Build/check report for BioC 3.23 - BUILD results for crlmm on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4428
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BUILD results for crlmm on nebbiolo1

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

Version: 1.69.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data crlmm

StartedAt: 2025-10-30 16:41:57 -0400 (Thu, 30 Oct 2025)

EndedAt: 2025-10-30 16:42:48 -0400 (Thu, 30 Oct 2025)

EllapsedTime: 51.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data crlmm
###
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* checking for file ‘crlmm/DESCRIPTION’ ... OK
* preparing ‘crlmm’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘AffyGW.Rnw’ using Sweave
--- finished re-building ‘AffyGW.Rnw’

--- re-building ‘CopyNumberOverview.Rnw’ using Sweave
--- finished re-building ‘CopyNumberOverview.Rnw’

--- re-building ‘IlluminaPreprocessCN.Rnw’ using Sweave
--- finished re-building ‘IlluminaPreprocessCN.Rnw’

--- re-building ‘Infrastructure.Rnw’ using Sweave
--- finished re-building ‘Infrastructure.Rnw’

--- re-building ‘genotyping.Rnw’ using Sweave
Loading required package: oligoClasses
Welcome to oligoClasses version 1.73.0
Loading required package: preprocessCore
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
Welcome to crlmm version 1.69.0
/-------------------------------------------\
|         SAMPLE HAPMAP SNP 6.0             |
|-------------------------------------------|
| Data obtained from http://www.hapmap.org  |
| This package is meant to be used only for |
| demonstration of BioConductor packages.   |
| Access http://www.hapmap.org for details. |
|-------------------------------------------|
| The contents of this package are provided |
| in good faith and the maintainer does not |
| warrant their accuracy.                   |
\-------------------------------------------/
If genomewidesnp6Crlmm is installed on an alternativelocation, please load it manually by usinglibrary(genomewidesnp6Crlmm,lib.loc='/Altern/Lib/Loc')
Timing stopped at: 0.001 0.003 0.005

Error: processing vignette 'genotyping.Rnw' failed with diagnostics:
 chunk 2 (label = crlmm) 
Error in snprma(filenames, fitMixture = TRUE, mixtureSampleSize = mixtureSampleSize,  : 
  Package genomewidesnp6Crlmm could not be found.

--- failed re-building ‘genotyping.Rnw’

--- re-building ‘gtypeDownstream.Rnw’ using Sweave
--- finished re-building ‘gtypeDownstream.Rnw’

cp ../inst/scripts/AffyGW.pdf .
cp ../inst/scripts/IlluminaPreprocessCN.pdf .
cp ../inst/scripts/Infrastructure.pdf .
cp ../inst/scripts/gtypeDownstream.pdf .
cp ../inst/scripts/crlmmIllumina.pdf .
"/home/biocbuild/bbs-3.23-bioc/R/bin/R" CMD pdflatex genotyping.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./genotyping.tex
LaTeX2e <2023-11-01> patch level 1
L3 programming layer <2024-01-22>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2023/05/17 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/home/biocbuild/bbs-3.23-bioc/R/share/texmf/tex/latex/Sweave.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
No file genotyping.aux.
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/grfext/grfext.sty
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/base/t1cmss.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd))
Runaway argument?
! File ended while scanning use of \FancyVerbGetLine.
<inserted text> 
                \par 
<*> genotyping.tex
                  
? 
! Emergency stop.
<inserted text> 
                \par 
<*> genotyping.tex
                  
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on genotyping.log.
make: *** [Makefile:10: vignettes] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted