[Bioc-devel] Request for comment metagenomeFeatures package

[Hector Corrada Bravo]

Thanks Vince,
I think we just fixed that:
https://github.com/HCBravoLab/greengenes13.5MgDb/issues/1#issuecomment-127649449

Cheers,
Hector

On Tue, Aug 4, 2015 at 10:45 AM, Vincent Carey <stvjc at channing.harvard.edu>
wrote:

> very interesting development, we have several folks who will take a look.
>
> FYI
>
> %vjcair> R CMD INSTALL greeng*b
>
> Bioconductor version 3.2 (BiocInstaller 1.19.9), ?biocLite for help
>
> Loading required package: digest
>
> Loading required package: tools
>
> Loading required package: utils
>
> Loading required package: codetools
>
> * installing to library
> ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’
>
> * installing *source* package ‘greengenes13.5MgDb’ ...
>
> ** R
>
> ** preparing package for lazy loading
>
> Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
>
>   undefined subclass "externalRefMethod" of class "functionORNULL";
> definition not updated
>
> ** help
>
> No man pages found in package  ‘greengenes13.5MgDb’
>
> *** installing help indices
>
> ** building package indices
>
> ** testing if installed package can be loaded
>
> Bioconductor version 3.2 (BiocInstaller 1.19.9), ?biocLite for help
>
> Loading required package: digest
>
> Loading required package: tools
>
> Loading required package: utils
>
> Loading required package: codetools
>
> Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
>
>   undefined subclass "externalRefMethod" of class "functionORNULL";
> definition not updated
>
> /gg_13_5.fasta.gz: Permission denied
>
> On Tue, Aug 4, 2015 at 9:43 AM, Nathan Olson <nathandavidolson at gmail.com>
> wrote:
>
> > We are starting to work on an infrastructure for annotation of 16S
> > metagenomic sequencing datasets and would like your comments and/or
> > contributions. Below are links to two github repositories:
> > metagenomeFeatures and greengenes13.5MgDb.  The metagenomeFeatures
> package
> > contains two classes; mgDb, for 16S sequence databases, and
> > metagenomeAnnotation, for annotating a sequence dataset with taxonomic
> > information from a mgDb object.  The greengenes13.5MgDb package, loads a
> > mgDb object with the greengenes 13.5 database.  greengenes 13.5 was used
> as
> > an example database, we plan on adding additional packages for other
> > commonly used databases, e.g RDP and Silva.
> >
> > The metagenomeFeatures includes two vignettes to demonstrating the mgDb
> and
> > metagenomeAnnotation class methods using the greengenes13.5MgDb as an
> > example database.
> >
> > We are planning on adding additional methods for the mgDb and
> > metagenomeAnnotation classes.  For the mgDb class, assigning query
> > sequences to database sequences using rRDP classifier, and/or sequence
> > alignment methods that are part of the Biostrings package.  For the
> > metagenomeAnnotation class we plan to include the ability to create a
> > phylogenetic tree from a metagenomeAnnotation object.
> > We would appreciate comments on the package and suggestions for
> additional
> > features.
> >
> > Links to package github repositories
> >
> > https://github.com/HCBravoLab/metagenomeFeatures
> >
> > https://github.com/HCBravoLab/greengenes13.5MgDb
> >
> > Thanks
> >
> > Nate Olson and Hector Corrada Bravo
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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>
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