[mira_talk] Re: Compiling MIRA -> error
- From: "Martin A. Hansen" <mail@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 14 Aug 2009 09:01:47 +0200
OK, here goes:
1) Linux node1 2.6.18-84.el5 #1 SMP Fri Feb 29 16:26:52 EST 2008 x86_64
x86_64 x86_64 GNU/Linux
2) flex 2.5.35
3) ~/maasha_install/bin/flex
4) ./configure --prefix=/home/maasha/maasha_install
--with-boost=/home/maasha/maasha_install
5)
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... x86_64-unknown-linux-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 for style of include used by make... GNU
checking dependency style of gcc... 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
+++++++++++++++++++++++++++++++++++++
systemuname: Linux
CFLAGS now:
CXXFLAGS now:
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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 int64_t... yes
+++++++++++++++++++++++++++++++++++++
CFLAGS now:
CXXFLAGS now: -DAJ_Linux64
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
checking whether long long has 64bit... yes
checking whether enabling 64bit compilation support... yes
checking for compiler optimisation settings... -O3 -funroll-loops
+++++++++++++++++++++++++++++++++++++
CFLAGS now: -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -O3 -funroll-loops
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
checking host system type... x86_64-unknown-linux-gnu
checking for a sed that does not truncate output... /bin/sed
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 for dlfcn.h... yes
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 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 -m elf_x86_64) 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 ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) 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 -m elf_x86_64) 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... none needed
checking whether yytext is a pointer... no
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 for isblank... yes
+++++++++++++++++++++++++++++++++++++
CFLAGS now: -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -O3 -funroll-loops
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++
CFLAGS now: -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -O3 -funroll-loops
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
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
+++++++++++++++++++++++++++++++++++++
CFLAGS now: -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -O3 -funroll-loops
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
checking for Expat XML Parser... no
+++++++++++++++++++++++++++++++++++++
CFLAGS now: -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -O3 -funroll-loops
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
checking for boostlib >= 1.35.0... yes
+++++++++++++++++++++++++++++++++++++
BOOST_CPPFLAGS: -I/home/maasha/maasha_install/include/boost-1_39
BOOST LDFLAGS: -L/home/maasha/maasha_install/lib
CFLAGS now: -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -O3 -funroll-loops
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++
BOOST_CPPFLAGS: -I/home/maasha/maasha_install/include/boost-1_39
BOOST LDFLAGS: -L/home/maasha/maasha_install/lib
CFLAGS now: -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -O3 -funroll-loops
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread-gcc41-mt-1_39... yes
+++++++++++++++++++++++++++++++++++++
BOOST_CPPFLAGS: -pthread
-I/home/maasha/maasha_install/include/boost-1_39
BOOST LDFLAGS: -L/home/maasha/maasha_install/lib
ac_boost_path: /home/maasha/maasha_install
ac_boost_lib_path:
BOOST_THREAD_LIB: -lboost_thread-gcc41-mt-1_39
CFLAGS now: -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -O3 -funroll-loops
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++
BOOST_CPPFLAGS: -pthread
-I/home/maasha/maasha_install/include/boost-1_39
BOOST LDFLAGS: -L/home/maasha/maasha_install/lib
ac_boost_path: /home/maasha/maasha_install
ac_boost_lib_path:
BOOST_THREAD_LIB: -lboost_thread-gcc41-mt-1_39
CFLAGS now: -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -O3 -funroll-loops -pthread
-I/home/maasha/maasha_install/include/boost-1_39
LDFLAGS now: -L/home/maasha/maasha_install/lib -lboost_thread-gcc41-mt-1_39
+++++++++++++++++++++++++++++++++++++
checking for flex version compatible with MIRA... yes
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 .................................
3rc2_dev_linux-gnu_x86_64_dynamic
Production or development version?................ development
We are building on ............................... Linux
CPU supports 64 bit? ......... ................... yes
Compiler ......................................... gcc
Compiler optimisation flags used ................. -O3 -funroll-loops
Do we compile in 64 bit? ......................... yes
Building completely static? ...................... no
BOOST expected to compile and link?............... yes
Can MIRA be built on this system? ................ yes
Using CFLAGS : -O3 -funroll-loops
Using CXXFLAGS : -DPUBLICQUIET -DAJ_Linux64 -O3 -funroll-loops -pthread
-I/home/maasha/maasha_install/include/boost-1_39
Using LDFLAGS : -L/home/maasha/maasha_install/lib
-lboost_thread-gcc41-mt-1_39
Looks good, we do not expect compilation problems.
--------------------------------------------------------------------------------
Type 'make' to make the binaries
and then 'make install' to install them.
6) attached.
7) bonus-info - the make error:
make
Making all in src
make[1]: Entering directory `/home/maasha/sletmig/mira-3rc2/src'
Making all in lec
make[2]: Entering directory `/home/maasha/sletmig/mira-3rc2/src/lec'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/maasha/sletmig/mira-3rc2/src/lec'
Making all in io
make[2]: Entering directory `/home/maasha/sletmig/mira-3rc2/src/io'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"3rc2\" -DPACKAGE_STRING=\"mira\ 3rc2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3rc2\"
-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/\"
-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_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DDEVELOPMENTVERSION=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -DENABLE64=1 -I.
-I../ -DPUBLICQUIET -DAJ_Linux64 -O3 -funroll-loops -pthread
-I/home/maasha/maasha_install/include/boost-1_39 -MT gbf.o -MD -MP -MF
.deps/gbf.Tpo -c -o gbf.o gbf.C
In file included from ../io/gbf.H:38,
from gbf.C:28:
../io/exp.H:49:23: error: FlexLexer.h: No such file or directory
../io/exp.H:163: error: ‘FlexLexer’ has not been declared
../io/exp.H:164: error: ‘FlexLexer’ has not been declared
make[2]: *** [gbf.o] Error 1
make[2]: Leaving directory `/home/maasha/sletmig/mira-3rc2/src/io'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/maasha/sletmig/mira-3rc2/src'
make: *** [all-recursive] Error 1
I ran
find . -name "*.flex.C" -exec rm -f {} \;
before make.
Cheers,
Martin
On Fri, Aug 14, 2009 at 8:30 AM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Donnerstag 13 August 2009 Martin A. Hansen wrote:
> > On the server, another type of flex related err:
> > :o(
>
> Did you do a "find . -name "*flex.C" before compiling? If not, please do
> that
> and try again.
>
> If yes and it still does not work, can you please send me the following:
>
> Output of
> 1) uname -a
> 2) flex --version
> 3) which flex
>
> Additionally, when you ran configure
> 4) with which options
> 5) the ouput of the configure script
> 6) the config.log file
>
> B.
>
>
> --
> You have received this mail because you are subscribed to the mira_talk
> mailing list. For information on how to subscribe or unsubscribe, please
> visit http://www.chevreux.org/mira_mailinglists.html
>
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