rsbml 2.2.1
Michael Lawrence
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/rsbml | | Last Changed Rev: 39231 / Revision: 42512 | | Last Changed Date: 2009-04-29 15:36:12 -0700 (Wed, 29 Apr 2009) |
| wilson1 | 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_2.2.1.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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c StringMap.c -o StringMap.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c check.c -o check.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c doc.c -o doc.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c dom.c -o dom.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c graph.c -o graph.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c init.c -o init.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c io.c -o io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c mathml.c -o mathml.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -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
** help
*** installing help indices
>>> Building/Updating help pages for package 'rsbml'
Formats: text html latex example
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read text html latex example
** building package indices ...
* DONE (rsbml)
INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=rsbml.buildbin-libdir --libs-only rsbml_2.2.1.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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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)