BioC 3.3: CHECK report for acde on oaxaca

Package: acde

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings acde_1.2.0.tar.gz

StartedAt: 2016-10-12 23:03:50 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 23:05:15 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 84.2 seconds

RetCode: 0

Status:  OK

CheckDir: acde.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 acde_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/acde.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 ‘acde/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘acde’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘acde’ 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
ac: no visible global function definition for ‘var’
ac2: no visible global function definition for ‘var’
fdr: no visible global function definition for ‘quantile’
plot.STP: no visible global function definition for ‘par’
plot.STP: no visible global function definition for ‘plot’
plot.STP: no visible global function definition for ‘polygon’
plot.STP: no visible global function definition for ‘abline’
plot.STP: no visible global function definition for ‘lines’
plot.STP: no visible global function definition for ‘legend’
plot.STP: no visible global function definition for ‘points’
plot.TC: no visible global function definition for ‘par’
plot.TC: no visible global function definition for ‘barplot’
plot.TC: no visible global function definition for ‘plot’
plot.TC: no visible global function definition for ‘mtext’
stp: no visible global function definition for ‘var’
stp: no visible global function definition for ‘cor’
summary.TC: no visible global function definition for ‘addmargins’
tc: no visible global function definition for ‘var’
tc: no visible global function definition for ‘cor’
Undefined global functions or variables:
  abline addmargins barplot cor legend lines mtext par plot points
  polygon quantile var
Consider adding
  importFrom("graphics", "abline", "barplot", "legend", "lines", "mtext",
             "par", "plot", "points", "polygon")
  importFrom("stats", "addmargins", "cor", "quantile", "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 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
bcaFDR 46.955   0.38  47.419
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/acde.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
ac	0.204	0.023	0.227
acde-package	3.024	0.048	3.089
bcaFDR	46.955	0.380	47.419
fdr	0.690	0.006	0.699
phytophthora	0.021	0.003	0.022
plot.STP	0.767	0.005	0.774
plot.TC	2.176	0.013	2.197
print.STP	0.733	0.005	0.740
print.TC	2.229	0.036	2.273
qval	0.714	0.004	0.720
stp	0.705	0.002	0.709
tc	2.102	0.030	2.139