[ Started: 2023-04-25 01:05:05 CEST ] [ OmnipathR v3.6.6 for BioC-3.16 from https://github.com/saezlab/OmnipathR@RELEASE_3_16 ] * 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 [2023-04-25 01:05:14] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-04-25 01:05:14] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-25 01:05:14] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-04-25 01:05:14] [TRACE] [OmnipathR] Contains 1 files. [2023-04-25 01:05:14] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-25 01:05:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-04-25 01:05:14] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-04-25 01:05:14] [TRACE] [OmnipathR] Cache locked: FALSE [2023-04-25 01:05:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:05:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:05:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:05:14] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: HTTP error 500. [2023-04-25 01:05:19] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:05:19] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: HTTP error 500. [2023-04-25 01:05:24] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:05:25] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&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 [2023-04-25 01:05:25] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2023-04-25 01:05:25] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `genes(PREFERRED)`, for organism 9606 (only reviewed: TRUE) [2023-04-25 01:05:25] [INFO] [OmnipathR] Loading database `Ensembl organism names`. [2023-04-25 01:05:25] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2023-04-25 01:05:25] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2023-04-25 01:05:25] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2023-04-25 01:05:25] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2023-04-25 01:05:25] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2023-04-25 01:05:25] [TRACE] [OmnipathR] HTTP 200 [2023-04-25 01:05:25] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2023-04-25 01:05:25] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. Warning in length(row) : closing unused connection 5 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic) Warning in length(row) : closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic) [2023-04-25 01:05:25] [INFO] [OmnipathR] Loaded database `Ensembl organism names`. [2023-04-25 01:05:25] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,genes(PREFERRED) [2023-04-25 01:05:25] [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`. [2023-04-25 01:05:25] [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` [2023-04-25 01:05:25] [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`. [2023-04-25 01:05:25] [INFO] [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `unknown` to `started`. [2023-04-25 01:05:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`. [2023-04-25 01:05:25] [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` [2023-04-25 01:05:25] [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` [2023-04-25 01:05:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ada9cda5e2120624b9e561db9e74f4ddcc5185b-1.rds`. [2023-04-25 01:05:32] [INFO] [OmnipathR] Download ready [key=1ada9cda5e2120624b9e561db9e74f4ddcc5185b, version=1] [2023-04-25 01:05:32] [INFO] [OmnipathR] Cache item `1ada9cda5e2120624b9e561db9e74f4ddcc5185b` version 1: status changed from `started` to `ready`. [2023-04-25 01:05:32] [SUCCESS] [OmnipathR] UniProt (legacy.uniprot.org): downloaded 20404 records [2023-04-25 01:05:32] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2023-04-25 01:05:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:05:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:05:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:05:44] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2023-04-25 01:05:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2023-04-25 01:05:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2023-04-25 01:05:44] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2023-04-25 01:05:44] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. Warning: closing unused connection 6 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic) [2023-04-25 01:05:47] [SUCCESS] [OmnipathR] Downloaded 92262 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2023-04-25 01:05:51] [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` [2023-04-25 01:05:51] [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` [2023-04-25 01:05:51] [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` [2023-04-25 01:05:51] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2023-04-25 01:05:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2023-04-25 01:05:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2023-04-25 01:05:52] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2023-04-25 01:05:52] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2023-04-25 01:06:01] [SUCCESS] [OmnipathR] Downloaded 134592 interactions. [2023-04-25 01:09:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2023-04-25 01:09:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2023-04-25 01:09:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2023-04-25 01:09:32] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2023-04-25 01:09:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2023-04-25 01:09:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2023-04-25 01:09:32] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2023-04-25 01:09:32] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2023-04-25 01:09:32] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records. [2023-04-25 01:09:33] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2023-04-25 01:09:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2023-04-25 01:09:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2023-04-25 01:09:33] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2023-04-25 01:09:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2023-04-25 01:09:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2023-04-25 01:09:33] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2023-04-25 