Multiple platform build/check report for BioC 3.19 - BUILD results for SCnorm on palomino3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4755
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4489
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4520
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (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*

BUILD results for SCnorm on palomino3

To the developers/maintainers of the SCnorm package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SCnorm.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: SCnorm

Version: 1.26.0

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

StartedAt: 2024-06-05 22:43:22 -0400 (Wed, 05 Jun 2024)

EndedAt: 2024-06-05 22:49:16 -0400 (Wed, 05 Jun 2024)

EllapsedTime: 354.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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


* checking for file 'SCnorm/DESCRIPTION' ... OK
* preparing 'SCnorm':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'SCnorm.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 in parse(text = code, keep.source = FALSE) : 
  <text>:12:19: unexpected symbol
11:                   PrintProgressPlots = TRUE
12:                   FilterCellNum
                      ^
Warning in highr::hilight(x, format, prompt = options$prompt, markup = opts$markup) :
  the syntax of the source code is invalid; the fallback mode is used
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 "SCnorm.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 'SCnorm.Rnw' failed with diagnostics:
running 'texi2dvi' on 'SCnorm.tex' failed

LaTeX errors:
s/SCnorm.tex:82: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:101: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:115: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:136: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:163: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:172: Package xcolor Error: Undefined color `fgcolor'.

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

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:224: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:279: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:355: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:418: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:432: Package xcolor Error: Undefined color `fgcolor'.

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

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:510: Package xcolor Error: Undefined color `fgcolor'.

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

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:554: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:605: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:630: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:664: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:695: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:725: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:745: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:849: Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
s/SCnorm.tex:890: Package xcolor Error: Undefined color `fgcolor'.

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

--- failed re-building 'SCnorm.Rnw'

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

Error: Vignette re-building failed.
Execution halted