Package: pint

Version: 1.33.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pint.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pint_1.33.0.tar.gz

StartedAt: 2019-04-09 02:52:45 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:55:25 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 159.3 seconds

RetCode: 0

Status:  OK

CheckDir: pint.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pint.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pint_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/pint.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pint/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pint’ version ‘1.33.0’
* 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 ‘pint’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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:
  ‘Matrix’ ‘methods’ ‘mvtnorm’
  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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.ChromosomeModels plot.GeneDependencyModel plot.GenomeModels
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
W.effects: no visible global function definition for ‘princomp’
W.effects: no visible global function definition for ‘cor’
calculate.arm: no visible global function definition for ‘as’
calculate.arm: no visible global function definition for ‘new’
calculate.arm.sparse: no visible global function definition for ‘new’
calculate.chr: no visible global function definition for ‘new’
calculate.chr.sparse: no visible global function definition for ‘new’
calculate.genome: no visible global function definition for ‘new’
calculate.genome.sparse: no visible global function definition for
  ‘new’
imputation: no visible global function definition for ‘rnorm’
imputation: no visible global function definition for ‘sd’
join.top.regions: no visible global function definition for ‘quantile’
plot.ChromosomeModels: no visible global function definition for ‘par’
plot.ChromosomeModels: no visible global function definition for
  ‘abline’
plot.ChromosomeModels: no visible global function definition for
  ‘points’
plot.ChromosomeModels: no visible global function definition for ‘text’
plot.ChromosomeModels: no visible global function definition for
  ‘lines’
plot.GeneDependencyModel: no visible global function definition for
  ‘gray’
plot.GeneDependencyModel: no visible global function definition for
  ‘par’
plot.GeneDependencyModel: no visible global function definition for
  ‘layout’
plot.GeneDependencyModel: no visible global function definition for
  ‘barplot’
plot.GeneDependencyModel: no visible global function definition for
  ‘legend’
plot.GeneDependencyModel: no visible global function definition for
  ‘mtext’
plot.GenomeModels: no visible global function definition for ‘par’
plot.GenomeModels: no visible global function definition for ‘abline’
plot.GenomeModels: no visible global function definition for ‘points’
plot.GenomeModels: no visible global function definition for ‘text’
plot.GenomeModels: no visible global function definition for ‘lines’
plot.GenomeModels: no visible global function definition for ‘axis’
summarize.region.parameters: no visible global function definition for
  ‘na.omit’
summarize.region.parameters: no visible global function definition for
  ‘cor’
z.effects: no visible global function definition for ‘princomp’
coerce,GeneDependencyModel-DependencyModel: no visible global function
  definition for ‘new’
coerce<-,GeneDependencyModel-DependencyModel: no visible global
  function definition for ‘slot<-’
coerce<-,GeneDependencyModel-DependencyModel: no visible global
  function definition for ‘slot’
getPArm,ChromosomeModels: no visible global function definition for
  ‘new’
getQArm,ChromosomeModels: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  abline as axis barplot cor gray layout legend lines mtext na.omit new
  par points princomp quantile rnorm sd slot slot<- text
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "barplot", "layout", "legend",
             "lines", "mtext", "par", "points", "text")
  importFrom("methods", "as", "new", "slot", "slot<-")
  importFrom("stats", "cor", "na.omit", "princomp", "quantile", "rnorm",
             "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
screen                    41.413  0.840  42.519
ChromosomeModels-class    33.442  0.911  34.456
plot                      10.304  0.144  10.509
GeneDependencyModel-class  9.464  0.170   9.659
* 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/pint.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pint
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘pint’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pint)

name	user	system	elapsed
ChromosomeModels-class	33.442	0.911	34.456
GeneDependencyModel-class	9.464	0.170	9.659
fit.byname	0.098	0.003	0.102
get.neighboring.probes	0	0	0
get.neighs	0.000	0.000	0.001
join.top.regions	0.001	0.000	0.000
order.feature.info	0.001	0.000	0.000
pint.data	0.062	0.002	0.064
plot	10.304	0.144	10.509
screen	41.413	0.840	42.519
summarize.region.parameters	0.000	0.000	0.001
window	0.152	0.003	0.159
z.effect	0.118	0.007	0.124