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

[Martin Morgan]

On 05/06/2014 04:30 AM, E N wrote:
> Hi,
>
> Let's me quote Ed Borasky
> <https://support.rstudio.com/hc/communities/public/questions/201046993-Library-dependency-issue-on-Fedora-20->:
> "When Fedora 20 migrated from R 3.0.2 to R 3.1.0, they switched from using
> the BLAS and LAPACK shipped with R to the BLAS and LAPACK from Fedora." Tom
> Callaway, R packager for Fedora, explained that here:
> <https://bugzilla.redhat.com/show_bug.cgi?id=1074975#c16>
>
> That causes packages depending on libRblas or/and libRlapack to fail
> installation on Fedora 20 systems running R version 3.1.0. I tried to upgrade
> some packages to BioConductor 2.14 and all those having those libraries in
> dependencies failed the upgrade. Platform: x86_64-redhat-linux-gnu (64-bit).
> The failing packages are:
>
> ChIPseqR, edgeR, IdMappingAnalysis, preprocessCore, RamiGO, RcppArmadillo,
> affy, DESeq2, DiffBind, oligo, ArrayExpress, gcrma, panp, ReportingTools,
> vsn, affycoretools, bgx, Ringo, simpleaffy, tilingArray, AgiMicroRna.
>
> Is there any way to solve that issue upstream (R-Core), or will Fedora 20
> users have to find workarounds themselves ?

Let's focus on preprocessCore, which does not have any additional dependencies.

Also, I assume you mean that you are using R that comes with the fedora package 
manager, rather than the R that is redistributed by Rstudio.

If you could provide the output of

   R CMD config BLAS_LIBS

and the full output of

   R -e "library(BiocInstaller); biocLite('preprocessCore')"

again using the R that is installed with the fedora package manager, then that 
would help to understand your problem.

If your problem is only with the version of R distributed by Rstudio, then as I 
understand it the solution is in the hands of Rstudio, and I am sure they will 
respond promptly.

Martin

>
> Regards, Eric. _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


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