[Bioc-devel] shrunken vignette

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.

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