search

pachterlab / voyager

From geospatial to spatial -omics
https://pachterlab.github.io/voyager/
Artistic License 2.0
79 stars 9 forks source link

Matrix >= 1.6.2 breaks Voyager #15

Closed rsbivand closed 11 months ago

rsbivand commented 12 months ago

In running reverse dependency checks for spdep, I see a failure: function as_cholmod_sparse not provided by package 'Matrix' not caused by changes in spdep.

lambdamoses commented 12 months ago

The issue comes from irlba (https://github.com/bwlewis/irlba/issues/70), which is used by the scater package to run PCA (https://github.com/alanocallaghan/scater/issues/201), which is done in some unit tests. It seems that reinstalling irlba from source would solve this problem. There has been a notice for developers of packages that link to Matrix: https://stat.ethz.ch/pipermail/r-package-devel/2023q4/010051.html. Since this problem isn't from Voyager itself and other packages using irlba are affected, all I can do is to wait for an update in irlba.

lambdamoses commented 11 months ago

Confirmed on GitHub Actions that installing irlba from source solves the problem, before say the next release of irlba.