BioC 2.13: CHECK report for CMA on zin1

Package: CMA

Version: 1.20.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings CMA_1.20.0.tar.gz

StartedAt: 2014-04-05 00:25:16 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:26:26 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 69.6 seconds

RetCode: 0

Status:  OK

CheckDir: CMA.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/CMA.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.20.0’
* 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 ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘CMA_vignette.rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [15s/15s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	3.036	0.048	3.089
GeneSelection	0.120	0.000	0.123
GenerateLearningsets	0.020	0.000	0.017
LassoCMA	0.524	0.008	0.543
Planarplot	0.192	0.008	0.199
classification	0.004	0.000	0.005
compBoostCMA	1.396	0.004	1.405
compare	0.004	0.000	0.003
dldaCMA	0.180	0.004	0.186
evaluation	0.152	0.004	0.156
fdaCMA	0.120	0.000	0.121
flexdaCMA	0.236	0.000	0.238
gbmCMA	2.568	0.012	2.589
golub	0.032	0.000	0.032
khan	0.048	0.000	0.048
knnCMA	0.192	0.008	0.202
ldaCMA	0.132	0.008	0.138
nnetCMA	0.092	0.008	0.098
pknnCMA	0.128	0.008	0.136
plrCMA	0.468	0.000	0.471
pls_ldaCMA	0.132	0.012	0.146
pls_lrCMA	0.248	0.008	0.255
pls_rfCMA	0.068	0.000	0.068
pnnCMA	0.044	0.000	0.042
prediction	0.004	0.000	0.003
qdaCMA	0.116	0.000	0.120
rfCMA	0.080	0.000	0.082
scdaCMA	0.108	0.000	0.108
shrinkldaCMA	0.132	0.000	0.131
svmCMA	0.500	0.008	0.511
tune	0.004	0.000	0.004
weighted_mcr	2.412	0.016	2.450