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June 20, 2018 20:16
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| ~/Projects/gene-converter $ p build_and_convert.py | |
| docker build -t convert/elegene10st --build-arg package=pd.elegene.1.0.st_3.12.0.tar.gz --build-arg db=elegene10st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| Removing intermediate container a0118890d985 | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Running in 475050347cd0 | |
| Removing intermediate container 475050347cd0 | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Running in 07e2a1244c34 | |
| Removing intermediate container 07e2a1244c34 | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in efb870c49c06 | |
| Removing intermediate container efb870c49c06 | |
| ---> 3d7ce725ef4f | |
| Step 7/13 : ARG db | |
| ---> Running in fb40ec396952 | |
| Removing intermediate container fb40ec396952 | |
| ---> 4b4d2f2dc247 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in a2d7f0d0f1a4 | |
| Removing intermediate container a2d7f0d0f1a4 | |
| ---> 2db0d7b68e07 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 6589c1c84c6e | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'elegene10st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'elegene10st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.elegene.1.0.st_3.12.0.tar.gz | |
| Installing pd.elegene.1.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpuPG0Nk/devtools76fe33c13/pd.elegene.1.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.elegene.1.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ^[[A** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.elegene.1.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 6589c1c84c6e | |
| ---> f80d10417c06 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 794ac02dd915 | |
| Removing intermediate container 794ac02dd915 | |
| ---> 7389853cb3b5 | |
| Step 11/13 : COPY convert.R . | |
| ---> 2fb10b6f8cd3 | |
| Step 12/13 : USER user | |
| ---> Running in a05b852f4963 | |
| Removing intermediate container a05b852f4963 | |
| ---> 1f8e676cfe08 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in c15f254f1fcb | |
| Removing intermediate container c15f254f1fcb | |
| ---> 2f02699c9689 | |
| Successfully built 2f02699c9689 | |
| Successfully tagged convert/elegene10st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/elegene10st Rscript convert.R -p elegene10st -o /home/user/data/out/ -i /home/user/data/elegene10st/GSM1816552_GSM1816552_AW2.CEL.gz -d elegene10st -s ce -g GSM1816552_GSM1816552_AW2 | |
| ^[[ALoading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'elegene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/elegene10st Rscript convert.R -p elegene10st -o /home/user/data/out/ -i /home/user/data/elegene10st/GSM2648100_GSM2648100_Affy0272_13_JI2.CEL.gz -d elegene10st -s ce -g GSM2648100_GSM2648100_Affy0272_13_JI2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'elegene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/elegene10st Rscript convert.R -p elegene10st -o /home/user/data/out/ -i /home/user/data/elegene10st/GSM1816553_GSM1816553_AW3.CEL.gz -d elegene10st -s ce -g GSM1816553_GSM1816553_AW3 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'elegene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/elegene10st Rscript convert.R -p elegene10st -o /home/user/data/out/ -i /home/user/data/elegene10st/GSM2816667_GSM2816667_02_Daf-21A966.CEL.gz -d elegene10st -s ce -g GSM2816667_GSM2816667_02_Daf-21A966 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'elegene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/elegene10st Rscript convert.R -p elegene10st -o /home/user/data/out/ -i /home/user/data/elegene10st/GSM2648108_GSM2648108_Affy0272_21_6I5.CEL.gz -d elegene10st -s ce -g GSM2648108_GSM2648108_Affy0272_21_6I5 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'elegene10st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/cangene10st --build-arg package=pd.cangene.1.0.st_3.12.0.tar.gz --build-arg db=cangene10st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in ad29a023a437 | |
| Removing intermediate container ad29a023a437 | |
| ---> 0b8d4f987ba3 | |
| Step 7/13 : ARG db | |
| ---> Running in 8094e59ffe49 | |
| Removing intermediate container 8094e59ffe49 | |
| ---> a5b932ac565b | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 88337921c360 | |
| Removing intermediate container 88337921c360 | |
| ---> f43152af7d5a | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 61f2e6ce72f3 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'cangene10st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'cangene10st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.cangene.1.0.st_3.12.0.tar.gz | |
| Installing pd.cangene.1.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpRh6hts/devtools775013b81/pd.cangene.1.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.cangene.1.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.cangene.1.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 61f2e6ce72f3 | |
| ---> 120ed9465f4f | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in ad8eab712d5e | |
| Removing intermediate container ad8eab712d5e | |
| ---> d8be7a9249f3 | |
| Step 11/13 : COPY convert.R . | |
| ---> 2b4c8f3b28b6 | |
| Step 12/13 : USER user | |
| ---> Running in 2b81397438f9 | |
| Removing intermediate container 2b81397438f9 | |
| ---> 5982ba3020d3 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 72a6aed5160b | |
| Removing intermediate container 72a6aed5160b | |
| ---> b57eb70e3f1f | |
| Successfully built b57eb70e3f1f | |
| Successfully tagged convert/cangene10st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/cangene10st Rscript convert.R -p cangene10st -o /home/user/data/out/ -i /home/user/data/cangene10st/GSM1677434_GSM1677434_2656CLG0023-20131001-Canine1.0.CEL.gz -d cangene10st -s cf -g GSM1677434_GSM1677434_2656CLG0023-20131001-Canine1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'cangene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/cangene10st Rscript convert.R -p cangene10st -o /home/user/data/out/ -i /home/user/data/cangene10st/GSM1677428_GSM1677428_2656CLG0017-20131001-Canine1.0.CEL.gz -d cangene10st -s cf -g GSM1677428_GSM1677428_2656CLG0017-20131001-Canine1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'cangene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/cangene10st Rscript convert.R -p cangene10st -o /home/user/data/out/ -i /home/user/data/cangene10st/GSM1701881_GSM1701881_191.CEL.gz -d cangene10st -s cf -g GSM1701881_GSM1701881_191 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'cangene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/cangene10st Rscript convert.R -p cangene10st -o /home/user/data/out/ -i /home/user/data/cangene10st/GSM1677418_GSM1677418_2656CLG0007-20131001-Canine1.0.CEL.gz -d cangene10st -s cf -g GSM1677418_GSM1677418_2656CLG0007-20131001-Canine1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'cangene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/cangene10st Rscript convert.R -p cangene10st -o /home/user/data/out/ -i /home/user/data/cangene10st/GSM1701867_GSM1701867_162.CEL.gz -d cangene10st -s cf -g GSM1701867_GSM1701867_162 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'cangene10st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/ovigene11st --build-arg package=pd.ovigene.1.1.st_3.12.0.tar.gz --build-arg db=ovigene11st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 12c22770371e | |
| Removing intermediate container 12c22770371e | |
| ---> ed8f6cef637c | |
| Step 7/13 : ARG db | |
| ---> Running in 98925382c08a | |
| Removing intermediate container 98925382c08a | |
| ---> b8e1cca7c13a | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 704afcf68e59 | |
| Removing intermediate container 704afcf68e59 | |
| ---> 19fe7ddc96f0 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 5a35a2bd4c0b | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'ovigene11st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'ovigene11st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.ovigene.1.1.st_3.12.0.tar.gz | |
| Installing pd.ovigene.1.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmp8iuxh3/devtools726822ac3/pd.ovigene.1.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.ovigene.1.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.ovigene.1.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 5a35a2bd4c0b | |
| ---> 7a67908e7b05 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 7263ac2e3ed4 | |
| Removing intermediate container 7263ac2e3ed4 | |
| ---> 37d8a9c6183a | |
| Step 11/13 : COPY convert.R . | |
| ---> 2d4bf529b79b | |
| Step 12/13 : USER user | |
| ---> Running in 690c59aea37e | |
| Removing intermediate container 690c59aea37e | |
| ---> c55a83882be0 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in ec326444094f | |
| Removing intermediate container ec326444094f | |
| ---> a60ca2d1206e | |
| Successfully built a60ca2d1206e | |
| Successfully tagged convert/ovigene11st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ovigene11st Rscript convert.R -p ovigene11st -o /home/user/data/out/ -i /home/user/data/ovigene11st/GSM1556961_GSM1556961_1883.CEL.gz -d ovigene11st -s oa -g GSM1556961_GSM1556961_1883 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'ovigene11st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ovigene11st Rscript convert.R -p ovigene11st -o /home/user/data/out/ -i /home/user/data/ovigene11st/GSM1556974_GSM1556974_1947.CEL.gz -d ovigene11st -s oa -g GSM1556974_GSM1556974_1947 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'ovigene11st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/hugene20st --build-arg package=pd.hugene.2.0.st_3.14.1.tar.gz --build-arg db=hugene20stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in de30520db63d | |
| Removing intermediate container de30520db63d | |
| ---> 6d8c9f0bac8b | |
| Step 7/13 : ARG db | |
| ---> Running in 6329e9c9e8ce | |
| Removing intermediate container 6329e9c9e8ce | |
| ---> 2124b99a4817 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 10a5733eda98 | |
| Removing intermediate container 10a5733eda98 | |
| ---> 0822bbb1d589 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 2d3dfc7f47a9 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hugene20stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hugene20stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 30602383 bytes (29.2 MB) | |
| ================================================== | |
| downloaded 29.2 MB | |
| * installing *source* package 'hugene20stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hugene20stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpHhkYp5/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hugene.2.0.st_3.14.1.tar.gz | |
| Installing pd.hugene.2.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpHhkYp5/devtools6596af61/pd.hugene.2.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hugene.2.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hugene.2.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 2d3dfc7f47a9 | |
| ---> c54443f4a7f8 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 73faeea6c135 | |
| Removing intermediate container 73faeea6c135 | |
| ---> 16a7a913e327 | |
| Step 11/13 : COPY convert.R . | |
| ---> 246071e32bca | |
| Step 12/13 : USER user | |
| ---> Running in ade11701e946 | |
| Removing intermediate container ade11701e946 | |
| ---> d3cba171257a | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 3b4bff5de490 | |
| Removing intermediate container 3b4bff5de490 | |
| ---> 6b928d84aa2c | |
| Successfully built 6b928d84aa2c | |
| Successfully tagged convert/hugene20st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_.CEL -d hugene20stprobeset -s hs -g GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hugene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hugene20st/GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_.CEL | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080886_GSM2080886_6_th_stim_HuGene-2_0-st_.CEL.gz -d hugene20stprobeset -s hs -g GSM2080886_GSM2080886_6_th_stim_HuGene-2_0-st_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hugene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hugene20st/GSM2080886_GSM2080886_6_th_stim_HuGene-2_0-st_.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_.CEL.gz -d hugene20stprobeset -s hs -g GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
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| Attaching package: 'S4Vectors' | |
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| expand.grid | |
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| Reading.. | |
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| strsplit | |
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| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hugene20st/GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| ^[[Adocker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080887_GSM2080887_7_treg_ctr_HuGene-2_0-st_.CEL.gz -d hugene20stprobeset -s hs -g GSM2080887_GSM2080887_7_treg_ctr_HuGene-2_0-st_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
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| Attaching package: 'BiocGenerics' | |
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| parLapplyLB, parRapply, parSapply, parSapplyLB | |
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| IQR, mad, sd, var, xtabs | |
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| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
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| Attaching package: 'S4Vectors' | |
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| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hugene.2.0.st | |
| Loading required package: Biostrings | |
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| strsplit | |
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| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hugene20st/GSM2080887_GSM2080887_7_treg_ctr_HuGene-2_0-st_.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080885_GSM2080885_5_th_ctr_HuGene-2_0-st_.CEL.gz -d hugene20stprobeset -s hs -g GSM2080885_GSM2080885_5_th_ctr_HuGene-2_0-st_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
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| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hugene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hugene20st/GSM2080885_GSM2080885_5_th_ctr_HuGene-2_0-st_.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080883_GSM2080883_3_treg_ctr_HuGene-2_0-st_.CEL.gz -d hugene20stprobeset -s hs -g GSM2080883_GSM2080883_3_treg_ctr_HuGene-2_0-st_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
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| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hugene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hugene20st/GSM2080883_GSM2080883_3_treg_ctr_HuGene-2_0-st_.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| Ran a whole brain! | |
| docker build -t convert/mogene11st --build-arg package=pd.mogene.1.1.st.v1_3.14.1.tar.gz --build-arg db=mogene11stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in d19fa305a6ce | |
| Removing intermediate container d19fa305a6ce | |
| ---> c8c788f3723a | |
| Step 7/13 : ARG db | |
| ---> Running in cf8205ab7de3 | |
| Removing intermediate container cf8205ab7de3 | |
| ---> 9187d93cc46f | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in fb57f0df7c3c | |
| Removing intermediate container fb57f0df7c3c | |
| ---> d313f1389cee | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 7ee5e849e6c8 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'mogene11stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mogene11stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 19287229 bytes (18.4 MB) | |
| ================================================== | |
| downloaded 18.4 MB | |
| * installing *source* package 'mogene11stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (mogene11stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmpu0ObUF/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mogene.1.1.st.v1_3.14.1.tar.gz | |
| Installing pd.mogene.1.1.st.v1 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmpu0ObUF/devtools7572a4ea/pd.mogene.1.1.st.v1' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.mogene.1.1.st.v1' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.mogene.1.1.st.v1) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 7ee5e849e6c8 | |
| ---> 11e6e09836bd | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 47c33d94520b | |
| Removing intermediate container 47c33d94520b | |
| ---> 25307936c617 | |
| Step 11/13 : COPY convert.R . | |
| ---> 8f6107d8c529 | |
| Step 12/13 : USER user | |
| ---> Running in 1d04864adc2e | |
| Removing intermediate container 1d04864adc2e | |
| ---> 1cf446c0806c | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in bbdfdb6718ae | |
| Removing intermediate container bbdfdb6718ae | |
| ---> c8f2c729ce4e | |
| Successfully built c8f2c729ce4e | |
| Successfully tagged convert/mogene11st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene11st Rscript convert.R -p mogene11st -o /home/user/data/out/ -i /home/user/data/mogene11st/GSM1495810_GSM1495810_HTMoGene11_022312W_PB115_S374_7_RNA.CEL.gz -d mogene11stprobeset -s mm -g GSM1495810_GSM1495810_HTMoGene11_022312W_PB115_S374_7_RNA | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene11st Rscript convert.R -p mogene11st -o /home/user/data/out/ -i /home/user/data/mogene11st/GSM1495834_GSM1495834_HTMoGene11_022312W_PB99_S386_13LiverB.CEL.gz -d mogene11stprobeset -s mm -g GSM1495834_GSM1495834_HTMoGene11_022312W_PB99_S386_13LiverB | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene11st Rscript convert.R -p mogene11st -o /home/user/data/out/ -i /home/user/data/mogene11st/GSM1495805_GSM1495805_HTMoGene11_022312W_PB110_S374_2_RNA.CEL.gz -d mogene11stprobeset -s mm -g GSM1495805_GSM1495805_HTMoGene11_022312W_PB110_S374_2_RNA | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene11st Rscript convert.R -p mogene11st -o /home/user/data/out/ -i /home/user/data/mogene11st/GSM1495809_GSM1495809_HTMoGene11_022312W_PB114_S374_6_RNA.CEL.gz -d mogene11stprobeset -s mm -g GSM1495809_GSM1495809_HTMoGene11_022312W_PB114_S374_6_RNA | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene11st Rscript convert.R -p mogene11st -o /home/user/data/out/ -i /home/user/data/mogene11st/GSM1495822_GSM1495822_HTMoGene11_022912W_PB127_S374_19_RNA.CEL.gz -d mogene11stprobeset -s mm -g GSM1495822_GSM1495822_HTMoGene11_022912W_PB127_S374_19_RNA | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/bovgene11st --build-arg package=pd.bovgene.1.1.st_3.12.0.tar.gz --build-arg db=bovgene11st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in ad367bf351da | |
| Removing intermediate container ad367bf351da | |
| ---> f28e2e8150a1 | |
| Step 7/13 : ARG db | |
| ---> Running in a643869d5aee | |
| Removing intermediate container a643869d5aee | |
| ---> 477c99a159ab | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in f034dfbce986 | |
| Removing intermediate container f034dfbce986 | |
| ---> b6ab68b02d75 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 196d0239233a | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'bovgene11st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'bovgene11st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.bovgene.1.1.st_3.12.0.tar.gz | |
| Installing pd.bovgene.1.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpA4t6tr/devtools722089cea/pd.bovgene.1.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.bovgene.1.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.bovgene.1.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 196d0239233a | |
| ---> af0d1286094c | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in a2ace11db845 | |
| Removing intermediate container a2ace11db845 | |
| ---> d63d6f236e31 | |
| Step 11/13 : COPY convert.R . | |
| ---> fb75ef8fe4db | |
| Step 12/13 : USER user | |
| ---> Running in 3ef7fb2ec319 | |
| Removing intermediate container 3ef7fb2ec319 | |
| ---> 31a202560151 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in b710207d47e2 | |
| Removing intermediate container b710207d47e2 | |
| ---> 7d8dc8346778 | |
| Successfully built 7d8dc8346778 | |
| Successfully tagged convert/bovgene11st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene11st Rscript convert.R -p bovgene11st -o /home/user/data/out/ -i /home/user/data/bovgene11st/GSM1843302_GSM1843302_2031M0024_NCP+LPS.CEL.gz -d bovgene11st -s bt -g GSM1843302_GSM1843302_2031M0024_NCP+LPS | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'bovgene11st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene11st Rscript convert.R -p bovgene11st -o /home/user/data/out/ -i /home/user/data/bovgene11st/GSM1843300_GSM1843300_2031M0022_CONT+LPS.CEL.gz -d bovgene11st -s bt -g GSM1843300_GSM1843300_2031M0022_CONT+LPS | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'bovgene11st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/clariomshumanht --build-arg package=pd.clariom.s.human.ht_3.14.1.tar.gz --build-arg db=clariomshumanht -f Dockerfile.pd . | |
| Sending build context to Docker daemon 2.627GB | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in dded58c4545d | |
| Removing intermediate container dded58c4545d | |
| ---> 49178a8f8169 | |
| Step 7/13 : ARG db | |
| ---> Running in a897f65fadae | |
| Removing intermediate container a897f65fadae | |
| ---> f2441683d3a8 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in a0041ebe74e4 | |
| Removing intermediate container a0041ebe74e4 | |
| ---> b9202be60dec | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 938584e0021d | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'clariomshumanht.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'clariomshumanht.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.clariom.s.human.ht_3.14.1.tar.gz | |
| Installing pd.clariom.s.human.ht | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpjHUH1F/devtools74f377e2c/pd.clariom.s.human.ht' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.clariom.s.human.ht' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.clariom.s.human.ht) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 938584e0021d | |
| ---> 500e9fb98c15 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in c323e9612fbe | |
| Removing intermediate container c323e9612fbe | |
| ---> 51ef25010dac | |
| Step 11/13 : COPY convert.R . | |
| ---> 9d828343e351 | |
| Step 12/13 : USER user | |
| ---> Running in f982f18fc57b | |
| Removing intermediate container f982f18fc57b | |
| ---> a865c2edde01 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 958bdf989942 | |
| Removing intermediate container 958bdf989942 | |
| ---> 397a5e176257 | |
| Successfully built 397a5e176257 | |
| Successfully tagged convert/clariomshumanht:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/clariomshumanht' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/mgu74bv2 --build-arg package=pd.mg.u74bv2_3.12.0.tar.gz --build-arg db=mgu74bv2 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in b960c3d15d1f | |
| Removing intermediate container b960c3d15d1f | |
| ---> d9cfbc8e05a6 | |
| Step 7/13 : ARG db | |
| ---> Running in 067ddeb966c0 | |
| Removing intermediate container 067ddeb966c0 | |
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| Step 8/13 : ENV DB=$db | |
| ---> Running in 935bf8d606a7 | |
| Removing intermediate container 935bf8d606a7 | |
| ---> 25a4878e94a7 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in aa5772098c07 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'mgu74bv2.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mgu74bv2.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 459531 bytes (448 KB) | |
| ================================================== | |
| downloaded 448 KB | |
| * installing *source* package 'mgu74bv2.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (mgu74bv2.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmpxr1nF4/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mg.u74bv2_3.12.0.tar.gz | |
| Installing pd.mg.u74bv2 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmpxr1nF4/devtools712d74ac8/pd.mg.u74bv2' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.mg.u74bv2' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.mg.u74bv2) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container aa5772098c07 | |
| ---> 7a0ef883c2ba | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in dd8dad0c67c6 | |
| Removing intermediate container dd8dad0c67c6 | |
| ---> 20b69864b47f | |
| Step 11/13 : COPY convert.R . | |
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| Step 12/13 : USER user | |
| ---> Running in b1c856d505aa | |
| Removing intermediate container b1c856d505aa | |
| ---> 6c95f0e87b77 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 659c1c9e85a5 | |
| Removing intermediate container 659c1c9e85a5 | |
| ---> d9bd88af1fc5 | |
| Successfully built d9bd88af1fc5 | |
| Successfully tagged convert/mgu74bv2:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/mgu74bv2' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/htmg430a --build-arg package=pd.ht.mg.430a_3.12.0.tar.gz --build-arg db=htmg430a -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in acd0c9250cdf | |
| Removing intermediate container acd0c9250cdf | |
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| Step 7/13 : ARG db | |
| ---> Running in 75876237787a | |
| Removing intermediate container 75876237787a | |
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| Step 8/13 : ENV DB=$db | |
| ---> Running in 796a30904531 | |
| Removing intermediate container 796a30904531 | |
| ---> 0a7f36781551 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 3b3ce2b2f843 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'htmg430a.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'htmg430a.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.ht.mg.430a_3.12.0.tar.gz | |
| Installing pd.ht.mg.430a | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmptUjD9Z/devtools767eb97b9/pd.ht.mg.430a' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.ht.mg.430a' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.ht.mg.430a) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 3b3ce2b2f843 | |
| ---> c6a206589d4e | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 535e54c408d3 | |
| Removing intermediate container 535e54c408d3 | |
| ---> 635227162fd1 | |
| Step 11/13 : COPY convert.R . | |
| ---> 5c21f668bd22 | |
| Step 12/13 : USER user | |
| ---> Running in cf71b1341711 | |
| Removing intermediate container cf71b1341711 | |
| ---> 78ad2e00f3ca | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 225b566a2b75 | |
| Removing intermediate container 225b566a2b75 | |
| ---> 19e966cd0163 | |
| Successfully built 19e966cd0163 | |
| Successfully tagged convert/htmg430a:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/htmg430a' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/bovgene10st --build-arg package=pd.bovgene.1.0.st_3.12.0.tar.gz --build-arg db=bovgene10st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 12b6e27f3fce | |
| Removing intermediate container 12b6e27f3fce | |
| ---> 9437b99a3dc8 | |
| Step 7/13 : ARG db | |
| ---> Running in 49099e3b7129 | |
| Removing intermediate container 49099e3b7129 | |
| ---> 0c2e90c3829c | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in f9158d2a08e6 | |
| Removing intermediate container f9158d2a08e6 | |
| ---> 87ae7a1662fb | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 683513f073d5 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'bovgene10st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'bovgene10st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.bovgene.1.0.st_3.12.0.tar.gz | |
