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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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SummarizedExperiment Error with import10xFeatureMatrix function #2152

Open yojetsharma opened 6 months ago

yojetsharma commented 6 months ago 
> ArrowFiles <- c('eb01.arrow', 'eb02.arrow','eb03.arrow','eb04.arrow')
> archr <- ArchRProject(ArrowFiles) 
Using GeneAnnotation set by addArchRGenome(Hg38)!
Using GeneAnnotation set by addArchRGenome(Hg38)!
Validating Arrows...
Getting SampleNames...
1 2 3 4 
Copying ArrowFiles to Ouptut Directory! If you want to save disk space set copyArrows = FALSE
1 2 3 4 
Getting Cell Metadata...
1 2 3 4 
Merging Cell Metadata...
Initializing ArchRProject...

                                                   / |
                                                 /    \
            .                                  /      |.
            \\\                              /        |.
              \\\                          /           `|.
                \\\                      /              |.
                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|

> seRNA <-
+   import10xFeatureMatrix(
+     input = c(
+       "~/Desktop/yojet/RNA/d149/filtered_feature_bc_matrix.h5",
+       "~/Desktop/yojet/RNA/ls002/filtered_feature_bc_matrix.h5",
+       "~/Desktop/yojet/RNA/ls003/filtered_feature_bc_matrix.h5",
+       "~/Desktop/yojet/RNA/ls004/filtered_feature_bc_matrix.h5"
+     ),
+     names = c('eb01', 'eb02', 'eb03', 'eb04')
+   )
Importing Feature Matrix 1 of 4
Importing Feature Matrix 2 of 4
Importing Feature Matrix 3 of 4
Importing Feature Matrix 4 of 4
Re-ordering RNA matricies for consistency.
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'rep.int': error in evaluating the argument 'x' in selecting a method for function 'runValue': error in evaluating the argument 'x' in selecting a method for function 'seqnames': error in evaluating the argument 'x' in selecting a method for function 'sortSeqlevels': error in evaluating the argument 'x' in selecting a method for function 'seqlevels': unable to find an inherited method for function ‘seqinfo’ for signature ‘"SummarizedExperiment"’
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 

locale:
 [1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8        LC_COLLATE=en_IN.UTF-8     LC_MONETARY=en_IN.UTF-8   
 [6] LC_MESSAGES=en_IN.UTF-8    LC_PAPER=en_IN.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C       

time zone: Asia/Kolkata
tzcode source: system (glibc)

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

other attached packages:
 [1] Rsamtools_2.18.0                  chromVARmotifs_0.2.0              rhdf5_2.46.1                      SummarizedExperiment_1.32.0      
 [5] MatrixGenerics_1.14.0             Rcpp_1.0.12                       matrixStats_1.3.0                 plyr_1.8.9                       
 [9] magrittr_2.0.3                    gtable_0.3.4                      gtools_3.9.5                      gridExtra_2.3                    
[13] ArchR_1.0.2                       reshape2_1.4.4                    tidyr_1.3.1                       clustree_0.5.1                   
[17] ggraph_2.2.1.9000                 BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.2                   rtracklayer_1.62.0               
[21] BiocIO_1.12.0                     Biostrings_2.70.3                 XVector_0.42.0                    CellChat_2.1.2                   
[25] Biobase_2.62.0                    igraph_2.0.3                      data.table_1.15.4                 GenomicRanges_1.54.1             
[29] GenomeInfoDb_1.38.8               IRanges_2.36.0                    S4Vectors_0.40.2                  BiocGenerics_0.48.1              
[33] glmGamPoi_1.14.3                  EnhancedVolcano_1.20.0            ggrepel_0.9.5                     MetBrewer_0.2.0                  
[37] patchwork_1.2.0                   RColorBrewer_1.1-3                future_1.33.2                     ggplot2_3.5.0                    
[41] stringr_1.5.1                     Matrix_1.6-5                      dplyr_1.1.4                       SeuratData_0.2.2.9001            
[45] Seurat_5.0.3                      SeuratObject_5.0.1                sp_2.1-3                         

