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 <st...@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@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@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 <nathandavidol...@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@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
