Peter,
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 [email protected]
--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.
-
Dave Bouvier
http://galaxyproject.org
http://usegalaxy.org
On 08/23/2017 08:38 AM, Peter Briggs wrote:
Dear devs
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 protected] and [email protected]) by moving the relevant
directories from 'tool_dependencies/_conda/envs' and then doing e.g.
conda_/bin/conda create -n [email protected] --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
Best wishes
Peter
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.
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