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

[Neumann, Steffen]

Hi BioC, 

since that build error we have updated xcms to 2.99.6,
and have started to convert the xcmsDirect vignette to Rmd.
Now, we have the same kind of build error on the xcmsMsn vignette,
http://bioconductor.org/checkResults/devel/bioc-LATEST/xcms/tokay1-buildsrc.html

I think that just converting the vignettes will fix the symptoms, 
but we should really fix the cause of the error, for that 
we need some more diagnostics, we weren't yet able to reproduce.

Any ideas ?

Yours,
Steffen


On Sun, 2017-07-30 at 19:42 +0000, Neumann, Steffen wrote:
> 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-outp
> ut-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]]
> > 
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> -- 
> 
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- 

IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409