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

Fri Jul 8 00:36:34 CEST 2016

Thanks Martin! That is a very interesting solution!

Best,

Julie

On 7/7/16 5:29 PM, "Martin Morgan" <martin.morgan at roswellpark.org> wrote:

>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/H
>tmlStyle.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
>>>
>>> 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
>>> privileged information. Any unauthorized review, use, disclosure or
>>> distribution is prohibited. If you are not the intended recipient,
>>> please
>>> 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.or
>>>g>
>>> 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
>>> Confidentiality
>>> Notice:\ This e-mail message, including ...{{dropped:11}}
>>>
>>>
>>> ________________________________
>>>
>>> Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>     [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>
>
>This email message may contain legally privileged and/or confidential
>information.  If you are not the intended recipient(s), or the employee
>or agent responsible for the delivery of this message to the intended
>recipient(s), you are hereby notified that any disclosure, copying,
>distribution, or use of this email message is prohibited.  If you have
>received this message in error, please notify the sender immediately by
>e-mail and delete this email message from your computer. Thank you.