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

[Martin Morgan]

On 05/06/2014 02:12 PM, E N wrote:
> Mr Morgan,
>
> I'm afraid the issue is not completely over. Among the packages that were failing installation, all now success after your guidance but three remain failing. Here are excerpts of the dumps:
>
> ChIPseqR
> gcc -m64 -std=gnu99 -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -flto -fpic -Wl,-z,relro -o ChIPseqR.so startScore.o -L/usr/lib64/R/lib -lR
> installing to /usr/lib64/R/library/ChIPseqR/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object '/usr/lib64/R/library/fBasics/libs/fBasics.so':
> libRblas.so: cannot open shared object file: No such file or directory

The problem here (and in each of the following examples) is that the R package 
fBasics was installed with an R from before your recent update; the fBasics 
package is looking for libRblas.so, but the fedora package manager has removed 
this so it is no longer present. The solution is to re-install fBasics (and 
mculst and igraph).

These packages are installed in a system directory, so updating requires sudo.

Likely other packages are in a similar state; this R command

   xx = installed.packages()
   table(xx[,Built"])

might point to packages installed with different R versions than your current 
version (embarrassingly, I get

2.14.1  3.1.0  3.2.0
      2    568      6

indicating 2 packages were installed with a previous version of R and 6 with a 
latter version than the one I'm actually using -- R 3.1.0). The offenders are

   xx[xx[,"Built"] != "3.1.0",]

this test would not be sufficient for identifying problem packages.

Martin

>
>
> IdMappingAnalysis
> ** preparing package for lazy loading
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>    unable to load shared object '/usr/lib64/R/library/mclust/libs/mclust.so':
>    libRlapack.so: cannot open shared object file: No such file or directory
>
> RamiGO:
> ** preparing package for lazy loading
> Error : .onLoad failed in loadNamespace() for 'igraph', details:
>    call: dyn.load(file, DLLpath = DLLpath, ...)
>    error: unable to load shared object '/usr/lib64/R/library/igraph/libs/igraph.so':
>    libRlapack.so: cannot open shared object file: No such file or directory
>
> Perhaps it's better to get someone with a Fedora 20 that understand better than I do debugging package installation, since I'm not far abusing your patience.
>
> Eric. 		 	   		
>


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