Packrat incorrectly inferring that Seurat package should be restored from Bioconductor

[pcantalupo]

Hello,

The problem is described in the following Github issues for two repositories: Seurat issue 2545 and rsconnect issue 399

Can packrat be updated to account for this situation?

Thank you

[KinSimon96]

Hello,

I'm having the same problem than yours. Did you figure it out ?

Thanks

[mattfemia]

Hey @KinSimon96

I've been using a work-around of installing/loading a previous version of Seurat (3.1.0) that didn't have the dependency yet. I also haven't checked to see if this was resolved yet though.

Running this works for me: ` library(devtools) library(rsconnect)

options(repos = BiocManager::repositories()) install_url('https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_3.1.0.tar.gz') install_url('https://cran.r-project.org/src/contrib/Archive/SDMTools/SDMTools_1.1-221.2.tar.gz')

deployApp() `

-Matt

[pcantalupo]

Hi ... I did not figure it out. I eventually gave up on Packrat as it was too cumbersome to implement in my workflows. Good luck.

[KinSimon96]

Hey @pcantalupo @mattfemia ,

Thank you for your fast reply! Installing previous version of Seurat seems a good alternative, but won't work for my app: it allows users to subset their own data either for quality control than for deeper cluster analysis. Unfortunately, the 3.1.0 does not recognize inputs in a enclosed environement (i.e pbmc <- subset(pbmc, subset = input$gene > 1). This has been corrected by sending them a report but only for the 3.1.5 version...

Really don't know what to do, i've spent hundreds of hours on it, i hope it will get fixed soon.

Have a nice day!

[YTLogos]

SO the package genetics is the same situation when run rsconnect::appDependencies()

[KinSimon96]

I've finally solved it by installing the dev version of Seurat, which corrects dependencies.

[aronatkins]

Seurat no longer indicates biocViews in its DESCRIPTION. https://github.com/satijalab/seurat/commit/1592346e83bef247c41a5f1d1ad698a56e8be38b