Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-02 11:40 -0400 (Thu, 02 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4831 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4612 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4584 |
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 207/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biodbHmdb 1.14.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the biodbHmdb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbHmdb.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. |
Package: biodbHmdb |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbHmdb |
StartedAt: 2025-09-29 20:09:42 -0400 (Mon, 29 Sep 2025) |
EndedAt: 2025-09-29 20:10:24 -0400 (Mon, 29 Sep 2025) |
EllapsedTime: 42.4 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbHmdb ### ############################################################################## ############################################################################## * checking for file ‘biodbHmdb/DESCRIPTION’ ... OK * preparing ‘biodbHmdb’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘biodbHmdb.Rmd’ using rmarkdown INFO [20:10:21.156] Loading definitions from package biodb version 1.16.1. INFO [20:10:23.338] Loading definitions from package biodbChebi version 1.14.0. INFO [20:10:23.371] Loading definitions from package biodbHmdb version 1.14.0. INFO [20:10:23.405] Loading definitions from package biodbNcbi version 1.12.0. INFO [20:10:23.431] Loading definitions from package biodbNci version 1.12.0. INFO [20:10:23.440] Loading definitions from package biodbUniprot version 1.14.0. INFO [20:10:23.796] Downloading whole database of hmdb.metabolites. INFO [20:10:23.798] Downloading HMDB metabolite database at "/private/tmp/RtmpH59p3h/Rinst1189a23d90860/biodbHmdb/extdata/generated/hmdb_extract.zip" ... INFO [20:10:23.832] copy 1 files to /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34. INFO [20:10:23.835] Done importing files. INFO [20:10:23.838] Extract whole database of hmdb.metabolites. INFO [20:10:23.839] Extracting content of downloaded', ' HMDB metabolite database... Quitting from biodbHmdb.Rmd:76-78 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `private$doExtractDownload()`: ! attempt to apply non-function --- Backtrace: ▆ 1. └─conn$getNbEntries() 2. └─private$doGetNbEntries(count = count) 3. └─self$getEntryIds() 4. └─private$doGetEntryIds(max.results = max.results, ...) 5. └─self$download() 6. └─private$doExtractDownload() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'biodbHmdb.Rmd' failed with diagnostics: attempt to apply non-function --- failed re-building ‘biodbHmdb.Rmd’ SUMMARY: processing the following file failed: ‘biodbHmdb.Rmd’ Error: Vignette re-building failed. Execution halted