BioC 3.1: CHECK report for MLInterfaces on moscato2

Package: MLInterfaces

Version: 1.48.0

Command: rm -rf MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && mkdir MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLInterfaces.buildbin-libdir MLInterfaces_1.48.0.tar.gz >MLInterfaces.Rcheck\00install.out 2>&1 && cp MLInterfaces.Rcheck\00install.out MLInterfaces-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=MLInterfaces.buildbin-libdir --install="check:MLInterfaces-install.out" --force-multiarch --no-vignettes --timings MLInterfaces_1.48.0.tar.gz

StartedAt: 2015-10-09 03:56:07 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:59:58 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 230.8 seconds

RetCode: 0

Status:  OK

CheckDir: MLInterfaces.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && mkdir MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLInterfaces.buildbin-libdir MLInterfaces_1.48.0.tar.gz >MLInterfaces.Rcheck\00install.out 2>&1 && cp MLInterfaces.Rcheck\00install.out MLInterfaces-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=MLInterfaces.buildbin-libdir --install="check:MLInterfaces-install.out" --force-multiarch --no-vignettes --timings MLInterfaces_1.48.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/MLInterfaces.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.48.0'
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' calls in package code:
  'RColorBrewer' 'gbm' 'kernlab'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  '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
gbm2: no visible global function definition for 'gbm'
predict.gbm2: no visible global function definition for 'predict.gbm'
planarPlot,classifierOutput-ExpressionSet-character: no visible global
  function definition for 'brewer.pal'
* checking Rd files ... OK
* 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' ... [36s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
MLearn-new             17.96   0.19   19.09
classifierOutput-class  5.11   0.00    5.11
** running examples for arch 'x64' ... [40s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
MLearn-new 20.02   0.27   20.93
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [4s]
 [4s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [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: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/MLInterfaces.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MLInterfaces' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'MLInterfaces' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'MLInterfaces' as MLInterfaces_1.48.0.zip
* DONE (MLInterfaces)

name	user	system	elapsed
MLearn-new	17.96	0.19	19.09
RAB	0.12	0.02	0.14
balKfold.xvspec	0.03	0.00	0.04
classifierOutput-class	5.11	0.00	5.11
clusteringOutput-class	0	0	0
confuMat-methods	0.39	0.03	0.42
confuTab	0	0	0
fs.absT	0.06	0.00	0.07
fsHistory	0.1	0.0	0.1
learnerSchema-class	0	0	0
performance-analytics	0.01	0.00	0.01
planarPlot-methods	3.58	0.12	3.70
predict.classifierOutput	2.56	0.05	2.63
raboostCont-class	0.01	0.00	0.01
varImpStruct-class	0.93	0.01	0.94
xvalLoop	0	0	0
xvalSpec	0.20	0.00	0.21

name	user	system	elapsed
MLearn-new	20.02	0.27	20.93
RAB	0.13	0.01	0.14
balKfold.xvspec	0.03	0.00	0.04
classifierOutput-class	4.79	0.00	4.78
clusteringOutput-class	0	0	0
confuMat-methods	0.27	0.02	0.29
confuTab	0.01	0.00	0.01
fs.absT	0.05	0.00	0.05
fsHistory	0.08	0.00	0.08
learnerSchema-class	0	0	0
performance-analytics	0	0	0
planarPlot-methods	2.93	0.15	3.08
predict.classifierOutput	2.90	0.00	2.97
raboostCont-class	0	0	0
varImpStruct-class	0.80	0.03	0.83
xvalLoop	0	0	0
xvalSpec	0.24	0.00	0.24