| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-11-20 12:03 -0500 (Thu, 20 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 213/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the biodbNci package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbNci.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: biodbNci |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 biodbNci |
| StartedAt: 2025-11-17 19:46:26 -0500 (Mon, 17 Nov 2025) |
| EndedAt: 2025-11-17 19:47:00 -0500 (Mon, 17 Nov 2025) |
| EllapsedTime: 33.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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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 biodbNci
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* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* preparing ‘biodbNci’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodbNci.Rmd’ using rmarkdown
INFO [19:46:57.857] Loading definitions from package biodb version 1.18.0.
INFO [19:46:59.275] Loading definitions from package biodbChebi version 1.16.0.
INFO [19:46:59.307] Loading definitions from package biodbHmdb version 1.16.0.
INFO [19:46:59.337] Loading definitions from package biodbNcbi version 1.14.0.
INFO [19:46:59.361] Loading definitions from package biodbNci version 1.14.0.
INFO [19:46:59.368] Loading definitions from package biodbUniprot version 1.16.0.
INFO [19:46:59.508] Create cache folder "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427".
INFO [19:46:59.509] Downloading whole database of nci.cactus.
INFO [19:46:59.511] Downloading NCI CACTUS database at "/tmp/RtmpIeS9Bc/Rinst1b000f5bd1d899/biodbNci/extdata/generated/cactus_extract.txt.gz" ...
INFO [19:46:59.540] copy 1 files to /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427.
INFO [19:46:59.541] Done importing files.
INFO [19:46:59.544] Extract whole database of nci.cactus.
INFO [19:46:59.545] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Quitting from biodbNci.Rmd:72-75 [unnamed-chunk-5]
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<error/rlang_error>
Error in `private$doExtractDownload()`:
! attempt to apply non-function
---
Backtrace:
▆
1. └─conn$getEntryIds(2)
2. └─private$doGetEntryIds(max.results = max.results, ...)
3. └─self$download()
4. └─private$doExtractDownload()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'biodbNci.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘biodbNci.Rmd’
SUMMARY: processing the following file failed:
‘biodbNci.Rmd’
Error: Vignette re-building failed.
Execution halted