BioC 3.5: CHECK report for MLInterfaces on malbec2

Package: MLInterfaces

Version: 1.56.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MLInterfaces_1.56.0.tar.gz

StartedAt: 2017-10-18 00:54:22 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:57:07 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 164.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MLInterfaces.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MLInterfaces_1.56.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/MLInterfaces.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.56.0’
* 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 ‘/home/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 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 14.572  0.728  15.247
* 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
  ‘/home/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	14.572	0.728	15.247
RAB	0.132	0.000	0.130
balKfold.xvspec	0.024	0.004	0.032
classifierOutput-class	1.336	0.132	1.902
clusteringOutput-class	0.004	0.000	0.002
confuMat-methods	0.264	0.012	0.275
confuTab	0.004	0.000	0.006
fs.absT	0.036	0.000	0.038
fsHistory	1.608	0.268	0.089
hclustWidget	0.000	0.004	0.002
learnerSchema-class	0.000	0.000	0.001
performance-analytics	0.004	0.000	0.008
planarPlot-methods	3.004	0.132	3.153
plspinHcube	0.000	0.000	0.001
predict.classifierOutput	3.228	0.004	3.235
projectLearnerToGrid	0.636	0.052	0.714
projectedLearner-class	0.000	0.000	0.001
raboostCont-class	0.000	0.000	0.002
varImpStruct-class	0.736	0.052	0.824
xvalLoop	0.004	0.000	0.001
xvalSpec	0.120	0.048	0.252