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AddDoubletScore - TileMatrix/chr5/rowSums does not exist #2224

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shamer3 opened this issue Oct 23, 2024 · 1 comment
Open

AddDoubletScore - TileMatrix/chr5/rowSums does not exist #2224

shamer3 opened this issue Oct 23, 2024 · 1 comment
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@shamer3
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shamer3 commented Oct 23, 2024

I am having some issues with AddDoubletScore(), I have used before on these samples however I am now getting this error message indicating there is an issue with the HDF5 file, which I have never had before and have processed them no problem.

************************************************************
2024-10-23 13:59:52.868972 : ERROR Found in addIterativeLSI for Cis_4weeksOFF (5 of 5) :  
LogFile = ArchRLogs/ArchR-addDoubletScores-435b5c4d2e0-Date-2024-10-23_Time-13-30-55.887278.log

<simpleError in h5read(ArrowFiles[y], paste0(useMatrix, "/", seqnames[x], "/rowSums")): Object 'TileMatrix/chr5/rowSums' does not exist in this HDF5 file.>

************************************************************

Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile),  : 
  Exiting See Error Above

Session information is as follows:

─ Session info ─────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.3 (2024-02-29)
 os       macOS 15.0.1
 system   x86_64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/London
 date     2024-10-23
 rstudio  2024.09.0+375 Cranberry Hibiscus (desktop)
 pandoc   NA

