Closed aLostMedStudent closed 5 months ago
RijndertAriese
commented
1 year ago Hi, I have the same error unfortunately. It appeared that this was a result from the graphs embedded. If I removed the nn/snn graphs it will subset just fine for me, but I cannot use the subset for subsequent analysis. What worked for me was downgrading to a v4.x Seurat package.
Cheers
frac2738
commented
1 year ago Same here.
options(Seurat.object.assay.version = "v3")
> Idents(exp_Integrated) <- "ScType"
> exp_Integrated <- subset(exp_Integrated, idents = c("Platelet","HSPC","Eryth","CD4 Proliferating"), invert = TRUE)
Error in getClassDef(x@superClass, package = packageSlot(x))@virtual :
no applicable method for `@` applied to an object of class "NULL"
> class(exp_Integrated)
[1] "Seurat"
attr(,"package")
[1] "SeuratObject"
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/libf77blas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=fr_FR.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris
tzcode source: system (glibc)
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.1.3 HGNChelper_0.8.1 scR_0.9.4 ggpubr_0.6.0 doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2
[8] pROC_1.18.5 Boruta_8.0.0 ranger_0.15.1 caretEnsemble_2.0.3 caret_6.0-94 lattice_0.22-5 corrplot_0.92
[15] kableExtra_1.3.4 SCpubr_2.0.2 DESeq2_1.40.2 RColorBrewer_1.1-3 RUVSeq_1.34.0 edgeR_3.42.4 limma_3.56.2
[22] EDASeq_2.34.0 ShortRead_1.58.0 GenomicAlignments_1.36.0 SummarizedExperiment_1.30.2 MatrixGenerics_1.12.3 matrixStats_1.1.0 Rsamtools_2.16.0
[29] GenomicRanges_1.52.1 Biostrings_2.68.1 GenomeInfoDb_1.36.4 XVector_0.40.0 IRanges_2.34.1 S4Vectors_0.38.2 BiocParallel_1.34.2
[36] Biobase_2.60.0 BiocGenerics_0.46.0 factoextra_1.0.7 Seurat_5.0.0 SeuratObject_5.0.0 sp_2.1-1 ggrepel_0.9.4
[43] data.table_1.14.8 ggplot2_3.4.4 viridis_0.6.4 viridisLite_0.4.2 pheatmap_1.0.12
loaded via a namespace (and not attached):
[1] R.methodsS3_1.8.2 progress_1.2.2 nnet_7.3-19 goftest_1.2-3 vctrs_0.6.4 spatstat.random_3.2-1 digest_0.6.33 png_0.1-8
[9] shape_1.4.6 deldir_1.0-9 parallelly_1.36.0 MASS_7.3-60 reshape2_1.4.4 httpuv_1.6.12 withr_2.5.2 xfun_0.41
[17] ellipsis_0.3.2 survival_3.5-7 memoise_2.0.1 systemfonts_1.0.5 ragg_1.2.6 zoo_1.8-12 GlobalOptions_0.1.2 pbapply_1.7-2
[25] R.oo_1.25.0 prettyunits_1.2.0 KEGGREST_1.40.1 promises_1.2.1 httr_1.4.7 rstatix_0.7.2 restfulr_0.0.15 globals_0.16.2
[33] fitdistrplus_1.1-11 ps_1.7.5 rstudioapi_0.15.0 miniUI_0.1.1.1 generics_0.1.3 processx_3.8.2 curl_5.1.0 zlibbioc_1.46.0
[41] polyclip_1.10-6 GenomeInfoDbData_1.2.10 desc_1.4.2 xtable_1.8-4 stringr_1.5.0 evaluate_0.23 S4Arrays_1.0.6 BiocFileCache_2.8.0
[49] hms_1.1.3 irlba_2.3.5.1 colorspace_2.1-0 filelock_1.0.2 ROCR_1.0-11 reticulate_1.34.0 spatstat.data_3.0-3 magrittr_2.0.3
[57] lmtest_0.9-40 later_1.3.1 spatstat.geom_3.2-7 future.apply_1.11.0 scattermore_1.2 XML_3.99-0.15 cowplot_1.1.1 RcppAnnoy_0.0.21
