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

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

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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
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