BioC 3.4: CHECK report for quantro on malbec1

Package: quantro

Version: 1.8.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings quantro_1.8.0.tar.gz

StartedAt: 2017-04-15 00:39:22 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:42:52 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 210.4 seconds

RetCode: 0

Status:  OK

CheckDir: quantro.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings quantro_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/quantro.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘quantro/DESCRIPTION’ ... OK
* this is package ‘quantro’ version ‘1.8.0’
* 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 ‘quantro’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
matboxplot: no visible global function definition for ‘palette’
matboxplot: no visible global function definition for ‘boxplot’
matdensity : getdensity : <anonymous>: no visible global function
  definition for ‘density’
matdensity: no visible global function definition for ‘palette’
matdensity: no visible global function definition for ‘matplot’
quantro: no visible binding for global variable ‘median’
quantro: no visible global function definition for ‘lm’
quantro: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  boxplot density lm matplot median palette quantile
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "boxplot", "matplot")
  importFrom("stats", "density", "lm", "median", "quantile")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/quantro.Rcheck/00check.log’
for details.

* installing *source* package ‘quantro’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (quantro)

name	user	system	elapsed
MSbetween	2.436	0.020	2.455
MSwithin	1.124	0.016	1.139
anova	1.136	0.008	1.145
matboxplot	1.020	0.012	1.031
matdensity	0.640	0.012	0.653
quantro	1.600	0.004	1.602
quantroPlot	0	0	0
quantroPvalPerm	1.604	0.004	1.608
quantroStat	1.168	0.004	1.175
quantroStatPerm	1.236	0.004	1.241
summary	1.596	0.008	1.605