[65] class_7.3-22 pillar_1.9.0 nlme_3.1-163 compiler_4.3.1 RSpectra_0.16-1 stringi_1.7.12 gower_1.0.1 tensor_1.5
[73] lubridate_1.9.3 plyr_1.8.9 crayon_1.5.2 abind_1.4-5 BiocIO_1.10.0 gridGraphics_0.5-1 locfit_1.5-9.8 bit_4.0.5
[81] codetools_0.2-19 textshaping_0.3.7 recipes_1.0.8 plotly_4.10.3 mime_0.12 splines_4.3.1 circlize_0.4.15 Rcpp_1.0.11
[89] fastDummies_1.7.3 dbplyr_2.4.0 interp_1.1-4 knitr_1.45 blob_1.2.4 utf8_1.2.4 fs_1.6.3 listenv_0.9.0
[97] pkgbuild_1.4.2 openxlsx_4.2.5.2 ggsignif_0.6.4 ggplotify_0.1.2 tibble_3.2.1 Matrix_1.6-2 callr_3.7.3 svglite_2.1.2
[105] pkgconfig_2.0.3 tools_4.3.1 cachem_1.0.8 RSQLite_2.3.3 rvest_1.0.3 DBI_1.1.3 fastmap_1.1.1 rmarkdown_2.25
[113] scales_1.2.1 grid_4.3.1 ica_1.0-3 broom_1.0.5 patchwork_1.1.3 dotCall64_1.1-0 carData_3.0-5 RANN_2.6.1
[121] rpart_4.1.21 farver_2.1.1 yaml_2.3.7 latticeExtra_0.6-30 rtracklayer_1.60.1 cli_3.6.1 purrr_1.0.2 webshot_0.5.5
[129] leiden_0.4.3 lifecycle_1.0.4 uwot_0.1.16 lava_1.7.3 backports_1.4.1 timechange_0.2.0 gtable_0.3.4 rjson_0.2.21
[137] ggridges_0.5.4 progressr_0.14.0 jsonlite_1.8.7 RcppHNSW_0.5.0 bitops_1.0-7 bit64_4.0.5 assertthat_0.2.1 Rtsne_0.16
[145] yulab.utils_0.1.0 spatstat.utils_3.0-4 zip_2.3.0 R.utils_2.12.2 timeDate_4022.108 lazyeval_0.2.2 shiny_1.7.5.1 htmltools_0.5.7
[153] sctransform_0.4.1 rappdirs_0.3.3 glue_1.6.2 spam_2.10-0 RCurl_1.98-1.13 rprojroot_2.0.4 jpeg_0.1-10 gridExtra_2.3
[161] igraph_1.5.1 R6_2.5.1 tidyr_1.3.0 forcats_1.0.0 labeling_0.4.3 GenomicFeatures_1.52.2 cluster_2.1.4 ipred_0.9-14
[169] DelayedArray_0.26.7 tidyselect_1.2.0 xml2_1.3.5 car_3.1-2 AnnotationDbi_1.62.2 future_1.33.0 ModelMetrics_1.2.2.2 munsell_0.5.0
[177] KernSmooth_2.23-22 htmlwidgets_1.6.2 aroma.light_3.30.0 hwriter_1.3.2.1 biomaRt_2.56.1 rlang_1.1.2 spatstat.sparse_3.0-3 spatstat.explore_3.2-5
[185] remotes_2.4.2.1 fansi_1.0.5 hardhat_1.3.0 prodlim_2023.08.28 I also get the same error when I try to split.by the feature plot in SCpubr.
mhkowalski
commented
1 year ago Hi, thanks for reporting this issue. Could you please try running UpdateSeuratObject on your object and then subsetting?
aLostMedStudent
commented
1 year ago Hi, I have done this and it did not fix the error. Thank you for your suggestion though! On Nov 10, 2023 at 3:58 PM -0500, mhkowalski @.***>, wrote:
Hi, thanks for reporting this issue. Could you please try running UpdateSeuratObject on your object and then subsetting? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>
longmanz
commented
1 year ago Hi,
Thanks for reporting this. This has been reported multiple times (https://github.com/satijalab/seurat/issues/7983, https://github.com/satijalab/seurat/issues/7993, https://github.com/satijalab/seurat/issues/7999), and is caused by the Matrix package version 1.6-2. Please down-grade your Matrix back to 1.6-1.1 to temporarily avoid this error: remotes::install_version("Matrix", version = "1.6-1.1").
afletch00
commented
1 year ago I downgraded Matrix and I still cannot subset...
