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###
### Running command:
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### 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
###
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% 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<T>::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<int>::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<int>::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<T>::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<int>::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<int>::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<int>::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<int>::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<char>::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<T>::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<int>::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<int>::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<T>::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<int>::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<int>::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<int>::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<int>::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<char>::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
