[ Started: 2025-07-23 18:58:46 CEST ]
[ OmnipathR v3.17.4 for BioC-3.22 from https://github.com/saezlab/OmnipathR@devel (a7f3b9d 2025-07-16 16:03:35) ]

* 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
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-23 16:58:47 UTC; unix
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-07-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-07-23 18:59:01] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.37.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); 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 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); 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 1.4.2(2025-04-08); 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 3.17.4(2025-07-23); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); 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 2.3.3(2025-05-13)
[2025-07-23 18:59:01] [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
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpgQeTsr/Rinst5963858ae98ba/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpgQeTsr/Rinst5963858ae98ba/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpgQeTsr/Rinst5963858ae98ba/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpgQeTsr/Rinst5963858ae98ba/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-07-23 18:59:01] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-07-23 18:59:01] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Downloaded 31.4 Kb in 0.208815s from www.ensembl.org (150.4 Kb/s); Redirect: 0s, DNS look up: 0.008317s, Connection: 0.02695s, Pretransfer: 0.087446s, First byte at: 0.190079s
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Jul 2025 16:59:02 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32150; 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, 24 Jul 2025 16:59:02 GMT; Set-cookie: ENSEMBL_HINX_SESSION=d34e9feec198fec40e4d607068d02ed60563daf4b56eb580b6e18b1e; 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, 24 Jul 2025 16:59:02 GMT; Set-cookie: ENSEMBL_HINX_SESSION=d34e9feec198fec40e4d607068d02ed60563daf4b56eb580b6e18b1e; 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-p1m2-31.ebi.ac.uk
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Response headers: [Date=Wed, 23 Jul 2025 16:59:02 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32150,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, 24 Jul 2025 16:59:02 GMT,Set-cookie=ENSEMBL_HINX_SESSION=d34e9feec198fec40e4d607068d02ed60563daf4b56eb580b6e18b1e; 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, 24 Jul 2025 16:59:02 GMT,Set-cookie=ENSEMBL_HINX_SESSION=d34e9feec198fec40e4d607068d02ed60563daf4b56eb580b6e18b1e; 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-p1m2-31.ebi.ac.uk]
[2025-07-23 18:59:02] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:02] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-07-23 18:59:02] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:02] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-07-23 18:59:02] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.114499s from omabrowser.org (75.9 Kb/s); Redirect: 0s, DNS look up: 0.032328s, Connection: 0.042897s, Pretransfer: 0.099633s, First byte at: 0.114352s
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 23 Jul 2025 16:59:02 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
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-07-23 18:59:02] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:02] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-07-23 18:59:02] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:02] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-07-23 18:59:02] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-07-23 18:59:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-07-23 18:59:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-07-23 18:59:24] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-07-23 18:59:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:24] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:24] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-07-23 18:59:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:24] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:24] [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`
[2025-07-23 18:59:24] [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`
[2025-07-23 18:59:24] [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`
[2025-07-23 18:59:24] [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`
[2025-07-23 18:59:24] [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`
[2025-07-23 18:59:24] [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`
[2025-07-23 18:59:24] [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`
[2025-07-23 18:59:24] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:24] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:24] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 18:59:24] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.124871s from omnipathdb.org (125.5 Kb/s); Redirect: 0s, DNS look up: 0.017406s, Connection: 0.034678s, Pretransfer: 0.092004s, First byte at: 0.124543s
[2025-07-23 18:59:24] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 16:59:24 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, 23 Jul 2025 17:59:24 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 18:59:25] [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`
[2025-07-23 18:59:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:25] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-07-23 18:59:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-07-23 18:59:25] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2025-07-23 18:59:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:25] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:29] [SUCCESS] [OmnipathR] Downloaded 128218 interactions.
