Error in get_dorothea

[DylanPostmus]

Hi,

I am having some trouble with the get_dorothea function of the decoupleR package (version 2.4.0).
When I run

net <- decoupleR::get_dorothea(organism='human', levels=c('A', 'B', 'C'))

I get the following error:

Error in mutate():
ℹ In argument: n_references = ifelse(...).
Caused by error in map():
ℹ In index: 1.
Caused by error in .f():
! Arguments in ... must be passed by position, not name.
✖ Problematic argument:
• outsep = outsep
Run rlang::last_trace() to see where the error occurred.

Could this be an issue with a tidyverse package?

Thanks in advance.

[PauBadiaM]

Hi @DylanPostmus ,

Could you please try to install the latest version of OmnipathR and try again?

devtools::install_github('saezlab/OmnipathR')

[DylanPostmus]

Works now! Many thanks.

[hemantgujar]

I am having similar issue. can you please help. Thanks

net <- get_dorothea(organism='human', levels=c('A', 'B', 'C'))

Error in mutate():
ℹ In argument: n_references = ifelse(...).
Caused by error in map():
ℹ In index: 1.
Caused by error in .f():
! Arguments in ... must be passed by position, not name.
✖ Problematic argument:
• outsep = outsep
Run rlang::last_trace() to see where the error occurred.

sessionInfo()

R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

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

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

other attached packages:
[1] pheatmap_1.0.12 ggplot2_3.4.2 patchwork_1.1.2 tidyr_1.3.0 tibble_3.2.1
[6] dplyr_1.1.1 decoupleR_2.4.0 SeuratObject_4.1.3 Seurat_4.3.0

loaded via a namespace (and not attached):
[1] Rtsne_0.16 colorspace_2.1-0 deldir_1.0-6 ellipsis_0.3.2
[5] ggridges_0.5.4 rstudioapi_0.14 spatstat.data_3.0-1 leiden_0.4.3
[9] listenv_0.9.0 farver_2.1.1 bit64_4.0.5 ggrepel_0.9.3
[13] fansi_1.0.4 xml2_1.3.3 codetools_0.2-19 splines_4.2.3
[17] knitr_1.42 polyclip_1.10-4 jsonlite_1.8.4 ica_1.0-3
[21] cluster_2.1.4 png_0.1-8 uwot_0.1.14 shiny_1.7.4
[25] sctransform_0.3.5 spatstat.sparse_3.0-1 readr_2.1.4 compiler_4.2.3
[29] httr_1.4.5 backports_1.4.1 Matrix_1.5-3 fastmap_1.1.1
[33] lazyeval_0.2.2 cli_3.6.1 later_1.3.0 prettyunits_1.1.1
[37] htmltools_0.5.5 tools_4.2.3 igraph_1.4.2 gtable_0.3.3
[41] glue_1.6.2 RANN_2.6.1 reshape2_1.4.4 rappdirs_0.3.3
[45] Rcpp_1.0.10 scattermore_0.8 cellranger_1.1.0 vctrs_0.6.1
[49] spatstat.explore_3.1-0 nlme_3.1-162 progressr_0.13.0 lmtest_0.9-40
[53] spatstat.random_3.1-4 xfun_0.38 OmnipathR_3.6.0 stringr_1.5.0
[57] globals_0.16.2 rvest_1.0.3 mime_0.12 miniUI_0.1.1.1
[61] lifecycle_1.0.3 irlba_2.3.5.1 goftest_1.2-3 future_1.32.0
[65] MASS_7.3-58.3 zoo_1.8-12 scales_1.2.1 vroom_1.6.1
[69] hms_1.1.3 promises_1.2.0.1 spatstat.utils_3.0-2 parallel_4.2.3
[73] RColorBrewer_1.1-3 yaml_2.3.7 curl_5.0.0 reticulate_1.28
[77] pbapply_1.7-0 gridExtra_2.3 stringi_1.7.12 checkmate_2.1.0
[81] rlang_1.1.0 pkgconfig_2.0.3 matrixStats_0.63.0 evaluate_0.20
[85] lattice_0.20-45 ROCR_1.0-11 purrr_1.0.1 tensor_1.5
[89] htmlwidgets_1.6.2 labeling_0.4.2 bit_4.0.5 cowplot_1.1.1
[93] tidyselect_1.2.0 parallelly_1.35.0 RcppAnnoy_0.0.20 plyr_1.8.8
[97] logger_0.2.2 magrittr_2.0.3 R6_2.5.1 generics_0.1.3
[101] pillar_1.9.0 withr_2.5.0 fitdistrplus_1.1-8 survival_3.5-5
[105] abind_1.4-5 sp_1.6-0 future.apply_1.10.0 crayon_1.5.2
[109] KernSmooth_2.23-20 utf8_1.2.3 spatstat.geom_3.1-0 plotly_4.10.1
[113] rmarkdown_2.21 tzdb_0.3.0 progress_1.2.2 readxl_1.4.2
[117] grid_4.2.3 data.table_1.14.8 digest_0.6.31 xtable_1.8-4
[121] httpuv_1.6.9 munsell_0.5.0 viridisLite_0.4.1

[hemantgujar]

After running
devtools::install_github('saezlab/OmnipathR')
net <- get_dorothea(organism='human', levels=c('A', 'B', 'C'))

Error in original_appender_console(lines) :
lazy-load database 'C:/xxxR/win-library/4.2/OmnipathR/R/OmnipathR.rdb' is corrupt
In addition: Warning messages:
1: 'OmnipathR::import_dorothea_interactions' is deprecated.
Use 'dorothea' instead.
See help("Deprecated")
2: In original_appender_console(lines) :
restarting interrupted promise evaluation
3: In original_appender_console(lines) :
internal error -3 in R_decompress1

[deeenes]

The error in your previous comment is the same as in #57, and has been fixed some weeks ago. The next error that you experience is not a problem with this package, but an issue with the installation or loading on your system, and most likely can be addressed by simply restarting R.

[hemantgujar]

Well this is weird. I restarted R and my computer and the problem was solved. I wonder why this issue occurred.
Thanks a lot.