##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Rchemcpp
###
##############################################################################
##############################################################################
* checking for file ‘Rchemcpp/DESCRIPTION’ ... OK
* preparing ‘Rchemcpp’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘Rchemcpp’ ...
** using staged installation
** libs
make[1]: Entering directory '/tmp/RtmpnzUsBO/Rbuild15a5738c68d1/Rchemcpp/src/chemcpp/src'
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o constant.o constant.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o node.o node.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o atom.o atom.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o bond.o bond.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o cerror.o cerror.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o chemcpp.o chemcpp.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o datacontainer.o datacontainer.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o descriptor.o descriptor.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o elements.o elements.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o jlpioutils.o jlpioutils.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o kcfmolecule.o kcfmolecule.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o molecule.o molecule.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o moleculeset.o moleculeset.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o moleculeutils.o moleculeutils.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o ring.o ring.cpp
g++ -std=gnu++11 -g -O2 -Wall -w -fPIC -I../src/ -c -o stringutils.o stringutils.cpp
g++ -std=gnu++11 -shared -o ../../libchemcpp.dll -g -O2 -Wall -w -fPIC -I../src/ constant.o node.o atom.o bond.o cerror.o chemcpp.o datacontainer.o descriptor.o elements.o jlpioutils.o kcfmolecule.o molecule.o moleculeset.o moleculeutils.o ring.o stringutils.o
g++ -std=gnu++11 -shared -o ../../libchemcpp.so -g -O2 -Wall -w -fPIC -I../src/ constant.o node.o atom.o bond.o cerror.o chemcpp.o datacontainer.o descriptor.o elements.o jlpioutils.o kcfmolecule.o molecule.o moleculeset.o moleculeutils.o ring.o stringutils.o
make[1]: Leaving directory '/tmp/RtmpnzUsBO/Rbuild15a5738c68d1/Rchemcpp/src/chemcpp/src'
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./chemcpp/src -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c Relements.cpp -o Relements.o
In file included from ./chemcpp/src/datacontainer.h:41:0,
from ./chemcpp/src/elements.h:38,
from Relements.h:7,
from Relements.cpp:2:
./chemcpp/src/descriptor.h:115:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T getValue( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/descriptor.h:217:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T Descriptor<T>::getValue( bool silentError ) throw( CError ){
^˜˜˜˜
In file included from ./chemcpp/src/elements.h:38:0,
from Relements.h:7,
from Relements.cpp:2:
./chemcpp/src/datacontainer.h:198:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< int >* getIntDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:207:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< float >* getFloatDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:211:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< string >* getStringDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:267:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:271:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describeShort() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/bond.h:37:0,
from ./chemcpp/src/atom.h:40,
from ./chemcpp/src/elements.h:39,
from Relements.h:7,
from Relements.cpp:2:
./chemcpp/src/ring.h:66:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBond( Bond* aBond, bool silentError = false ) throw ( CError );
^˜˜˜˜
./chemcpp/src/ring.h:70:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addAtom( Atom* anAtom, bool silentError = false ) throw ( CError );
^˜˜˜˜
In file included from ./chemcpp/src/atom.h:40:0,
from ./chemcpp/src/elements.h:39,
from Relements.h:7,
from Relements.cpp:2:
./chemcpp/src/bond.h:107:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getTarget() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:115:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getSource() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:234:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getReverse() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/elements.h:39:0,
from Relements.h:7,
from Relements.cpp:2:
./chemcpp/src/atom.h:122:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* addBond( Bond *aBond ) throw ( CError );
^˜˜˜˜
./chemcpp/src/atom.h:238:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getUniqueMorganIndex( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:251:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getMorganLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:256:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setPerretLabel() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:261:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getPerretLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:347:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Bond* aBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:351:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Atom* aTarget ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:402:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getBondWithTarget( Atom* otherAtom ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:407:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* nextUnvisitedAtom() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:413:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Ring* getRingBFS( vector<Atom*>* toVisit, vector<Bond*>* toVisitBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:465:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./chemcpp/src -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c Rmolecule.cpp -o Rmolecule.o
In file included from ./chemcpp/src/datacontainer.h:41:0,
from ./chemcpp/src/molecule.h:39,
from Rmolecule.h:7,
from Rmolecule.cpp:2:
./chemcpp/src/descriptor.h:115:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T getValue( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/descriptor.h:217:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T Descriptor<T>::getValue( bool silentError ) throw( CError ){
^˜˜˜˜
In file included from ./chemcpp/src/molecule.h:39:0,
from Rmolecule.h:7,
from Rmolecule.cpp:2:
./chemcpp/src/datacontainer.h:198:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< int >* getIntDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:207:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< float >* getFloatDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:211:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< string >* getStringDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:267:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:271:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describeShort() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/bond.h:37:0,
from ./chemcpp/src/atom.h:40,
from ./chemcpp/src/molecule.h:40,
from Rmolecule.h:7,
from Rmolecule.cpp:2:
./chemcpp/src/ring.h:66:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBond( Bond* aBond, bool silentError = false ) throw ( CError );
^˜˜˜˜
./chemcpp/src/ring.h:70:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addAtom( Atom* anAtom, bool silentError = false ) throw ( CError );
^˜˜˜˜
In file included from ./chemcpp/src/atom.h:40:0,
from ./chemcpp/src/molecule.h:40,
