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

Neumann, Steffen sneumann at ipb-halle.de
Wed Aug 16 00:06:08 CEST 2017


Indeed, is magically fixed today. 
Thanks for the clarification.
Yours,
Steffen

On Fri, 2017-08-11 at 11:38 -0400, Martin Morgan wrote:
> On 08/10/2017 04:14 PM, Neumann, Steffen wrote:
> > 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 ?
> 
> This generally looks like a transient problem we see, maybe related
> to 
> disk latency associated with large files (e.g., plots) produced
> during 
> the vignette processing, but we really don't have a clear handle on
> this.
> 
> Martin
> 
> > 
> > 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
> 
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-- 

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


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