R devel - Jul 2015 - ' --enable-R-shlib' problem when setting up R-devel in Linux Mint 17.1 64-bit

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

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

On 21 July 2015 at 02:15, MAURICIO ZAMBRANO BIGIARINI wrote:
| 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

That is most likely spurious.  Your errors may be due to, say, you not having
run 'make clean' or 'make distclean' in the previous repo
checkout you had so
that the effect of the _initial_ configure call still lingered.

There is no magic here. Lots of people have built R this way, and even more
people use configure regularly.  These things work.  

You somehow boxed yourself into a corner, out of which you now seem to have
escaped, which is good.  The proper sequence (svn checkout ...; configure
...; make ...) will work no matter what name you give the directory you work
in.

Regards, Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org