[ Started: 2026-06-01 21:13:44 CEST ] [ OmnipathR v3.18.4 for BioC-3.22 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_22 (efaae39 2026-01-20 15:40:26) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-01_2101/OmnipathR/OmnipathR.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.18.4’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... INFO installed size is 6.8Mb sub-directories of 1Mb or more: doc 5.4Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2026-06-01 21:14:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-01 21:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:15] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-06-01 21:14:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-06-01 19:12:19 UTC; omnipath [2026-06-01 21:14:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-06-01 21:14:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-06-01 19:13:47 UTC; unix [2026-06-01 21:14:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-06-01 21:14:15] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-06-01 21:14:15] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-06-01; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-06-01 21:14:15] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-06-01 21:14:16] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-06-01); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.58(2026-06-01); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-06-01 21:14:16] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-06-01 21:14:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-06-01 21:14:16] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-06-01 21:14:16] [TRACE] [OmnipathR] Contains 1 files. [2026-06-01 21:14:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-06-01 21:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-01 21:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-06-01 21:14:16] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-06-01 21:14:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-01_2101/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-06-01 21:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-01_2101/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-06-01 21:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-01_2101/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-06-01 21:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-01_2101/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-06-01 21:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:16] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2026-06-01 21:14:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-01 21:14:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:26] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-06-01 21:14:26] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-06-01 19:12:19 UTC; omnipath [2026-06-01 21:14:26] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-06-01 21:14:26] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-06-01 19:13:47 UTC; unix [2026-06-01 21:14:26] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-06-01 21:14:26] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-06-01 21:14:27] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-06-01; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-06-01 21:14:27] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-06-01 21:14:27] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-06-01); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.58(2026-06-01); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-06-01 21:14:27] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-06-01 21:14:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-06-01 21:14:27] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-06-01 21:14:27] [TRACE] [OmnipathR] Contains 1 files. [2026-06-01 21:14:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-06-01 21:14:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-01 21:14:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-06-01 21:14:27] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-06-01 21:14:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-01_2101/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-06-01 21:14:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-01_2101/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-06-01 21:14:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-01_2101/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-06-01 21:14:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-01_2101/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-06-01 21:14:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:14:27] [TRACE] [OmnipathR] Cache locked: FALSE cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’ patch_httr2_keep_handle: no visible binding for global variable ‘handle’ patch_httr2_keep_handle: no visible global function definition for ‘ORIGINAL’ Undefined global functions or variables: ORIGINAL enzyme_genesymbol handle * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: omnipath_for_cosmos > ### Title: OmniPath PPI for the COSMOS PKN > ### Aliases: omnipath_for_cosmos > > ### ** Examples > > op_cosmos <- omnipath_for_cosmos() [2026-06-01 21:22:29] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2026-06-01 21:22:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-06-01 21:22:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2026-06-01 21:22:29] [TRACE] [OmnipathR] Organism(s): 9606 [2026-06-01 21:22:29] [TRACE] [OmnipathR] Orthology targets: [2026-06-01 21:22:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-06-01 21:22:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-06-01 21:22:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-06-01 21:22:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-06-01 21:22:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-06-01 21:22:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-06-01 21:22:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-06-01 21:22:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-06-01 21:22:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-06-01 21:22:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-06-01 21:22:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-06-01 21:22:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.109537s from omnipathdb.org (143.3 Kb/s); Redirect: 0s, DNS look up: 0.000952s, Connection: 0.022191s, Pretransfer: 0.066073s, First byte at: 0.109202s [2026-06-01 21:22:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 01 Jun 2026 19:22:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 01 Jun 2026 20:22:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-06-01 21:22:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-06-01 21:22:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-01 21:22:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:22:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-01 21:22:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:22:30] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-06-01 21:22:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-06-01 21:22:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-06-01 21:22:30] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-06-01 21:22:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-01 21:22:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:22:30] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-06-01 21:22:33] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-06-01 21:22:33] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-06-01 21:22:33] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-06-01 21:22:33] [TRACE] [OmnipathR] BioMart query: [2026-06-01 21:22:33] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-06-01 21:22:33] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2026-06-01 21:22:33] [INFO] [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2026-06-01 21:22:33] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2026-06-01 21:22:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-01 21:22:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:22:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-01 21:22:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:22:33] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2026-06-01 21:22:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-06-01 21:22:33] [INFO] [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2026-06-01 21:22:33] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-06-01 21:22:33] [TRACE] [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2026-06-01 21:22:33] [TRACE] [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2026-06-01 21:22:33] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-06-01 21:22:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-06-01 21:22:33] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-06-01 21:22:33] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-06-01 21:22:33] [TRACE] [OmnipathR] Sending HTTP request. [2026-06-01 21:22:33] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-06-01 21:22:33] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-06-01 21:22:33] [TRACE] [OmnipathR] Downloaded 1014 bytes in 0.075875s from www.ensembl.org (13.1 Kb/s); Redirect: 0s, DNS look up: 0.006633s, Connection: 0.035663s, Pretransfer: 0.035717s, First byte at: 0.075776s [2026-06-01 21:22:33] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: D5EA:BF13D:3B5AAF:3E3A6F:6A0E4CF0; Server: GitHub.com; X-Cache-Hits: 27; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: 10280cb219caa51403f6554d2110f52aaffd21d9; Content-Encoding: gzip; Date: Mon, 01 Jun 2026 19:22:33 GMT; Expires: 0; X-Served-By: cache-lcy-egml8630021-LCY; Pragma: no-cache; X-Timer: S1780341753.488533,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"68b6c2f9-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 300; Content-Length: 1014 [2026-06-01 21:22:33] [TRACE] [OmnipathR] Response headers: [X-GitHub-Request-Id=D5EA:BF13D:3B5AAF:3E3A6F:6A0E4CF0,Server=GitHub.com,X-Cache-Hits=27,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=10280cb219caa51403f6554d2110f52aaffd21d9,Content-Encoding=gzip,Date=Mon, 01 Jun 2026 19:22:33 GMT,Expires=0,X-Served-By=cache-lcy-egml8630021-LCY,Pragma=no-cache,X-Timer=S1780341753.488533,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"68b6c2f9-8aa",Via=1.1 varnish,Connection=keep-alive,Age=300,Content-Length=1014] [2026-06-01 21:22:33] [TRACE] [OmnipathR] Calling reader callback on response. [2026-06-01 21:22:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-06-01 21:22:33] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2026-06-01 21:22:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-01 21:22:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-01 21:22:33] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2026-06-01 21:22:33] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message! [2026-06-01 21:22:33] [WARN] [OmnipathR] [2026-06-01 21:22:33] [WARN] [OmnipathR] [2026-06-01 21:22:33] [WARN] [OmnipathR] Service unavailable [2026-06-01 21:22:33] [WARN] [OmnipathR] [2026-06-01 21:22:33] [WARN] [OmnipathR] [2026-06-01 21:22:33] [WARN] [OmnipathR] [2026-06-01 21:22:33] [WARN] [OmnipathR] [2026-06-01 21:22:33] [WARN] [OmnipathR] [2026-06-01 21:22:33] [WARN] [OmnipathR]
[2026-06-01 21:22:33] [WARN] [OmnipathR] ensembl-logo [2026-06-01 21:22:33] [WARN] [OmnipathR]
[2026-06-01 21:22:33] [WARN] [OmnipathR]
[2026-06-01 21:22:33] [WARN] [OmnipathR]

