##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf fmcsR.buildbin-libdir && mkdir fmcsR.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/fmcsR_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=fmcsR.buildbin-libdir --merge-multiarch fmcsR_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL fmcsR_1.18.0.zip && rm fmcsR_1.18.0.tar.gz fmcsR_1.18.0.zip
###
##############################################################################
##############################################################################
% 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 77790 100 77790 0 0 5082k 0 --:--:-- --:--:-- --:--:-- 5426k
install for i386
* installing *source* package 'fmcsR' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/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]
size_t originalId;
^
MCSCompound.h:33:17: warning: 'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
int atomType;
^
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
Atom(size_t id, size_t originalId, int atomType, std::string atomSymbol)
^
In file included from MCS.cpp:3:0:
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]
const MCSCompound& compoundTwo;
^
MCS.h:145:16: warning: 'size_t FMCS::MCS::userDefinedLowerBound' [-Wreorder]
size_t userDefinedLowerBound;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:152:16: warning: 'FMCS::MCS::atomMismatchLowerBound' will be initialized after [-Wreorder]
size_t atomMismatchLowerBound;
^
MCS.h:149:16: warning: 'size_t FMCS::MCS::atomMismatchUpperBound' [-Wreorder]
size_t atomMismatchUpperBound;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:153:16: warning: 'FMCS::MCS::bondMismatchLowerBound' will be initialized after [-Wreorder]
size_t bondMismatchLowerBound;
^
MCS.h:150:16: warning: 'size_t FMCS::MCS::bondMismatchUpperBound' [-Wreorder]
size_t bondMismatchUpperBound;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:150:16: warning: 'FMCS::MCS::bondMismatchUpperBound' will be initialized after [-Wreorder]
size_t bondMismatchUpperBound;
^
MCS.h:143:19: warning: 'FMCS::MCS::MatchType FMCS::MCS::matchType' [-Wreorder]
MatchType matchType;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:143:19: warning: 'FMCS::MCS::matchType' will be initialized after [-Wreorder]
MatchType matchType;
^
MCS.h:129:21: warning: 'FMCS::MCS::RunningMode FMCS::MCS::runningMode' [-Wreorder]
RunningMode runningMode;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:129:21: warning: 'FMCS::MCS::runningMode' will be initialized after [-Wreorder]
RunningMode runningMode;
^
MCS.h:125:13: warning: 'int FMCS::MCS::_timeout' [-Wreorder]
int _timeout;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:156:16: warning: 'FMCS::MCS::bondMismatchCurr' will be initialized after [-Wreorder]
size_t bondMismatchCurr;
^
MCS.h:147:16: warning: 'size_t FMCS::MCS::currSubstructureNum' [-Wreorder]
size_t currSubstructureNum;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:147:16: warning: 'FMCS::MCS::currSubstructureNum' will be initialized after [-Wreorder]
size_t currSubstructureNum;
^
MCS.h:136:16: warning: 'double FMCS::MCS::timeUsed' [-Wreorder]
double timeUsed;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:137:13: warning: 'FMCS::MCS::startTime' will be initialized after [-Wreorder]
clock_t startTime;
^
MCS.h:133:16: warning: 'size_t FMCS::MCS::bestSize' [-Wreorder]
size_t bestSize;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:133:16: warning: 'FMCS::MCS::bestSize' will be initialized after [-Wreorder]
size_t bestSize;
^
MCS.h:131:14: warning: 'bool FMCS::MCS::identicalGraph' [-Wreorder]
bool identicalGraph;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:131:14: warning: 'FMCS::MCS::identicalGraph' will be initialized after [-Wreorder]
bool identicalGraph;
^
MCS.h:127:14: warning: 'bool FMCS::MCS::_isTimeout' [-Wreorder]
bool _isTimeout;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:127:14: warning: 'FMCS::MCS::_isTimeout' will be initialized after [-Wreorder]
bool _isTimeout;
^
MCS.h:123:14: warning: 'bool FMCS::MCS::haveBeenSwapped' [-Wreorder]
bool haveBeenSwapped;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
MCS.cpp: In member function 'void FMCS::MCS::calculate()':
MCS.cpp:108:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < atomCountOne; ++i) {
^
MCS.cpp:116:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < atomCountTwo; ++i) {
^
In file included from MCSCompound.h:15:0,
from MCS.h:12,
from MCS.cpp:3:
MCSList.h: In instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = unsigned int]':
MCS.cpp:381:69: required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < length; ++i) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/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]
