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Package 237/671HostnameOS / ArchBUILDCHECKBUILD BIN
fmcsR 1.2.0
ChemmineR Team
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/fmcsR
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: fmcsR
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch fmcsR_1.2.0.tar.gz
StartedAt: 2013-05-01 05:27:14 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 05:28:55 -0700 (Wed, 01 May 2013)
EllapsedTime: 101.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: fmcsR.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/fmcsR.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'fmcsR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fmcsR' version '1.2.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'fmcsR' can be installed ... [12s/14s] WARNING
Found the following significant warnings:
  fmcs_R_wrap.cpp:56:13: warning: variable 'runningMode' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
  fmcs_R_wrap.cpp:47:13: warning: variable 'matchType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
See '/Users/biocbuild/bbs-2.12-bioc/meat/fmcsR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... 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' ... NOTE
The following directories should probably not be installed:
  'images'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [48s/49s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
fmcsR-package 16.735  0.072  16.950
fmcs           8.727  0.035   8.844
fmcsBatch      8.449  0.031   8.560
MCS-class      7.491  0.027   7.634
* 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/fmcsR.Rcheck/00check.log'
for details.

fmcsR.Rcheck/00install.out:

* 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... /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... no
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
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c MCS.cpp -o MCS.o
In file included from MCS.cpp:3:
In file included from ./MCS.h:11:
./MCSCompound.h:40:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Atom() : atomType(0), atomId(-1), originalId(-1) {}
                                        ˜^˜
./MCSCompound.h:40:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Atom() : atomType(0), atomId(-1), originalId(-1) {}
                                                        ˜^˜
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
                : atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
                              ^
./MCSCompound.h:72:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                           ˜^˜
./MCSCompound.h:72:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                                          ˜^˜
./MCSCompound.h:72:60: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                                                          ˜^˜
MCS.cpp:46:11: warning: field 'compoundTwo' will be initialized after field 'userDefinedLowerBound' [-Wreorder]
          compoundTwo(compoundOne.size() > compoundTwo.size() ? compoundOne : compoundTwo),
          ^
MCS.cpp:48:8: warning: field 'atomMismatchLowerBound' will be initialized after field 'atomMismatchUpperBound' [-Wreorder]
          atomMismatchLowerBound(atomMishmatchLower), atomMismatchUpperBound(atomMismatchUpper),
          ^
MCS.cpp:49:8: warning: field 'bondMismatchLowerBound' will be initialized after field 'bondMismatchUpperBound' [-Wreorder]
          bondMismatchLowerBound(bondMismatchLower), bondMismatchUpperBound(bondMismatchUpper),
          ^
MCS.cpp:49:51: warning: field 'bondMismatchUpperBound' will be initialized after field 'matchType' [-Wreorder]
          bondMismatchLowerBound(bondMismatchLower), bondMismatchUpperBound(bondMismatchUpper),
                                                     ^
MCS.cpp:50:8: warning: field 'matchType' will be initialized after field 'runningMode' [-Wreorder]
          matchType(matchType), runningMode(runningMode), _timeout(timeout),
          ^
MCS.cpp:50:30: warning: field 'runningMode' will be initialized after field '_timeout' [-Wreorder]
          matchType(matchType), runningMode(runningMode), _timeout(timeout),
                                ^
MCS.cpp:51:29: warning: field 'bondMismatchCurr' will be initialized after field 'currSubstructureNum' [-Wreorder]
          atomMismatchCurr(0), bondMismatchCurr(0), currSubstructureNum(0),
                               ^
MCS.cpp:51:50: warning: field 'currSubstructureNum' will be initialized after field 'timeUsed' [-Wreorder]
          atomMismatchCurr(0), bondMismatchCurr(0), currSubstructureNum(0),
                                                    ^
MCS.cpp:52:8: warning: field 'timeUsed' will be initialized after field 'bestSize' [-Wreorder]
          timeUsed(0.0),  bestSize(0), identicalGraph(false), _isTimeout(false),
          ^
MCS.cpp:52:24: warning: field 'bestSize' will be initialized after field 'identicalGraph' [-Wreorder]
          timeUsed(0.0),  bestSize(0), identicalGraph(false), _isTimeout(false),
                          ^
MCS.cpp:52:37: warning: field 'identicalGraph' will be initialized after field '_isTimeout' [-Wreorder]
          timeUsed(0.0),  bestSize(0), identicalGraph(false), _isTimeout(false),
                                       ^
MCS.cpp:52:60: warning: field '_isTimeout' will be initialized after field 'haveBeenSwapped' [-Wreorder]
