Hi John The OS is CentOS 6.5 and I installed the 'Development Tools' package.
Mike 2014-07-29 17:38 GMT+02:00 K. John Wu <[email protected]>: > Hi, Mike, > > I am looking into this now. > > Seems like you are on a system that I have not tried recently, would > you mind tell me your setup, mostly the type and the version of the > compiler you are using, so that I can reproduce your errors and not > have you report each one separately. > > Alternatively, you might run 'make -k' and send me the report. > > Thanks. > > John > > > > On 7/29/14 8:24 AM, Mike Carter wrote: > > Hi John, > > > > thank you again! I got a new error while compiling. > > > > make[2]: *** [dictionary.lo] Error 1 > > make[2]: Leaving directory `/root/fastbit/src' > > make[1]: *** [all] Error 2 > > make[1]: Leaving directory `/root/fastbit/src' > > > > Mike > > > > > > > > 2014-07-29 16:23 GMT+02:00 K. John Wu <[email protected]>: > > > >> Hi, Mike, > >> > >> Thanks for the report. I see the compilation problem now. It should > >> be fixed in SVN Revision 741. Please give it a try. > >> > >> John > >> > >> > >> On 7/29/14 1:01 AM, Mike Carter wrote: > >>> Hi John > >>> > >>> I appended the make and configure - process "logs" . > >>> > >>> Mike > >>> > >>> > >>> 2014-07-28 16:58 GMT+02:00 K. John Wu <[email protected]>: > >>> > >>>> Hi, Mike, > >>>> > >>>> Thanks for the report of compilation problem. Would it be possible > >>>> for you to capture the whole error message from make? The lines you > >>>> included shows something about stl_map.h, which is a standard header > >>>> file. It would be more useful to me to see where in FastBit code this > >>>> error originates. > >>>> > >>>> John > >>>> > >>>> > >>>> On 7/28/14 5:23 AM, Mike Carter wrote: > >>>>> Hi John, > >>>>> > >>>>> thank you for your help. I tried it with following command from the > >> new > >>>>> svn version (revision 740) > >>>>> > >>>>> ./configure --with-java=/usr/java/jdk1.8.0_11 > >>>>> ... > >>>>> checking if /usr/java/jdk1.8.0_11/bin/java works... yes > >>>>> checking jni.h usability... yes > >>>>> checking jni.h presence... yes > >>>>> checking for jni.h... yes > >>>>> ... > >>>>> > >>>>> After the configuration I got an error by using make > >>>>> > >>>>> > >>>> > >> > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_map.h:581: > >>>>> note: typename std::_Rb_tree<_Key, std::pair<const > >> _Key, > >>>>> _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, > typename > >>>>> _Alloc::rebind<std::pair<const _Key, _Tp> >::other>::size_type > >>>>> std::map<_Key, _Tp, _Compare, _Alloc>::erase(const _Key&) [with _Key > = > >>>>> const char*, _Tp = ibis::part*, _Compare = ibis::lessi, _Alloc = > >>>>> std::allocator<std::pair<const char* const, ibis::part*> >] > >>>>> > >>>> > >> > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_map.h:596: > >>>>> note: void std::map<_Key, _Tp, _Compare, > >>>>> _Alloc>::erase(typename std::_Rb_tree<_Key, std::pair<const _Key, > _Tp>, > >>>>> std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename > >>>>> _Alloc::rebind<std::pair<const _Key, _Tp> >::other>::iterator, > typename > >>>>> std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, > >>>>> std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename > >>>>> _Alloc::rebind<std::pair<const _Key, _Tp> >::other>::iterator) [with > >>>> _Key = > >>>>> const char*, _Tp = ibis::part*, _Compare = ibis::lessi, _Alloc = > >>>>> std::allocator<std::pair<const char* const, ibis::part*> >] > >>>>> make[2]: *** [capi.lo] Error 1 > >>>>> make[2]: Leaving directory `/root/fastbit/src' > >>>>> make[1]: *** [all] Error 2 > >>>>> make[1]: Leaving directory `/root/fastbit/src' > >>>>> make: *** [all-recursive] Error 1 > >>>>> > >>>>> > >>>>> > >>>>> Mike > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> 2014-07-27 9:43 GMT+02:00 K. John Wu <[email protected]>: > >>>>> > >>>>>> Hi, Mike, > >>>>>> > >>>>>> Thanks for your interest in our work. There was a problem in > >>>>>> detecting whether you javac could be used safely in configure.ac. > >>>>>> This problem should be fixed in the code from the SVN archive. > Would > >>>>>> you mind check out the source code with > >>>>>> > >>>>>> svn checkout https://codeforge.lbl.gov/anonscm/fastbit > >>>>>> > >>>>>> and give it another try. > >>>>>> > >>>>>> One thing to watch for is that when you run configure script (for > >>>>>> example, through