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:32] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:32] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:32] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.106639s from omnipathdb.org (146.9 Kb/s); Redirect: 0s, DNS look up: 0.000948s, Connection: 0.02328s, Pretransfer: 0.061263s, First byte at: 0.106245s
[2025-07-23 18:59:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 16:59:32 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, 23 Jul 2025 17:59:32 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 18:59:33] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:33] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-07-23 18:59:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-07-23 18:59:33] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-07-23 18:59:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:33] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:34] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:35] [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`
[2025-07-23 18:59:35] [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`
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.100912s from omnipathdb.org (155.3 Kb/s); Redirect: 0s, DNS look up: 0.001027s, Connection: 0.019313s, Pretransfer: 0.064181s, First byte at: 0.100642s
[2025-07-23 18:59:35] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 16:59:35 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, 23 Jul 2025 17:59:35 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 18:59:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:36] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-07-23 18:59:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-07-23 18:59:36] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-07-23 18:59:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:36] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:38] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2025-07-23 18:59:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-07-23 18:59:39] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2025-07-23 18:59:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 0.676534s from omnipathdb.org (46.8 Kb/s); Redirect: 0s, DNS look up: 0.000866s, Connection: 0.019885s, Pretransfer: 0.058979s, First byte at: 0.674486s
[2025-07-23 18:59:39] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 16:59:39 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, 23 Jul 2025 17:59:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 18:59:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:40] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-07-23 18:59:40] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:40] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:40] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 18:59:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 18:59:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 18:59:41] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 18:59:41] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 18:59:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 18:59:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 18:59:41] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:41] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:41] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 18:59:41] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 0.631014s from omnipathdb.org (50.2 Kb/s); Redirect: 0s, DNS look up: 0.000899s, Connection: 0.020952s, Pretransfer: 0.055509s, First byte at: 0.629059s
[2025-07-23 18:59:41] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 16:59:41 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, 23 Jul 2025 17:59:41 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 18:59:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:42] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-07-23 18:59:42] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:42] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:42] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-07-23 18:59:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-07-23 18:59:42] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-07-23 18:59:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] Downloaded 60 bytes in 0.085635s from omnipathdb.org (700 bytes/s); Redirect: 0s, DNS look up: 0.00089s, Connection: 0.020045s, Pretransfer: 0.053668s, First byte at: 0.085616s
[2025-07-23 18:59:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 16:59:42 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, 23 Jul 2025 17:59:42 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-07-23 18:59:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:43] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-07-23 18:59:43] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:43] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:43] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2025-07-23 18:59:43] [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.
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-07-23 18:59:43] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 18:59:43] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-07-23 18:59:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-07-23 18:59:43] [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`
[2025-07-23 18:59:43] [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`
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-07-23 18:59:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Downloaded 22.3 Kb in 2.383887s from omnipathdb.org (9.3 Kb/s); Redirect: 0s, DNS look up: 0.000966s, Connection: 0.020991s, Pretransfer: 0.054862s, First byte at: 2.38229s
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 16:59:46 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, 23 Jul 2025 17:59:46 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 18:59:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:46] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-07-23 18:59:46] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:46] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:46] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-07-23 18:59:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-07-23 18:59:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-07-23 18:59:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:46] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Downloaded 36.9 Kb in 0.22182s from omnipathdb.org (166.3 Kb/s); Redirect: 0s, DNS look up: 0.00094s, Connection: 0.023154s, Pretransfer: 0.070369s, First byte at: 0.21981s
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 16:59:47 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, 23 Jul 2025 17:59:47 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 18:59:47] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:47] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-07-23 18:59:47] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:47] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:47] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-07-23 18:59:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 18:59:50] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-07-23 18:59:50] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-07-23 18:59:50] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2025-07-23 18:59:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-07-23 18:59:50] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2025-07-23 18:59:50] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:50] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 18:59:54] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 3.701933s from omnipathdb.org (8.6 Kb/s); Redirect: 0s, DNS look up: 0.000953s, Connection: 0.019442s, Pretransfer: 0.064815s, First byte at: 3.699376s
[2025-07-23 18:59:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 16:59:54 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, 23 Jul 2025 17:59:54 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 18:59:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2025-07-23 18:59:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:55] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-07-23 18:59:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-07-23 18:59:57] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2025-07-23 18:59:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:57] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:57] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-07-23 18:59:58] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-07-23 18:59:58] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-07-23 18:59:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.07818s from omnipathdb.org (111.5 Kb/s); Redirect: 0s, DNS look up: 0.001048s, Connection: 0.019054s, Pretransfer: 0.052743s, First byte at: 0.078012s
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 16:59:58 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, 23 Jul 2025 17:59:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 18:59:58] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:58] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-07-23 18:59:58] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:58] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-07-23 18:59:58] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-23 18:59:58] [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`.
