bwlewis
AddDoubletScore in ArchR throws error irlba : <simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'as_cholmod_sparse' not provided by package 'Matrix'>
Hey. I have the same error showing up. Please note that i have run ArchR on the same dataset previously and it had worked. Here is the error and the sessioninfo along with output of the logfile. I get the error when i try to run DoubletScores. Please note, i have tried installing RSpectre, tried using 1 thread and nothing has worked so far. Please help me..
The error :
2024-02-22 17:07:55 : ERROR Found in .computeLSI for LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log
<simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'as_cholmod_sparse' not provided by package 'Matrix'>
2024-02-22 17:07:55 : ERROR Found in .LSIPartialMatrix for LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log
<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
2024-02-22 17:07:55 : ERROR Found in addIterativeLSI for Sample1 (1 of 5) : LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log
<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), : Exiting See Error Above
Here is the sessioninfo()
─ Session info ─────────────────────────────────────────────────────────────────────── setting value version R version 4.2.3 (2023-03-15) os macOS Big Sur 11.0.1 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/New_York date 2024-02-22 rstudio 2023.03.0+386 Cherry Blossom (desktop) pandoc 2.11.3.2 @ /usr/local/bin/pandoc
─ Packages ─────────────────────────────────────────────────────────────────────────── package * version date (UTC) lib source ArchR * 1.0.3 2023-11-08 [1] Github (https://github.com/GreenleafLab/ArchR/commit/65968a4) Biobase * 2.58.0 2022-11-01 [1] Bioconductor BiocGenerics * 0.44.0 2022-11-01 [1] Bioconductor BiocIO 1.8.0 2022-11-01 [1] Bioconductor BiocManager 1.30.22 2023-08-08 [1] CRAN (R 4.2.0) BiocParallel 1.32.6 2023-03-17 [1] Bioconductor Biostrings * 2.66.0 2022-11-01 [1] Bioconductor bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0) BSgenome * 1.66.3 2023-02-16 [1] Bioconductor BSgenome.Hsapiens.UCSC.hg38 * 1.4.5 2023-07-11 [1] Bioconductor cachem 1.0.8 2023-05-01 [1] CRAN (R 4.2.0) Cairo 1.6-2 2023-11-28 [1] CRAN (R 4.2.3) cli 3.6.2 2023-12-11 [1] CRAN (R 4.2.3) codetools 0.2-19 2023-02-01 [1] CRAN (R 4.2.3) colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0) crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0) data.table * 1.15.0 2024-01-30 [1] CRAN (R 4.2.3) DelayedArray 0.24.0 2022-11-01 [1] Bioconductor devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.2.0) digest 0.6.34 2024-01-11 [1] CRAN (R 4.2.3) dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.2.3) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) fansi 1.0.6 2023-12-08 [1] CRAN (R 4.2.3) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.2.0) fs 1.6.3 2023-07-20 [1] CRAN (R 4.2.0) generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0) GenomeInfoDb * 1.34.9 2023-02-02 [1] Bioconductor GenomeInfoDbData 1.2.9 2023-03-26 [1] Bioconductor GenomicAlignments 1.34.1 2023-03-09 [1] Bioconductor GenomicRanges * 1.50.2 2022-12-16 [1] Bioconductor ggplot2 * 3.4.4 2023-10-12 [1] CRAN (R 4.2.0) glue 1.7.0 2024-01-09 [1] CRAN (R 