from Rmolecule.h:7,
from Rmolecule.cpp:2:
./chemcpp/src/bond.h:107:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getTarget() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:115:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getSource() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:234:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getReverse() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/molecule.h:40:0,
from Rmolecule.h:7,
from Rmolecule.cpp:2:
./chemcpp/src/atom.h:122:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* addBond( Bond *aBond ) throw ( CError );
^˜˜˜˜
./chemcpp/src/atom.h:238:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getUniqueMorganIndex( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:251:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getMorganLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:256:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setPerretLabel() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:261:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getPerretLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:347:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Bond* aBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:351:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Atom* aTarget ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:402:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getBondWithTarget( Atom* otherAtom ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:407:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* nextUnvisitedAtom() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:413:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Ring* getRingBFS( vector<Atom*>* toVisit, vector<Bond*>* toVisitBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:465:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
In file included from Rmolecule.h:7:0,
from Rmolecule.cpp:2:
./chemcpp/src/molecule.h:133:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* addAtom( Atom*, bool resetSSSR = true, bool resetMorganIndex = true ) throw( CError);
^˜˜˜˜
In file included from Rmolecule.h:7:0,
from Rmolecule.cpp:2:
./chemcpp/src/molecule.h:153:187: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* linkAtoms( string aSource, string aTarget, int aBondLabel, int aBondStereo = 0, int aBondNotUsed = 0, int aBondTopology = 0, int aBondReactionCenter = 0, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:159:186: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* linkAtoms( int firstAtom, int secondAtom, int aBondLabel, int aBondStereo = 0, int aBondNotUsed = 0, int aBondTopology = 0, int aBondReactionCenter = 0, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:171:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readMOL( string aFilename, bool genericAtomType = false ) throw(CError);
^˜˜˜˜
./chemcpp/src/molecule.h:175:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readMOLOld( string aFilename ) throw(CError);
^˜˜˜˜
./chemcpp/src/molecule.h:230:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
float getActivity( bool silentMode = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:248:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getAtom(int anId) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:314:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Ring* getRingWithID( int anID, bool createIfMissing) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:319:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasRing( Ring* newRing, bool detectingRing = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:324:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasRing() throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:328:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int numRings() throw( CError ){
^˜˜˜˜
./chemcpp/src/molecule.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
float getMW( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:421:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void eraseAtom( Atom* anAtom ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:730:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSelfKernel() throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:1033:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void linkAtomsNoReturn( int firstAtom, int secondAtom, int aBondLabel ) throw( CError );
^˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./chemcpp/src -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c Rmoleculeset.cpp -o Rmoleculeset.o
In file included from ./chemcpp/src/datacontainer.h:41:0,
from ./chemcpp/src/molecule.h:39,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from Rmoleculeset.cpp:2:
./chemcpp/src/descriptor.h:115:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T getValue( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/descriptor.h:217:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T Descriptor<T>::getValue( bool silentError ) throw( CError ){
^˜˜˜˜
In file included from ./chemcpp/src/molecule.h:39:0,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from Rmoleculeset.cpp:2:
./chemcpp/src/datacontainer.h:198:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< int >* getIntDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:207:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< float >* getFloatDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:211:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< string >* getStringDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:267:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:271:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describeShort() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/bond.h:37:0,
from ./chemcpp/src/atom.h:40,
from ./chemcpp/src/molecule.h:40,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from Rmoleculeset.cpp:2:
./chemcpp/src/ring.h:66:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBond( Bond* aBond, bool silentError = false ) throw ( CError );
^˜˜˜˜
./chemcpp/src/ring.h:70:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addAtom( Atom* anAtom, bool silentError = false ) throw ( CError );
^˜˜˜˜
In file included from ./chemcpp/src/atom.h:40:0,
from ./chemcpp/src/molecule.h:40,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from Rmoleculeset.cpp:2:
./chemcpp/src/bond.h:107:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getTarget() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:115:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getSource() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:234:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getReverse() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/molecule.h:40:0,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from Rmoleculeset.cpp:2:
./chemcpp/src/atom.h:122:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* addBond( Bond *aBond ) throw ( CError );
^˜˜˜˜
./chemcpp/src/atom.h:238:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getUniqueMorganIndex( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:251:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getMorganLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:256:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setPerretLabel() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:261:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getPerretLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:347:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Bond* aBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:351:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Atom* aTarget ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:402:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getBondWithTarget( Atom* otherAtom ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:407:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* nextUnvisitedAtom() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:413:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Ring* getRingBFS( vector<Atom*>* toVisit, vector<Bond*>* toVisitBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:465:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
