RunFastMNN Error in normarg_grid(grid, x)

[zezhuo]

Hi, I got an issue when running RunFastMNN (SeuratWrappers_0.3.1) below: Computing 2000 integration features 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.

Same issue was reported in Seurat: https://github.com/satijalab/seurat/issues/7295 SeuratWrappers_0.3.0 works well in another windows device. But v0.3.0 is not available anymore. Please check it out. Thanks!

Regards, Nelson

sessionInfo() R version 4.3.0 (2023-04-21 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: Etc/GMT-8 tzcode source: internal

attached base packages: [1] stats4 grid parallel stats graphics grDevices utils datasets [9] methods base

other attached packages: [1] SeuratWrappers_0.3.1 DelayedArray_0.26.2 S4Arrays_1.0.1
[4] IRanges_2.34.0 S4Vectors_0.38.1 MatrixGenerics_1.12.0 [7] matrixStats_0.63.0 BiocGenerics_0.46.0 Matrix_1.5-4
[10] plyr_1.8.8 stringr_1.5.0 patchwork_1.1.2
[13] gridtext_0.1.5 officer_0.6.2 gridExtra_2.3
[16] magick_2.7.4 cowplot_1.1.1 ggrepel_0.9.3
[19] ggrastr_1.0.1 ggplot2_3.4.2 ComplexHeatmap_2.16.0 [22] doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2
[25] dplyr_1.1.2 KernSmooth_2.23-20 RColorBrewer_1.1-3
[28] SCopeLoomR_0.13.0 BiocParallel_1.34.1 SCENIC_1.3.1
[31] gprofiler2_0.2.1 future_1.32.0 sceasy_0.0.7
[34] reticulate_1.28 SeuratObject_4.1.3 Seurat_4.3.0

