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August 30, 2017 20:09
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SRA2R Mac OS installation log
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| sdavis2@Seans-MBP-3:~/Documents/git$ R CMD INSTALL SRA2R | |
| * installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’ | |
| * installing *source* package ‘SRA2R’ ... | |
| ** libs | |
| clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o | |
| clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c Functions.cpp -o Functions.o | |
| clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c GetReads.cpp -o GetReads.o | |
| clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o | |
| clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o | |
| clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o | |
| clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o | |
| clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c abc.cpp -o abc.o | |
| abc.cpp:94:8: warning: unused variable 'r_ans_width' [-Wunused-variable] | |
| SEXP r_ans_width, r_ans; | |
| ^ | |
| 1 warning generated. | |
| clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c alignReads.cpp -o alignReads.o | |
| clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c getPileUp.cpp -o getPileUp.o | |
| clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c getReferences.cpp -o getReferences.o | |
| clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c refBases.cpp -o refBases.o | |
| clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include" -fPIC -Wall -g -O2 -c stats.cpp -o stats.o | |
| clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/opt/openssl/lib -o SRA2R.so Biostrings_stubs.o Functions.o GetReads.o IRanges_stubs.o RcppExports.o S4Vectors_stubs.o XVector_stubs.o abc.o alignReads.o getPileUp.o getReferences.o refBases.o stats.o -L/Users/sdavis2/lib -L/Users/sdavis2/lib -lncbi-ngs-c++ -lngs-c++ -lncbi-ngs-c++ -lncbi-vdb-static -lngs-adapt-c++ -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation | |
| installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/SRA2R/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| Error: package or namespace load failed for ‘SRA2R’ in dyn.load(file, DLLpath = DLLpath, ...): | |
| unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/SRA2R/libs/SRA2R.so': | |
| dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/SRA2R/libs/SRA2R.so, 6): Symbol not found: __ZNSs4_Rep20_S_empty_rep_storageE | |
| Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/SRA2R/libs/SRA2R.so | |
| Expected in: flat namespace | |
| in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/SRA2R/libs/SRA2R.so | |
| Error: loading failed | |
| Execution halted | |
| ERROR: loading failed | |
| * removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/SRA2R’ | |
| sdavis2@Seans-MBP-3:~/Documents/git$ cd SRA2R | |
| sdavis2@Seans-MBP-3:~/Documents/git/SRA2R$ git log | |
| commit 9408c4f0c9956c7cad1259fcbf5414444fbb79d7 | |
| Author: Sean Davis <[email protected]> | |
| Date: Thu Aug 25 02:18:31 2016 +0000 | |
| Fixed srrRegex to deal with 6 or seven digit numbers. |
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