rsbml 2.10.0
Michael Lawrence
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/rsbml | | Last Changed Rev: 54800 / Revision: 59457 | | Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=rsbml.buildbin-libdir rsbml_2.10.0.tar.gz'
>>>>>>>
* installing *source* package 'rsbml' ...
checking for pkg-config... /usr/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... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking build system type... i386-apple-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
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... /usr/bin/swig
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/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... checking for SUNDIALS Library... checking correct functioning of SUNDIALS... no:
CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990
LDFLAGS=
LIBS= -lm -lstdc++
configure: error: Can not link to SUNDIALS Library
configure: === End local SOSLib build ===
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c StringMap.c -o StringMap.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c check.c -o check.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c doc.c -o doc.o
doc.c: In function 'rsbml_build_doc_cvterm':
doc.c:126: warning: ISO C forbids braced-groups within expressions
doc.c:128: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_s_base':
doc.c:141: warning: ISO C forbids braced-groups within expressions
doc.c:143: warning: ISO C forbids braced-groups within expressions
doc.c:144: warning: ISO C forbids braced-groups within expressions
doc.c:145: warning: ISO C forbids braced-groups within expressions
doc.c:146: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_species_type':
doc.c:167: warning: ISO C forbids braced-groups within expressions
doc.c:168: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_species':
doc.c:187: warning: ISO C forbids braced-groups within expressions
doc.c:188: warning: ISO C forbids braced-groups within expressions
doc.c:189: warning: ISO C forbids braced-groups within expressions
doc.c:190: warning: ISO C forbids braced-groups within expressions
doc.c:191: warning: ISO C forbids braced-groups within expressions
doc.c:192: warning: ISO C forbids braced-groups within expressions
doc.c:193: warning: ISO C forbids braced-groups within expressions
doc.c:194: warning: ISO C forbids braced-groups within expressions
doc.c:195: warning: ISO C forbids braced-groups within expressions
doc.c:196: warning: ISO C forbids braced-groups within expressions
doc.c:197: warning: ISO C forbids braced-groups within expressions
doc.c:198: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_function_definition':
doc.c:216: warning: ISO C forbids braced-groups within expressions
doc.c:217: warning: ISO C forbids braced-groups within expressions
doc.c:218: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_unit':
doc.c:236: warning: ISO C forbids braced-groups within expressions
doc.c:237: warning: ISO C forbids braced-groups within expressions
doc.c:238: warning: ISO C forbids braced-groups within expressions
doc.c:239: warning: ISO C forbids braced-groups within expressions
doc.c:240: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_unit_definition':
doc.c:258: warning: ISO C forbids braced-groups within expressions
doc.c:259: warning: ISO C forbids braced-groups within expressions
doc.c:260: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_compartment_type':
doc.c:279: warning: ISO C forbids braced-groups within expressions
doc.c:280: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_compartment':
doc.c:299: warning: ISO C forbids braced-groups within expressions
doc.c:300: warning: ISO C forbids braced-groups within expressions
doc.c:301: warning: ISO C forbids braced-groups within expressions
doc.c:302: warning: ISO C forbids braced-groups within expressions
doc.c:303: warning: ISO C forbids braced-groups within expressions
doc.c:304: warning: ISO C forbids braced-groups within expressions
doc.c:305: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_parameter':
doc.c:323: warning: ISO C forbids braced-groups within expressions
doc.c:324: warning: ISO C forbids braced-groups within expressions
doc.c:325: warning: ISO C forbids braced-groups within expressions
doc.c:326: warning: ISO C forbids braced-groups within expressions
doc.c:327: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_kinetic_law':
doc.c:345: warning: ISO C forbids braced-groups within expressions
doc.c:346: warning: ISO C forbids braced-groups within expressions
doc.c:347: warning: ISO C forbids braced-groups within expressions
doc.c:348: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_simple_species_reference':
doc.c:362: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_stoichiometry_math':
doc.c:386: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_species_reference':
doc.c:411: warning: ISO C forbids braced-groups within expressions
doc.c:415: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_reaction':
doc.c:477: warning: ISO C forbids braced-groups within expressions
doc.c:478: warning: ISO C forbids braced-groups within expressions
doc.c:479: warning: ISO C forbids braced-groups within expressions
