[Bioc-devel] Examples of reading files of not allowed type

2018-05-24 Thread Jordan Bisanz 
Hello,

I have a developed a package called qiime2R which serves to facilitate the 
analysis of files from QIIME 2 (qiime2.org), one of the most commonly used 16S 
rRNA amplicon packages for microbiome analysis. It allows advanced analysis and 
data visualization in R without the loss of associated provenance tracking 
aiding in reproducible analyses. The situation I am running in to is that 
during the bioccheck, I can not have a runnable example as it requires the 
qiime2-specific file format (.qza). Inclusion of these files leads to a warning 
during R CMD check due to the inclusion of a type not allowed in data/. I have 
usage examples wrapped in \dontrun{}. Is it possible for this requirement to be 
waved?

Thanks,

Jordan

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Re: [Bioc-devel] Examples of reading files of not allowed type

2018-05-24 Thread Martin Morgan 

Save these under a folder inst/, conventionally inst/extdata/.

Access them using

  system.file(package="YourPackage", "extdata", "")

Martin

On 05/23/2018 06:44 PM, Jordan Bisanz wrote:

Hello,

I have a developed a package called qiime2R which serves to facilitate the 
analysis of files from QIIME 2 (qiime2.org), one of the most commonly used 16S 
rRNA amplicon packages for microbiome analysis. It allows advanced analysis and 
data visualization in R without the loss of associated provenance tracking 
aiding in reproducible analyses. The situation I am running in to is that 
during the bioccheck, I can not have a runnable example as it requires the 
qiime2-specific file format (.qza). Inclusion of these files leads to a warning 
during R CMD check due to the inclusion of a type not allowed in data/. I have 
usage examples wrapped in \dontrun{}. Is it possible for this requirement to be 
waved?

Thanks,

Jordan

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Re: [Bioc-devel] How best to remap S4Vectors::Hits indices?

2018-05-24 Thread Pariksheet Nanda 
Hi all,

> I want to compare a subset of GRanges for hits, but revert to
> the original GRanges indices when returning the results.

For now I will recreate the Hits object:
https://github.com/coregenomics/nascentrna/commit/e04e52b6db37bccde1dde7e85b262afe5c3d723c#diff-ee43ece522f0957d1699554637a9b9a3R67
That's the best I can think of till I hear any other suggestions.

Pariksheet

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Re: [Bioc-devel] BiocInstaller: next generation

2018-05-24 Thread Neumann, Steffen 
Hi,

On Fri, 2018-05-18 at 10:00 -0400, Martin Morgan wrote:
> 
> > ...
> > i.e. a package from a given BioC release, or a specific version
> > of a package, regardless from which release it comes.
> 
> I guess there are so many ways to shoot oneself in the foot that it
> is a wonder that we still have feet! I'm with Jim on this one...

Alright then, looking forward 
to the new BiocManager package.

Yours,
Steffen



-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409

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