############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/fmcsR_1.36.0.tar.gz && rm -rf fmcsR.buildbin-libdir && mkdir fmcsR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fmcsR.buildbin-libdir fmcsR_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL fmcsR_1.36.0.zip && rm fmcsR_1.36.0.tar.gz fmcsR_1.36.0.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 81031 100 81031 0 0 142k 0 --:--:-- --:--:-- --:--:-- 143k install for i386 * installing *source* package 'fmcsR' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MCS.cpp -o MCS.o MCS.cpp: In member function 'void FMCS::MCS::calculate()': MCS.cpp:108:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < atomCountOne; ++i) { ~~^~~~~~~~~~~~~~ MCS.cpp:116:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < atomCountTwo; ++i) { ~~^~~~~~~~~~~~~~ In file included from MCSCompound.h:15, from MCS.h:12, from MCS.cpp:3: MCSList.h: In instantiation of 'bool FMCS::MCSList::contains(const T&) const [with T = unsigned int]': MCS.cpp:381:69: required from here MCSList.h:143:27: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare] for (int i = 0; i < length; ++i) { ~~^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MCSCompound.cpp -o MCSCompound.o In file included from MCSCompound.cpp:5: MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)': MCSRingDetector.h:86:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if (vertexIndex < vertexPath.size()-1) { ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ MCSCompound.cpp: In copy constructor 'FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)': MCSCompound.cpp:87:74: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct FMCS::MCSCompound::Atom' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(atoms, other.atoms, sizeof(Atom) * other.atomCount); ^ In file included from MCSCompound.cpp:4: MCSCompound.h:26:16: note: 'struct FMCS::MCSCompound::Atom' declared here struct Atom { ^~~~ MCSCompound.cpp: In member function 'const FMCS::MCSCompound& FMCS::MCSCompound::operator=(const FMCS::MCSCompound&)': MCSCompound.cpp:123:68: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct FMCS::MCSCompound::Atom' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(atoms, that.atoms, sizeof(Atom) * that.atomCount); ^ In file included from MCSCompound.cpp:4: MCSCompound.h:26:16: note: 'struct FMCS::MCSCompound::Atom' declared here struct Atom { ^~~~ MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const string&)': MCSCompound.cpp:157:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < bondCount; ++i) { ~~^~~~~~~~~~~ MCSCompound.cpp: In member function 'std::__cxx11::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const string&) const': MCSCompound.cpp:194:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare] for(int i = 0; i < bondCount; ++i) { ~~^~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MCSMap.cpp -o MCSMap.o In file included from MCSMap.h:8, from MCSMap.cpp:3: MCSList.h: In instantiation of 'bool FMCS::MCSList::contains(const T&) const [with T = unsigned int]': MCSMap.cpp:28:36: required from here MCSList.h:143:27: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare] for (int i = 0; i < length; ++i) { ~~^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MCSRingDetector.cpp -o MCSRingDetector.o In file included from MCSRingDetector.cpp:13: MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)': MCSRingDetector.h:86:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if (vertexIndex < vertexPath.size()-1) { ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()': MCSRingDetector.cpp:93:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < vertexQueue.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~~ MCSRingDetector.cpp:94:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if (level > vertexPath.size()) { ~~~~~~^~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o 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:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o util.cpp: In function 'std::__cxx11::string getUpper(const string&)': util.cpp:11:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < upper.length(); ++i) { ~~^~~~~~~~~~~~~~~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/fmcsR.buildbin-libdir/00LOCK-fmcsR/00new/fmcsR/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'fmcsR' finding HTML links ... done MCS-class html fmcs html fmcsBatch html fmcsR-package html fmcstest html mcs2sdfset html plotMCS html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'fmcsR' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MCS.cpp -o MCS.o MCS.cpp: In member function 'void FMCS::MCS::calculate()': MCS.cpp:108:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < atomCountOne; ++i) { ~~^~~~~~~~~~~~~~ MCS.cpp:116:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < atomCountTwo; ++i) { ~~^~~~~~~~~~~~~~ In file included from MCSCompound.h:15, from MCS.h:12, from MCS.cpp:3: MCSList.h: In instantiation of 'bool FMCS::MCSList::contains(const T&) const [with T = long long unsigned int]': MCS.cpp:381:69: required from here MCSList.h:143:27: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] for (int i = 0; i < length; ++i) { ~~^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MCSCompound.cpp -o MCSCompound.o In file included from MCSCompound.cpp:5: MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)': MCSRingDetector.h:86:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if (vertexIndex < vertexPath.size()-1) { ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ MCSCompound.cpp: In copy constructor 'FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)': MCSCompound.cpp:87:74: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct FMCS::MCSCompound::Atom' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(atoms, other.atoms, sizeof(Atom) * other.atomCount); ^ In file included from MCSCompound.cpp:4: MCSCompound.h:26:16: note: 'struct FMCS::MCSCompound::Atom' declared here struct Atom { ^~~~ MCSCompound.cpp: In member function 'const FMCS::MCSCompound& FMCS::MCSCompound::operator=(const FMCS::MCSCompound&)': MCSCompound.cpp:123:68: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct FMCS::MCSCompound::Atom' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(atoms, that.atoms, sizeof(Atom) * that.atomCount); ^ In file included from MCSCompound.cpp:4: MCSCompound.h:26:16: note: 'struct FMCS::MCSCompound::Atom' declared here struct Atom { ^~~~ MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const string&)': MCSCompound.cpp:157:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < bondCount; ++i) { ~~^~~~~~~~~~~ MCSCompound.cpp: In member function 'std::__cxx11::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const string&) const': MCSCompound.cpp:194:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] for(int i = 0; i < bondCount; ++i) { ~~^~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MCSMap.cpp -o MCSMap.o In file included from MCSMap.h:8, from MCSMap.cpp:3: MCSList.h: In instantiation of 'bool FMCS::MCSList::contains(const T&) const [with T = long long unsigned int]': MCSMap.cpp:28:36: required from here MCSList.h:143:27: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] for (int i = 0; i < length; ++i) { ~~^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MCSRingDetector.cpp -o MCSRingDetector.o In file included from MCSRingDetector.cpp:13: MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)': MCSRingDetector.h:86:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if (vertexIndex < vertexPath.size()-1) { ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()': MCSRingDetector.cpp:93:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < vertexQueue.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~~ MCSRingDetector.cpp:94:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if (level > vertexPath.size()) { ~~~~~~^~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o 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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o util.cpp: In function 'std::__cxx11::string getUpper(const string&)': util.cpp:11:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < upper.length(); ++i) { ~~^~~~~~~~~~~~~~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'fmcsR' as fmcsR_1.36.0.zip * DONE (fmcsR) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'fmcsR' successfully unpacked and MD5 sums checked