From f.buske@uq.edu.au Fri May 06 06:16:40 2011 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 <1QICT0-0002Bu-9X>; Fri, 06 May 2011 06:16:38 +0200 Received: from mailhub3.uq.edu.au ([130.102.148.131]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QICSz-00070y-Fx>; Fri, 06 May 2011 06:16:38 +0200 Received: from smtp4.uq.edu.au (smtp4.uq.edu.au [130.102.128.19]) by mailhub3.uq.edu.au (8.13.8/8.13.8) with ESMTP id p464GWdG031703 for ; Fri, 6 May 2011 14:16:33 +1000 Received: from imb10-008701.imb.uq.edu.au (imb10-008701.imb.uq.edu.au [130.102.118.152]) (authenticated bits=0) by smtp4.uq.edu.au (8.13.8/8.13.8) with ESMTP id p464GUwE020170 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 6 May 2011 14:16:32 +1000 Message-ID: <4DC3761E.40303@uq.edu.au> Date: Fri, 06 May 2011 14:16:30 +1000 From: Fabian Buske User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.17) Gecko/20110414 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-UQ-FilterTime: 1304655393 X-Scanned-By: MIMEDefang 2.58 on UQ Mailhub on 130.102.148.131 X-Originating-IP: 130.102.148.131 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1304655398-00005A17-61DF073B/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] SeqAn Restructuring Done 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, 06 May 2011 04:16:40 -0000 Hi, I just tried to get a clean checkout but unfortunately got an error: >svn co http://svn.mi.fu-berlin.de/seqan/trunk/seqan seqan-trunk svn: REPORT request failed on '/seqan/!svn/vcc/default' svn: Can't find a temporary directory: Internal error I got this on a mac and a linux machine so problem might by on the server side. Cheers, Fabian On 8/04/11 2:37 AM, Holtgrewe, Manuel wrote: > Dear all, > > we have completed the restructuring and there should be no major glitches left. We moved the files, updated the source code, tutorial and documentation. Please report any problems with the update to the mailing list or in a ticket. If you have any further questions we would be more than happy to answer them! > > In order to circumvent problems, we recommend you to perform a clean checkout of SeqAn: > > svn co http://svn.mi.fu-berlin.de/seqan/trunk/seqan seqan-trunk > > The following should work then (assuming you are using Makefiles on Linux/Os X): > > $ mkdir build/Debug > $ cd build/Debug > $ cmake ../.. > $ make test_basic > $ ./core/tests/test_basic/test_basic > ... the basic test will run ... > > We are sorry for any caused inconvenience. > > Kind Regards, > The SeqAn Development Team > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev -- Fabian Buske Institute for Molecular Bioscience The University of Queensland Brisbane, Qld. 4072 Australia Phone: (61)-(7)-334-62641 From matthias.dodt@mdc-berlin.de Fri May 06 14:55:07 2011 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 <1QIKYk-0005Yt-Go>; Fri, 06 May 2011 14:55:06 +0200 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QIKYi-0000WE-Rx>; Fri, 06 May 2011 14:55:04 +0200 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 7307C17C8D7 for ; Fri, 6 May 2011 14:55:03 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:subject:subject:mime-version :user-agent:from:from:date:date:message-id:received:received :received:received; s=dkim1; t=1304686497; x=1306500897; bh=bcn3 GQ6lk1JvLI2mbkp6YspSiSZH8Y3i/IzHzrbgqy4=; b=s8t9YjyaTxsMBNjlhD2A heMevBQmIgDfxhzdckxkVhgRpxiKk1FIEK5XQ2xOWTX8zQObZYDBAxijt+evBBH/ fktKCGFs8/Ik3roYnDRGKsZsJp6jy3IHsj2+pCsBjEBiNsAuNHHdspsQ7r+EyMnx G/HASxzhy0WNzLM0Eqhf6Ns= X-Virus-Scanned: amavisd-new at bbbm.mdc-berlin.de Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id mL5LLIP6DJ3s for ; Fri, 6 May 2011 14:54:57 +0200 (CEST) Received: from mdcmail.mdc-berlin.de (mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 6 May 2011 14:54:57 +0200 (CEST) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.4675); Fri, 6 May 2011 14:53:58 +0200 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Fri, 6 May 2011 14:53:56 +0200 Message-ID: <4DC3EFB5.9080301@mdc-berlin.de> Date: Fri, 06 May 2011 14:55:17 +0200 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.17) Gecko/20110414 Lightning/1.0b2 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development Content-Type: multipart/alternative; boundary="------------000706080909020804040200" X-OriginalArrivalTime: 06 May 2011 12:53:56.0734 (UTC) FILETIME=[A94AC9E0:01CC0BEC] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-18118.002 X-TM-AS-Result: No--3.964200-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.23 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1304686506-00005A17-D6B532D3/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.027570, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.9 required=5.0 tests=HTML_50_60,HTML_MESSAGE, RATWARE_GECKO_BUILD Subject: [Seqan-dev] adding contig to fragmentStore.contigStore 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, 06 May 2011 12:55:07 -0000 This is a multi-part message in MIME format. --------------000706080909020804040200 Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit Hey guys! Does anybody have an advice on how to add a single contig (from a CharString) to a contigStore? I only found "assingSeq()" which seems to work only on memory mapped files-? I guess it should be something like: ... CharString newContig; .. .. unsigned seqOfs = length(TDataManager::getInstance()->fragStore.contigStore); resize(TDataManager::getInstance()->fragStore.contigStore, seqOfs + 1, Generous()); resize(TDataManager::getInstance()->fragStore.contigNameStore, seqOfs + 1, Generous()); assignSeq(TDataManager::getInstance()->fragStore.contigStore[seqOfs + i].seq, newContig, ?); And how to add a name later on to the contigNameStore? Thanks! --------------000706080909020804040200 Content-Type: text/html; charset=ISO-8859-15 Content-Transfer-Encoding: 7bit Hey guys!

Does anybody have an advice on how to add a single contig (from a CharString) to a contigStore? I only found "assingSeq()" which seems to work only on memory mapped files-?

I guess it should be something like:

...
CharString newContig;
..
..

unsigned seqOfs = length(TDataManager::getInstance()->fragStore.contigStore);
resize(TDataManager::getInstance()->fragStore.contigStore, seqOfs + 1, Generous());
resize(TDataManager::getInstance()->fragStore.contigNameStore, seqOfs + 1, Generous());


assignSeq(TDataManager::getInstance()->fragStore.contigStore[seqOfs + i].seq, newContig, ?);

And how to add a name later on to the contigNameStore?