4.2.3) gridExtra * 2.3 2017-09-09 [1] CRAN (R 4.2.0) gtable * 0.3.4 2023-08-21 [1] CRAN (R 4.2.0) gtools * 3.9.5 2023-11-20 [1] CRAN (R 4.2.3) htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.2.3) htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.2.3) httpuv 1.6.14 2024-01-26 [1] CRAN (R 4.2.3) IRanges * 2.32.0 2022-11-01 [1] Bioconductor irlba * 2.3.5.1 2022-10-03 [1] CRAN (R 4.2.0) later 1.3.2 2023-12-06 [1] CRAN (R 4.2.3) lattice 0.22-5 2023-10-24 [1] CRAN (R 4.2.3) lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.2.3) magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) Matrix * 1.6-4 2023-11-30 [1] CRAN (R 4.2.0) MatrixGenerics * 1.10.0 2022-11-01 [1] Bioconductor matrixStats * 1.2.0 2023-12-11 [1] CRAN (R 4.2.0) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0) mime 0.12 2021-09-28 [1] CRAN (R 4.2.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0) pillar 1.9.0 2023-03-22 [1] CRAN (R 4.2.0) pkgbuild 1.4.3 2023-12-10 [1] CRAN (R 4.2.3) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.2.3) plyr * 1.8.9 2023-10-02 [1] CRAN (R 4.2.0) profvis 0.3.8 2023-05-02 [1] CRAN (R 4.2.0) promises 1.2.1 2023-08-10 [1] CRAN (R 4.2.0) purrr 1.0.2 2023-08-10 [1] CRAN (R 4.2.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) Rcpp * 1.0.12 2024-01-09 [1] CRAN (R 4.2.3) RcppArmadillo * 0.12.6.6.1 2023-12-04 [1] CRAN (R 4.2.0) RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.2.3) remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.2.0) restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.2.0) rhdf5 * 2.42.1 2023-04-07 [1] Bioconductor rhdf5filters 1.10.1 2023-03-24 [1] Bioconductor Rhdf5lib 1.20.0 2022-11-01 [1] Bioconductor rjson 0.2.21 2022-01-09 [1] CRAN (R 4.2.0) rlang 1.1.3 2024-01-10 [1] CRAN (R 4.2.3) Rsamtools * 2.14.0 2022-11-01 [1] Bioconductor RSpectra * 0.16-1 2022-04-24 [1] CRAN (R 4.2.0) rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.2.0) rtracklayer * 1.58.0 2022-11-01 [1] Bioconductor S4Vectors * 0.36.2 2023-02-26 [1] Bioconductor scales 1.3.0 2023-11-28 [1] CRAN (R 4.2.3) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) shiny 1.8.0 2023-11-17 [1] CRAN (R 4.2.3) sparseMatrixStats * 1.10.0 2022-11-01 [1] Bioconductor stringi 1.8.3 2023-12-11 [1] CRAN (R 4.2.3) stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.2.3) SummarizedExperiment * 1.28.0 2022-11-01 [1] Bioconductor tibble 3.2.1 2023-03-20 [1] CRAN (R 4.2.0) tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0) urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0) usethis * 2.2.2 2023-07-06 [1] CRAN (R 4.2.0) utf8 1.2.4 2023-10-22 [1] CRAN (R 4.2.3) vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.2.3) withr 3.0.0 2024-01-16 [1] CRAN (R 4.2.3) XML 3.99-0.16.1 2024-01-22 [1] CRAN (R 4.2.3) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0) XVector * 0.38.0 2022-11-01 [1] Bioconductor yaml 2.3.8 2023-12-11 [1] CRAN (R 4.2.3) zlibbioc 1.44.0 2022-11-01 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
──────────────────────────────────────────────────────────────────────────────────────
And here is the output of the logfile
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \___ | ----.| | | | | |\ \\___. /__/ \__\ | _| .| _||| || | _| `._____|
Logging With ArchR!
