BioC 3.3: CHECK report for MLInterfaces on morelia

Package: MLInterfaces

Version: 1.51.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MLInterfaces_1.51.0.tar.gz

StartedAt: 2015-10-22 08:32:46 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 08:35:07 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 140.3 seconds

RetCode: 0

Status:  OK

CheckDir: MLInterfaces.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MLInterfaces_1.51.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MLInterfaces.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [9s/10s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [30s/29s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
MLearn-new 14.424  1.237  16.482
* 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
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/MLInterfaces.Rcheck/00check.log’
for details.

* installing *source* package ‘MLInterfaces’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
* DONE (MLInterfaces)

name	user	system	elapsed
MLearn-new	14.424	1.237	16.482
RAB	0.112	0.002	0.114
balKfold.xvspec	0.024	0.001	0.025
classifierOutput-class	1.357	0.423	1.752
clusteringOutput-class	0.001	0.003	0.004
confuMat-methods	0.285	0.028	0.313
confuTab	0.008	0.001	0.010
fs.absT	0.062	0.011	0.072
fsHistory	1.552	0.205	0.133
hclustWidget	0.001	0.000	0.002
learnerSchema-class	0.001	0.001	0.002
performance-analytics	0.003	0.001	0.004
planarPlot-methods	2.103	0.174	2.294
plspinHcube	0.001	0.000	0.000
predict.classifierOutput	1.434	0.041	1.497
projectLearnerToGrid	0.533	0.037	0.613
projectedLearner-class	0.001	0.000	0.001
raboostCont-class	0.001	0.000	0.002
varImpStruct-class	0.529	0.023	0.606
xvalLoop	0.002	0.000	0.002
xvalSpec	0.188	0.106	0.230