Error in .local(x, na.rm, dims, ...) : object 'CRsparse_colSums' not found error from RunAzimuth()

annstrange commented 11 months ago

After upgrading Seurat, SeuratData, and Azimuth to the most recent versions, then when I load Azimuth with library(Azimuth) I first get a warning that Registered S3 method overwritten by 'SeuratDisk': method from
as.sparse.H5Group Seurat

and then a number of methods stop working including Seurat::LoadNanostring(), Azimuth::RunAzimuth(), and Seurat::SCTransform(). The error does not happen until I've loaded library(Azimuth). These were all working before I updated to Seurat v5, but Azimuth seems to be breaking things by insisting on overwriting the as.sparse.H5Group method.

Example code:

seurat_obj <- Azimuth::RunAzimuth(seurat_obj, reference="./lungref.SeuratData/inst/azimuth") Warning: Overwriting miscellanous data for model Warning: Adding a dimensional reduction (refUMAP) without the associated assay being present detected inputs from HUMAN with id type Gene.name reference rownames detected HUMAN with id type Gene.name Error in .local(x, na.rm, dims, ...) : object 'CRsparse_colSums' not found

Steps to reproduce:

Install Seurat v5 as instructed here: https://satijalab.org/seurat/articles/install_v5
library(Seurat)
for some basic Seurat object you have already, load it as obj
obj <- SCTransform(obj, assay="RNA") # it'll work
library(Azimuth)
obj <- SCTransform(obj, assay="RNA") # it'll fail with CRsparse_colSums not found error.
obj <- RunAzimuth(obj, <whatever parameters>) # it'll fail too.

sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.1.1

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/Denver tzcode source: internal

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

other attached packages: [1] Azimuth_0.5.0 shinyBS_0.61.1 dplyr_1.1.4 BPCells_0.1.0
[5] Seurat_5.0.1 ifnb.SeuratData_3.1.0 SeuratData_0.2.2.9001 SeuratObject_5.0.1
[9] sp_2.1-1

