We recently resolved a similar issue on usegalaxy.org, part of which involved rebuilding some of deseq2's dependencies for R version 3.3.1, which is the currently preferred version for bioconda R packages. You should be able to get the right versions and builds of deseq2 and its dependencies with the following command:
conda_/bin/conda create --name firstname.lastname@example.org --override-channels -c iuc -c bioconda -c conda-forge -c defaults -c r bioconductor-deseq2=1.14.1 r-base=3.3.1
This will force installation of R 3.3.1 bioconda builds of r-getopt and other dependencies, which were rebuilt with conda-build > 2.0 a few months ago.
On 08/23/2017 08:38 AM, Peter Briggs wrote:
I'm experiencing problems with the conda dependencies for the DESeq2 tool (https://toolshed.g2.bx.psu.edu/repository?repository_id=1f158f7565dc70f9) installed into our production instance.
When this tool is run the only output is:
/PATH/TO/job_working_directory/025/25029/conda-env/lib/R/bin/exec/R: symbol lookup error: /PATH/TO/job_working_directory/025/25029/conda-env/lib/R/bin /exec/../../lib/../../libreadline.so.6: undefined symbol: PC
I've tried manually reinstalling the two dependencies (email@example.com and firstname.lastname@example.org) by moving the relevant directories from 'tool_dependencies/_conda/envs' and then doing e.g.
conda_/bin/conda create -n email@example.com --override-channels -c iuc -c bioconda -c conda-forge -c defaults -c r r-getopt=1.20.0
to see if this fixes the problem.
However while it completes okay for the bioconductor-deseq2 package, for r-getopt I get the following failure:
PaddingError: Placeholder of length '80' too short in package r::r-base-3.2.2-0. The package must be rebuilt with conda-build > 2.0.
I've tried doing 'conda_/bin/conda clean -pt' and retrying but I get the same error.
Any help to fix this is greatly appreciated, many thanks
Ps conda version is 4.2.13 and Galaxy is release_17.05; I'm trying to rebuild the conda environments manually because I couldn't see anything within the Galaxy UI which would let me do it there.