Error in retrieving interactions from Omnipath

[EugeniaRadulescu]

Dear authors,

When running the command:

interactions = import_omnipath_interactions( resources =c( "BioGRID"), organism = 9606 )

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 Backtrace:

1. OmnipathR::import_omnipath_interactions(...)
   19. purrr::map(., method, ...)
   20. purrr:::map_("list", .x, .f, ..., .progress = .progress)
   21. dplyr (local) .f(.x[[i]], ...)

This is my session info:

R version 4.2.2 Patched (2022-11-10 r83330) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.5 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] magrittr_2.0.3 ggraph_2.1.0 igraph_1.3.5
[4] WGCNA_1.72-1 fastcluster_1.2.3 dynamicTreeCut_1.63-1 [7] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[10] dplyr_1.1.0 purrr_1.0.1 readr_2.1.4
[13] tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.1
[16] tidyverse_2.0.0 OmnipathR_3.9.6 nichenetr_2.0.0

loaded via a namespace (and not attached): [1] rappdirs_0.3.3 scattermore_0.8 ModelMetrics_1.2.2.2
[4] SeuratObject_4.1.3 bit64_4.0.5 knitr_1.42
[7] irlba_2.3.5.1 data.table_1.14.6 rpart_4.1.19
[10] RCurl_1.98-1.10 KEGGREST_1.38.0 hardhat_1.3.0
[13] doParallel_1.0.17 generics_0.1.3 preprocessCore_1.60.2 [16] BiocGenerics_0.44.0 callr_3.7.3 cowplot_1.1.1
[19] RSQLite_2.2.20 usethis_2.1.6 shadowtext_0.1.2
[22] RANN_2.6.1 proxy_0.4-27 future_1.31.0
[25] DiagrammeR_1.0.10 bit_4.0.5 tzdb_0.3.0
[28] spatstat.data_3.0-0 xml2_1.3.3 httpuv_1.6.8
[31] viridis_0.6.2 gower_1.0.1 xfun_0.37
[34] hms_1.1.2 evaluate_0.20 promises_1.2.0.1
[37] fansi_1.0.4 progress_1.2.2 caTools_1.18.2
[40] readxl_1.4.2 DBI_1.1.3 htmlwidgets_1.6.1
[43] spatstat.geom_3.0-6 stats4_4.2.2 ellipsis_0.3.2
[46] ggnewscale_0.4.8 backports_1.4.1 deldir_1.0-6
[49] Biobase_2.58.0 vctrs_0.6.1 remotes_2.4.2
[52] ROCR_1.0-11 abind_1.4-5 caret_6.0-94
[55] cachem_1.0.6 withr_2.5.0 ggforce_0.4.1
[58] progressr_0.13.0 vroom_1.6.1 checkmate_2.1.0
[61] sctransform_0.3.5 fdrtool_1.2.17 prettyunits_1.1.1
[64] goftest_1.2-3 cluster_2.1.4 lazyeval_0.2.2
[67] crayon_1.5.2 spatstat.explore_3.0-6 labeling_0.4.2
[70] recipes_1.0.5 pkgconfig_2.0.3 GenomeInfoDb_1.34.9
[73] tweenr_2.0.2 nlme_3.1-162 pkgload_1.3.2
[76] nnet_7.3-18 devtools_2.4.5 rlang_1.1.0
[79] globals_0.16.2 lifecycle_1.0.3 miniUI_0.1.1.1
[82] rprojroot_2.0.3 cellranger_1.1.0 randomForest_4.7-1.1
[85] polyclip_1.10-4 matrixStats_0.63.0 lmtest_0.9-40
[88] Matrix_1.5-3 zoo_1.8-11 base64enc_0.1-3
[91] ggridges_0.5.4 GlobalOptions_0.1.2 processx_3.8.0
[94] png_0.1-8 viridisLite_0.4.1 rjson_0.2.21
[97] bitops_1.0-7 KernSmooth_2.23-20 visNetwork_2.1.2
[100] pROC_1.18.0 Biostrings_2.66.0 blob_1.2.3
[103] shape_1.4.6 parallelly_1.34.0 spatstat.random_3.1-3 [106] jpeg_0.1-10 S4Vectors_0.36.1 scales_1.2.1
[109] memoise_2.0.1 plyr_1.8.8 ica_1.0-3
[112] zlibbioc_1.44.0 compiler_4.2.2 RColorBrewer_1.1-3
[115] clue_0.3-64 fitdistrplus_1.1-8 cli_3.6.0