loaded via a [1] fs_1.6.3 [4] spatstat.sparse_3.0-3 [7] TFBSTools_1.40.0 [10] tools_4.3.2 [13] R6_2.5.1 [16] uwot_0.1.16 [19] prettyunits_1.2.0 [22] cli_3.6.1 [25] fastDummies_1.7.3 [28] spatstat.data_3.0-3 [31] pbapply_1.7-2 [34] parallelly_1.36.0 [37] RSQLite_2.3.3 [40] gtools_3.9.4 [43] googlesheets4_1.1.1 [46] fansi_1.0.5 [49] R.methodsS3_1.8.2 [52] SummarizedExperiment_1.32.0 [55] BiocFileCache_2.10.1 [58] blob_1.2.4 [61] crayon_1.5.2 [64] cowplot_1.1.1 [67] KEGGREST_1.42.0 [70] rjson_0.2.21 [73] fastmatch_1.1-4 [76] data.table_1.14.8 [79] spam_2.10-0 [82] poweRlaw_0.70.6 [85] S4Arrays_1.2.0 [88] survival_3.5-7 [91] ellipsis_0.3.2 [94] nlme_3.1-163 [97] filelock_1.0.2 [100] irlba_2.3.5.1 [103] colorspace_2.1-0 [106] DBI_1.1.3 [109] compiler_4.3.2 [112] xml2_1.3.5 [115] rtracklayer_1.62.0 [118] lmtest_0.9-40 [121] digest_0.6.33 [124] spatstat.utils_3.0-4 [127] pkgconfig_2.0.3 [130] fastmap_1.1.1 [133] htmlwidgets_1.6.2 [136] jsonlite_1.8.7 [139] RCurl_1.98-1.13 [142] dotCall64_1.1-0 [145] munsell_0.5.0 [148] stringi_1.8.1 [151] plyr_1.8.9 [154] ggrepel_0.9.4 [157] Biostrings_2.70.1 [160] hms_1.1.3 [163] spatstat.geom_3.2-7 [166] biomaRt_2.58.0 [169] XML_3.99-0.15 [172] httpuv_1.6.12 [175] purrr_1.0.2 [178] scattermore_1.2 [181] restfulr_0.0.15 [184] later_1.3.1 [187] tibble_3.2.1 [190] GenomicAlignments_1.38.0 [193] globals_0.16.2 namespace (and not attached): ProtGenerics_1.34.0 matrixStats_1.1.0
bitops_1.0-7 DirichletMultinomial_1.44.0
httr_1.4.7 RColorBrewer_1.1-3
sctransform_0.4.1 utf8_1.2.4
DT_0.30 lazyeval_0.2.2
rhdf5filters_1.14.1 withr_2.5.2
gridExtra_2.3 progressr_0.14.0
Biobase_2.62.0 spatstat.explore_3.2-5
EnsDb.Hsapiens.v86_2.99.0 shinyjs_2.1.0
readr_2.1.4 ggridges_0.5.4
Rsamtools_2.18.0 R.utils_2.12.3
BSgenome_1.70.1 rstudioapi_0.15.0
generics_0.1.3 BiocIO_1.12.0
ica_1.0-3 spatstat.random_3.2-1
GO.db_3.18.0 Matrix_1.6-3
S4Vectors_0.40.1 abind_1.4-5
lifecycle_1.0.4 yaml_2.3.7
rhdf5_2.46.0 SparseArray_1.2.2
Rtsne_0.16 grid_4.3.2
promises_1.2.1 shinydashboard_0.7.2
miniUI_0.1.1.1 lattice_0.22-5
GenomicFeatures_1.54.1 annotate_1.80.0
pillar_1.9.0 GenomicRanges_1.54.1
future.apply_1.11.0 codetools_0.2-19
leiden_0.4.3.1 glue_1.6.2
vctrs_0.6.4 png_0.1-8
cellranger_1.1.0 gtable_0.3.4
cachem_1.0.8 Signac_1.12.0
mime_0.12 pracma_2.4.4
gargle_1.5.2 RcppRoll_0.3.0
fitdistrplus_1.1-11 ROCR_1.0-11
bit64_4.0.5 progress_1.2.2
RcppAnnoy_0.0.21 GenomeInfoDb_1.38.1
KernSmooth_2.23-22 SeuratDisk_0.0.0.9021
seqLogo_1.68.0 BiocGenerics_0.48.1
tidyselect_1.2.0 bit_4.0.5
curl_5.1.0 hdf5r_1.3.8
DelayedArray_0.28.0 plotly_4.10.3
scales_1.2.1 caTools_1.18.2
rappdirs_0.3.3 stringr_1.5.1
goftest_1.2-3 presto_1.0.0
XVector_0.42.0 htmltools_0.5.7
MatrixGenerics_1.14.0 dbplyr_2.4.0
ensembldb_2.26.0 rlang_1.1.2
shiny_1.8.0 zoo_1.8-12
BiocParallel_1.36.0 R.oo_1.25.0
magrittr_2.0.3 GenomeInfoDbData_1.2.11
patchwork_1.1.3 Rhdf5lib_1.24.0
Rcpp_1.0.11 reticulate_1.34.0
zlibbioc_1.48.0 MASS_7.3-60
parallel_4.3.2 listenv_0.9.0
deldir_1.0-9 CNEr_1.38.0
splines_4.3.2 tensor_1.5
BSgenome.Hsapiens.UCSC.hg38_1.4.5 igraph_1.5.1
RcppHNSW_0.5.0 reshape2_1.4.4
stats4_4.3.2 TFMPvalue_0.0.9
JASPAR2020_0.99.10 tzdb_0.4.0
RANN_2.6.1 tidyr_1.3.0
polyclip_1.10-6 future_1.33.0
ggplot2_3.4.4 xtable_1.8-4
AnnotationFilter_1.26.0 RSpectra_0.16-1
googledrive_2.1.1 viridisLite_0.4.2
memoise_2.0.1 AnnotationDbi_1.64.1
IRanges_2.36.0 cluster_2.1.4

ian-coccimiglio commented 10 months ago

I'm getting the same issue, setup is on Windows 10 with Seurat v5 and updated Azimuth.

Niubile001 commented 10 months ago

After upgrading Seurat, SeuratData, and Azimuth to the most recent versions, then when I load Azimuth with library(Azimuth) I first get a warning that Registered S3 method overwritten by 'SeuratDisk': method from as.sparse.H5Group Seurat

and then a number of methods stop working including Seurat::LoadNanostring(), Azimuth::RunAzimuth(), and Seurat::SCTransform(). The error does not happen until I've loaded library(Azimuth). These were all working before I updated to Seurat v5, but Azimuth seems to be breaking things by insisting on overwriting the as.sparse.H5Group method.

