Question: jellyfish failing to install while building gkno
0
gravatar for brettin
5.0 years ago by
brettin0
United States
brettin0 wrote:

When installing gnko, it continues to fail when installing jellyfish. I have confirmed that jellyfish will compile and deploy outside of gkno using the standard install instructions for jellyfish and then setting the LD_LIBRARY_PATH=/usr/local/lib.

I am installing on a bare ubuntu image, so it is possible that I'm missing a dependency. Here is what the bootstrap.sh script looks like:

apt-get update

apt-get install -y build-essential

apt-get install -y openjdk-7-jdk

apt-get install -y ant

apt-get install -y git

apt-get install -y cmake

apt-get install -y ruby1.9.1

apt-get install -y libncurses5-dev

apt-get install -y libncurses5

apt-get install -y zlib1g-dev

# I tried this because I was unsure if yaggo was installing correctly.

gem install rake

git clone https://github.com/gmarcais/yaggo.git

cd yaggo/

rake gem

gem install ./pkg/yaggo-1.5.4.gem

 

The installation stops here:

  jellyfish...Traceback (most recent call last):

  File "/home/ubuntu/gkno_launcher/src/gkno.py", line 502, in <module>

    main()

  File "/home/ubuntu/gkno_launcher/src/gkno.py", line 291, in main

    success = admin.run(sys.argv)

  File "/home/ubuntu/gkno_launcher/src/gkno/adminUtils.py", line 84, in run

    if   self.mode == "build"    : success = self.build()

  File "/home/ubuntu/gkno_launcher/src/gkno/adminUtils.py", line 153, in build

    if self.buildTool(tool):

  File "/home/ubuntu/gkno_launcher/src/gkno/adminUtils.py", line 539, in buildTool

    success = tool.build(out, err)

  File "/home/ubuntu/gkno_launcher/src/gkno/conf/gknoTools.py", line 73, in build

    return self.doBuild()

  File "/home/ubuntu/gkno_launcher/src/gkno/conf/gknoTools.py", line 350, in doBuild

    if not self.runCommand("autoreconf -i") : return False

  File "/home/ubuntu/gkno_launcher/src/gkno/conf/gknoTools.py", line 90, in runCommand

    p = subprocess.Popen(command.split(), env=self.environ, stdout=self.out, stderr=self.err)

  File "/usr/lib/python2.7/subprocess.py", line 679, in __init__

    errread, errwrite)

  File "/usr/lib/python2.7/subprocess.py", line 1249, in _execute_child

    raise child_exception

OSError: [Errno 2] No such file or directory

 

Here is the err log:

 

root@precise64:/home/vagrant/gkno_launcher/logs# more build_jellyfish.err 

setup.rb:788: Use RbConfig instead of obsolete and deprecated Config.

---> bin

<--- bin

---> lib

---> lib/yaggo

<--- lib/yaggo

<--- lib

setup.rb:788: Use RbConfig instead of obsolete and deprecated Config.

---> bin

updating shebang: yaggo

updating shebang: create_yaggo_one_file

<--- bin

---> lib

---> lib/yaggo

<--- lib/yaggo

<--- lib

setup.rb:788: Use RbConfig instead of obsolete and deprecated Config.

rm -f InstalledFiles

---> bin

mkdir -p /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/bin

install yaggo /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/bin/

install create_yaggo_one_file /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/bin/

<--- bin

---> lib

mkdir -p /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib

---> lib/yaggo

mkdir -p /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo

install stub.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo

install library.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo

install parser.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo

install version.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo

install zsh_completion.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo

install dsl.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo

install general.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo

install man_page.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo

<--- lib/yaggo

<--- lib

 

 

and here is the stdout log:

root@precise64:/home/vagrant/gkno_launcher/logs# more build_jellyfish.out 

Cloning into 'yaggo'...

 

This is why I tried putting the yaggo installation into the bootstrap script. 

When I run the ./gkno build again, the remaining tools install, except for jellyfish. The log messages for the jellyfish failure are different, but apparently the failure in this case is not sufficient for the install program to stop. The install program successfully installs the remaining tools.

 

Any help would be appreciated. I'm working in two environments, both ubuntu, both virtualized, having the same problem with both.

 

 

gkno • 2.3k views
ADD COMMENTlink modified 5.0 years ago by alistairnward210 • written 5.0 years ago by brettin0

Some additional information. From what I can tell, the call to autoreconf  generates a configure file that is not valid. I can replicate this now when building Jellyfish outside of gkno. If autoreconf is run first, then the Jellyfish build fails. If autoreconf is not run, Jellyfish will build. When configure is run, this error is occurring:

./configure: line 15287: syntax error near unexpected token `VALGRIND,'

./configure: line 15287: `      PKG_CHECK_MODULES(VALGRIND, valgrind >= 1.8.0)'

And a bit more information, the call to autoreconf generates this snippet:

libtoolize: `./install-sh' is newer: use `--force' to overwrite

 

In any case, here is the entire typescript showing two different situations, one using autoreconf and one not using autoreconf. The error is identical to the error message I'm seeing when building Jelllyfish from  the gkno build command.