Thanks!
 --------------000706080909020804040200-- From manuel.holtgrewe@fu-berlin.de Fri May 06 15:18:45 2011 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 <1QIKvc-0006Vw-J8>; Fri, 06 May 2011 15:18:44 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QIKvc-0002vq-B0>; Fri, 06 May 2011 15:18:44 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QIKvc-0006Sc-5p>; Fri, 06 May 2011 15:18:44 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Fri, 6 May 2011 15:18:44 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Date: Fri, 6 May 2011 15:18:43 +0200 Thread-Topic: [Seqan-dev] adding contig to fragmentStore.contigStore Thread-Index: AcwL8B+9UBjEyKJnQ6K0vRRmqBzLig== Message-ID: References: <4DC3EFB5.9080301@mdc-berlin.de> In-Reply-To: <4DC3EFB5.9080301@mdc-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1304687924-00005A17-E1A279D3/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] adding contig to fragmentStore.contigStore 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, 06 May 2011 13:18:45 -0000 Hi Mat, I do not think that this works right now. What exactly are you trying to do? Do you want to load a file? Or is the fi= le already in memory? Maybe looking at the loadContigs function can help you to implement the req= uired functionality? http://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/core/include/seqan/st= ore/store_io.h#L868 Bests, Manuel Am 06.05.2011 um 14:55 schrieb Mat: > Hey guys! >=20 > Does anybody have an advice on how to add a single contig (from a CharStr= ing) to a contigStore? I only found "assingSeq()" which seems to work only = on memory mapped files-? >=20 > I guess it should be something like: >=20 > ... > CharString newContig; > .. > .. >=20 > unsigned seqOfs =3D length(TDataManager::getInstance()->fragStore.contigS= tore); > resize(TDataManager::getInstance()->fragStore.contigStore, seqOfs + 1, Ge= nerous()); > resize(TDataManager::getInstance()->fragStore.contigNameStore, seqOfs + 1= , Generous()); >=20 >=20 > assignSeq(TDataManager::getInstance()->fragStore.contigStore[seqOfs + i].= seq, newContig, ?); >=20 > And how to add a name later on to the contigNameStore? >=20 > Thanks! > From matthias.dodt@mdc-berlin.de Fri May 06 15:27:18 2011 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 <1QIL3t-0006qO-91>; Fri, 06 May 2011 15:27:17 +0200 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QIL3t-00066a-6a>; Fri, 06 May 2011 15:27:17 +0200 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id EFC7963170 for ; Fri, 6 May 2011 15:27:16 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:in-reply-to:references:subject:subject :mime-version:user-agent:from:from:date:date:message-id:received :received:received:received; s=dkim1; t=1304688431; x= 1306502831; bh=wjBFu7viU9zrELEU3kWdQka2erm+jw7rEeh0FALMPzs=; b=E //RXRSizzxwL5yOmLh1UkcGg58TE/usGd/WF+04Sxt3AbwowwhfLoA+vLEU/VMUi 9l63j/MOkgNR6ULDTFcgGXggRH083K4YSp/sOLRZei/c2hP73O1Wjimrp6AAwAUI i/+DIcESQo5KC5VeFvnI/sZoYvwdKeaztqM6IouqM8= X-Virus-Scanned: amavisd-new at bbbm.mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id nPtkLnn+7Mm9 for ; Fri, 6 May 2011 15:27:11 +0200 (CEST) Received: from mdcmail.mdc-berlin.de (mab.citx.mdc-berlin.de [141.80.36.102]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 6 May 2011 15:27:11 +0200 (CEST) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.4675); Fri, 6 May 2011 15:26:12 +0200 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Fri, 6 May 2011 15:26:11 +0200 Message-ID: <4DC3F743.4080904@mdc-berlin.de> Date: Fri, 06 May 2011 15:27:31 +0200 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.17) Gecko/20110414 Lightning/1.0b2 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development References: <4DC3EFB5.9080301@mdc-berlin.de> In-Reply-To: Content-Type: multipart/alternative; boundary="------------050005050801070209040508" X-OriginalArrivalTime: 06 May 2011 13:26:11.0018 (UTC) FILETIME=[2A371AA0:01CC0BF1] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-18118.002 X-TM-AS-Result: No--17.087200-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.20 X-ZEDAT-Hint: A X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1304688437-00005A17-50EF7009/3349369167-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000033, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.9 required=5.0 tests=FU_XPURGATE_SUSP,HTML_40_50, HTML_MESSAGE,RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] adding contig to fragmentStore.contigStore 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, 06 May 2011 13:27:18 -0000 This is a multi-part message in MIME format. --------------050005050801070209040508 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Manuel! Yes, i already checked that. The new contig sequence get's created during runtime from several input sources (FASTA and SAM files). cheers, mat Am 5/6/11 3:18 PM, schrieb Holtgrewe, Manuel: > Hi Mat, > > I do not think that this works right now. > > What exactly are you trying to do? Do you want to load a file? Or is the file already in memory? > > Maybe looking at the loadContigs function can help you to implement the required functionality? > > http://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/core/include/seqan/store/store_io.h#L868 > > Bests, > Manuel > > Am 06.05.2011 um 14:55 schrieb Mat: > >> Hey guys! >> >> Does anybody have an advice on how to add a single contig (from a CharString) to a contigStore? I only found "assingSeq()" which seems to work only on memory mapped files-? >> >> I guess it should be something like: >> >> ... >> CharString newContig; >> .. >> .. >> >> unsigned seqOfs = length(TDataManager::getInstance()->fragStore.contigStore); >> resize(TDataManager::getInstance()->fragStore.contigStore, seqOfs + 1, Generous()); >> resize(TDataManager::getInstance()->fragStore.contigNameStore, seqOfs + 1, Generous()); >> >> >> assignSeq(TDataManager::getInstance()->fragStore.contigStore[seqOfs + i].seq, newContig, ?); >> >> And how to add a name later on to the contigNameStore? >> >> Thanks! >> > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --------------050005050801070209040508 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Manuel!

Yes, i already checked that. The new contig sequence get's created during runtime from several input sources (FASTA and SAM files).

cheers,

mat

Am 5/6/11 3:18 PM, schrieb Holtgrewe, Manuel: 
Hi Mat,

I do not think that this works right now.

What exactly are you trying to do? Do you want to load a file? Or is the file already in memory?

Maybe looking at the loadContigs function can help you to implement the required functionality?

http://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/core/include/seqan/store/store_io.h#L868

Bests,
Manuel

Am 06.05.2011 um 14:55 schrieb Mat:


Hey guys!

Does anybody have an advice on how to add a single contig (from a CharString) to a contigStore? I only found "assingSeq()" which seems to work only on memory mapped files-?

