[ Started: 2025-03-21 01:12:04 CET ]
[ liana v0.1.14 for BioC-3.21 from https://github.com/saezlab/liana@master (6cab46c 2024-08-07 08:58:01) ]
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘liana’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘liana_cc2tensor.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
unable to open connection to X11 display ''
[2025-03-21 01:12:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:12:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:12:43] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-21 01:12:43] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-21 00:11:39 UTC; omnipath
[2025-03-21 01:12:43] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-21 01:12:43] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-21 00:11:40 UTC; unix
[2025-03-21 01:12:43] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-03-21 01:12:43] [INFO] [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-21 01:12:44] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-21 01:12:44] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-21 01:12:44] [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
[2025-03-21 01:12:44] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-21 01:12:44] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-21 01:12:44] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-21 01:12:44] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-21 01:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:12:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-21 01:12:44] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-21 01:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-21 01:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-21 01:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-21 01:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-21 01:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:12:44] [TRACE] [OmnipathR] Cache locked: FALSE
Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering.
For better results use image_read_svg() which uses the rsvg package.
Quitting from liana_cc2tensor.Rmd:122-137 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274
---
Backtrace:
▆
1. ├─tools::buildVignettes(dir = ".", tangle = TRUE)
2. │ ├─base::tryCatch(...)
3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. │ └─engine$weave(file, quiet = quiet, encoding = enc)
7. │ └─knitr:::vweave_rmarkdown(...)
8. │ └─rmarkdown::render(...)
9. │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
10. │ └─knitr:::process_file(text, output)
11. │ ├─xfun:::handle_error(...)
12. │ ├─base::withCallingHandlers(...)
13. │ └─knitr:::process_group(group)
14. │ └─knitr:::call_block(x)
15. │ └─knitr:::block_exec(params)
16. │ └─knitr:::eng_r(options)
17. │ └─knitr:::run_hooks(before = FALSE, options, env)
18. │ └─base::do.call(hook, args, envir = envir)
19. └─knitr (local) `<fn>`(...)
20. ├─knitr:::in_base_dir(for (f in get_plot_files()) plot_crop(f))
21. │ └─knitr:::in_dir(d, expr)
22. └─knitr::plot_crop(f)
23. └─magick::image_write(magick::image_trim(img), x)
24. └─magick:::magick_image_write(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'liana_cc2tensor.Rmd' failed with diagnostics:
R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274
--- failed re-building ‘liana_cc2tensor.Rmd’
--- re-building ‘liana_custom_op.Rmd’ using rmarkdown
[2025-03-21 01:13:00] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-21 01:13:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions]
[2025-03-21 01:13:00] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-03-21 01:13:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:00] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-03-21 01:13:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:00] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-03-21 01:13:00] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-03-21 01:13:00] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-03-21 01:13:00] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-03-21 01:13:00] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-03-21 01:13:00] [TRACE] [OmnipathR] Preparing httr2 request.
[2025-03-21 01:13:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-21 01:13:00] [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=TRUE,ssl_verifyhost=TRUE]
[2025-03-21 01:13:00] [TRACE] [OmnipathR] Sending HTTP request.
[2025-03-21 01:13:00] [TRACE] [OmnipathR] HTTP 200
[2025-03-21 01:13:01] [TRACE] [OmnipathR] Downloaded 31 Kb in 0.225821s from www.ensembl.org (137.3 Kb/s); Redirect: 0s, DNS look up: 0.029975s, Connection: 0.049027s, Pretransfer: 0.106347s, First byte at: 0.208934s
[2025-03-21 01:13:01] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-03-21 01:13:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:01] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-03-21 01:13:01] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-03-21 01:13:01] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-21 01:13:01] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-03-21 01:13:01] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-21 01:13:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:01] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-03-21 01:13:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-21 01:13:01] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-03-21 01:13:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-03-21 01:13:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-21 01:13:01] [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=TRUE,ssl_verifyhost=TRUE]
[2025-03-21 01:13:02] [TRACE] [OmnipathR] Downloaded 108 Kb in 0.10674s from omabrowser.org (1012.2 Kb/s); Redirect: 0s, DNS look up: 0.001113s, Connection: 0.010822s, Pretransfer: 0.045814s, First byte at: 0.05857s
[2025-03-21 01:13:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-21 01:13:02] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-03-21 01:13:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:02] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-03-21 01:13:02] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-03-21 01:13:02] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-21 01:13:02] [TRACE] [OmnipathR] Orthology targets:
[2025-03-21 01:13:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-21 01:13:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-21 01:13:02] [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=TRUE,ssl_verifyhost=TRUE]
[2025-03-21 01:13:03] [TRACE] [OmnipathR] Downloaded 236.8 Kb in 0.175259s from omnipathdb.org (1.3 Mb/s); Redirect: 0s, DNS look up: 0.000965s, Connection: 0.019211s, Pretransfer: 0.07235s, First byte at: 0.11461s
[2025-03-21 01:13:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:03] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `unknown` to `started`.