In file included from Rmolecule.h:7:0,
from Rmoleculeset.h:8,
from Rmoleculeset.cpp:2:
./chemcpp/src/molecule.h:133:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* addAtom( Atom*, bool resetSSSR = true, bool resetMorganIndex = true ) throw( CError);
^˜˜˜˜
In file included from Rmolecule.h:7:0,
from Rmoleculeset.h:8,
from Rmoleculeset.cpp:2:
./chemcpp/src/molecule.h:153:187: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* linkAtoms( string aSource, string aTarget, int aBondLabel, int aBondStereo = 0, int aBondNotUsed = 0, int aBondTopology = 0, int aBondReactionCenter = 0, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:159:186: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* linkAtoms( int firstAtom, int secondAtom, int aBondLabel, int aBondStereo = 0, int aBondNotUsed = 0, int aBondTopology = 0, int aBondReactionCenter = 0, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:171:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readMOL( string aFilename, bool genericAtomType = false ) throw(CError);
^˜˜˜˜
./chemcpp/src/molecule.h:175:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readMOLOld( string aFilename ) throw(CError);
^˜˜˜˜
./chemcpp/src/molecule.h:230:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
float getActivity( bool silentMode = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:248:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getAtom(int anId) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:314:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Ring* getRingWithID( int anID, bool createIfMissing) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:319:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasRing( Ring* newRing, bool detectingRing = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:324:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasRing() throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:328:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int numRings() throw( CError ){
^˜˜˜˜
./chemcpp/src/molecule.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
float getMW( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:421:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void eraseAtom( Atom* anAtom ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:730:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSelfKernel() throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:1033:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void linkAtomsNoReturn( int firstAtom, int secondAtom, int aBondLabel ) throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/moleculeset.h:39:0,
from Rmoleculeset.h:10,
from Rmoleculeset.cpp:2:
./chemcpp/src/kcfmolecule.h:53:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readKCF( string aFileName ) throw( CError );
^˜˜˜˜
./chemcpp/src/kcfmolecule.h:61:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Atom* addAtom(string aSymbol) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:10:0,
from Rmoleculeset.cpp:2:
./chemcpp/src/moleculeset.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* operator[]( string aName ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:243:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* getMolByName( string aName ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:247:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* operator[]( int anInd ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:251:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* getMolByIndex( int anInd ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:411:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* findFirstMoleculeWithName( string aName ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:10:0,
from Rmoleculeset.cpp:2:
./chemcpp/src/moleculeset.h:711:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeDescriptors( string aFileName, bool selectedOnly = false ) throw( CError ) ;
^˜˜˜˜
./chemcpp/src/moleculeset.h:787:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSortDescriptor( string aName, int aType, bool reverse = false ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:11:0,
from Rmoleculeset.cpp:2:
./chemcpp/src/moleculeutils.h:73:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:82:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void readMDLNSDBlock( Molecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:92:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void skipMDLEntry( Molecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:121:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool readKCFMolecule( KCFMolecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:11:0,
from Rmoleculeset.cpp:2:
./chemcpp/src/moleculeutils.h:154:181: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelUntilN( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int maxPower, int minLength = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:160:181: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelOrderN( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int anOrder, int parameter2 = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:167:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelConverge( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int converge, int parameter2 = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:282:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static string getRingString( Bond* aBond ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.cpp:2:0:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./chemcpp/src -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c spectrum3Dhelper.cpp -o spectrum3Dhelper.o
In file included from ./chemcpp/src/datacontainer.h:41:0,
from ./chemcpp/src/molecule.h:39,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/descriptor.h:115:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T getValue( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/descriptor.h:217:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T Descriptor<T>::getValue( bool silentError ) throw( CError ){
^˜˜˜˜
In file included from ./chemcpp/src/molecule.h:39:0,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/datacontainer.h:198:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< int >* getIntDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:207:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< float >* getFloatDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:211:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< string >* getStringDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:267:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:271:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describeShort() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/bond.h:37:0,
from ./chemcpp/src/atom.h:40,
from ./chemcpp/src/molecule.h:40,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/ring.h:66:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBond( Bond* aBond, bool silentError = false ) throw ( CError );
^˜˜˜˜
./chemcpp/src/ring.h:70:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addAtom( Atom* anAtom, bool silentError = false ) throw ( CError );
