##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL fmcsR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘fmcsR’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for size_t... yes
checking for alarm... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating config.h
config.status: config.h is unchanged
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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 unsigned int’} [-Wsign-compare]
  108 |                 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 unsigned int’} [-Wsign-compare]
  116 |                 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 unsigned int]’:
MCS.cpp:381:44:   required from here
MCSList.h:143:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  143 |         for (int i = 0; i < length; ++i) {
      |                         ~~^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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 unsigned int’} [-Wsign-compare]
   86 |                 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 unsigned int’} [-Wsign-compare]
  142 |                 if (vertexIndex < vertexPath.size()-1) {
      |                     ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
MCSCompound.cpp: In copy constructor ‘FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)’:
MCSCompound.cpp:87:23: 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]
   87 |                 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
   26 |         struct Atom {
      |                ^~~~
MCSCompound.cpp: In member function ‘const FMCS::MCSCompound& FMCS::MCSCompound::operator=(const FMCS::MCSCompound&)’:
MCSCompound.cpp:123:19: 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]
  123 |             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
   26 |         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 unsigned int’} [-Wsign-compare]
  157 |         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 of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  194 |         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 unsigned int’} [-Wsign-compare]
  467 |         for(int i = 0; i < bondCount; ++i) {
      |                        ~~^~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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 unsigned int]’:
MCSMap.cpp:28:32:   required from here
MCSList.h:143:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  143 |         for (int i = 0; i < length; ++i) {
      |                         ~~^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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 unsigned int’} [-Wsign-compare]
   86 |                 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 unsigned int’} [-Wsign-compare]
  142 |                 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 unsigned int’} [-Wsign-compare]
   93 |         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 unsigned int’} [-Wsign-compare]
   94 |             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 unsigned int’} [-Wsign-compare]
  149 |             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]
  175 |         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 unsigned int’} [-Wsign-compare]
  194 |         if (level > vertexPath.size()) {
      |             ~~~~~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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]
   74 |             matchType, runningMode, *timeout);
      |                                             ^
fmcs_R_wrap.cpp:74:45: warning: ‘matchType’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c util.cpp -o util.o
util.cpp: In function ‘std::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 unsigned int’} [-Wsign-compare]
   11 |     for (int i = 0; i < upper.length(); ++i) {
      |                     ~~^~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o fmcsR.so MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-fmcsR/00new/fmcsR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fmcsR)