Trouble building package using R in development

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Trouble building package using R in development

Gavin Simpson
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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Re: Trouble building package using R in development

Gavin Simpson
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
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

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Re: Trouble building package using R in development

Henrik Bengtsson-3
On Wed, Jan 16, 2013 at 7:25 AM, Gavin Simpson <[hidden email]> 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
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: Trouble building package using R in development

Henrik Bengtsson-3
On Wed, Jan 16, 2013 at 8:59 AM, Henrik Bengtsson <[hidden email]> wrote:

> On Wed, Jan 16, 2013 at 7:25 AM, Gavin Simpson <[hidden email]> 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

Should have clarified that in your case you need to add '--no-environ'.

/Henrik

>
> /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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Re: Trouble building package using R in development

hadley wickham
In reply to this post by Henrik Bengtsson-3
> To circumvent this, I check using:
>
> R --no-init-file CMD check foo_1.0.tar.gz

In devtools, we take considerable care to match the R you're running
with the R you're checking in, so we also set the following
environmental variables:

env <- c(
    "LC_ALL" = "C",
    "R_LIBS" = paste(.libPaths(), collapse = .Platform$path.sep),
    "CYGWIN" = "nodosfilewarning",
    "R_TESTS" = "",
    "NOT_CRAN" = "true",
    "TAR" = auto_tar(),
)

and always run /path/to/current/R --vanilla CMD check ...

Hadley

--
Chief Scientist, RStudio
http://had.co.nz/

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Re: Trouble building package using R in development

Gavin Simpson
On Wed, 2013-01-16 at 14:39 -0600, Hadley Wickham wrote:
> > To circumvent this, I check using:
> >
> > R --no-init-file CMD check foo_1.0.tar.gz
>
> In devtools, we take considerable care to match the R you're running
> with the R you're checking in, so we also set the following
> environmental variables:
<snip />

Thanks Henrik & Hadley,

> and always run /path/to/current/R --vanilla CMD check ...

To what end is the --vanilla here? Writing R Extensions says that R CMD
check (and R CMD build) are invoked via R --vanilla so that would seem
redundant, although my experience from several hours working this
through today suggests there is a difference between R --vanilla CMD
check and R CMD check.

G

> Hadley
>

--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 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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Re: Trouble building package using R in development

hadley wickham
> To what end is the --vanilla here? Writing R Extensions says that R CMD
> check (and R CMD build) are invoked via R --vanilla so that would seem
> redundant, although my experience from several hours working this
> through today suggests there is a difference between R --vanilla CMD
> check and R CMD check.

Maybe that's new? We've certainly had problems with R CMD reading user
startup files, which is why we starting using --vanilla.

Hadley

--
Chief Scientist, RStudio
http://had.co.nz/

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