Example code:

seurat_obj <- Azimuth::RunAzimuth(seurat_obj, reference="./lungref.SeuratData/inst/azimuth") Warning: Overwriting miscellanous data for model Warning: Adding a dimensional reduction (refUMAP) without the associated assay being present detected inputs from HUMAN with id type Gene.name reference rownames detected HUMAN with id type Gene.name Error in .local(x, na.rm, dims, ...) : object 'CRsparse_colSums' not found

Steps to reproduce:

Install Seurat v5 as instructed here: https://satijalab.org/seurat/articles/install_v5

library(Seurat)

for some basic Seurat object you have already, load it as obj

obj <- SCTransform(obj, assay="RNA") # it'll work

library(Azimuth)

obj <- SCTransform(obj, assay="RNA") # it'll fail with CRsparse_colSums not found error.

obj <- RunAzimuth(obj, <whatever parameters>) # it'll fail too.

sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.1.1

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/Denver tzcode source: internal

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

other attached packages: [1] Azimuth_0.5.0 shinyBS_0.61.1 dplyr_1.1.4 BPCells_0.1.0 [5] Seurat_5.0.1 ifnb.SeuratData_3.1.0 SeuratData_0.2.2.9001 SeuratObject_5.0.1 [9] sp_2.1-1

loaded via a namespace (and not attached): [1] fs_1.6.3 ProtGenerics_1.34.0 matrixStats_1.1.0 [4] spatstat.sparse_3.0-3 bitops_1.0-7 DirichletMultinomial_1.44.0 [7] TFBSTools_1.40.0 httr_1.4.7 RColorBrewer_1.1-3 [10] tools_4.3.2 sctransform_0.4.1 utf8_1.2.4 [13] R6_2.5.1 DT_0.30 lazyeval_0.2.2 [16] uwot_0.1.16 rhdf5filters_1.14.1 withr_2.5.2 [19] prettyunits_1.2.0 gridExtra_2.3 progressr_0.14.0 [22] cli_3.6.1 Biobase_2.62.0 spatstat.explore_3.2-5 [25] fastDummies_1.7.3 EnsDb.Hsapiens.v86_2.99.0 shinyjs_2.1.0 [28] spatstat.data_3.0-3 readr_2.1.4 ggridges_0.5.4 [31] pbapply_1.7-2 Rsamtools_2.18.0 R.utils_2.12.3 [34] parallelly_1.36.0 BSgenome_1.70.1 rstudioapi_0.15.0 [37] RSQLite_2.3.3 generics_0.1.3 BiocIO_1.12.0 [40] gtools_3.9.4 ica_1.0-3 spatstat.random_3.2-1 [43] googlesheets4_1.1.1 GO.db_3.18.0 Matrix_1.6-3 [46] fansi_1.0.5 S4Vectors_0.40.1 abind_1.4-5 [49] R.methodsS3_1.8.2 lifecycle_1.0.4 yaml_2.3.7 [52] SummarizedExperiment_1.32.0 rhdf5_2.46.0 SparseArray_1.2.2 [55] BiocFileCache_2.10.1 Rtsne_0.16 grid_4.3.2 [58] blob_1.2.4 promises_1.2.1 shinydashboard_0.7.2 [61] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.22-5 [64] cowplot_1.1.1 GenomicFeatures_1.54.1 annotate_1.80.0 [67] KEGGREST_1.42.0 pillar_1.9.0 GenomicRanges_1.54.1 [70] rjson_0.2.21 future.apply_1.11.0 codetools_0.2-19 [73] fastmatch_1.1-4 leiden_0.4.3.1 glue_1.6.2 [76] data.table_1.14.8 vctrs_0.6.4 png_0.1-8 [79] spam_2.10-0 cellranger_1.1.0 gtable_0.3.4 [82] poweRlaw_0.70.6 cachem_1.0.8 Signac_1.12.0 [85] S4Arrays_1.2.0 mime_0.12 pracma_2.4.4 [88] survival_3.5-7 gargle_1.5.2 RcppRoll_0.3.0 [91] ellipsis_0.3.2 fitdistrplus_1.1-11 ROCR_1.0-11 [94] nlme_3.1-163 bit64_4.0.5 progress_1.2.2 [97] filelock_1.0.2 RcppAnnoy_0.0.21 GenomeInfoDb_1.38.1 [100] irlba_2.3.5.1 KernSmooth_2.23-22 SeuratDisk_0.0.0.9021 [103] colorspace_2.1-0 seqLogo_1.68.0 BiocGenerics_0.48.1 [106] DBI_1.1.3 tidyselect_1.2.0 bit_4.0.5 [109] compiler_4.3.2 curl_5.1.0 hdf5r_1.3.8 [112] xml2_1.3.5 DelayedArray_0.28.0 plotly_4.10.3 [115] rtracklayer_1.62.0 scales_1.2.1 caTools_1.18.2 [118] lmtest_0.9-40 rappdirs_0.3.3 stringr_1.5.1 [121] digest_0.6.33 goftest_1.2-3 presto_1.0.0 [124] spatstat.utils_3.0-4 XVector_0.42.0 htmltools_0.5.7 [127] pkgconfig_2.0.3 MatrixGenerics_1.14.0 dbplyr_2.4.0 [130] fastmap_1.1.1 ensembldb_2.26.0 rlang_1.1.2 [133] htmlwidgets_1.6.2 shiny_1.8.0 zoo_1.8-12 [136] jsonlite_1.8.7 BiocParallel_1.36.0 R.oo_1.25.0 [139] RCurl_1.98-1.13 magrittr_2.0.3 GenomeInfoDbData_1.2.11 [142] dotCall64_1.1-0 patchwork_1.1.3 Rhdf5lib_1.24.0 [145] munsell_0.5.0 Rcpp_1.0.11 reticulate_1.34.0 [148] stringi_1.8.1 zlibbioc_1.48.0 MASS_7.3-60 [151] plyr_1.8.9 parallel_4.3.2 listenv_0.9.0 [154] ggrepel_0.9.4 deldir_1.0-9 CNEr_1.38.0 [157] Biostrings_2.70.1 splines_4.3.2 tensor_1.5 [160] hms_1.1.3 BSgenome.Hsapiens.UCSC.hg38_1.4.5 igraph_1.5.1 [163] spatstat.geom_3.2-7 RcppHNSW_0.5.0 reshape2_1.4.4 [166] biomaRt_2.58.0 stats4_4.3.2 TFMPvalue_0.0.9 [169] XML_3.99-0.15 JASPAR2020_0.99.10 tzdb_0.4.0 [172] httpuv_1.6.12 RANN_2.6.1 tidyr_1.3.0 [175] purrr_1.0.2 polyclip_1.10-6 future_1.33.0 [178] scattermore_1.2 ggplot2_3.4.4 xtable_1.8-4 [181] restfulr_0.0.15 AnnotationFilter_1.26.0 RSpectra_0.16-1 [184] later_1.3.1 googledrive_2.1.1 viridisLite_0.4.2 [187] tibble_3.2.1 memoise_2.0.1 AnnotationDbi_1.64.1 [190] GenomicAlignments_1.38.0 IRanges_2.36.0 cluster_2.1.4 [193] globals_0.16.2

Try reinstall irlba package may be helpful. It seems to be a conflict raised by latest Matrix (1.6.3) package.

annstrange commented 10 months ago

thanks for the quick response! However, after doing that, I'm still getting the same issue.

Gesmira commented 10 months ago

Thank you for the reproducible example, this was also reported here. RunAzimuth actually worked fine for me and I only got your error message with SCTransform. I don't think this is related to overwriting the as.sparse.H5Group method, as that has always been done. It seems to specifically be an issue with running colSums() on a sparse matrix due to a conflict with TFBSTools that is now loaded with Azimuth for Azimuth ATAC.

> head(colSums(obj[["RNA"]]$counts))
# this works
> head(TFBSTools::colSums(obj[["RNA"]]$counts))
Error in .local(x, na.rm, dims, ...) : 
  object 'CRsparse_colSums' not found

Specifically, this is only an issue if you have Matrix 1.6-3. TFBSTools::colSums runs fine if I have an older Matrix version. Looking into this now and if it's even fixable on our end or which packages we should reach out to. Will update here.