doc.c:480: warning: ISO C forbids braced-groups within expressions
doc.c:482: warning: ISO C forbids braced-groups within expressions
doc.c:486: warning: ISO C forbids braced-groups within expressions
doc.c:487: warning: ISO C forbids braced-groups within expressions
doc.c:488: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_rule':
doc.c:511: warning: ISO C forbids braced-groups within expressions
doc.c:518: warning: ISO C forbids braced-groups within expressions
doc.c:523: warning: ISO C forbids braced-groups within expressions
doc.c:555: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_event_assignment':
doc.c:573: warning: ISO C forbids braced-groups within expressions
doc.c:574: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_trigger':
doc.c:593: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_delay':
doc.c:610: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_event':
doc.c:629: warning: ISO C forbids braced-groups within expressions
doc.c:630: warning: ISO C forbids braced-groups within expressions
doc.c:632: warning: ISO C forbids braced-groups within expressions
doc.c:633: warning: ISO C forbids braced-groups within expressions
doc.c:638: warning: ISO C forbids braced-groups within expressions
doc.c:639: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_initial_assignment':
doc.c:864: warning: ISO C forbids braced-groups within expressions
doc.c:865: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_constraint':
doc.c:882: warning: ISO C forbids braced-groups within expressions
doc.c:883: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_model_creator':
doc.c:901: warning: ISO C forbids braced-groups within expressions
doc.c:902: warning: ISO C forbids braced-groups within expressions
doc.c:903: warning: ISO C forbids braced-groups within expressions
doc.c:904: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_model_history':
doc.c:920: warning: ISO C forbids braced-groups within expressions
doc.c:922: warning: ISO C forbids braced-groups within expressions
doc.c:924: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_model':
doc.c:942: warning: ISO C forbids braced-groups within expressions
doc.c:943: warning: ISO C forbids braced-groups within expressions
doc.c:945: warning: ISO C forbids braced-groups within expressions
doc.c:946: warning: ISO C forbids braced-groups within expressions
doc.c:948: warning: ISO C forbids braced-groups within expressions
doc.c:950: warning: ISO C forbids braced-groups within expressions
doc.c:951: warning: ISO C forbids braced-groups within expressions
doc.c:952: warning: ISO C forbids braced-groups within expressions
doc.c:953: warning: ISO C forbids braced-groups within expressions
doc.c:954: warning: ISO C forbids braced-groups within expressions
doc.c:956: warning: ISO C forbids braced-groups within expressions
doc.c:957: warning: ISO C forbids braced-groups within expressions
doc.c:959: warning: ISO C forbids braced-groups within expressions
doc.c:961: warning: ISO C forbids braced-groups within expressions
doc.c:968: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc':
doc.c:1003: warning: ISO C forbids braced-groups within expressions
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c dom.c -o dom.o
dom.c: In function 'rsbml_build_dom_s_base':
dom.c:154: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_kinetic_law':
dom.c:233: warning: ISO C forbids braced-groups within expressions
dom.c:241: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_stoichiometry_math':
dom.c:290: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_reaction':
dom.c:386: warning: ISO C forbids braced-groups within expressions
dom.c:387: warning: ISO C forbids braced-groups within expressions
dom.c:388: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_unit_definition':
dom.c:458: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_function_definition':
dom.c:479: warning: ISO C forbids braced-groups within expressions
dom.c:511:7: warning: embedding a directive within macro arguments is not portable
dom.c:520:5: warning: embedding a directive within macro arguments is not portable
dom.c:529:5: warning: embedding a directive within macro arguments is not portable
dom.c: In function 'rsbml_build_dom_rule':
dom.c:571: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_event_assignment':
dom.c:591: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_delay':
dom.c:608: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_trigger':
dom.c:623: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_event':
dom.c:661: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_initial_assignment':
dom.c:974: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_constraint':
dom.c:991: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_model_history':
dom.c:1030: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_model':
dom.c:1074: warning: ISO C forbids braced-groups within expressions
dom.c:1075: warning: ISO C forbids braced-groups within expressions
dom.c:1076: warning: ISO C forbids braced-groups within expressions
dom.c:1077: warning: ISO C forbids braced-groups within expressions
