[Bioc-devel] build error only occurs in window system

Hervé Pagès hpages at fredhutch.org
Thu Jul 7 22:29:31 CEST 2016

Hi Julie,

On 07/07/2016 12:36 PM, Zhu, Lihua (Julie) wrote:
> Thanks Dan! I did came across a similar post a few years ago regarding its non-reproducibility  http://r.789695.n4.nabble.com/quot-Failed-to-locate-the-texi2pdf-output-file-quot-td4664111.html
> In this case, is it possible not to show build error on the main page of the package http://bioconductor.org/packages/release/bioc/html/GUIDEseq.html? I am afraid that reviewers will most likely think that the software is not working.

It's a little bit complicated for us to put something like this in
place. Our efforts should rather be on troubleshooting and addressing
the issue, which, unfortunately, we've not managed to do so far.
Hopefully things will improve in general on the Windows build machines
when we replace the current moscatos with new hardware that run Windows
Server 2012 (not sure about this particular issue though).

In the meantime, you could temporarily mark GUIDEseq as unsupported on
Windows by adding a .BBSoptions file in the top-level folder with the
following line in it:

UnsupportedPlatforms: win

Once the review process is over, just remove that file.


> Best,
> Julie
> From: Dan Tenenbaum <dtenenba at fredhutch.org<mailto:dtenenba at fredhutch.org>>
> Date: Thursday, July 7, 2016 3:15 PM
> To: Jianhong Ou <jianhong.ou at umassmed.edu<mailto:jianhong.ou at umassmed.edu>>, Lihua Julie Zhu <julie.zhu at umassmed.edu<mailto:julie.zhu at umassmed.edu>>, "bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>" <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
> Subject: Re: [Bioc-devel] build error only occurs in window system
> Don't bother. The issue is a long-standing one and very difficult to reproduce which is why it has not been fixed. It happens sporadically so the solution is to wait for the next day's build and it will clear itself up.
> Dan
> On July 7, 2016 11:05:22 AM PDT, "Ou, Jianhong" <Jianhong.Ou at umassmed.edu<mailto:Jianhong.Ou at umassmed.edu>> wrote:
> Hi Julie,
> You could try to install windows 10 in a virtualBox for debugging.
> virtualBox: https://www.virtualbox.org/wiki/Downloads
> Windows 10: https://www.microsoft.com/en-us/software-download/windows10/
> Yours Sincerely,
> Jianhong Ou
> TEL: 508-856-5379
> LRB 608
> Bioinformatician of Bioinformatics core at
> Department of Molecular, Cell and Cancer Biology
> UMASS Medical School
> 364 Plantation Street Worcester,
> MA 01605
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> On 7/7/16 1:15 PM, "Bioc-devel on behalf of Zhu, Lihua (Julie)"
> <bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org> on behalf of Julie.Zhu at umassmed.edu<mailto:Julie.Zhu at umassmed.edu>>
> wrote:
> Dan,
> I recently noticed that GUIDEseq page has a error build status at
> http://bioconductor.org/packages/release/bioc/html/GUIDEseq.html. Oddly,
> the error only occurs in the window server.
> Is this something related to the window server solvable by the core team,
> or should I change something to make it work? I am preparing a
> manuscript. It would  not look good if the reviewers see a red error
> status on the page.
> Could you please help me? Many thanks!
> Best regards,
> Julie
>   running command
> '"C:\Users\BIOCBU�1\AppData\Local\Programs\MIKTEX�1.9\miktex\bin\texify.ex
> e" --quiet --pdf "GUIDEseq.tex" --max-iterations=20 -I
> "E:/biocbld/bbs-3.3-bioc/R/share/texmf/tex/latex" -I
> "E:/biocbld/bbs-3.3-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 'GUIDEseq'. The following files exist in directory
> '.': 'GUIDEseq-concordance.tex', 'GUIDEseq.Rnw', 'GUIDEseq.tex',
> 'gRNA-PlusMinusPeaksMerged.bed', 'gRNA-PlusMinusPeaksMerged.xls',
> 'gRNA-peaks.xls', 'gRNAHEK293_site4_chr13.bamReadSummary.xls',
> 'mergedPeaks.bed', 'offTargetsInPeakRegions.xls'
> Calls: <Anonymous> -> find_vignette_product
> Execution halted
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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