01:09:33] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2023-04-25 01:09:33] [SUCCESS] [OmnipathR] Downloaded 70 enzyme-substrate relationships. --- finished re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2023-04-25 01:09:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:36] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2023-04-25 01:09:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2023-04-25 01:09:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2023-04-25 01:09:37] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2023-04-25 01:09:37] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2023-04-25 01:09:39] [SUCCESS] [OmnipathR] Downloaded 64574 interactions. [2023-04-25 01:09:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:44] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`. [2023-04-25 01:09:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`. [2023-04-25 01:09:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`. [2023-04-25 01:09:44] [INFO] [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1] [2023-04-25 01:09:44] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`. [2023-04-25 01:09:44] [SUCCESS] [OmnipathR] Downloaded 1526 interactions. [2023-04-25 01:09:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:45] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2023-04-25 01:09:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2023-04-25 01:09:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2023-04-25 01:09:45] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2023-04-25 01:09:45] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2023-04-25 01:09:45] [SUCCESS] [OmnipathR] Downloaded 6880 interactions. [2023-04-25 01:09:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-04-25 01:09:45] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2023-04-25 01:09:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2023-04-25 01:09:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2023-04-25 01:09:45] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2023-04-25 01:09:45] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2023-04-25 01:09:46] [SUCCESS] [OmnipathR] Downloaded 3008 interactions. [2023-04-25 01:09:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:09:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:09:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:09:46] [INFO] [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `unknown` to `started`. [2023-04-25 01:09:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`. [2023-04-25 01:09:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cde98994cdbb4dd0e43d69b43a01b3491332287d-1.rds`. [2023-04-25 01:09:46] [INFO] [OmnipathR] Download ready [key=cde98994cdbb4dd0e43d69b43a01b3491332287d, version=1] [2023-04-25 01:09:46] [INFO] [OmnipathR] Cache item `cde98994cdbb4dd0e43d69b43a01b3491332287d` version 1: status changed from `started` to `ready`. [2023-04-25 01:09:47] [SUCCESS] [OmnipathR] Downloaded 6127 interactions. [2023-04-25 01:09:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:09:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:09:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:09:47] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: HTTP error 500. [2023-04-25 01:09:52] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:09:52] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: HTTP error 500. [2023-04-25 01:09:57] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-04-25 01:09:57] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,DoRothEA&datasets=dorothea,tf_target&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 339-359 (omnipath_intro.Rmd) Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics: HTTP error 500. --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2023-04-25 01:09:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2023-04-25 01:09:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2023-04-25 01:09:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2023-04-25 01:09:58] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2023-04-25 01:09:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2023-04-25 01:09:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2023-04-25 01:09:58] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2023-04-25 01:09:58] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2023-04-25 01:09:58] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2023-04-25 01:09:58] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2023-04-25 01:09:58] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2023-04-25 01:09:58] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2023-04-25 01:09:58] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2023-04-25 01:09:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2023-04-25 01:09:58] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2023-04-25 01:09:58] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2023-04-25 01:09:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2023-04-25 01:09:58] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2023-04-25 01:09:58] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2023-04-25 01:09:58] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2023-04-25 01:09:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2023-04-25 01:09:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2023-04-25 01:09:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2023-04-25 01:09:58] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` (attempt 1/3); error: HTTP error 500. [2023-04-25 01:10:03] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2023-04-25 01:10:03] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` (attempt 2/3); error: HTTP error 500. [2023-04-25 01:10:08] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2023-04-25 01:10:09] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` (attempt 3/3); error: HTTP error 500. Quitting from lines 88-97 (paths.Rmd) Error: processing vignette 'paths.Rmd' failed with diagnostics: HTTP error 500. --- failed re-building ‘paths.Rmd’ SUMMARY: processing the following files failed: ‘bioc_workshop.Rmd’ ‘omnipath_intro.Rmd’ ‘paths.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2023-04-25 01:10:09 CEST ]