[2025-03-21 01:13:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2025-03-21 01:13:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2025-03-21 01:13:03] [INFO] [OmnipathR] Download ready [key=69503cb1a01671e7c77c0e80e6ca0ce4110a89fe, version=1]
[2025-03-21 01:13:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:03] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `started` to `ready`.
[2025-03-21 01:13:03] [SUCCESS] [OmnipathR] Downloaded 4568 interactions.
[2025-03-21 01:13:04] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-21 01:13:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions]
[2025-03-21 01:13:04] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-21 01:13:04] [TRACE] [OmnipathR] Orthology targets:
[2025-03-21 01:13:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-21 01:13:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-21 01:13:04] [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=TRUE,ssl_verifyhost=TRUE]
[2025-03-21 01:13:04] [TRACE] [OmnipathR] Downloaded 128.2 Kb in 0.163137s from omnipathdb.org (785.7 Kb/s); Redirect: 0s, DNS look up: 0.000941s, Connection: 0.023812s, Pretransfer: 0.059471s, First byte at: 0.105266s
[2025-03-21 01:13:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:05] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `unknown` to `started`.
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2025-03-21 01:13:05] [INFO] [OmnipathR] Download ready [key=ec8c89037e2c920468342c7c2326c74a5474eedc, version=1]
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:05] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `started` to `ready`.
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-21 01:13:05] [SUCCESS] [OmnipathR] Downloaded 2879 interactions.
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions]
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Orthology targets:
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-21 01:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-21 01:13:05] [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=TRUE,ssl_verifyhost=TRUE]
[2025-03-21 01:13:05] [TRACE] [OmnipathR] Downloaded 224.3 Kb in 0.16536s from omnipathdb.org (1.3 Mb/s); Redirect: 0s, DNS look up: 0.001006s, Connection: 0.022237s, Pretransfer: 0.057778s, First byte at: 0.100682s
[2025-03-21 01:13:06] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:06] [INFO] [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `unknown` to `started`.
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2025-03-21 01:13:06] [INFO] [OmnipathR] Download ready [key=8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5, version=1]
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:06] [INFO] [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `started` to `ready`.
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-21 01:13:06] [SUCCESS] [OmnipathR] Downloaded 3765 interactions.
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions]
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Orthology targets:
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-21 01:13:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:06] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-21 01:13:06] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-21 01:13:07] [TRACE] [OmnipathR] Downloaded 207 Kb in 0.154674s from omnipathdb.org (1.3 Mb/s); Redirect: 0s, DNS look up: 0.000971s, Connection: 0.020598s, Pretransfer: 0.056192s, First byte at: 0.095668s
[2025-03-21 01:13:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:07] [INFO] [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `unknown` to `started`.
[2025-03-21 01:13:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2025-03-21 01:13:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2025-03-21 01:13:07] [INFO] [OmnipathR] Download ready [key=b2de51666493a9c70a7b375972a2557903c14763, version=1]
[2025-03-21 01:13:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:07] [INFO] [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `started` to `ready`.
[2025-03-21 01:13:07] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-21 01:13:07] [SUCCESS] [OmnipathR] Downloaded 2484 interactions.
[2025-03-21 01:13:08] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-21 01:13:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions]
[2025-03-21 01:13:08] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-21 01:13:08] [TRACE] [OmnipathR] Orthology targets:
[2025-03-21 01:13:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-21 01:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-21 01:13:08] [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=TRUE,ssl_verifyhost=TRUE]
[2025-03-21 01:13:08] [TRACE] [OmnipathR] Downloaded 111.9 Kb in 0.153588s from omnipathdb.org (728.5 Kb/s); Redirect: 0s, DNS look up: 0.000915s, Connection: 0.020318s, Pretransfer: 0.072998s, First byte at: 0.111698s
[2025-03-21 01:13:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:09] [INFO] [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `unknown` to `started`.
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2025-03-21 01:13:09] [INFO] [OmnipathR] Download ready [key=fedf7fd37a8e863f804aa073f2ae480ff78001e5, version=1]
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:09] [INFO] [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `started` to `ready`.
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-21 01:13:09] [SUCCESS] [OmnipathR] Downloaded 1894 interactions.
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions]
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Orthology targets:
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-21 01:13:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-21 01:13:09] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Downloaded 172.1 Kb in 0.178403s from omnipathdb.org (964.5 Kb/s); Redirect: 0s, DNS look up: 0.001037s, Connection: 0.023101s, Pretransfer: 0.058341s, First byte at: 0.11164s
[2025-03-21 01:13:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:10] [INFO] [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `unknown` to `started`.
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2025-03-21 01:13:10] [INFO] [OmnipathR] Download ready [key=95ee739b50bbfea2c48e5c86a64525084a1dab30, version=1]
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:10] [INFO] [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `started` to `ready`.
[2025-03-21 01:13:10] [SUCCESS] [OmnipathR] Downloaded 1796 interactions.
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_function,query_type=annotations]
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Orthology targets:
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-21 01:13:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-21 01:13:10] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-21 01:13:10] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-21 01:13:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-21 01:13:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-21 01:13:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-21 01:13:10] [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=TRUE,ssl_verifyhost=TRUE]
[2025-03-21 01:13:11] [TRACE] [OmnipathR] Downloaded 26 Kb in 0.113999s from omnipathdb.org (228.5 Kb/s); Redirect: 0s, DNS look up: 0.000997s, Connection: 0.01948s, Pretransfer: 0.073473s, First byte at: 0.110751s
[2025-03-21 01:13:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-21 01:13:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:11] [INFO] [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `unknown` to `started`.
[2025-03-21 01:13:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2025-03-21 01:13:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2025-03-21 01:13:11] [INFO] [OmnipathR] Download ready [key=4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd, version=1]
[2025-03-21 01:13:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 01:13:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-21 01:13:11] [INFO] [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `started` to `ready`.
[2025-03-21 01:13:11] [SUCCESS] [OmnipathR] Downloaded 2001 annotation records.
[2025-03-21 01:13:12] [TRACE] [OmnipathR] Bypassing call: `OmnipathR::filter_intercell_network(., simplify = FALSE, ...)`.
[2025-03-21 01:13:12] [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.
Quitting from liana_custom_op.Rmd:158-196 [pm_omni]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'tbl_vars' applied to an object of class "NULL"
---
Backtrace:
▆
1. ├─liana::generate_omni(...)
2. │ └─... %>% ...
3. └─dplyr::distinct_at(...)
4. └─dplyr:::manip_at(...)
5. └─dplyr:::tbl_at_syms(...)
6. └─dplyr:::tbl_at_vars(...)
7. └─dplyr::tbl_vars(tbl)
8. ├─dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x))
9. │ └─base::structure(...)
