BioC 2.12: CHECK report for CMA on petty

Package: CMA

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CMA_1.18.0.tar.gz

StartedAt: 2013-10-08 22:00:35 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:02:55 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 140.3 seconds

RetCode: 0

Status:  OK

CheckDir: CMA.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/CMA.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CMA' version '1.18.0'
* 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 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 ... [9s/9s] 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 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 ... [26s/26s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ElasticNetCMA 6.204  0.179    6.46
* 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-2.12-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
** testing if installed package can be loaded
* DONE (CMA)

name	user	system	elapsed
ElasticNetCMA	6.204	0.179	6.460
GeneSelection	0.277	0.037	0.315
GenerateLearningsets	0.038	0.006	0.043
LassoCMA	0.812	0.070	0.884
Planarplot	0.351	0.040	0.397
classification	0.009	0.010	0.020
compBoostCMA	1.932	0.193	2.143
compare	0.011	0.007	0.018
dldaCMA	0.383	0.048	0.464
evaluation	0.519	0.025	0.546
fdaCMA	0.194	0.041	0.240
flexdaCMA	0.418	0.044	0.464
gbmCMA	4.768	0.075	4.868
golub	0.059	0.009	0.068
khan	0.088	0.018	0.106
knnCMA	0.428	0.048	0.488
ldaCMA	0.245	0.043	0.302
nnetCMA	0.184	0.027	0.216
pknnCMA	0.264	0.028	0.294
plrCMA	0.955	0.076	1.036
pls_ldaCMA	0.295	0.033	0.328
pls_lrCMA	0.271	0.028	0.300
pls_rfCMA	0.159	0.017	0.177
pnnCMA	0.080	0.019	0.099
prediction	0.009	0.009	0.018
qdaCMA	0.234	0.035	0.270
rfCMA	0.148	0.026	0.177
scdaCMA	0.213	0.034	0.248
shrinkldaCMA	0.237	0.034	0.270
svmCMA	1.449	0.053	1.507
tune	0.008	0.006	0.015