Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2024-06-07 20:26 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 2135/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetSearch 2.6.0  (landing page)
Alvaro Cuadros-Inostroza
Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024)
git_url: https://git.bioconductor.org/packages/TargetSearch
git_branch: RELEASE_3_19
git_last_commit: dd7a8c0
git_last_commit_date: 2024-04-30 10:19:56 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for TargetSearch on palomino3

To the developers/maintainers of the TargetSearch package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TargetSearch.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: TargetSearch
Version: 2.6.0
Command: chmod a+r TargetSearch -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TargetSearch
StartedAt: 2024-06-05 23:26:34 -0400 (Wed, 05 Jun 2024)
EndedAt: 2024-06-05 23:28:02 -0400 (Wed, 05 Jun 2024)
EllapsedTime: 88.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r TargetSearch -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TargetSearch
###
##############################################################################
##############################################################################


* checking for file 'TargetSearch/DESCRIPTION' ... OK
* preparing 'TargetSearch':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'RICorrection.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 "RICorrection.tex" --max-iterations=20 -I "F:/biocbuild/bbs-3.19-bioc/R/share/texmf/tex/latex" -I "F:/biocbuild/bbs-3.19-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'RICorrection.Rnw' failed with diagnostics:
running 'texi2dvi' on 'RICorrection.tex' failed

LaTeX errors:
nettes/RICorrection.tex:111: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/RICorrection.tex:124: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/RICorrection.tex:144: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/RICorrection.tex:157: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/RICorrection.tex:189: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/RICorrection.tex:228: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/RICorrection.tex:249: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/RICorrection.tex:264: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/RICorrection.tex:293: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/RICorrection.tex:303: Package xcolor Error: Undefined color `fgcolor'.

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

--- failed re-building 'RICorrection.Rnw'

--- re-building 'TargetSearch.Rnw' using knitr
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
texify: major issue: User/administrator updates are out-of-sync.
Error: processing vignette 'TargetSearch.Rnw' failed with diagnostics:
running 'texi2dvi' on 'TargetSearch.tex' failed

LaTeX errors:
nettes/TargetSearch.tex:139: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:158: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:185: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:232: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:262: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:302: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:334: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:365: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:387: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:462: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:488: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:501: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:518: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:533: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:548: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:601: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:661: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:687: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:707: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:743: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:758: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:770: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
nettes/TargetSearch.tex:787: Package xcolor Error: Undefined color `fgcolor'.

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

--- failed re-building 'TargetSearch.Rnw'

SUMMARY: processing the following files failed:
  'RICorrection.Rnw' 'TargetSearch.Rnw'

Error: Vignette re-building failed.
In addition: Warning message:
In system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "TargetSearch.tex" --max-iterations=20 -I "F:/biocbuild/bbs-3.19-bioc/R/share/texmf/tex/latex" -I "F:/biocbuild/bbs-3.19-bioc/R/share/texmf/bibtex/bst"' had status 1
Execution halted