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Package 458/462HostnameOS / ArchBUILDCHECKBUILD BIN
XDE 1.99.0
Robert Scharpf
Snapshot Date: 2011-05-10 07:21:10 -0700 (Tue, 10 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/XDE
Last Changed Rev: 55381 / Revision: 55381
Last Changed Date: 2011-05-10 06:48:51 -0700 (Tue, 10 May 2011)
wilson2 Linux (openSUSE 11.4) / 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: XDE
Version: 1.99.0
Command: /Users/biocbuild/BBS/utils/build-universal.sh XDE_1.99.0.tar.gz /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R XDE.buildbin-libdir
StartedAt: 2011-05-10 18:17:31 -0700 (Tue, 10 May 2011)
EndedAt: 2011-05-10 18:20:07 -0700 (Tue, 10 May 2011)
EllapsedTime: 155.5 seconds
RetCode: 0
Status:  OK 
PackageFile: XDE_1.99.0.tgz
PackageFileSize: 2.924 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=XDE.buildbin-libdir XDE_1.99.0.tar.gz'
>>>>>>> 

* installing *source* package ‘XDE’ ...
** libs
*** arch - i386
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Cholesky.cpp -o Cholesky.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Matrix.cpp -o Matrix.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Random.cpp -o Random.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Structure.cpp -o Structure.o
In file included from /usr/include/c++/4.0.0/backward/strstream:51,
                 from Structure.cpp:1:
/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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -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:19:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Versions/2.14/Resources/include/R.h:38,
                 from diffExpressed_main.cpp:1:
/Library/Frameworks/R.framework/Versions/2.14/Resources/include/R_ext/Constants.h:30:1: warning: this is the location of the previous definition
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c main.cpp -o main.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -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
installing to /Users/biocbuild/bbs-2.9-bioc/meat/XDE.buildbin-libdir/XDE/libs/i386
*** arch - ppc
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c Cholesky.cpp -o Cholesky.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c Matrix.cpp -o Matrix.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c Random.cpp -o Random.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c Structure.cpp -o Structure.o
In file included from /usr/include/c++/4.0.0/backward/strstream:51,
                 from Structure.cpp:1:
/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++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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:19:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Versions/2.14/Resources/include/R.h:38,
                 from diffExpressed_main.cpp:1:
/Library/Frameworks/R.framework/Versions/2.14/Resources/include/R_ext/Constants.h:30:1: warning: this is the location of the previous definition
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c main.cpp -o main.o
g++-4.2 -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -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
installing to /Users/biocbuild/bbs-2.9-bioc/meat/XDE.buildbin-libdir/XDE/libs/ppc
*** arch - x86_64
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -c Cholesky.cpp -o Cholesky.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -c Matrix.cpp -o Matrix.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -c Random.cpp -o Random.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -c Structure.cpp -o Structure.o
In file included from /usr/include/c++/4.0.0/backward/strstream:51,
                 from Structure.cpp:1:
/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++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64  -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:19:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Versions/2.14/Resources/include/R.h:38,
                 from diffExpressed_main.cpp:1:
/Library/Frameworks/R.framework/Versions/2.14/Resources/include/R_ext/Constants.h:30:1: warning: this is the location of the previous definition
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -c main.cpp -o main.o
g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -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
installing to /Users/biocbuild/bbs-2.9-bioc/meat/XDE.buildbin-libdir/XDE/libs/x86_64
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. 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 "lapply" in "XDE"
Creating a new generic function for "nrow" in "XDE"
Creating a new generic function for "plot" in "XDE"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘XDE.Rnw’ 
   ‘XdeParameterClass.Rnw’ 
** testing if installed package can be loaded

* DONE (XDE)


>>>>>>> 
>>>>>>> FIXING LINKS FOR XDE.buildbin-libdir/XDE/libs/i386/XDE.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "XDE.buildbin-libdir/XDE/libs/i386/XDE.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "XDE.buildbin-libdir/XDE/libs/i386/XDE.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "XDE.buildbin-libdir/XDE/libs/i386/XDE.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "XDE.buildbin-libdir/XDE/libs/i386/XDE.so"


>>>>>>> 
>>>>>>> FIXING LINKS FOR XDE.buildbin-libdir/XDE/libs/ppc/XDE.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "XDE.buildbin-libdir/XDE/libs/ppc/XDE.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "XDE.buildbin-libdir/XDE/libs/ppc/XDE.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "XDE.buildbin-libdir/XDE/libs/ppc/XDE.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "XDE.buildbin-libdir/XDE/libs/ppc/XDE.so"


>>>>>>> 
>>>>>>> FIXING LINKS FOR XDE.buildbin-libdir/XDE/libs/x86_64/XDE.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "XDE.buildbin-libdir/XDE/libs/x86_64/XDE.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "XDE.buildbin-libdir/XDE/libs/x86_64/XDE.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "XDE.buildbin-libdir/XDE/libs/x86_64/XDE.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "XDE.buildbin-libdir/XDE/libs/x86_64/XDE.so"