dom.c:1078: warning: ISO C forbids braced-groups within expressions
dom.c:1079: warning: ISO C forbids braced-groups within expressions
dom.c:1080: warning: ISO C forbids braced-groups within expressions
dom.c:1082: warning: ISO C forbids braced-groups within expressions
dom.c:1083: warning: ISO C forbids braced-groups within expressions
dom.c:1084: warning: ISO C forbids braced-groups within expressions
dom.c:1085: warning: ISO C forbids braced-groups within expressions
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c graph.c -o graph.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c init.c -o init.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c io.c -o io.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c mathml.c -o mathml.o
mathml.c: In function 'rmathml_SEXP':
mathml.c:56: warning: unused variable 'closure'
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c simulate.c -o simulate.o
simulate.c:1: warning: ISO C forbids an empty source file
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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 -lpthread -licucore -lz -lbz2 -lsbml -lstdc++ -lm -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (rsbml)
>>>>>>>
>>>>>>> FIXING LINKS FOR rsbml.buildbin-libdir/rsbml/libs/i386/rsbml.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "rsbml.buildbin-libdir/rsbml/libs/i386/rsbml.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "rsbml.buildbin-libdir/rsbml/libs/i386/rsbml.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "rsbml.buildbin-libdir/rsbml/libs/i386/rsbml.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "rsbml.buildbin-libdir/rsbml/libs/i386/rsbml.so"
>>>>>>>
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=rsbml.buildbin-libdir --libs-only rsbml_2.10.0.tar.gz'
>>>>>>>
* installing *source* package 'rsbml' ...
checking for pkg-config... /usr/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... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking build system type... i386-apple-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
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... /usr/bin/swig
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/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... checking for SUNDIALS Library... checking correct functioning of SUNDIALS... no:
CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990
LDFLAGS=
LIBS= -lm -lstdc++
configure: error: Can not link to SUNDIALS Library
configure: === End local SOSLib build ===
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c StringMap.c -o StringMap.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c check.c -o check.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c doc.c -o doc.o
doc.c: In function 'rsbml_build_doc_cvterm':
doc.c:126: warning: ISO C forbids braced-groups within expressions
doc.c:128: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_s_base':
doc.c:141: warning: ISO C forbids braced-groups within expressions
doc.c:143: warning: ISO C forbids braced-groups within expressions
doc.c:144: warning: ISO C forbids braced-groups within expressions
doc.c:145: warning: ISO C forbids braced-groups within expressions
doc.c:146: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_species_type':
doc.c:167: warning: ISO C forbids braced-groups within expressions
doc.c:168: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_species':
doc.c:187: warning: ISO C forbids braced-groups within expressions
doc.c:188: warning: ISO C forbids braced-groups within expressions
doc.c:189: warning: ISO C forbids braced-groups within expressions
doc.c:190: warning: ISO C forbids braced-groups within expressions
doc.c:191: warning: ISO C forbids braced-groups within expressions
doc.c:192: warning: ISO C forbids braced-groups within expressions
doc.c:193: warning: ISO C forbids braced-groups within expressions
doc.c:194: warning: ISO C forbids braced-groups within expressions
doc.c:195: warning: ISO C forbids braced-groups within expressions
doc.c:196: warning: ISO C forbids braced-groups within expressions
doc.c:197: warning: ISO C forbids braced-groups within expressions
doc.c:198: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_function_definition':
doc.c:216: warning: ISO C forbids braced-groups within expressions
doc.c:217: warning: ISO C forbids braced-groups within expressions
doc.c:218: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_unit':
doc.c:236: warning: ISO C forbids braced-groups within expressions
doc.c:237: warning: ISO C forbids braced-groups within expressions
doc.c:238: warning: ISO C forbids braced-groups within expressions
doc.c:239: warning: ISO C forbids braced-groups within expressions
doc.c:240: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_unit_definition':
doc.c:258: warning: ISO C forbids braced-groups within expressions
doc.c:259: warning: ISO C forbids braced-groups within expressions
doc.c:260: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_compartment_type':
doc.c:279: warning: ISO C forbids braced-groups within expressions
doc.c:280: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_compartment':
doc.c:299: warning: ISO C forbids braced-groups within expressions
