Package: OTUbase

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch OTUbase_1.4.0.tar.gz

StartedAt: 2012-03-24 02:59:49 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:03:59 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 249.9 seconds

RetCode: 0

Status:  OK

CheckDir: OTUbase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/OTUbase.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 sizes of PDF files under 'inst/doc' ... 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
Warning in .simpleDuplicateClass(def, prev) :
  A specification for class ".ShortReadBase" in package 'OTUbase' seems equivalent to one from package 'ShortRead' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Introduction_to_OTUbase.Rnw' 
** testing if installed package can be loaded

* DONE (OTUbase)

name	user	system	elapsed
OTUset-class	1.012	0.014	1.261
TAXset-class	0.735	0.008	0.784
abundance	0.214	0.024	0.249
accessors	0.129	0.015	0.161
assignmentData	0.127	0.004	0.140
clusterSamples	0.130	0.004	0.157
other_functions	0.141	0.005	0.178
other_generics	0.119	0.003	0.141
readOTUset	0.127	0.004	0.182
readTAXset	0.124	0.004	0.144
sampleData	0.124	0.004	0.135
subOTUset	0.164	0.004	0.169
subTAXset	0.133	0.004	0.137