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Package 216/609HostnameOS / ArchBUILDCHECKBUILD BIN
fmcsR 1.0.5
ChemmineR Team
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/fmcsR
Last Changed Rev: 74515 / Revision: 74773
Last Changed Date: 2013-03-18 11:05:36 -0700 (Mon, 18 Mar 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: fmcsR
Version: 1.0.5
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings fmcsR_1.0.5.tar.gz
StartedAt: 2013-03-25 01:10:00 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:10:55 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 54.8 seconds
RetCode: 0
Status:  OK 
CheckDir: fmcsR.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/fmcsR.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fmcsR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fmcsR’ version ‘1.0.5’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘fmcsR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

fmcsR.Rcheck/00install.out:

* installing *source* package ‘fmcsR’ ...
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
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... /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
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c MCS.cpp -o MCS.o
In file included from MCS.h:11:0,
                 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:157:28: warning: ‘FMCS::MCS::compoundTwo’ will be initialized after [-Wreorder]
MCS.h:141:16: warning:   ‘size_t FMCS::MCS::userDefinedLowerBound’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.h:148:16: warning: ‘FMCS::MCS::atomMismatchLowerBound’ will be initialized after [-Wreorder]
MCS.h:145:16: warning:   ‘size_t FMCS::MCS::atomMismatchUpperBound’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.h:149:16: warning: ‘FMCS::MCS::bondMismatchLowerBound’ will be initialized after [-Wreorder]
MCS.h:146:16: warning:   ‘size_t FMCS::MCS::bondMismatchUpperBound’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.h:146:16: warning: ‘FMCS::MCS::bondMismatchUpperBound’ will be initialized after [-Wreorder]
MCS.h:139:19: warning:   ‘FMCS::MCS::MatchType FMCS::MCS::matchType’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.h:139:19: warning: ‘FMCS::MCS::matchType’ will be initialized after [-Wreorder]
MCS.h:126:21: warning:   ‘FMCS::MCS::RunningMode FMCS::MCS::runningMode’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.h:126:21: warning: ‘FMCS::MCS::runningMode’ will be initialized after [-Wreorder]
MCS.h:122:13: warning:   ‘int FMCS::MCS::_timeout’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.h:152:16: warning: ‘FMCS::MCS::bondMismatchCurr’ will be initialized after [-Wreorder]
MCS.h:143:16: warning:   ‘size_t FMCS::MCS::currSubstructureNum’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.h:143:16: warning: ‘FMCS::MCS::currSubstructureNum’ will be initialized after [-Wreorder]
MCS.h:133:16: warning:   ‘double FMCS::MCS::timeUsed’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.h:133:16: warning: ‘FMCS::MCS::timeUsed’ will be initialized after [-Wreorder]
MCS.h:130:16: warning:   ‘size_t FMCS::MCS::bestSize’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.h:130:16: warning: ‘FMCS::MCS::bestSize’ will be initialized after [-Wreorder]
MCS.h:128:14: warning:   ‘bool FMCS::MCS::identicalGraph’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.h:128:14: warning: ‘FMCS::MCS::identicalGraph’ will be initialized after [-Wreorder]
MCS.h:124:14: warning:   ‘bool FMCS::MCS::_isTimeout’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.h:124:14: warning: ‘FMCS::MCS::_isTimeout’ will be initialized after [-Wreorder]
MCS.h:120:14: warning:   ‘bool FMCS::MCS::haveBeenSwapped’ [-Wreorder]
MCS.cpp:39:5: warning:   when initialized here [-Wreorder]
MCS.cpp: In member function ‘void FMCS::MCS::calculate()’:
MCS.cpp:105:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCS.cpp:113:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from MCSCompound.h:15:0,
                 from MCS.h:11,
                 from MCS.cpp:3:
MCSList.h: In member function ‘bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]’:
MCS.cpp:371:69:   instantiated from here
MCSList.h:143:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.11-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-2.11-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-2.11-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-2.11-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:11:0,
                 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-2.11-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/lib64 -o fmcsR.so MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/fmcsR.Rcheck/fmcsR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘fmcsR.Rnw’ 
** testing if installed package can be loaded

* DONE (fmcsR)

fmcsR.Rcheck/fmcsR-Ex.timings:

nameusersystemelapsed
MCS-class1.5200.0081.550
fmcs1.6800.0121.846
fmcsBatch1.6880.0041.820
fmcsR-package3.2120.0123.377
fmcstest0.0400.0040.068
mcs2sdfset0.5280.0000.537
plotMCS0.4920.0000.491