ABauer26
commented
1 year ago Hello! I've also updated to Seurat v5 under R/4.2.3. I'm reaching a similar subsetting error with the spatial transcriptomics 10X Genomics Visium analysis under the seurat5 spatial vignette. While using the provided mouse brain spatial data and brain object, I run into the error that an object of type 'S4' is not subsettable while trying to execute a GroupCorrelation command. I have tried the referenced solutions above, including the UpdateSeuratObject as well as the Matrix package down-grade to 1.6-1.1. Nothing seems to work, so I thought I would also chime in to see if solutions become available. Cheers ~
frac2738
commented
1 year ago Downgrading to Matrix 1.6-1 (which is the minimum required by seurat5 ) fixed it.
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/libf77blas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=fr_FR.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris
tzcode source: system (glibc)
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] Matrix_1.6-1 dplyr_1.1.3 HGNChelper_0.8.1 scR_0.9.4 ggpubr_0.6.0 doParallel_1.0.17
[7] iterators_1.0.14 foreach_1.5.2 pROC_1.18.5 Boruta_8.0.0 ranger_0.15.1 caretEnsemble_2.0.3
[13] caret_6.0-94 lattice_0.22-5 corrplot_0.92 kableExtra_1.3.4 SCpubr_2.0.2 DESeq2_1.40.2
[19] RColorBrewer_1.1-3 wesanderson_0.3.7 paletteer_1.5.0 RUVSeq_1.34.0 edgeR_3.42.4 limma_3.56.2
[25] EDASeq_2.34.0 ShortRead_1.58.0 GenomicAlignments_1.36.0 SummarizedExperiment_1.30.2 MatrixGenerics_1.12.3 matrixStats_1.1.0
[31] Rsamtools_2.16.0 GenomicRanges_1.52.1 Biostrings_2.68.1 GenomeInfoDb_1.36.4 XVector_0.40.0 IRanges_2.34.1
[37] S4Vectors_0.38.2 BiocParallel_1.34.2 Biobase_2.60.0 BiocGenerics_0.46.0 factoextra_1.0.7 Seurat_5.0.0
[43] SeuratObject_5.0.0 sp_2.1-1 ggrepel_0.9.4 data.table_1.14.8 ggplot2_3.4.4 viridis_0.6.4
[49] viridisLite_0.4.2 pheatmap_1.0.12
loaded via a namespace (and not attached):
[1] spatstat.sparse_3.0-3 bitops_1.0-7 lubridate_1.9.3 httr_1.4.7 webshot_0.5.5 backports_1.4.1 tools_4.3.1 sctransform_0.4.1
[9] utf8_1.2.4 R6_2.5.1 lazyeval_0.2.2 uwot_0.1.16 withr_2.5.2 prettyunits_1.2.0 gridExtra_2.3 progressr_0.14.0
[17] cli_3.6.1 spatstat.explore_3.2-5 fastDummies_1.7.3 spatstat.data_3.0-3 ggridges_0.5.4 pbapply_1.7-2 systemfonts_1.0.5 svglite_2.1.2
[25] R.utils_2.12.2 parallelly_1.36.0 rstudioapi_0.15.0 RSQLite_2.3.3 shape_1.4.6 generics_0.1.3 BiocIO_1.10.0 hwriter_1.3.2.1
[33] ica_1.0-3 spatstat.random_3.2-1 car_3.1-2 zip_2.3.0 interp_1.1-4 fansi_1.0.5 abind_1.4-5 R.methodsS3_1.8.2
[41] lifecycle_1.0.4 yaml_2.3.7 carData_3.0-5 recipes_1.0.8 BiocFileCache_2.8.0 Rtsne_0.16 grid_4.3.1 blob_1.2.4
[49] promises_1.2.1 crayon_1.5.2 miniUI_0.1.1.1 cowplot_1.1.1 GenomicFeatures_1.52.2 KEGGREST_1.40.1 pillar_1.9.0 knitr_1.45