runconf), you will notice something like > >>>>>> > >>>>>> checking for jni.h... yes > >>>>>> > >>>>>> If you don't see this like, it means that the configure script has > not > >>>>>> figured out how to deal with JNI stuff on your system. In which > case, > >>>>>> you might tell it where to find you JDK installation by giving the > >>>>>> following option to the configure script > >>>>>> > >>>>>> --with-java=path-to-jdk > >>>>>> > >>>>>> Hope this helps. > >>>>>> > >>>>>> John > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> On 7/18/14 6:50 AM, Mike Carter wrote: > >>>>>>> Hello everybody! > >>>>>>> > >>>>>>> After installing Fastbit successfully on CentOS, I tried to run the > >>>> milky > >>>>>>> example by using the command [java milky ../tests/tmp/t1 "a>10 and > c > >>>>>>> between 50 and 70"]. > >>>>>>> > >>>>>>> [root@vm001 java]# java milky ../tests/tmp/t1 "a>10 and c between > 50 > >>>>>> and 70" > >>>>>>> Exception in thread "main" java.lang.UnsatisfiedLinkError: no > >>>> fastbitjni > >>>>>> in > >>>>>>> java.library.path > >>>>>>> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1857) > >>>>>>> at java.lang.Runtime.loadLibrary0(Runtime.java:870) > >>>>>>> at java.lang.System.loadLibrary(System.java:1119) > >>>>>>> at gov.lbl.fastbit.FastBit.<clinit>(FastBit.java:188) > >>>>>>> at milky.main(milky.java:69) > >>>>>>> > >>>>>>> So I was looking for the file "libfastbitjni.so", but I couldn't > find > >>>> it. > >>>>>>> It doesn't exist in the folder fastbit/src/.libs nor in the folder > >>>>>>> /usr/local/lib (the java.library.path). > >>>>>>> In the documentation I found the following command to produce the > >>>>>>> libfastbitjni.so. I'm not sure how to use it to produce > >>>> libfastbitjni.so. > >>>>>>> Additionally, the libfastbitjni.so doesn't exist in the folder > >>>> src/.libs, > >>>>>>> which is a presumption to run this command. > >>>>>>> > >>>>>>> > >>>>>>> gcc -O -shared -o libfastbitjni.so -Wl,-soname,libfastbitjni.so \ > >>>>>>> -I/export/home/jdk1.2/include \ > >>>>>>> -I/export/home/jdk1.2/include/linux FastBit.c \ > >>>>>>> ..\src\libfastbit.lo -lm > >>>>>>> > >>>>>>> Any hints and advices? What I am doing wrong? I unpacket > >>>>>>> fastbit-ibis1.3.8.tar.gz and first I executed. Ibis and ardea > works, > >>>> but > >>>>>> I > >>>>>>> need to access fastbit through Java. > >>>>>>> > >>>>>>> ./configure > >>>>>>> gmake -j 3 all > >>>>>>> make install > >>>>>>> > >>>>>>> Thank you! > >>>>>>> Mike Carter > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> FastBit-users mailing list > >>>>>>> [email protected] > >>>>>>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > >>>>>>> > >>>>>> _______________________________________________ > >>>>>> FastBit-users mailing list > >>>>>> [email protected] > >>>>>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > >>>>>> > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> FastBit-users mailing list > >>>>> [email protected] > >>>>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > >>>>> > >>>> _______________________________________________ > >>>> FastBit-users mailing list > >>>> [email protected] > >>>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > >>>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> FastBit-users mailing list > >>> [email protected] > >>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > >>> > >> _______________________________________________ > >> FastBit-users mailing list > >> [email protected] > >> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > >> > > > > > > > > _______________________________________________ > > FastBit-users mailing list > > [email protected] > > https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > > > _______________________________________________ > FastBit-users mailing list > [email protected] > https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >
[root@vm001 fastbit]# make -k Making all in src make[1]: Entering directory `/root/fastbit/src' make all-am make[2]: Entering directory `/root/fastbit/src' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT dictionary.lo -MD -MP -MF .deps/dictionary.Tpo -c -o dictionary.lo dictionary.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT dictionary.lo -MD -MP -MF .deps/dictionary.Tpo -c dictionary.cpp -fPIC -DPIC -o .libs/dictionary.o dictionary.cpp: In member function 'int ibis::dictionary::readKeys0(const char*, FILE*)': dictionary.cpp:426: error: 'class ibis::dictionary::MYMAP' has no member named 'reserve' dictionary.cpp: In member function 'int ibis::dictionary::readKeys1(const char*, FILE*)': dictionary.cpp:489: error: 'class ibis::dictionary::MYMAP' has no member named 'reserve' make[2]: *** [dictionary.lo] Error 1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT whereClause.lo -MD -MP -MF .deps/whereClause.Tpo -c -o whereClause.lo whereClause.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT whereClause.lo -MD -MP -MF .deps/whereClause.Tpo -c whereClause.cpp -fPIC -DPIC -o .libs/whereClause.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT whereClause.lo -MD -MP -MF .deps/whereClause.Tpo -c whereClause.cpp -o whereClause.o >/dev/null 2>&1 mv -f .deps/whereClause.Tpo .deps/whereClause.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT idbak.lo -MD -MP -MF .deps/idbak.Tpo -c -o idbak.lo idbak.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT idbak.lo -MD -MP -MF .deps/idbak.Tpo -c idbak.cpp -fPIC -DPIC -o .libs/idbak.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT idbak.lo -MD -MP -MF .deps/idbak.Tpo -c idbak.cpp -o idbak.o >/dev/null 2>&1 mv -f .deps/idbak.Tpo .deps/idbak.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT icmoins.lo -MD -MP -MF .deps/icmoins.Tpo -c -o icmoins.lo icmoins.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT icmoins.lo -MD -MP -MF .deps/icmoins.Tpo -c icmoins.cpp -fPIC -DPIC -o .libs/icmoins.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT icmoins.lo -MD -MP -MF .deps/icmoins.Tpo -c icmoins.cpp -o icmoins.o >/dev/null 2>&1 mv -f .deps/icmoins.Tpo .deps/icmoins.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT resource.lo -MD -MP -MF .deps/resource.Tpo -c -o resource.lo resource.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT resource.lo -MD -MP -MF .deps/resource.Tpo -c resource.cpp -fPIC -DPIC -o .libs/resource.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT resource.lo -MD -MP -MF .deps/resource.Tpo -c resource.cpp -o resource.o >/dev/null 2>&1 mv -f .deps/resource.Tpo .deps/resource.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT fromClause.lo -MD -MP -MF .deps/fromClause.Tpo -c -o fromClause.lo fromClause.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT fromClause.lo -MD -MP -MF .deps/fromClause.Tpo -c fromClause.cpp -fPIC -DPIC -o .libs/fromClause.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT fromClause.lo -MD -MP -MF .deps/fromClause.Tpo -c fromClause.cpp -o fromClause.o >/dev/null 2>&1 mv -f .deps/fromClause.Tpo .deps/fromClause.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT rids.lo -MD -MP -MF .deps/rids.Tpo -c -o rids.lo rids.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT rids.lo -MD -MP -MF .deps/rids.Tpo -c rids.cpp -fPIC -DPIC -o .libs/rids.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT rids.lo -MD -MP -MF .deps/rids.Tpo -c rids.cpp -o rids.o >/dev/null 2>&1 mv -f .deps/rids.Tpo .deps/rids.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT selectParser.lo -MD -MP -MF .deps/selectParser.Tpo -c -o selectParser.lo selectParser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT selectParser.lo -MD -MP -MF .deps/selectParser.Tpo -c selectParser.cc -fPIC -DPIC -o .libs/selectParser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT selectParser.lo -MD -MP -MF .deps/selectParser.Tpo -c selectParser.cc -o selectParser.o >/dev/null 2>&1 mv -f .deps/selectParser.Tpo .deps/selectParser.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT fromLexer.lo -MD -MP -MF .deps/fromLexer.Tpo -c -o fromLexer.lo fromLexer.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT fromLexer.lo -MD -MP -MF .deps/fromLexer.Tpo -c fromLexer.cc -fPIC -DPIC -o .libs/fromLexer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT fromLexer.lo -MD -MP -MF .deps/fromLexer.Tpo -c fromLexer.cc -o fromLexer.o >/dev/null 2>&1 mv -f .deps/fromLexer.Tpo .deps/fromLexer.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT whereParser.lo -MD -MP -MF .deps/whereParser.Tpo -c -o whereParser.lo whereParser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT whereParser.lo -MD -MP -MF .deps/whereParser.Tpo -c whereParser.cc -fPIC -DPIC -o .libs/whereParser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT whereParser.lo -MD -MP -MF .deps/whereParser.Tpo -c whereParser.cc -o whereParser.o >/dev/null 2>&1 mv -f .deps/whereParser.Tpo .deps/whereParser.