BioC 3.2: CHECK report for LiquidAssociation on perceval

Package: LiquidAssociation

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LiquidAssociation_1.24.0.tar.gz

StartedAt: 2015-11-10 06:25:51 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 06:27:43 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 112.3 seconds

RetCode: 0

Status:  OK

CheckDir: LiquidAssociation.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LiquidAssociation_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/LiquidAssociation.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LiquidAssociation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LiquidAssociation’ version ‘1.24.0’
* 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 ‘LiquidAssociation’ can be installed ... [11s/11s] 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
Packages in Depends field not imported from:
  ‘geepack’ ‘org.Sc.sgd.db’ ‘yeastCC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CNM.full,matrix : .local: no visible global function definition for
  ‘geese’
CNM.full,matrix : .local: no visible binding for global variable
  ‘groupid’
CNM.full,matrix : .local: no visible binding for global variable
  ‘visit’
CNM.full,matrix : .local: no visible global function definition for
  ‘geese.control’
CNM.simple,matrix : .local: no visible global function definition for
  ‘geese’
CNM.simple,matrix : .local: no visible binding for global variable
  ‘groupid’
CNM.simple,matrix : .local: no visible binding for global variable
  ‘visit’
CNM.simple,matrix : .local: no visible global function definition for
  ‘geese.control’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [15s/16s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getsGLA-methods 6.652  0.089   6.741
* 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

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/LiquidAssociation.Rcheck/00check.log’
for details.

* installing *source* package ‘LiquidAssociation’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘LiquidAssociation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LiquidAssociation)

name	user	system	elapsed
CNM-class	0.001	0.000	0.001
CNM.full-methods	0.050	0.002	0.051
CNM.simple-methods	0.034	0.001	0.034
GLA-methods	0.015	0.000	0.015
LA-methods	0.002	0.000	0.002
LiquidAssociation-package	0.038	0.001	0.038
getsGLA-methods	6.652	0.089	6.741
getsLA-methods	3.958	0.066	4.024
plotGLA-methods	0.012	0.002	1.014