doc.c:300: warning: ISO C forbids braced-groups within expressions
doc.c:301: warning: ISO C forbids braced-groups within expressions
doc.c:302: warning: ISO C forbids braced-groups within expressions
doc.c:303: warning: ISO C forbids braced-groups within expressions
doc.c:304: warning: ISO C forbids braced-groups within expressions
doc.c:305: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_parameter':
doc.c:323: warning: ISO C forbids braced-groups within expressions
doc.c:324: warning: ISO C forbids braced-groups within expressions
doc.c:325: warning: ISO C forbids braced-groups within expressions
doc.c:326: warning: ISO C forbids braced-groups within expressions
doc.c:327: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_kinetic_law':
doc.c:345: warning: ISO C forbids braced-groups within expressions
doc.c:346: warning: ISO C forbids braced-groups within expressions
doc.c:347: warning: ISO C forbids braced-groups within expressions
doc.c:348: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_simple_species_reference':
doc.c:362: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_stoichiometry_math':
doc.c:386: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_species_reference':
doc.c:411: warning: ISO C forbids braced-groups within expressions
doc.c:415: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_reaction':
doc.c:477: warning: ISO C forbids braced-groups within expressions
doc.c:478: warning: ISO C forbids braced-groups within expressions
doc.c:479: warning: ISO C forbids braced-groups within expressions
doc.c:480: warning: ISO C forbids braced-groups within expressions
doc.c:482: warning: ISO C forbids braced-groups within expressions
doc.c:486: warning: ISO C forbids braced-groups within expressions
doc.c:487: warning: ISO C forbids braced-groups within expressions
doc.c:488: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_rule':
doc.c:511: warning: ISO C forbids braced-groups within expressions
doc.c:518: warning: ISO C forbids braced-groups within expressions
doc.c:523: warning: ISO C forbids braced-groups within expressions
doc.c:555: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_event_assignment':
doc.c:573: warning: ISO C forbids braced-groups within expressions
doc.c:574: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_trigger':
doc.c:593: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_delay':
doc.c:610: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_event':
doc.c:629: warning: ISO C forbids braced-groups within expressions
doc.c:630: warning: ISO C forbids braced-groups within expressions
doc.c:632: warning: ISO C forbids braced-groups within expressions
doc.c:633: warning: ISO C forbids braced-groups within expressions
doc.c:638: warning: ISO C forbids braced-groups within expressions
doc.c:639: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_initial_assignment':
doc.c:864: warning: ISO C forbids braced-groups within expressions
doc.c:865: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_constraint':
doc.c:882: warning: ISO C forbids braced-groups within expressions
doc.c:883: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_model_creator':
doc.c:901: warning: ISO C forbids braced-groups within expressions
doc.c:902: warning: ISO C forbids braced-groups within expressions
doc.c:903: warning: ISO C forbids braced-groups within expressions
doc.c:904: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_model_history':
doc.c:920: warning: ISO C forbids braced-groups within expressions
doc.c:922: warning: ISO C forbids braced-groups within expressions
doc.c:924: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_model':
doc.c:942: warning: ISO C forbids braced-groups within expressions
doc.c:943: warning: ISO C forbids braced-groups within expressions
doc.c:945: warning: ISO C forbids braced-groups within expressions
doc.c:946: warning: ISO C forbids braced-groups within expressions
doc.c:948: warning: ISO C forbids braced-groups within expressions
doc.c:950: warning: ISO C forbids braced-groups within expressions
doc.c:951: warning: ISO C forbids braced-groups within expressions
doc.c:952: warning: ISO C forbids braced-groups within expressions
doc.c:953: warning: ISO C forbids braced-groups within expressions
doc.c:954: warning: ISO C forbids braced-groups within expressions
doc.c:956: warning: ISO C forbids braced-groups within expressions
doc.c:957: warning: ISO C forbids braced-groups within expressions
doc.c:959: warning: ISO C forbids braced-groups within expressions
doc.c:961: warning: ISO C forbids braced-groups within expressions
doc.c:968: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc':
doc.c:1003: warning: ISO C forbids braced-groups within expressions
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c dom.c -o dom.o
dom.c: In function 'rsbml_build_dom_s_base':
dom.c:154: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_kinetic_law':
dom.c:233: warning: ISO C forbids braced-groups within expressions
dom.c:241: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_stoichiometry_math':
dom.c:290: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_reaction':
