[mira_talk] Re: error in compilation mira-2.9.46

Bastien Chevreux a écrit :
it returns the same error: exp_flexer.flex.C:324: error: no 'int EXPFlexLexer::yywrap()' memberfunction declared in class 'EXPFlexLexer' 
i have flex 2.5.33.


Hmmm, I'm at the ISMB right now and have only limited possibilities to help. A 
quick Google-search pointed at the possibility that several parallel 
installations of Flex might fool automatic configuration checks.

What you can try: search your filesystem for all occurrences of FlexLexer.h 
and, in case there are several of them, remove/rename those which are from 
older installations.

Hope this helps.

Bastien



i have only one file: /usr/local/include/FlexLexer.h
see the attached logs files.




checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
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 dependency style of gcc... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 98304
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking how to run the C preprocessor... gcc -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 dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for a sed that does not truncate output... (cached) /bin/sed
checking for flex... flex
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for ANSI C header files... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for C/C++ restrict keyword... __restrict
checking whether struct tm is in sys/time.h or time.h... time.h
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking whether lstat dereferences a symlink specified with a trailing 
slash... yes
checking whether stat accepts an empty string... no
checking for strftime... yes
checking for floor... no
checking for memset... yes
checking for pow... no
checking for sqrt... no
checking whether the compiler implements namespaces... yes
checking whether the compiler supports ISO C++ standard library... yes
checking whether the compiler supports Standard Template Library... yes
checking for Expat XML Parser headers in /usr/include... found
checking for Expat XML Parser libraries... found
checking for Expat XML Parser... yes
checking for int64_t... yes
checking whether long long has 64bit... no
checking whether enabling 64bit compilation support... no
checking for boostlib >= 1.35.0... yes
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread-gcc-mt-1_33_1... no
checking for exit in -lboost_thread-gcc-mt-d-1_33_1... no
checking for exit in -lboost_thread-gcc42-mt-1_35... yes
checking for flex version compatible with MIRA... yes
checking for compiler optimisation settings... -O2 -funroll-loops
checking for purify... no
checking whether mira should compile in public quiet mode... yes
checking whether mira should compile a development version... yes
checking whether mira should compile with bound tracking... yes
checking whether mira should compile with bug tracking... yes
checking whether mira should compile with extended bug tracking... no
checking whether mira should compile with function trace... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/stdinc/Makefile
config.status: creating src/lec/Makefile
config.status: creating src/errorhandling/Makefile
config.status: creating src/util/Makefile
config.status: creating src/io/Makefile
config.status: creating src/mira/Makefile
config.status: creating src/EdIt/Makefile
config.status: creating src/caf/Makefile
config.status: creating src/examine/Makefile
config.status: creating src/knn_abi373/Makefile
config.status: creating src/knn_alf/Makefile
config.status: creating src/support/Makefile
config.status: creating src/scripts/Makefile
config.status: creating src/test/Makefile
config.status: creating src/test/io/Makefile
config.status: creating src/test/io/scf/Makefile
config.status: creating src/test/io/fasta/Makefile
config.status: creating src/test/io/generalio/Makefile
config.status: creating src/test/mira/Makefile
config.status: creating src/test/mira/align/Makefile
config.status: creating src/test/mira/read/Makefile
config.status: creating src/test/mira/readpool/Makefile
config.status: creating src/examples_programming/Makefile
config.status: creating src/progs/Makefile
config.status: creating doc/Makefile
config.status: creating distribution/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands

--------------------------------------------------------------------------------
                       Summary of MIRA configuration
--------------------------------------------------------------------------------

Building version ................................. 
2.9.46x2_dev_linux-gnu_i686_32_dynamic
Production or development version?................ development

We are building on ............................... Linux
CPU supports 64 bit? ......... ................... no
Compiler ......................................... gcc
Compiler optimisation flags used ................. -O2 -funroll-loops
Building completely static? ...................... no
BOOST expected to compile and link?............... yes

Can MIRA be built on this system? ................ yes

Looks good, we do not expect compilation problems.
--------------------------------------------------------------------------------

Type 'make' to make the binaries
and then 'make install' to install them.

Making all in src
make[1]: Entering directory `/home/lolo/mira-2.9.46x2/src'
Making all in lec
make[2]: Entering directory `/home/lolo/mira-2.9.46x2/src/lec'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/lolo/mira-2.9.46x2/src/lec'
Making all in io
make[2]: Entering directory `/home/lolo/mira-2.9.46x2/src/io'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" 
-DPACKAGE_VERSION=\"2.9.46x2\" -DPACKAGE_STRING=\"mira\ 2.9.46x2\" 
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"mira\" -DVERSION=\"2.9.46x2\" 
-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 -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_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ 
-DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=1 
-DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../    -DPUBLICQUIET   -O2 
-funroll-loops -MT exp_flexer.flex.o -MD -MP -MF .deps/exp_flexer.flex.Tpo -c 
-o exp_flexer.flex.o exp_flexer.flex.C
exp_flexer.flex.C:324: error: no 'int EXPFlexLexer::yywrap()' member function 
declared in class 'EXPFlexLexer'
make[2]: *** [exp_flexer.flex.o] Error 1
make[2]: Leaving directory `/home/lolo/mira-2.9.46x2/src/io'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/lolo/mira-2.9.46x2/src'
make: *** [all-recursive] Error 1

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