From owner-freebsd-ports-bugs@FreeBSD.ORG Fri Oct 24 12:20:04 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 688E910656A3 for ; Fri, 24 Oct 2008 12:20:04 +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 518A28FC12 for ; Fri, 24 Oct 2008 12:20:04 +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 m9OCK4LI062950 for ; Fri, 24 Oct 2008 12:20:04 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.3/8.14.3/Submit) id m9OCK4V7062949; Fri, 24 Oct 2008 12:20:04 GMT (envelope-from gnats) Date: Fri, 24 Oct 2008 12:20:04 GMT Message-Id: <200810241220.m9OCK4V7062949@freefall.freebsd.org> To: freebsd-ports-bugs@FreeBSD.org From: "Fernan Aguero" Cc: Subject: Re: ports/128271: biology/ncbi-toolkit - 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 Reply-To: Fernan Aguero List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 24 Oct 2008 12:20:04 -0000 The following reply was made to PR ports/128271; it has been noted by GNATS. From: "Fernan Aguero" To: bug-followup@freebsd.org, jcigar@ulb.ac.be Cc: Subject: Re: ports/128271: biology/ncbi-toolkit - blastall segfaults when output is set to XML (-m 7) Date: Fri, 24 Oct 2008 09:56:43 -0200 ------=_Part_6844_16388911.1224849403956 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Julie, I can confirm this bug with blastall 2.2.14 (see attached typescript). I have just updated the ncbi-toolkit port to the latest version (blast 2.2.18) in my box and I can no longer reproduce it, so I understand the bug seems has been fixed. I will try to submit the update as soon as possible, but it may take some days, as I'm flooded with work right now. In the meantime, please notice that the segfault when requesting XML format does not occur in all cases (i.e. if XML is what you need you probably don't need to wait for the updated port). fetch ftp://ftp.ncbi.nih.gov/blast/db/FASTA/vector.gz gzip -d vector.gz formatdb -i vector.gz -p F echo "CGAATCGTAACCGTTCGTACGAGAATCGCTGTCCTCTCCTTC" > test.fna Three ways of doing the same thing: i) blastall -p blastn -d vector -i test.fna -m7 vs ii) echo "CGAATCGTAACCGTTCGTACGAGAATCGCTGTCCTCTCCTTC" | blastall -p blastn -d vector -m7 vs iii) cat test.fna | blastall -p blastn -d vector -m7 In my hands (see attached typescript) I can only reproduce the bug when calling blastall as in (ii). I have never been able to get a core dump when calling blastall as in (i) or (iii). Cheers, -- fernan ------=_Part_6844_16388911.1224849403956 Content-Type: text/plain; name=test.txt Content-Transfer-Encoding: base64 X-Attachment-Id: f_fmoroghi1 Content-Disposition: attachment; filename=test.txt U2NyaXB0IHN0YXJ0ZWQgb24gRnJpIE9jdCAyNCAwODoxODo0OCAyMDA4CltmZXJuYW5AZ2FtYSB+ L3Rlc3RfYmxhc3RdIGJsYXN0YWxsIC1wIGJsYXN0biAtZCB2ZWN0b3IgLWkgdGVzdC5mbmEgLW04 IA0NCnRlc3QJZ2l8NTEzNjk5fGVtYnxBMTQxNTMuMXwJMTAwLjAwCTQyCTAJMAkxCTQyCTI3CTY4 CThlLTE4CTgzLjgNCnRlc3QJZ2l8NTEzNjUyfGVtYnxBMTM3NzUuMXwJMTAwLjAwCTQyCTAJMAkx CTQyCTEJNDIJOGUtMTgJODMuOA0KClsgdHJpbW1lZCBvdXRwdXQgXQoKW2Zlcm5hbkBnYW1hIH4v