[ Started: 2023-04-03 12:36:28 CEST ]
[ 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 ''
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:37:00] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:37:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:37:00] [TRACE]   [OmnipathR] Cache locked: FALSE
The magick package is required to crop "/tmp/RtmpfzkDcO/Rbuild2afcf53640f7b7/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/RtmpfzkDcO/Rbuild2afcf53640f7b7/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-7-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpfzkDcO/Rbuild2afcf53640f7b7/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-9-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpfzkDcO/Rbuild2afcf53640f7b7/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-10-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpfzkDcO/Rbuild2afcf53640f7b7/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-11-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpfzkDcO/Rbuild2afcf53640f7b7/liana/vignettes/liana_cc2tensor_files/figure-html/ccpairs-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpfzkDcO/Rbuild2afcf53640f7b7/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-14-1.svg" but not available.
Quitting from lines 389-399 (liana_cc2tensor.Rmd) 
Error: processing vignette 'liana_cc2tensor.Rmd' failed with diagnostics:
cannot open the connection to 'https://omnipathdb.org/resources'
--- failed re-building ‘liana_cc2tensor.Rmd’

--- re-building ‘liana_custom_op.Rmd’ using rmarkdown
Quitting from lines 116-142 (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 `file()`:
! cannot open the connection to 'https://omnipathdb.org/resources'
--- 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 (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
[2023-04-03 12:46:02] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`.
[2023-04-03 12:46:02] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`
[2023-04-03 12:46:02] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`.
[2023-04-03 12:46:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-03 12:46:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:46:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-03 12:46:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:46:02] [INFO]    [OmnipathR] Cache item `2ccc1998f0ab26ea421885e1334896d25db4554f` version 1: status changed from `unknown` to `started`.
[2023-04-03 12:46:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2ccc1998f0ab26ea421885e1334896d25db4554f-1.rds`.
[2023-04-03 12:46:02] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`
[2023-04-03 12:46:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`
[2023-04-03 12:46:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2ccc1998f0ab26ea421885e1334896d25db4554f-1.rds`.
[2023-04-03 12:46:09] [INFO]    [OmnipathR] Download ready [key=2ccc1998f0ab26ea421885e1334896d25db4554f, version=1]
[2023-04-03 12:46:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-03 12:46:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:46:09] [INFO]    [OmnipathR] Cache item `2ccc1998f0ab26ea421885e1334896d25db4554f` version 1: status changed from `started` to `ready`.
[2023-04-03 12:46:09] [SUCCESS] [OmnipathR] NCBI HomoloGene (ftp.ncbi.nih.gov): downloaded 275237 records
[2023-04-03 12:46:09] [INFO]    [OmnipathR] Loading database `Ensembl organism names`.
[2023-04-03 12:46:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-03 12:46:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:46:09] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2023-04-03 12:46:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-03 12:46:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:46:09] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2023-04-03 12:46:10] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2023-04-03 12:46:10] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2023-04-03 12:46:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2023-04-03 12:46:10] [TRACE]   [OmnipathR] HTTP 200
[2023-04-03 12:46:10] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2023-04-03 12:46:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-03 12:46:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-03 12:46:10] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2023-04-03 12:46:10] [INFO]    [OmnipathR] Loaded database `Ensembl organism names`.
[2023-04-03 12:46:11] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`.
[2023-04-03 12:46:11] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/2ccc1998f0ab26ea421885e1334896d25db4554f-1.rds`.
[2023-04-03 12:46:11] [SUCCESS] [OmnipathR] NCBI HomoloGene (ftp.ncbi.nih.gov): loaded 275237 records from cache
The magick package is required to crop "/tmp/RtmpfzkDcO/Rbuild2afcf53640f7b7/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/RtmpfzkDcO/Rbuild2afcf53640f7b7/liana/vignettes/liana_tutorial_files/figure-html/liana_dotplot-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpfzkDcO/Rbuild2afcf53640f7b7/liana/vignettes/liana_tutorial_files/figure-html/heatfreq-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpfzkDcO/Rbuild2afcf53640f7b7/liana/vignettes/liana_tutorial_files/figure-html/chordfreq-1.svg" but not available.
The magick package is required to crop "/tmp/RtmpfzkDcO/Rbuild2afcf53640f7b7/liana/vignettes/liana_tutorial_files/figure-html/cpdb_test-1.svg" but not available.
--- finished re-building ‘liana_tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘liana_cc2tensor.Rmd’ ‘liana_custom_op.Rmd’ ‘liana_nichenet.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-04-03 12:48:14 CEST ]