^˜˜˜˜
In file included from ./chemcpp/src/atom.h:40:0,
from ./chemcpp/src/molecule.h:40,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/bond.h:107:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getTarget() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:115:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getSource() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:234:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getReverse() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/molecule.h:40:0,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/atom.h:122:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* addBond( Bond *aBond ) throw ( CError );
^˜˜˜˜
./chemcpp/src/atom.h:238:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getUniqueMorganIndex( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:251:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getMorganLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:256:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setPerretLabel() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:261:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getPerretLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:347:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Bond* aBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:351:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Atom* aTarget ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:402:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getBondWithTarget( Atom* otherAtom ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:407:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* nextUnvisitedAtom() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:413:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Ring* getRingBFS( vector<Atom*>* toVisit, vector<Bond*>* toVisitBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:465:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
In file included from Rmolecule.h:7:0,
from Rmoleculeset.h:8,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/molecule.h:133:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* addAtom( Atom*, bool resetSSSR = true, bool resetMorganIndex = true ) throw( CError);
^˜˜˜˜
In file included from Rmolecule.h:7:0,
from Rmoleculeset.h:8,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/molecule.h:153:187: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* linkAtoms( string aSource, string aTarget, int aBondLabel, int aBondStereo = 0, int aBondNotUsed = 0, int aBondTopology = 0, int aBondReactionCenter = 0, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:159:186: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* linkAtoms( int firstAtom, int secondAtom, int aBondLabel, int aBondStereo = 0, int aBondNotUsed = 0, int aBondTopology = 0, int aBondReactionCenter = 0, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:171:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readMOL( string aFilename, bool genericAtomType = false ) throw(CError);
^˜˜˜˜
./chemcpp/src/molecule.h:175:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readMOLOld( string aFilename ) throw(CError);
^˜˜˜˜
./chemcpp/src/molecule.h:230:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
float getActivity( bool silentMode = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:248:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getAtom(int anId) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:314:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Ring* getRingWithID( int anID, bool createIfMissing) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:319:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasRing( Ring* newRing, bool detectingRing = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:324:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasRing() throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:328:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int numRings() throw( CError ){
^˜˜˜˜
./chemcpp/src/molecule.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
float getMW( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:421:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void eraseAtom( Atom* anAtom ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:730:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSelfKernel() throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:1033:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void linkAtomsNoReturn( int firstAtom, int secondAtom, int aBondLabel ) throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/moleculeset.h:39:0,
from Rmoleculeset.h:10,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/kcfmolecule.h:53:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readKCF( string aFileName ) throw( CError );
^˜˜˜˜
./chemcpp/src/kcfmolecule.h:61:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Atom* addAtom(string aSymbol) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:10:0,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/moleculeset.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* operator[]( string aName ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:243:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* getMolByName( string aName ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:247:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* operator[]( int anInd ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:251:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* getMolByIndex( int anInd ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:411:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* findFirstMoleculeWithName( string aName ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:10:0,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/moleculeset.h:711:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeDescriptors( string aFileName, bool selectedOnly = false ) throw( CError ) ;
^˜˜˜˜
./chemcpp/src/moleculeset.h:787:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSortDescriptor( string aName, int aType, bool reverse = false ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:11:0,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/moleculeutils.h:73:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:82:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void readMDLNSDBlock( Molecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:92:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void skipMDLEntry( Molecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:121:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool readKCFMolecule( KCFMolecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:11:0,
from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
./chemcpp/src/moleculeutils.h:154:181: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelUntilN( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int maxPower, int minLength = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:160:181: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelOrderN( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int anOrder, int parameter2 = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:167:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelConverge( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int converge, int parameter2 = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:282:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static string getRingString( Bond* aBond ) throw( CError );
^˜˜˜˜
In file included from spectrum3Dhelper.h:38:0,
