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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 OmnipathR
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* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:15] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-07 19:04:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-07 19:04:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-07
[2026-04-07 19:04:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-04-07 23:03:55 UTC; unix
[2026-04-07 19:04:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-04-07 19:04:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-04-07 19:04:15] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-07; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-07 19:04:15] [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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-07 19:04:15] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2026-04-07); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); 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 1.8.0(2024-09-30); 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 2.2.3(2026-04-07); jquerylib 0.1.4(2021-04-26); 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 0.4.1(2025-09-11); 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(2026-04-07); 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); processx 3.8.7(2026-04-01); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); purrr 1.2.1(2026-01-09); 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(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); 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 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); 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)
[2026-04-07 19:04:15] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Contains 1 files.
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpuizKkv/Rinst19d6ed729eae40/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-07 19:04:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpuizKkv/Rinst19d6ed729eae40/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-07 19:04:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpuizKkv/Rinst19d6ed729eae40/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-07 19:04:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpuizKkv/Rinst19d6ed729eae40/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-07 19:04:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Cache locked: FALSE
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2026-04-07 19:04:15] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:15] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-04-07 19:04:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:16] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-04-07 19:04:16] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-04-07 19:04:16] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-04-07 19:04:16] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-04-07 19:04:16] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-04-07 19:04:16] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-04-07 19:04:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-04-07 19:04:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:04:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:04:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-04-07 19:04:16] [TRACE] [OmnipathR] Sending HTTP request.
[2026-04-07 19:04:16] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-04-07 19:04:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:04:16] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.683433s from rescued.omnipathdb.org (58.3 Kb/s); Redirect: 0s, DNS look up: 0.020343s, Connection: 0.021085s, Pretransfer: 0.384035s, First byte at: 0.535282s
[2026-04-07 19:04:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:04:16 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Wed, 08 Apr 2026 00:04:16 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-04-07 19:04:16] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 07 Apr 2026 23:04:16 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Wed, 08 Apr 2026 00:04:16 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-04-07 19:04:17] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-04-07 19:04:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:17] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-04-07 19:04:17] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-07 19:04:17] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-07 19:04:17] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-04-07 19:04:17] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-07 19:04:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:17] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:04:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-07 19:04:17] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-04-07 19:04:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-04-07 19:04:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:04:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:04:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:04:18] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-07 19:04:18] [TRACE] [OmnipathR] Downloaded 6.7 Kb in 0.643414s from omabrowser.org (10.4 Kb/s); Redirect: 0s, DNS look up: 0.182993s, Connection: 0.196004s, Pretransfer: 0.30494s, First byte at: 0.642995s
[2026-04-07 19:04:18] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 07 Apr 2026 23:04:18 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=oVsubDQtgNoPmOgMpMlbu18RkBixyHBJWJbQNHX2EOhJskFCMNGiyPs43wgoJlWdJG8ew%2FgL732pW9x%2Bbh4DBCrwe5XHSie3zU5szsqzEs4ctFpwNAFJgbEFqqCYG%2F%2BLfg%3D%3D"}]}; cf-ray: 9e8caba6dd3f597a-IAD; alt-svc: h3=":443"; ma=86400
[2026-04-07 19:04:18] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-07 19:04:18] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-04-07 19:04:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:18] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-04-07 19:04:18] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-07 19:04:18] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-04-07 19:04:18] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-07 19:04:18] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-04-07 19:04:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:18] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:04:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-04-07 19:04:18] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-07 19:04:18] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-07 19:04:50] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-04-07 19:04:50] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-04-07 19:04:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:50] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-04-07 19:04:50] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-04-07 19:04:50] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:04:50] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:04:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:04:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:04:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:04:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:04:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:04:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:04:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:04:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:04:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:04:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:04:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:04:50] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.640719s from omnipathdb.org (24.5 Kb/s); Redirect: 0s, DNS look up: 0.098465s, Connection: 0.099213s, Pretransfer: 0.479959s, First byte at: 0.639639s
[2026-04-07 19:04:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:04:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:04:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:04:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:04:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:53] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:04:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2026-04-07 19:04:54] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2026-04-07 19:04:54] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2026-04-07 19:04:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:04:54] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2026-04-07 19:04:58] [SUCCESS] [OmnipathR] Downloaded 131398 interactions.
[2026-04-07 19:05:03] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2026-04-07 19:05:03] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:03] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:03] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:03] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:05:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:05:03] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:05:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:05:03] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.511353s from omnipathdb.org (30.7 Kb/s); Redirect: 0s, DNS look up: 0.001734s, Connection: 0.002641s, Pretransfer: 0.358716s, First byte at: 0.510828s
[2026-04-07 19:05:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:05:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:05:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:05:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:05] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:05:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-04-07 19:05:05] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-04-07 19:05:05] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2026-04-07 19:05:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:05] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2026-04-07 19:05:07] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships.