I guess it should be something like:

...
CharString newContig;
..
..

unsigned seqOfs = length(TDataManager::getInstance()->fragStore.contigStore);
resize(TDataManager::getInstance()->fragStore.contigStore, seqOfs + 1, Generous());
resize(TDataManager::getInstance()->fragStore.contigNameStore, seqOfs + 1, Generous());


assignSeq(TDataManager::getInstance()->fragStore.contigStore[seqOfs + i].seq, newContig, ?);

And how to add a name later on to the contigNameStore?

Thanks!
<ATT00001..txt>


_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev
--------------050005050801070209040508-- From Knut.Reinert@fu-berlin.de Fri May 06 21:17:44 2011 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 <1QIQWz-0002vV-Ko>; Fri, 06 May 2011 21:17:41 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QIQWz-0002zB-I5>; Fri, 06 May 2011 21:17:41 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QIQWz-0006wH-Bu>; Fri, 06 May 2011 21:17:41 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Fri, 6 May 2011 21:17:41 +0200 From: "Reinert, Knut" To: SeqAn Development Date: Fri, 6 May 2011 21:17:38 +0200 Thread-Topic: 3rd SeqAn workshop - mark your calendars in the week from Sept. 12-16 Thread-Index: AcwMIkRaJr9ug1sIR4mOU94YExr0qQ== Message-ID: <811BDE89-783E-4728-A052-E9F56C9EE29C@fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: multipart/signed; boundary="Apple-Mail-61--15255555"; protocol="application/pkcs7-signature"; micalg=sha1 MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1304709461-00005A17-08B23B6B/3349532562-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000190, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP, HTML_MESSAGE Subject: [Seqan-dev] 3rd SeqAn workshop - mark your calendars in the week from Sept. 12-16 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, 06 May 2011 19:17:44 -0000 --Apple-Mail-61--15255555 Content-Type: multipart/alternative; boundary=Apple-Mail-60--15255590 --Apple-Mail-60--15255590 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Dear friends, SeqAn users, and algorithm developers, I invite you (or coworkers) to participate in the 3rd SeqAn workshop = (www.seqan.de),=20 which will be in the week from September 12. to 16. 2011 in Berlin, = Germany (exact dates, venue and more info will follow soon).=20 The content of the workshop will be: SeqAn: Overview of new features in SeqAn 1.3 (new repository structure, tests, = functional extensions, etc.) Tutorials for new and advanced users Tutorials of how to write your own SeqAn modules and contribute them = (How to become a SeqAn developer) Plans for the parallelization of SeqAn (with a presentation of Convey = Computers) Plans about SeqAn tool integration into workflow engines (e.g. KNIME) Science: What do users wish in terms of functionality and infrastructure in = current and planned projects. Case Studies: Overview of successful projects using SeqAn (from the = SeqAn group and external users) and discussion about the experience. Discussions (this list will be dynamic and depend on your feedback):=20 How can SeqAn functionally be advanced to meet tomorrows needs for = sequence analysis? (Metagenomics, Genome comparison, Variant analysis, = etc.) Algorithm engineering meets clinical problems: What are the = algorithms/implementations/infrastructure needed for analyzing data in a = clinical context? ? The workshop will also have breakout sessions for ongoing projects, most = notably the DFG SPP 1307 "Algorithm engineering" and=20 (most likely) the BMBF VIP project "BioStore".=20 Please forward this invitation to interested members of your groups or = colleagues and mark the dates. Up-to-date information can be found under https://www.mi.fu-berlin.de/w/ABI/SeqAnRetreat2011 Please drop us a short line under Anja.kasseckert@fu-berlin.de about HOW MANY people of your group might come. (THIS IS FOR PLANNING PURPOSES and does not imply any commitment from = your side). I am hoping that you can find time to join us in late summer in Berlin. Yours, Knut Reinert and the SeqAn team ----------------------------------------------------------------------- Prof. Dr.-Ing. Knut Reinert Phone/fax : +49 30 838 75 222/218 = (GE) : +1 858 8826656 (US) Algorithmic Bioinformatics Mobile : +49 160 7195754 (GE) : +1 858405 8323 (US) Freie Universit=E4t Berlin Skype : knut.reinert Takustrasse 9 E-Mail : = knut.reinert@fu-berlin.de D-14195 Berlin, Germany Web : http://knut.reinert.ws ------------------------------------------------------------------------ --Apple-Mail-60--15255590 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 Dear = friends, SeqAn users, and algorithm developers,

I invite you (or = coworkers) to participate in the 3rd SeqAn workshop (www.seqan.de), 
which will be = in the week from September 12. to 16. 2011 in Berlin, = Germany (exact dates, venue and more info will follow = soon). 

The content of the workshop will = be:
SeqAn:
  • Overview of new features in SeqAn 1.3 (new = repository structure, tests, functional extensions, = etc.)
  • Tutorials for new and advanced users
  • Tutorials of = how to write your own SeqAn modules and contribute them (How to become a = SeqAn developer)
  • Plans for the parallelization of SeqAn (with a = presentation of Convey Computers)
  • Plans about SeqAn = tool integration into workflow engines (e.g. = KNIME)
Science:
  • What do users wish in terms of functionality = and infrastructure in current and planned projects.
  • Case = Studies: Overview of successful projects using SeqAn (from the SeqAn = group and external users) and discussion about the = experience.
  • Discussions (this list will be dynamic and depend = on your feedback): 
    • How can SeqAn functionally be = advanced to meet tomorrows needs for sequence analysis? (Metagenomics, = Genome comparison, Variant analysis, etc.)
    • Algorithm engineering = meets clinical problems: What are the = algorithms/implementations/infrastructure needed for analyzing data in a = clinical context?
    • ?

The = workshop will also have breakout sessions for ongoing projects, most = notably the DFG SPP 1307 "Algorithm = engineering" and 
(most = likely) the BMBF VIP project = "BioStore". 

Please forward this = invitation to interested members of your groups or colleagues = and mark the dates.

