[ Started: 2025-03-02 00:21:20 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 ''
[2025-03-02 00:21:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-02 00:21:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:21:59] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-02 00:21:59] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-01 23:21:01 UTC; omnipath
[2025-03-02 00:21:59] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-02 00:21:59] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-01 23:21:02 UTC; unix
[2025-03-02 00:21:59] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-03-02 00:21:59] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-02 00:22:00] [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=2025-03-02; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-02 00:22:00] [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]
[2025-03-02 00:22:00] [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
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-02 00:22:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:00] [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 lines 123-137 [unnamed-chunk-4] (liana_cc2tensor.Rmd)
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
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions]
[2025-03-02 00:22:16] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:16] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:16] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-03-02 00:22:16] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-02 00:22:16] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] HTTP 200
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] Downloaded 31 Kb in 0.390038s from www.ensembl.org (79.4 Kb/s); Redirect: 0s, DNS look up: 0.007498s, Connection: 0.02706s, Pretransfer: 0.091219s, First byte at: 0.373084s
[2025-03-02 00:22:17] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:17] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-02 00:22:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:17] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-02 00:22:17] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-03-02 00:22:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-02 00:22:17] [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=TRUE,ssl_verifyhost=TRUE]
[2025-03-02 00:22:18] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.109858s from omabrowser.org (983.4 Kb/s); Redirect: 0s, DNS look up: 0.000846s, Connection: 0.011464s, Pretransfer: 0.048487s, First byte at: 0.062009s
[2025-03-02 00:22:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-02 00:22:18] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-03-02 00:22:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-02 00:22:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:18] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-03-02 00:22:18] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-03-02 00:22:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-02 00:22:18] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-02 00:22:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-02 00:22:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:18] [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`
[2025-03-02 00:22:18] [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`
[2025-03-02 00:22:18] [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`
[2025-03-02 00:22:18] [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`
[2025-03-02 00:22:18] [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`
[2025-03-02 00:22:18] [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`
[2025-03-02 00:22:18] [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`
[2025-03-02 00:22:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-02 00:22:18] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-02 00:22:18] [WARN]    [OmnipathR] Failed to download `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` (attempt 1/3); error: cannot open the connection
[2025-03-02 00:22:23] [TRACE]   [OmnipathR] Attempt 2/3: `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`
[2025-03-02 00:22:23] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-02 00:22:23] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-02 00:22:24] [WARN]    [OmnipathR] Failed to download `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` (attempt 2/3); error: cannot open the connection
[2025-03-02 00:22:29] [TRACE]   [OmnipathR] Attempt 3/3: `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`
[2025-03-02 00:22:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-02 00:22:29] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-02 00:22:29] [ERROR]   [OmnipathR] Failed to download `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` (attempt 3/3); error: cannot open the connection
[2025-03-02 00:22:29] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-01 23:21:01 UTC; omnipath
[2025-03-02 00:22:29] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-02 00:22:29] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-01 23:21:02 UTC; unix
[2025-03-02 00:22:29] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-03-02 00:22:29] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-02 00:22:29] [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=2025-03-02; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-02 00:22:29] [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]
[2025-03-02 00:22:29] [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
[2025-03-02 00:22:30] [WARN]    [OmnipathR] Failed to download: `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`; error: cannot open the connection
[2025-03-02 00:22:30] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-01 23:21:01 UTC; omnipath
[2025-03-02 00:22:30] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-02 00:22:30] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-01 23:21:02 UTC; unix
[2025-03-02 00:22:30] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-03-02 00:22:30] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-02 00:22:30] [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=2025-03-02; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-02 00:22:30] [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]
[2025-03-02 00:22:30] [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
[2025-03-02 00:22:30] [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`
[2025-03-02 00:22:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-02 00:22:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-02 00:22:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:30] [INFO]    [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `unknown` to `started`.
[2025-03-02 00:22:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2025-03-02 00:22:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2025-03-02 00:22:30] [INFO]    [OmnipathR] Download ready [key=69503cb1a01671e7c77c0e80e6ca0ce4110a89fe, version=1]
[2025-03-02 00:22:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-02 00:22:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-02 00:22:30] [INFO]    [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `started` to `ready`.
[2025-03-02 00:22:30] [SUCCESS] [OmnipathR] Downloaded 2 interactions.

Quitting from lines 116-142 [curation_effort] (liana_custom_op.Rmd)
Error: processing vignette 'liana_custom_op.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'filter' applied to an object of class "list"
--- 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 lines 43-50 [unnamed-chunk-2] (liana_nichenet.Rmd)
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
[2025-03-02 00:23:43] [TRACE]   [OmnipathR] Bypassing call: `homologene_raw()`.
[2025-03-02 00:23:43] [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 lines 73-74 [show_taxid] (liana_ortho.Rmd)
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 lines 151-155 [liana_dotplot] (liana_tutorial.Rmd)
Error: processing vignette 'liana_tutorial.Rmd' failed with diagnostics:
R: geometry does not contain image `/tmp/RtmpdHwxHi/Rbuild2493256afa8a0e/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: 2025-03-02 00:24:54 CET ]