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

Michael R. Crusoe mcrusoe at msu.edu
Mon Oct 27 13:25:04 PDT 2014

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
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

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.idyll.org/pipermail/khmer/attachments/20141027/2202fcf5/attachment.htm>

More information about the khmer mailing list