RcisTarget::addSignificantGenes error

[ysu2015]

Hi RcisTarget,

I got errors when running "RcisTarget::addSignificantGenes" by following the tutorial posted on "https://www.bioconductor.org/packages/release/bioc/vignettes/RcisTarget/inst/doc/RcisTarget_MainTutorial.html#Running_RcisTarget".
my script (and the results not the same as the tutorial):
txtFile <- paste(file.path(system.file('examples', package='RcisTarget')),
"hypoxiaGeneSet.txt", sep="/")
geneLists <- list(hypoxia=read.table(txtFile, stringsAsFactors=FALSE)[,1])
head(geneLists$hypoxia)
motifRankings <- importRankings("mc_v10_clust/gene_based/hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather")

data(motifAnnotations_hgnc)
motifAnnotations_hgnc[199:202,]
(my results is the same as shown in the tutorial)

motif	TF	directAnnotation	inferred_Orthology	inferred_MotifSimil	annotationSource
bergman__tin	NKX2-8	FALSE	TRUE	TRUE	inferredBy_MotifSimilarity_n_Orthology
bergman__tll	DUX4	FALSE	FALSE	TRUE	inferredBy_MotifSimilarity
bergman__tll	NR2E1	FALSE	TRUE	FALSE	inferredBy_Orthology
bergman__usp	RXRA	FALSE	TRUE	FALSE	inferredBy_Orthology

4 rows | 1-6 of 7 columns

###############################
motifs_AUC <- calcAUC(geneLists, motifRankings, nCores=1)
motifEnrichmentTable <- addMotifAnnotation(
motifs_AUC,
nesThreshold=3,
motifAnnot=motifAnnotations_hgnc,
highlightTFs=list(hypoxia=c("HIF1A", "EPAS1")))

class(motifEnrichmentTable)
[1] "data.table" "data.frame"

dim(motifEnrichmentTable)
[1] 24 8

head(motifEnrichmentTable[,-"TF_lowConf", with=FALSE]) (not the same as tutorial)

geneSet	motif	NES	AUC	highlightedTFs	TFinDB	TF_highConf
hypoxia	23459	4.13	0.0667	HIF1A, EPAS1
hypoxia	19265	3.91	0.0643	HIF1A, EPAS1
hypoxia	10830	3.58	0.0608	HIF1A, EPAS1
hypoxia	10469	3.42	0.0591	HIF1A, EPAS1
hypoxia	18527	3.41	0.0590	HIF1A, EPAS1
hypoxia	19969	3.38	0.0586	HIF1A, EPAS1

6 rows

follow the solution suggested by "jdenavascues" (Thanks a lot!!)
motifRankings@rankings <- dplyr::relocate(motifRankings@rankings, motifs)

and then it still did not go through.
motifEnrichmentTable_wGenes <- addSignificantGenes(motifEnrichmentTable,
geneSets=geneLists,
rankings=motifRankings,
nCores=1,
method="iCisTarget")

[1] 27090
Error in rccs[, sr] : subscript out of bounds

I have noticed that some users are having trouble with RcisTarget, especially regarding the different versions of the database.
Does anyone figure these out?

Y