On Wed, Jan 16, 2013 at 8:59 AM, Henrik Bengtsson <h...@biostat.ucsf.edu> wrote: > On Wed, Jan 16, 2013 at 7:25 AM, Gavin Simpson <gavin.simp...@ucl.ac.uk> > wrote: >> As a follow-up, shortly after I clicked send I decided to do something >> silly and rename my ~/.Renviron (which set R_LIBS too). Silly because >> the Writing R Extensions (WRE) manual says that these startup files are >> not read as R is invoked with --vanilla. >> >> Once I renamed ~/.Renviron so it was not being read I was able to build >> the package using R Under Development following the remaining >> instructions in the WRE note [1] >> >> So I do wonder if I have misunderstood the note in WRE or if there is >> some other issue here? Starting R --vanilla with R Under Development >> wasn't reading ~/.Renviron, and by renaming ~/.Renviron that I was able >> to build the package indicates that this file was implicated in the >> problem I described. >> >> Is it intentional that R CMD build reads ~/.Renviron ? If it is, then >> WRE should ideally clarify this or make it explicit. If it wasn't >> supposed to be read, is there a bug here? > > FYI, related posts: > > * Rd thread 'R devel [and R 2.14.1 patched]: R CMD build now sources > ~/.Rprofile' on Feb 23, 2012 > [https://stat.ethz.ch/pipermail/r-devel/2012-February/063365.html] > * Rd thread 'R CMD build/check on Windows 7' on Jul 17, 2012 > [https://stat.ethz.ch/pipermail/r-devel/2012-July/064427.html] > > To circumvent this, I check using: > > R --no-init-file CMD check foo_1.0.tar.gz
Should have clarified that in your case you need to add '--no-environ'. /Henrik > > /Henrik > >> >> All the best, >> >> Gavin >> >> [1] >> http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Checking-and-building-packages >> >> On Wed, 2013-01-16 at 16:05 +0100, Gavin Simpson wrote: >>> Dear List, >>> >>> I'm having considerable trouble setting up my environment (Linux, Fedora >>> 16, Bash) to build and check packages under R Under Development >>> (r61660). I'm doing this to better get a handle on difference in the >>> output from running checks on examples in one of my packages. Note I >>> compiled R Under Development myself >>> >>> The problem I am now having is whenever I try to build my analogue >>> package using R Under Development, R complains about a dependency having >>> been built before R 3.0.0. I obviously don't have my environment >>> variables set correctly, but I don't see why or how R is finding my >>> daily-use package library; if anything I would have expected it to fail >>> with a missing dependency. >>> >>> If I start Rdevel with --vanilla (to mimic Rdevel CMD build) I see: >>> >>> > .libPaths() >>> [1] "/home/gavin/R/devlibs" "/home/gavin/R/devel/build/library" >>> >>> the first entry there is because I have temporarily set R_LIBS to that >>> directory via export R_LIBS=/home/gavin/R/devlibs. From there we see I >>> have versions of the dependencies installed in this library and they are >>> built with 3.0.0: >>> >>> > installed.packages("~/R/devlibs/")[, "Built", drop = FALSE] >>> Built >>> analogue "3.0.0" >>> ctv "3.0.0" >>> permute "3.0.0" >>> princurve "3.0.0" >>> rgl "3.0.0" >>> scatterplot3d "3.0.0" >>> vegan "3.0.0" >>> >>> Note that there are no other versions of vegan inadvertently installed >>> to the build directory for R Under Development. >>> >>> Following advice in Writing R Extensions I have also created >>> ~/build.Renviron and ~/check.Renviron and as these are non-standard I >>> also followed the advice to set R_BUILD_ENVIRON and R_CHECK_ENVIRON >>> again temporarily via export: >>> >>> $ cat $R_CHECK_ENVIRON >>> R_LIBS=/home/gavin/R/devlibs >>> >>> $ cat $R_BUILD_ENVIRON >>> R_LIBS=/home/gavin/R/devlibs >>> >>> Yet still I get errors building analogue: >>> >>> $ Rdevel CMD build ../analogue/pkg/ >>> * checking for file ‘../analogue/pkg/DESCRIPTION’ ... OK >>> * preparing ‘analogue’: >>> * checking DESCRIPTION meta-information ... OK >>> * cleaning src >>> * installing the package to re-build vignettes >>> ----------------------------------- >>> * installing *source* package ‘analogue’ ... >>> ** libs >>> gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG >>> -I/usr/local/include -fpic -g -O2 -pipe -m64 -Wall >>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector >>> --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c >>> c_distx.c -o c_distx.o >>> gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG >>> -I/usr/local/include -fpic -g -O2 -pipe -m64 -Wall >>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector >>> --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c >>> c_distxy.c -o c_distxy.o >>> gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG >>> -I/usr/local/include -fpic -g -O2 -pipe -m64 -Wall >>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector >>> --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c >>> distx.c -o distx.o >>> gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG >>> -I/usr/local/include -fpic -g -O2 -pipe -m64 -Wall >>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector >>> --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c >>> distxy.c -o distxy.o >>> gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG >>> -I/usr/local/include -fpic -g -O2 -pipe -m64 -Wall >>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector >>> --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c >>> wastats.c -o wastats.o >>> gcc -std=gnu99 -shared -L/usr/local/lib64 -o analogue.so c_distx.o >>> c_distxy.o distx.o distxy.o wastats.o >>> installing to /tmp/Rtmpctxbtv/Rinst30e3f762569/analogue/libs >>> ** R >>> ** data >>> ** inst >>> ** byte-compile and prepare package for lazy loading >>> Error : package ‘vegan’ was built before R 3.0.0: please re-install it >>> ERROR: lazy loading failed for package ‘analogue’ >>> * removing ‘/tmp/Rtmpctxbtv/Rinst30e3f762569/analogue’ >>> ----------------------------------- >>> ERROR: package installation failed >>> >>> Can anyone suggest where to go from here? >>> >>> TIA >>> >>> Gavin >> >> -- >> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% >> 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@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