| Installing pd.bovgene.1.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpCpTMQB/devtools747def76a/pd.bovgene.1.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.bovgene.1.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.bovgene.1.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 683513f073d5 | |
| ---> e9be9d554b4c | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 76eceb097098 | |
| Removing intermediate container 76eceb097098 | |
| ---> 9cf61f5af347 | |
| Step 11/13 : COPY convert.R . | |
| ---> b1bfbc1df3de | |
| Step 12/13 : USER user | |
| ---> Running in e6e06acaa1e3 | |
| Removing intermediate container e6e06acaa1e3 | |
| ---> 09c0dce2caa8 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 8eeede1ce702 | |
| Removing intermediate container 8eeede1ce702 | |
| ---> 19ae02c1aead | |
| Successfully built 19ae02c1aead | |
| Successfully tagged convert/bovgene10st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene10st Rscript convert.R -p bovgene10st -o /home/user/data/out/ -i /home/user/data/bovgene10st/GSM2844206_GSM2844206_V_66042_s30_LLC4.CEL.gz -d bovgene10st -s bt -g GSM2844206_GSM2844206_V_66042_s30_LLC4 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'bovgene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene10st Rscript convert.R -p bovgene10st -o /home/user/data/out/ -i /home/user/data/bovgene10st/GSM1954042_GSM1954042_Segfam_NNR_WT_2.CEL.gz -d bovgene10st -s bt -g GSM1954042_GSM1954042_Segfam_NNR_WT_2 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene10st Rscript convert.R -p bovgene10st -o /home/user/data/out/ -i /home/user/data/bovgene10st/GSM1954065_GSM1954065_Segfam_NNR_WT_25.CEL.gz -d bovgene10st -s bt -g GSM1954065_GSM1954065_Segfam_NNR_WT_25 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene10st Rscript convert.R -p bovgene10st -o /home/user/data/out/ -i /home/user/data/bovgene10st/GSM2882755_GSM2882755_4161_050416_BovGene-1_0-st_.CEL.gz -d bovgene10st -s bt -g GSM2882755_GSM2882755_4161_050416_BovGene-1_0-st_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'bovgene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene10st Rscript convert.R -p bovgene10st -o /home/user/data/out/ -i /home/user/data/bovgene10st/GSM2561719_GSM2561719_5_BoMac_CIT24_T1.CEL.gz -d bovgene10st -s bt -g GSM2561719_GSM2561719_5_BoMac_CIT24_T1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'bovgene10st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/equgene10st --build-arg package=pd.equgene.1.0.st_3.12.0.tar.gz --build-arg db=equgene10st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 694569b0d631 | |
| Removing intermediate container 694569b0d631 | |
| ---> 209eacbaffe5 | |
| Step 7/13 : ARG db | |
| ---> Running in aa730a0aa615 | |
| Removing intermediate container aa730a0aa615 | |
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| Step 8/13 : ENV DB=$db | |
| ---> Running in b893b9b26fa1 | |
| Removing intermediate container b893b9b26fa1 | |
| ---> d3942c56ae6a | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in fc8c6feddba5 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'equgene10st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'equgene10st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.equgene.1.0.st_3.12.0.tar.gz | |
| Installing pd.equgene.1.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmpo9i6jQ/devtools72fbe50f4/pd.equgene.1.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.equgene.1.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.equgene.1.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container fc8c6feddba5 | |
| ---> 82c2b7d942eb | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in a33680260a7d | |
| Removing intermediate container a33680260a7d | |
| ---> 3ff79e2285a2 | |
| Step 11/13 : COPY convert.R . | |
| ---> bde9c4102805 | |
| Step 12/13 : USER user | |
| ---> Running in ed7f41f51a7f | |
| Removing intermediate container ed7f41f51a7f | |
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| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 029505ddceb5 | |
| Removing intermediate container 029505ddceb5 | |
| ---> 33a8146d642b | |
| Successfully built 33a8146d642b | |
| Successfully tagged convert/equgene10st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/equgene10st Rscript convert.R -p equgene10st -o /home/user/data/out/ -i /home/user/data/equgene10st/GSM2671023_GSM2671023_PA261_Ex_3_Dag_15_IL-1b_151015_EquGene-1_0-st.CEL.gz -d equgene10st -s ec -g GSM2671023_GSM2671023_PA261_Ex_3_Dag_15_IL-1b_151015_EquGene-1_0-st | |
| Error in library(ba_package_name, character.only = TRUE) : | |
| there is no package called 'equgene10stecensgprobe' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/equgene10st Rscript convert.R -p equgene10st -o /home/user/data/out/ -i /home/user/data/equgene10st/GSM2671033_GSM2671033_PA261_Ex_4_Dag_9_K_151015_EquGene-1_0-st.CEL.gz -d equgene10st -s ec -g GSM2671033_GSM2671033_PA261_Ex_4_Dag_9_K_151015_EquGene-1_0-st | |
| Error in library(ba_package_name, character.only = TRUE) : | |
| there is no package called 'equgene10stecensgprobe' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/equgene10st Rscript convert.R -p equgene10st -o /home/user/data/out/ -i /home/user/data/equgene10st/GSM2098343_GSM2098343_My_Crafty_Life_Week4_ESC_EquGene.CEL.gz -d equgene10st -s ec -g GSM2098343_GSM2098343_My_Crafty_Life_Week4_ESC_EquGene | |
| Error in library(ba_package_name, character.only = TRUE) : | |
| there is no package called 'equgene10stecensgprobe' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/equgene10st Rscript convert.R -p equgene10st -o /home/user/data/out/ -i /home/user/data/equgene10st/GSM2671012_GSM2671012_PA261_Ex_2_Dag_15_IL-1b_151007_EquGene-1_0-st.CEL.gz -d equgene10st -s ec -g GSM2671012_GSM2671012_PA261_Ex_2_Dag_15_IL-1b_151007_EquGene-1_0-st | |
| Error in library(ba_package_name, character.only = TRUE) : | |
| there is no package called 'equgene10stecensgprobe' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/equgene10st Rscript convert.R -p equgene10st -o /home/user/data/out/ -i /home/user/data/equgene10st/GSM1299430_GSM1299430_MG-Am3.CEL.gz -d equgene10st -s ec -g GSM1299430_GSM1299430_MG-Am3 | |
| Error in library(ba_package_name, character.only = TRUE) : | |
| there is no package called 'equgene10stecensgprobe' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/chicken --build-arg package=pd.chicken_3.12.0.tar.gz --build-arg db=chicken -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 21bfd7505bba | |
| Removing intermediate container 21bfd7505bba | |
| ---> 851869501e47 | |
| Step 7/13 : ARG db | |
| ---> Running in c2ea7e76d1ea | |
| Removing intermediate container c2ea7e76d1ea | |
| ---> 1094a7e62617 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 51c6e0b3852e | |
| Removing intermediate container 51c6e0b3852e | |
| ---> de9486bce352 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 4504c25e2d48 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'chicken.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/chicken.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 1520746 bytes (1.5 MB) | |
| ================================================== | |
| downloaded 1.5 MB | |
| * installing *source* package 'chicken.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (chicken.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpLh4ljG/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.chicken_3.12.0.tar.gz | |
| Installing pd.chicken | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpLh4ljG/devtools76d54f044/pd.chicken' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.chicken' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.chicken) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 4504c25e2d48 | |
| ---> 4066fba31783 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in f6674f1996cf | |
| Removing intermediate container f6674f1996cf | |
| ---> 688881c46d02 | |
| Step 11/13 : COPY convert.R . | |
| ---> 58f59f6e5cd4 | |
| Step 12/13 : USER user | |
| ---> Running in d0dfa9fc9a55 | |
| Removing intermediate container d0dfa9fc9a55 | |
| ---> b01f1874286e | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in e58f119d4349 | |
| Removing intermediate container e58f119d4349 | |
| ---> 8b0529028855 | |
| Successfully built 8b0529028855 | |
| Successfully tagged convert/chicken:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/chicken' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/rae230a --build-arg package=pd.rae230a_3.12.0.tar.gz --build-arg db=rae230a -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in b4f4727df4ff | |
| Removing intermediate container b4f4727df4ff | |
| ---> d3f14d0f71f8 | |
| Step 7/13 : ARG db | |
| ---> Running in dd5c0b238f87 | |
| Removing intermediate container dd5c0b238f87 | |
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| Step 8/13 : ENV DB=$db | |
| ---> Running in 53b0b095baa3 | |
| Removing intermediate container 53b0b095baa3 | |
| ---> ebbf30113613 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 54d515390f88 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'rae230a.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/rae230a.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 564338 bytes (551 KB) | |
| ================================================== | |
| downloaded 551 KB | |
| * installing *source* package 'rae230a.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (rae230a.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpPOMnmq/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.rae230a_3.12.0.tar.gz | |
| Installing pd.rae230a | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpPOMnmq/devtools76b0bc727/pd.rae230a' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.rae230a' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.rae230a) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 54d515390f88 | |
| ---> 70393c997183 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 339b26dd8a91 | |
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| ---> 23de53eb16cc | |
| Step 11/13 : COPY convert.R . | |
| ---> b4645aa451ad | |
| Step 12/13 : USER user | |
| ---> Running in 28a4bbddce78 | |
| Removing intermediate container 28a4bbddce78 | |
| ---> 68c687dfeb13 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in fedf65bdf2d8 | |
| Removing intermediate container fedf65bdf2d8 | |
| ---> 8a3a4efb80bc | |
| Successfully built 8a3a4efb80bc | |
| Successfully tagged convert/rae230a:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/rae230a' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/hugene21st --build-arg package=pd.hugene.2.1.st_3.14.1.tar.gz --build-arg db=hugene21stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 90d50000829d | |
| Removing intermediate container 90d50000829d | |
| ---> ff6090be2e3e | |
| Step 7/13 : ARG db | |
| ---> Running in e3d2f96514c2 | |
| Removing intermediate container e3d2f96514c2 | |
| ---> 6b911648204a | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 00719090e862 | |
| Removing intermediate container 00719090e862 | |
| ---> 60a8cec9ab42 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in ed942fb5281e | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hugene21stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hugene21stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 30602388 bytes (29.2 MB) | |
| ================================================== | |
| downloaded 29.2 MB | |
| * installing *source* package 'hugene21stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hugene21stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmphQJcWi/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hugene.2.1.st_3.14.1.tar.gz | |
| Installing pd.hugene.2.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmphQJcWi/devtools71c7305e3/pd.hugene.2.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hugene.2.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hugene.2.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container ed942fb5281e | |
| ---> 242cbc3afce1 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 57f821778551 | |
| Removing intermediate container 57f821778551 | |
| ---> 9dfc757722cd | |
| Step 11/13 : COPY convert.R . | |
| ---> 9ff55c8b1681 | |
| Step 12/13 : USER user | |
| ---> Running in 0acd66a22dbf | |
| Removing intermediate container 0acd66a22dbf | |
| ---> cd8b23886444 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 7923bfd2af63 | |
| Removing intermediate container 7923bfd2af63 | |
| ---> ff734400a975 | |
| Successfully built ff734400a975 | |
| Successfully tagged convert/hugene21st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene21st Rscript convert.R -p hugene21st -o /home/user/data/out/ -i /home/user/data/hugene21st/GSM1437827_GSM1437827_HTHuGene21_102912H_SL253_810462-1.CEL.gz -d hugene21stprobeset -s hs -g GSM1437827_GSM1437827_HTHuGene21_102912H_SL253_810462-1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hugene.2.1.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hugene21st/GSM1437827_GSM1437827_HTHuGene21_102912H_SL253_810462-1.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene21st Rscript convert.R -p hugene21st -o /home/user/data/out/ -i /home/user/data/hugene21st/GSM1437964_GSM1437964_HTHuGene21_082912H_SL22_815163-2.CEL.gz -d hugene21stprobeset -s hs -g GSM1437964_GSM1437964_HTHuGene21_082912H_SL22_815163-2 | |
| Loading required package: AnnotationDbi | |
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| Attaching package: 'BiocGenerics' | |
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| parLapplyLB, parRapply, parSapply, parSapplyLB | |
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| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
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| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hugene21st/GSM1437964_GSM1437964_HTHuGene21_082912H_SL22_815163-2.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene21st Rscript convert.R -p hugene21st -o /home/user/data/out/ -i /home/user/data/hugene21st/GSM1437826_GSM1437826_HTHuGene21_100212H_SL103_810460-2.CEL.gz -d hugene21stprobeset -s hs -g GSM1437826_GSM1437826_HTHuGene21_100212H_SL103_810460-2 | |
| Loading required package: AnnotationDbi | |
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| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
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| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
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| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hugene21st/GSM1437826_GSM1437826_HTHuGene21_100212H_SL103_810460-2.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene21st Rscript convert.R -p hugene21st -o /home/user/data/out/ -i /home/user/data/hugene21st/GSM1437906_GSM1437906_HTHuGene21_110512H_SL284_812407-2.CEL.gz -d hugene21stprobeset -s hs -g GSM1437906_GSM1437906_HTHuGene21_110512H_SL284_812407-2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
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| Loading required package: BiocGenerics | |
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| Attaching package: 'BiocGenerics' | |
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| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
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| Attaching package: 'S4Vectors' | |
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| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
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| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
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| strsplit | |
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| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hugene21st/GSM1437906_GSM1437906_HTHuGene21_110512H_SL284_812407-2.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene21st Rscript convert.R -p hugene21st -o /home/user/data/out/ -i /home/user/data/hugene21st/GSM1437845_GSM1437845_HTHuGene21_102512H_SL228_810529-2.CEL.gz -d hugene21stprobeset -s hs -g GSM1437845_GSM1437845_HTHuGene21_102512H_SL228_810529-2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
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| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
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| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hugene.2.1.st | |
| Loading required package: Biostrings | |
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| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hugene21st/GSM1437845_GSM1437845_HTHuGene21_102512H_SL228_810529-2.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| Ran a whole brain! | |
| docker build -t convert/rhesus --build-arg package=pd.rhesus_3.12.0.tar.gz --build-arg db=rhesus -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
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| Step 3/13 : USER root | |
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| Step 4/13 : COPY install_pd.R . | |
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| Step 5/13 : ARG package | |
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| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 2856c748bfb4 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'rhesus.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'rhesus.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.rhesus_3.12.0.tar.gz | |
| Installing pd.rhesus | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpcZ8S9e/devtools73934c076/pd.rhesus' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.rhesus' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.rhesus) | |
| [[1]] | |
| [1] TRUE | |
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| Successfully built de24f9e53371 | |
| Successfully tagged convert/rhesus:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/rhesus' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/clariomsrat --build-arg package=pd.clariom.s.rat_3.14.1.tar.gz --build-arg db=clariomsrat -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
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| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
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| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in cbaa8e51ef22 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'clariomsrat.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'clariomsrat.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.clariom.s.rat_3.14.1.tar.gz | |
| Installing pd.clariom.s.rat | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpKk3G2K/devtools722a76e7b/pd.clariom.s.rat' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.clariom.s.rat' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.clariom.s.rat) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container cbaa8e51ef22 | |
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| ---> Running in f17ba760adc7 | |
| Removing intermediate container f17ba760adc7 | |
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| Step 11/13 : COPY convert.R . | |
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| ---> Running in b947b569c706 | |
| Removing intermediate container b947b569c706 | |
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| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in cd4bda6d3edf | |
| Removing intermediate container cd4bda6d3edf | |
| ---> 6c794f4250e6 | |
| Successfully built 6c794f4250e6 | |
| Successfully tagged convert/clariomsrat:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsrat Rscript convert.R -p clariomsrat -o /home/user/data/out/ -i /home/user/data/clariomsrat/GSM2479542_GSM2479542_kchip2shRNA2.CEL.gz -d clariomsrat -s rn -g GSM2479542_GSM2479542_kchip2shRNA2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'clariomsrat.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsrat Rscript convert.R -p clariomsrat -o /home/user/data/out/ -i /home/user/data/clariomsrat/GSM2479540_GSM2479540_control3.CEL.gz -d clariomsrat -s rn -g GSM2479540_GSM2479540_control3 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'clariomsrat.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsrat Rscript convert.R -p clariomsrat -o /home/user/data/out/ -i /home/user/data/clariomsrat/GSM2479539_GSM2479539_control2.CEL.gz -d clariomsrat -s rn -g GSM2479539_GSM2479539_control2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'clariomsrat.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsrat Rscript convert.R -p clariomsrat -o /home/user/data/out/ -i /home/user/data/clariomsrat/GSM2479541_GSM2479541_kchip2shRNA1.CEL.gz -d clariomsrat -s rn -g GSM2479541_GSM2479541_kchip2shRNA1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'clariomsrat.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsrat Rscript convert.R -p clariomsrat -o /home/user/data/out/ -i /home/user/data/clariomsrat/GSM2479543_GSM2479543_kchip2shRNA3.CEL.gz -d clariomsrat -s rn -g GSM2479543_GSM2479543_kchip2shRNA3 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'clariomsrat.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/chigene11st --build-arg package=pd.chigene.1.1.st_3.12.0.tar.gz --build-arg db=chigene11st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 5c847520823a | |
| Removing intermediate container 5c847520823a | |
| ---> ed7e0355857e | |
| Step 7/13 : ARG db | |
| ---> Running in e551cbf85f51 | |
| Removing intermediate container e551cbf85f51 | |
| ---> 76a735bd24fb | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in d69c4f996e55 | |
| Removing intermediate container d69c4f996e55 | |
| ---> ee520fd18fd8 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 787b2e827d13 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'chigene11st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'chigene11st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.chigene.1.1.st_3.12.0.tar.gz | |
| Installing pd.chigene.1.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmpoa1kIH/devtools7e876dbf/pd.chigene.1.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.chigene.1.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.chigene.1.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 787b2e827d13 | |
| ---> 9e4f8c3c8353 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 14bb9af71b9a | |
| Removing intermediate container 14bb9af71b9a | |
| ---> fd9da35460a9 | |
| Step 11/13 : COPY convert.R . | |
| ---> a540e0fda29b | |
| Step 12/13 : USER user | |
| ---> Running in 1173c21c53d8 | |
| Removing intermediate container 1173c21c53d8 | |
| ---> 2a73ea14328c | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in fb915d548320 | |
| Removing intermediate container fb915d548320 | |
| ---> e7f44665d4c8 | |
| Successfully built e7f44665d4c8 | |
| Successfully tagged convert/chigene11st:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/chigene11st' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/drosgenome1 --build-arg package=pd.drosgenome1_3.12.0.tar.gz --build-arg db=drosgenome1 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 187cb9fc1b24 | |
| Removing intermediate container 187cb9fc1b24 | |
| ---> 1a83b48c606b | |
| Step 7/13 : ARG db | |
| ---> Running in 30d8d41c95ae | |
| Removing intermediate container 30d8d41c95ae | |
| ---> b326191e6456 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 3ee1d6ec16e7 | |
| Removing intermediate container 3ee1d6ec16e7 | |
| ---> 382c7cb0f47d | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in e2124c445089 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'drosgenome1.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/drosgenome1.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 437744 bytes (427 KB) | |
| ================================================== | |
| downloaded 427 KB | |
| * installing *source* package 'drosgenome1.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (drosgenome1.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmp3NUqmD/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.drosgenome1_3.12.0.tar.gz | |
| Installing pd.drosgenome1 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmp3NUqmD/devtools73f457c20/pd.drosgenome1' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.drosgenome1' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.drosgenome1) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container e2124c445089 | |
| ---> 7a45b17dfdf1 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 888b4088e27f | |
| Removing intermediate container 888b4088e27f | |
| ---> 3d5bafcb42f2 | |
| Step 11/13 : COPY convert.R . | |
| ---> 864926c5481a | |
| Step 12/13 : USER user | |
| ---> Running in 3d52e1f77fb2 | |
| Removing intermediate container 3d52e1f77fb2 | |
| ---> 7bc9a64fb05b | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 87f0a7b84ba1 | |
| Removing intermediate container 87f0a7b84ba1 | |
| ---> d0c3a7f43195 | |
| Successfully built d0c3a7f43195 | |
| Successfully tagged convert/drosgenome1:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/drosgenome1' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/porgene11st --build-arg package=pd.porgene.1.1.st_3.12.0.tar.gz --build-arg db=porgene11st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 716507d7ed4b | |
| Removing intermediate container 716507d7ed4b | |
| ---> 2d0259afd3cb | |
| Step 7/13 : ARG db | |
| ---> Running in ffd06341a11f | |
| Removing intermediate container ffd06341a11f | |
| ---> 9310829062b6 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in fc3ff5ba7b32 | |
| Removing intermediate container fc3ff5ba7b32 | |
| ---> 59827bd0c276 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 4d28c9038c78 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'porgene11st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'porgene11st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.porgene.1.1.st_3.12.0.tar.gz | |
| Installing pd.porgene.1.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmp5wp8yQ/devtools76e316f1/pd.porgene.1.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.porgene.1.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.porgene.1.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 4d28c9038c78 | |
| ---> a5cbc5fab950 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in ec2107e414d1 | |
| Removing intermediate container ec2107e414d1 | |
| ---> a086924e473d | |
| Step 11/13 : COPY convert.R . | |
| ---> d5f4d472a028 | |
| Step 12/13 : USER user | |
| ---> Running in 82274b5625d0 | |
| Removing intermediate container 82274b5625d0 | |
| ---> 830af06e1510 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 7ad83d0db4ed | |
| Removing intermediate container 7ad83d0db4ed | |
| ---> 4e932cae2096 | |
| Successfully built 4e932cae2096 | |
| Successfully tagged convert/porgene11st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/porgene11st Rscript convert.R -p porgene11st -o /home/user/data/out/ -i /home/user/data/porgene11st/GSM2059244_GSM2059244_SA_LS_Pig1.CEL.gz -d porgene11st -s ss -g GSM2059244_GSM2059244_SA_LS_Pig1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'porgene11st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/porgene11st Rscript convert.R -p porgene11st -o /home/user/data/out/ -i /home/user/data/porgene11st/GSM2059275_GSM2059275_SA_ET_Pig9.CEL.gz -d porgene11st -s ss -g GSM2059275_GSM2059275_SA_ET_Pig9 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'porgene11st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/porgene11st Rscript convert.R -p porgene11st -o /home/user/data/out/ -i /home/user/data/porgene11st/GSM1847753_GSM1847753_9-2.CEL.gz -d porgene11st -s ss -g GSM1847753_GSM1847753_9-2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'porgene11st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/ragene21st --build-arg package=pd.ragene.2.1.st_3.14.1.tar.gz --build-arg db=ragene21stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 13f419901492 | |