[2026-04-07 19:05:08] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2026-04-07 19:05:08] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:08] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:08] [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`
[2026-04-07 19:05:08] [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`
[2026-04-07 19:05:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:05:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:05:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:05:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:05:08] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.418975s from omnipathdb.org (37.5 Kb/s); Redirect: 0s, DNS look up: 0.001471s, Connection: 0.002109s, Pretransfer: 0.269731s, First byte at: 0.418579s
[2026-04-07 19:05:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:05:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:05:08 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:05:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:11] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:05:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-04-07 19:05:11] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-04-07 19:05:11] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-04-07 19:05:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:11] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-04-07 19:05:14] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2026-04-07 19:05:15] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2026-04-07 19:05:15] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:15] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2026-04-07 19:05:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2026-04-07 19:05:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2026-04-07 19:05:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2026-04-07 19:05:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2026-04-07 19:05:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2026-04-07 19:05:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2026-04-07 19:05:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:05:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:05:15] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:05:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:05:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.346863s from omnipathdb.org (45.3 Kb/s); Redirect: 0s, DNS look up: 0.009789s, Connection: 0.010554s, Pretransfer: 0.201064s, First byte at: 0.346149s
[2026-04-07 19:05:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:05:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:05:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:05:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2026-04-07 19:05:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:17] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:05:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2026-04-07 19:05:17] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2026-04-07 19:05:17] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2026-04-07 19:05:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:17] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2026-04-07 19:05:17] [SUCCESS] [OmnipathR] Downloaded 37629 protein complexes.
[2026-04-07 19:05:18] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2026-04-07 19:05:18] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:18] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:05:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:05:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:05:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:05:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:05:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:05:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:05:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:05:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:05:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:05:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:05:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:05:19] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.339401s from omnipathdb.org (46.3 Kb/s); Redirect: 0s, DNS look up: 0.001281s, Connection: 0.001857s, Pretransfer: 0.19369s, First byte at: 0.33892s
[2026-04-07 19:05:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:05:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:05:19 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:05:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:05:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:21] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:05:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-04-07 19:05:21] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-04-07 19:05:21] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2026-04-07 19:05:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:21] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2026-04-07 19:05:21] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records.
[2026-04-07 19:05:21] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2026-04-07 19:05:21] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:21] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:05:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-04-07 19:05:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-04-07 19:05:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-04-07 19:05:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-04-07 19:05:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-04-07 19:05:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-04-07 19:05:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-04-07 19:05:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:05:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:05:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:05:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Downloaded 72 bytes in 0.27106s from omnipathdb.org (265 bytes/s); Redirect: 0s, DNS look up: 0.001525s, Connection: 0.00236s, Pretransfer: 0.199066s, First byte at: 0.27101s
[2026-04-07 19:05:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:05:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:05:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:05:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:23] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2026-04-07 19:05:23] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:23] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2026-04-07 19:05:23] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2026-04-07 19:05:23] [FATAL] [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest.
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:05:24] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-04-07 19:05:24] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:05:24] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-04-07 19:05:25] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2026-04-07 19:05:25] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:25] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:05:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-04-07 19:05:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-04-07 19:05:26] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-04-07 19:05:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-04-07 19:05:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:05:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:05:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Downloaded 16.7 Kb in 0.35754s from omnipathdb.org (46.6 Kb/s); Redirect: 0s, DNS look up: 0.001204s, Connection: 0.001818s, Pretransfer: 0.201897s, First byte at: 0.356964s
[2026-04-07 19:05:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:05:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:05:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:05:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:26] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2026-04-07 19:05:26] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:26] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2026-04-07 19:05:26] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records.
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2026-04-07 19:05:27] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:27] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:05:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:05:28] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:05:28] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:05:28] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:05:28] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:05:28] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:05:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:05:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:05:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:05:28] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:05:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:05:28] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.342163s from omnipathdb.org (45.9 Kb/s); Redirect: 0s, DNS look up: 0.001627s, Connection: 0.002423s, Pretransfer: 0.194868s, First byte at: 0.341438s
[2026-04-07 19:05:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:05:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:05:28 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:05:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:28] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:05:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-04-07 19:05:28] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-04-07 19:05:28] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2026-04-07 19:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:28] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2026-04-07 19:05:28] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records.
[2026-04-07 19:05:29] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-04-07 19:05:29] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-04-07 19:05:29] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:29] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:29] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-04-07 19:05:29] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:32] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-04-07 19:05:32] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2026-04-07 19:05:32] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:32] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:05:33] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-04-07 19:05:33] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:05:33] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache.
[2026-04-07 19:05:33] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:33] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2026-04-07 19:05:33] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2026-04-07 19:05:33] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-04-07 19:05:33] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-04-07 19:05:33] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2026-04-07 19:05:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2026-04-07 19:05:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2026-04-07 19:05:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:05:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:05:33] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:05:34] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:05:34] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.388881s from omnipathdb.org (40.4 Kb/s); Redirect: 0s, DNS look up: 0.001536s, Connection: 0.002357s, Pretransfer: 0.201591s, First byte at: 0.388263s
[2026-04-07 19:05:34] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:05:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:05:34 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:05:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2026-04-07 19:05:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:40] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:05:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-04-07 19:05:42] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-04-07 19:05:42] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2026-04-07 19:05:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:42] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2026-04-07 19:05:43] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records.
[2026-04-07 19:05:44] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2026-04-07 19:05:44] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-04-07 19:05:44] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`.
[2026-04-07 19:05:44] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-04-07 19:05:44] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2026-04-07 19:05:44] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`.
