[ Started: 2023-03-18 23:40:53 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 '' [2023-03-18 23:41:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:41:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:41:25] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-03-18 23:41:25] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-03-18 23:41:25] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-03-18 23:41:25] [TRACE] [OmnipathR] Contains 1 files. [2023-03-18 23:41:25] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-03-18 23:41:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:41:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:41:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-03-18 23:41:25] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-03-18 23:41:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-03-18 23:41:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:41:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-03-18 23:41:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:41:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-03-18 23:41:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:41:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-03-18 23:41:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:41:25] [TRACE] [OmnipathR] Cache locked: FALSE The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/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/RtmpuiZ0vv/Rbuild33f1d96871b043/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-7-1.svg" but not available. The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-9-1.svg" but not available. The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-10-1.svg" but not available. The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-11-1.svg" but not available. The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/liana/vignettes/liana_cc2tensor_files/figure-html/ccpairs-1.svg" but not available. The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-14-1.svg" but not available. [2023-03-18 23:49:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2023-03-18 23:49:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2023-03-18 23:49:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-03-18 23:49:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-03-18 23:49:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2023-03-18 23:49:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:49:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:49:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:43] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2023-03-18 23:49:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2023-03-18 23:49:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2023-03-18 23:49:45] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2023-03-18 23:49:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:49:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:45] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2023-03-18 23:49:45] [SUCCESS] [OmnipathR] Downloaded 700257 annotation records. The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/liana/vignettes/liana_cc2tensor_files/figure-html/unnamed-chunk-16-1.svg" but not available. The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/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 [2023-03-18 23:49:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2023-03-18 23:49:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:53] [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` [2023-03-18 23:49:54] [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` [2023-03-18 23:49:54] [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` [2023-03-18 23:49:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:49:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:49:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:54] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `unknown` to `started`. [2023-03-18 23:49:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2023-03-18 23:49:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2023-03-18 23:49:54] [INFO] [OmnipathR] Download ready [key=69503cb1a01671e7c77c0e80e6ca0ce4110a89fe, version=1] [2023-03-18 23:49:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:49:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:54] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `started` to `ready`. [2023-03-18 23:49:55] [SUCCESS] [OmnipathR] Downloaded 4580 interactions. [2023-03-18 23:49:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2023-03-18 23:49:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:55] [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` [2023-03-18 23:49:55] [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` [2023-03-18 23:49:55] [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` [2023-03-18 23:49:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:49:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:49:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:55] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `unknown` to `started`. [2023-03-18 23:49:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2023-03-18 23:49:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2023-03-18 23:49:55] [INFO] [OmnipathR] Download ready [key=ec8c89037e2c920468342c7c2326c74a5474eedc, version=1] [2023-03-18 23:49:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:49:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:49:55] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `started` to `ready`. [2023-03-18 23:49:56] [SUCCESS] [OmnipathR] Downloaded 1475 interactions. 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 `mutate()`: ℹ In argument: `CellPhoneDB_type = map(CellPhoneDB_type, first) %>% null_to_na %>% unlist`. Caused by error in `map()`: ℹ In index: 6. Caused by error in `vec_init()`: ! `x` must be a vector, not `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 (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 [2023-03-18 23:51:13] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`. [2023-03-18 23:51:13] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data` [2023-03-18 23:51:13] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`. [2023-03-18 23:51:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:51:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:51:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:51:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:51:13] [INFO] [OmnipathR] Cache item `2ccc1998f0ab26ea421885e1334896d25db4554f` version 1: status changed from `unknown` to `started`. [2023-03-18 23:51:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2ccc1998f0ab26ea421885e1334896d25db4554f-1.rds`. [2023-03-18 23:51:13] [INFO] [OmnipathR] Retrieving URL: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data` [2023-03-18 23:51:13] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data` [2023-03-18 23:51:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2ccc1998f0ab26ea421885e1334896d25db4554f-1.rds`. [2023-03-18 23:51:21] [INFO] [OmnipathR] Download ready [key=2ccc1998f0ab26ea421885e1334896d25db4554f, version=1] [2023-03-18 23:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:51:21] [INFO] [OmnipathR] Cache item `2ccc1998f0ab26ea421885e1334896d25db4554f` version 1: status changed from `started` to `ready`. [2023-03-18 23:51:21] [SUCCESS] [OmnipathR] NCBI HomoloGene (ftp.ncbi.nih.gov): downloaded 275237 records [2023-03-18 23:51:21] [INFO] [OmnipathR] Loading database `Ensembl organism names`. [2023-03-18 23:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:51:21] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2023-03-18 23:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:51:21] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2023-03-18 23:51:21] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2023-03-18 23:51:21] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2023-03-18 23:51:21] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2023-03-18 23:51:22] [TRACE] [OmnipathR] HTTP 200 [2023-03-18 23:51:22] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2023-03-18 23:51:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-18 23:51:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-18 23:51:22] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2023-03-18 23:51:22] [INFO] [OmnipathR] Loaded database `Ensembl organism names`. [2023-03-18 23:51:23] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data`. [2023-03-18 23:51:23] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/2ccc1998f0ab26ea421885e1334896d25db4554f-1.rds`. [2023-03-18 23:51:23] [SUCCESS] [OmnipathR] NCBI HomoloGene (ftp.ncbi.nih.gov): loaded 275237 records from cache The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/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/RtmpuiZ0vv/Rbuild33f1d96871b043/liana/vignettes/liana_tutorial_files/figure-html/liana_dotplot-1.svg" but not available. The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/liana/vignettes/liana_tutorial_files/figure-html/heatfreq-1.svg" but not available. The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/liana/vignettes/liana_tutorial_files/figure-html/chordfreq-1.svg" but not available. The magick package is required to crop "/tmp/RtmpuiZ0vv/Rbuild33f1d96871b043/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_custom_op.Rmd’ ‘liana_nichenet.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2023-03-18 23:53:40 CET ]