Gavin Simpson
2013-Jan-16 20:13 UTC
[Rd] R CMD check not reading R_LIBS from ~/.R/check.Renviron
Dear List,
Further to my earlier email, I note that, for me at least, R CMD check
is *not* reading R_LIBS from ~/.R/check.Renviron on R 2.15.2 patched
(r61228) and R Under Development (r61660). The only way I can get R CMD
check to look for packages in a user-supplied library is by explicitly
exporting R_LIBS set to the relevant directory.
R CMD build *does* read R_LIBS from ~/.R/build.Renviron for the same
versions of R on the same Fedora 16 laptop. So I am in the strange
situation of being able to build but not check a source package having
followed the instructions in Writing R Extensions.
I have tried exporting R_CHECK_ENVIRON via
export R_CHECK_ENVIRON=/home/gavin/.R/check.Renviron
and that doesn't work either.
~/.R/check.Renviron contains:
R_LIBS=/home/gavin/R/libs/
#R_LIBS=/home/gavin/R/devlibs/
Anyone suggest how/where I am going wrong?
More complete system info follows below.
TIA
Gavin
> sessionInfo()
R version 2.15.2 Patched (2012-12-05 r61228)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
> sessionInfo()
R Under development (unstable) (2013-01-16 r61660)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
--
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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Jari Oksanen
2013-Jan-17 08:55 UTC
[Rd] R CMD check not reading R_LIBS from ~/.R/check.Renviron
Gav, This is off-list since I only wonder what you are trying to do. It seems to me that you're trying something much too elegant and complicated. One thing that I have learnt to avoid is muck up with environments: that is calling trouble. One day they will change R and you will get errors that are very difficult to track (I had that once with gnome: I did not edit the config file manually, but only used configuration GUI tools, but then gnome changed and I could not start X11 after distro upgrade -- and it was difficult to track the reason). What I do with R-devel and R release co-existence is that I keep them completely separate. I do not install (make install) R-devel, but I leave it in its working directory. I have now a symbolic link in ~/bin ($HOME/bin): cd ~/bin ln -s ~/R-devel/bin/R R3 So when I want to run R 3.0.0 I use 'R3' and when I want to use stock R of my distro (no 2.15.1) use R. These are completely different beasts, and packages are installed separately for each so that they are 3.0.0 version in R3 and 2.15 versions in R. I don't edit environments, but always use defaults. With this setup, analogue checks up smoothly with only comment coming from examples: * checking differences from ?analogue-Ex.Rout? to ?analogue-Ex.Rout.save? ... 2c2 < This is vegan 2.1-23 ---> This is vegan 2.0-51104d1103 < Warning: argument 'tol.dw' is not used (yet) 4894d4892 < Warning: argument 'tol.dw' is not used (yet) 4933d4930 < Warning: argument 'tol.dw' is not used (yet) 6139d6135 < Warning: argument 'tol.dw' is not used (yet) 7078d7073 < Warning: argument 'tol.dw' is not used (yet) 7116d7110 < Warning: argument 'tol.dw' is not used (yet) OK Cheers, Jari ________________________________________ From: r-devel-bounces at r-project.org [r-devel-bounces at r-project.org] on behalf of Gavin Simpson [gavin.simpson at ucl.ac.uk] Sent: 16 January 2013 22:13 To: R Devel Mailing List Subject: [Rd] R CMD check not reading R_LIBS from ~/.R/check.Renviron Dear List, Further to my earlier email, I note that, for me at least, R CMD check is *not* reading R_LIBS from ~/.R/check.Renviron on R 2.15.2 patched (r61228) and R Under Development (r61660). The only way I can get R CMD check to look for packages in a user-supplied library is by explicitly exporting R_LIBS set to the relevant directory. R CMD build *does* read R_LIBS from ~/.R/build.Renviron for the same versions of R on the same Fedora 16 laptop. So I am in the strange situation of being able to build but not check a source package having followed the instructions in Writing R Extensions. I have tried exporting R_CHECK_ENVIRON via export R_CHECK_ENVIRON=/home/gavin/.R/check.Renviron and that doesn't work either. ~/.R/check.Renviron contains: R_LIBS=/home/gavin/R/libs/ #R_LIBS=/home/gavin/R/devlibs/ Anyone suggest how/where I am going wrong? More complete system info follows below. TIA Gavin> sessionInfo()R version 2.15.2 Patched (2012-12-05 r61228) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base> sessionInfo()R Under development (unstable) (2013-01-16 r61660) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel