Conda dependency install problems for DESeq2 tool

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Conda dependency install problems for DESeq2 tool

Peter Briggs
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.

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: Conda dependency install problems for DESeq2 tool

Dave Bouvier
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.
>
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: Conda dependency install problems for DESeq2 tool

Peter Briggs
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.
>>

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/