Package: OTUbase

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch OTUbase_1.1.1.tar.gz

StartedAt: 2011-03-17 17:02:19 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:04:42 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 142.7 seconds

RetCode: 0

Status:  OK

CheckDir: OTUbase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/OTUbase.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'OTUbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OTUbase' version '1.1.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'OTUbase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'OTUbase' ...
** R
** inst
** preparing package for lazy loading
Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object(s) are masked from 'package:IRanges':

    updateObject

This is vegan 1.17-8
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Welcome to OTUbase version 1.1.1

* DONE (OTUbase)

name	user	system	elapsed
OTUset-class	0.667	0.002	0.670
TAXset-class	0.537	0.002	0.539
abundance	0.187	0.014	0.201
accessors	0.127	0.009	0.136
assignmentData	0.118	0.001	0.120
clusterSamples	0.123	0.002	0.126
other_functions	0.139	0.002	0.141
other_generics	0.114	0.002	0.116
readOTUset	0.115	0.001	0.116
readTAXset	0.116	0.002	0.117
sampleData	0.120	0.002	0.122
subOTUset	0.144	0.002	0.145
subTAXset	0.123	0.002	0.125