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

[Martin Morgan]

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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