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT selectLexer.lo -MD -MP -MF .deps/selectLexer.Tpo -c -o selectLexer.lo selectLexer.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT selectLexer.lo -MD -MP -MF .deps/selectLexer.Tpo -c selectLexer.cc -fPIC -DPIC -o .libs/selectLexer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT selectLexer.lo -MD -MP -MF .deps/selectLexer.Tpo -c selectLexer.cc -o selectLexer.o >/dev/null 2>&1 mv -f .deps/selectLexer.Tpo .deps/selectLexer.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT whereLexer.lo -MD -MP -MF .deps/whereLexer.Tpo -c -o whereLexer.lo whereLexer.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT whereLexer.lo -MD -MP -MF .deps/whereLexer.Tpo -c whereLexer.cc -fPIC -DPIC -o .libs/whereLexer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT whereLexer.lo -MD -MP -MF .deps/whereLexer.Tpo -c whereLexer.cc -o whereLexer.o >/dev/null 2>&1 mv -f .deps/whereLexer.Tpo .deps/whereLexer.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT fromParser.lo -MD -MP -MF .deps/fromParser.Tpo -c -o fromParser.lo fromParser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT fromParser.lo -MD -MP -MF .deps/fromParser.Tpo -c fromParser.cc -fPIC -DPIC -o .libs/fromParser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT fromParser.lo -MD -MP -MF .deps/fromParser.Tpo -c fromParser.cc -o fromParser.o >/dev/null 2>&1 mv -f .deps/fromParser.Tpo .deps/fromParser.Plo make[2]: Target `all-am' not remade because of errors. make[2]: Leaving directory `/root/fastbit/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/fastbit/src' Making all in examples make[1]: Entering directory `/root/fastbit/examples' g++ -DHAVE_CONFIG_H -I. -I../src -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT ibis.o -MD -MP -MF .deps/ibis.Tpo -c -o ibis.o ibis.cpp mv -f .deps/ibis.Tpo .deps/ibis.Po cd ../src && make libfastbit.la make[2]: Entering directory `/root/fastbit/src' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT dictionary.lo -MD -MP -MF .deps/dictionary.Tpo -c -o dictionary.lo dictionary.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT dictionary.lo -MD -MP -MF .deps/dictionary.Tpo -c dictionary.cpp -fPIC -DPIC -o .libs/dictionary.o dictionary.cpp: In member function 'int ibis::dictionary::readKeys0(const char*, FILE*)': dictionary.cpp:426: error: 'class ibis::dictionary::MYMAP' has no member named 'reserve' dictionary.cpp: In member function 'int ibis::dictionary::readKeys1(const char*, FILE*)': dictionary.cpp:489: error: 'class ibis::dictionary::MYMAP' has no member named 'reserve' make[2]: *** [dictionary.lo] Error 1 make[2]: Target `libfastbit.la' not remade because of errors. make[2]: Leaving directory `/root/fastbit/src' make[1]: *** [../src/libfastbit.la] Error 2 gcc -DHAVE_CONFIG_H -I. -I../src -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT tcapi.o -MD -MP -MF .deps/tcapi.Tpo -c -o tcapi.o tcapi.c mv -f .deps/tcapi.Tpo .deps/tcapi.Po g++ -DHAVE_CONFIG_H -I. -I../src -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT thula.o -MD -MP -MF .deps/thula.Tpo -c -o thula.o thula.cpp mv -f .deps/thula.Tpo .deps/thula.Po g++ -DHAVE_CONFIG_H -I. -I../src -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT ardea.o -MD -MP -MF .deps/ardea.Tpo -c -o ardea.o ardea.cpp mv -f .deps/ardea.Tpo .deps/ardea.Po g++ -DHAVE_CONFIG_H -I. -I../src -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT rara.o -MD -MP -MF .deps/rara.Tpo -c -o rara.o rara.cpp mv -f .deps/rara.Tpo .deps/rara.Po gcc -DHAVE_CONFIG_H -I. -I../src -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT tiapi.o -MD -MP -MF .deps/tiapi.Tpo -c -o tiapi.o tiapi.c mv -f .deps/tiapi.Tpo .deps/tiapi.Po make[1]: Target `all' not remade because of errors. make[1]: Leaving directory `/root/fastbit/examples' Making all in java make[1]: Entering directory `/root/fastbit/java' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../src -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT FastBit.lo -MD -MP -MF .deps/FastBit.Tpo -c -o FastBit.lo FastBit.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../src -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT FastBit.lo -MD -MP -MF .deps/FastBit.Tpo -c FastBit.c -fPIC -DPIC -o .libs/FastBit.