Up-to-date information can be = found under
Please = drop us a short line under Anja.kasseckert@fu-berlin.de<= /a>






: +49 30 838 75 222/218 = (GE)
= : +1 858 8826656 (US)
Algorithmic Bioinformatics   =       Mobile : +49 160 7195754 = (GE)
) id <1QJHhz-0000i1-FV>; Mon, 09 May 2011 06:04:35 +0200 Received: from mailhub3.uq.edu.au ([130.102.148.131]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QJHhy-0002s3-LZ>; Mon, 09 May 2011 06:04:35 +0200 Received: from smtp4.uq.edu.au (smtp4.uq.edu.au [130.102.128.19]) by mailhub3.uq.edu.au (8.13.8/8.13.8) with ESMTP id p4944TW8006860 for ; Mon, 9 May 2011 14:04:30 +1000 Received: from imb10-008701.imb.uq.edu.au (imb10-008701.imb.uq.edu.au [130.102.118.152]) (authenticated bits=0) by smtp4.uq.edu.au (8.13.8/8.13.8) with ESMTP id p4944RDX019635 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 9 May 2011 14:04:29 +1000 Message-ID: <4DC767CB.6050604@uq.edu.au> Date: Mon, 09 May 2011 14:04:27 +1000 From: Fabian Buske User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.17) Gecko/20110414 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-UQ-FilterTime: 1304913870 X-Scanned-By: MIMEDefang 2.58 on UQ Mailhub on 130.102.148.131 X-Originating-IP: 130.102.148.131 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1304913875-00005A17-C93FD441/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: [Seqan-dev] compatibility of repeat_base's operators with stl container adaptations 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: Mon, 09 May 2011 04:04:36 -0000 Hi, I observed that findRepeats() from repeat_base.h relies on _operator[]_ and _resize()_ to work for the given type TRepeatStore &repString. line 504: findRepeats(TRepeatStore &repString, ..){ ... // copy low-complex regions to result string resize(repString, list.size()); typename TRepeatList::const_iterator lit = list.begin(); typename TRepeatList::const_iterator litEnd = list.end(); for (TSize i = 0; lit != litEnd; ++lit, ++i) repString[i] = (*lit).second; } I'm currently the adaptation of std::list rather than a StringSet, which does not (yet) contain proper functionality for these functions. I like to propose the following change to this class: findRepeats(TRepeatStore &repString, ..){ ... // copy low-complex regions to result string typename TRepeatList::const_iterator lit = list.begin(); typename TRepeatList::const_iterator litEnd = list.end(); for (TSize i = 0; lit != litEnd; ++lit, ++i) appendValue(repString, (*lit).second); } Alternatively, the adaptions from the STL should probably get some additional functionality. Cheers, Fabian -- Fabian Buske Institute for Molecular Bioscience The University of Queensland Brisbane, Qld. 4072 Australia Phone: (61)-(7)-334-62641 From f.buske@uq.edu.au Mon May 09 06:35:41 2011 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 <1QJIC4-0001uC-Mi>; Mon, 09 May 2011 06:35:40 +0200 Received: from mailhub4.uq.edu.au ([130.102.149.131]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QJIC3-00056m-T2>; Mon, 09 May 2011 06:35:40 +0200 Received: from smtp3.uq.edu.au (smtp3.uq.edu.au [130.102.128.18]) by mailhub4.uq.edu.au (8.13.8/8.13.8) with ESMTP id p494Zapb010319 for ; Mon, 9 May 2011 14:35:36 +1000 Received: from imb10-008701.imb.uq.edu.au (imb10-008701.imb.uq.edu.au [130.102.118.152]) (authenticated bits=0) by smtp3.uq.edu.au (8.13.8/8.13.8) with ESMTP id p494Zatj010682 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Mon, 9 May 2011 14:35:36 +1000 Message-ID: <4DC76F18.4040901@uq.edu.au> Date: Mon, 09 May 2011 14:35:36 +1000 From: Fabian Buske User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.17) Gecko/20110414 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-UQ-FilterTime: 1304915736 X-Scanned-By: MIMEDefang 2.58 on UQ Mailhub on 130.102.149.131 X-Originating-IP: 130.102.149.131 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1304915740-00005A17-532133A3/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] SeqAn Restructuring Done 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: Mon, 09 May 2011 04:35:41 -0000 Hi, I like the new structure of seqan. Below are, however, a couple of things I notices on Macs (with Xcode). 1.) When following the tutorial for "getting started" and jumping right to the Mac section and following from there I noticed that the "forwards" are not generated when opening the sandbox and trying to compile the example resulting in plenty of compiler errors. # mkdir Debug # cd Debug # cmake ../.. -DCMAKE_BUILD_TYPE=Debug -G "Xcode" # open sandbox/my_sandbox/seqan_sandbox_my_sandbox.xcodeproj or # open core/demos/seqan_core_demos.xcodeproj Opening the overall project build/Debug/seqan.xcodeproj and compiling anything at all first seems to be a workaround to get the "forwards" generated. 2.) Running the cmake command after populating the app folder does not seem to pick up additional header files in an app. cmake ../.. -DCMAKE_BUILD_TYPE=Debug -G "Xcode" 3.) The same seems to be true for the sandbox tests. Here neither header nor cpp files dropped into the sandbox/test/testapp-folder are picked up by cmake. Best, Fabian On 8/04/11 2:37 AM, Holtgrewe, Manuel wrote: > Dear all, > > we have completed the restructuring and there should be no major glitches left. We moved the files, updated the source code, tutorial and documentation. Please report any problems with the update to the mailing list or in a ticket. If you have any further questions we would be more than happy to answer them! > > In order to circumvent problems, we recommend you to perform a clean checkout of SeqAn: > > svn co http://svn.mi.fu-berlin.de/seqan/trunk/seqan seqan-trunk > > The following should work then (assuming you are using Makefiles on Linux/Os X): > > $ mkdir build/Debug > $ cd build/Debug > $ cmake ../.. > $ make test_basic > $ ./core/tests/test_basic/test_basic > ... the basic test will run ... > > We are sorry for any caused inconvenience. > > Kind Regards, > The SeqAn Development Team > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev -- Fabian Buske Institute for Molecular Bioscience The University of Queensland Brisbane, Qld. 4072 Australia Phone: (61)-(7)-334-62641 From Knut.Reinert@fu-berlin.de Mon May 09 07:26:13 2011 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 <1QJIyy-0003mP-Rp>; Mon, 09 May 2011 07:26:12 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QJIyy-0002Kp-Px>; Mon, 09 May 2011 07:26:12 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QJIyy-00011F-KQ>; Mon, 09 May 2011 07:26:12 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 9 May 2011 07:26:12 +0200 From: "Reinert, Knut" To: SeqAn Development Date: Mon, 9 May 2011 07:26:28 +0200 Thread-Topic: [Seqan-dev] SeqAn Restructuring Done Thread-Index: AcwOCZvl/EkYg3XVTKCs/a2M7O3iyA== Message-ID: References: <4DC76F18.4040901@uq.edu.au> In-Reply-To: <4DC76F18.4040901@uq.edu.au> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1304918772-00005A17-5FD3ECDC/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] SeqAn Restructuring Done 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: Mon, 09 May 2011 05:26:13 -0000 Hallo Fabian, Ich habe auch solche Probleme. Wir werden da mal reinschauen. Knut=20 Sent from my iPad On May 8, 2011, at 9:35 PM, "Fabian Buske" wrote: > Hi, >=20 > I like the new structure of seqan. > Below are, however, a couple of things I notices on Macs (with Xcode). >=20 > 1.) When following the tutorial for "getting started" and jumping right=20 > to the Mac section and following from there I noticed that