From jared.wilkening@gmail.com Tue Nov 10 00:05:34 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1N7dIi-00066X-RC>; Tue, 10 Nov 2009 00:05:32 +0100 Received: from mail-vw0-f192.google.com ([209.85.212.192]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1N7dIi-0001xa-Cf>; Tue, 10 Nov 2009 00:05:32 +0100 Received: by vws30 with SMTP id 30so1029194vws.33 for ; Mon, 09 Nov 2009 15:05:31 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:mime-version:sender:reply-to:received:from:date :x-google-sender-auth:message-id:subject:to:content-type :content-transfer-encoding; bh=LjByWk0W7QriNlsW1Fcb3RaWcMmO8/61cEvxkmkc32k=; b=gxTU+Q/bqDia+eONUK5bQVDx31g7Joh840c3YCdhfBGoT78e3eSbmXD1kbSxaaTJgz iYgTjBaAPG10K5zVx8MPHR56dargxV4eVhtSFwLAuAsU59FEAgZh7t62yPB2iAUomTDZ veULpnxmBFVOkZYGToEt9Vqn52Cet2gNYgfA0= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=mime-version:sender:reply-to:from:date:x-google-sender-auth :message-id:subject:to:content-type:content-transfer-encoding; b=BKZofAlCPxhgRgdjNf637ASiFZiQS1R4XZMn2azfUajRouJL0bV8RZGhFdvG4QnWWe pPuQ07/F0usIU0XiQmp6BQ2u1T16xRBu22pgezTWW780KoFwwAV3mDLrwZAK0ZhoiYu3 BsXmXxw2m04f30JRvy3QKm1Mvto1cDU5X7fDQ= MIME-Version: 1.0 Sender: jared.wilkening@gmail.com Received: by 10.220.125.40 with SMTP id w40mr3970547vcr.77.1257807931099; Mon, 09 Nov 2009 15:05:31 -0800 (PST) From: Jared Wilkening Date: Mon, 9 Nov 2009 17:05:11 -0600 X-Google-Sender-Auth: d4d1a624eb14ed17 Message-ID: To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable X-Originating-IP: 209.85.212.192 X-purgate: clean X-purgate-ID: 151147::1257807932-00000DDD-45E5E642/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000075, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST, RCVD_BY_IP, SPF_HELO_PASS,SPF_PASS X-Mailman-Approved-At: Tue, 10 Nov 2009 10:34:28 +0100 Subject: [Seqan-dev] find() build woes X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: jared@mcs.anl.gov, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 09 Nov 2009 23:05:34 -0000 Hi all, I have been trying to get a bit of code running using the SeqAn lib but keep hitting an issue when I have find in my code. To check if it was an issue with my code or something else I attempted to build test_index.cpp from svn_repo .../projects/tests/index/. My setup: gcc version 4.1.2 Seqan_Release_1.2 from the website g++ -c -I. test_index.cpp =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0//No issues g++ test_index.o -o test_index =A0 =A0 =A0//This blows up with the same issues that I get in my code: see errors below errors: test_index.o: In function `main': test_index.cpp:(.text+0xe0e2): undefined reference to `testQGramIndex()' test_index.cpp:(.text+0xe11f): undefined reference to `testShapes()' test_index.cpp:(.text+0xe18c): undefined reference to `testBWTWalk(char con= st*)' test_index.cpp:(.text+0xe1f4): undefined reference to `testIndexCreation()' test_index.o: In function `bool seqan::awriteAt >, seqan::Tuple, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Pair >, seqan::Tuple, seqan::Tag > const*, unsigned long, long, aiocb&)': test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_4PairINS1_ImmNS_3TagINS_11_Com= pressedEEEEENS_5TupleIhLj7EvEES4_EEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T= 2_R5aiocb[bool seqan::awriteAt >, seqan::Tuple, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Pair >, seqan::Tuple, seqan::Tag > const*, unsigned long, long, aiocb&)]+0xb8): undefined reference to `aio_write64' test_index.o: In function `bool seqan::awriteAt >, unsigned long, long>(seqan::File >&, seqan::Pair > const*, unsigned long, long, aiocb&)': test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_4PairImmNS_3TagINS_11_Compress= edEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb[bool seqan::awriteAt >, unsigned long, long>(seqan::File >&, seqan::Pair > const*, unsigned long, long, aiocb&)]+0x9a): undefined reference to `aio_write64' test_index.o: In function `bool seqan::awriteAt, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Pair, seqan::Tag > const*, unsigned long, long, aiocb&)': test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_4PairImNS_5TupleImLj7EvEENS_3T= agINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb[b= ool seqan::awriteAt, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Pair, seqan::Tag > const*, unsigned long, long, aiocb&)]+0x9a): undefined reference to `aio_write64' test_index.o: In function `bool seqan::awriteAt, seqan::Tuple, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple, seqan::Tuple, seqan::Tag > const*, unsigned long, long, aiocb&)': test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_6TripleImNS_5TupleImLj3EvEENS2= _ImLj6EvEENS_3TagINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_= T1_T2_R5aiocb[bool seqan::awriteAt, seqan::Tuple, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple, seqan::Tuple, seqan::Tag > const*, unsigned long, long, aiocb&)]+0xb1): undefined reference to `aio_write64' test_index.o: In function `bool seqan::awriteAt, seqan::Tuple, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple, seqan::Tuple, seqan::Tag > const*, unsigned long, long, aiocb&)': test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_6TripleImNS_5TupleImLj3EvEENS2= _ImLj4EvEENS_3TagINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_= T1_T2_R5aiocb[bool seqan::awriteAt, seqan::Tuple, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple, seqan::Tuple, seqan::Tag > const*, unsigned long, long, aiocb&)]+0x9a): undefined reference to `aio_write64' test_index.o:test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_6TripleImNS_5Tupl= eImLj3EvEENS2_ImLj5EvEENS_3TagINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5Asyn= cIT_EEEEPKT0_T1_T2_R5aiocb[bool seqan::awriteAt, seqan::Tuple, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple, seqan::Tuple, seqan::Tag > const*, unsigned long, long, aiocb&)]+0xb1): more undefined references to `aio_write64' follow test_index.o: In function `seqan::waitFor(aiocb&)': test_index.cpp:(.text._ZN5seqan7waitForER5aiocb[seqan::waitFor(aiocb&)]+0x2= 3): undefined reference to `aio_suspend64' test_index.o: In function `seqan::waitFor(aiocb&, long)': test_index.cpp:(.text._ZN5seqan7waitForER5aiocbl[seqan::waitFor(aiocb&, long)]+0x1d): undefined reference to `aio_error64' test_index.cpp:(.text._ZN5seqan7waitForER5aiocbl[seqan::waitFor(aiocb&, long)]+0xbc): undefined reference to `aio_suspend64' test_index.o: In function `bool seqan::cancel(seqan::File >&, aiocb&)': test_index.cpp:(.text._ZN5seqan6cancelIvEEbRNS_4FileINS_5AsyncIT_EEEER5aioc= b[bool