dom.c:386: warning: ISO C forbids braced-groups within expressions
dom.c:387: warning: ISO C forbids braced-groups within expressions
dom.c:388: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_unit_definition':
dom.c:458: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_function_definition':
dom.c:479: warning: ISO C forbids braced-groups within expressions
dom.c:511:7: warning: embedding a directive within macro arguments is not portable
dom.c:520:5: warning: embedding a directive within macro arguments is not portable
dom.c:529:5: warning: embedding a directive within macro arguments is not portable
dom.c: In function 'rsbml_build_dom_rule':
dom.c:571: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_event_assignment':
dom.c:591: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_delay':
dom.c:608: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_trigger':
dom.c:623: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_event':
dom.c:661: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_initial_assignment':
dom.c:974: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_constraint':
dom.c:991: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_model_history':
dom.c:1030: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_model':
dom.c:1074: warning: ISO C forbids braced-groups within expressions
dom.c:1075: warning: ISO C forbids braced-groups within expressions
dom.c:1076: warning: ISO C forbids braced-groups within expressions
dom.c:1077: warning: ISO C forbids braced-groups within expressions
dom.c:1078: warning: ISO C forbids braced-groups within expressions
dom.c:1079: warning: ISO C forbids braced-groups within expressions
dom.c:1080: warning: ISO C forbids braced-groups within expressions
dom.c:1082: warning: ISO C forbids braced-groups within expressions
dom.c:1083: warning: ISO C forbids braced-groups within expressions
dom.c:1084: warning: ISO C forbids braced-groups within expressions
dom.c:1085: warning: ISO C forbids braced-groups within expressions
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c graph.c -o graph.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c init.c -o init.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c io.c -o io.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c mathml.c -o mathml.o
mathml.c: In function 'rmathml_SEXP':
mathml.c:56: warning: unused variable 'closure'
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c simulate.c -o simulate.o
simulate.c:1: warning: ISO C forbids an empty source file
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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 -lpthread -licucore -lz -lbz2 -lsbml -lstdc++ -lm -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld warning: in /usr/local/lib/libsbml.dylib, file is not of required architecture
installing to /Users/biocbuild/bbs-2.8-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/ppc
* DONE (rsbml)
>>>>>>>
>>>>>>> FIXING LINKS FOR rsbml.buildbin-libdir/rsbml/libs/ppc/rsbml.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "rsbml.buildbin-libdir/rsbml/libs/ppc/rsbml.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "rsbml.buildbin-libdir/rsbml/libs/ppc/rsbml.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "rsbml.buildbin-libdir/rsbml/libs/ppc/rsbml.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "rsbml.buildbin-libdir/rsbml/libs/ppc/rsbml.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --library=rsbml.buildbin-libdir --libs-only rsbml_2.10.0.tar.gz'
>>>>>>>
* installing *source* package 'rsbml' ...
checking for pkg-config... /usr/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... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking build system type... i386-apple-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
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... /usr/bin/swig
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/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... checking for SUNDIALS Library... checking correct functioning of SUNDIALS... no:
CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990
LDFLAGS=
LIBS= -lm -lstdc++
configure: error: Can not link to SUNDIALS Library
configure: === End local SOSLib build ===
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c StringMap.c -o StringMap.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c check.c -o check.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c doc.c -o doc.o
doc.c: In function 'rsbml_build_doc_cvterm':
doc.c:126: warning: ISO C forbids braced-groups within expressions
doc.c:128: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_s_base':
doc.c:141: warning: ISO C forbids braced-groups within expressions
doc.c:143: warning: ISO C forbids braced-groups within expressions
doc.c:144: warning: ISO C forbids braced-groups within expressions
doc.c:145: warning: ISO C forbids braced-groups within expressions
doc.c:146: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_species_type':
doc.c:167: warning: ISO C forbids braced-groups within expressions
doc.c:168: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_species':
doc.c:187: warning: ISO C forbids braced-groups within expressions