          timeUsed(0.0),  bestSize(0), identicalGraph(false), _isTimeout(false),
                                                              ^
MCS.cpp:141:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                int length = size();
                    ˜˜˜˜˜˜   ^˜˜˜˜˜
MCS.cpp:223:86: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
                const MCSCompound::Bond bondOne = compoundOne.atoms[atomOne].getBond(targetNeighborMappingPtr[i]);
                                                  ˜˜˜˜˜˜˜˜˜˜˜                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCS.cpp:224:86: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                const MCSCompound::Bond bondTwo = compoundTwo.atoms[atomTwo].getBond(n);
                                                  ˜˜˜˜˜˜˜˜˜˜˜                        ^
MCS.cpp:232:88: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
                const MCSCompound::Bond bondOne = compoundOne.getAtom(atomOne).getBond(targetNeighborMappingPtr[i]);
                                                  ˜˜˜˜˜˜˜˜˜˜˜                          ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCS.cpp:233:88: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                const MCSCompound::Bond bondTwo = compoundTwo.getAtom(atomTwo).getBond(n);
                                                  ˜˜˜˜˜˜˜˜˜˜˜                          ^
MCS.cpp:243:88: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
                const MCSCompound::Bond bondOne = compoundOne.getAtom(atomOne).getBond(targetNeighborMappingPtr[i]);
                                                  ˜˜˜˜˜˜˜˜˜˜˜                          ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCS.cpp:244:88: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                const MCSCompound::Bond bondTwo = compoundTwo.getAtom(atomTwo).getBond(n);
                                                  ˜˜˜˜˜˜˜˜˜˜˜                          ^
MCS.cpp:346:46: warning: implicit conversion changes signedness: 'int' to 'const unsigned long' [-Wsign-conversion]
                atomListOneDegrees.push_back(degree);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
MCS.cpp:363:46: warning: implicit conversion changes signedness: 'int' to 'const unsigned long' [-Wsign-conversion]
                atomListTwoDegrees.push_back(degree);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
27 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:4:
./MCSCompound.h:40:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Atom() : atomType(0), atomId(-1), originalId(-1) {}
                                        ˜^˜
./MCSCompound.h:40:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Atom() : atomType(0), atomId(-1), originalId(-1) {}
                                                        ˜^˜
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
                : atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
                              ^
./MCSCompound.h:72:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                           ˜^˜
./MCSCompound.h:72:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                                          ˜^˜
./MCSCompound.h:72:60: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                                                          ˜^˜
In file included from MCSCompound.cpp:5:
./MCSRingDetector.h:87:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    vertexIndexMap[vertexPath[i]] = i;
                                   ˜˜˜˜˜˜˜˜˜˜ ^
./MCSRingDetector.h:133:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return vertexPath[vertexIndex-1];
                           ˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜
./MCSRingDetector.h:130:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
                int vertexIndex = vertexIndexMap.find(vertex)->second;
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜
./MCSRingDetector.h:143:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return vertexPath[vertexIndex + 1];
                           ˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./MCSRingDetector.h:140:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
                int vertexIndex = vertexIndexMap.find(vertex)->second;
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜
./MCSRingDetector.h:152:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return edgePath[vertexIndex-1];
                           ˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜
./MCSRingDetector.h:150:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
                int vertexIndex = vertexIndexMap.find(vertex)->second;
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜
./MCSRingDetector.h:160:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                return edgePath[vertexIndex];
                       ˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
./MCSRingDetector.h:159:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
                int vertexIndex = vertexIndexMap.find(vertex)->second;
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜
./MCSRingDetector.h:191:50: warning: field 'compound' will be initialized after field 'vertexId' [-Wreorder]
        MCSRingDetector(MCSCompound& compound) : compound(compound), vertexId(-1), edgeId(-1) {
