##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf flipflop.buildbin-libdir && mkdir flipflop.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flipflop_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flipflop.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flipflop.buildbin-libdir flipflop_1.12.0.tar.gz'
>>>>>>>
* installing *source* package ‘flipflop’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c FileSplitter.cpp -o FileSplitter.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_init_flipflop.c -o R_init_flipflop.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c align.cpp -o align.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c auxiliaryio.cpp -o auxiliaryio.o
In file included from auxiliaryio.cpp:6:
In file included from ./auxiliaryio.h:11:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
auxiliaryio.cpp:904:9: warning: unused variable 'id' [-Wunused-variable]
int id;
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c bedio.cpp -o bedio.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c common.cpp -o common.o
In file included from common.cpp:5:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c cvganalysis.cpp -o cvganalysis.o
In file included from cvganalysis.cpp:2:
In file included from ./cvganalysis.h:9:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
cvganalysis.cpp:156:12: warning: unused variable 'prevjump' [-Wunused-variable]
bool prevjump=false;
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c ffProcesssam.cpp -o ffProcesssam.o
In file included from ffProcesssam.cpp:3:
In file included from ./samio.h:10:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c instanceio.cpp -o instanceio.o
In file included from instanceio.cpp:2:
In file included from ./instanceio.h:7:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
instanceio.cpp:125:9: warning: unused variable 'currenttypeorder' [-Wunused-variable]
int currenttypeorder=-1;
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c parseopt.cpp -o parseopt.o
In file included from parseopt.cpp:1:
In file included from ./parseopt.h:9:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c rangeset.cpp -o rangeset.o
rangeset.cpp:331:8: warning: unused variable 't' [-Wunused-variable]
long t=0;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c readgroup.cpp -o readgroup.o
In file included from readgroup.cpp:3:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
readgroup.cpp:408:31: warning: unused variable 'vr_end' [-Wunused-variable]
vector<ReadGroup>::iterator vr_end = vr.end();
^
readgroup.cpp:1274:7: warning: unused variable 'npos' [-Wunused-variable]
int npos=0,nneg=0;
^
readgroup.cpp:1274:14: warning: unused variable 'nneg' [-Wunused-variable]
int npos=0,nneg=0;
^
readgroup.cpp:1273:7: warning: unused variable 'r' [-Wunused-variable]
int r=0;
^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c samio.cpp -o samio.o
In file included from samio.cpp:12:
In file included from ./samio.h:10:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
samio.cpp:153:7: warning: unused variable 'currentreadlen' [-Wunused-variable]
int currentreadlen=0;
^
samio.cpp:145:11: warning: unused variable 'dp2' [-Wunused-variable]
range_t dp2=dp;
^
samio.cpp:149:7: warning: unused variable 'rangecounter' [-Wunused-variable]
int rangecounter=1;
^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c samples.cpp -o samples.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c spams.cpp -o spams.o
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
In file included from spams/prox/fista.h:24:
spams/prox/project.h:3111:17: warning: unused variable 'pr' [-Wunused-variable]
const int pr=_pr_node[i];
^
spams/prox/project.h:3450:12: warning: 10 enumeration values not handled in switch: 'FLOW_LINEAR', 'FLOW_SQUARE', 'FLOW_SQUARE_POS'... [-Wswitch]
switch (loss) {
^
spams/prox/project.h:3709:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
switch (loss) {
^
spams/prox/project.h:3738:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
switch (loss) {
^
spams/prox/project.h:3761:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
switch (loss) {
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:83:15: warning: 9 enumeration values not handled in switch: 'SQUARE', 'SQUARE_MISSING', 'LOG'... [-Wswitch]
switch (loss) {
^
spams/prox/fista.h:101:15: warning: 36 enumeration values not handled in switch: 'L0', 'L1', 'RIDGE'... [-Wswitch]
switch (regul) {
^
spams/prox/fista.h:3588:24: warning: unused variable 'duality' [-Wunused-variable]
const bool duality = losses[0]->is_fenchel() && regularizers[0]->is_fenchel();
^
spams/prox/fista.h:3635:24: warning: unused variable 'duality' [-Wunused-variable]
const bool duality = losses[0]->is_fenchel() && regularizers[0]->is_fenchel();
^
spams/prox/fista.h:3788:30: warning: unused variable 'duality' [-Wunused-variable]
const bool duality = loss->is_fenchel() && regularizer->is_fenchel();
^
spams/prox/fista.h:3963:21: warning: 6 enumeration values not handled in switch: 'FLOW_LINEAR', 'FLOW_SQUARE_POS', 'FLOW_SQUARE_POS_WEIGHTS'... [-Wswitch]
switch (loss) {
^
spams/prox/fista.h:3693:24: warning: 7 enumeration values not handled in switch: 'SQUARE_MISSING', 'LOG', 'LOGWEIGHT'... [-Wswitch]
