AFAIU, 'R CMD check --as-cran' tries to hide any site and user package
libraries by setting R_LIBS_SITE and R_LIBS_USER. However, contrary
to R_LIBS_SITE, it fails for R_LIBS_USER and the user's personal
library is still available for test scripts. Should I revise my
assumptions, or is that intentional?
The short version. Shouldn't:
$ R_LIBS_USER='' Rscript --vanilla -e ".libPaths()"
[1] "/home/hb/R/x86_64-pc-linux-gnu-library/4.0"
[2] "/home/hb/software/R-devel/trunk/lib/R/library"
give the same output as:
$ R_LIBS_USER="no_such_dir" Rscript --vanilla -e ".libPaths()"
[1] "/home/hb/software/R-devel/trunk/lib/R/library"
?
The long version:
R_LIBS_SITE='no_such_dir' and R_LIBS_USER='' is set up at the very
end of tools:::setRlibs():
setRlibs <-
...
c(paste0("R_LIBS=", rlibs),
if(WINDOWS) " R_ENVIRON_USER='no_such_file'" else "R_ENVIRON_USER=''",
if(WINDOWS) " R_LIBS_USER='no_such_dir'" else "R_LIBS_USER=''",
" R_LIBS_SITE='no_such_dir'")
}
Monitoring with 'pstree' confirms this. On Linux with R 3.6.3, the
call stack of a 'R CMD check --as-cran teeny_0.1.0.tar.gz' call looks
like this when a test script is running:
`-sh /usr/lib/R/bin/check --as-cran teeny_0.1.0.tar.gz
`-R --no-restore --slave --args nextArg--as-crannextArgteeny_0.1.0.tar.gz
`-sh -c LANGUAGE=en _R_CHECK_INTERNALS2_=1
R_LIBS=/tmp/hb/RtmpQj4hXb/RLIBS_26e766e32c18 R_ENVIRON_USER=''
R_LIBS_USER='' R_LIBS_SITE='no_such_dir' '/usr/lib/R/bin/R' --vanilla
--slave < '/tmp/hb/RtmpQj4hXb/file26e763770b6a'
`-R --vanilla --slave
`-sh -c LANGUAGE=C R_TESTS=startup.Rs '/usr/lib/R/bin/R' CMD BATCH
--vanilla 'env.R' 'env.Rout'
`-sh /usr/lib/R/bin/BATCH --vanilla env.R env.Rout
`-R -f env.R --restore --save --no-readline --vanilla
`-sh -c 'pstree' --arguments --long --show-parents 10558
`-pstree --arguments --long --show-parents 10558
However, if I call print(Sys.getenv("R_LIBS_USER")) in my tests/env.R,
I'll find that it is no longer empty but it is indeed set to my
personal library "~/R/x86_64-pc-linux-gnu-library/3.6".
TROUBLESHOOTING:
It looks like R_LIBS_USER is set if and only if it's empty by Renviron
in my system folder:
$ grep R_LIBS < "$(Rscript -e "cat(file.path(R.home('etc'), 'Renviron'))")"
R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.6'}
#R_LIBS_USER=${R_LIBS_USER-'~/Library/R/3.6/library'}
# edd Jul 2007 Now use R_LIBS_SITE, not R_LIBS
R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}
This is from installing R on Ubuntu 18.04 using 'apt install
r-base-core'. To make sure it's not an issue with that distribution,
I also check a 'configure/make/make install' from SVN trunk and there
I see the same:
$ grep R_LIBS < "$(Rscript -e "cat(file.path(R.home('etc'), 'Renviron'))")"
R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/4.0'}
#R_LIBS_USER=${R_LIBS_USER-'~/Library/R/4.0/library'}
Printing it during tests/env.R confirms that it is indeed set to
"~/R/x86_64-pc-linux-gnu-library/4.0".
/Henrik
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