From biopython-bugs at bioperl.org Thu Nov 7 09:52:55 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:16 2005 Subject: [Biopython-dev] Notification: incoming/93 Message-ID: <200211071452.gA7Eqt6J025570@pw600a.bioperl.org> JitterBug notification new message incoming/93 Message summary for PR#93 From: andreas.kuntzagk@mdc-berlin.de Subject: GenBank-Format (Feature-Qualifier /motif) Date: Thu, 7 Nov 2002 09:52:51 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From andreas.kuntzagk@mdc-berlin.de Thu Nov 7 09:52:52 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gA7Eqp6J025565 for ; Thu, 7 Nov 2002 09:52:52 -0500 Date: Thu, 7 Nov 2002 09:52:51 -0500 Message-Id: <200211071452.gA7Eqp6J025565@pw600a.bioperl.org> From: andreas.kuntzagk@mdc-berlin.de To: biopython-bugs@bioperl.org Subject: GenBank-Format (Feature-Qualifier /motif) Full_Name: Andreas Kuntzagk Module: genbank_format.py Version: OS: Submission from: sulawesi.bioinf.mdc-berlin.de (141.80.80.60) In Entry GI:4165449 (and others) there is a qualifier /motif in a CDS -Feature. Currently the genbank_format.py doesn't allow this. Fix: insert "motif" into the feature_qualifier_names diff -r1.20 genbank_format.py 528a529 > "motif", From thomas at cbs.dtu.dk Fri Nov 8 06:22:21 2002 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] fast N-mer seach? Message-ID: Hej, What is the current best/fastest way to count all oligos of a given size in a sequence? Is this something one could use mx.TextTools for? Or is it still faster to use the naive way by looping over i, extract all seq[i:i+size] and increase the count in a dictionary ...? What if I'd like to count all word/oligo frequencies up to size N? stepping-into-the-optimization-swamp'ly y'rs -thomas -- Sicheritz-Ponten Thomas, Ph.D, thomas@biopython.org ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From biopython-bugs at bioperl.org Tue Nov 12 03:58:59 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/94 Message-ID: <200211120858.gAC8wx6J018639@pw600a.bioperl.org> JitterBug notification new message incoming/94 Message summary for PR#94 From: hikokabu@hotmail.com Subject: GebBankParser Date: Tue, 12 Nov 2002 03:58:57 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From hikokabu@hotmail.com Tue Nov 12 03:58:58 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gAC8wv6J018633 for ; Tue, 12 Nov 2002 03:58:58 -0500 Date: Tue, 12 Nov 2002 03:58:57 -0500 Message-Id: <200211120858.gAC8wv6J018633@pw600a.bioperl.org> From: hikokabu@hotmail.com To: biopython-bugs@bioperl.org Subject: GebBankParser Full_Name: Hisahiko Sato Module: biopython-1.00a4.win32-py2.2.exe Version: biopython-1.00a4.win32-py2.2.exe OS: win2000 Submission from: pvgw.m.chiba-u.ac.jp (133.82.145.42) while parsing a GenBankFile I got stucked saying "" E:\>F:\Desktop\SearchSeaquence.py 1 Homo sapiens Traceback (most recent call last): File "F:\Desktop\SearchSeaquence.py", line 9, in ? cur=iterator.next() File "E:\Python22\Lib\site-packages\Bio\GenBank\__init__.py", line 183, in nex t return self._parser.parse(File.StringHandle(data)) File "E:\Python22\Lib\site-packages\Bio\GenBank\__init__.py", line 268, in par se self._scanner.feed(handle, self._consumer) File "E:\Python22\Lib\site-packages\Bio\GenBank\__init__.py", line 1250, in fe ed self._parser.parseFile(handle) File "E:\Python22\Lib\site-packages\Martel\Parser.py", line 230, in parseFile self.parseString(fileobj.read()) File "E:\Python22\Lib\site-packages\Martel\Parser.py", line 258, in parseStrin g self._err_handler.fatalError(result) File "E:\Python22\lib\xml\sax\handler.py", line 38, in fatalError raise exception Martel.Parser.ParserPositionException: error parsing at or beyond character 1681 """ the entry which makes error is like this LOCUS HSU40580 4467 bp DNA linear PRI 16-OCT-2001 DEFINITION Human U22 snoRNA host gene (UHG) gene, complete sequence. ACCESSION U40580 VERSION U40580.1 GI:1200185 KEYWORDS . SOURCE Homo sapiens ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 4467) AUTHORS Tycowski,K.T., Shu,M.D. and Steitz,J.A. TITLE A mammalian gene with introns instead of exons generating stable RNA products JOURNAL Nature 379 (6564), 464-466 (1996) MEDLINE 96158882 PUBMED 8559254 REFERENCE 2 (bases 1 to 4467) AUTHORS Tycowski,K.T., Shu,M.-D. and Steitz,J.A. TITLE Direct Submission JOURNAL Submitted (13-NOV-1995) Kazimierz T. Tycowski, Molecular Biophysics & Biochemistry, Yale University, 295 Congress Ave., New Haven, CT 06536, USA FEATURES Location/Qualifiers source 1..4467 /organism="Homo sapiens" /db_xref="taxon:9606" gene 466..4391 /gene="UHG" TATA_signal 466..477 /gene="UHG" misc_RNA join(496..516,915..957,1165..1248,1443..1493,1830..1862, 2319..2365,2550..2582,2792..2830,3266..3306,3541..3569, 3700..4390) /gene="UHG" exon 496..516 /gene="UHG" /number=1 intron 517..914 /gene="UHG" /number=1 snoRNA 750..816 /gene="UHG" /product="U25 snoRNA" /note="U25 snoRNA gene" exon 915..957 /gene="UHG" /number=2 intron 958..1164 /gene="UHG" /number=2 snoRNA 1015..1089 /gene="UHG" /product="U26 snoRNA" /note="U26 snoRNA gene" exon 1165..1248 /gene="UHG" /number=3 intron 1249..1442 /gene="UHG" /number=3 snoRNA 1298..1369 /gene="UHG" /product="U27 snoRNA" /note="U27 snoRNA gene" exon 1443..1493 /gene="UHG" /number=4 intron 1494..1829 /gene="UHG" /number=4 snoRNA 1686..1760 /gene="UHG" /product="U28 snoRNA" /note="U28 snoRNA gene" exon 1830..1862 /gene="UHG" /number=5 intron 1863..2318 /gene="UHG" /number=5 misc_feature 2098..2222 /gene="UHG" /note="U22 snoRNA pseudogene" exon 2319..2365 /gene="UHG" /number=6 intron 2366..2549 /gene="UHG" /number=6 snoRNA 2415..2479 /gene="UHG" /product="U29 snoRNA" /note="U29 snoRNA gene" exon 2550..2582 /gene="UHG" /number=7 intron 2583..2791 /gene="UHG" /number=7 snoRNA 2651..2720 /gene="UHG" /product="U30 snoRNA" /note="U30 snoRNA gene" exon 2792..2830 /gene="UHG" /number=8 intron 2831..3265 /gene="UHG" /number=8 snoRNA 2989..3056 /gene="UHG" /product="U31 snoRNA" /note="U31 snoRNA gene" exon 3266..3306 /gene="UHG" /number=9 intron 3307..3540 /gene="UHG" /number=9 snoRNA 3346..3470 /gene="UHG" /product="U22 snoRNA" /note="U22 snoRNA gene" exon 3541..3569 /gene="UHG" /number=10 intron 3570..3699 /gene="UHG" /number=10 exon 3700..4390 /gene="UHG" /number=11 repeat_unit 3955..4065 /gene="UHG" /note="Alu-repeat" polyA_signal 4373..4378 /gene="UHG" polyA_site 4390 /gene="UHG" BASE COUNT 1106 a 927 c 1041 g 1392 t 1 others ORIGIN 1 gagtcgtccc ccgcgctgag accctggaca ccagcctccg aatgtgagcc aggcaactgg 61 cgcggaatcg acacgacggc gatcgaggct tcaggagnct gtagctccat ggaggcggat 121 cctgcacaca ggtttggggt gtgtgggcaa ggggcagctc agaacagggt tagagggtag 181 gcagtcgtga ccgtcagtcc aggatcgccg tgaggcagtg atctcaccgc tcctgccaca 241 tgcactgggt gagaaaacca agccgcaatg cggtcggtga gccagcacgc tcccgtagga 301 cgcatgcgcg cctttttcgc gccgcaagtt caggtggcgc tttgtctacg ccctccttcc 361 ctggaactct ctacccacaa ctccccgggg tcgcatgcgg tcaacgtatg cgcgtgcgct 421 cgccgtagcc ccgcccccaa atcccgtggg cccctgccgg catggtattt aatcgtctcc 481 ccggggagat tcgttctcat ttttctactg ctcgtggtaa gtggcttcgt ggtctttata 541 gctgttactc ttttgtactt tgtctttttc ttttattttc ttttgagcga ttgtgcgaac 601 atagcatagc acgcactatg ccttctgtgt tgtagctgcc tggccagggc gactggcgga 661 taaggtcttg tgcgtggcct cgaggcttaa aagtagcagt ggggctttgt gaaggacaaa 721 atggcgatgg cgggccgtgt aggtccccct tcctatgatg aggacctttt cacagacctg 781 tactgagctc cgtgaggata aataactctg aggagatggg ccctgcaagc ctcttgctta 841 gccgtctgtt cagaaaatag cgttttcgaa atgccctgag ttgacctaat gtcttattgg 901 gctcctgtct gcaggattta cgcgcacgtt ggaaccgaag agagctctgt tgttgcagta 961 agttcttacg gccatttctt aatctctgct ctttcgttga gtgtgtggaa gttgctacgg 1021 ggatgatttt acgaactgaa ctctctcttt ctgatggatt agtggagaaa acagaaaatt 1081 ctgagta ====> MESSAGE TRUNCATED AT 8192 <==== From biopython-bugs at bioperl.org Tue Nov 12 19:52:12 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/95 Message-ID: <200211130052.gAD0qC6J026846@pw600a.bioperl.org> JitterBug notification new message incoming/95 Message summary for PR#95 From: Jeffrey Chang Subject: Re: [Biopython-dev] Notification: incoming/94 Date: Tue, 12 Nov 2002 16:50:53 -0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From jchang@springfield.stanford.edu Tue Nov 12 19:52:12 2002 Received: from springfield.stanford.edu (springfield.Stanford.EDU [128.12.147.41]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gAD0qB6J026842 for ; Tue, 12 Nov 2002 19:52:12 -0500 Received: (from jchang@localhost) by springfield.stanford.edu (8.11.6/8.11.6) id gAD0osQ43464; Tue, 12 Nov 2002 16:50:54 -0800 (PST) (envelope-from jchang) Date: Tue, 12 Nov 2002 16:50:53 -0800 From: Jeffrey Chang To: hikokabu@hotmail.com Cc: biopython-bugs@bioperl.org Subject: Re: [Biopython-dev] Notification: incoming/94 Message-ID: <20021113005053.GB43356@springfield.stanford.edu> Mail-Followup-To: hikokabu@hotmail.com, biopython-bugs@bioperl.org References: <200211120858.gAC8wx6J018639@pw600a.bioperl.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <200211120858.gAC8wx6J018639@pw600a.bioperl.org> User-Agent: Mutt/1.4i Try updating the files inside the Bio/GenBank package from the CVS (cvs.biopython.org). There have been a number of updates to the format definitions since release 1.00a4. Jeff On Tue, Nov 12, 2002 at 03:58:59AM -0500, biopython-bugs@bioperl.org wrote: > JitterBug notification > > new message incoming/94 > > Message summary for PR#94 > From: hikokabu@hotmail.com > Subject: GebBankParser > Date: Tue, 12 Nov 2002 03:58:57 -0500 > 0 replies 0 followups > > ====> ORIGINAL MESSAGE FOLLOWS <==== > > >From hikokabu@hotmail.com Tue Nov 12 03:58:58 2002 > Received: from localhost (localhost [127.0.0.1]) > by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gAC8wv6J018633 > for ; Tue, 12 Nov 2002 03:58:58 -0500 > Date: Tue, 12 Nov 2002 03:58:57 -0500 > Message-Id: <200211120858.gAC8wv6J018633@pw600a.bioperl.org> > From: hikokabu@hotmail.com > To: biopython-bugs@bioperl.org > Subject: GebBankParser > > Full_Name: Hisahiko Sato > Module: biopython-1.00a4.win32-py2.2.exe > Version: biopython-1.00a4.win32-py2.2.exe > OS: win2000 > Submission from: pvgw.m.chiba-u.ac.jp (133.82.145.42) > > > while parsing a GenBankFile I got stucked saying > "" > E:\>F:\Desktop\SearchSeaquence.py > 1 > Homo sapiens > Traceback (most recent call last): > File "F:\Desktop\SearchSeaquence.py", line 9, in ? > cur=iterator.next() > File "E:\Python22\Lib\site-packages\Bio\GenBank\__init__.py", line 183, in > nex > t > return self._parser.parse(File.StringHandle(data)) > File "E:\Python22\Lib\site-packages\Bio\GenBank\__init__.py", line 268, in > par > se > self._scanner.feed(handle, self._consumer) > File "E:\Python22\Lib\site-packages\Bio\GenBank\__init__.py", line 1250, in > fe > ed > self._parser.parseFile(handle) > File "E:\Python22\Lib\site-packages\Martel\Parser.py", line 230, in parseFile > self.parseString(fileobj.read()) > File "E:\Python22\Lib\site-packages\Martel\Parser.py", line 258, in > parseStrin > g > self._err_handler.fatalError(result) > File "E:\Python22\lib\xml\sax\handler.py", line 38, in fatalError > raise exception > Martel.Parser.ParserPositionException: error parsing at or beyond character > 1681 > > """ > > the entry which makes error is like this > LOCUS HSU40580 4467 bp DNA linear PRI 16-OCT-2001 > DEFINITION Human U22 snoRNA host gene (UHG) gene, complete sequence. > ACCESSION U40580 > VERSION U40580.1 GI:1200185 > KEYWORDS . > SOURCE Homo sapiens > ORGANISM Homo sapiens > Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; > Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. > REFERENCE 1 (bases 1 to 4467) > AUTHORS Tycowski,K.T., Shu,M.D. and Steitz,J.A. > TITLE A mammalian gene with introns instead of exons generating stable > RNA products > JOURNAL Nature 379 (6564), 464-466 (1996) > MEDLINE 96158882 > PUBMED 8559254 > REFERENCE 2 (bases 1 to 4467) > AUTHORS Tycowski,K.T., Shu,M.-D. and Steitz,J.A. > TITLE Direct Submission > JOURNAL Submitted (13-NOV-1995) Kazimierz T. Tycowski, Molecular Biophysics > & Biochemistry, Yale University, 295 Congress Ave., New Haven, CT > 06536, USA > FEATURES Location/Qualifiers > source 1..4467 > /organism="Homo sapiens" > /db_xref="taxon:9606" > gene 466..4391 > /gene="UHG" > TATA_signal 466..477 > /gene="UHG" > misc_RNA join(496..516,915..957,1165..1248,1443..1493,1830..1862, > 2319..2365,2550..2582,2792..2830,3266..3306,3541..3569, > 3700..4390) > /gene="UHG" > exon 496..516 > /gene="UHG" > /number=1 > intron 517..914 > /gene="UHG" > /number=1 > snoRNA 750..816 > /gene="UHG" > /product="U25 snoRNA" > /note="U25 snoRNA gene" > exon 915..957 > /gene="UHG" > /number=2 > intron 958..1164 > /gene="UHG" > /number=2 > snoRNA 1015..1089 > /gene="UHG" > /product="U26 snoRNA" > /note="U26 snoRNA gene" > exon 1165..1248 > /gene="UHG" > /number=3 > intron 1249..1442 > /gene="UHG" > /number=3 > snoRNA 1298..1369 > /gene="UHG" > /product="U27 snoRNA" > /note="U27 snoRNA gene" > exon 1443..1493 > /gene="UHG" > /number=4 > intron 1494..1829 > /gene="UHG" > /number=4 > snoRNA 1686..1760 > /gene="UHG" > /product="U28 snoRNA" > /note="U28 snoRNA gene" > exon 1830..1862 > /gene="UHG" > /number=5 > intron 1863..2318 > /gene="UHG" > /number=5 > misc_feature 2098..2222 > /gene="UHG" > /note="U22 snoRNA pseudogene" > exon 2319..2365 > /gene="UHG" > /number=6 > intron 2366..2549 > /gene="UHG" > /number=6 > snoRNA 2415..2479 > /gene="UHG" > /product="U29 snoRNA" > /note="U29 snoRNA gene" > exon 2550..2582 > /gene="UHG" > /number=7 > intron 2583..2791 > /gene="UHG" > /number=7 > snoRNA 2651..2720 > /gene="UHG" > /product="U30 snoRNA" > /note="U30 snoRNA gene" > exon 2792..2830 > /gene="UHG" > /number=8 > intron 2831..3265 > /gene="UHG" > /number=8 > snoRNA 2989..3056 > /gene="UHG" > /product="U31 snoRNA" > /note="U31 snoRNA gene" > exon 3266..3306 > /gene="UHG" > /number=9 > intron 3307..3540 > /gene="UHG" > /number=9 > snoRNA 3346..3470 > /gene="UHG" > /product="U22 snoRNA" > /note="U22 snoRNA gene" > exon 3541..3569 > /gene="UHG" > /number=10 > intron ====> MESSAGE TRUNCATED AT 8192 <==== From biopython-bugs at bioperl.org Wed Nov 13 08:35:11 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/96 Message-ID: <200211131335.gADDZB6J002301@pw600a.bioperl.org> JitterBug notification new message incoming/96 Message summary for PR#96 From: "WALL STREET BULLETIN..47634" Subject: NEW STOCK PICK: PRCT - LAST PICK UP 150%......................................................................................................................................................................................................... ermom Date: Wed, 13 Nov 2002 07:34:52 -0600 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From Subscriber_Services78054@mho.net Wed Nov 13 08:35:11 2002 Received: from 24.132.88.113 ([210.212.0.3]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id gADDYS6J002270 for ; Wed, 13 Nov 2002 08:34:37 -0500 Message-Id: <200211131334.gADDYS6J002270@pw600a.bioperl.org> Received: from smtp-server1.cfl.rr.com ([5.151.138.187]) by rly-xl04.mx.aol.com with esmtp; Nov, 13 2002 7:14:12 AM +0400 Received: from 157.139.128.128 ([157.139.128.128]) by mta6.snfc21.pbi.net with asmtp; Nov, 13 2002 6:14:23 AM -0800 Received: from [195.98.27.144] by web13708.mail.yahoo.com with smtp; Nov, 13 2002 5:22:32 AM +0700 From: "WALL STREET BULLETIN..47634" To: WALL.STREET.BULLETIN..46400 Cc: Subject: NEW STOCK PICK: PRCT - LAST PICK UP 150%......................................................................................................................................................................................................... ermom Sender: "WALL STREET BULLETIN..47634" Mime-Version: 1.0 Content-Type: text/html; charset="iso-8859-1" Date: Wed, 13 Nov 2002 07:34:52 -0600 X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-Priority: 1

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cshwjkwxvmmkrvjapwtvfubctotfj From biopython-bugs at bioperl.org Wed Nov 13 08:45:14 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/97 Message-ID: <200211131345.gADDjE6J002468@pw600a.bioperl.org> JitterBug notification new message incoming/97 Message summary for PR#97 From: "WALL STREET BULLETIN..46389" Subject: NEW STOCK PICK: PRCT - LAST PICK UP 150%......................................................................................................................................................................................................... akglb Date: Wed, 13 Nov 2002 07:45:17 -0600 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From Subscriber_Services78054@vail.net Wed Nov 13 08:45:13 2002 Received: from 200.54.163.2 ([200.54.163.2]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id gADDj46J002437 for ; Wed, 13 Nov 2002 08:45:09 -0500 Message-Id: <200211131345.gADDj46J002437@pw600a.bioperl.org> Received: from unknown (170.127.231.172) by smtp013.mail.yahoo.com with local; Nov, 13 2002 7:16:59 AM +1100 Received: from 131.159.235.104 ([131.159.235.104]) by rly-yk05.mx.aol.com with local; Nov, 13 2002 6:23:52 AM -0000 Received: from [41.237.71.37] by f64.law4.hotmail.com with NNFMP; Nov, 13 2002 5:40:57 AM -0800 From: "WALL STREET BULLETIN..46389" To: WALL.STREET.BULLETIN..46758 Cc: Subject: NEW STOCK PICK: PRCT - LAST PICK UP 150%......................................................................................................................................................................................................... akglb Sender: "WALL STREET BULLETIN..46389" Mime-Version: 1.0 Content-Type: text/html; charset="iso-8859-1" Date: Wed, 13 Nov 2002 07:45:17 -0600 X-Mailer: Microsoft Outlook Build 10.0.2627 X-Priority: 1

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vmssgechtnytpgjdkfblkmahernsu From biopython-bugs at bioperl.org Wed Nov 13 09:52:58 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/98 Message-ID: <200211131452.gADEqw6J003450@pw600a.bioperl.org> JitterBug notification new message incoming/98 Message summary for PR#98 From: "WALL STREET BULLETIN..47814" Subject: NEW STOCK PICK: PRCT - LAST PICK UP 150%......................................................................................................................................................................................................... txmnr Date: Wed, 13 Nov 2002 08:53:03 -0600 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From Subscriber_Services78037@cac.net Wed Nov 13 09:52:57 2002 Received: from 200.207.156.165 (eevabelfort.net1.nerim.net [62.212.100.195]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id gADEqs6J003446 for ; Wed, 13 Nov 2002 09:52:56 -0500 Message-Id: <200211131452.gADEqs6J003446@pw600a.bioperl.org> Received: from rly-xl05.mx.aol.com ([147.119.50.98]) by smtp4.cyberec.com with NNFMP; Nov, 13 2002 8:50:41 AM +0300 Received: from 87.15.78.89 ([87.15.78.89]) by pet.vosn.net with local; Nov, 13 2002 7:36:43 AM +1200 Received: from 131.159.235.104 ([131.159.235.104]) by rly-yk05.mx.aol.com with local; Nov, 13 2002 6:23:59 AM -0200 Received: from [41.237.71.37] by f64.law4.hotmail.com with NNFMP; Nov, 13 2002 5:23:34 AM +0300 From: "WALL STREET BULLETIN..47814" To: biopython-bugs@bioperl.org Cc: Subject: NEW STOCK PICK: PRCT - LAST PICK UP 150%......................................................................................................................................................................................................... txmnr Sender: "WALL STREET BULLETIN..47814" Mime-Version: 1.0 Content-Type: text/html; charset="iso-8859-1" Date: Wed, 13 Nov 2002 08:53:03 -0600 X-Mailer: Microsoft Outlook Build 10.0.2616 X-Priority: 1

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hctiqmjvbnotoxe From jchang at smi.stanford.edu Wed Nov 13 18:09:45 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/93 In-Reply-To: <200211071452.gA7Eqt6J025570@pw600a.bioperl.org> References: <200211071452.gA7Eqt6J025570@pw600a.bioperl.org> Message-ID: <20021113230945.GA47117@springfield.stanford.edu> Thanks! I've applied the patch. Jeff On Thu, Nov 07, 2002 at 09:52:55AM -0500, biopython-bugs@bioperl.org wrote: > JitterBug notification > > new message incoming/93 > > Message summary for PR#93 > From: andreas.kuntzagk@mdc-berlin.de > Subject: GenBank-Format (Feature-Qualifier /motif) > Date: Thu, 7 Nov 2002 09:52:51 -0500 > 0 replies 0 followups > > ====> ORIGINAL MESSAGE FOLLOWS <==== > > >From andreas.kuntzagk@mdc-berlin.de Thu Nov 7 09:52:52 2002 > Received: from localhost (localhost [127.0.0.1]) > by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gA7Eqp6J025565 > for ; Thu, 7 Nov 2002 09:52:52 -0500 > Date: Thu, 7 Nov 2002 09:52:51 -0500 > Message-Id: <200211071452.gA7Eqp6J025565@pw600a.bioperl.org> > From: andreas.kuntzagk@mdc-berlin.de > To: biopython-bugs@bioperl.org > Subject: GenBank-Format (Feature-Qualifier /motif) > > Full_Name: Andreas Kuntzagk > Module: genbank_format.py > Version: > OS: > Submission from: sulawesi.bioinf.mdc-berlin.de (141.80.80.60) > > > In Entry GI:4165449 (and others) there is a qualifier /motif in a CDS -Feature. > Currently the genbank_format.py doesn't allow this. > > Fix: > insert "motif" into the feature_qualifier_names > > diff -r1.20 genbank_format.py > 528a529 > > "motif", > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From biopython-bugs at bioperl.org Thu Nov 14 09:42:15 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/99 Message-ID: <200211141442.gAEEgF6J015468@pw600a.bioperl.org> JitterBug notification new message incoming/99 Message summary for PR#99 From: "hiko" Subject: Re: [Biopython-dev] Notification: incoming/94 Date: Thu, 14 Nov 2002 23:43:06 0900 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From hikokabu@hotmail.com Thu Nov 14 09:42:14 2002 Received: from hotmail.com (oe72.law14.hotmail.com [64.4.20.207]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gAEEgD6J015451 for ; Thu, 14 Nov 2002 09:42:14 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 14 Nov 2002 06:42:18 -0800 X-Originating-IP: [133.82.145.42] From: "hiko" To: "Jeffrey Chang" Cc: References: <200211120858.gAC8wx6J018639@pw600a.bioperl.org> <20021113005053.GB43356@springfield.stanford.edu> Subject: Re: [Biopython-dev] Notification: incoming/94 Date: Thu, 14 Nov 2002 23:43:06 +0900 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_000C_01C28C37.94D0D880" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Message-ID: X-OriginalArrivalTime: 14 Nov 2002 14:42:18.0332 (UTC) FILETIME=[080BA9C0:01C28BEC] This is a multi-part message in MIME format. ------=_NextPart_000_000C_01C28C37.94D0D880 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit however I update the item, I still have a error...... I Check on Linux redhat .2 with python2.2.2 this File makes an error. regards. Hisahiko Sato ------=_NextPart_000_000C_01C28C37.94D0D880 Content-Type: application/octet-stream; name="ForTest.seq" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="ForTest.seq" LOCUS AF375472 148 bp snoRNA linear PRI = 16-OCT-2001=0A= DEFINITION Homo sapiens small nucleolar RNA M2, complete sequence and = LAMR1=0A= gene, intron 2.=0A= ACCESSION AF375472=0A= VERSION AF375472.1 GI:14248890=0A= KEYWORDS .