Error in pbMDS useNames = NA is defunct

[LeleDR]

Hello I have an issue that can't understand how to resolve.

CATALYST::pbMDS(sce, shape_by = "patient_id", size_by = FALSE)

Error: [matrixStats (>= 1.2.0)] useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. See also ?matrixStats::matrixStats.options

I am able to do the smoothed densities, the barplots and the heatmap but I can't make the MDS and I can't find how to fix the error

Thank you very much in advance for your help!

Léa

[HelenaLC]

Could you please post the output of your session info?

[LeleDR]

sessionInfo() R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22631)

Matrix products: default

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

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

other attached packages: [1] flowCore_2.10.0 CATALYST_1.22.0 SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0 [5] Biobase_2.58.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 IRanges_2.32.0
[9] S4Vectors_0.36.2 BiocGenerics_0.44.0 MatrixGenerics_1.10.0 matrixStats_1.3.0
[13] readxl_1.4.3

loaded via a namespace (and not attached): [1] backports_1.5.0 circlize_0.4.16 drc_3.0-1 plyr_1.8.9
[5] igraph_2.0.3 ConsensusClusterPlus_1.62.0 splines_4.2.1 BiocParallel_1.32.6
[9] usethis_3.0.0 ggplot2_3.5.1 scater_1.26.1 TH.data_1.1-2
[13] digest_0.6.36 foreach_1.5.2 htmltools_0.5.8.1 viridis_0.6.5
[17] fansi_1.0.6 magrittr_2.0.3 memoise_2.0.1 ScaledMatrix_1.6.0
[21] cluster_2.1.3 doParallel_1.0.17 remotes_2.5.0 ComplexHeatmap_2.14.0
[25] sandwich_3.1-1 cytolib_2.10.1 colorspace_2.1-0 ggrepel_0.9.5
[29] dplyr_1.1.4 crayon_1.5.3 RCurl_1.98-1.16 survival_3.3-1
[33] zoo_1.8-12 iterators_1.0.14 glue_1.7.0 polyclip_1.10-7
[37] gtable_0.3.5 nnls_1.5 zlibbioc_1.44.0 XVector_0.38.0
[41] GetoptLong_1.0.5 DelayedArray_0.24.0 pkgbuild_1.4.4 car_3.1-3
[45] BiocSingular_1.14.0 shape_1.4.6.1 abind_1.4-8 scales_1.3.0
[49] mvtnorm_1.3-1 rstatix_0.7.2 miniUI_0.1.1.1 Rcpp_1.0.12
[53] plotrix_3.8-4 xtable_1.8-4 viridisLite_0.4.2 clue_0.3-65
[57] rsvd_1.0.5 FlowSOM_2.6.0 Formula_1.2-5 profvis_0.3.8
[61] htmlwidgets_1.6.4 RColorBrewer_1.1-3 ellipsis_0.3.2 urlchecker_1.0.1
[65] pkgconfig_2.0.3 XML_3.99-0.17 farver_2.1.2 scuttle_1.8.4
[69] utf8_1.2.4 labeling_0.4.3 tidyselect_1.2.1 rlang_1.1.3
[73] reshape2_1.4.4 later_1.3.2 cellranger_1.1.0 munsell_0.5.1
[77] tools_4.2.1 cachem_1.1.0 cli_3.6.1 generics_0.1.3
[81] devtools_2.4.5 broom_1.0.7 ggridges_0.5.6 stringr_1.5.1
[85] fastmap_1.2.0 fs_1.6.4 purrr_1.0.2 sparseMatrixStats_1.10.0
[89] mime_0.12 compiler_4.2.1 rstudioapi_0.16.0 beeswarm_0.4.0
[93] png_0.1-8 ggsignif_0.6.4 tibble_3.2.1 tweenr_2.0.3
[97] stringi_1.8.4 lattice_0.20-45 Matrix_1.5-4 vctrs_0.6.5
[101] pillar_1.9.0 lifecycle_1.0.4 BiocManager_1.30.25 GlobalOptions_0.1.2
[105] BiocNeighbors_1.16.0 data.table_1.16.0 cowplot_1.1.3 bitops_1.0-8
[109] irlba_2.3.5.1 httpuv_1.6.15 colorRamps_2.3.4 R6_2.5.1
[113] promises_1.3.0 gridExtra_2.3 RProtoBufLib_2.10.0 vipor_0.4.7
[117] sessioninfo_1.2.2 codetools_0.2-18 pkgload_1.4.0 MASS_7.3-57
[121] gtools_3.9.5 rjson_0.2.21 withr_3.0.1 multcomp_1.4-26
[125] GenomeInfoDbData_1.2.9 parallel_4.2.1 grid_4.2.1 beachmat_2.14.2
[129] tidyr_1.3.1 DelayedMatrixStats_1.20.0 carData_3.0-5 Rtsne_0.17
[133] ggpubr_0.6.0 ggnewscale_0.5.0 ggforce_0.4.2 shiny_1.9.1
[137] ggbeeswarm_0.7.2

[HelenaLC]

R's current release version is 4.4.1 vs. yours: 4.2.1, which is 2.5 yo; accordingly, your package versions are severely outdated (e.g., CATALYST 1.22.0 instead of now: 1.28.0)... I'd suggest updating your software, as it is difficult to reproduce or lend advice regarding issues that are long outdated. If the issue persist with current software, I'll be happy to look into it!