BioC 2.13: CHECK report for MLInterfaces on zin1

Package: MLInterfaces

Version: 1.42.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings MLInterfaces_1.42.0.tar.gz

StartedAt: 2014-04-05 02:32:05 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:35:28 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 203.2 seconds

RetCode: 0

Status:  OK

CheckDir: MLInterfaces.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/MLInterfaces.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLInterfaces/DESCRIPTION’ ... OK
* this is package ‘MLInterfaces’ version ‘1.42.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MLInterfaces’ can be installed ... [15s/15s] 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
* 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 ... [36s/42s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
MLearn-new               17.049  0.604  19.253
predict.classifierOutput  3.232  0.012   5.963
* 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
  ‘/home/biocbuild/bbs-2.13-bioc/meat/MLInterfaces.Rcheck/00check.log’
for details.

* 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
* DONE (MLInterfaces)

name	user	system	elapsed
MLearn-new	17.049	0.604	19.253
RAB	0.144	0.000	0.162
balKfold.xvspec	0.020	0.004	0.025
classifierOutput-class	1.584	0.148	3.103
clusteringOutput-class	0.000	0.004	0.003
confuMat-methods	0.280	0.016	0.340
fs.absT	0.024	0.000	0.050
fsHistory	1.660	0.144	0.215
learnerSchema-class	0.004	0.004	0.008
planarPlot-methods	2.444	0.092	3.894
predict.classifierOutput	3.232	0.012	5.963
raboostCont-class	0.004	0.000	0.002
varImpStruct-class	0.768	0.036	1.027
xvalLoop	0.008	0.004	0.023
xvalSpec	0.152	0.084	0.354