stevensalvini
commented
1 year ago UPDATE:
Using Seurat_4.9.9.9045, the error message contains additional information:
obj <- IntegrateLayers(object = obj, method = FastMNNIntegration, new.reduction = "integrated.mnn")
Converting layers to SingleCellExperiment
Running fastMNN
Error in normarg_grid(grid, x) :
The current automatic grid maker returned an error when called on 'x'. Please use setAutoGridMaker()
to set a valid automatic grid maker.
In addition: Warning messages:
1: replacing previous import ‘S4Arrays::read_block’ by ‘DelayedArray::read_block’ when loading ‘SummarizedExperiment’
2: invoke() is deprecated as of rlang 0.4.0.Please use exec() or inject() instead.This warning is displayed once every 8 hours.
I have installed the Seurat 5 beta and it's all working well for me bar the FastNMM part.
I have the exactly same problem with the vignette code (so not giving an example of my own here). The issue is this...
Running:
obj <- IntegrateLayers( object = obj, method = FastMNNIntegration, new.reduction = "integrated.mnn", verbose = FALSE )
Results in the error:
Error in normarg_grid(grid, x) : The current automatic grid maker returned an error when called on 'x'. Please use setAutoGridMaker() to set a valid automatic grid maker.
I am guessing that I have maybe omitted one of the prequistes but I can't work out which if that is the case.
Any help, much appreciated!
Steve
-- R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.2 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8
[4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] patchwork_1.1.2 ggplot2_3.4.2 Azimuth_0.4.6.9002 shinyBS_0.61.1
[5] SeuratWrappers_0.3.19 pbmcsca.SeuratData_3.0.0 pbmcref.SeuratData_1.0.0 pbmc3k.SeuratData_3.1.4 [9] SeuratData_0.2.2.9001 Seurat_4.9.9.9044 SeuratObject_4.9.9.9084 sp_1.6-0
loaded via a namespace (and not attached): [1] fs_1.6.2 ProtGenerics_1.32.0 matrixStats_0.63.0
[4] spatstat.sparse_3.0-1 bitops_1.0-7 DirichletMultinomial_1.42.0
[7] TFBSTools_1.38.0 httr_1.4.6 RColorBrewer_1.1-3
[10] tools_4.3.0 sctransform_0.3.5 ResidualMatrix_1.10.0
[13] utf8_1.2.3 R6_2.5.1 DT_0.27
[16] lazyeval_0.2.2 uwot_0.1.14 rhdf5filters_1.12.1
[19] withr_2.5.0 prettyunits_1.1.1 gridExtra_2.3
[22] progressr_0.13.0 cli_3.6.1 Biobase_2.60.0
[25] spatstat.explore_3.1-0 fastDummies_1.6.3 EnsDb.Hsapiens.v86_2.99.0
[28] shinyjs_2.1.0 labeling_0.4.2 spatstat.data_3.0-1
[31] readr_2.1.4 ggridges_0.5.4 pbapply_1.7-0
[34] Rsamtools_2.16.0 R.utils_2.12.2 parallelly_1.35.0
[37] BSgenome_1.68.0 rstudioapi_0.14 RSQLite_2.3.1
[40] generics_0.1.3 BiocIO_1.10.0 gtools_3.9.4
[43] ica_1.0-3 spatstat.random_3.1-4 googlesheets4_1.1.0
[46] dplyr_1.1.2 GO.db_3.17.0 Matrix_1.5-4
[49] fansi_1.0.4 S4Vectors_0.38.1 abind_1.4-5
