bioconductor-genomeinfodbdata offline conda failure

[Netzach]

I have a local offline mirror of bioconda for a secure data research cluster. One of the prereqs for a popular package is bioconductor-genomeinfodbdata, but that can’t be installed offline, since it just contains hardcoded URLs instead of actually providing the package, which screws up a lot of functions in conda. Could this be changed in any way? (The file in question is only 17.1 MB)

[dpryan79]

You'll need to copy that file in yourself then. The various bioconductor data packages were changed in this way to save some space.

[krinsman]

I am also having issues with bioconductor-genomeinfodbdata, since even when online library("GenomeInfoDbData") fails with

Error in library("GenomeInfoDbData"): there is no package called ‘GenomeInfoDbData’

even after installing bioconductor-genomeinfodbdata. I am not sure whether this is actually related to your issue though, so I apologize for the unintentional thread hijacking if this is unrelated.

Anyway it GenomeInfoDbData doesn't show up in my R library, even though GenomeInfoDb does.

[dpryan79]

I just tried the following with success:

$ conda create -n genomeinfodb bioconductor-genomeinfodb bioconductor-genomeinfodbdata
$ source activate genomeinfodb
$ R
> .libPaths(R.home("library"))  # This causes R to ignore non-conda packages
> library(GenomeInfoDbData)
> data(specData)  # This is what the package actually contains
> head(specData)

The last command returned:

  tax_id        genus               species
1      1          all                  <NA>
2      1         root                  <NA>
3      2     Bacteria                  <NA>
4      2          not Bacteria Haeckel 1894
5      6 Azorhizobium                  <NA>
6      7 Azorhizobium           caulinodans

I can't reproduce any issues with the package when online.

[krinsman]

@dpryan79 Yes, that worked for me too. It must have been something else I installed in one of the new environments I created. Let me get back to you if I can figure out anything useful.

EDIT: I thought it might have been an issue with using Jupyter IRkernel, but when it didn't work, it didn't work with command-line R either, and now that it is working, it is working with Jupyter IRKernel too.

Also, now GenomeInfoDb and GenomeInfoDbData are showing up in <path to environment>/lib/R/library, whereas GenomeInfoDbData did not show up before (in other virtual environments). I guess it was probably a conflict with one of the million other packages I had installed in the original environment, but I have no idea which.

[dpryan79]

Closing for now, if this reoccurs then please feel free to reopen.