[ Started: 2025-04-03 00:13:43 CEST ] [ OmnipathR v3.15.12 for BioC-3.21 from https://github.com/saezlab/OmnipathR@devel (c8bbcd6 2025-03-28 23:24:47) ] * checking for file ‘./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 Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2025-04-03 00:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:57] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-03 00:13:57] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-03 00:13:57] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-03 00:13:57] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-02 22:13:43 UTC; unix [2025-04-03 00:13:57] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.12 [2025-04-03 00:13:57] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-03 00:13:57] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-03; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-03 00:13:57] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-03 00:13:57] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.35.0(2024-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.42(2025-01-07); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.12(2025-04-02); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.9(2024-03-15); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-03 00:13:57] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-03 00:13:57] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Contains 1 files. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpHznEmh/Rinst2ce7477fe49ac3/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-03 00:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:57] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpHznEmh/Rinst2ce7477fe49ac3/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-03 00:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:57] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpHznEmh/Rinst2ce7477fe49ac3/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-03 00:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:57] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpHznEmh/Rinst2ce7477fe49ac3/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-03 00:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:57] [TRACE] [OmnipathR] Cache locked: FALSE [2025-04-03 00:13:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:13:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2025-04-03 00:13:57] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:57] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:57] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-04-03 00:13:57] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-04-03 00:13:57] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-04-03 00:13:57] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-04-03 00:13:57] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-03 00:13:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:13:57] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:13:57] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-03 00:13:57] [TRACE] [OmnipathR] Sending HTTP request. [2025-04-03 00:13:57] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-04-03 00:13:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Downloaded 31.1 Kb in 0.259713s from www.ensembl.org (119.7 Kb/s); Redirect: 0s, DNS look up: 0.029034s, Connection: 0.047539s, Pretransfer: 0.11254s, First byte at: 0.236605s [2025-04-03 00:13:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 02 Apr 2025 22:13:57 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31821; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 03 Apr 2025 22:13:57 GMT; Set-cookie: ENSEMBL_HINX_SESSION=cb6ae7cacbce2b5b08d5a1e3683cd0a506ddb47fc82e61dc901ac3ce; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 03 Apr 2025 22:13:57 GMT; Set-cookie: ENSEMBL_HINX_SESSION=cb6ae7cacbce2b5b08d5a1e3683cd0a506ddb47fc82e61dc901ac3ce; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-32.ebi.ac.uk [2025-04-03 00:13:57] [TRACE] [OmnipathR] Response headers: [Date=Wed, 02 Apr 2025 22:13:57 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31821,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 03 Apr 2025 22:13:57 GMT,Set-cookie=ENSEMBL_HINX_SESSION=cb6ae7cacbce2b5b08d5a1e3683cd0a506ddb47fc82e61dc901ac3ce; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 03 Apr 2025 22:13:57 GMT,Set-cookie=ENSEMBL_HINX_SESSION=cb6ae7cacbce2b5b08d5a1e3683cd0a506ddb47fc82e61dc901ac3ce; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-32.ebi.ac.uk] [2025-04-03 00:13:57] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-04-03 00:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:57] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-04-03 00:13:57] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-04-03 00:13:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-04-03 00:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:58] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-04-03 00:13:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-03 00:13:58] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-04-03 00:13:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-04-03 00:13:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:13:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:13:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:13:58] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-03 00:13:58] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.123804s from omabrowser.org (70.2 Kb/s); Redirect: 0s, DNS look up: 0.047933s, Connection: 0.058638s, Pretransfer: 0.108451s, First byte at: 0.123661s [2025-04-03 00:13:58] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 02 Apr 2025 22:13:58 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-04-03 00:13:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-03 00:13:58] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-04-03 00:13:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:13:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:58] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-04-03 00:13:58] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-04-03 00:13:58] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:13:58] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:13:58] [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` [2025-04-03 00:13:58] [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` [2025-04-03 00:13:58] [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` [2025-04-03 00:13:58] [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` [2025-04-03 00:13:58] [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` [2025-04-03 00:13:58] [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` [2025-04-03 00:13:58] [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` [2025-04-03 00:13:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:13:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:13:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:13:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:13:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.119858s from omnipathdb.org (130.7 Kb/s); Redirect: 0s, DNS look up: 0.018264s, Connection: 0.040158s, Pretransfer: 0.075658s, First byte at: 0.119454s [2025-04-03 00:13:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:13:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:13:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:13:59] [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` [2025-04-03 00:13:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:13:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:13:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:59] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2025-04-03 00:13:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-04-03 00:13:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-04-03 00:13:59] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2025-04-03 00:13:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:13:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:13:59] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2025-04-03 00:14:03] [SUCCESS] [OmnipathR] Downloaded 128218 interactions. [2025-04-03 00:14:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2025-04-03 00:14:06] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:06] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:06] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:06] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:14:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:14:06] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:14:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:14:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09984s from omnipathdb.org (156.9 Kb/s); Redirect: 0s, DNS look up: 0.000927s, Connection: 0.022865s, Pretransfer: 0.056303s, First byte at: 0.099406s [2025-04-03 00:14:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:14:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:14:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:14:06] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:06] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2025-04-03 00:14:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-04-03 00:14:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-04-03 00:14:06] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2025-04-03 00:14:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:06] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2025-04-03 00:14:08] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships. [2025-04-03 00:14:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2025-04-03 00:14:08] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:08] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:08] [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` [2025-04-03 00:14:08] [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` [2025-04-03 00:14:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:14:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:14:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:14:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:14:08] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.109083s from omnipathdb.org (143.6 Kb/s); Redirect: 0s, DNS look up: 0.001002s, Connection: 0.021399s, Pretransfer: 0.067716s, First byte at: 0.108383s [2025-04-03 00:14:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:14:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:14:08 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:14:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:09] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-04-03 00:14:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-03 00:14:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-03 00:14:09] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-04-03 00:14:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:09] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-04-03 00:14:11] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. [2025-04-03 00:14:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2025-04-03 00:14:12] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:12] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2025-04-03 00:14:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2025-04-03 00:14:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2025-04-03 00:14:12] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2025-04-03 00:14:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2025-04-03 00:14:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2025-04-03 00:14:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2025-04-03 00:14:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:14:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:14:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:14:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:14:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089657s from omnipathdb.org (174.7 Kb/s); Redirect: 0s, DNS look up: 0.001032s, Connection: 0.019008s, Pretransfer: 0.05324s, First byte at: 0.089383s [2025-04-03 00:14:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:14:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:14:12 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:14:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2025-04-03 00:14:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:12] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2025-04-03 00:14:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2025-04-03 00:14:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2025-04-03 00:14:12] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2025-04-03 00:14:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:12] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2025-04-03 00:14:12] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes. [2025-04-03 00:14:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2025-04-03 00:14:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:13] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:14:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:14:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:14:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:14:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:14:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:14:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:14:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:14:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:14:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:14:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:14:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:14:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100344s from omnipathdb.org (156.1 Kb/s); Redirect: 0s, DNS look up: 0.001136s, Connection: 0.017492s, Pretransfer: 0.066773s, First byte at: 0.100043s [2025-04-03 00:14:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:14:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:14:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:14:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:14:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:13] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2025-04-03 00:14:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-04-03 00:14:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-04-03 00:14:13] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2025-04-03 00:14:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:14] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2025-04-03 00:14:14] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records. [2025-04-03 00:14:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2025-04-03 00:14:14] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:14] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-03 00:14:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-03 00:14:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-03 00:14:14] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-03 00:14:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-03 00:14:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-03 00:14:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-03 00:14:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:14:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:14:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:14:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:14:14] [TRACE] [OmnipathR] Downloaded 60 bytes in 0.084918s from omnipathdb.org (706 bytes/s); Redirect: 0s, DNS look up: 0.001006s, Connection: 0.025045s, Pretransfer: 0.058927s, First byte at: 0.084899s [2025-04-03 00:14:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:14:14 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 60; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:14:14 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-04-03 00:14:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-04-03 00:14:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:14] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2025-04-03 00:14:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2025-04-03 00:14:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2025-04-03 00:14:14] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2025-04-03 00:14:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:14] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2025-04-03 00:14:14] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2025-04-03 00:14:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations] [2025-04-03 00:14:14] [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. [2025-04-03 00:14:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2025-04-03 00:14:14] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:14] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:14:15] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-04-03 00:14:15] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:14:15] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2025-04-03 00:14:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations] [2025-04-03 00:14:15] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:15] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-03 00:14:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-03 00:14:15] [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` [2025-04-03 00:14:15] [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` [2025-04-03 00:14:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-03 00:14:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-03 00:14:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-03 00:14:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:14:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:14:15] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:14:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:14:15] [TRACE] [OmnipathR] Downloaded 22.3 Kb in 0.103203s from omnipathdb.org (215.7 Kb/s); Redirect: 0s, DNS look up: 0.001052s, Connection: 0.022712s, Pretransfer: 0.055981s, First byte at: 0.102689s [2025-04-03 00:14:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:14:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:14:15 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:14:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-04-03 00:14:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:15] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2025-04-03 00:14:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2025-04-03 00:14:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2025-04-03 00:14:15] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2025-04-03 00:14:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:15] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2025-04-03 00:14:15] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records. [2025-04-03 00:14:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2025-04-03 00:14:15] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:15] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:14:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:14:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:14:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:14:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:14:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:14:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:14:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:14:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:14:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:14:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:14:16] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.110681s from omnipathdb.org (141.6 Kb/s); Redirect: 0s, DNS look up: 0.000895s, Connection: 0.020612s, Pretransfer: 0.071323s, First byte at: 0.110377s [2025-04-03 00:14:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:14:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:14:16 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:14:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:16] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2025-04-03 00:14:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-04-03 00:14:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-04-03 00:14:16] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2025-04-03 00:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:16] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2025-04-03 00:14:16] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records. [2025-04-03 00:14:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-04-03 00:14:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-04-03 00:14:16] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:16] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:16] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-03 00:14:16] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:14:18] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2025-04-03 00:14:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:14:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations] [2025-04-03 00:14:18] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:18] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:14:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:14:19] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-04-03 00:14:19] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:14:19] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache. [2025-04-03 00:14:19] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:19] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic` [2025-04-03 00:14:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2025-04-03 00:14:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic` [2025-04-03 00:14:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic` [2025-04-03 00:14:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic` [2025-04-03 00:14:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2025-04-03 00:14:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2025-04-03 00:14:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:14:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:14:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:14:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:14:22] [TRACE] [OmnipathR] Downloaded 31.7 Kb in 3.129074s from omnipathdb.org (10.1 Kb/s); Redirect: 0s, DNS look up: 0.00095s, Connection: 0.021228s, Pretransfer: 0.065778s, First byte at: 3.126994s [2025-04-03 00:14:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:14:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:14:22 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:14:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic` [2025-04-03 00:14:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:23] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2025-04-03 00:14:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2025-04-03 00:14:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2025-04-03 00:14:25] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2025-04-03 00:14:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:25] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2025-04-03 00:14:25] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records. [2025-04-03 00:14:26] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2025-04-03 00:14:26] [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. [2025-04-03 00:14:26] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`. [2025-04-03 00:14:26] [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. [2025-04-03 00:14:26] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2025-04-03 00:14:26] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2025-04-03 00:14:26] [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. [2025-04-03 00:14:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:14:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:26] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:14:26] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:14:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2025-04-03 00:14:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2025-04-03 00:14:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2025-04-03 00:14:26] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2025-04-03 00:14:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2025-04-03 00:14:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2025-04-03 00:14:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2025-04-03 00:14:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:14:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:14:26] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:14:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:14:26] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.074625s from omnipathdb.org (116.8 Kb/s); Redirect: 0s, DNS look up: 0.001017s, Connection: 0.020114s, Pretransfer: 0.053896s, First byte at: 0.074454s [2025-04-03 00:14:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:14:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:14:26 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:14:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2025-04-03 00:14:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:26] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2025-04-03 