[52] R.methodsS3_1.8.2 lifecycle_1.0.3 yaml_2.3.7
[55] SummarizedExperiment_1.30.1 rhdf5_2.44.0 BiocFileCache_2.8.0
[58] Rtsne_0.16 grid_4.3.0 blob_1.2.4
[61] promises_1.2.0.1 shinydashboard_0.7.2 crayon_1.5.2
[64] miniUI_0.1.1.1 lattice_0.21-8 beachmat_2.16.0
[67] cowplot_1.1.1 annotate_1.78.0 GenomicFeatures_1.52.0
[70] KEGGREST_1.40.0 pillar_1.9.0 GenomicRanges_1.52.0
[73] rjson_0.2.21 future.apply_1.10.0 codetools_0.2-19
[76] fastmatch_1.1-3 leiden_0.4.3 glue_1.6.2
[79] data.table_1.14.8 remotes_2.4.2 vctrs_0.6.2
[82] png_0.1-8 spam_2.9-1 cellranger_1.1.0
[85] poweRlaw_0.70.6 gtable_0.3.3 cachem_1.0.8
[88] Signac_1.9.0.9000 S4Arrays_1.0.1 mime_0.12
[91] pracma_2.4.2 survival_3.5-5 gargle_1.4.0
[94] SingleCellExperiment_1.22.0 RcppRoll_0.3.0 ellipsis_0.3.2
[97] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-162
[100] bit64_4.0.5 progress_1.2.2 filelock_1.0.2
[103] RcppAnnoy_0.0.20 GenomeInfoDb_1.36.0 irlba_2.3.5.1
[106] KernSmooth_2.23-21 SeuratDisk_0.0.0.9020 colorspace_2.1-0
[109] seqLogo_1.66.0 BiocGenerics_0.46.0 DBI_1.1.3
[112] tidyselect_1.2.0 bit_4.0.5 compiler_4.3.0
[115] curl_5.0.0 BiocNeighbors_1.18.0 hdf5r_1.3.8
[118] xml2_1.3.4 DelayedArray_0.26.2 plotly_4.10.1
[121] rtracklayer_1.60.0 scales_1.2.1 caTools_1.18.2
[124] lmtest_0.9-40 rappdirs_0.3.3 stringr_1.5.0
[127] digest_0.6.31 goftest_1.2-3 presto_1.0.0
[130] spatstat.utils_3.0-2 XVector_0.40.0 htmltools_0.5.5
[133] pkgconfig_2.0.3 sparseMatrixStats_1.12.0 MatrixGenerics_1.12.0
[136] dbplyr_2.3.2 fastmap_1.1.1 ensembldb_2.24.0
[139] rlang_1.1.1 htmlwidgets_1.6.2 DelayedMatrixStats_1.22.0
[142] shiny_1.7.4 farver_2.1.1 zoo_1.8-12
[145] jsonlite_1.8.4 BiocParallel_1.34.1 R.oo_1.25.0
[148] BiocSingular_1.16.0 RCurl_1.98-1.12 magrittr_2.0.3
[151] scuttle_1.10.1 GenomeInfoDbData_1.2.10 dotCall64_1.0-2
[154] Rhdf5lib_1.22.0 munsell_0.5.0 Rcpp_1.0.10
[157] reticulate_1.28 stringi_1.7.12 zlibbioc_1.46.0
[160] MASS_7.3-60 plyr_1.8.8 parallel_4.3.0
[163] listenv_0.9.0 ggrepel_0.9.3 deldir_1.0-6
[166] CNEr_1.36.0 Biostrings_2.68.0 splines_4.3.0
[169] tensor_1.5 hms_1.1.3 BSgenome.Hsapiens.UCSC.hg38_1.4.5 [172] igraph_1.4.2 spatstat.geom_3.1-0 RcppHNSW_0.4.1
[175] ScaledMatrix_1.8.1 reshape2_1.4.4 biomaRt_2.56.0
[178] stats4_4.3.0 TFMPvalue_0.0.9 XML_3.99-0.14
[181] BiocManager_1.30.20 batchelor_1.16.0 JASPAR2020_0.99.10
[184] tzdb_0.3.0 httpuv_1.6.10 RANN_2.6.1
[187] tidyr_1.3.0 purrr_1.0.1 polyclip_1.10-4
[190] future_1.32.0 scattermore_1.0 rsvd_1.0.5
[193] xtable_1.8-4 restfulr_0.0.15 AnnotationFilter_1.24.0
[196] RSpectra_0.16-1 later_1.3.1 googledrive_2.1.0
[199] viridisLite_0.4.2 tibble_3.2.1 memoise_2.0.1
[202] AnnotationDbi_1.62.1 GenomicAlignments_1.36.0 IRanges_2.34.0
[205] cluster_2.1.4 globals_0.16.2