Hi all,
I'm trying to install R/bioconductor packages in galaxy and have trouble
with some of them.
I made a dependency package ("package_qdnaseq_1_0_5" in the
testtoolshed) that should install several R (bioconductor) packages
using "setup_r_environment" and for each package the
<package>http://link/to/package.tar.gz</package> structure.
It works for many but fails for the package "DNAcopy" with the error
below complaining about gfortran, but that seems to be installed on my
systems (tested two of them, ubuntu 12.04). When I install this with
"install.packages" in my default R installation it installs without
problems..
Anyway know how to deal with or debug this?
Thanks,
Stef
-----
install_environment.STDOUT DEBUG 2014-10-07 14:04:13,176 Error in
dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/home/stef/BASE/tools/galaxy/galaxy-dist/tool-dependency/qdnaseq/1.0.5/stef/package_qdnaseq_1_0_5/42096296e06f/DNAcopy/libs/DNAcopy.so':
/home/stef/BASE/tools/galaxy/galaxy-dist/tool-dependency/qdnaseq/1.0.5/stef/package_qdnaseq_1_0_5/42096296e06f/DNAcopy/libs/DNAcopy.so:
undefined symbol: _gfortran_os_error
Error: loading failed
Execution halted
Error in dyn.load(file, DLLpath = DLLpath, ...) :
ERROR: loading failed
* removing
‘/home/stef/BASE/tools/galaxy/galaxy-dist/tool-dependency/qdnaseq/1.0.5/stef/package_qdnaseq_1_0_5/42096296e06f/DNAcopy’
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