Package: OTUbase

Version: 1.1.1

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings OTUbase_1.1.1.tar.gz

StartedAt: 2011-02-24 21:38:20 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 21:40:13 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 112.6 seconds

RetCode: 0

Status:  OK

CheckDir: OTUbase.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/OTUbase.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-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	0.908	0.012	0.920
TAXset-class	0.432	0.000	0.435
abundance	0.176	0.008	0.187
accessors	0.112	0.008	0.124
assignmentData	0.112	0.008	0.144
clusterSamples	0.136	0.008	0.188
other_functions	0.128	0.016	0.204
other_generics	0.112	0.000	0.111
readOTUset	0.112	0.000	0.112
readTAXset	0.100	0.004	0.102
sampleData	0.116	0.000	0.114
subOTUset	0.140	0.000	0.141
subTAXset	0.112	0.000	0.116