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January 12, 2021 16:12
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rstudio/renv unexpected inclusion of MASS package from base system caused by pkgdown
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| ### -> pwd | |
| ~/DH/home/sandrews/Code/platform/kushy_example | |
| ### -> find . -maxdepth 6 | |
| . | |
| ./_pkgdown.yml | |
| ./.Rprofile | |
| ./renv | |
| ./renv/activate.R | |
| ./renv/library | |
| ./renv/library/R-3.6 | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0 | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/LICENSE | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/bin | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/NEWS.md | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/resources | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/R | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/Meta | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/NAMESPACE | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/html | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/DESCRIPTION | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/config.yml | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/INDEX | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/doc | |
| ./renv/library/R-3.6/x86_64-apple-darwin15.6.0/renv/help | |
| ./renv/.gitignore | |
| ./renv/settings.dcf | |
| ### -> cat _pkgdown.yml | |
| destination: docs | |
| ### -> cat .Rprofile | |
| source("renv/activate.R") | |
| ### -> R --no-environ --no-site-file --no-restore | |
| R version 3.6.1 (2019-07-05) -- "Action of the Toes" | |
| Copyright (C) 2019 The R Foundation for Statistical Computing | |
| Platform: x86_64-apple-darwin15.6.0 (64-bit) | |
| R is free software and comes with ABSOLUTELY NO WARRANTY. | |
| You are welcome to redistribute it under certain conditions. | |
| Type 'license()' or 'licence()' for distribution details. | |
| Natural language support but running in an English locale | |
| R is a collaborative project with many contributors. | |
| Type 'contributors()' for more information and | |
| 'citation()' on how to cite R or R packages in publications. | |
| Type 'demo()' for some demos, 'help()' for on-line help, or | |
| 'help.start()' for an HTML browser interface to help. | |
| Type 'q()' to quit R. | |
| * Project '~/DH/home/sandrews/Code/platform/kushy_example' loaded. [renv 0.12.5] | |
| > deps <- renv::dependencies() | |
| Finding R package dependencies ... Done! | |
| > pkgs <- sort(unique(deps$Package)) | |
| > all <- unlist(tools::package_dependencies(pkgs, recursive = TRUE)) | |
| > | |
| > | |
| > | |
| > | |
| > | |
| > | |
| > deps | |
| Source | |
| 1 /Users/stu/DH/home/sandrews/Code/platform/kushy_example/_pkgdown.yml | |
| Package Require Version Dev | |
| 1 pkgdown FALSE | |
| > | |
| > | |
| > | |
| > | |
| > pkgs | |
| [1] "pkgdown" | |
| > | |
| > | |
| > | |
| > | |
| > all | |
| pkgdown1 pkgdown2 pkgdown3 pkgdown4 pkgdown5 | |
| "callr" "crayon" "desc" "digest" "downlit" | |
| pkgdown6 pkgdown7 pkgdown8 pkgdown9 pkgdown10 | |
| "fs" "httr" "magrittr" "memoise" "openssl" | |
| pkgdown11 pkgdown12 pkgdown13 pkgdown14 pkgdown15 | |
| "purrr" "ragg" "rematch2" "rlang" "rmarkdown" | |
| pkgdown16 pkgdown17 pkgdown18 pkgdown19 pkgdown20 | |
| "tibble" "tools" "whisker" "withr" "xml2" | |
| pkgdown21 pkgdown22 pkgdown23 pkgdown24 pkgdown25 | |
