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Package 258/260HostnameOS / ArchBUILDCHECKBUILD BIN
XDE 1.0.0
Robert Scharpf
Snapshot Date: 2008-10-16 00:10:09 -0700 (Thu, 16 Oct 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/XDE
Last Changed Rev: 31430 / Revision: 34573
Last Changed Date: 2008-04-29 16:50:18 -0700 (Tue, 29 Apr 2008)
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 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK [ OK ]
Package: XDE
Version: 1.0.0
Command: /Users/biocbuild/BBS/utils/build-universal.sh XDE_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/2.7/Resources/bin/R XDE.buildbin-libdir
StartedAt: 2008-10-16 07:08:08 -0700 (Thu, 16 Oct 2008)
EndedAt: 2008-10-16 07:09:09 -0700 (Thu, 16 Oct 2008)
EllapsedTime: 61.3 seconds
RetCode: 0
Status: OK
PackageFile: XDE_1.0.0.tgz
PackageFileSize: 1.582 MiB

Command output

                INSTALLATION WITH 'R CMD INSTALL XDE_1.0.0.tar.gz'

* Installing to library 'XDE.buildbin-libdir'
* Installing *source* package 'XDE' ...
** libs
** arch - i386
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c Cholesky.cpp -o Cholesky.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c Matrix.cpp -o Matrix.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c Random.cpp -o Random.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c Structure.cpp -o Structure.o
In file included from /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/backward/strstream:51,
                 from Structure.cpp:1:
/Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:13:
Random.h:17:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:44,
                 from diffExpressed_main.cpp:1:
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:30:1: warning: this is the location of the previous definition
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c main.cpp -o main.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o XDE.so Cholesky.o Matrix.o Random.o Structure.o diffExpressed_main.o main.o -lm  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
g++ -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c Cholesky.cpp -o Cholesky.o
g++ -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c Matrix.cpp -o Matrix.o
g++ -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c Random.cpp -o Random.o
g++ -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c Structure.cpp -o Structure.o
In file included from /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/backward/strstream:51,
                 from Structure.cpp:1:
/Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
g++ -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:13:
Random.h:17:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:44,
                 from diffExpressed_main.cpp:1:
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:30:1: warning: this is the location of the previous definition
g++ -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c main.cpp -o main.o
g++ -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o XDE.so Cholesky.o Matrix.o Random.o Structure.o diffExpressed_main.o main.o -lm  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** 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)'.

Creating a new generic function for "pairs" in "XDE"
Creating a new generic function for "nrow" in "XDE"
Creating a new generic function for "plot" in "XDE"
** help
Note: removing empty section \details
Note: removing empty section \examples
 >>> Building/Updating help pages for package 'XDE'
     Formats: text html latex example 
  ExpressionSetList-class           text    html    latex   example
  XdeMcmc-class                     text    html    latex   example
  XdeParameter-class                text    html    latex   example
  burnin                            text    html    latex   example
  calculatePosteriorAvg             text    html    latex
  empiricalStart                    text    html    latex
  expressionSetList                 text    html    latex   example
  firstMcmc                         text    html    latex   example
  geneCenter                        text    html    latex   example
  hyperparameters                   text    html    latex   example
  iterations                        text    html    latex
  lastMcmc                          text    html    latex   example
  output                            text    html    latex   example
  pairs                             text    html    latex
  posteriorAvg                      text    html    latex
  seed                              text    html    latex
  ssStatistic                       text    html    latex   example
  standardizeSamples                text    html    latex
  studyCenter                       text    html    latex   example
  symbolsInteresting                text    html    latex   example
  thin                              text    html    latex
  tuning                            text    html    latex
  updates                           text    html    latex
  xapply                            text    html    latex
  xde                               text    html    latex   example
  xmcmc                             text    html    latex   example
  xsScores                          text    html    latex   example
  zeroNu                            text    html    latex
** building package indices ...
* DONE (XDE)