seqan::cancel(seqan::File >&, aiocb&)]+0x1c): undefined reference to `aio_cancel64' test_index.o: In function `bool seqan::areadAt >, unsigned long, long>(seqan::File >&, seqan::Pair >*, unsigned long, long, aiocb&)': test_index.cpp:(.text._ZN5seqan7areadAtIvNS_4PairImmNS_3TagINS_11_Compresse= dEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb[bool seqan::areadAt >, unsigned long, long>(seqan::File >&, seqan::Pair >*, unsigned long, long, aiocb&)]+0x9a): undefined reference to `aio_read64' test_index.o: In function `bool seqan::areadAt, seqan::Tuple, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple, seqan::Tuple, seqan::Tag >*, unsigned long, long, aiocb&)': test_index.cpp:(.text._ZN5seqan7areadAtIvNS_6TripleImNS_5TupleImLj3EvEENS2_= ImLj6EvEENS_3TagINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1= _T2_R5aiocb[bool seqan::areadAt, seqan::Tuple, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple, seqan::Tuple, seqan::Tag >*, unsigned long, long, aiocb&)]+0xb1): undefined reference to `aio_read64' test_index.o: In function `bool seqan::areadAt >, seqan::Tuple, seqan::Tuple, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple >, seqan::Tuple, seqan::Tuple, seqan::Tag >*, unsigned long, long, aiocb&)': test_index.cpp:(.text._ZN5seqan7areadAtIvNS_6TripleINS_4PairImmNS_3TagINS_1= 1_CompressedEEEEENS_5TupleImLj3EvEENS7_IhLj6EvEES5_EEmlEEbRNS_4FileINS_5Asy= ncIT_EEEEPT0_T1_T2_R5aiocb[bool seqan::areadAt >, seqan::Tuple, seqan::Tuple, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple >, seqan::Tuple, seqan::Tuple, seqan::Tag >*, unsigned long, long, aiocb&)]+0x97): undefined reference to `aio_read64' test_index.o: In function `bool seqan::areadAt >, seqan::Tuple, seqan::Tuple, 6u, seqan::Tag >, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple >, seqan::Tuple, seqan::Tuple, 6u, seqan::Tag >, seqan::Tag >*, unsigned long, long, aiocb&)': test_index.cpp:(.text._ZN5seqan7areadAtIvNS_6TripleINS_4PairImmNS_3TagINS_1= 1_CompressedEEEEENS_5TupleImLj3EvEENS7_INS_10SimpleTypeIhNS_4_DnaEEELj6ES5_= EES5_EEmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb[bool seqan::areadAt >, seqan::Tuple, seqan::Tuple, 6u, seqan::Tag >, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple >, seqan::Tuple, seqan::Tuple, 6u, seqan::Tag >, seqan::Tag >*, unsigned long, long, aiocb&)]+0xbd): undefined reference to `aio_read64' test_index.o: In function `bool seqan::areadAt >, seqan::Tuple, seqan::Tuple, 6u, seqan::Tag >, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple >, seqan::Tuple, seqan::Tuple, 6u, seqan::Tag >, seqan::Tag >*, unsigned long, long, aiocb&)': test_index.cpp:(.text._ZN5seqan7areadAtIvNS_6TripleINS_4PairImmNS_3TagINS_1= 1_CompressedEEEEENS_5TupleImLj3EvEENS7_INS_10SimpleTypeIhNS_5_Dna5EEELj6ES5= _EES5_EEmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb[bool seqan::areadAt >, seqan::Tuple, seqan::Tuple, 6u, seqan::Tag >, seqan::Tag >, unsigned long, long>(seqan::File >&, seqan::Triple >, seqan::Tuple, seqan::Tuple, 6u, seqan::Tag >, seqan::Tag >*, unsigned long, long, aiocb&)]+0xbd): undefined reference to `aio_read64' test_index.o:test_index.cpp:(.text._ZN5seqan7areadAtIvcmlEEbRNS_4FileINS_5A= syncIT_EEEEPT0_T1_T2_R5aiocb[bool seqan::areadAt(seqan::File >&, char*, unsigned long, long, aiocb&)]+0x8c): more