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Package 216/609HostnameOS / ArchBUILDCHECKBUILD BIN
fmcsR 1.0.5
ChemmineR Team
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/fmcsR
Last Changed Rev: 74515 / Revision: 74773
Last Changed Date: 2013-03-18 11:05:36 -0700 (Mon, 18 Mar 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: fmcsR
Version: 1.0.5
Command: rm -rf fmcsR.buildbin-libdir && mkdir fmcsR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh fmcsR_1.0.5.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R fmcsR.buildbin-libdir
StartedAt: 2013-03-25 01:52:40 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:53:12 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 32.8 seconds
RetCode: 0
Status:  OK 
PackageFile: fmcsR_1.0.5.tgz
PackageFileSize: 369.2 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=fmcsR.buildbin-libdir fmcsR_1.0.5.tar.gz'
>>>>>>> 

* installing *source* package 'fmcsR' ...
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for size_t... yes
checking for alarm... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating config.h
config.status: config.h is unchanged
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCS.cpp -o MCS.o
In file included from MCS.h:11,
                 from MCS.cpp:3:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
MCS.h: In constructor 'FMCS::MCS::MCS(const FMCS::MCSCompound&, const FMCS::MCSCompound&, size_t, size_t, size_t, size_t, size_t, size_t, FMCS::MCS::MatchType, FMCS::MCS::RunningMode, int)':
MCS.h:157: warning: 'FMCS::MCS::compoundTwo' will be initialized after
MCS.h:141: warning:   'size_t FMCS::MCS::userDefinedLowerBound'
MCS.cpp:43: warning:   when initialized here
MCS.h:148: warning: 'FMCS::MCS::atomMismatchLowerBound' will be initialized after
MCS.h:145: warning:   'size_t FMCS::MCS::atomMismatchUpperBound'
MCS.cpp:43: warning:   when initialized here
MCS.h:149: warning: 'FMCS::MCS::bondMismatchLowerBound' will be initialized after
MCS.h:146: warning:   'size_t FMCS::MCS::bondMismatchUpperBound'
MCS.cpp:43: warning:   when initialized here
MCS.h:146: warning: 'FMCS::MCS::bondMismatchUpperBound' will be initialized after
MCS.h:139: warning:   'FMCS::MCS::MatchType FMCS::MCS::matchType'
MCS.cpp:43: warning:   when initialized here
MCS.h:139: warning: 'FMCS::MCS::matchType' will be initialized after
MCS.h:126: warning:   'FMCS::MCS::RunningMode FMCS::MCS::runningMode'
MCS.cpp:43: warning:   when initialized here
MCS.h:126: warning: 'FMCS::MCS::runningMode' will be initialized after
MCS.h:122: warning:   'int FMCS::MCS::_timeout'
MCS.cpp:43: warning:   when initialized here
MCS.h:152: warning: 'FMCS::MCS::bondMismatchCurr' will be initialized after
MCS.h:143: warning:   'size_t FMCS::MCS::currSubstructureNum'
MCS.cpp:43: warning:   when initialized here
MCS.h:143: warning: 'FMCS::MCS::currSubstructureNum' will be initialized after
MCS.h:133: warning:   'double FMCS::MCS::timeUsed'
MCS.cpp:43: warning:   when initialized here
MCS.h:133: warning: 'FMCS::MCS::timeUsed' will be initialized after
MCS.h:130: warning:   'size_t FMCS::MCS::bestSize'
MCS.cpp:43: warning:   when initialized here
MCS.h:130: warning: 'FMCS::MCS::bestSize' will be initialized after
MCS.h:128: warning:   'bool FMCS::MCS::identicalGraph'
MCS.cpp:43: warning:   when initialized here
MCS.h:128: warning: 'FMCS::MCS::identicalGraph' will be initialized after
MCS.h:124: warning:   'bool FMCS::MCS::_isTimeout'
MCS.cpp:43: warning:   when initialized here
MCS.h:124: warning: 'FMCS::MCS::_isTimeout' will be initialized after
MCS.h:120: warning:   'bool FMCS::MCS::haveBeenSwapped'
MCS.cpp:43: warning:   when initialized here
MCS.cpp: In member function 'void FMCS::MCS::calculate()':
MCS.cpp:105: warning: comparison between signed and unsigned integer expressions
MCS.cpp:113: warning: comparison between signed and unsigned integer expressions
MCSList.h: In member function 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]':
MCS.cpp:371:   instantiated from here
MCSList.h:143: warning: comparison between signed and unsigned integer expressions
MCS.cpp: In member function 'size_t FMCS::MCS::top(FMCS::MCSList<long unsigned int>&)':
MCS.cpp:262: warning: 'candidateIdx' may be used uninitialized in this function
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:4:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
In file included from MCSCompound.cpp:5:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168: warning: 'FMCS::MCSRingDetector::compound' will be initialized after
MCSRingDetector.h:165: warning:   'int FMCS::MCSRingDetector::vertexId'
MCSRingDetector.h:191: warning:   when initialized here
MCSCompound.h: In copy constructor 'FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)':
MCSCompound.h:98: warning: 'FMCS::MCSCompound::bonds' will be initialized after
MCSCompound.h:88: warning:   'std::string FMCS::MCSCompound::SdfContentString'
MCSCompound.cpp:82: warning:   when initialized here
MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const std::string&)':
