BioC 3.1: CHECK report for CMA on morelia

Package: CMA

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CMA_1.26.0.tar.gz

StartedAt: 2015-10-09 00:25:09 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:26:22 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 72.6 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_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/CMA.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.26.0’
* 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/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 ... 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 : .local: no visible binding for global variable
  ‘xlab’
plot,genesel-missing : .local: no visible binding for global variable
  ‘ylab’
plot,genesel-missing : .local: no visible binding for global variable
  ‘main’
plot,genesel-missing : .local: no visible binding for global variable
  ‘cex.lab’
plot,genesel-missing : .local: no visible binding for global variable
  ‘ylim’
plot,tuningresult-missing : .local: no visible binding for global
  variable ‘main’
plot,tuningresult-missing : .local: no visible binding for global
  variable ‘xlab’
plot,tuningresult-missing : .local: no visible binding for global
  variable ‘ylab’
plot,tuningresult-missing : .local: 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’
* 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 ... [14s/14s] 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-3.1-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	2.037	0.367	2.543
GeneSelection	0.238	0.056	0.293
GenerateLearningsets	0.016	0.006	0.022
LassoCMA	0.374	0.018	0.392
Planarplot	0.173	0.051	0.223
classification	0.001	0.000	0.002
compBoostCMA	0.981	0.117	1.100
compare	0.001	0.000	0.001
dldaCMA	0.163	0.014	0.176
evaluation	0.134	0.006	0.141
fdaCMA	0.120	0.012	0.131
flexdaCMA	0.194	0.021	0.227
gbmCMA	2.165	0.169	2.385
golub	0.028	0.004	0.032
khan	0.044	0.005	0.049
knnCMA	0.169	0.023	0.217
ldaCMA	0.115	0.010	0.143
nnetCMA	0.063	0.006	0.068
pknnCMA	0.080	0.004	0.084
plrCMA	0.404	0.025	0.429
pls_ldaCMA	0.151	0.008	0.183
pls_lrCMA	0.118	0.005	0.124
pls_rfCMA	0.068	0.005	0.079
pnnCMA	0.044	0.015	0.059
prediction	0.001	0.000	0.001
qdaCMA	0.123	0.011	0.134
rfCMA	0.052	0.004	0.055
scdaCMA	0.089	0.005	0.094
shrinkldaCMA	0.095	0.006	0.100
svmCMA	0.511	0.016	0.548
tune	0.001	0.001	0.002
weighted_mcr	2.528	0.217	2.833