BioC 3.3: CHECK report for CMA on morelia

Package: CMA

Version: 1.29.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CMA_1.29.0.tar.gz

StartedAt: 2015-10-22 04:39:02 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 04:39:53 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 50.4 seconds

RetCode: 0

Status:  OK

CheckDir: CMA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CMA_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/CMA.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.29.0’
* 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 ... [3s/3s] 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 ... NOTE
'library' or 'require' calls in package code:
  ‘MASS’ ‘class’ ‘corpcor’ ‘e1071’ ‘gbm’ ‘glmnet’ ‘limma’ ‘mgcv’
  ‘mvtnorm’ ‘nnet’ ‘plsgenomics’ ‘randomForest’ ‘st’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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’
limmatest: no visible global function definition for ‘lmFit’
limmatest: no visible global function definition for ‘contrasts.fit’
limmatest: no visible global function definition for ‘eBayes’
limmatest: no visible global function definition for ‘classifyTestsF’
rfe: no visible binding for global variable ‘cost’
rfe: no visible binding for global variable ‘svm’
boxplot,evaloutput: no visible binding for global variable ‘main’
compare,list: no visible binding for global variable ‘main’
flexdaCMA,matrix-numeric-missing: no visible global function definition
  for ‘gam’
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’
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  ‘gbm.fit’
knnCMA,matrix-numeric-missing: no visible global function definition
  for ‘knn’
ldaCMA,matrix-numeric-missing: no visible global function definition
  for ‘lda’
nnetCMA,matrix-numeric-missing: no visible binding for global variable
  ‘size’
nnetCMA,matrix-numeric-missing: no visible binding for global variable
  ‘MaxNWts’
nnetCMA,matrix-numeric-missing: no visible global function definition
  for ‘class.ind’
plot,genesel-missing: no visible binding for global variable ‘xlab’
plot,genesel-missing: no visible binding for global variable ‘ylab’
plot,genesel-missing: no visible binding for global variable ‘main’
plot,genesel-missing: no visible binding for global variable ‘cex.lab’
plot,genesel-missing: no visible binding for global variable ‘ylim’
plot,tuningresult-missing: no visible binding for global variable
  ‘main’
plot,tuningresult-missing: no visible binding for global variable
  ‘xlab’
plot,tuningresult-missing: no visible binding for global variable
  ‘ylab’
plot,tuningresult-missing: no visible binding for global variable
  ‘ylim’
pls_ldaCMA,matrix-numeric-missing: no visible global function
  definition for ‘pls.regression’
pls_ldaCMA,matrix-numeric-missing: no visible global function
  definition for ‘transformy’
pls_ldaCMA,matrix-numeric-missing: no visible global function
  definition for ‘lda’
pls_lrCMA,matrix-numeric-missing: no visible global function definition
  for ‘pls.regression’
pls_lrCMA,matrix-numeric-missing: no visible global function definition
  for ‘transformy’
pls_rfCMA,matrix-numeric-missing: no visible global function definition
  for ‘pls.regression’
pls_rfCMA,matrix-numeric-missing: no visible global function definition
  for ‘transformy’
pls_rfCMA,matrix-numeric-missing: no visible global function definition
  for ‘randomForest’
prediction,data.frame-missing-data.frame-formula: no visible global
  function definition for ‘predicition’
qdaCMA,matrix-numeric-missing: no visible global function definition
  for ‘qda’
rfCMA,matrix-numeric-missing: no visible global function definition for
  ‘randomForest’
shrinkldaCMA,matrix-numeric-missing: no visible global function
  definition for ‘cov.shrink’
svmCMA,matrix-numeric-missing: no visible binding for global variable
  ‘cost’
weighted.mcr,character-character-numeric-character-matrix-numeric: no
  visible global function definition for ‘make.positive.definite’
weighted.mcr,character-character-numeric-character-matrix-numeric: no
  visible global function definition for ‘pmvnorm’
weighted.mcr,character-character-numeric-character-matrix-numeric: no
  visible global function definition for ‘rmvnorm’
wmc,matrix-numeric-numeric: no visible global function definition for
  ‘make.positive.definite’
wmc,matrix-numeric-numeric: no visible global function definition for
  ‘pmvnorm’
wmc,matrix-numeric-numeric: no visible global function definition for
  ‘rmvnorm’
Undefined global functions or variables:
  MaxNWts bag.fraction cex.lab class.ind classifyTestsF contrasts.fit
  cost cov.shrink eBayes gam gbm.fit knn lda lmFit lwd main
  make.positive.definite n.minobsinnode n.trees pls.regression pmvnorm
  predicition qda randomForest rmvnorm size svm transformy verbose xlab
  ylab ylim
* 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 ... [9s/9s] 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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	1.421	0.060	1.504
GeneSelection	0.198	0.009	0.207
GenerateLearningsets	0.009	0.001	0.009
LassoCMA	0.281	0.019	0.300
Planarplot	0.107	0.009	0.116
classification	0.001	0.000	0.001
compBoostCMA	0.770	0.038	0.811
compare	0.000	0.000	0.001
dldaCMA	0.138	0.011	0.150
evaluation	0.091	0.005	0.096
fdaCMA	0.084	0.007	0.092
flexdaCMA	0.124	0.006	0.130
gbmCMA	1.488	0.014	1.576
golub	0.023	0.003	0.026
khan	0.038	0.002	0.040
knnCMA	0.130	0.008	0.157
ldaCMA	0.085	0.006	0.109
nnetCMA	0.050	0.004	0.054
pknnCMA	0.069	0.004	0.073
plrCMA	0.310	0.017	0.328
pls_ldaCMA	0.096	0.007	0.124
pls_lrCMA	0.075	0.005	0.080
pls_rfCMA	0.042	0.003	0.045
pnnCMA	0.030	0.004	0.033
prediction	0.000	0.000	0.001
qdaCMA	0.088	0.007	0.096
rfCMA	0.051	0.003	0.055
scdaCMA	0.067	0.004	0.071
shrinkldaCMA	0.074	0.005	0.080
svmCMA	0.361	0.015	0.376
tune	0.001	0.000	0.001
weighted_mcr	1.544	0.159	1.728