RunChromVAR() error when computing deviations from background

[annaestevecodina]

Dear all,

I am encountering this error when running:
seurat_all <- RunChromVAR( object = seurat_all, genome = BSgenome.Mmusculus.UCSC.mm10 )

Computing GC bias per region
Selecting background regions
Computing deviations from background
Error in names(res) <- *vtmp* :
'names' attribute [107] must be the same length as the vector [53]

sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252
system code page: 65001

attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] motifmatchr_1.16.0 JASPAR2020_0.99.10 TFBSTools_1.32.0 chromVAR_1.16.0
[5] presto_1.0.0 data.table_1.14.2 devtools_2.4.3 usethis_2.1.5
[9] harmony_0.1.0 Rcpp_1.0.8 UpSetR_1.4.0 viridis_0.6.2
[13] viridisLite_0.4.0 RColorBrewer_1.1-2 slingshot_2.2.0 TrajectoryUtils_1.2.0
[17] princurve_2.1.6 tradeSeq_1.8.0 biomaRt_2.50.2 fgsea_1.20.0
[21] biovizBase_1.42.0 BSgenome.Mmusculus.UCSC.mm10_1.4.3 BSgenome_1.62.0 rtracklayer_1.54.0
[25] Biostrings_2.62.0 XVector_0.34.0 EnsDb.Mmusculus.v79_2.99.0 Signac_1.5.0
[29] gridExtra_2.3 shiny_1.7.1 ReactomeGSA_1.8.0 Repitools_1.40.0
[33] scales_1.1.1 ensembldb_2.18.2 AnnotationFilter_1.18.0 GenomicFeatures_1.46.3
[37] AnnotationDbi_1.56.2 AnnotationHub_3.2.0 BiocFileCache_2.2.0 dbplyr_2.1.1
[41] scater_1.22.0 scuttle_1.4.0 SingleCellExperiment_1.16.0 VennDiagram_1.7.1
[45] futile.logger_1.4.3 cowplot_1.1.1 enrichR_3.0 SingleR_1.8.0
[49] celldex_1.4.0 SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.1
[53] GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.3 BiocGenerics_0.40.0
[57] MatrixGenerics_1.6.0 matrixStats_0.61.0 limma_3.50.0 patchwork_1.1.1
[61] Matrix_1.3-4 ggpubr_0.4.0 forcats_0.5.1 stringr_1.4.0
[65] dplyr_1.0.7 purrr_0.3.4 readr_2.1.1 tidyr_1.1.4
[69] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1 SeuratObject_4.0.4
[73] Seurat_4.1.0

