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@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@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the > employee or agent responsible for the delivery of this message to the > intended recipient(s), you are hereby notified that any disclosure, > copying, distribution, or use of this email message is > prohibited. If you have received this message in error, please > notify the sender immediately by e-mail and delete this email message > from your computer. Thank you. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
