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CHECK report for Rchemcpp on malbec2

This page was generated on 2019-03-18 11:14:54 -0400 (Mon, 18 Mar 2019).

Package 1281/1676HostnameOS / ArchINSTALLBUILDCHECK
Rchemcpp 2.21.1
Guenter Klambauer
Snapshot Date: 2019-03-17 17:01:51 -0400 (Sun, 17 Mar 2019)
URL: https://git.bioconductor.org/packages/Rchemcpp
Branch: master
Last Commit: 1e538d9
Last Changed Date: 2019-01-04 13:46:16 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  ERROR  ERROR  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  ERROR  ERROR  skipped 

Summary

Package: Rchemcpp
Version: 2.21.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rchemcpp.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rchemcpp_2.21.1.tar.gz
StartedAt: 2019-03-18 04:00:01 -0400 (Mon, 18 Mar 2019)
EndedAt: 2019-03-18 04:01:21 -0400 (Mon, 18 Mar 2019)
EllapsedTime: 79.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Rchemcpp.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rchemcpp.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rchemcpp_2.21.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.Rcheck’
* using R Under development (unstable) (2019-01-21 r75999)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rchemcpp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rchemcpp’ version ‘2.21.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rchemcpp’ can be installed ... WARNING
Found the following significant warnings:
  ./chemcpp/src/descriptor.h:115:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/descriptor.h:217:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/datacontainer.h:198:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/datacontainer.h:207:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/datacontainer.h:211:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/datacontainer.h:267:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/datacontainer.h:271:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/ring.h:66:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/ring.h:70:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/bond.h:107:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/bond.h:115:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/bond.h:234:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/atom.h:122:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/atom.h:238:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/atom.h:251:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/atom.h:256:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/atom.h:261:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/atom.h:347:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/atom.h:351:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/atom.h:402:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/atom.h:407:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/atom.h:413:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/atom.h:465:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:133:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:153:187: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:159:186: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:171:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:175:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:230:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:248:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:314:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:319:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:324:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:328:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:421:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:730:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/molecule.h:1033:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/kcfmolecule.h:53:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/kcfmolecule.h:61:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeset.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeset.h:243:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeset.h:247:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeset.h:251:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeset.h:411:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeset.h:711:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeset.h:787:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeutils.h:73:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeutils.h:82:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeutils.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeutils.h:92:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeutils.h:121:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeutils.h:154:181: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeutils.h:160:181: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeutils.h:167:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  ./chemcpp/src/moleculeutils.h:282:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 15.9Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs     12.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotStruc: no visible global function definition for ‘lines’
plotStruc: no visible global function definition for ‘points’
plotStruc: no visible global function definition for ‘text’
plot,SDFset: no visible global function definition for ‘par’
Undefined global functions or variables:
  lines par points text
Consider adding
  importFrom("graphics", "lines", "par", "points", "text")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/Rchemcpp/libs/libchemcpp.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘exit’, possibly from ‘exit’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.Rcheck/00check.log’
for details.

Installation output

Rchemcpp.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Rchemcpp
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Rchemcpp’ ...
** libs
make[1]: Entering directory '/home/biocbuild/bbs-3.9-bioc/meat/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 '/home/biocbuild/bbs-3.9-bioc/meat/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,/home/biocbuild/bbs-3.9-bioc/R/library/Rchemcpp/libs -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/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
* DONE (Rchemcpp)

Tests output

Example timings

Rchemcpp.Rcheck/Rchemcpp-Ex.timings

nameusersystemelapsed
Rchemcpp-package3.0260.0313.562
Rcpp_Rmolecule-class0.0030.0000.002
Rcpp_Rmoleculeset-class0.0070.0000.007
createRMolecule0.0040.0000.004
getMoleculeNamesFromSDF0.0060.0000.005
getMoleculePropertyFromSDF0.0020.0000.002
sd2gram1.1530.0041.184
sd2gram3Dpharma1.0640.0121.089
sd2gram3Dspectrum0.2460.0000.403
sd2gramSpectrum0.0280.0070.035
sd2gramSubtree0.2320.0120.272