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Hello R-devel, Since Pavel has mentioned ABI-level dependencies between packages [1], it may be relevant to revisit the related problem mentioned ~1.5 years ago by Dirk [2]. While the current version of SeuratObject doesn't exhibit this problem, a combination of package versions described by Dirk still breaks each other on R-devel: 1. Install Matrix_1.5-1 2. Install SeuratObject_4.1.3 from source 3. Install Matrix_1.6-0 4. SeuratObject is now broken until reinstalled from source The problem is actually s...

...lout of that release (and not before, regrettably, ...), I programmatically scanned the namespaces of the reverse dependencies of Matrix for classRepresentation objects with package slot "Matrix", and sent those maintainers an e-mail asking them to add more importClassesFrom(Matrix, ...). SeuratObject was one of a few affected packages. These days we run two rounds of reverse dependency testing, one with the user library built entirely against the old Matrix and one with the user library built entirely against the new Matrix. The second catches breakage due to ABI changes and stale cached S4 c...

...t reproduction is by saving the code snippet below in the current directory as eg 'matrixIssue.R' and have it run in a container as docker run --rm -ti -v `pwd`:/mnt rocker/r2u Rscript /mnt/matrixIssue.R This runs in under two minutes, first installing the older Matrix, next installs SeuratObject, and then by removing the older Matrix making the (already installed) current Matrix version the default. This simulates a package update for Matrix. Which, as the final snippet demonstrates, silently breaks SeuratObject as the cached S4 method Csparse_validate is now missing. So when SeuratObject...