[BioC] Trouble installing topGO package

Eric Fournier Eric.Fournier at fsaa.ulaval.ca
Mon Sep 8 21:18:24 CEST 2014


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.


-----Message d'origine-----
De : Eric Fournier [mailto:Eric.Fournier at fsaa.ulaval.ca] 
Envoyé : Friday, September 05, 2014 1:50 PM
À : bioconductor at r-project.org
Objet : [BioC] Trouble installing topGO package


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?


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

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