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This page was generated on 2024-06-07 20:25 -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 413/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.36.0  (landing page)
Tiphaine Martin
Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024)
git_url: https://git.bioconductor.org/packages/coMET
git_branch: RELEASE_3_19
git_last_commit: 6d5fd0d
git_last_commit_date: 2024-04-30 11:45:58 -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 coMET on palomino3

To the developers/maintainers of the coMET package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/coMET.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: coMET
Version: 1.36.0
Command: chmod a+r coMET -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data coMET
StartedAt: 2024-06-05 18:16:41 -0400 (Wed, 05 Jun 2024)
EndedAt: 2024-06-05 18:19:53 -0400 (Wed, 05 Jun 2024)
EllapsedTime: 191.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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


* checking for file 'coMET/DESCRIPTION' ... OK
* preparing 'coMET':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'coMET.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.
!!! 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.
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
!!! 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.
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family '1' not found, will use 'sans' instead
!!! 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.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "coMET.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 'coMET.Rnw' failed with diagnostics:
running 'texi2dvi' on 'coMET.tex' failed

LaTeX errors:
coMET.tex:80: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:129: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:141: Package xcolor Error: Undefined color `fgcolor'.

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

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:212: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:225: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:238: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:274: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:299: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:363: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:430: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:487: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:503: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:583: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:627: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:647: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:696: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:713: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:749: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:767: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:802: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:830: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:917: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:936: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1162: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1198: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1220: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1241: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1256: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1279: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1309: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1342: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1362: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1386: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1398: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1433: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1468: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1507: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.tex:1561: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
coMET.te
--- failed re-building 'coMET.Rnw'

SUMMARY: processing the following file failed:
  'coMET.Rnw'

Error: Vignette re-building failed.
Execution halted