BioC 3.3: CHECK report for MLInterfaces on linux2.bioconductor.org

Package: MLInterfaces

Version: 1.51.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MLInterfaces_1.51.0.tar.gz

StartedAt: 2015-10-27 05:54:39 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:56:52 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 132.9 seconds

RetCode: 0

Status:  OK

CheckDir: MLInterfaces.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MLInterfaces_1.51.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/MLInterfaces.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLInterfaces/DESCRIPTION’ ... OK
* this is package ‘MLInterfaces’ version ‘1.51.0’
* 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 ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘MLInterfaces’ for: ‘plot’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘MASS:::predict.lda’ ‘ada:::predict.ada’ ‘e1071:::predict.svm’
  ‘rpart:::predict.rpart’ ‘stats:::plot.hclust’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
hclustWidget : <anonymous>: no visible global function definition for
  ‘:=’
hclustWidget : <anonymous>: no visible binding for global variable
  ‘key’
Undefined global functions or variables:
  := key
* checking Rd files ... NOTE
prepare_Rd: plspinHcube.Rd:17-19: Dropping empty section \details
* 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 files in ‘vignettes’ ... OK
* checking examples ... [26s/25s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
MLearn-new 12.453  0.475  12.444
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [5s/5s]
 [5s/5s] OK
* 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
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-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	12.453	0.475	12.444
RAB	0.109	0.000	0.109
balKfold.xvspec	0.018	0.000	0.018
classifierOutput-class	1.350	0.128	1.603
clusteringOutput-class	0.001	0.000	0.001
confuMat-methods	0.204	0.012	0.217
confuTab	0.003	0.000	0.005
fs.absT	0.024	0.004	0.028
fsHistory	1.454	0.100	0.064
hclustWidget	0.002	0.000	0.002
learnerSchema-class	0.001	0.000	0.000
performance-analytics	0.003	0.000	0.004
planarPlot-methods	2.192	0.076	2.273
plspinHcube	0.001	0.000	0.001
predict.classifierOutput	1.209	0.012	1.223
projectLearnerToGrid	0.714	0.020	0.736
projectedLearner-class	0.002	0.000	0.002
raboostCont-class	0.002	0.000	0.002
varImpStruct-class	0.702	0.004	0.708
xvalLoop	0.003	0.000	0.003
xvalSpec	0.154	0.071	0.187