Is MKL dependency missing on conda?
skoren opened this issue · 2 comments
There was a user who hit a verkko error with mashmap installed through conda (see: marbl/verkko#162). Couldn't confirm mashmap version since it won't run to report version but I would guess this is not 2.0. I didn't see any reference to this library in the code so not sure why it's there in conda.
mkl was listed as an osx dependency in conda for v2.0, but I removed it for v3.0 and up since we don't link to it. Nevertheless, someone from our lab experienced this issue last week w/ v3.0.4 on Ubuntu 18.04 and I haven't been able to figure out the cause yet. Seems to only happen w/ v3.0.2 and v3.0.4 and only w/ the conda build. The issue is fixed for them by updating to v3.0.5.
Conda was going through some infrastructure changes/issues around the time of those builds, so perhaps that contributed to the issue.
For verkko, you'll have specify mashmap>=v3.0.5. In the meantime, I'll see if I can get conda to rebuild the impacted versions.
Thanks for the info, I asked them to try upgrading and will see if that works.