Start Time : 2024-02-22 17:07:46
------- ArchR Info
ArchRThreads = 1 ArchRGenome = Hg38
------- System Info
Computer OS = unix
------- Session Info
R version 4.2.3 (2023-03-15) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.0.1
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
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
attached base packages: [1] stats4 grid stats graphics grDevices utils datasets methods [9] base
other attached packages: [1] Rsamtools_2.14.0 BSgenome.Hsapiens.UCSC.hg38_1.4.5 [3] BSgenome_1.66.3 rtracklayer_1.58.0 [5] Biostrings_2.66.0 XVector_0.38.0 [7] rhdf5_2.42.1 SummarizedExperiment_1.28.0 [9] Biobase_2.58.0 RcppArmadillo_0.12.6.6.1 [11] Rcpp_1.0.12 GenomicRanges_1.50.2 [13] GenomeInfoDb_1.34.9 IRanges_2.32.0 [15] S4Vectors_0.36.2 BiocGenerics_0.44.0 [17] sparseMatrixStats_1.10.0 MatrixGenerics_1.10.0 [19] matrixStats_1.2.0 data.table_1.15.0 [21] stringr_1.5.1 plyr_1.8.9 [23] magrittr_2.0.3 ggplot2_3.4.4 [25] gtable_0.3.4 gtools_3.9.5 [27] gridExtra_2.3 devtools_2.4.5 [29] usethis_2.2.2 ArchR_1.0.3 [31] RSpectra_0.16-1 irlba_2.3.5.1 [33] Matrix_1.6-4
loaded via a namespace (and not attached): [1] bitops_1.0-7 fs_1.6.3 tools_4.2.3 [4] profvis_0.3.8 utf8_1.2.4 R6_2.5.1 [7] colorspace_2.1-0 rhdf5filters_1.10.1 urlchecker_1.0.1 [10] withr_3.0.0 tidyselect_1.2.0 compiler_4.2.3 [13] cli_3.6.2 Cairo_1.6-2 DelayedArray_0.24.0 [16] scales_1.3.0 digest_0.6.34 pkgconfig_2.0.3 [19] htmltools_0.5.7 sessioninfo_1.2.2 fastmap_1.1.1 [22] htmlwidgets_1.6.4 rlang_1.1.3 rstudioapi_0.15.0 [25] shiny_1.8.0 BiocIO_1.8.0 generics_0.1.3 [28] BiocParallel_1.32.6 dplyr_1.1.4 RCurl_1.98-1.14 [31] GenomeInfoDbData_1.2.9 munsell_0.5.0 Rhdf5lib_1.20.0 [34] fansi_1.0.6 lifecycle_1.0.4 yaml_2.3.8 [37] stringi_1.8.3 zlibbioc_1.44.0 pkgbuild_1.4.3 [40] parallel_4.2.3 promises_1.2.1 crayon_1.5.2 [43] miniUI_0.1.1.1 lattice_0.22-5 pillar_1.9.0 [46] rjson_0.2.21 codetools_0.2-19 pkgload_1.3.4 [49] XML_3.99-0.16.1 glue_1.7.0 remotes_2.4.2.1 [52] BiocManager_1.30.22 vctrs_0.6.5 httpuv_1.6.14 [55] purrr_1.0.2 cachem_1.0.8 mime_0.12 [58] xtable_1.8-4 restfulr_0.0.15 later_1.3.2 [61] tibble_3.2.1 GenomicAlignments_1.34.1 memoise_2.0.1 [64] ellipsis_0.3.2
------- Log Info
2024-02-22 17:07:46 : addDoubletScores Input-Parameters, Class = list
addDoubletScores Input-Parameters$input: length = 5 [1] "Sample1.arrow" "Sample2.arrow" "Sample3.arrow" [4] "Sample4.arrow" "Sample5.arrow"
addDoubletScores Input-Parameters$useMatrix: length = 1 [1] "TileMatrix"
addDoubletScores Input-Parameters$k: length = 1 [1] 10
addDoubletScores Input-Parameters$nTrials: length = 1 [1] 5
addDoubletScores Input-Parameters$dimsToUse: length = 30 [1] 1 2 3 4 5 6
addDoubletScores Input-Parameters$LSIMethod: length = 1 [1] 1
addDoubletScores Input-Parameters$scaleDims: length = 1 [1] FALSE
addDoubletScores Input-Parameters$corCutOff: length = 1 [1] 0.75
addDoubletScores Input-Parameters$knnMethod: length = 1 [1] "UMAP"
addDoubletScores Input-Parameters$outDir: length = 1 [1] "QualityControl"
addDoubletScores Input-Parameters$threads: length = 1 [1] 1
addDoubletScores Input-Parameters$force: length = 1 [1] FALSE
addDoubletScores Input-Parameters$parallelParam: length = 0 NULL
addDoubletScores Input-Parameters$verbose: length = 1 [1] TRUE
addDoubletScores Input-Parameters$logFile: length = 1 [1] "ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"
2024-02-22 17:07:46 : Batch Execution w/ safelapply!, 0 mins elapsed. 2024-02-22 17:07:46 : Sample1(1 of 5) : Computing Doublet Statistics, 0 mins elapsed. 2024-02-22 17:07:46 : Running IterativeLSI, 0.004 mins elapsed.
