Question: how to resolve , configure: error: Stopping here as BOOST thread lib must be available at this stage. Sorry.
0
gravatar for iamtuttu5
22 months ago by
iamtuttu540
United States
iamtuttu540 wrote:

Dear all

 

I was trying to install mira 4 in my ubuntu server but it result the following errorr while i run ./configure command

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 whether to add --prefix as include path... no

+++++++++++++++++++++++++++++++++++++
systemuname: Linux
CFLAGS now:
CXXFLAGS now:
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
checking for gcc... gcc
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 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 has 64bit... yes
checking whether enabling 64bit compilation support... yes
checking build system type... x86_64-unknown-linux-gnu
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 how to print strings... printf
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... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
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 dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
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 -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 how to run the C++ preprocessor... g++ -E
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... (cached) 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... yes
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for flex++... yes
checking for xxd... 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 correctly handles 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 special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for isblank... yes

+++++++++++++++++++++++++++++++++++++
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
checking for boostlib >= 1.46.0... configure: We could not detect the boost libraries (version 1.46 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option.  If you are sure you have boost installed, then check your version number looking in <boost version.hpp="">. See http://randspringer.de/boost for more documentation.

+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -I/include/boost-0
 BOOST LDFLAGS:     -L/lib64
 ac_boost_path:     /opt/local
 ac_boost_lib_path:
CFLAGS now:   -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64   -O3 -funroll-loops
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
Setting rescue value for ac_boost_lib_path: /opt/local/lib

+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -I/include/boost-0
 BOOST LDFLAGS:     -L/lib64
CFLAGS now:   -O3 -funroll-loops -Wl,-rpath,/opt/local/lib
CXXFLAGS now: -DAJ_Linux64   -O3 -funroll-loops
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
checking whether the Boost::Thread library is available... no

+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -I/include/boost-0
 BOOST LDFLAGS:     -L/lib64
 ac_boost_path:     /opt/local
 ac_boost_lib_path: /opt/local/lib
 BOOST_THREAD_LIB:
CFLAGS now:   -O3 -funroll-loops -Wl,-rpath,/opt/local/lib
CXXFLAGS now: -DAJ_Linux64   -O3 -funroll-loops
LDFLAGS now:
+++++++++++++++++++++++++++++++++++++
Automatic recognition of Boost thread lib failed? I have
////// BOOST_CPPFLAGS:    -I/include/boost-0
////// BOOST LDFLAGS:     -L/lib64
////// ac_boost_path:     /opt/local
////// ac_boost_lib_path: /opt/local/lib
////// BOOST_THREAD_LIB:
////// BOOST_ROOT:
Please give the configure script the location of your BOOST
 libraries. Or, if needed, the name of your thread library (without
 'lib' in front):
   --with-boost=DIR
or --with-boost-libdir=LIB_DIR
or --with-boost-thread=special-lib

configure: error: Stopping here as BOOST thread lib must be available at this stage. Sorry.

 

 

any help will be appreciated 

Thank you

rna-seq ngs assembly • 1.6k views
ADD COMMENTlink modified 22 months ago by novice710 • written 22 months ago by iamtuttu540
1
gravatar for JC
22 months ago by
JC6.3k
Mexico
JC6.3k wrote:

Boost Libs are missing, solution ->  http://stackoverflow.com/questions/12578499/how-to-install-boost-on-ubuntu

ADD COMMENTlink written 22 months ago by JC6.3k
1
gravatar for novice
22 months ago by
novice710
United States
novice710 wrote:

Spare yourself the headache (especially if you don't have root access) and just use the compiled binaries of Mira instead.

ADD COMMENTlink written 22 months ago by novice710

Dear novice

so how to install the compiled binaries of mira ?

ADD REPLYlink written 22 months ago by iamtuttu540

Say you downloaded mira_linux.tar.bz2:

  1. Extract the compressed file
    $ tar xvf mira_linux.tar.bz2
    Now you can run Mira with 
    $ ./mira_linux/bin/mira
    But you could also continue to step 2 & 3.
     
  2. Add the binaries to your PATH
    $ cd mira_linux/bin/
    $ export PATH=$PATH:$PWD

    Now you can run Mira from any directory
    $ mira -h
    Next time you connect, however, Mira won't be in your PATH. To make it add automatically at each new session:
     
  3. While inside /mira_linux/bin/
    $ echo "export PATH=\$PATH:$PWD" >> ~/.bash_profile
    Make sure to use >> NOT >.
     
ADD REPLYlink modified 22 months ago • written 22 months ago by novice710

Thank you so much novice

ADD REPLYlink written 16 months ago by iamtuttu540
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