[mira_talk] Re: Problem with installation, even with GCC version 4.8.1, its asking for updated version of GCC

  • From: Hukum rawal <hukam.rawal@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 12 Aug 2016 12:33:28 +0530

Thanks. Its really amazed me that how you sort it out that my system having
2 versions of BOOST. Now I have only 1.61.0 version. but having almost
similar kind of error:

...
.
..
Making all in memorc
make[4]: Entering directory `/root/mira-4.0.2/src/memorc'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src
 -I/root/libunwind/include  -DPUBLICQUIET -DAJ_Linux64 -I/root/flex/include
 -I/root/mira/include -O3 -funroll-loops -pthread -I/root/boost/include
-I/root/expat/include -Werror=uninitialized -Werror=return-type
-Werror=parentheses -std=c++0x -Werror=unused-value -MT memorc.o -MD -MP
-MF .deps/memorc.Tpo -c -o memorc.o memorc.C
mv -f .deps/memorc.Tpo .deps/memorc.Po
rm -f libmemorc.a
ar cru libmemorc.a memorc.o
ranlib libmemorc.a
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src
 -I/root/libunwind/include  -DPUBLICQUIET -DAJ_Linux64 -I/root/flex/include
 -I/root/mira/include -O3 -funroll-loops -pthread -I/root/boost/include
-I/root/expat/include -Werror=uninitialized -Werror=return-type
-Werror=parentheses -std=c++0x -Werror=unused-value -MT main.o -MD -MP -MF
.deps/main.Tpo -c -o main.o main.C
mv -f .deps/main.Tpo .deps/main.Po
/bin/sh ../../libtool --tag=CXX   --mode=link g++  -DPUBLICQUIET
-DAJ_Linux64 -I/root/flex/include  -I/root/mira/include -O3 -funroll-loops
-pthread -I/root/boost/include -I/root/expat/include -Werror=uninitialized
-Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value
 -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/
-L/root/boost/lib -all-static -L/root/libunwind/lib -L/root/mira/lib
-L/root/boost/lib -L/root/expat/lib -o main main.o  -lmiraerrorhandling
-lboost_thread -lboost_regex -lboost_system -lboost_filesystem
-lboost_iostreams -lrt -lexpat -lm -lz -lbz2
/root/google-perftools/lib//libtcmalloc_minimal.a
libtool: link: g++ -DPUBLICQUIET -DAJ_Linux64 -I/root/flex/include
-I/root/mira/include -O3 -funroll-loops -pthread -I/root/boost/include
-I/root/expat/include -Werror=uninitialized -Werror=return-type
-Werror=parentheses -std=c++0x -Werror=unused-value -static -o main main.o
 -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/
-L/root/boost/lib -L/root/libunwind/lib -L/root/mira/lib -L/root/expat/lib
-lmiraerrorhandling -lboost_thread -lboost_regex -lboost_system
-lboost_filesystem -lboost_iostreams -lrt /root/expat/lib/libexpat.a -lm
-lz -lbz2 /root/google-perftools/lib//libtcmalloc_minimal.a -pthread
make[4]: Leaving directory `/root/mira-4.0.2/src/memorc'
Making all in modules
make[4]: Entering directory `/root/mira-4.0.2/src/modules'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src
 -I/root/libunwind/include  -DPUBLICQUIET -DAJ_Linux64 -I/root/flex/include
 -I/root/mira/include -O3 -funroll-loops -pthread -I/root/boost/include
-I/root/expat/include -Werror=uninitialized -Werror=return-type
-Werror=parentheses -std=c++0x -Werror=unused-value -MT mod_bait.o -MD -MP
-MF .deps/mod_bait.Tpo -c -o mod_bait.o mod_bait.C
mv -f .deps/mod_bait.Tpo .deps/mod_bait.Po
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src
 -I/root/libunwind/include  -DPUBLICQUIET -DAJ_Linux64 -I/root/flex/include
 -I/root/mira/include -O3 -funroll-loops -pthread -I/root/boost/include
-I/root/expat/include -Werror=uninitialized -Werror=return-type
-Werror=parentheses -std=c++0x -Werror=unused-value -MT mod_dbgreplay.o -MD
-MP -MF .deps/mod_dbgreplay.Tpo -c -o mod_dbgreplay.o mod_dbgreplay.C
mv -f .deps/mod_dbgreplay.Tpo .deps/mod_dbgreplay.Po
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src
 -I/root/libunwind/include  -DPUBLICQUIET -DAJ_Linux64 -I/root/flex/include
 -I/root/mira/include -O3 -funroll-loops -pthread -I/root/boost/include
-I/root/expat/include -Werror=uninitialized -Werror=return-type
-Werror=parentheses -std=c++0x -Werror=unused-value -MT mod_mira.o -MD -MP
-MF .deps/mod_mira.Tpo -c -o mod_mira.o mod_mira.C
mv -f .deps/mod_mira.Tpo .deps/mod_mira.Po
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src
 -I/root/libunwind/include  -DPUBLICQUIET -DAJ_Linux64 -I/root/flex/include
 -I/root/mira/include -O3 -funroll-loops -pthread -I/root/boost/include
-I/root/expat/include -Werror=uninitialized -Werror=return-type
-Werror=parentheses -std=c++0x -Werror=unused-value -MT mod_convert.o -MD
-MP -MF .deps/mod_convert.Tpo -c -o mod_convert.o mod_convert.C
mod_convert.C: In static member function ‘static void
ConvPro::saveContigList_helper(std::list<Contig>&, ReadPool&)’:
mod_convert.C:708:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:712:11: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".html");
           ^
mod_convert.C:722:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:726:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".txt");
          ^
mod_convert.C:733:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:737:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".txt");
          ^
mod_convert.C:747:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:751:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".txt");
          ^
mod_convert.C:762:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:766:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:770:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:774:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:778:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".txt");
          ^
mod_convert.C:781:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".txt");
          ^
mod_convert.C:784:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".txt");
          ^
mod_convert.C:787:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".txt");
          ^
mod_convert.C:804:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:809:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".txt");
          ^
mod_convert.C:820:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:824:6: warning: deprecated conversion from string constant to
‘char*’ [-Wwrite-strings]
    "");
      ^
mod_convert.C:843:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:847:6: warning: deprecated conversion from string constant to
‘char*’ [-Wwrite-strings]
    "");
      ^
mod_convert.C:874:22: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
        &clist.front());
                      ^
mod_convert.C:879:15: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
        nullptr);
               ^
mod_convert.C:915:22: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
        &clist.front());
                      ^
mod_convert.C:920:15: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
        nullptr);
               ^
mod_convert.C:938:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:942:11: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".html");
           ^
mod_convert.C:952:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:956:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".txt");
          ^
mod_convert.C:966:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:970:6: warning: deprecated conversion from string constant to
‘char*’ [-Wwrite-strings]
    "");
      ^
mod_convert.C:980:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:984:6: warning: deprecated conversion from string constant to
‘char*’ [-Wwrite-strings]
    "");
      ^
mod_convert.C:1001:20: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
      &clist.front());
                    ^
mod_convert.C:1009:8: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
      "");
        ^
mod_convert.C:1023:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:1027:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".ace");
          ^
mod_convert.C:1037:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:1041:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".tcs");
          ^
mod_convert.C:1051:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:1055:10: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    ".wig");
          ^
mod_convert.C:1065:18: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    &clist.front());
                  ^
mod_convert.C:1069:20: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
    "_gccontent.wig");
                    ^
mod_convert.C: In static member function ‘static uint32
ConvPro::openOFSlist(Contig*, std::list<std::basic_ofstream<char>*>&)’:
mod_convert.C:1318:108: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

