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BioC 3.0: INSTALL report for fmcsR on moscato1

This page was generated on 2015-04-10 09:48:09 -0700 (Fri, 10 Apr 2015).

Package 325/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fmcsR 1.8.0
ChemmineR Team
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/fmcsR
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: fmcsR
Version: 1.8.0
Command: C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.0/bioc/src/contrib/fmcsR_1.8.0.tar.gz && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch fmcsR_1.8.0.tar.gz && rm fmcsR_1.8.0.tar.gz
StartedAt: 2015-04-09 17:34:39 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 17:36:07 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 88.8 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.0/bioc/src/contrib/fmcsR_1.8.0.tar.gz && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch fmcsR_1.8.0.tar.gz && rm fmcsR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 76536  100 76536    0     0  7286k      0 --:--:-- --:--:-- --:--:-- 36.4M

install for i386

* installing to library 'D:/biocbld/bbs-3.0-bioc/R/library'
* installing *source* package 'fmcsR' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c MCS.cpp -o MCS.o
In file included from MCS.h:12:0,
                 from MCS.cpp:3:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38:20: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after [-Wreorder]
MCSCompound.h:33:17: warning:   'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
MCSCompound.h:46:13: warning:   when initialized here [-Wreorder]
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:161:28: warning: 'FMCS::MCS::compoundTwo' will be initialized after [-Wreorder]
MCS.h:145:16: warning:   'size_t FMCS::MCS::userDefinedLowerBound' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:152:16: warning: 'FMCS::MCS::atomMismatchLowerBound' will be initialized after [-Wreorder]
MCS.h:149:16: warning:   'size_t FMCS::MCS::atomMismatchUpperBound' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:153:16: warning: 'FMCS::MCS::bondMismatchLowerBound' will be initialized after [-Wreorder]
MCS.h:150:16: warning:   'size_t FMCS::MCS::bondMismatchUpperBound' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:150:16: warning: 'FMCS::MCS::bondMismatchUpperBound' will be initialized after [-Wreorder]
MCS.h:143:19: warning:   'FMCS::MCS::MatchType FMCS::MCS::matchType' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:143:19: warning: 'FMCS::MCS::matchType' will be initialized after [-Wreorder]
MCS.h:129:21: warning:   'FMCS::MCS::RunningMode FMCS::MCS::runningMode' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:129:21: warning: 'FMCS::MCS::runningMode' will be initialized after [-Wreorder]
MCS.h:125:13: warning:   'int FMCS::MCS::_timeout' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:156:16: warning: 'FMCS::MCS::bondMismatchCurr' will be initialized after [-Wreorder]
MCS.h:147:16: warning:   'size_t FMCS::MCS::currSubstructureNum' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:147:16: warning: 'FMCS::MCS::currSubstructureNum' will be initialized after [-Wreorder]
MCS.h:136:16: warning:   'double FMCS::MCS::timeUsed' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:137:13: warning: 'FMCS::MCS::startTime' will be initialized after [-Wreorder]
MCS.h:133:16: warning:   'size_t FMCS::MCS::bestSize' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:133:16: warning: 'FMCS::MCS::bestSize' will be initialized after [-Wreorder]
MCS.h:131:14: warning:   'bool FMCS::MCS::identicalGraph' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:131:14: warning: 'FMCS::MCS::identicalGraph' will be initialized after [-Wreorder]
MCS.h:127:14: warning:   'bool FMCS::MCS::_isTimeout' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:127:14: warning: 'FMCS::MCS::_isTimeout' will be initialized after [-Wreorder]
MCS.h:123:14: warning:   'bool FMCS::MCS::haveBeenSwapped' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.cpp: In member function 'void FMCS::MCS::calculate()':
MCS.cpp:108:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCS.cpp:116:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from MCSCompound.h:15:0,
                 from MCS.h:12,
                 from MCS.cpp:3:
MCSList.h: In member function 'bool FMCS::MCSList<T>::contains(const T&) const [with T = unsigned int]':
MCS.cpp:381:69:   instantiated from here
MCSList.h:143:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:4:0:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38:20: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after [-Wreorder]
MCSCompound.h:33:17: warning:   'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
MCSCompound.h:46:13: warning:   when initialized here [-Wreorder]
In file included from MCSCompound.cpp:5:0:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168:22: warning: 'FMCS::MCSRingDetector::compound' will be initialized after [-Wreorder]
MCSRingDetector.h:165:13: warning:   'int FMCS::MCSRingDetector::vertexId' [-Wreorder]
MCSRingDetector.h:191:9: warning:   when initialized here [-Wreorder]
MCSCompound.h: In copy constructor 'FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)':
