| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 72/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AnnotationForge 1.46.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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: 1.46.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data AnnotationForge |
| StartedAt: 2024-06-09 18:01:33 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 18:05:37 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 243.6 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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘makeProbePackage.Rmd’ using rmarkdown
See
‘/private/tmp/RtmpTCwKip/hgu95av2probe.Rcheck/00check.log’
for details.
Warning in gsub(r2, "\\1\\3", x[i]) :
closing unused connection 4 (/private/tmp/Rtmpl7Wu2z/Rinst110382df8fa3a/AnnotationForge/extdata/HG-U95Av2_probe_tab.gz)
--- finished re-building ‘makeProbePackage.Rmd’
--- re-building ‘MakingNewAnnotationPackages.Rnw’ using knitr
trying URL 'http://rest.uniprot.org/uniprotkb/search?query=P13368%20OR%20Q6GZX4&format=xml'
Content type 'application/xml' length 45246 bytes (44 KB)
==================================================
downloaded 44 KB
Error: processing vignette 'MakingNewAnnotationPackages.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'MakingNewAnnotationPackages.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `fgcolor'.
See the xcolor package documentation for explanation.
Type H <return> for immediate help.
...
! Emergency stop.
...
l.78 ...}{rgb}{0.941, 0.941, 0.941}\color{fgcolor}
\begin{kframe}
! ==> Fatal error occurred, no output PDF file produced!
--- 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
Error: processing vignette 'SQLForge.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SQLForge.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `fgcolor'.
See the xcolor package documentation for explanation.
Type H <return> for immediate help.
...
! Emergency stop.
...
l.67 ...}{rgb}{0.941, 0.941, 0.941}\color{fgcolor}
\begin{kframe}
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SQLForge.Rnw’
SUMMARY: processing the following files failed:
‘MakingNewAnnotationPackages.Rnw’ ‘SQLForge.Rnw’
Error: Vignette re-building failed.
Execution halted