BioC 3.3: CHECK report for flowPlots on oaxaca

Package: flowPlots

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowPlots_1.20.0.tar.gz

StartedAt: 2016-10-13 01:35:50 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 01:36:27 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 37.3 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 --no-vignettes --timings flowPlots_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/flowPlots.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.20.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
StackedData-class 6.062  0.035   6.102
* 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-3.3-bioc/meat/flowPlots.Rcheck/00check.log’
for details.

* installing *source* package ‘flowPlots’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowPlots)

name	user	system	elapsed
GroupListBoxplot	0.122	0.005	0.128
StackedData-class	6.062	0.035	6.102
adultsNeonates	0.002	0.000	0.003
computeMarginalData-methods	1.666	0.008	1.676
computeMarkers-methods	0.001	0.000	0.002
computePFDData-methods	1.305	0.008	1.314
computePFDGroupStatsList	0.224	0.006	0.230
computePFDPartsData-methods	1.832	0.005	1.840
computeProfileData-methods	1.800	0.008	1.811
legendPFDStatsGroupNames	0.066	0.002	0.068
makeBarplotData	0.012	0.002	0.012
makeDataList	0.038	0.001	0.039
makeTernaryData	0.072	0.002	0.074
marginalDF	0.002	0.001	0.002
marginalData-methods	0.003	0.001	0.003
markerMatrix	0.002	0.001	0.003
markers-methods	0.002	0.001	0.003
pfdDF	0.001	0.000	0.002
pfdData-methods	0.003	0.001	0.003
pfdPartsData-methods	0.003	0.001	0.003
pfdPartsList	0.001	0.001	0.003
profileDF	0.001	0.000	0.002
profileData-methods	0.002	0.000	0.003
readStackedData-methods	0.102	0.002	0.103
stackedData-methods	0.127	0.002	0.130