[2026-04-07 19:05:44] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-04-07 19:05:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:05:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:45] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:45] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2026-04-07 19:05:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2026-04-07 19:05:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-04-07 19:05:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-04-07 19:05:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2026-04-07 19:05:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2026-04-07 19:05:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2026-04-07 19:05:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:05:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:05:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:05:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:05:45] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.266879s from omnipathdb.org (28.4 Kb/s); Redirect: 0s, DNS look up: 0.001241s, Connection: 0.002059s, Pretransfer: 0.192387s, First byte at: 0.266605s
[2026-04-07 19:05:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:05:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:05:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:05:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:46] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-04-07 19:05:46] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:46] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2026-04-07 19:05:46] [SUCCESS] [OmnipathR] Downloaded 1190 records.
[2026-04-07 19:05:46] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-04-07 19:05:46] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:46] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-04-07 19:05:46] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-07 19:05:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:05:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:05:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:05:47] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-07 19:05:47] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.794414s from rest.uniprot.org (54 bytes/s); Redirect: 0s, DNS look up: 0.002932s, Connection: 0.003589s, Pretransfer: 0.470523s, First byte at: 0.794349s
[2026-04-07 19:05:47] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Tue, 07 Apr 2026 23:05:47 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-07 19:05:56] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-04-07 19:05:56] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2026-04-07 19:05:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:05:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:05:56] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2026-04-07 19:05:56] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-04-07 19:05:56] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-04-07 19:05:56] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-04-07 19:05:56] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-04-07 19:05:56] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2026-04-07 19:05:56] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2026-04-07 19:05:56] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`.
[2026-04-07 19:05:56] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-04-07 19:05:56] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2026-04-07 19:05:56] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-04-07 19:05:57] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2026-04-07 19:05:57] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘bioc_workshop.Rmd’
--- re-building ‘cosmos.Rmd’ using rmarkdown
[2026-04-07 19:05:58] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2026-04-07 19:05:58] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-04-07 19:05:58] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`.
[2026-04-07 19:05:58] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-04-07 19:05:58] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2026-04-07 19:05:58] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-04-07 19:05:58] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2026-04-07 19:05:58] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:05:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2026-04-07 19:05:58] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:05:58] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:05:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:05:58] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-04-07 19:05:58] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:06:01] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-04-07 19:06:01] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2026-04-07 19:06:01] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2026-04-07 19:06:02] [TRACE] [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
<Dataset name="hsapiens_gene_ensembl" interface="default" >
<Attribute name="uniprotswissprot"/>
<Attribute name="external_gene_name"/>
</Dataset>
</Query>
[2026-04-07 19:06:02] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-07 19:06:02] [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`.
[2026-04-07 19:06:02] [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`
[2026-04-07 19:06:02] [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`.
[2026-04-07 19:06:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:06:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:06:02] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:06:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2026-04-07 19:06:02] [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`
[2026-04-07 19:06:02] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-04-07 19:06:02] [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`
[2026-04-07 19:06:02] [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`.
[2026-04-07 19:06:02] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-04-07 19:06:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:06:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:06:02] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-04-07 19:06:02] [TRACE] [OmnipathR] Sending HTTP request.
[2026-04-07 19:06:02] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-04-07 19:06:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:06:02] [TRACE] [OmnipathR] Downloaded 346 bytes in 0.26831s from www.ensembl.org (1.3 Kb/s); Redirect: 0s, DNS look up: 0.005446s, Connection: 0.006173s, Pretransfer: 0.006254s, First byte at: 0.268251s
[2026-04-07 19:06:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: Apache; Content-Security-Policy: frame-ancestors 'self'; Date: Tue, 07 Apr 2026 23:06:02 GMT; X-Frame-Options: SAMEORIGIN; Transfer-Encoding: chunked; Content-Type: text/plain; charset=utf-8; Via: 1.1 phswsa12.partners.org:80 (Cisco-WSA/15.2.0-164); Connection: keep-alive
[2026-04-07 19:06:02] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Security-Policy=frame-ancestors 'self',Date=Tue, 07 Apr 2026 23:06:02 GMT,X-Frame-Options=SAMEORIGIN,Transfer-Encoding=chunked,Content-Type=text/plain; charset=utf-8,Via=1.1 phswsa12.partners.org:80 (Cisco-WSA/15.2.0-164),Connection=keep-alive]
[2026-04-07 19:06:02] [TRACE] [OmnipathR] Calling reader callback on response.
[2026-04-07 19:06:03] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2026-04-07 19:06:03] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2026-04-07 19:06:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:06:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:06:03] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2026-04-07 19:06:03] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2026-04-07 19:06:03] [WARN] [OmnipathR] Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
[2026-04-07 19:06:03] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 1 records
Quitting from cosmos.Rmd:175-179 [omnipath]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'cosmos.Rmd' failed with diagnostics:
The size of `nm` (2) must be compatible with the size of `x` (1).
