<div dir="ltr"><div class="gmail_quote">On Mon Oct 27 2014 at 12:34:21 PM Evan Bollig PhD <<a href="mailto:boll0107@umn.edu" target="_blank">boll0107@umn.edu</a>> wrote:</div><div class="gmail_quote"><br></div><div class="gmail_quote">Hello Evan,</div><div class="gmail_quote"><br></div><div class="gmail_quote">Thank you for using khmer and sending us your installation report.</div><div class="gmail_quote"><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Installing via pip assumes that libpython2.7 is on the system default<br>
paths. Wrong assumption. What if I'm building against Enthought<br>
python? Also, why does the installer assume /home/builder/jenkins<br>
exists?<br></blockquote><div><br></div><div>What operating system and distribution are you using?<br></div><div>Which install instuctions are you following?</div><div><br></div><div>For end-users our install instructions are at <a href="http://khmer.readthedocs.org/en/v1.1/install.html" target="_blank">http://khmer.readthedocs.org/en/v1.1/install.html</a></div><div>We've re-written them for the pending release: <a href="http://khmer.readthedocs.org/en/latest/user/install.html" target="_blank">http://khmer.readthedocs.org/en/latest/user/install.html</a> They should still work with v1.1</div><div><br></div><div>Developers should start at <a href="http://khmer.readthedocs.org/en/latest/dev/getting-started.html" target="_blank">http://khmer.readthedocs.org/en/latest/dev/getting-started.html</a></div><div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>I hope this helps,</div><div> <br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
#####<br>
$> pip install khmer<br>
Downloading/unpacking khmer<br>
Downloading khmer-1.1.tar.gz (3.6MB): 3.6MB downloaded<br>
<br>
[... CUT ...]<br>
<br>
g++ -pthread -shared -Wl,-rpath,$ORIGIN/../lib -g<br>
-L/home/builder/jenkins/<u></u>worksp<u></u>ace/Python_Masters/ARCH/<u></u>x86_<u></u>64/label/Linux/core/lib<br>
build/temp.linux-x86_64-2.7/<u></u>kh<u></u>mer/_khmermodule.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/khmer_config.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/thread_id_map.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/trace_logger.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/perf_metrics.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/read_parsers.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/kmer_hash.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/hashtable.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/hashbits.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/labelhash.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/counting.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/subset.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/aligner.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/scoringmatrix.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/node.o<br>
build/temp.linux-x86_64-2.7/<u></u>li<u></u>b/kmer.o third-party/zlib/adler32.lo<br>
third-party/zlib/compress.lo third-party/zlib/crc32.lo<br>
third-party/zlib/deflate.lo third-party/zlib/gzclose.lo<br>
third-party/zlib/gzlib.lo third-party/zlib/gzread.lo<br>
third-party/zlib/gzwrite.lo third-party/zlib/infback.lo<br>
third-party/zlib/inffast.lo third-party/zlib/inflate.lo<br>
third-party/zlib/inftrees.lo third-party/zlib/trees.lo<br>
third-party/zlib/uncompr.lo third-party/zlib/zutil.lo<br>
third-party/bzip2/blocksort.o third-party/bzip2/huffman.o<br>
third-party/bzip2/crctable.o third-party/bzip2/randtable.o<br>
third-party/bzip2/compress.o third-party/bzip2/decompress.o<br>
third-party/bzip2/bzlib.o<br>
-L/home/builder/jenkins/<u></u>worksp<u></u>ace/Python_Masters/ARCH/<u></u>x86_<u></u>64/label/Linux/core/lib<br>
-lpython2.7 -o build/lib.linux-x86_64-2.7/<u></u>khm<u></u>er/_khmermodule.so<br>
<br>
/usr/bin/ld: cannot find -lpython2.7<br>
##########<br></blockquote></div><div><br></div>-- <br><div dir="ltr"><font face="courier new, monospace"><span style="font-size:small">Michael R. Crusoe: Programmer & Bioinformatician </span><a href="mailto:mcrusoe@msu.edu" style="color:rgb(17,85,204);font-size:small" target="_blank">mcrusoe@msu.edu</a><br style="font-size:small"><span style="font-size:small"> @ the Genomics, Evolution, and Development lab; Michigan State U</span><br style="font-size:small"><a href="https://impactstory.org/MichaelRCrusoe" style="color:rgb(17,85,204);font-size:small" target="_blank">https://impactstory.org/MichaelRCrusoe</a><font> <a href="http://twitter.com/biocrusoe" target="_blank">http://twitter.com/biocrusoe</a></font></font><br></div></div>