=0A= SOURCE Homo sapiens=0A= ORGANISM Homo sapiens=0A= Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; = Euteleostomi;=0A= Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.=0A= REFERENCE 1 (bases 1 to 148)=0A= AUTHORS de la Pena,M.J., Wrathall,L., Le,P. and Sobel,M.E.=0A= TITLE Identification of additional members of the H/ACA family of = snoRNAs=0A= in human, chicken, and fruit fly=0A= JOURNAL Unpublished=0A= REFERENCE 2 (bases 1 to 148)=0A= AUTHORS de la Pena,M.J., Wrathall,L., Le,P. and Sobel,M.E.=0A= TITLE Direct Submission=0A= JOURNAL Submitted (02-MAY-2001) Laboratory of Pathology/Molecular = Pathology=0A= Section, National Cancer Institute - NIH, 9000 Rockville Pike=0A= B10/B1B53, Bethesda, MD 20892-1200, USA=0A= FEATURES Location/Qualifiers=0A= source 1..148=0A= /organism=3D"Homo sapiens"=0A= /db_xref=3D"taxon:9606"=0A= gene <1..>148=0A= /gene=3D"LAMR1"=0A= /note=3D"RPSA"=0A= snoRNA 1..148=0A= /gene=3D"LAMR1"=0A= /product=3D"snoRNA M2"=0A= intron <1..>148=0A= /gene=3D"LAMR1"=0A= /number=3D2=0A= misc_feature 70..75=0A= /gene=3D"LAMR1"=0A= /note=3D"H box"=0A= misc_feature 144..146=0A= /gene=3D"LAMR1"=0A= /note=3D"ACA box"=0A= BASE COUNT 35 a 32 c 39 g 42 t=0A= ORIGIN =0A= 1 tgcacactat taaagctcag ggtggaggcc agtcttggct catgaacttc = tgagtgtcgg=0A= 61 aagtgtgcta tatcaatggc aggattttcg ctaacaccag tagagcttgc = ctctatgact=0A= 121 ggagtttggt agtactcgct gccacata=0A= //=0A= ------=_NextPart_000_000C_01C28C37.94D0D880-- From biopython-bugs at bioperl.org Fri Nov 15 01:32:18 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/100 Message-ID: <200211150632.gAF6WI6J024403@pw600a.bioperl.org> JitterBug notification new message incoming/100 Message summary for PR#100 From: Jeffrey Chang Subject: Re: [Biopython-dev] Notification: incoming/94 Date: Thu, 14 Nov 2002 22:30:55 -0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From jchang@springfield.stanford.edu Fri Nov 15 01:32:17 2002 Received: from springfield.stanford.edu (springfield.Stanford.EDU [128.12.147.41]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gAF6WG6J024399 for ; Fri, 15 Nov 2002 01:32:17 -0500 Received: (from jchang@localhost) by springfield.stanford.edu (8.11.6/8.11.6) id gAF6UtS51880; Thu, 14 Nov 2002 22:30:56 -0800 (PST) (envelope-from jchang) Date: Thu, 14 Nov 2002 22:30:55 -0800 From: Jeffrey Chang To: hiko Cc: biopython-bugs@bioperl.org Subject: Re: [Biopython-dev] Notification: incoming/94 Message-ID: <20021115063055.GA51858@springfield.stanford.edu> Mail-Followup-To: hiko , biopython-bugs@bioperl.org References: <200211120858.gAC8wx6J018639@pw600a.bioperl.org> <20021113005053.GB43356@springfield.stanford.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.4i This file seems to have a residue type of "snoRNA", which the parser didn't handle. I have updated the genbank_format.py file to handle it. Please download the latest file at cvs.biopython.org, and let me know if that fixes things. Thanks for the bug report! Jeff On Thu, Nov 14, 2002 at 11:43:06PM +0900, hiko wrote: > however I update the item, I still have a error...... > I Check on Linux redhat .2 with python2.2.2 > this File makes an error. > > regards. > > Hisahiko Sato From ybastide at irisa.fr Mon Nov 18 17:15:37 2002 From: ybastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] BioSQL and PostgreSQL Message-ID: <3DD96689.60002@irisa.fr> Hi, I've adapted BioSQL/*.py to work with PostgreSQL. Well, at least the tests pass... Patch attached, comments are welcome. A few points: * I've made utility classes for nonstandard SQL/DBAPI operations, e.g. retrieving the id of the last inserted record. (The implementation is so-so, I know :). There are Generic_dbutils, Mysql_dbutils and Pg_dbutils. The choice is made according to the DBAPI module's name; only MySQLdb and psycopg are currently recognised. * Replaced count = self.cursor.execute by self.cursor.execute and fetch * Likewise, self.adaptor.execute_one("INSERT ...") --> self.adaptor.execute() * SUBSTRING(biosequence_str, %s, %s) --> SUBSTRING(biosequence_str FROM %s FOR %s). SQL is beautiful... * I've modified test_BioSQL.py so that the first doesn't require a schema (it will DROP DATABASE/CREATE DATABASE like the other ones). I've also added tearDown()'s to close the database connections; otherwise, psycopg cannot drop the db. * Modified open_database: psycopg uses a dsn, not keyword arguments. (Done but not included in the patch: adaptations to the current biosql-schema CVS.) Regards, Yves -------------- next part -------------- Index: BioSQL/BioSeqDatabase.py =================================================================== RCS file: /home/repository/biopython/biopython/BioSQL/BioSeqDatabase.py,v retrieving revision 1.10 diff -u -p -r1.10 BioSeqDatabase.py --- BioSQL/BioSeqDatabase.py 2002/03/01 08:39:24 1.10 +++ BioSQL/BioSeqDatabase.py 2002/11/18 21:18:43 @@ -5,6 +5,7 @@ database, and is compatible with the Bio """ import BioSeq import Loader +import DBUtils def open_database(driver = "MySQLdb", *args, **kwargs): """Main interface for loading a existing BioSQL-style database. @@ -26,16 +27,49 @@ def open_database(driver = "MySQLdb", *a """ module = __import__(driver) connect = getattr(module, "connect") - conn = connect(*args, **kwargs) + try: + conn = connect(*args, **kwargs) + except TypeError: + # Perhaps a version of psycopg with different parameter style + # (i.e., dsn="dbname= host= user=..." + # FIXME: doesn't use the args array + kw = kwargs.copy() + + for k in kw.keys(): + if kw[k] == '': del kw[k] + + if kw.has_key('db'): + kw['dbname'] = kw['db'] + del kw['db'] + if kw.has_key('passwd'): + kw['password'] = kw['passwd'] + del kw['passwd'] + + # PostgreSQL needs a database to connect to, so use a + # system one if needed + # FIXME: might be a security risk? + # So currently, we keep dbname=user +## if not kw.has_key('dbname'): +## kw['dbname'] = 'template1' + + dsn = ' '.join(['='.join(i) for i in kw.items()]) + conn = connect(dsn) + return DBServer(conn, module) class DBServer: def __init__(self, conn, module): - self.conn = conn self.module = module - self.adaptor = Adaptor(self.conn) + if module.__name__ == 'psycopg': + create_dbutils = DBUtils.create_Pg_dbutils + elif module.__name__ == 'MySQLdb': + create_dbutils = DBUtils.create_Mysql_dbutils + else: + create_dbutils = DBUtils.create_Generic_dbutils + self.adaptor = Adaptor(conn, create_dbutils) + def __repr__(self): - return self.__class__.__name__ + "(%r)" % self.conn + return self.__class__.__name__ + "(%r)" % self.adaptor.conn def __getitem__(self, name): return BioSeqDatabase(self.adaptor, name) def keys(self): @@ -58,7 +92,7 @@ class DBServer: # make the database sql = r"INSERT INTO biodatabase (name) VALUES" \ r" (%s)" - self.adaptor.execute_one(sql, (db_name)) + self.adaptor.execute(sql, (db_name,)) return BioSeqDatabase(self.adaptor, db_name) def load_database_sql(self, sql_file): @@ -74,6 +108,8 @@ class DBServer: for line in sql_handle.xreadlines(): if line.find("#") == 0: # don't include comment lines pass + elif line.find("--") == 0: # ditto, SQL std. comments + pass elif line.strip(): # only include non-blank lines sql += line.strip() sql += ' ' @@ -84,40 +120,48 @@ class DBServer: self.adaptor.cursor.execute(sql_line, ()) class Adaptor: - def __init__(self, conn): + def __init__(self, conn, create_dbutils): self.conn = conn self.cursor = conn.cursor() + self.dbutils = create_dbutils()##self.conn, self.cursor) + + def last_id(self, table): + return self.dbutils.last_id(self.cursor, table) + def autocommit(self, y = 1): + return self.dbutils.autocommit(self.conn, y) + def fetch_dbid_by_dbname(self, dbname): - count = self.cursor.execute( + self.cursor.execute( r"select biodatabase_id from biodatabase where name = %s", (dbname,)) - if count == 0: + rv = self.cursor.fetchall() + if not rv: raise KeyError("Cannot find biodatabase with name %r" % dbname) - assert count == 1, "More than one biodatabase with name %r" % dbname - return self.cursor.fetchone()[0] + assert len(rv) == 1, "More than one biodatabase with name %r" % dbname + return rv[0][0] def fetch_seqid_by_display_id(self, dbid, name): - count = self.cursor.execute( + self.cursor.execute( r"select bioentry_id from bioentry where " r" biodatabase_id = %s and display_id = %s", (dbid, name)) - if count == 0: + rv = self.cursor.fetchall() + if not rv: raise IndexError("Cannot find display id %r" % name) - assert count == 1, "More than one entry with display id of %r" % name - seqid, = self.cursor.fetchone() - return seqid + assert len(rv) == 1, "More than one entry with display id of %r" % name + return rv[0][0] def fetch_seqid_by_accession(self, dbid, name): - count = self.cursor.execute( + self.cursor.execute( r"select bioentry_id from bioentry where " r" biodatabase_id = %s and accession = %s", (dbid, name)) - if count == 0: + rv = self.cursor.fetchall() + if not rv: raise IndexError("Cannot find accession %r" % name) - assert count == 1, "More than one entry with accession of %r" % name - seqid, = self.cursor.fetchone() - return seqid + assert len(rv) == 1, "More than one entry with accession of %r" % name + return rv[0][0] def fetch_seqid_by_seqid(self, dbid, seqid): # XXX can't implement this right since it doesn't seem like the @@ -151,9 +196,10 @@ class Adaptor: return [field[0] for field in self.cursor.fetchall()] def execute_one(self, sql, args): - count = self.cursor.execute(sql, args) - assert count == 1, "Expected 1 response, got %s" % count - return self.cursor.fetchone() + self.cursor.execute(sql, args) + rv = self.cursor.fetchall() + assert len(rv) == 1, "Expected 1 response, got %s" % count + return rv[0] def execute(self, sql, args): """Just execute an sql command. @@ -163,7 +209,7 @@ class Adaptor: def get_subseq_as_string(self, seqid, start, end): length = end - start return self.execute_one( - """select SUBSTRING(biosequence_str, %s, %s) + """select SUBSTRING(biosequence_str FROM %s FOR %s) from biosequence where bioentry_id = %s""", (start+1, length, seqid))[0] Index: BioSQL/Loader.py =================================================================== RCS file: /home/repository/biopython/biopython/BioSQL/Loader.py,v retrieving revision 1.8 diff -u -p -r1.8 Loader.py --- BioSQL/Loader.py 2002/05/28 13:05:42 1.8 +++ BioSQL/Loader.py 2002/11/18 21:18:43 @@ -57,7 +57,7 @@ class DatabaseLoader: else: sql = r"INSERT INTO ontology_term (term_name, term_definition)" \ r"VALUES (%s, %s)" - self.adaptor.execute_one(sql, (term_name, term_description)) + self.adaptor.execute(sql, (term_name, term_description)) # recursively call this to give back the id return self._get_ontology_id(term_name, term_description) @@ -78,12 +78,10 @@ class DatabaseLoader: sql = r"INSERT INTO bioentry (biodatabase_id, display_id, " \ r"accession, entry_version, division) VALUES" \ r" (%s, %s, %s, %s, %s)" - self.adaptor.execute_one(sql, (self.dbid, record.name, - accession, version, division)) + self.adaptor.execute(sql, (self.dbid, record.name, + accession, version, division)) # now retrieve the id for the bioentry - sql = r"SELECT max(bioentry_id) FROM bioentry" - results = self.adaptor.execute_one(sql, ()) - bioentry_id = results[0] + bioentry_id = self.adaptor.last_id('bioentry') return bioentry_id @@ -100,7 +98,7 @@ class DatabaseLoader: date_id = self._get_ontology_id("date", "Sequence date") sql = r"INSERT INTO bioentry_qualifier_value VALUES" \ r" (%s, %s, %s)" - self.adaptor.execute_one(sql, (bioentry_id, date_id, date)) + self.adaptor.execute(sql, (bioentry_id, date_id, date)) def _load_bioentry_taxa(self, record, bioentry_id): """Add taxa information to the database. @@ -109,9 +107,9 @@ class DatabaseLoader: try: # XXX this isn't right, we need taxa ids and other junk taxa = record.annotations["taxa"] - sql = r"INSERT INTO bioentry_taxa VALUES" \ + sql = r"INSERT INTO bioentry_taxa(bioentry_id, taxa_id) VALUES" \ r" (%s, %s)" - self.adapter.execute_one(sql, (bioentry_id, taxa)) + self.adapter.execute(sql, (bioentry_id, taxa)) except KeyError: pass @@ -121,26 +119,26 @@ class DatabaseLoader: accession, version = record.id.split(".") # determine the string representation of the alphabet if isinstance(record.seq.alphabet, Alphabet.DNAAlphabet): - mol_type = "DNA" + alphabet = "DNA" elif isinstance(record.seq.alphabet, Alphabet.RNAAlphabet): - mol_type = "RNA" + alphabet = "RNA" elif isinstance(record.seq.alphabet, Alphabet.ProteinAlphabet): - mol_type = "PROTEIN" + alphabet = "PROTEIN" else: - mol_type = "UNKNOWN" + alphabet = "UNKNOWN" sql = r"INSERT INTO biosequence (bioentry_id, seq_version, " \ r"biosequence_str, molecule) VALUES (%s, %s, %s, %s)" - self.adaptor.execute_one(sql, (bioentry_id, version, record.seq.data, - mol_type)) + self.adaptor.execute(sql, (bioentry_id, version, record.seq.data, + alphabet)) def _load_bioentry_description(self, record, bioentry_id): """Load the description table. """ descr_id = self._get_ontology_id("description", "Sequence description") sql = r"INSERT INTO bioentry_qualifier_value VALUES (%s, %s, %s)" - self.adaptor.execute_one(sql, (bioentry_id, descr_id, - record.description)) + self.adaptor.execute(sql, (bioentry_id, descr_id, + record.description)) def _load_seqfeature(self, feature, feature_rank, bioentry_id): """Load a biopython SeqFeature into the database. @@ -161,11 +159,9 @@ class DatabaseLoader: # XXX This doesn't do source yet, since I'm not sure I understand it. sql = r"INSERT INTO seqfeature (bioentry_id, seqfeature_key_id, " \ r"seqfeature_rank) VALUES (%s, %s, %s)" - self.adaptor.execute_one(sql, (bioentry_id, seqfeature_key_id, - feature_rank)) - sql = r"SELECT max(seqfeature_id) FROM seqfeature" - results = self.adaptor.execute_one(sql, ()) - seqfeature_id = results[0] + self.adaptor.execute(sql, (bioentry_id, seqfeature_key_id, + feature_rank)) + seqfeature_id = self.adaptor.last_id('seqfeature') return seqfeature_id @@ -212,7 +208,7 @@ class DatabaseLoader: start = feature.location.nofuzzy_start + 1 end = feature.location.nofuzzy_end - self.adaptor.execute_one(sql, (seqfeature_id, start, end, strand, rank)) + self.adaptor.execute(sql, (seqfeature_id, start, end, strand, rank)) def _load_seqfeature_qualifiers(self, qualifiers, seqfeature_id): """Insert the (key, value) pair qualifiers relating to a feature. @@ -228,11 +224,11 @@ class DatabaseLoader: qualifier_value = qualifiers[qualifier_key][qual_value_rank] sql = r"INSERT INTO seqfeature_qualifier_value VALUES" \ r" (%s, %s, %s, %s)" - self.adaptor.execute_one(sql, (seqfeature_id, + self.adaptor.execute(sql, (seqfeature_id, qualifier_key_id, qual_value_rank, qualifier_value)) class DatabaseRemover: - """Compliment the Loader functionality by fully removing a database. + """Complement the Loader functionality by fully removing a database. This probably isn't really useful for normal purposes, since you can just do a: @@ -242,6 +238,7 @@ class DatabaseRemover: XXX I think this might be the worst optimized SQL in the history of the world. There is probably a much better way to do it. + [The "right" way is of course to have FKs--YB] """ def __init__(self, adaptor, dbid): """Initialize with a database id and adaptor connection. Index: Doc/Tutorial.tex =================================================================== RCS file: /home/repository/biopython/biopython/Doc/Tutorial.tex,v retrieving revision 1.28 diff -u -p -r1.28 Tutorial.tex --- Doc/Tutorial.tex 2002/10/17 03:21:32 1.28 +++ Doc/Tutorial.tex 2002/11/18 21:18:45 @@ -3323,7 +3323,7 @@ detect likely problems. I will give seve \ref{problem structures}. \begin{figure} -{\par\centering \resizebox*{0.75\textwidth}{!}{\includegraphics{smcra.eps}} \par} +{\par\centering \resizebox*{0.75\textwidth}{!}{\includegraphics{smcra}} \par} \caption{\label{SMCRA UML diagram}UML diagram of the SMCRA data structure used to represent a macromolecular structure.} \end{figure} Index: Tests/test_BioSQL.py =================================================================== RCS file: /home/repository/biopython/biopython/Tests/test_BioSQL.py,v retrieving revision 1.9 diff -u -p -r1.9 test_BioSQL.py --- Tests/test_BioSQL.py 2002/01/31 18:31:07 1.9 +++ Tests/test_BioSQL.py 2002/11/18 21:18:45 @@ -1,8 +1,5 @@ #!/usr/bin/env python """Tests for dealing with storage of biopython objects in a relational db. - -Currently these tests require a MySQL db loaded with the GenBank info -in GenBank/cor6_6.gb. This loading can be done with bioperl-db. """ # standard library import sys @@ -20,14 +17,21 @@ from Bio import GenBank from BioSQL import BioSeqDatabase from BioSQL import BioSeq -# Constants for the MySQL database +##DBDRIVER = 'MySQLdb' +##DBTYPE = 'mysql' +DBDRIVER = 'psycopg' +DBTYPE = 'pg' + +# Works for mysql and postgresql, not oracle +DBSCHEMA = "biosqldb-" + DBTYPE + ".sql" +# Constants for the database driver DBHOST = 'localhost' -DBUSER = 'chapmanb' +DBUSER = '' DBPASSWD = '' TESTDB = 'biosql' # XXX I need to put these SQL files somewhere in biopython SQL_FILE = os.path.join(os.pardir, os.pardir, "biosql-schema", "sql", - "biosqldb-mysql.sql") + DBSCHEMA) def run_tests(argv): test_suite = testing_suite() @@ -49,31 +53,57 @@ def testing_suite(): return test_suite -def load_database(gb_handle): - """Load a GenBank file into a BioSQL database. - - This is useful for running tests against a newly created database. - """ +def create_database(): + """Create an empty BioSQL database.""" # first open a connection to create the database - server = BioSeqDatabase.open_database(user = DBUSER, passwd = DBPASSWD, + server = BioSeqDatabase.open_database(driver = DBDRIVER, + user = DBUSER, passwd = DBPASSWD, host = DBHOST) - + + # Auto-commit: postgresql cannot drop database in a transaction + try: + server.adaptor.autocommit() + except AttributeError: + pass + # drop anything in the database try: sql = r"DROP DATABASE " + TESTDB server.adaptor.cursor.execute(sql, ()) except server.module.OperationalError: # the database doesn't exist pass + except server.module.IntegrityError, e: # ditto--perhaps + if str(e).find('database "%s" does not exist' % TESTDB) > 0: + pass + else: + raise # create a new database sql = r"CREATE DATABASE " + TESTDB - server.adaptor.execute_one(sql, ()) + server.adaptor.execute(sql, ()) + + server.adaptor.conn.close() + + # now open a connection to load the database + server = BioSeqDatabase.open_database(driver = DBDRIVER, + user = DBUSER, passwd = DBPASSWD, + host = DBHOST, db = TESTDB) + server.load_database_sql(SQL_FILE) + server.adaptor.conn.commit() + server.adaptor.conn.close() + +def load_database(gb_handle): + """Load a GenBank file into a BioSQL database. + This is useful for running tests against a newly created database. + """ + + create_database() # now open a connection to load the database db_name = "biosql-test" - server = BioSeqDatabase.open_database(user = DBUSER, passwd = DBPASSWD, + server = BioSeqDatabase.open_database(driver = DBDRIVER, + user = DBUSER, passwd = DBPASSWD, host = DBHOST, db = TESTDB) - server.load_database_sql(SQL_FILE) db = server.new_database(db_name) # get the GenBank file we are going to put into it @@ -81,6 +111,8 @@ def load_database(gb_handle): iterator = GenBank.Iterator(gb_handle, parser) # finally put it in the database db.load(iterator) + server.adaptor.conn.commit() + server.adaptor.conn.close() class ReadTest(unittest.TestCase): """Test reading a database from an already built database. @@ -95,11 +127,17 @@ class ReadTest(unittest.TestCase): load_database(gb_handle) gb_handle.close() - server = BioSeqDatabase.open_database(user = DBUSER, - passwd = DBPASSWD, host = DBHOST, db = TESTDB) + server = BioSeqDatabase.open_database(driver = DBDRIVER, + user = DBUSER, + passwd = DBPASSWD, + host = DBHOST, db = TESTDB) self.db = server["biosql-test"] + def tearDown(self): + self.db.adaptor.conn.close() + del self.db + def t_get_db_items(self): """Get a list of all items in the database. """ @@ -139,10 +177,16 @@ class SeqInterfaceTest(unittest.TestCase load_database(gb_handle) gb_handle.close() - server = BioSeqDatabase.open_database(user = DBUSER, passwd = DBPASSWD, + server = BioSeqDatabase.open_database(driver = DBDRIVER, + user = DBUSER, passwd = DBPASSWD, host = DBHOST, db = TESTDB) - db = server["biosql-test"] - self.item = db.lookup(accession = "X62281") + self.db = server["biosql-test"] + self.item = self.db.lookup(accession = "X62281") + + def tearDown(self): + self.db.adaptor.conn.close() + del self.db + del self.item def t_seq_record(self): """Make sure SeqRecords from BioSQL implement the right interface. @@ -217,9 +261,14 @@ class LoaderTest(unittest.TestCase): """Load a database from a GenBank file. """ def setUp(self): + + # create TESTDB + create_database() + # load the database db_name = "biosql-test" - server = BioSeqDatabase.open_database(user = DBUSER, passwd = DBPASSWD, + server = BioSeqDatabase.open_database(driver = DBDRIVER, + user = DBUSER, passwd = DBPASSWD, host = DBHOST, db = TESTDB) # remove the database if it already exists @@ -237,6 +286,10 @@ class LoaderTest(unittest.TestCase): parser = GenBank.FeatureParser() self.iterator = GenBank.Iterator(handle, parser) + def tearDown(self): + self.db.adaptor.conn.close() + del self.db + def t_load_database(self): """Load SeqRecord objects into a BioSQL database. """ @@ -267,9 +320,14 @@ class InDepthLoadTest(unittest.TestCase) load_database(gb_handle) gb_handle.close() - server = BioSeqDatabase.open_database(user = DBUSER, passwd = DBPASSWD, + server = BioSeqDatabase.open_database(driver = DBDRIVER, + user = DBUSER, passwd = DBPASSWD, host = DBHOST, db = TESTDB) self.db = server["biosql-test"] + + def tearDown(self): + self.db.adaptor.conn.close() + del self.db def t_record_loading(self): """Make sure all records are correctly loaded. --- /dev/null 1970-01-01 01:00:00.000000000 +0100 +++ BioSQL/DBUtils.py 2002-11-18 22:19:07.000000000 +0100 @@ -0,0 +1,59 @@ +class Generic_dbutils: + def __init__(self): + pass + + def tname(self, table): + if table != 'biosequence': return table + else: return 'bioentry' + +# Disabled: better safe than sorry +## def next_id(self, cursor, table): +## # XXX brain-dead! Hopefully, the database will enforce PK unicity.. +## table = self.tname(table) +## sql = r"select 1+max(%s_id) from %s" % (table, table) +## cursor.execute(sql) +## rv = cursor.fetchone() +## return rv[0] + + def last_id(self, cursor, table): + # XXX: Unsafe without transactions isolation + table = self.tname(table) + sql = r"select max(%s_id) from %s" % table + cursor.execute(sql) + rv = cursor.fetchone() + return rv[0] + + def autocommit(self, conn, y = 1): + # Let's hope it was not really needed + pass + +class Mysql_dbutils(Generic_dbutils): + def last_id(self, cursor, table): + return cursor.insert_id() + +class Pg_dbutils(Generic_dbutils): + def next_id(self, cursor, table): + table = self.tname(table) + sql = r"select nextval('%s_pk_seq')" % table + cursor.execute(sql) + rv = cursor.fetchone() + return rv[0] + + def last_id(self, cursor, table): + table = self.tname(table) + sql = r"select currval('%s_pk_seq')" % table + cursor.execute(sql) + rv = cursor.fetchone() + return rv[0] + + def autocommit(self, conn, y = 1): + conn.autocommit(y) + +def create_Generic_dbutils(): + return