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

peter dalgaard pdalgd at gmail.com
Tue Jul 21 01:29:56 CEST 2015 

Oi!

Could you guys move to r-devel? This has nothing to do with _package_ development.

-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
> 
> ______________________________________________
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> 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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