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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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register error in runSCENIC_2_createRegulons #178

Open hsd676 opened 3 years ago

hsd676 commented 3 years ago

I keep getting the "Error in UseMethod("register", x) : "register" has no method "c('MulticoreParam', 'SnowParam', 'BiocParallelParam', 'envRefClass', '.environment', 'refClass', 'environment', 'refObject')" for the target object" error.

I have already tried resetting core parameters = 1. Please help. I am stuck.

runSCENIC_1_coexNetwork2modules(scenicOptions) 20:36 Creating TF modules Number of links between TFs and targets: 3504334 [,1] nTFs 872 nTargets 9437 nGeneSets 4902 nLinks 4257482 runSCENIC_2_createRegulons(scenicOptions, coexMethod=c("top5perTarget")) Error in runSCENIC_2_createRegulons(scenicOptions, coexMethod = c("top5perTarget")) : Parameters are useless, (coexMethod = c("top5perTarget")) runSCENIC_2_createRegulons(scenicOptions) Error in UseMethod("register", x) : "register" has no method "c('MulticoreParam', 'SnowParam', 'BiocParallelParam', 'envRefClass', '.environment', 'refClass', 'environment', 'refObject')" for the target object

Anyone have the same error? Please share your solution, Thank you!

ryrl970311 commented 3 years ago

Has your error been solved?

vida-change commented 2 years ago

Has your error been solved?

JokerOuO commented 8 months ago

I have the same problem. I found was caused by a conflict between the register function of the NMF package and the BiocParallel package. Run detach("package:NMF") before runSCENIC_2_createRegulons function or change register(MulticoreParam(nCores), default = FALSE) to BiocParallel::register(MulticoreParam(nCores), default = FALSE) in the source code.