Script started on Wed 18 Jun 2014 12:34:59 AM UTC
]0;root@ubuntu-brettin-dev-2: ~root@ubuntu-brettin-dev-2:~# tar -xf jellyfish-2.1.3.tar
]0;root@ubuntu-brettin-dev-2: ~root@ubuntu-brettin-dev-2:~# cd jellyfish-2.1.3
]0;root@ubuntu-brettin-dev-2: ~/jellyfish-2.1.3root@ubuntu-brettin-dev-2:~/jellyfish-2.1.3# autoreconf -i
libtoolize: `./install-sh' is newer: use `--force' to overwrite
]0;root@ubuntu-brettin-dev-2: ~/jellyfish-2.1.3root@ubuntu-brettin-dev-2:~/jellyfish-2.1.3# ./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 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 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/local/bin/yaggo
./configure: line 15287: syntax error near unexpected token `VALGRIND,'
./configure: line 15287: `      PKG_CHECK_MODULES(VALGRIND, valgrind >= 1.8.0)'
]0;root@ubuntu-brettin-dev-2: ~/jellyfish-2.1.3root@ubuntu-brettin-dev-2:~/jellyfish-2.1.3# cd ..
]0;root@ubuntu-brettin-dev-2: ~root@ubuntu-brettin-dev-2:~# rm -r jellyfish-2.1.3
]0;root@ubuntu-brettin-dev-2: ~root@ubuntu-brettin-dev-2:~# tar -xf jellyfish-2.1.3.tar
]0;root@ubuntu-brettin-dev-2: ~root@ubuntu-brettin-dev-2:~# cd jellyfish-2.1.3.
]0;root@ubuntu-brettin-dev-2: ~/jellyfish-2.1.3root@ubuntu-brettin-dev-2:~/jellyfish-2.1.3# ./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 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 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/local/bin/yaggo
checking for pkg-config... no
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
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
]0;root@ubuntu-brettin-dev-2: ~/jellyfish-2.1.3root@ubuntu-brettin-dev-2:~/jellyfish-2.1.3# make
make  all-am
make[1]: Entering directory `/root/jellyfish-2.1.3'
  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/err.lo
  CXX    lib/jsoncpp.lo
  CXX    lib/time.lo
  CXX    lib/generator_manager.lo
  CXXLD  libjellyfish-2.0.la
  CXX    sub_commands/jellyfish.o
  CXX    sub_commands/count_main.o
  CXX    sub_commands/info_main.o
  CXX    sub_commands/dump_main.o
  CXX    sub_commands/histo_main.o
  CXX    sub_commands/stats_main.o
  CXX    sub_commands/merge_main.o
  CXX    sub_commands/bc_main.o
  CXX    sub_commands/query_main.o
  CXX    sub_commands/cite_main.o
  CXX    jellyfish/merge_files.o
  CXXLD  bin/jellyfish
make[1]: Leaving directory `/root/jellyfish-2.1.3'
]0;root@ubuntu-brettin-dev-2: ~/jellyfish-2.1.3root@ubuntu-brettin-dev-2:~/jellyfish-2.1.3# cd ..
]0;root@ubuntu-brettin-dev-2: ~root@ubuntu-brettin-dev-2:~# exit

Script done on Wed 18 Jun 2014 12:38:54 AM UTC

ADD REPLYlink written 5.0 years ago by brettin0
1
gravatar for alistairnward
5.0 years ago by
alistairnward210
United States
alistairnward210 wrote:

If you take a fresh clone of gkno and build it, what is the error log from gkno that you get from the Jellyfish failure? Jellyfish is the tool that we've had the most trouble getting to run on most systems, but seems to be running on all the systems we've tested so far. There could be some dependency problem (this was a big problem for Mac installations) - so you definitely need valgrind and automake setup.

We don't want to be setting system level parameters, or requiring users to do additional steps themselves (as far as is possible), so I'd like to see exactly what gkno is seeing as a problem and try and get an integrated solution.

Thanks for the report.

ADD COMMENTlink written 5.0 years ago by alistairnward210

Working with a fresh clone, and a base ubuntu image (precise64), the problem was isolated to the pkg.m4 macro not being installed. This was solved by including pkg-config. Isolated the problem late last night.

The resulting bootstrap works now on two different ubuntu builds, The bootstrap looks like this:

!/usr/bin/env bash

set up for gnko

apt-get update apt-get install -y build-essential apt-get install -y openjdk-7-jdk apt-get install -y ant apt-get install -y git apt-get install -y cmake apt-get install -y ruby1.9.1 apt-get install -y libncurses5-dev apt-get install -y libncurses5 apt-get install -y dh-autoreconf apt-get install -y pkg-config

git clone https://github.com/gkno/gkno_launcher.git pushd gkno_launcher ./gkno build popd

ADD REPLYlink written 5.0 years ago by brettin0
0
gravatar for alistairnward
5.0 years ago by
alistairnward210
United States
alistairnward210 wrote:

Ok, thanks for this. I need to go and check on the dependency checking at the start of building gkno. I think I found that pkg-config was also a problem for Mac installations, so we weren't explicitly checking for it. I need to get these updated and then provide instructions on installing all of these dependencies. These reports are very helpful to us, so thank you again.

ADD COMMENTlink written 5.0 years ago by alistairnward210
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