00:14:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-04-03 00:14:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-04-03 00:14:26] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2025-04-03 00:14:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:26] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2025-04-03 00:14:26] [SUCCESS] [OmnipathR] Downloaded 1098 records. [2025-04-03 00:14:26] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2025-04-03 00:14:26] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2025-04-03 00:14:26] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2025-04-03 00:14:26] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-03 00:14:26] [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`. [2025-04-03 00:14:26] [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` [2025-04-03 00:14:26] [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`. [2025-04-03 00:14:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:14:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:14:26] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2025-04-03 00:14:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-04-03 00:14:26] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-03 00:14:26] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-03 00:14:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:14:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:14:26] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:15:15] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-03 00:15:15] [TRACE] [OmnipathR] Downloaded 43 bytes in 48.822334s from rest.uniprot.org (0 bytes/s); Redirect: 0s, DNS look up: 0.019259s, Connection: 0.038269s, Pretransfer: 0.096793s, First byte at: 48.822262s [2025-04-03 00:15:15] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; 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: 05-February-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 02 Apr 2025 22:15:15 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_01; access-control-allow-origin: *; 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: 05-February-2025 [2025-04-03 00:16:15] [WARN] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` (attempt 1/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) [2025-04-03 00:16:20] [TRACE] [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-03 00:16:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:16:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:16:20] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:17:00] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-03 00:17:00] [TRACE] [OmnipathR] Downloaded 43 bytes in 39.219287s from rest.uniprot.org (1 bytes/s); Redirect: 0s, DNS look up: 0.048387s, Connection: 0.066584s, Pretransfer: 0.120343s, First byte at: 39.219214s [2025-04-03 00:17:00] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; 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: 05-February-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 02 Apr 2025 22:17:00 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_01; access-control-allow-origin: *; 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: 05-February-2025 [2025-04-03 00:18:00] [WARN] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` (attempt 2/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) [2025-04-03 00:18:05] [TRACE] [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-03 00:18:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:18:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:18:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:18:42] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-03 00:18:42] [TRACE] [OmnipathR] Downloaded 43 bytes in 37.336047s from rest.uniprot.org (1 bytes/s); Redirect: 0s, DNS look up: 0.001681s, Connection: 0.020451s, Pretransfer: 0.075221s, First byte at: 37.335977s [2025-04-03 00:18:42] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; 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: 05-February-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 02 Apr 2025 22:18:42 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_01; access-control-allow-origin: *; 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: 05-February-2025 [2025-04-03 00:19:42] [ERROR] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` (attempt 3/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) [2025-04-03 00:19:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-03 00:19:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-03 00:19:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-02 22:13:43 UTC; unix [2025-04-03 00:19:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.12 [2025-04-03 00:19:42] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-03 00:19:42] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-03; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-03 00:19:42] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-03 00:19:42] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.35.0(2024-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.42(2025-01-07); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.12(2025-04-02); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.9(2024-03-15); selectr 0.4-2(2019-11-20); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); utf8 1.2.4(2023-10-22); vctrs 0.6.5(2023-12-01); vroom 1.6.5(2023-12-05); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-03 00:19:42] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE Quitting from bioc_workshop.Rmd:451-459 [id-translate-vector] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) --- Backtrace: ▆ 1. ├─OmnipathR::translate_ids(d, uniprot_id = uniprot, genesymbol) 2. │ └─... %>% ... 3. ├─purrr::reduce2(...) 4. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE) 5. │ └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...) 6. │ ├─... %>% ... 7. │ └─OmnipathR:::id_translation_table(...) 8. │ └─OmnipathR::uniprot_full_id_mapping_table(...) 9. │ └─... %>% trim_and_distinct 10. ├─OmnipathR:::ensure_character(., From, To) 11. │ └─d %>% mutate(across(c(!!!cols), as.character)) 12. ├─dplyr::mutate(., across(c(!!!cols), as.character)) 13. ├─OmnipathR:::trim_and_distinct(.) 14. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct 15. ├─dplyr::distinct(.) 16. ├─dplyr::mutate(., across(everything(), str_trim)) 17. ├─dplyr::filter(., !is.na(From) & !is.na(To)) 18. ├─tidyr::separate_rows(., To, sep = "[; ]") 19. ├─tidyr::separate_rows(., From, sep = "[; ]") 20. ├─dplyr::mutate(., From = strip_semicol(From), To = strip_semicol(To)) 21. ├─dplyr::rename(., From = 1, To = 2) 22. ├─OmnipathR::all_uniprots(., reviewed = reviewed, organism = organism) 23. │ ├─... %T>% load_success() 24. │ └─OmnipathR:::generic_downloader(...) 25. │ ├─... %>% omnipath_cache_save(url = url, post = post) 26. │ ├─rlang::exec(...) 27. │ └─OmnipathR (local) ``(...) 28. ├─OmnipathR:::load_success(.) 29. │ └─from_cache %<>% if_null(data %>% is_from_cache) 30. ├─OmnipathR:::if_null(., data %>% is_from_cache) 31. │ └─value1 %>% is.null %>% if (value2) value1 32. ├─data %>% is_from_cache 33. ├─OmnipathR:::is_from_cache(.) 34. │ └─obj %>% attr("origin") %>% ... 35. └─OmnipathR::omnipath_cache_save(., url = url, post = post) 36. └─base::saveRDS(data, target_path) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) --- failed re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2025-04-03 00:19:44] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2025-04-03 00:19:44] [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. [2025-04-03 00:19:44] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2025-04-03 00:19:44] [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. [2025-04-03 00:19:44] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2025-04-03 00:19:44] [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. [2025-04-03 00:19:44] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2025-04-03 00:19:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:19:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2025-04-03 00:19:44] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:19:44] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:19:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:19:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-03 00:19:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:19:46] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2025-04-03 00:19:46] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2025-04-03 00:19:46] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2025-04-03 00:19:46] [TRACE] [OmnipathR] BioMart query: [2025-04-03 00:19:46] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-03 00:19:46] [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`. [2025-04-03 00:19:46] [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` [2025-04-03 00:19:46] [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`. [2025-04-03 00:19:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:19:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:19:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:19:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:19:47] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2025-04-03 00:19:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2025-04-03 00:19:47] [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` [2025-04-03 00:19:47] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-04-03 00:19:47] [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` [2025-04-03 00:19:47] [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`. [2025-04-03 00:19:47] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-03 00:19:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:19:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:19:47] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-03 00:19:47] [TRACE] [OmnipathR] Sending HTTP request. [2025-04-03 00:19:47] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-04-03 00:19:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:19:47] [TRACE] [OmnipathR] Downloaded 1015 bytes in 0.107903s from www.ensembl.org (9.2 Kb/s); Redirect: 0s, DNS look up: 0.064191s, Connection: 0.083193s, Pretransfer: 0.083398s, First byte at: 0.107655s [2025-04-03 00:19:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: 946B:216992:1CA676:1EA808:67ECD591; Server: GitHub.com; X-Cache-Hits: 1; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: cbf907cbb3c99c5cca8e133a1a915f2703a904d3; Content-Encoding: gzip; Date: Wed, 02 Apr 2025 22:19:47 GMT; Expires: 0; X-Served-By: cache-lcy-eglc8600073-LCY; Pragma: no-cache; X-Timer: S1743632387.135564,VS0,VE2; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"67177dde-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 39; Content-Length: 1015 [2025-04-03 00:19:47] [TRACE] [OmnipathR] Response headers: [X-GitHub-Request-Id=946B:216992:1CA676:1EA808:67ECD591,Server=GitHub.com,X-Cache-Hits=1,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=cbf907cbb3c99c5cca8e133a1a915f2703a904d3,Content-Encoding=gzip,Date=Wed, 02 Apr 2025 22:19:47 GMT,Expires=0,X-Served-By=cache-lcy-eglc8600073-LCY,Pragma=no-cache,X-Timer=S1743632387.135564,VS0,VE2,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"67177dde-8aa",Via=1.1 varnish,Connection=keep-alive,Age=39,Content-Length=1015] [2025-04-03 00:19:47] [TRACE] [OmnipathR] Calling reader callback on response. [2025-04-03 00:19:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2025-04-03 00:19:47] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2025-04-03 00:19:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:19:47] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2025-04-03 00:19:47] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message! [2025-04-03 00:19:47] [WARN] [OmnipathR] [2025-04-03 00:19:47] [WARN] [OmnipathR] [2025-04-03 00:19:47] [WARN] [OmnipathR] Service unavailable [2025-04-03 00:19:47] [WARN] [OmnipathR] [2025-04-03 00:19:47] [WARN] [OmnipathR] [2025-04-03 00:19:47] [WARN] [OmnipathR] [2025-04-03 00:19:47] [WARN] [OmnipathR] [2025-04-03 00:19:47] [WARN] [OmnipathR] [2025-04-03 00:19:47] [WARN] [OmnipathR]
[2025-04-03 00:19:47] [WARN] [OmnipathR] ensembl-logo [2025-04-03 00:19:47] [WARN] [OmnipathR]
[2025-04-03 00:19:47] [WARN] [OmnipathR]
[2025-04-03 00:19:47] [WARN] [OmnipathR]

Server Status

[2025-04-03 00:19:47] [WARN] [OmnipathR]

[2025-04-03 00:19:47] [WARN] [OmnipathR] [!] [2025-04-03 00:19:47] [WARN] [OmnipathR] The Ensembl web service you requested is temporarily unavailable. [2025-04-03 00:19:47] [WARN] [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused. [2025-04-03 00:19:47] [WARN] [OmnipathR]

[2025-04-03 00:19:47] [WARN] [OmnipathR]

For all enquiries, please contact our HelpDesk.

