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
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