Generic_dbutils() + +def create_Mysql_dbutils(): + return Mysql_dbutils() + +def create_Pg_dbutils(): + return Pg_dbutils() From biopython-bugs at bioperl.org Mon Nov 18 22:25:43 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/101 Message-ID: <200211190325.gAJ3Ph6J007720@pw600a.bioperl.org> JitterBug notification new message incoming/101 Message summary for PR#101 From: "Thierry Vanhoudt" Subject: Discounted Tobacco Date: Mon, 18 Nov 2002 19:21:14 0100 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From sales@smoking.com.net Mon Nov 18 22:25:42 2002 Received: from linux.local ([213.9.245.34]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id gAJ3Pe6J007716 for ; Mon, 18 Nov 2002 22:25:41 -0500 Message-Id: <200211190325.gAJ3Pe6J007716@pw600a.bioperl.org> Received: (qmail 8883 invoked from network); 18 Nov 2002 19:22:47 -0000 Received: from unknown (HELO admin) (192.168.0.1) by linux.local with SMTP; 18 Nov 2002 19:22:47 -0000 From: "Thierry Vanhoudt" Subject: Discounted Tobacco To: biopython-bugs@bioperl.org Sender: Thierry Vanhoudt Reply-To: sales@smoking.com.net Date: Mon, 18 Nov 2002 19:21:14 +0100 X-Priority: 3 X-Library: Indy 8.0.25 Dear Sir or Madam In the past you have requested information on discounted products. If you are not a smoker, and find this email offensive, then we sincerely apologise. We will be only too happy to take you off our database. If you are a smoker, however, you are probably fed up with paying high prices for your cigarettes and tobacco. Take a look at what we can do for you at http://www.britishsmokers.com/?S=26&ID=2&E=2836924 We can send you, legally, by registered air mail, direct to your door, 4 cartons of cigarettes or 40 pouches of rolling tobacco (all brands are available) from only 170 Euros - about 105 pounds - fully inclusive of postage and packing. Why pay more? If you would rather not hear from us any more, this link will ensure that you are not bothered again. http://www.britishsmokers.com/off/index.php Yours faithfully. British Smokers http://www.britishsmokers.com/?S=26&ID=2&E=2836924 w2y12836924563 From biopython-bugs at bioperl.org Mon Nov 18 22:25:46 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/102 Message-ID: <200211190325.gAJ3Pk6J007730@pw600a.bioperl.org> JitterBug notification new message incoming/102 Message summary for PR#102 From: "Thierry Vanhoudt" Subject: Discounted Smokes Date: Mon, 18 Nov 2002 19:21:14 0100 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From sales@smoking.com.net Mon Nov 18 22:25:46 2002 Received: from linux.local ([213.9.245.34]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id gAJ3Pi6J007724 for ; Mon, 18 Nov 2002 22:25:45 -0500 Message-Id: <200211190325.gAJ3Pi6J007724@pw600a.bioperl.org> Received: (qmail 8886 invoked from network); 18 Nov 2002 19:22:48 -0000 Received: from unknown (HELO admin) (192.168.0.1) by linux.local with SMTP; 18 Nov 2002 19:22:48 -0000 From: "Thierry Vanhoudt" Subject: Discounted Smokes To: biopython-bugs@bioperl.org Sender: Thierry Vanhoudt Reply-To: sales@smoking.com.net Date: Mon, 18 Nov 2002 19:21:14 +0100 X-Priority: 3 X-Library: Indy 8.0.25 Dear Sir or Madam In the past you have requested information on discounted products. If you are not a smoker, and find this email offensive, then we sincerely apologise. We will be only too happy to take you off our database. If you are a smoker, however, you are probably fed up with paying high prices for your cigarettes and tobacco. Take a look at what we can do for you at http://www.britishsmokers.com/?S=26&ID=2&E=2836925 We can send you, legally, by registered air mail, direct to your door, 4 cartons of cigarettes or 40 pouches of rolling tobacco (all brands are available) from only 170 Euros - about 105 pounds - fully inclusive of postage and packing. Why pay more? If you would rather not hear from us any more, this link will ensure that you are not bothered again. http://www.britishsmokers.com/off/index.php Yours faithfully. British Smokers http://www.britishsmokers.com/?S=26&ID=2&E=2836925 w2y12836925563 From biopython-bugs at bioperl.org Mon Nov 18 22:48:00 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/103 Message-ID: <200211190348.gAJ3m06J008057@pw600a.bioperl.org> JitterBug notification new message incoming/103 Message summary for PR#103 From: StopForeclosure148 Subject: STOP YOUR FORECLOSURE.............................................................................................................................................................................................. jdhbm Date: Mon, 18 Nov 2002 21:52:23 -0600 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From StopForeclosure98807@mindspring.com Mon Nov 18 22:48:00 2002 Received: from 200.253.196.70 ([200.253.196.70]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id gAJ3ls6J008050 for ; Mon, 18 Nov 2002 22:47:56 -0500 Message-Id: <200211190347.gAJ3ls6J008050@pw600a.bioperl.org> Received: from unknown (156.54.224.23) by a231242.upc-a.chello.nl with local; Nov, 18 2002 9:42:11 PM +0600 Received: from [14.42.188.81] by sydint1.microthin.com.au with asmtp; Nov, 18 2002 8:23:02 PM -0200 Received: from [121.102.119.231] by a231242.upc-a.chello.nl with NNFMP; Nov, 18 2002 7:36:10 PM +0300 From: StopForeclosure148 To: HOMEOWNER97253 Cc: Subject: STOP YOUR FORECLOSURE.............................................................................................................................................................................................. jdhbm Sender: StopForeclosure148 Mime-Version: 1.0 Content-Type: text/html; charset="iso-8859-1" Date: Mon, 18 Nov 2002 21:52:23 -0600 X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-Priority: 1

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mpshhwadfkhtujaucgrbkjpcetpsgwbv From biopython-bugs at bioperl.org Mon Nov 18 23:40:18 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/104 Message-ID: <200211190440.gAJ4eI6J009118@pw600a.bioperl.org> JitterBug notification new message incoming/104 Message summary for PR#104 From: StopForeclosure158 Subject: STOP YOUR FORECLOSURE.............................................................................................................................................................................................. xvd Date: Mon, 18 Nov 2002 22:44:40 -0600 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From StopForeclosure98585@compuserve.com Mon Nov 18 23:40:17 2002 Received: from 194.126.46.244 ([194.126.46.244]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id gAJ4e56J009105 for ; Mon, 18 Nov 2002 23:40:13 -0500 Message-Id: <200211190440.gAJ4e56J009105@pw600a.bioperl.org> Received: from ssymail.ssy.co.kr ([113.236.31.212]) by a231242.upc-a.chello.nl with local; Nov, 18 2002 10:21:26 PM -0200 Received: from [14.42.188.81] by sydint1.microthin.com.au with asmtp; Nov, 18 2002 9:15:14 PM -0700 Received: from unknown (70.133.86.252) by da001d2020.lax-ca.osd.concentric.net with esmtp; Nov, 18 2002 8:20:27 PM -0200 From: StopForeclosure158 To: HOMEOWNER97263 Cc: Subject: STOP YOUR FORECLOSURE.............................................................................................................................................................................................. xvd Sender: StopForeclosure158 Mime-Version: 1.0 Content-Type: text/html; charset="iso-8859-1" Date: Mon, 18 Nov 2002 22:44:40 -0600 X-Mailer: Internet Mail Service (5.5.2650.21) X-Priority: 1

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jhoccytpyyonfeshfbwdgeytabsvdncdhrhng From chapmanb at arches.uga.edu Wed Nov 20 11:09:35 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] BioSQL and PostgreSQL In-Reply-To: <3DD96689.60002@irisa.fr> References: <3DD96689.60002@irisa.fr> Message-ID: <20021120160935.GE91535@ci350185-a.athen1.ga.home.com> Yves; > I've adapted BioSQL/*.py to work with PostgreSQL. Well, at least the > tests pass... Patch attached, comments are welcome. Thanks much! I have committed these. The MySQL still seems to work fine for me, although the PostgreSQL does give me errors in the sql schema I have: IntegrityError: ERROR: pg_ownercheck: class "bioentry_entry" not found CREATE INDEX bioentryentry ON bioentry_entry ( entry_id ) I know that there is tons happening on the BioSQL development front that I just plain haven't been following, so I am really out of the loop on what the current schema is or what schema we should be working with or if anything is stable. That being said, if the postgres works for you and MySQL doesn't break, I'm happy :-). > * I've made utility classes for nonstandard SQL/DBAPI operations, e.g. > retrieving the id of the last inserted record. (The implementation is > so-so, I know :). There are Generic_dbutils, Mysql_dbutils and > Pg_dbutils. The choice is made according to the DBAPI module's name; > only MySQLdb and psycopg are currently recognised. Sure. Sounds find to me as this is cleaner then my implementation. Thanks. I am no database expert, so I appreciate anything making this better. > (Done but not included in the patch: adaptations to the current > biosql-schema CVS.) Hmmmm, so maybe you understand better than I do what is going on with the current schema :-). I guess the best place to talk about this is the BioSQL list: http://obda.open-bio.org/mailman/listinfo/biosql-l I wish I knew what was going on so I could offer more advice, but mostly I am a simpleton when it comes to designing SQL schemas so I just let the smart folks figure out what is best and then implement it. Certaintly we do want to stay up to date whenever they have something stable. What do you think about talking up your patches over there? Thanks again for this work; much appreciated! Brad From jchang at smi.stanford.edu Wed Nov 20 23:32:45 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Making biopython release Message-ID: <20021121043244.GA7777@springfield.stanford.edu> Hello everybody, Biopython's *way* overdue for a release -- most of our bug fixes seem to be of the get-files-from-CVS variety. Let's try to get things stabilized so we can ship out another version. Here's what we need to do. Please let me know, with a well-reasoned argument, if you disagree. Bug fixes --------- We have a bugzilla database at bugzilla.bioperl.org. Here are the bugs I think should be fixed before we release. I've made a best guess at who should be working on them. 4 jchang GenBank search should support "limits" 10 dalke BerkeleyDB.py Problem? 11 cayte Tests/MetaTool/Meta9.out conflicts with meta9.out 12 cayte potential conflict between Bio/Rebase/Rebase.py and Bio/Rebase/__init__.py 16 idoerg test_FSSP takes a long time to run 17 gec Bio/SCOP/tests should be integrated with rest of regression tests 22 jchang Some NCBI scripts will be obsolete Dec 2002 XX jchang make the seqdb load _ini files on access Please take ownership of your bug in the database. All the regression tests must pass (on a properly configured system) before we can make a release. I ran the tests today (BioSQL stuff was skipped) and found 7 tests to be failing. Please check your code and make sure the tests pass! test_locuslink test_FSSP test_ais test_align test_easy test_format_registry test_locus_http Thomas, I've gotten some reports that people are having trouble compiling the C++ KDTree module. Do you know what the issues are in compiling C++ software, and where problems might be? Sorry to be so vague about it. I don't have a reproducible. I'll try and hunt down the reports. If people have problems compiling it, we will have to back it out. Michael, do you mind moving easy.py and GenericTools.py somewhere else, e.g. into GFF? I'm not sure I like them directly in the Bio namespace. Misc Tasks ---------- Other things to do are: 1. Update the README file, making sure requirements, etc are still up to date. 2. Make sure the tutorial is still current. Modules have moved around. 3. Make sure example scripts are still work. Either fix or remove them. 4. Update the NEWS file. Figure out all new features, etc. Let me know if you can take charge of any of these tasks. Addendum -------- In an earlier email, Brad had wanted to shoot for a next Wednesday release. That means that all the above must be done by Tuesday, so that I will have a change to make the final tarball. Let me know your status, and whether you think this is realistic, given holidays, etc. Nevertheless, let's keep communicating through the dev mailing list on progress, updates, concerns, etc. Anybody with code in the repository should let me know when your code is ready to go. Thanks, Brad, for getting the ball rolling! This is going to be a beefy release. Jeff From thamelry at vub.ac.be Thu Nov 21 03:18:42 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Making biopython release In-Reply-To: <20021121043244.GA7777@springfield.stanford.edu> References: <20021121043244.GA7777@springfield.stanford.edu> Message-ID: <200211210813.gAL8D2010716@durendal.skynet.be> Jeff wrote: > Thomas, I've gotten some reports that people are having trouble > compiling the C++ KDTree module. As far as I remember there was once one trivial problem with a default argument that was defined twice but that has been corrected. I haven't heard of any problems since. > Sorry to be so vague about it. I don't have a reproducible. I'll try and > hunt down the reports. If people have problems compiling it, we will have > to back it out. Well, I hope you can at least send me the problem reports then, so I can solve the problems! :-) Regards, --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode Belgium http://ultr.vub.ac.be/~thomas From ybastide at IRISA.fr Thu Nov 21 04:28:25 2002 From: ybastide at IRISA.fr (Yves Bastide) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Re: Making biopython release In-Reply-To: <20021121043244.GA7777@springfield.stanford.edu> References: <20021121043244.GA7777@springfield.stanford.edu> Message-ID: <3DDCA739.2070403@IRISA.fr> Hello, Which version of python is aimed at in this release? It seems that triemodule.c needs 2.2 to compile. yves From Yves.Bastide at irisa.fr Thu Nov 21 05:18:25 2002 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Re: BioSQL and PostgreSQL Message-ID: <3DDCB2F1.6080000@irisa.fr> Brad Chapman wrote: > Yves; > > >>I've adapted BioSQL/*.py to work with PostgreSQL. Well, at least the >>tests pass... Patch attached, comments are welcome. > > > Thanks much! I have committed these. The MySQL still seems to work fine > for me, although the PostgreSQL does give me errors in the sql schema I > have: > > IntegrityError: ERROR: pg_ownercheck: class "bioentry_entry" not found > > CREATE INDEX bioentryentry ON bioentry_entry ( entry_id ) > > I know that there is tons happening on the BioSQL development front that > I just plain haven't been following, so I am really out of the loop on > what the current schema is or what schema we should be working with or > if anything is stable. Hmm, you must have a weird version of the schema :) (this said, the current one in CVS doesn't work with the corresponding bioperl-db) > > That being said, if the postgres works for you and MySQL doesn't break, > I'm happy :-). > > >>* I've made utility classes for nonstandard SQL/DBAPI operations, e.g. >>retrieving the id of the last inserted record. (The implementation is >>so-so, I know :). There are Generic_dbutils, Mysql_dbutils and >>Pg_dbutils. The choice is made according to the DBAPI module's name; >>only MySQLdb and psycopg are currently recognised. > > > Sure. Sounds find to me as this is cleaner then my implementation. > Thanks. I am no database expert, so I appreciate anything making this > better. Yep. But my implementation is a hack: it hardcodes the name of two adaptors, MySQLdb and psycopg -- while there are at least 3 ones for postgresql. > > >>(Done but not included in the patch: adaptations to the current >>biosql-schema CVS.) > > > Hmmmm, so maybe you understand better than I do what is going on with > the current schema :-). I guess the best place to talk about this is the > BioSQL list: > > http://obda.open-bio.org/mailman/listinfo/biosql-l > For discussing about the schema itself: you're right. But at the moment, I suppose you would prefer to stick to its old version, since the new biopython release is slated for next week while I think a new BioSQL won't come out before December... > I wish I knew what was going on so I could offer more advice, but > mostly I am a simpleton when it comes to designing SQL schemas so I just > let the smart folks figure out what is best and then implement it. > Certaintly we do want to stay up to date whenever they have something > stable. > > What do you think about talking up your patches over there? Hmm, not sure the perl and java guys are interested a lot in biopython's biosql guts :) But yes, I've got some questions to ask Hilmar. > > Thanks again for this work; much appreciated! Thank you! > > Brad yves From idoerg at burnham.org Thu Nov 21 12:47:08 2002 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Making biopython release References: <20021121043244.GA7777@springfield.stanford.edu> Message-ID: <3DDD1C1C.5050806@burnham.org> Jeff, I updated the test_FSSP 3 weeks ago, should be clean & fast. (Well, faster). Can you email me the errors you are getting? Good move on the release. I. Jeffrey Chang wrote: > Hello everybody, > > Biopython's *way* overdue for a release -- most of our bug fixes seem > to be of the get-files-from-CVS variety. Let's try to get things > stabilized so we can ship out another version. Here's what we need to > do. Please let me know, with a well-reasoned argument, if you > disagree. > > > Bug fixes > --------- > > We have a bugzilla database at bugzilla.bioperl.org. Here are the > bugs I think should be fixed before we release. I've made a best > guess at who should be working on them. > > 4 jchang GenBank search should support "limits" > 10 dalke BerkeleyDB.py Problem? > 11 cayte Tests/MetaTool/Meta9.out conflicts with meta9.out > 12 cayte potential conflict between Bio/Rebase/Rebase.py and Bio/Rebase/__init__.py > 16 idoerg test_FSSP takes a long time to run > 17 gec Bio/SCOP/tests should be integrated with rest of regression tests > 22 jchang Some NCBI scripts will be obsolete Dec 2002 > XX jchang make the seqdb load _ini files on access > > Please take ownership of your bug in the database. > > All the regression tests must pass (on a properly configured system) > before we can make a release. I ran the tests today (BioSQL stuff was > skipped) and found 7 tests to be failing. Please check your code and > make sure the tests pass! > test_locuslink > test_FSSP > test_ais > test_align > test_easy > test_format_registry > test_locus_http > > Thomas, I've gotten some reports that people are having trouble > compiling the C++ KDTree module. Do you know what the issues are in > compiling C++ software, and where problems might be? Sorry to be so > vague about it. I don't have a reproducible. I'll try and hunt down > the reports. If people have problems compiling it, we will have to > back it out. > > Michael, do you mind moving easy.py and GenericTools.py somewhere > else, e.g. into GFF? I'm not sure I like them directly in the Bio > namespace. > > > Misc Tasks > ---------- > > Other things to do are: > > 1. Update the README file, making sure requirements, etc are still up > to date. > > 2. Make sure the tutorial is still current. Modules have moved > around. > > 3. Make sure example scripts are still work. Either fix or remove > them. > > 4. Update the NEWS file. Figure out all new features, etc. > > > Let me know if you can take charge of any of these tasks. > > > > Addendum > -------- > > In an earlier email, Brad had wanted to shoot for a next Wednesday > release. That means that all the above must be done by Tuesday, so > that I will have a change to make the final tarball. Let me know your > status, and whether you think this is realistic, given holidays, etc. > > Nevertheless, let's keep communicating through the dev mailing list on > progress, updates, concerns, etc. Anybody with code in the repository > should let me know when your code is ready to go. > > Thanks, Brad, for getting the ball rolling! This is going to be a > beefy release. > > Jeff > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > > -- Iddo Friedberg The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 From jchang at smi.stanford.edu Thu Nov 21 13:27:58 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Re: Making biopython release In-Reply-To: <3DDCA739.2070403@IRISA.fr> References: <20021121043244.GA7777@springfield.stanford.edu> <3DDCA739.2070403@IRISA.fr> Message-ID: <20021121182758.GA9800@springfield.stanford.edu> Yes, 2.2. Martel requires some of the 2.2 features, so some of the parsers won't operate correctly without them. Plus, there are various other 2.2-isms scattered in the code... Jeff On Thu, Nov 21, 2002 at 10:28:25AM +0100, Yves Bastide wrote: > Hello, > > Which version of python is aimed at in this release? It seems that > triemodule.c needs 2.2 to compile. > > yves > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From biopython-bugs at bioperl.org Thu Nov 21 14:38:35 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Notification: incoming/105 Message-ID: <200211211938.gALJcZ6J007765@pw600a.bioperl.org> JitterBug notification new message incoming/105 Message summary for PR#105 From: "WALL STREET BULLETIN..47804" Subject: NEW STOCK PICK: TBIN - SYPY UP 309%....................................................................................................................................................................... auvcl Date: Thu, 21 Nov 2002 13:42:11 -0600 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From Subscriber_Services78059@adelphia.net Thu Nov 21 14:38:35 2002 Received: from 218.108.26.226 ([218.108.26.226]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id gALJcV6J007761 for ; Thu, 21 Nov 2002 14:38:33 -0500 Message-Id: <200211211938.gALJcV6J007761@pw600a.bioperl.org> Received: from [49.164.250.3] by rly-xw01.mx.aol.com with SMTP; Nov, 21 2002 1:40:59 PM -0000 Received: from [72.62.68.193] by rly-yk04.mx.aol.com with asmtp; Nov, 21 2002 12:38:10 PM +0700 Received: from unknown (74.38.244.167) by asy100.as122.sol.superonline.com with NNFMP; Nov, 21 2002 11:42:03 AM +0700 Received: from 87.15.78.89 ([87.15.78.89]) by pet.vosn.net with local; Nov, 21 2002 10:20:57 AM -0100 From: "WALL STREET BULLETIN..47804" To: WALL.STREET.BULLETIN..47299 Cc: biopython-bugs@bioperl.org Subject: NEW STOCK PICK: TBIN - SYPY UP 309%....................................................................................................................................................................... auvcl Sender: "WALL STREET BULLETIN..47804" Mime-Version: 1.0 Content-Type: text/html; charset="iso-8859-1" Date: Thu, 21 Nov 2002 13:42:11 -0600 X-Mailer: Microsoft Outlook IMO Build 9.0.2416 (9.0.2910.0) X-Priority: 1

