[ Started: 2023-03-21 16:50:11 CET ]
[ liana v0.1.12 for BioC-3.17 from https://github.com/saezlab/liana@master ]

* 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 ''
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:50:44] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Contains 1 files.
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:50:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:50:44] [TRACE]   [OmnipathR] Cache locked: FALSE
The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-4-1.svg" but not available.
sh: 5: /home/omnipath/.cache/R/basilisk/1.11.3/liana/0.1.12/liana_cell2cell/etc/conda/activate.d/activate-r-base.sh: [[: not found
The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-7-1.svg" but not available.
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The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-10-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-11-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_cc2tensor_files/figure-html/ccpairs-1.svg" but not available.
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[2023-03-21 16:59:06] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-21 16:59:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:06] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-21 16:59:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-03-21 16:59:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-03-21 16:59:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-03-21 16:59:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:07] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-03-21 16:59:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-03-21 16:59:09] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2023-03-21 16:59:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:09] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:09] [SUCCESS] [OmnipathR] Downloaded 700257 annotation records.
The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-16-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-17-1.svg" but not available.
--- finished re-building ‘liana_cc2tensor.Rmd’

--- re-building ‘liana_custom_op.Rmd’ using rmarkdown
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:18] [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`
[2023-03-21 16:59:18] [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`
[2023-03-21 16:59:18] [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`
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:18] [INFO]    [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2023-03-21 16:59:18] [INFO]    [OmnipathR] Download ready [key=69503cb1a01671e7c77c0e80e6ca0ce4110a89fe, version=1]
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:18] [INFO]    [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:18] [SUCCESS] [OmnipathR] Downloaded 4580 interactions.
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-21 16:59:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:18] [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`
[2023-03-21 16:59:18] [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`
[2023-03-21 16:59:18] [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`
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:19] [INFO]    [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2023-03-21 16:59:19] [INFO]    [OmnipathR] Download ready [key=ec8c89037e2c920468342c7c2326c74a5474eedc, version=1]
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:19] [INFO]    [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:19] [SUCCESS] [OmnipathR] Downloaded 1475 interactions.
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:19] [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`
[2023-03-21 16:59:19] [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`
[2023-03-21 16:59:19] [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`
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:19] [INFO]    [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2023-03-21 16:59:19] [INFO]    [OmnipathR] Download ready [key=8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5, version=1]
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:19] [INFO]    [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:20] [SUCCESS] [OmnipathR] Downloaded 3765 interactions.
[2023-03-21 16:59:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-21 16:59:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:20] [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`
[2023-03-21 16:59:20] [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`
[2023-03-21 16:59:20] [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`
[2023-03-21 16:59:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:20] [INFO]    [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2023-03-21 16:59:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2023-03-21 16:59:20] [INFO]    [OmnipathR] Download ready [key=b2de51666493a9c70a7b375972a2557903c14763, version=1]
[2023-03-21 16:59:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:20] [INFO]    [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:21] [SUCCESS] [OmnipathR] Downloaded 2485 interactions.
[2023-03-21 16:59:21] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-21 16:59:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:21] [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`
[2023-03-21 16:59:21] [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`
[2023-03-21 16:59:21] [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`
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:22] [INFO]    [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2023-03-21 16:59:22] [INFO]    [OmnipathR] Download ready [key=fedf7fd37a8e863f804aa073f2ae480ff78001e5, version=1]
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:22] [INFO]    [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:22] [SUCCESS] [OmnipathR] Downloaded 1894 interactions.
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:22] [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`
[2023-03-21 16:59:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:22] [INFO]    [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2023-03-21 16:59:22] [INFO]    [OmnipathR] Download ready [key=95ee739b50bbfea2c48e5c86a64525084a1dab30, version=1]
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:22] [INFO]    [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:22] [SUCCESS] [OmnipathR] Downloaded 1797 interactions.
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2023-03-21 16:59:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:23] [INFO]    [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2023-03-21 16:59:23] [INFO]    [OmnipathR] Download ready [key=4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd, version=1]
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:23] [INFO]    [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:23] [SUCCESS] [OmnipathR] Downloaded 1981 annotation records.
[2023-03-21 16:59:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2023-03-21 16:59:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2023-03-21 16:59:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2023-03-21 16:59:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:24] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-03-21 16:59:26] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-03-21 16:59:26] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2023-03-21 16:59:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:26] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:26] [SUCCESS] [OmnipathR] Downloaded 323572 intercellular communication role records.
