BioC 3.5: CHECK report for MLInterfaces on tokay2

Package: MLInterfaces

Version: 1.56.0

Command: rm -rf MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && mkdir MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLInterfaces.buildbin-libdir MLInterfaces_1.56.0.tar.gz >MLInterfaces.Rcheck\00install.out 2>&1 && cp MLInterfaces.Rcheck\00install.out MLInterfaces-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MLInterfaces.buildbin-libdir --install="check:MLInterfaces-install.out" --force-multiarch --no-vignettes --timings MLInterfaces_1.56.0.tar.gz

StartedAt: 2017-10-18 01:27:23 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:32:37 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 314.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MLInterfaces.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && mkdir MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLInterfaces.buildbin-libdir MLInterfaces_1.56.0.tar.gz >MLInterfaces.Rcheck\00install.out 2>&1 && cp MLInterfaces.Rcheck\00install.out MLInterfaces-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MLInterfaces.buildbin-libdir --install="check:MLInterfaces-install.out" --force-multiarch --no-vignettes --timings MLInterfaces_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MLInterfaces.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 'C:/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
MLearn-new 18.6   0.45   20.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
MLearn-new         23.94   0.27   24.47
planarPlot-methods  4.92   0.16    5.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MLInterfaces.Rcheck/00check.log'
for details.

install for i386

* 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'

install for x64

* installing *source* package 'MLInterfaces' ...
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces'
* MD5 sums
packaged installation of 'MLInterfaces' as MLInterfaces_1.56.0.zip
* DONE (MLInterfaces)

name	user	system	elapsed
MLearn-new	18.60	0.45	20.14
RAB	0.21	0.01	0.22
balKfold.xvspec	0.05	0.00	0.05
classifierOutput-class	3.64	0.02	3.65
clusteringOutput-class	0	0	0
confuMat-methods	0.45	0.02	0.47
confuTab	0	0	0
fs.absT	0.06	0.00	0.06
fsHistory	0.09	0.00	0.09
hclustWidget	0.02	0.00	0.02
learnerSchema-class	0	0	0
performance-analytics	0	0	0
planarPlot-methods	3.92	0.15	4.08
plspinHcube	0	0	0
predict.classifierOutput	2.30	0.00	2.29
projectLearnerToGrid	0.94	0.08	1.01
projectedLearner-class	0	0	0
raboostCont-class	0	0	0
varImpStruct-class	0.90	0.03	0.94
xvalLoop	0	0	0
xvalSpec	0.27	0.00	0.26

name	user	system	elapsed
MLearn-new	23.94	0.27	24.47
RAB	0.17	0.00	0.17
balKfold.xvspec	0.05	0.00	0.05
classifierOutput-class	2.22	0.00	2.22
clusteringOutput-class	0	0	0
confuMat-methods	0.28	0.00	0.28
confuTab	0.02	0.00	0.01
fs.absT	0.04	0.00	0.05
fsHistory	0.08	0.00	0.08
hclustWidget	0	0	0
learnerSchema-class	0	0	0
performance-analytics	0	0	0
planarPlot-methods	4.92	0.16	5.08
plspinHcube	0	0	0
predict.classifierOutput	3.45	0.00	3.63
projectLearnerToGrid	0.88	0.09	0.96
projectedLearner-class	0	0	0
raboostCont-class	0	0	0
varImpStruct-class	0.75	0.05	0.80
xvalLoop	0	0	0
xvalSpec	0.25	0.00	0.25