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BioC 3.4: CHECK report for fmcsR on tokay1

This page was generated on 2017-04-15 16:17:24 -0400 (Sat, 15 Apr 2017).

Package 452/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fmcsR 1.16.0
Thomas Girke
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/fmcsR
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: fmcsR
Version: 1.16.0
Command: rm -rf fmcsR.buildbin-libdir fmcsR.Rcheck && mkdir fmcsR.buildbin-libdir fmcsR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=fmcsR.buildbin-libdir fmcsR_1.16.0.tar.gz >fmcsR.Rcheck\00install.out 2>&1 && cp fmcsR.Rcheck\00install.out fmcsR-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=fmcsR.buildbin-libdir --install="check:fmcsR-install.out" --force-multiarch --no-vignettes --timings fmcsR_1.16.0.tar.gz
StartedAt: 2017-04-14 22:23:09 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:24:47 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 97.6 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 && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=fmcsR.buildbin-libdir fmcsR_1.16.0.tar.gz >fmcsR.Rcheck\00install.out 2>&1 && cp fmcsR.Rcheck\00install.out fmcsR-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=fmcsR.buildbin-libdir --install="check:fmcsR-install.out" --force-multiarch --no-vignettes --timings fmcsR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/fmcsR.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-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 '1.16.0'
* 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 ... NOTE
fmcs: no visible global function definition for 'as'
fmcs: no visible global function definition for 'new'
fmcsBatch: no visible global function definition for 'as'
fmcsBatch : score: no visible global function definition for 'as'
plotMCS: no visible global function definition for 'par'
coerce,list-MCS: no visible global function definition for 'new'
Undefined global functions or variables:
  as new par
Consider adding
  importFrom("graphics", "par")
  importFrom("methods", "as", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 'C:/Users/biocbuild/bbs-3.4-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/i386/fmcsR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
fmcsR-package 1.49      0    5.88
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
fmcsR-package 1.31   0.02    7.03
fmcsBatch     0.05   0.03    5.42
* checking for unstated dependencies in vignettes ... NOTE
'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

Status: 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-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
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/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]
             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&, std::size_t, std::size_t, std::size_t, std::size_t, std::size_t, std::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:108:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < atomCountOne; ++i) {
                                   ^
MCS.cpp:116:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < atomCountTwo; ++i) {
                                   ^
In file included from MCSCompound.h:15:0,
                 from MCS.h:12,
                 from MCS.cpp:3:
MCSList.h: In instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = unsigned int]':
MCS.cpp:381:69:   required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                           ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/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]
             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:86:35: 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:142:33: 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:157:27: 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:194:27: 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:467:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int i = 0; i < bondCount; ++i) {
                          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/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 instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = unsigned int]':
MCSMap.cpp:28:36:   required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                           ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/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]
             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:86:35: 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:142:33: 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:93:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < vertexQueue.size(); ++i) {
                           ^
MCSRingDetector.cpp:94:31: 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:149:31: 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:194:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (level > vertexPath.size()) {
                   ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/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]
             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]
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c util.cpp -o util.o
util.cpp: In function 'std::string getUpper(const string&)':
util.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < upper.length(); ++i) {
                       ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-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
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/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]
             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&, std::size_t, std::size_t, std::size_t, std::size_t, std::size_t, std::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:108:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < atomCountOne; ++i) {
                                   ^
MCS.cpp:116:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < atomCountTwo; ++i) {
                                   ^
In file included from MCSCompound.h:15:0,
                 from MCS.h:12,
                 from MCS.cpp:3:
MCSList.h: In instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long long unsigned int]':
MCS.cpp:381:69:   required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                           ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/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]
             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:86:35: 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:142:33: 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:157:27: 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:194:27: 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:467:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int i = 0; i < bondCount; ++i) {
                          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/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 instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long long unsigned int]':
MCSMap.cpp:28:36:   required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                           ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/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]
             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:86:35: 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:142:33: 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:93:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < vertexQueue.size(); ++i) {
                           ^
MCSRingDetector.cpp:94:31: 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:149:31: 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:194:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (level > vertexPath.size()) {
                   ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/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]
             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]
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c util.cpp -o util.o
util.cpp: In function 'std::string getUpper(const string&)':
util.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < upper.length(); ++i) {
                       ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fmcsR' as fmcsR_1.16.0.zip
* DONE (fmcsR)

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

nameusersystemelapsed
MCS-class2.030.022.07
fmcs2.440.012.45
fmcsBatch0.090.024.81
fmcsR-package1.490.005.88
fmcstest0.030.000.03
mcs2sdfset0.740.000.74
plotMCS0.530.000.53

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

nameusersystemelapsed
MCS-class1.260.021.28
fmcs1.390.001.39
fmcsBatch0.050.035.42
fmcsR-package1.310.027.03
fmcstest0.020.000.02
mcs2sdfset0.420.000.42
plotMCS0.390.000.39