[57] rjson_0.2.21 future.apply_1.11.0 codetools_0.2-19 leiden_0.4.3 glue_1.6.2 remotes_2.4.2.1 vctrs_0.6.4 png_0.1-8
[65] spam_2.10-0 gtable_0.3.4 rematch2_2.1.2 cachem_1.0.8 gower_1.0.1 aroma.light_3.30.0 xfun_0.41 openxlsx_4.2.5.2
[73] prodlim_2023.08.28 S4Arrays_1.0.6 mime_0.12 survival_3.5-7 timeDate_4022.108 hardhat_1.3.0 lava_1.7.3 ellipsis_0.3.2
[81] fitdistrplus_1.1-11 ipred_0.9-14 ROCR_1.0-11 nlme_3.1-163 bit64_4.0.5 progress_1.2.2 filelock_1.0.2 RcppAnnoy_0.0.21
[89] irlba_2.3.5.1 rpart_4.1.21 KernSmooth_2.23-22 colorspace_2.1-0 DBI_1.1.3 nnet_7.3-19 tidyselect_1.2.0 processx_3.8.2
[97] bit_4.0.5 compiler_4.3.1 curl_5.1.0 rvest_1.0.3 xml2_1.3.5 DelayedArray_0.26.7 plotly_4.10.3 rtracklayer_1.60.1
[105] scales_1.2.1 lmtest_0.9-40 callr_3.7.3 rappdirs_0.3.3 stringr_1.5.0 digest_0.6.33 goftest_1.2-3 spatstat.utils_3.0-4
[113] rmarkdown_2.25 htmltools_0.5.7 pkgconfig_2.0.3 jpeg_0.1-10 dbplyr_2.4.0 fastmap_1.1.1 GlobalOptions_0.1.2 rlang_1.1.2
[121] htmlwidgets_1.6.2 shiny_1.7.5.1 zoo_1.8-12 jsonlite_1.8.7 ModelMetrics_1.2.2.2 R.oo_1.25.0 RCurl_1.98-1.13 magrittr_2.0.3
[129] GenomeInfoDbData_1.2.10 dotCall64_1.1-0 patchwork_1.1.3 munsell_0.5.0 Rcpp_1.0.11 reticulate_1.34.0 stringi_1.7.12 zlibbioc_1.46.0
[137] MASS_7.3-60 plyr_1.8.9 pkgbuild_1.4.2 listenv_0.9.0 deldir_1.0-9 splines_4.3.1 tensor_1.5 circlize_0.4.15
[145] hms_1.1.3 locfit_1.5-9.8 ps_1.7.5 igraph_1.5.1 spatstat.geom_3.2-7 ggsignif_0.6.4 RcppHNSW_0.5.0 reshape2_1.4.4
[153] biomaRt_2.56.1 XML_3.99-0.15 evaluate_0.23 latticeExtra_0.6-30 httpuv_1.6.12 RANN_2.6.1 tidyr_1.3.0 purrr_1.0.2
[161] polyclip_1.10-6 future_1.33.0 scattermore_1.2 broom_1.0.5 xtable_1.8-4 restfulr_0.0.15 RSpectra_0.16-1 rstatix_0.7.2
[169] later_1.3.1 class_7.3-22 tibble_3.2.1 memoise_2.0.1 AnnotationDbi_1.62.2 cluster_2.1.4 timechange_0.2.0 globals_0.16.2 
izumidk
commented
6 months ago I'm trying to fix this issue by downgrading to Matrix 1.6-1 however, I am running into the issue that SeuratObject (5.0.2) depends on Matrix 1.6-4 and Seurat V5 depends on SeuratObect 5.0.2. So when I load Seurat with downgraded Matrix package I get this error
Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace ‘Matrix’ 1.6-1 is being loaded, but >= 1.6.4 is required
Error: package ‘SeuratObject’ could not be loaded
eds35016
commented
6 months ago Is there a solution to this? Matrix >= 1.6.4 is required for SeuratObect 5.0.2
eds35016
commented
6 months ago Reinstalling irlba after updating Matrix to >= 1.6.4 seems to have fixed the issue. See here.
igrabski
commented
5 months ago Thanks, as @eds35016 suggests, you should now be able to resolve this issue by updating Seurat, SeuratObject, and Matrix.
