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Package 170/233HostnameOS / ArchBUILDCHECKBUILD BIN
puma 1.4.3
Richard Pearson
Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008)
Last Changed Rev: 28570 / Revision: 30966
Last Changed Date: 2007-11-08 04:31:11 -0800 (Thu, 08 Nov 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK [ OK ] OK 
Package: puma
Version: 1.4.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check puma_1.4.3.tar.gz
StartedAt: 2008-04-09 16:39:47 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 16:45:44 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 357.9 seconds
RetCode: 0
Status: OK
CheckDir: puma.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/puma.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'puma/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'puma' version '1.4.3'
* 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 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 ... OK


* Installing *source* package 'puma' ...
** libs
** arch - i386
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c cregistration.c -o cregistration.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c donlp2.c -o donlp2.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c multimgmos.c -o multimgmos.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c newx.c -o newx.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c pplr_c.c -o pplr_c.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c pumaclust_c.c -o pumaclust_c.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c user_eval.c -o user_eval.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o cregistration.o donlp2.o multimgmos.o newx.o pplr_c.o pumaclust_c.o user_eval.o   -F/Library/Frameworks/R.framework/.. -framework R 
** arch - ppc
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c cregistration.c -o cregistration.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c donlp2.c -o donlp2.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c multimgmos.c -o multimgmos.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c newx.c -o newx.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c pplr_c.c -o pplr_c.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c pumaclust_c.c -o pumaclust_c.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c user_eval.c -o user_eval.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o cregistration.o donlp2.o multimgmos.o newx.o pplr_c.o pumaclust_c.o user_eval.o   -F/Library/Frameworks/R.framework/.. -framework R 
** 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
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: limma
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: ROCR
Loading required package: gplots
Loading required package: gtools
Loading required package: gdata

Attaching package: 'gdata'

	The following object(s) are masked from package:Biobase :


Attaching package: 'gplots'

	The following object(s) are masked from package:stats :


** 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
  exampleE                          text    html    latex
  exampleStd                        text    html    latex
  exprReslt-class                   text    html    latex   example
  hgu95aphis                        text    html    latex
  justmgMOS                         text    html    latex   example
  justmmgMOS                        text    html    latex   example
  legend2                           text    html    latex   example
  license.puma                      text    html    latex   example
  matrixDistance                    text    html    latex   example
  mgmos                             text    html    latex   example
  mmgmos                            text    html    latex   example                  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)