[2025-07-23 18:59:58] [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`
[2025-07-23 18:59:58] [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`.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 18:59:58] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-07-23 18:59:58] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 18:59:58] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 18:59:59] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-07-23 18:59:59] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.582705s from rest.uniprot.org (73 bytes/s); Redirect: 0s, DNS look up: 0.015897s, Connection: 0.034186s, Pretransfer: 0.096877s, First byte at: 0.582635s
[2025-07-23 18:59:59] [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: 18-June-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 23 Jul 2025 16:59:59 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_03; 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: 18-June-2025
[2025-07-23 19:00:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-07-23 19:00:12] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-07-23 19:00:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:00:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:00:12] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-07-23 19:00:12] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records
[2025-07-23 19:00:12] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2025-07-23 19:00:12] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-07-23 19:00:12] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2025-07-23 19:00:12] [TRACE]   [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2025-07-23 19:00:12] [TRACE]   [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2025-07-23 19:00:12] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2025-07-23 19:00:12] [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.
[2025-07-23 19:00:12] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2025-07-23 19:00:12] [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.
[2025-07-23 19:00:13] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2025-07-23 19:00:13] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
[2025-07-23 19:00:13] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-07-23 19:00:13] [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.
[2025-07-23 19:00:13] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-07-23 19:00:13] [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.
[2025-07-23 19:00:13] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-07-23 19:00:13] [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.
[2025-07-23 19:00:13] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-07-23 19:00:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:00:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-07-23 19:00:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:00:13] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:00:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:00:14] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-07-23 19:00:14] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:00:16] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-07-23 19:00:16] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="external_gene_name"/>
    </Dataset>
</Query>
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-23 19:00:17] [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`.
[2025-07-23 19:00:17] [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`
[2025-07-23 19:00:17] [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`.
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:00:17] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-07-23 19:00:17] [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`
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-07-23 19:00:17] [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`
[2025-07-23 19:00:17] [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`.
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-07-23 19:00:17] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-07-23 19:00:23] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-07-23 19:00:23] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:00:23] [TRACE]   [OmnipathR] Downloaded 1.2 Mb in 6.254035s from www.ensembl.org (188.6 Kb/s); Redirect: 0s, DNS look up: 0.001697s, Connection: 0.02059s, Pretransfer: 0.020866s, First byte at: 0.083947s
[2025-07-23 19:00:23] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: Apache; Content-Type: text/plain; charset=utf-8; Content-Security-Policy: frame-ancestors 'self'; Date: Wed, 23 Jul 2025 17:00:17 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN
[2025-07-23 19:00:23] [TRACE]   [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Wed, 23 Jul 2025 17:00:17 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN]
[2025-07-23 19:00:23] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-07-23 19:00:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-07-23 19:00:23] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-07-23 19:00:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:00:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:00:23] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-07-23 19:00:24] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 122455 records
[2025-07-23 19:00:24] [TRACE]   [OmnipathR] Translating complexes: 592 complexes in data.
[2025-07-23 19:00:24] [TRACE]   [OmnipathR] 433 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-07-23 19:00:25] [TRACE]   [OmnipathR] Translated 433 complexes to 433.
[2025-07-23 19:00:25] [TRACE]   [OmnipathR] 67526 rows before translation, 4551 uniprot IDs in column `source`.
[2025-07-23 19:00:25] [TRACE]   [OmnipathR] 67598 rows after translation; translated 4551 `uniprot` IDs in column `source` to 4391 `genesymbol` IDs in column `genesymbol_source`.
[2025-07-23 19:00:25] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-07-23 19:00:25] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-07-23 19:00:25] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="external_gene_name"/>
    </Dataset>
</Query>
[2025-07-23 19:00:25] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-23 19:00:25] [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`.
[2025-07-23 19:00:25] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-07-23 19:00:25] [SUCCESS] [OmnipathR] www.ensembl.org: loaded 122455 records from cache
[2025-07-23 19:00:25] [TRACE]   [OmnipathR] Translating complexes: 311 complexes in data.
[2025-07-23 19:00:25] [TRACE]   [OmnipathR] 220 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-07-23 19:00:26] [TRACE]   [OmnipathR] Translated 220 complexes to 220.
[2025-07-23 19:00:26] [TRACE]   [OmnipathR] 67598 rows before translation, 4638 uniprot IDs in column `target`.
