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This page was generated on 2023-02-27 02:34:45 -0000 (Mon, 27 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4259
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BUILD results for wppi on kunpeng1


To the developers/maintainers of the wppi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wppi.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
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raw results

Package 2152/2169HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.7.0  (landing page)
Ana Galhoz
Snapshot Date: 2023-02-23 09:40:21 -0000 (Thu, 23 Feb 2023)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: master
git_last_commit: c0740ca
git_last_commit_date: 2022-11-01 15:24:35 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    ERROR  skipped

Summary

Package: wppi
Version: 1.7.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data wppi
StartedAt: 2023-02-24 04:41:44 -0000 (Fri, 24 Feb 2023)
EndedAt: 2023-02-24 04:42:48 -0000 (Fri, 24 Feb 2023)
EllapsedTime: 64.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data wppi
###
##############################################################################
##############################################################################


* checking for file ‘wppi/DESCRIPTION’ ... OK
* preparing ‘wppi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:41:59] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Contains 1 files.
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:41:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:41:59] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-02-24 04:42:00] [INFO]    [wppi] Executing WPPI workflow.
[2023-02-24 04:42:00] [INFO]    [wppi] Collecting database knowledge.
[2023-02-24 04:42:00] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-02-24 04:42:00] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-02-24 04:42:00] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-02-24 04:42:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 04:42:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:42:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 04:42:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:42:00] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2023-02-24 04:42:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-02-24 04:42:00] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-02-24 04:42:00] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-02-24 04:42:18] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-02-24 04:42:18] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2023-02-24 04:42:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 04:42:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:42:18] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2023-02-24 04:42:19] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 268983 records
[2023-02-24 04:42:19] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2023-02-24 04:42:19] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2023-02-24 04:42:19] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2023-02-24 04:42:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 04:42:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:42:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 04:42:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:42:19] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2023-02-24 04:42:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2023-02-24 04:42:19] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2023-02-24 04:42:19] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2023-02-24 04:42:33] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2023-02-24 04:42:33] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2023-02-24 04:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 04:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-24 04:42:33] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2023-02-24 04:42:35] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 626136 records
[2023-02-24 04:42:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-02-24 04:42:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-02-24 04:42:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-02-24 04:42:36] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-02-24 04:42:41] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-02-24 04:42:41] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-02-24 04:42:46] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2023-02-24 04:42:47] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 3/3); error: HTTP error 500.
Quitting from lines 80-102 (wppi_workflow.Rmd) 
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘wppi_workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘wppi_workflow.Rmd’

Error: Vignette re-building failed.
Execution halted