Valid 'mctype': 'snow' or 'doMC'
XiaofeiSunUCSF opened this issue · comments
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'
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.
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!
save error with aucell 1.12.0
conda list |grep aucell
bioconductor-aucell 1.12.0 r40_0 bioconda
AUCell 1.12.0 on Bioconductor not work
AUCell 1.13.0 install from GitHub works
I can confirm that it only works with the AUCell 1.13 from GitHub.
Double confirm again, only AUCell 1.13.0 installed from Github works.
AUCell 1.13.1 installed from GItHub still works
AUCell 1.13.3 from GitHub didn't work ...
AUCell 1.13.3 from GitHub works for me after restarting R
AUCell 1.13.3 from GitHub didn't work ...
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