Gesmira commented 10 months ago

Hi, A solution is detailed in Seurat: https://github.com/satijalab/seurat/issues/8089#issuecomment-1847816493

Ensure you have R version 4.3 or update to it.
In a fresh R session, update Bioconductor with the following call:
```
BiocManager::install(version = "3.18")
```
When prompted if you would like to update all packages, say yes. This will then update a series of Bioconductor packages which may take up to an hour.
At this point, the issue should be fixed. Let us know if you continue to encounter problems.

JarneBelien commented 10 months ago

Dear @Gesmira,

I have done the above fix but I keep getting this error when I run RunAzimuth:

Error in .local(x, na.rm, dims, ...) : object 'CRsparse_colSums' not found

My R version is 4.3.1 and I ran the BiocManager::install(version = "3.18") command as suggested above.

I also saw in another thread that a possible fix might be to unload Azimuth, however as I am trying to run the RunAzimuth command this is of course not an option. Might it still be due to some other dependency conflicts?

Do you have any other fix suggestions?

Gesmira commented 10 months ago

Hi @JarneBelien , I'm afraid I can't reproduce this. Did you restart your R session before updating the packages? If you're still experiencing the error, can you include the full output of sessionInfo()?

JarneBelien commented 10 months ago

Yes, I did restart the R session before the update. I tried again and get the same error. My session info is as follows:

`R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=Dutch_Belgium.utf8 LC_CTYPE=Dutch_Belgium.utf8 LC_MONETARY=Dutch_Belgium.utf8 [4] LC_NUMERIC=C LC_TIME=Dutch_Belgium.utf8

time zone: Europe/Brussels tzcode source: internal

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

other attached packages: [1] Azimuth_0.5.0 shinyBS_0.61.1 writexl_1.4.2 viridis_0.6.4 viridisLite_0.4.2
[6] showtext_0.9-6 showtextdb_3.0 sysfonts_0.8.8 Seurat_5.0.1 RColorBrewer_1.1-3
[11] ggplot2_3.4.4 FSA_0.9.5 dplyr_1.1.4 ComplexHeatmap_2.18.0 SeuratObject_5.0.1
[16] sp_2.1-2