undefined references to `aio_read64' follow collect2: ld returned 1 exit status Any ideas? Cheers, Jared Wilkening From weese@campus.fu-berlin.de Wed Nov 11 11:26:03 2009 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1N8AOo-0003DO-7h>; Wed, 11 Nov 2009 11:26:02 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1N8AOo-0001Oc-16>; Wed, 11 Nov 2009 11:26:02 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1N8AN5-0004zd-LN>; Wed, 11 Nov 2009 11:24:15 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Wed, 11 Nov 2009 11:26:01 +0100 From: "Weese, David" To: "jared@mcs.anl.gov" , SeqAn Development Date: Wed, 11 Nov 2009 11:25:59 +0100 Thread-Topic: [Seqan-dev] find() build woes Thread-Index: AcpiuV2Jqdcimze2S2eue91Ktj30Vg== Message-ID: <13EA5A3C-F265-4591-80C3-8C3458A01A90@fu-berlin.de> References: In-Reply-To: Accept-Language: de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-ID: 151147::1257935162-00000DDD-B5999EEB/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.259696, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Niger.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] find() build woes X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 11 Nov 2009 10:26:03 -0000 Hi Jared, you have to compile all .cpp files within a test folder (like test/ index/). Then you need to link all of them and also link against the rt-library with the "-lrt" option. You find general information about building on our website and in the Trac Wiki (Development Link), see "Getting Started". Regards, David -- David Weese weese@inf.fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75246 Takustra=DFe 9 Algorithmic Bioinformatic= s 14195 Berlin Room 021 Am 09.11.2009 um 23:05 schrieb Jared Wilkening: > Hi all, > > I have been trying to get a bit of code running using the SeqAn lib > but keep hitting an issue when I have find in my > code. > > To check if it was an issue with my code or something else I attempted > to build test_index.cpp from svn_repo .../projects/tests/index/. > > My setup: > gcc version 4.1.2 > Seqan_Release_1.2 from the website > > g++ -c -I. test_index.cpp //No issues > g++ test_index.o -o test_index //This blows up with the same > issues that I get in my code: see errors below > > errors: > test_index.o: In function `main': > test_index.cpp:(.text+0xe0e2): undefined reference to `testQGramIndex > ()' > test_index.cpp:(.text+0xe11f): undefined reference to `testShapes()' > test_index.cpp:(.text+0xe18c): undefined reference to `testBWTWalk > (char const*)' > test_index.cpp:(.text+0xe1f4): undefined reference to > `testIndexCreation()' > test_index.o: In function `bool seqan::awriteAt seqan::Pair seqan::Tag >, seqan::Tuple void>, seqan::Tag >, unsigned long, > long>(seqan::File >&, > seqan::Pair seqan::Tag >, seqan::Tuple void>, seqan::Tag > const*, unsigned long, long, > aiocb&)': > test_index.cpp: > (.text > ._ZN5seqan8awriteAtIvNS_4PairINS1_ImmNS_3TagINS_11_CompressedEEEEENS_5Tup= leIhLj7EvEES4_EEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb > [bool > seqan::awriteAt long, seqan::Tag >, seqan::Tuple 7u, void>, seqan::Tag >, unsigned long, > long>(seqan::File >&, > seqan::Pair seqan::Tag >, seqan::Tuple void>, seqan::Tag > const*, unsigned long, long, > aiocb&)]+0xb8): undefined