Re: [Rd] R-devel/Linux x64/Sun Studio 12: Problem with Matrix

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Sat, 21 Feb 2009 08:44:33 +0000 (GMT)

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


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