| Removing intermediate container 13f419901492 | |
| ---> 1b5294778adb | |
| Step 7/13 : ARG db | |
| ---> Running in 6e672a7e2b8b | |
| Removing intermediate container 6e672a7e2b8b | |
| ---> 549547992f93 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 8895101daf48 | |
| Removing intermediate container 8895101daf48 | |
| ---> 54507fb3656f | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in b17cd5a648a5 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'ragene21stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/ragene21stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 11254209 bytes (10.7 MB) | |
| ================================================== | |
| downloaded 10.7 MB | |
| * installing *source* package 'ragene21stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (ragene21stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpN8aBu0/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.ragene.2.1.st_3.14.1.tar.gz | |
| Installing pd.ragene.2.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpN8aBu0/devtools7565b296a/pd.ragene.2.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.ragene.2.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.ragene.2.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container b17cd5a648a5 | |
| ---> ca757742286d | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 01e72c371e94 | |
| Removing intermediate container 01e72c371e94 | |
| ---> ed63aa83c1aa | |
| Step 11/13 : COPY convert.R . | |
| ---> 43fbcaddbbaa | |
| Step 12/13 : USER user | |
| ---> Running in 72eee6850983 | |
| Removing intermediate container 72eee6850983 | |
| ---> 7ddc094fd0ba | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 7ca782ba7bd9 | |
| Removing intermediate container 7ca782ba7bd9 | |
| ---> 18d52974fb79 | |
| Successfully built 18d52974fb79 | |
| Successfully tagged convert/ragene21st:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/ragene21st' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/ovigene10st --build-arg package=pd.ovigene.1.0.st_3.12.0.tar.gz --build-arg db=ovigene10st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 3f00a5bc7d36 | |
| Removing intermediate container 3f00a5bc7d36 | |
| ---> c28eed26b9ab | |
| Step 7/13 : ARG db | |
| ---> Running in 5757ed9c14e6 | |
| Removing intermediate container 5757ed9c14e6 | |
| ---> 046a5d12a4e0 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in dfa2f4f7daf0 | |
| Removing intermediate container dfa2f4f7daf0 | |
| ---> c74cfba90455 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 457c6694e613 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'ovigene10st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'ovigene10st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.ovigene.1.0.st_3.12.0.tar.gz | |
| Installing pd.ovigene.1.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpfquhvL/devtools75b79db58/pd.ovigene.1.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.ovigene.1.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.ovigene.1.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 457c6694e613 | |
| ---> 8d96cd69f1a9 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 1c86f75874d4 | |
| Removing intermediate container 1c86f75874d4 | |
| ---> 117d993fe3e4 | |
| Step 11/13 : COPY convert.R . | |
| ---> f36323f66d72 | |
| Step 12/13 : USER user | |
| ---> Running in 6b8bdc412f5a | |
| Removing intermediate container 6b8bdc412f5a | |
| ---> 12612aeb1bf6 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 5010eefac2e0 | |
| Removing intermediate container 5010eefac2e0 | |
| ---> e1fc5ac08d25 | |
| Successfully built e1fc5ac08d25 | |
| Successfully tagged convert/ovigene10st:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/ovigene10st' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/hgu95c --build-arg package=pd.hg.u95c_3.12.0.tar.gz --build-arg db=hgu95c -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in ea64ee5a9961 | |
| Removing intermediate container ea64ee5a9961 | |
| ---> dd0939c76168 | |
| Step 7/13 : ARG db | |
| ---> Running in 584b7e2e14a5 | |
| Removing intermediate container 584b7e2e14a5 | |
| ---> 76293801474c | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 5e9a23388c61 | |
| Removing intermediate container 5e9a23388c61 | |
| ---> ededddbb5bd7 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in adf6587b4948 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hgu95c.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu95c.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 499631 bytes (487 KB) | |
| ================================================== | |
| downloaded 487 KB | |
| * installing *source* package 'hgu95c.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hgu95c.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpelCghj/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hg.u95c_3.12.0.tar.gz | |
| Installing pd.hg.u95c | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpelCghj/devtools767a7393e/pd.hg.u95c' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hg.u95c' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hg.u95c) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container adf6587b4948 | |
| ---> 2ba514738e8d | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 3a8ee102bb58 | |
| Removing intermediate container 3a8ee102bb58 | |
| ---> 0131a284bc6e | |
| Step 11/13 : COPY convert.R . | |
| ---> e62bed7ddaad | |
| Step 12/13 : USER user | |
| ---> Running in 8630cd03e68e | |
| Removing intermediate container 8630cd03e68e | |
| ---> f24f599f2175 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 6207ccfce6b5 | |
| Removing intermediate container 6207ccfce6b5 | |
| ---> 0f94068a7bfb | |
| Successfully built 0f94068a7bfb | |
| Successfully tagged convert/hgu95c:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu95c Rscript convert.R -p hgu95c -o /home/user/data/out/ -i /home/user/data/hgu95c/GSM1249616_GSM1249616_24C.CEL.gz -d hgu95c -s hs -g GSM1249616_GSM1249616_24C | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u95c | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu95c/GSM1249616_GSM1249616_24C.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu95c_GSM1249616_GSM1249616_24C_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu95c Rscript convert.R -p hgu95c -o /home/user/data/out/ -i /home/user/data/hgu95c/GSM16215_GSM16215.CEL.gz -d hgu95c -s hs -g GSM16215_GSM16215 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u95c | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu95c/GSM16215_GSM16215.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu95c_GSM16215_GSM16215_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu95c Rscript convert.R -p hgu95c -o /home/user/data/out/ -i /home/user/data/hgu95c/GSM153247_GSM153247.CEL.gz -d hgu95c -s hs -g GSM153247_GSM153247 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u95c | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu95c/GSM153247_GSM153247.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu95c_GSM153247_GSM153247_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu95c Rscript convert.R -p hgu95c -o /home/user/data/out/ -i /home/user/data/hgu95c/GSM152921_GSM152921.CEL.gz -d hgu95c -s hs -g GSM152921_GSM152921 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u95c | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu95c/GSM152921_GSM152921.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu95c_GSM152921_GSM152921_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu95c Rscript convert.R -p hgu95c -o /home/user/data/out/ -i /home/user/data/hgu95c/GSM1675152_GSM1675152_PN68_u95c.CEL.gz -d hgu95c -s hs -g GSM1675152_GSM1675152_PN68_u95c | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u95c | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu95c/GSM1675152_GSM1675152_PN68_u95c.CEL.gz | |
| Mutating.. | |
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| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu95c_GSM1675152_GSM1675152_PN68_u95c_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/celegans --build-arg package=pd.celegans_3.12.0.tar.gz --build-arg db=celegans -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
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| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
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| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
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| ---> Running in 6538a9325e18 | |
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| ---> Running in b68bd921647a | |
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| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 0ce2abdb901f | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'celegans.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/celegans.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 807983 bytes (789 KB) | |
| ================================================== | |
| downloaded 789 KB | |
| * installing *source* package 'celegans.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (celegans.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpQR1TXf/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.celegans_3.12.0.tar.gz | |
| Installing pd.celegans | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpQR1TXf/devtools771b1c73f/pd.celegans' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.celegans' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.celegans) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 0ce2abdb901f | |
| ---> f9a9be3d1d27 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 718592f62041 | |
| Removing intermediate container 718592f62041 | |
| ---> 467a6dc23b4c | |
| Step 11/13 : COPY convert.R . | |
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| Step 12/13 : USER user | |
| ---> Running in 6d177597a94b | |
| Removing intermediate container 6d177597a94b | |
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| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 62b1ad8d7e43 | |
| Removing intermediate container 62b1ad8d7e43 | |
| ---> 3b9435c6d06f | |
| Successfully built 3b9435c6d06f | |
| Successfully tagged convert/celegans:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/celegans Rscript convert.R -p celegans -o /home/user/data/out/ -i /home/user/data/celegans/GSM1627902_GSM1627902_47_Gas1_LipoicAcid_L1_5.CEL.gz -d celegans -s ce -g GSM1627902_GSM1627902_47_Gas1_LipoicAcid_L1_5 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Ce.eg.db | |
| Reading.. | |
| Loading required package: pd.celegans | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/celegans/GSM1627902_GSM1627902_47_Gas1_LipoicAcid_L1_5.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//celegans_GSM1627902_GSM1627902_47_Gas1_LipoicAcid_L1_5_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/celegans Rscript convert.R -p celegans -o /home/user/data/out/ -i /home/user/data/celegans/GSM1627892_GSM1627892_37_Gas1_CoQ10_A_1.CEL.gz -d celegans -s ce -g GSM1627892_GSM1627892_37_Gas1_CoQ10_A_1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Ce.eg.db | |
| Reading.. | |
| Loading required package: pd.celegans | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/celegans/GSM1627892_GSM1627892_37_Gas1_CoQ10_A_1.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//celegans_GSM1627892_GSM1627892_37_Gas1_CoQ10_A_1_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/celegans Rscript convert.R -p celegans -o /home/user/data/out/ -i /home/user/data/celegans/GSM1627929_GSM1627929_74_Gas1_CoQ10_L1_2.CEL.gz -d celegans -s ce -g GSM1627929_GSM1627929_74_Gas1_CoQ10_L1_2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Ce.eg.db | |
| Reading.. | |
| Loading required package: pd.celegans | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/celegans/GSM1627929_GSM1627929_74_Gas1_CoQ10_L1_2.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//celegans_GSM1627929_GSM1627929_74_Gas1_CoQ10_L1_2_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/celegans Rscript convert.R -p celegans -o /home/user/data/out/ -i /home/user/data/celegans/GSM1627857_GSM1627857_2_N2_H2O_A_5.CEL.gz -d celegans -s ce -g GSM1627857_GSM1627857_2_N2_H2O_A_5 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Ce.eg.db | |
| Reading.. | |
| Loading required package: pd.celegans | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/celegans/GSM1627857_GSM1627857_2_N2_H2O_A_5.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//celegans_GSM1627857_GSM1627857_2_N2_H2O_A_5_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/celegans Rscript convert.R -p celegans -o /home/user/data/out/ -i /home/user/data/celegans/GSM1627917_GSM1627917_62_Gas1_OroticAcid_L1_1.CEL.gz -d celegans -s ce -g GSM1627917_GSM1627917_62_Gas1_OroticAcid_L1_1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Ce.eg.db | |
| Reading.. | |
| Loading required package: pd.celegans | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/celegans/GSM1627917_GSM1627917_62_Gas1_OroticAcid_L1_1.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//celegans_GSM1627917_GSM1627917_62_Gas1_OroticAcid_L1_1_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/canine2 --build-arg package=pd.canine.2_3.12.0.tar.gz --build-arg db=canine2 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 1af7d750d797 | |
| Removing intermediate container 1af7d750d797 | |
| ---> 68bf369d8243 | |
| Step 7/13 : ARG db | |
| ---> Running in ba27964607d9 | |
| Removing intermediate container ba27964607d9 | |
| ---> 79a4bead4372 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in ccab8e844873 | |
| Removing intermediate container ccab8e844873 | |
| ---> a5e7b7ff9b2e | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 8ebbce6c07cc | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'canine2.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/canine2.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 1724323 bytes (1.6 MB) | |
| ================================================== | |
| downloaded 1.6 MB | |
| * installing *source* package 'canine2.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (canine2.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpIVrCgf/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.canine.2_3.12.0.tar.gz | |
| Installing pd.canine.2 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpIVrCgf/devtools74a6d74e8/pd.canine.2' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.canine.2' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.canine.2) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 8ebbce6c07cc | |
| ---> 6f837e40c93d | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 4e74ca786ab2 | |
| Removing intermediate container 4e74ca786ab2 | |
| ---> ae18a5a58531 | |
| Step 11/13 : COPY convert.R . | |
| ---> 4e07aa7e292d | |
| Step 12/13 : USER user | |
| ---> Running in c5f61db47a2f | |
| Removing intermediate container c5f61db47a2f | |
| ---> 93b44e784408 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in fb8a893a451c | |
| Removing intermediate container fb8a893a451c | |
| ---> 580fc9e0e6f2 | |
| Successfully built 580fc9e0e6f2 | |
| Successfully tagged convert/canine2:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/canine2' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/mu11ksubb --build-arg package=pd.mu11ksubb_3.12.0.tar.gz --build-arg db=mu11ksubb -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 62bf2e85238b | |
| Removing intermediate container 62bf2e85238b | |
| ---> dc01c37b2452 | |
| Step 7/13 : ARG db | |
| ---> Running in 2a760d8b9159 | |
| Removing intermediate container 2a760d8b9159 | |
| ---> 76d02e17ed78 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 80882cc8e721 | |
| Removing intermediate container 80882cc8e721 | |
| ---> 57add5c26967 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 3ae5f66cc9a2 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'mu11ksubb.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mu11ksubb.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 300766 bytes (293 KB) | |
| ================================================== | |
| downloaded 293 KB | |
| * installing *source* package 'mu11ksubb.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (mu11ksubb.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmprtRhTt/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mu11ksubb_3.12.0.tar.gz | |
| Installing pd.mu11ksubb | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmprtRhTt/devtools866fc08c2/pd.mu11ksubb' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.mu11ksubb' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| Warning: call dbDisconnect() when finished working with a connection | |
| ** testing if installed package can be loaded | |
| * DONE (pd.mu11ksubb) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 3ae5f66cc9a2 | |
| ---> 6da5bdda4d09 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in bcc765b1cfe9 | |
| Removing intermediate container bcc765b1cfe9 | |
| ---> 0590fbf3e52c | |
| Step 11/13 : COPY convert.R . | |
| ---> ec4efe5fb918 | |
| Step 12/13 : USER user | |
| ---> Running in 32e58eaa6649 | |
| Removing intermediate container 32e58eaa6649 | |
| ---> 0fc156e260a8 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 4ed6397200a8 | |
| Removing intermediate container 4ed6397200a8 | |
| ---> 0a0599fb2c39 | |
| Successfully built 0a0599fb2c39 | |
| Successfully tagged convert/mu11ksubb:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/mu11ksubb' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/mgu74av2 --build-arg package=pd.mg.u74av2_3.12.0.tar.gz --build-arg db=mgu74av2 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in d3342a0253df | |
| Removing intermediate container d3342a0253df | |
| ---> 45a35c1f6117 | |
| Step 7/13 : ARG db | |
| ---> Running in eb5f1faf6205 | |
| Removing intermediate container eb5f1faf6205 | |
| ---> 7ede1342110f | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 91fec98a1820 | |
| Removing intermediate container 91fec98a1820 | |
| ---> 58a1cd980e69 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 1a27ed31c10b | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'mgu74av2.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mgu74av2.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 491976 bytes (480 KB) | |
| ================================================== | |
| downloaded 480 KB | |
| * installing *source* package 'mgu74av2.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (mgu74av2.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpoOrYZ5/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mg.u74av2_3.12.0.tar.gz | |
| Installing pd.mg.u74av2 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpoOrYZ5/devtools72b5463e7/pd.mg.u74av2' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.mg.u74av2' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.mg.u74av2) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 1a27ed31c10b | |
| ---> e4f731dd2851 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in c492e15212ed | |
| Removing intermediate container c492e15212ed | |
| ---> 165cdb3d089e | |
| Step 11/13 : COPY convert.R . | |
| ---> ceaed37c5c56 | |
| Step 12/13 : USER user | |
| ---> Running in 7f18b9c096b7 | |
| Removing intermediate container 7f18b9c096b7 | |
| ---> f7e038efaf95 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 109a6caec265 | |
| Removing intermediate container 109a6caec265 | |
| ---> 638fc38da801 | |
| Successfully built 638fc38da801 | |
| Successfully tagged convert/mgu74av2:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/mgu74av2' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/hgu219 --build-arg package=pd.hg.u219_3.12.0.tar.gz --build-arg db=hgu219 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in a6e21dab2563 | |
| Removing intermediate container a6e21dab2563 | |
| ---> e61cf77dc8e7 | |
| Step 7/13 : ARG db | |
| ---> Running in 11bb86d4d553 | |
| Removing intermediate container 11bb86d4d553 | |
| ---> 2e22511714a3 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 41822bfa264f | |
| Removing intermediate container 41822bfa264f | |
| ---> b67785b7f2eb | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in c70494fbc4e2 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hgu219.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu219.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 2002040 bytes (1.9 MB) | |
| ================================================== | |
| downloaded 1.9 MB | |
| * installing *source* package 'hgu219.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hgu219.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmp1mmELs/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hg.u219_3.12.0.tar.gz | |
| Installing pd.hg.u219 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmp1mmELs/devtools72b6ab640/pd.hg.u219' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hg.u219' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hg.u219) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container c70494fbc4e2 | |
| ---> 7d0d36e5f73a | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 9ac2a1674c7e | |
| Removing intermediate container 9ac2a1674c7e | |
| ---> 598fd4706545 | |
| Step 11/13 : COPY convert.R . | |
| ---> 5588bf0f2e1b | |
| Step 12/13 : USER user | |
| ---> Running in f72e1d2ea43c | |
| Removing intermediate container f72e1d2ea43c | |
| ---> 095b3e630b65 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 296ffbcfa30f | |
| Removing intermediate container 296ffbcfa30f | |
| ---> 2364eb45a8b5 | |
| Successfully built 2364eb45a8b5 | |
| Successfully tagged convert/hgu219:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu219 Rscript convert.R -p hgu219 -o /home/user/data/out/ -i /home/user/data/hgu219/GSM1692201_GSM1692201_13_03_2013_D11_2441106.CEL.gz -d hgu219 -s hs -g GSM1692201_GSM1692201_13_03_2013_D11_2441106 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u219 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu219/GSM1692201_GSM1692201_13_03_2013_D11_2441106.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu219_GSM1692201_GSM1692201_13_03_2013_D11_2441106_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu219 Rscript convert.R -p hgu219 -o /home/user/data/out/ -i /home/user/data/hgu219/GSM1237162_GSM1237162_TH001_AP_12hrs_040810_C02_E01.CEL.gz -d hgu219 -s hs -g GSM1237162_GSM1237162_TH001_AP_12hrs_040810_C02_E01 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u219 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu219/GSM1237162_GSM1237162_TH001_AP_12hrs_040810_C02_E01.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu219_GSM1237162_GSM1237162_TH001_AP_12hrs_040810_C02_E01_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/mogene21st --build-arg package=pd.mogene.2.1.st_3.14.1.tar.gz --build-arg db=mogene21stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 3a783dd639a0 | |
| Removing intermediate container 3a783dd639a0 | |
| ---> 0bd77615b9cd | |
| Step 7/13 : ARG db | |
| ---> Running in b6834a0d5fa9 | |
| Removing intermediate container b6834a0d5fa9 | |
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| Step 8/13 : ENV DB=$db | |
| ---> Running in b44407a1f75d | |
| Removing intermediate container b44407a1f75d | |
| ---> 6c405e1114a8 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in a113ab7cf493 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'mogene21stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mogene21stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 19142056 bytes (18.3 MB) | |
| ================================================== | |
| downloaded 18.3 MB | |
| * installing *source* package 'mogene21stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (mogene21stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmp7DDI4Q/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mogene.2.1.st_3.14.1.tar.gz | |
| Installing pd.mogene.2.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmp7DDI4Q/devtools736d0c26f/pd.mogene.2.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.mogene.2.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.mogene.2.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container a113ab7cf493 | |
| ---> 748a6521f9e6 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 85f9c3916a15 | |
| Removing intermediate container 85f9c3916a15 | |
| ---> 862e8b664451 | |
| Step 11/13 : COPY convert.R . | |
| ---> a9f05dc0b5a8 | |
| Step 12/13 : USER user | |
| ---> Running in f61f75f3fa1b | |
| Removing intermediate container f61f75f3fa1b | |
| ---> 845637bd0778 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in fbd3788fdd29 | |
| Removing intermediate container fbd3788fdd29 | |
| ---> a85c25cc27f9 | |
| Successfully built a85c25cc27f9 | |
| Successfully tagged convert/mogene21st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene21st Rscript convert.R -p mogene21st -o /home/user/data/out/ -i /home/user/data/mogene21st/GSM2138279_GSM2138279_34_MoGene-2_1-st_G07.CEL.gz -d mogene21stprobeset -s mm -g GSM2138279_GSM2138279_34_MoGene-2_1-st_G07 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mogene.2.1.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mogene21st/GSM2138279_GSM2138279_34_MoGene-2_1-st_G07.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mogene21st_GSM2138279_GSM2138279_34_MoGene-2_1-st_G07_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene21st Rscript convert.R -p mogene21st -o /home/user/data/out/ -i /home/user/data/mogene21st/GSM2138292_GSM2138292_64_100216MoGene2.1ST_F07.CEL.gz -d mogene21stprobeset -s mm -g GSM2138292_GSM2138292_64_100216MoGene2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mogene.2.1.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mogene21st/GSM2138292_GSM2138292_64_100216MoGene2.1ST_F07.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mogene21st_GSM2138292_GSM2138292_64_100216MoGene2_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene21st Rscript convert.R -p mogene21st -o /home/user/data/out/ -i /home/user/data/mogene21st/GSM2138278_GSM2138278_32_MoGene-2_1-st_F07.CEL.gz -d mogene21stprobeset -s mm -g GSM2138278_GSM2138278_32_MoGene-2_1-st_F07 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mogene.2.1.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mogene21st/GSM2138278_GSM2138278_32_MoGene-2_1-st_F07.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mogene21st_GSM2138278_GSM2138278_32_MoGene-2_1-st_F07_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene21st Rscript convert.R -p mogene21st -o /home/user/data/out/ -i /home/user/data/mogene21st/GSM2138298_GSM2138298_70_100216MoGene2.1ST_D09.CEL.gz -d mogene21stprobeset -s mm -g GSM2138298_GSM2138298_70_100216MoGene2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mogene.2.1.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mogene21st/GSM2138298_GSM2138298_70_100216MoGene2.1ST_D09.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mogene21st_GSM2138298_GSM2138298_70_100216MoGene2_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene21st Rscript convert.R -p mogene21st -o /home/user/data/out/ -i /home/user/data/mogene21st/GSM2138282_GSM2138282_38_MoGene-2_1-st_B09.CEL.gz -d mogene21stprobeset -s mm -g GSM2138282_GSM2138282_38_MoGene-2_1-st_B09 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mogene.2.1.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mogene21st/GSM2138282_GSM2138282_38_MoGene-2_1-st_B09.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mogene21st_GSM2138282_GSM2138282_38_MoGene-2_1-st_B09_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/chigene10st --build-arg package=pd.chigene.1.0.st_3.12.0.tar.gz --build-arg db=chigene10st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 255324890c4e | |
| Removing intermediate container 255324890c4e | |
| ---> c29819c63136 | |
