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

Evan Bollig PhD boll0107 at umn.edu
Mon Oct 27 09:17:51 PDT 2014


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?

#####
$> 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
##########

-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



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