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../src -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT FastBit.lo -MD -MP -MF .deps/FastBit.Tpo -c FastBit.c -o FastBit.o >/dev/null 2>&1 mv -f .deps/FastBit.Tpo .deps/FastBit.Plo cd ../src && make libfastbit.la make[2]: Entering directory `/root/fastbit/src' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT dictionary.lo -MD -MP -MF .deps/dictionary.Tpo -c -o dictionary.lo dictionary.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -g -O2 -std=c++0x -I/usr/java/jdk1.8.0_11/include -I/usr/java/jdk1.8.0_11/include/linux -MT dictionary.lo -MD -MP -MF .deps/dictionary.Tpo -c dictionary.cpp -fPIC -DPIC -o .libs/dictionary.o dictionary.cpp: In member function 'int ibis::dictionary::readKeys0(const char*, FILE*)': dictionary.cpp:426: error: 'class ibis::dictionary::MYMAP' has no member named 'reserve' dictionary.cpp: In member function 'int ibis::dictionary::readKeys1(const char*, FILE*)': dictionary.cpp:489: error: 'class ibis::dictionary::MYMAP' has no member named 'reserve' make[2]: *** [dictionary.lo] Error 1 make[2]: Target `libfastbit.la' not remade because of errors. make[2]: Leaving directory `/root/fastbit/src' make[1]: *** [../src/libfastbit.la] Error 2 echo "fastbit.library.path=/root/fastbit/java/.libs:/root/fastbit/java/../src/.libs" >| build.properties make[1]: Target `all' not remade because of errors. make[1]: Leaving directory `/root/fastbit/java' Making all in tests make[1]: Entering directory `/root/fastbit/tests' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/root/fastbit/tests' make[1]: Entering directory `/root/fastbit' make[1]: Nothing to be done for `all-am'. make[1]: Leaving directory `/root/fastbit' make: *** [all-recursive] Error 1 make: Target `all' not remade because of errors.
[root@vm001 fastbit]# yum groupupdate "Development Tools" Loaded plugins: fastestmirror, security Loading mirror speeds from cached hostfile * base: mirror.switch.ch * extras: mirror.switch.ch * updates: mirror.switch.ch Setting up Group Process Checking for new repos for mirrors Package flex-2.5.35-8.el6.x86_64 already installed and latest version Package gcc-4.4.7-4.el6.x86_64 already installed and latest version Package redhat-rpm-config-9.0.3-42.el6.centos.noarch already installed and latest version Package rpm-build-4.8.0-37.el6.x86_64 already installed and latest version Package 1:make-3.81-20.el6.x86_64 already installed and latest version Package patch-2.6-6.el6.x86_64 already installed and latest version Package 1:pkgconfig-0.23-9.1.el6.x86_64 already installed and latest version Package gettext-0.17-16.el6.x86_64 already installed and latest version Package automake-1.11.1-4.el6.noarch already installed and latest version Package bison-2.4.1-5.el6.x86_64 already installed and latest version Package libtool-2.2.6-15.5.el6.x86_64 already installed and latest version Package autoconf-2.63-5.1.el6.noarch already installed and latest version Package gcc-c++-4.4.7-4.el6.x86_64 already installed and latest version Package binutils-2.20.51.0.2-5.36.el6.x86_64 already installed and latest version Package patchutils-0.3.1-3.1.el6.x86_64 already installed and latest version Package byacc-1.9.20070509-7.el6.x86_64 already installed and latest version Package indent-2.2.10-7.el6.x86_64 already installed and latest version Package systemtap-2.3-4.el6_5.x86_64 already installed and latest version Package diffstat-1.51-2.el6.x86_64 already installed and latest version Package elfutils-0.152-1.el6.x86_64 already installed and latest version Package cvs-1.11.23-16.el6.x86_64 already installed and latest version Package rcs-5.7-37.el6.x86_64 already installed and latest version Package subversion-1.6.11-10.el6_5.x86_64 already installed and latest version Package gcc-gfortran-4.4.7-4.el6.x86_64 already installed and latest version Package 1:doxygen-1.6.1-6.el6.x86_64 already installed and latest version Package intltool-0.41.0-1.1.el6.noarch already installed and latest version Package git-1.7.1-3.el6_4.1.x86_64 already installed and latest version Package ctags-5.8-2.el6.x86_64 already installed and latest version Package cscope-15.6-6.el6.x86_64 already installed and latest version Package swig-1.3.40-6.el6.x86_64 already installed and latest version Warning: Group development does not have any packages. No packages in any requested group available to install or update
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