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...@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: dtene...@fredhutch.org > > To: anand...@hotmail.com > > CC: kasperdanielhan...@gmail.com; bioc-devel@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...@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 > > [[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
