rsbml 2.4.0
Michael Lawrence
| Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/rsbml | | Last Changed Rev: 42684 / Revision: 43539 | | Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | [ OK ] |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
INSTALLATION WITH 'R CMD INSTALL --preclean --library=rsbml.buildbin-libdir rsbml_2.4.0.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... yes
checking for SUNDIALS Library headers... yes
checking for SUNDIALS Library... yes
checking correct functioning of SUNDIALS... yes
checking correct functioning of GRACE... no:
CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -Ino/include
LDFLAGS= -Lno/lib
LIBS=-lgrace_np -lm -lstdc++
Can not link to GRACE Library!
odeSolver will be installed without XMGrace functionality
checking for isnan in -lm... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/libODES.pc
config.status: creating src/sbmlsolver/config.h
config.status: executing depfiles commands
Build Settings for SBML_odeSolver v1.7.0beta:
----------------------------------
host type = darwin
shared lib extension = dylib
install dir = /private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local
CC = gcc
CFLAGS = -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990
LDFLAGS =
LIBS = -lm -ldl -lm -lstdc++
SBML Library = yes
CFLAGS = -I/usr/include/libxml2 -I/usr/local/include
LDFLAGS =
LIBS = -L/usr/local/lib -lsbml -lstdc++ -lm -lxml2
SUNDIALS Library = yes
CFLAGS = -I/usr/local/include
LDFLAGS = -L/usr/local/lib
LIBS = -lsundials_kinsol -lsundials_cvodes -lsundials_nvecserial
GRACE = no
XMGRACE functionality will NOT be installed!
GRAPHVIZ = no
GRAPHVIZ functionality will NOT be installed!
NOTE:
SOSlib has the following dependencies:
(*) SUNDIALS suite v2.3.0
(*) libSBML v3.0.2 or CVS
Making all in src
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT arithmeticCompiler.o -MD -MP -MF .deps/arithmeticCompiler.Tpo -c -o arithmeticCompiler.o arithmeticCompiler.c
mv -f .deps/arithmeticCompiler.Tpo .deps/arithmeticCompiler.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT compiler.o -MD -MP -MF .deps/compiler.Tpo -c -o compiler.o compiler.c
mv -f .deps/compiler.Tpo .deps/compiler.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT cvodeData.o -MD -MP -MF .deps/cvodeData.Tpo -c -o cvodeData.o cvodeData.c
mv -f .deps/cvodeData.Tpo .deps/cvodeData.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT cvodeSolver.o -MD -MP -MF .deps/cvodeSolver.Tpo -c -o cvodeSolver.o cvodeSolver.c
mv -f .deps/cvodeSolver.Tpo .deps/cvodeSolver.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT daeSolver.o -MD -MP -MF .deps/daeSolver.Tpo -c -o daeSolver.o daeSolver.c
daeSolver.c:412: warning: 'JacRes' defined but not used
daeSolver.c:335: warning: 'IntegratorInstance_freeIDASpecSolverStructures' defined but not used
mv -f .deps/daeSolver.Tpo .deps/daeSolver.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT drawGraph.o -MD -MP -MF .deps/drawGraph.Tpo -c -o drawGraph.o drawGraph.c
drawGraph.c: In function 'drawModelTxt':
drawGraph.c:978: warning: assignment from incompatible pointer type
drawGraph.c:1001: warning: assignment from incompatible pointer type
mv -f .deps/drawGraph.Tpo .deps/drawGraph.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT integratorInstance.o -MD -MP -MF .deps/integratorInstance.Tpo -c -o integratorInstance.o integratorInstance.c
mv -f .deps/integratorInstance.Tpo .deps/integratorInstance.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT modelSimplify.o -MD -MP -MF .deps/modelSimplify.Tpo -c -o modelSimplify.o modelSimplify.c
mv -f .deps/modelSimplify.Tpo .deps/modelSimplify.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT nullSolver.o -MD -MP -MF .deps/nullSolver.Tpo -c -o nullSolver.o nullSolver.c
nullSolver.c:327: warning: 'JacV' defined but not used
mv -f .deps/nullSolver.Tpo .deps/nullSolver.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT odeConstruct.o -MD -MP -MF .deps/odeConstruct.Tpo -c -o odeConstruct.o odeConstruct.c
mv -f .deps/odeConstruct.Tpo .deps/odeConstruct.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT odeModel.o -MD -MP -MF .deps/odeModel.Tpo -c -o odeModel.o odeModel.c
odeModel.c:798: warning: 'List_append' defined but not used
mv -f .deps/odeModel.Tpo .deps/odeModel.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT odeSolver.o -MD -MP -MF .deps/odeSolver.Tpo -c -o odeSolver.o odeSolver.c
mv -f .deps/odeSolver.Tpo .deps/odeSolver.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT processAST.o -MD -MP -MF .deps/processAST.Tpo -c -o processAST.o processAST.c
mv -f .deps/processAST.Tpo .deps/processAST.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT sensSolver.o -MD -MP -MF .deps/sensSolver.Tpo -c -o sensSolver.o sensSolver.c
mv -f .deps/sensSolver.Tpo .deps/sensSolver.Po
rm -f libODES.a
/usr/bin/ar cru libODES.a ASTIndexNameNode.o arithmeticCompiler.o charBuffer.o compiler.o cvodeData.o cvodeSolver.o daeSolver.o drawGraph.o integratorInstance.o integratorSettings.o interpol.o modelSimplify.o nullSolver.o odeConstruct.o odeModel.o odeSolver.o processAST.o sbml.o sbmlResults.o sensSolver.o solverError.o util.o
ranlib libODES.a
make[1]: Nothing to be done for `all-am'.
