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saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.
https://saezlab.github.io/decoupleR/
GNU General Public License v3.0
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Error in if (.keep) . else select(., -!!evs_col) from get_collectri(organism='human', split_complexes=FALSE) #140

Open kasayadior opened 2 days ago

kasayadior commented 2 days ago

Hi, I am trying to get the TF enrichment using the command and get the error. Please help, thank you.

library(decoupleR) library(OmnipathR) omnipath_cache_wipe() [2024-10-07 19:14:03] [SUCCESS] [OmnipathR] Removing all cache contents from /home/.cache/OmnipathR. net <- get_collectri(organism='human', split_complexes=FALSE)

[2024-10-07 19:14:13] [WARN] [OmnipathR] Failed to download https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic (attempt 1/3); error: HTTP error 500. [2024-10-07 19:14:18] [WARN] [OmnipathR] Failed to download https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic (attempt 2/3); error: HTTP error 500. [2024-10-07 19:14:23] [ERROR] [OmnipathR] Failed to download https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic (attempt 3/3); error: HTTP error 500. [2024-10-07 19:14:23] [WARN] [OmnipathR] Failed to download: https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic; error: HTTP error 500. [2024-10-07 19:14:23] [WARN] [OmnipathR] Accessing collectri as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. Error in if (.keep) . else select(., -!!evs_col) : argument is of length zero

sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux 8.4 (Ootpa)

Matrix products: default BLAS/LAPACK: /software/openblas-0.3.13-el8-x86_64/lib/libopenblas_skylakexp-r0.3.13.so; LAPACK version 3.9.0

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

other attached packages: [1] OmnipathR_3.13.27 decoupleR_2.9.7

loaded via a namespace (and not attached): [1] xfun_0.48 lattice_0.22-5 tzdb_0.4.0
[4] vctrs_0.6.5 tools_4.3.1 generics_0.1.3
[7] curl_5.2.3 parallel_4.3.1 tibble_3.2.1
[10] fansi_1.0.6 RSQLite_2.3.7 blob_1.2.4
[13] pkgconfig_2.0.3 R.oo_1.26.0 Matrix_1.6-5
[16] checkmate_2.3.2 readxl_1.4.3 lifecycle_1.0.4
[19] compiler_4.3.1 stringr_1.5.1 progress_1.2.3
[22] codetools_0.2-20 htmltools_0.5.8.1 yaml_2.3.10
[25] pillar_1.9.0 later_1.3.2 crayon_1.5.3
[28] tidyr_1.3.1 R.utils_2.12.3 BiocParallel_1.36.0 [31] cachem_1.1.0 parallelly_1.38.0 zip_2.3.1
[34] rvest_1.0.4 tidyselect_1.2.1 digest_0.6.37
[37] stringi_1.8.4 dplyr_1.1.4 purrr_1.0.2
[40] fastmap_1.2.0 grid_4.3.1 cli_3.6.3
[43] logger_0.3.0 magrittr_2.0.3 XML_3.99-0.17
[46] utf8_1.2.4 readr_2.1.5 withr_3.0.1
[49] prettyunits_1.2.0 backports_1.5.0 rappdirs_0.3.3
[52] bit64_4.5.2 lubridate_1.9.3 timechange_0.3.0
[55] rmarkdown_2.28 httr_1.4.7 igraph_2.0.3
[58] bit_4.5.0 cellranger_1.1.0 R.methodsS3_1.8.2
[61] hms_1.1.3 evaluate_1.0.0 memoise_2.0.1
[64] knitr_1.48 rlang_1.1.4 Rcpp_1.0.13
[67] glue_1.8.0 DBI_1.2.3 selectr_0.4-2
[70] xml2_1.3.6 vroom_1.6.5 rstudioapi_0.16.0
[73] jsonlite_1.8.9 R6_2.5.1

deeenes commented 1 day ago

Hello,

Between noon yesterday and today our server experienced a service outage. Now it should be working again. I recommend to wipe the cache again before loading CollecTRI, just like you've done it above.