[R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit

MAURICIO ZAMBRANO BIGIARINI mauricio.zambrano at ufrontera.cl
Tue Jul 21 04:57:55 CEST 2015 

On 20 July 2015 at 20:29, peter dalgaard <pdalgd at gmail.com> wrote:
> Oi!
>
> Could you guys move to r-devel? This has nothing to do with _package_ development.

Thanks for the advice. I was not sure about the list I should have
submitted this message, but looking at
http://www.r-project.org/mail.html:

R-package-devel
is to get help about package development in R,...
If you are having problems developing a package or passing R CMD
check, this is the place to ask!
....

R-devel:
This list is intended for questions and discussion about code
development in R.  ...
The list is also for proposals of new functionality for R, and
pre-testing of new versions. It is meant particularly for those who
maintain an active position in the development of R.


and as my original intend was to passing R CMD check--as-cran using
the development version of R, I chose r-package-devel.


I'll create a shorten version of this message in r-devel (not sure if
this is the right way of moving a message from one mailing list to
another).

Mauricio

>
> -Peter D
>
>> On 21 Jul 2015, at 00:49 , MAURICIO ZAMBRANO BIGIARINI <mauricio.zambrano at ufrontera.cl> wrote:
>>
>> ---------- Forwarded message ----------
>> From: Dirk Eddelbuettel <edd at debian.org>
>> Date: 20 July 2015 at 19:21
>> Subject: Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit
>> To: MAURICIO ZAMBRANO BIGIARINI <mauricio.zambrano at ufrontera.cl>
>> Cc: Dirk Eddelbuettel <edd at debian.org>, r-package-devel at r-project.org
>>
>>
>>
>> On 20 July 2015 at 18:56, MAURICIO ZAMBRANO BIGIARINI wrote:
>> | how can I be sure that I I enabled the shared library support ?
>>
>> edd at max:~/svn/r-devel$ ./configure --help | grep enable-R-sh
>>  --enable-R-shlib        build the shared/dynamic library 'libR' [no]
>> edd at max:~/svn/r-devel$
>>
>> Make sure you set --enable-R-shlib.
>>
>> It is in the script which you linked to in your previous email.
>>
>>
>> I thought I did it already when running configure:
>>
>> ./configure --prefix=/usr/local/lib/R-devel --enable-R-shlib
>> --with-blas --with-lapack --with-readline
>> --without-recommended-packages
>>
>>
>>
>> I just tried to run again your script (mentioned in my previous
>> e-mail) from scratch and I'm still getting an error:
>>
>> R is now configured for x86_64-unknown-linux-gnu
>>
>>  Source directory:          .
>>  Installation directory:    /usr/local/lib/R-devel
>>
>>  C compiler:                ccache gcc  -ggdb -pipe -std=gnu99 -Wall -pedantic
>>  Fortran 77 compiler:       ccache gfortran  -g -O2
>>
>>  C++ compiler:              ccache g++  -ggdb -pipe -Wall -pedantic
>>  C++11 compiler:            ccache g++  -std=c++11 -ggdb -pipe -Wall -pedantic
>>  Fortran 90/95 compiler:    ccache gfortran -g -O2
>>  Obj-C compiler:
>>
>>  Interfaces supported:      X11, tcltk
>>  External libraries:        readline, BLAS(generic), LAPACK(generic), curl
>>  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
>>  Options enabled:           shared R library, R profiling
>>
>>  Capabilities skipped:
>>  Options not enabled:       shared BLAS, memory profiling
>>
>>  Recommended packages:      no
>>
>> make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/manual'
>> make[1]: Nothing to be done for `front-matter'.
>> make[1]: Nothing to be done for `html-non-svn'.
>> make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/manual'
>> SVN-REVISION is unchanged
>> make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/m4'
>> make[1]: Nothing to be done for `R'.
>> make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/m4'
>> make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/tools'
>> make[1]: Nothing to be done for `R'.
>> make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/tools'
>> make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc'
>> make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/html'
>> make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/html'
>> make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/manual'
>> make[2]: Nothing to be done for `R'.
>> make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/manual'
>> make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc'
>> make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/etc'
>> make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/etc'
>> make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/share'
>> make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/share'
>> make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src'
>> make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/scripts'
>> creating src/scripts/R.fe
>> make[3]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/scripts'
>> make[3]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/scripts'
>> make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/scripts'
>> make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/include'
>> config.status: creating src/include/config.h
>> config.status: src/include/config.h is unchanged
>> Rmath.h is unchanged
>> make[3]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/include/R_ext'
>> make[3]: Nothing to be done for `R'.
>> make[3]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/include/R_ext'
>> make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/include'
>> make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/extra'
>> make[3]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/extra/tre'
>> make[4]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/extra/tre'
>> make[4]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/extra/tre'
>> make[4]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/extra/tre'
>> make[4]: `libtre.a' is up to date.
>> make[4]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/extra/tre'
>> make[3]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/extra/tre'
>> make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/extra'
>> make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/appl'
>> make[3]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/appl'
>> make[3]: `libappl.a' is up to date.
>> make[3]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/appl'
>> make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/appl'
>> make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/nmath'
>> make[3]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/nmath'
>> make[3]: `libnmath.a' is up to date.
>> make[3]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/nmath'
>> make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/nmath'
>> make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/unix'
>> make[3]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/unix'
>> make[3]: `libunix.a' is up to date.
>> make[3]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/unix'
>> make[3]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/unix'
>> ccache gcc -I. -I../../src/include -I../../src/include
>> -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -ggdb -pipe
>> -std=gnu99 -Wall -pedantic  -L/usr/local/lib
>> -DR_HOME='"/home/hzambran/SVN/R-devel/trunk"' \
>> -o Rscript ./Rscript.c
>> make[3]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/unix'
>> make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/unix'
>> make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/main'
>> make[3]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/main'
>> ccache gcc -shared -fopenmp -L/usr/local/lib  -o libR.so
>> CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o
>> arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o
>> colors.o complex.o connections.o context.o cum.o dcf.o datetime.o
>> debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o
>> edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o
>> gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o
>> iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o
>> match.o memory.o names.o objects.o options.o paste.o platform.o plot.o
>> plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o
>> qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o
>> scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o
>> subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o
>> util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o
>> xxxpr.o   `ls ../unix/*.o ../appl/*.o ../nmath/*.o`
>> ../extra/tre/libtre.a    -lblas -lgfortran -lm -lquadmath   -lreadline
>> -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
>> /usr/bin/ld: ../appl/dchdc.o: relocation R_X86_64_32 against `.rodata'
>> can not be used when making a shared object; recompile with -fPIC
>> ../appl/dchdc.o: error adding symbols: Bad value
>> collect2: error: ld returned 1 exit status
>> make[3]: *** [libR.so] Error 1
>> make[3]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/main'
>> make[2]: *** [R] Error 2
>> make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/main'
>> make[1]: *** [R] Error 1
>> make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src'
>> make: *** [R] Error 1
>> *** Done -- now run 'make install'
>>
>>
>> Any thoughts what I'm doing wrong ?
>>
>>
>> Mauricio
>>
>> ______________________________________________
>> R-package-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
>
>
>
>
>
>
>
>

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