[Bioc-devel] shrunken vignette

[Andrzej Oleś]

Hi Anand, Kasper,

thank you for reporting the problems with `BiocStyle::html_document2`
format function. As already noted by Kasper, the new HTML output style is
still work in progress.
I will look into improving the formatting of TOC, see
https://github.com/Bioconductor/BiocStyle/issues/6.

Cheers,
Andrzej

On Sun, Jul 17, 2016 at 5:08 AM, Anand MT <anand_mt at hotmail.com> wrote:

> Hi Dan,
> Figured it out. Sorry it was my fault. Turns out I was using output style -
> "BiocStyle::html_document2",  instead of "BiocStyle::html_document" in
> vignette metadata.
> Changing it solved the issue. I think earlier template center aligns
> everything.
> Thank you.
>
>
> > Date: Sat, 16 Jul 2016 18:39:43 -0700
> > From: dtenenba at fredhutch.org
> > To: anand_mt at hotmail.com
> > CC: kasperdanielhansen at gmail.com; bioc-devel at r-project.org
> > Subject: Re: [Bioc-devel] shrunken vignette
> >
> > It can be changed if we can identify the problem.
> >
> > Bioconductor package developers should be using the devel version of
> Bioconductor in order to identify problems like this.
> >
> > Dan
> >
> >
> > ----- Original Message -----
> > > From: "Anand MT" <anand_mt at hotmail.com>
> > > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "Kasper Daniel Hansen" <
> kasperdanielhansen at gmail.com>
> > > Cc: "bioc-devel" <bioc-devel at r-project.org>
> > > Sent: Saturday, July 16, 2016 6:37:01 PM
> > > Subject: RE: [Bioc-devel] shrunken vignette
> >
> > > Hi Dan and Kasper,
> > > Thank you. I will add sessionInfo. vignette built with R CMD build
> also looks
> > > good with cleaner toc. Maybe its the devel BiocStyle level as
> suggested. So no
> > > way to change it now?
> > >
> > >> Date: Fri, 15 Jul 2016 20:46:01 -0700
> > >> From: dtenenba at fredhutch.org
> > >> To: kasperdanielhansen at gmail.com
> > >> CC: anand_mt at hotmail.com; bioc-devel at r-project.org
> > >> Subject: Re: [Bioc-devel] shrunken vignette
> > >>
> > >> Also note that the build system does not use devtools to build
> vignettes, it
> > >> uses R CMD build.
> > >>
> > >>
> > >> ----- Original Message -----
> > >> > From: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> > >> > To: "Anand MT" <anand_mt at hotmail.com>
> > >> > Cc: "bioc-devel" <bioc-devel at r-project.org>
> > >> > Sent: Friday, July 15, 2016 8:43:00 PM
> > >> > Subject: Re: [Bioc-devel] shrunken vignette
> > >>
> > >> > If you add a sessionInfo() section to your document (which I highly
> > >> > recommend) you'll probably realize the two versions are using
> different
> > >> > versions of BiocStyle (anything in devel uses BiocStyle level).  The
> > >> > default layout is changing, and I am sure comments or bug reports
> are
> > >> > welcome.  For example, as rendered right now I would agree the TOC
> sucks.
> > >> >
> > >> > Best,
> > >> > Kasper
> > >> >
> > >> > On Fri, Jul 15, 2016 at 9:53 PM, Anand MT <anand_mt at hotmail.com>
> wrote:
> > >> >
> > >> >> Hi all,
> > >> >> My package 'maftools' finally found its homepage today. But when I
> checked
> > >> >> the vignette, it has been shrunken. It appears to be html vignette
> is
> > >> >> center aligned rather than left aligned. It makes things cluttered
> and and
> > >> >> toc looks messy.
> > >> >> Vignette is here:
> > >> >>
> http://bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html
> > >> >> When I build it manually on my computer with
> devtools::build_vignettes()
> > >> >> it looks like this. http://poisonalien.github.io   - A much
> cleaner look.
> > >> >> Do I need to change any thing in markdown file?
> > >> >> Meta data on my vignette markdown looks like this.
> > >> >> ---title: "maftools : Summarize, Analyze and Visualize MAF
> files"author:
> > >> >> "Anand Mayakonda"date: "`r Sys.Date()`"output:
> > >> >> BiocStyle::html_document2vignette: >
> %\VignetteIndexEntry{Summarize,
> > >> >> Analyze and Visualize MAF files}
> %\VignetteEngine{knitr::rmarkdown}
> > >> >> %\VignetteEncoding{UTF-8}---
> > >> >>
> > >> >> Thank you.
> > >> >>
> > >> >>         [[alternative HTML version deleted]]
> > >> >>
> > >> >> _______________________________________________
> > >> >> Bioc-devel at r-project.org mailing list
> > >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >> >>
> > >> >
> > >> >  [[alternative HTML version deleted]]
> > >> >
> > >> > _______________________________________________
> > >> > Bioc-devel at r-project.org mailing list
> > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>         [[alternative HTML version deleted]]
>
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