size_t originalId;
^
MCSCompound.h:33:17: warning: 'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
int atomType;
^
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
Atom(size_t id, size_t originalId, int atomType, std::string atomSymbol)
^
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:86:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < this->vertexPath.size(); ++i) {
^
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (vertexIndex < vertexPath.size()-1) {
^
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168:22: warning: 'FMCS::MCSRingDetector::compound' will be initialized after [-Wreorder]
MCSCompound& compound;
^
MCSRingDetector.h:165:13: warning: 'int FMCS::MCSRingDetector::vertexId' [-Wreorder]
int vertexId;
^
MCSRingDetector.h:191:9: warning: when initialized here [-Wreorder]
MCSRingDetector(MCSCompound& compound) : compound(compound), vertexId(-1), edgeId(-1) {
^
In file included from MCSCompound.cpp:4:0:
MCSCompound.h: In copy constructor 'FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)':
MCSCompound.h:98:15: warning: 'FMCS::MCSCompound::bonds' will be initialized after [-Wreorder]
Bond *bonds;
^
MCSCompound.h:88:21: warning: 'std::string FMCS::MCSCompound::SdfContentString' [-Wreorder]
std::string SdfContentString;
^
MCSCompound.cpp:82:5: warning: when initialized here [-Wreorder]
MCSCompound::MCSCompound(const MCSCompound& other)
^
MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const string&)':
MCSCompound.cpp:157:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < bondCount; ++i) {
^
MCSCompound.cpp: In member function 'std::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const string&) const':
MCSCompound.cpp:194:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < indexLength; ++i) {
^
MCSCompound.cpp: In member function 'const FMCS::MCSCompound::Bond* FMCS::MCSCompound::getBond(size_t, size_t) const':
MCSCompound.cpp:467:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < bondCount; ++i) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/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 instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = unsigned int]':
MCSMap.cpp:28:36: required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < length; ++i) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/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]
size_t originalId;
^
MCSCompound.h:33:17: warning: 'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
int atomType;
^
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
Atom(size_t id, size_t originalId, int atomType, std::string atomSymbol)
^
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:86:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < this->vertexPath.size(); ++i) {
^
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (vertexIndex < vertexPath.size()-1) {
^
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168:22: warning: 'FMCS::MCSRingDetector::compound' will be initialized after [-Wreorder]
MCSCompound& compound;
^
MCSRingDetector.h:165:13: warning: 'int FMCS::MCSRingDetector::vertexId' [-Wreorder]
int vertexId;
^
MCSRingDetector.h:191:9: warning: when initialized here [-Wreorder]
MCSRingDetector(MCSCompound& compound) : compound(compound), vertexId(-1), edgeId(-1) {
^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()':
MCSRingDetector.cpp:93:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < vertexQueue.size(); ++i) {
^
MCSRingDetector.cpp:94:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < queueSize-1-i; ++j ) {
^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::convert()':
MCSRingDetector.cpp:149:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < degree; ++j) {
^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::detect()':
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
int aromaticCount = 0;
^
MCSRingDetector.cpp: In member function 'bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const':
MCSRingDetector.cpp:194:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (level > vertexPath.size()) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/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]
size_t originalId;
^
MCSCompound.h:33:17: warning: 'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
int atomType;
^
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
Atom(size_t id, size_t originalId, int atomType, std::string atomSymbol)
^
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 [-Wmaybe-uninitialized]
matchType, runningMode, *timeout);
^
fmcs_R_wrap.cpp:74:45: warning: 'matchType' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c util.cpp -o util.o
util.cpp: In function 'std::string getUpper(const string&)':