loaded via a namespace (and not attached):
  [1] spatstat.sparse_3.0-3       bitops_1.0-7                DirichletMultinomial_1.44.0 TFBSTools_1.40.0            httr_1.4.7                 
  [6] doParallel_1.0.17           tools_4.3.3                 sctransform_0.4.1           backports_1.4.1             utf8_1.2.4                 
 [11] R6_2.5.1                    lazyeval_0.2.2              uwot_0.2.1                  rhdf5filters_1.14.1         GetoptLong_1.0.5           
 [16] withr_3.0.0                 progressr_0.14.0            cli_3.6.2                   Cairo_1.6-2                 spatstat.explore_3.2-7     
 [21] fastDummies_1.7.3           network_1.18.2              labeling_0.4.3              sass_0.4.9                  spatstat.data_3.0-4        
 [26] readr_2.1.5                 ggridges_0.5.6              pbapply_1.7-2               systemfonts_1.0.6           R.utils_2.12.3             
 [31] svglite_2.1.3               parallelly_1.37.1           RSQLite_2.3.6               rstudioapi_0.16.0           FNN_1.1.4                  
 [36] generics_0.1.3              shape_1.4.6.1               ica_1.0-3                   spatstat.random_3.2-3       car_3.1-2                  
 [41] GO.db_3.18.0                fansi_1.0.6                 abind_1.4-5                 R.methodsS3_1.8.2           lifecycle_1.0.4            
 [46] yaml_2.3.8                  carData_3.0-5               SparseArray_1.2.4           Rtsne_0.17                  blob_1.2.4                 
 [51] promises_1.3.0              crayon_1.5.2                miniUI_0.1.1.1              lattice_0.22-6              cowplot_1.1.3              
 [56] annotate_1.80.0             KEGGREST_1.42.0             sna_2.7-2                   pillar_1.9.0                knitr_1.46                 
 [61] ComplexHeatmap_2.18.0       rjson_0.2.21                future.apply_1.11.2         codetools_0.2-18            leiden_0.4.3.1             
 [66] glue_1.7.0                  vctrs_0.6.5                 png_0.1-8                   spam_2.10-0                 poweRlaw_0.80.0            
 [71] cachem_1.0.8                xfun_0.43                   S4Arrays_1.2.1              mime_0.12                   tidygraph_1.3.1            
 [76] pracma_2.4.4                coda_0.19-4.1               survival_3.5-8              iterators_1.0.14            fitdistrplus_1.1-11        
 [81] ROCR_1.0-11                 nlme_3.1-164                bit64_4.0.5                 RcppAnnoy_0.0.22            bslib_0.7.0                
 [86] irlba_2.3.5.1               KernSmooth_2.23-22          DBI_1.2.2                   seqLogo_1.68.0              colorspace_2.1-0           
 [91] tidyselect_1.2.1            bit_4.0.5                   compiler_4.3.3              BiocNeighbors_1.20.2        DelayedArray_0.28.0        
 [96] plotly_4.10.4               caTools_1.18.2              scales_1.3.0                lmtest_0.9-40               NMF_0.27                   
[101] rappdirs_0.3.3              digest_0.6.35               goftest_1.2-3               spatstat.utils_3.0-4        htmltools_0.5.8.1          
[106] pkgconfig_2.0.3             fastmap_1.1.1               rlang_1.1.3                 GlobalOptions_0.1.2         htmlwidgets_1.6.4          
[111] shiny_1.8.1.1               farver_2.1.1                jquerylib_0.1.4             zoo_1.8-12                  jsonlite_1.8.8             
[116] BiocParallel_1.36.0         statnet.common_4.9.0        R.oo_1.26.0                 RCurl_1.98-1.14             GenomeInfoDbData_1.2.11    
[121] ggnetwork_0.5.13            dotCall64_1.1-1             Rhdf5lib_1.24.2             munsell_0.5.1               viridis_0.6.5              
[126] reticulate_1.36.0           stringi_1.8.3               ggalluvial_0.12.5           zlibbioc_1.48.2             MASS_7.3-60.0.1            
[131] listenv_0.9.1               CNEr_1.38.0                 deldir_2.0-4                graphlayouts_1.1.1          splines_4.3.3              
[136] tensor_1.5                  hms_1.1.3                   circlize_0.4.16             ggpubr_0.6.0                spatstat.geom_3.2-9        
[141] ggsignif_0.6.4              RcppHNSW_0.6.0              rngtools_1.5.2              TFMPvalue_0.0.9             XML_3.99-0.16.1            
[146] BiocManager_1.30.22         tzdb_0.4.0                  foreach_1.5.2               tweenr_2.0.3                httpuv_1.6.15              
[151] RANN_2.6.1                  purrr_1.0.2                 polyclip_1.10-6             clue_0.3-65                 scattermore_1.2            
[156] gridBase_0.4-7              ggforce_0.4.2               broom_1.0.5                 xtable_1.8-4                restfulr_0.0.15            
[161] RSpectra_0.16-1             rstatix_0.7.2               later_1.3.2                 viridisLite_0.4.2           tibble_3.2.1               
[166] AnnotationDbi_1.64.1        memoise_2.0.1               registry_0.5-1              GenomicAlignments_1.38.2    cluster_2.1.6              
[171] globals_0.16.3
rcorces commented 6 months ago

Hi @yojetsharma! 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.

juliabelk commented 2 months ago

@yojetsharma this sounds similar to an issue I ran into - #2199 may provide some guidance if it is in fact the same issue