fmcsR 1.6.5
ChemmineR Team
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/fmcsR | | Last Changed Rev: 93218 / Revision: 95116 | | Last Changed Date: 2014-08-06 10:19:29 -0700 (Wed, 06 Aug 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | [ OK ] | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| morelia | 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-2.14-bioc/R/bin/R CMD INSTALL fmcsR
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* installing to library ‘/home/biocbuild/bbs-2.14-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-2.14-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]
MCSCompound.h:33:17: warning: ‘int FMCS::MCSCompound::Atom::atomType’ [-Wreorder]
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
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]
MCS.h:145:16: warning: ‘size_t FMCS::MCS::userDefinedLowerBound’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.h:152:16: warning: ‘FMCS::MCS::atomMismatchLowerBound’ will be initialized after [-Wreorder]
MCS.h:149:16: warning: ‘size_t FMCS::MCS::atomMismatchUpperBound’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.h:153:16: warning: ‘FMCS::MCS::bondMismatchLowerBound’ will be initialized after [-Wreorder]
MCS.h:150:16: warning: ‘size_t FMCS::MCS::bondMismatchUpperBound’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.h:150:16: warning: ‘FMCS::MCS::bondMismatchUpperBound’ will be initialized after [-Wreorder]
MCS.h:143:19: warning: ‘FMCS::MCS::MatchType FMCS::MCS::matchType’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.h:143:19: warning: ‘FMCS::MCS::matchType’ will be initialized after [-Wreorder]
MCS.h:129:21: warning: ‘FMCS::MCS::RunningMode FMCS::MCS::runningMode’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.h:129:21: warning: ‘FMCS::MCS::runningMode’ will be initialized after [-Wreorder]
MCS.h:125:13: warning: ‘int FMCS::MCS::_timeout’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.h:156:16: warning: ‘FMCS::MCS::bondMismatchCurr’ will be initialized after [-Wreorder]
MCS.h:147:16: warning: ‘size_t FMCS::MCS::currSubstructureNum’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.h:147:16: warning: ‘FMCS::MCS::currSubstructureNum’ will be initialized after [-Wreorder]
MCS.h:136:16: warning: ‘double FMCS::MCS::timeUsed’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.h:137:13: warning: ‘FMCS::MCS::startTime’ will be initialized after [-Wreorder]
MCS.h:133:16: warning: ‘size_t FMCS::MCS::bestSize’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.h:133:16: warning: ‘FMCS::MCS::bestSize’ will be initialized after [-Wreorder]
MCS.h:131:14: warning: ‘bool FMCS::MCS::identicalGraph’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.h:131:14: warning: ‘FMCS::MCS::identicalGraph’ will be initialized after [-Wreorder]
MCS.h:127:14: warning: ‘bool FMCS::MCS::_isTimeout’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.h:127:14: warning: ‘FMCS::MCS::_isTimeout’ will be initialized after [-Wreorder]
MCS.h:123:14: warning: ‘bool FMCS::MCS::haveBeenSwapped’ [-Wreorder]
MCS.cpp:41:5: warning: when initialized here [-Wreorder]
MCS.cpp: In member function ‘void FMCS::MCS::calculate()’:
MCS.cpp:108:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCS.cpp:116:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from MCSCompound.h:15:0,
from MCS.h:12,
from MCS.cpp:3:
MCSList.h: In member function ‘bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]’:
MCS.cpp:381:69: instantiated from here
MCSList.h:143:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-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]
MCSCompound.h:33:17: warning: ‘int FMCS::MCSCompound::Atom::atomType’ [-Wreorder]
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
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]
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]
MCSRingDetector.h: In constructor ‘FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)’:
MCSRingDetector.h:168:22: warning: ‘FMCS::MCSRingDetector::compound’ will be initialized after [-Wreorder]
MCSRingDetector.h:165:13: warning: ‘int FMCS::MCSRingDetector::vertexId’ [-Wreorder]
MCSRingDetector.h:191:9: warning: when initialized here [-Wreorder]
MCSCompound.h: In copy constructor ‘FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)’:
MCSCompound.h:98:15: warning: ‘FMCS::MCSCompound::bonds’ will be initialized after [-Wreorder]
MCSCompound.h:88:21: warning: ‘std::string FMCS::MCSCompound::SdfContentString’ [-Wreorder]
MCSCompound.cpp:82:5: warning: when initialized here [-Wreorder]
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]
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]
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]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c MCSMap.cpp -o MCSMap.o
In file included from MCSMap.h:8:0,
from MCSMap.cpp:3:
MCSList.h: In member function ‘bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]’:
MCSMap.cpp:28:36: instantiated from here
MCSList.h:143:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-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]
MCSCompound.h:33:17: warning: ‘int FMCS::MCSCompound::Atom::atomType’ [-Wreorder]
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
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]
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]
MCSRingDetector.h: In constructor ‘FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)’:
MCSRingDetector.h:168:22: warning: ‘FMCS::MCSRingDetector::compound’ will be initialized after [-Wreorder]
MCSRingDetector.h:165:13: warning: ‘int FMCS::MCSRingDetector::vertexId’ [-Wreorder]
MCSRingDetector.h:191:9: warning: when initialized here [-Wreorder]
MCSRingDetector.cpp: In member function ‘void FMCS::MCSRingDetector::sortVertexQueue()’:
MCSRingDetector.cpp:93:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.cpp:94:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.cpp: In member function ‘void FMCS::MCSRingDetector::convert()’:
MCSRingDetector.cpp:149:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCSRingDetector.cpp: In member function ‘void FMCS::MCSRingDetector::detect()’:
MCSRingDetector.cpp:175:13: warning: unused variable ‘aromaticCount’ [-Wunused-variable]
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]
g++ -I/home/biocbuild/bbs-2.14-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]
MCSCompound.h:33:17: warning: ‘int FMCS::MCSCompound::Atom::atomType’ [-Wreorder]
MCSCompound.h:46:13: warning: when initialized here [-Wreorder]
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 [-Wuninitialized]
fmcs_R_wrap.cpp:74:45: warning: ‘matchType’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.14-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]
g++ -shared -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-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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)