| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-03-11 11:33 -0400 (Wed, 11 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" | 4719 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 2847 |
| 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 78/2360 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AnnotationForge 1.53.0 (landing page) Bioconductor Package Maintainer
| 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 AnnotationForge in R Universe. | ||||||||||||||
|
To the developers/maintainers of the AnnotationForge package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnnotationForge.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: AnnotationForge |
| Version: 1.53.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data AnnotationForge |
| StartedAt: 2026-03-10 15:17:06 -0400 (Tue, 10 Mar 2026) |
| EndedAt: 2026-03-10 15:17:22 -0400 (Tue, 10 Mar 2026) |
| EllapsedTime: 16.2 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 AnnotationForge
###
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* checking for file ‘AnnotationForge/DESCRIPTION’ ... OK
* preparing ‘AnnotationForge’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘makeProbePackage.Rmd’ using rmarkdown
Quitting from makeProbePackage.Rmd:38-51 [makeprobepackage]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'affy'
---
Backtrace:
▆
1. └─AnnotationForge::makeProbePackage(...)
2. ├─BiocGenerics::do.call(...)
3. ├─base::do.call(...)
4. └─AnnotationForge::getProbeDataAffy(arraytype = "HG-U95Av2", datafile = `<gzfile>`)
5. └─base::loadNamespace("affy")
6. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
7. └─base (local) withOneRestart(expr, restarts[[1L]])
8. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'makeProbePackage.Rmd' failed with diagnostics:
there is no package called 'affy'
--- failed re-building ‘makeProbePackage.Rmd’
--- re-building ‘MakingNewAnnotationPackages.Rnw’ using knitr
Quitting from MakingNewAnnotationPackages.Rnw:53-57 [Homo.sapiens]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'Homo.sapiens'
---
Backtrace:
x
1. \-base::library(Homo.sapiens)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MakingNewAnnotationPackages.Rnw' failed with diagnostics:
there is no package called 'Homo.sapiens'
--- failed re-building ‘MakingNewAnnotationPackages.Rnw’
--- re-building ‘MakingNewOrganismPackages.Rmd’ using knitr
--- finished re-building ‘MakingNewOrganismPackages.Rmd’
--- re-building ‘SQLForge.Rnw’ using knitr
Warning: call dbDisconnect() when finished working with a connection
Warning in for (Cl in classes) if (is(object, Cl)) return(object) :
closing unused connection 4 (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp6ws26k/Rinst8d9a5763945b/AnnotationForge/extdata/HG-U95Av2_probe_tab.gz)
--- finished re-building ‘SQLForge.Rnw’
SUMMARY: processing the following files failed:
‘makeProbePackage.Rmd’ ‘MakingNewAnnotationPackages.Rnw’
Error: Vignette re-building failed.
Execution halted