BioC 2.13: CHECK report for procoil on perceval

Package: procoil

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch procoil_1.12.0.tar.gz

StartedAt: 2014-04-05 03:30:49 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:31:30 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 41.3 seconds

RetCode: 0

Status:  OK

CheckDir: procoil.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/procoil.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 ‘procoil/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘procoil’ version ‘1.12.0’
* 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 ‘procoil’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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: ‘utils’
  All declared Imports should be used.
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 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 files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] 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/procoil.Rcheck/00check.log’
for details.

* installing *source* package ‘procoil’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘procoil’
Creating a generic function for ‘predict’ from package ‘stats’ in package ‘procoil’
Creating a generic function for ‘weights’ from package ‘stats’ in package ‘procoil’
Creating a generic function for ‘profile’ from package ‘stats’ in package ‘procoil’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (procoil)

name	user	system	elapsed
CCModel-class	0.296	0.012	0.339
CCProfile-class	0.121	0.005	0.141
plot-methods	0.175	0.004	0.181
predict-methods	0.211	0.003	0.236
procoil-package	0.263	0.005	0.269
profile-methods	0.082	0.001	0.084
readCCModel	0.012	0.000	0.013
show-methods	0.344	0.313	0.810
weights-methods	0.028	0.002	0.030