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

[Dirk Eddelbuettel]

On 18 March 2020 at 19:19, Henrik Bengtsson wrote:
| 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

What makes you think that? AFAIK --as-cran just sets a bunch of the (nearly
countless) environment variables (all described in R Inst+Admin, as I recall)
to a set of values "close to" values CRAN uses.

| 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 using rob:~$ Rscript --vanilla -e ".libPaths()"
  [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"      
  [3] "/usr/lib/R/library"           
  edd using 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 using 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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http://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org