BioC 3.5: CHECK report for pcot2 on toluca2

Package: pcot2

Version: 1.43.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pcot2_1.43.0.tar.gz

StartedAt: 2017-04-23 07:50:09 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 07:51:10 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 61.1 seconds

RetCode: 0

Status:  OK

CheckDir: pcot2.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 pcot2_1.43.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/pcot2.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcot2/DESCRIPTION’ ... OK
* this is package ‘pcot2’ version ‘1.43.0’
* 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 ‘pcot2’ 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
'library' or 'require' call to ‘amap’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Cor: no visible global function definition for ‘var’
Cor: no visible global function definition for ‘cov2cor’
aveProbe: no visible binding for global variable ‘median’
corplot: no visible global function definition for ‘hclust’
corplot2: no visible global function definition for ‘cor’
corplot2: no visible global function definition for ‘layout’
corplot2: no visible global function definition for ‘par’
corplot2: no visible global function definition for ‘hclust’
corplot2: no visible global function definition for ‘image’
corplot2: no visible global function definition for ‘title’
corplot2: no visible global function definition for ‘box’
corplot2: no visible global function definition for ‘axis’
corplot2: no visible global function definition for ‘plot.new’
geneLocator: no visible global function definition for ‘plot.new’
geneLocator: no visible global function definition for ‘par’
geneLocator: no visible global function definition for ‘image’
geneLocator: no visible global function definition for ‘title’
geneLocator: no visible global function definition for ‘axis’
geneLocator: no visible global function definition for ‘locator’
pco: no visible global function definition for ‘cmdscale’
pcot2: no visible global function definition for ‘p.adjust’
plotCor: no visible global function definition for ‘par’
plotCor: no visible global function definition for ‘layout’
plotCor: no visible global function definition for ‘image’
plotCor: no visible global function definition for ‘title’
plotCor: no visible global function definition for ‘box’
plotCor: no visible global function definition for ‘axis’
rb: no visible global function definition for ‘rgb’
rg: no visible global function definition for ‘rgb’
rg: no visible global function definition for ‘dnorm’
t2: no visible global function definition for ‘var’
t2: no visible global function definition for ‘pf’
t2.unequ: no visible global function definition for ‘var’
wb: no visible global function definition for ‘rgb’
wb: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  axis box cmdscale cor cov2cor dnorm hclust image layout locator
  median p.adjust par pf plot.new rgb title var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "box", "image", "layout", "locator",
             "par", "plot.new", "title")
  importFrom("stats", "cmdscale", "cor", "cov2cor", "dnorm", "hclust",
             "median", "p.adjust", "pf", "var")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
pcot2    13.276  1.110  14.855
aveProbe  9.225  0.268   9.562
* 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-3.5-bioc/meat/pcot2.Rcheck/00check.log’
for details.

* installing *source* package ‘pcot2’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pcot2)

name	user	system	elapsed
aveProbe	9.225	0.268	9.562
corplot	1.402	0.093	1.756
corplot2	1.848	0.086	2.577
getImat	0.493	0.035	0.530
pcot2	13.276	1.110	14.855