--- failed re-building ‘cosmos.Rmd’
--- re-building ‘db_manager.Rmd’ using rmarkdown
[2026-04-07 19:06:04] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2026-04-07 19:06:04] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2026-04-07 19:06:04] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2026-04-07 19:06:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-07 19:06:04] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-04-07 19:06:04] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-04-07 19:06:04] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): loaded 20431 records from cache
[2026-04-07 19:06:05] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’
--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2026-04-07 19:06:17] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:06:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-04-07 19:06:17] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:06:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-04-07 19:06:17] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:06:17] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:06:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:06:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-04-07 19:06:17] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:06:20] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
--- finished re-building ‘drug_targets.Rmd’
--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2026-04-07 19:06:28] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:06:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2026-04-07 19:06:28] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:06:28] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:06:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-04-07 19:06:28] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-04-07 19:06:28] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-04-07 19:06:28] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-04-07 19:06:28] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-04-07 19:06:28] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-04-07 19:06:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-04-07 19:06:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:06:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:06:28] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:06:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:06:28] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.377013s from omnipathdb.org (41.6 Kb/s); Redirect: 0s, DNS look up: 0.001283s, Connection: 0.001943s, Pretransfer: 0.221085s, First byte at: 0.376563s
[2026-04-07 19:06:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:06:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:06:28 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:06:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-04-07 19:06:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:06:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:06:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:06:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:06:32] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:06:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2026-04-07 19:06:33] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2026-04-07 19:06:33] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2026-04-07 19:06:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:06:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:06:33] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2026-04-07 19:06:33] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2026-04-07 19:06:55] [SUCCESS] [OmnipathR] Downloaded 139054 interactions.
[2026-04-07 19:15:57] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:15:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2026-04-07 19:15:57] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:15:57] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:15:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:15:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:15:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-04-07 19:15:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-04-07 19:15:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-04-07 19:15:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-04-07 19:15:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-04-07 19:15:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-04-07 19:15:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-04-07 19:15:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:15:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:15:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:15:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:15:59] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.363544s from omnipathdb.org (43.2 Kb/s); Redirect: 0s, DNS look up: 0.001206s, Connection: 0.001956s, Pretransfer: 0.202014s, First byte at: 0.363049s
[2026-04-07 19:15:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:15:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:15:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:16:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-04-07 19:16:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:02] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:16:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2026-04-07 19:16:02] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2026-04-07 19:16:02] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2026-04-07 19:16:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:02] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2026-04-07 19:16:02] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records.
[2026-04-07 19:16:03] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2026-04-07 19:16:03] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:16:03] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-04-07 19:16:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-04-07 19:16:03] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-04-07 19:16:03] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-04-07 19:16:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-04-07 19:16:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-04-07 19:16:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-04-07 19:16:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:16:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:16:03] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:16:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:16:03] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.286699s from omnipathdb.org (4.4 Kb/s); Redirect: 0s, DNS look up: 0.001903s, Connection: 0.002874s, Pretransfer: 0.211507s, First byte at: 0.286551s
[2026-04-07 19:16:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:16:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:16:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:16:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-04-07 19:16:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:04] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:16:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2026-04-07 19:16:04] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2026-04-07 19:16:04] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2026-04-07 19:16:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:04] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2026-04-07 19:16:04] [SUCCESS] [OmnipathR] Downloaded 68 enzyme-substrate relationships.
--- finished re-building ‘extra_attrs.Rmd’
--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’
--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2026-04-07 19:16:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:16:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:07] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2026-04-07 19:16:07] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2026-04-07 19:16:08] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:16:08] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:16:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:16:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:16:09] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:16:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:16:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.380642s from omnipathdb.org (41.2 Kb/s); Redirect: 0s, DNS look up: 0.002222s, Connection: 0.009605s, Pretransfer: 0.222981s, First byte at: 0.379509s
[2026-04-07 19:16:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:16:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:16:09 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:16:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:12] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:16:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2026-04-07 19:16:13] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2026-04-07 19:16:13] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2026-04-07 19:16:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:13] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2026-04-07 19:16:15] [SUCCESS] [OmnipathR] Downloaded 67773 interactions.
[2026-04-07 19:16:17] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2026-04-07 19:16:17] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2026-04-07 19:16:17] [TRACE] [OmnipathR] Organism(s): 10090
[2026-04-07 19:16:17] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:16:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:16:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:16:18] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:16:18] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:16:18] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.362393s from omnipathdb.org (43.3 Kb/s); Redirect: 0s, DNS look up: 0.001714s, Connection: 0.002595s, Pretransfer: 0.205152s, First byte at: 0.361651s
[2026-04-07 19:16:18] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:16:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:16:18 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:16:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:21] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:16:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2026-04-07 19:16:22] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2026-04-07 19:16:22] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2026-04-07 19:16:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:22] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2026-04-07 19:16:23] [SUCCESS] [OmnipathR] Downloaded 41476 interactions.
[2026-04-07 19:16:23] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2026-04-07 19:16:23] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2026-04-07 19:16:23] [TRACE] [OmnipathR] Organism(s): 10116
[2026-04-07 19:16:23] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:16:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:24] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:24] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:24] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:24] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:16:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:16:24] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:16:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:16:25] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.39974s from omnipathdb.org (39.3 Kb/s); Redirect: 0s, DNS look up: 0.001742s, Connection: 0.00252s, Pretransfer: 0.242311s, First byte at: 0.399188s
[2026-04-07 19:16:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:16:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:16:25 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:16:27] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:27] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:16:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2026-04-07 19:16:28] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2026-04-07 19:16:28] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2026-04-07 19:16:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:28] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2026-04-07 19:16:28] [SUCCESS] [OmnipathR] Downloaded 11083 interactions.
