R devel - Feb 2009 - R-devel/Linux x64/Sun Studio 12: Problem with Matrix

This seems to be a problem with your OS installation. I have

gannet% file /lib64/libpthread.so.0
/lib64/libpthread.so.0: symbolic link to `libpthread-2.9.so'
gannet% file /lib64/libpthread-2.9.so
/lib64/libpthread-2.9.so: ELF 64-bit LSB shared object, x86-64, 
version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 
2.6.9, not stripped

gannet% rpm -q --whatprovides /lib64/libpthread-2.9.so
glibc-2.9-3.x86_64

and of course building (current) Matrix works for me.

On Sat, 21 Feb 2009, Thomas Petzoldt wrote:
> Dear Developers,
>
> motivated by the new Sun Studio checks I compiled R-devel and several of
> our packages with Sun Studio 12 on Fedora x64.
>
> Everything worked fine and R-devel runs, with the exception of package
> Matrix where compilation crashes with the following message. The error
> occurs during building of the recommended packages and also if Matrix is
> compiled separately:
>
> [...]
> CC -G -lCstd  -L/opt/sun/sunstudio12/lib/amd64 -o Matrix.so CHMfactor.o
> Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o
> cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o
> dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o
> dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o
> CHOLMOD.a COLAMD.a AMD.a -L/home/user/R/R-devel/lib -lRlapack
> -L/home/user/R/R-devel/lib -lRblas
>
-R/opt/sun/sunstudio12/lib/amd64:/opt/sun/sunstudio12/lib/amd64:/opt/sun/lib/rtlibs/amd64:/opt/sun/lib/rtlibs/amd64
-L/opt/sun/sunstudio12/rtlibs/amd64 -L/opt/sun/sunstudio12/prod/lib/amd64 -lfui
-lfai -lfsu -lmtsk -lpthread -lm /opt/sun/sunstudio12/prod/lib/amd64/libc_supp.a
> /lib64/libpthread.so.0: file not recognized: File format not recognized
> make: *** [Matrix.so] Error 1
> ERROR: compilation failed for package ?Matrix?
> * Removing ?/home/user/R/R-devel/library/Matrix?
>
> Can someone help me or give me a pointer what I'm making wrong? How can
> I get/include the missing shared library?
>
> Many thanks in advance
>
> Thomas Petzoldt
>
>
> #file: config.site
>
> CC=cc
> CFLAGS="-xO5 -xc99 -xlibmil -nofstore"
> CPICFLAGS=-Kpic
> F77=f95
> FFLAGS="-O5 -libmil -nofstore"
> FPICFLAGS=-Kpic
> CXX=CC
> CXXFLAGS="-xO5 -xlibmil -nofstore"
> CXXPICFLAGS=-Kpic
> FC=f95
> FCFLAGS=$FFLAGS
> FCPICFLAGS=-Kpic
> LDFLAGS=-L/opt/sun/sunstudio12/lib/amd64
> SHLIB_LDFLAGS=-shared
> SHLIB_CXXLDFLAGS="-G -lCstd"
> SHLIB_FCLDFLAGS=-G
> SAFE_FFLAGS="-O5 -libmil"
>
> platform 86_64-unknown-linux-gnu
> arch x86_64
> os linux-gnu
> system x86_64, linux-gnu
> status Under development (unstable)
> major 2
> minor 9.0
> year  2009
> month 02
> day   20
> svn rev 47964
> language R
> version.string R version 2.9.0 Under development (unstable) (2009-02-20
> r47964)
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Dear Developers,

motivated by the new Sun Studio checks I compiled R-devel and several of
our packages with Sun Studio 12 on Fedora x64.

Everything worked fine and R-devel runs, with the exception of package
Matrix where compilation crashes with the following message. The error
occurs during building of the recommended packages and also if Matrix is
compiled separately:

[...]
CC -G -lCstd  -L/opt/sun/sunstudio12/lib/amd64 -o Matrix.so CHMfactor.o
Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o
cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o
dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o
dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o
CHOLMOD.a COLAMD.a AMD.a -L/home/user/R/R-devel/lib -lRlapack
-L/home/user/R/R-devel/lib -lRblas
-R/opt/sun/sunstudio12/lib/amd64:/opt/sun/sunstudio12/lib/amd64:/opt/sun/lib/rtlibs/amd64:/opt/sun/lib/rtlibs/amd64
-L/opt/sun/sunstudio12/rtlibs/amd64 -L/opt/sun/sunstudio12/prod/lib/amd64 -lfui
-lfai -lfsu -lmtsk -lpthread -lm /opt/sun/sunstudio12/prod/lib/amd64/libc_supp.a
/lib64/libpthread.so.0: file not recognized: File format not recognized
make: *** [Matrix.so] Error 1
ERROR: compilation failed for package ?Matrix?
* Removing ?/home/user/R/R-devel/library/Matrix?

Can someone help me or give me a pointer what I'm making wrong? How can
I get/include the missing shared library?

Many thanks in advance

Thomas Petzoldt


#file: config.site

CC=cc
CFLAGS="-xO5 -xc99 -xlibmil -nofstore"
CPICFLAGS=-Kpic
F77=f95
FFLAGS="-O5 -libmil -nofstore"
FPICFLAGS=-Kpic
CXX=CC
CXXFLAGS="-xO5 -xlibmil -nofstore"
CXXPICFLAGS=-Kpic
FC=f95
FCFLAGS=$FFLAGS
FCPICFLAGS=-Kpic
LDFLAGS=-L/opt/sun/sunstudio12/lib/amd64
SHLIB_LDFLAGS=-shared
SHLIB_CXXLDFLAGS="-G -lCstd"
SHLIB_FCLDFLAGS=-G
SAFE_FFLAGS="-O5 -libmil"

platform 86_64-unknown-linux-gnu                                        
arch x86_64                                                          
os linux-gnu                                                       
system x86_64, linux-gnu                                               
status Under development (unstable)                                    
major 2                                                               
minor 9.0                                                             
year  2009                                                            
month 02                                                              
day   20                                                              
svn rev 47964                                                           
language R
version.string R version 2.9.0 Under development (unstable) (2009-02-20
r47964)