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aertslab / AUCell

AUCell: score single cells with gene regulatory networks
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At risk of removal from Bioconductor #42

Open lshep opened 5 months ago

lshep commented 5 months ago

We have tried to contact the maintainer email in the package. The package is currently failing across all platforms in devel and will soon start to fail across all platforms in release. The rbokeh package was removed from CRAN on 10-29-2023. You will have to adjust your package to not depend on rbokeh or your package will be removed from Bioconductor. We appreciate your quick attention to this matter.

ghuls commented 4 months ago

@lshep Can you try this, to see if it solves it? https://github.com/aertslab/AUCell/pull/44

I am not an R user, so there can be issues with it.

lshep commented 4 months ago

Their is still R code that references rbokeh. You would have to remove the code that uses rbokeh in aux_createViewerApp.R as well

ghuls commented 4 months ago

Would that not be only be executed if rbokeh is installed?

lshep commented 4 months ago

Our system checks for dependencies and it will ERROR because it will look for rbokeh for being installed. The code must be removed since rbokeh is not longer on CRAN

ghuls commented 4 months ago

aux_createViewerApp.R is removed now.

lshep commented 4 months ago

someone with R experience will likely have to review and check. on a quick local check myself there is still clean up needed 

lorikern@jbcj433:~/PkgReview$ R CMD build AUCell 
* checking for file 'AUCell/DESCRIPTION' ... OK
* preparing 'AUCell':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'AUCell' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'AUCell' in namespaceExport(ns, exports):
 undefined exports: AUCell_createViewerApp
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/tmp/RtmpH2Fsu1/Rinste4bf5a00e1b/AUCell'
      -----------------------------------
ERROR: package installation failed

once changes are approved and merged over these will still need to be pushed to git.bioconductor.org by the maintainer as well.

ghuls commented 4 months ago

Another attempt.

Version number is also updated to 1.26.0 (assuming this is the correct thing to do: https://code.bioconductor.org/browse/AUCell/commit/32bf58ee019f245e2fca448e5fa97fcd236a1fe4)

ghuls commented 4 months ago

@lshep The devel branch now contains this commit and is based on the latest devel branch on https://code.bioconductor.org/browse/AUCell/ . I don't have access to the repo on bioconductor, so I can't push it myself.

lshep commented 4 months ago

The correct version bump for devel should have been 1.25.1 so version numbers are something we will have to straighten out. Is Sara Aibar sara.aibar@kuleuven.vib.be no longer maintaining the package? Is there a way to have Sara request access be given to you to push changes?