Package: BiocGenerics

Version: 0.5.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiocGenerics_0.5.6.tar.gz

StartedAt: 2013-03-25 01:23:10 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:24:15 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 64.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocGenerics.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BiocGenerics.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '0.5.6'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'BiocGenerics' can be installed ... [4s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... WARNING
Missing link or links in documentation object '/Users/biocbuild/bbs-2.12-bioc/meat/BiocGenerics.Rcheck/00_pkg_src/BiocGenerics/man/rank.Rd':
  '[IRanges]{rank,Vector-method}'

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* 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 ... [9s/9s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'BiocGenerics_unit_tests.R' [2s/2s]
 [3s/3s] OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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 'as.data.frame' in package 'BiocGenerics'
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 'match' 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 'rank' 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 'sort' 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 'unlist' in package 'BiocGenerics'
Creating a new generic function for 'xtabs' in package 'BiocGenerics'
Creating a new generic function for 'clusterCall' in package 'BiocGenerics'
Creating a new generic function for 'clusterApply' in package 'BiocGenerics'
Creating a new generic function for 'clusterApplyLB' in package 'BiocGenerics'
Creating a new generic function for 'clusterEvalQ' in package 'BiocGenerics'
Warning in getPackageName(environment(fdef)) :
  Created a package name, '2013-03-25 01:23:13', when none found
Creating a new generic function for 'clusterExport' in package 'BiocGenerics'
Creating a new generic function for 'clusterMap' in package 'BiocGenerics'
Creating a new generic function for 'parLapply' in package 'BiocGenerics'
Creating a new generic function for 'parSapply' in package 'BiocGenerics'
Creating a new generic function for 'parApply' in package 'BiocGenerics'
Creating a new generic function for 'parRapply' in package 'BiocGenerics'
Creating a new generic function for 'parCapply' in package 'BiocGenerics'
Creating a new generic function for 'parLapplyLB' in package 'BiocGenerics'
Creating a new generic function for 'parSapplyLB' 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	0.008	0.006	0.013
Extremes	0.031	0.017	0.052
annotation	0.740	0.036	0.777
as.data.frame	0.017	0.007	0.024
boxplot	0.012	0.007	0.021
cbind	0.019	0.010	0.027
clusterApply	0.092	0.045	0.136
combine	0.235	0.033	0.268
density	0.010	0.007	0.018
duplicated	0.015	0.009	0.024
eval	0.011	0.008	0.018
funprog	0.033	0.021	0.057
get	0.014	0.011	0.026
image	0.010	0.008	0.017
lapply	0.018	0.011	0.029
mapply	0.011	0.008	0.019
match	0.011	0.008	0.020
nrow	0.027	0.017	0.045
order	0.011	0.008	0.019
paste	0.010	0.008	0.017
rank	0.010	0.010	0.019
rep	0.011	0.009	0.019
residuals	0.011	0.008	0.019
row_colnames	0.018	0.011	0.029
sets	0.023	0.014	0.037
sort	0.012	0.007	0.019
strand	4.803	0.117	4.925
table	0.013	0.008	0.019
tapply	0.012	0.008	0.021
unique	0.011	0.008	0.019
unlist	0.012	0.008	0.020
updateObject	0.518	0.046	0.564
weights	0.012	0.006	0.018
xtabs	0.015	0.007	0.022