the=20 > "forwards" are not generated when opening the sandbox and trying to=20 > compile the example resulting in plenty of compiler errors. >=20 > # mkdir Debug > # cd Debug > # cmake ../.. -DCMAKE_BUILD_TYPE=3DDebug -G "Xcode" > # open sandbox/my_sandbox/seqan_sandbox_my_sandbox.xcodeproj > or > # open core/demos/seqan_core_demos.xcodeproj >=20 > Opening the overall project build/Debug/seqan.xcodeproj and compiling=20 > anything at all first seems to be a workaround to get the "forwards"=20 > generated. >=20 > 2.) Running the cmake command after populating the app folder does not=20 > seem to pick up additional header files in an app. > cmake ../.. -DCMAKE_BUILD_TYPE=3DDebug -G "Xcode" >=20 > 3.) The same seems to be true for the sandbox tests. Here neither header= =20 > nor cpp files dropped into the sandbox/test/testapp-folder are picked up= =20 > by cmake. >=20 > Best, > Fabian >=20 >=20 > On 8/04/11 2:37 AM, Holtgrewe, Manuel wrote: >> Dear all, >>=20 >> we have completed the restructuring and there should be no major glitche= s left. We moved the files, updated the source code, tutorial and documenta= tion. Please report any problems with the update to the mailing list or in = a ticket. If you have any further questions we would be more than happy to = answer them! >>=20 >> In order to circumvent problems, we recommend you to perform a clean che= ckout of SeqAn: >>=20 >> svn co http://svn.mi.fu-berlin.de/seqan/trunk/seqan seqan-trunk >>=20 >> The following should work then (assuming you are using Makefiles on Linu= x/Os X): >>=20 >> $ mkdir build/Debug >> $ cd build/Debug >> $ cmake ../.. >> $ make test_basic >> $ ./core/tests/test_basic/test_basic >> ... the basic test will run ... >>=20 >> We are sorry for any caused inconvenience. >>=20 >> Kind Regards, >> The SeqAn Development Team >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >=20 >=20 > --=20 > Fabian Buske > Institute for Molecular Bioscience > The University of Queensland > Brisbane, Qld. 4072 Australia > Phone: (61)-(7)-334-62641 >=20 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From manuel.holtgrewe@fu-berlin.de Mon May 09 09:23:02 2011 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 <1QJKo1-0008VV-7N>; Mon, 09 May 2011 09:23:01 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1QJKo1-0007va-5a>; Mon, 09 May 2011 09:23:01 +0200 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.102]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1QJKo1-0000g7-1V>; Mon, 09 May 2011 09:23:01 +0200 Message-Id: From: Manuel Holtgrewe To: SeqAn Development In-Reply-To: <4DC76F18.4040901@uq.edu.au> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Mime-Version: 1.0 (Apple Message framework v936) Date: Mon, 9 May 2011 09:22:59 +0200 References: <4DC76F18.4040901@uq.edu.au> X-Mailer: Apple Mail (2.936) X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1304925781-00005A17-81EE7AD5/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] SeqAn Restructuring Done 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: Mon, 09 May 2011 07:23:02 -0000 Am 09.05.2011 um 06:35 schrieb Fabian Buske: > Hi, > > I like the new structure of seqan. > Below are, however, a couple of things I notices on Macs (with Xcode). > > 1.) When following the tutorial for "getting started" and jumping > right > to the Mac section and following from there I noticed that the > "forwards" are not generated when opening the sandbox and trying to > compile the example resulting in plenty of compiler errors. > > # mkdir Debug > # cd Debug > # cmake ../.. -DCMAKE_BUILD_TYPE=Debug -G "Xcode" > # open sandbox/my_sandbox/seqan_sandbox_my_sandbox.xcodeproj > or > # open core/demos/seqan_core_demos.xcodeproj > > Opening the overall project build/Debug/seqan.xcodeproj and compiling > anything at all first seems to be a workaround to get the "forwards" > generated. Did you use the skel generator script or the zip file with the example sandbox? I remember that there were some issues with the generator that I fixed in [9570]. I forgot to update the ZIP file in the tutorial and just did this. > 2.) Running the cmake command after populating the app folder does not > seem to pick up additional header files in an app. > cmake ../.. -DCMAKE_BUILD_TYPE=Debug -G "Xcode" > > 3.) The same seems to be true for the sandbox tests. Here neither > header > nor cpp files dropped into the sandbox/test/testapp-folder are > picked up > by cmake. Did you look into the existing apps and tests? Headers have to be added manually to the seqan command adding a new test/app executable. Bests, Manuel From matthias.dodt@mdc-berlin.de Mon May 09 12:49:23 2011 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 <1QJO1i-0001D6-Lq>; Mon, 09 May 2011 12:49:22 +0200 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QJO1i-0007NA-JP>; Mon, 09 May 2011 12:49:22 +0200 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 32D7C40533 for ; Mon, 9 May 2011 12:49:22 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:subject:subject:mime-version :user-agent:from:from:date:date:message-id:received:received :received:received; s=dkim1; t=1304938156; x=1306752556; bh=btY0 2CXRzuQkx0U837ETpzu4Z7NTN9zKA0xu8R/IVnA=; b=gwCLZvdKYt0scXaETqVp KsPRTMUwoPqTCNtvcrZyzJJIDv0SAA15WwZ9XD9At0mJm9XS1ro2HBO5zYnMSYNB CcWtJUenw3msFkrQFaJJP9GrSuwyIB4W/kEbVfeuctqDiRD1vx4kUR53aNIF2x4t qnp+aSHmOUkXZZgukZbRpnk= X-Virus-Scanned: amavisd-new at bbbm.mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id i+xX18ENKkWd for ; Mon, 9 May 2011 12:49:16 +0200 (CEST) Received: from mdcmail.mdc-berlin.de (mab.citx.mdc-berlin.de [141.80.36.102]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Mon, 9 May 2011 12:49:16 +0200 (CEST) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.4675); Mon, 9 May 2011 12:49:09 +0200 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Mon, 9 May 2011 12:49:08 +0200 Message-ID: <4DC7C6F7.4050500@mdc-berlin.de> Date: Mon, 09 May 2011 12:50:31 +0200 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.17) Gecko/20110414 Lightning/1.0b2 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development Content-Type: multipart/alternative; boundary="------------010505090302030509030306" X-OriginalArrivalTime: 09 May 2011 10:49:08.0694 (UTC) FILETIME=[B94FCF60:01CC0E36] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-18122.007 X-TM-AS-Result: No--6.318500-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.30 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1304938162-00005A17-B37358EB/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.047614, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.9 required=5.0 tests=HTML_40_50,HTML_MESSAGE, RATWARE_GECKO_BUILD Subject: [Seqan-dev] new release 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: Mon, 09 May 2011 10:49:23 -0000 This is a multi-part message in MIME format. --------------010505090302030509030306 Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit Hey guys! I checked out the latest repository and got the following error from seqan.h: /home/mat/seqan/seqan-trunk/core/include/seqan.h:40:25: error: seqan/blast.h: No such file or directory /home/mat/seqan/seqan-trunk/core/include/seqan.h:45:30: error: seqan/find_motif.h: No such file or directory /home/mat/seqan/seqan-trunk/core/include/seqan.h:58:30: error: seqan/statistics.h: No such file or directory I think these files are missing? thanks! best --------------010505090302030509030306 Content-Type: text/html; charset=ISO-8859-15 Content-Transfer-Encoding: 7bit Hey guys!