10. └─dplyr:::tbl_vars_dispatch(x)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'liana_custom_op.Rmd' failed with diagnostics:
no applicable method for 'tbl_vars' applied to an object of class "NULL"
--- failed re-building ‘liana_custom_op.Rmd’
--- re-building ‘liana_devel.Rmd’ using rmarkdown
--- finished re-building ‘liana_devel.Rmd’
--- re-building ‘liana_nichenet.Rmd’ using rmarkdown
Quitting from liana_nichenet.Rmd:42-50 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'nichenetr'
---
Backtrace:
▆
1. └─base::library(nichenetr)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'liana_nichenet.Rmd' failed with diagnostics:
there is no package called 'nichenetr'
--- failed re-building ‘liana_nichenet.Rmd’
--- re-building ‘liana_ortho.Rmd’ using rmarkdown
[2025-03-21 01:14:24] [TRACE] [OmnipathR] Bypassing call: `homologene_raw()`.
[2025-03-21 01:14:24] [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.
Quitting from liana_ortho.Rmd:72-74 [show_taxid]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'object' in selecting a method for function 'na.omit': no applicable method for 'pull' applied to an object of class "list"
---
Backtrace:
▆
1. ├─liana::show_homologene()
2. │ └─... %>% print(n = nrow(.))
3. ├─base::print(., n = nrow(.))
4. ├─dplyr::arrange(., name)
5. ├─stats::na.omit(.)
6. ├─tibble::tibble(ncbi_taxid = ., name = common_name(.), latin = latin_name(.))
7. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
8. │ └─rlang::eval_tidy(xs[[j]], mask)
9. ├─base::unique(.)
10. ├─dplyr::pull(., ncbi_taxid)
11. └─base::.handleSimpleError(...)
12. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'liana_ortho.Rmd' failed with diagnostics:
error in evaluating the argument 'object' in selecting a method for function 'na.omit': no applicable method for 'pull' applied to an object of class "list"
--- failed re-building ‘liana_ortho.Rmd’
--- re-building ‘liana_tutorial.Rmd’ using rmarkdown
Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering.
For better results use image_read_svg() which uses the rsvg package.
Quitting from liana_tutorial.Rmd:150-155 [liana_dotplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! R: geometry does not contain image `/tmp/Rtmp3JDLPD/Rbuild1af8e74172cab5/liana/vignettes/liana_tutorial_files/figure-html/liana_dotplot-1.svg' @ warning/attribute.c/GetImageBoundingBox/534
---
Backtrace:
▆
1. ├─tools::buildVignettes(dir = ".", tangle = TRUE)
2. │ ├─base::tryCatch(...)
3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. │ └─engine$weave(file, quiet = quiet, encoding = enc)
7. │ └─knitr:::vweave_rmarkdown(...)
8. │ └─rmarkdown::render(...)
9. │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
10. │ └─knitr:::process_file(text, output)
11. │ ├─xfun:::handle_error(...)
12. │ ├─base::withCallingHandlers(...)
13. │ └─knitr:::process_group(group)
14. │ └─knitr:::call_block(x)
15. │ └─knitr:::block_exec(params)
16. │ └─knitr:::eng_r(options)
17. │ └─knitr:::run_hooks(before = FALSE, options, env)
18. │ └─base::do.call(hook, args, envir = envir)
19. └─knitr (local) `<fn>`(...)
20. ├─knitr:::in_base_dir(for (f in get_plot_files()) plot_crop(f))
21. │ └─knitr:::in_dir(d, expr)
22. └─knitr::plot_crop(f)
23. ├─magick::image_write(magick::image_trim(img), x)
24. │ └─magick:::assert_image(image)
25. └─magick::image_trim(img)
26. └─magick:::magick_image_trim(image, fuzz)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'liana_tutorial.Rmd' failed with diagnostics:
R: geometry does not contain image `/tmp/Rtmp3JDLPD/Rbuild1af8e74172cab5/liana/vignettes/liana_tutorial_files/figure-html/liana_dotplot-1.svg' @ warning/attribute.c/GetImageBoundingBox/534
--- failed re-building ‘liana_tutorial.Rmd’
SUMMARY: processing the following files failed:
‘liana_cc2tensor.Rmd’ ‘liana_custom_op.Rmd’ ‘liana_nichenet.Rmd’
‘liana_ortho.Rmd’ ‘liana_tutorial.Rmd’
Error: Vignette re-building failed.
Execution halted
[ Finished: 2025-03-21 01:15:37 CET ]