reference to `aio_write64' > test_index.o: In function `bool seqan::awriteAt seqan::Pair seqan::Tag >, unsigned long, > long>(seqan::File >&, seqan::Pair unsigned long, seqan::Tag > const*, unsigned long, > long, aiocb&)': > test_index.cpp: > (.text > ._ZN5seqan8awriteAtIvNS_4PairImmNS_3TagINS_11_CompressedEEEEEmlEEbRNS_4Fi= leINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb > [bool > seqan::awriteAt seqan::Tag >, unsigned long, > long>(seqan::File >&, seqan::Pair unsigned long, seqan::Tag > const*, unsigned long, > long, aiocb&)]+0x9a): undefined reference to `aio_write64' > test_index.o: In function `bool seqan::awriteAt seqan::Pair, > seqan::Tag >, unsigned long, > long>(seqan::File >&, seqan::Pair seqan::Tuple, seqan::Tag >> const*, unsigned long, long, aiocb&)': > test_index.cpp: > (.text > ._ZN5seqan8awriteAtIvNS_4PairImNS_5TupleImLj7EvEENS_3TagINS_11_Compressed= EEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb > [bool > seqan::awriteAt long, 7u, void>, seqan::Tag >, unsigned long, > long>(seqan::File >&, seqan::Pair seqan::Tuple, seqan::Tag >> const*, unsigned long, long, aiocb&)]+0x9a): undefined reference to > `aio_write64' > test_index.o: In function `bool seqan::awriteAt seqan::Triple, > seqan::Tuple, seqan::Tag >> , unsigned long, long>(seqan::File >&, > seqan::Triple, > seqan::Tuple, seqan::Tag >> const*, unsigned long, long, aiocb&)': > test_index.cpp: > (.text > ._ZN5seqan8awriteAtIvNS_6TripleImNS_5TupleImLj3EvEENS2_ImLj6EvEENS_3TagIN= S_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb > [bool > seqan::awriteAt seqan::Tuple, seqan::Tuple void>, seqan::Tag >, unsigned long, > long>(seqan::File >&, seqan::Triple seqan::Tuple, seqan::Tuple void>, seqan::Tag > const*, unsigned long, long, > aiocb&)]+0xb1): undefined reference to `aio_write64' > test_index.o: In function `bool seqan::awriteAt seqan::Triple, > seqan::Tuple, seqan::Tag >> , unsigned long, long>(seqan::File >&, > seqan::Triple, > seqan::Tuple, seqan::Tag >> const*, unsigned long, long, aiocb&)': > test_index.cpp: > (.text > ._ZN5seqan8awriteAtIvNS_6TripleImNS_5TupleImLj3EvEENS2_ImLj4EvEENS_3TagIN= S_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb > [bool > seqan::awriteAt seqan::Tuple, seqan::Tuple void>, seqan::Tag >, unsigned long, > long>(seqan::File >&, seqan::Triple seqan::Tuple, seqan::Tuple void>, seqan::Tag > const*, unsigned long, long, > aiocb&)]+0x9a): undefined reference to `aio_write64' > test_index.o:test_index.cpp: > (.text > ._ZN5seqan8awriteAtIvNS_6TripleImNS_5TupleImLj3EvEENS2_ImLj5EvEENS_3TagIN= S_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb > [bool > seqan::awriteAt seqan::Tuple, seqan::Tuple void>, seqan::Tag >, unsigned long, > long>(seqan::File >&, seqan::Triple seqan::Tuple, seqan::Tuple void>, seqan::Tag > const*, unsigned long, long, > aiocb&)]+0xb1): more undefined references to `aio_write64' follow > test_index.o: In function `seqan::waitFor(aiocb&)': > test_index.cpp:(.text._ZN5seqan7waitForER5aiocb[seqan::waitFor > (aiocb&)]+0x23): > undefined reference to `aio_suspend64' > test_index.o: In function `seqan::waitFor(aiocb&, long)': > test_index.cpp:(.text._ZN5seqan7waitForER5aiocbl[seqan::waitFor > (aiocb&, > long)]+0x1d): undefined reference to `aio_error64' > test_index.cpp:(.text._ZN5seqan7waitForER5aiocbl[seqan::waitFor > (aiocb&, > long)]+0xbc): undefined reference to `aio_suspend64' > test_index.o: In function `bool > seqan::cancel(seqan::File >&, aiocb&)': > test_index.cpp: > (.text._ZN5seqan6cancelIvEEbRNS_4FileINS_5AsyncIT_EEEER5aiocb[bool > seqan::cancel(seqan::File >&, aiocb&)]+0x1c): > undefined reference to `aio_cancel64' > test_index.o: In function `bool seqan::areadAt seqan::Pair seqan::Tag >, unsigned long, > long>(seqan::File >&, seqan::Pair unsigned long, seqan::Tag >*, unsigned long, long, > aiocb&)': > test_index.cpp: > (.text > ._ZN5seqan7areadAtIvNS_4PairImmNS_3TagINS_11_CompressedEEEEEmlEEbRNS_4Fil= eINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb > [bool > seqan::areadAt seqan::Tag >, unsigned long, > long>(seqan::File >&, seqan::Pair unsigned long, seqan::Tag >*, unsigned long, long, > aiocb&)]+0x9a): undefined reference to `aio_read64' > test_index.o: In function `bool seqan::areadAt seqan::Triple, > seqan::Tuple, seqan::Tag >> , unsigned long, long>(seqan::File >&, > seqan::Triple, > seqan::Tuple, seqan::Tag >> *, unsigned long, long, aiocb&)': > test_index.cpp: > (.text > ._ZN5seqan7areadAtIvNS_6TripleImNS_5TupleImLj3EvEENS2_ImLj6EvEENS_3TagINS= _11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb > [bool > seqan::areadAt seqan::Tuple, seqan::Tuple void>, seqan::Tag >, unsigned long, > long>(seqan::File >&, seqan::Triple seqan::Tuple, seqan::Tuple void>, seqan::Tag >*, unsigned long, long, > aiocb&)]+0xb1): undefined reference to `aio_read64' > test_index.o: In function `bool seqan::areadAt seqan::Triple seqan::Tag >, seqan::Tuple void>, seqan::Tuple, > seqan::Tag >, unsigned long, > long>(seqan::File >&, > seqan::Triple seqan::Tag >, seqan::Tuple void>, seqan::Tuple, > seqan::Tag >*, unsigned long, long, aiocb&)': > test_index.cpp: > (.text > ._ZN5seqan7areadAtIvNS_6TripleINS_4PairImmNS_3TagINS_11_CompressedEEEEENS= _5TupleImLj3EvEENS7_IhLj6EvEES5_EEmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_= R5aiocb > [bool > seqan::areadAt long, seqan::Tag >, seqan::Tuple 3u, void>, seqan::Tuple, > seqan::Tag >, unsigned long, > long>(seqan::File >&, > seqan::Triple seqan::Tag >, seqan::Tuple void>, seqan::Tuple, > seqan::Tag >*, unsigned long, long, > aiocb&)]+0x97): undefined reference to `aio_read64' > test_index.o: In function `bool seqan::areadAt seqan::Triple seqan::Tag >, seqan::Tuple void>, seqan::Tuple, 6u, > seqan::Tag >, seqan::Tag >, > unsigned long, long>(seqan::File >&, > seqan::Triple seqan::Tag >, seqan::Tuple void>, seqan::Tuple, 6u, > seqan::Tag >, seqan::Tag >*, > unsigned long, long, aiocb&)': > test_index.cpp: > (.text > ._ZN5seqan7areadAtIvNS_6TripleINS_4PairImmNS_3TagINS_11_CompressedEEEEENS= _5TupleImLj3EvEENS7_INS_10SimpleTypeIhNS_4_DnaEEELj6ES5_EES5_EEmlEEbRNS_4Fi= leINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb > [bool > seqan::areadAt long, seqan::Tag >, seqan::Tuple 3u, void>, seqan::Tuple, > 6u, seqan::Tag >, seqan::Tag >> , unsigned long, long>(seqan::File >&, > seqan::Triple seqan::Tag >, seqan::Tuple void>, seqan::Tuple, 6u, > seqan::Tag >, seqan::Tag >*, > unsigned long, long, aiocb&)]+0xbd): undefined reference to > `aio_read64' > test_index.o: In function `bool seqan::areadAt seqan::Triple seqan::Tag >, seqan::Tuple void>, seqan::Tuple, > 6u, seqan::Tag >, seqan::Tag >> , unsigned long, long>(seqan::File >&, > seqan::Triple seqan::Tag >, seqan::Tuple void>, seqan::Tuple, > 6u, seqan::Tag >, seqan::Tag >> *, unsigned long, long, aiocb&)': > test_index.cpp: > (.text > ._ZN5seqan7areadAtIvNS_6TripleINS_4PairImmNS_3TagINS_11_CompressedEEEEENS= _5TupleImLj3EvEENS7_INS_10SimpleTypeIhNS_5_Dna5EEELj6ES5_EES5_EEmlEEbRNS_4F= ileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb > [bool > seqan::areadAt long, seqan::Tag >, seqan::Tuple 3u, void>, seqan::Tuple seqan::_Dna5>, 6u, seqan::Tag >, > seqan::Tag >, unsigned long, > long>(seqan::File >&, > seqan::Triple seqan::Tag >, seqan::Tuple void>, seqan::Tuple, > 6u, seqan::Tag >, seqan::Tag >> *, unsigned long, long, aiocb&)]+0xbd): undefined reference to > `aio_read64' > test_index.o:test_index.cpp: > (.text > ._ZN5seqan7areadAtIvcmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb > [bool > seqan::areadAt long>(seqan::File >&, char*, unsigned long, long, > aiocb&)]+0x8c): more undefined references to `aio_read64' follow > collect2: ld returned 1 exit status > > Any ideas? > > Cheers, > Jared Wilkening > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From j.reid@mail.cryst.bbk.ac.uk Thu Nov 12 17:13:02 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1N8cI9-0000DJ-0z>; Thu, 12 Nov 2009 17:13:01 +0100 Received: from adora-ext.cryst.bbk.ac.uk ([193.61.32.13] helo=adora.cryst.bbk.ac.uk) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1N8cI8-0007V7-TK>; Thu, 12 Nov 2009 17:13:01 +0100 Received: from [127.0.0.1] (axon-ext.cryst.bbk.ac.uk [193.61.32.77]) by adora.cryst.bbk.ac.uk (8.13.8/8.13.8) with ESMTP id nACGJspf011641 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO) for ; Thu, 12 Nov 2009 16:19:56 GMT Message-ID: <4AFC3406.9080404@mail.cryst.bbk.ac.uk> Date: Thu, 12 Nov 2009 16:12:54 +0000 From: John Reid User-Agent: Thunderbird 2.0.0.23 (X11/20090817) MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: In-Reply-To: Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit X-Cryst-BBK-MailScanner-Information: Please contact CCSG for more information (http://www. cryst.bbk.ac.uk/CCSG) X-Cryst-BBK-MailScanner-ID: nACGJspf011641 X-Cryst-BBK-MailScanner: Found to be clean X-Cryst-BBK-MailScanner-SpamCheck: not spam, SpamAssassin (not cached, score=1.673, required 5, HTML_MESSAGE 0.00, MIME_HTML_ONLY 1.67) X-Cryst-BBK-MailScanner-SpamScore: s X-Cryst-BBK-MailScanner-From: j.reid@mail.cryst.bbk.ac.uk X-Cryst-BBK-MailScanner-Watermark: 1258647596.39939@fy7UelhlUrBFtsDxX2/+wQ X-Originating-IP: 193.61.32.13 X-purgate: clean X-purgate-ID: 151147::1258042381-00000DDD-EA0D1B5C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.024966, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_40_50, HTML_MESSAGE,HTML_TAG_EXIST_TBODY,MIME_HTML_ONLY,SPF_HELO_PASS, SPF_PASS Subject: Re: [Seqan-dev] MarkovModel X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 12 Nov 2009 16:13:02 -0000
Subject:
Re: [Seqan-dev] MarkovModel
From:
David Weese <weese@campus.fu-berlin.de>
Date:
Sat, 31 Oct 2009 10:10:36 +0100
To:
SeqAn Development <seqan-dev@lists.fu-berlin.de>
To:
SeqAn Development <seqan-dev@lists.fu-berlin.de>		 

Hi John,

you are absolutely right. I fixed that. Just make an SVN update. I
reported the Trac problem to our admins.

