Added a new vignette to GenomicRanges that explains this stuff.
On Mon, Sep 29, 2014 at 6:54 PM, Michael Lawrence wrote:
> I admit negligence in not document this. But if you look at VRanges, you
> can see how we set a method for "extraColumnSlotNames" returns a character
> vector of slot names
Hi Gordon, James,
thank you for pointing this out! At the time BiocStyle for markdown
documents was developed 'rmarkdown' was not yet on CRAN and couldn't
be used as a vignette builder engine.
As things changed in the meantime, the approach described by Gordon
should be just fine. I will update th
On Thu, 02-10-2014, at 22:42, Hervé Pagès wrote:
> Hi,
>
> This makes a lot of sense. I also find a bit disturbing that the main
> text cannot immediately be distinguished from other things like captions
> or page headers (BiocStyle places the title of the vignette at the top
> of each page but
- Original Message -
> From: "Andrzej Oleś"
> To: "Wolfgang Huber"
> Cc: bioc-devel@r-project.org
> Sent: Friday, October 3, 2014 3:25:30 AM
> Subject: Re: [Bioc-devel] Add a new developer/maintainer
>
> Hi Setia,
>
> you will probably also need an account with write permissions to th
- Original Message -
> From: "Henrik Bengtsson"
> To: jmac...@u.washington.edu
> Cc: bioc-devel@r-project.org
> Sent: Friday, October 3, 2014 6:56:59 AM
> Subject: Re: [Bioc-devel] RMarkdown for vignettes
>
> I think it requires Bioc core to make a statement that pandoc will be
> added
I think it requires Bioc core to make a statement that pandoc will be added
to the list of external software that can be assume to exist on the servers.
If it is also expected that users should be able to rebuild all
vignettes/documents themselves, then that assumption has to be extended to
the us
Hi Gordon,
Sean Davis has something about this on his blog:
http://watson.nci.nih.gov/~sdavis/blog/convert_from_sweave_to_r_markdown_vignettes/
Best,
Jim
On Fri, Oct 3, 2014 at 9:06 AM, Gordon Ball wrote:
> Hello
>
> Is it possible to use (RStudio's) rmarkdown package as a vignette
> build
Hello
Is it possible to use (RStudio's) rmarkdown package as a vignette
builder for the upcoming release?
ie, with the (at least locally working) configuration
DESCRIPTION
Suggests: knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
vignette/vignette.Rmd
---
title: ...
out
Hi Setia,
you will probably also need an account with write permissions to the
package SVN for the new maintainer. For this its probably best to
contact Dan Tenenbaum
Cheers,
Andrzej
On Fri, Oct 3, 2014 at 11:48 AM, Wolfgang Huber wrote:
> Dear Setia
>
> just edit the “DESCRIPTION” file.
>
> F
Dear Setia
just edit the “DESCRIPTION” file.
For maintainers, note the CRAN Repository Policy at
http://cran.r-project.org/web/packages/policies.html which I think we generally
also apply in Bioconductor: "The package’s DESCRIPTION file must show both the
name and email address of a single des
Dear Bioc Developer,
I would like to add another person as developer and maintainer of my package
IsoGeneGUI. Please let me know the procedure for that. Look forward to your
suggestion. Thank you.
Best regards,
Setia
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