doc.c:188: warning: ISO C forbids braced-groups within expressions
doc.c:189: warning: ISO C forbids braced-groups within expressions
doc.c:190: warning: ISO C forbids braced-groups within expressions
doc.c:191: warning: ISO C forbids braced-groups within expressions
doc.c:192: warning: ISO C forbids braced-groups within expressions
doc.c:193: warning: ISO C forbids braced-groups within expressions
doc.c:194: warning: ISO C forbids braced-groups within expressions
doc.c:195: warning: ISO C forbids braced-groups within expressions
doc.c:196: warning: ISO C forbids braced-groups within expressions
doc.c:197: warning: ISO C forbids braced-groups within expressions
doc.c:198: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_function_definition':
doc.c:216: warning: ISO C forbids braced-groups within expressions
doc.c:217: warning: ISO C forbids braced-groups within expressions
doc.c:218: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_unit':
doc.c:236: warning: ISO C forbids braced-groups within expressions
doc.c:237: warning: ISO C forbids braced-groups within expressions
doc.c:238: warning: ISO C forbids braced-groups within expressions
doc.c:239: warning: ISO C forbids braced-groups within expressions
doc.c:240: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_unit_definition':
doc.c:258: warning: ISO C forbids braced-groups within expressions
doc.c:259: warning: ISO C forbids braced-groups within expressions
doc.c:260: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_compartment_type':
doc.c:279: warning: ISO C forbids braced-groups within expressions
doc.c:280: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_compartment':
doc.c:299: warning: ISO C forbids braced-groups within expressions
doc.c:300: warning: ISO C forbids braced-groups within expressions
doc.c:301: warning: ISO C forbids braced-groups within expressions
doc.c:302: warning: ISO C forbids braced-groups within expressions
doc.c:303: warning: ISO C forbids braced-groups within expressions
doc.c:304: warning: ISO C forbids braced-groups within expressions
doc.c:305: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_parameter':
doc.c:323: warning: ISO C forbids braced-groups within expressions
doc.c:324: warning: ISO C forbids braced-groups within expressions
doc.c:325: warning: ISO C forbids braced-groups within expressions
doc.c:326: warning: ISO C forbids braced-groups within expressions
doc.c:327: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_kinetic_law':
doc.c:345: warning: ISO C forbids braced-groups within expressions
doc.c:346: warning: ISO C forbids braced-groups within expressions
doc.c:347: warning: ISO C forbids braced-groups within expressions
doc.c:348: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_simple_species_reference':
doc.c:362: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_stoichiometry_math':
doc.c:386: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_species_reference':
doc.c:411: warning: ISO C forbids braced-groups within expressions
doc.c:415: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_reaction':
doc.c:477: warning: ISO C forbids braced-groups within expressions
doc.c:478: warning: ISO C forbids braced-groups within expressions
doc.c:479: warning: ISO C forbids braced-groups within expressions
doc.c:480: warning: ISO C forbids braced-groups within expressions
doc.c:482: warning: ISO C forbids braced-groups within expressions
doc.c:486: warning: ISO C forbids braced-groups within expressions
doc.c:487: warning: ISO C forbids braced-groups within expressions
doc.c:488: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_rule':
doc.c:511: warning: ISO C forbids braced-groups within expressions
doc.c:518: warning: ISO C forbids braced-groups within expressions
doc.c:523: warning: ISO C forbids braced-groups within expressions
doc.c:555: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_event_assignment':
doc.c:573: warning: ISO C forbids braced-groups within expressions
doc.c:574: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_trigger':
doc.c:593: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_delay':
doc.c:610: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_event':
doc.c:629: warning: ISO C forbids braced-groups within expressions
doc.c:630: warning: ISO C forbids braced-groups within expressions
doc.c:632: warning: ISO C forbids braced-groups within expressions
doc.c:633: warning: ISO C forbids braced-groups within expressions
doc.c:638: warning: ISO C forbids braced-groups within expressions
doc.c:639: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_initial_assignment':
doc.c:864: warning: ISO C forbids braced-groups within expressions
doc.c:865: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_constraint':
doc.c:882: warning: ISO C forbids braced-groups within expressions
doc.c:883: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_model_creator':
doc.c:901: warning: ISO C forbids braced-groups within expressions
doc.c:902: warning: ISO C forbids braced-groups within expressions
doc.c:903: warning: ISO C forbids braced-groups within expressions
doc.c:904: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_model_history':
