gseWP() enrichWP() R functions error - GMT files absent from WP data downloads current directory

[Yann Aubert]

Hi, 

The gseWP() and enrichWP() functions from the clusterProfiler/enricher R packages which were previously working fine are throwing an error due to missing GMT files in the current WP data downloads directory. (https://wikipathways-data.wmcloud.org/current/gmt/) 

Would be great if this could be fixed ! 

Thanks in advance. 

Best 

Yann Aubert, PhD

[Egon Willighagen]

Hi Yann,

On Tue, 17 Jan 2023 at 11:47, Yann Aubert <yann....@inserm.fr> wrote:

The gseWP() and enrichWP() functions from the clusterProfiler/enricher R packages which were previously working fine are throwing an error due to missing GMT files in the current WP data downloads directory. (https://wikipathways-data.wmcloud.org/current/gmt/) 

Due to the changes in upgrading the WikIPathways platform and maintaining the old platform, we have had trouble creating the GMT files for January. We are working on it.

Is there an option that clusterProfiler/enricher continues using the December release? (Alex, Kristina, maybe current can continue to point to the last Released version, since we did not formally release January yet?)

Egon

--

Lipidomics is increasing to be a fascinating new method to look at biology. This Nature Methods article includes how we use WikiPathways and related tools: https://doi.org/10.1038/s41592-022-01710-0 

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: https://egonw.github.io/
Blog: https://chem-bla-ics.blogspot.com/
Mastodon: https://scholar.social/@egonw
PubList: https://orcid.org/0000-0001-7542-0286

[Yann AUBERT]

Hi Egon, 

Thanks for your answer.

Actually a workaround has been submitted here on stackoverflow. 

However it requires modification of the original gseWP() function and creation of a number of additional functions in order to use GMT files from the previous WikiPathways data download release (20221210). To be complete, the additional functions described in the stackoverflow post mentionned above can also be used to modify the enrichWP() in order to use GMT files from the previous WikiPathways data download release (20221210). However, it would be great if the GMT files could be accessible in the current directory as expected by those two functions. 

Yann

[alex.pico]

The GMT data are now live and everything should be working as normal. Sorry for the inconvenience!  The systematic bug was fixed and future monthly releases should be on schedule.