MCSCompound.h:98:15: warning: 'FMCS::MCSCompound::bonds' will be initialized after [-Wreorder]
MCSCompound.h:88:21: warning:   'std::string FMCS::MCSCompound::SdfContentString' [-Wreorder]
MCSCompound.cpp:82:5: warning:   when initialized here [-Wreorder]
MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const string&)':
MCSCompound.cpp:157:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSCompound.cpp: In member function 'std::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const string&) const':
MCSCompound.cpp:194:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSCompound.cpp: In member function 'const FMCS::MCSCompound::Bond* FMCS::MCSCompound::getBond(size_t, size_t) const':
MCSCompound.cpp:467:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c MCSMap.cpp -o MCSMap.o
In file included from MCSMap.h:8:0,
                 from MCSMap.cpp:3:
MCSList.h: In member function 'bool FMCS::MCSList<T>::contains(const T&) const [with T = unsigned int]':
MCSMap.cpp:28:36:   instantiated from here
MCSList.h:143:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.h:16:0,
                 from MCSRingDetector.cpp:13:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38:20: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after [-Wreorder]
MCSCompound.h:33:17: warning:   'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
MCSCompound.h:46:13: warning:   when initialized here [-Wreorder]
In file included from MCSRingDetector.cpp:13:0:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168:22: warning: 'FMCS::MCSRingDetector::compound' will be initialized after [-Wreorder]
MCSRingDetector.h:165:13: warning:   'int FMCS::MCSRingDetector::vertexId' [-Wreorder]
MCSRingDetector.h:191:9: warning:   when initialized here [-Wreorder]
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()':
MCSRingDetector.cpp:93:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.cpp:94:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::convert()':
MCSRingDetector.cpp:149:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::detect()':
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
MCSRingDetector.cpp: In member function 'bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const':
MCSRingDetector.cpp:194:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
In file included from MCS.h:12:0,
                 from fmcs_R_wrap.cpp:11:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38:20: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after [-Wreorder]
MCSCompound.h:33:17: warning:   'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
MCSCompound.h:46:13: warning:   when initialized here [-Wreorder]
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:74:45: warning: 'runningMode' may be used uninitialized in this function [-Wuninitialized]
fmcs_R_wrap.cpp:74:45: warning: 'matchType' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c util.cpp -o util.o
util.cpp: In function 'std::string getUpper(const string&)':
util.cpp:11:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/R/library/fmcsR/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing to library 'D:/biocbld/bbs-3.0-bioc/R/library'
* installing *source* package 'fmcsR' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c MCS.cpp -o MCS.o
In file included from MCS.h:12:0,
                 from MCS.cpp:3:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38:20: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after [-Wreorder]
MCSCompound.h:33:17: warning:   'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
MCSCompound.h:46:13: warning:   when initialized here [-Wreorder]
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:161:28: warning: 'FMCS::MCS::compoundTwo' will be initialized after [-Wreorder]
MCS.h:145:16: warning:   'size_t FMCS::MCS::userDefinedLowerBound' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:152:16: warning: 'FMCS::MCS::atomMismatchLowerBound' will be initialized after [-Wreorder]
MCS.h:149:16: warning:   'size_t FMCS::MCS::atomMismatchUpperBound' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:153:16: warning: 'FMCS::MCS::bondMismatchLowerBound' will be initialized after [-Wreorder]
MCS.h:150:16: warning:   'size_t FMCS::MCS::bondMismatchUpperBound' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:150:16: warning: 'FMCS::MCS::bondMismatchUpperBound' will be initialized after [-Wreorder]
MCS.h:143:19: warning:   'FMCS::MCS::MatchType FMCS::MCS::matchType' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:143:19: warning: 'FMCS::MCS::matchType' will be initialized after [-Wreorder]
MCS.h:129:21: warning:   'FMCS::MCS::RunningMode FMCS::MCS::runningMode' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:129:21: warning: 'FMCS::MCS::runningMode' will be initialized after [-Wreorder]
MCS.h:125:13: warning:   'int FMCS::MCS::_timeout' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:156:16: warning: 'FMCS::MCS::bondMismatchCurr' will be initialized after [-Wreorder]
MCS.h:147:16: warning:   'size_t FMCS::MCS::currSubstructureNum' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:147:16: warning: 'FMCS::MCS::currSubstructureNum' will be initialized after [-Wreorder]
