Package: pint

Version: 1.34.0

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_1.34.0.tar.gz

StartedAt: 2019-10-16 05:35:22 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:38:47 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 204.3 seconds

RetCode: 0

Status:  OK

CheckDir: pint.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:pint.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pint_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/pint.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 ‘pint/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pint’ version ‘1.34.0’
* 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                    51.172  2.117  53.402
ChromosomeModels-class    43.962  2.512  46.519
plot                      12.760  0.505  13.416
GeneDependencyModel-class 12.538  0.526  13.157
* 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.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pint
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘pint’ ...
** using staged installation
** 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 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 (pint)

name	user	system	elapsed
ChromosomeModels-class	43.962	2.512	46.519
GeneDependencyModel-class	12.538	0.526	13.157
fit.byname	0.120	0.005	0.124
get.neighboring.probes	0.000	0.000	0.001
get.neighs	0.000	0.001	0.000
join.top.regions	0	0	0
order.feature.info	0.000	0.000	0.001
pint.data	0.059	0.004	0.063
plot	12.760	0.505	13.416
screen	51.172	2.117	53.402
summarize.region.parameters	0	0	0
window	0.140	0.012	0.152
z.effect	0.086	0.005	0.092