Package: CNORode

Version: 1.1.4

Command: rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNORode_1.1.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CNORode.buildbin-libdir

StartedAt: 2013-03-25 05:21:43 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:22:15 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 31.9 seconds

RetCode: 0

Status:  OK

PackageFile: CNORode_1.1.4.tgz

PackageFileSize: 612.7 KiB

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNORode.buildbin-libdir CNORode_1.1.4.tar.gz'
>>>>>>> 

* installing *source* package 'CNORode' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodea.c -o cvodea.o
cvodea.c: In function 'CVodeB':
cvodea.c:1263: warning: 'flag' may be used uninitialized in this function
cvodea.c: In function 'CVAhermiteGetY':
cvodea.c:2507: warning: 'ySd0' may be used uninitialized in this function
cvodea.c:2507: warning: 'yS0' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodea_io.c -o cvodea_io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes.c -o cvodes.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_band.c -o cvodes_band.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_bandpre.c -o cvodes_bandpre.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_bbdpre.c -o cvodes_bbdpre.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_dense.c -o cvodes_dense.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_diag.c -o cvodes_diag.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_direct.c -o cvodes_direct.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_io.c -o cvodes_io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_spbcgs.c -o cvodes_spbcgs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_spgmr.c -o cvodes_spgmr.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_spils.c -o cvodes_spils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c decimal2binary.c -o decimal2binary.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c findStates.c -o findStates.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c fnvector_serial.c -o fnvector_serial.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getNumBits.c -o getNumBits.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getNumInputs.c -o getNumInputs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getStateIndex.c -o getStateIndex.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getTruthTables.c -o getTruthTables.o
getTruthTables.c: In function 'getTruthTables':
getTruthTables.c:17: warning: unused variable 'n'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c get_count_bits.c -o get_count_bits.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c get_input_index.c -o get_input_index.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c: In function 'get_support_truth_tables':
get_support_truth_tables.c:16: warning: unused variable 'k'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c get_truth_tables_index.c -o get_truth_tables_index.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c hill_function.c -o hill_function.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c linear_transfer_function.c -o linear_transfer_function.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c normHill.c -o normHill.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c nvector_serial.c -o nvector_serial.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printAdjMat.c -o printAdjMat.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printInterMat.c -o printInterMat.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printNminiTerms.c -o printNminiTerms.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printTruthTables.c -o printTruthTables.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c rhsODE.c -o rhsODE.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sim_logic_ode.c -o sim_logic_ode.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:150: warning: implicit declaration of function 'CVDense'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_band.c -o sundials_band.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_dense.c -o sundials_dense.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_direct.c -o sundials_direct.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_iterative.c -o sundials_iterative.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_math.c -o sundials_math.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_nvector.c -o sundials_nvector.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_spbcgs.c -o sundials_spbcgs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_spgmr.c -o sundials_spgmr.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_sptfqmr.c -o sundials_sptfqmr.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o CNORode.so cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CNORode.buildbin-libdir/CNORode/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'CNORode-vignette.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
Warning: ignoring .First.lib() for package 'CNORode'
* DONE (CNORode)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "CNORode.buildbin-libdir/CNORode/libs/i386/CNORode.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "CNORode.buildbin-libdir/CNORode/libs/i386/CNORode.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "CNORode.buildbin-libdir/CNORode/libs/i386/CNORode.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "CNORode.buildbin-libdir/CNORode/libs/i386/CNORode.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=CNORode.buildbin-libdir --libs-only CNORode_1.1.4.tar.gz'
>>>>>>> 

* installing *source* package 'CNORode' ...
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodea.c -o cvodea.o
cvodea.c: In function 'CVodeB':
cvodea.c:1263: warning: 'flag' may be used uninitialized in this function
cvodea.c: In function 'CVAhermiteGetY':
cvodea.c:2507: warning: 'ySd0' may be used uninitialized in this function
cvodea.c:2507: warning: 'yS0' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodea_io.c -o cvodea_io.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes.c -o cvodes.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_band.c -o cvodes_band.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_bandpre.c -o cvodes_bandpre.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_bbdpre.c -o cvodes_bbdpre.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_dense.c -o cvodes_dense.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_diag.c -o cvodes_diag.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_direct.c -o cvodes_direct.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_io.c -o cvodes_io.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_spbcgs.c -o cvodes_spbcgs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_spgmr.c -o cvodes_spgmr.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_spils.c -o cvodes_spils.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c decimal2binary.c -o decimal2binary.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c findStates.c -o findStates.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c fnvector_serial.c -o fnvector_serial.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getNumBits.c -o getNumBits.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getNumInputs.c -o getNumInputs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getStateIndex.c -o getStateIndex.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c getTruthTables.c -o getTruthTables.o
getTruthTables.c: In function 'getTruthTables':
getTruthTables.c:17: warning: unused variable 'n'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c get_count_bits.c -o get_count_bits.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c get_input_index.c -o get_input_index.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c: In function 'get_support_truth_tables':
get_support_truth_tables.c:16: warning: unused variable 'k'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c get_truth_tables_index.c -o get_truth_tables_index.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c hill_function.c -o hill_function.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c linear_transfer_function.c -o linear_transfer_function.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c normHill.c -o normHill.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c nvector_serial.c -o nvector_serial.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printAdjMat.c -o printAdjMat.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printInterMat.c -o printInterMat.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printNminiTerms.c -o printNminiTerms.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c printTruthTables.c -o printTruthTables.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c rhsODE.c -o rhsODE.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sim_logic_ode.c -o sim_logic_ode.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:150: warning: implicit declaration of function 'CVDense'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_band.c -o sundials_band.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_dense.c -o sundials_dense.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_direct.c -o sundials_direct.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_iterative.c -o sundials_iterative.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_math.c -o sundials_math.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_nvector.c -o sundials_nvector.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_spbcgs.c -o sundials_spbcgs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_spgmr.c -o sundials_spgmr.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -g -O2 -Wall -pedantic  -c sundials_sptfqmr.c -o sundials_sptfqmr.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o CNORode.so cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CNORode.buildbin-libdir/CNORode/libs/x86_64
* DONE (CNORode)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "CNORode.buildbin-libdir/CNORode/libs/x86_64/CNORode.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "CNORode.buildbin-libdir/CNORode/libs/x86_64/CNORode.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "CNORode.buildbin-libdir/CNORode/libs/x86_64/CNORode.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "CNORode.buildbin-libdir/CNORode/libs/x86_64/CNORode.so"