From mauricio.zambrano at ufrontera.cl  Tue Jul 21 07:15:35 2015
From: mauricio.zambrano at ufrontera.cl (MAURICIO ZAMBRANO BIGIARINI)
Date: Tue, 21 Jul 2015 02:15:35 -0300
Subject: [Rd] ' --enable-R-shlib' problem when setting up R-devel in
 Linux Mint 17.1 64-bit
In-Reply-To: <CAP6VaruUVAAEj-V0JxYB0Ueq7oBNyysUB-9kzKxG-9aa5mfujA@mail.gmail.com>
References: <CAP6VaruUVAAEj-V0JxYB0Ueq7oBNyysUB-9kzKxG-9aa5mfujA@mail.gmail.com>
Message-ID: <CAP6Varse6imZoxzGearqG-7nBLmrmKyuB=N6TG3Bcc=CTkTw4A@mail.gmail.com>

Regarding the previous problem with setting up r-devel in Linux Mint
17.1 64-bit, I deleted all the r-devel files I previously had, and
then I did the check out to the

'~/svn/r-devel'

directory originally mentioned by by Dirk  on
https://stat.ethz.ch/pipermail/r-sig-debian/2012-August/001935.html,
instead of the customised location I previously chose:

'~/SVN/R-devel/trunk'

and now I everything worked perfectly fine.

However, I'm still wondering what should I change in the first script
proposed by Dirk on
https://stat.ethz.ch/pipermail/r-sig-debian/2012-August/001935.html if
i want to use a user-defined location for the development files (e.g.,
'~/SVN/R-devel/trunk'). I meant, in addition to the line:

cd ~/svn/r-devel



Kind regards,

Mauricio

=====================================
"When the pupil is ready, the master arrives."
(Zen proverb)
=====================================
Linux user #454569 -- Linux Mint user


On 21 July 2015 at 00:21, MAURICIO ZAMBRANO BIGIARINI
<mauricio.zambrano at ufrontera.cl> wrote:
> Dear list,
>
> This is my first time trying to set up the development version of R
> (R-devel ) in my local machine to test some packages before submitting
> them to CRAN. I'm using Linux Mint 17.1 64-bit, which is an
> Ubuntu-based distro.
>
> However, I'm not able to correctly set up r-devel, apparently due to a
> problem with enabling the shared library support.
>
>
> I run the first script given by Dirk Eddelbuettel (changing
> '~/SVN/R-devel/trunk' by '~/svn/r-devel' as my local copy of r-devel)
> on:
> https://stat.ethz.ch/pipermail/r-sig-debian/2012-August/001935.html
>
>
> After running that script, the error message I get is:
>
>  `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'
>
>
> and the complete output of the make part of that script is below:
>
> 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'
>
>
> I would highly appreciate any advice on how to solve this issue or how
> to correctly set up r-devel.
>
>
> Thanks in advance,
>
> Mauricio Zambrano-Bigiarini, PhD
>
> =====================================
> Dept. of Civil Engineering
> Faculty of Engineering and Sciences
> Universidad de La Frontera
> PO Box 54-D, Temuco, Chile
> =====================================
> mailto     : mauricio.zambrano at ufrontera.cl
> work-phone : +56 45 259 2812
> http://ingenieriacivil.ufro.cl/
> =====================================
> "When the pupil is ready, the master arrives."
> (Zen proverb)
> =====================================
> Linux user #454569 -- Linux Mint user



[Rd] ' --enable-R-shlib' problem when setting up R-devel in Linux Mint 17.1 64-bit
MAURICIO ZAMBRANO BIGIARINI