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

[Iddo Friedberg]

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/