[Bioc-devel] Package Without a Vignette

From: "Zhilong Jia" <zhilongjia at gmail.com>
To: "Stefan Haunsberger" <stefan.haunsberger at gmail.com>
Cc: "bioc-devel" <bioc-devel at r-project.org>
Sent: Saturday, April 2, 2016 5:48:59 PM
Subject: Re: [Bioc-devel] Package Without a Vignette

Hi,

I just found no vignette for my updated package cogena
<http://bioconductor.org/packages/3.3/bioc/html/cogena.html> (1.5.2),
though there are vignettes  in the code. And the check CMD is
/home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings
cogena_1.5.2.tar.gz in
http://bioconductor.org/checkResults/3.3/bioc-LATEST/cogena/zin2-checksrc.html

And the similar section is here:

vignette: >
 %\VignetteIndexEntry{Vignette Title}
 %\VignetteEngine{knitr::rmarkdown}
 %\usepackage[utf8]{inputenc}

No \\ here.


Thank you.

Regards,
Zhilong


On 22 March 2016 at 18:24, Stefan Haunsberger <stefan.haunsberger at gmail.com>
wrote:

Hi,

Yes, my bad. I'm already on it.

Thanks,
Stefan

On Tue, Mar 22, 2016 at 10:14 AM Martin Morgan <
martin.morgan at roswellpark.org> wrote:

On 03/22/2016 03:00 AM, Dario Strbenac wrote:

Hello,

The newly added Bioconductor package miRNAmeConverter has no vignette,

although a vignette is a requirement for Bioconductor packages which are
not simply annotation databases.

Rather, the package has a vignette, but it is not built.

This is because of the '\\' in the vignette header. Also, the 'html' and
'pdf' versions of the vignette should not be in SVN.

I've cc'd the maintainer.

Martin


Index: miRNAmeConverter-vignette.Rmd
===================================================================
--- miRNAmeConverter-vignette.Rmd       (revision 115094)
+++ miRNAmeConverter-vignette.Rmd       (working copy)
@@ -9,9 +9,9 @@
  csl: apa.csl
  bibliography: references.bib
  vignette: >
-   %\\VignetteIndexEntry{miRNAmeConverter-vignette}
-   %\\VignetteEncoding{UTF-8}
-   %\\VignetteEngine{knitr::rmarkdown}
+   %\VignetteIndexEntry{miRNAmeConverter-vignette}
+   %\VignetteEncoding{UTF-8}
+   %\VignetteEngine{knitr::rmarkdown}
  ---

  <!-- output:

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia

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--
Zhilong JIA
zhilongjia at gmail.com
https://github.com/zhilongjia

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