[ Started: 2023-12-24 12:01:22 CET ] [ decoupleR v2.6.0 for BioC-3.17 from https://github.com/saezlab/decoupleR@RELEASE_3_17 ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘decoupleR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘decoupleR.Rmd’ using rmarkdown The magick package is required to crop "/tmp/Rtmp2P54jm/Rbuild2e5f77722a26e1/decoupleR/vignettes/decoupleR_files/figure-html/show_matrix-1.png" but not available. The magick package is required to crop "/tmp/Rtmp2P54jm/Rbuild2e5f77722a26e1/decoupleR/vignettes/decoupleR_files/figure-html/res_gsea-1.png" but not available. The magick package is required to crop "/tmp/Rtmp2P54jm/Rbuild2e5f77722a26e1/decoupleR/vignettes/decoupleR_files/figure-html/res_ulm-1.png" but not available. The magick package is required to crop "/tmp/Rtmp2P54jm/Rbuild2e5f77722a26e1/decoupleR/vignettes/decoupleR_files/figure-html/res_decouple-1.png" but not available. --- finished re-building ‘decoupleR.Rmd’ --- re-building ‘pw_bk.Rmd’ using rmarkdown [2023-12-24 12:01:38] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2023-12-24 12:01:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-12-24 12:01:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:38] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-12-24 12:01:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-12-24 12:01:38] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-12-24 12:01:38] [TRACE] [OmnipathR] Contains 1 files. [2023-12-24 12:01:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-12-24 12:01:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-12-24 12:01:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-12-24 12:01:38] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-12-24 12:01:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-12-24 12:01:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-12-24 12:01:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-12-24 12:01:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-12-24 12:01:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:39] [TRACE] [OmnipathR] Cache locked: FALSE Quitting from lines 101-103 [progeny] (pw_bk.Rmd) Error: processing vignette 'pw_bk.Rmd' failed with diagnostics: cannot open the connection to 'https://omnipathdb.org/resources' --- failed re-building ‘pw_bk.Rmd’ --- re-building ‘pw_sc.Rmd’ using rmarkdown The magick package is required to crop "/tmp/Rtmp2P54jm/Rbuild2e5f77722a26e1/decoupleR/vignettes/pw_sc_files/figure-html/umap-1.png" but not available. Quitting from lines 78-80 [progeny] (pw_sc.Rmd) Error: processing vignette 'pw_sc.Rmd' failed with diagnostics: cannot open the connection to 'https://omnipathdb.org/resources' --- failed re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2023-12-24 12:01:42] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2023-12-24 12:01:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-12-24 12:01:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:42] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2023-12-24 12:01:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-12-24 12:01:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:42] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2023-12-24 12:01:42] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2023-12-24 12:01:42] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2023-12-24 12:01:42] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2023-12-24 12:01:42] [TRACE] [OmnipathR] HTTP 200 [2023-12-24 12:01:42] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2023-12-24 12:01:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-12-24 12:01:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:42] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2023-12-24 12:01:43] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2023-12-24 12:01:43] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2023-12-24 12:01:43] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2023-12-24 12:01:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-12-24 12:01:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-12-24 12:01:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:43] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2023-12-24 12:01:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2023-12-24 12:01:43] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2023-12-24 12:01:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2023-12-24 12:01:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2023-12-24 12:01:43] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2023-12-24 12:01:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-12-24 12:01:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-12-24 12:01:43] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2023-12-24 12:01:43] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2023-12-24 12:01:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:43] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:43] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:43] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 1/3); error: HTTP error 500. [2023-12-24 12:01:48] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:48] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 2/3); error: HTTP error 500. [2023-12-24 12:01:53] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:53] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 3/3); error: HTTP error 500. [2023-12-24 12:01:53] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`; error: HTTP error 500. [2023-12-24 12:01:53] [TRACE] [OmnipathR] Attempting `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:53] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:53] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:53] [WARN] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 1/3); error: HTTP error 500. [2023-12-24 12:01:59] [TRACE] [OmnipathR] Attempt 2/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:01:59] [WARN] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 2/3); error: HTTP error 500. [2023-12-24 12:02:04] [TRACE] [OmnipathR] Attempt 3/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:04] [ERROR] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 3/3); error: HTTP error 500. [2023-12-24 12:02:04] [WARN] [OmnipathR] Failed to download: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`; error: HTTP error 500. [2023-12-24 12:02:04] [ERROR] [OmnipathR] `only_from` can be called only on data frames with `evidences` column. Quitting from lines 109-111 [collectri] (tf_bk.Rmd) Error: processing vignette 'tf_bk.Rmd' failed with diagnostics: `only_from` can be called only on data frames with `evidences` column. --- failed re-building ‘tf_bk.Rmd’ --- re-building ‘tf_sc.Rmd’ using rmarkdown The magick package is required to crop "/tmp/Rtmp2P54jm/Rbuild2e5f77722a26e1/decoupleR/vignettes/tf_sc_files/figure-html/umap-1.png" but not available. [2023-12-24 12:02:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:04] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 1/3); error: HTTP error 500. [2023-12-24 12:02:09] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:09] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 2/3); error: HTTP error 500. [2023-12-24 12:02:14] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:15] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 3/3); error: HTTP error 500. [2023-12-24 12:02:15] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`; error: HTTP error 500. [2023-12-24 12:02:15] [TRACE] [OmnipathR] Attempting `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:15] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:15] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:15] [WARN] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 1/3); error: HTTP error 500. [2023-12-24 12:02:20] [TRACE] [OmnipathR] Attempt 2/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:20] [WARN] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 2/3); error: HTTP error 500. [2023-12-24 12:02:25] [TRACE] [OmnipathR] Attempt 3/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-12-24 12:02:25] [ERROR] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 3/3); error: HTTP error 500. [2023-12-24 12:02:25] [WARN] [OmnipathR] Failed to download: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`; error: HTTP error 500. [2023-12-24 12:02:25] [ERROR] [OmnipathR] `only_from` can be called only on data frames with `evidences` column. Quitting from lines 86-88 [collectri] (tf_sc.Rmd) Error: processing vignette 'tf_sc.Rmd' failed with diagnostics: `only_from` can be called only on data frames with `evidences` column. --- failed re-building ‘tf_sc.Rmd’ SUMMARY: processing the following files failed: ‘pw_bk.Rmd’ ‘pw_sc.Rmd’ ‘tf_bk.Rmd’ ‘tf_sc.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2023-12-24 12:02:25 CET ]