BioC 3.2: CHECK report for MLInterfaces on perceval

Package: MLInterfaces

Version: 1.50.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MLInterfaces_1.50.0.tar.gz

StartedAt: 2015-11-10 07:08:57 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 07:12:19 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 202.4 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_1.50.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MLInterfaces.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.50.0’
* 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 ... [15s/15s] 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘ada:::predict.ada’ ‘e1071:::predict.svm’ ‘MASS:::predict.lda’
  ‘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’
* 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 ... [43s/41s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
MLearn-new 18.6  1.852   20.69
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [8s/8s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	18.600	1.852	20.690
RAB	0.234	0.002	0.236
balKfold.xvspec	0.067	0.002	0.069
classifierOutput-class	2.614	0.763	3.236
clusteringOutput-class	0.002	0.002	0.002
confuMat-methods	0.351	0.056	0.406
confuTab	0.009	0.003	0.011
fs.absT	0.085	0.014	0.099
fsHistory	2.840	0.357	0.180
hclustWidget	0.003	0.000	0.003
learnerSchema-class	0.002	0.002	0.002
performance-analytics	0.006	0.003	0.009
planarPlot-methods	2.915	0.390	3.362
plspinHcube	0.001	0.000	0.001
predict.classifierOutput	2.182	0.055	2.237
projectLearnerToGrid	0.920	0.068	1.016
projectedLearner-class	0.002	0.000	0.003
raboostCont-class	0.001	0.000	0.002
varImpStruct-class	0.923	0.039	1.007
xvalLoop	0.002	0.000	0.002
xvalSpec	0.248	0.185	0.351