From owner-freebsd-python@FreeBSD.ORG Sat Aug 31 17:04:56 2013 Return-Path: Delivered-To: freebsd-python@FreeBSD.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTP id 42CFB174; Sat, 31 Aug 2013 17:04:56 +0000 (UTC) (envelope-from john@saltant.com) Received: from homiemail-a98.g.dreamhost.com (caiajhbdcbbj.dreamhost.com [208.97.132.119]) by mx1.freebsd.org (Postfix) with ESMTP id 18E422B2F; Sat, 31 Aug 2013 17:04:55 +0000 (UTC) Received: from homiemail-a98.g.dreamhost.com (localhost [127.0.0.1]) by homiemail-a98.g.dreamhost.com (Postfix) with ESMTP id 6F45D2C2079; Sat, 31 Aug 2013 10:04:49 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=saltant.com; h=message-id :date:from:mime-version:to:cc:subject:content-type; s= saltant.com; bh=aQ0EHDed1Hs+Q86tcf6C/yaSCqo=; b=n0BwtsiDA3dtvdTO gACOiorR+KcMO4rbp4ejYNlfRfbZUKwDBkOHgkf+ToEtKC9x0XmKDyDEQv7g2eRE v+jhCgXl1tgb4tJl63dd9LnnOPIGU7N4Gb1JOTaPlQNAeSkdPuBD3D8RqpHDYVBm 35sF0oHgnXwLqLM+aE+OiZdUNhE= Received: from omnific.local (drivel.saltant.net [72.78.188.146]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) (Authenticated sender: john@saltant.com) by homiemail-a98.g.dreamhost.com (Postfix) with ESMTPSA id 184EF2C206E; Sat, 31 Aug 2013 10:04:49 -0700 (PDT) Message-ID: <52222229.6070303@saltant.com> Date: Sat, 31 Aug 2013 13:04:41 -0400 From: "John W. O'Brien" Organization: Saltant Solutions User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:17.0) Gecko/20130801 Thunderbird/17.0.8 MIME-Version: 1.0 To: wen@freebsd.org, sunpoet@freebsd.org Subject: devel/py-tables dumps core after science/hdf5-18 upgrade to 1.8.10 (r325778) X-Enigmail-Version: 1.5.2 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="dfS2CvT4QhJ1897HTFt8vTKJLKsOABiW2" Cc: freebsd-python@FreeBSD.org X-BeenThere: freebsd-python@freebsd.org X-Mailman-Version: 2.1.14 Precedence: list List-Id: FreeBSD-specific Python issues List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 31 Aug 2013 17:04:56 -0000 This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --dfS2CvT4QhJ1897HTFt8vTKJLKsOABiW2 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello wen@, sunpoet@, and python@, I just wanted to call your attention to this because it might warrant a mention in UPDATING, though the hdf5 error message is helpfully verbose. Rebuilding devel/py-tables after the upgrade fixes this. Other ports that depend upon science/hdf5-18 are likely affected too. % pkg_info -xI tables hdf hdf5-1.8.10 Hierarchical Data Format library (from NCSA) py27-tables-3.0.0 Hierarchical database for Python % python -c 'import tables; print(tables.get_hdf5_version())' 1.8.9 % nosetests tables.tests.test_basics Warning! ***HDF5 library version mismatched error*** The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked.= Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 b= ut linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related= settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environmen= t variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.8.9, library is 1.8.10 SUMMARY OF THE HDF5 CONFIGURATION =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D General Information: ------------------- HDF5 Version: 1.8.10-patch1 [...] Bye... Abort (core dumped) % Thank you, John --dfS2CvT4QhJ1897HTFt8vTKJLKsOABiW2 Content-Type: application/pgp-signature; name="signature.asc" Content-Description: OpenPGP digital signature Content-Disposition: attachment; filename="signature.asc" -----BEGIN PGP SIGNATURE----- Version: GnuPG/MacGPG2 v2.0.20 (Darwin) Comment: GPGTools - http://gpgtools.org Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBCgAGBQJSIiIwAAoJEBRzAKlhyP/Ff6oH/2+D05/xCHpiEEtr0wMiEQo5 UccS+kZOGYScXsTbsuhoT/WUvURByC9e+BMqC8Fg2yjEkb28AQA1q3abU9t+dzqH cQuwdHsx/E1QMrJ0aUwSASmg8WaguFWvOVo4fwsEnah0NPmvUpY1JHIa6YCuJm16 cpQvFPH5vygR+BcuMN1PsbLpGEXczrr2sugVlaqNaCcUwTMAoQ/flZ48kuRC3t2w 7xmxnOZyW1hmwn43dUzGM6ujIdtBxKqxb7Fm2vR5ruowoNireBICHdAqxms4lBSS kw5zzFiFsEE8RAqU4U7fj6nlFNim8tQ6Q2jh9jWzGzM4kWeJyHhXQkGaj+Ghs08= =E22T -----END PGP SIGNATURE----- --dfS2CvT4QhJ1897HTFt8vTKJLKsOABiW2--