Package: flowPlots

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowPlots.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowPlots_1.32.0.tar.gz

StartedAt: 2019-10-16 02:52:51 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:53:43 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 52.1 seconds

RetCode: 0

Status:  OK

CheckDir: flowPlots.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:flowPlots.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowPlots_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowPlots.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 ‘flowPlots/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowPlots’ version ‘1.32.0’
* 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 ‘flowPlots’ 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
Package in Depends field not imported from: ‘methods’
  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
GroupListBoxplot: no visible global function definition for ‘boxplot’
GroupListBoxplot: no visible global function definition for ‘points’
GroupListBoxplot: no visible global function definition for ‘axis’
GroupListBoxplot: no visible global function definition for ‘mtext’
GroupListBoxplot: no visible global function definition for ‘box’
GroupListBoxplot: no visible global function definition for ‘legend’
GroupListBoxplot: no visible global function definition for ‘title’
GroupListBoxplot: no visible global function definition for ‘text’
computePFDGroupStatsList: no visible global function definition for
  ‘sd’
get2GroupPValues: no visible global function definition for
  ‘wilcox.test’
getMultiGroupPValues: no visible global function definition for
  ‘kruskal.test’
readStackedData,character: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  axis box boxplot kruskal.test legend mtext points read.csv sd text
  title wilcox.test
Consider adding
  importFrom("graphics", "axis", "box", "boxplot", "legend", "mtext",
             "points", "text", "title")
  importFrom("stats", "kruskal.test", "sd", "wilcox.test")
  importFrom("utils", "read.csv")
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 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
StackedData-class 7.924  0.176   8.103
* 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/flowPlots.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 flowPlots
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘flowPlots’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (flowPlots)

name	user	system	elapsed
GroupListBoxplot	0.133	0.012	0.145
StackedData-class	7.924	0.176	8.103
adultsNeonates	0.001	0.002	0.004
computeMarginalData-methods	1.799	0.009	1.809
computeMarkers-methods	0.001	0.000	0.002
computePFDData-methods	1.807	0.101	1.908
computePFDGroupStatsList	0.306	0.019	0.332
computePFDPartsData-methods	2.224	0.060	2.284
computeProfileData-methods	2.029	0.043	2.072
legendPFDStatsGroupNames	0.096	0.004	0.100
makeBarplotData	0.013	0.004	0.017
makeDataList	0.055	0.003	0.059
makeTernaryData	0.096	0.006	0.102
marginalDF	0.002	0.002	0.003
marginalData-methods	0.002	0.002	0.004
markerMatrix	0.001	0.001	0.003
markers-methods	0.002	0.001	0.004
pfdDF	0.002	0.002	0.004
pfdData-methods	0.003	0.002	0.005
pfdPartsData-methods	0.004	0.003	0.005
pfdPartsList	0.001	0.001	0.002
profileDF	0.002	0.001	0.003
profileData-methods	0.003	0.002	0.005
readStackedData-methods	0.045	0.003	0.049
stackedData-methods	0.064	0.006	0.071