glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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Build troubles #4

Closed iminkin closed 10 years ago

iminkin commented 10 years ago

I'm using Open Suse 12.3 installed just from scratch (Live CD). Content of stderr is at:

http://pastebin.com/download.php?i=47nBVaG5

On which distro it is possible to install progressiveCactus without problems?

joelarmstrong commented 10 years ago

Hi,

We test it regularly on Ubuntu and CentOS (and Mac OS).

That said, using suse shouldn't be a problem, or hopefully anything with a gnu toolkit. The problem is in compiling an upstream library that we've included. Other people seem to have trouble building the library as well:

http://leaf.dragonflybsd.org/~marino/boomlogs/kyototycoon-0.9.56.log

I'm a bit stumped as to what's causing this. I'll run a suse VM over the weekend and try to figure it out.

benedictpaten commented 10 years ago

Seems like those are mostly strict compile warnings - can we/should we turn those off in the distributed version?

On Fri, Oct 11, 2013 at 12:24 PM, Joel Armstrong notifications@github.comwrote:

Hi,

We test it regularly on Ubuntu and CentOS (and Mac OS).

That said, using suse shouldn't be a problem, or hopefully anything with a gnu toolkit. The problem is in compiling an upstream library that we've included. Other people seem to have trouble building the library as well:

http://leaf.dragonflybsd.org/~marino/boomlogs/kyototycoon-0.9.56.log

I'm a bit stumped as to what's causing this. I'll run a suse VM over the weekend and try to figure it out.

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/4#issuecomment-26164698 .

glennhickey commented 10 years ago

I don't think the compiler warnings are hurting anyone here... unless they're related to the fatal linker errors at the end... but then I don't think turning the warnings off will fix those!

On Fri, Oct 11, 2013 at 3:43 PM, Benedict Paten notifications@github.comwrote:

Seems like those are mostly strict compile warnings - can we/should we turn those off in the distributed version?

On Fri, Oct 11, 2013 at 12:24 PM, Joel Armstrong notifications@github.comwrote:

Hi,

We test it regularly on Ubuntu and CentOS (and Mac OS).

That said, using suse shouldn't be a problem, or hopefully anything with a gnu toolkit. The problem is in compiling an upstream library that we've included. Other people seem to have trouble building the library as well:

http://leaf.dragonflybsd.org/~marino/boomlogs/kyototycoon-0.9.56.log

I'm a bit stumped as to what's causing this. I'll run a suse VM over the weekend and try to figure it out.

— Reply to this email directly or view it on GitHub< https://github.com/glennhickey/progressiveCactus/issues/4#issuecomment-26164698>

.

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/4#issuecomment-26166235 .

joelarmstrong commented 10 years ago

We may not even be able to turn off the strict compile warnings in some of the submodules, since they mostly (all?) have their own makefiles and we just cd in and call make.

iminkin commented 10 years ago

Thanks for the answer, I will try an Ubuntu machine.

joelarmstrong commented 10 years ago

I've tried to replicate this with a openSUSE 12.3 virtual machine with no luck, it might be some specific gcc/libc version or env variable issue.

Just for the record, it appears to work for gcc 4.7.2, glibc 2.17-4.71, 64-bit. I think it's an upstream problem regardless, closing. If we run into it again we can take another look.

fbemm commented 9 years ago

Trying to setup pCactus I get:

cd submodules && make all make[1]: Entering directory `software/progressiveCactus/submodules' rm -f software/progressiveCactus/submodules/../environment python software/progressiveCactus/submodules/virtualenv/virtualenv.py software/progressiveCactus/python New python executable in software/progressiveCactus/python/bin/python Installing setuptools............ Complete output from command sof...us/python/bin/python -c "#!python \"\"\"Bootstra...sys.argv[1:])

" sof...ols-0.6c11-py2.7.egg: Traceback (most recent call last): File "", line 279, in File "", line 239, in main File "software/progressiveCactus/submodules/virtualenv/virtualenv_support/setuptools-0.6c11-py2.7.egg/setuptools/command/easy_install.py", line 12, in File "software/anaconda-2.1.0/lib/python2.7/tempfile.py", line 32, in import io as _io File "software/anaconda-2.1.0/lib/python2.7/io.py", line 51, in import _io

ImportError: software/progressiveCactus/python/lib/python2.7/lib-dynload/_io.so: undefined symbol: _PyLong_AsInt

...Installing setuptools...done. Traceback (most recent call last): File "software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 2471, in main() File "software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 942, in main never_download=options.never_download) File "software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 1052, in create_environment search_dirs=search_dirs, never_download=never_download) File "software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 599, in install_setuptools search_dirs=search_dirs, never_download=never_download) File "software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 571, in _install_req cwd=cwd) File "software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 1020, in call_subprocess % (cmd_desc, proc.returncode)) OSError: Command sof...us/python/bin/python -c "#!python \"\"\"Bootstra...sys.argv[1:])

" sof...ols-0.6c11-py2.7.egg failed with error code 1 make[1]: * [virtPyRule] Error 1 make[1]: Leaving directory `software/progressiveCactus/submodules' make: * [all] Error 2

Any Ideas? make starts failing during setting up setup tools. I am using anaconda as python distribution. Thx!