2024-02-22 17:07:46 : IterativeLSI Input-Parameters, Class = list
IterativeLSI Input-Parameters$ArchRProj: length = 1
IterativeLSI Input-Parameters$useMatrix: length = 1 [1] "TileMatrix"
IterativeLSI Input-Parameters$name: length = 1 [1] "IterativeLSI"
IterativeLSI Input-Parameters$iterations: length = 1 [1] 2
IterativeLSI Input-Parameters$firstSelection: length = 1 [1] "top"
IterativeLSI Input-Parameters$depthCol: length = 1 [1] "nFrags"
IterativeLSI Input-Parameters$varFeatures: length = 1 [1] 25000
IterativeLSI Input-Parameters$dimsToUse: length = 30 [1] 1 2 3 4 5 6
IterativeLSI Input-Parameters$LSIMethod: length = 1 [1] 1
IterativeLSI Input-Parameters$scaleDims: length = 1 [1] FALSE
IterativeLSI Input-Parameters$corCutOff: length = 1 [1] 0.75
IterativeLSI Input-Parameters$binarize: length = 1 [1] TRUE
IterativeLSI Input-Parameters$outlierQuantiles: length = 0 NULL
IterativeLSI Input-Parameters$filterBias: length = 1 [1] FALSE
IterativeLSI Input-Parameters$sampleCellsPre: length = 1 [1] 10000
IterativeLSI Input-Parameters$projectCellsPre: length = 1 [1] FALSE
IterativeLSI Input-Parameters$sampleCellsFinal: length = 0 NULL
IterativeLSI Input-Parameters$selectionMethod: length = 1 [1] "var"
IterativeLSI Input-Parameters$scaleTo: length = 1 [1] 10000
IterativeLSI Input-Parameters$totalFeatures: length = 1 [1] 5e+05
IterativeLSI Input-Parameters$filterQuantile: length = 1 [1] 0.995
IterativeLSI Input-Parameters$excludeChr: length = 0 NULL
IterativeLSI Input-Parameters$keep0lsi: length = 1 [1] FALSE
IterativeLSI Input-Parameters$saveIterations: length = 1 [1] FALSE
IterativeLSI Input-Parameters$nPlot: length = 1 [1] 10000
IterativeLSI Input-Parameters$outDir: length = 1 [1] "/Users/hiraanis/Desktop/PhD/Hira-multiome/ArchR_analysis/tmp/tmp-2ee34c5ab8c5-Date-2024-02-22_Time-17-07-46"
IterativeLSI Input-Parameters$threads: length = 1 [1] 1
IterativeLSI Input-Parameters$seed: length = 1 [1] 1
IterativeLSI Input-Parameters$verbose: length = 1 [1] FALSE
IterativeLSI Input-Parameters$force: length = 1 [1] TRUE
IterativeLSI Input-Parameters$logFile: length = 1 [1] "ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"
2024-02-22 17:07:46 : Computing Total Across All Features, 0 mins elapsed. 2024-02-22 17:07:47 : Computing Top Features, 0.023 mins elapsed. ########### 2024-02-22 17:07:48 : Running LSI (1 of 2) on Top Features, 0.038 mins elapsed. ########### 2024-02-22 17:07:48 : Creating Partial Matrix, 0.038 mins elapsed. 2024-02-22 17:07:54 : Computing LSI, 0.13 mins elapsed.
