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’