─ Packages ─────────────────────────────────────────────────────────────────
 package                     * version    date (UTC) lib source
 abind                         1.4-8      2024-09-12 [1] CRAN (R 4.3.3)
 AnnotationDbi               * 1.64.1     2023-11-03 [1] Bioconductor
 AnnotationFilter            * 1.26.0     2023-10-24 [1] Bioconductor
 ArchR                       * 1.0.2      2024-10-23 [1] Github (GreenleafLab/ArchR@6a0ec0c)
 Biobase                     * 2.62.0     2023-10-24 [1] Bioconductor
 BiocFileCache                 2.10.2     2024-03-27 [1] Bioconductor 3.18 (R 4.3.3)
 BiocGenerics                * 0.48.1     2023-11-01 [1] Bioconductor
 BiocIO                      * 1.12.0     2023-10-24 [1] Bioconductor
 BiocManager                 * 1.30.23    2024-05-04 [1] CRAN (R 4.3.2)
 BiocParallel                  1.36.0     2023-10-24 [1] Bioconductor
 biomaRt                       2.58.2     2024-01-30 [1] Bioconductor 3.18 (R 4.3.2)
 Biostrings                  * 2.70.3     2024-03-13 [1] Bioconductor 3.18 (R 4.3.3)
 bit                           4.5.0      2024-09-20 [1] CRAN (R 4.3.3)
 bit64                         4.5.2      2024-09-22 [1] CRAN (R 4.3.3)
 bitops                        1.0-9      2024-10-03 [1] CRAN (R 4.3.3)
 blob                          1.2.4      2023-03-17 [1] CRAN (R 4.3.0)
 BSgenome                    * 1.70.2     2024-02-08 [1] Bioconductor 3.18 (R 4.3.2)
 BSgenome.Hsapiens.UCSC.hg38 * 1.4.5      2024-05-01 [1] Bioconductor
 cachem                        1.1.0      2024-05-16 [1] CRAN (R 4.3.3)
 Cairo                         1.6-2      2023-11-28 [1] CRAN (R 4.3.0)
 callr                         3.7.6      2024-03-25 [1] CRAN (R 4.3.2)
 cli                           3.6.3      2024-06-21 [1] CRAN (R 4.3.3)
 cluster                       2.1.6      2023-12-01 [2] CRAN (R 4.3.3)
 codetools                     0.2-19     2023-02-01 [2] CRAN (R 4.3.3)
 colorspace                    2.1-1      2024-07-26 [1] CRAN (R 4.3.3)
 cowplot                       1.1.3      2024-01-22 [1] CRAN (R 4.3.2)
 crayon                        1.5.3      2024-06-20 [1] CRAN (R 4.3.3)
 curl                          5.2.3      2024-09-20 [1] CRAN (R 4.3.3)
 data.table                  * 1.16.2     2024-10-10 [1] CRAN (R 4.3.3)
 DBI                           1.2.3      2024-06-02 [1] CRAN (R 4.3.3)
 dbplyr                        2.5.0      2024-03-19 [1] CRAN (R 4.3.2)
 DelayedArray                  0.28.0     2023-10-24 [1] Bioconductor
 deldir                        2.0-4      2024-02-28 [1] CRAN (R 4.3.2)
 desc                          1.4.3      2023-12-10 [1] CRAN (R 4.3.0)
 devtools                    * 2.4.5      2022-10-11 [1] CRAN (R 4.3.0)
 digest                        0.6.37     2024-08-19 [1] CRAN (R 4.3.3)
 doParallel                  * 1.0.17     2022-02-07 [1] CRAN (R 4.3.0)
 dotCall64                     1.1-1      2023-11-28 [1] CRAN (R 4.3.0)
 dplyr                       * 1.1.4      2023-11-17 [1] CRAN (R 4.3.0)
 ellipsis                      0.3.2      2021-04-29 [1] CRAN (R 4.3.0)
 EnsDb.Hsapiens.v86          * 2.99.0     2024-05-14 [1] Bioconductor
 ensembldb                   * 2.26.1     2024-04-15 [1] Bioconductor 3.18 (R 4.3.3)
 fansi                         1.0.6      2023-12-08 [1] CRAN (R 4.3.0)
 farver                        2.1.2      2024-05-13 [1] CRAN (R 4.3.3)
 fastmap                       1.2.0      2024-05-15 [1] CRAN (R 4.3.3)
 filelock                      1.0.3      2023-12-11 [1] CRAN (R 4.3.0)
 fitdistrplus                  1.2-1      2024-07-12 [1] CRAN (R 4.3.3)