2024-02-22 17:07:54 : LSI Parameters, Class = list
LSI Parameters$: length = 1
1 function (name) 2 .Internal(args(name))
LSI Parameters$mat: nRows = 25000, nCols = 1788 LSI Parameters$mat: NonZeroEntries = 10513861, EntryRange = [ 1 , 1 ] 5 x 5 sparse Matrix of class "dgCMatrix" Sample1#GTCTTGCTCATGGTTA-1 Sample1#GACCTTTGTGTCCTGC-1 [1,] 1 1 [2,] 1 1 [3,] . 1 [4,] 1 1 [5,] 1 1 Sample1#CCCAGTTTCTTGATGA-1 Sample1#CCGCAAATCGATTATG-1 [1,] 1 . [2,] 1 . [3,] . 1 [4,] 1 1 [5,] 1 1 Sample1#CCAAGTTAGCCACATG-1 [1,] 1 [2,] 1 [3,] . [4,] . [5,] 1
LSI Parameters$LSIMethod: length = 1 [1] 1
LSI Parameters$scaleTo: length = 1 [1] 10000
LSI Parameters$nDimensions: length = 1 [1] 30
LSI Parameters$binarize: length = 1 [1] TRUE
LSI Parameters$outlierQuantiles: length = 0 NULL
LSI Parameters$keep0lsi: length = 1 [1] FALSE
LSI Parameters$seed: length = 1 [1] 1
LSI Parameters$verbose: length = 1 [1] FALSE
LSI Parameters$tstart: length = 1 [1] "2024-02-22 17:07:46 EST"
LSI Parameters$logFile: length = 1 [1] "ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"
2024-02-22 17:07:54 : Running LSI, Input Matrix = 0.126 GB, 0.132 mins elapsed. 2024-02-22 17:07:54 : Binarizing Matrix, 0.132 mins elapsed. 2024-02-22 17:07:54 : Computing Term Frequency, 0.133 mins elapsed. 2024-02-22 17:07:54 : Removing 0 Sum Rows, 0.133 mins elapsed. 2024-02-22 17:07:54 : Computing Inverse Document Frequency, 0.135 mins elapsed. 2024-02-22 17:07:54 : Computing TF-IDF Matrix, 0.135 mins elapsed. 2024-02-22 17:07:55 : Computing SVD using irlba, 0.145 mins elapsed.
2024-02-22 17:07:55 : ERROR Found in .computeLSI for LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log
<simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'as_cholmod_sparse' not provided by package 'Matrix'>
2024-02-22 17:07:55 : errorList, Class = list
errorList$mat: nRows = 25000, nCols = 1788 errorList$mat: NonZeroEntries = 10513861, EntryRange = [ 6.05921387773296e-05 , 0.019743480836276 ] 5 x 5 sparse Matrix of class "dgCMatrix" Sample1#GTCTTGCTCATGGTTA-1 Sample1#GACCTTTGTGTCCTGC-1 [1,] 1.003779e-04 9.683009e-05 [2,] 8.973452e-05 8.656289e-05 [3,] . 9.005340e-05 [4,] 7.383138e-05 7.122185e-05 [5,] 9.618878e-05 9.278904e-05 Sample1#CCCAGTTTCTTGATGA-1 Sample1#CCGCAAATCGATTATG-1 [1,] 1.026353e-04 . [2,] 9.175255e-05 . [3,] . 9.387405e-05 [4,] 7.549177e-05 7.424354e-05 [5,] 9.835197e-05 9.672575e-05 Sample1#CCAAGTTAGCCACATG-1 [1,] 9.992355e-05 [2,] 8.932835e-05 [3,] . [4,] . [5,] 9.575340e-05
errorList$colSm: length = 1 [1] "Error with colSm!"
errorList$idf: length = 1 [1] "Error with idf!"
errorList$V: length = 1 [1] "Error with V!"
errorList$matSVD: length = 1 [1] "Error with matSVD!"
errorList$out: length = 1 [1] "Error with out!"
