On Wed, Mar 18, 2020 at 8:04 PM Dirk Eddelbuettel <e...@debian.org> wrote:
>
>
> 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.
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="$PWD"
R --vanilla CMD check --as-cran teeny_0.1.0.tar.gz
then tests scripts still get R_LIBS_USER="~/R/x86_64-pc-linux-gnu-library/3.6".
But, then why is there a difference between Windows and Linux in this
essential behavior? To me, this suggests there is a mistake
somewhere. OTH, I know that lots of oddities in R exist for a reason.
/Henrik
>
> | to R_LIBS_SITE, it fails for R_LIBS_USER and the user's personal
> | library is still available for test scripts. Should I revise my
> | assumptions, or is that intentional?
>
> I would place a nickel on the former if betting was allowed in Illinois.
>
> edd@rob:~$ Rscript --vanilla -e ".libPaths()"
> [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
> [3] "/usr/lib/R/library"
> edd@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@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 | e...@debian.org
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