‘package ‘GenomeInfoDb’ could not be loaded’

[cgirardot]

Hi,

Version : 1.42.1+galaxy6 installed today on latest 20.09 version
First run gives me this error:

Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GenomeInfoDbData’
Failed with error:  ‘package ‘GenomeInfoDb’ could not be loaded’
Error in import(opt$gtf_file, feature.type = opt$feature_type) : 
  could not find function "import"
Execution halted

I am not sure why GenomeInfoDbData does not get installed in the first place as a dep but this is not the first time I see this (I had the issue with other tools as well). Maybe force install GenomeInfoDbData would do ?

For now, I solved the issue as an admin by installing the missing GenomeInfoDbData in the conda env

[pcm32]

Thanks for reporting this @cgirardot! Could you clarify please about what tool is this? Thanks!

[cgirardot]

Oh sorry, it is GTF2GeneList

[pcm32]

@pinin4fjords could you take a look and see if there is something wrong with the underlying conda package?

[pinin4fjords]

I've seen this error come up periodically myself, it's something faulty with the way that conda environments initialise with that package. I always fix it by forcing a reinstall of the package in the conda env, as you have done.

[pcm32]

I wonder if this comes up when running from the container.... so then the package is part of the conda dependencies already?

[pinin4fjords]

Yes, I think it's a fairly base bioconductor dependency, but for some reason it fails to install correctly sometimes.