BioC 2.14: CHECK report for a4Base on morelia

Package: a4Base

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Base_1.12.0.tar.gz

StartedAt: 2014-10-07 20:58:28 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:02:56 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 267.7 seconds

RetCode: 0

Status:  OK

CheckDir: a4Base.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Base_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/a4Base.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘JavaGD’

Depends: includes the non-default packages:
  ‘grid’ ‘Biobase’ ‘AnnotationDbi’ ‘annaffy’ ‘mpm’ ‘genefilter’ ‘limma’
  ‘multtest’ ‘glmnet’ ‘a4Preproc’ ‘a4Core’ ‘gplots’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘a4Base’ can be installed ... [20s/21s] OK
* checking installed package size ... OK
* checking package 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘Biobase’ ‘grid’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘AnnotationDbi’ ‘a4Preproc’ ‘annaffy’ ‘genefilter’ ‘glmnet’ ‘gplots’
  ‘mpm’ ‘multtest’
  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
plotLogRatio: no visible global function definition for ‘JavaGD’
plotLogRatio: no visible global function definition for ‘grid.garnish’
plotLogRatio: no visible global function definition for
  ‘grid.hyperlink’
plotLogRatio: no visible global function definition for ‘grid.script’
plotLogRatio: no visible global function definition for ‘gridToSVG’
* 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 examples ... [86s/88s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
spectralMap     13.922  0.724  14.731
computeLogRatio 10.526  0.189  10.914
plotLogRatio     9.728  0.152   9.948
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/a4Base.Rcheck/00check.log’
for details.

* installing *source* package ‘a4Base’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (a4Base)

name	user	system	elapsed
a4palette	0.019	0.000	0.020
addQuantilesColors	3.171	0.162	3.347
boxPlot	2.950	0.105	3.061
combineTwoExpressionSet	0.001	0.001	0.001
computeLogRatio	10.526	0.189	10.914
createExpressionSet	0.101	0.001	0.102
filterVarInt	2.474	0.102	2.580
heatmap.expressionSet	0.005	0.001	0.006
histPvalue	2.592	0.088	2.929
histpvalueplotter	2.599	0.091	2.728
lassoReg	2.577	0.086	2.686
logReg	0.001	0.000	0.001
nlcvTT	0.001	0.000	0.001
plot1gene	2.626	0.099	2.873
plotComb2Samples	2.456	0.086	2.694
plotCombMultSamples	2.824	0.122	4.134
plotCombination2genes	2.419	0.080	2.503
plotLogRatio	9.728	0.152	9.948
probabilitiesPlot	0.001	0.001	0.001
probe2gene	2.624	0.070	2.696
profilesPlot	2.361	0.052	2.430
propdegenescalculation	2.678	0.074	2.758
replicates	0.003	0.000	0.003
spectralMap	13.922	0.724	14.731
tTest	2.463	0.080	2.591
volcanoPlot	3.025	0.123	3.657