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 15:26:10 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 15:27:29 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 78.5 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: ASCII
* 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	3.078	0.109	3.201
GeneSelection	0.294	0.018	0.313
GenerateLearningsets	0.018	0.000	0.019
LassoCMA	0.624	0.034	0.657
Planarplot	0.301	0.010	0.311
classification	0.001	0.000	0.001
compBoostCMA	1.463	0.024	1.487
compare	0	0	0
dldaCMA	0.294	0.008	0.303
evaluation	0.217	0.003	0.220
fdaCMA	0.127	0.003	0.131
flexdaCMA	0.344	0.011	0.354
gbmCMA	4.465	0.018	4.483
golub	0.040	0.001	0.041
khan	0.049	0.001	0.050
knnCMA	0.413	0.011	0.424
ldaCMA	0.154	0.005	0.175
nnetCMA	0.117	0.004	0.120
pknnCMA	0.283	0.007	0.290
plrCMA	0.669	0.028	0.697
pls_ldaCMA	0.306	0.008	0.314
pls_lrCMA	0.221	0.007	0.229
pls_rfCMA	0.208	0.004	0.212
pnnCMA	0.053	0.001	0.053
prediction	0	0	0
qdaCMA	0.151	0.004	0.155
rfCMA	0.118	0.003	0.121
scdaCMA	0.156	0.007	0.162
shrinkldaCMA	0.195	0.006	0.202
svmCMA	1.221	0.027	1.249
tune	0.000	0.000	0.001