biomformat

Package: biomformat
Version: 1.0.2
Date: 2016-04-16
Maintainer: Paul J. McMurdie <mcmurdie@stanford.edu>
License: GPL-2
Title: An interface package for the BIOM file format
Type: Package
Author: Paul J. McMurdie <mcmurdie@stanford.edu> and Joseph N Paulson <jpaulson@jimmy.harvard.edu>
BugReports: https://github.com/joey711/biomformat/issues
URL: https://github.com/joey711/biomformat/, http://biom-format.org/
Description: This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and
subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object
back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format
project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of
common core functions/methods.
Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5
Depends: R (>= 3.2), methods
Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6),
rmarkdown (>= 0.7)
VignetteBuilder: knitr
Collate: 'allClasses.R' 'allPackage.R' 'IO-methods.R' 'BIOM-class.R'
'validity-methods.R'
biocViews: DataImport, Metagenomics, Microbiome
NeedsCompilation: no
Packaged: 2016-05-16 05:51:54 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'biomformat' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nrow' from package 'base' in package 'biomformat'
Creating a generic function for 'ncol' from package 'base' in package 'biomformat'
Creating a generic function for 'rownames' from package 'base' in package 'biomformat'
Creating a generic function for 'colnames' from package 'base' in package 'biomformat'
** help
*** installing help indices
  converting help for package 'biomformat'
    finding HTML links ... done
    biom-class                              html  
    biom-methods                            html  
    finding level-2 HTML links ... done

    biom-package                            html  
    biom_data-methods                       html  
    biom_shape-methods                      html  
    colnames-methods                        html  
    header-methods                          html  
    make_biom                               html  
    matrix_element_type-methods             html  
    ncol-methods                            html  
Rd warning: /tmp/Rtmp26YbXH/R.INSTALL3e5150ea1c32/biomformat/man/ncol-methods.Rd:6: missing file link 'ncol'
Rd warning: /tmp/Rtmp26YbXH/R.INSTALL3e5150ea1c32/biomformat/man/ncol-methods.Rd:19: missing file link 'ncol'
Rd warning: /tmp/Rtmp26YbXH/R.INSTALL3e5150ea1c32/biomformat/man/ncol-methods.Rd:31: missing file link 'ncol'
    nrow-methods                            html  
    observation_metadata-methods            html  
    read_biom                               html  
    read_hdf5_biom                          html  
    rownames-methods                        html  
Rd warning: /tmp/Rtmp26YbXH/R.INSTALL3e5150ea1c32/biomformat/man/rownames-methods.Rd:6: missing file link 'rownames'
Rd warning: /tmp/Rtmp26YbXH/R.INSTALL3e5150ea1c32/biomformat/man/rownames-methods.Rd:19: missing file link 'rownames'
Rd warning: /tmp/Rtmp26YbXH/R.INSTALL3e5150ea1c32/biomformat/man/rownames-methods.Rd:31: missing file link 'rownames'
    sample_metadata-methods                 html  
    show-methods                            html  
    write_biom                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biomformat)
Making 'packages.html' ... done