[BioC] Trouble installing topGO package

Eric Fournier Eric.Fournier at fsaa.ulaval.ca
Fri Sep 5 19:49:43 CEST 2014


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 âSparseMâ ...
** package âSparseMâ 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 âSparseMâ

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?


Eric Fournier, B. Sc.
Research Assistant in Bioinformatics
Université Laval, Qc, Canada
eric.fournier.4 at ulaval.ca
418-656-2131 x 11465

	[[alternative HTML version deleted]]

More information about the Bioconductor mailing list