BioC 3.4: CHECK report for KEGGprofile on morelia

Package: KEGGprofile

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGprofile_1.15.0.tar.gz

StartedAt: 2016-09-20 08:26:25 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:28:05 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 100.5 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGprofile.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 KEGGprofile_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/KEGGprofile.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 ‘KEGGprofile/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGprofile’ version ‘1.15.0’
* 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 ‘KEGGprofile’ 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
col_by_value: no visible global function definition for ‘image’
col_by_value: no visible global function definition for ‘box’
col_by_value: no visible global function definition for ‘par’
col_by_value: no visible global function definition for ‘axis’
convertId: no visible global function definition for ‘flush.console’
download_KEGGfile: no visible global function definition for
  ‘download.file’
find_enriched_pathway: no visible global function definition for
  ‘phyper’
find_enriched_pathway: no visible global function definition for
  ‘p.adjust’
newIdMatrix: no visible binding for global variable ‘var’
pieGlyph2: no visible global function definition for ‘par’
pieGlyph2: no visible global function definition for ‘polygon’
pieGlyph2: no visible global function definition for ‘text’
plot_pathway_cor : <anonymous>: no visible global function definition
  for ‘sd’
plot_pathway_cor : <anonymous>: no visible global function definition
  for ‘cor’
plot_pathway_cor : <anonymous> : <anonymous>: no visible global
  function definition for ‘cor’
plot_pathway_cor : <anonymous>: no visible global function definition
  for ‘median’
plot_pathway_cor: no visible global function definition for
  ‘wilcox.test’
plot_pathway_cor: no visible global function definition for ‘par’
plot_pathway_cor: no visible global function definition for ‘boxplot’
plot_pathway_cor: no visible global function definition for ‘abline’
plot_polygon: no visible global function definition for ‘polygon’
plot_profile: no visible global function definition for ‘rainbow’
plot_profile: no visible global function definition for ‘png’
plot_profile: no visible global function definition for ‘par’
plot_profile: no visible global function definition for ‘plot’
plot_profile: no visible global function definition for ‘rasterImage’
plot_profile: no visible binding for global variable ‘var’
plot_profile: no visible global function definition for ‘matplot’
plot_profile: no visible global function definition for ‘text’
plot_profile: no visible global function definition for ‘legend’
plot_profile: no visible global function definition for ‘polygon’
plot_profile: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline axis box boxplot cor dev.off download.file flush.console image
  legend matplot median p.adjust par phyper plot png polygon rainbow
  rasterImage sd text var wilcox.test
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "abline", "axis", "box", "boxplot", "image",
             "legend", "matplot", "par", "plot", "polygon",
             "rasterImage", "text")
  importFrom("stats", "cor", "median", "p.adjust", "phyper", "sd", "var",
             "wilcox.test")
  importFrom("utils", "download.file", "flush.console")
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
plot_pathway 5.084  0.505  15.267
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/KEGGprofile.Rcheck/00check.log’
for details.

* installing *source* package ‘KEGGprofile’ ...
** 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 (KEGGprofile)

name	user	system	elapsed
col_by_value	0.021	0.002	0.024
convertId	0.601	0.010	1.705
download_KEGGfile	0.003	0.003	4.233
download_latest_pathway	0.001	0.000	0.000
find_enriched_pathway	1.690	0.056	1.765
newIdMatrix	0.001	0.000	0.002
parse_XMLfile	0.062	0.002	0.064
plot_pathway	5.084	0.505	15.267
plot_pathway_cor	1.866	0.080	1.947
plot_profile	1.146	0.095	1.257