 
openOFStream(*ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".fasta",optcontig),ios::out);

                                ^
mod_convert.C:1321:113: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

 
openOFStream(*ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".fasta.qual",optcontig),ios::out);

                                     ^
mod_convert.C:1324:108: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

 
openOFStream(*ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".fasta",optcontig),ios::out);

                                ^
mod_convert.C:1327:113: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

 
openOFStream(*ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".fasta.qual",optcontig),ios::out);

                                     ^
mod_convert.C:1330:108: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

 
openOFStream(*ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".fastq",optcontig),ios::out);

                                ^
mod_convert.C:1333:106: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

 
openOFStream(*ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".caf",optcontig),ios::out);

                              ^
mod_convert.C:1336:106: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

 
openOFStream(*ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".maf",optcontig),ios::out);

                              ^
mod_convert.C:1340:106: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

 
openOFStream(*ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".sam",optcontig),ios::out);

                              ^
mod_convert.C:1344:98: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

 
CP_gffsave.open(createFileNameFromBasePostfixContigAndRead(CP_outbasename,".gff3",optcontig));

                      ^
mod_convert.C: In member function ‘int ConvPro::mainConvPro(int, char**)’:
mod_convert.C:1733:96: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

openOFStream(*CP_ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".fasta"),ios::out);

                    ^
mod_convert.C:1738:101: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

openOFStream(*CP_ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".fasta.qual"),ios::out);

                         ^
mod_convert.C:1742:96: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

openOFStream(*CP_ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".fasta"),ios::out);

                    ^
mod_convert.C:1747:101: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

openOFStream(*CP_ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".fasta.qual"),ios::out);

                         ^
mod_convert.C:1751:96: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

openOFStream(*CP_ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".fastq"),ios::out);

                    ^
mod_convert.C:1755:94: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

openOFStream(*CP_ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".caf"),ios::out);

                  ^
mod_convert.C:1759:94: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

openOFStream(*CP_ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".maf"),ios::out);

