[Rd] Trouble building package using R in development

Gavin Simpson gavin.simpson at ucl.ac.uk
Wed Jan 16 16:05:06 CET 2013

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]
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:



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?


 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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