[Biopython-dev] Re: bug 37 (fwd)

Iddo Friedberg idoerg at cc.huji.ac.il
Wed Jul 11 06:03:01 EDT 2001


Hi,

You're up bright and early, Brad!

OK, I'm out of ideas. This should be documented somewhere (where do we
document known bugs?), but I'm out of ideas as to a fix. Besides a
python2.1 update.


Iddo

On Wed, 11 Jul 2001, Brad Chapman wrote:

: > Iddo:
: > >Can anyone reproduce the segfault bug on python2.0?
:
: Andrew:
: > The biopython.org machine is an Alpha machine running Linux
: > and Python 2.0 - no segfault:
:
: I do get the segfault with Python 2.0 on FreeBSD:
:
: [chapmanb]$ uname -a
: FreeBSD insomniac.athen1.ga.home.com 4.3-STABLE FreeBSD 4.3-STABLE #5: Fri Jun
: 8 01:44:22 EDT 2001   chapmanb at insomniac.athen1.ga.home.com:/usr/src/sys/compi
: le/INSOMNIACi386
: [chapmanb]$ python
: Python 2.0 (#2, Oct 31 2000, 15:45:46)
: [GCC 2.95.2 19991024 (release)] on freebsd4
: Type "copyright", "credits" or "license" for more information.
: >>> from Bio import Seq
: >>> l = Seq.MutableSeq('ACDEFG')
: >>> print l
: MutableSeq('ACDEFG', Alphabet())
: >>> l
: Segmentation fault (core dumped)
:
: but I don't see it with NetBSD/Python2.1:
:
: [chapmanb]$ uname -a
: NetBSD taxus.athen1.ga.home.com 1.5.1 NetBSD 1.5.1 (TAXUS) #1: Tue Jun 12 09:13:48 EDT 2001   chapmanb at taxus:/usr/src/sys/arch/macppc/compile/TAXUS macppc
: [chapmanb]$ python
: Python 2.1(#6, Jul8 2001, 17:18:01)
: [GCC egcs-2.91.66 19990314 (egcs-1.1.2 release)] on netbsd1
: Type "copyright", "credits" or "license" for more information.
: >>> from Bio import Seq
: >>> l = Seq.MutableSeq('ACDEFGHIKL')
: >>> print l
: MutableSeq('ACDEFGHIKL', Alphabet())
: >>> l
: MutableSeq(array('c', 'ACDEFGHIKL'), Alphabet())
:
: I'd suspect this is a tricky bug in 2.0 that got fixed somewhere along
: the line in 2.1.
:
: only-use-old-versions-of-software-if-you-like-to-run-into-fixed-bugs<wink>-ly
: yr's,
:
: Brad
:
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:

--

Iddo Friedberg                                  | Tel: +972-2-6758647
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |
http://bioinfo.md.huji.ac.il/marg/people-home/iddo/




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