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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 72/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationForge 1.47.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/AnnotationForge
git_branch: devel
git_last_commit: 007e1ad
git_last_commit_date: 2024-05-20 11:25:03 -0400 (Mon, 20 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for AnnotationForge on palomino4

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.

raw results


Summary

Package: AnnotationForge
Version: 1.47.1
Command: chmod a+r AnnotationForge -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data AnnotationForge
StartedAt: 2024-06-09 17:12:01 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 17:16:34 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 273.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r AnnotationForge -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data AnnotationForge
###
##############################################################################
##############################################################################


* 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
  'F:/biocbuild/bbs-3.20-bioc/tmpdir/RtmpKW3c91/hgu95av2probe.Rcheck/00check.log'
for details.

The filename, directory name, or volume label syntax is incorrect.
Warning: closing unused connection 4 (F:/biocbuild/bbs-3.20-bioc/tmpdir/RtmpMJxYhp/Rinst3ebc425a6dac/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

texify: major issue: User/administrator updates are out-of-sync.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "MakingNewAnnotationPackages.tex" --max-iterations=20 -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/tex/latex" -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'MakingNewAnnotationPackages.Rnw' failed with diagnostics:
running 'texi2dvi' on 'MakingNewAnnotationPackages.tex' failed

LaTeX errors:
/vignettes/MakingNewAnnotationPackages.tex:78: Package xcolor Error: Undefined 
color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:126: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:148: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:163: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:300: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:339: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
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/vignettes/MakingNewAnnotationPackages.tex:390: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:413: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:459: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
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/vignettes/MakingNewAnnotationPackages.tex:471: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:485: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:506: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:531: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:552: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:573: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:593: Package xcolor Error: Undefined
 color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:632: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:644: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:658: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:689: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:707: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:735: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:752: Package xcolor Error: Undefined
 color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:772: Package xcolor Error: Undefined
 color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:786: Package xcolor Error: Undefined
 color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:810: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:832: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:959: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:972: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:990: Package xcolor Error: Undefined
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See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1015: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1039: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1095: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1107: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1151: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1189: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1242: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1282: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1300: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1319: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1332: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1346: Package xcolor Error: Undefine
d color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
/vignettes/MakingNewAnnotationPackages.tex:1375: Package xcolor Error: Undefine
--- failed re-building 'MakingNewAnnotationPackages.Rnw'

--- re-building 'MakingNewOrganismPackages.Rmd' using knitr
--- finished re-building 'MakingNewOrganismPackages.Rmd'

--- re-building 'SQLForge.Rnw' using knitr
texify: major issue: User/administrator updates are out-of-sync.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "SQLForge.tex" --max-iterations=20 -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/tex/latex" -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'SQLForge.Rnw' failed with diagnostics:
running 'texi2dvi' on 'SQLForge.tex' failed

LaTeX errors:
/vignettes/SQLForge.tex:67: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
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/vignettes/SQLForge.tex:151: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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/vignettes/SQLForge.tex:173: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
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/vignettes/SQLForge.tex:182: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
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/vignettes/SQLForge.tex:203: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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/vignettes/SQLForge.tex:228: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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/vignettes/SQLForge.tex:252: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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/vignettes/SQLForge.tex:332: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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/vignettes/SQLForge.tex:357: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
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/vignettes/SQLForge.tex:402: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
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/vignettes/SQLForge.tex:456: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              

--- failed re-building 'SQLForge.Rnw'

SUMMARY: processing the following files failed:
  'MakingNewAnnotationPackages.Rnw' 'SQLForge.Rnw'

Error: Vignette re-building failed.
Execution halted