BioC 2.12: CHECK report for parody on petty

Package: parody

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch parody_1.18.0.tar.gz

StartedAt: 2013-10-08 23:21:58 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:22:31 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 32.9 seconds

RetCode: 0

Status:  OK

CheckDir: parody.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/parody.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'parody/DESCRIPTION' ... OK
* this is package 'parody' version '1.18.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'parody' can be installed ... [2s/2s] 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 ... NOTE
ddcovGen : <anonymous>: warning in matrix(x[i, ], nc = 1): partial
  argument match of 'nc' to 'ncol'
ddcovGen : <anonymous>: warning in matrix((N * mx - om)/(N - 1), nc =
  1): partial argument match of 'nc' to 'ncol'
* checking Rd files ... NOTE
prepare_Rd: mv.calout.detect.Rd:40: Dropping empty section \references
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [1s/1s] 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/parody.Rcheck/00check.log'
for details.

* installing *source* package 'parody' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (parody)

name	user	system	elapsed
box.scale	0.013	0.001	0.014
bushfire	0.031	0.002	0.034
calout.detect	0.019	0.001	0.021
mv.calout.detect	0.041	0.001	0.043
tcost	0.028	0.001	0.030
tukeyor	0.016	0.002	0.018