| "yaml" "processx" "R6" "utils" "grDevices" | |
| pkgdown26 pkgdown27 pkgdown28 pkgdown29 pkgdown30 | |
| "methods" "assertthat" "rprojroot" "brio" "evaluate" | |
| pkgdown31 pkgdown32 pkgdown33 pkgdown34 pkgdown35 | |
| "fansi" "vctrs" "curl" "jsonlite" "mime" | |
| pkgdown36 pkgdown37 pkgdown38 pkgdown39 pkgdown40 | |
| "askpass" "systemfonts" "textshaping" "knitr" "htmltools" | |
| pkgdown41 pkgdown42 pkgdown43 pkgdown44 pkgdown45 | |
| "tinytex" "xfun" "stringr" "cli" "ellipsis" | |
| pkgdown46 pkgdown47 pkgdown48 pkgdown49 pkgdown50 | |
| "lifecycle" "pillar" "pkgconfig" "graphics" "stats" | |
| pkgdown51 pkgdown52 pkgdown53 pkgdown54 pkgdown55 | |
| "sys" "glue" "base64enc" "highr" "markdown" | |
| pkgdown56 pkgdown57 pkgdown58 pkgdown59 | |
| "utf8" "ps" "stringi" "cpp11" | |
| > | |
| > | |
| > | |
| > | |
| > | |
| > | |
| > renv::diagnostics() | |
| Diagnostics Report -- renv [0.12.5] | |
| =================================== | |
| # Session Info ======================= | |
| R version 3.6.1 (2019-07-05) | |
| Platform: x86_64-apple-darwin15.6.0 (64-bit) | |
| Running under: macOS Catalina 10.15.7 | |
| Matrix products: default | |
| BLAS: /Library/Frameworks/R.framework/Versions/3.6.1/Resources/lib/libRblas.0.dylib | |
| LAPACK: /Library/Frameworks/R.framework/Versions/3.6.1/Resources/lib/libRlapack.dylib | |
| locale: | |
| [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 | |
| attached base packages: | |
| [1] stats graphics grDevices datasets utils methods base | |
| loaded via a namespace (and not attached): | |
| [1] compiler_3.6.1 tools_3.6.1 renv_0.12.5 | |
| # Project ============================ | |
| Project path: "~/DH/home/sandrews/Code/platform/kushy_example" | |
| # Status ============================= | |
| * This project has not yet been snapshotted -- 'renv.lock' does not exist. | |
| The following package(s) are installed but not recorded in the lockfile: | |
| _ | |
| MASS [7.3-51.4] | |
| renv [0.12.5] | |
| Use `renv::snapshot()` to add these packages to your lockfile. | |
| # Packages =========================== | |
| This project has not yet been snapshotted: 'renv.lock' does not exist. | |
| Library Source Lockfile Source Path Dependency | |
| KernSmooth 2.23-15 CRAN <NA> <NA> [2] <NA> | |
| MASS 7.3-51.4 CRAN <NA> <NA> [2] indirect | |
| Matrix 1.2-17 CRAN <NA> <NA> [2] <NA> | |
| R6 <NA> <NA> <NA> <NA> <NA> indirect | |
| askpass <NA> <NA> <NA> <NA> <NA> indirect | |
| assertthat <NA> <NA> <NA> <NA> <NA> indirect | |
| backports <NA> <NA> <NA> <NA> <NA> indirect | |
| base64enc <NA> <NA> <NA> <NA> <NA> indirect | |
| boot 1.3-22 CRAN <NA> <NA> [2] <NA> | |
| callr <NA> <NA> <NA> <NA> <NA> indirect | |
| class 7.3-15 CRAN <NA> <NA> [2] <NA> | |
| cli <NA> <NA> <NA> <NA> <NA> indirect | |
| cluster 2.1.0 CRAN <NA> <NA> [2] <NA> | |
| codetools 0.2-16 CRAN <NA> <NA> [2] <NA> | |
| crayon <NA> <NA> <NA> <NA> <NA> indirect | |
| curl <NA> <NA> <NA> <NA> <NA> indirect | |
| desc <NA> <NA> <NA> <NA> <NA> indirect | |
| digest <NA> <NA> <NA> <NA> <NA> indirect | |
| ellipsis <NA> <NA> <NA> <NA> <NA> indirect | |
| evaluate <NA> <NA> <NA> <NA> <NA> indirect | |
| fansi <NA> <NA> <NA> <NA> <NA> indirect | |
| foreign 0.8-71 CRAN <NA> <NA> [2] <NA> | |
| fs <NA> <NA> <NA> <NA> <NA> indirect | |
| glue <NA> <NA> <NA> <NA> <NA> indirect | |
| grDevices <NA> <NA> <NA> <NA> [2] indirect | |
| graphics <NA> <NA> <NA> <NA> [2] indirect | |
| highlight <NA> <NA> <NA> <NA> <NA> indirect | |
