First time seeing this bug after years of decoupleR use #179
Description
Recently, got stuck with an issue that is not due to my wrapper script. This issue points to a deeper bug inside decoupleR and I'm convinced now it also points to OmnipathR. On my Linux machine, I've been using the same package for a year now without any problems, however now I can't use it anymore due to this issue. It seems like this issue is of some form of new incompatibillity of decoupleR with OmnipathR
decoupleR::get_dorothea(organism = 'human')
#> Error in `if (.keep) ...`:
#> ! argument is of length zeroCreated on 2026-01-22 with reprex v2.1.1
SessionInfo:
sessionInfo()
R version 4.5.2 (2025-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Linux Mint 21.3
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_1.12.1 reprex_2.1.1 crayon_1.5.3 SummarizedExperiment_1.40.0 GenomicRanges_1.62.1 Seqinfo_1.0.0
[7] MatrixGenerics_1.22.0 matrixStats_1.5.0 mesocore_0.2.10 data.table_1.18.0 BiocManager_1.30.27 pacman_0.5.1
[13] nortest_1.0-4 org.Hs.eg.db_3.22.0 AnnotationDbi_1.72.0 IRanges_2.44.0 S4Vectors_0.48.0 Biobase_2.70.0
[19] BiocGenerics_0.56.0 generics_0.1.4 ggplot2_4.0.1 readxl_1.4.5 here_1.0.2 pheatmap_1.0.13
[25] decoupleR_2.16.0 docopt_0.7.2
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.18.0 jsonlite_2.0.0 magrittr_2.0.4 farver_2.1.2 rmarkdown_2.30 fs_1.6.6 vctrs_0.7.0
[9] memoise_2.0.1 htmltools_0.5.9 S4Arrays_1.10.1 usethis_3.2.1 progress_1.2.3 curl_7.0.0 cellranger_1.1.0 SparseArray_1.10.8
[17] sass_0.4.10 parallelly_1.46.1 bslib_0.9.0 desc_1.4.3 httr2_1.2.2 lubridate_1.9.4 cachem_1.1.0 igraph_2.2.1
[25] mime_0.13 lifecycle_1.0.5 pkgconfig_2.0.3 Matrix_1.7-4 R6_2.6.1 fastmap_1.2.0 digest_0.6.39 selectr_0.5-1
[33] ps_1.9.1 DESeq2_1.50.2 rprojroot_2.1.1 pkgload_1.4.1 RSQLite_2.4.5 timechange_0.3.0 httr_1.4.7 abind_1.4-8
[41] compiler_4.5.2 remotes_2.5.0 bit64_4.6.0-1 withr_3.0.2 S7_0.2.1 backports_1.5.0 BiocParallel_1.44.0 DBI_1.2.3
[49] logger_0.4.1 OmnipathR_3.19.6 pkgbuild_1.4.8 R.utils_2.13.0 rappdirs_0.3.4 DelayedArray_0.36.0 sessioninfo_1.2.3 tools_4.5.2
[57] otel_0.2.0 httpuv_1.6.16 zip_2.3.3 clipr_0.8.0 R.oo_1.27.1 glue_1.8.0 callr_3.7.6 promises_1.5.0
[65] grid_4.5.2 checkmate_2.3.3 gtable_0.3.6 tzdb_0.5.0 R.methodsS3_1.8.2 tidyr_1.3.2 hms_1.1.4 xml2_1.5.2
[73] XVector_0.50.0 pillar_1.11.1 stringr_1.6.0 vroom_1.6.7 later_1.4.5 dplyr_1.1.4 lattice_0.22-7 bit_4.6.0
[81] tidyselect_1.2.1 locfit_1.5-9.12 miniUI_0.1.2 Biostrings_2.78.0 knitr_1.51 xfun_0.56 devtools_2.4.6 stringi_1.8.7
[89] yaml_2.3.12 evaluate_1.0.5 codetools_0.2-20 tcltk_4.5.2 tibble_3.3.1 cli_3.6.5 xtable_1.8-4 jquerylib_0.1.4
[97] processx_3.8.6 Rcpp_1.1.1 png_0.1-8 XML_3.99-0.20 parallel_4.5.2 ellipsis_0.3.2 readr_2.1.6 blob_1.3.0
[105] prettyunits_1.2.0 scales_1.4.0 purrr_1.2.1 rlang_1.1.7 KEGGREST_1.50.0 rvest_1.0.5