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Package 86/436HostnameOS / ArchBUILDCHECKBUILD BIN
CMA 1.9.1
Christoph Bernau
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CMA
Last Changed Rev: 51804 / Revision: 53255
Last Changed Date: 2011-01-07 06:25:59 -0800 (Fri, 07 Jan 2011)
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 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: CMA
Version: 1.9.1
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings CMA_1.9.1.tar.gz
StartedAt: 2011-02-24 18:57:25 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 18:58:55 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 90.6 seconds
RetCode: 0
Status:  OK 
CheckDir: CMA.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/CMA.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.9.1’
* 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
  'browseVignettes()'. 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
ElasticNetCMA3.8760.1284.020
GeneSelection0.3920.0000.390
GenerateLearningsets0.0240.0000.022
LassoCMA0.8400.0120.858
Planarplot0.4760.0000.491
classification0.0000.0000.001
compBoostCMA1.5160.0041.526
compare000
dldaCMA0.4120.0080.420
evaluation0.1880.0040.194
fdaCMA0.0800.0080.086
flexdaCMA0.2080.0040.226
gbmCMA4.1400.0004.183
golub0.0200.0000.027
khan0.0360.0000.039
knnCMA0.2720.0040.282
ldaCMA0.1240.0000.136
nnetCMA0.0960.0000.097
pknnCMA0.1720.0040.185
plrCMA0.6640.0080.685
pls_ldaCMA0.1880.0000.195
pls_lrCMA0.2000.0000.199
pls_rfCMA0.1080.0000.106
pnnCMA0.0360.0000.037
prediction000
qdaCMA0.1000.0120.116
rfCMA0.0960.0000.096
scdaCMA0.1320.0000.133
shrinkldaCMA0.1640.0000.172
svmCMA1.1330.0081.162
tune0.0000.0000.001