BioC 3.6: BUILD BIN report for CNORode on veracruz1

Package: CNORode

Version: 1.19.0

Command: rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNORode_1.19.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CNORode.buildbin-libdir

StartedAt: 2017-08-16 10:04:41 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 10:04:56 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 15.0 seconds

RetCode: 0

Status:  OK

PackageFile: CNORode_1.19.0.tgz

PackageFileSize: 531 KiB

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### Running command:
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###   rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNORode_1.19.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CNORode.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNORode.buildbin-libdir CNORode_1.19.0.tar.gz'
>>>>>>> 

* installing *source* package ‘CNORode’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodea.c -o cvodea.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodea_io.c -o cvodea_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes.c -o cvodes.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes_band.c -o cvodes_band.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes_bandpre.c -o cvodes_bandpre.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes_bbdpre.c -o cvodes_bbdpre.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes_dense.c -o cvodes_dense.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes_diag.c -o cvodes_diag.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes_direct.c -o cvodes_direct.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes_io.c -o cvodes_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes_spbcgs.c -o cvodes_spbcgs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes_spgmr.c -o cvodes_spgmr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes_spils.c -o cvodes_spils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c decimal2binary.c -o decimal2binary.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c findStates.c -o findStates.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c fnvector_serial.c -o fnvector_serial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c getNumBits.c -o getNumBits.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c getNumInputs.c -o getNumInputs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c getStateIndex.c -o getStateIndex.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c getTruthTables.c -o getTruthTables.o
getTruthTables.c:17:14: warning: unused variable 'n' [-Wunused-variable]
        int i,j,k,m,n,counter1,input,miniterm;
                    ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c get_count_bits.c -o get_count_bits.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c get_input_index.c -o get_input_index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c:16:10: warning: unused variable 'k' [-Wunused-variable]
        int i,j,k;
                ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c get_truth_tables_index.c -o get_truth_tables_index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c hill_function.c -o hill_function.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c linear_transfer_function.c -o linear_transfer_function.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c normHill.c -o normHill.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c nvector_serial.c -o nvector_serial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c printAdjMat.c -o printAdjMat.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c printInterMat.c -o printInterMat.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c printNminiTerms.c -o printNminiTerms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c printTruthTables.c -o printTruthTables.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c rhsODE.c -o rhsODE.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c sim_logic_ode.c -o sim_logic_ode.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c simulateODE.c -o simulateODE.o
simulateODE.c:150:11: warning: implicit declaration of function 'CVDense' is invalid in C99 [-Wimplicit-function-declaration]
          flag = CVDense(cvode_mem, neq);
                 ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c sundials_band.c -o sundials_band.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c sundials_dense.c -o sundials_dense.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c sundials_direct.c -o sundials_direct.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c sundials_iterative.c -o sundials_iterative.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c sundials_math.c -o sundials_math.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c sundials_nvector.c -o sundials_nvector.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c sundials_spbcgs.c -o sundials_spbcgs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c sundials_spgmr.c -o sundials_spgmr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c sundials_sptfqmr.c -o sundials_sptfqmr.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -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-3.6-bioc/meat/CNORode.buildbin-libdir/CNORode/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNORode)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "CNORode.buildbin-libdir/CNORode/libs//CNORode.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "CNORode.buildbin-libdir/CNORode/libs//CNORode.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "CNORode.buildbin-libdir/CNORode/libs//CNORode.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "CNORode.buildbin-libdir/CNORode/libs//CNORode.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "CNORode.buildbin-libdir/CNORode/libs//CNORode.so"