Making install in src
test -z "/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/lib" || ../config/install-sh -c -d "/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/lib"
/usr/bin/install -c -m 644 'libODES.a' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/lib/libODES.a'
ranlib '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/lib/libODES.a'
test -z "/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/lib/pkgconfig" || ../config/install-sh -c -d "/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/lib/pkgconfig"
/usr/bin/install -c -m 644 'libODES.pc' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/lib/pkgconfig/libODES.pc'
test -z "/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver" || ../config/install-sh -c -d "/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver"
/usr/bin/install -c -m 644 'sbmlsolver/ASTIndexNameNode.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/ASTIndexNameNode.h'
/usr/bin/install -c -m 644 'sbmlsolver/arithmeticCompiler.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/arithmeticCompiler.h'
/usr/bin/install -c -m 644 'sbmlsolver/charBuffer.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/charBuffer.h'
/usr/bin/install -c -m 644 'sbmlsolver/compiler.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/compiler.h'
/usr/bin/install -c -m 644 'sbmlsolver/config.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/config.h'
/usr/bin/install -c -m 644 'sbmlsolver/cvodeData.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/cvodeData.h'
/usr/bin/install -c -m 644 'sbmlsolver/cvodeSolver.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/cvodeSolver.h'
/usr/bin/install -c -m 644 'sbmlsolver/daeSolver.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/daeSolver.h'
/usr/bin/install -c -m 644 'sbmlsolver/drawGraph.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/drawGraph.h'
/usr/bin/install -c -m 644 'sbmlsolver/exportdefs.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/exportdefs.h'
/usr/bin/install -c -m 644 'sbmlsolver/integratorInstance.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/integratorInstance.h'
/usr/bin/install -c -m 644 'sbmlsolver/integratorSettings.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/integratorSettings.h'
/usr/bin/install -c -m 644 'sbmlsolver/interpol.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/interpol.h'
/usr/bin/install -c -m 644 'sbmlsolver/modelSimplify.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/modelSimplify.h'
/usr/bin/install -c -m 644 'sbmlsolver/nullSolver.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/nullSolver.h'
/usr/bin/install -c -m 644 'sbmlsolver/odeConstruct.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/odeConstruct.h'
/usr/bin/install -c -m 644 'sbmlsolver/odeModel.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/odeModel.h'
/usr/bin/install -c -m 644 'sbmlsolver/odeSolver.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/odeSolver.h'
/usr/bin/install -c -m 644 'sbmlsolver/processAST.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/processAST.h'
/usr/bin/install -c -m 644 'sbmlsolver/sbml.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/sbml.h'
/usr/bin/install -c -m 644 'sbmlsolver/sbmlResults.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/sbmlResults.h'
/usr/bin/install -c -m 644 'sbmlsolver/sensSolver.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/sensSolver.h'
/usr/bin/install -c -m 644 'sbmlsolver/solverError.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/solverError.h'
/usr/bin/install -c -m 644 'sbmlsolver/util.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/util.h'
/usr/bin/install -c -m 644 'sbmlsolver/variableIndex.h' '/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/variableIndex.h'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c StringMap.c -o StringMap.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c check.c -o check.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c doc.c -o doc.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c dom.c -o dom.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c graph.c -o graph.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c init.c -o init.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c io.c -o io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c mathml.c -o mathml.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/include -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 -L/private/tmp/RtmphHJpdP/R.INSTALL10d63af1/rsbml/local/lib -lODES -lsundials_kinsol -lsundials_cvodes -lsundials_nvecserial -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
* DONE (rsbml)
INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=rsbml.buildbin-libdir --libs-only rsbml_2.4.0.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... yes
checking for SUNDIALS Library headers... yes
checking for SUNDIALS Library... yes
checking correct functioning of SUNDIALS... yes
checking correct functioning of GRACE... no:
CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -Ino/include
LDFLAGS= -Lno/lib
LIBS=-lgrace_np -lm -lstdc++
Can not link to GRACE Library!