| highr <NA> <NA> <NA> <NA> <NA> indirect | |
| htmltools <NA> <NA> <NA> <NA> <NA> indirect | |
| httr <NA> <NA> <NA> <NA> <NA> indirect | |
| jsonlite <NA> <NA> <NA> <NA> <NA> indirect | |
| knitr <NA> <NA> <NA> <NA> <NA> indirect | |
| lattice 0.20-38 CRAN <NA> <NA> [2] <NA> | |
| lifecycle <NA> <NA> <NA> <NA> <NA> indirect | |
| magrittr <NA> <NA> <NA> <NA> <NA> indirect | |
| markdown <NA> <NA> <NA> <NA> <NA> indirect | |
| memoise <NA> <NA> <NA> <NA> <NA> indirect | |
| methods <NA> <NA> <NA> <NA> [2] indirect | |
| mgcv 1.8-28 CRAN <NA> <NA> [2] <NA> | |
| mime <NA> <NA> <NA> <NA> <NA> indirect | |
| nlme 3.1-140 CRAN <NA> <NA> [2] <NA> | |
| nnet 7.3-12 CRAN <NA> <NA> [2] <NA> | |
| openssl <NA> <NA> <NA> <NA> <NA> indirect | |
| pillar <NA> <NA> <NA> <NA> <NA> indirect | |
| pkgconfig <NA> <NA> <NA> <NA> <NA> indirect | |
| pkgdown <NA> <NA> <NA> <NA> <NA> direct | |
| processx <NA> <NA> <NA> <NA> <NA> indirect | |
| ps <NA> <NA> <NA> <NA> <NA> indirect | |
| purrr <NA> <NA> <NA> <NA> <NA> indirect | |
| rematch2 <NA> <NA> <NA> <NA> <NA> indirect | |
| renv 0.12.5 CRAN <NA> <NA> [1] <NA> | |
| rlang <NA> <NA> <NA> <NA> <NA> indirect | |
| rmarkdown <NA> <NA> <NA> <NA> <NA> indirect | |
| rpart 4.1-15 CRAN <NA> <NA> [2] <NA> | |
| rprojroot <NA> <NA> <NA> <NA> <NA> indirect | |
| rstudioapi <NA> <NA> <NA> <NA> <NA> indirect | |
| spatial 7.3-11 CRAN <NA> <NA> [2] <NA> | |
| stats <NA> <NA> <NA> <NA> [2] indirect | |
| stringi <NA> <NA> <NA> <NA> <NA> indirect | |
| stringr <NA> <NA> <NA> <NA> <NA> indirect | |
| survival 2.44-1.1 CRAN <NA> <NA> [2] <NA> | |
| sys <NA> <NA> <NA> <NA> <NA> indirect | |
| tibble <NA> <NA> <NA> <NA> <NA> indirect | |
| tinytex <NA> <NA> <NA> <NA> <NA> indirect | |
| tools <NA> <NA> <NA> <NA> [2] indirect | |
| utf8 <NA> <NA> <NA> <NA> <NA> indirect | |
| utils <NA> <NA> <NA> <NA> [2] indirect | |
| vctrs <NA> <NA> <NA> <NA> <NA> indirect | |
| whisker <NA> <NA> <NA> <NA> <NA> indirect | |
| withr <NA> <NA> <NA> <NA> <NA> indirect | |
| xfun <NA> <NA> <NA> <NA> <NA> indirect | |
| xml2 <NA> <NA> <NA> <NA> <NA> indirect | |
| yaml <NA> <NA> <NA> <NA> <NA> indirect | |
| [1]: /Users/stu/DH/home/sandrews/Code/platform/kushy_example/renv/library/R-3.6/x86_64-apple-darwin15.6.0 | |
| [2]: /private/var/folders/s2/fw4yx0qx35nb3mrls_fkqtbh0000gr/T/Rtmps1c6bx/renv-system-library | |
| # User Profile ======================= | |
| [no R packages referenced in user profile | |
| # Settings =========================== | |
| List of 7 | |
| $ external.libraries : chr(0) | |
| $ ignored.packages : chr(0) | |
| $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo" | |
| $ r.version : chr(0) | |
| $ snapshot.type : chr "implicit" | |
| $ use.cache : logi TRUE | |
| $ vcs.ignore.library : logi TRUE | |
| # Options ============================ | |
| List of 2 | |
| $ renv.consent: logi TRUE | |
| $ renv.verbose: logi TRUE | |
| # Environment Variables ============== | |
| HOME = /Users/stu | |
| LANG = en_US.UTF-8 | |
| R_LIBS = renv/library/R-3.6/x86_64-apple-darwin15.6.0 | |
| R_LIBS_SITE = | |
| R_LIBS_USER = /Users/stu/DH/home/sandrews/Code/platform/kushy_example/renv/library/R-3.6/x86_64-apple-darwin15.6.0:/private/var/folders/s2/fw4yx0qx35nb3mrls_fkqtbh0000gr/T/Rtmps1c6bx/renv-system-library | |
| RENV_DEFAULT_R_ENVIRON = | |
| RENV_DEFAULT_R_ENVIRON_USER = | |
| RENV_DEFAULT_R_LIBS = renv/library/R-3.6/x86_64-apple-darwin15.6.0 | |
| RENV_DEFAULT_R_LIBS_SITE = | |
