BioC 2.12: CHECK report for CMA on george2

Package: CMA

Version: 1.18.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings CMA_1.18.0.tar.gz

StartedAt: 2013-10-09 01:02:58 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:05:17 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 139.6 seconds

RetCode: 0

Status:  OK

CheckDir: CMA.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/CMA.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.18.0’
* 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/10s] 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 ... [25s/28s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ElasticNetCMA 7.62  0.156   8.517
* 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
  ‘/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
** testing if installed package can be loaded
* DONE (CMA)

name	user	system	elapsed
ElasticNetCMA	7.620	0.156	8.517
GeneSelection	0.280	0.012	0.306
GenerateLearningsets	0.048	0.000	0.049
LassoCMA	0.960	0.040	1.046
Planarplot	0.268	0.012	0.289
classification	0.024	0.000	0.024
compBoostCMA	1.964	0.012	2.107
compare	0.024	0.004	0.031
dldaCMA	0.660	0.004	0.709
evaluation	0.188	0.016	0.207
fdaCMA	0.156	0.008	0.178
flexdaCMA	0.336	0.032	0.511
gbmCMA	3.901	0.052	4.594
golub	0.060	0.004	0.107
khan	0.048	0.008	0.058
knnCMA	0.336	0.012	0.387
ldaCMA	0.244	0.004	0.264
nnetCMA	0.192	0.008	0.270
pknnCMA	0.228	0.012	0.263
plrCMA	1.116	0.016	1.378
pls_ldaCMA	0.212	0.016	0.231
pls_lrCMA	0.248	0.008	0.257
pls_rfCMA	0.140	0.008	0.148
pnnCMA	0.088	0.004	0.092
prediction	0.012	0.004	0.018
qdaCMA	0.196	0.008	0.212
rfCMA	0.128	0.000	0.155
scdaCMA	0.192	0.008	0.215
shrinkldaCMA	0.240	0.004	0.244
svmCMA	1.540	0.032	1.642
tune	0.02	0.00	0.02