| Step 7/13 : ARG db | |
| ---> Running in 420d7401636f | |
| Removing intermediate container 420d7401636f | |
| ---> 3b0e4c1f0572 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 842765b5ec50 | |
| Removing intermediate container 842765b5ec50 | |
| ---> 684d411ce6d2 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 9785df98b9fb | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'chigene10st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'chigene10st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.chigene.1.0.st_3.12.0.tar.gz | |
| Installing pd.chigene.1.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpTaACjD/devtools725078046/pd.chigene.1.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.chigene.1.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.chigene.1.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 9785df98b9fb | |
| ---> 22aafef37a40 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 88fa9c7e95dd | |
| Removing intermediate container 88fa9c7e95dd | |
| ---> 150bc055cb1d | |
| Step 11/13 : COPY convert.R . | |
| ---> 578b2df6e827 | |
| Step 12/13 : USER user | |
| ---> Running in 47f60b697e6c | |
| Removing intermediate container 47f60b697e6c | |
| ---> 6bc10f7b2632 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 2a923b361614 | |
| Removing intermediate container 2a923b361614 | |
| ---> 92000f8da32a | |
| Successfully built 92000f8da32a | |
| Successfully tagged convert/chigene10st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/chigene10st Rscript convert.R -p chigene10st -o /home/user/data/out/ -i /home/user/data/chigene10st/GSM2033382_GSM2033382_ChiMaBrL10_76.CEL.gz -d chigene10st -s gg -g GSM2033382_GSM2033382_ChiMaBrL10_76 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'chigene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/chigene10st Rscript convert.R -p chigene10st -o /home/user/data/out/ -i /home/user/data/chigene10st/GSM2033265_GSM2033265_ChiMaLegH13_34.CEL.gz -d chigene10st -s gg -g GSM2033265_GSM2033265_ChiMaLegH13_34 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'chigene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/chigene10st Rscript convert.R -p chigene10st -o /home/user/data/out/ -i /home/user/data/chigene10st/GSM2033328_GSM2033328_ChiEmBrL10_60.CEL.gz -d chigene10st -s gg -g GSM2033328_GSM2033328_ChiEmBrL10_60 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'chigene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/chigene10st Rscript convert.R -p chigene10st -o /home/user/data/out/ -i /home/user/data/chigene10st/GSM2033355_GSM2033355_ChiMaBrH13_43.CEL.gz -d chigene10st -s gg -g GSM2033355_GSM2033355_ChiMaBrH13_43 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'chigene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/chigene10st Rscript convert.R -p chigene10st -o /home/user/data/out/ -i /home/user/data/chigene10st/GSM2033339_GSM2033339_ChiEmBrL13_77.CEL.gz -d chigene10st -s gg -g GSM2033339_GSM2033339_ChiEmBrL13_77 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'chigene10st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/mouse4302 --build-arg package=pd.mouse430.2_3.12.0.tar.gz --build-arg db=mouse4302 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in c718550e920f | |
| Removing intermediate container c718550e920f | |
| ---> a0335718c07e | |
| Step 7/13 : ARG db | |
| ---> Running in f770abbd47b8 | |
| Removing intermediate container f770abbd47b8 | |
| ---> e17fe2c2a8f1 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 49583cf0ae55 | |
| Removing intermediate container 49583cf0ae55 | |
| ---> 382af416c8f9 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in eb466a535462 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'mouse4302.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mouse4302.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 1700696 bytes (1.6 MB) | |
| ================================================== | |
| downloaded 1.6 MB | |
| * installing *source* package 'mouse4302.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (mouse4302.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpWDdkGn/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mouse430.2_3.12.0.tar.gz | |
| Installing pd.mouse430.2 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpWDdkGn/devtools771f5150a/pd.mouse430.2' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.mouse430.2' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.mouse430.2) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container eb466a535462 | |
| ---> 20eb2449a73a | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 9bca2be7193c | |
| Removing intermediate container 9bca2be7193c | |
| ---> 059657795ade | |
| Step 11/13 : COPY convert.R . | |
| ---> fe6aaa523f4b | |
| Step 12/13 : USER user | |
| ---> Running in 9847931ab7dd | |
| Removing intermediate container 9847931ab7dd | |
| ---> 01eb5cf1835b | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 2d697e066df3 | |
| Removing intermediate container 2d697e066df3 | |
| ---> aa5dd8ab3714 | |
| Successfully built aa5dd8ab3714 | |
| Successfully tagged convert/mouse4302:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mouse4302 Rscript convert.R -p mouse4302 -o /home/user/data/out/ -i /home/user/data/mouse4302/GSM1162179_GSM1162179_Rappold_130309_7_E12.5-WT-limb_Mou430_2.CEL.gz -d mouse4302 -s mm -g GSM1162179_GSM1162179_Rappold_130309_7_E12 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mouse430.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mouse4302/GSM1162179_GSM1162179_Rappold_130309_7_E12.5-WT-limb_Mou430_2.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mouse4302_GSM1162179_GSM1162179_Rappold_130309_7_E12_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mouse4302 Rscript convert.R -p mouse4302 -o /home/user/data/out/ -i /home/user/data/mouse4302/GSM984788_GSM984788_ko-normal2.CEL.gz -d mouse4302 -s mm -g GSM984788_GSM984788_ko-normal2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mouse430.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mouse4302/GSM984788_GSM984788_ko-normal2.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mouse4302_GSM984788_GSM984788_ko-normal2_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mouse4302 Rscript convert.R -p mouse4302 -o /home/user/data/out/ -i /home/user/data/mouse4302/GSM984790_GSM984790_ko-normal4.CEL.gz -d mouse4302 -s mm -g GSM984790_GSM984790_ko-normal4 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mouse430.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mouse4302/GSM984790_GSM984790_ko-normal4.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mouse4302_GSM984790_GSM984790_ko-normal4_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mouse4302 Rscript convert.R -p mouse4302 -o /home/user/data/out/ -i /home/user/data/mouse4302/GSM984783_GSM984783_wt-normal1.CEL.gz -d mouse4302 -s mm -g GSM984783_GSM984783_wt-normal1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mouse430.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mouse4302/GSM984783_GSM984783_wt-normal1.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mouse4302_GSM984783_GSM984783_wt-normal1_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mouse4302 Rscript convert.R -p mouse4302 -o /home/user/data/out/ -i /home/user/data/mouse4302/GSM2096882_GSM2096882_Kzhyshkowska_081210_empty_Vector_Klon_4_Mouse430_2_.CEL.gz -d mouse4302 -s mm -g GSM2096882_GSM2096882_Kzhyshkowska_081210_empty_Vector_Klon_4_Mouse430_2_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mouse430.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mouse4302/GSM2096882_GSM2096882_Kzhyshkowska_081210_empty_Vector_Klon_4_Mouse430_2_.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mouse4302_GSM2096882_GSM2096882_Kzhyshkowska_081210_empty_Vector_Klon_4_Mouse430_2__master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/drogene11st --build-arg package=pd.drogene.1.1.st_3.12.0.tar.gz --build-arg db=drogene11st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 2e94d0078c36 | |
| Removing intermediate container 2e94d0078c36 | |
| ---> 96897513d9d5 | |
| Step 7/13 : ARG db | |
| ---> Running in 24cc8f7aae68 | |
| Removing intermediate container 24cc8f7aae68 | |
| ---> c2741c229b75 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 8577451eab0a | |
| Removing intermediate container 8577451eab0a | |
| ---> 384219885be9 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in a6cf1ba6d14c | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'drogene11st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'drogene11st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.drogene.1.1.st_3.12.0.tar.gz | |
| Installing pd.drogene.1.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpElyRUI/devtools72289f03b/pd.drogene.1.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.drogene.1.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.drogene.1.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container a6cf1ba6d14c | |
| ---> 97df240611e7 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in d482687a5b4e | |
| Removing intermediate container d482687a5b4e | |
| ---> 942e3e71f0c5 | |
| Step 11/13 : COPY convert.R . | |
| ---> 20d7d271ea4e | |
| Step 12/13 : USER user | |
| ---> Running in e64a55696a21 | |
| Removing intermediate container e64a55696a21 | |
| ---> c33a0ddb03f9 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 0d14f3ad326e | |
| Removing intermediate container 0d14f3ad326e | |
| ---> 642050c7ca8b | |
| Successfully built 642050c7ca8b | |
| Successfully tagged convert/drogene11st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drogene11st Rscript convert.R -p drogene11st -o /home/user/data/out/ -i /home/user/data/drogene11st/GSM1684611_GSM1684611_Drosophila_8re.CEL.gz -d drogene11st -s dm -g GSM1684611_GSM1684611_Drosophila_8re | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'drogene11st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drogene11st Rscript convert.R -p drogene11st -o /home/user/data/out/ -i /home/user/data/drogene11st/GSM1684601_GSM1684601_Drosophila_2re.CEL.gz -d drogene11st -s dm -g GSM1684601_GSM1684601_Drosophila_2re | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'drogene11st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drogene11st Rscript convert.R -p drogene11st -o /home/user/data/out/ -i /home/user/data/drogene11st/GSM1684610_GSM1684610_Drosophila_8.CEL.gz -d drogene11st -s dm -g GSM1684610_GSM1684610_Drosophila_8 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'drogene11st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drogene11st Rscript convert.R -p drogene11st -o /home/user/data/out/ -i /home/user/data/drogene11st/GSM1684598_GSM1684598_Drosophila_1.CEL.gz -d drogene11st -s dm -g GSM1684598_GSM1684598_Drosophila_1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'drogene11st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/ygs98 --build-arg package=pd.yg.s98_3.12.0.tar.gz --build-arg db=ygs98 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in dfe2e464ee0d | |
| Removing intermediate container dfe2e464ee0d | |
| ---> a25a27418a10 | |
| Step 7/13 : ARG db | |
| ---> Running in 5e25331d9b6e | |
| Removing intermediate container 5e25331d9b6e | |
| ---> 42353b6f907b | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 6a5a7543c9d0 | |
| Removing intermediate container 6a5a7543c9d0 | |
| ---> 51ca6d725f05 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 12b3d65c0565 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'ygs98.db' | |
| also installing the dependency 'org.Sc.sgd.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Sc.sgd.db_3.5.0.tar.gz' | |
| Content type 'application/x-gzip' length 21146339 bytes (20.2 MB) | |
| ================================================== | |
| downloaded 20.2 MB | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/ygs98.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 221818 bytes (216 KB) | |
| ================================================== | |
| downloaded 216 KB | |
| * installing *source* package 'org.Sc.sgd.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (org.Sc.sgd.db) | |
| * installing *source* package 'ygs98.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (ygs98.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpjM2LRc/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.yg.s98_3.12.0.tar.gz | |
| Installing pd.yg.s98 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpjM2LRc/devtools74d74ef1/pd.yg.s98' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.yg.s98' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| Warning: call dbDisconnect() when finished working with a connection | |
| ** testing if installed package can be loaded | |
| * DONE (pd.yg.s98) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 12b3d65c0565 | |
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| ---> Running in b1d4c6cc890f | |
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| ---> Running in 7d159440ece5 | |
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| Removing intermediate container d1533c7ce50d | |
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| Successfully built 706f1b0f7d35 | |
| Successfully tagged convert/ygs98:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/ygs98' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/porcine --build-arg package=pd.porcine_3.12.0.tar.gz --build-arg db=porcine -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
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| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
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| Step 6/13 : ENV PACKAGE=$package | |
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| Step 7/13 : ARG db | |
| ---> Running in 6fa9413a9edf | |
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| Step 8/13 : ENV DB=$db | |
| ---> Running in 77d843dff10a | |
| Removing intermediate container 77d843dff10a | |
| ---> b8dae277c082 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 36e1ceeaf3b9 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'porcine.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/porcine.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 900443 bytes (879 KB) | |
| ================================================== | |
| downloaded 879 KB | |
| * installing *source* package 'porcine.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (porcine.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmphOPzBC/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.porcine_3.12.0.tar.gz | |
| Installing pd.porcine | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmphOPzBC/devtools718a856b0/pd.porcine' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.porcine' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.porcine) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 36e1ceeaf3b9 | |
| ---> af6fceb6a4c7 | |
| Step 10/13 : VOLUME /home/user/data | |
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| ---> Running in 8d52405cef5a | |
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| ---> Running in 2d950878c4bd | |
| Removing intermediate container 2d950878c4bd | |
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| Successfully built 431e167b0b98 | |
| Successfully tagged convert/porcine:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/porcine' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/mogene20st --build-arg package=pd.mogene.2.0.st_3.14.1.tar.gz --build-arg db=mogene20stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in d488bf938cb0 | |
| Removing intermediate container d488bf938cb0 | |
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| Step 7/13 : ARG db | |
| ---> Running in dbbe203e8538 | |
| Removing intermediate container dbbe203e8538 | |
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| Step 8/13 : ENV DB=$db | |
| ---> Running in 9090a3dafbe1 | |
| Removing intermediate container 9090a3dafbe1 | |
| ---> 21d023b6c17e | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 2fa539e93d91 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'mogene20stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mogene20stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 19142058 bytes (18.3 MB) | |
| ================================================== | |
| downloaded 18.3 MB | |
| * installing *source* package 'mogene20stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (mogene20stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpwEklxa/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mogene.2.0.st_3.14.1.tar.gz | |
| Installing pd.mogene.2.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpwEklxa/devtools75092bc04/pd.mogene.2.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.mogene.2.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.mogene.2.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 2fa539e93d91 | |
| ---> 58a0bfa6ce02 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 6ffcf2be6938 | |
| Removing intermediate container 6ffcf2be6938 | |
| ---> 3b65b4a66f78 | |
| Step 11/13 : COPY convert.R . | |
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| Step 12/13 : USER user | |
| ---> Running in ed957b88cba8 | |
| Removing intermediate container ed957b88cba8 | |
| ---> 663e0d2dcc49 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 8be0bd3a2406 | |
| Removing intermediate container 8be0bd3a2406 | |
| ---> 0d42bb2c212e | |
| Successfully built 0d42bb2c212e | |
| Successfully tagged convert/mogene20st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene20st Rscript convert.R -p mogene20st -o /home/user/data/out/ -i /home/user/data/mogene20st/GSM1318174_GSM1318174_K5001_shRNA-Cdca7l_2_-1.CEL.gz -d mogene20stprobeset -s mm -g GSM1318174_GSM1318174_K5001_shRNA-Cdca7l_2_-1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mogene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mogene20st/GSM1318174_GSM1318174_K5001_shRNA-Cdca7l_2_-1.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mogene20st_GSM1318174_GSM1318174_K5001_shRNA-Cdca7l_2_-1_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene20st Rscript convert.R -p mogene20st -o /home/user/data/out/ -i /home/user/data/mogene20st/GSM1967970_GSM1967970_3_MYB-tr_Pool_1.CEL.gz -d mogene20stprobeset -s mm -g GSM1967970_GSM1967970_3_MYB-tr_Pool_1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mogene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mogene20st/GSM1967970_GSM1967970_3_MYB-tr_Pool_1.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mogene20st_GSM1967970_GSM1967970_3_MYB-tr_Pool_1_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene20st Rscript convert.R -p mogene20st -o /home/user/data/out/ -i /home/user/data/mogene20st/GSM2630715_GSM2630715_PMS-MoGene_2-12195.CEL.gz -d mogene20stprobeset -s mm -g GSM2630715_GSM2630715_PMS-MoGene_2-12195 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mogene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mogene20st/GSM2630715_GSM2630715_PMS-MoGene_2-12195.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mogene20st_GSM2630715_GSM2630715_PMS-MoGene_2-12195_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene20st Rscript convert.R -p mogene20st -o /home/user/data/out/ -i /home/user/data/mogene20st/GSM2630708_GSM2630708_PMS-MoGene_2-14755.CEL.gz -d mogene20stprobeset -s mm -g GSM2630708_GSM2630708_PMS-MoGene_2-14755 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mogene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mogene20st/GSM2630708_GSM2630708_PMS-MoGene_2-14755.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mogene20st_GSM2630708_GSM2630708_PMS-MoGene_2-14755_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene20st Rscript convert.R -p mogene20st -o /home/user/data/out/ -i /home/user/data/mogene20st/GSM1939042_GSM1939042_2_PA2681.CEL.gz -d mogene20stprobeset -s mm -g GSM1939042_GSM1939042_2_PA2681 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.mogene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/mogene20st/GSM1939042_GSM1939042_2_PA2681.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//mogene20st_GSM1939042_GSM1939042_2_PA2681_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/moe430b --build-arg package=pd.moe430b_3.12.0.tar.gz --build-arg db=moe430b -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 53eca264d42e | |
| Removing intermediate container 53eca264d42e | |
| ---> a6fb21f79362 | |
| Step 7/13 : ARG db | |
| ---> Running in a72be2b5d147 | |
| Removing intermediate container a72be2b5d147 | |
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| Step 8/13 : ENV DB=$db | |
| ---> Running in 25aa47dd7732 | |
| Removing intermediate container 25aa47dd7732 | |
| ---> 0422ab39e04c | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 463c77d71304 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'moe430b.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/moe430b.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 789949 bytes (771 KB) | |
| ================================================== | |
| downloaded 771 KB | |
| * installing *source* package 'moe430b.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (moe430b.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpkSds7B/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.moe430b_3.12.0.tar.gz | |
| Installing pd.moe430b | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpkSds7B/devtools7badbe64/pd.moe430b' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.moe430b' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.moe430b) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 463c77d71304 | |
| ---> ae6071fd5d20 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in b4309f6174e2 | |
| Removing intermediate container b4309f6174e2 | |
| ---> a533c997c57d | |
| Step 11/13 : COPY convert.R . | |
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| Step 12/13 : USER user | |
| ---> Running in df44e213030c | |
| Removing intermediate container df44e213030c | |
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| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in ad6268ff1000 | |
| Removing intermediate container ad6268ff1000 | |
| ---> e2ab998e4986 | |
| Successfully built e2ab998e4986 | |
| Successfully tagged convert/moe430b:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/moe430b' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/hthgu133a --build-arg package=pd.ht.hg.u133a_3.12.0.tar.gz --build-arg db=hthgu133a -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 4c9daeaa9f54 | |
| Removing intermediate container 4c9daeaa9f54 | |
| ---> 817f9ca2f4d0 | |
| Step 7/13 : ARG db | |
| ---> Running in 172a79244eae | |
| Removing intermediate container 172a79244eae | |
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| Step 8/13 : ENV DB=$db | |
| ---> Running in 76e38d42d988 | |
| Removing intermediate container 76e38d42d988 | |
| ---> 416475c051fc | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 0d01a1a03faf | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hthgu133a.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hthgu133a.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 903509 bytes (882 KB) | |
| ================================================== | |
| downloaded 882 KB | |
| * installing *source* package 'hthgu133a.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hthgu133a.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmppgu6na/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.ht.hg.u133a_3.12.0.tar.gz | |
| Installing pd.ht.hg.u133a | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmppgu6na/devtools85ca5f470/pd.ht.hg.u133a' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.ht.hg.u133a' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.ht.hg.u133a) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 0d01a1a03faf | |
| ---> 39a1cd8a2687 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 3c52b5f66a19 | |
| Removing intermediate container 3c52b5f66a19 | |
| ---> e715dd83068d | |
| Step 11/13 : COPY convert.R . | |
| ---> bd908d0011ac | |
| Step 12/13 : USER user | |
| ---> Running in f110fc62b505 | |
| Removing intermediate container f110fc62b505 | |
| ---> 420ede1c067f | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in ccca7ed15bb7 | |
| Removing intermediate container ccca7ed15bb7 | |
| ---> 1cfc95570ea0 | |
| Successfully built 1cfc95570ea0 | |
| Successfully tagged convert/hthgu133a:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hthgu133a Rscript convert.R -p hthgu133a -o /home/user/data/out/ -i /home/user/data/hthgu133a/GSM363121_GSM363121.CEL.gz -d hthgu133a -s hs -g GSM363121_GSM363121 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.ht.hg.u133a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hthgu133a/GSM363121_GSM363121.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hthgu133a_GSM363121_GSM363121_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hthgu133a Rscript convert.R -p hthgu133a -o /home/user/data/out/ -i /home/user/data/hthgu133a/GSM753704_GSM753704.CEL.gz -d hthgu133a -s hs -g GSM753704_GSM753704 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.ht.hg.u133a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hthgu133a/GSM753704_GSM753704.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hthgu133a_GSM753704_GSM753704_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hthgu133a Rscript convert.R -p hthgu133a -o /home/user/data/out/ -i /home/user/data/hthgu133a/GSM528637_GSM528637_plate1_H08.CEL.gz -d hthgu133a -s hs -g GSM528637_GSM528637_plate1_H08 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.ht.hg.u133a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hthgu133a/GSM528637_GSM528637_plate1_H08.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hthgu133a_GSM528637_GSM528637_plate1_H08_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hthgu133a Rscript convert.R -p hthgu133a -o /home/user/data/out/ -i /home/user/data/hthgu133a/GSM498516_GSM498516_UZHRCC072_HG-U133.CEL.gz -d hthgu133a -s hs -g GSM498516_GSM498516_UZHRCC072_HG-U133 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.ht.hg.u133a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hthgu133a/GSM498516_GSM498516_UZHRCC072_HG-U133.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hthgu133a_GSM498516_GSM498516_UZHRCC072_HG-U133_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/drogene10st --build-arg package=pd.drogene.1.0.st_3.12.0.tar.gz --build-arg db=drogene10st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 7ada6d468a53 | |
| Removing intermediate container 7ada6d468a53 | |
| ---> 62e978838a1a | |
| Step 7/13 : ARG db | |
| ---> Running in 9fd479e7efd6 | |
| Removing intermediate container 9fd479e7efd6 | |
| ---> 824d472ada5f | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in f4cfd8c50c18 | |
| Removing intermediate container f4cfd8c50c18 | |
| ---> d27b8b23ca4a | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 20496aae9eca | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'drogene10st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'drogene10st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.drogene.1.0.st_3.12.0.tar.gz | |
| Installing pd.drogene.1.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpQxrbF5/devtools74f8f33f8/pd.drogene.1.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.drogene.1.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.drogene.1.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 20496aae9eca | |
| ---> 45d7caad9ad3 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 841fb4c53e4d | |
| Removing intermediate container 841fb4c53e4d | |
| ---> b600d3cc2656 | |
| Step 11/13 : COPY convert.R . | |
| ---> f405ac8d1ab1 | |
| Step 12/13 : USER user | |
| ---> Running in 01493bccdbd0 | |
| Removing intermediate container 01493bccdbd0 | |