util.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < upper.length(); ++i) {
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-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
** testing if installed package can be loaded
install for x64
* installing *source* package 'fmcsR' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/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]
size_t originalId;
^
MCSCompound.h:33:17: warning: 'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
int atomType;
^
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
Atom(size_t id, size_t originalId, int atomType, std::string atomSymbol)
^
In file included from MCS.cpp:3:0:
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]
const MCSCompound& compoundTwo;
^
MCS.h:145:16: warning: 'size_t FMCS::MCS::userDefinedLowerBound' [-Wreorder]
size_t userDefinedLowerBound;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:152:16: warning: 'FMCS::MCS::atomMismatchLowerBound' will be initialized after [-Wreorder]
size_t atomMismatchLowerBound;
^
MCS.h:149:16: warning: 'size_t FMCS::MCS::atomMismatchUpperBound' [-Wreorder]
size_t atomMismatchUpperBound;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:153:16: warning: 'FMCS::MCS::bondMismatchLowerBound' will be initialized after [-Wreorder]
size_t bondMismatchLowerBound;
^
MCS.h:150:16: warning: 'size_t FMCS::MCS::bondMismatchUpperBound' [-Wreorder]
size_t bondMismatchUpperBound;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:150:16: warning: 'FMCS::MCS::bondMismatchUpperBound' will be initialized after [-Wreorder]
size_t bondMismatchUpperBound;
^
MCS.h:143:19: warning: 'FMCS::MCS::MatchType FMCS::MCS::matchType' [-Wreorder]
MatchType matchType;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:143:19: warning: 'FMCS::MCS::matchType' will be initialized after [-Wreorder]
MatchType matchType;
^
MCS.h:129:21: warning: 'FMCS::MCS::RunningMode FMCS::MCS::runningMode' [-Wreorder]
RunningMode runningMode;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:129:21: warning: 'FMCS::MCS::runningMode' will be initialized after [-Wreorder]
RunningMode runningMode;
^
MCS.h:125:13: warning: 'int FMCS::MCS::_timeout' [-Wreorder]
int _timeout;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:156:16: warning: 'FMCS::MCS::bondMismatchCurr' will be initialized after [-Wreorder]
size_t bondMismatchCurr;
^
MCS.h:147:16: warning: 'size_t FMCS::MCS::currSubstructureNum' [-Wreorder]
size_t currSubstructureNum;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:147:16: warning: 'FMCS::MCS::currSubstructureNum' will be initialized after [-Wreorder]
size_t currSubstructureNum;
^
MCS.h:136:16: warning: 'double FMCS::MCS::timeUsed' [-Wreorder]
double timeUsed;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:137:13: warning: 'FMCS::MCS::startTime' will be initialized after [-Wreorder]
clock_t startTime;
^
MCS.h:133:16: warning: 'size_t FMCS::MCS::bestSize' [-Wreorder]
size_t bestSize;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:133:16: warning: 'FMCS::MCS::bestSize' will be initialized after [-Wreorder]
size_t bestSize;
^
MCS.h:131:14: warning: 'bool FMCS::MCS::identicalGraph' [-Wreorder]
bool identicalGraph;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:131:14: warning: 'FMCS::MCS::identicalGraph' will be initialized after [-Wreorder]
bool identicalGraph;
^
MCS.h:127:14: warning: 'bool FMCS::MCS::_isTimeout' [-Wreorder]
bool _isTimeout;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
In file included from MCS.cpp:3:0:
MCS.h:127:14: warning: 'FMCS::MCS::_isTimeout' will be initialized after [-Wreorder]
bool _isTimeout;
^
MCS.h:123:14: warning: 'bool FMCS::MCS::haveBeenSwapped' [-Wreorder]
bool haveBeenSwapped;
^
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS::MCS(const MCSCompound& compoundOne, const MCSCompound& compoundTwo,
^
MCS.cpp: In member function 'void FMCS::MCS::calculate()':
MCS.cpp:108:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < atomCountOne; ++i) {
^
MCS.cpp:116:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < atomCountTwo; ++i) {
^
In file included from MCSCompound.h:15:0,
from MCS.h:12,
from MCS.cpp:3:
MCSList.h: In instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long long unsigned int]':
MCS.cpp:381:69: required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < length; ++i) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/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]
size_t originalId;
^
MCSCompound.h:33:17: warning: 'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
int atomType;
^
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
Atom(size_t id, size_t originalId, int atomType, std::string atomSymbol)
^
