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 /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