[2023-03-21 16:59:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-03-21 16:59:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-03-21 16:59:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-03-21 16:59:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:27] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-03-21 16:59:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-03-21 16:59:27] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2023-03-21 16:59:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:27] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:27] [SUCCESS] [OmnipathR] Downloaded 21325 intercellular communication role records.
[2023-03-21 16:59:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-21 16:59:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-21 16:59:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-21 16:59:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:28] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-03-21 16:59:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-03-21 16:59:28] [INFO]    [OmnipathR] Download ready [key=3098404926bc0cf155d043ff0c6efe64e3424b74, version=1]
[2023-03-21 16:59:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:28] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:30] [SUCCESS] [OmnipathR] Downloaded 80237 interactions.
[2023-03-21 16:59:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-03-21 16:59:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-03-21 16:59:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-03-21 16:59:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:30] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-03-21 16:59:31] [INFO]    [OmnipathR] Download ready [key=1ac430724a20c137fc374a8499adabb468a12835, version=1]
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:31] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:31] [SUCCESS] [OmnipathR] Downloaded 27928 intercellular communication role records.
[2023-03-21 16:59:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-03-21 16:59:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:31] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `unknown` to `started`.
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-03-21 16:59:31] [INFO]    [OmnipathR] Download ready [key=552757063f9934c7b745a9c4247c3b5282a66c88, version=1]
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 16:59:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 16:59:31] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `started` to `ready`.
[2023-03-21 16:59:31] [SUCCESS] [OmnipathR] Downloaded 43967 intercellular communication role records.
[2023-03-21 17:06:32] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-03-21 17:06:32] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2023-03-21 17:06:32] [SUCCESS] [OmnipathR] Loaded 323572 intercellular communication role records from cache.
[2023-03-21 17:06:33] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-03-21 17:06:33] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-03-21 17:06:33] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
[2023-03-21 17:06:33] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-03-21 17:06:33] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-21 17:06:36] [SUCCESS] [OmnipathR] Loaded 80237 interactions from cache.
[2023-03-21 17:06:36] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-03-21 17:06:36] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-03-21 17:06:36] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache.
[2023-03-21 17:06:36] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-03-21 17:06:36] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-03-21 17:06:36] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache.
[2023-03-21 17:14:45] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2023-03-21 17:14:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2023-03-21 17:14:46] [SUCCESS] [OmnipathR] Loaded 80237 interactions from cache.
[2023-03-21 17:14:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2023-03-21 17:14:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2023-03-21 17:14:47] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache.
[2023-03-21 17:14:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2023-03-21 17:14:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2023-03-21 17:14:47] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache.
[2023-03-21 17:21:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2023-03-21 17:21:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2023-03-21 17:21:47] [SUCCESS] [OmnipathR] Loaded 323572 intercellular communication role records from cache.
[2023-03-21 17:21:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2023-03-21 17:21:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2023-03-21 17:21:47] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
--- finished 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 (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
[2023-03-21 17:23:05] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`.
[2023-03-21 17:23:05] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`
[2023-03-21 17:23:05] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`.
[2023-03-21 17:23:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 17:23:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 17:23:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 17:23:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 17:23:05] [INFO]    [OmnipathR] Cache item `2ccc1998f0ab26ea421885e1334896d25db4554f` version 1: status changed from `unknown` to `started`.
[2023-03-21 17:23:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2ccc1998f0ab26ea421885e1334896d25db4554f-1.rds`.
[2023-03-21 17:23:05] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`
[2023-03-21 17:23:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2ccc1998f0ab26ea421885e1334896d25db4554f-1.rds`.
[2023-03-21 17:23:17] [INFO]    [OmnipathR] Download ready [key=2ccc1998f0ab26ea421885e1334896d25db4554f, version=1]
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 17:23:17] [INFO]    [OmnipathR] Cache item `2ccc1998f0ab26ea421885e1334896d25db4554f` version 1: status changed from `started` to `ready`.
[2023-03-21 17:23:17] [SUCCESS] [OmnipathR] NCBI HomoloGene (ftp.ncbi.nih.gov): downloaded 275237 records
[2023-03-21 17:23:17] [INFO]    [OmnipathR] Loading database `Ensembl organism names`.
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 17:23:17] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 17:23:17] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2023-03-21 17:23:17] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] HTTP 200
[2023-03-21 17:23:17] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 17:23:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 17:23:17] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2023-03-21 17:23:18] [INFO]    [OmnipathR] Loaded database `Ensembl organism names`.
[2023-03-21 17:23:19] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`.
[2023-03-21 17:23:19] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/2ccc1998f0ab26ea421885e1334896d25db4554f-1.rds`.
[2023-03-21 17:23:19] [SUCCESS] [OmnipathR] NCBI HomoloGene (ftp.ncbi.nih.gov): loaded 275237 records from cache
The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_ortho_files/figure-html/orthology-1.svg" but not available.
--- finished re-building ‘liana_ortho.Rmd’

--- re-building ‘liana_tutorial.Rmd’ using rmarkdown
The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_tutorial_files/figure-html/liana_dotplot-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_tutorial_files/figure-html/heatfreq-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_tutorial_files/figure-html/chordfreq-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpzOATLO/Rbuildcc2e32ea007de/liana/vignettes/liana_tutorial_files/figure-html/cpdb_test-1.svg" but not available.
--- finished re-building ‘liana_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-03-21 17:25:37 CET ]