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Created January 12, 2021 16:12
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rstudio/renv unexpected inclusion of MASS package from base system caused by pkgdown
Raw
debug-2021-01-12.log
### -> 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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