Error message during running runSCENIC_3_scoreCells()

[jiuquzjw]

Catched error in AUCell_buildRankings() or in the histogram plot:

[jiuquzjw]

Hello, thanks for this great tool!

When I run 'runSCENIC_3_scoreCells()' with SCENIC version 1.3.1, I got the following error:

Catched error in AUCell_buildRankings() or in the histogram plot: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Error in saveRDS(aucellRankings, file = getIntName(scenicOptions, "aucell_rankings")) :
object 'aucellRankings' not found

What should I do

[MDMotlagh]

@jiuquzjw Hi,
This is a problem with Bioconductor 3.18 and AUCell package. Downgrade Bioconductor to 3.17 and then install AUCell and other packages including SCENIC. This should solve the problem.

[jiuquzjw]

@jiuquzjw Hi, This is a problem with Bioconductor 3.18 and AUCell package. Downgrade Bioconductor to 3.17 and then install AUCell and other packages including SCENIC. This should solve the problem.

Thank you. It really helps.

[PKatarina]

Just an FYI. I am trying to run AUCell_run with the example from the documentation and I get the same error. But I am using R 4.2.1 and Bioconductor 3.16.

I am going to try even older versions of Bioconductor to find if there is some combinaton that works with older versions of R. Any other suggestions are most welcome.

library(AUCell)

# Print session info
print(sessionInfo())

# Fake run of AUCell
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="")))
geneSets <- list(geneSet1=sample(rownames(exprMatrix), 10),
geneSet2=sample(rownames(exprMatrix), 5))
cells_rankings <- AUCell_buildRankings(exprMatrix, plotStats = FALSE)
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5, nCores=1)
selectedThresholds <- rowMeans(getAUC(cells_AUC))
cellsTsne<- Rtsne::Rtsne(t(exprMatrix),max_iter = 10)$Y
# cellsTsne<- tsne::tsne(t(exprMatrix),max_iter = 10)
rownames(cellsTsne) <- colnames(exprMatrix)
######
par(mfrow=c(2,3))
thrs <- AUCell_plotTSNE(tSNE=cellsTsne, exprMat=NULL,
cellsAUC=cells_AUC, thresholds=selectedThresholds,
plots = c("histogram", "binaryAUC", "AUC"))
#####
# Color based on the known phenodata:
cellInfo <- data.frame(cellType1=sample(LETTERS[1:3],ncol(exprMatrix), replace=TRUE),
cellType2=sample(letters[5:7],ncol(exprMatrix), replace=TRUE),
nGenes=abs(rnorm(ncol(exprMatrix))),
row.names=colnames(exprMatrix))
colVars <- list(cellType2=setNames(c("skyblue","magenta", "darkorange"),letters[5:7]))
# dev.off()
plotTsne_cellProps(cellsTsne, cellInfo, colVars=colVars)

version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /apps/spack/opt/spack/linux-centos7-cascadelake/gcc-11.2.0/r-4.2.1-zh3inedhayocwcuck33iojfmatdhhye3/rlib/R/lib/libRblas.so
LAPACK: /apps/spack/opt/spack/linux-centos7-cascadelake/gcc-11.2.0/r-4.2.1-zh3inedhayocwcuck33iojfmatdhhye3/rlib/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=hr_HR.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=hr_HR.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=hr_HR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=hr_HR.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] AUCell_1.20.2

loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.28.0 KEGGREST_1.38.0
[3] lattice_0.22-5 vctrs_0.6.5
[5] htmltools_0.5.7 stats4_4.2.1
[7] blob_1.2.4 XML_3.99-0.16.1
[9] rlang_1.1.3 R.oo_1.26.0
[11] later_1.3.2 DBI_1.2.1
[13] R.utils_2.12.3 BiocGenerics_0.44.0
[15] bit64_4.0.5 matrixStats_1.2.0
[17] GenomeInfoDbData_1.2.9 lifecycle_1.0.4
[19] zlibbioc_1.44.0 MatrixGenerics_1.10.0
[21] Biostrings_2.66.0 R.methodsS3_1.8.2
[23] memoise_2.0.1 Biobase_2.58.0
[25] IRanges_2.32.0 fastmap_1.1.1
[27] httpuv_1.6.14 GenomeInfoDb_1.34.9
[29] AnnotationDbi_1.60.2 GSEABase_1.60.0
[31] Rcpp_1.0.12 xtable_1.8-4
[33] promises_1.2.1 cachem_1.0.8
[35] DelayedArray_0.24.0 S4Vectors_0.36.2
[37] graph_1.76.0 annotate_1.76.0
[39] XVector_0.38.0 mime_0.12
[41] bit_4.0.5 png_0.1-8
[43] digest_0.6.34 shiny_1.8.0
[45] GenomicRanges_1.50.2 grid_4.2.1
[47] cli_3.6.2 tools_4.2.1
[49] bitops_1.0-7 magrittr_2.0.3
[51] RCurl_1.98-1.14 RSQLite_2.3.5
[53] crayon_1.5.2 ellipsis_0.3.2
[55] Matrix_1.6-5 data.table_1.15.0
[57] DelayedMatrixStats_1.20.0 sparseMatrixStats_1.10.0
[59] httr_1.4.7 R6_2.5.1
[61] compiler_4.2.1
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Execution halted

[zhangbaobao123-abc]

Hello, thanks for this great tool!

When I run 'runSCENIC_3_scoreCells()' with SCENIC version 1.3.1, I got the following error:

Catched error in AUCell_buildRankings() or in the histogram plot: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. Error in saveRDS(aucellRankings, file = getIntName(scenicOptions, "aucell_rankings")) : object 'aucellRankings' not found

What should I do

hi，i have same problem same as you.if you have solved it. "Can you tell me the version of the AUCell package?

[PKatarina]

The problem is not with AUCell but matrixStats. My sys-admin solved it for me so I don't have the details but this worked in another case I got the same error remotes::install_version("matrixStats", version="1.1.0") # restart your session and run previous scripts Good luck

…

On Fri, Jun 21, 2024 at 3:52 PM zhangbaobao123-abc ***@***.***> wrote: Hello, thanks for this great tool! When I run 'runSCENIC_3_scoreCells()' with SCENIC version 1.3.1, I got the following error: Catched error in AUCell_buildRankings() or in the histogram plot: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. Error in saveRDS(aucellRankings, file = getIntName(scenicOptions, "aucell_rankings")) : object 'aucellRankings' not found What should I do hi，i have same problem same as you.if you have solved it. "Can you tell me the version of the AUCell package? — Reply to this email directly, view it on GitHub <#439 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AK2UYJTCGTF5GALC3WG2JKDZIQVYVAVCNFSM6AAAAABCAMEE4KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBSG44TQMRXGA> . You are receiving this because you commented.Message ID: ***@***.***>