ArchR
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Published
20 hours ago •
GreenleafLab
GreenleafLab
peakAnnoEnrichment() Error
Error running peakAnnoEnrichment()
> motifs.neg <- peakAnnoEnrichment(
+ seMarker = tumour.normal.sample,
+ ArchRProj = patient.project,
+ peakAnnotation = "Motif",
+ cutOff = "FDR <= 0.05 & Log2FC <= -1")
ArchR logging to : ArchRLogs/ArchR-peakAnnoEnrichment-3fec4a854be7-Date-2024-08-16_Time-14-14-42.584608.log
If there is an issue, please report to github with logFile!
2024-08-16 14:14:47.061325 : Computing Enrichments 1 of 1, 0.075 mins elapsed.
Error in .local(x, na.rm, dims, ...) :
object 'CRsparse_colSums' not found
Session info:
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] parallel stats4 grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] motifmatchr_1.24.0 chromVARmotifs_0.2.0 BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.2
[5] rtracklayer_1.62.0 BiocIO_1.12.0 Biostrings_2.70.3 XVector_0.42.0
[9] viridis_0.6.5 viridisLite_0.4.2 Signac_1.13.0 Seurat_5.1.0
[13] SeuratObject_5.0.2 sp_2.1-4 rhdf5_2.46.1 SummarizedExperiment_1.32.0
[17] Biobase_2.62.0 MatrixGenerics_1.14.0 Rcpp_1.0.13 Matrix_1.6-5
[21] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 IRanges_2.36.0 S4Vectors_0.40.2
[25] BiocGenerics_0.48.1 matrixStats_1.3.0 data.table_1.15.4 stringr_1.5.1
[29] plyr_1.8.9 magrittr_2.0.3 ggplot2_3.4.2 gtable_0.3.5
[33] gtools_3.9.5 gridExtra_2.3 ArchR_1.0.2
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.3.3 later_1.3.2 bitops_1.0-8 R.oo_1.26.0
[6] tibble_3.2.1 polyclip_1.10-7 DirichletMultinomial_1.44.0 XML_3.99-0.17 fastDummies_1.7.3
[11] lifecycle_1.0.4 globals_0.16.3 lattice_0.22-5 MASS_7.3-60.0.1 plotly_4.10.4
[16] yaml_2.3.10 httpuv_1.6.15 sctransform_0.4.1 spam_2.10-0 spatstat.sparse_3.1-0
[21] reticulate_1.37.0 CNEr_1.38.0 DBI_1.2.3 cowplot_1.1.3 pbapply_1.7-2
[26] RColorBrewer_1.1-3 abind_1.4-5 zlibbioc_1.48.2 Rtsne_0.17 R.utils_2.12.3
[31] purrr_1.0.2 RCurl_1.98-1.16 pracma_2.4.4 GenomeInfoDbData_1.2.11 ggrepel_0.9.5
[36] irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.0-5 seqLogo_1.68.0 goftest_1.2-3
[41] RSpectra_0.16-2 annotate_1.80.0 spatstat.random_3.3-1 fitdistrplus_1.2-1 parallelly_1.38.0
[46] leiden_0.4.3.1 codetools_0.2-19 DelayedArray_0.28.0 RcppRoll_0.3.1 tidyselect_1.2.1
[51] spatstat.explore_3.3-1 GenomicAlignments_1.38.2 jsonlite_1.8.8 progressr_0.14.0 ggridges_0.5.6
[56] survival_3.5-8 tools_4.3.3 TFMPvalue_0.0.9 ica_1.0-3 glue_1.7.0
[61] SparseArray_1.2.4 dplyr_1.1.4 withr_3.0.1 fastmap_1.2.0 rhdf5filters_1.14.1
[66] fansi_1.0.6 caTools_1.18.2 digest_0.6.36 R6_2.5.1 mime_0.12
[71] colorspace_2.1-1 GO.db_3.18.0 scattermore_1.2 Cairo_1.6-2 poweRlaw_0.80.0
[76] tensor_1.5 spatstat.data_3.1-2 RSQLite_2.3.7 R.methodsS3_1.8.2 utf8_1.2.4
[81] tidyr_1.3.1 generics_0.1.3 httr_1.4.7 htmlwidgets_1.6.4 S4Arrays_1.2.1
[86] TFBSTools_1.40.0 uwot_0.2.2 pkgconfig_2.0.3 blob_1.2.4 lmtest_0.9-40
[91] htmltools_0.5.8.1 dotCall64_1.1-1 scales_1.3.0 png_0.1-8 spatstat.univar_3.0-0
[96] rstudioapi_0.16.0 tzdb_0.4.0 reshape2_1.4.4 rjson_0.2.21 nlme_3.1-164
[101] cachem_1.1.0 zoo_1.8-12 KernSmooth_2.23-22 miniUI_0.1.1.1 AnnotationDbi_1.64.1
[106] restfulr_0.0.15 pillar_1.9.0 vctrs_0.6.5 RANN_2.6.1 promises_1.3.0
[111] xtable_1.8-4 cluster_2.1.6 readr_2.1.5 cli_3.6.3 compiler_4.3.3
[116] Rsamtools_2.18.0 rlang_1.1.4 crayon_1.5.3 future.apply_1.11.2 stringi_1.8.4
[121] deldir_2.0-4 BiocParallel_1.36.0 munsell_0.5.1 lazyeval_0.2.2 spatstat.geom_3.3-2
[126] RcppHNSW_0.6.0 hms_1.1.3 patchwork_1.2.0 bit64_4.0.5 future_1.34.0
[131] Rhdf5lib_1.24.2 KEGGREST_1.42.0 shiny_1.9.1 ROCR_1.0-11 memoise_2.0.1
[136] igraph_2.0.3 fastmatch_1.1-4 bit_4.0.5
Hi @eblchen! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.
https://github.com/GreenleafLab/ArchR/issues/2140#issuecomment-2429357308
