Package: CMA

Version: 1.9.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CMA_1.9.1.tar.gz

StartedAt: 2011-02-24 18:51:08 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:52:58 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 109.7 seconds

RetCode: 0

Status:  OK

CheckDir: CMA.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/CMA.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-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

* 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)

name	user	system	elapsed
ElasticNetCMA	4.055	0.273	4.445
GeneSelection	0.404	0.055	0.462
GenerateLearningsets	0.027	0.000	0.028
LassoCMA	0.882	0.089	0.976
Planarplot	0.441	0.030	0.474
classification	0.001	0.000	0.001
compBoostCMA	2.152	0.499	2.666
compare	0.000	0.000	0.001
dldaCMA	0.423	0.040	0.470
evaluation	0.291	0.006	0.309
fdaCMA	0.187	0.006	0.193
flexdaCMA	0.483	0.019	0.536
gbmCMA	7.145	0.045	7.237
golub	0.057	0.002	0.060
khan	0.077	0.003	0.081
knnCMA	0.583	0.027	0.617
ldaCMA	0.226	0.009	0.245
nnetCMA	0.163	0.008	0.171
pknnCMA	0.372	0.011	0.385
plrCMA	0.922	0.052	0.977
pls_ldaCMA	0.434	0.032	0.467
pls_lrCMA	0.314	0.024	0.339
pls_rfCMA	0.298	0.006	0.306
pnnCMA	0.074	0.002	0.076
prediction	0.001	0.000	0.001
qdaCMA	0.220	0.008	0.230
rfCMA	0.175	0.006	0.182
scdaCMA	0.235	0.028	0.267
shrinkldaCMA	0.276	0.018	0.303
svmCMA	1.781	0.080	1.899
tune	0	0	0