Bug 194683 - parts science/py-scikit-learn (py27-scikit-learn-0.15.0_1) fail due to unresolved symbols
Summary: parts science/py-scikit-learn (py27-scikit-learn-0.15.0_1) fail due to unreso...
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: amd64 Any
: --- Affects Only Me
Assignee: Dmitry Sivachenko
URL:
Keywords:
Depends on:
Blocks:
 
Reported: 2014-10-29 13:33 UTC by Jacob Frelinger
Modified: 2019-12-17 01:23 UTC (History)
0 users

See Also:
jacob.frelinger: maintainer-feedback? (demon)


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Description Jacob Frelinger 2014-10-29 13:33:22 UTC
Parts of py27-scikit-learn-0.15.0_1 can't be used/loaded do to unresolved symbols.

trying to import the PCA module from sklearn.decomposition results in:
ImportError: /usr/local/lib/libcblas.so.2: Undefined symbol "cgemv_"
due to it trying to import pairwise_fast.so

ldd of pairwise_fast.so shows no missing libraries:
[jolly@kapu metrics]$ ldd ./pairwise_fast.so 
./pairwise_fast.so:
	libcblas.so.2 => /usr/local/lib/libcblas.so.2 (0x80162e000)
	libm.so.5 => /lib/libm.so.5 (0x801844000)
	libpython2.7.so.1 => /usr/local/lib/libpython2.7.so.1 (0x801a6c000)
	libc.so.7 => /lib/libc.so.7 (0x80081f000)
	libgfortran.so.3 => /usr/local/lib/gcc48/libgfortran.so.3 (0x801e26000)
	libgcc_s.so.1 => /usr/local/lib/gcc48/libgcc_s.so.1 (0x80213b000)
	libquadmath.so.0 => /usr/local/lib/gcc48/libquadmath.so.0 (0x802351000)
	libintl.so.9 => /usr/local/lib/libintl.so.9 (0x80258c000)
	libutil.so.9 => /lib/libutil.so.9 (0x802796000)
	libthr.so.3 => /lib/libthr.so.3 (0x8029a8000)


running nosetests on the site-packages/sklearn directory shows several tests failing due to the same unresolved symbol (most of which are from trying to import pairwise_fast, and one from trying to import liblinear)

libmap.conf is empty and no files in /usr/local/etc/libmap.conf.d
Comment 1 Bugzilla Automation freebsd_committer 2014-10-29 13:33:22 UTC
Auto-assigned to maintainer demon@FreeBSD.org
Comment 2 commit-hook freebsd_committer 2014-10-30 11:53:11 UTC
A commit references this bug:

Author: demon
Date: Thu Oct 30 11:52:49 UTC 2014
New revision: 371746
URL: https://svnweb.freebsd.org/changeset/ports/371746

Log:
  Explicitly link with libblas to avoid errors like
  import sklearn.decomposition.pca
  ImportError: /usr/local/lib/libcblas.so.2: Undefined symbol "cgemv_"
  due to it trying to import pairwise_fast.so

  PR:             194683

  Update to version 0.15.2.

Changes:
  head/science/py-scikit-learn/Makefile
  head/science/py-scikit-learn/distinfo