[118] XVector_0.38.0 urlchecker_1.0.1 listenv_0.9.0
[121] patchwork_1.1.2 pbapply_1.7-0 ps_1.7.2
[124] htmlTable_2.4.1 Formula_1.2-4 MASS_7.3-58.2
[127] tidyselect_1.2.0 stringi_1.7.12 highr_0.10
[130] yaml_2.3.7 latticeExtra_0.6-30 ggrepel_0.9.3
[133] grid_4.2.2 tools_4.2.2 timechange_0.2.0
[136] future.apply_1.10.0 parallel_4.2.2 circlize_0.4.15
[139] rstudioapi_0.14 foreach_1.5.2 foreign_0.8-84
[142] gridExtra_2.3 prodlim_2023.03.31 farver_2.1.1
[145] Rtsne_0.16 digest_0.6.31 BiocManager_1.30.19
[148] shiny_1.7.4 lava_1.7.2.1 Rcpp_1.0.10
[151] later_1.3.0 RcppAnnoy_0.0.20 httr_1.4.4
[154] AnnotationDbi_1.60.0 ComplexHeatmap_2.14.0 colorspace_2.1-0
[157] rvest_1.0.3 fs_1.6.1 tensor_1.5
[160] reticulate_1.28 IRanges_2.32.0 splines_4.2.2
[163] uwot_0.1.14 spatstat.utils_3.0-1 graphlayouts_0.8.4
[166] sp_1.6-0 plotly_4.10.1 sessioninfo_1.2.2
[169] xtable_1.8-4 jsonlite_1.8.4 BBmisc_1.13
[172] tidygraph_1.2.3 timeDate_4022.108 ipred_0.9-14
[175] R6_2.5.1 profvis_0.3.7 Hmisc_4.7-2
[178] pillar_1.8.1 htmltools_0.5.4 mime_0.12
[181] glue_1.6.2 fastmap_1.1.0 class_7.3-21
[184] codetools_0.2-19 pkgbuild_1.4.0 utf8_1.2.3
[187] lattice_0.20-45 spatstat.sparse_3.0-0 logger_0.2.2
[190] curl_5.0.0 leiden_0.4.3 zip_2.2.2
[193] GO.db_3.16.0 openxlsx_4.2.5.2 interp_1.1-3
[196] survival_3.5-0 limma_3.54.2 rmarkdown_2.20
[199] desc_1.4.2 munsell_0.5.0 GenomeInfoDbData_1.2.9 [202] e1071_1.7-13 GetoptLong_1.0.5 iterators_1.0.14
[205] impute_1.72.3 reshape2_1.4.4 gtable_0.3.1
[208] Seurat_4.3.0

Could you please help with this error?

Thanks!

Eugenia

[ritsuya-niwayama-servier]

Dear OmniPath team, I have the same problem in R while it could be due to my setting. For Python client, it works for me. Thanks!

Kind regards Ritsuya

[deeenes]

Dear Eugenia,

Sorry for the very late answer. This issue is the same as the pinned issue, and the problem has been fixed in February. Please try to install the latest version of the package:

remotes::install_github('saezlab/OmnipathR')

Best,

Denes

[lmassenet-regad]

Hello, I get the following error, even after reinstalling with the latest version of the package mentioned on your last post. Do you know what I can do to solve this problem ? Thank you in advance for your help, Best, Lucile

[deeenes]

Hi Lucile,

I think the most likely reason is that you have the old version loaded in your session despite you've already installed the new one. If even after starting a new session you experience the error, please check if the path where you updated OmnipathR is in the library paths of your R session (.libPaths()).

If you're indeed using the latest version of the package, that means you found a new error which has different reasons than the one above. In this case, please post here the output of traceback() and rlang::last_error().

Best,

Denes

[lmassenet-regad]

Hi Denes, it worked after starting a new session. Thanks !