Error in xtfrm.data.frame(x) : cannot xtfrm data frames

[StefanosVoglis]

Hi, I got a new error using the version 2.0 of the package.

When running the example workflow I get the following error message

cell_predictions <- run_scATOMIC(lung_cancer_demo_data) [1] "Starting Layer 1" Error in xtfrm.data.frame(x) : cannot xtfrm data frames

And in contrast to the vignette its not a warning but an error message and causes an interruption of the function.

Any ideas what the reason could be?

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=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C
[5] LC_TIME=German_Germany.utf8

time zone: Europe/Berlin tzcode source: internal

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

other attached packages: [1] data.table_1.14.8 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2 purrr_1.0.1
[7] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 tidyverse_2.0.0 pbmcapply_1.5.1 DISCOtoolkit_1.0.0
[13] copykat_1.1.0 cutoff.scATOMIC_0.1.0 agrmt_1.42.8 SeuratObject_4.1.3 Seurat_4.3.0 Rmagic_2.0.3
[19] Matrix_1.5-4 reticulate_1.28 caret_6.0-94 lattice_0.21-8 ggplot2_3.4.2 randomForest_4.7-1.1 [25] scATOMIC_2.0.0

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.14 jsonlite_1.8.4 magrittr_2.0.3 spatstat.utils_3.0-3 rmarkdown_2.21
[7] vctrs_0.6.2 ROCR_1.0-11 spatstat.explore_3.2-1 htmltools_0.5.5 pROC_1.18.2 sctransform_0.3.5
[13] parallelly_1.35.0 KernSmooth_2.23-20 htmlwidgets_1.6.2 ica_1.0-3 plyr_1.8.8 plotly_4.10.1
[19] zoo_1.8-12 igraph_1.4.2 mime_0.12 lifecycle_1.0.3 iterators_1.0.14 pkgconfig_2.0.3
[25] R6_2.5.1 fastmap_1.1.1 fitdistrplus_1.1-11 future_1.32.0 shiny_1.7.4 digest_0.6.31
[31] colorspace_2.1-0 patchwork_1.1.2 rprojroot_2.0.3 tensor_1.5 irlba_2.3.5.1 progressr_0.13.0
[37] fansi_1.0.4 spatstat.sparse_3.0-1 timechange_0.2.0 polyclip_1.10-4 httr_1.4.6 abind_1.4-5
[43] compiler_4.3.0 here_1.0.1 withr_2.5.0 MASS_7.3-58.4 lava_1.7.2.1 rappdirs_0.3.3
[49] ModelMetrics_1.2.2.2 tools_4.3.0 lmtest_0.9-40 httpuv_1.6.11 future.apply_1.10.0 goftest_1.2-3
[55] nnet_7.3-18 glue_1.6.2 nlme_3.1-162 promises_1.2.0.1 grid_4.3.0 Rtsne_0.16
[61] cluster_2.1.4 reshape2_1.4.4 generics_0.1.3 recipes_1.0.6 gtable_0.3.3 spatstat.data_3.0-1
[67] tzdb_0.4.0 class_7.3-21 hms_1.1.3 sp_1.6-0 utf8_1.2.3 spatstat.geom_3.2-1
[73] RcppAnnoy_0.0.20 ggrepel_0.9.3 RANN_2.6.1 foreach_1.5.2 pillar_1.9.0 later_1.3.1
[79] splines_4.3.0 deldir_1.0-9 survival_3.5-5 tidyselect_1.2.0 miniUI_0.1.1.1 pbapply_1.7-0
[85] knitr_1.42 gridExtra_2.3 scattermore_1.1 stats4_4.3.0 xfun_0.39 hardhat_1.3.0
[91] timeDate_4022.108 matrixStats_0.63.0 stringi_1.7.12 lazyeval_0.2.2 yaml_2.3.7 evaluate_0.21
[97] codetools_0.2-19 cli_3.6.1 uwot_0.1.14 rpart_4.1.19 xtable_1.8-4 munsell_0.5.0
[103] Rcpp_1.0.10 spatstat.random_3.1-5 globals_0.16.2 png_0.1-8 ellipsis_0.3.2 gower_1.0.1
[109] listenv_0.9.0 viridisLite_0.4.2 ipred_0.9-14 scales_1.2.1 prodlim_2023.03.31 ggridges_0.5.4
[115] leiden_0.4.3 rlang_1.1.1 cowplot_1.1.1

[inofechm]

Hi Stefanos, Thank you for bringing up this issue! I believe what was once a warning in R versions < 4.3 is now an error. I will work on a fix ASAP and update the package

[inofechm]

Hi Stefanos, I have modified the code to avoid this error/warning. Could you please re-install scATOMIC version 2.0.1 with devtools::install_github("abelson-lab/scATOMIC") Let me know if the workflow works on your end now and I'll close the issue Thanks again for raising this important issue

[StefanosVoglis]

Hi, now it works! Many thanks!