BioC 3.5: CHECK report for plgem on oaxaca

Package: plgem

Version: 1.47.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings plgem_1.47.0.tar.gz

StartedAt: 2017-03-04 07:10:16 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:11:07 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 51.1 seconds

RetCode: 0

Status:  OK

CheckDir: plgem.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 plgem_1.47.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/plgem.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plgem/DESCRIPTION’ ... OK
* this is package ‘plgem’ version ‘1.47.0’
* 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 ‘plgem’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plgem.fit : <anonymous>: no visible global function definition for ‘sd’
plgem.fit: no visible global function definition for ‘quantile’
plgem.fit: no visible global function definition for ‘median’
plgem.fit: no visible global function definition for ‘lm’
plgem.fit: no visible global function definition for ‘coef’
plgem.fit: no visible global function definition for ‘summary.lm’
plgem.fit: no visible global function definition for ‘cor’
plgem.fit: no visible global function definition for ‘png’
plgem.fit: no visible global function definition for ‘layout’
plgem.fit: no visible global function definition for ‘par’
plgem.fit: no visible global function definition for ‘contour’
plgem.fit: no visible global function definition for ‘colors’
plgem.fit: no visible global function definition for ‘points’
plgem.fit: no visible global function definition for ‘abline’
plgem.fit: no visible global function definition for ‘text’
plgem.fit: no visible global function definition for ‘hist’
plgem.fit: no visible global function definition for ‘box’
plgem.fit: no visible global function definition for ‘qqnorm’
plgem.fit: no visible global function definition for ‘dev.off’
plgem.fit: no visible global function definition for ‘mtext’
plgem.pValue: no visible binding for global variable ‘ecdf’
Undefined global functions or variables:
  abline box coef colors contour cor dev.off ecdf hist layout lm median
  mtext par png points qqnorm quantile sd summary.lm text
Consider adding
  importFrom("grDevices", "colors", "dev.off", "png")
  importFrom("graphics", "abline", "box", "contour", "hist", "layout",
             "mtext", "par", "points", "text")
  importFrom("stats", "coef", "cor", "ecdf", "lm", "median", "qqnorm",
             "quantile", "sd", "summary.lm")
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
plgem.deg    5.100  0.555   5.661
plgem.pValue 4.934  0.514   5.450
run.plgem    4.745  0.592   5.340
* 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-3.5-bioc/meat/plgem.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
LPSeset	0.078	0.007	0.085
plgem.deg	5.100	0.555	5.661
plgem.fit	1.209	0.158	1.367
plgem.obsStn	0.786	0.019	0.805
plgem.pValue	4.934	0.514	5.450
plgem.resampledStn	2.336	0.467	2.806
plgem.write.summary	0.001	0.000	0.001
run.plgem	4.745	0.592	5.340
setGpar	0.000	0.000	0.001