[Bioc-devel] build error only occurs in window system
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, Herv? Pag?s 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}}
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