| ---> 6c9269315872 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in ec73c4ba4095 | |
| Removing intermediate container ec73c4ba4095 | |
| ---> b538f3fb0acb | |
| Successfully built b538f3fb0acb | |
| Successfully tagged convert/drogene10st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drogene10st Rscript convert.R -p drogene10st -o /home/user/data/out/ -i /home/user/data/drogene10st/GSM1295070_GSM1295070_AG_12.CEL.gz -d drogene10st -s dm -g GSM1295070_GSM1295070_AG_12 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'drogene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drogene10st Rscript convert.R -p drogene10st -o /home/user/data/out/ -i /home/user/data/drogene10st/GSM1295071_GSM1295071_AG_13.CEL.gz -d drogene10st -s dm -g GSM1295071_GSM1295071_AG_13 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'drogene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drogene10st Rscript convert.R -p drogene10st -o /home/user/data/out/ -i /home/user/data/drogene10st/GSM1588215_GSM1588215_AG_9.CEL.gz -d drogene10st -s dm -g GSM1588215_GSM1588215_AG_9 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'drogene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drogene10st Rscript convert.R -p drogene10st -o /home/user/data/out/ -i /home/user/data/drogene10st/GSM1295075_GSM1295075_AG_4.CEL.gz -d drogene10st -s dm -g GSM1295075_GSM1295075_AG_4 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'drogene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drogene10st Rscript convert.R -p drogene10st -o /home/user/data/out/ -i /home/user/data/drogene10st/GSM1588213_GSM1588213_AG_7.CEL.gz -d drogene10st -s dm -g GSM1588213_GSM1588213_AG_7 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'drogene10st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/hgu95d --build-arg package=pd.hg.u95d_3.12.0.tar.gz --build-arg db=hgu95d -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in b050e2f4a8c1 | |
| Removing intermediate container b050e2f4a8c1 | |
| ---> b0e86106ab94 | |
| Step 7/13 : ARG db | |
| ---> Running in a445e6463e66 | |
| Removing intermediate container a445e6463e66 | |
| ---> c771c2e7f137 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in bfed39bb9757 | |
| Removing intermediate container bfed39bb9757 | |
| ---> 49fe30eecb79 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 4cb95ff3d49f | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hgu95d.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu95d.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 468612 bytes (457 KB) | |
| ================================================== | |
| downloaded 457 KB | |
| * installing *source* package 'hgu95d.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hgu95d.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpwVaBVg/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hg.u95d_3.12.0.tar.gz | |
| Installing pd.hg.u95d | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpwVaBVg/devtools773e08420/pd.hg.u95d' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hg.u95d' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hg.u95d) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 4cb95ff3d49f | |
| ---> f82f08c392b0 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 831fcdec2661 | |
| Removing intermediate container 831fcdec2661 | |
| ---> 0275e704347a | |
| Step 11/13 : COPY convert.R . | |
| ---> 617406dd7664 | |
| Step 12/13 : USER user | |
| ---> Running in 83b88a51b61e | |
| Removing intermediate container 83b88a51b61e | |
| ---> 53fe96b2389f | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 45e2c9bfd196 | |
| Removing intermediate container 45e2c9bfd196 | |
| ---> c3dd62e65722 | |
| Successfully built c3dd62e65722 | |
| Successfully tagged convert/hgu95d:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/hgu95d' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/hgu95e --build-arg package=pd.hg.u95e_3.12.0.tar.gz --build-arg db=hgu95e -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 47a49ce6be24 | |
| Removing intermediate container 47a49ce6be24 | |
| ---> 0df363476ec1 | |
| Step 7/13 : ARG db | |
| ---> Running in e13aea1e031f | |
| Removing intermediate container e13aea1e031f | |
| ---> 8f060c91d8f3 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 3d2a6bebdd4b | |
| Removing intermediate container 3d2a6bebdd4b | |
| ---> 43f0d86bb40e | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 955d7e591424 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hgu95e.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu95e.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 490931 bytes (479 KB) | |
| ================================================== | |
| downloaded 479 KB | |
| * installing *source* package 'hgu95e.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hgu95e.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpexyUwF/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hg.u95e_3.12.0.tar.gz | |
| Installing pd.hg.u95e | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpexyUwF/devtools75141da30/pd.hg.u95e' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hg.u95e' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hg.u95e) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 955d7e591424 | |
| ---> 52df6c512f78 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 3b9e54a7aa1f | |
| Removing intermediate container 3b9e54a7aa1f | |
| ---> 4d15f02d622f | |
| Step 11/13 : COPY convert.R . | |
| ---> 3e30d7cdc8bd | |
| Step 12/13 : USER user | |
| ---> Running in 98252eb277b6 | |
| Removing intermediate container 98252eb277b6 | |
| ---> fed795f3ddcb | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 837381cfa36e | |
| Removing intermediate container 837381cfa36e | |
| ---> bf6973de1947 | |
| Successfully built bf6973de1947 | |
| Successfully tagged convert/hgu95e:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/hgu95e' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/hgu133b --build-arg package=pd.hg.u133b_3.12.0.tar.gz --build-arg db=hgu133b -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 13ac8cc38f7a | |
| Removing intermediate container 13ac8cc38f7a | |
| ---> 64865f7d27b9 | |
| Step 7/13 : ARG db | |
| ---> Running in 3fbe66120c17 | |
| Removing intermediate container 3fbe66120c17 | |
| ---> ece2e3aa89d5 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 886785b9a352 | |
| Removing intermediate container 886785b9a352 | |
| ---> 7fd803505057 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 4db3967fd0a8 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hgu133b.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu133b.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 846016 bytes (826 KB) | |
| ================================================== | |
| downloaded 826 KB | |
| * installing *source* package 'hgu133b.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hgu133b.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpIhN9li/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hg.u133b_3.12.0.tar.gz | |
| Installing pd.hg.u133b | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpIhN9li/devtools73673e06b/pd.hg.u133b' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hg.u133b' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hg.u133b) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 4db3967fd0a8 | |
| ---> 085f7971a6f2 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 3ea794b9f764 | |
| Removing intermediate container 3ea794b9f764 | |
| ---> f47ffd3f6572 | |
| Step 11/13 : COPY convert.R . | |
| ---> 7155e4024388 | |
| Step 12/13 : USER user | |
| ---> Running in 9e04bd2750e6 | |
| Removing intermediate container 9e04bd2750e6 | |
| ---> 0e9298b83ef8 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in dca8a46b6d28 | |
| Removing intermediate container dca8a46b6d28 | |
| ---> 4476cedd9c31 | |
| Successfully built 4476cedd9c31 | |
| Successfully tagged convert/hgu133b:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133b Rscript convert.R -p hgu133b -o /home/user/data/out/ -i /home/user/data/hgu133b/GSM2235452_GSM2235452_45013hg133b11.CEL.gz -d hgu133b -s hs -g GSM2235452_GSM2235452_45013hg133b11 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133b | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133b/GSM2235452_GSM2235452_45013hg133b11.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133b_GSM2235452_GSM2235452_45013hg133b11_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133b Rscript convert.R -p hgu133b -o /home/user/data/out/ -i /home/user/data/hgu133b/GSM79507_GSM79507.CEL.gz -d hgu133b -s hs -g GSM79507_GSM79507 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133b | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133b/GSM79507_GSM79507.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133b_GSM79507_GSM79507_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133b Rscript convert.R -p hgu133b -o /home/user/data/out/ -i /home/user/data/hgu133b/GSM254203_GSM254203.CEL.gz -d hgu133b -s hs -g GSM254203_GSM254203 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133b | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133b/GSM254203_GSM254203.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133b_GSM254203_GSM254203_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133b Rscript convert.R -p hgu133b -o /home/user/data/out/ -i /home/user/data/hgu133b/GSM79416_GSM79416.CEL.gz -d hgu133b -s hs -g GSM79416_GSM79416 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133b | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133b/GSM79416_GSM79416.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133b_GSM79416_GSM79416_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133b Rscript convert.R -p hgu133b -o /home/user/data/out/ -i /home/user/data/hgu133b/GSM64892_GSM64892.CEL.gz -d hgu133b -s hs -g GSM64892_GSM64892 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133b | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133b/GSM64892_GSM64892.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133b_GSM64892_GSM64892_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/hgu95a --build-arg package=pd.hg.u95a_3.12.0.tar.gz --build-arg db=hgu95a -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in bfa75cd8c95b | |
| Removing intermediate container bfa75cd8c95b | |
| ---> ecf0b677b715 | |
| Step 7/13 : ARG db | |
| ---> Running in baf96a4be406 | |
| Removing intermediate container baf96a4be406 | |
| ---> 00582bb98162 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in d040ae1762b4 | |
| Removing intermediate container d040ae1762b4 | |
| ---> 0884c0682a15 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in c9b5535a5d39 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hgu95a.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu95a.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 501956 bytes (490 KB) | |
| ================================================== | |
| downloaded 490 KB | |
| * installing *source* package 'hgu95a.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hgu95a.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpMCxMge/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hg.u95a_3.12.0.tar.gz | |
| Installing pd.hg.u95a | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpMCxMge/devtools6e07fb97/pd.hg.u95a' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hg.u95a' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hg.u95a) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container c9b5535a5d39 | |
| ---> bbf5112cb66a | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 4ad401f32587 | |
| Removing intermediate container 4ad401f32587 | |
| ---> c4c7abc4d9e2 | |
| Step 11/13 : COPY convert.R . | |
| ---> f55fb5ef4656 | |
| Step 12/13 : USER user | |
| ---> Running in feadaa63e376 | |
| Removing intermediate container feadaa63e376 | |
| ---> 79fbacb3da64 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 2ac95da78d14 | |
| Removing intermediate container 2ac95da78d14 | |
| ---> f442f3fdaf78 | |
| Successfully built f442f3fdaf78 | |
| Successfully tagged convert/hgu95a:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/hgu95a' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/hgu95b --build-arg package=pd.hg.u95b_3.12.0.tar.gz --build-arg db=hgu95b -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in bfbd56fbbcbc | |
| Removing intermediate container bfbd56fbbcbc | |
| ---> 70012239fe7b | |
| Step 7/13 : ARG db | |
| ---> Running in bf5b6eb4fbbd | |
| Removing intermediate container bf5b6eb4fbbd | |
| ---> 9347c3b7b047 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 76a4cfd5458a | |
| Removing intermediate container 76a4cfd5458a | |
| ---> d5e8daec8e5d | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 6f720420bbdd | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hgu95b.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu95b.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 481099 bytes (469 KB) | |
| ================================================== | |
| downloaded 469 KB | |
| * installing *source* package 'hgu95b.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hgu95b.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpnYMQgb/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hg.u95b_3.12.0.tar.gz | |
| Installing pd.hg.u95b | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpnYMQgb/devtools77b53e8f8/pd.hg.u95b' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hg.u95b' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hg.u95b) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 6f720420bbdd | |
| ---> e1810dc6c70b | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in b0e1b04cbc9b | |
| Removing intermediate container b0e1b04cbc9b | |
| ---> 65f053561117 | |
| Step 11/13 : COPY convert.R . | |
| ---> 0ab57bec1a14 | |
| Step 12/13 : USER user | |
| ---> Running in 07eeb7a15741 | |
| Removing intermediate container 07eeb7a15741 | |
| ---> 66a4176b297a | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in a6752b00c83b | |
| Removing intermediate container a6752b00c83b | |
| ---> 7f51214190ef | |
| Successfully built 7f51214190ef | |
| Successfully tagged convert/hgu95b:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu95b Rscript convert.R -p hgu95b -o /home/user/data/out/ -i /home/user/data/hgu95b/GSM1675160_GSM1675160_PN71_U95b.CEL.gz -d hgu95b -s hs -g GSM1675160_GSM1675160_PN71_U95b | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u95b | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu95b/GSM1675160_GSM1675160_PN71_U95b.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu95b_GSM1675160_GSM1675160_PN71_U95b_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu95b Rscript convert.R -p hgu95b -o /home/user/data/out/ -i /home/user/data/hgu95b/GSM1675395_GSM1675395_PT87_U95b.CEL.gz -d hgu95b -s hs -g GSM1675395_GSM1675395_PT87_U95b | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u95b | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu95b/GSM1675395_GSM1675395_PT87_U95b.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu95b_GSM1675395_GSM1675395_PT87_U95b_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu95b Rscript convert.R -p hgu95b -o /home/user/data/out/ -i /home/user/data/hgu95b/GSM134141_GSM134141.CEL.gz -d hgu95b -s hs -g GSM134141_GSM134141 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u95b | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu95b/GSM134141_GSM134141.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu95b_GSM134141_GSM134141_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/hgu133a --build-arg package=pd.hg.u133a_3.12.0.tar.gz --build-arg db=hgu133a -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 47e293294c51 | |
| Removing intermediate container 47e293294c51 | |
| ---> 9b32d860841a | |
| Step 7/13 : ARG db | |
| ---> Running in 618b190f859d | |
| Removing intermediate container 618b190f859d | |
| ---> d5f50e8b34eb | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 0e600edbbdd2 | |
| Removing intermediate container 0e600edbbdd2 | |
| ---> e161544e2cc8 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in b36727259140 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hgu133a.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu133a.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 903473 bytes (882 KB) | |
| ================================================== | |
| downloaded 882 KB | |
| * installing *source* package 'hgu133a.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hgu133a.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmp6Ozuo7/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hg.u133a_3.12.0.tar.gz | |
| Installing pd.hg.u133a | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmp6Ozuo7/devtools778a2dda/pd.hg.u133a' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hg.u133a' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hg.u133a) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container b36727259140 | |
| ---> dcec9ec479b6 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 9d9c1fe974c4 | |
| Removing intermediate container 9d9c1fe974c4 | |
| ---> e5a8b1514fb3 | |
| Step 11/13 : COPY convert.R . | |
| ---> cbf676463ab7 | |
| Step 12/13 : USER user | |
| ---> Running in 78a36e290af5 | |
| Removing intermediate container 78a36e290af5 | |
| ---> 9c44ee5edfe4 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 50e4453a8459 | |
| Removing intermediate container 50e4453a8459 | |
| ---> 1a18189b2ecf | |
| Successfully built 1a18189b2ecf | |
| Successfully tagged convert/hgu133a:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133a Rscript convert.R -p hgu133a -o /home/user/data/out/ -i /home/user/data/hgu133a/GSM1024732_GSM1024732_NBM5E.U133A_C2E.CEL.gz -d hgu133a -s hs -g GSM1024732_GSM1024732_NBM5E | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133a/GSM1024732_GSM1024732_NBM5E.U133A_C2E.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133a_GSM1024732_GSM1024732_NBM5E_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133a Rscript convert.R -p hgu133a -o /home/user/data/out/ -i /home/user/data/hgu133a/GSM1024731_GSM1024731_NBM4E.U133A_C1E.CEL.gz -d hgu133a -s hs -g GSM1024731_GSM1024731_NBM4E | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
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| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133a/GSM1024731_GSM1024731_NBM4E.U133A_C1E.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133a_GSM1024731_GSM1024731_NBM4E_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133a Rscript convert.R -p hgu133a -o /home/user/data/out/ -i /home/user/data/hgu133a/GSM1024730_GSM1024730_BMRG-E.U133A_P3E.CEL.gz -d hgu133a -s hs -g GSM1024730_GSM1024730_BMRG-E | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133a/GSM1024730_GSM1024730_BMRG-E.U133A_P3E.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133a_GSM1024730_GSM1024730_BMRG-E_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133a Rscript convert.R -p hgu133a -o /home/user/data/out/ -i /home/user/data/hgu133a/GSM1024733_GSM1024733_NBM6E.U133A_C3E.CEL.gz -d hgu133a -s hs -g GSM1024733_GSM1024733_NBM6E | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133a/GSM1024733_GSM1024733_NBM6E.U133A_C3E.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133a_GSM1024733_GSM1024733_NBM6E_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133a Rscript convert.R -p hgu133a -o /home/user/data/out/ -i /home/user/data/hgu133a/GSM1024729_GSM1024729_BMZJ2-E.U133A_P2E.CEL.gz -d hgu133a -s hs -g GSM1024729_GSM1024729_BMZJ2-E | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133a/GSM1024729_GSM1024729_BMZJ2-E.U133A_P2E.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133a_GSM1024729_GSM1024729_BMZJ2-E_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/equgene11st --build-arg package=pd.equgene.1.1.st_3.12.0.tar.gz --build-arg db=equgene11st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 2b85d8f312c2 | |
| Removing intermediate container 2b85d8f312c2 | |
| ---> 60b36a91e822 | |
| Step 7/13 : ARG db | |
| ---> Running in a39d2adbaa8c | |
| Removing intermediate container a39d2adbaa8c | |
| ---> 51aa5a5485a3 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 63d833aa3465 | |
| Removing intermediate container 63d833aa3465 | |
| ---> 90bdfab4f54f | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 7cb0963d23f1 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'equgene11st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'equgene11st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.equgene.1.1.st_3.12.0.tar.gz | |
| Installing pd.equgene.1.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpzNg6j2/devtools768f4ed1c/pd.equgene.1.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.equgene.1.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.equgene.1.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 7cb0963d23f1 | |
| ---> 04bc19f3e5e9 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 6f2d2e842024 | |
| Removing intermediate container 6f2d2e842024 | |
| ---> 8eca86066038 | |
| Step 11/13 : COPY convert.R . | |
| ---> 2bc373a8c692 | |
| Step 12/13 : USER user | |
| ---> Running in ed6733bf3ca5 | |
| Removing intermediate container ed6733bf3ca5 | |
| ---> 02bfe8caa122 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 5f9fdd19eea5 | |
| Removing intermediate container 5f9fdd19eea5 | |
| ---> 89e260c0e8b8 | |
| Successfully built 89e260c0e8b8 | |
| Successfully tagged convert/equgene11st:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/equgene11st' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/zebrafish --build-arg package=pd.zebrafish_3.12.0.tar.gz --build-arg db=zebrafish -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 6aeb8daa544e | |
| Removing intermediate container 6aeb8daa544e | |
| ---> 9536a9874ea7 | |
| Step 7/13 : ARG db | |
| ---> Running in cfebcb5f69c2 | |
| Removing intermediate container cfebcb5f69c2 | |
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| Step 8/13 : ENV DB=$db | |
| ---> Running in 2fe6e73648e8 | |
| Removing intermediate container 2fe6e73648e8 | |
| ---> d51ff091db3f | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 91e3bbbc2f37 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'zebrafish.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/zebrafish.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 618087 bytes (603 KB) | |
| ================================================== | |
| downloaded 603 KB | |
| * installing *source* package 'zebrafish.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (zebrafish.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpC3XK4m/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.zebrafish_3.12.0.tar.gz | |
| Installing pd.zebrafish | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpC3XK4m/devtools714e269e4/pd.zebrafish' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.zebrafish' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.zebrafish) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 91e3bbbc2f37 | |
| ---> 16797c64e358 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 18e29771b036 | |
| Removing intermediate container 18e29771b036 | |
| ---> e9dcc6a90441 | |
| Step 11/13 : COPY convert.R . | |
| ---> dc7fdaf8cf15 | |
| Step 12/13 : USER user | |
| ---> Running in 3c10508f2ae5 | |
| Removing intermediate container 3c10508f2ae5 | |
| ---> 9ba7e3394085 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in b5319d88bf79 | |
| Removing intermediate container b5319d88bf79 | |
| ---> 5943b5f8e6d5 | |
| Successfully built 5943b5f8e6d5 | |
| Successfully tagged convert/zebrafish:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebrafish Rscript convert.R -p zebrafish -o /home/user/data/out/ -i /home/user/data/zebrafish/GSM1122074_GSM1122074_L11._D2_Zebrafish_.CEL.gz -d zebrafish -s dr -g GSM1122074_GSM1122074_L11 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Dr.eg.db | |
| Reading.. | |
| Loading required package: pd.zebrafish | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/zebrafish/GSM1122074_GSM1122074_L11._D2_Zebrafish_.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//zebrafish_GSM1122074_GSM1122074_L11_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebrafish Rscript convert.R -p zebrafish -o /home/user/data/out/ -i /home/user/data/zebrafish/GSM683599_GSM683599.CEL.gz -d zebrafish -s dr -g GSM683599_GSM683599 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Dr.eg.db | |
| Reading.. | |
| Loading required package: pd.zebrafish | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/zebrafish/GSM683599_GSM683599.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//zebrafish_GSM683599_GSM683599_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebrafish Rscript convert.R -p zebrafish -o /home/user/data/out/ -i /home/user/data/zebrafish/GSM1088004_GSM1088004_Robison-122-031009.CEL.gz -d zebrafish -s dr -g GSM1088004_GSM1088004_Robison-122-031009 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Dr.eg.db | |
| Reading.. | |
| Loading required package: pd.zebrafish | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/zebrafish/GSM1088004_GSM1088004_Robison-122-031009.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//zebrafish_GSM1088004_GSM1088004_Robison-122-031009_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebrafish Rscript convert.R -p zebrafish -o /home/user/data/out/ -i /home/user/data/zebrafish/GSM1129280_GSM1129280_24_CA.CEL.gz -d zebrafish -s dr -g GSM1129280_GSM1129280_24_CA | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Dr.eg.db | |
| Reading.. | |
| Loading required package: pd.zebrafish | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/zebrafish/GSM1129280_GSM1129280_24_CA.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//zebrafish_GSM1129280_GSM1129280_24_CA_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/hthgu133pluspm --build-arg package=pd.ht.hg.u133.plus.pm_3.12.0.tar.gz --build-arg db=hthgu133pluspm -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 166edad93b36 | |
| Removing intermediate container 166edad93b36 | |
| ---> 56f031e5cefa | |
| Step 7/13 : ARG db | |
| ---> Running in 37d83a74901f | |
| Removing intermediate container 37d83a74901f | |
| ---> 8340efc88486 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 6e3152a1f719 | |
| Removing intermediate container 6e3152a1f719 | |
| ---> 19b0979e8620 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 654c5178e220 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hthgu133pluspm.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'hthgu133pluspm.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.ht.hg.u133.plus.pm_3.12.0.tar.gz | |
| Installing pd.ht.hg.u133.plus.pm | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpXzKIOz/devtools72edbc719/pd.ht.hg.u133.plus.pm' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.ht.hg.u133.plus.pm' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.ht.hg.u133.plus.pm) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 654c5178e220 | |
| ---> 0c4041bbc777 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 8d383ce99f8b | |
| Removing intermediate container 8d383ce99f8b | |
| ---> 1a98af0cc63d | |
| Step 11/13 : COPY convert.R . | |
| ---> 024d42a3f3b8 | |
| Step 12/13 : USER user | |
| ---> Running in 81a89b82023a | |
| Removing intermediate container 81a89b82023a | |
| ---> 088acb78f920 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 401435ef8f9f | |
| Removing intermediate container 401435ef8f9f | |
| ---> 6747c33aa49e | |
| Successfully built 6747c33aa49e | |
