R SIG Fedora - Mar 2011 - CentOS 5 install won't make with shared libs enabled

Hi,
I've been trying to get a shared library version of the R package(version
2.12.1) installed on a CentOS 5 system. (It installs fine without but other
packages demand shared libs - namely Rapache).
I've tried this with yum but don't know of any flags to set to tell it
to
installl with shared libs enabled. I then tried a local R install as
non-root with source packages:

after downloading the latest tarball and unzipping:
./configure --prefix=/opt --enable-R-shlib
make

make[3]: Entering directory
`/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main'
gcc -std=gnu99 -shared -L/usr/local/lib64  -o libR.so CConverters.o
CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o
array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o
complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o
deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o
engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o
gram-ex.o gramLatex.o gramRd.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 model.o names.o objects.o optim.o
optimize.o options.o par.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 size.o
sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o
summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o
../unix/Rembedded.o ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a
../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
../extra/tre/libtre.a  ../extra/xz/liblzma.a  -L../../lib -lRblas -lgfortran
-lm   -lreadline -lncurses  -ldl -lm
/usr/bin/ld: CConverters.o: relocation R_X86_64_32S against `R_FunTab' can
not be used when making a shared object; recompile with -fPIC
CConverters.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libR.so] Error 1
make[3]: Leaving directory
`/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main'
make[2]: *** [R] Error 2
make[2]: Leaving directory
`/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src'
make: *** [R] Error 1


I then added the -fPIC to the CC line in Makeconf and did a new make but no
joy:

make[3]: Entering directory
`/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main'
gcc -std=gnu99 -fPIC -shared -L/usr/local/lib64  -o libR.so CConverters.o
CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o
array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o
complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o
deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o
engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o
gram-ex.o gramLatex.o gramRd.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 model.o names.o objects.o optim.o
optimize.o options.o par.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 size.o
sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o
summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o
../unix/Rembedded.o ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a
../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
../extra/tre/libtre.a  ../extra/xz/liblzma.a  -L../../lib -lRblas -lgfortran
-lm   -lreadline -lncurses  -ldl -lm
/usr/bin/ld: CConverters.o: relocation R_X86_64_32S against `R_FunTab' can
not be used when making a shared object; recompile with -fPIC
CConverters.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libR.so] Error 1

I've checked all the faq's and been googling this with no joy.
I'd be grateful for any help on installing this dependency to get Rapache
installed

Thanks,
Sean.

	[[alternative HTML version deleted]]

On 03/02/2011 10:46 AM, Sean O'Keeffe wrote:
> Hi,
> I've been trying to get a shared library version of the R
package(version
> 2.12.1) installed on a CentOS 5 system. (It installs fine without but other
> packages demand shared libs - namely Rapache).
> I've tried this with yum but don't know of any flags to set to tell
it to
> installl with shared libs enabled. I then tried a local R install as
> non-root with source packages:
The R package in EPEL should work fine on CentOS, and it is built with
shared libs. If you have EPEL enabled, and run "yum install R",
you'll
get everything.

~tom

=Fedora Project

On Mar 2, 2011, at 9:46 AM, Sean O'Keeffe wrote:
> Hi,
> I've been trying to get a shared library version of the R
package(version
> 2.12.1) installed on a CentOS 5 system. (It installs fine without but other
> packages demand shared libs - namely Rapache).
> I've tried this with yum but don't know of any flags to set to tell
it to
> installl with shared libs enabled. I then tried a local R install as
> non-root with source packages:
> 
> after downloading the latest tarball and unzipping:
> ./configure --prefix=/opt --enable-R-shlib
> make
> 
> make[3]: Entering directory
> `/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main'
> gcc -std=gnu99 -shared -L/usr/local/lib64  -o libR.so CConverters.o
> CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o
> array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o
> complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o
> deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o
> engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o
> gram-ex.o gramLatex.o gramRd.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 model.o names.o objects.o optim.o
> optimize.o options.o par.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 size.o
> sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o
subset.o
> summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o
> ../unix/Rembedded.o ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a
> ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
> ../extra/tre/libtre.a  ../extra/xz/liblzma.a  -L../../lib -lRblas
-lgfortran
> -lm   -lreadline -lncurses  -ldl -lm
> /usr/bin/ld: CConverters.o: relocation R_X86_64_32S against `R_FunTab'
can
> not be used when making a shared object; recompile with -fPIC
> CConverters.o: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[3]: *** [libR.so] Error 1
> make[3]: Leaving directory
> `/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main'
> make[2]: *** [R] Error 2
> make[2]: Leaving directory
> `/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main'
> make[1]: *** [R] Error 1
> make[1]: Leaving directory
`/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src'
> make: *** [R] Error 1
> 
> 
> I then added the -fPIC to the CC line in Makeconf and did a new make but no
> joy:
> 
> make[3]: Entering directory
> `/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main'
> gcc -std=gnu99 -fPIC -shared -L/usr/local/lib64  -o libR.so CConverters.o
> CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o
> array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o
> complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o
> deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o
> engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o
> gram-ex.o gramLatex.o gramRd.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 model.o names.o objects.o optim.o
> optimize.o options.o par.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 size.o
> sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o
subset.o
> summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o
> ../unix/Rembedded.o ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a
> ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
> ../extra/tre/libtre.a  ../extra/xz/liblzma.a  -L../../lib -lRblas
-lgfortran
> -lm   -lreadline -lncurses  -ldl -lm
> /usr/bin/ld: CConverters.o: relocation R_X86_64_32S against `R_FunTab'
can
> not be used when making a shared object; recompile with -fPIC
> CConverters.o: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[3]: *** [libR.so] Error 1
> 
> I've checked all the faq's and been googling this with no joy.
> I'd be grateful for any help on installing this dependency to get
Rapache
> installed
> 
> Thanks,
> Sean.

