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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