Ciao,
Dave
I did a svn update and I still have the following problem. This is the content of the ticket I could not create:

The following code does not compile with the latest svn version of seqan (rev 5003)

{{{
#include <seqan/index.h>
#include <seqan/statistical_index.h>

using namespace seqan;

int main()
{
    const size_t order = 0;
    MarkovModel< Dna5 > mm( order );
    typedef String< Dna5 > string_t;
    StringSet< string_t > X;
    mm.build( X );
    return 0;
}
}}}

With gcc 4.4.1 I get the following compilation error:
{{{
In file included from /home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index.h:35,
from src/sandbox/seqan_sandbox_markov_model.cpp:6:
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h: In member function ‘void seqan::MarkovModel<
        seqan::SimpleType<unsigned char, seqan::_Dna5>, double, const seqan::Tag<seqan::Default_> >::_computeAuxiliaryMatrices()’:
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:180:   instantiated from ‘void seqan::MarkovModel<
        seqan::SimpleType<unsigned char, seqan::_Dna5>, double, const seqan::Tag<seqan::Default_>
    >::build(seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, seqan::Owner<const seqan::Tag<seqan::Default_> > > &)’
src/sandbox/seqan_sandbox_markov_model.cpp:16:   instantiated from here
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:400: error: No match for ‘_matricialSum(
        seqan::String<double, seqan::Alloc<void> >, seqan::String<double, seqan::Alloc<void> > &, const unsigned int &)’
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:522: candidates are: seqan::String<
        TValue, seqan::Alloc<void> > seqan::_matricialSum(seqan::String<TValue, TSpec> &, seqan::String<TValue, TStringSpec> &, unsigned int)
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:403: error: invalid initialization of non-const reference of type ‘seqan::String<
        double, seqan::Alloc<void> > &’ from a temporary of type ‘seqan::String<double, seqan::Alloc<void>>’
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:485: error: in passing argument 1 of ‘seqan::String<TValue, seqan::Alloc<void> >
    seqan::_matricialProduct(seqan::String<TValue, TSpec> &, seqan::String<TValue, TStringSpec> &, unsigned int)’
}}}

From tzuchien.chiu@gmail.com Fri Nov 27 12:13:51 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1NDylq-0004Ml-GY>; Fri, 27 Nov 2009 12:13:50 +0100 Received: from mail-bw0-f218.google.com ([209.85.218.218]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1NDylq-0007EU-De>; Fri, 27 Nov 2009 12:13:50 +0100 Received: by bwz10 with SMTP id 10so1197682bwz.15 for ; Fri, 27 Nov 2009 03:13:49 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:mime-version:sender:received:date :x-google-sender-auth:message-id:subject:from:to:content-type; bh=k8CR4VWdrFogfaJxDCDEdPW31uqY0xCivoggc+W2xUM=; b=hKQVdKyw3xzMOMX2oUcAsjlrHQdkYb+d9i43DY8utdTI1vvddL5le/LUXLDro6d2bg jNTdT0cDjjpmx15bPwHsFImrpen/Y+/WKtgb4YkkWk2KLMhv40bE6HAAvuTiaSWGxtCA 2UwMalFNpg1nKw8IrapGT3+NsCLRxO2qzcxTs= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=mime-version:sender:date:x-google-sender-auth:message-id:subject :from:to:content-type; b=BZxmKWnsE+2eN39yghkQRzCz45LcL5iM2p6D55dD7cO7S172GBlidUvSLqLPXOzEVL Yqv6jD0/+tvhvHE4WnJu5Db8br2xEZ3sZa5lSAYvWJ+2/9v7Gv4Adx9uG3CtaL6tntyP ALE7iAAgAce+AQ1Q09YE98OrcZWjKzbr80njA= MIME-Version: 1.0 Sender: tzuchien.chiu@gmail.com Received: by 10.204.27.21 with SMTP id g21mr927444bkc.133.1259320429885; Fri, 27 Nov 2009 03:13:49 -0800 (PST) Date: Fri, 27 Nov 2009 12:13:49 +0100 X-Google-Sender-Auth: 29013cecd02557ed Message-ID: <4d77c5f20911270313y2bda654ieae317c2b2cbab54@mail.gmail.com> From: Alex To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1 X-Originating-IP: 209.85.218.218 X-purgate: clean X-purgate-ID: 151147::1259320430-00000DDD-82EE3278/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000004, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST, RCVD_BY_IP, SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] Serialization a Pattern class X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 27 Nov 2009 11:13:51 -0000 I am using Seqan to do multiple pattern matching. I have a lot of substrings (needles) and it takes up to 3 minutes to create the Pattern class. I am thinking of "serializing" the created Pattern class to a file (do it once), and load it after for future uses. This includes saving the data structure of Graph and property maps, etc, to a file and load them back. Could somebody please suggest me a easy way to implement this ? Alex.