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Package 80/389HostnameOS / ArchBUILDCHECKBUILD BIN
CMA 1.6.0
Christoph Bernau
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/CMA
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: CMA
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings CMA_1.6.0.tar.gz
StartedAt: 2010-10-04 16:33:21 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 16:35:17 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 116.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CMA.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/CMA.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CMA' version '1.6.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'CMA' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

CMA.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package ‘CMA’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (CMA)

CMA.Rcheck/CMA-Ex.timings:

nameusersystemelapsed
ElasticNetCMA4.3680.2554.701
GeneSelection0.4520.0640.519
GenerateLearningsets0.0330.0010.034
LassoCMA1.1570.0941.277
Planarplot0.4550.0310.490
classification0.0010.0010.001
compBoostCMA1.9990.5482.598
compare0.0000.0010.001
dldaCMA0.4360.0360.485
evaluation0.3300.0110.353
fdaCMA0.1880.0060.196
flexdaCMA0.3820.0150.444
gbmCMA7.8480.0658.057
golub0.0580.0020.060
khan0.0780.0030.083
knnCMA0.6000.0320.664
ldaCMA0.2320.0090.264
nnetCMA0.1790.0100.212
pknnCMA0.2670.0120.290
plrCMA0.8450.0610.924
pls_ldaCMA0.3370.0360.374
pls_lrCMA0.4230.0260.453
pls_rfCMA0.3820.0400.429
pnnCMA0.0750.0020.077
prediction0.0000.0010.000
qdaCMA0.2310.0090.243
rfCMA2.8420.0362.952
scdaCMA0.2430.0280.300
shrinkldaCMA0.2860.0210.339
svmCMA1.9070.0852.105
tune0.0000.0000.001