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Package 62/294HostnameOS / ArchBUILDCHECKBUILD BIN
CMA 1.0.0
Martin Slawski
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/CMA
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64 N O T   S U P P O R T E D
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK [ OK ] OK 
Package: CMA
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes CMA_1.0.0.tar.gz
StartedAt: 2009-04-18 17:14:06 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 17:16:05 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 119.6 seconds
RetCode: 0
Status: OK
CheckDir: CMA.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/CMA.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'CMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CMA' version '1.0.0'
* 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 name space can be loaded with stated dependencies ... 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'
svmCMA,matrix-numeric-missing: no visible binding for global variable
  'cost'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating CMA-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating CMA-manual.tex ... OK
* checking CMA-manual.tex using pdflatex ... OK

CMA.Rcheck/00install.out:

* Installing *source* package 'CMA' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

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

Warning in conformMethod(signature, mnames, fnames, f, fdef, definition) :
  In method for function "Planarplot": formal arguments in method and function do not appear in the same order
Warning in conformMethod(signature, mnames, fnames, f, fdef, definition) :
  In method for function "fdaCMA": formal arguments in method and function do not appear in the same order
Warning in rematchDefinition(definition, fdef, mnames, fnames, signature) :
  Arguments of method and generic are not in the same order
Warning in conformMethod(signature, mnames, fnames, f, fdef, definition) :
  In method for function "flexdaCMA": formal arguments in method and function do not appear in the same order
** help
 >>> Building/Updating help pages for package 'CMA'
     Formats: text html latex example 
  CMA-package                       text    html    latex
  ElasticNetCMA-methods             text    html    latex
  ElasticNetCMA                     text    html    latex   example
  GeneSelection-methods             text    html    latex
  GeneSelection                     text    html    latex   example
  GenerateLearningsets              text    html    latex   example
  LassoCMA-methods                  text    html    latex
  LassoCMA                          text    html    latex   example
  Planarplot-methods                text    html    latex
  Planarplot                        text    html    latex   example
  best                              text    html    latex
  boxplot                           text    html    latex
  classification-methods            text    html    latex
  classification                    text    html    latex   example
  cloutput-class                    text    html    latex
  clvarseloutput-class              text    html    latex
  compBoostCMA-methods              text    html    latex
  compBoostCMA                      text    html    latex   example
  compare-methods                   text    html    latex
  compare                           text    html    latex   example
  dldaCMA-methods                   text    html    latex
  dldaCMA                           text    html    latex   example
  evaloutput-class                  text    html    latex
  evaluation-methods                text    html    latex
  evaluation                        text    html    latex   example
  fdaCMA-methods                    text    html    latex
  fdaCMA                            text    html    latex   example
  filter                            text    html    latex
  flexdaCMA-methods                 text    html    latex
  flexdaCMA                         text    html    latex   example
  ftable                            text    html    latex
  gbmCMA-methods                    text    html    latex
  gbmCMA                            text    html    latex   example
  genesel-class                     text    html    latex
  golub                             text    html    latex   example
  internals                         text    html    latex
  join-methods                      text    html    latex
  join                              text    html    latex
  khan                              text    html    latex   example
  knnCMA-methods                    text    html    latex
  knnCMA                            text    html    latex   example
  ldaCMA-methods                    text    html    latex
  ldaCMA                            text    html    latex   example
  learningsets-class                text    html    latex
  nnetCMA-methods                   text    html    latex
  nnetCMA                           text    html    latex   example
  obsinfo                           text    html    latex
  pknnCMA-methods                   text    html    latex
  pknnCMA                           text    html    latex   example
  plot,cloutput-method              text    html    latex
  plot,genesel-method               text    html    latex
  plot,tuningresult-method          text    html    latex
  plrCMA-methods                    text    html    latex
  plrCMA                            text    html    latex   example
  pls_ldaCMA-methods                text    html    latex
  pls_ldaCMA                        text    html    latex   example
  pls_lrCMA-methods                 text    html    latex
  pls_lrCMA                         text    html    latex   example
  pls_rfCMA-methods                 text    html    latex
  pls_rfCMA                         text    html    latex   example
  pnnCMA-methods                    text    html    latex
  pnnCMA                            text    html    latex   example
  qdaCMA-methods                    text    html    latex
  qdaCMA                            text    html    latex   example
  rfCMA-methods                     text    html    latex
  rfCMA                             text    html    latex   example
  roc                               text    html    latex
  scdaCMA-methods                   text    html    latex
  scdaCMA                           text    html    latex   example
  shrinkldaCMA-methods              text    html    latex
  shrinkldaCMA                      text    html    latex   example
  summary                           text    html    latex
  svmCMA-methods                    text    html    latex
  svmCMA                            text    html    latex   example
  toplist                           text    html    latex
  tune-methods                      text    html    latex
  tune                              text    html    latex   example
  tuningresult-class                text    html    latex
  varseloutput-class                text    html    latex
** building package indices ...
* DONE (CMA)