| Successfully tagged convert/hthgu133pluspm:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hthgu133pluspm Rscript convert.R -p hthgu133pluspm -o /home/user/data/out/ -i /home/user/data/hthgu133pluspm/GSM1527618_GSM1527618_16023.CEL.gz -d hthgu133pluspm -s hs -g GSM1527618_GSM1527618_16023 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'hthgu133pluspm.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hthgu133pluspm Rscript convert.R -p hthgu133pluspm -o /home/user/data/out/ -i /home/user/data/hthgu133pluspm/GSM1527617_GSM1527617_16020.CEL.gz -d hthgu133pluspm -s hs -g GSM1527617_GSM1527617_16020 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'hthgu133pluspm.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hthgu133pluspm Rscript convert.R -p hthgu133pluspm -o /home/user/data/out/ -i /home/user/data/hthgu133pluspm/GSM1527612_GSM1527612_15986.CEL.gz -d hthgu133pluspm -s hs -g GSM1527612_GSM1527612_15986 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'hthgu133pluspm.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hthgu133pluspm Rscript convert.R -p hthgu133pluspm -o /home/user/data/out/ -i /home/user/data/hthgu133pluspm/GSM1527624_GSM1527624_16002.CEL.gz -d hthgu133pluspm -s hs -g GSM1527624_GSM1527624_16002 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'hthgu133pluspm.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hthgu133pluspm Rscript convert.R -p hthgu133pluspm -o /home/user/data/out/ -i /home/user/data/hthgu133pluspm/GSM1527613_GSM1527613_15988.CEL.gz -d hthgu133pluspm -s hs -g GSM1527613_GSM1527613_15988 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'hthgu133pluspm.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/canine --build-arg package=pd.canine_3.12.0.tar.gz --build-arg db=canine -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in fc10c6af5cf4 | |
| Removing intermediate container fc10c6af5cf4 | |
| ---> f4e34d2b90b6 | |
| Step 7/13 : ARG db | |
| ---> Running in 66903a5e0898 | |
| Removing intermediate container 66903a5e0898 | |
| ---> 6f307c234347 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in b42b2ffaff5b | |
| Removing intermediate container b42b2ffaff5b | |
| ---> eb02ca4767e2 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in ac096cc6bf49 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'canine.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/canine.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 796354 bytes (777 KB) | |
| ================================================== | |
| downloaded 777 KB | |
| * installing *source* package 'canine.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (canine.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpinAb1N/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.canine_3.12.0.tar.gz | |
| Installing pd.canine | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpinAb1N/devtools7431ffbc/pd.canine' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.canine' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.canine) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container ac096cc6bf49 | |
| ---> 475b7743c9f5 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 2b809b606913 | |
| Removing intermediate container 2b809b606913 | |
| ---> ba5b4949c2ca | |
| Step 11/13 : COPY convert.R . | |
| ---> 6d046dafb8ca | |
| Step 12/13 : USER user | |
| ---> Running in ee92bb466da7 | |
| Removing intermediate container ee92bb466da7 | |
| ---> fca7d3bdf723 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in f1ea53a2c6aa | |
| Removing intermediate container f1ea53a2c6aa | |
| ---> f4cadb151307 | |
| Successfully built f4cadb151307 | |
| Successfully tagged convert/canine:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/canine' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/clariomshuman --build-arg package=pd.clariom.s.human_3.14.1.tar.gz --build-arg db=clariomshuman -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in db52808233c6 | |
| Removing intermediate container db52808233c6 | |
| ---> 8cfd1f1c90c6 | |
| Step 7/13 : ARG db | |
| ---> Running in 9d79bae9296e | |
| Removing intermediate container 9d79bae9296e | |
| ---> 8c037ed626cf | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in cf94fcf116f4 | |
| Removing intermediate container cf94fcf116f4 | |
| ---> e745063efa7a | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 88daab3a470a | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'clariomshuman.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'clariomshuman.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.clariom.s.human_3.14.1.tar.gz | |
| Installing pd.clariom.s.human | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpfmoC2l/devtools776c71595/pd.clariom.s.human' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.clariom.s.human' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.clariom.s.human) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 88daab3a470a | |
| ---> 4246a9e72b02 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in cdd4a88e944f | |
| Removing intermediate container cdd4a88e944f | |
| ---> 908f17fd2128 | |
| Step 11/13 : COPY convert.R . | |
| ---> e8b790840b09 | |
| Step 12/13 : USER user | |
| ---> Running in 08561537ff5a | |
| Removing intermediate container 08561537ff5a | |
| ---> 5fe732f499d6 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 95382a8697b8 | |
| Removing intermediate container 95382a8697b8 | |
| ---> b9984b5173f0 | |
| Successfully built b9984b5173f0 | |
| Successfully tagged convert/clariomshuman:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/clariomshuman' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/hgu133plus2 --build-arg package=pd.hg.u133.plus.2_3.12.0.tar.gz --build-arg db=hgu133plus2 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 7766aa7481a0 | |
| Removing intermediate container 7766aa7481a0 | |
| ---> 01941dfe2665 | |
| Step 7/13 : ARG db | |
| ---> Running in d478bb3ab6db | |
| Removing intermediate container d478bb3ab6db | |
| ---> eeaa67b92843 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 8ac08510d746 | |
| Removing intermediate container 8ac08510d746 | |
| ---> f8a582dda283 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in e34cf71e4ff9 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hgu133plus2.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu133plus2.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 2139642 bytes (2.0 MB) | |
| ================================================== | |
| downloaded 2.0 MB | |
| * installing *source* package 'hgu133plus2.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hgu133plus2.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmpaov6wg/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hg.u133.plus.2_3.12.0.tar.gz | |
| Installing pd.hg.u133.plus.2 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmpaov6wg/devtools77cc9b64e/pd.hg.u133.plus.2' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hg.u133.plus.2' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hg.u133.plus.2) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container e34cf71e4ff9 | |
| ---> 46b684b9796f | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 9e6dba3b0f12 | |
| Removing intermediate container 9e6dba3b0f12 | |
| ---> f0b3233c5929 | |
| Step 11/13 : COPY convert.R . | |
| ---> 74a2b787e9d3 | |
| Step 12/13 : USER user | |
| ---> Running in 022ecacfc20c | |
| Removing intermediate container 022ecacfc20c | |
| ---> 3de4ad41cc04 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 10f3508f34ad | |
| Removing intermediate container 10f3508f34ad | |
| ---> 66b13d4460c9 | |
| Successfully built 66b13d4460c9 | |
| Successfully tagged convert/hgu133plus2:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133plus2 Rscript convert.R -p hgu133plus2 -o /home/user/data/out/ -i /home/user/data/hgu133plus2/GSM465285_GSM465285.CEL.gz -d hgu133plus2 -s hs -g GSM465285_GSM465285 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133.plus.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133plus2/GSM465285_GSM465285.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133plus2_GSM465285_GSM465285_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133plus2 Rscript convert.R -p hgu133plus2 -o /home/user/data/out/ -i /home/user/data/hgu133plus2/GSM465301_GSM465301.CEL.gz -d hgu133plus2 -s hs -g GSM465301_GSM465301 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133.plus.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133plus2/GSM465301_GSM465301.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133plus2_GSM465301_GSM465301_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133plus2 Rscript convert.R -p hgu133plus2 -o /home/user/data/out/ -i /home/user/data/hgu133plus2/GSM465287_GSM465287.CEL.gz -d hgu133plus2 -s hs -g GSM465287_GSM465287 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133.plus.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133plus2/GSM465287_GSM465287.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133plus2_GSM465287_GSM465287_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133plus2 Rscript convert.R -p hgu133plus2 -o /home/user/data/out/ -i /home/user/data/hgu133plus2/GSM465356_GSM465356.CEL.gz -d hgu133plus2 -s hs -g GSM465356_GSM465356 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133.plus.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133plus2/GSM465356_GSM465356.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133plus2_GSM465356_GSM465356_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133plus2 Rscript convert.R -p hgu133plus2 -o /home/user/data/out/ -i /home/user/data/hgu133plus2/GSM465362_GSM465362.CEL.gz -d hgu133plus2 -s hs -g GSM465362_GSM465362 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133.plus.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133plus2/GSM465362_GSM465362.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133plus2_GSM465362_GSM465362_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/cangene11st --build-arg package=pd.cangene.1.1.st_3.12.0.tar.gz --build-arg db=cangene11st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in a019038df1a6 | |
| Removing intermediate container a019038df1a6 | |
| ---> d676a9bb45c6 | |
| Step 7/13 : ARG db | |
| ---> Running in 4f5f74bc628e | |
| Removing intermediate container 4f5f74bc628e | |
| ---> 870d831faa68 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 4a98bbdf549f | |
| Removing intermediate container 4a98bbdf549f | |
| ---> 3eb67833d2b5 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 96408afdffb3 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'cangene11st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'cangene11st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.cangene.1.1.st_3.12.0.tar.gz | |
| Installing pd.cangene.1.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpMIONo7/devtools76d863bea/pd.cangene.1.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.cangene.1.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.cangene.1.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 96408afdffb3 | |
| ---> aaf8b51053f2 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 94cfe55809f9 | |
| Removing intermediate container 94cfe55809f9 | |
| ---> d50d8221ac40 | |
| Step 11/13 : COPY convert.R . | |
| ---> 869f8cf37da8 | |
| Step 12/13 : USER user | |
| ---> Running in 6103112caa63 | |
| Removing intermediate container 6103112caa63 | |
| ---> 83126e334958 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 77326689fe23 | |
| Removing intermediate container 77326689fe23 | |
| ---> a7f5611b9e4f | |
| Successfully built a7f5611b9e4f | |
| Successfully tagged convert/cangene11st:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/cangene11st' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/moe430a --build-arg package=pd.moe430a_3.12.0.tar.gz --build-arg db=moe430a -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 1dcaadcb664e | |
| Removing intermediate container 1dcaadcb664e | |
| ---> dd256040f29a | |
| Step 7/13 : ARG db | |
| ---> Running in f5ecd2428d66 | |
| Removing intermediate container f5ecd2428d66 | |
| ---> 875d305c766a | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in ec715e991784 | |
| Removing intermediate container ec715e991784 | |
| ---> 6feed03d5706 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 289914e13baa | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'moe430a.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/moe430a.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 889709 bytes (868 KB) | |
| ================================================== | |
| downloaded 868 KB | |
| * installing *source* package 'moe430a.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (moe430a.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpxvE6j4/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.moe430a_3.12.0.tar.gz | |
| Installing pd.moe430a | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpxvE6j4/devtools73ed29d6c/pd.moe430a' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.moe430a' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.moe430a) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 289914e13baa | |
| ---> 9463d1e723dc | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 727b5f1c16ac | |
| Removing intermediate container 727b5f1c16ac | |
| ---> 6b6d5d2b4773 | |
| Step 11/13 : COPY convert.R . | |
| ---> 30bd4a17bc1d | |
| Step 12/13 : USER user | |
| ---> Running in d549706488a7 | |
| Removing intermediate container d549706488a7 | |
| ---> e33698eb8842 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in bec17e2c0935 | |
| Removing intermediate container bec17e2c0935 | |
| ---> 97adf6b317e5 | |
| Successfully built 97adf6b317e5 | |
| Successfully tagged convert/moe430a:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/moe430a Rscript convert.R -p moe430a -o /home/user/data/out/ -i /home/user/data/moe430a/GSM299067_GSM299067.CEL.gz -d moe430a -s mm -g GSM299067_GSM299067 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.moe430a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/moe430a/GSM299067_GSM299067.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//moe430a_GSM299067_GSM299067_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/moe430a Rscript convert.R -p moe430a -o /home/user/data/out/ -i /home/user/data/moe430a/GSM370684_GSM370684.CEL.gz -d moe430a -s mm -g GSM370684_GSM370684 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.moe430a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/moe430a/GSM370684_GSM370684.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//moe430a_GSM370684_GSM370684_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/moe430a Rscript convert.R -p moe430a -o /home/user/data/out/ -i /home/user/data/moe430a/GSM98658_GSM98658.CEL.gz -d moe430a -s mm -g GSM98658_GSM98658 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.moe430a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/moe430a/GSM98658_GSM98658.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//moe430a_GSM98658_GSM98658_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/moe430a Rscript convert.R -p moe430a -o /home/user/data/out/ -i /home/user/data/moe430a/GSM276720_GSM276720.CEL.gz -d moe430a -s mm -g GSM276720_GSM276720 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Mm.eg.db | |
| Reading.. | |
| Loading required package: pd.moe430a | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/moe430a/GSM276720_GSM276720.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//moe430a_GSM276720_GSM276720_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/drosophila2 --build-arg package=pd.drosophila.2_3.12.0.tar.gz --build-arg db=drosophila2 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 1ce5663bc564 | |
| Removing intermediate container 1ce5663bc564 | |
| ---> 11969799d9fb | |
| Step 7/13 : ARG db | |
| ---> Running in e74d1fcf1618 | |
| Removing intermediate container e74d1fcf1618 | |
| ---> 84363714e786 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 4dd51fa28593 | |
| Removing intermediate container 4dd51fa28593 | |
| ---> 594adc8f2fb3 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in cc3ce4849920 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'drosophila2.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/drosophila2.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 717518 bytes (700 KB) | |
| ================================================== | |
| downloaded 700 KB | |
| * installing *source* package 'drosophila2.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (drosophila2.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpuRiwTt/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.drosophila.2_3.12.0.tar.gz | |
| Installing pd.drosophila.2 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpuRiwTt/devtools66a1667f6/pd.drosophila.2' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.drosophila.2' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.drosophila.2) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container cc3ce4849920 | |
| ---> f2c27c5058bd | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in c57543e75ceb | |
| Removing intermediate container c57543e75ceb | |
| ---> 859b3ec2700a | |
| Step 11/13 : COPY convert.R . | |
| ---> eb37ca61e3f1 | |
| Step 12/13 : USER user | |
| ---> Running in c37d00c77a2d | |
| Removing intermediate container c37d00c77a2d | |
| ---> f0a80f973563 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in d14821730cce | |
| Removing intermediate container d14821730cce | |
| ---> ec10e39b22b1 | |
| Successfully built ec10e39b22b1 | |
| Successfully tagged convert/drosophila2:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drosophila2 Rscript convert.R -p drosophila2 -o /home/user/data/out/ -i /home/user/data/drosophila2/GSM748808_GSM748808_Embryo1-uas-ttk.CEL.gz -d drosophila2 -s dm -g GSM748808_GSM748808_Embryo1-uas-ttk | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Dm.eg.db | |
| Reading.. | |
| Loading required package: pd.drosophila.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/drosophila2/GSM748808_GSM748808_Embryo1-uas-ttk.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//drosophila2_GSM748808_GSM748808_Embryo1-uas-ttk_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drosophila2 Rscript convert.R -p drosophila2 -o /home/user/data/out/ -i /home/user/data/drosophila2/GSM748798_GSM748798_BRJune09--476-2009--CON020609.CEL.gz -d drosophila2 -s dm -g GSM748798_GSM748798_BRJune09--476-2009--CON020609 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Dm.eg.db | |
| Reading.. | |
| Loading required package: pd.drosophila.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/drosophila2/GSM748798_GSM748798_BRJune09--476-2009--CON020609.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//drosophila2_GSM748798_GSM748798_BRJune09--476-2009--CON020609_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drosophila2 Rscript convert.R -p drosophila2 -o /home/user/data/out/ -i /home/user/data/drosophila2/GSM748801_GSM748801_BRJune09--382-2009--CON140509.CEL.gz -d drosophila2 -s dm -g GSM748801_GSM748801_BRJune09--382-2009--CON140509 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Dm.eg.db | |
| Reading.. | |
| Loading required package: pd.drosophila.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/drosophila2/GSM748801_GSM748801_BRJune09--382-2009--CON140509.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//drosophila2_GSM748801_GSM748801_BRJune09--382-2009--CON140509_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drosophila2 Rscript convert.R -p drosophila2 -o /home/user/data/out/ -i /home/user/data/drosophila2/GSM748812_GSM748812_control-UAS-cels3.CEL.gz -d drosophila2 -s dm -g GSM748812_GSM748812_control-UAS-cels3 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Dm.eg.db | |
| Reading.. | |
| Loading required package: pd.drosophila.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/drosophila2/GSM748812_GSM748812_control-UAS-cels3.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//drosophila2_GSM748812_GSM748812_control-UAS-cels3_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/drosophila2 Rscript convert.R -p drosophila2 -o /home/user/data/out/ -i /home/user/data/drosophila2/GSM748799_GSM748799_BRJune09--477-2009--TTK020609.CEL.gz -d drosophila2 -s dm -g GSM748799_GSM748799_BRJune09--477-2009--TTK020609 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Dm.eg.db | |
| Reading.. | |
| Loading required package: pd.drosophila.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/drosophila2/GSM748799_GSM748799_BRJune09--477-2009--TTK020609.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//drosophila2_GSM748799_GSM748799_BRJune09--477-2009--TTK020609_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/elegene11st --build-arg package=pd.elegene.1.1.st_3.12.0.tar.gz --build-arg db=elegene11st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 268e7a5477bd | |
| Removing intermediate container 268e7a5477bd | |
| ---> 452e1e9abd1e | |
| Step 7/13 : ARG db | |
| ---> Running in bf3dc13e19a2 | |
| Removing intermediate container bf3dc13e19a2 | |
| ---> 723e25099c7b | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 65f8e6b49a6f | |
| Removing intermediate container 65f8e6b49a6f | |
| ---> 70d601528d66 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 9eb05dba2839 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'elegene11st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'elegene11st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.elegene.1.1.st_3.12.0.tar.gz | |
| Installing pd.elegene.1.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmpc8e6ow/devtools76d7d41d4/pd.elegene.1.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.elegene.1.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.elegene.1.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 9eb05dba2839 | |
| ---> 7b1d542aa98d | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in cdd946390778 | |
| Removing intermediate container cdd946390778 | |
| ---> 292a20480c94 | |
| Step 11/13 : COPY convert.R . | |
| ---> ac4036366638 | |
| Step 12/13 : USER user | |
| ---> Running in 6f0c03ea02f0 | |
| Removing intermediate container 6f0c03ea02f0 | |
| ---> f75ee40250b9 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 7aa8efb5c100 | |
| Removing intermediate container 7aa8efb5c100 | |
| ---> 6bfe8ebfc882 | |
| Successfully built 6bfe8ebfc882 | |
| Successfully tagged convert/elegene11st:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/elegene11st' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/ragene10st --build-arg package=pd.ragene.1.0.st.v1_3.14.1.tar.gz --build-arg db=ragene10stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in c50d325f0328 | |
| Removing intermediate container c50d325f0328 | |
| ---> e0dc7a9371f1 | |
| Step 7/13 : ARG db | |
| ---> Running in 8276d7181072 | |
| Removing intermediate container 8276d7181072 | |
| ---> 0fd4355e9ad4 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 1a451bd5631e | |
| Removing intermediate container 1a451bd5631e | |
| ---> e20abf365371 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 6b830613c8c9 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'ragene10stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/ragene10stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 11490046 bytes (11.0 MB) | |
| ================================================== | |
| downloaded 11.0 MB | |
| * installing *source* package 'ragene10stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (ragene10stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpQG1jVs/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.ragene.1.0.st.v1_3.14.1.tar.gz | |
| Installing pd.ragene.1.0.st.v1 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpQG1jVs/devtools737677e84/pd.ragene.1.0.st.v1' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.ragene.1.0.st.v1' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.ragene.1.0.st.v1) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 6b830613c8c9 | |
| ---> d9da0f5161bf | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 083d94b4038e | |
| Removing intermediate container 083d94b4038e | |
| ---> 2187fd15945e | |
| Step 11/13 : COPY convert.R . | |
| ---> c7abc674d4ca | |
| Step 12/13 : USER user | |
| ---> Running in 8ac1c04d9d9c | |
| Removing intermediate container 8ac1c04d9d9c | |
| ---> 507a23e2dcb6 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 27a79c18b7d4 | |
| Removing intermediate container 27a79c18b7d4 | |
| ---> 45c255f75c75 | |
| Successfully built 45c255f75c75 | |
| Successfully tagged convert/ragene10st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ragene10st Rscript convert.R -p ragene10st -o /home/user/data/out/ -i /home/user/data/ragene10st/GSM1040120_GSM1040120_ILC_02_Con_070610_RatGe_St1_0.CEL.gz -d ragene10stprobeset -s rn -g GSM1040120_GSM1040120_ILC_02_Con_070610_RatGe_St1_0 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ragene10st Rscript convert.R -p ragene10st -o /home/user/data/out/ -i /home/user/data/ragene10st/GSM2344830_GSM2344830_16G_LD+_LID-_nigra_C.CEL.gz -d ragene10stprobeset -s rn -g GSM2344830_GSM2344830_16G_LD+_LID-_nigra_C | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ragene10st Rscript convert.R -p ragene10st -o /home/user/data/out/ -i /home/user/data/ragene10st/GSM1040119_GSM1040119_ILC_01_Con_070610_RatGe_St1_0.CEL.gz -d ragene10stprobeset -s rn -g GSM1040119_GSM1040119_ILC_01_Con_070610_RatGe_St1_0 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ragene10st Rscript convert.R -p ragene10st -o /home/user/data/out/ -i /home/user/data/ragene10st/GSM2344820_GSM2344820_15C_LD-_6-OHDA_Striatum_B.CEL.gz -d ragene10stprobeset -s rn -g GSM2344820_GSM2344820_15C_LD-_6-OHDA_Striatum_B | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ragene10st Rscript convert.R -p ragene10st -o /home/user/data/out/ -i /home/user/data/ragene10st/GSM2344829_GSM2344829_13G_LD+_LID-_nigra_B.CEL.gz -d ragene10stprobeset -s rn -g GSM2344829_GSM2344829_13G_LD+_LID-_nigra_B | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/mgu74a --build-arg package=pd.mg.u74a_3.12.0.tar.gz --build-arg db=mgu74a -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in fc34a4308c6a | |
| Removing intermediate container fc34a4308c6a | |
| ---> a654765b66c7 | |
| Step 7/13 : ARG db | |
| ---> Running in 9f195219a5f4 | |
| Removing intermediate container 9f195219a5f4 | |
| ---> 260738fd6b9c | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 0ec1376d88e3 | |
| Removing intermediate container 0ec1376d88e3 | |
| ---> 79bc5aad2427 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 1213c43374f7 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'mgu74a.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mgu74a.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 496797 bytes (485 KB) | |
| ================================================== | |
| downloaded 485 KB | |
| * installing *source* package 'mgu74a.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (mgu74a.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmp0YtAyf/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mg.u74a_3.12.0.tar.gz | |
| Installing pd.mg.u74a | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmp0YtAyf/devtools71c020706/pd.mg.u74a' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.mg.u74a' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.mg.u74a) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 1213c43374f7 | |
| ---> 7697e7d57923 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 6c4e83801943 | |
| Removing intermediate container 6c4e83801943 | |
| ---> a4d3279a2f11 | |
| Step 11/13 : COPY convert.R . | |
| ---> cbe33abcfe75 | |
| Step 12/13 : USER user | |
| ---> Running in 356ee96cb34c | |
| Removing intermediate container 356ee96cb34c | |
| ---> ac176096aaf2 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 93c412e47f5d | |
| Removing intermediate container 93c412e47f5d | |
| ---> 013e11281b82 | |
| Successfully built 013e11281b82 | |
