Open
Description
What happened?
When running the example of tm_g_quality I see an error:
Problem during calculation of variance-stabilized transformation (VST), try again with more genes. More details: Error in validObject(.Object): invalid class "DESeqDataSet" object: superclass "ExpData" not defined in the environment of the object's class
Not sure if there is some updates on DESeq or DESeq2 that has lead to this error (or BiocGenerics) but in any case is seems a problem processing the data inside the module not a teal issue.
sessionInfo()
R version 4.5.0 (2025-04-11 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=Spanish_Spain.utf8 LC_CTYPE=Spanish_Spain.utf8
[3] LC_MONETARY=Spanish_Spain.utf8 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.utf8
time zone: Europe/Madrid
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.1.4 shinytest2_0.4.1
[3] teal.modules.hermes_0.2.0.9003 testthat_3.2.3
[5] teal_0.16.0.9005 teal.slice_0.6.0.9003
[7] teal.data_0.7.0.9002 teal.code_0.6.1.9000
[9] shiny_1.10.0 ggplot2_3.5.2
[11] pkgdown_2.1.2 devtools_2.4.5
[13] usethis_3.1.0
loaded via a namespace (and not attached):
[1] splines_4.5.0 later_1.4.2 hermes_1.12.0
[4] filelock_1.0.3 tibble_3.2.1 lifecycle_1.0.4
[7] httr2_1.1.2 rutils_0.0.2.92 Rdpack_2.6.4
[10] nestcolor_0.1.3.9000 gert_2.1.5 edgeR_4.6.1
[13] doParallel_1.0.17 rprojroot_2.0.4 processx_3.8.6
[16] lattice_0.22-7 crosstalk_1.2.1 credentials_2.0.2
[19] MultiAssayExperiment_1.34.0 backports_1.5.0 magrittr_2.0.3
[22] limma_3.64.0 sass_0.4.10 rmarkdown_2.29
[25] jquerylib_0.1.4 yaml_2.3.10 remotes_2.5.0
[28] httpuv_1.6.16 askpass_1.2.1 sessioninfo_1.2.3
[31] pkgbuild_1.4.7 cowplot_1.1.3 DBI_1.2.3
[34] RColorBrewer_1.1-3 abind_1.4-8 pkgload_1.4.0
[37] GenomicRanges_1.60.0 purrr_1.0.4 BiocGenerics_0.54.0
[40] rappdirs_0.3.3 circlize_0.4.16 GenomeInfoDbData_1.2.14
[43] IRanges_2.42.0 S4Vectors_0.46.0 ggrepel_0.9.6
[46] gitcreds_0.1.2 teal.widgets_0.4.3.9002 teal.reporter_0.4.0.9004
[49] codetools_0.2-20 DelayedArray_0.34.1 DT_0.33
[52] xml2_1.3.8 tidyselect_1.2.1 shape_1.4.6.1
[55] UCSC.utils_1.4.0 shinyRadioMatrix_0.2.1 farver_2.1.2
[58] shinyWidgets_0.9.0 matrixStats_1.5.0 stats4_4.5.0
[61] BiocFileCache_2.16.0 jsonlite_2.0.0 GetoptLong_1.0.5
[64] ellipsis_0.3.2 survival_3.8-3 iterators_1.0.14
[67] systemfonts_1.2.3 foreach_1.5.2 tools_4.5.0
[70] progress_1.2.3 ragg_1.4.0 rtables_0.6.12.9000
[73] Rcpp_1.0.14 glue_1.8.0 gridExtra_2.3
[76] SparseArray_1.8.0 BiocBaseUtils_1.10.0 DESeq2_1.48.0
[79] xfun_0.52 MatrixGenerics_1.20.0 ggfortify_0.4.17
[82] GenomeInfoDb_1.44.0 withr_3.0.2 formatR_1.14
[85] fastmap_1.2.0 shinyjs_2.1.0 openssl_2.3.2
[88] callr_3.7.6 digest_0.6.37 R6_2.6.1
[91] mime_0.13 textshaping_1.0.1 colorspace_2.1-1
[94] biomaRt_2.64.0 RSQLite_2.3.11 tidyr_1.3.1
[97] generics_0.1.4 renv_1.1.4 prettyunits_1.2.0
[100] httr_1.4.7
[ reached 'max' / getOption("max.print") -- omitted 70 entries ]Relevant log output
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