fmcsR 1.11.4
Thomas Girke
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/fmcsR | | Last Changed Rev: 104621 / Revision: 107696 | | Last Changed Date: 2015-06-05 15:53:41 -0700 (Fri, 05 Jun 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | [ 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 | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD INSTALL fmcsR
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* installing to library ‘/home/biocbuild/bbs-3.2-bioc/R/library’
* installing *source* package ‘fmcsR’ ...
checking for g++... g++
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++ 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... /bin/grep
checking for egrep... /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
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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:108:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < atomCountOne; ++i) {
^
MCS.cpp:116:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < atomCountTwo; ++i) {
^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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:86:59: 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:142:53: 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:157:29: 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:194:29: 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:467:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < bondCount; ++i) {
^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c MCSMap.cpp -o MCSMap.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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:86:59: 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:142:53: 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:93:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < vertexQueue.size(); ++i) {
^
MCSRingDetector.cpp:94:45: 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:149:33: 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:194:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (level > vertexPath.size()) {
^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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]
g++ -I/home/biocbuild/bbs-3.2-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:11:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < upper.length(); ++i) {
^
g++ -shared -L/home/biocbuild/bbs-3.2-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-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/R/library/fmcsR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (fmcsR)