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? 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