from spectrum3Dhelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp: In function ‘void gramSpectrum3D_self(SEXP, int, int, int, double, double, bool)’:
spectrum3Dhelper.cpp:74:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i = 0 ; i < atomLabels.size() ; i++ ){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp: In function ‘void gramSpectrum3D_test(SEXP, int, int, int, double, double, bool)’:
spectrum3Dhelper.cpp:174:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i = 0 ; i < atomLabels.size() ; i++ ){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp: In function ‘void gramComputeSpectrum3D_self(MoleculeSet*, int, int, int, std::vector<pathsInMol3D>*, std::vector<std::__cxx11::basic_string<char> >*, std::vector<int>*, bool)’:
spectrum3Dhelper.cpp:225:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < atomLabels->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp:241:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0 ; j < atomLabels->size() ; j++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp:242:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int k = 0 ; k < bondTypes->size() ; k++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp: In function ‘void gramComputeSpectrum3D_test(MoleculeSet*, MoleculeSet*, int, int, int, std::vector<pathsInMol3D>*, std::vector<pathsInMol3D>*, std::vector<std::__cxx11::basic_string<char> >*, std::vector<int>*, bool)’:
spectrum3Dhelper.cpp:279:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < atomLabels->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp:295:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0 ; j < atomLabels->size() ; j++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp:296:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int k = 0 ; k < bondTypes->size() ; k++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp: In function ‘void updatePaths3D(MoleculeSet*, std::__cxx11::string, int, std::vector<pathsInMol3D>*, std::vector<pathsInMol3D>*, int, int)’:
spectrum3Dhelper.cpp:384:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp:388:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp: In function ‘void updateGram3D_self(MoleculeSet*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:445:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp:446:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = i ; j < molPaths->size() ; j++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp: In function ‘void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol3D>*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:488:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp:489:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0 ; j < molPaths_test->size() ; j++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp: In function ‘void updateSelfKernel3D(MoleculeSet*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:530:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp: In function ‘void updateGram3D_self(MoleculeSet*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:472:19: warning: ‘update’ may be used uninitialized in this function [-Wmaybe-uninitialized]
(*aSet).addToGram( (*molPaths)[j].molInd , (*molPaths)[i].molInd, update);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp: In function ‘void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol3D>*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:513:19: warning: ‘update’ may be used uninitialized in this function [-Wmaybe-uninitialized]
(*aSet).addToGram( (*molPaths)[i].molInd , (*molPaths_test)[j].molInd, update);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrum3Dhelper.cpp: In function ‘void updateSelfKernel3D(MoleculeSet*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:557:26: warning: ‘update’ may be used uninitialized in this function [-Wmaybe-uninitialized]
aMol->addToSelfKernel(update);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./chemcpp/src -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c spectrumhelper.cpp -o spectrumhelper.o
In file included from ./chemcpp/src/datacontainer.h:41:0,
from ./chemcpp/src/molecule.h:39,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/descriptor.h:115:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T getValue( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/descriptor.h:217:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T Descriptor<T>::getValue( bool silentError ) throw( CError ){
^˜˜˜˜
In file included from ./chemcpp/src/molecule.h:39:0,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/datacontainer.h:198:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< int >* getIntDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:207:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< float >* getFloatDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:211:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< string >* getStringDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:267:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:271:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describeShort() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/bond.h:37:0,
from ./chemcpp/src/atom.h:40,
from ./chemcpp/src/molecule.h:40,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/ring.h:66:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBond( Bond* aBond, bool silentError = false ) throw ( CError );
^˜˜˜˜
./chemcpp/src/ring.h:70:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addAtom( Atom* anAtom, bool silentError = false ) throw ( CError );
^˜˜˜˜
In file included from ./chemcpp/src/atom.h:40:0,
from ./chemcpp/src/molecule.h:40,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/bond.h:107:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getTarget() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:115:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getSource() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:234:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getReverse() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/molecule.h:40:0,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/atom.h:122:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* addBond( Bond *aBond ) throw ( CError );
^˜˜˜˜
./chemcpp/src/atom.h:238:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getUniqueMorganIndex( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:251:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getMorganLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:256:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setPerretLabel() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:261:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getPerretLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:347:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Bond* aBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:351:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Atom* aTarget ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:402:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getBondWithTarget( Atom* otherAtom ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:407:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* nextUnvisitedAtom() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:413:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Ring* getRingBFS( vector<Atom*>* toVisit, vector<Bond*>* toVisitBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:465:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
In file included from Rmolecule.h:7:0,
from Rmoleculeset.h:8,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/molecule.h:133:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* addAtom( Atom*, bool resetSSSR = true, bool resetMorganIndex = true ) throw( CError);
