Hi all,
I have trouble to compile Matrix packages on Solar10 x86-64 with Sun compilers.
I saw some postings on this but am not sure how to solve this problem.
It is becoming critical as I cannot install biocLite() because of its
dependency on Matrix.
Could you direct me how to resolve the issue?
Thanks in advance!
Dongseok
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> install.packages("Matrix")
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://cran.fhcrc.org/src/contrib/Matrix_0.999375-20.tar.gz'
Content type 'application/x-gzip' length 1954872 bytes (1.9 Mb)
opened URL
==================================================
downloaded 1.9 Mb
* Installing *source* package 'Matrix' ...
** libs
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c CHMfactor.c -o CHMfactor.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c Csparse.c -o Csparse.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c TMatrix_as.c -o TMatrix_as.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c Tsparse.c -o Tsparse.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c init.c -o init.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c Mutils.c -o Mutils.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c chm_common.c -o chm_common.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c cs.c -o cs.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c cs_utils.c -o cs_utils.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dense.c -o dense.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dgCMatrix.c -o dgCMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dgTMatrix.c -o dgTMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dgeMatrix.c -o dgeMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dpoMatrix.c -o dpoMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dppMatrix.c -o dppMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dsCMatrix.c -o dsCMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dsyMatrix.c -o dsyMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dspMatrix.c -o dspMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dtCMatrix.c -o dtCMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dtTMatrix.c -o dtTMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dtrMatrix.c -o dtrMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c dtpMatrix.c -o dtpMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c factorizations.c -o factorizations.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ldense.c -o ldense.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c lgCMatrix.c -o lgCMatrix.o
cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c sparseQR.c -o sparseQR.o
( cd Lib ; make clean )
( cd Lib ; make clean )
( cd Source ; make clean )
( cd Source ; make clean )
( cd Lib ; make lib )
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/spqr_rmap.cpp
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/SuiteSparseQR_C.cpp
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/SuiteSparseQR_expert.cpp
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/spqr_parallel.cpp
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/spqr_kernel.cpp
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/spqr_analyze.cpp
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/spqr_assemble.cpp
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/spqr_cpack.cpp
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/spqr_csize.cpp
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/spqr_fcsize.cpp
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/spqr_debug.cpp
CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig
-I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include
-I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O
-I/opt/SUNWspro/prod/include -c ../Source/spqr_front.cpp
"../Source/spqr_front.cpp", line 184: Error: Could not find a match for larfg
needed in house<double>(int, double*, cholmod_common_struct*).
"../Source/spqr_front.cpp", line 413: Where: While instantiating
"house<double>(int, double*, cholmod_common_struct*)".
"../Source/spqr_front.cpp", line 413: Where: Instantiated from
spqr_front<double>(int, int, int, double, int, int, double*, int*, char*,
double*, double*, cholmod_common_struct*).
"../Source/spqr_front.cpp", line 564: Where: Instantiated from non-template
code.
1 Error(s) detected.
*** Error code 1
make: Fatal error: Command failed for target `spqr_front.o'
Current working directory /tmp/R.INSTALL.KwaqDb/Matrix/src/SPQR/Lib
*** Error code 1
make: Fatal error: Command failed for target `library'
Current working directory /tmp/R.INSTALL.KwaqDb/Matrix/src/SPQR
*** Error code 1
The following command caused the error:
for d in SPQR CHOLMOD COLAMD AMD; do \
(cd ${d} && CFLAGS="-O -I/opt/SUNWspro/prod/include" CXXFLAGS="-O
-I/opt/SUNWspro/prod/include"
MkInclude="/home/choid/bin/R281/lib/R/etc/Makeconf" make library) || exit 1; \
done
make: Fatal error: Command failed for target `sublibs'
ERROR: compilation failed for package 'Matrix'
** Removing '/home/choid/bin/R281/lib/R/library/Matrix'
The downloaded packages are in
/tmp/RtmpjvNsHB/downloaded_packages
Updating HTML index of packages in '.Library'
Warning message:
In install.packages("Matrix") :
installation of package 'Matrix' had non-zero exit status
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