R CMD check --as-cran attempts to hide R_LIBS_USER but fails

Wed, Mar 18, 2020 9:38 PM

On Wed, Mar 18, 2020 at 8:04 PM Dirk Eddelbuettel <edd at debian.org> wrote:

1. --as-cran sets R_LIBS_SITE='no_such_dir' and R_LIBS_USER='',
whereas without --as-cran they're not set.

2. --as-cran sets R_LIBS_USER='no_such_dir' on Windows and there it is
masked, i.e. tests scripts do NOT see user's personal library because
print(Sys.getenv("R_LIBS_USER")) is reported as "'no_such_dir'"
(sic!).

The only other interpretation I can imagine from using R_LIBS_USER=''
on Linux is that is exists there to force the default settings in case
it is already set externally by user.  For example, if one do

  export R_LIBS_USER="$PWD"
  R --vanilla CMD check --as-cran teeny_0.1.0.tar.gz

then tests scripts still get R_LIBS_USER="~/R/x86_64-pc-linux-gnu-library/3.6".

But, then why is there a difference between Windows and Linux in this
essential behavior?  To me, this suggests there is a mistake
somewhere.  OTH, I know that lots of oddities in R exist for a reason.

/Henrik

| 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?

I would place a nickel on the former if betting was allowed in Illinois.

  edd at rob:~$ Rscript --vanilla -e ".libPaths()"
  [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
  [3] "/usr/lib/R/library"
  edd at rob:~$ R_LIBS_USER='' Rscript --vanilla -e ".libPaths()"
  [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
  [3] "/usr/lib/R/library"
  edd at rob:~$

I happen to turn per-user libraries off by default, which may affect things.
That said, I actually quite like having the same paths. Your mileage, as they
say, may vary.

Dirk


| 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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| https://stat.ethz.ch/mailman/listinfo/r-devel

--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

R CMD check --as-cran attempts to hide R_LIBS_USER but fails

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