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
<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.org>
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...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
