BioC 2.14: CHECK report for MLInterfaces on petty

Package: MLInterfaces

Version: 1.44.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MLInterfaces_1.44.1.tar.gz

StartedAt: 2014-10-07 22:58:45 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:05:56 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 431.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MLInterfaces.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MLInterfaces_1.44.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/MLInterfaces.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.44.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘MASS’ ‘genefilter’ ‘rpart’ ‘rda’ ‘annotate’ ‘cluster’
  ‘sfsmisc’
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 ‘MLInterfaces’ can be installed ... [33s/35s] 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 ... WARNING
Unknown package ‘multicore’ in Rd xrefs
* 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 files in ‘vignettes’ ... OK
* checking examples ... [75s/70s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
MLearn-new               32.94  2.735  34.824
predict.classifierOutput  6.35  0.062   6.452
* 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 was 1 warning.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	32.940	2.735	34.824
RAB	0.263	0.007	0.270
balKfold.xvspec	0.023	0.002	0.025
classifierOutput-class	3.439	1.024	4.130
clusteringOutput-class	0.003	0.000	0.004
confuMat-methods	0.551	0.105	0.657
fs.absT	0.040	0.006	0.044
fsHistory	3.498	0.535	0.301
learnerSchema-class	0.002	0.001	0.002
planarPlot-methods	3.913	0.534	4.685
predict.classifierOutput	6.350	0.062	6.452
raboostCont-class	0.002	0.000	0.003
varImpStruct-class	1.550	0.102	1.695
xvalLoop	0.003	0.001	0.004
xvalSpec	0.309	0.265	0.426