I was previously capable of manipulating this Seurat object with the subset function no without issue. Yesterday I updated my R from 4.1 to 4.3.2 and updated to Seurat V5. The weird thing is that this error is specific to this seurat object (i.e. when I loaded in a different object and used the subset function there was no such error). I would prefer not to have to re-create this object as it is rather larger. Thank you in advance!
The error is listed below:
sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.1
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
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: America/New_York tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] Seurat_5.0.0 SeuratObject_5.0.0 sp_2.1-1
loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.7 magrittr_2.0.3 spatstat.utils_3.0-4 farver_2.1.1
[7] fs_1.6.3 vctrs_0.6.4 ROCR_1.0-11 memoise_2.0.1 spatstat.explore_3.2-5 htmltools_0.5.7
[13] usethis_2.2.2 sctransform_0.4.1 parallelly_1.36.0 KernSmooth_2.23-22 htmlwidgets_1.6.2 ica_1.0-3
[19] plyr_1.8.9 plotly_4.10.3 zoo_1.8-12 cachem_1.0.8 igraph_1.5.1 mime_0.12
[25] lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.6-2 R6_2.5.1 fastmap_1.1.1 fitdistrplus_1.1-11
[31] future_1.33.0 shiny_1.7.5.1 digest_0.6.33 colorspace_2.1-0 patchwork_1.1.3 ps_1.7.5
[37] tensor_1.5 RSpectra_0.16-1 irlba_2.3.5.1 pkgload_1.3.3 labeling_0.4.3 progressr_0.14.0
[43] fansi_1.0.5 spatstat.sparse_3.0-3 httr_1.4.7 polyclip_1.10-6 abind_1.4-5 compiler_4.3.2
[49] remotes_2.4.2.1 withr_2.5.2 fastDummies_1.7.3 pkgbuild_1.4.2 MASS_7.3-60 sessioninfo_1.2.2
[55] tools_4.3.2 lmtest_0.9-40 httpuv_1.6.12 future.apply_1.11.0 goftest_1.2-3 glue_1.6.2
[61] callr_3.7.3 nlme_3.1-163 promises_1.2.1 grid_4.3.2 Rtsne_0.16 cluster_2.1.4
[67] reshape2_1.4.4 generics_0.1.3 gtable_0.3.4 spatstat.data_3.0-3 tidyr_1.3.0 data.table_1.14.8
[73] utf8_1.2.4 spatstat.geom_3.2-7 RcppAnnoy_0.0.21 ggrepel_0.9.4 RANN_2.6.1 pillar_1.9.0
[79] stringr_1.5.0 spam_2.10-0 RcppHNSW_0.5.0 later_1.3.1 splines_4.3.2 dplyr_1.1.3
[85] lattice_0.22-5 survival_3.5-7 deldir_1.0-9 tidyselect_1.2.0 miniUI_0.1.1.1 pbapply_1.7-2
[91] gridExtra_2.3 scattermore_1.2 devtools_2.4.5 matrixStats_1.1.0 stringi_1.7.12 lazyeval_0.2.2
[97] codetools_0.2-19 tibble_3.2.1 cli_3.6.1 uwot_0.1.16 xtable_1.8-4 reticulate_1.34.0
[103] munsell_0.5.0 processx_3.8.2 Rcpp_1.0.11 globals_0.16.2 spatstat.random_3.2-1 png_0.1-8
[109] parallel_4.3.2 ellipsis_0.3.2 ggplot2_3.4.4 prettyunits_1.2.0 dotCall64_1.1-0 profvis_0.3.8
[115] urlchecker_1.0.1 listenv_0.9.0 viridisLite_0.4.2 scales_1.2.1 ggridges_0.5.4 leiden_0.4.3
[121] purrr_1.0.2 crayon_1.5.2 rlang_1.1.2 cowplot_1.1.1