switch (param.loss) {
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3720:27: warning: 4 enumeration values not handled in switch: 'MULTILOG', 'CUR', 'HINGE'... [-Wswitch]
switch (param.loss) {
^
spams/prox/fista.h:3752:27: warning: 8 enumeration values not handled in switch: 'SQUARE', 'SQUARE_MISSING', 'LOG'... [-Wswitch]
switch (param.loss) {
^
spams/prox/fista.h:3772:24: warning: enumeration values 'MULTILOG', 'HINGE', and 'INCORRECT_LOSS' not handled in switch [-Wswitch]
switch (param.loss) {
^
spams/prox/fista.h:3396:18: warning: 33 enumeration values not handled in switch: 'L0', 'L1', 'RIDGE'... [-Wswitch]
switch (param.regul) {
^
spams/prox/fista.h:3692:32: note: in instantiation of function template specialization 'FISTA::setRegularizerADMM<double>' requested here
regularizers[i]=setRegularizerADMM(param,graph_st,tree_st);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3426:18: warning: 11 enumeration values not handled in switch: 'L1L2', 'L1LINF', 'L1L2_L1'... [-Wswitch]
switch (param.regul) {
^
spams/prox/fista.h:3719:35: note: in instantiation of function template specialization 'FISTA::setRegularizerVectors<double>' requested here
regularizers[i]=setRegularizerVectors(param,graph_st,tree_st,graph_path_st);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
In file included from spams/prox/fista.h:24:
spams/prox/project.h:3738:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
switch (loss) {
^
spams/prox/project.h:3991:40: note: in instantiation of member function 'DoubleMinCostFlow<double>::eval_flow_derivative_arc' requested here
const T reduced_cost=this->eval_flow_derivative_arc(node,j)-target;
^
spams/prox/project.h:3804:14: note: in instantiation of member function 'DoubleMinCostFlow<double>::check_reduced_costs' requested here
eps=this->check_reduced_costs();
^
spams/prox/project.h:4624:13: note: in instantiation of member function 'DoubleMinCostFlow<double>::solve_min_cost' requested here
_solver->solve_min_cost();
^
spams/prox/fista.h:2254:28: note: in instantiation of member function 'DoubleGraphPath<double>::proximal_conv' requested here
_graph2.proximal_conv(y.rawX(),lambda,_alt_norm);
^
spams/prox/fista.h:3449:45: note: in instantiation of member function 'FISTA::GraphPathConv<double>::prox' requested here
case GRAPH_PATH_CONV: reg = new GraphPathConv<T>(param_reg); break;
^
spams/prox/fista.h:3719:35: note: in instantiation of function template specialization 'FISTA::setRegularizerVectors<double>' requested here
regularizers[i]=setRegularizerVectors(param,graph_st,tree_st,graph_path_st);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
In file included from spams/prox/fista.h:24:
spams/prox/project.h:3761:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
switch (loss) {
^
spams/prox/project.h:4019:43: note: in instantiation of member function 'DoubleMinCostFlow<double>::eval_flow_saturate_arc' requested here
const T saturated_amount = this->eval_flow_saturate_arc(node,arc,target);
^
spams/prox/project.h:3859:16: note: in instantiation of member function 'DoubleMinCostFlow<double>::saturate_arc' requested here
this->saturate_arc(i,j);
^
spams/prox/project.h:3817:13: note: in instantiation of member function 'DoubleMinCostFlow<double>::refine' requested here
this->refine(eps);
^
spams/prox/project.h:4624:13: note: in instantiation of member function 'DoubleMinCostFlow<double>::solve_min_cost' requested here
_solver->solve_min_cost();
^
spams/prox/fista.h:2254:28: note: in instantiation of member function 'DoubleGraphPath<double>::proximal_conv' requested here
_graph2.proximal_conv(y.rawX(),lambda,_alt_norm);
^
spams/prox/fista.h:3449:45: note: in instantiation of member function 'FISTA::GraphPathConv<double>::prox' requested here
case GRAPH_PATH_CONV: reg = new GraphPathConv<T>(param_reg); break;
^
spams/prox/fista.h:3719:35: note: in instantiation of function template specialization 'FISTA::setRegularizerVectors<double>' requested here
regularizers[i]=setRegularizerVectors(param,graph_st,tree_st,graph_path_st);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
In file included from spams/prox/fista.h:24:
spams/prox/project.h:3709:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
switch (loss) {
^
spams/prox/project.h:3696:22: note: in instantiation of member function 'DoubleMinCostFlow<double>::eval_flow_arc' requested here
cost+=this->eval_flow_arc(i,j);
^
spams/prox/project.h:4545:29: note: in instantiation of member function 'DoubleMinCostFlow<double>::compute_cost' requested here
const T val=0.5*_solver->compute_cost();
^
spams/prox/fista.h:2265:71: note: in instantiation of member function 'DoubleGraphPath<double>::eval_conv' requested here
return const_cast<DoubleGraphPath<T>* >(&_graph2)->eval_conv(x.rawX(),NULL,_alt_norm);
^
spams/prox/fista.h:3449:45: note: in instantiation of member function 'FISTA::GraphPathConv<double>::eval' requested here
case GRAPH_PATH_CONV: reg = new GraphPathConv<T>(param_reg); break;
^
spams/prox/fista.h:3719:35: note: in instantiation of function template specialization 'FISTA::setRegularizerVectors<double>' requested here
regularizers[i]=setRegularizerVectors(param,graph_st,tree_st,graph_path_st);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
T sec=time.getElapsed();
^
spams/prox/fista.h:3620:16: note: in instantiation of function template specialization 'FISTA::ISTA_Generic<double, Vector<double>, Vector<double> >' requested here
ISTA_Generic(*(losses[numT]),*(regularizers[numT]),alpha0i,alphai,optim_infoi,param);
^
spams/prox/fista.h:3735:16: note: in instantiation of function template specialization 'FISTA::solver_aux1<double>' requested here
solver_aux1(X, alpha0, alpha, optim_info, regularizers,losses,param);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
T sec=time.getElapsed();
^
spams/prox/fista.h:3624:16: note: in instantiation of function template specialization 'FISTA::FISTA_Generic<double, Vector<double>, Vector<double> >' requested here
FISTA_Generic(*(losses[numT]),*(regularizers[numT]),alpha0i,alphai,optim_infoi,param);
^
spams/prox/fista.h:3735:16: note: in instantiation of function template specialization 'FISTA::solver_aux1<double>' requested here
solver_aux1(X, alpha0, alpha, optim_info, regularizers,losses,param);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3477:18: warning: 11 enumeration values not handled in switch: 'GROUPLASSO_L2', 'GROUPLASSO_LINF', 'GROUPLASSO_L2_L1'... [-Wswitch]
switch (param.regul) {
^
spams/prox/fista.h:3751:35: note: in instantiation of function template specialization 'FISTA::setRegularizerMatrices<double>' requested here
regularizers[i]=setRegularizerMatrices(param,alpha0.m(),N,graph_st,tree_st,graph_path_st);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
T sec=time.getElapsed();
^
spams/prox/fista.h:3662:16: note: in instantiation of function template specialization 'FISTA::ISTA_Generic<double, Matrix<double>, Vector<double> >' requested here
ISTA_Generic(*(losses[numT]),*(regularizers[numT]),alpha0i,alphai,optim_infoi,param);
^
spams/prox/fista.h:3757:16: note: in instantiation of function template specialization 'FISTA::solver_aux2<double>' requested here
solver_aux2(X, alpha0, alpha, optim_info, regularizers,losses,param);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
T sec=time.getElapsed();
^
spams/prox/fista.h:3666:16: note: in instantiation of function template specialization 'FISTA::FISTA_Generic<double, Matrix<double>, Vector<double> >' requested here
FISTA_Generic(*(losses[numT]),*(regularizers[numT]),alpha0i,alphai,optim_infoi,param);
^
spams/prox/fista.h:3757:16: note: in instantiation of function template specialization 'FISTA::solver_aux2<double>' requested here
solver_aux2(X, alpha0, alpha, optim_info, regularizers,losses,param);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
T sec=time.getElapsed();
^
spams/prox/fista.h:3796:19: note: in instantiation of function template specialization 'FISTA::ISTA_Generic<double, Matrix<double>, Matrix<double> >' requested here
ISTA_Generic(*loss,*regularizer,alpha0,alpha,optim_infoi,param);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
T sec=time.getElapsed();
^
spams/prox/fista.h:3800:19: note: in instantiation of function template specialization 'FISTA::FISTA_Generic<double, Matrix<double>, Matrix<double> >' requested here
FISTA_Generic(*loss,*regularizer,alpha0,alpha,optim_infoi,param);
^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3963:21: warning: 6 enumeration values not handled in switch: 'FLOW_LINEAR', 'FLOW_SQUARE_POS', 'FLOW_SQUARE_POS_WEIGHTS'... [-Wswitch]
switch (loss) {
^
./spams.h:1065:10: note: in instantiation of function template specialization 'FISTA::SepLossPathCoding<double>' requested here
FISTA::SepLossPathCoding<T>((Matrix<T> &)(*alpha0),(Matrix<T>&)(*alpha),param,loss,&graph,path_out);
^
spams.cpp:4813:36: note: in instantiation of function template specialization '_sepCostsPathCoding<double>' requested here
result = (SpMatrix< double > *)_sepCostsPathCoding< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19);
^
28 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC -Wall -mtune=core2 -g -O2 -c structdef.cpp -o structdef.o
In file included from structdef.cpp:6:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
1 warning generated.
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 flipflop.so FileSplitter.o R_init_flipflop.o align.o auxiliaryio.o bedio.o common.o cvganalysis.o ffProcesssam.o instanceio.o parseopt.o rangeset.o readgroup.o samio.o samples.o spams.o structdef.o -lstdc++ -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -lcblas -stdlib=libstdc++ -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/flipflop.buildbin-libdir/flipflop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flipflop)
>>>>>>>
>>>>>>> FIXING LINKS FOR flipflop.buildbin-libdir/flipflop/libs//flipflop.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "flipflop.buildbin-libdir/flipflop/libs//flipflop.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "flipflop.buildbin-libdir/flipflop/libs//flipflop.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "flipflop.buildbin-libdir/flipflop/libs//flipflop.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "flipflop.buildbin-libdir/flipflop/libs//flipflop.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "flipflop.buildbin-libdir/flipflop/libs//flipflop.so"
