BioC 2.13: CHECK report for MLInterfaces on perceval

Package: MLInterfaces

Version: 1.42.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MLInterfaces_1.42.0.tar.gz

StartedAt: 2014-04-05 02:42:31 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:49:16 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 404.6 seconds

RetCode: 0

Status:  OK

CheckDir: MLInterfaces.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/MLInterfaces.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 ‘MLInterfaces/DESCRIPTION’ ... OK
* this is package ‘MLInterfaces’ 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 ‘MLInterfaces’ can be installed ... [27s/28s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘rpart’ ‘MASS’ ‘gbm’ ‘mboost’ ‘sfsmisc’
A package should be listed in only one of these fields.
* 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’ call to ‘sfsmisc’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘genefilter’ ‘MASS’ ‘rda’ ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ‘:::’ call: ‘rpart:::predict.rpart’
  See the note in ?`:::` about the use of this operator.
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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘multicore’
* 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’:
  ‘MLint_devel.Rnw’, ‘MLInterfaces.Rnw’, ‘MLprac2_2.Rnw’,
  ‘xvalComputerClusters.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [70s/100s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
MLearn-new               30.866  4.834  53.274
predict.classifierOutput  6.252  0.161  11.907
planarPlot-methods        3.341  0.724   7.890
classifierOutput-class    2.287  0.870   6.460
* 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/MLInterfaces.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
MLearn-new	30.866	4.834	53.274
RAB	0.252	0.019	0.555
balKfold.xvspec	0.095	0.019	0.224
classifierOutput-class	2.287	0.870	6.460
clusteringOutput-class	0.005	0.006	0.021
confuMat-methods	0.426	0.099	1.005
fs.absT	0.057	0.013	0.124
fsHistory	2.863	0.652	0.532
learnerSchema-class	0.004	0.005	0.010
planarPlot-methods	3.341	0.724	7.890
predict.classifierOutput	6.252	0.161	11.907
raboostCont-class	0.003	0.004	0.018
varImpStruct-class	1.250	0.138	2.680
xvalLoop	0.008	0.017	0.056
xvalSpec	0.280	0.382	0.677