 foreach                     * 1.5.2      2022-02-02 [1] CRAN (R 4.3.0)
 fs                            1.6.4      2024-04-25 [1] CRAN (R 4.3.2)
 future                        1.34.0     2024-07-29 [1] CRAN (R 4.3.3)
 future.apply                  1.11.2     2024-03-28 [1] CRAN (R 4.3.2)
 generics                      0.1.3      2022-07-05 [1] CRAN (R 4.3.0)
 GenomeInfoDb                * 1.38.8     2024-03-15 [1] Bioconductor 3.18 (R 4.3.3)
 GenomeInfoDbData              1.2.11     2024-05-01 [1] Bioconductor
 GenomicAlignments             1.38.2     2024-01-16 [1] Bioconductor 3.18 (R 4.3.2)
 GenomicFeatures             * 1.54.4     2024-03-13 [1] Bioconductor 3.18 (R 4.3.3)
 GenomicRanges               * 1.54.1     2023-10-29 [1] Bioconductor
 ggplot2                     * 3.4.2      2023-04-03 [1] CRAN (R 4.3.3)
 ggrepel                       0.9.6      2024-09-07 [1] CRAN (R 4.3.3)
 ggridges                      0.5.6      2024-01-23 [1] CRAN (R 4.3.2)
 globals                       0.16.3     2024-03-08 [1] CRAN (R 4.3.2)
 glue                          1.8.0      2024-09-30 [1] CRAN (R 4.3.3)
 goftest                       1.2-3      2021-10-07 [1] CRAN (R 4.3.0)
 gridExtra                   * 2.3        2017-09-09 [1] CRAN (R 4.3.0)
 gtable                      * 0.3.5      2024-04-22 [1] CRAN (R 4.3.2)
 gtools                      * 3.9.5      2023-11-20 [1] CRAN (R 4.3.0)
 harmony                       1.2.0      2024-05-01 [1] Github (immunogenomics/harmony@f054b03)
 hdf5r                       * 1.3.11     2024-07-07 [1] CRAN (R 4.3.3)
 hexbin                      * 1.28.4     2024-09-04 [1] CRAN (R 4.3.3)
 hms                           1.1.3      2023-03-21 [1] CRAN (R 4.3.0)
 htmltools                     0.5.8.1    2024-04-04 [1] CRAN (R 4.3.2)
 htmlwidgets                   1.6.4      2023-12-06 [1] CRAN (R 4.3.0)
 httpuv                        1.6.15     2024-03-26 [1] CRAN (R 4.3.2)
 httr                          1.4.7      2023-08-15 [1] CRAN (R 4.3.0)
 ica                           1.0-3      2022-07-08 [1] CRAN (R 4.3.0)
 igraph                        2.0.3      2024-03-13 [1] CRAN (R 4.3.2)
 IRanges                     * 2.36.0     2023-10-24 [1] Bioconductor
 irlba                         2.3.5.1    2022-10-03 [1] CRAN (R 4.3.3)
 iterators                   * 1.0.14     2022-02-05 [1] CRAN (R 4.3.0)
 jsonlite                      1.8.9      2024-09-20 [1] CRAN (R 4.3.3)
 KEGGREST                      1.42.0     2023-10-24 [1] Bioconductor
 KernSmooth                    2.23-22    2023-07-10 [2] CRAN (R 4.3.3)
 labeling                      0.4.3      2023-08-29 [1] CRAN (R 4.3.0)
 later                         1.3.2      2023-12-06 [1] CRAN (R 4.3.0)
 lattice                       0.22-5     2023-10-24 [2] CRAN (R 4.3.3)
 lazyeval                      0.2.2      2019-03-15 [1] CRAN (R 4.3.0)
 leiden                        0.4.3.1    2023-11-17 [1] CRAN (R 4.3.0)
 lifecycle                     1.0.4      2023-11-07 [1] CRAN (R 4.3.0)
 listenv                       0.9.1      2024-01-29 [1] CRAN (R 4.3.2)
 lmtest                        0.9-40     2022-03-21 [1] CRAN (R 4.3.0)
 magrittr                    * 2.0.3      2022-03-30 [1] CRAN (R 4.3.0)
 MASS                          7.3-60.0.1 2024-01-13 [2] CRAN (R 4.3.3)
 Matrix                      * 1.6-5      2024-01-11 [1] CRAN (R 4.3.3)
 MatrixGenerics              * 1.14.0     2023-10-24 [1] Bioconductor
 matrixStats                 * 1.4.1      2024-09-08 [1] CRAN (R 4.3.3)
