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###
### Running command:
###
### rm -rf ternarynet.buildbin-libdir && mkdir ternarynet.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ternarynet_1.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ternarynet.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ternarynet.buildbin-libdir ternarynet_1.42.0.tar.gz'
>>>>>>>
* installing *source* package ‘ternarynet’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c array.c -o array.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gn.c -o gn.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gn_Rwrap.c -o gn_Rwrap.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c tnetfit.cc -o tnetfit.o
tnetfit.cc:24:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage, maxStage, maxTransition;
^
tnetfit.cc:24:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage, maxStage, maxTransition;
^
tnetfit.cc:24:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage, maxStage, maxTransition;
^
tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable]
int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c tnetfuncs.cc -o tnetfuncs.o
tnetfuncs.cc:427:5: warning: unused variable 'tableWidth' [-Wunused-variable]
int tableWidth = powi(nOutcomes,maxDegree);
^
tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
^
tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable]
int m1, m2, i;
^
tnetfuncs.cc:517:6: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c tnetpost.cc -o tnetpost.o
tnetpost.cc:41:9: warning: variable 'Rf_beta' set but not used [-Wunused-but-set-variable]
int beta;
^
/Library/Frameworks/R.framework/Resources/include/Rmath.h:210:15: note: expanded from macro 'beta'
#define beta Rf_beta
^
tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable]
double newScore, oldScore, minScore, finalScore;
^
tnetpost.cc:28:32: warning: variable 'minScore' set but not used [-Wunused-but-set-variable]
double newScore, oldScore, minScore, finalScore;
^
tnetpost.cc:40:27: warning: variable 'delta' set but not used [-Wunused-but-set-variable]
double epsilon, chi0, delta, rho;
^
tnetpost.cc:40:34: warning: variable 'rho' set but not used [-Wunused-but-set-variable]
double epsilon, chi0, delta, rho;
^
tnetpost.cc:30:13: warning: unused variable 'stage_count' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
tnetpost.cc:44:9: warning: variable 'ne' set but not used [-Wunused-but-set-variable]
int ne, maxDegree;
^
tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
tnetpost.cc:30:33: warning: unused variable 'jtrans' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
tnetpost.cc:30:26: warning: unused variable 'tempi' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
tnetpost.cc:30:41: warning: unused variable 'nTransition' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
tnetpost.cc:36:21: warning: variable 'xSeedFit' set but not used [-Wunused-but-set-variable]
int m0, mdelta, xSeedFit;
^
tnetpost.cc:150:10: warning: variable 'minDump' set but not used [-Wunused-but-set-variable]
bool minDump = true;
^
tnetpost.cc:38:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage;
^
tnetpost.cc:38:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage;
^
tnetpost.cc:39:9: warning: variable 'maxStage' set but not used [-Wunused-but-set-variable]
int maxStage, maxTransition;
^
tnetpost.cc:38:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage;
^
tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
^
tnetpost.cc:39:19: warning: variable 'maxTransition' set but not used [-Wunused-but-set-variable]
int maxStage, maxTransition;
^
tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable]
int m0fit;
^
tnetpost.cc:40:21: warning: variable 'chi0' set but not used [-Wunused-but-set-variable]
double epsilon, chi0, delta, rho;
^
tnetpost.cc:40:12: warning: variable 'epsilon' set but not used [-Wunused-but-set-variable]
double epsilon, chi0, delta, rho;
^
22 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c util.c -o util.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 ternarynet.so array.o gn.o gn_Rwrap.o init.o tnetfit.o tnetfuncs.o tnetpost.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-bioc/meat/ternarynet.buildbin-libdir/00LOCK-ternarynet/00new/ternarynet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ternarynet)
>>>>>>>
>>>>>>> FIXING LINKS FOR ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so"
