BioC 2.13: CHECK report for plethy on perceval

Package: plethy

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch plethy_1.0.0.tar.gz

StartedAt: 2014-04-05 03:24:55 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:29:23 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 267.1 seconds

RetCode: 0

Status:  OK

CheckDir: plethy.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/plethy.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plethy/DESCRIPTION’ ... OK
* this is package ‘plethy’ version ‘1.0.0’
* 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 ‘plethy’ can be installed ... [11s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘csv.to.table’ ‘find.break.ranges.integer’ ‘fix.time’ ‘multi.grep’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘plethy.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [30s/32s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
utilities 7.881  1.587  10.032
parsing   4.938  1.313   7.020
plethy    4.449  1.308   6.366
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [112s/117s]
 [113s/117s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/plethy.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
BuxcoDB	1.310	0.091	1.662
add_query_funcs	0.421	0.047	0.501
dbImport	0.812	0.044	1.042
parsing	4.938	1.313	7.020
plethy	4.449	1.308	6.366
utilities	7.881	1.587	10.032