Zlib dependency problem?

[znruss]

I'm having a lot of trouble getting khmer to work without administrator privileges. I managed to get virtualenv and pip working, and khmer installs without issue using these commands:

cd a/writeable/directory/
virtualenv khmerEnv
source khmerEnv/bin/activate
pip install --allow-external argparse git+https://github.com/ged-lab/khmer.git@master#egg=khmer

or the stable branch; tried both. However, there's a problem: Make test fails, as does interleave-reads.py.

(test)-bash-4.1$ interleave-reads.py
Traceback (most recent call last):
  File "/auto/sahara/namib/home/znruss/test/bin/interleave-reads.py", line 5, in <module>
    pkg_resources.run_script('khmer==1.0', 'interleave-reads.py')
  File "/auto/sahara/namib/home/znruss/test/lib/python2.7/site-packages/pkg_resources.py", line 528, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/auto/sahara/namib/home/znruss/test/lib/python2.7/site-packages/pkg_resources.py", line 1394, in run_script
    execfile(script_filename, namespace, namespace)
  File "/auto/sahara/namib/home/znruss/test/lib/python2.7/site-packages/khmer-1.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/interleave-reads.py", line 27, in <module>
    import khmer
  File "/auto/sahara/namib/home/znruss/test/lib/python2.7/site-packages/khmer-1.0-py2.7-linux-x86_64.egg/khmer/__init__.py", line 9, in <module>
    from khmer._khmer import _new_counting_hash
ImportError: /auto/sahara/namib/home/znruss/test/lib/python2.7/site-packages/khmer-1.0-py2.7-linux-x86_64.egg/khmer/_khmermodule.so: undefined symbol: gzopen

I've tried making my own python and zlib and also setting LD_LIBRARY_PATH and LD_RUN_PATH to no avail.

[ctb]

On Tue, Apr 22, 2014 at 11:52:38AM -0700, znruss wrote:

I'm having a lot of trouble getting khmer to work without administrator privileges. I managed to get virtualenv and pip working, and khmer installs without issue using these commands:

Hi, znruss, take a look at this:

https://github.com/ged-lab/khmer/issues/365

it's just been merged, so things might work now!

best, --titus

cd a/writeable/directory/
virtualenv khmerEnv
source khmerEnv/bin/activate
pip install --allow-external argparse git+https://github.com/ged-lab/khmer.git@master#egg=khmer

or the stable branch; tried both. However, there's a problem: Make test fails, as does interleave-reads.py.

(test)-bash-4.1$ interleave-reads.py
Traceback (most recent call last):
  File "/auto/sahara/namib/home/znruss/test/bin/interleave-reads.py", line 5, in <module>
    pkg_resources.run_script('khmer==1.0', 'interleave-reads.py')
  File "/auto/sahara/namib/home/znruss/test/lib/python2.7/site-packages/pkg_resources.py", line 528, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/auto/sahara/namib/home/znruss/test/lib/python2.7/site-packages/pkg_resources.py", line 1394, in run_script
    execfile(script_filename, namespace, namespace)
  File "/auto/sahara/namib/home/znruss/test/lib/python2.7/site-packages/khmer-1.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/interleave-reads.py", line 27, in <module>
    import khmer
  File "/auto/sahara/namib/home/znruss/test/lib/python2.7/site-packages/khmer-1.0-py2.7-linux-x86_64.egg/khmer/__init__.py", line 9, in <module>
    from khmer._khmer import _new_counting_hash
ImportError: /auto/sahara/namib/home/znruss/test/lib/python2.7/site-packages/khmer-1.0-py2.7-linux-x86_64.egg/khmer/_khmermodule.so: undefined symbol: gzopen

I've tried making my own python and zlib and also setting LD_LIBRARY_PATH and LD_RUN_PATH to no avail.

---

Reply to this email directly or view it on GitHub:

https://github.com/ged-lab/khmer-protocols/issues/85

C. Titus Brown, ctb@msu.edu

[znruss]

That worked perfectly! Thanks very much!