XiaofeiSunUCSF commented 3 years ago

Hi, Thank you for this wonderful package. I got one error while running the code, could you please help me figure it out?

Error in .AUCell_calcAUC(geneSets = geneSets, rankings = rankings, nCores = nCores, : Valid 'mctype': 'snow' or 'doMC'

fchen365 commented 3 years ago

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wzcaltech commented 3 years ago

same here, I use to be able to run SCENIC earlier this year (April-May) and didn't encounter this issue. Now I see the same error as described above.

s-aibar commented 3 years ago

Hello,

Sorry, that was a bug that was introduced in one of the previous releases from AUCell. It should now be corrected, but you might still have that version.

To solve it, just install the new version:

BiocManager::install("AUCell")
packageVersion("AUCell")

If it installs a version older than 1.12 (might be determined by Bioconductor based on your R version), then you can try installing the latest version directly from Github: devtools::install_github("aertslab/AUCell")

Then the error should be fixed:

set.seed(123)
exprMatrix <- matrix(data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
                     nrow=20, 
                     dimnames=list(paste("Gene", 1:20, sep=""), 
                                   paste("Cell", 1:500, sep="")))
cells_rankings <- AUCell_buildRankings(exprMatrix, nCores=2)

fewGenes <- sample(rownames(exprMatrix), 10)
cells_AUC <- AUCell_calcAUC(fewGenes, cells_rankings, aucMaxRank=5, nCores=2)

Sorry for the inconvenience!

Lix1993 commented 3 years ago

save error with aucell 1.12.0

conda list |grep aucell
bioconductor-aucell       1.12.0                    r40_0    bioconda

liuyifang commented 3 years ago

AUCell 1.12.0 on Bioconductor not work AUCell 1.13.0 install from GitHub works

Florian411 commented 3 years ago

I can confirm that it only works with the AUCell 1.13 from GitHub.

rsggsr commented 3 years ago

Double confirm again, only AUCell 1.13.0 installed from Github works.

mlbfalchetti commented 3 years ago

AUCell 1.13.1 installed from GItHub still works

martin-jeremy commented 3 years ago

AUCell 1.13.3 from GitHub didn't work ...

dxw5099 commented 3 years ago

AUCell 1.13.3 from GitHub works for me after restarting R

AUCell 1.13.3 from GitHub didn't work ...

xf78 commented 3 years ago

hi @Florian411 ,where can I download AUCell 1.13.0,i can not find AUCell 1.13.0 in https://github.com/aertslab/AUCell,thanks

aertslab / AUCell

Valid 'mctype': 'snow' or 'doMC' #10

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