From owner-freebsd-ports-bugs@FreeBSD.ORG Tue Oct 21 15:30:04 2008 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 7E1301065676 for ; Tue, 21 Oct 2008 15:30:04 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 5AF088FC18 for ; Tue, 21 Oct 2008 15:30:04 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.14.3/8.14.3) with ESMTP id m9LFU4Mn067269 for ; Tue, 21 Oct 2008 15:30:04 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.3/8.14.3/Submit) id m9LFU4RU067266; Tue, 21 Oct 2008 15:30:04 GMT (envelope-from gnats) Resent-Date: Tue, 21 Oct 2008 15:30:04 GMT Resent-Message-Id: <200810211530.m9LFU4RU067266@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Julien Cigar Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 8E4AA1065682 for ; Tue, 21 Oct 2008 15:26:54 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (www.freebsd.org [IPv6:2001:4f8:fff6::21]) by mx1.freebsd.org (Postfix) with ESMTP id 7D4278FC20 for ; Tue, 21 Oct 2008 15:26:54 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.14.3/8.14.3) with ESMTP id m9LFQrbe053483 for ; Tue, 21 Oct 2008 15:26:53 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.14.3/8.14.3/Submit) id m9LFQrPF053482; Tue, 21 Oct 2008 15:26:53 GMT (envelope-from nobody) Message-Id: <200810211526.m9LFQrPF053482@www.freebsd.org> Date: Tue, 21 Oct 2008 15:26:53 GMT From: Julien Cigar To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-3.1 Cc: Subject: ports/128271: blastall segfaults when output is set to XML (-m 7) X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 21 Oct 2008 15:30:04 -0000 >Number: 128271 >Category: ports >Synopsis: blastall segfaults when output is set to XML (-m 7) >Confidential: no >Severity: serious >Priority: high >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: sw-bug >Submitter-Id: current-users >Arrival-Date: Tue Oct 21 15:30:04 UTC 2008 >Closed-Date: >Last-Modified: >Originator: Julien Cigar >Release: 7.0-RELEASE >Organization: ULB >Environment: FreeBSD bccm-it.vub.ac.be 7.0-RELEASE-p4 FreeBSD 7.0-RELEASE-p4 #2: Wed Sep 10 09:56:56 CEST 2008 root@bccm-it.vub.ac.be:/usr/obj/usr/src/sys/CUSTOM i386 >Description: Hello, All is in the title, blastall segfaults on my machine when output is set to XML, default (text) output however works. >How-To-Repeat: jcigar@bccm-it rodentia % cat /tmp/98b284018c5e0f5dabd8eee9fc07def7.txt ATGACAAATTTTCGAAAAACACACCCACTACTCAAAATTATTAATAACACATTTATTGACCTCCCAACCCCCTCAAAT jcigar@bccm-it rodentia % blastall -p blastn -i /tmp/98b284018c5e0f5dabd8eee9fc07def7.txt -d rodentia.fasta -m 7 zsh: segmentation fault (core dumped) blastall -p blastn -i /tmp/98b284018c5e0f5dabd8eee9fc07def7.txt -d -m 7 >Fix: upgrade to ncbi-toolkit 2.2.18 (current version is very outdated) ? >Release-Note: >Audit-Trail: >Unformatted: