Re: [Bioc-devel] shrunken vignette

[Dan Tenenbaum]

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


- Original Message -
> From: "Kasper Daniel Hansen" 
> To: "Anand MT" 
> Cc: "bioc-devel" 
> 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  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]]
>>
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Re: [Bioc-devel] BioC check error for flowClust on windows

[Dan Tenenbaum]

When you don't see a specific error message, it's often a hint that R actually 
crashed (popped up a dialog box that you can't see in the build report. 

And indeed that is the case here. 

I can reproduce it easily as follows: 

R --arch i386 

library(flowClust) 
example(flowClust) 

It works fine under the default (x64) architecture. Did you test it under i386? 

Here's the build report url, BTW: 

https://bioconductor.org/checkResults/devel/bioc-LATEST/flowClust/moscato1-checksrc.html
 

By debugging the flowClust() function I can see that the crash happens after 
invoking .flowClustK() via mclapply(). 

Dan 

> From: "Mike" 
> To: "bioc-devel" 
> Sent: Friday, July 15, 2016 1:53:37 PM
> Subject: [Bioc-devel] BioC check error for flowClust on windows

> Hi,

> Here is the CHECK report for flowClust on moscato1. There is not pacific
> error message on that page and I can't reproduce it on my local windows.

> Mike

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[Bioc-devel] BioC check error for flowClust on windows

[Mike]

Hi,

Here is the CHECK report for flowClust on moscato1. There is not pacific 
error message on that page and I can't reproduce it on my local windows.


Mike

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[Bioc-devel] Looking for small RNA-seq fastq files - to use in Rmarkdown

[Krithika Bhuvaneshwar]

Dear Bioconductor community,

I'm exploring options to create a Bioconductor or package related to
RNA-seq data. Specifically, I am looking for an example RNA-seq
dataset (fastq files, human genome, preferably liver cancer) to use in
Rmarkdown files.

As you know the input files to be used in Rmarkdown cannot be large files.

Question - Does anyone know of well-known small RNA-seq fastq files
ready to be used in Bioconductor Rmarkdown ? If not, my only other
option would be to take a sample of a publicly available RNA-seq fastq
file.

Thanks,
Krithika

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