Package: flowFit

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowFit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowFit_1.22.0.tar.gz

StartedAt: 2019-10-16 02:51:27 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:53:08 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 100.8 seconds

RetCode: 0

Status:  OK

CheckDir: flowFit.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:flowFit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowFit_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowFit.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 ‘flowFit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowFit’ version ‘1.22.0’
* 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 ‘flowFit’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.generationsPercent: no visible global function definition for
  ‘integrate’
parentFitting: no visible global function definition for ‘sd’
parentFitting: no visible global function definition for ‘hist’
proliferationFitting: no visible global function definition for ‘hist’
proliferationGrid: no visible global function definition for ‘rgb’
proliferationGrid: no visible global function definition for ‘dev.cur’
proliferationGrid: no visible global function definition for ‘abline’
plot,parentFittingData-ANY: no visible global function definition for
  ‘par’
plot,parentFittingData-ANY: no visible global function definition for
  ‘layout’
plot,parentFittingData-ANY: no visible global function definition for
  ‘lines’
plot,parentFittingData-ANY: no visible global function definition for
  ‘axis’
plot,parentFittingData-ANY: no visible global function definition for
  ‘plot.new’
plot,parentFittingData-ANY: no visible binding for global variable
  ‘black’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘dev.interactive’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘par’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘rainbow’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘layout’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘lines’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘axis’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘plot.new’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘polygon’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘text’
plot,proliferationFittingData-ANY: no visible binding for global
  variable ‘black’
summary,parentFittingData: no visible global function definition for
  ‘df.residual’
summary,proliferationFittingData: no visible global function definition
  for ‘df.residual’
Undefined global functions or variables:
  abline axis black dev.cur dev.interactive df.residual hist integrate
  layout lines par plot.new polygon rainbow rgb sd text
Consider adding
  importFrom("grDevices", "dev.cur", "dev.interactive", "rainbow", "rgb")
  importFrom("graphics", "abline", "axis", "hist", "layout", "lines",
             "par", "plot.new", "polygon", "text")
  importFrom("stats", "df.residual", "integrate", "sd")
to your NAMESPACE file.
* 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
flowFit-package      6.417  0.777   7.216
proliferationFitting 4.975  0.563   5.548
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowFit.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 flowFit
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘flowFit’ ...
** using staged installation
** R
** demo
** 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 (flowFit)

name	user	system	elapsed
flowFit-package	6.417	0.777	7.216
generationsDistance	0.000	0.000	0.001
getGenerations	0.511	0.032	0.543
logTicks	0.061	0.011	0.073
parentFitting	0.489	0.036	0.526
parentFittingData-class	0.055	0.011	0.066
proliferationFitting	4.975	0.563	5.548
proliferationFittingData-class	0.350	0.042	0.465
proliferationGrid	0.003	0.001	0.005
proliferationIndex	0.306	0.034	0.341