Hello Dave

Thanks for the quick response, that seems to have fixed it - the r-getopt conda package installs without a problem and the readline.so.6/missing symbol error has gone away.

(DESeq2 is failing with an R error now, but I suspect that's a separate problem.)

Thanks again,

Best wishes

Peter

On 23/08/17 15:28, Dave Bouvier wrote:

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 __bioconductor-deseq2@1.14.1 --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 (bioconductor-deseq2@1.14.2 and r-getopt@1.20.0) by moving the relevant directories from 'tool_dependencies/_conda/envs' and then doing e.g.

conda_/bin/conda create -n __r-getopt@1.20.0 --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.