I checked out the latest repository and got the following error from seqan.h:

/home/mat/seqan/seqan-trunk/core/include/seqan.h:40:25: error: seqan/blast.h: No such file or directory
/home/mat/seqan/seqan-trunk/core/include/seqan.h:45:30: error: seqan/find_motif.h: No such file or directory
/home/mat/seqan/seqan-trunk/core/include/seqan.h:58:30: error: seqan/statistics.h: No such file or directory

I think these files are missing?

thanks!

best
 --------------010505090302030509030306-- From manuel.holtgrewe@fu-berlin.de Mon May 09 16:30:50 2011 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 <1QJRU1-0002Si-3F>; Mon, 09 May 2011 16:30:49 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QJRU1-0005TB-1K>; Mon, 09 May 2011 16:30:49 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QJRU0-00025M-SK>; Mon, 09 May 2011 16:30:49 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 9 May 2011 16:30:48 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Date: Mon, 9 May 2011 16:30:47 +0200 Thread-Topic: [Seqan-dev] compatibility of repeat_base's operators with stl container adaptations Thread-Index: AcwOVbBMyQGH6/c+T8eGneBUqMGM8g== Message-ID: References: <4DC767CB.6050604@uq.edu.au> In-Reply-To: <4DC767CB.6050604@uq.edu.au> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1304951449-00005A17-ECEE931E/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] compatibility of repeat_base's operators with stl container adaptations 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: Mon, 09 May 2011 14:30:50 -0000 Hi Fabian, changesets [9609] [9610] should make findRepeats() more generic. Note that = I used reserve() regardless of the type of repString since it can be implem= ented for both lists and strings. The code using appendValue() will then be= roughly equivalent to the existing code for Strings, i.e. only one realloc= ation of space. For lists, reserve() does nothing, but appendValue() always= works efficiently for lists. Please test whether this works and report back any problems. Bests, Manuel Am 09.05.2011 um 06:04 schrieb Fabian Buske: > Hi, >=20 > I observed that findRepeats() from repeat_base.h relies on _operator[]_=20 > and _resize()_ to work for the given type TRepeatStore &repString. >=20 > line 504: > findRepeats(TRepeatStore &repString, ..){ > ... > // copy low-complex regions to result string > resize(repString, list.size()); > typename TRepeatList::const_iterator lit =3D list.begin(); > typename TRepeatList::const_iterator litEnd =3D list.end(); > for (TSize i =3D 0; lit !=3D litEnd; ++lit, ++i) > repString[i] =3D (*lit).second; > } >=20 > I'm currently the adaptation of std::list rather than a StringSet, which= =20 > does not (yet) contain proper functionality for these functions. >=20 > I like to propose the following change to this class: >=20 > findRepeats(TRepeatStore &repString, ..){ > ... > // copy low-complex regions to result string > typename TRepeatList::const_iterator lit =3D list.begin(); > typename TRepeatList::const_iterator litEnd =3D list.end(); > for (TSize i =3D 0; lit !=3D litEnd; ++lit, ++i) > appendValue(repString, (*lit).second); > } >=20 > Alternatively, the adaptions from the STL should probably get some=20 > additional functionality. >=20 > Cheers, > Fabian >=20 > --=20 > Fabian Buske > Institute for Molecular Bioscience > The University of Queensland > Brisbane, Qld. 4072 Australia > Phone: (61)-(7)-334-62641 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From f.buske@uq.edu.au Tue May 10 01:20:38 2011 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 <1QJZki-00067H-NX>; Tue, 10 May 2011 01:20:36 +0200 Received: from mailhub4.uq.edu.au ([130.102.149.131]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QJZkh-0004iw-Tg>; Tue, 10 May 2011 01:20:36 +0200 Received: from smtp4.uq.edu.au (smtp4.uq.edu.au [130.102.128.19]) by mailhub4.uq.edu.au (8.13.8/8.13.8) with ESMTP id p49NKWxF002345 for ; Tue, 10 May 2011 09:20:32 +1000 Received: from imb10-008701.imb.uq.edu.au (imb10-008701.imb.uq.edu.au [130.102.118.152]) (authenticated bits=0) by smtp4.uq.edu.au (8.13.8/8.13.8) with ESMTP id p49NKUHF007065 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 10 May 2011 09:20:32 +1000 Message-ID: <4DC876BE.8000409@uq.edu.au> Date: Tue, 10 May 2011 09:20:30 +1000 From: Fabian Buske User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.17) Gecko/20110414 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development References: <4DC767CB.6050604@uq.edu.au> In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-UQ-FilterTime: 1304983232 X-Scanned-By: MIMEDefang 2.58 on UQ Mailhub on 130.102.149.131 X-Originating-IP: 130.102.149.131 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1304983236-00005A17-A48A1721/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] compatibility of repeat_base's operators with stl container adaptations 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: Mon, 09 May 2011 23:20:38 -0000 Hi Manuel, your update on findRepeats() works just fine. Thanks a lot! Best, Fabian On 10/05/11 12:30 AM, Holtgrewe, Manuel wrote: > Hi Fabian, > > changesets [9609] [9610] should make findRepeats() more generic. Note that I used reserve() regardless of the type of repString since it can be implemented for both lists and strings. The code using appendValue() will then be roughly equivalent to the existing code for Strings, i.e. only one reallocation of space. For lists, reserve() does nothing, but appendValue() always works efficiently for lists. > > Please test whether this works and report back any problems. > > Bests, > Manuel > > Am 09.05.2011 um 06:04 schrieb Fabian Buske: > >> Hi, >> >> I observed that findRepeats() from repeat_base.h relies on _operator[]_ >> and _resize()_ to work for the given type TRepeatStore&repString. >> >> line 504: >> findRepeats(TRepeatStore&repString, ..){ >> ... >> // copy low-complex regions to result string >> resize(repString, list.size()); >> typename TRepeatList::const_iterator lit = list.begin(); >> typename TRepeatList::const_iterator litEnd = list.end(); >> for (TSize i = 0; lit != litEnd; ++lit, ++i) >> repString[i] = (*lit).second; >> } >> >> I'm currently the adaptation of std::list rather than a StringSet, which >> does not (yet) contain proper functionality for these functions. >> >> I like to propose the following change to this class: >> >> findRepeats(TRepeatStore&repString, ..){ >> ... >> // copy low-complex regions to result string >> typename TRepeatList::const_iterator lit = list.begin(); >> typename TRepeatList::const_iterator litEnd = list.end(); >> for (TSize i = 0; lit != litEnd; ++lit, ++i) >> appendValue(repString, (*lit).second); >> } >> >> Alternatively, the adaptions from the STL should probably get some >> additional functionality. >> >> Cheers, >> Fabian >> >> -- >> Fabian Buske >> Institute for Molecular Bioscience >> The University of Queensland >> Brisbane, Qld. 4072 Australia >> Phone: (61)-(7)-334-62641 >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev -- Fabian Buske Institute for Molecular Bioscience The University of Queensland Brisbane, Qld. 4072 Australia Phone: (61)-(7)-334-62641 From f.buske@uq.edu.au Tue May 10 01:38:29 2011 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 <1QJa20-0006mO-Kp>; Tue, 10 May 2011 01:38:28 +0200 Received: from mailhub3.uq.edu.au ([130.102.148.131]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QJa1z-00065K-Qn>; Tue, 10 May 2011 01:38:28 +0200 Received: from smtp4.uq.edu.au (smtp4.uq.edu.au [130.102.128.19]) by mailhub3.uq.edu.au (8.13.8/8.13.8) with ESMTP id p49NcOY4001896 for ; Tue, 10 May 2011 09:38:24 +1000 Received: from imb10-008701.imb.uq.edu.au (imb10-008701.imb.uq.edu.au [130.102.118.152]) (authenticated bits=0) by smtp4.uq.edu.au (8.13.8/8.13.8) with ESMTP id p49NcOPk019291 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 10 May 2011 09:38:24 +1000 Message-ID: <4DC87AEF.3060404@uq.edu.au> Date: Tue, 10 May 2011 09:38:23 +1000 From: Fabian Buske User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.17) Gecko/20110414 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development References: <4DC76F18.4040901@uq.edu.au> In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-UQ-FilterTime: 1304984304 X-Scanned-By: MIMEDefang 2.58 on UQ Mailhub on 130.102.148.131 X-Originating-IP: 130.102.148.131 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1304984308-00005A17-6105AF86/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] SeqAn Restructuring Done 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: Mon, 09 May 2011 23:38:29 -0000 Hi Manuel, >> 1.) When following the tutorial for "getting started" and jumping >> right >> to the Mac section and following from there I noticed that the >> "forwards" are not generated when opening the sandbox and trying to >> compile the example resulting in plenty of compiler errors. >> >> # mkdir Debug >> # cd Debug >> # cmake ../.. -DCMAKE_BUILD_TYPE=Debug -G "Xcode" >> # open sandbox/my_sandbox/seqan_sandbox_my_sandbox.xcodeproj >> or >> # open core/demos/seqan_core_demos.xcodeproj >> >> Opening the overall project build/Debug/seqan.xcodeproj and compiling >> anything at all first seems to be a workaround to get the "forwards" >> generated. > Did you use the skel generator script or the zip file with the example > sandbox? I remember that there were some issues with the generator > that I fixed in [9570]. I forgot to update the ZIP file in the > tutorial and just did this. I used the skel generator script for the sandbox establishment and its still a problem. >> 2.) Running the cmake command after populating the app folder does not >> seem to pick up additional header files in an app. >> cmake ../.. -DCMAKE_BUILD_TYPE=Debug -G "Xcode" >> >> 3.) The same seems to be true for the sandbox tests. Here neither >> header >> nor cpp files dropped into the sandbox/test/testapp-folder are >> picked up >> by cmake. > Did you look into the existing apps and tests? Headers have to be > added manually to the seqan command adding a new test/app executable. > Ok, I was thinking (for some reason) that the CMakeList.txt is generated from the folder content so I didn't even think about touching them. After adding the header and cpp files manually they appear in the project. Looks like I have managed to fully port my project to the new structure now. Thanks again! Best, Fabian -- Fabian Buske Institute for Molecular Bioscience The University of Queensland Brisbane, Qld. 4072 Australia Phone: (61)-(7)-334-62641 From f.buske@uq.edu.au Tue May 10 08:42:33 2011 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 <1QJgeN-0005hy-Rg>; Tue, 10 May 2011 08:42:32 +0200 Received: from mailhub4.uq.edu.au ([130.102.149.131]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QJgeN-0000jm-21>; Tue, 10 May 2011 08:42:31 +0200 Received: from smtp4.uq.edu.au (smtp4.uq.edu.au [130.102.128.19]) by mailhub4.uq.edu.au (8.13.8/8.13.8) with ESMTP id p4A6gReU022607 for ; Tue, 10 May 2011 16:42:27 +1000 Received: from imb10-008701.imb.uq.edu.au (imb10-008701.imb.uq.edu.au [130.102.118.152]) (authenticated bits=0) by smtp4.uq.edu.au (8.13.8/8.13.8) with ESMTP id p4A6gOGt006910 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 10 May 2011 16:42:26 +1000 Message-ID: <4DC8DE50.7000204@uq.edu.au> Date: Tue, 10 May 2011 16:42:24 +1000 From: Fabian Buske User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.17) Gecko/20110414 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-UQ-FilterTime: 1305009747 X-Scanned-By: MIMEDefang 2.58 on UQ Mailhub on 130.102.149.131 X-Originating-IP: 130.102.149.131 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1305009751-00005A17-4E940A64/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: [Seqan-dev] FYI: CMake - Seqan - OpenMP support 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: Tue, 10 May 2011 06:42:33 -0000 Hi, After porting my project to the new structure I noticed that the OpenMP support didn't work properly anymore. In Xcode you always have to tick the "Enable OpenMP Support" checkbox in "Project Info/Build" after running the cmake command (which isn't too much of a hassle). For the Makefile version one, however, seems to have to add some flags to tell the compiler to do as it is told, i.e. for gcc: cmake ../.. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-fopenmp" seems to work. I assumed cmake would take care of this. Cheers, Fabian -- Fabian Buske Institute for Molecular Bioscience The University of Queensland Brisbane, Qld. 4072 Australia Phone: (61)-(7)-334-62641 From manuel.holtgrewe@fu-berlin.de Tue May 10 08:45:07 2011 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 <1QJggs-0005pa-GS>; Tue, 10 May 2011 08:45:06 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1QJggs-00030v-EW>; Tue, 10 May 2011 08:45:06 +0200 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.102]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1QJggs-00056E-AU>; Tue, 10 May 2011 08:45:06 +0200 Message-Id: <38702A9A-255D-4A8D-95B5-A5331170DF84@fu-berlin.de> From: Manuel Holtgrewe To: SeqAn Development In-Reply-To: <4DC8DE50.7000204@uq.