odeSolver will be installed without XMGrace functionality
checking for isnan in -lm... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/libODES.pc
config.status: creating src/sbmlsolver/config.h
config.status: executing depfiles commands
Build Settings for SBML_odeSolver v1.7.0beta:
----------------------------------
host type = darwin
shared lib extension = dylib
install dir = /private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local
CC = gcc
CFLAGS = -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990
LDFLAGS =
LIBS = -lm -ldl -lm -lstdc++
SBML Library = yes
CFLAGS = -I/usr/include/libxml2 -I/usr/local/include
LDFLAGS =
LIBS = -L/usr/local/lib -lsbml -lstdc++ -lm -lxml2
SUNDIALS Library = yes
CFLAGS = -I/usr/local/include
LDFLAGS = -L/usr/local/lib
LIBS = -lsundials_kinsol -lsundials_cvodes -lsundials_nvecserial
GRACE = no
XMGRACE functionality will NOT be installed!
GRAPHVIZ = no
GRAPHVIZ functionality will NOT be installed!
NOTE:
SOSlib has the following dependencies:
(*) SUNDIALS suite v2.3.0
(*) libSBML v3.0.2 or CVS
Making all in src
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT arithmeticCompiler.o -MD -MP -MF .deps/arithmeticCompiler.Tpo -c -o arithmeticCompiler.o arithmeticCompiler.c
mv -f .deps/arithmeticCompiler.Tpo .deps/arithmeticCompiler.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT compiler.o -MD -MP -MF .deps/compiler.Tpo -c -o compiler.o compiler.c
mv -f .deps/compiler.Tpo .deps/compiler.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT cvodeData.o -MD -MP -MF .deps/cvodeData.Tpo -c -o cvodeData.o cvodeData.c
mv -f .deps/cvodeData.Tpo .deps/cvodeData.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT cvodeSolver.o -MD -MP -MF .deps/cvodeSolver.Tpo -c -o cvodeSolver.o cvodeSolver.c
mv -f .deps/cvodeSolver.Tpo .deps/cvodeSolver.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT daeSolver.o -MD -MP -MF .deps/daeSolver.Tpo -c -o daeSolver.o daeSolver.c
daeSolver.c:412: warning: 'JacRes' defined but not used
daeSolver.c:335: warning: 'IntegratorInstance_freeIDASpecSolverStructures' defined but not used
mv -f .deps/daeSolver.Tpo .deps/daeSolver.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT drawGraph.o -MD -MP -MF .deps/drawGraph.Tpo -c -o drawGraph.o drawGraph.c
drawGraph.c: In function 'drawModelTxt':
drawGraph.c:978: warning: assignment from incompatible pointer type
drawGraph.c:1001: warning: assignment from incompatible pointer type
mv -f .deps/drawGraph.Tpo .deps/drawGraph.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT integratorInstance.o -MD -MP -MF .deps/integratorInstance.Tpo -c -o integratorInstance.o integratorInstance.c
mv -f .deps/integratorInstance.Tpo .deps/integratorInstance.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT modelSimplify.o -MD -MP -MF .deps/modelSimplify.Tpo -c -o modelSimplify.o modelSimplify.c
mv -f .deps/modelSimplify.Tpo .deps/modelSimplify.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT nullSolver.o -MD -MP -MF .deps/nullSolver.Tpo -c -o nullSolver.o nullSolver.c
nullSolver.c:327: warning: 'JacV' defined but not used
mv -f .deps/nullSolver.Tpo .deps/nullSolver.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT odeConstruct.o -MD -MP -MF .deps/odeConstruct.Tpo -c -o odeConstruct.o odeConstruct.c
mv -f .deps/odeConstruct.Tpo .deps/odeConstruct.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT odeModel.o -MD -MP -MF .deps/odeModel.Tpo -c -o odeModel.o odeModel.c
odeModel.c:798: warning: 'List_append' defined but not used
mv -f .deps/odeModel.Tpo .deps/odeModel.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT odeSolver.o -MD -MP -MF .deps/odeSolver.Tpo -c -o odeSolver.o odeSolver.c
mv -f .deps/odeSolver.Tpo .deps/odeSolver.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT processAST.o -MD -MP -MF .deps/processAST.Tpo -c -o processAST.o processAST.c
mv -f .deps/processAST.Tpo .deps/processAST.Po
gcc -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -I. -fPIC -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -MT sensSolver.o -MD -MP -MF .deps/sensSolver.Tpo -c -o sensSolver.o sensSolver.c
mv -f .deps/sensSolver.Tpo .deps/sensSolver.Po
rm -f libODES.a
/usr/bin/ar cru libODES.a ASTIndexNameNode.o arithmeticCompiler.o charBuffer.o compiler.o cvodeData.o cvodeSolver.o daeSolver.o drawGraph.o integratorInstance.o integratorSettings.o interpol.o modelSimplify.o nullSolver.o odeConstruct.o odeModel.o odeSolver.o processAST.o sbml.o sbmlResults.o sensSolver.o solverError.o util.o
ranlib libODES.a
make[1]: Nothing to be done for `all-am'.