MCS.h:136:16: warning:   'double FMCS::MCS::timeUsed' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:137:13: warning: 'FMCS::MCS::startTime' will be initialized after [-Wreorder]
MCS.h:133:16: warning:   'size_t FMCS::MCS::bestSize' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:133:16: warning: 'FMCS::MCS::bestSize' will be initialized after [-Wreorder]
MCS.h:131:14: warning:   'bool FMCS::MCS::identicalGraph' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:131:14: warning: 'FMCS::MCS::identicalGraph' will be initialized after [-Wreorder]
MCS.h:127:14: warning:   'bool FMCS::MCS::_isTimeout' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.h:127:14: warning: 'FMCS::MCS::_isTimeout' will be initialized after [-Wreorder]
MCS.h:123:14: warning:   'bool FMCS::MCS::haveBeenSwapped' [-Wreorder]
MCS.cpp:41:5: warning:   when initialized here [-Wreorder]
MCS.cpp: In member function 'void FMCS::MCS::calculate()':
MCS.cpp:108:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCS.cpp:116:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from MCSCompound.h:15:0,
                 from MCS.h:12,
                 from MCS.cpp:3:
MCSList.h: In member function 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long long unsigned int]':
MCS.cpp:381:69:   instantiated from here
MCSList.h:143:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:4:0:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38:20: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after [-Wreorder]
MCSCompound.h:33:17: warning:   'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
MCSCompound.h:46:13: warning:   when initialized here [-Wreorder]
In file included from MCSCompound.cpp:5:0:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168:22: warning: 'FMCS::MCSRingDetector::compound' will be initialized after [-Wreorder]
MCSRingDetector.h:165:13: warning:   'int FMCS::MCSRingDetector::vertexId' [-Wreorder]
MCSRingDetector.h:191:9: warning:   when initialized here [-Wreorder]
MCSCompound.h: In copy constructor 'FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)':
MCSCompound.h:98:15: warning: 'FMCS::MCSCompound::bonds' will be initialized after [-Wreorder]
MCSCompound.h:88:21: warning:   'std::string FMCS::MCSCompound::SdfContentString' [-Wreorder]
MCSCompound.cpp:82:5: warning:   when initialized here [-Wreorder]
MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const string&)':
MCSCompound.cpp:157:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSCompound.cpp: In member function 'std::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const string&) const':
MCSCompound.cpp:194:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSCompound.cpp: In member function 'const FMCS::MCSCompound::Bond* FMCS::MCSCompound::getBond(size_t, size_t) const':
MCSCompound.cpp:467:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c MCSMap.cpp -o MCSMap.o
In file included from MCSMap.h:8:0,
                 from MCSMap.cpp:3:
MCSList.h: In member function 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long long unsigned int]':
MCSMap.cpp:28:36:   instantiated from here
MCSList.h:143:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.h:16:0,
                 from MCSRingDetector.cpp:13:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38:20: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after [-Wreorder]
MCSCompound.h:33:17: warning:   'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
MCSCompound.h:46:13: warning:   when initialized here [-Wreorder]
In file included from MCSRingDetector.cpp:13:0:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168:22: warning: 'FMCS::MCSRingDetector::compound' will be initialized after [-Wreorder]
MCSRingDetector.h:165:13: warning:   'int FMCS::MCSRingDetector::vertexId' [-Wreorder]
MCSRingDetector.h:191:9: warning:   when initialized here [-Wreorder]
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()':
MCSRingDetector.cpp:93:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.cpp:94:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::convert()':
MCSRingDetector.cpp:149:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::detect()':
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
MCSRingDetector.cpp: In member function 'bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const':
MCSRingDetector.cpp:194:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
In file included from MCS.h:12:0,
                 from fmcs_R_wrap.cpp:11:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38:20: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after [-Wreorder]
MCSCompound.h:33:17: warning:   'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
MCSCompound.h:46:13: warning:   when initialized here [-Wreorder]
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:74:45: warning: 'runningMode' may be used uninitialized in this function [-Wuninitialized]
fmcs_R_wrap.cpp:74:45: warning: 'matchType' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c util.cpp -o util.o
util.cpp: In function 'std::string getUpper(const string&)':
util.cpp:11:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/R/library/fmcsR/libs/x64
** testing if installed package can be loaded
* DONE (fmcsR)