Server Status

[2026-06-01 21:22:33] [WARN] [OmnipathR]

[2026-06-01 21:22:33] [WARN] [OmnipathR] [!] [2026-06-01 21:22:33] [WARN] [OmnipathR] The Ensembl web service you requested is temporarily unavailable. [2026-06-01 21:22:33] [WARN] [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused. [2026-06-01 21:22:33] [WARN] [OmnipathR]

[2026-06-01 21:22:33] [WARN] [OmnipathR]

For all enquiries, please contact our HelpDesk.

[2026-06-01 21:22:33] [WARN] [OmnipathR]
[2026-06-01 21:22:33] [WARN] [OmnipathR]

Ensembl mirrors

[2026-06-01 21:22:33] [WARN] [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud: [2026-06-01 21:22:33] [WARN] [OmnipathR] [2026-06-01 21:22:33] [WARN] [OmnipathR] These will be available while the main service is unavailable, although please note that some of the [2026-06-01 21:22:33] [WARN] [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main [2026-06-01 21:22:33] [WARN] [OmnipathR] data centre. [2026-06-01 21:22:33] [WARN] [OmnipathR]
[2026-06-01 21:22:33] [WARN] [OmnipathR]
[2026-06-01 21:22:33] [WARN] [OmnipathR] [2026-06-01 21:22:33] [WARN] [OmnipathR] [2026-06-01 21:22:33] [WARN] [OmnipathR] [2026-06-01 21:22:33] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 records Error in `set_names()`: ! The size of `nm` (2) must be compatible with the size of `x` (1). Backtrace: ▆ 1. ├─OmnipathR::omnipath_for_cosmos() 2. │ └─... %T>% ... 3. ├─dplyr::bind_rows(...) 4. │ └─rlang::list2(...) 5. ├─OmnipathR::translate_ids_multi(...) 6. │ └─source_cols %>% seq_along %>% ... 7. ├─purrr::reduce(...) 8. │ └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir) 9. │ └─OmnipathR (local) fn(out, elt, ...) 10. │ └─OmnipathR::translate_ids(...) 11. │ └─... %>% ... 12. ├─purrr::reduce2(...) 13. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE) 14. │ └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...) 15. │ ├─... %>% ... 16. │ └─OmnipathR:::id_translation_table(...) 17. │ └─OmnipathR::ensembl_id_mapping_table(...) 18. │ └─... %>% trim_and_distinct 19. ├─OmnipathR:::ensure_character(., From, To) 20. │ └─d %>% mutate(across(c(!!!cols), as.character)) 21. ├─dplyr::mutate(., across(c(!!!cols), as.character)) 22. ├─OmnipathR:::trim_and_distinct(.) 23. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct 24. ├─dplyr::distinct(.) 25. ├─dplyr::mutate(., across(everything(), str_trim)) 26. ├─rlang::set_names(., c("From", "To")) 27. └─rlang::abort(message = message) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotation_categories 68.509 0.048 68.679 curated_ligrec_stats 28.748 1.506 39.036 omnipath-interactions 22.043 0.953 26.091 filter_extra_attrs 18.838 3.159 22.148 all_uniprots 17.857 0.950 29.138 nichenet_gr_network_omnipath 13.239 0.515 14.399 nichenet_signaling_network_omnipath 12.757 0.433 13.919 extra_attrs_to_cols 9.849 0.799 11.010 extra_attr_values 9.602 0.974 10.944 go_annot_download 8.288 0.495 8.316 giant_component 7.055 0.373 7.772 filter_by_resource 6.075 0.291 6.762 has_extra_attrs 5.476 0.587 6.091 extra_attrs 4.928 0.657 5.647 filter_intercell 4.853 0.367 5.186 curated_ligand_receptor_interactions 4.678 0.286 6.033 ensembl_id_mapping_table 1.506 0.163 36.134 kegg_conv 1.025 0.095 13.270 kinasephos 0.787 0.097 80.588 kegg_link 0.528 0.081 5.194 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-01_2101/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2026-06-01 21:40:48 CEST ]