IOBR Error in IOBR::calculate_sig_score() -- GSVA::gsva() defunc

Hi,

The IOBR::calculate_sig_score() function no longer works with R version 4.4.0, Bioconductor release 3.19. Particularly the function calculate_sig_score_ssgsea() fails because the previous GSVA API is defunc:

Error in GSVA::gsva(expr = bulkExp, gset.idx.list = signatures, method = statMethod, : Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva'). as you can see also here: https://github.com/rcastelo/GSVA/issues/172

Would it be possible to update the IOBR package so that it works with the newest Bioconductor release?

Thank you!

Jun 06 '24 15:06 AimSchina

I encountered the same problem. This seems to be caused by the update of GSVA package. I switched to GSVA 1.50 version and it solved the problem. I hope the author will update it as soon as possible to adapt to the GSVA package.

Oct 02 '24 15:10 Mincana-Huang

For those who encountered the same problem, you can download the source package of GSVA (https://bioconductor.org/packages/3.18/bioc/src/contrib/GSVA_1.50.5.tar.gz) from bioconductor and install it in your environment. Once you loaded this version of GSVA, the problem could be bypassed.

Oct 06 '24 06:10 CC-DrDU

My package versions are GSVA v1.46.0 matrixStats v1.4.1 one workaround is

options(matrixStats.useNames.NA = "deprecated")

not sure if it's the right solution but anyway GSVA runs

Dec 11 '24 01:12 ZJURenyi