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Package 245/294HostnameOS / ArchBUILDCHECKBUILD BIN
rsbml 2.0.0
Michael Lawrence
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/rsbml
Last Changed Rev: 34841 / Revision: 38965
Last Changed Date: 2008-10-22 10:15:39 -0700 (Wed, 22 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: rsbml
Version: 2.0.0
Command: /Users/biocbuild/BBS/utils/build-universal.sh rsbml_2.0.0.tar.gz /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R rsbml.buildbin-libdir
StartedAt: 2009-04-18 18:36:01 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 18:36:58 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 56.4 seconds
RetCode: 0
Status: OK
PackageFile: rsbml_2.0.0.tgz
PackageFileSize: 992.4 KiB

Command output

                INSTALLATION WITH 'R CMD INSTALL --library=rsbml.buildbin-libdir rsbml_2.0.0.tar.gz'

* Installing *source* package 'rsbml' ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LIBSBML3... yes
configure: === Begin local SOSLib build ===
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... awk
checking whether make sets $(MAKE)... yes
checking build system type... i386-apple-darwin8.11.1
checking host system type... i386-apple-darwin8.11.1
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether gcc accepts -fpic... yes
checking how to run the C preprocessor... gcc -E
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets $(MAKE)... (cached) yes
checking for autoconf... /usr/bin/autoconf
checking for aclocal... /usr/bin/aclocal
checking for make... /usr/bin/make
checking for ar... /usr/bin/ar
checking for swig... swig
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for SBML... yes
checking for correct functioning of SBML... no:
                   CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -I/usr/include/libxml2 -I/usr/local/include  
                   LDFLAGS=  
                   LIBS=-lm -lstdc++ -L/usr/local/lib -lsbml -lstdc++ -lm -lxml2  
configure: error: Can not link to SBML Library:
		  Please, make sure to use libSBML version >= 3.0.2 or CVS
configure: === End local SOSLib build ===
configure: creating ./config.status
config.status: creating src/Makevars
** 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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c StringMap.c -o StringMap.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c check.c -o check.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c doc.c -o doc.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c dom.c -o dom.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c graph.c -o graph.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c init.c -o init.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c io.c -o io.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c mathml.c -o mathml.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c simulate.c -o simulate.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 rsbml.so StringMap.o check.o doc.o dom.o graph.o init.o io.o mathml.o simulate.o -L/usr/local/lib -lsbml -lstdc++ -lm -lxml2     -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading
Loading required package: graph
** help
 >>> Building/Updating help pages for package 'rsbml'
     Formats: text html latex example 
  AlgebraicRule-class               text    html    latex
  AssignmentRule-class              text    html    latex
  BoundingBox-class                 text    html    latex
  CVTerm-class                      text    html    latex
  Compartment-class                 text    html    latex
  CompartmentGlyph-class            text    html    latex
  CompartmentType-class             text    html    latex
  CompartmentVolumeRule-class       text    html    latex
  Constraint-class                  text    html    latex
  CubicBezier-class                 text    html    latex
  Curve-class                       text    html    latex
  Delay-class                       text    html    latex
  Describable-class                 text    html    latex
  Dimensions-class                  text    html    latex
  Event-class                       text    html    latex
  EventAssignment-class             text    html    latex
  Experiment-class                  text    html    latex
  FunctionDefinition-class          text    html    latex
  GraphicalObject-class             text    html    latex
  InitialAssignment-class           text    html    latex
  KineticLaw-class                  text    html    latex
  Layout-class                      text    html    latex
  LineSegment-class                 text    html    latex
  Model-class                       text    html    latex
  ModelCreator-class                text    html    latex
  ModelHistory-class                text    html    latex
  ModifierSpeciesReference-class    text    html    latex
  Parameter-class                   text    html    latex
  ParameterRule-class               text    html    latex
  Point-class                       text    html    latex
  RateRule-class                    text    html    latex
  Reaction-class                    text    html    latex
  ReactionGlyph-class               text    html    latex
  Rule-class                        text    html    latex
  SBML-class                        text    html    latex   example
  SBMLDocument-class                text    html    latex   example
  SBMLProblem-class                 text    html    latex
  SBMLProblems-class                text    html    latex
  SBase-class                       text    html    latex
  SOSDesign-class                   text    html    latex
  SOSExperiment-class               text    html    latex
  SOSProtocol-class                 text    html    latex
  SOSResult-class                   text    html    latex
  SOSSubject-class                  text    html    latex
  SimpleSpeciesReference-class      text    html    latex
  Species-class                     text    html    latex
  SpeciesConcentrationRule-class    text    html    latex
  SpeciesGlyph-class                text    html    latex
  SpeciesReference-class            text    html    latex
  SpeciesReferenceGlyph-class       text    html    latex
  SpeciesType-class                 text    html    latex
  StoichiometryMath-class           text    html    latex
  TextGlyph-class                   text    html    latex
  Trigger-class                     text    html    latex
  Unit-class                        text    html    latex
  UnitDefinition-class              text    html    latex
  math                              text    html    latex
  read                              text    html    latex   example
** building package indices ...
* DONE (rsbml)

                INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --library=rsbml.buildbin-libdir --libs-only rsbml_2.0.0.tar.gz'

* Installing *source* package 'rsbml' ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LIBSBML3... yes
configure: === Begin local SOSLib build ===
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... awk
checking whether make sets $(MAKE)... yes
checking build system type... i386-apple-darwin8.11.1
checking host system type... i386-apple-darwin8.11.1
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether gcc accepts -fpic... yes
checking how to run the C preprocessor... gcc -E
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets $(MAKE)... (cached) yes
checking for autoconf... /usr/bin/autoconf
checking for aclocal... /usr/bin/aclocal
checking for make... /usr/bin/make
checking for ar... /usr/bin/ar
checking for swig... swig
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for SBML... yes
checking for correct functioning of SBML... no:
                   CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -I/usr/include/libxml2 -I/usr/local/include  
                   LDFLAGS=  
                   LIBS=-lm -lstdc++ -L/usr/local/lib -lsbml -lstdc++ -lm -lxml2  
configure: error: Can not link to SBML Library:
		  Please, make sure to use libSBML version >= 3.0.2 or CVS
configure: === End local SOSLib build ===
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** 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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c StringMap.c -o StringMap.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c check.c -o check.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c doc.c -o doc.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c dom.c -o dom.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c graph.c -o graph.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c init.c -o init.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c io.c -o io.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c mathml.c -o mathml.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/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -c simulate.c -o simulate.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 rsbml.so StringMap.o check.o doc.o dom.o graph.o init.o io.o mathml.o simulate.o -L/usr/local/lib -lsbml -lstdc++ -lm -lxml2     -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/usr/libexec/gcc/powerpc-apple-darwin8/4.2.1/ld: warning /usr/local/lib/libsbml.dylib cputype (7, architecture i386) does not match cputype (18) for specified -arch flag: ppc (file not loaded)
* DONE (rsbml)