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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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RazerS3 binary appears to be broken #15384

Open messersc opened 5 years ago

messersc commented 5 years ago 
$ razers3 --help
Illegal instruction

See https://github.com/FRED-2/OptiType/issues/90

Downgrading to an older version helps. Not sure what the problem is.

npavlovikj commented 5 years ago

@messersc , not sure if this helps, but can you please make sure you use the proper order of the conda channels when installing "razers3" (e.g. -c conda-forge -c bioconda -c defaults as defined here, https://bioconda.github.io/#set-up-channels)?

I tried installing "razers3" 3.5.3 myself, and everything worked fine:

(razers3) [fedora@npavlovikj-conda bioconda-recipes]$ razers3 --help
...
VERSION
    Last update:
    razers3 version: 3.5.3 [tarball]
    SeqAn version: 2.1.1

And here is a list of the dependencies and the respective channels for you to compare with yours:

(razers3) [fedora@npavlovikj-conda bioconda-recipes]$ conda list
# packages in environment at /anaconda/envs/razers3:
#
# Name                    Version                   Build  Channel
bzip2                     1.0.6                h470a237_2    conda-forge
libgcc-ng                 7.2.0                hdf63c60_3    conda-forge/label/cf201901
libstdcxx-ng              7.2.0                hdf63c60_3    conda-forge/label/cf201901
razers3                   3.5.3                h21aa3a5_2    bioconda
zlib                      1.2.11               h470a237_4    conda-forge
messersc commented 5 years ago

Hi,

that's interesting, although it might not be what causes the crash. I just created a new environment:

$ conda list
# packages in environment at /fast/users/messersc_c/work/miniconda/envs/razers3:
#
# Name                    Version                   Build  Channel
bzip2                     1.0.6             h14c3975_1002    conda-forge
libgcc-ng                 8.2.0                hdf63c60_1  
libstdcxx-ng              8.2.0                hdf63c60_1  
razers3                   3.5.3                h21aa3a5_2    bioconda
zlib                      1.2.11            h14c3975_1004    conda-forge

$ razers3
Illegal instruction

Downgrading the libs to 7.2.0 does not change anything.

$ conda list
# packages in environment at /fast/users/messersc_c/work/miniconda/envs/razers3:
#
# Name                    Version                   Build  Channel
bzip2                     1.0.6                h470a237_2    conda-forge
libgcc-ng                 7.2.0                hdf63c60_3  
libstdcxx-ng              7.2.0                hdf63c60_3  
razers3                   3.5.3                h21aa3a5_2    bioconda
zlib                      1.2.11               h470a237_4    conda-forge

$ razers3 
Illegal instruction

This is on a Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz.

npavlovikj commented 5 years ago

You are right Clemens, this is specific to your machine and not the channels - I tried using the exact packages from your env and "razers3" worked fine for me...

Looks like there is similar issue reported for bioconda package on Xeon machine, https://github.com/bioconda/bioconda-recipes/issues/14613. If you have the time, you can try buildling the conda recipe locally with the suggested flags to see if that helps... Probably the compilers used with the older recipe had some additional flags set that work on your machine, https://github.com/bioconda/bioconda-recipes/blob/fc8284ce0c953b33ae4015cf115fda683bf81663/recipes/razers3.

holtgrewe commented 5 years ago

cf #11790