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BioC 3.1: CHECK report for CMA on petty

This page was generated on 2015-10-09 09:33:36 -0700 (Fri, 09 Oct 2015).

Package 181/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CMA 1.26.0
Christoph Bernau
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/CMA
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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: 2015-10-08 22:09:33 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:11:20 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 106.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CMA.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/CMA.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.26.0’
* 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 ... [7s/8s] 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’
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 ... [22s/22s] 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.


CMA.Rcheck/00install.out:

* 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)

CMA.Rcheck/CMA-Ex.timings:

nameusersystemelapsed
ElasticNetCMA3.6880.1683.881
GeneSelection0.3850.0220.408
GenerateLearningsets0.0230.0010.024
LassoCMA0.6500.0320.682
Planarplot0.2720.0160.287
classification0.0030.0010.004
compBoostCMA1.5640.0401.608
compare0.0020.0000.003
dldaCMA0.2520.0320.286
evaluation0.4870.0250.513
fdaCMA0.1660.0220.192
flexdaCMA0.4130.0150.447
gbmCMA3.8480.0273.933
golub0.0540.0070.061
khan0.0810.0090.090
knnCMA0.3310.0260.358
ldaCMA0.2270.0190.260
nnetCMA0.1530.0140.168
pknnCMA0.1860.0130.201
plrCMA0.7400.0570.802
pls_ldaCMA0.3280.0170.391
pls_lrCMA0.2820.0120.294
pls_rfCMA0.0900.0080.099
pnnCMA0.0730.0080.083
prediction0.0010.0000.001
qdaCMA0.2310.0200.252
rfCMA0.1030.0110.114
scdaCMA0.1690.0170.187
shrinkldaCMA0.1980.0120.210
svmCMA0.7810.0360.819
tune0.0020.0000.002
weighted_mcr3.3790.3663.765