[2026-04-07 19:16:28] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2026-04-07 19:16:28] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2026-04-07 19:16:28] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:16:28] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:16:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:16:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:16:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:16:30] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:16:30] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.40469s from omnipathdb.org (38.8 Kb/s); Redirect: 0s, DNS look up: 0.001656s, Connection: 0.002622s, Pretransfer: 0.199821s, First byte at: 0.403704s
[2026-04-07 19:16:30] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:16:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:16:30 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:16:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:31] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:16:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2026-04-07 19:16:31] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2026-04-07 19:16:31] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2026-04-07 19:16:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:31] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2026-04-07 19:16:32] [SUCCESS] [OmnipathR] Downloaded 2840 interactions.
[2026-04-07 19:16:32] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-04-07 19:16:32] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-04-07 19:16:32] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:16:32] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:32] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-04-07 19:16:32] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:35] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-04-07 19:16:37] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2026-04-07 19:16:37] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:16:37] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:16:37] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:16:37] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:16:37] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:16:37] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:16:37] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:16:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:16:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:16:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:16:37] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:16:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:16:37] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.364597s from omnipathdb.org (43.1 Kb/s); Redirect: 0s, DNS look up: 0.001591s, Connection: 0.002303s, Pretransfer: 0.207327s, First byte at: 0.363831s
[2026-04-07 19:16:37] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:16:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:16:37 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:16:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-07 19:16:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:39] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:16:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2026-04-07 19:16:39] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2026-04-07 19:16:39] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2026-04-07 19:16:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:39] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2026-04-07 19:16:39] [SUCCESS] [OmnipathR] Downloaded 6128 interactions.
[2026-04-07 19:16:40] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2026-04-07 19:16:40] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:16:40] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:16:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:16:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:16:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:16:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:16:41] [TRACE] [OmnipathR] Downloaded 19.1 Kb in 0.399141s from omnipathdb.org (47.8 Kb/s); Redirect: 0s, DNS look up: 0.001292s, Connection: 0.002216s, Pretransfer: 0.210274s, First byte at: 0.398524s
[2026-04-07 19:16:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:16:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:16:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:16:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:42] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:16:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2026-04-07 19:16:42] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2026-04-07 19:16:42] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2026-04-07 19:16:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:42] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2026-04-07 19:16:42] [SUCCESS] [OmnipathR] Downloaded 648 interactions.
[2026-04-07 19:16:42] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2026-04-07 19:16:43] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:16:43] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-04-07 19:16:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-04-07 19:16:43] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-04-07 19:16:43] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-04-07 19:16:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-04-07 19:16:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-04-07 19:16:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-04-07 19:16:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:16:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:16:43] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:16:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:16:43] [TRACE] [OmnipathR] Downloaded 112 bytes in 0.383642s from omnipathdb.org (291 bytes/s); Redirect: 0s, DNS look up: 0.001392s, Connection: 0.002262s, Pretransfer: 0.278966s, First byte at: 0.383584s
[2026-04-07 19:16:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:16:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:16:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:16:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-04-07 19:16:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:44] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:16:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2026-04-07 19:16:44] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2026-04-07 19:16:44] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2026-04-07 19:16:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:44] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2026-04-07 19:16:44] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2026-04-07 19:16:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:16:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:45] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2026-04-07 19:16:45] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:16:45] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:45] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-04-07 19:16:45] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:46] [SUCCESS] [OmnipathR] Loaded 41506 enzyme-substrate relationships from cache.
[2026-04-07 19:16:46] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-04-07 19:16:46] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-04-07 19:16:47] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:16:47] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:47] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-04-07 19:16:47] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:50] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-04-07 19:16:51] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2026-04-07 19:16:51] [TRACE] [OmnipathR] Organism(s): 10090
[2026-04-07 19:16:51] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:16:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:16:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:16:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:16:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:16:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.36102s from omnipathdb.org (43.5 Kb/s); Redirect: 0s, DNS look up: 0.001109s, Connection: 0.00178s, Pretransfer: 0.202041s, First byte at: 0.359478s
[2026-04-07 19:16:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:16:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:16:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:16:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-04-07 19:16:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:54] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:16:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2026-04-07 19:16:54] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2026-04-07 19:16:54] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2026-04-07 19:16:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:54] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2026-04-07 19:16:55] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships.
[2026-04-07 19:16:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:16:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:56] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:16:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2026-04-07 19:16:56] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:16:56] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:16:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:16:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-04-07 19:16:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-04-07 19:16:57] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-04-07 19:16:57] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-04-07 19:16:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-04-07 19:16:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-04-07 19:16:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-04-07 19:16:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:16:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:16:57] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:16:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:16:57] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.344902s from omnipathdb.org (45.5 Kb/s); Redirect: 0s, DNS look up: 0.001272s, Connection: 0.002089s, Pretransfer: 0.198912s, First byte at: 0.344065s
[2026-04-07 19:16:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:16:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:16:57 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:16:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-04-07 19:16:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:59] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:16:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2026-04-07 19:16:59] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2026-04-07 19:16:59] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2026-04-07 19:16:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:16:59] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2026-04-07 19:16:59] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes.
