Package: dyebias

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch dyebias_1.18.0.tar.gz

StartedAt: 2013-05-01 04:53:56 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 04:56:14 -0700 (Wed, 01 May 2013)

EllapsedTime: 137.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: dyebias.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/dyebias.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'dyebias/DESCRIPTION' ... OK
* this is package 'dyebias' version '1.18.0'
* 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 'dyebias' can be installed ... [6s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 for unstated 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
dyebias.apply.correction: no visible global function definition for
  'maR<-'
dyebias.apply.correction: no visible global function definition for
  'maG<-'
* checking Rd files ... WARNING
checkRd: (3) dyebias.application.subset.Rd:16-20: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.apply.correction.Rd:10-19: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.boxplot.Rd:17-23: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.estimate.iGSDBs.Rd:12-14: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.rgplot.Rd:17-32: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.trendplot.Rd:22-38: \synopsis will be removed in R 3.1.0
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [73s/74s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
dyebias.rgplot             12.969  0.830  14.069
dyebias.trendplot          12.791  0.852  14.097
dyebias.boxplot            12.616  0.746  13.623
dyebias.application.subset 12.516  0.545  13.427
dyebias.apply.correction   11.579  0.749  12.708
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/dyebias.Rcheck/00check.log'
for details.

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

name	user	system	elapsed
dyebias.application.subset	12.516	0.545	13.427
dyebias.apply.correction	11.579	0.749	12.708
dyebias.boxplot	12.616	0.746	13.623
dyebias.estimate.iGSDBs	3.230	0.106	3.442
dyebias.monotonicity	0.041	0.021	0.064
dyebias.monotonicityplot	0.040	0.019	0.060
dyebias.rgplot	12.969	0.830	14.069
dyebias.trendplot	12.791	0.852	14.097