[2025-04-03 00:19:47] [WARN] [OmnipathR]
[2025-04-03 00:19:47] [WARN] [OmnipathR]

Ensembl mirrors

[2025-04-03 00:19:47] [WARN] [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud: [2025-04-03 00:19:47] [WARN] [OmnipathR] [2025-04-03 00:19:47] [WARN] [OmnipathR] These will be available while the main service is unavailable, although please note that some of the [2025-04-03 00:19:47] [WARN] [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main [2025-04-03 00:19:47] [WARN] [OmnipathR] data centre. [2025-04-03 00:19:47] [WARN] [OmnipathR]
[2025-04-03 00:19:47] [WARN] [OmnipathR]
[2025-04-03 00:19:47] [WARN] [OmnipathR]
[2025-04-03 00:19:47] [WARN] [OmnipathR]

© 2024 EMBL-EBI

[2025-04-03 00:19:47] [WARN] [OmnipathR]
[2025-04-03 00:19:47] [WARN] [OmnipathR] [2025-04-03 00:19:47] [WARN] [OmnipathR] [2025-04-03 00:19:47] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 records Quitting from cosmos.Rmd:175-179 [omnipath] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 [2025-04-03 00:19:47] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2025-04-03 00:19:47] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2025-04-03 00:19:47] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2025-04-03 00:19:47] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-03 00:19:47] [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`. [2025-04-03 00:19:47] [INFO] [OmnipathR] No version is available for key `5edbb7050189a96382506b82b49b51a411621af7` (https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true). [2025-04-03 00:19:47] [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`. [2025-04-03 00:19:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:19:47] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 2: status changed from `unknown` to `started`. [2025-04-03 00:19:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-2.rds`. [2025-04-03 00:19:47] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-03 00:19:47] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-03 00:19:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:19:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:19:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:19:53] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-03 00:19:53] [TRACE] [OmnipathR] Downloaded 43 bytes in 5.946477s from rest.uniprot.org (7 bytes/s); Redirect: 0s, DNS look up: 0.000974s, Connection: 0.019797s, Pretransfer: 0.094876s, First byte at: 5.946411s [2025-04-03 00:19:53] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; 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: 05-February-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 02 Apr 2025 22:19:53 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_01; access-control-allow-origin: *; 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: 05-February-2025 [2025-04-03 00:20:53] [WARN] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` (attempt 1/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) [2025-04-03 00:20:58] [TRACE] [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-03 00:20:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:20:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:20:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:21:28] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-03 00:21:28] [TRACE] [OmnipathR] Downloaded 43 bytes in 29.41866s from rest.uniprot.org (1 bytes/s); Redirect: 0s, DNS look up: 0.001917s, Connection: 0.020619s, Pretransfer: 0.09458s, First byte at: 29.41859s [2025-04-03 00:21:28] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; 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: 05-February-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 02 Apr 2025 22:21:28 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_01; access-control-allow-origin: *; 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: 05-February-2025 [2025-04-03 00:22:28] [WARN] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` (attempt 2/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) [2025-04-03 00:22:33] [TRACE] [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-04-03 00:22:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:22:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:22:33] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:23:02] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-03 00:23:02] [TRACE] [OmnipathR] Downloaded 43 bytes in 29.366501s from rest.uniprot.org (1 bytes/s); Redirect: 0s, DNS look up: 0.001025s, Connection: 0.019852s, Pretransfer: 0.088774s, First byte at: 29.366429s [2025-04-03 00:23:02] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; 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: 05-February-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 02 Apr 2025 22:23:02 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_01; access-control-allow-origin: *; 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: 05-February-2025 [2025-04-03 00:24:02] [ERROR] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` (attempt 3/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) [2025-04-03 00:24:02] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-03 00:24:02] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-03 00:24:02] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-02 22:13:43 UTC; unix [2025-04-03 00:24:02] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.12 [2025-04-03 00:24:02] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-03 00:24:02] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-03; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-03 00:24:02] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-03 00:24:02] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.35.0(2024-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.42(2025-01-07); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.12(2025-04-02); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.9(2024-03-15); selectr 0.4-2(2019-11-20); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); utf8 1.2.4(2023-10-22); vctrs 0.6.5(2023-12-01); vroom 1.6.5(2023-12-05); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-03 00:24:02] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE Quitting from db_manager.Rmd:66-69 [get] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) --- Backtrace: ▆ 1. ├─OmnipathR::get_db("up_gs") 2. │ └─OmnipathR::load_db(key, param = param) 3. │ ├─rlang::exec(loader, !!!param) 4. │ └─OmnipathR (local) ``(to = "genesymbol", organism = 9606L) 5. │ └─... %>% trim_and_distinct 6. ├─OmnipathR:::trim_and_distinct(.) 7. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct 8. ├─dplyr::distinct(.) 9. ├─dplyr::mutate(., across(everything(), str_trim)) 10. ├─dplyr::filter(., !is.na(From) & !is.na(To)) 11. ├─tidyr::separate_rows(., To, sep = "[; ]") 12. ├─tidyr::separate_rows(., From, sep = "[; ]") 13. ├─dplyr::mutate(., From = strip_semicol(From), To = strip_semicol(To)) 14. ├─dplyr::rename(., From = 1, To = 2) 15. ├─OmnipathR::all_uniprots(., reviewed = reviewed, organism = organism) 16. │ ├─... %T>% load_success() 17. │ └─OmnipathR:::generic_downloader(...) 18. │ ├─... %>% omnipath_cache_save(url = url, post = post) 19. │ ├─rlang::exec(...) 20. │ └─OmnipathR (local) ``(...) 21. ├─OmnipathR:::load_success(.) 22. │ └─from_cache %<>% if_null(data %>% is_from_cache) 23. ├─OmnipathR:::if_null(., data %>% is_from_cache) 24. │ └─value1 %>% is.null %>% if (value2) value1 25. ├─data %>% is_from_cache 26. ├─OmnipathR:::is_from_cache(.) 27. │ └─obj %>% attr("origin") %>% ... 28. └─OmnipathR::omnipath_cache_save(., url = url, post = post) 29. └─base::saveRDS(data, target_path) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'db_manager.Rmd' failed with diagnostics: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) --- failed re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2025-04-03 00:24:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:24:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-04-03 00:24:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:24:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-04-03 00:24:03] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:24:03] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:24:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:24:04] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-03 00:24:04] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:24:06] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2025-04-03 00:24:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:24:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2025-04-03 00:24:08] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:24:08] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:24:08] [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` [2025-04-03 00:24:08] [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` [2025-04-03 00:24:08] [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` [2025-04-03 00:24:08] [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` [2025-04-03 00:24:08] [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` [2025-04-03 00:24:08] [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` [2025-04-03 00:24:08] [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` [2025-04-03 00:24:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:24:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:24:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:24:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:24:08] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.105944s from omnipathdb.org (147.9 Kb/s); Redirect: 0s, DNS look up: 0.009828s, Connection: 0.030839s, Pretransfer: 0.064542s, First byte at: 0.105623s [2025-04-03 00:24:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:24:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:24:08 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:24:09] [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` [2025-04-03 00:24:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:24:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:24:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:24:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:24:09] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2025-04-03 00:24:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2025-04-03 00:24:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2025-04-03 00:24:09] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2025-04-03 00:24:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:24:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:24:09] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2025-04-03 00:24:09] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-04-03 00:24:18] [SUCCESS] [OmnipathR] Downloaded 134282 interactions. [2025-04-03 00:29:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:29:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2025-04-03 00:29:54] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:29:54] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:29:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:29:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-03 00:29:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-03 00:29:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-03 00:29:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-03 00:29:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-03 00:29:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-03 00:29:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-03 00:29:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:29:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:29:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:29:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:29:54] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10921s from omnipathdb.org (143.5 Kb/s); Redirect: 0s, DNS look up: 0.001103s, Connection: 0.021676s, Pretransfer: 0.06757s, First byte at: 0.108889s [2025-04-03 00:29:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:29:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:29:54 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:29:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-04-03 00:29:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:29:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:29:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:55] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2025-04-03 00:29:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2025-04-03 00:29:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2025-04-03 00:29:55] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2025-04-03 00:29:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:29:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:56] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2025-04-03 00:29:56] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records. [2025-04-03 