| Successfully tagged convert/mgu74a:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/mgu74a' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/zebgene10st --build-arg package=pd.zebgene.1.0.st_3.12.0.tar.gz --build-arg db=zebgene10st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 286087912d05 | |
| Removing intermediate container 286087912d05 | |
| ---> d46edfbdf58a | |
| Step 7/13 : ARG db | |
| ---> Running in 58f3413d1c38 | |
| Removing intermediate container 58f3413d1c38 | |
| ---> 93b2fe841c87 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 7a0f578f0ab5 | |
| Removing intermediate container 7a0f578f0ab5 | |
| ---> 8913d0f1cb76 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in b0ccf05fa826 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'zebgene10st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'zebgene10st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.zebgene.1.0.st_3.12.0.tar.gz | |
| Installing pd.zebgene.1.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpJxvFJe/devtools731aa3bb1/pd.zebgene.1.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.zebgene.1.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.zebgene.1.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container b0ccf05fa826 | |
| ---> 10cf95f13072 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 713da91c8835 | |
| Removing intermediate container 713da91c8835 | |
| ---> 87e2ab7389f8 | |
| Step 11/13 : COPY convert.R . | |
| ---> f999ee75ad92 | |
| Step 12/13 : USER user | |
| ---> Running in 667f84dd4f2c | |
| Removing intermediate container 667f84dd4f2c | |
| ---> d732625a20f7 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in bf7f1f4d1ca0 | |
| Removing intermediate container bf7f1f4d1ca0 | |
| ---> 1926dc2a7534 | |
| Successfully built 1926dc2a7534 | |
| Successfully tagged convert/zebgene10st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebgene10st Rscript convert.R -p zebgene10st -o /home/user/data/out/ -i /home/user/data/zebgene10st/GSM1716329_GSM1716329_Control1.CEL.gz -d zebgene10st -s dr -g GSM1716329_GSM1716329_Control1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'zebgene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebgene10st Rscript convert.R -p zebgene10st -o /home/user/data/out/ -i /home/user/data/zebgene10st/GSM2258542_GSM2258542_HMN_Hyp-brain1_ZebGene-1_0-st_.CEL.gz -d zebgene10st -s dr -g GSM2258542_GSM2258542_HMN_Hyp-brain1_ZebGene-1_0-st_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'zebgene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebgene10st Rscript convert.R -p zebgene10st -o /home/user/data/out/ -i /home/user/data/zebgene10st/GSM1821239_GSM1821239_E.070611_ZebGene-1_0-st_.CEL.gz -d zebgene10st -s dr -g GSM1821239_GSM1821239_E | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'zebgene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebgene10st Rscript convert.R -p zebgene10st -o /home/user/data/out/ -i /home/user/data/zebgene10st/GSM1350439_GSM1350439_9LN.071813.CEL.gz -d zebgene10st -s dr -g GSM1350439_GSM1350439_9LN | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'zebgene10st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/clariomdhuman --build-arg package=pd.clariom.d.human_3.14.1.tar.gz --build-arg db=clariomdhumanprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in e828299e0dec | |
| Removing intermediate container e828299e0dec | |
| ---> 06248bad045e | |
| Step 7/13 : ARG db | |
| ---> Running in 5b38effc6933 | |
| Removing intermediate container 5b38effc6933 | |
| ---> 55101d57f1fb | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in c3650b291bdc | |
| Removing intermediate container c3650b291bdc | |
| ---> 20a2ce1d7407 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 60491fc415bb | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'clariomdhumanprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/clariomdhumanprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 55757652 bytes (53.2 MB) | |
| ================================================== | |
| downloaded 53.2 MB | |
| * installing *source* package 'clariomdhumanprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (clariomdhumanprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpJUDnSw/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.clariom.d.human_3.14.1.tar.gz | |
| Installing pd.clariom.d.human | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpJUDnSw/devtools86a81b26/pd.clariom.d.human' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.clariom.d.human' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.clariom.d.human) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 60491fc415bb | |
| ---> 2a5df6f1b5e1 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 667a17e8d4d2 | |
| Removing intermediate container 667a17e8d4d2 | |
| ---> 7e7116de088a | |
| Step 11/13 : COPY convert.R . | |
| ---> 18c8f14dbcd9 | |
| Step 12/13 : USER user | |
| ---> Running in 8239b9dbf506 | |
| Removing intermediate container 8239b9dbf506 | |
| ---> abc1b5cb343a | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 0aeb461e4d8b | |
| Removing intermediate container 0aeb461e4d8b | |
| ---> 2029e2ccea48 | |
| Successfully built 2029e2ccea48 | |
| Successfully tagged convert/clariomdhuman:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/clariomdhuman' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/ragene20st --build-arg package=pd.ragene.2.0.st_3.14.1.tar.gz --build-arg db=ragene20stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 6a97e48ccf39 | |
| Removing intermediate container 6a97e48ccf39 | |
| ---> ecedbafd7923 | |
| Step 7/13 : ARG db | |
| ---> Running in 6df38b5fffa4 | |
| Removing intermediate container 6df38b5fffa4 | |
| ---> cc85003e5812 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 7ed506fa79e7 | |
| Removing intermediate container 7ed506fa79e7 | |
| ---> b0f210c48a11 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 32ae82670b40 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'ragene20stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/ragene20stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 11254205 bytes (10.7 MB) | |
| ================================================== | |
| downloaded 10.7 MB | |
| * installing *source* package 'ragene20stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (ragene20stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpzwVVvD/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.ragene.2.0.st_3.14.1.tar.gz | |
| Installing pd.ragene.2.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpzwVVvD/devtools769249d1d/pd.ragene.2.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.ragene.2.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.ragene.2.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 32ae82670b40 | |
| ---> b76d63186a08 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 8dc11e853bc5 | |
| Removing intermediate container 8dc11e853bc5 | |
| ---> 27add69bc713 | |
| Step 11/13 : COPY convert.R . | |
| ---> 62094a60815c | |
| Step 12/13 : USER user | |
| ---> Running in 965f5fc07f8a | |
| Removing intermediate container 965f5fc07f8a | |
| ---> fbf39acc4775 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 33e760a35bc0 | |
| Removing intermediate container 33e760a35bc0 | |
| ---> 244e8ba2d5ab | |
| Successfully built 244e8ba2d5ab | |
| Successfully tagged convert/ragene20st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ragene20st Rscript convert.R -p ragene20st -o /home/user/data/out/ -i /home/user/data/ragene20st/GSM1664281_GSM1664281_80_M6_CO_d28_UCB.CEL.gz -d ragene20stprobeset -s rn -g GSM1664281_GSM1664281_80_M6_CO_d28_UCB | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.ragene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/ragene20st/GSM1664281_GSM1664281_80_M6_CO_d28_UCB.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//ragene20st_GSM1664281_GSM1664281_80_M6_CO_d28_UCB_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ragene20st Rscript convert.R -p ragene20st -o /home/user/data/out/ -i /home/user/data/ragene20st/GSM1664258_GSM1664258_23_3_C_d90_LUB.CEL.gz -d ragene20stprobeset -s rn -g GSM1664258_GSM1664258_23_3_C_d90_LUB | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.ragene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/ragene20st/GSM1664258_GSM1664258_23_3_C_d90_LUB.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//ragene20st_GSM1664258_GSM1664258_23_3_C_d90_LUB_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ragene20st Rscript convert.R -p ragene20st -o /home/user/data/out/ -i /home/user/data/ragene20st/GSM1664326_GSM1664326_70_M17_MPy_LD_d28_UCB_1.CEL.gz -d ragene20stprobeset -s rn -g GSM1664326_GSM1664326_70_M17_MPy_LD_d28_UCB_1 | |
| ^[[ALoading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.ragene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/ragene20st/GSM1664326_GSM1664326_70_M17_MPy_LD_d28_UCB_1.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//ragene20st_GSM1664326_GSM1664326_70_M17_MPy_LD_d28_UCB_1_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ragene20st Rscript convert.R -p ragene20st -o /home/user/data/out/ -i /home/user/data/ragene20st/GSM1664350_GSM1664350_110_13_Pio_LD_d28_LUB.CEL.gz -d ragene20stprobeset -s rn -g GSM1664350_GSM1664350_110_13_Pio_LD_d28_LUB | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.ragene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/ragene20st/GSM1664350_GSM1664350_110_13_Pio_LD_d28_LUB.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//ragene20st_GSM1664350_GSM1664350_110_13_Pio_LD_d28_LUB_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ragene20st Rscript convert.R -p ragene20st -o /home/user/data/out/ -i /home/user/data/ragene20st/GSM1664268_GSM1664268_53_M03_CMC_d14_UCB_1.CEL.gz -d ragene20stprobeset -s rn -g GSM1664268_GSM1664268_53_M03_CMC_d14_UCB_1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.ragene.2.0.st | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/ragene20st/GSM1664268_GSM1664268_53_M03_CMC_d14_UCB_1.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//ragene20st_GSM1664268_GSM1664268_53_M03_CMC_d14_UCB_1_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/hugene11st --build-arg package=pd.hugene.1.1.st.v1_3.14.1.tar.gz --build-arg db=hugene11stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 202867f063ca | |
| Removing intermediate container 202867f063ca | |
| ---> 909c4569a886 | |
| Step 7/13 : ARG db | |
| ---> Running in a5466680e856 | |
| Removing intermediate container a5466680e856 | |
| ---> 2a8b61c387a8 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 9729b5248a98 | |
| Removing intermediate container 9729b5248a98 | |
| ---> bc488e1e4f1d | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 3652c794e764 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hugene11stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hugene11stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 28600168 bytes (27.3 MB) | |
| ================================================== | |
| downloaded 27.3 MB | |
| * installing *source* package 'hugene11stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hugene11stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmphvoQmQ/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hugene.1.1.st.v1_3.14.1.tar.gz | |
| Installing pd.hugene.1.1.st.v1 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmphvoQmQ/devtools77a1b6585/pd.hugene.1.1.st.v1' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hugene.1.1.st.v1' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hugene.1.1.st.v1) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 3652c794e764 | |
| ---> 87c0fd0a789c | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 55e5a160c7a2 | |
| Removing intermediate container 55e5a160c7a2 | |
| ---> ef81268242fd | |
| Step 11/13 : COPY convert.R . | |
| ---> c3eeddcb2cc6 | |
| Step 12/13 : USER user | |
| ---> Running in 7144fd5c39c4 | |
| Removing intermediate container 7144fd5c39c4 | |
| ---> baebba153b3e | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 60ef4e4d8fe0 | |
| Removing intermediate container 60ef4e4d8fe0 | |
| ---> f96053d9e27f | |
| Successfully built f96053d9e27f | |
| Successfully tagged convert/hugene11st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene11st Rscript convert.R -p hugene11st -o /home/user/data/out/ -i /home/user/data/hugene11st/GSM2062511_GSM2062511_AP19_3_LCD_B10.CEL.gz -d hugene11stprobeset -s hs -g GSM2062511_GSM2062511_AP19_3_LCD_B10 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene11st Rscript convert.R -p hugene11st -o /home/user/data/out/ -i /home/user/data/hugene11st/GSM1644560_GSM1644560_F037_2.CEL.gz -d hugene11stprobeset -s hs -g GSM1644560_GSM1644560_F037_2 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene11st Rscript convert.R -p hugene11st -o /home/user/data/out/ -i /home/user/data/hugene11st/GSM1341616_GSM1341616_HG01_D05.CEL.gz -d hugene11stprobeset -s hs -g GSM1341616_GSM1341616_HG01_D05 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene11st Rscript convert.R -p hugene11st -o /home/user/data/out/ -i /home/user/data/hugene11st/GSM1501053_GSM1501053_A1891-15.CEL.gz -d hugene11stprobeset -s hs -g GSM1501053_GSM1501053_A1891-15 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene11st Rscript convert.R -p hugene11st -o /home/user/data/out/ -i /home/user/data/hugene11st/GSM1228715_GSM1228715_HTHuGene11_020411K_MT32_327.CEL.gz -d hugene11stprobeset -s hs -g GSM1228715_GSM1228715_HTHuGene11_020411K_MT32_327 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/ragene11st --build-arg package=pd.ragene.1.1.st.v1_3.14.1.tar.gz --build-arg db=ragene11stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in a8461bd50fd5 | |
| Removing intermediate container a8461bd50fd5 | |
| ---> 3545b5b072dc | |
| Step 7/13 : ARG db | |
| ---> Running in 0c8db9a850b1 | |
| Removing intermediate container 0c8db9a850b1 | |
| ---> 26a0b1615329 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in b506cc9c022a | |
| Removing intermediate container b506cc9c022a | |
| ---> 68ca8cb9af53 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in d58890997842 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'ragene11stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/ragene11stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 11490023 bytes (11.0 MB) | |
| ================================================== | |
| downloaded 11.0 MB | |
| * installing *source* package 'ragene11stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (ragene11stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpiPnm5Z/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.ragene.1.1.st.v1_3.14.1.tar.gz | |
| Installing pd.ragene.1.1.st.v1 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpiPnm5Z/devtools77d46076d/pd.ragene.1.1.st.v1' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.ragene.1.1.st.v1' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.ragene.1.1.st.v1) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container d58890997842 | |
| ---> 2eefa48794dd | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 691efaeb9cc1 | |
| Removing intermediate container 691efaeb9cc1 | |
| ---> b06d53915ac8 | |
| Step 11/13 : COPY convert.R . | |
| ---> e59b7e216054 | |
| Step 12/13 : USER user | |
| ---> Running in 9d01fd19c3fd | |
| Removing intermediate container 9d01fd19c3fd | |
| ---> bf8ace952d95 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 8f3426b09960 | |
| Removing intermediate container 8f3426b09960 | |
| ---> 169d69f06075 | |
| Successfully built 169d69f06075 | |
| Successfully tagged convert/ragene11st:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/ragene11st' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/yeast2 --build-arg package=pd.yeast.2_3.12.0.tar.gz --build-arg db=yeast2 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 673aada17b2b | |
| Removing intermediate container 673aada17b2b | |
| ---> ae3856263296 | |
| Step 7/13 : ARG db | |
| ---> Running in 209fe7712a46 | |
| Removing intermediate container 209fe7712a46 | |
| ---> c34999147234 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in b252ca4dc272 | |
| Removing intermediate container b252ca4dc272 | |
| ---> a9faa741946e | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 4bbeee53dee8 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'yeast2.db' | |
| also installing the dependency 'org.Sc.sgd.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Sc.sgd.db_3.5.0.tar.gz' | |
| Content type 'application/x-gzip' length 21146339 bytes (20.2 MB) | |
| ================================================== | |
| downloaded 20.2 MB | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/yeast2.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 254373 bytes (248 KB) | |
| ================================================== | |
| downloaded 248 KB | |
| * installing *source* package 'org.Sc.sgd.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (org.Sc.sgd.db) | |
| * installing *source* package 'yeast2.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (yeast2.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpFZS8g9/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.yeast.2_3.12.0.tar.gz | |
| Installing pd.yeast.2 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpFZS8g9/devtools763f0c1fc/pd.yeast.2' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.yeast.2' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| Warning: call dbDisconnect() when finished working with a connection | |
| ** testing if installed package can be loaded | |
| * DONE (pd.yeast.2) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 4bbeee53dee8 | |
| ---> fcb99110b5ee | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in af09d6caf3f2 | |
| Removing intermediate container af09d6caf3f2 | |
| ---> 3c23fcbff4ec | |
| Step 11/13 : COPY convert.R . | |
| ---> cad96a0d8b03 | |
| Step 12/13 : USER user | |
| ---> Running in 64c2909bde50 | |
| Removing intermediate container 64c2909bde50 | |
| ---> 68adb3b1de37 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 60e819ecb19e | |
| Removing intermediate container 60e819ecb19e | |
| ---> a62ee7ebd600 | |
| Successfully built a62ee7ebd600 | |
| Successfully tagged convert/yeast2:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/yeast2 Rscript convert.R -p yeast2 -o /home/user/data/out/ -i /home/user/data/yeast2/GSM414682_GSM414682.CEL.gz -d yeast2 -s sc -g GSM414682_GSM414682 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Sc.sgd.db | |
| Reading.. | |
| Loading required package: pd.yeast.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/yeast2/GSM414682_GSM414682.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//yeast2_GSM414682_GSM414682_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/mgu74cv2 --build-arg package=pd.mg.u74cv2_3.12.0.tar.gz --build-arg db=mgu74cv2 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in e525dd3c80de | |
| Removing intermediate container e525dd3c80de | |
| ---> 386309d43628 | |
| Step 7/13 : ARG db | |
| ---> Running in 36870c93a2f2 | |
| Removing intermediate container 36870c93a2f2 | |
| ---> 4f57021ec411 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 249443f4a079 | |
| Removing intermediate container 249443f4a079 | |
| ---> 391d4ac6c24a | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in a5a378c1e72e | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'mgu74cv2.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mgu74cv2.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 467300 bytes (456 KB) | |
| ================================================== | |
| downloaded 456 KB | |
| * installing *source* package 'mgu74cv2.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (mgu74cv2.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpRsT0IL/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mg.u74cv2_3.12.0.tar.gz | |
| Installing pd.mg.u74cv2 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpRsT0IL/devtools77416ed0a/pd.mg.u74cv2' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.mg.u74cv2' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.mg.u74cv2) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container a5a378c1e72e | |
| ---> 2d79dc523970 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 3244067f0abf | |
| Removing intermediate container 3244067f0abf | |
| ---> 4c7615e161ff | |
| Step 11/13 : COPY convert.R . | |
| ---> ede09e98f55b | |
| Step 12/13 : USER user | |
| ---> Running in 59223ade2f28 | |
| Removing intermediate container 59223ade2f28 | |
| ---> 5f62e2009087 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 4e215aafd8aa | |
| Removing intermediate container 4e215aafd8aa | |
| ---> 3e1f5cdd8701 | |
| Successfully built 3e1f5cdd8701 | |
| Successfully tagged convert/mgu74cv2:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/mgu74cv2' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/zebgene11st --build-arg package=pd.zebgene.1.1.st_3.12.0.tar.gz --build-arg db=zebgene11st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 4eec72a8d542 | |
| Removing intermediate container 4eec72a8d542 | |
| ---> e95d38fc2fd6 | |
| Step 7/13 : ARG db | |
| ---> Running in e48a65169e57 | |
| Removing intermediate container e48a65169e57 | |
| ---> 64a141dc624a | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 7fcd00c2ed27 | |
| Removing intermediate container 7fcd00c2ed27 | |
| ---> 6d5242b397ad | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 92751b699ff3 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'zebgene11st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'zebgene11st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.zebgene.1.1.st_3.12.0.tar.gz | |
| Installing pd.zebgene.1.1.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmpfoo1OR/devtools7298a544/pd.zebgene.1.1.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.zebgene.1.1.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.zebgene.1.1.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 92751b699ff3 | |
| ---> 63c67ba08ded | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in b6ce15642f72 | |
| Removing intermediate container b6ce15642f72 | |
| ---> 4d3fdbb590a3 | |
| Step 11/13 : COPY convert.R . | |
| ---> 2f0714e83a5b | |
| Step 12/13 : USER user | |
| ---> Running in 8cee465d93c7 | |
| Removing intermediate container 8cee465d93c7 | |
| ---> f3c785b16c6f | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 11a5b057218b | |
| Removing intermediate container 11a5b057218b | |
| ---> 76a20d2e849c | |
| Successfully built 76a20d2e849c | |
| Successfully tagged convert/zebgene11st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebgene11st Rscript convert.R -p zebgene11st -o /home/user/data/out/ -i /home/user/data/zebgene11st/GSM1340438_GSM1340438_101639-172.CEL.gz -d zebgene11st -s dr -g GSM1340438_GSM1340438_101639-172 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'zebgene11st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebgene11st Rscript convert.R -p zebgene11st -o /home/user/data/out/ -i /home/user/data/zebgene11st/GSM1340453_GSM1340453_101639-187.CEL.gz -d zebgene11st -s dr -g GSM1340453_GSM1340453_101639-187 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'zebgene11st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebgene11st Rscript convert.R -p zebgene11st -o /home/user/data/out/ -i /home/user/data/zebgene11st/GSM1340342_GSM1340342_101639-074.CEL.gz -d zebgene11st -s dr -g GSM1340342_GSM1340342_101639-074 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'zebgene11st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebgene11st Rscript convert.R -p zebgene11st -o /home/user/data/out/ -i /home/user/data/zebgene11st/GSM1340408_GSM1340408_101639-142.CEL.gz -d zebgene11st -s dr -g GSM1340408_GSM1340408_101639-142 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'zebgene11st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/zebgene11st Rscript convert.R -p zebgene11st -o /home/user/data/out/ -i /home/user/data/zebgene11st/GSM1340436_GSM1340436_101639-170.CEL.gz -d zebgene11st -s dr -g GSM1340436_GSM1340436_101639-170 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'zebgene11st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/hugene10st --build-arg package=pd.hugene.1.0.st.v1_3.14.1.tar.gz --build-arg db=hugene10stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in a20d7e6162d8 | |
| Removing intermediate container a20d7e6162d8 | |
| ---> 3618b6254c91 | |
| Step 7/13 : ARG db | |
| ---> Running in ab391085602a | |
| Removing intermediate container ab391085602a | |
| ---> 1b36f390916a | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in e78f25d0c459 | |
| Removing intermediate container e78f25d0c459 | |
| ---> 9d077456ee6c | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 573d3a83f107 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hugene10stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hugene10stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 28600188 bytes (27.3 MB) | |
| ================================================== | |
| downloaded 27.3 MB | |
| * installing *source* package 'hugene10stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hugene10stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpcCLxhM/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hugene.1.0.st.v1_3.14.1.tar.gz | |
| Installing pd.hugene.1.0.st.v1 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpcCLxhM/devtools718ed811f/pd.hugene.1.0.st.v1' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hugene.1.0.st.v1' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hugene.1.0.st.v1) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 573d3a83f107 | |
| ---> 2188a9e87919 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 91974ea7f809 | |
| Removing intermediate container 91974ea7f809 | |
| ---> 14d98dc977db | |
| Step 11/13 : COPY convert.R . | |
| ---> e534945b9c81 | |
| Step 12/13 : USER user | |
| ---> Running in 13d3b399b32e | |
| Removing intermediate container 13d3b399b32e | |
| ---> 6236c73b5d08 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 64fb8bd178ea | |
| Removing intermediate container 64fb8bd178ea | |
| ---> 01e0118bd0da | |
| Successfully built 01e0118bd0da | |
| Successfully tagged convert/hugene10st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene10st Rscript convert.R -p hugene10st -o /home/user/data/out/ -i /home/user/data/hugene10st/GSM912379_GSM912379_AS_SL_F7_576.CEL.gz -d hugene10stprobeset -s hs -g GSM912379_GSM912379_AS_SL_F7_576 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene10st Rscript convert.R -p hugene10st -o /home/user/data/out/ -i /home/user/data/hugene10st/GSM912374_GSM912374_AS_COPD_D_C4_5000061.CEL.gz -d hugene10stprobeset -s hs -g GSM912374_GSM912374_AS_COPD_D_C4_5000061 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene10st Rscript convert.R -p hugene10st -o /home/user/data/out/ -i /home/user/data/hugene10st/GSM912422_GSM912422_AS_COPD_C_C6_5000730.CEL.gz -d hugene10stprobeset -s hs -g GSM912422_GSM912422_AS_COPD_C_C6_5000730 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene10st Rscript convert.R -p hugene10st -o /home/user/data/out/ -i /home/user/data/hugene10st/GSM912253_GSM912253_AS_SL399.CEL.gz -d hugene10stprobeset -s hs -g GSM912253_GSM912253_AS_SL399 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene10st Rscript convert.R -p hugene10st -o /home/user/data/out/ -i /home/user/data/hugene10st/GSM912221_GSM912221_AS_COPD_D_A5_5000075.CEL.gz -d hugene10stprobeset -s hs -g GSM912221_GSM912221_AS_COPD_D_A5_5000075 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/rae230b --build-arg package=pd.rae230b_3.12.0.tar.gz --build-arg db=rae230b -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in b1db8028e103 | |
| Removing intermediate container b1db8028e103 | |
| ---> 4dd3ebb18412 | |
| Step 7/13 : ARG db | |
| ---> Running in 3fb1241dbd48 | |
| Removing intermediate container 3fb1241dbd48 | |
