[Bioc-devel] libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20

E N gifi2007 at hotmail.com
Tue May 6 22:32:20 CEST 2014

>>> [...] Presumably you can
>>> work around this by installing the lapack / blas dependency manually (i.e.,
>>> through the fedora package manager), and getting Tom Callaway to update the
>>> dependencies in R-3.1.0-4.fc20.src.rpm (although I see there that bals-devel>=
>>> 3.0 is already require'd.
>>> Partly I am 'shooting in the dark', so if I am missing something please excuse
>>> my errors.

>>>> /usr/bin/ld: cannot find -llapack
>>>> /usr/bin/ld: cannot find -lblas
>. I guess
> the following simple commands fail for you -- create a simple C source code file
> $ cat> tmp.c
> int main(int argc, const char **argv) {}
> (press cntrl-D after typing the above, so you have a file 'tmp.c' with that
> single line of code) and try to
> $ gcc -m64 -lblas tmp.c
> $ ./a.out
> $
> For me gcc finds libblas, and creates an executable file a.out, which actually
> does nothing. For you I guess you'll see something like the following, where
> I've replaced '-lblas' with a reference to some imaginary library that my system
> knows nothing about
> $ gcc -m64 -limaginary tmp.c
> /usr/bin/ld: cannot find -limaginary
> collect2: error: ld returned 1 exit status
> $
> If this is the case, then somehow your package manager has installed the lapack
> and blas packages without making their location known to other programs.
> Libraries are usually discovered via ldconfig, and I have for instance
> $ ldconfig -p|grep blas
> libgslcblas.so.0 (libc6,x86-64) => /usr/lib/libgslcblas.so.0
> libgslcblas.so (libc6,x86-64) => /usr/lib/libgslcblas.so
> libf77blas.so.3 (libc6,x86-64) => /usr/lib/libf77blas.so.3
> libcblas.so.3 (libc6,x86-64) => /usr/lib/libcblas.so.3
> libblas.so.3 (libc6,x86-64) => /usr/lib/libblas.so.3
> libblas.so (libc6,x86-64) => /usr/lib/libblas.so
> You might have success with
> $ sudo ldconfig
> but after this I'll let someone with access to a fedora system step in.
> Martin

Indeed, you are right M. Morgan ! After a <sudo yum install lapack-devel blas-devel>, GCC passes the <gcc -m64 -lblas tmp.c> example which wasn't the case before lapack-devel and blas-devel were installed. Thereafter, even the biocLite("preprocessCore") is now running quite well.

That's weird because at <http://koji.fedoraproject.org/koji/rpminfo?rpmID=4985034> blas-devel and lapack-devel are listed in dependency list, but this is no more a Bioconductor or R problem, it's Fedora R package's. Thanks a lot!

Best wishes,


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