On a fresh install of R & decoupleR, get_collectri() fails to fetch the resources. Therre is a gateway error once (552), then a warning about the static table collection, then an error.
Example code:
library(decoupleR)
db <- decoupleR::get_celloectri()
Output:
library(decoupleR)
db <- decoupleR::get_collectri()
[2026-06-22 10:09:10] [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
After clearing the cache:
library(decoupleR)
decoupleR::get_collectri()
[2026-06-22 10:18:20] [WARN] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 1/3); error: Failed to perform HTTP request.
Caused by error in curl::curl_fetch_disk():
! Timeout was reached [www.ensembl.org]:
Resolving timed out after 10000 milliseconds
[2026-06-22 10:18:51] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522
[2026-06-22 10:18:51] [WARN] [OmnipathR] Failed to download https://omabrowser.org/All/oma-species.txt (attempt 1/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522
[2026-06-22 10:18:57] [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.
[100%] Downloaded 2551921 bytes...
Error in if (.keep) . else select(., -!!evs_col) :
argument is of length zero
I've attached the omnipathR log.
omnipathr-20260622-1018.log
sessionInfo()
R version 4.6.0 (2026-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS
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_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Berlin
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] decoupleR_2.9.7
loaded via a namespace (and not attached):
[1] xfun_0.58 httr2_1.2.2 websocket_1.4.4 processx_3.9.0 lattice_0.22-9 OmnipathR_4.1.0 tzdb_0.5.0 ps_1.9.3 vctrs_0.7.3
[10] tools_4.6.0 generics_0.1.4 curl_7.1.0 parallel_4.6.0 tibble_3.3.1 RSQLite_3.53.1 blob_1.3.0 pkgconfig_2.0.3 R.oo_1.27.1
[19] Matrix_1.7-5 checkmate_2.3.4 readxl_1.5.0 lifecycle_1.0.5 compiler_4.6.0 stringr_1.6.0 progress_1.2.3 chromote_0.5.1 codetools_0.2-20
[28] htmltools_0.5.9 yaml_2.3.12 pillar_1.11.1 later_1.4.8 crayon_1.5.3 tidyr_1.3.2 R.utils_2.13.0 BiocParallel_1.46.0 cachem_1.1.0
[37] sessioninfo_1.2.4 parallelly_1.47.0 zip_3.0.0 rvest_1.0.5 tidyselect_1.2.1 digest_0.6.39 stringi_1.8.7 dplyr_1.2.1 purrr_1.2.2
[46] fastmap_1.2.0 grid_4.6.0 cli_3.6.6 logger_0.4.2 magrittr_2.0.5 XML_3.99-0.23 readr_2.2.0 withr_3.0.2 promises_1.5.0
[55] prettyunits_1.2.0 backports_1.5.1 rappdirs_0.3.4 bit64_4.8.2 lubridate_1.9.5 timechange_0.4.0 httr_1.4.8 rmarkdown_2.31 igraph_2.3.2
[64] bit_4.6.0 otel_0.2.0 cellranger_1.1.0 R.methodsS3_1.8.2 hms_1.1.4 memoise_2.0.1 evaluate_1.0.5 knitr_1.51 tcltk_4.6.0
[73] rlang_1.2.0 Rcpp_1.1.1-1.1 glue_1.8.1 DBI_1.3.0 selectr_0.5-1 xml2_1.5.2 vroom_1.7.1 rstudioapi_0.19.0 jsonlite_2.0.0
[82] R6_2.6.1 fs_2.1.0
On a fresh install of R & decoupleR,
get_collectri()fails to fetch the resources. Therre is a gateway error once (552), then a warning about the static table collection, then an error.Example code:
Output:
After clearing the cache:
I've attached the omnipathR log.
omnipathr-20260622-1018.log
sessionInfo()R version 4.6.0 (2026-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS
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_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Berlin
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] decoupleR_2.9.7
loaded via a namespace (and not attached):
[1] xfun_0.58 httr2_1.2.2 websocket_1.4.4 processx_3.9.0 lattice_0.22-9 OmnipathR_4.1.0 tzdb_0.5.0 ps_1.9.3 vctrs_0.7.3
[10] tools_4.6.0 generics_0.1.4 curl_7.1.0 parallel_4.6.0 tibble_3.3.1 RSQLite_3.53.1 blob_1.3.0 pkgconfig_2.0.3 R.oo_1.27.1
[19] Matrix_1.7-5 checkmate_2.3.4 readxl_1.5.0 lifecycle_1.0.5 compiler_4.6.0 stringr_1.6.0 progress_1.2.3 chromote_0.5.1 codetools_0.2-20
[28] htmltools_0.5.9 yaml_2.3.12 pillar_1.11.1 later_1.4.8 crayon_1.5.3 tidyr_1.3.2 R.utils_2.13.0 BiocParallel_1.46.0 cachem_1.1.0
[37] sessioninfo_1.2.4 parallelly_1.47.0 zip_3.0.0 rvest_1.0.5 tidyselect_1.2.1 digest_0.6.39 stringi_1.8.7 dplyr_1.2.1 purrr_1.2.2
[46] fastmap_1.2.0 grid_4.6.0 cli_3.6.6 logger_0.4.2 magrittr_2.0.5 XML_3.99-0.23 readr_2.2.0 withr_3.0.2 promises_1.5.0
[55] prettyunits_1.2.0 backports_1.5.1 rappdirs_0.3.4 bit64_4.8.2 lubridate_1.9.5 timechange_0.4.0 httr_1.4.8 rmarkdown_2.31 igraph_2.3.2
[64] bit_4.6.0 otel_0.2.0 cellranger_1.1.0 R.methodsS3_1.8.2 hms_1.1.4 memoise_2.0.1 evaluate_1.0.5 knitr_1.51 tcltk_4.6.0
[73] rlang_1.2.0 Rcpp_1.1.1-1.1 glue_1.8.1 DBI_1.3.0 selectr_0.5-1 xml2_1.5.2 vroom_1.7.1 rstudioapi_0.19.0 jsonlite_2.0.0
[82] R6_2.6.1 fs_2.1.0