| RENV_DEFAULT_R_LIBS_USER = ~/Library/R/3.6/library | |
| RENV_DEFAULT_R_PROFILE = | |
| RENV_DEFAULT_R_PROFILE_USER = <NA> | |
| RENV_PATHS_ROOT = /Users/stu/Research/Tools/RENV-HOME | |
| RENV_PROJECT = /Users/stu/DH/home/sandrews/Code/platform/kushy_example | |
| # PATH =============================== | |
| - . | |
| - /usr/local/bin | |
| - /usr/local/sbin | |
| - /usr/local/bin | |
| - /usr/bin | |
| - /bin | |
| - /usr/sbin | |
| - /sbin | |
| - /opt/X11/bin | |
| - /Users/stu/Research/Tools/Bio-Tools/bin | |
| - /Users/stu/bin | |
| # Cache ============================== | |
| There are a total of 221 package(s) installed in the renv cache. | |
| Cache path: "~/Research/Tools/RENV-HOME/cache/v5/R-3.6/x86_64-apple-darwin15.6.0" | |
| > | |
| > | |
| > | |
| > | |
| > q() | |
| Save workspace image? [y/n/c]: n | |
| ### -> echo "_pkgdown.yml" >> .renvignore | |
| ### -> R --no-environ --no-site-file --no-restore | |
| R version 3.6.1 (2019-07-05) -- "Action of the Toes" | |
| Copyright (C) 2019 The R Foundation for Statistical Computing | |
| Platform: x86_64-apple-darwin15.6.0 (64-bit) | |
| R is free software and comes with ABSOLUTELY NO WARRANTY. | |
| You are welcome to redistribute it under certain conditions. | |
| Type 'license()' or 'licence()' for distribution details. | |
| Natural language support but running in an English locale | |
| R is a collaborative project with many contributors. | |
| Type 'contributors()' for more information and | |
| 'citation()' on how to cite R or R packages in publications. | |
| Type 'demo()' for some demos, 'help()' for on-line help, or | |
| 'help.start()' for an HTML browser interface to help. | |
| Type 'q()' to quit R. | |
| * Project '~/DH/home/sandrews/Code/platform/kushy_example' loaded. [renv 0.12.5] | |
| > deps <- renv::dependencies() | |
| Finding R package dependencies ... Done! | |
| > pkgs <- sort(unique(deps$Package)) | |
| > all <- unlist(tools::package_dependencies(pkgs, recursive = TRUE)) | |
| > | |
| > deps | |
| NULL | |
| > | |
| > | |
| > | |
| > | |
| > pkgs | |
| NULL | |
| > | |
| > | |
| > | |
| > | |
| > length(all) | |
| [1] 489240 | |
| > head(all) | |
| A31 A32 A33 A34 A35 aaSEA1 | |
| "xtable" "pbapply" "parallel" "stats" "utils" "DT" | |
| > head(all, 50) | |
| A31 A32 A33 A34 | |
| "xtable" "pbapply" "parallel" "stats" | |
| A35 aaSEA1 aaSEA2 aaSEA3 | |
| "utils" "DT" "networkD3" "shiny" | |
| aaSEA4 aaSEA5 aaSEA6 aaSEA7 | |
| "shinydashboard" "magrittr" "Bios2cor" "seqinr" | |
| aaSEA8 aaSEA9 aaSEA10 aaSEA11 | |
| "plotly" "Hmisc" "bio3d" "circular" | |
| aaSEA12 aaSEA13 aaSEA14 aaSEA15 | |
| "bigmemory" "parallel" "igraph" "htmltools" | |
| aaSEA16 aaSEA17 aaSEA18 aaSEA19 | |
| "htmlwidgets" "jsonlite" "crosstalk" "promises" | |
| aaSEA20 aaSEA21 aaSEA22 aaSEA23 | |
| "lattice" "survival" "Formula" "ggplot2" | |
| aaSEA24 aaSEA25 aaSEA26 aaSEA27 | |
| "methods" "latticeExtra" "cluster" "rpart" | |
| aaSEA28 aaSEA29 aaSEA30 aaSEA31 | |
| "nnet" "foreign" "gtable" "grid" | |
| aaSEA32 aaSEA33 aaSEA34 aaSEA35 | |
| "gridExtra" "data.table" "htmlTable" "viridis" | |
| aaSEA36 aaSEA37 aaSEA38 aaSEA39 | |
| "base64enc" "tools" "scales" "httr" | |
| aaSEA40 aaSEA41 aaSEA42 aaSEA43 | |
| "digest" "viridisLite" "tidyr" "RColorBrewer" | |
| aaSEA44 aaSEA45 | |
| "dplyr" "vctrs" | |
| > | |
| > | |
| > | |
| > | |
| > renv::diagnostics() | |
| Diagnostics Report -- renv [0.12.5] | |
| =================================== | |
