[ Started: 2025-03-01 01:12:51 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 '' [2025-03-01 01:13:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:30] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-01 01:13:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-01 00:12:31 UTC; omnipath [2025-03-01 01:13:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-01 01:13:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-01 00:12:32 UTC; unix [2025-03-01 01:13:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-03-01 01:13:30] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-01 01:13:30] [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=2025-03-01; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-01 01:13:31] [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] [2025-03-01 01:13:31] [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 [2025-03-01 01:13:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-01 01:13:31] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-01 01:13:31] [TRACE] [OmnipathR] Contains 1 files. [2025-03-01 01:13:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-01 01:13:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-01 01:13:31] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-01 01:13:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-01 01:13:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-01 01:13:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-01 01:13:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-01 01:13:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:31] [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 [2025-03-01 01:13:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-01 01:13:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions] [2025-03-01 01:13:50] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-03-01 01:13:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:50] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-03-01 01:13:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:50] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-03-01 01:13:50] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-03-01 01:13:50] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-03-01 01:13:50] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-03-01 01:13:50] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-03-01 01:13:50] [TRACE] [OmnipathR] Preparing httr2 request. [2025-03-01 01:13:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-01 01:13:50] [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=TRUE,ssl_verifyhost=TRUE] [2025-03-01 01:13:50] [TRACE] [OmnipathR] Sending HTTP request. [2025-03-01 01:13:51] [TRACE] [OmnipathR] HTTP 200 [2025-03-01 01:13:51] [TRACE] [OmnipathR] Downloaded 30.9 Kb in 0.54262s from www.ensembl.org (56.9 Kb/s); Redirect: 0s, DNS look up: 0.122085s, Connection: 0.142541s, Pretransfer: 0.229681s, First byte at: 0.525166s [2025-03-01 01:13:51] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-03-01 01:13:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:51] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-03-01 01:13:51] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-03-01 01:13:51] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-03-01 01:13:51] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-03-01 01:13:51] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-03-01 01:13:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:51] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-03-01 01:13:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-03-01 01:13:51] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-03-01 01:13:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-03-01 01:13:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-01 01:13:51] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-03-01 01:13:52] [TRACE] [OmnipathR] Downloaded 108 Kb in 0.146975s from omabrowser.org (735.1 Kb/s); Redirect: 0s, DNS look up: 0.032418s, Connection: 0.042802s, Pretransfer: 0.084855s, First byte at: 0.098587s [2025-03-01 01:13:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-03-01 01:13:52] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-03-01 01:13:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:52] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-03-01 01:13:52] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-03-01 01:13:52] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-01 01:13:52] [TRACE] [OmnipathR] Orthology targets: [2025-03-01 01:13:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-01 01:13:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:52] [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` [2025-03-01 01:13:52] [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` [2025-03-01 01:13:52] [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` [2025-03-01 01:13:52] [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` [2025-03-01 01:13:52] [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` [2025-03-01 01:13:52] [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` [2025-03-01 01:13:52] [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` [2025-03-01 01:13:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-01 01:13:52] [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=TRUE,ssl_verifyhost=TRUE] [2025-03-01 01:13:53] [TRACE] [OmnipathR] Downloaded 236.8 Kb in 0.175459s from omnipathdb.org (1.3 Mb/s); Redirect: 0s, DNS look up: 0.001044s, Connection: 0.020705s, Pretransfer: 0.075946s, First byte at: 0.115193s [2025-03-01 01:13:53] [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` [2025-03-01 01:13:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:53] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `unknown` to `started`. [2025-03-01 01:13:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2025-03-01 01:13:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2025-03-01 01:13:53] [INFO] [OmnipathR] Download ready [key=69503cb1a01671e7c77c0e80e6ca0ce4110a89fe, version=1] [2025-03-01 01:13:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:53] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `started` to `ready`. [2025-03-01 01:13:53] [SUCCESS] [OmnipathR] Downloaded 4568 interactions. [2025-03-01 01:13:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-01 01:13:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions] [2025-03-01 01:13:54] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-01 01:13:54] [TRACE] [OmnipathR] Orthology targets: [2025-03-01 