BioC 3.5: CHECK report for MLInterfaces on oaxaca

Package: MLInterfaces

Version: 1.55.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MLInterfaces_1.55.0.tar.gz

StartedAt: 2017-03-04 05:58:10 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 06:01:28 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 198.2 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 MLInterfaces_1.55.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MLInterfaces.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.55.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘MLInterfaces’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/MLInterfaces.Rcheck/00install.out’ for details.
* 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:
  ‘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 ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
MLearn-new 20.284  1.536  21.658
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/MLInterfaces.Rcheck/00check.log’
for details.

* installing *source* package ‘MLInterfaces’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘MLInterfaces’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘MLInterfaces’
* DONE (MLInterfaces)

name	user	system	elapsed
MLearn-new	20.284	1.536	21.658
RAB	0.152	0.013	0.166
balKfold.xvspec	0.028	0.003	0.031
classifierOutput-class	1.339	0.280	1.433
clusteringOutput-class	0.002	0.001	0.002
confuMat-methods	0.273	0.037	0.326
confuTab	0.009	0.002	0.010
fs.absT	0.067	0.014	0.082
fsHistory	1.219	0.200	0.138
hclustWidget	0.001	0.000	0.002
learnerSchema-class	0.001	0.000	0.001
performance-analytics	0.006	0.004	0.010
planarPlot-methods	3.361	0.252	3.616
plspinHcube	0	0	0
predict.classifierOutput	4.042	0.051	4.124
projectLearnerToGrid	0.752	0.054	0.863
projectedLearner-class	0.002	0.000	0.003
raboostCont-class	0.002	0.000	0.002
varImpStruct-class	0.760	0.035	0.879
xvalLoop	0.001	0.001	0.001
xvalSpec	0.172	0.105	0.226