BioC 2.14: CHECK report for CMA on morelia

Package: CMA

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CMA_1.22.0.tar.gz

StartedAt: 2014-10-07 22:03:20 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:04:44 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 83.7 seconds

RetCode: 0

Status:  OK

CheckDir: CMA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CMA_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/CMA.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.22.0’
* 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 ... [5s/5s] 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 loading without being on the library search path ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/16s] 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	3.286	0.081	3.383
GeneSelection	0.254	0.011	0.267
GenerateLearningsets	0.016	0.000	0.018
LassoCMA	0.449	0.030	0.479
Planarplot	0.316	0.014	0.331
classification	0.001	0.001	0.002
compBoostCMA	1.072	0.053	1.129
compare	0.002	0.001	0.001
dldaCMA	0.210	0.013	0.239
evaluation	0.158	0.007	0.165
fdaCMA	0.115	0.010	0.126
flexdaCMA	0.243	0.013	0.257
gbmCMA	2.607	0.020	2.644
golub	0.039	0.004	0.043
khan	0.054	0.006	0.059
knnCMA	0.221	0.014	0.236
ldaCMA	0.145	0.012	0.157
nnetCMA	0.087	0.009	0.096
pknnCMA	0.126	0.006	0.133
plrCMA	0.40	0.02	0.42
pls_ldaCMA	0.181	0.011	0.223
pls_lrCMA	0.287	0.008	0.297
pls_rfCMA	0.081	0.005	0.086
pnnCMA	0.045	0.005	0.049
prediction	0.001	0.000	0.002
qdaCMA	0.139	0.011	0.149
rfCMA	0.087	0.004	0.091
scdaCMA	0.110	0.008	0.118
shrinkldaCMA	0.124	0.008	0.133
svmCMA	0.616	0.015	0.631
tune	0.000	0.000	0.001
weighted_mcr	2.838	0.175	3.016