From hb at biostat.ucsf.edu  Wed Jan 16 17:59:42 2013
From: hb at biostat.ucsf.edu (Henrik Bengtsson)
Date: Wed, 16 Jan 2013 08:59:42 -0800
Subject: [Rd] Trouble building package using R in development
In-Reply-To: <1358349920.4687.34.camel@chrysothemis.geog.ucl.ac.uk>
References: <1358348706.4687.25.camel@chrysothemis.geog.ucl.ac.uk>
	<1358349920.4687.34.camel@chrysothemis.geog.ucl.ac.uk>
Message-ID: <CAFDcVCQmyZYLpT=vkFaT5feJSS4VcSBKR+VoNAtosVKXBhzU_A@mail.gmail.com>

On Wed, Jan 16, 2013 at 7:25 AM, Gavin Simpson <gavin.simpson at 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
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>
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[Rd] Trouble building package using R in development
Henrik Bengtsson