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BioC 3.0: CHECK report for fmcsR on moscato1

This page was generated on 2015-04-10 09:48:10 -0700 (Fri, 10 Apr 2015).

Package 325/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fmcsR 1.8.0
ChemmineR Team
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/fmcsR
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  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 

Summary

Package: fmcsR
Version: 1.8.0
Command: rm -rf fmcsR.buildbin-libdir fmcsR.Rcheck && mkdir fmcsR.buildbin-libdir fmcsR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=fmcsR.buildbin-libdir fmcsR_1.8.0.tar.gz >fmcsR.Rcheck\00install.out 2>&1 && cp fmcsR.Rcheck\00install.out fmcsR-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=fmcsR.buildbin-libdir --install="check:fmcsR-install.out" --force-multiarch --no-vignettes --timings fmcsR_1.8.0.tar.gz
StartedAt: 2015-04-10 01:11:43 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:14:11 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 147.3 seconds
RetCode: 0
Status:  OK  
CheckDir: fmcsR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf fmcsR.buildbin-libdir fmcsR.Rcheck && mkdir fmcsR.buildbin-libdir fmcsR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=fmcsR.buildbin-libdir fmcsR_1.8.0.tar.gz >fmcsR.Rcheck\00install.out 2>&1 && cp fmcsR.Rcheck\00install.out fmcsR-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=fmcsR.buildbin-libdir --install="check:fmcsR-install.out" --force-multiarch --no-vignettes --timings fmcsR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/fmcsR.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fmcsR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fmcsR' version '1.8.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'fmcsR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'ChemmineR'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
'library' or 'require' call to 'ChemmineR' which was already attached by Depends.
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  'BiocGenerics' 'RUnit' 'methods'
  All declared Imports should be used.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.0-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/i386/fmcsR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/x64/fmcsR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [32s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
fmcsR-package 3.72   0.02   11.37
fmcsBatch     0.11   0.03    9.50
** running examples for arch 'x64' ... [32s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
fmcsR-package 2.71   0.00   12.96
fmcsBatch     0.05   0.02    9.38
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: 'RefManageR'
'library' or 'require' call not declared from: 'ChemmineOB'
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 5 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/fmcsR.Rcheck/00check.log'
for details.

fmcsR.Rcheck/00install.out:


install for i386

* installing *source* package 'fmcsR' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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 = unsigned int]':
MCS.cpp:381:69:   instantiated from here
MCSList.h:143:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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 = unsigned int]':
MCSMap.cpp:28:36:   instantiated from here
MCSList.h:143:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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++ -m32 -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'fmcsR' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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 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++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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 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++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -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++ -m64 -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fmcsR' as fmcsR_1.8.0.zip
* DONE (fmcsR)

fmcsR.Rcheck/examples_i386/fmcsR-Ex.timings:

nameusersystemelapsed
MCS-class2.840.002.84
fmcs3.710.003.72
fmcsBatch0.110.039.50
fmcsR-package 3.72 0.0211.37
fmcstest0.060.000.06
mcs2sdfset1.450.011.47
plotMCS1.080.001.07

fmcsR.Rcheck/examples_x64/fmcsR-Ex.timings:

nameusersystemelapsed
MCS-class2.340.012.35
fmcs2.890.002.88
fmcsBatch0.050.029.38
fmcsR-package 2.71 0.0012.96
fmcstest0.050.010.38
mcs2sdfset1.610.001.60
plotMCS1.120.001.13