| # Session Info ======================= | |
| R version 3.6.1 (2019-07-05) | |
| Platform: x86_64-apple-darwin15.6.0 (64-bit) | |
| Running under: macOS Catalina 10.15.7 | |
| Matrix products: default | |
| BLAS: /Library/Frameworks/R.framework/Versions/3.6.1/Resources/lib/libRblas.0.dylib | |
| LAPACK: /Library/Frameworks/R.framework/Versions/3.6.1/Resources/lib/libRlapack.dylib | |
| locale: | |
| [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 | |
| attached base packages: | |
| [1] stats graphics grDevices datasets utils methods base | |
| loaded via a namespace (and not attached): | |
| [1] compiler_3.6.1 tools_3.6.1 renv_0.12.5 | |
| # Project ============================ | |
| Project path: "~/DH/home/sandrews/Code/platform/kushy_example" | |
| # Status ============================= | |
| * This project has not yet been snapshotted -- 'renv.lock' does not exist. | |
| The following package(s) are installed but not recorded in the lockfile: | |
| _ | |
| renv [0.12.5] | |
| Use `renv::snapshot()` to add these packages to your lockfile. | |
| # Packages =========================== | |
| This project has not yet been snapshotted: 'renv.lock' does not exist. | |
| Library Source Lockfile Source Path Dependency | |
| KernSmooth 2.23-15 CRAN <NA> <NA> [2] <NA> | |
| MASS 7.3-51.4 CRAN <NA> <NA> [2] <NA> | |
| Matrix 1.2-17 CRAN <NA> <NA> [2] <NA> | |
| boot 1.3-22 CRAN <NA> <NA> [2] <NA> | |
| class 7.3-15 CRAN <NA> <NA> [2] <NA> | |
| cluster 2.1.0 CRAN <NA> <NA> [2] <NA> | |
| codetools 0.2-16 CRAN <NA> <NA> [2] <NA> | |
| foreign 0.8-71 CRAN <NA> <NA> [2] <NA> | |
| lattice 0.20-38 CRAN <NA> <NA> [2] <NA> | |
| mgcv 1.8-28 CRAN <NA> <NA> [2] <NA> | |
| nlme 3.1-140 CRAN <NA> <NA> [2] <NA> | |
| nnet 7.3-12 CRAN <NA> <NA> [2] <NA> | |
| renv 0.12.5 CRAN <NA> <NA> [1] <NA> | |
| rpart 4.1-15 CRAN <NA> <NA> [2] <NA> | |
| spatial 7.3-11 CRAN <NA> <NA> [2] <NA> | |
| survival 2.44-1.1 CRAN <NA> <NA> [2] <NA> | |
| [1]: /Users/stu/DH/home/sandrews/Code/platform/kushy_example/renv/library/R-3.6/x86_64-apple-darwin15.6.0 | |
| [2]: /private/var/folders/s2/fw4yx0qx35nb3mrls_fkqtbh0000gr/T/RtmpEaXpon/renv-system-library | |
| # User Profile ======================= | |
| [no R packages referenced in user profile | |
| # Settings =========================== | |
| List of 7 | |
| $ external.libraries : chr(0) | |
| $ ignored.packages : chr(0) | |
| $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo" | |
| $ r.version : chr(0) | |
| $ snapshot.type : chr "implicit" | |
| $ use.cache : logi TRUE | |
| $ vcs.ignore.library : logi TRUE | |
| # Options ============================ | |
| List of 2 | |
| $ renv.consent: logi TRUE | |
| $ renv.verbose: logi TRUE | |
| # Environment Variables ============== | |
| HOME = /Users/stu | |
| LANG = en_US.UTF-8 | |
| R_LIBS = renv/library/R-3.6/x86_64-apple-darwin15.6.0 | |
| R_LIBS_SITE = | |
| R_LIBS_USER = /Users/stu/DH/home/sandrews/Code/platform/kushy_example/renv/library/R-3.6/x86_64-apple-darwin15.6.0:/private/var/folders/s2/fw4yx0qx35nb3mrls_fkqtbh0000gr/T/RtmpEaXpon/renv-system-library | |
| RENV_DEFAULT_R_ENVIRON = | |
| RENV_DEFAULT_R_ENVIRON_USER = | |
| RENV_DEFAULT_R_LIBS = renv/library/R-3.6/x86_64-apple-darwin15.6.0 | |
| RENV_DEFAULT_R_LIBS_SITE = | |
| RENV_DEFAULT_R_LIBS_USER = ~/Library/R/3.6/library | |
| RENV_DEFAULT_R_PROFILE = | |
| RENV_DEFAULT_R_PROFILE_USER = <NA> | |
| RENV_PATHS_ROOT = /Users/stu/Research/Tools/RENV-HOME | |