 memoise                       2.0.1      2021-11-26 [1] CRAN (R 4.3.0)
 mime                          0.12       2021-09-28 [1] CRAN (R 4.3.0)
 miniUI                        0.1.1.1    2018-05-18 [1] CRAN (R 4.3.0)
 munsell                       0.5.1      2024-04-01 [1] CRAN (R 4.3.2)
 nabor                       * 0.5.0      2018-07-11 [1] CRAN (R 4.3.0)
 nlme                          3.1-164    2023-11-27 [2] CRAN (R 4.3.3)
 parallelly                    1.38.0     2024-07-27 [1] CRAN (R 4.3.3)
 patchwork                     1.2.0      2024-01-08 [1] CRAN (R 4.3.0)
 pbapply                       1.7-2      2023-06-27 [1] CRAN (R 4.3.0)
 pillar                        1.9.0      2023-03-22 [1] CRAN (R 4.3.0)
 pkgbuild                      1.4.4      2024-03-17 [1] CRAN (R 4.3.2)
 pkgconfig                     2.0.3      2019-09-22 [1] CRAN (R 4.3.0)
 pkgload                       1.4.0      2024-06-28 [1] CRAN (R 4.3.3)
 plotly                        4.10.4     2024-01-13 [1] CRAN (R 4.3.0)
 plyr                        * 1.8.9      2023-10-02 [1] CRAN (R 4.3.0)
 png                           0.1-8      2022-11-29 [1] CRAN (R 4.3.0)
 polyclip                      1.10-7     2024-07-23 [1] CRAN (R 4.3.3)
 presto                        1.0.0      2024-05-01 [1] Github (immunogenomics/presto@7636b3d)
 prettyunits                   1.2.0      2023-09-24 [1] CRAN (R 4.3.0)
 processx                      3.8.4      2024-03-16 [1] CRAN (R 4.3.2)
 profvis                       0.3.8      2023-05-02 [1] CRAN (R 4.3.0)
 progress                      1.2.3      2023-12-06 [1] CRAN (R 4.3.0)
 progressr                     0.14.0     2023-08-10 [1] CRAN (R 4.3.0)
 promises                      1.3.0      2024-04-05 [1] CRAN (R 4.3.2)
 ProtGenerics                  1.34.0     2023-10-24 [1] Bioconductor
 ps                            1.7.7      2024-07-02 [1] CRAN (R 4.3.3)
 purrr                         1.0.2      2023-08-10 [1] CRAN (R 4.3.0)
 R6                            2.5.1      2021-08-19 [1] CRAN (R 4.3.0)
 RANN                          2.6.1      2019-01-08 [1] CRAN (R 4.3.0)
 rappdirs                      0.3.3      2021-01-31 [1] CRAN (R 4.3.0)
 RColorBrewer                  1.1-3      2022-04-03 [1] CRAN (R 4.3.0)
 Rcpp                        * 1.0.13     2024-07-17 [1] CRAN (R 4.3.3)
 RcppAnnoy                     0.0.22     2024-01-23 [1] CRAN (R 4.3.2)
 RCurl                         1.98-1.16  2024-07-11 [1] CRAN (R 4.3.3)
 remotes                       2.5.0      2024-03-17 [1] CRAN (R 4.3.2)
 renv                          1.0.7      2024-04-11 [1] CRAN (R 4.3.2)
 reshape2                      1.4.4      2020-04-09 [1] CRAN (R 4.3.0)
 restfulr                      0.0.15     2022-06-16 [1] CRAN (R 4.3.0)
 reticulate                    1.37.0     2024-05-21 [1] CRAN (R 4.3.3)
 rhandsontable                 0.3.8      2021-05-27 [1] CRAN (R 4.3.0)
 rhdf5                       * 2.46.1     2023-11-29 [1] Bioconductor
 rhdf5filters                  1.14.1     2023-11-06 [1] Bioconductor
 Rhdf5lib                      1.24.2     2024-02-07 [1] Bioconductor 3.18 (R 4.3.2)
 rjson                         0.2.23     2024-09-16 [1] CRAN (R 4.3.3)
 rlang                         1.1.4      2024-06-04 [1] CRAN (R 4.3.3)
 ROCR                          1.0-11     2020-05-02 [1] CRAN (R 4.3.0)
 Rsamtools                     2.18.0     2023-10-24 [1] Bioconductor
 RSQLite                       2.3.7      2024-05-27 [1] CRAN (R 4.3.3)
 rstudioapi                    0.16.0     2024-03-24 [1] CRAN (R 4.3.2)
 rtracklayer                 * 1.62.0     2023-10-24 [1] Bioconductor