00:29:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:29:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2025-04-03 00:29:56] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:29:56] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:29:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-03 00:29:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-03 00:29:56] [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` [2025-04-03 00:29:56] [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` [2025-04-03 00:29:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-03 00:29:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-03 00:29:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-03 00:29:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:29:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:29:56] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:29:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:29:56] [TRACE] [OmnipathR] Downloaded 5.1 Kb in 0.098114s from omnipathdb.org (51.9 Kb/s); Redirect: 0s, DNS look up: 0.000935s, Connection: 0.024407s, Pretransfer: 0.075338s, First byte at: 0.098098s [2025-04-03 00:29:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:29:56 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 5219; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:29:56 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-04-03 00:29:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-04-03 00:29:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:56] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2025-04-03 00:29:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2025-04-03 00:29:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2025-04-03 00:29:56] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2025-04-03 00:29:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:56] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2025-04-03 00:29:56] [SUCCESS] [OmnipathR] Downloaded 70 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 [2025-04-03 00:29:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:29:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:29:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2025-04-03 00:29:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:29:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2025-04-03 00:29:58] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:29:58] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:29:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:29:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:58] [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` [2025-04-03 00:29:58] [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` [2025-04-03 00:29:58] [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` [2025-04-03 00:29:58] [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` [2025-04-03 00:29:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:29:58] [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` [2025-04-03 00:29:58] [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` [2025-04-03 00:29:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:29:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:29:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:29:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:29:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092945s from omnipathdb.org (168.6 Kb/s); Redirect: 0s, DNS look up: 0.000902s, Connection: 0.02052s, Pretransfer: 0.053899s, First byte at: 0.092602s [2025-04-03 00:29:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:29:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:29:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:29:59] [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` [2025-04-03 00:29:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:59] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2025-04-03 00:29:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2025-04-03 00:29:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2025-04-03 00:29:59] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2025-04-03 00:29:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:29:59] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:01] [SUCCESS] [OmnipathR] Downloaded 64485 interactions. [2025-04-03 00:30:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2025-04-03 00:30:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2025-04-03 00:30:05] [TRACE] [OmnipathR] Organism(s): 10090 [2025-04-03 00:30:05] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:05] [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` [2025-04-03 00:30:05] [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` [2025-04-03 00:30:05] [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` [2025-04-03 00:30:05] [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` [2025-04-03 00:30:05] [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` [2025-04-03 00:30:05] [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` [2025-04-03 00:30:05] [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` [2025-04-03 00:30:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:05] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102016s from omnipathdb.org (153.6 Kb/s); Redirect: 0s, DNS look up: 0.000906s, Connection: 0.022608s, Pretransfer: 0.056264s, First byte at: 0.101655s [2025-04-03 00:30:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:05 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:06] [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` [2025-04-03 00:30:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:06] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2025-04-03 00:30:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2025-04-03 00:30:06] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2025-04-03 00:30:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:06] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:07] [SUCCESS] [OmnipathR] Downloaded 39742 interactions. [2025-04-03 00:30:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2025-04-03 00:30:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2025-04-03 00:30:07] [TRACE] [OmnipathR] Organism(s): 10116 [2025-04-03 00:30:07] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:07] [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` [2025-04-03 00:30:07] [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` [2025-04-03 00:30:07] [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` [2025-04-03 00:30:07] [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` [2025-04-03 00:30:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:07] [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` [2025-04-03 00:30:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:07] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099882s from omnipathdb.org (156.9 Kb/s); Redirect: 0s, DNS look up: 0.000842s, Connection: 0.01715s, Pretransfer: 0.067476s, First byte at: 0.099642s [2025-04-03 00:30:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:07 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:08] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2025-04-03 00:30:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2025-04-03 00:30:08] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2025-04-03 00:30:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:08] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:08] [SUCCESS] [OmnipathR] Downloaded 6869 interactions. [2025-04-03 00:30:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2025-04-03 00:30:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2025-04-03 00:30:08] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:08] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:08] [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` [2025-04-03 00:30:08] [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` [2025-04-03 00:30:08] [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` [2025-04-03 00:30:08] [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` [2025-04-03 00:30:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:08] [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` [2025-04-03 00:30:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:09] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:09] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101755s from omnipathdb.org (154 Kb/s); Redirect: 0s, DNS look up: 0.000934s, Connection: 0.022634s, Pretransfer: 0.057699s, First byte at: 0.101476s [2025-04-03 00:30:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:08 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:09] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2025-04-03 00:30:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2025-04-03 00:30:09] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2025-04-03 00:30:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:09] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:09] [SUCCESS] [OmnipathR] Downloaded 2834 interactions. [2025-04-03 00:30:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-04-03 00:30:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-04-03 00:30:09] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:09] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:09] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-03 00:30:09] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:12] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2025-04-03 00:30:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2025-04-03 00:30:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:13] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:13] [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` [2025-04-03 00:30:13] [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` [2025-04-03 00:30:13] [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` [2025-04-03 00:30:13] [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` [2025-04-03 00:30:13] [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` [2025-04-03 00:30:13] [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` [2025-04-03 00:30:13] [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` [2025-04-03 00:30:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.083806s from omnipathdb.org (186.9 Kb/s); Redirect: 0s, DNS look up: 0.001s, Connection: 0.016809s, Pretransfer: 0.051484s, First byte at: 0.083569s [2025-04-03 00:30:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:13] [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` [2025-04-03 00:30:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:13] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2025-04-03 00:30:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2025-04-03 00:30:13] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2025-04-03 00:30:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:13] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:13] [SUCCESS] [OmnipathR] Downloaded 6127 interactions. [2025-04-03 00:30:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2025-04-03 00:30:14] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:14] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:14] [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` [2025-04-03 00:30:14] [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` [2025-04-03 00:30:14] [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` [2025-04-03 00:30:14] [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` [2025-04-03 00:30:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:14] [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` [2025-04-03 00:30:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:14] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.115652s from omnipathdb.org (135.5 Kb/s); Redirect: 0s, DNS look up: 0.021975s, Connection: 0.041105s, Pretransfer: 0.076633s, First byte at: 0.115362s [2025-04-03 00:30:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:14 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:14] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2025-04-03 00:30:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2025-04-03 00:30:14] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2025-04-03 00:30:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:14] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:14] [SUCCESS] [OmnipathR] Downloaded 716 interactions. [2025-04-03 00:30:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2025-04-03 00:30:14] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:14] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:14] [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` [2025-04-03 00:30:14] [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` [2025-04-03 00:30:14] [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` [2025-04-03 00:30:14] [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` [2025-04-03 