[2026-04-07 19:17:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:17:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:03] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:17:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],wide=FALSE,query_type=annotations]
[2026-04-07 19:17:03] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:03] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-04-07 19:17:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-04-07 19:17:03] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-04-07 19:17:03] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-04-07 19:17:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-04-07 19:17:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-04-07 19:17:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-04-07 19:17:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:03] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:03] [TRACE] [OmnipathR] Downloaded 11.6 Kb in 0.349689s from omnipathdb.org (33.3 Kb/s); Redirect: 0s, DNS look up: 0.001658s, Connection: 0.002466s, Pretransfer: 0.202067s, First byte at: 0.348787s
[2026-04-07 19:17:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-04-07 19:17:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:04] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`.
[2026-04-07 19:17:04] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`.
[2026-04-07 19:17:04] [INFO] [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1]
[2026-04-07 19:17:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:04] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:04] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records.
[2026-04-07 19:17:04] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:17:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2026-04-07 19:17:04] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:04] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:17:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:06] [TRACE] [OmnipathR] Downloaded 1.2 Kb in 0.265604s from omnipathdb.org (4.5 Kb/s); Redirect: 0s, DNS look up: 0.001794s, Connection: 0.002621s, Pretransfer: 0.193184s, First byte at: 0.265542s
[2026-04-07 19:17:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:06] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:07] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`.
[2026-04-07 19:17:07] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`.
[2026-04-07 19:17:07] [INFO] [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1]
[2026-04-07 19:17:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:07] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:07] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2026-04-07 19:17:07] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:17:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2026-04-07 19:17:07] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:07] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:17:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:08] [TRACE] [OmnipathR] Downloaded 2.7 Kb in 0.594393s from omnipathdb.org (4.6 Kb/s); Redirect: 0s, DNS look up: 0.0014s, Connection: 0.002216s, Pretransfer: 0.515634s, First byte at: 0.594181s
[2026-04-07 19:17:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:08 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-04-07 19:17:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:09] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`.
[2026-04-07 19:17:09] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`.
[2026-04-07 19:17:09] [INFO] [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1]
[2026-04-07 19:17:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:09] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:09] [SUCCESS] [OmnipathR] Downloaded 366 annotation records.
[2026-04-07 19:17:09] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:17:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2026-04-07 19:17:09] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:09] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:17:10] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-04-07 19:17:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-04-07 19:17:10] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache.
[2026-04-07 19:17:10] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:10] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2026-04-07 19:17:10] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-04-07 19:17:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell_summary`
[2026-04-07 19:17:10] [SUCCESS] [OmnipathR] Loaded 1190 records from cache.
[2026-04-07 19:17:11] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:11] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-04-07 19:17:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-04-07 19:17:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-04-07 19:17:11] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-04-07 19:17:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-04-07 19:17:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-04-07 19:17:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-04-07 19:17:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:11] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:11] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.361445s from omnipathdb.org (43.4 Kb/s); Redirect: 0s, DNS look up: 0.001287s, Connection: 0.001987s, Pretransfer: 0.205193s, First byte at: 0.360812s
[2026-04-07 19:17:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:11 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-04-07 19:17:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:16] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2026-04-07 19:17:18] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2026-04-07 19:17:18] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2026-04-07 19:17:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:18] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:19] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records.
[2026-04-07 19:17:19] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2026-04-07 19:17:19] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-04-07 19:17:19] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2026-04-07 19:17:19] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘omnipath_intro.Rmd’
--- re-building ‘paths.Rmd’ using rmarkdown
[2026-04-07 19:17:21] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:17:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2026-04-07 19:17:21] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:21] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:17:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-04-07 19:17:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-04-07 19:17:21] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-04-07 19:17:21] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-04-07 19:17:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-04-07 19:17:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-04-07 19:17:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-04-07 19:17:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:21] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:22] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.413172s from omnipathdb.org (38 Kb/s); Redirect: 0s, DNS look up: 0.001286s, Connection: 0.001883s, Pretransfer: 0.199696s, First byte at: 0.412098s
[2026-04-07 19:17:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:23] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2026-04-07 19:17:23] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:23] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:23] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2026-04-07 19:17:23] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:23] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2026-04-07 19:17:23] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-04-07 19:17:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:23] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-07 19:17:23] [TRACE] [OmnipathR] Downloaded 9.4 Kb in 0.154439s from static-content.springer.com (60.9 Kb/s); Redirect: 0s, DNS look up: 0.003409s, Connection: 0.004236s, Pretransfer: 0.13631s, First byte at: 0.153246s
[2026-04-07 19:17:23] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; content-type: application/octet-stream; x-guploader-uploadid: AMNfjG1Gogb0uiNR7zhYPY9FRSYBHzH9dozuurv7tel_pYrEnPy0jEKVoGR6B3VvG7g6r4watkz3yow; cache-control: private, max-age=86400; last-modified: Thu, 16 Nov 2023 16:51:13 GMT; etag: "daa03c1eafd00cad9456b660ca85b849"; x-goog-generation: 1700153472991609; x-goog-metageneration: 1; x-goog-stored-content-encoding: identity; x-goog-stored-content-length: 160972; x-goog-hash: crc32c=v/3p0Q==; x-goog-hash: md5=2qA8Hq/QDK2UVrZgyoW4SQ==; x-goog-storage-class: MULTI_REGIONAL; server: UploadServer; x-cdn-origin: GCS, SNPaaS; accept-ranges: bytes; age: 179590; date: Tue, 07 Apr 2026 23:17:23 GMT; via: 1.1 varnish; x-served-by: cache-iad-kcgs7200171-IAD; x-cache: HIT; x-cache-hits: 0; x-timer: S1775603844.798753,VS0,VE3; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972
