Thanks Martin! That is a very interesting solution! Best,
Julie On 7/7/16 5:29 PM, "Martin Morgan" <martin.mor...@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 >>> <dtene...@fredhutch.org<mailto:dtene...@fredhutch.org>> >>> Date: Thursday, July 7, 2016 3:15 PM >>> To: Jianhong Ou >>> <jianhong...@umassmed.edu<mailto:jianhong...@umassmed.edu>>, Lihua >>> Julie Zhu <julie....@umassmed.edu<mailto:julie....@umassmed.edu>>, >>> "bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>" >>> <bioc-devel@r-project.org<mailto:bioc-devel@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...@umassmed.edu<mailto:jianhong...@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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.or >>>g> >>> on behalf of julie....@umassmed.edu<mailto:julie....@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@r-project.org<mailto:Bioc-devel@r-project.org> mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> > > >This email message may contain legally privileged and/or confidential >information. 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