Make error

[lufuhao]

Hi, I got make error when compiling the git version today. Please HELP. cmd:

git clone https://github.com/gmarcais/Jellyfish.git autoreconf -i ./configure --prefix=/path/to/jellyfish/v2.1.4/x86_64 make

CONFIGURE

checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu 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... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking for style of include used by make... GNU 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 whether gcc understands -c and -o together... yes 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... 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 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 -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 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 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 for md5sum... md5sum checking for yaggo... /usr/users/celldev/luf/local/yaggo/v1.5.4/x86_64/bin/yaggo checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for __int128... yes checking for std::numeric_limits<__int128>... no checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for siginfo_t.si_int... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating tests/compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands

config.status: executing libtool commands

Make error:

YAGGO sub_commands/count_main_cmdline.hpp YAGGO sub_commands/info_main_cmdline.hpp YAGGO sub_commands/dump_main_cmdline.hpp YAGGO sub_commands/histo_main_cmdline.hpp YAGGO sub_commands/stats_main_cmdline.hpp YAGGO sub_commands/merge_main_cmdline.hpp YAGGO sub_commands/bc_main_cmdline.hpp YAGGO sub_commands/query_main_cmdline.hpp YAGGO sub_commands/cite_main_cmdline.hpp YAGGO sub_commands/mem_main_cmdline.hpp YAGGO jellyfish/generate_sequence_cmdline.hpp YAGGO unit_tests/test_main_cmdline.hpp make all-am make[1]: Entering directory `/usr/users/celldev/luf/local/jellyfish/v2.1.4/Jellyfish'

CXX lib/rectangular_binary_matrix.lo

CXX lib/mer_dna.lo

CXX lib/storage.lo

CXX lib/allocators_mmap.lo

CXX lib/misc.lo

CXX lib/int128.lo

CXX lib/thread_exec.lo

CXX lib/jsoncpp.lo

CXX lib/time.lo

CXX lib/generator_manager.lo

CXX sub_commands/jellyfish.o

CXX sub_commands/count_main.o

sub_commands/jellyfish.cc: In function ‘int version(int, char**)’:

sub_commands/jellyfish.cc:130:16: error: ‘PACKAGE_STRING’ was not declared in this scope std::cout << PACKAGE_STRING << std::endl; ^

make[1]: *\ [sub_commands/jellyfish.o] Error 1

make[1]: *\ Waiting for unfinished jobs....

make[1]: Leaving directory `/usr/users/celldev/luf/local/jellyfish/v2.1.4/Jellyfish'

make: *\ [all] Error 2

[lufuhao]

Plus: ubuntu 14.04 x86_64 gcc 4.9.2 g++ 4.9.2

[gmarcais]

I don't understand how PACKAGE_STRING can be undefined. Configure is setting this in config.h. Can you apply this patch?

https://gist.github.com/440d5491de5c4cfb7d03.git

Let me know if this works for you.