[2026-04-07 19:17:24] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2026-04-07 19:17:24] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2026-04-07 19:17:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:24] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:24] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2026-04-07 19:17:24] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:17:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2026-04-07 19:17:25] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:25] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-04-07 19:17:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-04-07 19:17:25] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-04-07 19:17:25] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-04-07 19:17:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-04-07 19:17:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-04-07 19:17:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-04-07 19:17:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:25] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:25] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.368541s from omnipathdb.org (42.6 Kb/s); Redirect: 0s, DNS look up: 0.001602s, Connection: 0.002273s, Pretransfer: 0.207646s, First byte at: 0.36743s
[2026-04-07 19:17:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:25 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-04-07 19:17:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:29] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2026-04-07 19:17:30] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2026-04-07 19:17:30] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2026-04-07 19:17:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:30] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:35] [SUCCESS] [OmnipathR] Downloaded 147217 interactions.
[2026-04-07 19:17:35] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:17:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2026-04-07 19:17:35] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:35] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:17:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-04-07 19:17:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-04-07 19:17:36] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-04-07 19:17:36] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-04-07 19:17:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-04-07 19:17:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-04-07 19:17:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-04-07 19:17:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:36] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.424097s from omnipathdb.org (37 Kb/s); Redirect: 0s, DNS look up: 0.001302s, Connection: 0.002064s, Pretransfer: 0.266325s, First byte at: 0.422889s
[2026-04-07 19:17:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:36 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-04-07 19:17:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:40] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2026-04-07 19:17:42] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2026-04-07 19:17:42] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2026-04-07 19:17:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:42] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:42] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records.
[2026-04-07 19:17:43] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:43] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-04-07 19:17:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-04-07 19:17:43] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-04-07 19:17:43] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-04-07 19:17:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-04-07 19:17:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-04-07 19:17:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-04-07 19:17:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:43] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:44] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.572712s from omnipathdb.org (27.4 Kb/s); Redirect: 0s, DNS look up: 0.001241s, Connection: 0.00202s, Pretransfer: 0.291735s, First byte at: 0.57222s
[2026-04-07 19:17:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-04-07 19:17:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:45] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2026-04-07 19:17:45] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2026-04-07 19:17:45] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2026-04-07 19:17:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:45] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:45] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records.
[2026-04-07 19:17:46] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:46] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:46] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.376682s from omnipathdb.org (41.7 Kb/s); Redirect: 0s, DNS look up: 0.00122s, Connection: 0.00211s, Pretransfer: 0.219693s, First byte at: 0.3755s
[2026-04-07 19:17:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:46 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:48] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-04-07 19:17:48] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:48] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:48] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records.
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-04-07 19:17:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-04-07 19:17:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-04-07 19:17:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-04-07 19:17:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.346752s from omnipathdb.org (45.3 Kb/s); Redirect: 0s, DNS look up: 0.001289s, Connection: 0.002173s, Pretransfer: 0.196686s, First byte at: 0.345609s
[2026-04-07 19:17:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-04-07 19:17:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:50] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2026-04-07 19:17:50] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2026-04-07 19:17:50] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2026-04-07 19:17:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:50] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:50] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records.
[2026-04-07 19:17:50] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:50] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:50] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-04-07 19:17:50] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:50] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-04-07 19:17:51] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:51] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-04-07 19:17:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-04-07 19:17:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-04-07 19:17:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-04-07 19:17:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-04-07 19:17:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-04-07 19:17:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-04-07 19:17:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:51] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:51] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.476946s from omnipathdb.org (32.9 Kb/s); Redirect: 0s, DNS look up: 0.001618s, Connection: 0.002529s, Pretransfer: 0.226876s, First byte at: 0.475727s
[2026-04-07 19:17:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:51 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:53] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2026-04-07 19:17:53] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:53] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:53] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records.
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-04-07 19:17:53] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:53] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-04-07 19:17:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-04-07 19:17:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-04-07 19:17:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-04-07 19:17:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:53] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:54] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.36072s from omnipathdb.org (43.5 Kb/s); Redirect: 0s, DNS look up: 0.00119s, Connection: 0.002301s, Pretransfer: 0.202491s, First byte at: 0.359716s
[2026-04-07 19:17:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:17:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-04-07 19:17:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:55] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:17:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2026-04-07 19:17:56] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:17:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:17:56] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2026-04-07 19:17:56] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records.
