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

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Thu Jul 7 21:36:15 CEST 2016

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.



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.


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.org> on behalf of Julie.Zhu at umassmed.edu<mailto:Julie.Zhu at umassmed.edu>>


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,


 running command
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
Notice:\ This e-mail message, including ...{{dropped:11}}


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