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: 2011-02-24 20:38:33 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 20:40:54 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 140.7 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) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* 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 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 1.17-7
** 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	1.023	0.015	1.062
TAXset-class	0.682	0.004	0.686
abundance	0.288	0.024	0.314
accessors	0.192	0.014	0.207
assignmentData	0.164	0.003	0.168
clusterSamples	0.178	0.005	0.191
other_functions	0.188	0.004	0.194
other_generics	0.171	0.004	0.181
readOTUset	0.168	0.003	0.171
readTAXset	0.141	0.004	0.146
sampleData	0.169	0.003	0.174
subOTUset	0.208	0.004	0.213
subTAXset	0.157	0.005	0.166