Recent changes to **Matrix** break installed SeuratObject

[hpages]

Hi,

As you might know, the latest versions of Matrix have introduced changes that break a number of packages on machines where they were installed before Matrix got updated.

One of the victims is the SeuratObject package:

> library(SeuratObject)
> LogMap(y=letters)
Error in validObject(.Object) : 
  invalid class "LogMap" object: superclass "mMatrix" not defined in the environment of the object's class

This happens on any machine where SeuratObject got installed before the latest Matrix (1.6-3) got into the wild and landed on the machine.

Unfortunately, the approach of the Matrix maintainers is to simply assume that people will proactively reinstall packages affected by the changes they're doing. Even though it's really hard or even impossible for the end users or system admins to know what packages exactly need reinstallation.

However, the situation would greatly improve if SeuratObject's version was bumped and the bumped version resubmitted to CRAN. The new version would then naturally propagate to the user machine which in turn would trigger a reinstallation.

I'm kindly asking if you would consider doing that.

Note that 20+ Bioconductor packages depend directly or indirectly on SeuratObject and are currently broken on any machine where the latest Matrix has landed.

FWIW here is another CRAN package broken by the recent changes to Matrix.

Thanks,

H.

[mojaveazure]

Hi Hervé,

We've already submitted a new version of SeuratObject (5.0.1) to CRAN depending on the updated Matrix (out of habit, we pin to the current latest which is now 1.6-3). We've ahd some minor back-and-forth as CRAN currently only has Matrix 1.6-1.1 on r-devel for Windows, but hopefully this gets resolved quickly and the updated version gets accepted and propogated out

When it does get accepted, I'll merge #170 and tag a release on this repo. I've linked #170 to this issue so that the merge of #170 will close this. That way, you'll be notified when SeuratObject 5.0.1 hits CRAN

[hpages]

Awesome! Thanks for staying on top of this.

Have a nice day,
H.

[mojaveazure]

Hi Hervé,

Just an update, SeuratObject 5.0.1 has been accepted by CRAN and made its way to at least cloud.r-project.org and cran.rstudio.com. It is currently source-only; I expect binaries to be built and make their way to the mirrors over the weekend

[hpages]

Excellent! Thanks for the update.