From mauricio.zambrano at ufrontera.cl  Tue Jul 21 05:21:04 2015
From: mauricio.zambrano at ufrontera.cl (MAURICIO ZAMBRANO BIGIARINI)
Date: Tue, 21 Jul 2015 00:21:04 -0300
Subject: [Rd] ' --enable-R-shlib' problem when setting up R-devel in Linux
 Mint 17.1 64-bit
Message-ID: <CAP6VaruUVAAEj-V0JxYB0Ueq7oBNyysUB-9kzKxG-9aa5mfujA@mail.gmail.com>

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