 Rtsne                         0.17       2023-12-07 [1] CRAN (R 4.3.0)
 S4Arrays                      1.2.1      2024-03-06 [1] Bioconductor 3.18 (R 4.3.3)
 S4Vectors                   * 0.40.2     2023-11-23 [1] Bioconductor
 scales                        1.3.0      2023-11-28 [1] CRAN (R 4.3.0)
 scattermore                   1.2        2023-06-12 [1] CRAN (R 4.3.0)
 sctransform                   0.4.1      2023-10-19 [1] CRAN (R 4.3.0)
 sessioninfo                   1.2.2      2021-12-06 [1] CRAN (R 4.3.0)
 Seurat                      * 4.3.0      2022-11-18 [1] CRAN (R 4.3.3)
 SeuratObject                * 5.0.2      2024-05-08 [1] CRAN (R 4.3.2)
 shiny                         1.9.1      2024-08-01 [1] CRAN (R 4.3.3)
 shinythemes                   1.2.0      2021-01-25 [1] CRAN (R 4.3.0)
 sp                            2.1-4      2024-04-30 [1] CRAN (R 4.3.2)
 spam                          2.10-0     2023-10-23 [1] CRAN (R 4.3.0)
 SparseArray                   1.2.4      2024-02-11 [1] Bioconductor 3.18 (R 4.3.2)
 spatstat.data                 3.1-2      2024-06-21 [1] CRAN (R 4.3.3)
 spatstat.explore              3.3-1      2024-07-15 [1] CRAN (R 4.3.3)
 spatstat.geom                 3.3-2      2024-07-15 [1] CRAN (R 4.3.3)
 spatstat.random               3.3-1      2024-07-15 [1] CRAN (R 4.3.3)
 spatstat.sparse               3.1-0      2024-06-21 [1] CRAN (R 4.3.3)
 spatstat.univar               3.0-0      2024-06-28 [1] CRAN (R 4.3.3)
 spatstat.utils                3.1-0      2024-08-17 [1] CRAN (R 4.3.3)
 stringi                       1.8.4      2024-05-06 [1] CRAN (R 4.3.2)
 stringr                     * 1.5.1      2023-11-14 [1] CRAN (R 4.3.0)
 SummarizedExperiment        * 1.32.0     2023-10-24 [1] Bioconductor
 survival                      3.5-8      2024-02-14 [2] CRAN (R 4.3.3)
 tensor                        1.5        2012-05-05 [1] CRAN (R 4.3.0)
 tibble                        3.2.1      2023-03-20 [1] CRAN (R 4.3.0)
 tidyr                       * 1.3.1      2024-01-24 [1] CRAN (R 4.3.2)
 tidyselect                    1.2.1      2024-03-11 [1] CRAN (R 4.3.2)
 urlchecker                    1.0.1      2021-11-30 [1] CRAN (R 4.3.0)
 usethis                     * 3.0.0      2024-07-29 [1] CRAN (R 4.3.3)
 utf8                          1.2.4      2023-10-22 [1] CRAN (R 4.3.0)
 uwot                          0.2.2      2024-04-21 [1] CRAN (R 4.3.2)
 vctrs                         0.6.5      2023-12-01 [1] CRAN (R 4.3.0)
 viridisLite                   0.4.2      2023-05-02 [1] CRAN (R 4.3.0)
 withr                         3.0.1      2024-07-31 [1] CRAN (R 4.3.3)
 XML                           3.99-0.17  2024-06-25 [1] CRAN (R 4.3.3)
 xml2                          1.3.6      2023-12-04 [1] CRAN (R 4.3.0)
 xtable                        1.8-4      2019-04-21 [1] CRAN (R 4.3.0)
 XVector                     * 0.42.0     2023-10-24 [1] Bioconductor
 yaml                          2.3.10     2024-07-26 [1] CRAN (R 4.3.3)
 zlibbioc                      1.48.2     2024-03-13 [1] Bioconductor 3.18 (R 4.3.3)
 zoo                           1.8-12     2023-04-13 [1] CRAN (R 4.3.0)

 [1] /Users/shamer/Library/R/x86_64/4.3/library
 [2] /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library
@shamer3 shamer3 added the bug Something isn't working label Oct 23, 2024
@rcorces
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rcorces commented Oct 23, 2024

Hi @shamer3! 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.

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