<simpleError: 'coef.cv.glmnet' is not an exported object from 'namespace:glmnet'>

[evenDDDDD]

Hi, When I run classify_cells, there is such an error like #42 , I want to know why？ <simpleError: 'coef.cv.glmnet' is not an exported object from 'namespace:glmnet'>

my R sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: ,,,,,,,/python3/lib/libopenblasp-r0.3.9.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] org.Mm.eg.db_3.10.0 AnnotationDbi_1.48.0 [3] cowplot_1.1.0 dplyr_1.0.2 [5] Seurat_3.2.1 garnett_0.2.15 [7] monocle3_0.2.3.0 SingleCellExperiment_1.8.0 [9] SummarizedExperiment_1.16.1 DelayedArray_0.12.3 [11] BiocParallel_1.20.1 matrixStats_0.56.0 [13] GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 [15] IRanges_2.20.2 S4Vectors_0.24.4 [17] Biobase_2.46.0 BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] backports_1.1.9 plyr_1.8.6 igraph_1.2.5 [4] lazyeval_0.2.2 splines_3.6.3 listenv_0.8.0 [7] usethis_1.6.1 ggplot2_3.3.2 digest_0.6.25 [10] foreach_1.5.0 htmltools_0.5.0 viridis_0.5.1 [13] fansi_0.4.1 magrittr_1.5 memoise_1.1.0 [16] tensor_1.5 cluster_2.1.0 ROCR_1.0-11 [19] remotes_2.2.0 globals_0.12.5 prettyunits_1.1.1 [22] colorspace_1.4-1 blob_1.2.1 rappdirs_0.3.1 [25] ggrepel_0.8.2 callr_3.4.4 crayon_1.3.4 [28] RCurl_1.98-1.2 jsonlite_1.7.1 spatstat_1.64-1 [31] spatstat.data_1.4-3 iterators_1.0.12 survival_3.2-3 [34] zoo_1.8-8 glue_1.4.2 polyclip_1.10-0 [37] gtable_0.3.0 zlibbioc_1.32.0 XVector_0.26.0 [40] leiden_0.3.3 pkgbuild_1.1.0 shape_1.4.4 [43] future.apply_1.6.0 abind_1.4-5 scales_1.1.1 [46] DBI_1.1.0 miniUI_0.1.1.1 Rcpp_1.0.5 [49] viridisLite_0.3.0 xtable_1.8-4 reticulate_1.16 [52] bit_4.0.4 rsvd_1.0.3 glmnet_4.0-2 [55] htmlwidgets_1.5.1 httr_1.4.2 RColorBrewer_1.1-2 [58] ellipsis_0.3.1 ica_1.0-2 pkgconfig_2.0.3 [61] uwot_0.1.8 deldir_0.1-28 tidyselect_1.1.0 [64] rlang_0.4.7 reshape2_1.4.4 later_1.1.0.1 [67] munsell_0.5.0 tools_3.6.3 cli_2.0.2 [70] RSQLite_2.2.0 generics_0.0.2 devtools_2.3.1 [73] ggridges_0.5.2 stringr_1.4.0 fastmap_1.0.1 [76] goftest_1.2-2 bit64_4.0.5 processx_3.4.4 [79] fs_1.5.0 fitdistrplus_1.1-1 purrr_0.3.4 [82] RANN_2.6.1 pbapply_1.4-3 future_1.18.0 [85] nlme_3.1-149 mime_0.9 compiler_3.6.3 [88] plotly_4.9.2.1 curl_4.3 png_0.1-7 [91] testthat_2.3.2 spatstat.utils_1.17-0 tibble_3.0.3 [94] stringi_1.5.3 ps_1.3.4 desc_1.2.0 [97] lattice_0.20-41 Matrix_1.2-18 vctrs_0.3.4 [100] pillar_1.4.6 lifecycle_0.2.0 lmtest_0.9-38 [103] RcppAnnoy_0.0.16 data.table_1.13.0 bitops_1.0-6 [106] irlba_2.3.3 httpuv_1.5.4 patchwork_1.0.1 [109] R6_2.4.1 promises_1.1.1 KernSmooth_2.23-17 [112] gridExtra_2.3 sessioninfo_1.1.1 codetools_0.2-16 [115] MASS_7.3-53 assertthat_0.2.1 pkgload_1.1.0 [118] rprojroot_1.3-2 withr_2.2.0 sctransform_0.2.1 [121] GenomeInfoDbData_1.2.2 mgcv_1.8-33 grid_3.6.3 [124] rpart_4.1-15 tidyr_1.1.2 DelayedMatrixStats_1.8.0 [127] Rtsne_0.15 shiny_1.5.0

Thanks!

[evenDDDDD]

The result was that all cells were classified as “Unknown” `> table(pData(cds)$cell_type)

Unknown 20596 `

[hpliner]

Hi,

Not sure why this is happening on your setup given the versions that you have. I've tried one small fix in Garnett 0.2.16 to better point to the function in question. Can you please reinstall garnett, restart your session and give it another try?

[hpliner]

Closing, reopen if this is still an issue!