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This page was generated on 2023-02-08 01:15:35 -0000 (Wed, 08 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4164
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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 2147/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.7.0  (landing page)
Ana Galhoz
Snapshot Date: 2023-02-06 00:12:45 -0000 (Mon, 06 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: 2023-02-06 16:25:43 -0000 (Mon, 06 Feb 2023)
EndedAt: 2023-02-06 16:26:24 -0000 (Mon, 06 Feb 2023)
EllapsedTime: 41.1 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
###
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* 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
[2023-02-06 16:26:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 16:26:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-06 16:26:01] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-06 16:26:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-02-06 16:26:01] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Contains 1 files.
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-06 16:26:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-02-06 16:26:02] [INFO]    [wppi] Executing WPPI workflow.
[2023-02-06 16:26:02] [INFO]    [wppi] Collecting database knowledge.
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-02-06 16:26:02] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-06 16:26:02] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2023-02-06 16:26:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-02-06 16:26:03] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-02-06 16:26:03] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-02-06 16:26:23] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-02-06 16:26:23] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2023-02-06 16:26:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-06 16:26:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-06 16:26:23] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
Quitting from lines 80-102 (wppi_workflow.Rmd) 
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
ℹ In argument: `across(everything(), na_if, "-")`.
Caused by error in `across()`:
! Can't compute column `entrez_gene_id`.
Caused by error in `fn()`:
! Can't convert `y` <character> to match type of `x` <double>.
--- failed re-building ‘wppi_workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted