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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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LINKS not compiling Bloomfilter #13470

Open marchoeppner opened 5 years ago

marchoeppner commented 5 years ago

Hi, so I have been trying to run LINKS, a scaffolder for long reads (https://github.com/bcgsc/LINKS). This tool is available on bioconda in multiple versions.

When I try to run it (1.8.6), I get the following error - which is actually the same I get when trying to compile it myself (multiple machines). There seems to be a somewhat complex process to get the bloom filter compiled...?

Something went wrong running /mnt/lv_userdirs/software/links/1.8.6/LINKS Mo 4. Feb 08:55:43 CET 2019 Can't locate object method "new" via package "BloomFilter::BloomFilter" (perhaps you forgot to load "BloomFilter::BloomFilter"?) at /mnt/lv_userdirs/software/links/1.8.6/LINKS line 216.

ralanharris commented 5 years ago

marchoeppner did you ever get LINKS to work? I get the same error as you with a conda install. I also tried to compile it myself and ran into the same issue.

lcoombe commented 4 years ago

Hi all -- just an FYI that this issue is fixed in #20124