Sudden Error in DoubletScoring; worked perfectly fine previously

[shamer3]

I have been using ArchR for a while now and had got quite far in terms of analysing my data. I have recently started trying to analyse a new dataset and have now got stuck with addDoubletScores. I have not changed any of my package versions/ R version etc and now it does not work. I get the following error message:

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2024-05-02 10:38:53.118384 : ERROR Found in .computeLSI for  
LogFile = ArchRLogs/ArchR-addDoubletScores-1ffd21bc2644-Date-2024-05-02_Time-10-38-15.446085.log

<simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'sexp_as_cholmod_sparse' not provided by package 'Matrix'>

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2024-05-02 10:38:53.171964 : ERROR Found in .LSIPartialMatrix for  
LogFile = ArchRLogs/ArchR-addDoubletScores-1ffd21bc2644-Date-2024-05-02_Time-10-38-15.446085.log

<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>

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2024-05-02 10:38:53.176983 : ERROR Found in addIterativeLSI for BMA_3 (1 of 3) :  
LogFile = ArchRLogs/ArchR-addDoubletScores-1ffd21bc2644-Date-2024-05-02_Time-10-38-15.446085.log

<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>

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I have also attached the log file to this report. ArchR-addDoubletScores-1ffd21bc2644-Date-2024-05-02_Time-10-38-15.446085.log

I have tried all the fixes I can find in other comments on similar issues but with no success. Would be really appreciative if someone could help or has any suggestions. As I have come to the limit of troubleshooting I am able to do.

[rcorces]

Hi @shamer3! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

[liviuspenter]

This problem went away for me when I downgraded to Matrix 1.6-3 and reinstalled irlba.

Of note, there is another issue with ggplot2 which needs to be version 3.4.0 - I had to downgrade that one as well.

[zvittorio]

I had a similar error in addDoubletScores, but it traced back to Seurat's FindClusters in my case. My colleagues and I prepared a training for scATACseq data analysis where we used ArchR. During the preparation of the course we never encountered the error. Then, when showing the analysis during the hands-on training the error popped up. We didn't change anything in the meawhile, so libraries stayed exactly the same. In particular, we where using Matrix version 1.6-4 This is what fixed the error for us:

• updated Matrix to the latest version as possible. For us, this meant 1.6-5, because of R version constraints.
• restart R and/or clean the environment and go to Session > Restart R
• now load the updated Matrix library

Hopefully this will help!