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-04-07 19:17:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-04-07 19:17:56] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:17:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:17:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:17:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:17:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:17:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:17:56] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:17:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:17:57] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.360151s from omnipathdb.org (43.6 Kb/s); Redirect: 0s, DNS look up: 0.001526s, Connection: 0.002419s, Pretransfer: 0.20992s, First byte at: 0.359139s
[2026-04-07 19:17:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:17:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:17:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:18:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:18:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:01] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:18:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2026-04-07 19:18:01] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2026-04-07 19:18:01] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2026-04-07 19:18:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:01] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2026-04-07 19:18:04] [SUCCESS] [OmnipathR] Downloaded 84507 interactions.
[2026-04-07 19:18:04] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:18:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2026-04-07 19:18:04] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:18:04] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:18:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:18:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-04-07 19:18:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-04-07 19:18:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-04-07 19:18:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-04-07 19:18:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-04-07 19:18:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-04-07 19:18:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-04-07 19:18:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:18:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:18:06] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:18:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:18:06] [TRACE] [OmnipathR] Downloaded 11.4 Kb in 0.37186s from omnipathdb.org (30.7 Kb/s); Redirect: 0s, DNS look up: 0.001244s, Connection: 0.001851s, Pretransfer: 0.200384s, First byte at: 0.371323s
[2026-04-07 19:18:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:18:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:18:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:18:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-04-07 19:18:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:07] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:18:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2026-04-07 19:18:07] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2026-04-07 19:18:07] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2026-04-07 19:18:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:07] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2026-04-07 19:18:07] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records.
[2026-04-07 19:18:07] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:18:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2026-04-07 19:18:07] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:18:07] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:18:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:18:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-04-07 19:18:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-04-07 19:18:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-04-07 19:18:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-04-07 19:18:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-04-07 19:18:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-04-07 19:18:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-04-07 19:18:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:18:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:18:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:18:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:18:08] [TRACE] [OmnipathR] Downloaded 10.6 Kb in 0.418901s from omnipathdb.org (25.3 Kb/s); Redirect: 0s, DNS look up: 0.001237s, Connection: 0.001996s, Pretransfer: 0.202645s, First byte at: 0.418065s
[2026-04-07 19:18:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:18:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:18:08 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:18:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-04-07 19:18:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:09] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:18:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2026-04-07 19:18:09] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2026-04-07 19:18:09] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2026-04-07 19:18:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:09] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2026-04-07 19:18:09] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records.
[2026-04-07 19:18:11] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2026-04-07 19:18:11] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-04-07 19:18:11] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:18:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2026-04-07 19:18:11] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:18:11] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:18:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:18:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:18:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:18:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:18:12] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:18:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:18:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:18:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:18:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:18:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:18:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:18:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:18:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.342193s from omnipathdb.org (45.9 Kb/s); Redirect: 0s, DNS look up: 0.001845s, Connection: 0.002487s, Pretransfer: 0.191255s, First byte at: 0.33948s
[2026-04-07 19:18:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:18:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:18:12 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:18:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-04-07 19:18:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:14] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:18:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2026-04-07 19:18:14] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2026-04-07 19:18:14] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2026-04-07 19:18:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:14] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2026-04-07 19:18:14] [SUCCESS] [OmnipathR] Downloaded 4242 interactions.
[2026-04-07 19:18:14] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:18:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2026-04-07 19:18:14] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:18:14] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:18:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:18:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:18:15] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-04-07 19:18:15] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:18:15] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-04-07 19:18:16] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:18:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2026-04-07 19:18:16] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:18:16] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:18:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:18:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-04-07 19:18:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-04-07 19:18:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-04-07 19:18:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-04-07 19:18:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-04-07 19:18:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-04-07 19:18:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-04-07 19:18:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-07 19:18:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-07 19:18:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-07 19:18:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-07 19:18:17] [TRACE] [OmnipathR] Downloaded 17.1 Kb in 0.377861s from omnipathdb.org (45.3 Kb/s); Redirect: 0s, DNS look up: 0.00163s, Connection: 0.002424s, Pretransfer: 0.221407s, First byte at: 0.376545s
[2026-04-07 19:18:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 23:18:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 08 Apr 2026 00:18:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-07 19:18:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-04-07 19:18:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:19] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2026-04-07 19:18:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-04-07 19:18:19] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-04-07 19:18:19] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2026-04-07 19:18:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-07 19:18:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:19] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2026-04-07 19:18:19] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records.
[2026-04-07 19:18:28] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:18:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2026-04-07 19:18:28] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:18:28] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:18:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:18:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:18:29] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-04-07 19:18:29] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-04-07 19:18:29] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-04-07 19:18:30] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-07 19:18:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2026-04-07 19:18:30] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-07 19:18:30] [TRACE] [OmnipathR] Orthology targets:
[2026-04-07 19:18:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-07 19:18:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-07 19:18:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-04-07 19:18:31] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-04-07 19:18:31] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-04-07 19:18:31] [SUCCESS] [OmnipathR] Loaded 2102 annotation records from cache.
--- finished re-building ‘paths.Rmd’
SUMMARY: processing the following file failed:
‘cosmos.Rmd’
Error: Vignette re-building failed.
Execution halted