MCSCompound.cpp:157: warning: comparison between signed and unsigned integer expressions
MCSCompound.cpp: In member function 'std::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const std::string&) const':
MCSCompound.cpp:194: warning: comparison between signed and unsigned integer expressions
MCSCompound.cpp: In member function 'const FMCS::MCSCompound::Bond* FMCS::MCSCompound::getBond(size_t, size_t) const':
MCSCompound.cpp:467: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCSMap.cpp -o MCSMap.o
MCSList.h: In member function 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]':
MCSMap.cpp:28:   instantiated from here
MCSList.h:143: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.h:16,
                 from MCSRingDetector.cpp:13:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
In file included from MCSRingDetector.cpp:13:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168: warning: 'FMCS::MCSRingDetector::compound' will be initialized after
MCSRingDetector.h:165: warning:   'int FMCS::MCSRingDetector::vertexId'
MCSRingDetector.h:191: warning:   when initialized here
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()':
MCSRingDetector.cpp:93: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.cpp:94: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::convert()':
MCSRingDetector.cpp:149: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::detect()':
MCSRingDetector.cpp:175: warning: unused variable 'aromaticCount'
MCSRingDetector.cpp: In member function 'bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const':
MCSRingDetector.cpp:194: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
In file included from MCS.h:11,
                 from fmcs_R_wrap.cpp:11:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
fmcs_R_wrap.cpp: In function 'void fmcs_R_wrap(const char**, const char**, int*, int*, int*, int*, int*, int*, int*, const char**, const char**, const char**, const char**, const char**)':
fmcs_R_wrap.cpp:42: warning: 'matchType' may be used uninitialized in this function
fmcs_R_wrap.cpp:52: warning: 'runningMode' may be used uninitialized in this function
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c util.cpp -o util.o
util.cpp: In function 'std::string getUpper(const std::string&)':
util.cpp:11: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o fmcsR.so MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'fmcsR.Rnw' 
** testing if installed package can be loaded

* DONE (fmcsR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR fmcsR.buildbin-libdir/fmcsR/libs/i386/fmcsR.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/i386/fmcsR.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/i386/fmcsR.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/i386/fmcsR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/i386/fmcsR.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=fmcsR.buildbin-libdir --libs-only fmcsR_1.0.5.tar.gz'
>>>>>>> 

* installing *source* package 'fmcsR' ...
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for size_t... yes
checking for alarm... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating config.h
config.status: config.h is unchanged
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCS.cpp -o MCS.o
In file included from MCS.h:11,
                 from MCS.cpp:3:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
MCS.h: In constructor 'FMCS::MCS::MCS(const FMCS::MCSCompound&, const FMCS::MCSCompound&, size_t, size_t, size_t, size_t, size_t, size_t, FMCS::MCS::MatchType, FMCS::MCS::RunningMode, int)':
MCS.h:157: warning: 'FMCS::MCS::compoundTwo' will be initialized after
MCS.h:141: warning:   'size_t FMCS::MCS::userDefinedLowerBound'
MCS.cpp:43: warning:   when initialized here
MCS.h:148: warning: 'FMCS::MCS::atomMismatchLowerBound' will be initialized after
MCS.h:145: warning:   'size_t FMCS::MCS::atomMismatchUpperBound'
MCS.cpp:43: warning:   when initialized here
MCS.h:149: warning: 'FMCS::MCS::bondMismatchLowerBound' will be initialized after
MCS.h:146: warning:   'size_t FMCS::MCS::bondMismatchUpperBound'
MCS.cpp:43: warning:   when initialized here
MCS.h:146: warning: 'FMCS::MCS::bondMismatchUpperBound' will be initialized after
MCS.h:139: warning:   'FMCS::MCS::MatchType FMCS::MCS::matchType'
MCS.cpp:43: warning:   when initialized here
MCS.h:139: warning: 'FMCS::MCS::matchType' will be initialized after
MCS.h:126: warning:   'FMCS::MCS::RunningMode FMCS::MCS::runningMode'
MCS.cpp:43: warning:   when initialized here
MCS.h:126: warning: 'FMCS::MCS::runningMode' will be initialized after
MCS.h:122: warning:   'int FMCS::MCS::_timeout'
MCS.cpp:43: warning:   when initialized here
MCS.h:152: warning: 'FMCS::MCS::bondMismatchCurr' will be initialized after
MCS.h:143: warning:   'size_t FMCS::MCS::currSubstructureNum'
MCS.cpp:43: warning:   when initialized here
MCS.h:143: warning: 'FMCS::MCS::currSubstructureNum' will be initialized after
MCS.h:133: warning:   'double FMCS::MCS::timeUsed'
MCS.cpp:43: warning:   when initialized here
MCS.h:133: warning: 'FMCS::MCS::timeUsed' will be initialized after
