peakAnnoEnrichment() Error

[eblchen]

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        

[rcorces]

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.

[alekseybelikov]

https://github.com/GreenleafLab/ArchR/issues/2140#issuecomment-2429357308