^˜˜˜˜
In file included from Rmolecule.h:7:0,
from Rmoleculeset.h:8,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/molecule.h:153:187: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* linkAtoms( string aSource, string aTarget, int aBondLabel, int aBondStereo = 0, int aBondNotUsed = 0, int aBondTopology = 0, int aBondReactionCenter = 0, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:159:186: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* linkAtoms( int firstAtom, int secondAtom, int aBondLabel, int aBondStereo = 0, int aBondNotUsed = 0, int aBondTopology = 0, int aBondReactionCenter = 0, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:171:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readMOL( string aFilename, bool genericAtomType = false ) throw(CError);
^˜˜˜˜
./chemcpp/src/molecule.h:175:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readMOLOld( string aFilename ) throw(CError);
^˜˜˜˜
./chemcpp/src/molecule.h:230:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
float getActivity( bool silentMode = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:248:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getAtom(int anId) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:314:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Ring* getRingWithID( int anID, bool createIfMissing) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:319:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasRing( Ring* newRing, bool detectingRing = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:324:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasRing() throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:328:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int numRings() throw( CError ){
^˜˜˜˜
./chemcpp/src/molecule.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
float getMW( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:421:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void eraseAtom( Atom* anAtom ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:730:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSelfKernel() throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:1033:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void linkAtomsNoReturn( int firstAtom, int secondAtom, int aBondLabel ) throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/moleculeset.h:39:0,
from Rmoleculeset.h:10,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/kcfmolecule.h:53:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readKCF( string aFileName ) throw( CError );
^˜˜˜˜
./chemcpp/src/kcfmolecule.h:61:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Atom* addAtom(string aSymbol) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:10:0,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/moleculeset.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* operator[]( string aName ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:243:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* getMolByName( string aName ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:247:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* operator[]( int anInd ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:251:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* getMolByIndex( int anInd ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:411:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* findFirstMoleculeWithName( string aName ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:10:0,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/moleculeset.h:711:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeDescriptors( string aFileName, bool selectedOnly = false ) throw( CError ) ;
^˜˜˜˜
./chemcpp/src/moleculeset.h:787:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSortDescriptor( string aName, int aType, bool reverse = false ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:11:0,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/moleculeutils.h:73:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:82:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void readMDLNSDBlock( Molecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:92:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void skipMDLEntry( Molecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:121:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool readKCFMolecule( KCFMolecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:11:0,
from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
./chemcpp/src/moleculeutils.h:154:181: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelUntilN( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int maxPower, int minLength = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:160:181: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelOrderN( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int anOrder, int parameter2 = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:167:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelConverge( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int converge, int parameter2 = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:282:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static string getRingString( Bond* aBond ) throw( CError );
^˜˜˜˜
In file included from spectrumhelper.h:38:0,
from spectrumhelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp: In function ‘void gramSpectrum_self(SEXP, int, int, double, bool, bool)’:
spectrumhelper.cpp:72:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i = 0 ; i < atomLabels.size() ; i++ ){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:75:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i = 0 ; i < bondTypes.size() ; i++ ){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp: In function ‘void gramSpectrum_test(SEXP, int, int, double, bool, bool)’:
spectrumhelper.cpp:130:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i = 0 ; i < atomLabels.size() ; i++ ){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:133:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i = 0 ; i < bondTypes.size() ; i++ ){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp: In function ‘void gramComputeSpectrum_self(MoleculeSet*, int, int, int, double, std::vector<pathsInMol>*, std::vector<std::__cxx11::basic_string<char> >*, std::vector<int>*, bool, bool)’:
spectrumhelper.cpp:161:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < atomLabels->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:188:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0 ; j < atomLabels->size() ; j++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:189:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int k = 0 ; k < bondTypes->size() ; k++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp: In function ‘void gramComputeSpectrum_test(MoleculeSet*, MoleculeSet*, int, int, int, double, std::vector<pathsInMol>*, std::vector<pathsInMol>*, std::vector<std::__cxx11::basic_string<char> >*, std::vector<int>*, bool, bool)’:
spectrumhelper.cpp:229:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < atomLabels->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:258:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0 ; j < atomLabels->size() ; j++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:259:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int k = 0 ; k < bondTypes->size() ; k++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp: In function ‘void updatePaths(MoleculeSet*, std::__cxx11::string, int, std::vector<pathsInMol>*, std::vector<pathsInMol>*, int, int)’:
