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

Thu Jul 7 23:29:25 CEST 2016

On 07/07/2016 04:29 PM, Hervé Pagès wrote:
> 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.

another very hackish solution is, since the error always (??) involves 
the PDF command on the vignette, to convert the Rnw vignettte to Rmd. 
You can do this using the script at

https://github.com/seandavi/F1000R_BiocWorkflows/blob/master/rnwConversion/processesRnw.R

(actually, 
https://github.com/mtmorgan/F1000R_BiocWorkflows/blob/master/rnwConversion/processesRnw.R 
to support to issues with your Rnw file)

The vignette is in markdown immediately; a little hand-editing following

http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html

adds

---
author:
- |
     Lihua Julie Zhu, Michael Lawrence, Ankit Gupta,\
     Alper Kucukural, Manuel Garber, Scot Wolfe
title: 'GUIDEseq user guide'
output:
   BiocStyle::html_document
vignette: >
   %\VignetteIndexEntry{GUIDEseq user's guide}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
...

to the header and

Suggests: rmarkdown (...)

to the DESCRIPTION for a BiocStyle'd vignette

Martin

>
> Cheers,
> H.
>
>>
>> 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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