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

From: Thomas Petzoldt <Thomas.Petzoldt_at_TU-Dresden.de>
Date: Sat, 21 Feb 2009 09:46:52 +0100


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)

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