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.
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