| ---> 8755f2d5bf9f | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 2bc57bc4fb92 | |
| Removing intermediate container 2bc57bc4fb92 | |
| ---> c1335f7f821f | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 68d430d8c5c1 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'rae230b.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/rae230b.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 498700 bytes (487 KB) | |
| ================================================== | |
| downloaded 487 KB | |
| * installing *source* package 'rae230b.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (rae230b.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpCP0xeO/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.rae230b_3.12.0.tar.gz | |
| Installing pd.rae230b | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpCP0xeO/devtools75952ca64/pd.rae230b' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.rae230b' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.rae230b) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 68d430d8c5c1 | |
| ---> a7e61c276571 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 37c165790aac | |
| Removing intermediate container 37c165790aac | |
| ---> 0543e5024046 | |
| Step 11/13 : COPY convert.R . | |
| ---> ea3fc8e066fa | |
| Step 12/13 : USER user | |
| ---> Running in a3b44e22d904 | |
| Removing intermediate container a3b44e22d904 | |
| ---> 2f3e052d681c | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in b51ea9dd4773 | |
| Removing intermediate container b51ea9dd4773 | |
| ---> 6b35f5c65152 | |
| Successfully built 6b35f5c65152 | |
| Successfully tagged convert/rae230b:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/rae230b Rscript convert.R -p rae230b -o /home/user/data/out/ -i /home/user/data/rae230b/GSM312737_GSM312737.CEL.gz -d rae230b -s rn -g GSM312737_GSM312737 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.rae230b | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/rae230b/GSM312737_GSM312737.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//rae230b_GSM312737_GSM312737_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/rae230b Rscript convert.R -p rae230b -o /home/user/data/out/ -i /home/user/data/rae230b/GSM946782_GSM946782_RESTING_8_B.CEL.gz -d rae230b -s rn -g GSM946782_GSM946782_RESTING_8_B | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.rae230b | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/rae230b/GSM946782_GSM946782_RESTING_8_B.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//rae230b_GSM946782_GSM946782_RESTING_8_B_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/porgene10st --build-arg package=pd.porgene.1.0.st_3.12.0.tar.gz --build-arg db=porgene10st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 744d1de23e10 | |
| Removing intermediate container 744d1de23e10 | |
| ---> 5bfacb987326 | |
| Step 7/13 : ARG db | |
| ---> Running in 3231b4dda298 | |
| Removing intermediate container 3231b4dda298 | |
| ---> 694a378f632d | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in fb42f7c74b17 | |
| Removing intermediate container fb42f7c74b17 | |
| ---> 8ba6f53ddc79 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 71497116cd54 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'porgene10st.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'porgene10st.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.porgene.1.0.st_3.12.0.tar.gz | |
| Installing pd.porgene.1.0.st | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpZhU36M/devtools7256a9b02/pd.porgene.1.0.st' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.porgene.1.0.st' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.porgene.1.0.st) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 71497116cd54 | |
| ---> 82645c5a8349 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 54e174b3811b | |
| Removing intermediate container 54e174b3811b | |
| ---> be3355651d56 | |
| Step 11/13 : COPY convert.R . | |
| ---> 06e7f6ca1eee | |
| Step 12/13 : USER user | |
| ---> Running in 51297e21792c | |
| Removing intermediate container 51297e21792c | |
| ---> 22861ac5266b | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 0b11e5c584a8 | |
| Removing intermediate container 0b11e5c584a8 | |
| ---> f9bb97cd528f | |
| Successfully built f9bb97cd528f | |
| Successfully tagged convert/porgene10st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/porgene10st Rscript convert.R -p porgene10st -o /home/user/data/out/ -i /home/user/data/porgene10st/GSM1361245_GSM1361245_1326-LM_6.CEL.gz -d porgene10st -s ss -g GSM1361245_GSM1361245_1326-LM_6 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'porgene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/porgene10st Rscript convert.R -p porgene10st -o /home/user/data/out/ -i /home/user/data/porgene10st/GSM2056878_GSM2056878_M3_PorGene-1_0-st_.CEL.gz -d porgene10st -s ss -g GSM2056878_GSM2056878_M3_PorGene-1_0-st_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'porgene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/porgene10st Rscript convert.R -p porgene10st -o /home/user/data/out/ -i /home/user/data/porgene10st/GSM1361249_GSM1361249_1495-LW_12.CEL.gz -d porgene10st -s ss -g GSM1361249_GSM1361249_1495-LW_12 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'porgene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/porgene10st Rscript convert.R -p porgene10st -o /home/user/data/out/ -i /home/user/data/porgene10st/GSM2211171_GSM2211171_RUTJ_C-1_PorGene-1_0-st_.CEL.gz -d porgene10st -s ss -g GSM2211171_GSM2211171_RUTJ_C-1_PorGene-1_0-st_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'porgene10st.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/porgene10st Rscript convert.R -p porgene10st -o /home/user/data/out/ -i /home/user/data/porgene10st/GSM1109177_GSM1109177_A257_02_C_P1_2_RESIST_PORGENE-1_0-ST_.CEL.gz -d porgene10st -s ss -g GSM1109177_GSM1109177_A257_02_C_P1_2_RESIST_PORGENE-1_0-ST_ | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'porgene10st.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/hgu133a2 --build-arg package=pd.hg.u133a.2_3.12.0.tar.gz --build-arg db=hgu133a2 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in c1a4d096d5d8 | |
| Removing intermediate container c1a4d096d5d8 | |
| ---> 82b274413b83 | |
| Step 7/13 : ARG db | |
| ---> Running in d1e9f47e6a02 | |
| Removing intermediate container d1e9f47e6a02 | |
| ---> 060c26ab5c34 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in e7df69772ade | |
| Removing intermediate container e7df69772ade | |
| ---> 04d1677ff584 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in beb9beb45769 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'hgu133a2.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu133a2.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 901592 bytes (880 KB) | |
| ================================================== | |
| downloaded 880 KB | |
| * installing *source* package 'hgu133a2.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (hgu133a2.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmpn4j4Ao/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hg.u133a.2_3.12.0.tar.gz | |
| Installing pd.hg.u133a.2 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmpn4j4Ao/devtools627d2431e/pd.hg.u133a.2' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.hg.u133a.2' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.hg.u133a.2) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container beb9beb45769 | |
| ---> d63d727414ba | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in bdd70e4e5de1 | |
| Removing intermediate container bdd70e4e5de1 | |
| ---> 4d990dc94961 | |
| Step 11/13 : COPY convert.R . | |
| ---> 858f1c7ea2f4 | |
| Step 12/13 : USER user | |
| ---> Running in d57a27bbbb51 | |
| Removing intermediate container d57a27bbbb51 | |
| ---> 322a75c9fc48 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 71884f584e69 | |
| Removing intermediate container 71884f584e69 | |
| ---> f3a60b23bf7b | |
| Successfully built f3a60b23bf7b | |
| Successfully tagged convert/hgu133a2:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133a2 Rscript convert.R -p hgu133a2 -o /home/user/data/out/ -i /home/user/data/hgu133a2/GSM2149864_GSM2149864_RL_B6_26.CEL.gz -d hgu133a2 -s hs -g GSM2149864_GSM2149864_RL_B6_26 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133a.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133a2/GSM2149864_GSM2149864_RL_B6_26.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133a2_GSM2149864_GSM2149864_RL_B6_26_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133a2 Rscript convert.R -p hgu133a2 -o /home/user/data/out/ -i /home/user/data/hgu133a2/GSM1445573_GSM1445573_Fitzgerald_RC18_U133Av2.0.CEL.gz -d hgu133a2 -s hs -g GSM1445573_GSM1445573_Fitzgerald_RC18_U133Av2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133a.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133a2/GSM1445573_GSM1445573_Fitzgerald_RC18_U133Av2.0.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133a2_GSM1445573_GSM1445573_Fitzgerald_RC18_U133Av2_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133a2 Rscript convert.R -p hgu133a2 -o /home/user/data/out/ -i /home/user/data/hgu133a2/GSM2149859_GSM2149859_RL_A2_02.CEL.gz -d hgu133a2 -s hs -g GSM2149859_GSM2149859_RL_A2_02 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133a.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133a2/GSM2149859_GSM2149859_RL_A2_02.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133a2_GSM2149859_GSM2149859_RL_A2_02_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133a2 Rscript convert.R -p hgu133a2 -o /home/user/data/out/ -i /home/user/data/hgu133a2/GSM1445575_GSM1445575_Fitzgerald_RC44_U133Av2.0.CEL.gz -d hgu133a2 -s hs -g GSM1445575_GSM1445575_Fitzgerald_RC44_U133Av2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133a.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133a2/GSM1445575_GSM1445575_Fitzgerald_RC44_U133Av2.0.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133a2_GSM1445575_GSM1445575_Fitzgerald_RC44_U133Av2_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hgu133a2 Rscript convert.R -p hgu133a2 -o /home/user/data/out/ -i /home/user/data/hgu133a2/GSM1445574_GSM1445574_Fitzgerald_RC31_U133Av2.0.CEL.gz -d hgu133a2 -s hs -g GSM1445574_GSM1445574_Fitzgerald_RC31_U133Av2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Hs.eg.db | |
| Reading.. | |
| Loading required package: pd.hg.u133a.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/hgu133a2/GSM1445574_GSM1445574_Fitzgerald_RC31_U133Av2.0.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//hgu133a2_GSM1445574_GSM1445574_Fitzgerald_RC31_U133Av2_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/mogene10st --build-arg package=pd.mogene.1.0.st.v1_3.14.1.tar.gz --build-arg db=mogene10stprobeset -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in d6aa9d5593dc | |
| Removing intermediate container d6aa9d5593dc | |
| ---> 304ea3df1de6 | |
| Step 7/13 : ARG db | |
| ---> Running in 17f3b3dbf598 | |
| Removing intermediate container 17f3b3dbf598 | |
| ---> 7d4852150394 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 00d3e13714da | |
| Removing intermediate container 00d3e13714da | |
| ---> d31062852116 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 757a90facae0 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'mogene10stprobeset.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mogene10stprobeset.db_8.7.0.tar.gz' | |
| Content type 'application/x-gzip' length 19287224 bytes (18.4 MB) | |
| ================================================== | |
| downloaded 18.4 MB | |
| * installing *source* package 'mogene10stprobeset.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (mogene10stprobeset.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmp5FZz5k/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mogene.1.0.st.v1_3.14.1.tar.gz | |
| Installing pd.mogene.1.0.st.v1 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmp5FZz5k/devtools7297e2981/pd.mogene.1.0.st.v1' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.mogene.1.0.st.v1' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.mogene.1.0.st.v1) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 757a90facae0 | |
| ---> bc2b48473622 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in f0995d65da95 | |
| Removing intermediate container f0995d65da95 | |
| ---> 226648531c8a | |
| Step 11/13 : COPY convert.R . | |
| ---> 645523a2a62a | |
| Step 12/13 : USER user | |
| ---> Running in 96690c57b7f1 | |
| Removing intermediate container 96690c57b7f1 | |
| ---> eb112e34e05a | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 32d8284c67ba | |
| Removing intermediate container 32d8284c67ba | |
| ---> 810a56fde11b | |
| Successfully built 810a56fde11b | |
| Successfully tagged convert/mogene10st:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene10st Rscript convert.R -p mogene10st -o /home/user/data/out/ -i /home/user/data/mogene10st/GSM983053_GSM983053_05.952GFPPOS7MO.CEL.gz -d mogene10stprobeset -s mm -g GSM983053_GSM983053_05 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene10st Rscript convert.R -p mogene10st -o /home/user/data/out/ -i /home/user/data/mogene10st/GSM983050_GSM983050_02.693GFPPOS1Y9MO.CEL.gz -d mogene10stprobeset -s mm -g GSM983050_GSM983050_02 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene10st Rscript convert.R -p mogene10st -o /home/user/data/out/ -i /home/user/data/mogene10st/GSM983055_GSM983055_09.955GFPNEG7MO.CEL.gz -d mogene10stprobeset -s mm -g GSM983055_GSM983055_09 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene10st Rscript convert.R -p mogene10st -o /home/user/data/out/ -i /home/user/data/mogene10st/GSM983054_GSM983054_06.952GFPNEG7MO.CEL.gz -d mogene10stprobeset -s mm -g GSM983054_GSM983054_06 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene10st Rscript convert.R -p mogene10st -o /home/user/data/out/ -i /home/user/data/mogene10st/GSM983052_GSM983052_04.704GFPPOS1Y9MO.CEL.gz -d mogene10stprobeset -s mm -g GSM983052_GSM983052_04 | |
| Error: CEL file header does not match platform argument | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/clariomsmouse --build-arg package=pd.clariom.s.mouse_3.14.1.tar.gz --build-arg db=clariomsmouse -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in 87cc4b3134c1 | |
| Removing intermediate container 87cc4b3134c1 | |
| ---> d5b56ee93963 | |
| Step 7/13 : ARG db | |
| ---> Running in 56d3162d92ee | |
| Removing intermediate container 56d3162d92ee | |
| ---> a9f30c34a952 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 7809048a96d3 | |
| Removing intermediate container 7809048a96d3 | |
| ---> 22c4a63c5e12 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in ae2095faaecc | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'clariomsmouse.db' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Warning message: | |
| package 'clariomsmouse.db' is not available (for R version 3.4.4) | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.clariom.s.mouse_3.14.1.tar.gz | |
| Installing pd.clariom.s.mouse | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpbmqJBI/devtools729585366/pd.clariom.s.mouse' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.clariom.s.mouse' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.clariom.s.mouse) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container ae2095faaecc | |
| ---> 9c767b1e0673 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in df565cd2d888 | |
| Removing intermediate container df565cd2d888 | |
| ---> 790ef26b0080 | |
| Step 11/13 : COPY convert.R . | |
| ---> f27d82883192 | |
| Step 12/13 : USER user | |
| ---> Running in 22e99c230a89 | |
| Removing intermediate container 22e99c230a89 | |
| ---> 2a74f3215f1a | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 7041a3b626b7 | |
| Removing intermediate container 7041a3b626b7 | |
| ---> 972ee32c2540 | |
| Successfully built 972ee32c2540 | |
| Successfully tagged convert/clariomsmouse:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsmouse Rscript convert.R -p clariomsmouse -o /home/user/data/out/ -i /home/user/data/clariomsmouse/GSM3143080_GSM3143080_KRlow2.CEL.gz -d clariomsmouse -s mm -g GSM3143080_GSM3143080_KRlow2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'clariomsmouse.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsmouse Rscript convert.R -p clariomsmouse -o /home/user/data/out/ -i /home/user/data/clariomsmouse/GSM3143081_GSM3143081_KRlow3.CEL.gz -d clariomsmouse -s mm -g GSM3143081_GSM3143081_KRlow3 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'clariomsmouse.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsmouse Rscript convert.R -p clariomsmouse -o /home/user/data/out/ -i /home/user/data/clariomsmouse/GSM3143076_GSM3143076_KR1.CEL.gz -d clariomsmouse -s mm -g GSM3143076_GSM3143076_KR1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'clariomsmouse.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsmouse Rscript convert.R -p clariomsmouse -o /home/user/data/out/ -i /home/user/data/clariomsmouse/GSM3143079_GSM3143079_KRlow1.CEL.gz -d clariomsmouse -s mm -g GSM3143079_GSM3143079_KRlow1 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'clariomsmouse.db' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsmouse Rscript convert.R -p clariomsmouse -o /home/user/data/out/ -i /home/user/data/clariomsmouse/GSM3143077_GSM3143077_KR2.CEL.gz -d clariomsmouse -s mm -g GSM3143077_GSM3143077_KR2 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Error in library(db_package_name, character.only = TRUE) : | |
| there is no package called 'clariomsmouse.db' | |
| Execution halted | |
| Ran a whole brain! | |
| docker build -t convert/mu11ksuba --build-arg package=pd.mu11ksuba_3.12.0.tar.gz --build-arg db=mu11ksuba -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in e0b71c474213 | |
| Removing intermediate container e0b71c474213 | |
| ---> a725fb231fd8 | |
| Step 7/13 : ARG db | |
| ---> Running in aef8708ef84b | |
| Removing intermediate container aef8708ef84b | |
| ---> bbe883639634 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in aded81da5e9c | |
| Removing intermediate container aded81da5e9c | |
| ---> ba57731af421 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 06dfc53dcfab | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'mu11ksuba.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mu11ksuba.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 310997 bytes (303 KB) | |
| ================================================== | |
| downloaded 303 KB | |
| * installing *source* package 'mu11ksuba.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (mu11ksuba.db) | |
| The downloaded source packages are in | |
| '/tmp/RtmpUF3msH/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mu11ksuba_3.12.0.tar.gz | |
| Installing pd.mu11ksuba | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/RtmpUF3msH/devtools76a0e0db9/pd.mu11ksuba' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.mu11ksuba' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| Warning: call dbDisconnect() when finished working with a connection | |
| ** testing if installed package can be loaded | |
| * DONE (pd.mu11ksuba) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 06dfc53dcfab | |
| ---> 1467dbf24185 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in c0965d8b595f | |
| Removing intermediate container c0965d8b595f | |
| ---> 31563e8947a4 | |
| Step 11/13 : COPY convert.R . | |
| ---> 0bbc2f3f77d8 | |
| Step 12/13 : USER user | |
| ---> Running in f717e55dc695 | |
| Removing intermediate container f717e55dc695 | |
| ---> 43908c92fa59 | |
| Step 13/13 : ENTRYPOINT [] | |
| ---> Running in 1c80d6bd74b4 | |
| Removing intermediate container 1c80d6bd74b4 | |
| ---> 84251ff509c9 | |
| Successfully built 84251ff509c9 | |
| Successfully tagged convert/mu11ksuba:latest | |
| [Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/mu11ksuba' | |
| Ran a sample! | |
| Ran a whole brain! | |
| docker build -t convert/rat2302 --build-arg package=pd.rat230.2_3.12.0.tar.gz --build-arg db=rat2302 -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| ---> Using cache | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Using cache | |
| ---> c6cf6253bb3d | |
| Step 4/13 : COPY install_pd.R . | |
| ---> Using cache | |
| ---> 0e591293bbac | |
| Step 5/13 : ARG package | |
| ---> Using cache | |
| ---> 2a40e6020d31 | |
| Step 6/13 : ENV PACKAGE=$package | |
| ---> Running in e9be05e9125c | |
| Removing intermediate container e9be05e9125c | |
| ---> 213af460052f | |
| Step 7/13 : ARG db | |
| ---> Running in da981774074c | |
| Removing intermediate container da981774074c | |
| ---> 40802d5153d7 | |
| Step 8/13 : ENV DB=$db | |
| ---> Running in 5ac8d5e7842a | |
| Removing intermediate container 5ac8d5e7842a | |
| ---> 098ed91d9fe9 | |
| Step 9/13 : RUN Rscript install_pd.R | |
| ---> Running in 0759d709ab88 | |
| Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help | |
| A new version of Bioconductor is available after installing the most recent | |
| version of R; see http://bioconductor.org/install | |
| BioC_mirror: https://bioconductor.org | |
| Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). | |
| Installing package(s) 'rat2302.db' | |
| trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/rat2302.db_3.2.3.tar.gz' | |
| Content type 'application/x-gzip' length 1023160 bytes (999 KB) | |
| ================================================== | |
| downloaded 999 KB | |
| * installing *source* package 'rat2302.db' ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (rat2302.db) | |
| The downloaded source packages are in | |
| '/tmp/Rtmp1PI2AU/downloaded_packages' | |
| Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv', | |
| 'spatial' | |
| Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.rat230.2_3.12.0.tar.gz | |
| Installing pd.rat230.2 | |
| '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ | |
| CMD INSTALL '/tmp/Rtmp1PI2AU/devtools75d6fdd95/pd.rat230.2' \ | |
| --library='/usr/local/lib/R/site-library' --install-tests | |
| * installing *source* package 'pd.rat230.2' ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (pd.rat230.2) | |
| [[1]] | |
| [1] TRUE | |
| Removing intermediate container 0759d709ab88 | |
| ---> b5e283b7cd35 | |
| Step 10/13 : VOLUME /home/user/data | |
| ---> Running in 9294eb85dc00 | |
| Removing intermediate container 9294eb85dc00 | |
| ---> 2bec2194aecd | |
| Step 11/13 : COPY convert.R . | |
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| Removing intermediate container 2b3453786660 | |
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| ---> Running in d3a0f5acfd46 | |
| Removing intermediate container d3a0f5acfd46 | |
| ---> ae74849e66d7 | |
| Successfully built ae74849e66d7 | |
| Successfully tagged convert/rat2302:latest | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/rat2302 Rscript convert.R -p rat2302 -o /home/user/data/out/ -i /home/user/data/rat2302/GSM1495846_GSM1495846_RAE2302_061014H_PB3_LE4.CEL.gz -d rat2302 -s rn -g GSM1495846_GSM1495846_RAE2302_061014H_PB3_LE4 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.rat230.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/rat2302/GSM1495846_GSM1495846_RAE2302_061014H_PB3_LE4.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//rat2302_GSM1495846_GSM1495846_RAE2302_061014H_PB3_LE4_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/rat2302 Rscript convert.R -p rat2302 -o /home/user/data/out/ -i /home/user/data/rat2302/GSM1495845_GSM1495845_RAE2302_061014H_PB2_LE3.CEL.gz -d rat2302 -s rn -g GSM1495845_GSM1495845_RAE2302_061014H_PB2_LE3 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.rat230.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/rat2302/GSM1495845_GSM1495845_RAE2302_061014H_PB2_LE3.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//rat2302_GSM1495845_GSM1495845_RAE2302_061014H_PB2_LE3_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/rat2302 Rscript convert.R -p rat2302 -o /home/user/data/out/ -i /home/user/data/rat2302/GSM1495854_GSM1495854_RAE2302_061014H_PB11_HW27.CEL.gz -d rat2302 -s rn -g GSM1495854_GSM1495854_RAE2302_061014H_PB11_HW27 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.rat230.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/rat2302/GSM1495854_GSM1495854_RAE2302_061014H_PB11_HW27.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//rat2302_GSM1495854_GSM1495854_RAE2302_061014H_PB11_HW27_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/rat2302 Rscript convert.R -p rat2302 -o /home/user/data/out/ -i /home/user/data/rat2302/GSM1495847_GSM1495847_RAE2302_061014H_PB4_LE5.CEL.gz -d rat2302 -s rn -g GSM1495847_GSM1495847_RAE2302_061014H_PB4_LE5 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.rat230.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/rat2302/GSM1495847_GSM1495847_RAE2302_061014H_PB4_LE5.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//rat2302_GSM1495847_GSM1495847_RAE2302_061014H_PB4_LE5_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/rat2302 Rscript convert.R -p rat2302 -o /home/user/data/out/ -i /home/user/data/rat2302/GSM1495853_GSM1495853_RAE2302_061014H_PB10_HW26.CEL.gz -d rat2302 -s rn -g GSM1495853_GSM1495853_RAE2302_061014H_PB10_HW26 | |
| Loading required package: AnnotationDbi | |
| Loading required package: methods | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Loading required package: parallel | |
| Attaching package: 'BiocGenerics' | |
| The following objects are masked from 'package:parallel': | |
| clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
| clusterExport, clusterMap, parApply, parCapply, parLapply, | |
| parLapplyLB, parRapply, parSapply, parSapplyLB | |
| The following objects are masked from 'package:stats': | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from 'package:base': | |
| Filter, Find, Map, Position, Reduce, anyDuplicated, append, | |
| as.data.frame, cbind, colMeans, colSums, colnames, do.call, | |
| duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, | |
| lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, | |
| pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, | |
| setdiff, sort, table, tapply, union, unique, unsplit, which, | |
| which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:base': | |
| expand.grid | |
| Loading required package: org.Rn.eg.db | |
| Reading.. | |
| Loading required package: pd.rat230.2 | |
| Loading required package: Biostrings | |
| Loading required package: XVector | |
| Attaching package: 'Biostrings' | |
| The following object is masked from 'package:base': | |
| strsplit | |
| Loading required package: RSQLite | |
| Loading required package: oligoClasses | |
| Welcome to oligoClasses version 1.40.0 | |
| Loading required package: oligo | |
| ================================================================================ | |
| Welcome to oligo version 1.42.0 | |
| ================================================================================ | |
| Loading required package: DBI | |
| Platform design info loaded. | |
| Reading in : /home/user/data/rat2302/GSM1495853_GSM1495853_RAE2302_061014H_PB10_HW26.CEL.gz | |
| Mutating.. | |
| Joining.. | |
| Interesectiong.. | |
| Selecting.. | |
| 'select()' returned 1:many mapping between keys and columns | |
| Filtering.. | |
| Writing outfile.. | |
| Error in open.connection(path, "wb") : cannot open the connection | |
| Calls: <Anonymous> ... write_delim -> stream_delim -> open -> open.connection | |
| In addition: Warning message: | |
| In open.connection(path, "wb") : | |
| cannot open compressed file '/home/user/data/out//rat2302_GSM1495853_GSM1495853_RAE2302_061014H_PB10_HW26_master_conversion.tsv.gz', probable reason 'No such file or directory' | |
| Execution halted | |
| Ran a whole brain! |
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