doc.c:920: warning: ISO C forbids braced-groups within expressions
doc.c:922: warning: ISO C forbids braced-groups within expressions
doc.c:924: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc_model':
doc.c:942: warning: ISO C forbids braced-groups within expressions
doc.c:943: warning: ISO C forbids braced-groups within expressions
doc.c:945: warning: ISO C forbids braced-groups within expressions
doc.c:946: warning: ISO C forbids braced-groups within expressions
doc.c:948: warning: ISO C forbids braced-groups within expressions
doc.c:950: warning: ISO C forbids braced-groups within expressions
doc.c:951: warning: ISO C forbids braced-groups within expressions
doc.c:952: warning: ISO C forbids braced-groups within expressions
doc.c:953: warning: ISO C forbids braced-groups within expressions
doc.c:954: warning: ISO C forbids braced-groups within expressions
doc.c:956: warning: ISO C forbids braced-groups within expressions
doc.c:957: warning: ISO C forbids braced-groups within expressions
doc.c:959: warning: ISO C forbids braced-groups within expressions
doc.c:961: warning: ISO C forbids braced-groups within expressions
doc.c:968: warning: ISO C forbids braced-groups within expressions
doc.c: In function 'rsbml_build_doc':
doc.c:1003: warning: ISO C forbids braced-groups within expressions
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c dom.c -o dom.o
dom.c: In function 'rsbml_build_dom_s_base':
dom.c:154: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_kinetic_law':
dom.c:233: warning: ISO C forbids braced-groups within expressions
dom.c:241: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_stoichiometry_math':
dom.c:290: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_reaction':
dom.c:386: warning: ISO C forbids braced-groups within expressions
dom.c:387: warning: ISO C forbids braced-groups within expressions
dom.c:388: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_unit_definition':
dom.c:458: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_function_definition':
dom.c:479: warning: ISO C forbids braced-groups within expressions
dom.c:511:7: warning: embedding a directive within macro arguments is not portable
dom.c:520:5: warning: embedding a directive within macro arguments is not portable
dom.c:529:5: warning: embedding a directive within macro arguments is not portable
dom.c: In function 'rsbml_build_dom_rule':
dom.c:571: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_event_assignment':
dom.c:591: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_delay':
dom.c:608: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_trigger':
dom.c:623: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_event':
dom.c:661: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_initial_assignment':
dom.c:974: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_constraint':
dom.c:991: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_model_history':
dom.c:1030: warning: ISO C forbids braced-groups within expressions
dom.c: In function 'rsbml_build_dom_model':
dom.c:1074: warning: ISO C forbids braced-groups within expressions
dom.c:1075: warning: ISO C forbids braced-groups within expressions
dom.c:1076: warning: ISO C forbids braced-groups within expressions
dom.c:1077: warning: ISO C forbids braced-groups within expressions
dom.c:1078: warning: ISO C forbids braced-groups within expressions
dom.c:1079: warning: ISO C forbids braced-groups within expressions
dom.c:1080: warning: ISO C forbids braced-groups within expressions
dom.c:1082: warning: ISO C forbids braced-groups within expressions
dom.c:1083: warning: ISO C forbids braced-groups within expressions
dom.c:1084: warning: ISO C forbids braced-groups within expressions
dom.c:1085: warning: ISO C forbids braced-groups within expressions
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c graph.c -o graph.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c init.c -o init.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c io.c -o io.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c mathml.c -o mathml.o
mathml.c: In function 'rmathml_SEXP':
mathml.c:56: warning: unused variable 'closure'
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c simulate.c -o simulate.o
simulate.c:1: warning: ISO C forbids an empty source file
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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 -lpthread -licucore -lz -lbz2 -lsbml -lstdc++ -lm -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld warning: in /usr/local/lib/libsbml.dylib, file is not of required architecture
installing to /Users/biocbuild/bbs-2.8-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/x86_64
* DONE (rsbml)
>>>>>>>
>>>>>>> FIXING LINKS FOR rsbml.buildbin-libdir/rsbml/libs/x86_64/rsbml.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "rsbml.buildbin-libdir/rsbml/libs/x86_64/rsbml.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "rsbml.buildbin-libdir/rsbml/libs/x86_64/rsbml.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "rsbml.buildbin-libdir/rsbml/libs/x86_64/rsbml.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "rsbml.buildbin-libdir/rsbml/libs/x86_64/rsbml.so"