BioC 3.0: CHECK report for OrderedList on oaxaca

Package: OrderedList

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch OrderedList_1.38.0.tar.gz

StartedAt: 2015-04-10 01:55:05 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:55:53 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 47.5 seconds

RetCode: 0

Status:  OK

CheckDir: OrderedList.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch OrderedList_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/OrderedList.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OrderedList/DESCRIPTION’ ... OK
* this is package ‘OrderedList’ version ‘1.38.0’
* 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 ‘OrderedList’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘methods’ ‘twilight’
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 loading without being on the library search path ... OK
* checking 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘OrderedList/R/a.R’:
  .First.lib has wrong argument list ‘libname, pkgname, where’

Package startup functions should have two arguments with names starting
  with ‘lib’ and ‘pkg’, respectively.
See section ‘Good practice’ in '?.onAttach'.
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] 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
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/OrderedList.Rcheck/00check.log’
for details.

* installing *source* package ‘OrderedList’ ...
** 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 (OrderedList)

name	user	system	elapsed
OL.result	0.001	0.000	0.001
OrderedList	0.254	0.010	0.264
compareLists	0.940	0.016	0.963
getOverlap	0.900	0.005	0.906
plot.OrderedList	0.048	0.002	0.074
prepareData	0.118	0.002	0.122
print.OrderedList	0.003	0.000	0.004