[Biopython-dev] Notification: incoming/120

biopython-bugs at bioperl.org biopython-bugs at bioperl.org
Thu Jan 30 14:28:03 EST 2003

JitterBug notification

new message incoming/120

Message summary for PR#120
	From: ognen at kc.rr.com
	Subject: biopython fails to compile on tru64
	Date: Thu, 30 Jan 2003 14:28:02 -0500
	0 replies 	0 followups


>From ognen at kc.rr.com Thu Jan 30 14:28:02 2003
Received: from localhost (localhost [])
	by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h0UJS27E014046
	for <biopython-bugs at pw600a.bioperl.org>; Thu, 30 Jan 2003 14:28:02 -0500
Date: Thu, 30 Jan 2003 14:28:02 -0500
Message-Id: <200301301928.h0UJS27E014046 at pw600a.bioperl.org>
From: ognen at kc.rr.com
To: biopython-bugs at bioperl.org
Subject: biopython fails to compile on tru64
X-Spam-Status: No
X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang)

Full_Name: Ognen Duzlevski
Module: KDTree
Version: 1.1
OS: tru64
Submission from: (NULL) (

Using Compaq CC 6.4 on a Tru64 5.1 alpha system. Python 2.2.2 was compiled using
the same compiler (it would not compile using gcc 3.1 on the same machine).
Doing python setup.py build produced the following output:

ld -shared -expect_unresolved * build/temp.osf1-V5.1-alpha-2.2/_KDTree.o
build/temp.osf1-V5.1-alpha-2.2/_KDTree.swig.o -lstdc++ -o
Can't open: build/temp.osf1-V5.1-alpha-2.2/_KDTree.o (No such file or
error: command 'ld' failed with exit status 1

I worked around this by manually executing the following two lines:

gcc -DNDEBUG -O -I/usr/local/Python-2.2.2/include/python2.2 -c

gcc -DNDEBUG -O -O -I/usr/local/Python-2.2.2/include/python2.2 -c

and then copying the resulting .o files into build/temp.<architecture>. You will
notice that the biopython was compiled with Compaq C but these two modules I had
to compile with gcc and hopefully the mix will work ;)

More information about the Biopython-dev mailing list