BioC 3.1: CHECK report for OCplus on petty

Package: OCplus

Version: 1.42.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OCplus_1.42.0.tar.gz

StartedAt: 2015-10-09 00:53:15 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:54:49 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 93.8 seconds

RetCode: 0

Status:  OK

CheckDir: OCplus.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 OCplus_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/OCplus.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OCplus/DESCRIPTION’ ... OK
* this is package ‘OCplus’ version ‘1.42.0’
* 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 ‘OCplus’ can be installed ... [5s/5s] 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
Package in Depends field not imported from: ‘akima’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot.fdr2d.result: no visible global function definition for ‘interp’
Tornadoplot: no visible global function definition for ‘interp’
Volcanoplot: no visible global function definition for ‘interp’
* checking Rd files ... NOTE
prepare_Rd: tstatistics.Rd:38-39: Dropping empty section \examples
* 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.FDR.result':
  ‘plot.FDR.result’

S3 methods shown with full name in documentation object 'plot.fdr1d.result':
  ‘plot.fdr1d.result’

S3 methods shown with full name in documentation object 'plot.fdr2d.result':
  ‘plot.fdr2d.result’

S3 methods shown with full name in documentation object 'summary.fdr.result':
  ‘summary.fdr.result’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [32s/33s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
samplesize 10.672  0.414  11.582
tMixture    6.541  0.412   7.480
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/OCplus.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
EOC	1.040	0.054	1.113
FDR	0.005	0.000	0.006
MAsim.smyth	0.444	0.020	0.466
OCshow	1.981	0.102	2.085
TOC	0.618	0.057	0.820
average.fdr	1.782	0.144	1.930
fdr1d	0.768	0.097	0.867
fdr2d	1.007	0.076	1.085
plot.FDR.result	0.200	0.023	0.223
plot.fdr1d.result	0.726	0.069	0.798
plot.fdr2d.result	1.138	0.076	1.217
samplesize	10.672	0.414	11.582
smooth1d	0.064	0.010	0.073
summary.fdr.result	0.845	0.079	0.934
tMixture	6.541	0.412	7.480