Multiple platform build/check report for BioC 3.20 - BUILD results for crlmm on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4670
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4355
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4446
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4439
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4306
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 crlmm on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: crlmm

Version: 1.64.1

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

StartedAt: 2025-03-07 00:39:21 -0000 (Fri, 07 Mar 2025)

EndedAt: 2025-03-07 00:40:23 -0000 (Fri, 07 Mar 2025)

EllapsedTime: 62.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data crlmm
###
##############################################################################
##############################################################################


* checking for file ‘crlmm/DESCRIPTION’ ... OK
* preparing ‘crlmm’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package 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 1.68.0
Loading required package: preprocessCore
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
Welcome to crlmm version 1.64.1

Error: processing vignette 'genotyping.Rnw' failed with diagnostics:
 chunk 2 (label = crlmm) 
Error in library(hapmapsnp6) : there is no package called ‘hapmapsnp6’

--- 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/R/R-4.4.3/bin/R" CMD pdflatex genotyping.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./genotyping.tex
LaTeX2e <2020-10-01> patch level 4
L3 programming layer <2021-05-07>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2020/04/10 v1.4m Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/home/biocbuild/R/R-4.4.3/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/generic/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