[Bioc-devel] Missing vignette on my BioConductor page

[Marine Rohmer]

Hi Martin, thank you so much for you answer!

I'm not sure to have well understood what is my problem, maybe I missed 
somewhere some basic learning about how to package.

According to "The vignette" section from "Bioconductor: Package 
guidelines" and probably other guidelines I could have read, I've 
created a .Rnw document within a "vignettes" subdirectory. It compiles 
with pdflatex. No need for knitr. I have written some code examples but 
not included "evaluated code chunks" within my .Rnw file.

What is the problem: knitr, the code chunks, or another thing?

You can find attached my vignettes subdirectory + the compiled vignette 
(pdf file).

Thank you again for your help,

Regards,

Marine R.



Le 13/09/2016 à 16:35, Martin Morgan a écrit :
> Hi Marine -- mail sent to bioc-devel from non-subscribers is silently 
> dropped; I could not spot a subscription that might be yours, are you 
> subscribed?
>
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> I guess you mean the package ISoLDE. Here's the 'build' report for 
> release
>
> http://bioconductor.org/checkResults/release/bioc-LATEST/ISoLDE/zin2-buildsrc.html 
>
>
> and devel
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/ISoLDE/zin1-buildsrc.html 
>
>
> If the vignette were being built, it would indicate that in the 
> Command output section.
>
> packages using knitr need to have Suggests: knitr and VignetteBuilder: 
> knitr in the DESCRIPTION file; make these changes to both release and 
> devel branches, bumping the version as below in devel, and to 1.0.3 in 
> release.
>
> Bioconductor packages are *required* to have a 'real' vignette with 
> evaluated code chunks; the reviewer must have missed this part of the 
> review process. You'll need to update your vignette to this 
> specification, while remaining within the size and space limitations 
> in the Bioconductor guidelines
>
> http://bioconductor.org/developers/package-guidelines/#correctness
>
> Hope that helps, please don't hesitate to ask (preferably as a 
> subscribed member on the Bioc-devel mailing list) for any further 
> assistance.
>
> ISoLDE$ svn diff
> Index: DESCRIPTION
> ===================================================================
> --- DESCRIPTION    (revision 120902)
> +++ DESCRIPTION    (working copy)
> @@ -1,7 +1,7 @@
>  Package: ISoLDE
>  Type: Package
>  Title: Integrative Statistics of alleLe Dependent Expression
> -Version: 1.1.2
> +Version: 1.1.3
>  Date: 2015-10-29
>  Authors at R: c( person("Christelle", "Reynès", email =
>          "christelle.reynes at igf.cnrs.fr", role = c("aut","cre")),
> @@ -16,6 +16,7 @@
>  Encoding: UTF-8
>  License: GPL (>= 2.0)
>  Depends: R (>= 3.3.0),graphics,grDevices,stats,utils
> +Suggests: knitr
>  URL: www.r-project.org
>  LazyData: no
>  NeedsCompilation: yes
> @@ -26,3 +27,4 @@
>          Sequencing, RNASeq, MultipleComparison, SNP,
>          GeneticVariability, Epigenetics, MathematicalBiology,
>          GeneRegulation
> +VignetteBuilder: knitr
>
>
> Martin
>
>
> -------- Forwarded Message --------
> Subject: Auto-discard notification
> Date: Tue, 13 Sep 2016 15:17:52 +0200
> From: bioc-devel-bounces at r-project.org
> To: bioc-devel-owner at r-project.org
>
> The attached message has been automatically discarded.
>
>
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the 
> employee or agent responsible for the delivery of this message to the 
> intended recipient(s), you are hereby notified that any disclosure, 
> copying, distribution, or use of this email message is prohibited.  If 
> you have received this message in error, please notify the sender 
> immediately by e-mail and delete this email message from your 
> computer. Thank you.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: vignette.pdf
Type: application/pdf
Size: 231509 bytes
Desc: not available
URL: <https://stat.ethz.ch/pipermail/bioc-devel/attachments/20160914/c331c99d/attachment-0001.pdf>