| RENV_PROJECT = /Users/stu/DH/home/sandrews/Code/platform/kushy_example | |
| # PATH =============================== | |
| - . | |
| - /usr/local/bin | |
| - /usr/local/sbin | |
| - /usr/local/bin | |
| - /usr/bin | |
| - /bin | |
| - /usr/sbin | |
| - /sbin | |
| - /opt/X11/bin | |
| - /Users/stu/Research/Tools/Bio-Tools/bin | |
| - /Users/stu/bin | |
| # Cache ============================== | |
| There are a total of 221 package(s) installed in the renv cache. | |
| Cache path: "~/Research/Tools/RENV-HOME/cache/v5/R-3.6/x86_64-apple-darwin15.6.0" | |
| > q() | |
| Save workspace image? [y/n/c]: n | |
| ### -> echo "library(pkgdown)" >| depends.r | |
| ### -> R --no-environ --no-site-file --no-restore | |
| R version 3.6.1 (2019-07-05) -- "Action of the Toes" | |
| Copyright (C) 2019 The R Foundation for Statistical Computing | |
| Platform: x86_64-apple-darwin15.6.0 (64-bit) | |
| R is free software and comes with ABSOLUTELY NO WARRANTY. | |
| You are welcome to redistribute it under certain conditions. | |
| Type 'license()' or 'licence()' for distribution details. | |
| Natural language support but running in an English locale | |
| R is a collaborative project with many contributors. | |
| Type 'contributors()' for more information and | |
| 'citation()' on how to cite R or R packages in publications. | |
| Type 'demo()' for some demos, 'help()' for on-line help, or | |
| 'help.start()' for an HTML browser interface to help. | |
| Type 'q()' to quit R. | |
| * Project '~/DH/home/sandrews/Code/platform/kushy_example' loaded. [renv 0.12.5] | |
| > | |
| > | |
| > | |
| > deps <- renv::dependencies() | |
| Finding R package dependencies ... Done! | |
| > pkgs <- sort(unique(deps$Package)) | |
| > all <- unlist(tools::package_dependencies(pkgs, recursive = TRUE)) | |
| > | |
| > | |
| > | |
| > deps | |
| Source | |
| 1 /Users/stu/DH/home/sandrews/Code/platform/kushy_example/depends.r | |
| Package Require Version Dev | |
| 1 pkgdown FALSE | |
| > | |
| > | |
| > | |
| > pkgs | |
| [1] "pkgdown" | |
| > | |
| > | |
| > | |
| > | |
| > all | |
| pkgdown1 pkgdown2 pkgdown3 pkgdown4 pkgdown5 | |
| "callr" "crayon" "desc" "digest" "downlit" | |
| pkgdown6 pkgdown7 pkgdown8 pkgdown9 pkgdown10 | |
| "fs" "httr" "magrittr" "memoise" "openssl" | |
| pkgdown11 pkgdown12 pkgdown13 pkgdown14 pkgdown15 | |
| "purrr" "ragg" "rematch2" "rlang" "rmarkdown" | |
| pkgdown16 pkgdown17 pkgdown18 pkgdown19 pkgdown20 | |
| "tibble" "tools" "whisker" "withr" "xml2" | |
| pkgdown21 pkgdown22 pkgdown23 pkgdown24 pkgdown25 | |
| "yaml" "processx" "R6" "utils" "grDevices" | |
| pkgdown26 pkgdown27 pkgdown28 pkgdown29 pkgdown30 | |
| "methods" "assertthat" "rprojroot" "brio" "evaluate" | |
| pkgdown31 pkgdown32 pkgdown33 pkgdown34 pkgdown35 | |
| "fansi" "vctrs" "curl" "jsonlite" "mime" | |
| pkgdown36 pkgdown37 pkgdown38 pkgdown39 pkgdown40 | |
| "askpass" "systemfonts" "textshaping" "knitr" "htmltools" | |
| pkgdown41 pkgdown42 pkgdown43 pkgdown44 pkgdown45 | |
| "tinytex" "xfun" "stringr" "cli" "ellipsis" | |
| pkgdown46 pkgdown47 pkgdown48 pkgdown49 pkgdown50 | |
| "lifecycle" "pillar" "pkgconfig" "graphics" "stats" | |
| pkgdown51 pkgdown52 pkgdown53 pkgdown54 pkgdown55 | |
| "sys" "glue" "base64enc" "highr" "markdown" | |
| pkgdown56 pkgdown57 pkgdown58 pkgdown59 | |
| "utf8" "ps" "stringi" "cpp11" | |
| > | |
| > | |
| > | |
| > | |
| > renv::diagnostics() | |
| Diagnostics Report -- renv [0.12.5] | |
