BioC 2.13: CHECK report for MLInterfaces on moscato1

Package: MLInterfaces

Version: 1.42.0

Command: rm -rf MLInterfaces.buildbin-libdir && mkdir MLInterfaces.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLInterfaces.buildbin-libdir MLInterfaces_1.42.0.tar.gz >MLInterfaces-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=MLInterfaces.buildbin-libdir --install="check:MLInterfaces-install.out" --force-multiarch --no-vignettes --timings MLInterfaces_1.42.0.tar.gz && mv MLInterfaces.buildbin-libdir/* MLInterfaces.Rcheck/ && rmdir MLInterfaces.buildbin-libdir

StartedAt: 2014-04-05 05:13:34 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:20:10 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 396.3 seconds

RetCode: 0

Status:  OK

CheckDir: MLInterfaces.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/MLInterfaces.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MLInterfaces/DESCRIPTION' ... OK
* this is package 'MLInterfaces' version '1.42.0'
* 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
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'rpart' 'MASS' 'gbm' 'mboost' 'sfsmisc'
A package should be listed in only one of these fields.
* 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' call to 'sfsmisc' which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'pls'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'MASS' 'genefilter' 'rda' 'rpart'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'rpart:::predict.rpart'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'multicore'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'MLInterfaces.Rnw', 'MLint_devel.Rnw', 'MLprac2_2.Rnw',
  'xvalComputerClusters.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [59s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
MLearn-new               28.45   0.39   29.05
classifierOutput-class    6.49   0.00    6.49
predict.classifierOutput  5.24   0.05    5.29
** running examples for arch 'x64' ... [74s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
MLearn-new               36.25   0.58   37.50
predict.classifierOutput  7.10   0.01    7.61
classifierOutput-class    6.16   0.01    6.18
* 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/MLInterfaces.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MLInterfaces' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MLInterfaces' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MLInterfaces' as MLInterfaces_1.42.0.zip
* DONE (MLInterfaces)

name	user	system	elapsed
MLearn-new	28.45	0.39	29.05
RAB	0.27	0.00	0.26
balKfold.xvspec	0.03	0.02	0.05
classifierOutput-class	6.49	0.00	6.49
clusteringOutput-class	0.01	0.00	0.01
confuMat-methods	0.48	0.01	0.52
fs.absT	0.03	0.00	0.03
fsHistory	0.14	0.00	0.14
learnerSchema-class	0.02	0.00	0.02
planarPlot-methods	4.26	0.10	4.35
predict.classifierOutput	5.24	0.05	5.29
raboostCont-class	0	0	0
varImpStruct-class	1.26	0.09	1.36
xvalLoop	0.04	0.00	0.03
xvalSpec	0.34	0.00	0.35

name	user	system	elapsed
MLearn-new	36.25	0.58	37.50
RAB	0.33	0.00	0.33
balKfold.xvspec	0.05	0.00	0.05
classifierOutput-class	6.16	0.01	6.18
clusteringOutput-class	0.02	0.00	0.02
confuMat-methods	0.45	0.04	0.48
fs.absT	0.05	0.00	0.04
fsHistory	0.17	0.01	0.19
learnerSchema-class	0	0	0
planarPlot-methods	4.42	0.13	4.54
predict.classifierOutput	7.10	0.01	7.61
raboostCont-class	0.02	0.00	0.02
varImpStruct-class	1.46	0.10	1.56
xvalLoop	0.02	0.00	0.01
xvalSpec	0.33	0.01	0.35