[2025-07-23 19:00:26] [TRACE]   [OmnipathR] 69182 rows after translation; translated 4638 `uniprot` IDs in column `target` to 4555 `genesymbol` IDs in column `genesymbol_target`.
[2025-07-23 19:00:26] [INFO]    [OmnipathR] OmniPath PPI for COSMOS PKN ready: 138486 interactions.
--- finished re-building ‘cosmos.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2025-07-23 19:00:26] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-07-23 19:00:26] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-07-23 19:00:27] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-07-23 19:00:27] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-23 19:00:27] [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`.
[2025-07-23 19:00:27] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-07-23 19:00:27] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): loaded 20420 records from cache
[2025-07-23 19:00:27] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2025-07-23 19:00:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:00:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-07-23 19:00:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:00:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-07-23 19:00:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:00:38] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:00:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:00:38] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-07-23 19:00:38] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:00:41] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2025-07-23 19:00:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:00:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-07-23 19:00:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:00:43] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:00:43] [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`
[2025-07-23 19:00:43] [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`
[2025-07-23 19:00:43] [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`
[2025-07-23 19:00:43] [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`
[2025-07-23 19:00:43] [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`
[2025-07-23 19:00:43] [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`
[2025-07-23 19:00:43] [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`
[2025-07-23 19:00:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:00:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:00:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:00:46] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:00:46] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 2.813823s from omnipathdb.org (11.3 Kb/s); Redirect: 0s, DNS look up: 0.001113s, Connection: 0.017208s, Pretransfer: 0.051434s, First byte at: 2.812001s
[2025-07-23 19:00:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:00:46 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, 23 Jul 2025 18:00:46 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:00:47] [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`
[2025-07-23 19:00:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:00:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:00:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:00:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:00:47] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:00:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-07-23 19:00:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-07-23 19:00:47] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2025-07-23 19:00:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:00:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:00:47] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2025-07-23 19:00:47] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-07-23 19:00:57] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-07-23 19:06:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-07-23 19:06:50] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-07-23 19:06:50] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:06:50] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:06:52] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:06:52] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 1.907779s from omnipathdb.org (16.6 Kb/s); Redirect: 0s, DNS look up: 0.000954s, Connection: 0.023395s, Pretransfer: 0.079849s, First byte at: 1.905812s
[2025-07-23 19:06:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:06:52 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, 23 Jul 2025 18:06:52 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:06:52] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-07-23 19:06:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:06:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:06:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:53] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-07-23 19:06:53] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:53] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2025-07-23 19:06:53] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-07-23 19:06:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-07-23 19:06:53] [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`
[2025-07-23 19:06:53] [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`
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-07-23 19:06:53] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:06:53] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:06:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:06:54] [TRACE]   [OmnipathR] Downloaded 5.1 Kb in 0.100401s from omnipathdb.org (50.8 Kb/s); Redirect: 0s, DNS look up: 0.000924s, Connection: 0.018786s, Pretransfer: 0.068266s, First byte at: 0.100383s
[2025-07-23 19:06:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:06:54 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, 23 Jul 2025 18:06:54 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-07-23 19:06:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-07-23 19:06:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:06:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:06:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:54] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:06:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-07-23 19:06:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-07-23 19:06:54] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2025-07-23 19:06:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:06:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:54] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2025-07-23 19:06:54] [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
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:56] [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`
[2025-07-23 19:06:56] [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`
[2025-07-23 19:06:56] [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`
[2025-07-23 19:06:56] [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`
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:06:56] [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`
[2025-07-23 19:06:56] [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`
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:06:56] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:06:58] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:06:58] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 1.827274s from omnipathdb.org (17.3 Kb/s); Redirect: 0s, DNS look up: 0.00084s, Connection: 0.016991s, Pretransfer: 0.051413s, First byte at: 1.825451s
[2025-07-23 19:06:58] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:06:58 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, 23 Jul 2025 18:06:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:06:58] [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`