                  ^
mod_convert.C:1764:94: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

openOFStream(*CP_ofs.back(),createFileNameFromBasePostfixContigAndRead(CP_outbasename,".sam"),ios::out);

                  ^
mod_convert.C:1768:78: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]

CP_gffsave.open(createFileNameFromBasePostfixContigAndRead(CP_outbasename,"").c_str());

  ^
mv -f .deps/mod_convert.Tpo .deps/mod_convert.Po
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src
 -I/root/libunwind/include  -DPUBLICQUIET -DAJ_Linux64 -I/root/flex/include
 -I/root/mira/include -O3 -funroll-loops -pthread -I/root/boost/include
-I/root/expat/include -Werror=uninitialized -Werror=return-type
-Werror=parentheses -std=c++0x -Werror=unused-value -MT mod_memestim.o -MD
-MP -MF .deps/mod_memestim.Tpo -c -o mod_memestim.o mod_memestim.C
mv -f .deps/mod_memestim.Tpo .deps/mod_memestim.Po
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src
 -I/root/libunwind/include  -DPUBLICQUIET -DAJ_Linux64 -I/root/flex/include
 -I/root/mira/include -O3 -funroll-loops -pthread -I/root/boost/include
-I/root/expat/include -Werror=uninitialized -Werror=return-type
-Werror=parentheses -std=c++0x -Werror=unused-value -MT mod_tagsnp.o -MD
-MP -MF .deps/mod_tagsnp.Tpo -c -o mod_tagsnp.o mod_tagsnp.C
mv -f .deps/mod_tagsnp.Tpo .deps/mod_tagsnp.Po
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src
 -I/root/libunwind/include  -DPUBLICQUIET -DAJ_Linux64 -I/root/flex/include
 -I/root/mira/include -O3 -funroll-loops -pthread -I/root/boost/include
-I/root/expat/include -Werror=uninitialized -Werror=return-type
-Werror=parentheses -std=c++0x -Werror=unused-value -MT misc.o -MD -MP -MF
.deps/misc.Tpo -c -o misc.o misc.C
mv -f .deps/misc.Tpo .deps/misc.Po
rm -f libmiramodules.a
ar cru libmiramodules.a mod_bait.o mod_dbgreplay.o mod_mira.o mod_convert.o
mod_memestim.o mod_tagsnp.o misc.o
ranlib libmiramodules.a
make[4]: Leaving directory `/root/mira-4.0.2/src/modules'
Making all in progs
make[4]: Entering directory `/root/mira-4.0.2/src/progs'
Making .H out of .xxd compileinfo.itxt
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src
 -I/root/libunwind/include -pthread -I/root/boost/include -DPUBLICQUIET
-DAJ_Linux64 -I/root/flex/include  -I/root/mira/include -O3 -funroll-loops
-pthread -I/root/boost/include -I/root/expat/include -Werror=uninitialized
-Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -MT
mira.o -MD -MP -MF .deps/mira.Tpo -c -o mira.o mira.C
mv -f .deps/mira.Tpo .deps/mira.Po
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src
 -I/root/libunwind/include -pthread -I/root/boost/include -DPUBLICQUIET
-DAJ_Linux64 -I/root/flex/include  -I/root/mira/include -O3 -funroll-loops
-pthread -I/root/boost/include -I/root/expat/include -Werror=uninitialized
-Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -MT
quirks.o -MD -MP -MF .deps/quirks.Tpo -c -o quirks.o quirks.C
quirks.C: In function ‘void fixLocaleQuirk()’:
quirks.C:56:5: error: ‘cout’ is not a member of ‘std’
     std::cout << "Your system seems to be older or have some quirks with
locale settings."
     ^
make[4]: *** [quirks.o] Error 1
make[4]: Leaving directory `/root/mira-4.0.2/src/progs'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/root/mira-4.0.2/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/root/mira-4.0.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/root/mira-4.0.2'
make: *** [all] Error 2


On Thu, Aug 11, 2016 at 6:45 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:

On 11 Aug 2016, at 8:39 , Hukum rawal <hukam.rawal@xxxxxxxxx> wrote:
What is the possibility of this error in make install command?
[root@hpc12 mira-3.4.1.1]# make && make install
[…]
/usr/bin/ld: warning: libboost_system.so.1.61.0, needed by
/root/boost/lib/libboost_thread.so, may conflict with
libboost_system.so.1.48.0

Two things:
1. compilation and linking are mixing up two Boost versions present on
your system (61 and the older 48). Sooner or later this will got wrong (and
it does)
2. The above mentioned mixing up is due to you trying to compile a very
old version of MIRA (3.4.x). Don’t! Beside the compilation problems (which
I know took me quite a while to get ironed out), the 4.x series is so far
ahead of 3.x in terms of assembly quality that trying to use older versions
is simply a waste of time nowadays.

B.
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-- 
Hukam C. Rawal

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