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...@hotmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "Kasper Daniel Hansen" > <kasperdanielhan...@gmail.com> > Cc: "bioc-devel" <bioc-devel@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: dtene...@fredhutch.org >> To: kasperdanielhan...@gmail.com >> CC: anand...@hotmail.com; bioc-devel@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" <kasperdanielhan...@gmail.com> >> > To: "Anand MT" <anand...@hotmail.com> >> > Cc: "bioc-devel" <bioc-devel@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...@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@r-project.org mailing list >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioc-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