| =================================== | |
| # Session Info ======================= | |
| R version 3.6.1 (2019-07-05) | |
| Platform: x86_64-apple-darwin15.6.0 (64-bit) | |
| Running under: macOS Catalina 10.15.7 | |
| Matrix products: default | |
| BLAS: /Library/Frameworks/R.framework/Versions/3.6.1/Resources/lib/libRblas.0.dylib | |
| LAPACK: /Library/Frameworks/R.framework/Versions/3.6.1/Resources/lib/libRlapack.dylib | |
| locale: | |
| [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 | |
| attached base packages: | |
| [1] stats graphics grDevices datasets utils methods base | |
| loaded via a namespace (and not attached): | |
| [1] compiler_3.6.1 tools_3.6.1 renv_0.12.5 | |
| # Project ============================ | |
| Project path: "~/DH/home/sandrews/Code/platform/kushy_example" | |
| # Status ============================= | |
| * This project has not yet been snapshotted -- 'renv.lock' does not exist. | |
| The following package(s) are installed but not recorded in the lockfile: | |
| _ | |
| MASS [7.3-51.4] | |
| renv [0.12.5] | |
| Use `renv::snapshot()` to add these packages to your lockfile. | |
| # Packages =========================== | |
| This project has not yet been snapshotted: 'renv.lock' does not exist. | |
| Library Source Lockfile Source Path Dependency | |
| KernSmooth 2.23-15 CRAN <NA> <NA> [2] <NA> | |
| MASS 7.3-51.4 CRAN <NA> <NA> [2] indirect | |
| Matrix 1.2-17 CRAN <NA> <NA> [2] <NA> | |
| R6 <NA> <NA> <NA> <NA> <NA> indirect | |
| askpass <NA> <NA> <NA> <NA> <NA> indirect | |
| assertthat <NA> <NA> <NA> <NA> <NA> indirect | |
| backports <NA> <NA> <NA> <NA> <NA> indirect | |
| base64enc <NA> <NA> <NA> <NA> <NA> indirect | |
| boot 1.3-22 CRAN <NA> <NA> [2] <NA> | |
| callr <NA> <NA> <NA> <NA> <NA> indirect | |
| class 7.3-15 CRAN <NA> <NA> [2] <NA> | |
| cli <NA> <NA> <NA> <NA> <NA> indirect | |
| cluster 2.1.0 CRAN <NA> <NA> [2] <NA> | |
| codetools 0.2-16 CRAN <NA> <NA> [2] <NA> | |
| crayon <NA> <NA> <NA> <NA> <NA> indirect | |
| curl <NA> <NA> <NA> <NA> <NA> indirect | |
| desc <NA> <NA> <NA> <NA> <NA> indirect | |
| digest <NA> <NA> <NA> <NA> <NA> indirect | |
| ellipsis <NA> <NA> <NA> <NA> <NA> indirect | |
| evaluate <NA> <NA> <NA> <NA> <NA> indirect | |
| fansi <NA> <NA> <NA> <NA> <NA> indirect | |
| foreign 0.8-71 CRAN <NA> <NA> [2] <NA> | |
| fs <NA> <NA> <NA> <NA> <NA> indirect | |
| glue <NA> <NA> <NA> <NA> <NA> indirect | |
| grDevices <NA> <NA> <NA> <NA> [2] indirect | |
| graphics <NA> <NA> <NA> <NA> [2] indirect | |
| highlight <NA> <NA> <NA> <NA> <NA> indirect | |
| highr <NA> <NA> <NA> <NA> <NA> indirect | |
| htmltools <NA> <NA> <NA> <NA> <NA> indirect | |
| httr <NA> <NA> <NA> <NA> <NA> indirect | |
| jsonlite <NA> <NA> <NA> <NA> <NA> indirect | |
| knitr <NA> <NA> <NA> <NA> <NA> indirect | |
| lattice 0.20-38 CRAN <NA> <NA> [2] <NA> | |
| lifecycle <NA> <NA> <NA> <NA> <NA> indirect | |
| magrittr <NA> <NA> <NA> <NA> <NA> indirect | |
| markdown <NA> <NA> <NA> <NA> <NA> indirect | |
| memoise <NA> <NA> <NA> <NA> <NA> indirect | |
| methods <NA> <NA> <NA> <NA> [2] indirect | |
| mgcv 1.8-28 CRAN <NA> <NA> [2] <NA> | |
| mime <NA> <NA> <NA> <NA> <NA> indirect | |
| nlme 3.1-140 CRAN <NA> <NA> [2] <NA> | |
| nnet 7.3-12 CRAN <NA> <NA> [2] <NA> | |
| openssl <NA> <NA> <NA> <NA> <NA> indirect | |
| pillar <NA> <NA> <NA> <NA> <NA> indirect | |
| pkgconfig <NA> <NA> <NA> <NA> <NA> indirect | |
| pkgdown <NA> <NA> <NA> <NA> <NA> direct | |
