Package: flowFit

Version: 1.24.0

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_1.24.0.tar.gz

StartedAt: 2020-04-15 02:21:32 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:22:40 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 68.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowFit.Rcheck

Warnings: 1

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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_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/flowFit.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.24.0’
* 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 ‘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:
   use the Contact field instead
* 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 ... WARNING
Missing link or links in documentation object 'parentFittingData-class.Rd':
  ‘Data’

Missing link or links in documentation object 'proliferationFittingData-class.Rd':
  ‘Data’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 5.665  0.307   6.015
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-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	5.665	0.307	6.015
generationsDistance	0	0	0
getGenerations	0.423	0.016	0.440
logTicks	0.034	0.006	0.041
parentFitting	0.442	0.027	0.472
parentFittingData-class	0.053	0.007	0.060
proliferationFitting	4.166	0.171	4.356
proliferationFittingData-class	0.291	0.022	0.318
proliferationGrid	0.003	0.000	0.003
proliferationIndex	0.247	0.012	0.260