loaded via a namespace (and not attached): [1] fs_1.6.3 ProtGenerics_1.34.0 matrixStats_1.2.0
[4] spatstat.sparse_3.0-3 bitops_1.0-7 DirichletMultinomial_1.44.0
[7] TFBSTools_1.40.0 httr_1.4.7 doParallel_1.0.17
[10] tools_4.3.1 sctransform_0.4.1 utf8_1.2.4
[13] R6_2.5.1 DT_0.31 lazyeval_0.2.2
[16] uwot_0.1.16 rhdf5filters_1.14.1 GetoptLong_1.0.5
[19] withr_2.5.2 prettyunits_1.2.0 gridExtra_2.3
[22] progressr_0.14.0 cli_3.6.2 Biobase_2.62.0
[25] spatstat.explore_3.2-5 fastDummies_1.7.3 EnsDb.Hsapiens.v86_2.99.0
[28] shinyjs_2.1.0 labeling_0.4.3 spatstat.data_3.0-3
[31] readr_2.1.4 ggridges_0.5.4 pbapply_1.7-2
[34] Rsamtools_2.18.0 R.utils_2.12.3 parallelly_1.36.0
[37] BSgenome_1.70.1 limma_3.58.1 rstudioapi_0.15.0
[40] RSQLite_2.3.4 generics_0.1.3 shape_1.4.6
[43] BiocIO_1.12.0 gtools_3.9.5 ica_1.0-3
[46] spatstat.random_3.2-2 googlesheets4_1.1.1 GO.db_3.18.0
[49] Matrix_1.6-4 ggbeeswarm_0.7.2 fansi_1.0.6
[52] S4Vectors_0.40.2 abind_1.4-5 R.methodsS3_1.8.2
[55] lifecycle_1.0.4 yaml_2.3.8 SummarizedExperiment_1.32.0
[58] rhdf5_2.46.1 SparseArray_1.2.2 BiocFileCache_2.10.1
[61] Rtsne_0.17 blob_1.2.4 promises_1.2.1
[64] shinydashboard_0.7.2 crayon_1.5.2 miniUI_0.1.1.1
[67] lattice_0.22-5 cowplot_1.1.1 annotate_1.80.0
[70] GenomicFeatures_1.54.1 KEGGREST_1.42.0 pillar_1.9.0
[73] knitr_1.45 GenomicRanges_1.54.1 rjson_0.2.21
[76] future.apply_1.11.0 codetools_0.2-19 fastmatch_1.1-4
[79] leiden_0.4.3.1 glue_1.6.2 data.table_1.14.10
[82] vctrs_0.6.5 png_0.1-8 spam_2.10-0
[85] cellranger_1.1.0 poweRlaw_0.70.6 gtable_0.3.4
[88] cachem_1.0.8 xfun_0.41 Signac_1.12.0
[91] S4Arrays_1.2.0 mime_0.12 pracma_2.4.4
[94] survival_3.5-7 pbmcref.SeuratData_1.0.0 gargle_1.5.2
[97] RcppRoll_0.3.0 iterators_1.0.14 statmod_1.5.0
[100] ellipsis_0.3.2 fitdistrplus_1.1-11 ROCR_1.0-11
[103] nlme_3.1-164 bit64_4.0.5 progress_1.2.3
[106] filelock_1.0.3 RcppAnnoy_0.0.21 GenomeInfoDb_1.38.1
[109] irlba_2.3.5.1 vipor_0.4.5 KernSmooth_2.23-22
[112] seqLogo_1.68.0 SeuratDisk_0.0.0.9021 colorspace_2.1-0
[115] BiocGenerics_0.48.1 DBI_1.1.3 ggrastr_1.0.2
[118] tidyselect_1.2.0 bit_4.0.5 compiler_4.3.1
[121] curl_5.2.0 hdf5r_1.3.8 xml2_1.3.6
[124] DelayedArray_0.28.0 plotly_4.10.3 rtracklayer_1.62.0
[127] caTools_1.18.2 scales_1.3.0 lmtest_0.9-40
[130] rappdirs_0.3.3 stringr_1.5.1 digest_0.6.33
[133] goftest_1.2-3 spatstat.utils_3.0-4 presto_1.0.0
[136] rmarkdown_2.25 XVector_0.42.0 htmltools_0.5.7
[139] pkgconfig_2.0.3 MatrixGenerics_1.14.0 dbplyr_2.4.0
[142] fastmap_1.1.1 ensembldb_2.26.0 rlang_1.1.2
[145] GlobalOptions_0.1.2 htmlwidgets_1.6.4 shiny_1.8.0
[148] farver_2.1.1 zoo_1.8-12 jsonlite_1.8.8
[151] BiocParallel_1.36.0 R.oo_1.25.0 RCurl_1.98-1.13
[154] magrittr_2.0.3 GenomeInfoDbData_1.2.11 dotCall64_1.1-1
[157] patchwork_1.1.3 Rhdf5lib_1.24.0 munsell_0.5.0
[160] Rcpp_1.0.11 reticulate_1.34.0 stringi_1.8.3
[163] zlibbioc_1.48.0 MASS_7.3-60 plyr_1.8.9
[166] parallel_4.3.1 listenv_0.9.0 ggrepel_0.9.4
[169] CNEr_1.38.0 deldir_2.0-2 Biostrings_2.70.1
[172] splines_4.3.1 tensor_1.5 hms_1.1.3
[175] circlize_0.4.15 BSgenome.Hsapiens.UCSC.hg38_1.4.5 igraph_1.6.0
[178] spatstat.geom_3.2-7 RcppHNSW_0.5.0 reshape2_1.4.4
[181] biomaRt_2.58.0 stats4_4.3.1 TFMPvalue_0.0.9
[184] XML_3.99-0.16 evaluate_0.23 tzdb_0.4.0
[187] JASPAR2020_0.99.10 foreach_1.5.2 httpuv_1.6.13
[190] RANN_2.6.1 tidyr_1.3.0 purrr_1.0.2
[193] polyclip_1.10-6 SeuratData_0.2.2.9001 future_1.33.0
[196] clue_0.3-65 scattermore_1.2 xtable_1.8-4
[199] restfulr_0.0.15 AnnotationFilter_1.26.0 RSpectra_0.16-1
[202] later_1.3.2 googledrive_2.1.1 tibble_3.2.1
[205] memoise_2.0.1 beeswarm_0.4.0 AnnotationDbi_1.64.1
[208] GenomicAlignments_1.38.0 IRanges_2.36.0 cluster_2.1.6
[211] globals_0.16.2 `

satijalab / azimuth

Error in .local(x, na.rm, dims, ...) : object 'CRsparse_colSums' not found error from RunAzimuth() #192