[ Started: 2023-04-03 13:01:10 CEST ] [ OmnipathR v3.7.10 for BioC-3.17 from https://github.com/saezlab/OmnipathR@master ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘bioc_workshop.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2023-04-03 13:01:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-03 13:01:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:19] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-04-03 13:01:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-03 13:01:19] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-04-03 13:01:19] [TRACE] [OmnipathR] Contains 1 files. [2023-04-03 13:01:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-03 13:01:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-03 13:01:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-04-03 13:01:19] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-04-03 13:01:19] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpfaD8ZV/Rinst2b84bc261a3b24/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-03 13:01:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:19] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpfaD8ZV/Rinst2b84bc261a3b24/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-03 13:01:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:19] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpfaD8ZV/Rinst2b84bc261a3b24/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-03 13:01:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:19] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpfaD8ZV/Rinst2b84bc261a3b24/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-03 13:01:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:19] [TRACE] [OmnipathR] Cache locked: FALSE [2023-04-03 13:01:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-03 13:01:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-03 13:01:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-03 13:01:19] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: HTTP error 500. [2023-04-03 13:01:24] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-03 13:01:24] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: HTTP error 500. [2023-04-03 13:01:29] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-03 13:01:29] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 3/3); error: HTTP error 500. Quitting from lines 225-227 (bioc_workshop.Rmd) Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics: HTTP error 500. --- failed re-building ‘bioc_workshop.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2023-04-03 13:01:29] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2023-04-03 13:01:29] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE) [2023-04-03 13:01:29] [INFO] [OmnipathR] Loading database `Ensembl organism names`. [2023-04-03 13:01:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-03 13:01:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:29] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2023-04-03 13:01:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-03 13:01:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:29] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2023-04-03 13:01:29] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2023-04-03 13:01:29] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2023-04-03 13:01:29] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2023-04-03 13:01:30] [TRACE] [OmnipathR] HTTP 200 [2023-04-03 13:01:30] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2023-04-03 13:01:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-03 13:01:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:30] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2023-04-03 13:01:30] [INFO] [OmnipathR] Loaded database `Ensembl organism names`. [2023-04-03 13:01:30] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED) [2023-04-03 13:01:30] [TRACE] [OmnipathR] Looking up in cache: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`. [2023-04-03 13:01:30] [INFO] [OmnipathR] Cache record does not exist: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` [2023-04-03 13:01:30] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no`. [2023-04-03 13:01:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-03 13:01:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-03 13:01:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:30] [INFO] [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `unknown` to `started`. [2023-04-03 13:01:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`. [2023-04-03 13:01:30] [INFO] [OmnipathR] Retrieving URL: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` [2023-04-03 13:01:30] [TRACE] [OmnipathR] Attempt 1/3: `https://legacy.uniprot.org/uniprot/?query=*&format=tab&force=true&columns=id,genes(PREFERRED)&fil=organism:9606%20AND%20reviewed:yes&compress=no` [2023-04-03 13:01:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`. [2023-04-03 13:01:36] [INFO] [OmnipathR] Download ready [key=1ada9cda5e2120624b9e561db9e74f4ddcc5185b, version=1] [2023-04-03 13:01:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-03 13:01:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-03 13:01:36] [INFO] [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `started` to `ready`. [2023-04-03 13:01:36] [SUCCESS] [OmnipathR] UniProt (legacy.uniprot.org): downloaded 20404 records [2023-04-03 13:01:37] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2023-04-03 13:01:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-03 13:01:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-03 13:01:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-03 13:01:48] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 1/3); error: HTTP error 500. [2023-04-03 13:01:53] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-03 13:01:53] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 2/3); error: HTTP error 500. [2023-04-03 13:01:58] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-03 13:01:58] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 3/3); error: HTTP error 500. Quitting from lines 46-51 (drug_targets.Rmd) Error: processing vignette 'drug_targets.Rmd' failed with diagnostics: HTTP error 500. --- failed re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2023-04-03 13:01:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2023-04-03 13:01:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2023-04-03 13:01:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2023-04-03 13:01:58] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 1/3); error: HTTP error 500. [2023-04-03 13:02:03] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2023-04-03 13:02:03] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 2/3); error: HTTP error 500. [2023-04-03 13:02:08] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2023-04-03 13:02:09] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` (attempt 3/3); error: HTTP error 500. Quitting from lines 56-58 (extra_attrs.Rmd) Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics: HTTP error 500. --- failed re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown Quitting from lines 167-177 (omnipath_intro.Rmd) Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics: cannot open the connection to 'https://omnipathdb.org/resources' --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown Quitting from lines 56-67 (paths.Rmd) Error: processing vignette 'paths.Rmd' failed with diagnostics: cannot open the connection to 'https://omnipathdb.org/resources' --- failed re-building ‘paths.Rmd’ SUMMARY: processing the following files failed: ‘bioc_workshop.Rmd’ ‘drug_targets.Rmd’ ‘extra_attrs.Rmd’ ‘omnipath_intro.Rmd’ ‘paths.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2023-04-03 13:02:11 CEST ]