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[Bioc-devel] shrunken vignette

7 messages · Anand MT, Kasper Daniel Hansen, Dan Tenenbaum +1 more

Anand MT
# 
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.
Kasper Daniel Hansen
# 
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:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Dan Tenenbaum
    

    

      
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Also note that the build system does not use devtools to build vignettes, it uses R CMD build.


----- Original Message -----

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Anand MT
    

    

      
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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?

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Dan Tenenbaum
    

    

      
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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 -----

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Anand MT
    

    

      
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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.

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Andrzej Oleś
    

    

      
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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_mt at hotmail.com> wrote: