[Bioc-devel] Vignette for xcms fails to build on tokay1

[Neumann, Steffen]

Hi, 

Hi,

any suggestions or better diagnostics that could help us 
fixing this, in case it really is something in xcms ? 

There were a few earlier reports with similar messages, 

back in 2013, slightly hinting at virus scanners: 
http://r.789695.n4.nabble.com/quot-Failed-to-locate-the-texi2pdf-output-file-quot-td4664111.html

Back in 2015, but both referring to SPB:
https://github.com/Bioconductor/packagebuilder/issues/2
https://github.com/Bioconductor/packagebuilder/issues/26

And from 2016 without any resolution:
https://github.com/r-hub/rhub/issues/58

Yours,
Steffen



On Thu, 2017-07-27 at 10:23 +0000, Rainer Johannes wrote:
> Dear all,
> 
> one of the xcms vignettes fails to build on tokay1 recently with the
> error message:
> 
> Warning: running command
> '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf
> "xcmsDirect.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-3.6-
> bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.6-
> bioc/R/share/texmf/bibtex/bst"' had status 1
> Error in find_vignette_product(name, by = "texi2pdf", engine =
> engine) :
>   Failed to locate the 'texi2pdf' output file (by engine
> 'utils::Sweave') for vignette with name 'xcmsDirect'. The following
> files exist in directory '.': 'FlowChart.graffle', 'FlowChart.pdf',
> 'benchmarking.Rmd-notrun', 'biomed-central.csl', 'example.tsv',
> 'new_functionality.R', 'new_functionality.Rmd',
> 'new_functionality.html', 'new_functionality.org', 'references.bib',
> 'xcms.bib', 'xcms.org<http://xcms.org>', 'xcmsDirect-005.pdf',
> 'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw', 'xcmsMSn.Rnw',
> 'xcmsPreprocess.Rnw-notrun'
> Calls: <Anonymous> -> find_vignette_product
> Execution halted
> 
> is this some problem with tokay1 or is it related to the vignette (I
> have no problems building this vignette in my Windows build machine)?
> 
> thanks, jo
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 

IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
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                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409