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yfsmreihcthaidradwoadovns From chapmanb at arches.uga.edu Thu Nov 21 14:39:56 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Making biopython release In-Reply-To: <20021121043244.GA7777@springfield.stanford.edu> References: <20021121043244.GA7777@springfield.stanford.edu> Message-ID: <20021121193956.GC96650@ci350185-a.athen1.ga.home.com> Hey Jeff; Thanks for getting this together. Sweet, it doesn't look like any bugs belong to me. That bugzilla stuff is confuuuusing. Well, maybe only if you look at it for two seconds and scratch your head. And my tests work, still. Nice. I'll volunteer to do the following (probably this weekend): > 2. Make sure the tutorial is still current. Modules have moved > around. > > 3. Make sure example scripts are still work. Either fix or remove > them. I think any bad things here are mostly my doing, so I'll try to make sure they're all current. I also sign up for: => Figuring out what is up with bioSQL. Get a schema that works with the code and put it in the release. => Making the Windows installer (for python2.2 only, yay!) I agree with just targetting python 2.2 -- they are already on their second bugfix release of this release and it's been around for a long time. Also RedHat has finally moved away from 1.5.2, I think, so probably it's good to keep pushing people forward on having current versions. Plus it's easier for us. Man-this-release-stuff-is-hard-work-ly yr's, Brad From chapmanb at arches.uga.edu Thu Nov 21 14:47:05 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Re: BioSQL and PostgreSQL In-Reply-To: <3DDCB2F1.6080000@irisa.fr> References: <3DDCB2F1.6080000@irisa.fr> Message-ID: <20021121194705.GD96650@ci350185-a.athen1.ga.home.com> Hi Yves; > > I know that there is tons happening on the BioSQL development front that > > I just plain haven't been following, so I am really out of the loop on > > what the current schema is or what schema we should be working with or > > if anything is stable. > > Hmm, you must have a weird version of the schema :) (this said, the > current one in CVS doesn't work with the corresponding bioperl-db) I'm absolutely positive I was using a weird version :-). Wait, are there versions. I think the most important thing for this release is to have a SQL schema that works with the code we release. When the BioSQL decision making has settled down to a new "for sure" schema, then we can migrate over to that. Do you have an "almost official" version that works with both Postgres and MySQL? If so, I vote for including that. > Yep. But my implementation is a hack: it hardcodes the name of two > adaptors, MySQLdb and psycopg -- while there are at least 3 ones for > postgresql. No worries on that front from me -- psycopg is a semi-official Postgres driver, I reckon, since it's used in Zope. My only beef with it is that the name is damn hard to type properly. For right now, having one working driver with Postgres makes me happy, so the hack is right on as far as I'm concerned. > For discussing about the schema itself: you're right. But at the > moment, I suppose you would prefer to stick to its old version, since > the new biopython release is slated for next week while I think a new > BioSQL won't come out before December... Yup. This sounds good. I would like Postgres to work for this release, though -- do you want to send the schema you used that works and I can check it into CVS? There will be another hacking session going on and I imagine BioSQL will get beat around hard there, so for right now it's good to have something that works for people who want a relational database. > Hmm, not sure the perl and java guys are interested a lot in biopython's > biosql guts :) Well, they should be :-). Brad From jchang at SMI.Stanford.EDU Thu Nov 21 17:19:06 2002 From: jchang at SMI.Stanford.EDU (Jeffrey Chang) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Making biopython release In-Reply-To: <3DDD1C1C.5050806@burnham.org> References: <20021121043244.GA7777@springfield.stanford.edu> <3DDD1C1C.5050806@burnham.org> Message-ID: <20021121221906.GA10133@springfield.stanford.edu> On Thu, Nov 21, 2002 at 09:47:08AM -0800, Iddo Friedberg wrote: > I updated the test_FSSP 3 weeks ago, should be clean & fast. (Well, > faster). Can you email me the errors you are getting? Sure -- here ya go! Jeff [krusty:~/remotecvs/biopython/Tests] jchang% python run_tests.py test_FSSP test_FSSP ... FAIL ====================================================================== FAIL: test_FSSP ---------------------------------------------------------------------- Traceback (most recent call last): File "run_tests.py", line 131, in runTest self.runSafeTest() File "run_tests.py", line 168, in runSafeTest expected_handle) File "run_tests.py", line 237, in compare_output assert expected_test == test_name, "\nOutput: %s\nExpected: %s" % \ AssertionError: Output: test_FSSP Expected: ---------------------------------------------------------------------- Ran 1 tests in 122.241s FAILED (failures=1) From katel at worldpath.net Fri Nov 22 02:13:52 2002 From: katel at worldpath.net (katel@worldpath.net) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Making biopython release Message-ID: <244640-220021152271352187@M2W064.mail2web.com> I'll try to fix the bugs over the next few days. Cayte -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From jchang at smi.stanford.edu Fri Nov 22 03:00:23 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:17 2005 Subject: [Biopython-dev] Making biopython release In-Reply-To: <20021121193956.GC96650@ci350185-a.athen1.ga.home.com> References: <20021121043244.GA7777@springfield.stanford.edu> <20021121193956.GC96650@ci350185-a.athen1.ga.home.com> Message-ID: <20021122080023.GF11726@springfield.stanford.edu> On Thu, Nov 21, 2002 at 02:39:56PM -0500, Brad Chapman wrote: > I'll volunteer to do the following (probably this weekend): > > > 2. Make sure the tutorial is still current. Modules have moved > > around. > > > > 3. Make sure example scripts are still work. Either fix or remove > > them. Great! Thanks much. I think I broke some of those when I moved some modules around. :( Be sure the imports are all still working. > I also sign up for: > > => Figuring out what is up with bioSQL. Get a schema that works with the > code and put it in the release. > > => Making the Windows installer (for python2.2 only, yay!) Cool. I'll let you know when the CVS repository is stabilized so you can make the Windows version. > Man-this-release-stuff-is-hard-work-ly yr's, yeah-i-guess-that's-why-we-don't-do-it-enough-ly yr's, :) Jeff From jchang at SMI.Stanford.EDU Fri Nov 22 02:52:03 2002 From: jchang at SMI.Stanford.EDU (Jeffrey Chang) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] Making biopython release In-Reply-To: <200211210813.gAL8D2010716@durendal.skynet.be> References: <20021121043244.GA7777@springfield.stanford.edu> <200211210813.gAL8D2010716@durendal.skynet.be> Message-ID: <20021122075202.GD11726@springfield.stanford.edu> Hey Thomas, I'm getting an error when trying to link the KDTree module (attached). This is on Solaris 2.6, gcc 2.95.3, and python 2.2. Do you know where these errors are coming from? It's most likely an error with distutil's compiling options, but we need a workaround. Jeff On Thu, Nov 21, 2002 at 09:18:42AM +0100, Thomas Hamelryck wrote: > Jeff wrote: > > > Thomas, I've gotten some reports that people are having trouble > > compiling the C++ KDTree module. > > As far as I remember there was once one trivial problem with a default > argument that was defined twice but that has been corrected. I haven't heard > of any problems since. > > > Sorry to be so vague about it. I don't have a reproducible. I'll try and > > hunt down the reports. If people have problems compiling it, we will have > > to back it out. > > Well, I hope you can at least send me the problem reports then, > so I can solve the problems! :-) > > Regards, > > --- > Thomas Hamelryck Vrije Universiteit Brussel (VUB) > Intitute for Molecular Biology ULTR Department > Paardenstraat 65 1640 Sint-Gensius-Rode Belgium > http://ultr.vub.ac.be/~thomas -------------- next part -------------- running build running build_py not copying Bio/Index.py (output up-to-date) not copying Bio/__init__.py (output up-to-date) not copying Bio/ParserSupport.py (output up-to-date) not copying Bio/File.py (output up-to-date) not copying Bio/PubMed.py (output up-to-date) not copying Bio/sequtils.py (output up-to-date) not copying Bio/Seq.py (output up-to-date) not copying Bio/utils.py (output up-to-date) not copying Bio/SeqRecord.py (output up-to-date) not copying Bio/PropertyManager.py (output up-to-date) not copying Bio/SeqFeature.py (output up-to-date) not copying 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Bio/PDB/PDBIO.py (output up-to-date) not copying Bio/PDB/NeighborSearch.py (output up-to-date) not copying Bio/PDB/PDBExceptions.py (output up-to-date) not copying Bio/PDB/PDBParser.py (output up-to-date) not copying Bio/PDB/Residue.py (output up-to-date) not copying Bio/PDB/Selection.py (output up-to-date) not copying Bio/PDB/Structure.py (output up-to-date) not copying Bio/PDB/StructureBuilder.py (output up-to-date) not copying Bio/Parsers/__init__.py (output up-to-date) not copying Bio/Parsers/spark.py (output up-to-date) not copying Bio/Pathway/__init__.py (output up-to-date) not copying Bio/Pathway/Rep/MultiGraph.py (output up-to-date) not copying Bio/Pathway/Rep/HashSet.py (output up-to-date) not copying Bio/Pathway/Rep/__init__.py (output up-to-date) not copying Bio/Pathway/Rep/Graph.py (output up-to-date) not copying Bio/Prosite/__init__.py (output up-to-date) not copying Bio/Prosite/Prodoc.py (output up-to-date) not copying Bio/Prosite/Pattern.py (output up-to-date) not copying Bio/Rebase/__init__.py (output up-to-date) not copying Bio/Rebase/Rebase.py (output up-to-date) not copying Bio/SCOP/__init__.py (output up-to-date) not copying Bio/SCOP/Dom.py (output up-to-date) not copying Bio/SCOP/Residues.py (output up-to-date) not copying Bio/SCOP/Raf.py (output up-to-date) not copying Bio/SCOP/Cla.py (output up-to-date) not copying Bio/SCOP/Des.py (output up-to-date) not copying Bio/SCOP/Hie.py (output up-to-date) not copying Bio/SCOP/FileIndex.py (output up-to-date) not copying Bio/SVDSuperimposer/SVDSuperimposer.py (output up-to-date) not copying Bio/SVDSuperimposer/__init__.py (output up-to-date) not copying Bio/SeqIO/__init__.py (output up-to-date) not copying Bio/SeqIO/FASTA.py (output up-to-date) not copying Bio/SeqIO/generic.py (output up-to-date) not copying Bio/SeqUtils/__init__.py (output up-to-date) not copying Bio/SubsMat/FreqTable.py (output up-to-date) not copying Bio/SubsMat/MatrixInfo.py (output up-to-date) not copying Bio/SubsMat/__init__.py (output up-to-date) not copying Bio/SwissProt/__init__.py (output up-to-date) not copying Bio/SwissProt/KeyWList.py (output up-to-date) not copying Bio/SwissProt/SProt.py (output up-to-date) not copying Bio/UniGene/__init__.py (output up-to-date) not copying Bio/WWW/__init__.py (output up-to-date) not copying Bio/WWW/ExPASy.py (output up-to-date) not copying Bio/WWW/SCOP.py (output up-to-date) not copying Bio/WWW/NCBI.py (output up-to-date) not copying Bio/WWW/InterPro.py (output up-to-date) not copying Bio/builders/__init__.py (output up-to-date) not copying Bio/builders/SeqRecord/__init__.py (output up-to-date) not copying Bio/builders/SeqRecord/sequence.py (output up-to-date) not copying Bio/config/FormatRegistry.py (output up-to-date) not copying Bio/config/DBRegistry.py (output up-to-date) not copying Bio/config/Registry.py (output up-to-date) not copying Bio/config/__init__.py (output up-to-date) not copying Bio/config/_support.py (output up-to-date) not copying Bio/config/seqdatabase.py (output up-to-date) not copying Bio/dbdefs/__init__.py (output up-to-date) not copying Bio/dbdefs/_support.py (output up-to-date) not copying Bio/dbdefs/embl.py (output up-to-date) not copying Bio/dbdefs/genbank.py (output up-to-date) not copying Bio/dbdefs/interpro.py (output up-to-date) not copying Bio/dbdefs/pdb.py (output up-to-date) not copying Bio/dbdefs/prodoc.py (output up-to-date) not copying Bio/dbdefs/prosite.py (output up-to-date) not copying Bio/dbdefs/swissprot.py (output up-to-date) not copying Bio/expressions/__init__.py (output up-to-date) not copying Bio/expressions/blocks.py (output up-to-date) not copying Bio/expressions/fasta.py (output up-to-date) not copying Bio/expressions/genbank.py (output up-to-date) not copying Bio/expressions/embl/__init__.py (output up-to-date) not copying Bio/expressions/embl/embl65.py (output up-to-date) not copying Bio/expressions/swissprot/__init__.py (output up-to-date) not copying Bio/expressions/swissprot/sprot38.py (output up-to-date) not copying Bio/expressions/swissprot/sprot40.py (output up-to-date) not copying Bio/formatdefs/__init__.py (output up-to-date) not copying Bio/formatdefs/embl.py (output up-to-date) not copying Bio/formatdefs/genbank.py (output up-to-date) not copying Bio/formatdefs/sequence.py (output up-to-date) not copying Bio/formatdefs/swissprot.py (output up-to-date) not copying Bio/formatdefs/search.py (output up-to-date) not copying Bio/writers/__init__.py (output up-to-date) not copying Bio/writers/SeqRecord/__init__.py (output up-to-date) not copying Bio/writers/SeqRecord/fasta.py (output up-to-date) not copying Bio/writers/SeqRecord/empty.py (output up-to-date) not copying Martel/RecordReader.py (output up-to-date) not copying Martel/Expression.py (output up-to-date) not copying Martel/Generate.py (output up-to-date) not copying Martel/Iterator.py (output up-to-date) not copying Martel/Parser.py (output up-to-date) not copying Martel/__init__.py (output up-to-date) not copying Martel/convert_re.py (output up-to-date) not copying Martel/optimize.py (output up-to-date) not copying Martel/setup.py (output up-to-date) not copying Martel/msre_constants.py (output up-to-date) not copying Martel/Time.py (output up-to-date) not copying Martel/msre_parse.py (output up-to-date) not copying Martel/LAX.py (output up-to-date) not copying Martel/Dispatch.py (output up-to-date) not copying Martel/IterParser.py (output up-to-date) not copying BioSQL/__init__.py (output up-to-date) not copying BioSQL/BioSeq.py (output up-to-date) not copying BioSQL/Loader.py (output up-to-date) not copying BioSQL/BioSeqDatabase.py (output up-to-date) running build_ext skipping 'Bio.cSVM' extension (up-to-date) skipping 'Bio.ckMeans' extension (up-to-date) skipping 'Bio.clistfns' extension (up-to-date) skipping 'Bio.cmathfns' extension (up-to-date) skipping 'Bio.cstringfns' extension (up-to-date) skipping 'Bio.cdistance' extension (up-to-date) skipping 'Bio.cpairwise2' extension (up-to-date) skipping 'Bio.trie' extension (up-to-date) building 'Bio.KDTree._KDTreecmodule' extension Text relocation remains referenced against symbol offset in file _IO_do_write 0x194 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) _IO_do_write 0x6b0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_do_write 0x78 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) _IO_do_write 0x6f0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_do_write 0xc80 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_do_write 0x5c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_do_write 0x108 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_do_write 0x62c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_do_write 0x154 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) _IO_do_write 0x658 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_file_fopen 0x2d0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) __builtin_vec_delete 0x1d0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __builtin_vec_delete 0xc4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __builtin_vec_delete 0xc4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __builtin_vec_delete 0xb8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __builtin_vec_delete 0x10 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) __builtin_vec_delete 0x70 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __builtin_vec_delete 0x1d4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __builtin_vec_delete 0x100 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __builtin_vec_delete 0xb8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __builtin_vec_delete 0x70 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _Q_qtod 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) flush(ostream &) 0x1bdc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) free 0x84 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) free 0xea8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) free 0x9bc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) free 0x978 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) free 0x578 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) free 0x1f8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) free 0x2e8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) .rem 0x164 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_free_backup_area 0x460 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_free_backup_area 0x530 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_free_backup_area 0x3c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(ioseekoff.o) _IO_free_backup_area 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_free_backup_area 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(ioseekpos.o) _IO_free_backup_area 0xdc8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_free_backup_area 0x40 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_free_backup_area 0x1ec /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) malloc 0x8cc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) malloc 0xe28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) malloc 0xe78 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) malloc 0x40 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) malloc 0x88 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filedoalloc.o) malloc 0x26c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_sgetn 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_sgetn 0x3ec /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_sgetn 0x1818 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::operator<<(char const *) 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::operator<<(char const *) 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __builtin_vec_new 0x2f0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) terminate(void) 0xb0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) terminate(void) 0x1dc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) terminate(void) 0x1e0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) terminate(void) 0x11c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) terminate(void) 0x54 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) terminate(void) 0x4c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __throw 0x158 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __throw 0x160 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __throw 0x164 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __throw 0x15c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __throw 0x34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __throw 0x3c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) __throw 0x98 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) __throw 0x104 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) read 0xa8c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) .umul 0x4f4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) .umul 0x1cec /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) .umul 0x1cdc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) .umul 0x4d4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) .umul 0x57c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) .umul 0x554 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) .umul 0x144 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) .umul 0x154 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) .udiv 0x1080 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) .udiv 0x1cb0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) _IO_cleanup 0x50c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_cleanup 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(cleanup.o) _IO_cleanup 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(cleanup.o) istream::ios virtual table 0x78 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0xb8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x88 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x74 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0xb0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x5c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x60 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x94 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x7c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x6c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x1d84 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x1d7c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream::ios virtual table 0x6c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x17c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream::ios virtual table 0x74 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream::ios virtual table 0x1d78 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x170 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream::ios virtual table 0x174 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream::ios virtual table 0x64 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream::ios virtual table 0x68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream::ios virtual table 0x6c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream::ios virtual table 0x78 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::ios virtual table 0x70 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream::ios virtual table 0x70 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_default_finish 0x2d4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_default_finish 0x134 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_ungetc 0x868 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) _IO_ungetc 0xa4c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) _IO_ungetc 0x898 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) _IO_ungetc 0xa38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) _IO_ungetc 0x74 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) _IO_ungetc 0xa00 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) memmove 0x320 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) __urem64 0x1024 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __rtti_user 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) __rtti_user 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) open 0x20c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) open 0x254 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) cerr 0x5c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) cerr 0x70 