insightsengineering / insightsengineering/teal.modules.hermes

[Bug]: tm_g_quality example produces an error

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bug core sme
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R
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Description

### What happened?

When running the example of `tm_g_quality` I see an error:

![Image](https://github.com/user-attachments/assets/8e66678a-1dcf-45e6-8de5-35455509a2ff)

> 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
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

```R

```

### Code of Conduct

- [x] I agree to follow this project's Code of Conduct.

### Contribution Guidelines

- [x] I agree to follow this project's Contribution Guidelines.

### Security Policy

- [x] I agree to follow this project's Security Policy.

Contributor guide

Open the contributing guide

Research direction

Start by reproducing the tm_g_quality example with the reported R 4.5.0 and DESeq2 1.48.0 session, then inspect the variance-stabilized transformation error and the surrounding package behavior. Determine whether the failure is in teal.modules.hermes or a dependency; done means the example processes its data without the reported DESeqDataSet error.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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