gmarcais / Jellyfish

A fast multi-threaded k-mer counter
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trouble building the git tree #40

Closed douglasgscofield closed 9 years ago

douglasgscofield commented 9 years ago

Hi, having trouble getting the git tree built and it doesn't seem to be something with the compiler (gcc 4.4.7, 4.8.3 both fail), perhaps something with yaggo? Or perhaps I am confused.

Short version:

milou2: /sw/apps/bioinfo/jellyfish/src $ git clone https://github.com/gmarcais/Jellyfish.git
milou2: /sw/apps/bioinfo/jellyfish/src/Jellyfish $ mkdir build
milou2: /sw/apps/bioinfo/jellyfish/src/Jellyfish $ cd build
milou2: /sw/apps/bioinfo/jellyfish/src/Jellyfish/build $ yaggo -v
yaggo 1.5.6
milou2: /sw/apps/bioinfo/jellyfish/src/Jellyfish/build $ ../configure
milou2: /sw/apps/bioinfo/jellyfish/src/Jellyfish/build $ make -j 4
  YAGGO    sub_commands/count_main_cmdline.hpp
...
  CXX    sub_commands/info_main.o
In file included from ../sub_commands/count_main.cc:44:
./sub_commands/count_main_cmdline.hpp: In constructor ‘count_main_cmdline::count_main_cmdline()’:
./sub_commands/count_main_cmdline.hpp:353: error: expected primary-expression before ‘)’ token
./sub_commands/count_main_cmdline.hpp:354: error: expected primary-expression before ‘)’ token
...

Gcc 4.8.3 gives a more verbose error:

In file included from sub_commands/count_main.cc:44:0:
./sub_commands/count_main_cmdline.hpp: In constructor ‘count_main_cmdline::count_main_cmdline()’:
./sub_commands/count_main_cmdline.hpp:353:26: error: expected primary-expression before ‘)’ token
     mer_len_arg((uint32_t)), mer_len_given(false),
                          ^
./sub_commands/count_main_cmdline.hpp:354:23: error: expected primary-expression before ‘)’ token
     size_arg((uint64_t)), size_given(false),
                       ^
...

Same happens when I clone develop using git clone -b develop https://github.com/gmarcais/Jellyfish.git.

The long version for master, with gcc 4.4.7:

milou2: /sw/apps/bioinfo/jellyfish/src $ git clone https://github.com/gmarcais/Jellyfish.git
Initialized empty Git repository in /pica/sw/apps/bioinfo/jellyfish/src/Jellyfish/.git/
remote: Counting objects: 4662, done.
remote: Total 4662 (delta 0), reused 0 (delta 0), pack-reused 4662
Receiving objects: 100% (4662/4662), 3.26 MiB | 1.60 MiB/s, done.
Resolving deltas: 100% (3365/3365), done.
milou2: /sw/apps/bioinfo/jellyfish/src $ cd Jellyfish/
milou2: /sw/apps/bioinfo/jellyfish/src/Jellyfish $ autoreconf -i
libtoolize: putting auxiliary files in `.'.
libtoolize: copying file `./ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'.
libtoolize: copying file `m4/libtool.m4'
libtoolize: copying file `m4/ltoptions.m4'
libtoolize: copying file `m4/ltsugar.m4'
libtoolize: copying file `m4/ltversion.m4'
libtoolize: copying file `m4/lt~obsolete.m4'
configure.ac:2: installing `./config.guess'
configure.ac:2: installing `./config.sub'
configure.ac:4: installing `./install-sh'
configure.ac:4: installing `./missing'
swig/Makefile.am: installing `./depcomp'
milou2: /sw/apps/bioinfo/jellyfish/src/Jellyfish $ mkdir build
milou2: /sw/apps/bioinfo/jellyfish/src/Jellyfish $ cd build
milou2: /sw/apps/bioinfo/jellyfish/src/Jellyfish/build $ yaggo -v
yaggo 1.5.6
milou2: /sw/apps/bioinfo/jellyfish/src/Jellyfish/build $ ../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... gawk
checking whether make sets $(MAKE)... yes
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... 3458764513820540925
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 -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 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 -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 for md5sum... md5sum
checking for yaggo... /sw/apps/bioinfo/jellyfish/src/yaggo/yaggo
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for __int128... no
checking for std::numeric_limits<__int128>... no
checking for _NSGetExecutablePath... no
checking execinfo.h usability... yes
checking execinfo.h presence... yes
checking for execinfo.h... yes
checking ext/stdio_filebuf.h usability... yes
checking ext/stdio_filebuf.h presence... yes
checking for ext/stdio_filebuf.h... yes
checking for siginfo_t.si_int... yes
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
milou2: /sw/apps/bioinfo/jellyfish/src/Jellyfish/build $ make -j 4
  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    jellyfish/generate_sequence_cmdline.hpp
  YAGGO    sub_commands/mem_main_cmdline.hpp
  YAGGO    unit_tests/test_main_cmdline.hpp
make  all-recursive
make[1]: Entering directory `/pica/sw/apps/bioinfo/jellyfish/src/Jellyfish/build'
Making all in .
make[2]: Entering directory `/pica/sw/apps/bioinfo/jellyfish/src/Jellyfish/build'
  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
  CXX    sub_commands/info_main.o
In file included from ../sub_commands/count_main.cc:44:
./sub_commands/count_main_cmdline.hpp: In constructor ‘count_main_cmdline::count_main_cmdline()’:
./sub_commands/count_main_cmdline.hpp:353: error: expected primary-expression before ‘)’ token
./sub_commands/count_main_cmdline.hpp:354: error: expected primary-expression before ‘)’ token
./sub_commands/count_main_cmdline.hpp:365: error: expected primary-expression before ‘)’ token
./sub_commands/count_main_cmdline.hpp:374: error: expected primary-expression before ‘)’ token
./sub_commands/count_main_cmdline.hpp:375: error: expected primary-expression before ‘)’ token
./sub_commands/count_main_cmdline.hpp: In constructor ‘count_main_cmdline::count_main_cmdline(int, char**)’:
./sub_commands/count_main_cmdline.hpp:382: error: expected primary-expression before ‘)’ token
./sub_commands/count_main_cmdline.hpp:383: error: expected primary-expression before ‘)’ token
./sub_commands/count_main_cmdline.hpp:394: error: expected primary-expression before ‘)’ token
./sub_commands/count_main_cmdline.hpp:403: error: expected primary-expression before ‘)’ token
./sub_commands/count_main_cmdline.hpp:404: error: expected primary-expression before ‘)’ token
make[2]: *** [sub_commands/count_main.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory `/pica/sw/apps/bioinfo/jellyfish/src/Jellyfish/build'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/pica/sw/apps/bioinfo/jellyfish/src/Jellyfish/build'
make: *** [all] Error 2
gmarcais commented 9 years ago

Yes, my bad. I messed up yaggo. Install the latest release of yaggo to fix this.

douglasgscofield commented 9 years ago

That takes care of it, thanks!