BioC 2.13: CHECK report for dyebias on perceval

Package: dyebias

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch dyebias_1.20.0.tar.gz

StartedAt: 2014-04-05 00:58:58 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:01:23 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 144.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: dyebias.Rcheck

Warnings: 2

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/dyebias.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dyebias/DESCRIPTION’ ... OK
* this is package ‘dyebias’ version ‘1.20.0’
* 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 ‘build’ 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): object ‘msb.2009.21’ not found
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘marray’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘dyebias-vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [82s/83s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
dyebias.rgplot             15.606  0.442  16.186
dyebias.trendplot          15.293  0.520  15.985
dyebias.boxplot            14.397  0.457  15.054
dyebias.apply.correction   13.972  0.430  14.599
dyebias.application.subset 13.651  0.403  14.408
* 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

WARNING: There were 2 warnings.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	13.651	0.403	14.408
dyebias.apply.correction	13.972	0.430	14.599
dyebias.boxplot	14.397	0.457	15.054
dyebias.estimate.iGSDBs	3.550	0.065	3.697
dyebias.monotonicity	0.028	0.019	0.048
dyebias.monotonicityplot	0.020	0.015	0.036
dyebias.rgplot	15.606	0.442	16.186
dyebias.trendplot	15.293	0.520	15.985