Package: CMA

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CMA_1.16.0.tar.gz

StartedAt: 2013-03-24 23:04:15 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:05:54 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 99.4 seconds

RetCode: 0

Status:  OK

CheckDir: CMA.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/CMA.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'CMA' can be installed ... OK
* checking installed package size ... 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 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 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'preamble.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/CMA.Rcheck/00check.log'
for details.

* installing *source* package 'CMA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'CMA_vignette.rnw' 
** testing if installed package can be loaded

* DONE (CMA)

name	user	system	elapsed
ElasticNetCMA	4.190	0.272	4.755
GeneSelection	0.340	0.072	0.445
GenerateLearningsets	0.016	0.001	0.015
LassoCMA	0.618	0.112	0.845
Planarplot	0.246	0.040	0.327
classification	0.000	0.000	0.001
compBoostCMA	1.836	0.593	3.101
compare	0.000	0.000	0.001
dldaCMA	0.254	0.048	0.326
evaluation	0.180	0.013	0.199
fdaCMA	0.137	0.017	0.206
flexdaCMA	0.267	0.047	0.379
gbmCMA	4.103	0.077	4.283
golub	0.042	0.004	0.045
khan	0.061	0.005	0.067
knnCMA	0.271	0.027	0.312
ldaCMA	0.156	0.014	0.246
nnetCMA	0.109	0.015	0.140
pknnCMA	0.168	0.017	0.200
plrCMA	0.657	0.053	0.824
pls_ldaCMA	0.218	0.044	0.299
pls_lrCMA	0.189	0.035	0.275
pls_rfCMA	0.090	0.006	0.115
pnnCMA	0.052	0.005	0.072
prediction	0	0	0
qdaCMA	0.162	0.017	0.211
rfCMA	0.116	0.008	0.144
scdaCMA	0.143	0.028	0.208
shrinkldaCMA	0.166	0.023	0.228
svmCMA	0.953	0.070	1.129
tune	0	0	0