[khmer] pip install khmer fails (-lpython2.7)

[Evan Bollig PhD]

Michael,

The Jenkins requirement was in the snippet I sent you: g++ -pthread
-shared -Wl,-rpath,$ORIGIN/../lib -g
-L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib
[...]

== required ==>
-L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib

Commands I've run:

$ source
$ venv -s ~/khmer/
$ source ~/khmer/bin/activate
$ pip install khmer

Failure inside "building 'khmer._khmermodule' extension"

/usr/bin/ld: cannot find -lpython2.7

I attempted to set LD_LIBRARY_PATH. No luck resolving the issue. This
tells me that your build requires the path to libpython2.7.so to exist
on the ld.so path. I'm a user, not an administrator, which means I
have no control over this. However, you should be able to get
setuptools to test for libpython2.7.so on LD_LIBRARY_PATH, or use
python-config (python2-config) to get the lib path for the python
distribution.

-E

-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
evan at msi.umn.edu
boll0107 at umn.edu


On Mon, Oct 27, 2014 at 3:25 PM, Michael R. Crusoe <mcrusoe at msu.edu> wrote:
> On Mon Oct 27 2014 at 12:34:21 PM Evan Bollig PhD <boll0107 at umn.edu> wrote:
>
> Hello Evan,
>
> Thank you for using khmer and sending us your installation report.
>
>> Installing via pip assumes that libpython2.7 is on the system default
>> paths. Wrong assumption. What if I'm building against Enthought
>> python? Also, why does the installer assume /home/builder/jenkins
>> exists?
>
>
> What operating system and distribution are you using?
> Which install instuctions are you following?
>
> For end-users our install instructions are at
> http://khmer.readthedocs.org/en/v1.1/install.html
> We've re-written them for the pending release:
> http://khmer.readthedocs.org/en/latest/user/install.html They should still
> work with v1.1
>
> Developers should start at
> http://khmer.readthedocs.org/en/latest/dev/getting-started.html
>
> We use the standard Python packaging program Setuptools. At this time we
> support installation inside of a virtualenv only. We are happy to work with
> you to support other Python environments though Enthought should (and can)
> customize distutils/setuptools if they put libraries in different places.
>
> For example: to specify additional directories to find external libraries
> you can use the `--library-dirs` option to `./setup.py build_ext` or edit
> the appropriate line in the "setup.cfg" file.
>
> In your logs I don't see any reference to the path "/home/builder/jenkins"
> being required to exist so I don't know how to help you.
>
> I hope this helps,
>
>>
>>
>> #####
>> $> pip install khmer
>> Downloading/unpacking khmer
>>   Downloading khmer-1.1.tar.gz (3.6MB): 3.6MB downloaded
>>
>> [... CUT ...]
>>
>> g++ -pthread -shared -Wl,-rpath,$ORIGIN/../lib -g
>>
>> -L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib
>> build/temp.linux-x86_64-2.7/khmer/_khmermodule.o
>> build/temp.linux-x86_64-2.7/lib/khmer_config.o
>> build/temp.linux-x86_64-2.7/lib/thread_id_map.o
>> build/temp.linux-x86_64-2.7/lib/trace_logger.o
>> build/temp.linux-x86_64-2.7/lib/perf_metrics.o
>> build/temp.linux-x86_64-2.7/lib/read_parsers.o
>> build/temp.linux-x86_64-2.7/lib/kmer_hash.o
>> build/temp.linux-x86_64-2.7/lib/hashtable.o
>> build/temp.linux-x86_64-2.7/lib/hashbits.o
>> build/temp.linux-x86_64-2.7/lib/labelhash.o
>> build/temp.linux-x86_64-2.7/lib/counting.o
>> build/temp.linux-x86_64-2.7/lib/subset.o
>> build/temp.linux-x86_64-2.7/lib/aligner.o
>> build/temp.linux-x86_64-2.7/lib/scoringmatrix.o
>> build/temp.linux-x86_64-2.7/lib/node.o
>> build/temp.linux-x86_64-2.7/lib/kmer.o third-party/zlib/adler32.lo
>> third-party/zlib/compress.lo third-party/zlib/crc32.lo
>> third-party/zlib/deflate.lo third-party/zlib/gzclose.lo
>> third-party/zlib/gzlib.lo third-party/zlib/gzread.lo
>> third-party/zlib/gzwrite.lo third-party/zlib/infback.lo
>> third-party/zlib/inffast.lo third-party/zlib/inflate.lo
>> third-party/zlib/inftrees.lo third-party/zlib/trees.lo
>> third-party/zlib/uncompr.lo third-party/zlib/zutil.lo
>> third-party/bzip2/blocksort.o third-party/bzip2/huffman.o
>> third-party/bzip2/crctable.o third-party/bzip2/randtable.o
>> third-party/bzip2/compress.o third-party/bzip2/decompress.o
>> third-party/bzip2/bzlib.o
>>
>> -L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib
>> -lpython2.7 -o build/lib.linux-x86_64-2.7/khmer/_khmermodule.so
>>
>> /usr/bin/ld: cannot find -lpython2.7
>> ##########
>
>
> --
> Michael R. Crusoe:  Programmer & Bioinformatician   mcrusoe at msu.edu
>  @ the Genomics, Evolution, and Development lab; Michigan State U
> https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe