| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-26 06:18:06 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 450/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crlmm 1.59.0 (landing page) Benilton S Carvalho
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | |||||||||
| Package: crlmm |
| Version: 1.59.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data crlmm |
| StartedAt: 2023-05-25 21:37:02 -0000 (Thu, 25 May 2023) |
| EndedAt: 2023-05-25 21:38:13 -0000 (Thu, 25 May 2023) |
| EllapsedTime: 71.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R-4.3.0/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 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 1.63.0
Loading required package: preprocessCore
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
Welcome to crlmm version 1.59.0
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-4.3.0/bin/R" CMD pdflatex genotyping.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./genotyping.tex
LaTeX2e <2018-04-01> patch level 5
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/home/biocbuild/R/R-4.3.0/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
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)))
No file genotyping.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/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/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.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