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pachterlab / voyager

From geospatial to spatial -omics
https://pachterlab.github.io/voyager/
Artistic License 2.0
70 stars 8 forks source link

Matrix >= 1.6.2 breaks Voyager #15

Closed rsbivand closed 8 months ago

rsbivand commented 9 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 9 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 8 months ago

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