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) cin 0x54 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) cin 0x64 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) filebuf::overflow(int) 0x1ec /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) _IO_ostream_withassign type_info node0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_ostream_withassign type_info node0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_ostream_withassign type_info node0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_ostream_withassign type_info node0x70 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __builtin_delete 0x84 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __builtin_delete 0xd8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __builtin_delete 0x84 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __builtin_delete 0xd8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __builtin_delete 0x114 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __builtin_delete 0xcc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __builtin_delete 0x2e8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) __builtin_delete 0x424 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) __builtin_delete 0xcc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __builtin_delete 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_istream_withassign::ios virtual table0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_istream_withassign::ios virtual table0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_istream_withassign::ios virtual table0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostdiostream type_info node 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ostdiostream type_info node 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ostdiostream type_info node 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream type_info node 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream type_info node 0x54 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream type_info node 0x58 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream type_info node 0x64 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream type_info node 0xb4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream type_info node 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream type_info node 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream type_info node 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream type_info node 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream type_info node 0x84 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream type_info node 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream type_info node 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) streambuf type_info node 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf type_info node 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf type_info node 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf type_info node 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf type_info node 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf type_info node 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) strlen 0x16c8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_adjust_column 0x374 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_adjust_column 0x3e4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) 0xc70 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0xf14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0xd14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0xc68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x44 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x44 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0xd98 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0xf28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0xfb4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x54 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x58 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x16c0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x60 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x16c4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0xfbc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x3c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x44 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x48 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x70 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x9c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x64 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x64 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x74 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0xd18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x3c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x7c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x80 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x8c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x90 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x48 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x98 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x60 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0xfc4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x58 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0xd9c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0xfc0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x54 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x48 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) 0x3c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_putc 0x360 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_putc 0x49c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_putc 0x430 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_putc 0x47c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_putc 0x10 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_putc 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_putc 0xe38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_putc 0x115c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_putc 0x1bb8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_putc 0x1bd4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_putc 0xec0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_putc 0x10 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_putc 0x10 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_strtod 0xa64 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) istdiostream::ios virtual table 0xc4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istdiostream::ios virtual table 0xb0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istdiostream::ios virtual table 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istdiostream::ios virtual table 0xb4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istdiostream::ios virtual table 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istdiostream::ios virtual table 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) iostream::ios virtual table 0x1e00 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) iostream::ios virtual table 0xf4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) iostream::ios virtual table 0x10c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) iostream::ios virtual table 0x1e18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) iostream::ios virtual table 0x11c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) iostream::ios virtual table 0x1e28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) iostream::ios virtual table 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) iostream::ios virtual table 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) iostream::ios virtual table 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_file_init 0x80 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) _IO_file_init 0xdc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) _IO_file_init 0x30 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) _IO_file_init 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) _Q_dtoq 0xc88 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_stdin_ 0x4c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) _IO_stdin_ 0x3c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) iostream type_info node 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) iostream type_info node 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) iostream type_info node 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) iostream type_info node 0xa8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_getc 0xe4c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_getc 0x128 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_getc 0x1c0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_getc 0x7dc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_getc 0x70 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_getc 0x814 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_getc 0xbc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) _IO_getc 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_getc 0x350 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_getc 0x5b0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_getc 0x6a4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_getc 0x48 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) _IO_getc 0xb8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) _IO_getc 0x284 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) _IO_getc 0x8fc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_padn 0x10 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_padn 0x1720 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_padn 0x11b8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_padn 0x340 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_padn 0x394 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_padn 0x414 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_padn 0x4c4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_padn 0x508 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_padn 0x564 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_padn 0x1124 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_padn 0x177c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_padn 0x1210 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_ostream_withassign::ios virtual table0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_ostream_withassign::ios virtual table0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_ostream_withassign::ios virtual table0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) close 0xad4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) ostream::write(char const *, int) 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::write(char const *, int) 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::write(char const *, int) 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_outfloat 0x1630 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_istream_withassign type_info node0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_istream_withassign type_info node0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_istream_withassign type_info node0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_istream_withassign type_info node0x70 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_FILE type_info node 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_FILE type_info node 0x44 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_FILE type_info node 0x3c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_FILE type_info node 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_FILE type_info node 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_FILE type_info node 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_FILE type_info node 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) ios virtual table 0x18b0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0xf4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0xb0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0xac /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0xf8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x18b8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x60 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x1d30 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x60 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0xb0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0xac /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x1d38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ios virtual table 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0x0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) ios virtual table 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0xbc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0x1cc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0x1c4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0x1c0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0x1c8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0xb8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0xbc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0xb8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ios virtual table 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) ios virtual table 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) ios virtual table 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_ostream_withassign::operator=(ostream &)0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_istream_withassign::operator=(istream &)0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) streambuf::sungetc(void) 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) streambuf::sungetc(void) 0x11c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) fflush 0x210 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) fflush 0x1cf0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) fflush 0x1ce8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) fflush 0x1bc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream::get(char *, int, char) 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::get(char *, int, char) 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::read(char *, int) 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::read(char *, int) 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::read(char *, int) 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __mul64 0x8e0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __ctype 0x5c4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x5c8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x2ac /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x298 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x228 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x2a8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x650 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x44 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x40 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x30 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x59c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x294 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x224 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x67c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) __ctype 0x11c 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0x166c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::do_osfx(void) 0x1c98 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::do_osfx(void) 0xefc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::do_osfx(void) 0x123c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::do_osfx(void) 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::do_osfx(void) 0x1270 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::do_osfx(void) 0x1874 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::do_osfx(void) 0x17b8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::operator<<(unsigned int) 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) skip_ws(streambuf *) 0x1b1c 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ostream type_info node 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream type_info node 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream type_info node 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream type_info node 0x38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ostream type_info node 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream type_info node 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream type_info node 0x8c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream type_info node 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream type_info node 0xdc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream type_info function 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istream type_info function 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __rtti_class 0x4c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __rtti_class 0x34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __rtti_class 0x34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __rtti_class 0x84 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __rtti_class 0xa0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __rtti_class 0x68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __rtti_class 0x4c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __rtti_class 0x34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __rtti_class 0x68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __rtti_class 0x34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __rtti_class 0x4c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) streambuf::sputbackc(char) 0x8bc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) streambuf::sputbackc(char) 0x1b80 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) streambuf::sputbackc(char) 0x1b4c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) streambuf::sputbackc(char) 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) streambuf::sputbackc(char) 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) streambuf::sputbackc(char) 0x68c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) streambuf::sputbackc(char) 0x838 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __iob 0x1ce4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) __iob 0x1ce0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::operator>>(char *) 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::operator>>(char *) 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::operator>>(char &) 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::operator>>(char &) 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) streambuf::ignore(int) 0x320 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_seekpos 0x19a8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _IO_seekpos 0x244 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_seekpos 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_seekpos 0x48c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) filebuf::close(void) 0x1ed0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x1b00 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x50 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x4c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x1aa4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x1cc4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x17f0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x1568 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x1508 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x1478 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x16a4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x1410 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x138c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x1c34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x1a4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x6c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) ostream::flush(void) 0x44 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isscan.o) ostream::flush(void) 0x1cc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) ostream::flush(void) 0x58 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x132c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x12a8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x3cc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x574 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0xea0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x624 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x374 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) ostream::flush(void) 0x728 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x244 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0xc34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0xc8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isscan.o) ostream::flush(void) 0xde8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x2f8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0xd64 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0xce0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) ostream::flush(void) 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::_skip_ws(void) 0xe04 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::_skip_ws(void) 0xe4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isscan.o) istream::_skip_ws(void) 0xd80 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::_skip_ws(void) 0xcfc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::_skip_ws(void) 0x60 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isscan.o) istream::_skip_ws(void) 0xc50 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::_skip_ws(void) 0x80 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::_skip_ws(void) 0x58 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::_skip_ws(void) 0x744 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::_skip_ws(void) 0x640 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) istream::_skip_ws(void) 0x590 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iostream.o) _sb_readline(streambuf *, long &, char)0x3a0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) _sb_readline(streambuf *, long &, char)0x2c0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) memcpy 0x318 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) memcpy 0x110 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iogetline.o) memcpy 0x2d8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) memcpy 0x12c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iogetline.o) memcpy 0xea0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) memcpy 0x340 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) memcpy 0xbe8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) memcpy 0x2a0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) memcpy 0x2b8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) memcpy 