loaded via a namespace (and not attached):
[1] rsvd_1.0.5 Hmisc_4.6-0 ica_1.0-2 RcppRoll_0.3.0
[5] ps_1.6.0 Rsamtools_2.10.0 rprojroot_2.0.2 lmtest_0.9-39
[9] crayon_1.4.2 spatstat.core_2.3-2 MASS_7.3-54 nlme_3.1-153
[13] backports_1.4.1 qlcMatrix_0.9.7 reprex_2.0.1 rlang_1.0.0
[17] ROCR_1.0-11 readxl_1.3.1 irlba_2.3.5 callr_3.7.0
[21] filelock_1.0.2 BiocParallel_1.28.3 rjson_0.2.21 CNEr_1.30.0
[25] bit64_4.0.5 glue_1.6.1 poweRlaw_0.70.6 sctransform_0.3.3
[29] processx_3.5.2 parallel_4.1.2 vipor_0.4.5 spatstat.sparse_2.1-0
[33] vsn_3.62.0 spatstat.geom_2.3-1 haven_2.4.3 tidyselect_1.1.1
[37] fitdistrplus_1.1-6 XML_3.99-0.8 zoo_1.8-9 GenomicAlignments_1.30.0
[41] xtable_1.8-4 magrittr_2.0.2 cli_3.1.1 zlibbioc_1.40.0
[45] rstudioapi_0.13 miniUI_0.1.1.1 rpart_4.1-15 fastmatch_1.1-3
[49] lambda.r_1.2.4 BiocSingular_1.10.0 xfun_0.29 pkgbuild_1.3.1
[53] cluster_2.1.2 caTools_1.18.2 KEGGREST_1.34.0 interactiveDisplayBase_1.32.0
[57] ggrepel_0.9.1 listenv_0.8.0 TFMPvalue_0.0.8 png_0.1-7
[61] future_1.23.0 withr_2.4.3 lsa_0.73.2 bitops_1.0-7
[65] slam_0.1-50 ggforce_0.3.3 plyr_1.8.6 cellranger_1.1.0
[69] sparsesvd_0.2 pracma_2.3.6 pillar_1.6.5 gplots_3.1.1
[73] cachem_1.0.6 fs_1.5.2 DelayedMatrixStats_1.16.0 vctrs_0.3.8
[77] ellipsis_0.3.2 generics_0.1.1 tools_4.1.2 foreign_0.8-81
[81] beeswarm_0.4.0 munsell_0.5.0 tweenr_1.0.2 DelayedArray_0.20.0
[85] pkgload_1.2.4 fastmap_1.1.0 compiler_4.1.2 abind_1.4-5
[89] httpuv_1.6.5 Ringo_1.58.0 ExperimentHub_2.2.1 sessioninfo_1.2.2
[93] plotly_4.10.0 GenomeInfoDbData_1.2.7 DNAcopy_1.68.0 edgeR_3.36.0
[97] lattice_0.20-45 deldir_1.0-6 snow_0.4-4 utf8_1.2.2
[101] later_1.3.0 jsonlite_1.7.3 affy_1.72.0 docopt_0.7.1
[105] ScaledMatrix_1.2.0 pbapply_1.5-0 carData_3.0-5 sparseMatrixStats_1.6.0
[109] nabor_0.5.0 genefilter_1.76.0 lazyeval_0.2.2 promises_1.2.0.1
[113] car_3.0-12 R.utils_2.11.0 latticeExtra_0.6-29 goftest_1.2-3
[117] spatstat.utils_2.3-0 reticulate_1.24 checkmate_2.0.0 Rtsne_0.15
[121] dichromat_2.0-0 uwot_0.1.11 igraph_1.2.11 survival_3.2-13
[125] yaml_2.2.2 htmltools_0.5.2 memoise_2.0.1 VariantAnnotation_1.40.0
[129] BiocIO_1.4.0 locfit_1.5-9.4 gsmoothr_0.1.7 digest_0.6.29
[133] assertthat_0.2.1 mime_0.12 rappdirs_0.3.3 futile.options_1.0.1
[137] RSQLite_2.2.9 future.apply_1.8.1 remotes_2.4.2 blob_1.2.2
[141] R.oo_1.24.0 preprocessCore_1.56.0 labeling_0.4.2 splines_4.1.2
[145] Formula_1.2-4 ProtGenerics_1.26.0 RCurl_1.98-1.5 broom_0.7.11
[149] hms_1.1.1 modelr_0.1.8 colorspace_2.0-2 base64enc_0.1-3
[153] BiocManager_1.30.16 ggbeeswarm_0.6.0 nnet_7.3-16 RANN_2.6.1
[157] ggseqlogo_0.1 fansi_1.0.2 tzdb_0.2.0 brio_1.1.3
[161] truncnorm_1.0-8 parallelly_1.30.0 SnowballC_0.7.0 R6_2.5.1
[165] ggridges_0.5.3 lifecycle_1.0.1 formatR_1.11 curl_4.3.2
[169] ggsignif_0.6.3 affyio_1.64.0 testthat_3.1.2 leiden_0.3.9
[173] desc_1.4.0 RcppAnnoy_0.0.19 htmlwidgets_1.5.4 beachmat_2.10.0
[177] polyclip_1.10-0 seqLogo_1.60.0 rvest_1.0.2 mgcv_1.8-38
[181] globals_0.14.0 htmlTable_2.4.0 codetools_0.2-18 lubridate_1.8.0
[185] GO.db_3.14.0 gtools_3.9.2 prettyunits_1.1.1 R.methodsS3_1.8.1
[189] RSpectra_0.16-0 gtable_0.3.0 DBI_1.1.2 tensor_1.5
[193] httr_1.4.2 KernSmooth_2.23-20 stringi_1.7.6 progress_1.2.2
[197] reshape2_1.4.4 farver_2.1.0 annotate_1.72.0 DT_0.20
[201] xml2_1.3.3 BiocNeighbors_1.12.0 restfulr_0.0.13 scattermore_0.7
[205] BiocVersion_3.14.0 bit_4.0.4 jpeg_0.1-9 spatstat.data_2.1-2
[209] pkgconfig_2.0.3 DirichletMultinomial_1.36.0 rstatix_0.7.0 Rsolnp_1.16
[213] knitr_1.37