MCS.h:130: warning:   'size_t FMCS::MCS::bestSize'
MCS.cpp:43: warning:   when initialized here
MCS.h:130: warning: 'FMCS::MCS::bestSize' will be initialized after
MCS.h:128: warning:   'bool FMCS::MCS::identicalGraph'
MCS.cpp:43: warning:   when initialized here
MCS.h:128: warning: 'FMCS::MCS::identicalGraph' will be initialized after
MCS.h:124: warning:   'bool FMCS::MCS::_isTimeout'
MCS.cpp:43: warning:   when initialized here
MCS.h:124: warning: 'FMCS::MCS::_isTimeout' will be initialized after
MCS.h:120: warning:   'bool FMCS::MCS::haveBeenSwapped'
MCS.cpp:43: warning:   when initialized here
MCS.cpp: In member function 'void FMCS::MCS::calculate()':
MCS.cpp:105: warning: comparison between signed and unsigned integer expressions
MCS.cpp:113: warning: comparison between signed and unsigned integer expressions
MCSList.h: In member function 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]':
MCS.cpp:371:   instantiated from here
MCSList.h:143: warning: comparison between signed and unsigned integer expressions
MCS.cpp: In member function 'size_t FMCS::MCS::top(FMCS::MCSList<long unsigned int>&)':
MCS.cpp:262: warning: 'candidateIdx' may be used uninitialized in this function
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:4:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
In file included from MCSCompound.cpp:5:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168: warning: 'FMCS::MCSRingDetector::compound' will be initialized after
MCSRingDetector.h:165: warning:   'int FMCS::MCSRingDetector::vertexId'
MCSRingDetector.h:191: warning:   when initialized here
MCSCompound.h: In copy constructor 'FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)':
MCSCompound.h:98: warning: 'FMCS::MCSCompound::bonds' will be initialized after
MCSCompound.h:88: warning:   'std::string FMCS::MCSCompound::SdfContentString'
MCSCompound.cpp:82: warning:   when initialized here
MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const std::string&)':
MCSCompound.cpp:157: warning: comparison between signed and unsigned integer expressions
MCSCompound.cpp: In member function 'std::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const std::string&) const':
MCSCompound.cpp:194: warning: comparison between signed and unsigned integer expressions
MCSCompound.cpp: In member function 'const FMCS::MCSCompound::Bond* FMCS::MCSCompound::getBond(size_t, size_t) const':
MCSCompound.cpp:467: warning: comparison between signed and unsigned integer expressions
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCSMap.cpp -o MCSMap.o
MCSList.h: In member function 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]':
MCSMap.cpp:28:   instantiated from here
MCSList.h:143: warning: comparison between signed and unsigned integer expressions
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.h:16,
                 from MCSRingDetector.cpp:13:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
In file included from MCSRingDetector.cpp:13:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168: warning: 'FMCS::MCSRingDetector::compound' will be initialized after
MCSRingDetector.h:165: warning:   'int FMCS::MCSRingDetector::vertexId'
MCSRingDetector.h:191: warning:   when initialized here
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()':
MCSRingDetector.cpp:93: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.cpp:94: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::convert()':
MCSRingDetector.cpp:149: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::detect()':
MCSRingDetector.cpp:175: warning: unused variable 'aromaticCount'
MCSRingDetector.cpp: In member function 'bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const':
MCSRingDetector.cpp:194: warning: comparison between signed and unsigned integer expressions
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
In file included from MCS.h:11,
                 from fmcs_R_wrap.cpp:11:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
fmcs_R_wrap.cpp: In function 'void fmcs_R_wrap(const char**, const char**, int*, int*, int*, int*, int*, int*, int*, const char**, const char**, const char**, const char**, const char**)':
fmcs_R_wrap.cpp:42: warning: 'matchType' may be used uninitialized in this function
fmcs_R_wrap.cpp:52: warning: 'runningMode' may be used uninitialized in this function
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c util.cpp -o util.o
util.cpp: In function 'std::string getUpper(const std::string&)':
util.cpp:11: warning: comparison between signed and unsigned integer expressions
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o fmcsR.so MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/x86_64

* DONE (fmcsR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR fmcsR.buildbin-libdir/fmcsR/libs/x86_64/fmcsR.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/x86_64/fmcsR.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/x86_64/fmcsR.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/x86_64/fmcsR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/x86_64/fmcsR.so"