Package: BiocGenerics

Version: 0.3.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiocGenerics_0.3.0.tar.gz

StartedAt: 2012-06-20 22:12:35 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 22:13:36 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 60.9 seconds

RetCode: 0

Status:  OK

CheckDir: BiocGenerics.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/BiocGenerics.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BiocGenerics/DESCRIPTION' ... OK
* this is package 'BiocGenerics' version '0.3.0'
* 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 'BiocGenerics' 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 ... NOTE
S3 methods shown with full name in documentation object 'rep':
  'rep.int'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'BiocGenerics_unit_tests.R'
 OK
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.

* installing *source* package 'BiocGenerics' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'cbind' in package 'BiocGenerics'
Creating a new generic function for 'rbind' in package 'BiocGenerics'
Creating a new generic function for 'duplicated' in package 'BiocGenerics'
Creating a new generic function for 'anyDuplicated' in package 'BiocGenerics'
Creating a new generic function for 'eval' in package 'BiocGenerics'
Creating a new generic function for 'pmax' in package 'BiocGenerics'
Creating a new generic function for 'pmin' in package 'BiocGenerics'
Creating a new generic function for 'pmax.int' in package 'BiocGenerics'
Creating a new generic function for 'pmin.int' in package 'BiocGenerics'
Creating a new generic function for 'Reduce' in package 'BiocGenerics'
Creating a new generic function for 'Filter' in package 'BiocGenerics'
Creating a new generic function for 'Find' in package 'BiocGenerics'
Creating a new generic function for 'Map' in package 'BiocGenerics'
Creating a new generic function for 'Position' in package 'BiocGenerics'
Creating a new generic function for 'get' in package 'BiocGenerics'
Creating a new generic function for 'mget' in package 'BiocGenerics'
Creating a new generic function for 'lapply' in package 'BiocGenerics'
Creating a new generic function for 'sapply' in package 'BiocGenerics'
Creating a new generic function for 'mapply' in package 'BiocGenerics'
Creating a new generic function for 'order' in package 'BiocGenerics'
Creating a new generic function for 'paste' in package 'BiocGenerics'
Creating a new generic function for 'rep.int' in package 'BiocGenerics'
Creating a new generic function for 'rownames' in package 'BiocGenerics'
Creating a new generic function for 'colnames' in package 'BiocGenerics'
Creating a new generic function for 'union' in package 'BiocGenerics'
Creating a new generic function for 'intersect' in package 'BiocGenerics'
Creating a new generic function for 'setdiff' in package 'BiocGenerics'
Creating a new generic function for 'table' in package 'BiocGenerics'
Creating a new generic function for 'tapply' in package 'BiocGenerics'
Creating a new generic function for 'unique' in package 'BiocGenerics'
Creating a new generic function for 'xtabs' in package 'BiocGenerics'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (BiocGenerics)

name	user	system	elapsed
BiocGenerics-package	0.001	0.000	0.000
Extremes	0.014	0.001	0.015
boxplot	0.002	0.000	0.002
cbind	0.004	0.001	0.005
combine	0.125	0.006	0.131
density	0.002	0.000	0.003
duplicated	0.005	0.001	0.006
eval	0.003	0.001	0.003
funprog	0.010	0.002	0.012
get	0.004	0.001	0.005
image	0.002	0.000	0.003
lapply	0.006	0.001	0.007
mapply	0.002	0.001	0.002
nrow	0.008	0.001	0.010
order	0.002	0.001	0.002
paste	0.002	0.000	0.002
rep	0.002	0.000	0.002
residuals	0.002	0.001	0.002
row_colnames	0.006	0.001	0.007
sets	0.006	0.001	0.007
strand	4.010	0.093	4.151
table	0.005	0.001	0.005
tapply	0.003	0.000	0.003
unique	0.004	0.000	0.004
updateObject	1.208	0.031	1.259
weights	0.004	0.000	0.005
xtabs	0.003	0.000	0.004