Making install in src
test -z "/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/lib" || ../config/install-sh -c -d "/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/lib"
/usr/bin/install -c -m 644 'libODES.a' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/lib/libODES.a'
ranlib '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/lib/libODES.a'
test -z "/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/lib/pkgconfig" || ../config/install-sh -c -d "/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/lib/pkgconfig"
/usr/bin/install -c -m 644 'libODES.pc' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/lib/pkgconfig/libODES.pc'
test -z "/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver" || ../config/install-sh -c -d "/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver"
/usr/bin/install -c -m 644 'sbmlsolver/ASTIndexNameNode.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/ASTIndexNameNode.h'
/usr/bin/install -c -m 644 'sbmlsolver/arithmeticCompiler.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/arithmeticCompiler.h'
/usr/bin/install -c -m 644 'sbmlsolver/charBuffer.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/charBuffer.h'
/usr/bin/install -c -m 644 'sbmlsolver/compiler.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/compiler.h'
/usr/bin/install -c -m 644 'sbmlsolver/config.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/config.h'
/usr/bin/install -c -m 644 'sbmlsolver/cvodeData.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/cvodeData.h'
/usr/bin/install -c -m 644 'sbmlsolver/cvodeSolver.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/cvodeSolver.h'
/usr/bin/install -c -m 644 'sbmlsolver/daeSolver.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/daeSolver.h'
/usr/bin/install -c -m 644 'sbmlsolver/drawGraph.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/drawGraph.h'
/usr/bin/install -c -m 644 'sbmlsolver/exportdefs.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/exportdefs.h'
/usr/bin/install -c -m 644 'sbmlsolver/integratorInstance.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/integratorInstance.h'
/usr/bin/install -c -m 644 'sbmlsolver/integratorSettings.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/integratorSettings.h'
/usr/bin/install -c -m 644 'sbmlsolver/interpol.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/interpol.h'
/usr/bin/install -c -m 644 'sbmlsolver/modelSimplify.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/modelSimplify.h'
/usr/bin/install -c -m 644 'sbmlsolver/nullSolver.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/nullSolver.h'
/usr/bin/install -c -m 644 'sbmlsolver/odeConstruct.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/odeConstruct.h'
/usr/bin/install -c -m 644 'sbmlsolver/odeModel.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/odeModel.h'
/usr/bin/install -c -m 644 'sbmlsolver/odeSolver.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/odeSolver.h'
/usr/bin/install -c -m 644 'sbmlsolver/processAST.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/processAST.h'
/usr/bin/install -c -m 644 'sbmlsolver/sbml.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/sbml.h'
/usr/bin/install -c -m 644 'sbmlsolver/sbmlResults.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/sbmlResults.h'
/usr/bin/install -c -m 644 'sbmlsolver/sensSolver.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/sensSolver.h'
/usr/bin/install -c -m 644 'sbmlsolver/solverError.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/solverError.h'
/usr/bin/install -c -m 644 'sbmlsolver/util.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/util.h'
/usr/bin/install -c -m 644 'sbmlsolver/variableIndex.h' '/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include/sbmlsolver/variableIndex.h'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c StringMap.c -o StringMap.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c check.c -o check.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c doc.c -o doc.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c dom.c -o dom.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c graph.c -o graph.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c init.c -o init.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c io.c -o io.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include -I/usr/local/include -fPIC -g -O2 -c mathml.c -o mathml.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -DSOSLIB -I/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/include -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 -L/private/tmp/Rtmpy9OoNx/R.INSTALL10d63af1/rsbml/local/lib -lODES -lsundials_kinsol -lsundials_cvodes -lsundials_nvecserial -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
* DONE (rsbml)