Etienne A. Thevenot
| Snapshot Date: 2026-03-13 13:40 -0400 (Fri, 13 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/phenomis |
| git_branch: devel |
| git_last_commit: 2244e33 |
| git_last_commit_date: 2025-10-29 11:18:33 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-14 11:34 -0400 (Sat, 14 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4837 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4050 |
| 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 1591/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| phenomis 1.13.0 (landing page) Etienne A. Thevenot
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for phenomis in R Universe. | ||||||||||||||
|
To the developers/maintainers of the phenomis package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/phenomis.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: phenomis |
| Version: 1.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data phenomis |
| StartedAt: 2026-03-13 16:39:25 -0400 (Fri, 13 Mar 2026) |
| EndedAt: 2026-03-13 16:39:59 -0400 (Fri, 13 Mar 2026) |
| EllapsedTime: 34.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data phenomis
###
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* checking for file ‘phenomis/DESCRIPTION’ ... OK
* preparing ‘phenomis’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘phenomis-vignette.Rmd’ using rmarkdown
2026-03-13 16:39:46.818 R[75371:148368353] XType: Using static font registry.
INFO [16:39:54.534] Loading definitions from package biodb version 1.19.0.
INFO [16:39:55.190] Loading definitions from package biodbChebi version 1.17.1.
INFO [16:39:55.697] Closing BiodbMain instance...
INFO [16:39:55.698] Connector "mass.csv.file" deleted.
Quitting from phenomis-vignette.Rmd:671-674 [cll_load]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `find.package()`:
! there is no package called 'CLL'
---
Backtrace:
▆
1. └─utils::data(sCLLex, package = "CLL")
2. └─base::find.package(package, lib.loc, verbose = verbose)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'phenomis-vignette.Rmd' failed with diagnostics:
there is no package called 'CLL'
--- failed re-building ‘phenomis-vignette.Rmd’
SUMMARY: processing the following file failed:
‘phenomis-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted