BioC 2.14: CHECK report for timecourse on petty

Package: timecourse

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch timecourse_1.36.0.tar.gz

StartedAt: 2014-10-08 00:26:49 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:28:48 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 118.8 seconds

RetCode: 0

Status:  OK

CheckDir: timecourse.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch timecourse_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/timecourse.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘timecourse/DESCRIPTION’ ... OK
* this is package ‘timecourse’ version ‘1.36.0’
* 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 ‘timecourse’ can be installed ... [7s/8s] 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:
  ‘MASS’ ‘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 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 ‘timecourse/R/zzz.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'.

mb.2D : <anonymous>: no visible binding for global variable ‘n’
mb.2D : <anonymous>: no visible binding for global variable ‘T1’
mb.2D : <anonymous>: no visible binding for global variable ‘xbar’
mb.2D : <anonymous>: no visible binding for global variable ‘modS1’
* 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 ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
mb.long   10.565  0.102  10.728
mb.MANOVA  4.944  0.026   5.012
* 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-2.14-bioc/meat/timecourse.Rcheck/00check.log’
for details.

* installing *source* package ‘timecourse’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for class “LargeDataObject” in package ‘timecourse’ seems equivalent to one from package ‘limma’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (timecourse)

name	user	system	elapsed
mb.MANOVA	4.944	0.026	5.012
mb.long	10.565	0.102	10.728