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Package 85/419HostnameOS / ArchBUILDCHECKBUILD BIN
CMA 1.8.1
Christoph Bernau
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/CMA
Last Changed Rev: 51670 / Revision: 54281
Last Changed Date: 2010-12-23 01:47:05 -0800 (Thu, 23 Dec 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: CMA
Version: 1.8.1
Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings CMA_1.8.1.tar.gz
StartedAt: 2011-03-31 05:16:16 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 05:17:29 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 73.6 seconds
RetCode: 0
Status:  OK 
CheckDir: CMA.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/CMA.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CMA’ version ‘1.8.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘CMA’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ROCinternal: no visible binding for global variable ‘xlab’
ROCinternal: no visible binding for global variable ‘ylab’
ROCinternal: no visible binding for global variable ‘main’
ROCinternal: no visible binding for global variable ‘lwd’
rfe: no visible binding for global variable ‘cost’
boxplot,evaloutput: no visible binding for global variable ‘main’
compare,list: no visible binding for global variable ‘main’
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  ‘n.minobsinnode’
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  ‘bag.fraction’
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  ‘n.trees’
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  ‘verbose’
nnetCMA,matrix-numeric-missing: no visible binding for global variable
  ‘size’
nnetCMA,matrix-numeric-missing: no visible binding for global variable
  ‘MaxNWts’
prediction,data.frame-missing-data.frame-formula: no visible global
  function definition for ‘predicition’
svmCMA,matrix-numeric-missing: no visible binding for global variable
  ‘cost’
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

CMA.Rcheck/00install.out:

* installing *source* package ‘CMA’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (CMA)

CMA.Rcheck/CMA-Ex.timings:

nameusersystemelapsed
ElasticNetCMA4.2760.1204.394
GeneSelection0.3280.0040.336
GenerateLearningsets0.0120.0040.015
LassoCMA0.7720.0000.775
Planarplot0.4280.0000.427
classification000
compBoostCMA1.5440.0001.550
compare000
dldaCMA0.2400.0000.244
evaluation0.1760.0000.178
fdaCMA0.0840.0000.085
flexdaCMA0.2160.0080.221
gbmCMA4.3880.0004.389
golub0.0240.0000.025
khan0.0280.0000.030
knnCMA0.2800.0080.285
ldaCMA0.1120.0040.157
nnetCMA0.0920.0080.100
pknnCMA0.1880.0000.189
plrCMA0.6480.0120.658
pls_ldaCMA0.3560.0000.355
pls_lrCMA0.1840.0040.189
pls_rfCMA0.1000.0000.101
pnnCMA0.0360.0000.036
prediction000
qdaCMA0.1160.0040.117
rfCMA0.0920.0000.093
scdaCMA0.1280.0000.128
shrinkldaCMA0.1770.0000.177
svmCMA1.2840.0081.294
tune000