loaded via a namespace (and not attached): [1] spatstat.sparse_3.0-1 bitops_1.0-7 httr_1.4.6
[4] tools_4.3.0 sctransform_0.3.5 backports_1.4.1
[7] ResidualMatrix_1.10.0 utf8_1.2.3 R6_2.5.1
[10] lazyeval_0.2.2 uwot_0.1.14 GetoptLong_1.0.5
[13] withr_2.5.0 sp_1.6-0 prettyunits_1.1.1
[16] progressr_0.13.0 textshaping_0.3.6 cli_3.6.1
[19] Biobase_2.60.0 logging_0.10-108 spatstat.explore_3.1-0
[22] labeling_0.4.2 spatstat.data_3.0-1 askpass_1.1
[25] ggridges_0.5.4 pbapply_1.7-0 systemfonts_1.0.4
[28] ggradar2_1.1.0 R.utils_2.12.2 parallelly_1.35.0
[31] limma_3.56.1 readxl_1.4.2 rstudioapi_0.14
[34] RSQLite_2.3.1 generics_0.1.3 shape_1.4.6
[37] ica_1.0-3 spatstat.random_3.1-5 zip_2.3.0
[40] car_3.1-2 ggbeeswarm_0.7.2 fansi_1.0.4
[43] abind_1.4-5 R.methodsS3_1.8.2 lifecycle_1.0.3
[46] edgeR_3.42.2 carData_3.0-5 SummarizedExperiment_1.30.1 [49] Rtsne_0.16 blob_1.2.4 promises_1.2.0.1
[52] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.21-8
[55] beachmat_2.16.0 annotate_1.78.0 KEGGREST_1.40.0
[58] pillar_1.9.0 knitr_1.42 GenomicRanges_1.52.0
[61] rjson_0.2.21 future.apply_1.11.0 codetools_0.2-19
[64] leiden_0.4.3 glue_1.6.2 ggvenn_0.1.10
[67] data.table_1.14.8 remotes_2.4.2 vctrs_0.6.2
[70] png_0.1-8 cellranger_1.1.0 gtable_0.3.3
[73] cachem_1.0.8 xfun_0.39 mime_0.12
[76] ConsensusClusterPlus_1.64.0 survival_3.5-5 SingleCellExperiment_1.22.0 [79] pheatmap_1.0.12 ellipsis_0.3.2 fitdistrplus_1.1-11
[82] ROCR_1.0-11 lsa_0.73.3 nlme_3.1-162
[85] bit64_4.0.5 RcppAnnoy_0.0.20 rprojroot_2.0.3
[88] GenomeInfoDb_1.36.0 SnowballC_0.7.1 irlba_2.3.5.1
[91] vipor_0.4.5 colorspace_2.1-0 DBI_1.1.3
[94] processx_3.8.1 DESeq2_1.40.1 mnormt_2.1.1
[97] tidyselect_1.2.0 curl_5.0.0 bit_4.0.5
[100] compiler_4.3.0 AUCell_1.22.0 graph_1.78.0
[103] BiocNeighbors_1.18.0 hdf5r_1.3.8 xml2_1.3.4
[106] desc_1.4.2 ggdendro_0.1.23 plotly_4.10.1
[109] scales_1.2.1 psych_2.3.3 lmtest_0.9-40
[112] callr_3.7.3 digest_0.6.31 goftest_1.2-3
[115] spatstat.utils_3.0-3 XVector_0.40.0 htmltools_0.5.5
[118] pkgconfig_2.0.3 sparseMatrixStats_1.12.0 fastmap_1.1.1
[121] rlang_1.1.1 GlobalOptions_0.1.2 htmlwidgets_1.6.2
[124] shiny_1.7.4 DelayedMatrixStats_1.22.0 farver_2.1.1
[127] zoo_1.8-12 jsonlite_1.8.4 R.oo_1.25.0
[130] BiocSingular_1.16.0 RCurl_1.98-1.12 magrittr_2.0.3
[133] scuttle_1.10.1 GenomeInfoDbData_1.2.10 munsell_0.5.0
[136] Rcpp_1.0.10 ape_5.7-1 viridis_0.6.3
[139] stringi_1.7.12 zlibbioc_1.46.0 MASS_7.3-58.4
[142] pkgbuild_1.4.0 DEGreport_1.36.0 listenv_0.9.0
[145] deldir_1.0-6 Biostrings_2.68.1 splines_4.3.0
[148] tensor_1.5 circlize_0.4.15 locfit_1.5-9.7
[151] ps_1.7.5 uuid_1.1-0 igraph_1.4.2
[154] ggpubr_0.6.0 spatstat.geom_3.2-1 ggsignif_0.6.4
[157] ScaledMatrix_1.8.1 reshape2_1.4.4 XML_3.99-0.14
[160] BiocManager_1.30.20 batchelor_1.16.0 httpuv_1.6.11
[163] openssl_2.0.6 RANN_2.6.1 tidyr_1.3.0
[166] purrr_1.0.1 polyclip_1.10-4 reshape_0.8.9
[169] clue_0.3-64 scattermore_1.0 rsvd_1.0.5
[172] broom_1.0.4 xtable_1.8-4 rstatix_0.7.2
[175] later_1.3.1 ragg_1.2.5 viridisLite_0.4.2
[178] tibble_3.2.1 memoise_2.0.1 beeswarm_0.4.0
[181] AnnotationDbi_1.62.1 cluster_2.1.4 globals_0.16.2
[184] GSEABase_1.62.0

[liziyie]

The problem happened in this command: integrated[[reconstructed.assay]] <- CreateAssayObject( data = as(object = SummarizedExperiment::assay(x = out), Class = "sparseMatrix"), ) The function failed to extract the reconstructed assay from the output of fastmnn "out". I don't know how to do this as well... when check "out" it shows like this assay(out) Error in (function (cond) : error in evaluating the argument 'x' in selecting a method for function 'type': object of type 'S4' is not subsettable

[Lucyyang1991]

I have the same issue that was reported in Seurat: https://github.com/satijalab/seurat/issues/7295, so just want to follow a workaround.

[menage95]

I am also having this issue. Did anyone find a resolution?

[stevensalvini]

After spending time chasing a solution I gave up so I’m afraid my “resolution” was to do a bare metal reinstall of Linux and everything above! When I did so it all worked as it should.

[kmh005]

Also looking for guidance here, Seurat5, Windows 10 machine.

[bravedu01]

Same issue in macbook. Anyone has a resolution?