Package: OTUbase

Version: 1.3.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings OTUbase_1.3.0.tar.gz

StartedAt: 2011-05-09 13:33:18 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:35:51 -0700 (Mon, 09 May 2011)

EllapsedTime: 152.5 seconds

RetCode: 0

Status:  OK

CheckDir: OTUbase.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/OTUbase.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.3.0’
* 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 for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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 1.17-10
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘Introduction_to_OTUbase.Rnw’ 
** testing if installed package can be loaded
================================================================================
Welcome to OTUbase version 1.3.0

* DONE (OTUbase)

name	user	system	elapsed
OTUset-class	0.736	0.004	0.738
TAXset-class	0.476	0.000	0.474
abundance	0.168	0.016	0.183
accessors	0.116	0.012	0.132
assignmentData	0.112	0.004	0.117
clusterSamples	0.124	0.008	0.132
other_functions	0.144	0.000	0.144
other_generics	0.132	0.004	0.133
readOTUset	0.124	0.000	0.124
readTAXset	0.108	0.004	0.110
sampleData	0.116	0.000	0.114
subOTUset	0.140	0.004	0.142
subTAXset	0.112	0.008	0.120