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.)
On 23/08/17 15:28, Dave Bouvier wrote:
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(a)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.
On 08/23/2017 08:38 AM, Peter Briggs wrote:
> Dear devs
> I'm experiencing problems with the conda dependencies for the DESeq2 tool
) 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
> /exec/../../lib/../../libreadline.so.6: undefined symbol: PC
> I've tried manually reinstalling the two dependencies (bioconductor-deseq2(a)1.14.2
and r-getopt(a)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(a)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
> 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
> Any help to fix this is greatly appreciated, many thanks
> Best wishes
> 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.
Peter Briggs peter.briggs(a)manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482