pb-cdunn
commented
9 years ago Hmm. I'm not sure whether that error is in rdfextras or setuptools/distribute. They are both 3p software. I suspect the latter.
Try to install virtualenv for your python. It should work fine for 2.7.3, which I am using today. (I just did a fresh install without errors.) Then follow the instructions to activate it. If you've already done that, try to upgrade setuptools within your virtualenv first.
If all else fails, maybe it's safe to ignore.
dgordon562
when executing the following according to falcon_manual.md
git clone https://github.com/pb-jchin/pypeFLOW.git cd pypeFLOW python setup.py install
cd .. git clone https://github.com/PacificBiosciences/FALCON.git cd FALCON python setup.py install
cd .. git clone https://github.com/pb-jchin/DAZZ_DB.git cd DAZZ_DB/ make cp DBrm DBshow DBsplit DBstats fasta2DB ../fc_env/bin/
cd .. git clone https://github.com/pb-jchin/DALIGNER.git cd DALIGNER git checkout 97b0c27a26164dbdd6dc52923855501ca3d14d45 make cp daligner daligner_p DB2Falcon HPCdaligner LA4Falcon LAmerge LAsort ../fc_env/bin cd ..
I get the following error several times (below). Is this a problem or can I push ahead? Receiving objects: 100% (956/956), 1.96 MiB, done. Resolving deltas: 100% (457/457), done. Traceback (most recent call last): File "setup.py", line 14, in
'rdfextras >= 0.1'
File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/distutils/core.py", line 112, in setup
_setup_distribution = dist = klass(attrs)
File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 2025, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 2235, in requires
dm = self._dep_map
File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 2464, in _dep_map
self.__dep_map = self._compute_dependencies()
File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 2497, in _compute_dependencies
common = frozenset(reqs_for_extra(None))
File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 2494, in reqs_for_extra
if req.marker_fn(override={'extra':extra}):
File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/_markerlib/markers.py", line 109, in marker_fn
return eval(compiled_marker, environment)
File "", line 1, in
NameError: name 'sys_platform' is not defined
Initialized empty Git repository in /net/gs/vol1/home/dgordon/falcon150523/FALCON-master/install/FALCON/.git/
I just want to know if I can ignore this error and continue.