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tderrien / FEELnc

FEELnc : FlExible Extraction of LncRNA
GNU General Public License v3.0
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Conda install is broken #43

Closed daissi closed 3 years ago

daissi commented 3 years ago

Hi, I tried to install FEELnc through conda but FEELnc crashes with these errors: 

$conda create -n env_feelnc feelnc
...
...
$conda activate env_feelnc
$FEELnc_classifier.pl
Can't load '/gpfs/home/xxxx/miniconda3/envs/env_feelnc/lib/site_perl/5.26.2/x86_64-linux-thread-multi/auto/DB_File/DB_File.so' for module DB_File: libdb-6.1.so: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier ou dossier de ce type at /gpfs/home/xxxx/miniconda3/envs/env_feelnc/lib/site_perl/5.26.2/x86_64-linux-thread-multi/XSLoader.pm line 96.
 at /gpfs/home/xxxx/miniconda3/envs/env_feelnc/lib/site_perl/5.26.2/x86_64-linux-thread-multi/DB_File.pm line 257.
Compilation failed in require at /gpfs/home/xxxx/miniconda3/envs/env_feelnc/lib/site_perl/5.26.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 37.
BEGIN failed--compilation aborted at /gpfs/home/xxxx/miniconda3/envs/env_feelnc/lib/site_perl/5.26.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 37.
Compilation failed in require at /gpfs/home/xxxx/miniconda3/envs/env_feelnc/lib/site_perl/5.26.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
BEGIN failed--compilation aborted at /gpfs/home/xxxx/miniconda3/envs/env_feelnc/lib/site_perl/5.26.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
Compilation failed in require at /gpfs/home/xxxx/miniconda3/envs/env_feelnc/lib/site_perl/5.26.2/Bio/SeqFeature/database_part.pm line 6.
BEGIN failed--compilation aborted at /gpfs/home/xxxx/miniconda3/envs/env_feelnc/lib/site_perl/5.26.2/Bio/SeqFeature/database_part.pm line 6.
Compilation failed in require at /home/xxxx/miniconda3/envs/env_feelnc/bin/FEELnc_classifier.pl line 12.
BEGIN failed--compilation aborted at /home/xxxx/miniconda3/envs/env_feelnc/bin/FEELnc_classifier.pl line 12.

It seems related to https://github.com/bioconda/bioconda-recipes/issues/24688

vwucher commented 3 years ago

Hi,

It is weird, on the issue, the "perl-db-file" seems to be broken for at least 8 days but I managed to install FEELnc using conda yesterday from scratch. Did you lunched the: conda install -c bioconda feelnc or conda install -c bioconda/label/cf201901 feelnc today? Did you tried to redo everything from scratch if you installed FEELnc from bioconda some times ago? Otherwise, you can use FEELnc by installing manually bioperl and cloning FEELnc github. It is less convenient but it should work. Because if it is an issue with bioperl, I am not sure when it is going to get fixed.

Please, tell us if you need more help and sorry for the trouble. Valentin

daissi commented 3 years ago

Hi Valentin,

Thanks!

It works with "-c bioconda/label/cf201901" otherwise it fails.

Best, Dylan

vwucher commented 3 years ago

I am glad it worked!