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

[Zhu, Lihua (Julie)]

Herve,

I strongly agree that the ultimate goal is to fix the issue. Thanks for
the short term solution!

Best,

Julie

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On 7/7/16 4:29 PM, "Hervé Pagès" <hpages at fredhutch.org> 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-f
>>ile-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.
>
>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
>>
>> Confidentiality Notice:
>> This e-mail message, including any attachments, is for the sole use of
>>the
>> intended recipient(s) and may contain confidential, proprietary and
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>> contact the sender immediately and destroy or permanently delete all
>> copies of the original message.
>>
>>
>>
>>
>>
>>
>> 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.e
>>x
>> 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
>1100 Fairview Ave. N, M1-B514
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