dGVzdF9ibGFzdF0gYmxhc3RhbGwgLXAgYmxhc3RuIC1kIHZlY3RvciAtaSB0ZXN0LmZuYSAtbTcN DQo8P3htbCB2ZXJzaW9uPSIxLjAiPz4NCjwhRE9DVFlQRSBCbGFzdE91dHB1dCBQVUJMSUMgIi0v L05DQkkvL05DQkkgQmxhc3RPdXRwdXQvRU4iICJodHRwOi8vd3d3Lm5jYmkubmxtLm5paC5nb3Yv ZHRkL05DQklfQmxhc3RPdXRwdXQuZHRkIj4NCjxCbGFzdE91dHB1dD4NCiAgPEJsYXN0T3V0cHV0 X3Byb2dyYW0+Ymxhc3RuPC9CbGFzdE91dHB1dF9wcm9ncmFtPg0KICA8Qmxhc3RPdXRwdXRfdmVy c2lvbj5ibGFzdG4gMi4yLjE0IFtNYXktMDctMjAwNl08L0JsYXN0T3V0cHV0X3ZlcnNpb24+DQog IDxCbGFzdE91dHB1dF9yZWZlcmVuY2U+flJlZmVyZW5jZTogQWx0c2NodWwsIFN0ZXBoZW4gRi4s IFRob21hcyBMLiBNYWRkZW4sIEFsZWphbmRybyBBLiBTY2hhZmZlciwgfkppbmdodWkgWmhhbmcs IFpoZW5nIFpoYW5nLCBXZWJiIE1pbGxlciwgYW5kIERhdmlkIEouIExpcG1hbiAoMTk5NyksIH4m cXVvdDtHYXBwZWQgQkxBU1QgYW5kIFBTSS1CTEFTVDogYSBuZXcgZ2VuZXJhdGlvbiBvZiBwcm90 ZWluIGRhdGFiYXNlIHNlYXJjaH5wcm9ncmFtcyZxdW90OywgIE51Y2xlaWMgQWNpZHMgUmVzLiAy NTozMzg5LTM0MDIuPC9CbGFzdE91dHB1dF9yZWZlcmVuY2U+DQoKWyB0cmltbWVkIG91dHB1dCBd Cgo8L0JsYXN0T3V0cHV0Pg0KW2Zlcm5hbkBnYW1hIH4vdGVzdF9ibGFzdF0gZWNobyAiQ0dBQVRD R1RBQUNDR1RUQ0dUQUNHQUdBQVRDR0NUR1RDQ1RDVENDVFRDIiB8IGJsYXN0YWxsIC1wIGJsYXN0 biAtZCB2ZWN0b3IgLW03DQ0KU2VnbWVudGF0aW9uIGZhdWx0IChjb3JlIGR1bXBlZCkNCltmZXJu YW5AZ2FtYSB+L3Rlc3RfYmxhc3RdIGVjaG8gIkNHQUFUQ0dUQUFDQ0dUVENHVEFDR0FHQUFUQ0dD VEdUQ0NUQ1RDQ1RUQyIgfCBibGFzdGFsbCAtcCBibGFzdG4gLWQgdmVjdG9yIC1tOA0NCjFfMAln aXw1MTM2OTl8ZW1ifEExNDE1My4xfAkxMDAuMDAJNDIJMAkwCTEJNDIJMjcJNjgJOGUtMTgJODMu OA0KMV8wCWdpfDUxMzY1MnxlbWJ8QTEzNzc1LjF8CTEwMC4wMAk0MgkwCTAJMQk0MgkxCTQyCThl LTE4CTgzLjgNCgpbIHRyaW1tZWQgb3V0cHV0IF0KCltmZXJuYW5AZ2FtYSB+dGVzdF9ibGFzdF0g Y2F0IHRlc3QuZm5hIHwgYmxhc3RhbGwgLXAgYmxhc3RuIC1kIHZlY3RvciAtbTcNDQo8P3htbCB2 ZXJzaW9uPSIxLjAiPz4NCjwhRE9DVFlQRSBCbGFzdE91dHB1dCBQVUJMSUMgIi0vL05DQkkvL05D QkkgQmxhc3RPdXRwdXQvRU4iICJodHRwOi8vd3d3Lm5jYmkubmxtLm5paC5nb3YvZHRkL05DQklf Qmxhc3RPdXRwdXQuZHRkIj4NCjxCbGFzdE91dHB1dD4NCiAgPEJsYXN0T3V0cHV0X3Byb2dyYW0+ Ymxhc3RuPC9CbGFzdE91dHB1dF9wcm9ncmFtPg0KICA8Qmxhc3RPdXRwdXRfdmVyc2lvbj5ibGFz dG4gMi4yLjE0IFtNYXktMDctMjAwNl08L0JsYXN0T3V0cHV0X3ZlcnNpb24+DQogIDxCbGFzdE91 dHB1dF9yZWZlcmVuY2U+flJlZmVyZW5jZTogQWx0c2NodWwsIFN0ZXBoZW4gRi4sIFRob21hcyBM LiBNYWRkZW4sIEFsZWphbmRybyBBLiBTY2hhZmZlciwgfkppbmdodWkgWmhhbmcsIFpoZW5nIFpo YW5nLCBXZWJiIE1pbGxlciwgYW5kIERhdmlkIEouIExpcG1hbiAoMTk5NyksIH4mcXVvdDtHYXBw ZWQgQkxBU1QgYW5kIFBTSS1CTEFTVDogYSBuZXcgZ2VuZXJhdGlvbiBvZiBwcm90ZWluIGRhdGFi YXNlIHNlYXJjaH5wcm9ncmFtcyZxdW90OywgIE51Y2xlaWMgQWNpZHMgUmVzLiAyNTozMzg5LTM0 MDIuPC9CbGFzdE91dHB1dF9yZWZlcmVuY2U+DQoKWyB0cmltbWVkIG91dHB1dCBdCgo8L0JsYXN0 T3V0cHV0Pg0KW2Zlcm5hbkBnYW1hIH50ZXN0X2JsYXN0XSBjYXQgdGVzdC5mbmEgfCBibGFzdGFs bCAtcCBibGFzdG4gLWQgdmVjdG9yIC1tOA0NCnRlc3QJZ2l8NTEzNjk5fGVtYnxBMTQxNTMuMXwJ MTAwLjAwCTQyCTAJMAkxCTQyCTI3CTY4CThlLTE4CTgzLjgNCnRlc3QJZ2l8NTEzNjUyfGVtYnxB MTM3NzUuMXwJMTAwLjAwCTQyCTAJMAkxCTQyCTEJNDIJOGUtMTgJODMuOA0KClsgdHJpbW1lZCBv dXRwdXQgXQoKW2Zlcm5hbkBnYW1hIH50ZXN0X2JsYXN0XSBeRAgIZXhpdA0KClNjcmlwdCBkb25l IG9uIEZyaSBPY3QgMjQgMDg6NDg6NTUgMjAwOAo= ------=_Part_6844_16388911.1224849403956--