spectrumhelper.cpp:368:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:372:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp: In function ‘void updateGram_self(MoleculeSet*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:453:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:455:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:467:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:468:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = i ; j < molPaths->size() ; j++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp: In function ‘void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol>*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:518:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:520:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int k = 0 ; k < (*molPaths)[i].path_pointers.size() ; k++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:528:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths_test->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:530:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int k = 0 ; k < (*molPaths_test)[i].path_pointers.size() ; k++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:543:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:544:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0 ; j < molPaths_test->size() ; j++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp: In function ‘void updateSelfKernel(MoleculeSet*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:592:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:594:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp:606:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < molPaths->size() ; i++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp: In function ‘void updateGram_self(MoleculeSet*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:497:24: warning: ‘update’ may be used uninitialized in this function [-Wmaybe-uninitialized]
(*aSet).addToGram( (*molPaths)[i].molInd , (*molPaths)[j].molInd, update);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp: In function ‘void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol>*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:570:19: warning: ‘update’ may be used uninitialized in this function [-Wmaybe-uninitialized]
(*aSet).addToGram( (*molPaths)[i].molInd , (*molPaths_test)[j].molInd, update);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
spectrumhelper.cpp: In function ‘void updateSelfKernel(MoleculeSet*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:630:26: warning: ‘update’ may be used uninitialized in this function [-Wmaybe-uninitialized]
aMol->addToSelfKernel(update);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I./chemcpp/src -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c subtreehelper.cpp -o subtreehelper.o
In file included from ./chemcpp/src/datacontainer.h:41:0,
from ./chemcpp/src/molecule.h:39,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/descriptor.h:115:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T getValue( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/descriptor.h:217:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
T Descriptor<T>::getValue( bool silentError ) throw( CError ){
^˜˜˜˜
In file included from ./chemcpp/src/molecule.h:39:0,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/datacontainer.h:198:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< int >* getIntDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:207:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< float >* getFloatDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:211:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Descriptor< string >* getStringDescriptor( string aLabel, bool silentError = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:267:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
./chemcpp/src/datacontainer.h:271:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describeShort() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/bond.h:37:0,
from ./chemcpp/src/atom.h:40,
from ./chemcpp/src/molecule.h:40,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/ring.h:66:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBond( Bond* aBond, bool silentError = false ) throw ( CError );
^˜˜˜˜
./chemcpp/src/ring.h:70:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addAtom( Atom* anAtom, bool silentError = false ) throw ( CError );
^˜˜˜˜
In file included from ./chemcpp/src/atom.h:40:0,
from ./chemcpp/src/molecule.h:40,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/bond.h:107:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getTarget() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:115:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getSource() throw( CError );
^˜˜˜˜
./chemcpp/src/bond.h:234:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getReverse() throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/molecule.h:40:0,
from Rmolecule.h:7,
from Rmoleculeset.h:8,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/atom.h:122:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* addBond( Bond *aBond ) throw ( CError );
^˜˜˜˜
./chemcpp/src/atom.h:238:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getUniqueMorganIndex( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:251:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getMorganLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:256:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setPerretLabel() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:261:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string getPerretLabel( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:347:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Bond* aBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:351:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void restoreHiddenBond( Atom* aTarget ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:402:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* getBondWithTarget( Atom* otherAtom ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:407:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* nextUnvisitedAtom() throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:413:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Ring* getRingBFS( vector<Atom*>* toVisit, vector<Bond*>* toVisitBond ) throw( CError );
^˜˜˜˜
./chemcpp/src/atom.h:465:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void describe() throw( CError );
^˜˜˜˜
In file included from Rmolecule.h:7:0,
from Rmoleculeset.h:8,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/molecule.h:133:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* addAtom( Atom*, bool resetSSSR = true, bool resetMorganIndex = true ) throw( CError);
^˜˜˜˜
In file included from Rmolecule.h:7:0,
from Rmoleculeset.h:8,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/molecule.h:153:187: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* linkAtoms( string aSource, string aTarget, int aBondLabel, int aBondStereo = 0, int aBondNotUsed = 0, int aBondTopology = 0, int aBondReactionCenter = 0, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:159:186: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Bond* linkAtoms( int firstAtom, int secondAtom, int aBondLabel, int aBondStereo = 0, int aBondNotUsed = 0, int aBondTopology = 0, int aBondReactionCenter = 0, bool resetSSSR = true ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:171:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readMOL( string aFilename, bool genericAtomType = false ) throw(CError);
^˜˜˜˜