                                                 ^
MCSCompound.cpp:83:56: warning: field 'bonds' will be initialized after field 'SdfContentString' [-Wreorder]
            : bondCount(0), atomCount(0), atoms(NULL), bonds(NULL), SdfContentString(other.SdfContentString) {
                                                       ^
MCSCompound.cpp:196:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            atomMap.push_back(index[i], i);
            ˜˜˜˜˜˜˜                     ^
MCSCompound.cpp:200:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            string bondline = lines[4+numAtoms+i];
                              ˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
MCSCompound.cpp:205:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            if (atomMap.containsKey(beginAtom-1) && atomMap.containsKey(endAtom-1)) {
                ˜˜˜˜˜˜˜             ˜˜˜˜˜˜˜˜˜^˜
MCSCompound.cpp:205:80: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            if (atomMap.containsKey(beginAtom-1) && atomMap.containsKey(endAtom-1)) {
                                                    ˜˜˜˜˜˜˜             ˜˜˜˜˜˜˜^˜
MCSCompound.cpp:206:65: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                size_t newBeginAtom = atomMap.getValue(beginAtom-1)+1;
                                      ˜˜˜˜˜˜˜          ˜˜˜˜˜˜˜˜˜^˜
MCSCompound.cpp:207:61: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                size_t newEndAtom = atomMap.getValue(endAtom-1)+1;
                                    ˜˜˜˜˜˜˜          ˜˜˜˜˜˜˜^˜
MCSCompound.cpp:235:51: warning: implicit conversion changes signedness: 'int' to 'const unsigned long' [-Wsign-conversion]
        return *neighborBonds[neighborAtoms.where(anotherAtom)];
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜˜˜˜˜˜˜˜
MCSCompound.cpp:367:40: warning: implicit conversion changes signedness: 'int' to 'const value_type' (aka 'const unsigned long') [-Wsign-conversion]
                originalIds.push_back(i+1);
                ˜˜˜˜˜˜˜˜˜˜˜           ˜^˜
MCSCompound.cpp:434:18: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        atomCount = atoi(atomCountString.c_str());
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCSCompound.cpp:435:18: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        bondCount = atoi(bondCountString.c_str());
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCSCompound.cpp:459:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                bonds[i] = Bond(i, firstAtom, secondAtom, bondType, false, false);
                           ˜˜˜˜    ^˜˜˜˜˜˜˜˜
MCSCompound.cpp:459:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                bonds[i] = Bond(i, firstAtom, secondAtom, bondType, false, false);
                           ˜˜˜˜               ^˜˜˜˜˜˜˜˜˜
MCSCompound.cpp:459:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                bonds[i] = Bond(i, firstAtom, secondAtom, bondType, false, false);
                           ˜˜˜˜                           ^˜˜˜˜˜˜˜
30 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c MCSMap.cpp -o MCSMap.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.cpp:13:
In file included from ./MCSRingDetector.h:16:
./MCSCompound.h:40:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Atom() : atomType(0), atomId(-1), originalId(-1) {}
                                        ˜^˜
./MCSCompound.h:40:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Atom() : atomType(0), atomId(-1), originalId(-1) {}
                                                        ˜^˜
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
                : atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
                              ^
./MCSCompound.h:72:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                           ˜^˜
./MCSCompound.h:72:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                                          ˜^˜
./MCSCompound.h:72:60: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                                                          ˜^˜
In file included from MCSRingDetector.cpp:13:
./MCSRingDetector.h:87:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    vertexIndexMap[vertexPath[i]] = i;
                                   ˜˜˜˜˜˜˜˜˜˜ ^
./MCSRingDetector.h:133:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return vertexPath[vertexIndex-1];
                           ˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜
./MCSRingDetector.h:130:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
                int vertexIndex = vertexIndexMap.find(vertex)->second;
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜
./MCSRingDetector.h:143:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return vertexPath[vertexIndex + 1];
                           ˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
./MCSRingDetector.h:140:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
                int vertexIndex = vertexIndexMap.find(vertex)->second;
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜
./MCSRingDetector.h:152:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return edgePath[vertexIndex-1];
                           ˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜
