Package: LiquidAssociation

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LiquidAssociation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LiquidAssociation_1.38.0.tar.gz

StartedAt: 2019-10-16 04:06:20 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:08:30 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 130.1 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 --install=check:LiquidAssociation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LiquidAssociation_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/LiquidAssociation.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.38.0’
* 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 ‘LiquidAssociation’ can be installed ... 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: no visible global function definition for ‘geese’
CNM.full,matrix: no visible binding for global variable ‘groupid’
CNM.full,matrix: no visible binding for global variable ‘visit’
CNM.full,matrix: no visible global function definition for
  ‘geese.control’
CNM.simple,matrix: no visible global function definition for ‘geese’
CNM.simple,matrix: no visible binding for global variable ‘groupid’
CNM.simple,matrix: no visible binding for global variable ‘visit’
CNM.simple,matrix: no visible global function definition for
  ‘geese.control’
Undefined global functions or variables:
  geese geese.control groupid visit
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getsGLA-methods 7.155   0.34   7.495
* 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-3.9-bioc/meat/LiquidAssociation.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL LiquidAssociation
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘LiquidAssociation’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LiquidAssociation)

name	user	system	elapsed
CNM-class	0.001	0.001	0.001
CNM.full-methods	0.043	0.005	0.048
CNM.simple-methods	0.050	0.002	0.052
GLA-methods	0.008	0.002	0.011
LA-methods	0.003	0.001	0.004
LiquidAssociation-package	0.169	0.025	0.194
getsGLA-methods	7.155	0.340	7.495
getsLA-methods	4.157	0.113	4.270
plotGLA-methods	0.033	0.002	1.041