Trouble building package using R in development

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

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