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rmhubley / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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error while installing fresh with conda #237

Closed splaisan closed 7 months ago

splaisan commented 7 months ago

Hi,

I did the following on a ubuntu 22 server (conda 23.10.0)

conda create -n repeatmasker
conda activate repeatmasker
conda install -c bioconda repeatmasker

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: / 
SafetyError: The package for repeatmasker located at /opt/miniconda3/pkgs/repeatmasker-4.1.5-pl5321hdfd78af_1
appears to be corrupted. The path 'share/RepeatMasker/Libraries/Dfam.h5'
has an incorrect size.
  reported size: 68 bytes
  actual size: 5861387976 bytes

done
Executing transaction: done

# trying to call the exe
RepeatMasker 
Storable.c: loadable library and perl binaries are mismatched (got handshake key 0xeb00080, needed 0xed00080)

I tried this several times, always fail while it works on, a separate server (ubuntu20) Is this something normal?

thanks

splaisan commented 7 months ago

apparently it was a PERL5LIB definition in my .bashrc which was misleading the conda env. After unsetting PERL5LIB RepeatMasker accepts to run (dry run so far)

this other issue edit may be a fix too: https://github.com/conda/conda/issues/10709