00:30:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-04-03 00:30:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-04-03 00:30:14] [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` [2025-04-03 00:30:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:15] [TRACE] [OmnipathR] Downloaded 2.2 Kb in 0.073681s from omnipathdb.org (29.3 Kb/s); Redirect: 0s, DNS look up: 0.000993s, Connection: 0.019881s, Pretransfer: 0.054183s, First byte at: 0.073666s [2025-04-03 00:30:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:15 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 2210; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:15 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-04-03 00:30:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-04-03 00:30:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:15] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2025-04-03 00:30:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2025-04-03 00:30:15] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2025-04-03 00:30:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:15] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:15] [SUCCESS] [OmnipathR] Downloaded 32 interactions. [2025-04-03 00:30:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2025-04-03 00:30:15] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:15] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:15] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-04-03 00:30:15] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:17] [SUCCESS] [OmnipathR] Loaded 43269 enzyme-substrate relationships from cache. [2025-04-03 00:30:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-04-03 00:30:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-04-03 00:30:17] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:17] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-04-03 00:30:17] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:19] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2025-04-03 00:30:20] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2025-04-03 00:30:20] [TRACE] [OmnipathR] Organism(s): 10090 [2025-04-03 00:30:20] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:20] [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` [2025-04-03 00:30:20] [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` [2025-04-03 00:30:20] [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` [2025-04-03 00:30:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:20] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:20] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:20] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094469s from omnipathdb.org (165.8 Kb/s); Redirect: 0s, DNS look up: 0.000926s, Connection: 0.020662s, Pretransfer: 0.054281s, First byte at: 0.094147s [2025-04-03 00:30:20] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:20 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-04-03 00:30:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:20] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2025-04-03 00:30:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2025-04-03 00:30:21] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2025-04-03 00:30:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:21] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:21] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships. [2025-04-03 00:30:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2025-04-03 00:30:21] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:21] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-04-03 00:30:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-04-03 00:30:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-04-03 00:30:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-04-03 00:30:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-04-03 00:30:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-04-03 00:30:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-04-03 00:30:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:22] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.086122s from omnipathdb.org (181.9 Kb/s); Redirect: 0s, DNS look up: 0.000947s, Connection: 0.018012s, Pretransfer: 0.051261s, First byte at: 0.085867s [2025-04-03 00:30:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:22 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-04-03 00:30:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:22] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2025-04-03 00:30:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2025-04-03 00:30:22] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2025-04-03 00:30:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:22] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:22] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes. [2025-04-03 00:30:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:24] [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] [2025-04-03 00:30:24] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:24] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:24] [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_H3C1_H4C8_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` [2025-04-03 00:30:24] [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_H3C1_H4C8_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` [2025-04-03 00:30:24] [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_H3C1_H4C8_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` [2025-04-03 00:30:24] [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_H3C1_H4C8_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` [2025-04-03 00:30:24] [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_H3C1_H4C8_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` [2025-04-03 00:30:24] [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_H3C1_H4C8_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` [2025-04-03 00:30:24] [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_H3C1_H4C8_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` [2025-04-03 00:30:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:24] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:24] [TRACE] [OmnipathR] Downloaded 15 Kb in 0.114382s from omnipathdb.org (130.9 Kb/s); Redirect: 0s, DNS look up: 0.000908s, Connection: 0.019056s, Pretransfer: 0.077601s, First byte at: 0.114033s [2025-04-03 00:30:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:24 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:24 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:24] [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_H3C1_H4C8_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` [2025-04-03 00:30:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:24] [INFO] [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`. [2025-04-03 00:30:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`. [2025-04-03 00:30:24] [INFO] [OmnipathR] Download ready [key=e666cdf8b0e6e846fc6eb9319c9261ea08f0995d, version=1] [2025-04-03 00:30:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:24] [INFO] [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:24] [SUCCESS] [OmnipathR] Downloaded 1237 annotation records. [2025-04-03 00:30:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations] [2025-04-03 00:30:24] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:24] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:24] [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,H3C1,H4C8,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` [2025-04-03 00:30:24] [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,H3C1,H4C8,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` [2025-04-03 00:30:24] [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,H3C1,H4C8,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` [2025-04-03 00:30:24] [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,H3C1,H4C8,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` [2025-04-03 00:30:24] [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,H3C1,H4C8,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` [2025-04-03 00:30:24] [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,H3C1,H4C8,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` [2025-04-03 00:30:24] [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,H3C1,H4C8,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` [2025-04-03 00:30:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:24] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:25] [TRACE] [OmnipathR] Downloaded 5.8 Kb in 0.07605s from omnipathdb.org (76.4 Kb/s); Redirect: 0s, DNS look up: 0.000854s, Connection: 0.02146s, Pretransfer: 0.055022s, First byte at: 0.076009s [2025-04-03 00:30:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:24 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 5949; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:24 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-04-03 00:30:25] [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,H3C1,H4C8,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` [2025-04-03 00:30:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:25] [INFO] [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`. [2025-04-03 00:30:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`. [2025-04-03 00:30:25] [INFO] [OmnipathR] Download ready [key=72a8d891c5e3f648f5330031c8382decd1c9ce51, version=1] [2025-04-03 00:30:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:25] [INFO] [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:25] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2025-04-03 00:30:25] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations] [2025-04-03 00:30:25] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:25] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:25] [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,H3C1,H4C8,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` [2025-04-03 00:30:25] [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,H3C1,H4C8,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` [2025-04-03 00:30:25] [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,H3C1,H4C8,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` [2025-04-03 00:30:25] [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,H3C1,H4C8,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` [2025-04-03 00:30:25] [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,H3C1,H4C8,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` [2025-04-03 00:30:25] [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,H3C1,H4C8,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` [2025-04-03 00:30:25] [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,H3C1,H4C8,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` [2025-04-03 00:30:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:25] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:25] [TRACE] [OmnipathR] Downloaded 3.8 Kb in 0.096724s from omnipathdb.org (39 Kb/s); Redirect: 0s, DNS look up: 0.000926s, Connection: 0.023216s, Pretransfer: 0.07396s, First byte at: 0.096622s [2025-04-03 00:30:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:25 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:26] [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,H3C1,H4C8,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` [2025-04-03 00:30:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:26] [INFO] [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`. [2025-04-03 00:30:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`. [2025-04-03 00:30:26] [INFO] [OmnipathR] Download ready [key=ddeb1f70cb112e394ecedc8a102cdde6b3254ab7, version=1] [2025-04-03 00:30:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:26] [INFO] [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:26] [SUCCESS] [OmnipathR] Downloaded 424 annotation records. [2025-04-03 00:30:26] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2025-04-03 00:30:26] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:26] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:30:26] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-04-03 00:30:26] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-04-03 00:30:26] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache. [2025-04-03 00:30:26] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:26] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2025-04-03 00:30:26] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-04-03 00:30:26] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell_summary` [2025-04-03 00:30:26] [SUCCESS] [OmnipathR] Loaded 1098 records from cache. [2025-04-03 00:30:26] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:26] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-04-03 00:30:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-04-03 