Hi, I've been trying to install the topGO package on Linux (debian squeeze), but I keep getting this error when installing the SparseM dependency: * installing *source* package ?SparseM? ... ** package ?SparseM? successfully unpacked and MD5 sums checked ** libs gfortran -fpic -g -O2 -c bckslv.f -o bckslv.o gfortran -fpic -g -O2 -c chol.f -o chol.o gfortran -fpic -g -O2 -c chol2csr.f -o chol2csr.o gfortran -fpic -g -O2 -c cholesky.f -o cholesky.o gfortran -fpic -g -O2 -c csr.f -o csr.o gfortran -fpic -g -O2 -c extract.f -o extract.o gfortran -fpic -g -O2 -c sparskit.f -o sparskit.o gfortran -fpic -g -O2 -c subscr.f -o subscr.o gcc -std=gnu99 -shared -Wl,-z,relro -o SparseM.so bckslv.o chol.o chol2csr.o cholesky.o csr.o extract.o sparskit.o subscr.o -lgfortran -lm -L/usr/lib64/R/lib -lR /usr/bin/ld: /usr/lib64/R/lib/libgfortran.a(error.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/lib64/R/lib/libgfortran.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [SparseM.so] Error 1 ERROR: compilation failed for package ?SparseM? This is not strictly a Bioconductor issue, but I'm way over my head, and I thought the odds were good that someone else here has stumbled into a similar issue in the past. Can anyone offer suggestions on how to get this dependency to compile? Thanks, -Eric ________________________________________________________ Eric Fournier, B. Sc. Research Assistant in Bioinformatics Universit? Laval, Qc, Canada eric.fournier.4 at ulaval.ca 418-656-2131 x 11465 [[alternative HTML version deleted]]

Hi, for the benefit of anyone having the same issue as I did, a day and a half worth of trial and error taught me that redirecting the /usr/lib/R/lib/libgfortran.a symbolic link from /usr/lib/gcc/x86_64 -linux-gnu/4.4/libgfortran.a to /usr/lib/gcc/x86_64-linux- gnu/4.4/libgfortran.so was all I needed to do. Trying to rebuild gcc with --with-PIC is not necessary. Cheers, -Eric -----Message d'origine----- De?: Eric Fournier [mailto:Eric.Fournier at fsaa.ulaval.ca] Envoy??: Friday, September 05, 2014 1:50 PM ??: bioconductor at r-project.org Objet?: [BioC] Trouble installing topGO package Hi, I've been trying to install the topGO package on Linux (debian squeeze), but I keep getting this error when installing the SparseM dependency: * installing *source* package ?SparseM? ... ** package ?SparseM? successfully unpacked and MD5 sums checked ** libs gfortran -fpic -g -O2 -c bckslv.f -o bckslv.o gfortran -fpic -g -O2 -c chol.f -o chol.o gfortran -fpic -g -O2 -c chol2csr.f -o chol2csr.o gfortran -fpic -g -O2 -c cholesky.f -o cholesky.o gfortran -fpic -g -O2 -c csr.f -o csr.o gfortran -fpic -g -O2 -c extract.f -o extract.o gfortran -fpic -g -O2 -c sparskit.f -o sparskit.o gfortran -fpic -g -O2 -c subscr.f -o subscr.o gcc -std=gnu99 -shared -Wl,-z,relro -o SparseM.so bckslv.o chol.o chol2csr.o cholesky.o csr.o extract.o sparskit.o subscr.o -lgfortran -lm -L/usr/lib64/R/lib -lR /usr/bin/ld: /usr/lib64/R/lib/libgfortran.a(error.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/lib64/R/lib/libgfortran.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [SparseM.so] Error 1 ERROR: compilation failed for package ?SparseM? This is not strictly a Bioconductor issue, but I'm way over my head, and I thought the odds were good that someone else here has stumbled into a similar issue in the past. Can anyone offer suggestions on how to get this dependency to compile? Thanks, -Eric ________________________________________________________ Eric Fournier, B. Sc. Research Assistant in Bioinformatics Universit? Laval, Qc, Canada eric.fournier.4 at ulaval.ca 418-656-2131 x 11465 [[alternative HTML version deleted]]