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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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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