Sean,

Why not just use the RPMs provided by the EPEL:

 http://fedoraproject.org/wiki/EPEL

Config information is available from the above link.

R 2.12.1 is available:

 http://download.fedora.redhat.com/pub/epel/5/x86_64/repoview/R.html

The R RPMs are built for shlibs.

That will save you the hassle of building from source, unless you have other
compelling requirements.

HTH,

Marc Schwartz

On Wed, Mar 2, 2011 at 9:46 AM, Sean O'Keeffe <so2346 at columbia.edu>
wrote:
> Hi,
> I've been trying to get a shared library version of the R
package(version
> 2.12.1) installed on a CentOS 5 system. (It installs fine without but other
> packages demand shared libs - namely Rapache).
> I've tried this with yum but don't know of any flags to set to tell
it to
> installl with shared libs enabled. I then tried a local R install as
> non-root with source packages:
>
> after downloading the latest tarball and unzipping:
> ./configure --prefix=/opt --enable-R-shlib
> make
>
Wow. I'm stunned that Rapache shows up as a requirement.  I think the
other guys are right that  you should just use R from Epel, but if you
want to be a do-it-yourselfer, I would suggest he following.

DO NOT build R from source that way. DO get the SRPM file that is used
to build RPMS.  Then set your build directory in a file in your home
directory (.rpmmacros as I recall), then install the SRPM file, then
go read the SPEC file in the rpm tree. The SPEC file shows how the
thing is built, and you can rebuild in the command line like

$ rpmbuild -ba whatever.spec

This will give you an RPM that is exactly matching your system, same
as "configure ..  make" but more easily managed.  If you have trouble
getting started, I think I can double-check the instructions. I know
I've written them out before.

Here's another point.  The "default" configure statement for
R's RPM
is much more elaborate than you think.  So trying it from scratch is
probably a big mistake.  If you look at the SPEC file, you will see
what I mean.

If you do succeed in building RPMS, it will be then easy for you to
take the RPM for Rapache and rebuild that for your system.  Or it will
be VERY OBVIOUS in the R spec file what you need to do to get rid of
the Rapache package requirement.  It sounds to me like a very
aggressive piece  of packaging, there, since most R installations will
never need it.

 Until you posted, I did not know that Rapache had been packaged in
Fedora, while running a RedHat system, I built my own.  It is a very
simple build, actually, it is just an apache module and a apache
config file.  Next time I have spare time, i will see how their
packaging differs from mine.

Or you can check and tell me. The installable is
http://pj.free.faculty.org/Centos/5/i386/kups/packages/rapache-1.1.13-1.i386.rpm

Here's the SRPM, you could rebuild

http://pj.free.faculty.org/Centos/5/i386/kups/SRPMS/rapache-1.1.13-1.src.rpm

Good luck. I hope this will be an exciting chance for you to join the
smart, clever group of RPM building linux users.  Advice I got years
ago: Never install anything with "make install" because it puts
unaccountable damage all over your file system, and if you do that,
set the prefix in the configure to be a unique, separate thing. Never
manually install into /usr.

And if something is worth building by hand, it is worth building in a
package so you can remove it!

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas