BioC 3.0: CHECK report for CMA on perceval

Package: CMA

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CMA_1.24.0.tar.gz

StartedAt: 2015-04-10 00:02:24 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:05:21 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 176.8 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 --no-multiarch CMA_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/CMA.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.24.0’
* 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 ... [7s/35s] 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:
  ‘class’ ‘corpcor’ ‘e1071’ ‘gbm’ ‘glmnet’ ‘limma’ ‘MASS’ ‘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
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’
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’
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’
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 ... [21s/34s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ElasticNetCMA 5.334  0.186   6.344
weighted_mcr  3.619  0.305   5.045
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	5.334	0.186	6.344
GeneSelection	0.382	0.017	0.439
GenerateLearningsets	0.015	0.001	0.016
LassoCMA	0.624	0.035	0.915
Planarplot	0.228	0.020	0.318
classification	0.001	0.000	0.002
compBoostCMA	1.420	0.034	2.093
compare	0.001	0.000	0.001
dldaCMA	0.199	0.018	0.371
evaluation	0.166	0.011	0.261
fdaCMA	0.118	0.015	0.388
flexdaCMA	0.309	0.031	1.247
gbmCMA	2.795	0.034	4.481
golub	0.033	0.004	0.037
khan	0.048	0.005	0.054
knnCMA	0.282	0.021	1.030
ldaCMA	0.141	0.012	0.490
nnetCMA	0.130	0.014	0.564
pknnCMA	0.152	0.009	0.480
plrCMA	0.699	0.031	1.134
pls_ldaCMA	0.216	0.016	0.730
pls_lrCMA	0.181	0.009	0.229
pls_rfCMA	0.080	0.005	0.085
pnnCMA	0.044	0.006	0.056
prediction	0.002	0.000	0.001
qdaCMA	0.156	0.014	0.287
rfCMA	0.076	0.003	0.097
scdaCMA	0.111	0.007	0.620
shrinkldaCMA	0.144	0.009	0.345
svmCMA	0.677	0.027	2.442
tune	0.001	0.001	0.001
weighted_mcr	3.619	0.305	5.045