./chemcpp/src/molecule.h:175:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readMOLOld( string aFilename ) throw(CError);
^˜˜˜˜
./chemcpp/src/molecule.h:230:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
float getActivity( bool silentMode = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:248:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Atom* getAtom(int anId) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:314:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Ring* getRingWithID( int anID, bool createIfMissing) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:319:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasRing( Ring* newRing, bool detectingRing = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:324:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasRing() throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:328:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int numRings() throw( CError ){
^˜˜˜˜
./chemcpp/src/molecule.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
float getMW( bool silentError = false ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:421:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void eraseAtom( Atom* anAtom ) throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:730:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSelfKernel() throw( CError );
^˜˜˜˜
./chemcpp/src/molecule.h:1033:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void linkAtomsNoReturn( int firstAtom, int secondAtom, int aBondLabel ) throw( CError );
^˜˜˜˜
In file included from ./chemcpp/src/moleculeset.h:39:0,
from Rmoleculeset.h:10,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/kcfmolecule.h:53:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readKCF( string aFileName ) throw( CError );
^˜˜˜˜
./chemcpp/src/kcfmolecule.h:61:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Atom* addAtom(string aSymbol) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:10:0,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/moleculeset.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* operator[]( string aName ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:243:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* getMolByName( string aName ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:247:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* operator[]( int anInd ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:251:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* getMolByIndex( int anInd ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeset.h:411:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Molecule* findFirstMoleculeWithName( string aName ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:10:0,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/moleculeset.h:711:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeDescriptors( string aFileName, bool selectedOnly = false ) throw( CError ) ;
^˜˜˜˜
./chemcpp/src/moleculeset.h:787:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSortDescriptor( string aName, int aType, bool reverse = false ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:11:0,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/moleculeutils.h:73:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:82:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void readMDLNSDBlock( Molecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:92:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void skipMDLEntry( Molecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:121:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool readKCFMolecule( KCFMolecule& aMolecule, ifstream& inFile ) throw( CError );
^˜˜˜˜
In file included from Rmoleculeset.h:11:0,
from subtreehelper.h:37,
from subtreehelper.cpp:32:
./chemcpp/src/moleculeutils.h:154:181: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelUntilN( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int maxPower, int minLength = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:160:181: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelOrderN( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int anOrder, int parameter2 = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:167:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double powerKernelConverge( Molecule* mol1, Molecule* mol2, double (*pt2AtomKernel)( Atom*, Atom* ), double (*pt2BondKernel)(Bond*, Bond*), int converge, int parameter2 = 1 ) throw( CError );
^˜˜˜˜
./chemcpp/src/moleculeutils.h:282:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static string getRingString( Bond* aBond ) throw( CError );
^˜˜˜˜
In file included from subtreehelper.h:37:0,
from subtreehelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
subtreehelper.cpp: In function ‘void gramSubtree_self(SEXP, double, int, bool, bool, bool, bool)’:
subtreehelper.cpp:59:6: warning: unused variable ‘depth’ [-Wunused-variable]
int depth = -1;
^˜˜˜˜
subtreehelper.cpp: In function ‘void gramSubtree_test(SEXP, double, int, bool, bool, bool, bool)’:
subtreehelper.cpp:138:6: warning: unused variable ‘depth’ [-Wunused-variable]
int depth = -1;
^˜˜˜˜
subtreehelper.cpp: In function ‘void initialize_extended(MoleculeSet*, std::vector<std::vector<std::vector<Nextatom> > >*)’:
subtreehelper.cpp:215:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int k=0; k < edges->at(n)[i].size() ; k++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
subtreehelper.cpp: In function ‘double subTreeKernel(Molecule*, Molecule*, std::vector<std::vector<Nextatom> >*, std::vector<std::vector<Nextatom> >*, int, double, bool, bool, bool)’:
subtreehelper.cpp:297:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int istep=0 ; istep < toupdate1.size() ; istep++) {
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
subtreehelper.cpp:304:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
subtreehelper.cpp:304:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
subtreehelper.cpp:321:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int l = 0 ; l < tuples[natoms1-1][d-1].size() ; l++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
subtreehelper.cpp:322:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int m = 0 ; m < tuples[natoms2-1][d-1].size() ; m++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
subtreehelper.cpp:350:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int n = 1 ; n < tempKernel.size() ; n++){
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
subtreehelper.cpp: In function ‘void initialize_tuples(int)’:
subtreehelper.cpp:451:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0 ; i<tuples[n][p-1].size() ; i++) {
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
subtreehelper.cpp:457:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0 ; j<tuples[n][p-1][i].size() ; j++) {
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o Rchemcpp.so Relements.o Rmolecule.o Rmoleculeset.o spectrum3Dhelper.o spectrumhelper.o subtreehelper.o -L./ -lchemcpp -Wl,-rpath,/tmp/RtmpnzUsBO/Rinst15a571fff0f9/00LOCK-Rchemcpp/00new/Rchemcpp/libs -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /tmp/RtmpnzUsBO/Rinst15a571fff0f9/00LOCK-Rchemcpp/00new/Rchemcpp/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘length’ with signature ‘"Rcpp_Rmoleculeset"’: no definition for class “Rcpp_Rmoleculeset”
** 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
ERROR: absolute paths in ‘libs/Rchemcpp.so’ include the temporary installation directory: please report to the package maintainer and use ‘--no-staged-install’
* removing ‘/tmp/RtmpnzUsBO/Rinst15a571fff0f9/Rchemcpp’
-----------------------------------
ERROR: package installation failed
