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Package 219/294HostnameOS / ArchBUILDCHECKBUILD BIN
puma 1.8.1
Richard Pearson
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/puma
Last Changed Rev: 36981 / Revision: 38965
Last Changed Date: 2009-01-27 09:44:14 -0800 (Tue, 27 Jan 2009)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
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: puma
Version: 1.8.1
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes puma_1.8.1.tar.gz
StartedAt: 2009-04-18 17:44:18 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 17:50:39 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 380.8 seconds
RetCode: 0
Status: OK
CheckDir: puma.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/puma.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ASCII
* checking for file 'puma/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'puma' version '1.8.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'puma' 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 ... OK
* 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
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating puma-Ex.R ... OK
* checking examples ... OK
* creating puma-manual.tex ... OK
* checking puma-manual.tex using pdflatex ... OK

puma.Rcheck/00install.out:

* Installing *source* package 'puma' ...
** libs
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c cregistration.c -o cregistration.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c donlp2.c -o donlp2.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c multimgmos.c -o multimgmos.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c newx.c -o newx.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c pplr_c.c -o pplr_c.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c pumaclust_c.c -o pumaclust_c.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c user_eval.c -o user_eval.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o puma.so cregistration.o donlp2.o multimgmos.o newx.o pplr_c.o pumaclust_c.o user_eval.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c cregistration.c -o cregistration.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c donlp2.c -o donlp2.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c multimgmos.c -o multimgmos.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c newx.c -o newx.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c pplr_c.c -o pplr_c.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c pumaclust_c.c -o pumaclust_c.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c user_eval.c -o user_eval.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o puma.so cregistration.o donlp2.o multimgmos.o newx.o pplr_c.o pumaclust_c.o user_eval.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** demo
** 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)'.

Loading required package: affy
Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
  Class "ExpressionSet" is defined (with package slot "Biobase") but no metadata object found to revise subclass information---not exported?  Making a copy in package "puma"
Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
  Class "eSet" is defined (with package slot "Biobase") but no metadata object found to revise subclass information---not exported?  Making a copy in package "puma"
Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
  Class "VersionedBiobase" is defined (with package slot "Biobase") but no metadata object found to revise subclass information---not exported?  Making a copy in package "puma"
Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
  Class "Versioned" is defined (with package slot "Biobase") but no metadata object found to revise subclass information---not exported?  Making a copy in package "puma"
** help
 >>> Building/Updating help pages for package 'puma'
     Formats: text html latex example 
  Clust.exampleE                    text    html    latex
  Clust.exampleStd                  text    html    latex
  DEResult-class                    text    html    latex   example
  bcomb                             text    html    latex   example
  calcAUC                           text    html    latex   example
  calculateFC                       text    html    latex   example
  calculateLimma                    text    html    latex   example
  calculateTtest                    text    html    latex   example
  clusterApplyLBDots                text    html    latex
  clusterNormE                      text    html    latex   example
  clusterNormVar                    text    html    latex   example
  compareLimmapumaDE                text    html    latex
  createContrastMatrix              text    html    latex   example
  createDesignMatrix                text    html    latex   example
  create_eset_r                     text    html    latex
  erfc                              text    html    latex   example
  eset_mmgmos                       text    html    latex
  exampleE                          text    html    latex
  exampleStd                        text    html    latex
  exprReslt-class                   text    html    latex   example
  hgu95aphis                        text    html    latex
Note: removing empty section \examples in file 'justmgMOS.Rd'
  justmgMOS                         text    html    latex
Note: removing empty section \examples in file 'justmmgMOS.Rd'
  justmmgMOS                        text    html    latex
  legend2                           text    html    latex   example
Note: removing empty section \details in file 'license.puma.Rd'
Note: removing empty section \arguments in file 'license.puma.Rd'
Note: removing empty section \seealso in file 'license.puma.Rd'
  license.puma                      text    html    latex   example
  matrixDistance                    text    html    latex   example
  mgmos                             text    html    latex   example
  mmgmos                            text    html    latex   example
  normalisation.gs                  text    html    latex   example
  numFP                             text    html    latex   example
  numOfFactorsToUse                 text    html    latex   example
  numTP                             text    html    latex   example
  orig_pplr                         text    html    latex   example
  plot-methods                      text    html    latex   example
  plotErrorBars                     text    html    latex   example
  plotHistTwoClasses                text    html    latex   example
  plotROC                           text    html    latex   example
  plotWhiskers                      text    html    latex
  pplr                              text    html    latex   example
  pplrUnsorted                      text    html    latex
  puma-package                      text    html    latex   example
  pumaComb                          text    html    latex   example
  pumaDE                            text    html    latex   example
  pumaDEUnsorted                    text    html    latex
  pumaFull                          text    html    latex   example
  pumaNormalize                     text    html    latex   example
  pumaPCA                           text    html    latex   example
  pumaPCAExpectations-class         text    html    latex
  pumaPCAModel-class                text    html    latex
  pumaPCARes-class                  text    html    latex
  pumaclust                         text    html    latex   example
  removeUninformativeFactors        text    html    latex   example
** building package indices ...
* DONE (puma)