./MCSRingDetector.h:150:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
                int vertexIndex = vertexIndexMap.find(vertex)->second;
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜
./MCSRingDetector.h:160:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                return edgePath[vertexIndex];
                       ˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
./MCSRingDetector.h:159:55: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
                int vertexIndex = vertexIndexMap.find(vertex)->second;
                                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜
./MCSRingDetector.h:191:50: warning: field 'compound' will be initialized after field 'vertexId' [-Wreorder]
        MCSRingDetector(MCSCompound& compound) : compound(compound), vertexId(-1), edgeId(-1) {
                                                 ^
MCSRingDetector.cpp:94:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            for (int j = 0; j < queueSize-1-i; ++j ) {
                                           ˜^
MCSRingDetector.cpp:95:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if (vertexMap[vertexQueue[j]] < vertexMap[vertexQueue[j+1]]) {
                              ˜˜˜˜˜˜˜˜˜˜˜ ^
MCSRingDetector.cpp:95:72: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if (vertexMap[vertexQueue[j]] < vertexMap[vertexQueue[j+1]]) {
                                                          ˜˜˜˜˜˜˜˜˜˜˜ ˜^˜
MCSRingDetector.cpp:96:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    int tmp = vertexQueue[j];
                              ˜˜˜˜˜˜˜˜˜˜˜ ^
MCSRingDetector.cpp:97:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    vertexQueue[j] = vertexQueue[j+1];
                    ˜˜˜˜˜˜˜˜˜˜˜ ^
MCSRingDetector.cpp:97:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    vertexQueue[j] = vertexQueue[j+1];
                                     ˜˜˜˜˜˜˜˜˜˜˜ ˜^˜
MCSRingDetector.cpp:98:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    vertexQueue[j+1] = tmp;
                    ˜˜˜˜˜˜˜˜˜˜˜ ˜^˜
MCSRingDetector.cpp:110:76: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                const Edge& one = edgeMap[vertexMap[vertex].connectedEdges[i]];
                                          ˜˜˜˜˜˜˜˜˜                        ^
MCSRingDetector.cpp:111:80: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                const Edge& another = edgeMap[vertexMap[vertex].connectedEdges[j]];
                                              ˜˜˜˜˜˜˜˜˜                        ^
MCSRingDetector.cpp:126:59: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            int edgeId = vertexMap[vertex].connectedEdges[i];
                         ˜˜˜˜˜˜˜˜˜                        ^
MCSRingDetector.cpp:106:34: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        int connectedEdgeCount = vertexMap[vertex].connectedEdges.size();
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:150:65: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                connectedEdges.push_back(atoms[i].neighborBonds[j]->bondId); 
                                         ˜˜˜˜˜                  ^
MCSRingDetector.cpp:142:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        int atomCount = compound.getAtomCount();
            ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:144:25: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        int bondCount = compound.getBondCount();
            ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:150:69: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const value_type' (aka 'const int') [-Wshorten-64-to-32]
                connectedEdges.push_back(atoms[i].neighborBonds[j]->bondId); 
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
MCSRingDetector.cpp:158:43: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'const value_type' (aka 'const int') [-Wshorten-64-to-32]
            vertexPath.push_back(bonds[i].firstAtom);
            ˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:159:43: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'const value_type' (aka 'const int') [-Wshorten-64-to-32]
            vertexPath.push_back(bonds[i].secondAtom);
            ˜˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:179:38: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                compound.setRingBond(*ringEdgeIter);
                ˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:183:46: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                    compound.setAromaticBond(*ringEdgeIter);
                    ˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
        int aromaticCount = 0;
            ^
MCSRingDetector.cpp:243:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            return isSp2Hybridized(leftVertex(vertex), level+1, dumm) || isSp2Hybridized(rightVertex(vertex), level+1, dumm);
                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:243:90: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            return isSp2Hybridized(leftVertex(vertex), level+1, dumm) || isSp2Hybridized(rightVertex(vertex), level+1, dumm);
                                                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:206:29: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        int neighborCount = atom.neighborBonds.size();
            ˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:255:35: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            if (! isSp2Hybridized(*i, 1, hasLonePair)) {
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
MCSRingDetector.cpp:259:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            size_t leftEdge = this->leftEdge(*i);
                   ˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:259:46: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            size_t leftEdge = this->leftEdge(*i);
                              ˜˜˜˜           ^˜
MCSRingDetector.cpp:260:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            size_t rightEdge = this->rightEdge(*i);
                   ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCSRingDetector.cpp:260:48: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            size_t rightEdge = this->rightEdge(*i);
                               ˜˜˜˜            ^˜
44 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
In file included from fmcs_R_wrap.cpp:11:
In file included from ./MCS.h:11:
./MCSCompound.h:40:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Atom() : atomType(0), atomId(-1), originalId(-1) {}
                                        ˜^˜
./MCSCompound.h:40:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Atom() : atomType(0), atomId(-1), originalId(-1) {}
                                                        ˜^˜
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
                : atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
                              ^
./MCSCompound.h:72:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                           ˜^˜
./MCSCompound.h:72:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                                          ˜^˜
./MCSCompound.h:72:60: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            Bond() : bondId(-1), firstAtom(-1), secondAtom(-1), bondType(0), isAromatic(false), isInARing(false) {}
                                                          ˜^˜
fmcs_R_wrap.cpp:71:13: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            userDefinedLowerBound, substructureNumLimit,
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:71:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            userDefinedLowerBound, substructureNumLimit,
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:72:13: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            *atomMismatchLowerBound, *atomMismatchUpperBound,
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:72:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            *atomMismatchLowerBound, *atomMismatchUpperBound,
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:73:13: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            *bondMismatchLowerBound, *bondMismatchUpperBound,
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:73:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            *bondMismatchLowerBound, *bondMismatchUpperBound,
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:125:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        cmpOneSize = mcs.getCompoundOne().size();
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:126:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        cmpTwoSize = mcs.getCompoundTwo().size();
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:127:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        mSize = mcs.size();
              ˜ ^˜˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:56:13: warning: variable 'runningMode' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
            default:
            ^˜˜˜˜˜˜
fmcs_R_wrap.cpp:74:24: note: uninitialized use occurs here
            matchType, runningMode, *timeout);
                       ^˜˜˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:52:9: note: variable 'runningMode' is declared here
        MCS::RunningMode runningMode;
        ^
fmcs_R_wrap.cpp:47:13: warning: variable 'matchType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
            default: 
            ^˜˜˜˜˜˜
fmcs_R_wrap.cpp:74:13: note: uninitialized use occurs here
            matchType, runningMode, *timeout);
            ^˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:42:6: note: variable 'matchType' is declared here
        MCS::MatchType matchType;
        ^
17 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c util.cpp -o util.o
util.cpp:12:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        upper[i] = toupper(upper[i]);
        ˜˜˜˜˜ ^
util.cpp:12:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        upper[i] = toupper(upper[i]);
                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
util.cpp:12:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        upper[i] = toupper(upper[i]);
                           ˜˜˜˜˜ ^
3 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o fmcsR.so MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/fmcsR.Rcheck/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)

fmcsR.Rcheck/fmcsR-Ex.timings:

nameusersystemelapsed
MCS-class7.4910.0277.634
fmcs8.7270.0358.844
fmcsBatch8.4490.0318.560
fmcsR-package16.735 0.07216.950
fmcstest0.0630.0100.074
mcs2sdfset2.5200.0112.548
plotMCS2.4340.0172.489