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:86:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < this->vertexPath.size(); ++i) {
^
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (vertexIndex < vertexPath.size()-1) {
^
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168:22: warning: 'FMCS::MCSRingDetector::compound' will be initialized after [-Wreorder]
MCSCompound& compound;
^
MCSRingDetector.h:165:13: warning: 'int FMCS::MCSRingDetector::vertexId' [-Wreorder]
int vertexId;
^
MCSRingDetector.h:191:9: warning: when initialized here [-Wreorder]
MCSRingDetector(MCSCompound& compound) : compound(compound), vertexId(-1), edgeId(-1) {
^
In file included from MCSCompound.cpp:4:0:
MCSCompound.h: In copy constructor 'FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)':
MCSCompound.h:98:15: warning: 'FMCS::MCSCompound::bonds' will be initialized after [-Wreorder]
Bond *bonds;
^
MCSCompound.h:88:21: warning: 'std::string FMCS::MCSCompound::SdfContentString' [-Wreorder]
std::string SdfContentString;
^
MCSCompound.cpp:82:5: warning: when initialized here [-Wreorder]
MCSCompound::MCSCompound(const MCSCompound& other)
^
MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const string&)':
MCSCompound.cpp:157:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < bondCount; ++i) {
^
MCSCompound.cpp: In member function 'std::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const string&) const':
MCSCompound.cpp:194:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < indexLength; ++i) {
^
MCSCompound.cpp: In member function 'const FMCS::MCSCompound::Bond* FMCS::MCSCompound::getBond(size_t, size_t) const':
MCSCompound.cpp:467:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < bondCount; ++i) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/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 instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long long unsigned int]':
MCSMap.cpp:28:36: required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < length; ++i) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/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]
size_t originalId;
^
MCSCompound.h:33:17: warning: 'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
int atomType;
^
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
Atom(size_t id, size_t originalId, int atomType, std::string atomSymbol)
^
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:86:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < this->vertexPath.size(); ++i) {
^
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (vertexIndex < vertexPath.size()-1) {
^
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168:22: warning: 'FMCS::MCSRingDetector::compound' will be initialized after [-Wreorder]
MCSCompound& compound;
^
MCSRingDetector.h:165:13: warning: 'int FMCS::MCSRingDetector::vertexId' [-Wreorder]
int vertexId;
^
MCSRingDetector.h:191:9: warning: when initialized here [-Wreorder]
MCSRingDetector(MCSCompound& compound) : compound(compound), vertexId(-1), edgeId(-1) {
^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()':
MCSRingDetector.cpp:93:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < vertexQueue.size(); ++i) {
^
MCSRingDetector.cpp:94:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < queueSize-1-i; ++j ) {
^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::convert()':
MCSRingDetector.cpp:149:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < degree; ++j) {
^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::detect()':
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
int aromaticCount = 0;
^
MCSRingDetector.cpp: In member function 'bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const':
MCSRingDetector.cpp:194:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (level > vertexPath.size()) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/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]
size_t originalId;
^
MCSCompound.h:33:17: warning: 'int FMCS::MCSCompound::Atom::atomType' [-Wreorder]
int atomType;
^
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
Atom(size_t id, size_t originalId, int atomType, std::string atomSymbol)
^
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 [-Wmaybe-uninitialized]
matchType, runningMode, *timeout);
^
fmcs_R_wrap.cpp:74:45: warning: 'matchType' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c util.cpp -o util.o
util.cpp: In function 'std::string getUpper(const string&)':
util.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < upper.length(); ++i) {
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fmcsR' as fmcsR_1.18.0.zip
* DONE (fmcsR)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'fmcsR' successfully unpacked and MD5 sums checked
