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BioC 2.14: CHECK report for MLInterfaces on morelia

This page was generated on 2014-10-08 09:02:19 -0700 (Wed, 08 Oct 2014).

Package 505/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLInterfaces 1.44.1
V. Carey
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/MLInterfaces
Last Changed Rev: 94822 / Revision: 95116
Last Changed Date: 2014-10-01 15:26:30 -0700 (Wed, 01 Oct 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: MLInterfaces
Version: 1.44.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MLInterfaces_1.44.1.tar.gz
StartedAt: 2014-10-08 00:05:54 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:09:58 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 243.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MLInterfaces.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MLInterfaces_1.44.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/MLInterfaces.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLInterfaces/DESCRIPTION’ ... OK
* this is package ‘MLInterfaces’ version ‘1.44.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘MASS’ ‘genefilter’ ‘rpart’ ‘rda’ ‘annotate’ ‘cluster’
  ‘sfsmisc’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [17s/19s] 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 ... WARNING
Unknown package ‘multicore’ in Rd xrefs
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [43s/43s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
MLearn-new 19.36  1.584  21.752
* 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/MLInterfaces.Rcheck/00check.log’
for details.

MLInterfaces.Rcheck/00install.out:

* 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)

MLInterfaces.Rcheck/MLInterfaces-Ex.timings:

nameusersystemelapsed
MLearn-new19.360 1.58421.752
RAB0.1590.0020.162
balKfold.xvspec0.0140.0010.014
classifierOutput-class2.2750.7542.375
clusteringOutput-class0.0010.0010.002
confuMat-methods0.2990.0310.406
fs.absT0.0180.0020.020
fsHistory2.0580.2170.153
learnerSchema-class0.0020.0000.002
planarPlot-methods2.5400.2112.890
predict.classifierOutput3.4030.0383.544
raboostCont-class0.0020.0010.001
varImpStruct-class0.8320.0471.061
xvalLoop0.0010.0000.002
xvalSpec0.1730.1130.226