ArchR
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20 hours ago •
GreenleafLab
GreenleafLab
SummarizedExperiment Error with import10xFeatureMatrix function
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> 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
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.
@yojetsharma this sounds similar to an issue I ran into - #2199 may provide some guidance if it is in fact the same issue