00:30:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-04-03 00:30:26] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-04-03 00:30:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-04-03 00:30:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-04-03 00:30:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-04-03 00:30:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:26] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.113111s from omnipathdb.org (138.5 Kb/s); Redirect: 0s, DNS look up: 0.001018s, Connection: 0.023326s, Pretransfer: 0.067976s, First byte at: 0.112715s [2025-04-03 00:30:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:26 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:27] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-04-03 00:30:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:27] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2025-04-03 00:30:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2025-04-03 00:30:29] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2025-04-03 00:30:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:29] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:29] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records. [2025-04-03 00:30:29] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2025-04-03 00:30:29] [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. [2025-04-03 00:30:29] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2025-04-03 00:30:29] [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 [2025-04-03 00:30:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2025-04-03 00:30:30] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:30] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-03 00:30:30] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-03 00:30:30] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-03 00:30:30] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-03 00:30:30] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-03 00:30:30] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-03 00:30:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-03 00:30:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:30] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:30] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:30] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.108118s from omnipathdb.org (144.9 Kb/s); Redirect: 0s, DNS look up: 0.001104s, Connection: 0.019808s, Pretransfer: 0.070456s, First byte at: 0.107796s [2025-04-03 00:30:30] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:30 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-04-03 00:30:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:31] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2025-04-03 00:30:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2025-04-03 00:30:31] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2025-04-03 00:30:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:31] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:31] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2025-04-03 00:30:31] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-03 00:30:31] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2025-04-03 00:30:31] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-04-03 00:30:31] [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`. [2025-04-03 00:30:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:31] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2025-04-03 00:30:31] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-04-03 00:30:31] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-04-03 00:30:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:31] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:31] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-03 00:30:31] [TRACE] [OmnipathR] Downloaded 10.8 Kb in 0.070345s from static-content.springer.com (152.9 Kb/s); Redirect: 0s, DNS look up: 0.021143s, Connection: 0.027873s, Pretransfer: 0.060685s, First byte at: 0.069804s [2025-04-03 00:30:31] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; 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; content-type: application/octet-stream; x-goog-hash: crc32c=v/3p0Q==; x-goog-hash: md5=2qA8Hq/QDK2UVrZgyoW4SQ==; x-goog-storage-class: MULTI_REGIONAL; x-guploader-uploadid: AFiumC7ZpYKgxNZtW8bqZY8u8z2x9V62Ud4hs7Wz5zewS1xt8QPnURGT01ram66yNo-OgPW_uOsydnKUF6Xmdbs; server: UploadServer; x-cdn-origin: GCS, SNPaaS; accept-ranges: bytes; age: 86297; date: Wed, 02 Apr 2025 22:30:31 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230127-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1743633032.515202,VS0,VE2; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972 [2025-04-03 00:30:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2025-04-03 00:30:31] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2025-04-03 00:30:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:31] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:31] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2025-04-03 00:30:31] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:31] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2025-04-03 00:30:32] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:32] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:32] [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` [2025-04-03 00:30:32] [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` [2025-04-03 00:30:32] [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` [2025-04-03 00:30:32] [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` [2025-04-03 00:30:32] [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` [2025-04-03 00:30:32] [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` [2025-04-03 00:30:32] [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` [2025-04-03 00:30:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:32] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:32] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098696s from omnipathdb.org (158.7 Kb/s); Redirect: 0s, DNS look up: 0.001133s, Connection: 0.018972s, Pretransfer: 0.062648s, First byte at: 0.098412s [2025-04-03 00:30:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:32 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:32] [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` [2025-04-03 00:30:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:32] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2025-04-03 00:30:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2025-04-03 00:30:33] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2025-04-03 00:30:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:33] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:36] [SUCCESS] [OmnipathR] Downloaded 121170 interactions. [2025-04-03 00:30:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2025-04-03 00:30:36] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:36] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-03 00:30:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-03 00:30:36] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-03 00:30:36] [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` [2025-04-03 00:30:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-03 00:30:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-03 00:30:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-03 00:30:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:36] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.084272s from omnipathdb.org (185.9 Kb/s); Redirect: 0s, DNS look up: 0.001004s, Connection: 0.01743s, Pretransfer: 0.050557s, First byte at: 0.083882s [2025-04-03 00:30:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:36 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:37] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-04-03 00:30:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:37] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2025-04-03 00:30:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2025-04-03 00:30:38] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2025-04-03 00:30:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:38] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:38] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records. [2025-04-03 00:30:39] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:39] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-03 00:30:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-03 00:30:39] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-03 00:30:39] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-03 00:30:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-03 00:30:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-03 00:30:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-03 00:30:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:39] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:39] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.082927s from omnipathdb.org (188.9 Kb/s); Redirect: 0s, DNS look up: 0.000908s, Connection: 0.016937s, Pretransfer: 0.050212s, First byte at: 0.082604s [2025-04-03 00:30:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-04-03 00:30:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:39] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2025-04-03 00:30:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2025-04-03 00:30:39] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2025-04-03 00:30:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:39] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:39] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records. [2025-04-03 00:30:39] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:39] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:39] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:39] [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` [2025-04-03 00:30:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:39] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:39] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097553s from omnipathdb.org (160.6 Kb/s); Redirect: 0s, DNS look up: 0.001026s, Connection: 0.021634s, Pretransfer: 0.055307s, First byte at: 0.097184s [2025-04-03 00:30:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:40] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-04-03 00:30:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-04-03 00:30:40] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2025-04-03 00:30:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:40] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:40] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records. [2025-04-03 00:30:40] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:40] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-03 00:30:40] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-03 00:30:40] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-03 00:30:40] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-03 00:30:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-03 00:30:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-03 00:30:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-03 00:30:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:40] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:40] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096028s from omnipathdb.org (163.1 Kb/s); Redirect: 0s, DNS look up: 0.000969s, Connection: 0.021254s, Pretransfer: 0.054389s, First byte at: 0.095055s [2025-04-03 00:30:40] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:40 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:41] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-04-03 00:30:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:41] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2025-04-03 00:30:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2025-04-03 00:30:41] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2025-04-03 00:30:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:41] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:41] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records. [2025-04-03 00:30:41] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:41] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:41] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-04-03 00:30:41] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:41] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2025-04-03 00:30:41] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:41] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-03 00:30:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-03 00:30:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-03 00:30:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-03 00:30:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-03 00:30:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-03 