0x2d0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) memcpy 0x368 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) memcpy 0x694 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) memcpy 0x780 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_getline_info 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iogetline.o) _IO_getline_info 0xa0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) _IO_getline_info 0x1fc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) _IO_getline_info 0x268 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isgetline.o) _IO_file_doallocate 0x318 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) streambuf::vscan(char const *, void *, ios *)0x108 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isscan.o) streambuf::vscan(char const *, void *, ios *)0x84 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(isscan.o) _IO_list_all 0xb00 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0xb04 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0x34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0xb68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0xbc0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0x10 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0x84 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0xb64 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0x88 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0xbbc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_list_all 0x90 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_vfscanf 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(sbscan.o) _IO_vfscanf 0x60 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(sbscan.o) 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) 0x78 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) 0x0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) 0x74 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) ios::sync_with_stdio(int) 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_stderr_buf 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) _IO_stderr_buf 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) _IO_default_xsputn 0xca4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_default_xsputn 0xa4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_stdout_buf 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) _IO_stdout_buf 0x38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) clog 0x6c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) clog 0x60 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) _IO_stderr_ 0x44 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) _IO_stderr_ 0x48 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) _IO_stdout_ 0x50 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) _IO_stdout_ 0x40 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) cout 0x68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) cout 0x58 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdstreams.o) 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) 0x38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) 0x40 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) 0x50 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) 0x58 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_FILE type_info function 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_FILE type_info function 0x30 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_init_marker 0x3fc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf::streambuf(int) 0xc8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) streambuf::streambuf(int) 0x6c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) streambuf::streambuf(int) 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) streambuf::xsputn(char const *, int)0x258 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) _IO_flush_all_linebuffered 0x4a0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_flush_all_linebuffered 0x3b0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_setb 0x878 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_setb 0x8e8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_setb 0x854 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_setb 0xac /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filedoalloc.o) _IO_setb 0x5f8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_setb 0x264 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_setb 0x90 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_init 0x2b0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) strtol 0x244 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) strtol 0x248 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) strtol 0x160 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) strtol 0x15c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) fread 0x104 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) _ios_fields type_info function 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _ios_fields type_info node 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _ios_fields type_info node 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _ios_fields type_info node 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _ios_fields type_info node 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _ios_fields type_info node 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_seekmark 0x46c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) filebuf::~filebuf(void) 0x84 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) filebuf::~filebuf(void) 0x40 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) _IO_marker_delta 0x450 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) errno 0x1490 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) errno 0x1484 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) errno 0x3c8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) errno 0x19f0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) errno 0x74c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x73c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x1260 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) errno 0x1328 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) errno 0x574 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x56c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x454 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x2ec /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x1258 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) errno 0x44c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x178 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x2e8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x26c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x268 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x3c0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) errno 0x1c4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) errno 0x188 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_link_in 0x27c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_link_in 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_link_in 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_link_in 0x2b4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) filebuf virtual table 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) filebuf virtual table 0xd0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) filebuf virtual table 0x74 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) filebuf virtual table 0x78 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) filebuf virtual table 0x130 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) filebuf virtual table 0x138 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) filebuf virtual table 0xd4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) filebuf virtual table 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) streambuf::setb(char *, char *, int)0x1cc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf::setb(char *, char *, int)0x1a8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf virtual table 0x2a4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf virtual table 0x2c4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf virtual table 0x2c8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf virtual table 0x2a0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_file_attach 0x8c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) _IO_file_attach 0x2e8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) _IO_file_attach 0xe8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) _IO_sputbackc 0x10 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(ioungetc.o) _IO_sputbackc 0x32c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_sputbackc 0xac /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iogetline.o) _IO_flush_all 0xc14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_flush_all 0x39c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) stdiobuf::~stdiobuf(void) 0x5c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) stdiobuf::~stdiobuf(void) 0x5c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) stdiobuf virtual table 0x68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) stdiobuf virtual table 0x10 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) stdiobuf virtual table 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) stdiobuf virtual table 0x60 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) _IO_dtoa 0xdc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(outfloat.o) _IO_remove_marker 0x410 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_default_uflow 0x80 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_marker_difference 0x43c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_default_pbackfail 0x140 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) streambuf::doallocbuf(void) 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_doallocbuf 0x7fc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_doallocbuf 0x5a0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_doallocbuf 0x488 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_doallocbuf 0x28c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) filebuf type_info node 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) filebuf type_info node 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) filebuf type_info node 0x64 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) filebuf type_info node 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) filebuf type_info node 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) filebuf type_info node 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) filebuf type_info function 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) streambuf::xsgetn(char *, int) 0x458 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) ostdiostream::ios virtual table 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ostdiostream::ios virtual table 0xc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ostdiostream::ios virtual table 0xac /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ostdiostream::ios virtual table 0xc0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ostdiostream::ios virtual table 0xb0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) ostdiostream::ios virtual table 0x1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) streambuf::~streambuf(void) 0x180 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) streambuf::~streambuf(void) 0x110 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) streambuf::~streambuf(void) 0xa4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) streambuf::~streambuf(void) 0x48 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) filebuf::setbuf(char *, int) 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) filebuf::setbuf(char *, int) 0xf8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(filebuf.o) _IO_default_xsgetn 0xc0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_unsave_markers 0xa18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_unsave_markers 0x480 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_unsave_markers 0x68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_sungetc 0x340 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_un_link 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_un_link 0xb0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_un_link 0x9c8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) __rtti_si 0x30 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) __rtti_si 0x30 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __rtti_si 0x30 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) __rtti_si 0x48 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) __rtti_si 0x5c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_default_doallocate 0x278 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_switch_to_get_mode 0x49c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_switch_to_get_mode 0xc44 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_switch_to_get_mode 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(streambuf.o) _IO_switch_to_get_mode 0x3d0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_switch_to_get_mode 0x7d8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) _IO_switch_to_get_mode 0x4a8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) __overflow 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(ioputc.o) __overflow 0xc3c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) __overflow 0x700 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) stdiobuf::buffered(int) 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) stdiobuf::buffered(int) 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) _IO_switch_to_main_get_area 0x1f0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_switch_to_main_get_area 0x4d4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_switch_to_main_get_area 0xd64 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_switch_to_main_get_area 0x408 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) __uflow 0x58 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iogetline.o) __uflow 0x18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iogetc.o) _IO_switch_to_backup_area 0xe4c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_switch_to_backup_area 0xe10 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_switch_to_backup_area 0xd80 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(genops.o) _IO_default_setbuf 0x314 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) fclose 0x170 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) 0x798 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0x794 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0x780 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0x77c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0x314 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xa8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xa4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0x740 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0x924 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0x928 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0x310 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0x73c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) strtoul 0x188 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0x2488 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x248c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1b34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1b1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1b18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1b04 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1b00 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1a34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x25c4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1380 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x12ec /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x12e8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1384 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x13c4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1ae8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1a50 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x25c8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x253c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1a38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1288 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x18d4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1944 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x258c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1940 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x2590 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x18fc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x18f8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x18d8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x18ac /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x17fc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1874 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1824 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1820 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x17f8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x143c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1438 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1414 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1410 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x13c8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) result_k.68 0x1eb0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) result_k.68 0x1eac /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) result_k.68 0x22b0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) result_k.68 0x2280 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) result_k.68 0x2298 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) result_k.68 0x22f0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) result_k.68 0x22e8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) result_k.68 0x22cc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) result_k.68 0x22c8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) result_k.68 0x2290 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x22fc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x22b4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1e9c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1e98 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x22b8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x22c4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x22dc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x22e4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x22f4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x22f8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x630 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x62c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0xd0c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0xd08 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x21fc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x21f8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) __huge_val 0x1264 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) __huge_val 0x126c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) write 0xb00 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) lseek 0xaa8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) fstat 0xac0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(fileops.o) 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) 0x2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) 0x24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) 0x20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) 0x28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) stdiobuf type_info node 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) stdiobuf type_info node 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) stdiobuf type_info node 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istdiostream type_info node 0x14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istdiostream type_info node 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) istdiostream type_info node 0x4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) stdiobuf::stdiobuf(FILE *) 0x108 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) stdiobuf::stdiobuf(FILE *) 0x104 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) fseek 0x15c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) __filbuf 0xc0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) fwrite 0x128 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) fwrite 0x24c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(stdiostream.o) atexit 0x8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(cleanup.o) 0x2ee8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x2ee4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x2ee0 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x2edc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x2ed8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x2ed4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c68 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c64 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c60 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c5c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c58 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c54 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c50 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c4c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c48 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c44 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c40 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c3c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c30 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c10 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c0c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c08 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(floatconv.o) 0x1c04 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/usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb38 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb34 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb30 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb2c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb28 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb24 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb20 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb1c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb18 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb14 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb10 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb0c /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb08 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb04 