[Bioc-devel] shrunken vignette

[Dan Tenenbaum]

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]]
>> > 
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