[2025-07-23 19:06:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:06:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:06:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:59] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:06:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-07-23 19:06:59] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-07-23 19:06:59] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2025-07-23 19:06:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:06:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:06:59] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2025-07-23 19:07:01] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2025-07-23 19:07:04] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:07:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2025-07-23 19:07:04] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:07:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2025-07-23 19:07:05] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-07-23 19:07:05] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:07:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:07:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:05] [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`
[2025-07-23 19:07:05] [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`
[2025-07-23 19:07:05] [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`
[2025-07-23 19:07:05] [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`
[2025-07-23 19:07:05] [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`
[2025-07-23 19:07:05] [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`
[2025-07-23 19:07:05] [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`
[2025-07-23 19:07:05] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:07:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:07:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:07:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:07:06] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 1.066914s from omnipathdb.org (29.7 Kb/s); Redirect: 0s, DNS look up: 0.000848s, Connection: 0.021455s, Pretransfer: 0.066456s, First byte at: 1.065364s
[2025-07-23 19:07:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:07:06 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, 23 Jul 2025 18:07:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:07:06] [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`
[2025-07-23 19:07:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:06] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:07:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-07-23 19:07:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-07-23 19:07:07] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2025-07-23 19:07:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:07] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2025-07-23 19:07:08] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] Organism(s): 10116
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:08] [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`
[2025-07-23 19:07:08] [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`
[2025-07-23 19:07:08] [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`
[2025-07-23 19:07:08] [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`
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:07:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:07:08] [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`
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:07:08] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:07:09] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:07:09] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 0.468944s from omnipathdb.org (67.5 Kb/s); Redirect: 0s, DNS look up: 9e-04s, Connection: 0.020662s, Pretransfer: 0.078886s, First byte at: 0.467265s
[2025-07-23 19:07:09] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:07:09 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, 23 Jul 2025 18:07:09 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:07:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:07:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:09] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:07:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-07-23 19:07:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-07-23 19:07:09] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2025-07-23 19:07:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:09] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2025-07-23 19:07:10] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:10] [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`
[2025-07-23 19:07:10] [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`
[2025-07-23 19:07:10] [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`
[2025-07-23 19:07:10] [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`
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:07:10] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:07:10] [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`
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 0.311899s from omnipathdb.org (101.5 Kb/s); Redirect: 0s, DNS look up: 0.000851s, Connection: 0.020877s, Pretransfer: 0.054987s, First byte at: 0.310214s
[2025-07-23 19:07:10] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:07:10 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, 23 Jul 2025 18:07:10 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:07:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:11] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-07-23 19:07:11] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:11] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2025-07-23 19:07:11] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:07:11] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-07-23 19:07:11] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-23 19:07:14] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-07-23 19:07:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:07:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-07-23 19:07:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:07:15] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:07:15] [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`
[2025-07-23 19:07:15] [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`
[2025-07-23 19:07:15] [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`
[2025-07-23 19:07:15] [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`
[2025-07-23 19:07:15] [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`
[2025-07-23 19:07:15] [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`
[2025-07-23 19:07:15] [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`
[2025-07-23 19:07:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:07:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:07:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:07:23] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:07:23] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 7.927491s from omnipathdb.org (4 Kb/s); Redirect: 0s, DNS look up: 0.000878s, Connection: 0.023053s, Pretransfer: 0.068349s, First byte at: 7.925881s
[2025-07-23 19:07:23] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:07:16 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, 23 Jul 2025 18:07:16 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:07:23] [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`
[2025-07-23 19:07:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:23] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:07:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-07-23 19:07:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-07-23 19:07:23] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2025-07-23 19:07:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:07:23] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2025-07-23 19:07:24] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2025-07-23 19:07:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:07:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2025-07-23 19:07:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:07:24] [TRACE]   [OmnipathR] Orthology targets: 

Quitting from omnipath_intro.Rmd:413-431 [mirnatarget]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://omnipathdb.org/resources'
---
Backtrace:
    ▆
 1. ├─OmnipathR::mirna_target(resources = c("miR2Disease", "miRDeathDB"))
 2. │ ├─rlang::exec(omnipath_query, !!!args)
 3. │ └─OmnipathR (local) `<fn>`(resources = `<chr>`, query_type = "interactions", datasets = "mirnatarget")
 4. │   └─environment() %>% as.list %>% c(list(...)) %>% ...
 5. └─OmnipathR:::omnipath_check_param(.)