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xb00 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xafc /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xaf8 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) 0xaf4 /usr/pubsw/lib/gcc-lib/sparc-sun-solaris2.6/2.95.3/libstdc++.a(iovfscanf.o) ld: fatal: relocations remain against allocatable but non-writable sections collect2: ld returned 1 exit status skipping Bio/KDTree/_KDTree.C (build/temp.solaris-2.6-sun4u-2.2/_KDTree.o up-to-date) skipping Bio/KDTree/_KDTree.swig.C (build/temp.solaris-2.6-sun4u-2.2/_KDTree.swig.o up-to-date) gcc -shared build/temp.solaris-2.6-sun4u-2.2/_KDTree.o build/temp.solaris-2.6-sun4u-2.2/_KDTree.swig.o -lstdc++ -o build/lib.solaris-2.6-sun4u-2.2/Bio/KDTree/_KDTreecmodule.so error: command 'gcc' failed with exit status 1 From Yves.Bastide at irisa.fr Fri Nov 22 05:04:26 2002 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] Re: BioSQL and PostgreSQL In-Reply-To: <3DDDFDAB.7070508@irisa.fr> References: <3DDCB2F1.6080000@irisa.fr> <20021121194705.GD96650@ci350185-a.athen1.ga.home.com> <3DDDFDAB.7070508@irisa.fr> Message-ID: <3DDE012A.7030409@irisa.fr> Oops! Yves Bastide wrote in private, missing the list: > Hi, > > Brad Chapman wrote: > >> Hi Yves; >> >> > [...] > > Then let's use the current schema, including the not-done-yet > replacement of reference.reference_medline by reference.document_id, ok? > I'll send here my current diffs. > >> >>> Yep. But my implementation is a hack: it hardcodes the name of two >>> adaptors, MySQLdb and psycopg -- while there are at least 3 ones for >>> postgresql. >> >> >> >> No worries on that front from me -- psycopg is a semi-official Postgres >> driver, I reckon, since it's used in Zope. My only beef with it is that >> the name is damn hard to type properly. > > > Yes, but Zope won't be supported by biopython -- it still uses python 2.1. > > [...] > >> >> Brad > > > yves > > From Yves.Bastide at irisa.fr Fri Nov 22 05:23:46 2002 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] BioSQL questions Message-ID: <3DDE05B2.7020900@irisa.fr> Bioentries are retrieved via two classes, DBSeqRecord and DBInternalSeq. Why? I'm asking because it seems sound, but I don't understand why which data is retrieved by which class, e.g. sequence name by DBInternalSeq. Concerning the sequence name: a bioentry contains four ids: * bioentry_id, the internal id * display_id, called "name" by SeqRecord * accession, called "id" * identifier, not retrieved. In Genbank parlance, display_id == LOCUS, accession == ACCESSION (duh!) and identifier == GI. Obviously, the GI should be retrieved; and I think "id" should be renamed to "accession". Comments? yves From Yves.Bastide at irisa.fr Fri Nov 22 16:57:25 2002 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] GenBank alphabet Message-ID: <3DDEA845.1080101@irisa.fr> g'd'evening, what's the relation between an entry alphabet and its sequence? Case in point: Tests/cor6_6.gb, first entry. ATCOR66M is a mRNA, but the sequence is a DNA one (as documented by the NCBI). So: * what do biologists prefer? * what to store in a BioSQL record (BioPerl says dna)? Thanks, yves From Yves.Bastide at irisa.fr Fri Nov 22 17:40:15 2002 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] BioSQL upgrade [0 of 3] Message-ID: <3DDEB24F.8000202@irisa.fr> Here's a set of patches to update BioSQL. It: * uses an up-to-date biosql schema [1]; * can put about all of a Bio.SeqRecord.SeqRecord [2] in the database. [1] biosql-schema The schema used is what's currently in CVS (biosqldb-mysql.sql 1.18, and biosqldb-pg.sql created from it), with one exception: reference.reference_medline must be a VARCHAR(20). [2] Bio.SeqRecord.SeqRecord I believe this means in practice a GenBank record, as SProt uses another class. yves From Yves.Bastide at irisa.fr Fri Nov 22 17:45:09 2002 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] BioSQL upgrade [1 of 3] In-Reply-To: <3DDEB24F.8000202@irisa.fr> References: <3DDEB24F.8000202@irisa.fr> Message-ID: <3DDEB375.4080109@irisa.fr> The first patch creates a Bio.crc, with crc32 and crc64 methods; I needed a CRC64, and foud it clean to have it nicely with the usual CRC32 :-) The crc64 code is a translation of the BioPerl one (I will only claim the errors). -------------- next part -------------- --- /dev/null 1970-01-01 01:00:00.000000000 +0100 +++ Bio/crc.py 2002-11-22 21:34:16.000000000 +0100 @@ -0,0 +1,32 @@ +# crc32 and crc64 +# crc64 is adapted from BioPerl + +from binascii import crc32 + +_table_h = [] + +def crc64(s): + crcl = 0 + crch = 0 + for c in s: + shr = (crch & 0xFF) << 24 + temp1h = crch >> 8 + temp1l = (crcl >> 8) | shr + idx = (crcl ^ ord(c)) & 0xFF + crch = temp1h ^ _table_h[idx] + crcl = temp1l + + return "CRC-%08X%08X" % (crch, crcl) + +# Initialisation +for i in range(256): + l = i + part_h = 0 + for j in range(8): + rflag = l & 1 + l >>= 1 + if part_h & 1: l |= (1L << 31) + part_h >>= 1L + if rflag: part_h ^= 0xd8000000L + _table_h.append(part_h) + From Yves.Bastide at irisa.fr Fri Nov 22 17:47:10 2002 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] Re: BioSQL upgrade [2 of 3] In-Reply-To: <3DDEB375.4080109@irisa.fr> References: <3DDEB24F.8000202@irisa.fr> <3DDEB375.4080109@irisa.fr> Message-ID: <3DDEB3EE.90508@irisa.fr> Big e-mail, small payload :) -------------- next part -------------- Index: setup.py =================================================================== RCS file: /home/repository/biopython/biopython/setup.py,v retrieving revision 1.51 diff -u -p -r1.51 setup.py --- setup.py 2002/11/06 22:22:09 1.51 +++ setup.py 2002/11/22 22:12:07 @@ -221,6 +221,7 @@ biopython_packages = ['Bio', 'Bio.builders', 'Bio.builders.SeqRecord', 'Bio.config', + 'Bio.crc', 'Bio.dbdefs', 'Bio.expressions', 'Bio.expressions.embl', From Yves.Bastide at irisa.fr Fri Nov 22 17:48:53 2002 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] Re: BioSQL upgrade [3 of 3] In-Reply-To: <3DDEB3EE.90508@irisa.fr> References: <3DDEB24F.8000202@irisa.fr> <3DDEB375.4080109@irisa.fr> <3DDEB3EE.90508@irisa.fr> Message-ID: <3DDEB455.8010005@irisa.fr> The big one. -------------- next part -------------- Index: BioSQL/BioSeq.py =================================================================== RCS file: /home/repository/biopython/biopython/BioSQL/BioSeq.py,v retrieving revision 1.8 diff -u -p -r1.8 BioSeq.py --- BioSQL/BioSeq.py 2002/03/01 12:22:05 1.8 +++ BioSQL/BioSeq.py 2002/11/22 22:13:21 @@ -14,7 +14,7 @@ class DBSeq: # This implements the biop def __getattr__(self, name): if name == "data": return self.tostring() - raise AttributeError(name) + raise AttributeError, name def __len__(self): return self._length @@ -55,18 +55,20 @@ class DBInternalSeq: self.primary_id = primary_id self.adaptor = adaptor - self.name, self.id, _length, self.moltype = \ + self.name, self.id, _length, self.description, self.moltype = \ self.adaptor.execute_one( """select en.display_id, en.accession, length(bs.biosequence_str), - bs.molecule - from bioentry en, biosequence bs - where bs.bioentry_id = en.bioentry_id and - bs.bioentry_id = %s""", + en.description, bs.alphabet + from bioentry en, biosequence bs + where bs.bioentry_id = en.bioentry_id and + bs.bioentry_id = %d""", (self.primary_id,)) self._length = int(_length) - + def __getattr__(self, name): + if name[:1] == '_': + raise AttributeError, name if name == "seq": moltype = self.moltype.upper() from Bio.Alphabet import IUPAC @@ -84,23 +86,9 @@ class DBInternalSeq: return seq f = getattr(self, "_get_" + name, None) if f is None: - raise AttributeError(name) + raise AttributeError, name return f() - def _get_description(self): - descr_results = _get_ontology_terms("description", self.primary_id, - self.adaptor) - if len(descr_results) == 0: - description = "" - elif len(descr_results) == 1: - description = descr_results[0] - else: - raise ValueError("Got multiple unexpected descriptions: %s" % - descr_results) - - self.description = description - return description - def __len__(self): return self._length @@ -110,10 +98,13 @@ def _get_ontology_terms(ontology_name, b sql = r"SELECT ontology_term_id FROM ontology_term " \ r"WHERE term_name = %s" id_info = adaptor.execute_and_fetchall(sql, (ontology_name,)) + if id_info is None: + return None + ontology_id = id_info[0][0] sql = r"SELECT qualifier_value FROM bioentry_qualifier_value " \ - r"WHERE bioentry_id = %s AND ontology_term_id = %s" + r"WHERE bioentry_id = %d AND ontology_term_id = %s" values = adaptor.execute_and_fetch_col0(sql, (bioentry_id, ontology_id)) return values @@ -190,7 +181,7 @@ class Species: elif name == "genus": return self.classification[1] - raise AttributeError(name) + raise AttributeError, name def __setattr__(self, name, val): if name == "species": @@ -212,9 +203,11 @@ class Annotation: self.primary_id = primary_id def __getattr__(self, name): + if name[:1] == '_': + raise AttributeError, name f = getattr(self, "_get_" + name, None) if f is None: - raise AttributeError(name) + raise AttributeError, name return f() # functions to make this more like a dictionary @@ -222,7 +215,7 @@ class Annotation: if key in ["comments", "dblinks", "references"]: return getattr(self, key) else: - raise KeyError("Unexpected item: %s") + raise KeyError("Unexpected item: %s" % key) def has_key(self, key): if key in ["comments", "dblinks", "references"]: @@ -236,7 +229,7 @@ class Annotation: def _get_comments(self): comments = self.adaptor.execute_and_fetch_col0( - """select comment_text from comment where bioentry_id = %s""", + """select comment_text from comment where bioentry_id = %d""", (self.primary_id,)) self.comments = comments return comments @@ -244,7 +237,7 @@ class Annotation: def _get_dblinks(self): dblink_info = self.adaptor.execute_and_fetchall( """select dbname, accession from bioentry_direct_links - where source_bioentry_id = %s""", + where source_bioentry_id = %d""", (self.primary_id,)) dblinks = [DBLink(database, primary_id) for (database, primary_id) in dblink_info] @@ -255,7 +248,7 @@ class Annotation: results = self.adaptor.execute_and_fetchall( """select reference_id, reference_start,reference_end from bioentry_reference - where bioentry_id = %s + where bioentry_id = %d order by reference_rank""", (self.primary_id,)) @@ -284,8 +277,8 @@ def load_seq_features(adaptor, primary_i from Bio import SeqFeature # Get the seqfeature id list - sql = r"SELECT seqfeature_id, seqfeature_rank, seqfeature_key_id " \ - r"FROM seqfeature WHERE bioentry_id = %s" + sql = r"SELECT seqfeature_id, seqfeature_rank, ontology_term_id " \ + r"FROM seqfeature WHERE bioentry_id = %d" results = adaptor.execute_and_fetchall(sql, (primary_id,)) seq_feature_list = [] @@ -324,9 +317,9 @@ def load_seq_features(adaptor, primary_i # Get any remote reference information remote_results = adaptor.execute_and_fetchall(""" - SELECT rem.seqfeature_location_id, rem.accession, rem.version - FROM remote_seqfeature_name rem, seqfeature_location sfl - WHERE rem.seqfeature_location_id = sfl.seqfeature_location_id AND + SELECT seqfeature_location_id, accession, version + FROM seqfeature_location sfl, dbxref drf + WHERE drf.dbxref_id = sfl.dbxref_id AND sfl.seqfeature_id = %s""", (seqfeature_id,)) # Do the merge locally @@ -387,10 +380,10 @@ class DBSeqRecord: self.version, _length, self.division = \ self.adaptor.execute_one( - """select en.entry_version, length(bs.biosequence_str), en.division + """select en.entry_version, length(bs.biosequence_str), bs.division from bioentry en, biosequence bs where bs.bioentry_id = en.bioentry_id and - bs.bioentry_id = %s""", + bs.bioentry_id = %d""", (self.primary_id,)) self._length = int(_length) @@ -399,12 +392,12 @@ class DBSeqRecord: def __getattr__(self, name): if name[:1] == "_": - raise AttributeError(name) + raise AttributeError, name if name in self._forward_getattr: return getattr(self.primary_seq, name) f = getattr(self, "_get_" + name, None) if f is None: - raise AttributeError(name) + raise AttributeError, name return f() def _get_primary_seq(self): @@ -430,14 +423,14 @@ class DBSeqRecord: def _get_dates(self): self.dates = _get_ontology_terms("date", self.primary_id, self.adaptor) - return dates + return self.dates def _get_species(self): full_lineage, common_name = self.adaptor.execute_one( """select tx.full_lineage, tx.common_name - from taxa tx, bioentry_taxa bt - where tx.taxa_id = bt.taxa_id and - bt.bioentry_id = %s""", + from taxon tx, bioentry be + where tx.taxon_id = be.taxon_id and + be.bioentry_id = %d""", (self.primary_id,)) terms = full_lineage.split(":") species = Species(terms, common_name) @@ -448,9 +441,7 @@ class DBSeqRecord: return version def _get_keywords(self): - keywords = self.adaptor.execute_and_fetch_col0( - """select keywords from bioentry_keywords - where bioentry_id = %s""", - (self.primary_id,)) + keywords = _get_ontology_term('Keywords', self.primary_id, + self.adaptor) self.keywords = keywords return keywords Index: BioSQL/BioSeqDatabase.py =================================================================== RCS file: /home/repository/biopython/biopython/BioSQL/BioSeqDatabase.py,v retrieving revision 1.11 diff -u -p -r1.11 BioSeqDatabase.py --- BioSQL/BioSeqDatabase.py 2002/11/20 15:38:11 1.11 +++ BioSQL/BioSeqDatabase.py 2002/11/22 22:13:21 @@ -58,11 +58,12 @@ def open_database(driver = "MySQLdb", *a return DBServer(conn, module) class DBServer: - def __init__(self, conn, module): + def __init__(self, conn, module, module_name = None): self.module = module - if module.__name__ == 'psycopg': + if module_name is None: module_name = module.__name__ + if module_name == 'psycopg': create_dbutils = DBUtils.create_Pg_dbutils - elif module.__name__ == 'MySQLdb': + elif module_name == 'MySQLdb': create_dbutils = DBUtils.create_Mysql_dbutils else: create_dbutils = DBUtils.create_Generic_dbutils @@ -123,7 +124,7 @@ class Adaptor: def __init__(self, conn, create_dbutils): self.conn = conn self.cursor = conn.cursor() - self.dbutils = create_dbutils()##self.conn, self.cursor) + self.dbutils = create_dbutils() def last_id(self, table): return self.dbutils.last_id(self.cursor, table) @@ -131,6 +132,12 @@ class Adaptor: def autocommit(self, y = 1): return self.dbutils.autocommit(self.conn, y) + def commit(self): + return self.conn.commit() + + def rollback(self): + return self.conn.rollback() + def fetch_dbid_by_dbname(self, dbname): self.cursor.execute( r"select biodatabase_id from biodatabase where name = %s", @@ -138,14 +145,17 @@ class Adaptor: rv = self.cursor.fetchall() if not rv: raise KeyError("Cannot find biodatabase with name %r" % dbname) - assert len(rv) == 1, "More than one biodatabase with name %r" % dbname + # Cannot happen (UK) +## assert len(rv) == 1, "More than one biodatabase with name %r" % dbname return rv[0][0] def fetch_seqid_by_display_id(self, dbid, name): - self.cursor.execute( - r"select bioentry_id from bioentry where " - r" biodatabase_id = %s and display_id = %s", - (dbid, name)) + sql = r"select bioentry_id from bioentry where display_id = %s" + fields = [name] + if dbid: + sql += " and biodatabase_id = %d" + fields.append(dbid) + self.cursor.execute(sql, fields) rv = self.cursor.fetchall() if not rv: raise IndexError("Cannot find display id %r" % name) @@ -153,13 +163,17 @@ class Adaptor: return rv[0][0] def fetch_seqid_by_accession(self, dbid, name): - self.cursor.execute( - r"select bioentry_id from bioentry where " - r" biodatabase_id = %s and accession = %s", - (dbid, name)) + sql = r"select bioentry_id from bioentry where accession = %s" + fields = [name] + if dbid: + sql += " and biodatabase_id = %d" + fields.append(dbid) + + self.cursor.execute(sql, fields) rv = self.cursor.fetchall() if not rv: raise IndexError("Cannot find accession %r" % name) + # Can happen: several versions (or biodatabases) assert len(rv) == 1, "More than one entry with accession of %r" % name return rv[0][0] @@ -203,6 +217,8 @@ class Adaptor: def execute(self, sql, args): """Just execute an sql command. """ +## print "sql:", `sql` +## print "args:", `args` self.cursor.execute(sql, args) def get_subseq_as_string(self, seqid, start, end): Index: BioSQL/Loader.py =================================================================== RCS file: /home/repository/biopython/biopython/BioSQL/Loader.py,v retrieving revision 1.9 diff -u -p -r1.9 Loader.py --- BioSQL/Loader.py 2002/11/20 15:38:11 1.9 +++ BioSQL/Loader.py 2002/11/22 22:13:21 @@ -11,6 +11,8 @@ from time import gmtime, strftime # biopython from Bio import Alphabet +from Bio.crc import crc64 + class DatabaseLoader: """Load a database with biopython objects. """ @@ -27,40 +29,135 @@ class DatabaseLoader: """ bioentry_id = self._load_bioentry_table(record) self._load_bioentry_date(record, bioentry_id) - # self._load_bioentry_taxa(record, bioentry_id) self._load_biosequence(record, bioentry_id) - self._load_bioentry_description(record, bioentry_id) + self._load_comment(record, bioentry_id) + references = record.annotations.get('references', ()) + for reference, rank in zip(references, range(len(references))): + self._load_reference(reference, rank, bioentry_id) for seq_feature_num in range(len(record.features)): seq_feature = record.features[seq_feature_num] self._load_seqfeature(seq_feature, seq_feature_num, bioentry_id) - def _get_ontology_id(self, term_name, term_description = ""): + def _get_ontology_id(self, + term_name, + term_description = None, + term_identifier = None, + category_id = 0): """Get the id that corresponds to any term in an ontology. This looks through the ontology table for a the given term. If it is not found, a new id corresponding to this ontology is created. In either case, the id corresponding to that term is returned, so that you can reference it in another table. + + The category_id can be needed to disambiguate the term: + it will be used if != 0. """ + # try to get the ontology term sql = r"SELECT ontology_term_id FROM ontology_term " \ r"WHERE term_name = %s" - id_results = self.adaptor.execute_and_fetchall(sql, (term_name,)) + fields = [term_name] + if category_id != 0: # 'None' is legitimate + sql += ' AND category_id ' + if category_id is None: + sql += 'IS NULL' + else: + sql += '= %d' + fields.append(category_id) + id_results = self.adaptor.execute_and_fetchall(sql, fields) # something is wrong if len(id_results) > 1: raise ValueError("Multiple ontology ids for %s: %s" % - term_name, id_results) + (term_name, id_results)) # we already have the ontology term inserted elif len(id_results) == 1: return id_results[0][0] # we need to create it else: - sql = r"INSERT INTO ontology_term (term_name, term_definition)" \ - r"VALUES (%s, %s)" - self.adaptor.execute(sql, (term_name, term_description)) - # recursively call this to give back the id - return self._get_ontology_id(term_name, term_description) + # If no category_id specified, set it to null, as 0 isn't possible + if category_id == 0: category_id = None + + sql = r"INSERT INTO ontology_term (term_name, term_definition," \ + r" term_identifier, category_id)" \ + r" VALUES (%s, %s, %s, %d)" + self.adaptor.execute(sql, (term_name, term_description, + term_identifier, category_id)) + return self.adaptor.last_id('ontology_term') + def _get_taxon_id(self, record): + """Get the id corresponding to a taxon. + + If the species isn't in the taxon table, it is created. + + The code to find the species in the record is brittle. + """ + # Binomial and full lineage + try: + binomial = record.annotations["organism"] + except KeyError: + binomial = None + + # XXX no variant + variant = '-' + + if binomial and variant: + sql = "SELECT taxon_id FROM taxon WHERE binomial = %s" \ + " AND variant = %s" + taxa = self.adaptor.execute_and_fetchall(sql, (binomial, variant)) + if taxa: + return taxa[0][0] + + # Didn't found the binomial/variant... Let's try with the taxon id + ncbi_taxon_id = None + for f in record.features: + if (f.type == 'source' and getattr(f, 'qualifiers', None) + and f.qualifiers.has_key('db_xref')): + for db_xref in f.qualifiers['db_xref']: + if db_xref[:6] == 'taxon:': + ncbi_taxon_id = int(db_xref[6:]) + break + if ncbi_taxon_id: break + + if ncbi_taxon_id: + sql = "SELECT taxon_id FROM taxon WHERE ncbi_taxon_id = %u" + taxa = self.adaptor.execute_and_fetchall(sql, (ncbi_taxon_id,)) + if taxa: + return taxa[0][0] + + # OK, so we're gonna try to insert the taxon + + # Common name + try: + common_name = record.annotations["source"] + except KeyError: + common_name = None + + # Full lineage + try: + full_lineage = record.annotations["taxonomy"] + ante, last = binomial.split() + if full_lineage[-1] == ante: + full_lineage.append(last) + full_lineage.reverse() + full_lineage = ':'.join(full_lineage) + except KeyError: + full_lineage = None + + # Check for the NON NULLs + if binomial == None or variant == None or full_lineage == None: + return + + # Insert into the taxon table + sql = "INSERT INTO taxon (binomial, variant, common_name," \ + " ncbi_taxon_id, full_lineage)" \ + " VALUES (%s, %s, %s, %d, %s)" + self.adaptor.execute(sql, (binomial, variant, common_name, + ncbi_taxon_id, full_lineage)) + taxon_id = self.adaptor.last_id('taxon') + + return taxon_id + def _load_bioentry_table(self, record): """Fill the bioentry table with sequence information. """ @@ -68,18 +165,21 @@ class DatabaseLoader: if record.id.find('.') >= 0: # try to get a version from the id accession, version = record.id.split('.') - else: # otherwise just use a null version + version = int(version) + else: # otherwise just use a version of 0 accession = record.id version = 0 - try: - division = record.annotations["data_file_divison"] - except KeyError: - division = "No" - sql = r"INSERT INTO bioentry (biodatabase_id, display_id, " \ - r"accession, entry_version, division) VALUES" \ - r" (%s, %s, %s, %s, %s)" - self.adaptor.execute(sql, (self.dbid, record.name, - accession, version, division)) + + taxon_id = self._get_taxon_id(record) + identifier = record.annotations.get('gi') + description = getattr(record, 'description', None) + + sql = r"INSERT INTO bioentry (biodatabase_id, taxon_id, display_id, " \ + r"accession, identifier, description, entry_version) VALUES" \ + r" (%d, %d, %s, %s, %s, %s, %d)" + self.adaptor.execute(sql, (self.dbid, taxon_id, record.name, + accession, identifier, description, + version)) # now retrieve the id for the bioentry bioentry_id = self.adaptor.last_id('bioentry') @@ -100,46 +200,83 @@ class DatabaseLoader: r" (%s, %s, %s)" self.adaptor.execute(sql, (bioentry_id, date_id, date)) - def _load_bioentry_taxa(self, record, bioentry_id): - """Add taxa information to the database. - """ - return None # XXX don't do anything right now - try: - # XXX this isn't right, we need taxa ids and other junk - taxa = record.annotations["taxa"] - sql = r"INSERT INTO bioentry_taxa(bioentry_id, taxa_id) VALUES" \ - r" (%s, %s)" - self.adapter.execute(sql, (bioentry_id, taxa)) - except KeyError: - pass - def _load_biosequence(self, record, bioentry_id): """Load the biosequence table in the database. """ accession, version = record.id.split(".") + version = int(version) # determine the string representation of the alphabet if