| processx <NA> <NA> <NA> <NA> <NA> indirect | |
| ps <NA> <NA> <NA> <NA> <NA> indirect | |
| purrr <NA> <NA> <NA> <NA> <NA> indirect | |
| rematch2 <NA> <NA> <NA> <NA> <NA> indirect | |
| renv 0.12.5 CRAN <NA> <NA> [1] <NA> | |
| rlang <NA> <NA> <NA> <NA> <NA> indirect | |
| rmarkdown <NA> <NA> <NA> <NA> <NA> indirect | |
| rpart 4.1-15 CRAN <NA> <NA> [2] <NA> | |
| rprojroot <NA> <NA> <NA> <NA> <NA> indirect | |
| rstudioapi <NA> <NA> <NA> <NA> <NA> indirect | |
| spatial 7.3-11 CRAN <NA> <NA> [2] <NA> | |
| stats <NA> <NA> <NA> <NA> [2] indirect | |
| stringi <NA> <NA> <NA> <NA> <NA> indirect | |
| stringr <NA> <NA> <NA> <NA> <NA> indirect | |
| survival 2.44-1.1 CRAN <NA> <NA> [2] <NA> | |
| sys <NA> <NA> <NA> <NA> <NA> indirect | |
| tibble <NA> <NA> <NA> <NA> <NA> indirect | |
| tinytex <NA> <NA> <NA> <NA> <NA> indirect | |
| tools <NA> <NA> <NA> <NA> [2] indirect | |
| utf8 <NA> <NA> <NA> <NA> <NA> indirect | |
| utils <NA> <NA> <NA> <NA> [2] indirect | |
| vctrs <NA> <NA> <NA> <NA> <NA> indirect | |
| whisker <NA> <NA> <NA> <NA> <NA> indirect | |
| withr <NA> <NA> <NA> <NA> <NA> indirect | |
| xfun <NA> <NA> <NA> <NA> <NA> indirect | |
| xml2 <NA> <NA> <NA> <NA> <NA> indirect | |
| yaml <NA> <NA> <NA> <NA> <NA> indirect | |
| [1]: /Users/stu/DH/home/sandrews/Code/platform/kushy_example/renv/library/R-3.6/x86_64-apple-darwin15.6.0 | |
| [2]: /private/var/folders/s2/fw4yx0qx35nb3mrls_fkqtbh0000gr/T/RtmpGJfPFE/renv-system-library | |
| # User Profile ======================= | |
| [no R packages referenced in user profile | |
| # Settings =========================== | |
| List of 7 | |
| $ external.libraries : chr(0) | |
| $ ignored.packages : chr(0) | |
| $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo" | |
| $ r.version : chr(0) | |
| $ snapshot.type : chr "implicit" | |
| $ use.cache : logi TRUE | |
| $ vcs.ignore.library : logi TRUE | |
| # Options ============================ | |
| List of 2 | |
| $ renv.consent: logi TRUE | |
| $ renv.verbose: logi TRUE | |
| # Environment Variables ============== | |
| HOME = /Users/stu | |
| LANG = en_US.UTF-8 | |
| R_LIBS = renv/library/R-3.6/x86_64-apple-darwin15.6.0 | |
| R_LIBS_SITE = | |
| R_LIBS_USER = /Users/stu/DH/home/sandrews/Code/platform/kushy_example/renv/library/R-3.6/x86_64-apple-darwin15.6.0:/private/var/folders/s2/fw4yx0qx35nb3mrls_fkqtbh0000gr/T/RtmpGJfPFE/renv-system-library | |
| RENV_DEFAULT_R_ENVIRON = | |
| RENV_DEFAULT_R_ENVIRON_USER = | |
| RENV_DEFAULT_R_LIBS = renv/library/R-3.6/x86_64-apple-darwin15.6.0 | |
| RENV_DEFAULT_R_LIBS_SITE = | |
| RENV_DEFAULT_R_LIBS_USER = ~/Library/R/3.6/library | |
| RENV_DEFAULT_R_PROFILE = | |
| RENV_DEFAULT_R_PROFILE_USER = <NA> | |
| RENV_PATHS_ROOT = /Users/stu/Research/Tools/RENV-HOME | |
| RENV_PROJECT = /Users/stu/DH/home/sandrews/Code/platform/kushy_example | |
| # PATH =============================== | |
| - . | |
| - /usr/local/bin | |
| - /usr/local/sbin | |
| - /usr/local/bin | |
| - /usr/bin | |
| - /bin | |
| - /usr/sbin | |
| - /sbin | |
| - /opt/X11/bin | |
| - /Users/stu/Research/Tools/Bio-Tools/bin | |
| - /Users/stu/bin | |
| # Cache ============================== | |
| There are a total of 221 package(s) installed in the renv cache. | |
| Cache path: "~/Research/Tools/RENV-HOME/cache/v5/R-3.6/x86_64-apple-darwin15.6.0" | |
| > q() | |
| Save workspace image? [y/n/c]: n | |
| ### -> |
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