 6.   └─OmnipathR::resources(param$query_type)
 7.     └─OmnipathR:::safe_json(path = resources_url)
 8.       └─base::readLines(con = path, encoding = encoding)
 9.         └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
cannot open the connection to 'https://omnipathdb.org/resources'
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-07-23 19:08:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-07-23 19:08:24] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-07-23 19:08:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] Downloaded 29.2 Kb in 0.242599s from omnipathdb.org (120.2 Kb/s); Redirect: 0s, DNS look up: 0.001017s, Connection: 0.019608s, Pretransfer: 0.069039s, First byte at: 0.241004s
[2025-07-23 19:08:24] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:24 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, 23 Jul 2025 18:08:24 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:25] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:25] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-07-23 19:08:25] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:25] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:25] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2025-07-23 19:08:25] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-07-23 19:08:25] [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`.
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:25] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-07-23 19:08:25] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-07-23 19:08:25] [TRACE]   [OmnipathR] Downloaded 10.8 Kb in 0.102287s from static-content.springer.com (105.2 Kb/s); Redirect: 0s, DNS look up: 0.007849s, Connection: 0.014869s, Pretransfer: 0.055369s, First byte at: 0.100353s
[2025-07-23 19:08:25] [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: 0; date: Wed, 23 Jul 2025 17:08:25 GMT; via: 1.1 varnish; x-served-by: cache-fra-etou8220161-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1753290506.582587,VS0,VE37; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972
[2025-07-23 19:08:26] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-07-23 19:08:26] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2025-07-23 19:08:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:26] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:26] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2025-07-23 19:08:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2025-07-23 19:08:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:26] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:26] [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`
[2025-07-23 19:08:26] [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`
[2025-07-23 19:08:26] [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`
[2025-07-23 19:08:26] [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`
[2025-07-23 19:08:26] [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`
[2025-07-23 19:08:26] [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`
[2025-07-23 19:08:26] [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`
[2025-07-23 19:08:26] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:26] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:28] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:29] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 2.824469s from omnipathdb.org (11.2 Kb/s); Redirect: 0s, DNS look up: 0.000968s, Connection: 0.02034s, Pretransfer: 0.05422s, First byte at: 2.822774s
[2025-07-23 19:08:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:28 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, 23 Jul 2025 18:08:28 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-07-23 19:08:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:29] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-07-23 19:08:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-07-23 19:08:30] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2025-07-23 19:08:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:30] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:33] [SUCCESS] [OmnipathR] Downloaded 121170 interactions.
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-07-23 19:08:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-07-23 19:08:33] [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`
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-07-23 19:08:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:33] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:36] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:36] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 2.433638s from omnipathdb.org (13 Kb/s); Redirect: 0s, DNS look up: 0.000953s, Connection: 0.017471s, Pretransfer: 0.051409s, First byte at: 2.431335s
[2025-07-23 19:08:36] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:36 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, 23 Jul 2025 18:08:36 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:37] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-07-23 19:08:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:37] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-07-23 19:08:38] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:38] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:38] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-07-23 19:08:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-07-23 19:08:38] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-07-23 19:08:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 0.242729s from omnipathdb.org (130.4 Kb/s); Redirect: 0s, DNS look up: 0.000938s, Connection: 0.021901s, Pretransfer: 0.056823s, First byte at: 0.240891s
[2025-07-23 19:08:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:38 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, 23 Jul 2025 18:08:38 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:39] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:39] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-07-23 19:08:39] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:39] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:39] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:39] [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`
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 0.347022s from omnipathdb.org (91.2 Kb/s); Redirect: 0s, DNS look up: 0.000979s, Connection: 0.021069s, Pretransfer: 0.070664s, First byte at: 0.345025s
[2025-07-23 19:08:39] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:39 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, 23 Jul 2025 18:08:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:40] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-07-23 19:08:40] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:40] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:40] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-07-23 19:08:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-07-23 19:08:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-07-23 19:08:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 0.337714s from omnipathdb.org (93.7 Kb/s); Redirect: 0s, DNS look up: 0.000948s, Connection: 0.025645s, Pretransfer: 0.059802s, First byte at: 0.335561s
[2025-07-23 19:08:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:40 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, 23 Jul 2025 18:08:40 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:41] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-07-23 19:08:41] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:41] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:41] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-07-23 19:08:41] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:41] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-07-23 19:08:41] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-07-23 19:08:41] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-07-23 19:08:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 0.250794s from omnipathdb.org (126.2 Kb/s); Redirect: 0s, DNS look up: 0.001173s, Connection: 0.019415s, Pretransfer: 0.053555s, First byte at: 0.248788s
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:42 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, 23 Jul 2025 18:08:42 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:42] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-07-23 19:08:42] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:42] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:42] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-07-23 19:08:42] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:42] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-07-23 19:08:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-07-23 19:08:42] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-07-23 19:08:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-07-23 19:08:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 0.408494s from omnipathdb.org (77.5 Kb/s); Redirect: 0s, DNS look up: 0.00089s, Connection: 0.019351s, Pretransfer: 0.054053s, First byte at: 0.406309s
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:43 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, 23 Jul 2025 18:08:43 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:43] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-07-23 19:08:44] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:44] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:44] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-07-23 19:08:44] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-07-23 19:08:44] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:44] [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`
[2025-07-23 19:08:44] [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`
[2025-07-23 19:08:44] [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`
[2025-07-23 19:08:44] [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`
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-07-23 19:08:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-07-23 19:08:44] [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`
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:44] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:45] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:45] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 1.207355s from omnipathdb.org (26.2 Kb/s); Redirect: 0s, DNS look up: 0.00084s, Connection: 0.022458s, Pretransfer: 0.067582s, First byte at: 1.205554s
[2025-07-23 19:08:45] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:45 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, 23 Jul 2025 18:08:45 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-07-23 19:08:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:46] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-07-23 19:08:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-07-23 19:08:46] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2025-07-23 19:08:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:46] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:47] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-07-23 19:08:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-07-23 19:08:47] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-07-23 19:08:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:47] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Downloaded 13.1 Kb in 0.196365s from omnipathdb.org (66.7 Kb/s); Redirect: 0s, DNS look up: 0.000949s, Connection: 0.020934s, Pretransfer: 0.069996s, First byte at: 0.195655s
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:48 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, 23 Jul 2025 18:08:48 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:48] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:48] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-07-23 19:08:48] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:48] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:48] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-07-23 19:08:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-07-23 19:08:48] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-07-23 19:08:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:48] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:49] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:49] [TRACE]   [OmnipathR] Downloaded 12.1 Kb in 0.201579s from omnipathdb.org (60 Kb/s); Redirect: 0s, DNS look up: 0.000889s, Connection: 0.018724s, Pretransfer: 0.052681s, First byte at: 0.200908s
[2025-07-23 19:08:49] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:49 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, 23 Jul 2025 18:08:49 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:49] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-07-23 19:08:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:49] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:49] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-07-23 19:08:49] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-07-23 19:08:49] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2025-07-23 19:08:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:49] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:49] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2025-07-23 19:08:50] [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.
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:50] [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`
[2025-07-23 19:08:50] [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`
[2025-07-23 19:08:50] [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`
[2025-07-23 19:08:50] [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`
[2025-07-23 19:08:50] [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`
[2025-07-23 19:08:50] [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`
[2025-07-23 19:08:50] [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`
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] Downloaded 11.7 Kb in 0.199235s from omnipathdb.org (58.8 Kb/s); Redirect: 0s, DNS look up: 0.000942s, Connection: 0.02394s, Pretransfer: 0.058139s, First byte at: 0.198652s
[2025-07-23 19:08:50] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:50 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, 23 Jul 2025 18:08:50 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:51] [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`
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:51] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-07-23 19:08:51] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:51] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:51] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-07-23 19:08:51] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 19:08:51] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:08:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-07-23 19:08:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-07-23 19:08:52] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-07-23 19:08:52] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] Downloaded 20.2 Kb in 0.210642s from omnipathdb.org (95.7 Kb/s); Redirect: 0s, DNS look up: 0.000868s, Connection: 0.0225s, Pretransfer: 0.057013s, First byte at: 0.209526s
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Jul 2025 17:08:52 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, 23 Jul 2025 18:08:52 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-23 19:08:52] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:52] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-07-23 19:08:52] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-23 19:08:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:52] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2025-07-23 19:08:52] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-07-23 19:08:54] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-07-23 19:08:54] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Orthology targets: 
[2025-07-23 19:08:54] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-23 19:08:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-23 19:08:55] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-07-23 19:08:55] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-07-23 19:08:55] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-07-23 19:08:55] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache.
--- finished re-building ‘paths.Rmd’

SUMMARY: processing the following file failed:
  ‘omnipath_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2025-07-23 19:08:55 CEST ]