isinstance(record.seq.alphabet, Alphabet.DNAAlphabet): - alphabet = "DNA" + alphabet = "dna" elif isinstance(record.seq.alphabet, Alphabet.RNAAlphabet): - alphabet = "RNA" + alphabet = "rna" elif isinstance(record.seq.alphabet, Alphabet.ProteinAlphabet): - alphabet = "PROTEIN" + alphabet = "protein" else: - alphabet = "UNKNOWN" + alphabet = "unknown" - sql = r"INSERT INTO biosequence (bioentry_id, seq_version, " \ - r"biosequence_str, molecule) VALUES (%s, %s, %s, %s)" - self.adaptor.execute(sql, (bioentry_id, version, record.seq.data, - alphabet)) - - def _load_bioentry_description(self, record, bioentry_id): - """Load the description table. - """ - descr_id = self._get_ontology_id("description", "Sequence description") - sql = r"INSERT INTO bioentry_qualifier_value VALUES (%s, %s, %s)" - self.adaptor.execute(sql, (bioentry_id, descr_id, - record.description)) + try: + division = record.annotations["data_file_division"] + except KeyError: + division = "UNK" + sql = r"INSERT INTO biosequence (bioentry_id, seq_version, " \ + r"seq_length, biosequence_str, alphabet, division) " \ + r"VALUES (%d, %d, %d, %s, %s, %s)" + self.adaptor.execute(sql, (bioentry_id, version, + len(record.seq.data), + record.seq.data, + alphabet, division)) + + def _load_comment(self, record, bioentry_id): + # Assume annotations['comment'] is not a list + comment = record.annotations.get('comment') + if not comment: + return + comment = comment.replace('\n', ' ') + + sql = "INSERT INTO comment (bioentry_id, comment_text, comment_rank)" \ + " VALUES (%d, %s, %d)" + self.adaptor.execute(sql, (bioentry_id, comment, 1)) + + def _load_reference(self, reference, rank, bioentry_id): + # Currently, the UK is either the medline_id or a CRC64 + if reference.medline_id: + uk = reference.medline_id + else: + s = '' + for f in reference.authors, reference.title, reference.journal: + if f: s += f + else: s += "" + uk = crc64(s) + + sql = "SELECT reference_id FROM reference WHERE reference_medline = %s" + refs = self.adaptor.execute_and_fetch_col0(sql, (uk,)) + if not len(refs): + authors = reference.authors or None + title = reference.title or None + journal = reference.journal or None + sql = "INSERT INTO reference (reference_location," \ + " reference_title, reference_authors, reference_medline)" \ + " VALUES (%s, %s, %s, %s)" + self.adaptor.execute(sql, (journal, title, + authors, uk)) + reference_id = self.adaptor.last_id('reference') + else: + reference_id = refs[0] + if len(reference.location): + start = 1 + int(str(reference.location[0].start)) + end = int(str(reference.location[0].end)) + else: + start = None + end = None + + sql = "INSERT INTO bioentry_reference (bioentry_id, reference_id," \ + " reference_start, reference_end, reference_rank)" \ + " VALUES (%d, %d, %d, %d, %d)" + self.adaptor.execute(sql, (bioentry_id, reference_id, + start, end, rank + 1)) + def _load_seqfeature(self, feature, feature_rank, bioentry_id): """Load a biopython SeqFeature into the database. """ @@ -154,13 +291,20 @@ class DatabaseLoader: This loads the "key" of the seqfeature (ie. CDS, gene) and the basic seqfeature table itself. """ - seqfeature_key_id = self._get_ontology_id(feature_type) + category_id = self._get_ontology_id('SeqFeature Keys') + seqfeature_key_id = self._get_ontology_id(feature_type, + category_id = category_id) + + # XXX source is always EMBL/GenBank/SwissProt here; it should depend on + # the record + source_cat_id = self._get_ontology_id('SeqFeature Sources') + source_id = self._get_ontology_id('EMBL/GenBank/SwissProt', + category_id = source_cat_id) - # XXX This doesn't do source yet, since I'm not sure I understand it. - sql = r"INSERT INTO seqfeature (bioentry_id, seqfeature_key_id, " \ - r"seqfeature_rank) VALUES (%s, %s, %s)" + sql = r"INSERT INTO seqfeature (bioentry_id, ontology_term_id, " \ + r"seqfeature_source_id, seqfeature_rank) VALUES (%d, %d, %d, %d)" self.adaptor.execute(sql, (bioentry_id, seqfeature_key_id, - feature_rank)) + source_id, feature_rank + 1)) seqfeature_id = self.adaptor.last_id('seqfeature') return seqfeature_id @@ -193,7 +337,7 @@ class DatabaseLoader: """ sql = r"INSERT INTO seqfeature_location (seqfeature_id, " \ r"seq_start, seq_end, seq_strand, location_rank) " \ - r"VALUES (%s, %s, %s, %s, %s)" + r"VALUES (%d, %d, %d, %d, %d)" # hack for NOT NULL in strand -- we have None be the same as 0 # for strand information @@ -208,7 +352,7 @@ class DatabaseLoader: start = feature.location.nofuzzy_start + 1 end = feature.location.nofuzzy_end - self.adaptor.execute(sql, (seqfeature_id, start, end, strand, rank)) + self.adaptor.execute(sql, (seqfeature_id, start, end, strand, rank+1)) def _load_seqfeature_qualifiers(self, qualifiers, seqfeature_id): """Insert the (key, value) pair qualifiers relating to a feature. @@ -216,16 +360,18 @@ class DatabaseLoader: Qualifiers should be a dictionary of the form: {key : [value1, value2]} """ + tag_category_id = self._get_ontology_id('Annotation Tags') for qualifier_key in qualifiers.keys(): - qualifier_key_id = self._get_ontology_id(qualifier_key) + qualifier_key_id = self._get_ontology_id(qualifier_key, + category_id = tag_category_id) # now add all of the values to their table for qual_value_rank in range(len(qualifiers[qualifier_key])): qualifier_value = qualifiers[qualifier_key][qual_value_rank] sql = r"INSERT INTO seqfeature_qualifier_value VALUES" \ - r" (%s, %s, %s, %s)" + r" (%d, %d, %d, %s)" self.adaptor.execute(sql, (seqfeature_id, - qualifier_key_id, qual_value_rank, qualifier_value)) + qualifier_key_id, qual_value_rank + 1, qualifier_value)) class DatabaseRemover: """Complement the Loader functionality by fully removing a database. From biopython-bugs at bioperl.org Sat Nov 23 00:48:40 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] Notification: incoming/106 Message-ID: <200211230548.gAN5me6J025639@pw600a.bioperl.org> JitterBug notification new message incoming/106 Message summary for PR#106 From: Your_Health_Care_685 Subject: YOUR HEALTH CARE........................................................................................................................................................................... maso Date: Fri, 22 Nov 2002 23:44:12 -0600 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From Your_Health_Care_79@gte.net Sat Nov 23 00:48:39 2002 Received: from 66.127.101.180 (adsl-66-127-101-180.dsl.pltn13.pacbell.net [66.127.101.180]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id gAN5mQ6J025632 for ; Sat, 23 Nov 2002 00:48:31 -0500 Message-Id: <200211230548.gAN5mQ6J025632@pw600a.bioperl.org> Received: from unknown (HELO web13708.mail.yahoo.com) (141.52.163.69) by smtp4.cyberec.com with SMTP; Nov, 22 2002 11:36:04 PM +1200 Received: from mailout2-eri1.midsouth.rr.com ([110.220.177.171]) by rly-xr01.mx.aol.com with NNFMP; Nov, 22 2002 10:19:48 PM -0700 Received: from mx.rootsystems.net ([60.127.54.24]) by smtp-server6.tampabay.rr.com with SMTP; Nov, 22 2002 9:30:01 PM +0600 Received: from unknown (HELO mailout2-eri1.midsouth.rr.com) (184.119.91.62) by rly-xw05.mx.aol.com with asmtp; Nov, 22 2002 8:34:42 PM +1200 From: Your_Health_Care_685 To: Subscriber1946@vail.net Cc: Subject: YOUR HEALTH CARE........................................................................................................................................................................... maso Sender: Your_Health_Care_685 Mime-Version: 1.0 Content-Type: text/html; charset="iso-8859-1" Date: Fri, 22 Nov 2002 23:44:12 -0600 X-Mailer: QUALCOMM Windows Eudora Version 5.1 X-Priority: 1

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adimjcictevrmnsjteyjpwcsubnpkkvkpko From chapmanb at arches.uga.edu Sun Nov 24 15:26:38 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] BioSQL upgrade [0 of 3] In-Reply-To: <3DDEB24F.8000202@irisa.fr> References: <3DDEB24F.8000202@irisa.fr> Message-ID: <20021124202638.GB4918@ci350185-a.athen1.ga.home.com> Yves; > Here's a set of patches to update BioSQL. It: Sweet. Thanks much for this work! I've got it all checked in and tests pass on both Postgres and MySQL on my machine. I also checked a current biosqldb-mysql.sql and biosqldb-pg.sql into Tests/BioSQL so the Tests looks for them there -- this way we have the SQL that we know works in the test directory and all that kind of good stuff. Just one note on your implementations. In a lot of the SQL strings you used %d when an integer was expected in the schema. This seems to work fine in Postgres but MySQLdb craps out on it, complaining with a TypeError about an integer being needed. To solve this, everything should just be %s in the SQL string and then all the necessary magic just takes place -- this works with both databases. > [2] Bio.SeqRecord.SeqRecord > I believe this means in practice a GenBank record, as SProt uses another > class. Yup, I implemented this "generic" SeqRecord class when I did the GenBank stuff, and SwissProt was already finished at that time. Ideally, parsing into SeqRecords should be supported for everything, but it just hasn't been done yet. Thanks again for all this work! Hopefully I've got everything into CVS okay -- let me know if anything seems wonky or anything. Brad From chapmanb at arches.uga.edu Sun Nov 24 15:37:08 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] BioSQL questions In-Reply-To: <3DDE05B2.7020900@irisa.fr> References: <3DDE05B2.7020900@irisa.fr> Message-ID: <20021124203708.GC4918@ci350185-a.athen1.ga.home.com> > Bioentries are retrieved via two classes, DBSeqRecord and DBInternalSeq. > Why? > > I'm asking because it seems sound, but I don't understand why which data > is retrieved by which class, e.g. sequence name by DBInternalSeq. This is just an implementation detail that has carried over from the first stab at this by Andrew. He'll have to tell use why he split it like this; he probably had some mad idea in his head at the time, but I reckon now it is more arbitrary than anything. > Concerning the sequence name: a bioentry contains four ids: > > * bioentry_id, the internal id > > * display_id, called "name" by SeqRecord > > * accession, called "id" > > * identifier, not retrieved. > > In Genbank parlance, display_id == LOCUS, accession == ACCESSION (duh!) > and identifier == GI. Yeah, this is hideous and completely my fault. What I guess I think we should have is: name -- the LOCUS/display_id id -- the GI/identifier; this should not be the accession, that sucks. accessions -- a list of accession numbers; I think Jeff said something about multiple accession numbers recently, so we can support them all and then just jam the first one into BioSQL. > Obviously, the GI should be retrieved Right now GI is nastily jammed into data.accessions['gi']. Yuck. How does this sound for a plan? Does this take care of most of the ugliness? Brad From chapmanb at arches.uga.edu Sun Nov 24 15:55:21 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] GenBank alphabet In-Reply-To: <3DDEA845.1080101@irisa.fr> References: <3DDEA845.1080101@irisa.fr> Message-ID: <20021124205521.GE4918@ci350185-a.athen1.ga.home.com> Afternoon; > what's the relation between an entry alphabet and its sequence? > > Case in point: Tests/cor6_6.gb, first entry. > ATCOR66M is a mRNA, but the sequence is a DNA one (as documented by the > NCBI). So: Good point. I think this is something else I jacked up (what's new? :-). The sequence itself is DNA, so they should actually probably use cDNA to be "correct" about it. I never even thought about this. > * what do biologists prefer? We don't care :-). Seriously, this should be DNA 'cause it has Ts and not Us. > * what to store in a BioSQL record (BioPerl says dna)? Also DNA. We have to be consistent with the actual content of the string; the origin of the sequence as an mRNA should be stored somewhere else (presumedly) in the GenBank record. Also good to be consistent with BioPerl 'cause those guys are always right. I fixed this in CVS. Thanks for pointing it out. Brad From chapmanb at arches.uga.edu Sun Nov 24 17:02:49 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] The Status of the Tests Message-ID: <20021124220249.GF4918@ci350185-a.athen1.ga.home.com> Hey all; I gave a hack at the Tests today and I think I have them all working but five with the following problems: test_GFF -- We need the files for the tests. I'm not sure how this doctest stuff works exactly, but we need to put the NC_001802x.fna or whatever files somewhere in the Tests directory so it can find them. test_locuslink -- we are missing the file "LL_block" from the LocusLink directory. test_easy -- We seem to be missing '../Tests/easy/multi.fna' and '../Tests/easy/NC_001422.gbk.' test_ais and test_HotRand -- These tests takes waaaaaaaay too long to run and I guess it is because they are fetching stuff from the web (true random numbers). I just disabled them especially since they'll be a mess on a machine without an internet connection. test_trie -- I get the following import error with this: dynamic module does not define init function (inittrie). This is after adding it to the compiled extensions. I have zero idea what this means or how to fix it. Anyways, if people can fix their stuff in these tests (mostly missing files), we can get them all running smoothly and happily. Now I go to sleep. Man, am I ever sick. Brad From katel at worldpath.net Mon Nov 25 04:12:19 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] Tests Message-ID: <000701c29462$c332fe00$08a0940c@pcklindner> I wasn't able to ftp to bio.perl.org tonite. Did I miss the migration to a bigger computer? Cayte From jchang at smi.stanford.edu Mon Nov 25 04:52:55 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] Tests In-Reply-To: <000701c29462$c332fe00$08a0940c@pcklindner> References: <000701c29462$c332fe00$08a0940c@pcklindner> Message-ID: <20021125095255.GA22077@springfield.stanford.edu> Sort of. bio.perl.org was moved onto a different network. There were some issues with the firewall on that network having problems with FTP. I guess those haven't been resolved yet. Can you use scp to get the files you need? Jeff On Mon, Nov 25, 2002 at 01:12:19AM -0800, Cayte wrote: > I wasn't able to ftp to bio.perl.org tonite. Did I miss the migration to > a bigger computer? > Cayte > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From jchang at smi.stanford.edu Tue Nov 26 20:54:06 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] The Status of the Tests In-Reply-To: <20021124220249.GF4918@ci350185-a.athen1.ga.home.com> References: <20021124220249.GF4918@ci350185-a.athen1.ga.home.com> Message-ID: <20021127015406.GA27643@springfield.stanford.edu> On Sun, Nov 24, 2002 at 05:02:49PM -0500, Brad Chapman wrote: > test_trie -- I get the following import error with this: dynamic module does > not define init function (inittrie). This is after adding it to the > compiled extensions. I have zero idea what this means or how to fix it. Oops, I checked in the code and tests, but failed to add them to setup.py. I've checked this in now. Please let me know if it is still failing! Jeff From jchang at smi.stanford.edu Wed Nov 27 03:04:33 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] added requires_internet test Message-ID: <20021127080433.GB28480@springfield.stanford.edu> Hey all, I've added a file requires_internet.py to Bio/Tests. This is basically a modules that's used to detect whether the internet is available. If it is, then nothing happens. If it is not, then it raises an ImportError. This file is useful for the regression tests. Add "import requires_internet" to the top of each of the regression test files (test_*). This way, if the internet is available, then the tests run normally. Otherwise, the tests are skipped. I've already added it to test_ais and test_HotRand. Please add it to other test files as appropriate. Also, please give it a spin, and let me know if there are any bugs! Thanks, Jeff From jchang at smi.stanford.edu Wed Nov 27 03:05:39 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] The Status of the Tests In-Reply-To: <20021124220249.GF4918@ci350185-a.athen1.ga.home.com> References: <20021124220249.GF4918@ci350185-a.athen1.ga.home.com> Message-ID: <20021127080539.GC28480@springfield.stanford.edu> On Sun, Nov 24, 2002 at 05:02:49PM -0500, Brad Chapman wrote: > test_ais and test_HotRand -- These tests takes waaaaaaaay too long to run > and I guess it is because they are fetching stuff from the web (true random > numbers). I just disabled them especially since they'll be a mess on a machine > without an internet connection. I think I've addressed the case where there's no internet connection. Cayte, are these slow because of the web access, or some other reason? Is there any way to speed up the tests? Jeff From jchang at smi.stanford.edu Wed Nov 27 03:59:14 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] The Status of the Tests In-Reply-To: <20021124220249.GF4918@ci350185-a.athen1.ga.home.com> References: <20021124220249.GF4918@ci350185-a.athen1.ga.home.com> Message-ID: <20021127085914.GD28480@springfield.stanford.edu> I had been noticing some odd failures in test_format_registry and test_align. Basically, they would fail when running the whole regression suite. However, if run separately (python run_tests test_align), they worked. It turns out that this is due to a bug in the interface between the regression testing framework and some code in Biopython. The problem stems from functions (or class methods) defined as: def foobar(outhandle=sys.stdout, ...) ... This conflicted with the regression tests, because the regression tests reassigned sys.stdout. The outhandle parameter in the foobar function was getting bound to the old value of sys.stdout when imported. The fix was to change occurrences of this to: def foobar(outhandle=None, ...) outhandle = outhandle or sys.stdout Written this way, outhandle will get bound when the function is called, rather than when the module is first imported. I've checked these fixes in. test_format_registry and test_align are now happy again! Jeff From ybastide at irisa.fr Wed Nov 27 05:40:17 2002 From: ybastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] [patch] BioSQL: reference_docid Message-ID: <3DE4A111.4050605@irisa.fr> Hi, here's a patch to have references' CRC in a different field than medline_id, as discussed on BioSQL-l. This is a 20Kio diff mainly because of trivial differences in the schemas, so I gzipped it... Brad: I'm with you on moving around accession and GI in the sequence object. While on this, I guess all of them should be retrieved in the first SELECT (one SELECT for the bioentry record, and others for the biosequence, annotation data, etc.). Regards, yves -------------- next part -------------- A non-text attachment was scrubbed... Name: biosql.diff.gz Type: application/gzip Size: 4582 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython-dev/attachments/20021127/a05ccfe5/biosql.diff.bin From ybastide at irisa.fr Wed Nov 27 12:13:44 2002 From: ybastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] [patch] BioSQL.BioSeq.Annotation._get_dblinks Message-ID: <3DE4FD48.9060808@irisa.fr> Hi, quick patch to BioSQL.BioSeq, which used a nonexistant table for db links. Also add the NCBI taxon id in the Species class. yves -------------- next part -------------- Index: BioSQL/BioSeq.py =================================================================== RCS file: /home/repository/biopython/biopython/BioSQL/BioSeq.py,v retrieving revision 1.9 diff -u -p -r1.9 BioSeq.py --- BioSQL/BioSeq.py 2002/11/24 20:07:04 1.9 +++ BioSQL/BioSeq.py 2002/11/27 17:12:50 @@ -132,10 +132,11 @@ _is_title = re.compile(r"[A-Z][^A-Z]*$") _is_lower = re.compile(r"[^A-Z]+$") class Species: - def __init__(self, classification, common_name = None, sub_species = None, - organelle = None): + def __init__(self, classification, common_name = None, ncbi_id = None, + sub_species = None, organelle = None): self.classification = classification self.common_name = common_name + self.ncbi_id = ncbi_id self.sub_species = sub_species self.organelle = organelle @@ -236,8 +237,9 @@ class Annotation: def _get_dblinks(self): dblink_info = self.adaptor.execute_and_fetchall( - """select dbname, accession from bioentry_direct_links - where source_bioentry_id = %s""", + "SELECT dbname, accession FROM bioentry_dblink, dbxref" \ + " WHERE bioentry_dblink.dbxref_id = dbxref.dbxref_id" \ + " AND bioentry_id = %s""", (self.primary_id,)) dblinks = [DBLink(database, primary_id) for (database, primary_id) in dblink_info] @@ -426,14 +428,14 @@ class DBSeqRecord: return self.dates def _get_species(self): - full_lineage, common_name = self.adaptor.execute_one( - """select tx.full_lineage, tx.common_name + full_lineage, common_name, ncbi_id = self.adaptor.execute_one( + """select tx.full_lineage, tx.common_name, tx.ncbi_taxon_id from taxon tx, bioentry be where tx.taxon_id = be.taxon_id and be.bioentry_id = %s""", (self.primary_id,)) terms = full_lineage.split(":") - species = Species(terms, common_name) + species = Species(terms, common_name, ncbi_id) return species def _get_seq_version(self): From grouse at mail.utexas.edu Wed Nov 27 13:52:05 2002 From: grouse at mail.utexas.edu (Michael Hoffman) Date: Sat Mar 5 14:43:18 2005 Subject: [Biopython-dev] Re: The Status of the Tests In-Reply-To: <20021124220249.GF4918@ci350185-a.athen1.ga.home.com> References: <20021124220249.GF4918@ci350185-a.athen1.ga.home.com> Message-ID: On Sun, 24 Nov 2002, Brad Chapman wrote: > test_GFF -- We need the files for the tests. I'm not sure how this doctest > stuff works exactly, but we need to put the NC_001802x.fna or whatever files > somewhere in the Tests directory so it can find them. I'll get right on it. > test_easy -- We seem to be missing '../Tests/easy/multi.fna' and > '../Tests/easy/NC_001422.gbk.' Likewise. Last time I noticed these were missing I was having trouble with the developer CVS. Since this was right about the time of the machine switch I decided to wait until things settled down and then it dropped off my radar. Sorry. -- Michael Hoffman The University of Texas at Austin From jchang at smi.stanford.edu Wed Nov 27 18:12:23 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Re: The Status of the Tests In-Reply-To: References: <20021124220249.GF4918@ci350185-a.athen1.ga.home.com> Message-ID: <20021127231223.GD30559@springfield.stanford.edu> [regression tests with missing files] > I'll get right on it. Great! Also, do you mind moving easy.py and GenericTools.py into GFF, or somewhere besides the Bio namespace? I know I might have told you to put them there, but I do not want to be placing alternate API's in such an exposed place. Thanks, Jeff From katel at worldpath.net Wed Nov 27 21:59:40 2002 From: katel at worldpath.net (katel@worldpath.net) Date: Sat Mar 5 14:43:19 2005 Subject: [Biopython-dev] Tests Message-ID: <184670-220021142825940534@M2W075.mail2web.com> LL_block is on the path slash-home-slash-katel-slash-biopython-slash-Tests-slash-LocusLink Apparently the repository has changed because I couldn't check it in with the path I've used in the past. Cayte -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ .