Package: CMA

Version: 1.17.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings CMA_1.17.1.tar.gz

StartedAt: 2013-01-16 01:40:47 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 01:42:16 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 89.0 seconds

RetCode: 0

Status:  OK

CheckDir: CMA.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/CMA.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.17.1’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CMA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 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
  ‘/loc/home/biocbuild/bbs-2.12-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	4.808	0.084	4.895
GeneSelection	0.412	0.004	0.418
GenerateLearningsets	0.028	0.000	0.028
LassoCMA	0.616	0.024	0.644
Planarplot	0.216	0.012	0.228
classification	0.008	0.004	0.012
compBoostCMA	1.428	0.004	1.431
compare	0.008	0.000	0.009
dldaCMA	0.208	0.012	0.222
evaluation	0.168	0.004	0.172
fdaCMA	0.112	0.008	0.122
flexdaCMA	0.244	0.004	0.250
gbmCMA	3.184	0.044	3.230
golub	0.044	0.000	0.042
khan	0.052	0.000	0.053
knnCMA	0.244	0.028	0.275
ldaCMA	0.156	0.012	0.168
nnetCMA	0.108	0.008	0.117
pknnCMA	0.176	0.000	0.177
plrCMA	1.004	0.008	1.012
pls_ldaCMA	0.172	0.016	0.188
pls_lrCMA	0.156	0.008	0.169
pls_rfCMA	0.092	0.000	0.091
pnnCMA	0.056	0.000	0.057
prediction	0.012	0.000	0.012
qdaCMA	0.132	0.012	0.147
rfCMA	0.357	0.000	0.356
scdaCMA	0.120	0.008	0.129
shrinkldaCMA	0.148	0.008	0.158
svmCMA	0.736	0.020	0.759
tune	0.012	0.000	0.012