fmcsR 1.18.0
Thomas Girke
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/fmcsR | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
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### Running command:
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### rm -rf fmcsR.buildbin-libdir && mkdir fmcsR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh fmcsR_1.18.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R fmcsR.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=fmcsR.buildbin-libdir fmcsR_1.18.0.tar.gz'
>>>>>>>
* 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... yes
checking for _Bool... yes
checking for inline... inline
checking for size_t... yes
checking for alarm... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating config.h
config.status: config.h is unchanged
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c MCS.cpp -o MCS.o
In file included from MCS.cpp:3:
In file included from ./MCS.h:12:
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
: atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
^
MCS.cpp:48:11: warning: field 'compoundTwo' will be initialized after field 'userDefinedLowerBound' [-Wreorder]
compoundTwo(compoundOne.size() > compoundTwo.size() ? compoundOne : compoundTwo),
^
MCS.cpp:50:8: warning: field 'atomMismatchLowerBound' will be initialized after field 'atomMismatchUpperBound' [-Wreorder]
atomMismatchLowerBound(atomMishmatchLower), atomMismatchUpperBound(atomMismatchUpper),
^
MCS.cpp:51:8: warning: field 'bondMismatchLowerBound' will be initialized after field 'bondMismatchUpperBound' [-Wreorder]
bondMismatchLowerBound(bondMismatchLower), bondMismatchUpperBound(bondMismatchUpper),
^
MCS.cpp:51:51: warning: field 'bondMismatchUpperBound' will be initialized after field 'matchType' [-Wreorder]
bondMismatchLowerBound(bondMismatchLower), bondMismatchUpperBound(bondMismatchUpper),
^
MCS.cpp:52:8: warning: field 'matchType' will be initialized after field 'runningMode' [-Wreorder]
matchType(matchType), runningMode(runningMode), _timeout(timeout),
^
MCS.cpp:52:30: warning: field 'runningMode' will be initialized after field '_timeout' [-Wreorder]
matchType(matchType), runningMode(runningMode), _timeout(timeout),
^
MCS.cpp:53:29: warning: field 'bondMismatchCurr' will be initialized after field 'currSubstructureNum' [-Wreorder]
atomMismatchCurr(0), bondMismatchCurr(0), currSubstructureNum(0),
^
MCS.cpp:53:50: warning: field 'currSubstructureNum' will be initialized after field 'timeUsed' [-Wreorder]
atomMismatchCurr(0), bondMismatchCurr(0), currSubstructureNum(0),
^
MCS.cpp:54:22: warning: field 'startTime' will be initialized after field 'bestSize' [-Wreorder]
timeUsed(0.0),startTime(0), bestSize(0), identicalGraph(false), _isTimeout(false),
^
MCS.cpp:54:37: warning: field 'bestSize' will be initialized after field 'identicalGraph' [-Wreorder]
timeUsed(0.0),startTime(0), bestSize(0), identicalGraph(false), _isTimeout(false),
^
MCS.cpp:54:50: warning: field 'identicalGraph' will be initialized after field '_isTimeout' [-Wreorder]
timeUsed(0.0),startTime(0), bestSize(0), identicalGraph(false), _isTimeout(false),
^
MCS.cpp:54:73: warning: field '_isTimeout' will be initialized after field 'haveBeenSwapped' [-Wreorder]
timeUsed(0.0),startTime(0), bestSize(0), identicalGraph(false), _isTimeout(false),
^
13 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:4:
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
: atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
^
In file included from MCSCompound.cpp:5:
./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:401:6: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete newAtomIndex;
^
[]
MCSCompound.cpp:353:26: note: allocated with 'new[]' here
int *newAtomIndex = new int[oldAtomCount];
^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c MCSMap.cpp -o MCSMap.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.cpp:13:
In file included from ./MCSRingDetector.h:16:
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
: atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
^
In file included from MCSRingDetector.cpp:13:
./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:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
int aromaticCount = 0;
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -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:12:
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
: atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
^
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;
^
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;
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c util.cpp -o util.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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-3.5-bioc/meat/fmcsR.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR fmcsR.buildbin-libdir/fmcsR/libs//fmcsR.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "fmcsR.buildbin-libdir/fmcsR/libs//fmcsR.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "fmcsR.buildbin-libdir/fmcsR/libs//fmcsR.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "fmcsR.buildbin-libdir/fmcsR/libs//fmcsR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "fmcsR.buildbin-libdir/fmcsR/libs//fmcsR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "fmcsR.buildbin-libdir/fmcsR/libs//fmcsR.so"