Closed sbdaxia closed 11 months ago
please show the full code you're running and the output of sessionInfo()
@sbdaxia any update on this?
Sorry took me a bit of time to establish a reproducible example. It turns out the error is actually coming from a conflict between the chromVAR
package and the Signac
package.
I was able to run the following code with no error if chromVAR
is not loaded.
chrom_assay <- CreateChromatinAssay(
counts = atac_mtx,
assay = "sci",
genome = "mm10",
ranges = sci_geo_peaks,
project = 'sci'
)
However, as soon as chromVAR
is loaded, running the same code gives me the following error
Error in .local(x, na.rm, dims, ...) :
object 'R_sparse_marginsum' not found
I have changed the title of this thread to better describe this issue. Would this be something that I should post to the chromVAR
Github?
Below is my sessionInfo
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.5.1
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-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
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
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] chromVAR_1.24.0 lubridate_1.9.3 forcats_1.0.0 dplyr_1.1.3
[5] purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[9] tidyverse_2.0.0 ArchRtoSignac_1.0.3 rhdf5_2.46.0 SummarizedExperiment_1.32.0
[13] MatrixGenerics_1.14.0 Rcpp_1.0.11 matrixStats_1.1.0 data.table_1.14.8
[17] stringr_1.5.1 plyr_1.8.9 magrittr_2.0.3 gtable_0.3.4
[21] gtools_3.9.4 gridExtra_2.3 ArchR_1.0.2 EnsDb.Mmusculus.v79_2.99.0
[25] ensembldb_2.26.0 AnnotationFilter_1.26.0 GenomicFeatures_1.54.1 AnnotationDbi_1.64.1
[29] Biobase_2.62.0 rtracklayer_1.62.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.0
[33] IRanges_2.36.0 S4Vectors_0.40.1 BiocGenerics_0.48.1 Matrix_1.6-1
[37] ggplot2_3.4.4 Seurat_5.0.0 SeuratObject_5.0.0 sp_2.1-1
[41] Signac_1.12.0
loaded via a namespace (and not attached):
[1] ProtGenerics_1.34.0 spatstat.sparse_3.0-3 bitops_1.0-7 DirichletMultinomial_1.44.0
[5] TFBSTools_1.40.0 httr_1.4.7 RColorBrewer_1.1-3 tools_4.3.1
[9] sctransform_0.4.1 utf8_1.2.4 R6_2.5.1 DT_0.30
[13] lazyeval_0.2.2 uwot_0.1.16 rhdf5filters_1.14.1 withr_2.5.2
[17] prettyunits_1.2.0 progressr_0.14.0 cli_3.6.1 Cairo_1.6-1
[21] spatstat.explore_3.2-5 fastDummies_1.7.3 spatstat.data_3.0-3 ggridges_0.5.4
[25] pbapply_1.7-2 Rsamtools_2.18.0 R.utils_2.12.2 parallelly_1.36.0
[29] BSgenome_1.70.1 rstudioapi_0.15.0 RSQLite_2.3.3 generics_0.1.3
[33] BiocIO_1.12.0 ica_1.0-3 spatstat.random_3.2-1 GO.db_3.18.0
[37] fansi_1.0.5 abind_1.4-5 R.methodsS3_1.8.2 lifecycle_1.0.4
[41] yaml_2.3.7 SparseArray_1.2.2 BiocFileCache_2.10.1 Rtsne_0.16
[45] blob_1.2.4 promises_1.2.1 crayon_1.5.2 miniUI_0.1.1.1
[49] lattice_0.22-5 cowplot_1.1.1 annotate_1.80.0 KEGGREST_1.42.0
[53] pillar_1.9.0 knitr_1.45 rjson_0.2.21 future.apply_1.11.0
[57] codetools_0.2-19 fastmatch_1.1-4 leiden_0.4.3 glue_1.6.2
[61] vctrs_0.6.4 png_0.1-8 spam_2.10-0 poweRlaw_0.70.6
[65] cachem_1.0.8 xfun_0.41 S4Arrays_1.2.0 mime_0.12
[69] pracma_2.4.4 survival_3.5-7 RcppRoll_0.3.0 ellipsis_0.3.2
[73] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-163 bit64_4.0.5
[77] progress_1.2.2 filelock_1.0.2 RcppAnnoy_0.0.21 irlba_2.3.5.1
[81] KernSmooth_2.23-22 colorspace_2.1-0 seqLogo_1.68.0 DBI_1.1.3
[85] tidyselect_1.2.0 bit_4.0.5 compiler_4.3.1 curl_5.1.0
[89] xml2_1.3.5 DelayedArray_0.28.0 plotly_4.10.3 scales_1.2.1
[93] caTools_1.18.2 lmtest_0.9-40 rappdirs_0.3.3 digest_0.6.33
[97] goftest_1.2-3 spatstat.utils_3.0-4 rmarkdown_2.25 XVector_0.42.0
[101] htmltools_0.5.7 pkgconfig_2.0.3 dbplyr_2.4.0 fastmap_1.1.1
[105] rlang_1.1.2 htmlwidgets_1.6.2 shiny_1.7.5.1 zoo_1.8-12
[109] jsonlite_1.8.7 BiocParallel_1.36.0 R.oo_1.25.0 RCurl_1.98-1.13
[113] GenomeInfoDbData_1.2.11 dotCall64_1.1-0 patchwork_1.1.3 Rhdf5lib_1.24.0
[117] munsell_0.5.0 reticulate_1.34.0 stringi_1.8.1 zlibbioc_1.48.0
[121] MASS_7.3-60 parallel_4.3.1 listenv_0.9.0 ggrepel_0.9.4
[125] deldir_1.0-9 CNEr_1.38.0 Biostrings_2.70.1 splines_4.3.1
[129] tensor_1.5 hms_1.1.3 igraph_1.5.1 spatstat.geom_3.2-7
[133] RcppHNSW_0.5.0 reshape2_1.4.4 biomaRt_2.58.0 TFMPvalue_0.0.9
[137] XML_3.99-0.15 evaluate_0.23 tzdb_0.4.0 httpuv_1.6.12
[141] RANN_2.6.1 polyclip_1.10-6 future_1.33.0 scattermore_1.2
[145] xtable_1.8-4 restfulr_0.0.15 RSpectra_0.16-1 later_1.3.1
[149] viridisLite_0.4.2 memoise_2.0.1 GenomicAlignments_1.38.0 cluster_2.1.4
[153] timechange_0.2.0 globals_0.16.2
You can try re-installing SeuratObject, this could be related to some other issues reported here: https://github.com/mojaveazure/seurat-object/commit/d567ec8b0f49534bd51c29f153f2e0b877dedc34
I can confirm that after updating SeuratObject
to 5.0.1, the issue has been resolved. Thank you so much for your help!
Using the
CreateChromatinAssay
function with Seurat 5 loaded renders the following errorDowngrading Seurat to 4.4.0 resolved this issue. So I presume this error is coming from incompatibility between Seurat 5 and the current version of Signac.