00:30:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-03 00:30:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.087922s from omnipathdb.org (178.2 Kb/s); Redirect: 0s, DNS look up: 0.000945s, Connection: 0.018578s, Pretransfer: 0.051879s, First byte at: 0.087527s [2025-04-03 00:30:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:41 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-04-03 00:30:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:42] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2025-04-03 00:30:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2025-04-03 00:30:42] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2025-04-03 00:30:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:42] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:42] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records. [2025-04-03 00:30:42] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:42] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:42] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-04-03 00:30:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:42] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2025-04-03 00:30:42] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:42] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-03 00:30:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-03 00:30:42] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-03 00:30:42] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-03 00:30:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-03 00:30:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-03 00:30:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-03 00:30:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:42] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:42] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:42] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.086368s from omnipathdb.org (181.4 Kb/s); Redirect: 0s, DNS look up: 0.001096s, Connection: 0.018292s, Pretransfer: 0.051601s, First byte at: 0.086008s [2025-04-03 00:30:42] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:42 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:43] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-04-03 00:30:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:43] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2025-04-03 00:30:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2025-04-03 00:30:43] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2025-04-03 00:30:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:43] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:43] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records. [2025-04-03 00:30:43] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:43] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:43] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-04-03 00:30:43] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-04-03 00:30:43] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2025-04-03 00:30:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2025-04-03 00:30:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2025-04-03 00:30:43] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:43] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:43] [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` [2025-04-03 00:30:43] [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` [2025-04-03 00:30:43] [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` [2025-04-03 00:30:43] [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` [2025-04-03 00:30:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-03 00:30:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-03 00:30:43] [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` [2025-04-03 00:30:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:43] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:43] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094708s from omnipathdb.org (165.4 Kb/s); Redirect: 0s, DNS look up: 0.000882s, Connection: 0.02063s, Pretransfer: 0.053927s, First byte at: 0.094381s [2025-04-03 00:30:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:43 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-04-03 00:30:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:44] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-04-03 00:30:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-04-03 00:30:44] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2025-04-03 00:30:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:44] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:45] [SUCCESS] [OmnipathR] Downloaded 30053 interactions. [2025-04-03 00:30:45] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2025-04-03 00:30:45] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:45] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-03 00:30:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-03 00:30:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-03 00:30:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-03 00:30:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-03 00:30:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-03 00:30:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-03 00:30:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:45] [TRACE] [OmnipathR] Downloaded 13.1 Kb in 0.092178s from omnipathdb.org (142.2 Kb/s); Redirect: 0s, DNS look up: 0.000957s, Connection: 0.019607s, Pretransfer: 0.053378s, First byte at: 0.091504s [2025-04-03 00:30:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:45 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-04-03 00:30:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:46] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2025-04-03 00:30:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2025-04-03 00:30:46] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2025-04-03 00:30:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:46] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:46] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records. [2025-04-03 00:30:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2025-04-03 00:30:46] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:46] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-03 00:30:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-03 00:30:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-03 00:30:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-03 00:30:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-03 00:30:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-03 00:30:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-03 00:30:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:46] [TRACE] [OmnipathR] Downloaded 12.1 Kb in 0.107874s from omnipathdb.org (112.1 Kb/s); Redirect: 0s, DNS look up: 0.000969s, Connection: 0.01864s, Pretransfer: 0.07167s, First byte at: 0.107629s [2025-04-03 00:30:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:46 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-04-03 00:30:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:47] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2025-04-03 00:30:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2025-04-03 00:30:47] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2025-04-03 00:30:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:47] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:47] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records. [2025-04-03 00:30:47] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2025-04-03 00:30:47] [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. [2025-04-03 00:30:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions] [2025-04-03 00:30:47] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:47] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:48] [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` [2025-04-03 00:30:48] [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` [2025-04-03 00:30:48] [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` [2025-04-03 00:30:48] [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` [2025-04-03 00:30:48] [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` [2025-04-03 00:30:48] [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` [2025-04-03 00:30:48] [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` [2025-04-03 00:30:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:48] [TRACE] [OmnipathR] Downloaded 11.7 Kb in 0.095068s from omnipathdb.org (123.2 Kb/s); Redirect: 0s, DNS look up: 0.000993s, Connection: 0.020986s, Pretransfer: 0.054543s, First byte at: 0.094805s [2025-04-03 00:30:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:48 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:48] [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` [2025-04-03 00:30:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:48] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2025-04-03 00:30:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2025-04-03 00:30:48] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2025-04-03 00:30:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:48] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:48] [SUCCESS] [OmnipathR] Downloaded 322 interactions. [2025-04-03 00:30:48] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2025-04-03 00:30:48] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:48] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:30:49] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-04-03 00:30:49] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:30:49] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2025-04-03 00:30:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2025-04-03 00:30:49] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:49] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-03 00:30:49] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-03 00:30:49] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-03 00:30:49] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-03 00:30:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-03 00:30:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-03 00:30:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-03 00:30:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-03 00:30:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-03 00:30:49] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-03 00:30:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-03 00:30:49] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10796s from omnipathdb.org (145.1 Kb/s); Redirect: 0s, DNS look up: 0.000999s, Connection: 0.020186s, Pretransfer: 0.068328s, First byte at: 0.107595s [2025-04-03 00:30:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 02 Apr 2025 22:30:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 02 Apr 2025 23:30:49 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-03 00:30:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-03 00:30:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:50] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2025-04-03 00:30:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-04-03 00:30:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-04-03 00:30:50] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2025-04-03 00:30:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-03 00:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:50] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2025-04-03 00:30:50] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records. [2025-04-03 00:30:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2025-04-03 00:30:51] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:51] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:30:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-04-03 00:30:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-04-03 00:30:51] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2025-04-03 00:30:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-03 00:30:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2025-04-03 00:30:51] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-03 00:30:51] [TRACE] [OmnipathR] Orthology targets: [2025-04-03 00:30:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-04-03 00:30:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-03 00:30:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-03 00:30:52] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-04-03 00:30:52] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-04-03 00:30:52] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache. --- finished re-building ‘paths.Rmd’ SUMMARY: processing the following files failed: ‘bioc_workshop.Rmd’ ‘cosmos.Rmd’ ‘db_manager.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2025-04-03 00:30:52 CEST ]