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This page was generated on 2025-11-06 12:00 -0500 (Thu, 06 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4902
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4638
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 999/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hmdbQuery 1.30.0  (landing page)
VJ Carey
Snapshot Date: 2025-11-05 13:45 -0500 (Wed, 05 Nov 2025)
git_url: https://git.bioconductor.org/packages/hmdbQuery
git_branch: RELEASE_3_22
git_last_commit: 7b7f897
git_last_commit_date: 2025-10-29 10:42:41 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  

BUILD results for hmdbQuery on nebbiolo2

To the developers/maintainers of the hmdbQuery package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hmdbQuery.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: hmdbQuery
Version: 1.30.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 hmdbQuery
StartedAt: 2025-11-05 18:17:46 -0500 (Wed, 05 Nov 2025)
EndedAt: 2025-11-05 18:18:07 -0500 (Wed, 05 Nov 2025)
EllapsedTime: 21.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 hmdbQuery
###
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* checking for file ‘hmdbQuery/DESCRIPTION’ ... OK
* preparing ‘hmdbQuery’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘hmdbQuery.Rmd’ using rmarkdown

Quitting from hmdbQuery.Rmd:37-41 [lk1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'http://www.hmdb.ca/metabolites/HMDB0000001.xml'
---
Backtrace:
    ▆
 1. └─hmdbQuery::HmdbEntry(...)
 2.   └─hmdbQuery:::hmxToList(prefix = prefix, id = id)
 3.     └─base::readLines(.hmxPath(prefix = prefix, id = id, ...))
 4.       └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'hmdbQuery.Rmd' failed with diagnostics:
cannot open the connection to 'http://www.hmdb.ca/metabolites/HMDB0000001.xml'
--- failed re-building ‘hmdbQuery.Rmd’

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

Error: Vignette re-building failed.
Execution halted