01:13:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-01 01:13:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:54] [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` [2025-03-01 01:13:54] [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` [2025-03-01 01:13:54] [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` [2025-03-01 01:13:54] [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` [2025-03-01 01:13:54] [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` [2025-03-01 01:13:54] [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` [2025-03-01 01:13:54] [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` [2025-03-01 01:13:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-01 01:13:54] [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] [2025-03-01 01:13:54] [TRACE] [OmnipathR] Downloaded 128.2 Kb in 0.144248s from omnipathdb.org (888.6 Kb/s); Redirect: 0s, DNS look up: 0.001113s, Connection: 0.019803s, Pretransfer: 0.062476s, First byte at: 0.099966s [2025-03-01 01:13:54] [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` [2025-03-01 01:13:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:55] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `unknown` to `started`. [2025-03-01 01:13:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2025-03-01 01:13:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2025-03-01 01:13:55] [INFO] [OmnipathR] Download ready [key=ec8c89037e2c920468342c7c2326c74a5474eedc, version=1] [2025-03-01 01:13:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:55] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `started` to `ready`. [2025-03-01 01:13:55] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-03-01 01:13:55] [SUCCESS] [OmnipathR] Downloaded 2879 interactions. [2025-03-01 01:13:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-01 01:13:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions] [2025-03-01 01:13:55] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-01 01:13:55] [TRACE] [OmnipathR] Orthology targets: [2025-03-01 01:13:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-01 01:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:55] [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` [2025-03-01 01:13:55] [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` [2025-03-01 01:13:55] [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` [2025-03-01 01:13:55] [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` [2025-03-01 01:13:55] [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` [2025-03-01 01:13:55] [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` [2025-03-01 01:13:55] [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` [2025-03-01 01:13:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-01 01:13:55] [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] [2025-03-01 01:13:55] [TRACE] [OmnipathR] Downloaded 224.3 Kb in 0.140298s from omnipathdb.org (1.6 Mb/s); Redirect: 0s, DNS look up: 0.000992s, Connection: 0.017618s, Pretransfer: 0.055545s, First byte at: 0.089326s [2025-03-01 01:13:56] [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` [2025-03-01 01:13:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:56] [INFO] [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `unknown` to `started`. [2025-03-01 01:13:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2025-03-01 01:13:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2025-03-01 01:13:56] [INFO] [OmnipathR] Download ready [key=8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5, version=1] [2025-03-01 01:13:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:56] [INFO] [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `started` to `ready`. [2025-03-01 01:13:56] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-03-01 01:13:56] [SUCCESS] [OmnipathR] Downloaded 3765 interactions. [2025-03-01 01:13:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-01 01:13:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions] [2025-03-01 01:13:56] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-01 01:13:56] [TRACE] [OmnipathR] Orthology targets: [2025-03-01 01:13:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-01 01:13:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:56] [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` [2025-03-01 01:13:56] [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` [2025-03-01 01:13:56] [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` [2025-03-01 01:13:56] [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` [2025-03-01 01:13:56] [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` [2025-03-01 01:13:56] [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` [2025-03-01 01:13:56] [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` [2025-03-01 01:13:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-01 01:13:56] [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=TRUE,ssl_verifyhost=TRUE] [2025-03-01 01:13:57] [TRACE] [OmnipathR] Downloaded 207 Kb in 0.162158s from omnipathdb.org (1.2 Mb/s); Redirect: 0s, DNS look up: 0.001053s, Connection: 0.01894s, Pretransfer: 0.073687s, First byte at: 0.109296s [2025-03-01 01:13:57] [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` [2025-03-01 01:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:57] [INFO] [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `unknown` to `started`. [2025-03-01 01:13:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`. [2025-03-01 01:13:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`. [2025-03-01 01:13:57] [INFO] [OmnipathR] Download ready [key=b2de51666493a9c70a7b375972a2557903c14763, version=1] [2025-03-01 01:13:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:57] [INFO] [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `started` to `ready`. [2025-03-01 01:13:57] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-03-01 01:13:57] [SUCCESS] [OmnipathR] Downloaded 2484 interactions. [2025-03-01 01:13:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-01 01:13:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions] [2025-03-01 01:13:58] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-01 01:13:58] [TRACE] [OmnipathR] Orthology targets: [2025-03-01 01:13:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-01 01:13:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:58] [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` [2025-03-01 01:13:58] [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` [2025-03-01 01:13:58] [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` [2025-03-01 01:13:58] [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` [2025-03-01 01:13:58] [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` [2025-03-01 01:13:58] [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` [2025-03-01 01:13:58] [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` [2025-03-01 01:13:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-01 01:13:58] [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=TRUE,ssl_verifyhost=TRUE] [2025-03-01 01:13:58] [TRACE] [OmnipathR] Downloaded 111.9 Kb in 0.129828s from omnipathdb.org (861.8 Kb/s); Redirect: 0s, DNS look up: 0.000875s, Connection: 0.018682s, Pretransfer: 0.056898s, First byte at: 0.093015s [2025-03-01 01:13:59] [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` [2025-03-01 01:13:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:59] [INFO] [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `unknown` to `started`. [2025-03-01 01:13:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2025-03-01 01:13:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2025-03-01 01:13:59] [INFO] [OmnipathR] Download ready [key=fedf7fd37a8e863f804aa073f2ae480ff78001e5, version=1] [2025-03-01 01:13:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:13:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:59] [INFO] [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `started` to `ready`. [2025-03-01 01:13:59] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-03-01 01:13:59] [SUCCESS] [OmnipathR] Downloaded 1894 interactions. [2025-03-01 01:13:59] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-01 01:13:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions] [2025-03-01 01:13:59] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-01 01:13:59] [TRACE] [OmnipathR] Orthology targets: [2025-03-01 01:13:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-01 01:13:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:13:59] [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` [2025-03-01 01:13:59] [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` [2025-03-01 01:13:59] [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` [2025-03-01 01:13:59] [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` [2025-03-01 01:13:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-01 01:13:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-01 01:13:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-01 01:13:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-01 01:13:59] [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] [2025-03-01 01:13:59] [TRACE] [OmnipathR] Downloaded 172.1 Kb in 0.147383s from omnipathdb.org (1.1 Mb/s); Redirect: 0s, DNS look up: 0.000932s, Connection: 0.018198s, Pretransfer: 0.071651s, First byte at: 0.106179s [2025-03-01 01:14:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-01 01:14:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:14:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:14:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:14:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:14:00] [INFO] [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `unknown` to `started`. [2025-03-01 01:14:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2025-03-01 01:14:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2025-03-01 01:14:00] [INFO] [OmnipathR] Download ready [key=95ee739b50bbfea2c48e5c86a64525084a1dab30, version=1] [2025-03-01 01:14:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:14:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:14:00] [INFO] [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `started` to `ready`. [2025-03-01 01:14:00] [SUCCESS] [OmnipathR] Downloaded 1796 interactions. [2025-03-01 01:14:00] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-01 01:14:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_function,query_type=annotations] [2025-03-01 01:14:00] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-01 01:14:00] [TRACE] [OmnipathR] Orthology targets: [2025-03-01 01:14:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-01 01:14:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:14:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-03-01 01:14:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-03-01 01:14:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-03-01 01:14:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-03-01 01:14:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-03-01 01:14:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-03-01 01:14:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-03-01 01:14:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-01 01:14:00] [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] [2025-03-01 01:14:00] [TRACE] [OmnipathR] Downloaded 26 Kb in 0.110438s from omnipathdb.org (235.9 Kb/s); Redirect: 0s, DNS look up: 0.001071s, Connection: 0.023214s, Pretransfer: 0.061245s, First byte at: 0.1059s [2025-03-01 01:14:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-03-01 01:14:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:14:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:14:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:14:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:14:01] [INFO] [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `unknown` to `started`. [2025-03-01 01:14:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`. [2025-03-01 01:14:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`. [2025-03-01 01:14:01] [INFO] [OmnipathR] Download ready [key=4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd, version=1] [2025-03-01 01:14:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-01 01:14:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-01 01:14:01] [INFO] [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `started` to `ready`. [2025-03-01 01:14:01] [SUCCESS] [OmnipathR] Downloaded 2001 annotation records. [2025-03-01 01:14:02] [TRACE] [OmnipathR] Bypassing call: `OmnipathR::filter_intercell_network(., simplify = FALSE, ...)`. [2025-03-01 01:14:02] [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 159-196 [pm_omni] (liana_custom_op.Rmd) 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 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 [2025-03-01 01:15:15] [TRACE] [OmnipathR] Bypassing call: `homologene_raw()`. [2025-03-01 01:15:15] [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/RtmpB0XeeF/Rbuild1f24f63f32a719/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: 2025-03-01 01:16:26 CET ]