2024-02-22 17:07:55 : ERROR Found in .LSIPartialMatrix for LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log
<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
2024-02-22 17:07:55 : errorList, Class = list
errorList$: length = 1
1 function (name) 2 .Internal(args(name))
errorList$ArrowFiles: length = 1 [1] "Sample1.arrow"
errorList$useMatrix: length = 1 [1] "TileMatrix"
errorList$cellNames: length = 1788 [1] "Sample1#GTCTTGCTCATGGTTA-1" "Sample1#GACCTTTGTGTCCTGC-1" [3] "Sample1#CCCAGTTTCTTGATGA-1" "Sample1#CCGCAAATCGATTATG-1" [5] "Sample1#CCAAGTTAGCCACATG-1" "Sample1#AACCTAATCTTGTCCA-1"
errorList$cellDepth: length = 1788 Sample1#GTCTTGCTCATGGTTA-1 Sample1#GACCTTTGTGTCCTGC-1 4.982931 4.980317 Sample1#CCCAGTTTCTTGATGA-1Sample1#CCGCAAATCGATTATG-1 4.965225 4.961654 Sample1#CCAAGTTAGCCACATG-1 Sample1#AACCTAATCTTGTCCA-1 4.961169 4.958750
errorList$sampleNames: length = 1788 [1] "Sample1" "Sample1" "Sample1" "Sample1" "Sample1" [6] "Sample1"
errorList$dimsToUse: length = 30 [1] 1 2 3 4 5 6
errorList$binarize: length = 1 [1] TRUE
errorList$outlierQuantiles: length = 0 NULL
errorList$keep0lsi: length = 1 [1] FALSE
errorList$LSIMethod: length = 1 [1] 1
errorList$scaleTo: length = 1 [1] 10000
errorList$sampleCells: length = 0 NULL
errorList$projectAll: length = 0 logical(0)
errorList$threads: length = 1 [1] 1
errorList$seed: length = 1 [1] 1
errorList$useIndex: length = 1 [1] FALSE
errorList$tstart: length = 1 [1] "2024-02-22 17:07:46 EST"
errorList$verbose: length = 1 [1] FALSE
errorList$logFile: length = 1 [1] "ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"
errorList$outLSI: length = 1 [1] "Error with outLSI!"
errorList$matSVD: length = 1 [1] "Error with matSVD!"
2024-02-22 17:07:55 : ERROR Found in addIterativeLSI for Sample1 (1 of 5) : LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log
<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
2024-02-22 17:07:55 : errorList, Class = list
errorList$ArrowFile: length = 1 [1] "Sample1.arrow"
Is there any solutions now ? I meet the same problem and it does not work . even I changed Matrix version changes to 1.6.5 irlba v 2.3.51 ArchR v1.0.3
Hello, same error here, it was working fine not so long ago. Any idea how to solve it ? Tried to downgrade the matrix packages but nothings work
Did you try https://github.com/bwlewis/irlba/issues/70#issuecomment-1900350534 ? (i.e. reinstalling the packages from source so it recompiles without pre-caching).
Did you try #70 (comment) ? (i.e. reinstalling the packages from source so it recompiles without pre-caching).
Yes I tried but I get the "Error: package 'Matrix' is not available" error message, I am working on a cluster with R version 4.3.1 so that might be the problem, but I don't know how to resolve it so far.
If you have any idea it would be very helpful
Fixed it by installing from the repos : install.packages("Matrix", repos = "http://R-Forge.R-project.org")