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Content-Transfer-Encoding: quoted-printable Mime-Version: 1.0 (Apple Message framework v936) Date: Tue, 10 May 2011 08:45:05 +0200 References: <4DC8DE50.7000204@uq.edu.au> X-Mailer: Apple Mail (2.936) X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1305009906-00005A17-DBC96350/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] FYI: CMake - Seqan - OpenMP support 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: Tue, 10 May 2011 06:45:07 -0000 Using the new structure, you have to do this yourself. Currently, =20 OpenMP is already searched for on the top level structure, so the =20 OPENMP_FOUND flags are available. However, you have to add the define =20= yourself in your CMakeLists.txt. With the new structure, you are =20 mostly responsible for adding dependencies yourself. For example: cmake_minimum_required (VERSION 2.6) project (sandbox_weese_apps_razers3) if (OPENMP_FOUND) # We need a configuration header file. First, configure this file, =20= then # add the target directory to the inclue path. configure_file (${CMAKE_CURRENT_SOURCE_DIR}/config.h.in ${CMAKE_CURRENT_BINARY_DIR}/config.h) include_directories(${CMAKE_CURRENT_BINARY_DIR}) # Enable OpenMP. set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") # Add executable for RazerS 3. seqan_add_executable (razers3 razers.cpp) elseif (OPENMP_FOUND) message(STATUS "Not building RazerS3, since OpenMP could not be =20 found.") endif (OPENMP_FOUND) Am 10.05.2011 um 08:42 schrieb Fabian Buske: > Hi, > > After porting my project to the new structure I noticed that the =20 > OpenMP > support didn't work properly anymore. > > In Xcode you always have to tick the "Enable OpenMP Support" =20 > checkbox in > "Project Info/Build" after running the cmake command (which isn't too > much of a hassle). > > For the Makefile version one, however, seems to have to add some flags > to tell the compiler to do as it is told, i.e. for gcc: > > cmake ../.. -DCMAKE_BUILD_TYPE=3DRelease -DCMAKE_CXX_FLAGS=3D"-fopenmp" > > seems to work. I assumed cmake would take care of this. > > Cheers, > Fabian > > --=20 > Fabian Buske > Institute for Molecular Bioscience > The University of Queensland > Brisbane, Qld. 4072 Australia > Phone: (61)-(7)-334-62641 > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --=20 Manuel Holtgrewe manuel.holtgrewe@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 Bioinformatics 14195 Berlin Room 021 From manuel.holtgrewe@fu-berlin.de Tue May 10 08:48:51 2011 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 <1QJgkT-0005xH-Kl>; Tue, 10 May 2011 08:48:49 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1QJgkT-0003ji-J0>; Tue, 10 May 2011 08:48:49 +0200 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.102]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1QJgkT-0005II-Gf>; Tue, 10 May 2011 08:48:49 +0200 Message-Id: <793809C7-6089-494C-AE1A-0EFD19C7AA9D@fu-berlin.de> From: Manuel Holtgrewe To: SeqAn Development In-Reply-To: <4DC87AEF.3060404@uq.edu.au> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Mime-Version: 1.0 (Apple Message framework v936) Date: Tue, 10 May 2011 08:48:49 +0200 References: <4DC76F18.4040901@uq.edu.au> <4DC87AEF.3060404@uq.edu.au> X-Mailer: Apple Mail (2.936) X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1305010129-00005A17-0E762EAF/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] SeqAn Restructuring Done 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: Tue, 10 May 2011 06:48:51 -0000 >> Did you use the skel generator script or the zip file with the >> example >> sandbox? I remember that there were some issues with the generator >> that I fixed in [9570]. I forgot to update the ZIP file in the >> tutorial and just did this. > I used the skel generator script for the sandbox establishment and its > still a problem. Ah, I think I remember now... There are issues with targets being inherited from parent trees. I think this mostly concerns XCode but not Visual Studio, but I could be wrong. There is a thread on this on the CMake mailing list and it appears to be a limitation in XCode or the XCode CMake generator. http://www.cmake.org/pipermail/cmake/2011-April/043794.html My recommendation is to open the root project and build one target which will build all forwards. We are currently working on updating the library such that not forwards are required but will need to write some more tests so we can make sure that this change does not actually break anything... Bests, Manuel From f.buske@uq.edu.au Tue May 10 09:04:27 2011 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 <1QJgzZ-0006bQ-3w>; Tue, 10 May 2011 09:04:25 +0200 Received: from mailhub4.uq.edu.au ([130.102.149.131]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QJgzY-0005r3-AX>; Tue, 10 May 2011 09:04:25 +0200 Received: from smtp3.uq.edu.au (smtp3.uq.edu.au [130.102.128.18]) by mailhub4.uq.edu.au (8.13.8/8.13.8) with ESMTP id p4A74McC022478 for ; Tue, 10 May 2011 17:04:22 +1000 Received: from imb10-008701.imb.uq.edu.au (imb10-008701.imb.uq.edu.au [130.102.118.152]) (authenticated bits=0) by smtp3.uq.edu.au (8.13.8/8.13.8) with ESMTP id p4A74MIW017251 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 10 May 2011 17:04:22 +1000 Message-ID: <4DC8E375.6060201@uq.edu.au> Date: Tue, 10 May 2011 17:04:21 +1000 From: Fabian Buske User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.17) Gecko/20110414 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development References: <4DC8DE50.7000204@uq.edu.au> <38702A9A-255D-4A8D-95B5-A5331170DF84@fu-berlin.de> In-Reply-To: <38702A9A-255D-4A8D-95B5-A5331170DF84@fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-UQ-FilterTime: 1305011062 X-Scanned-By: MIMEDefang 2.58 on UQ Mailhub on 130.102.149.131 X-Originating-IP: 130.102.149.131 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1305011065-00005A17-2B94DE8E/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] FYI: CMake - Seqan - OpenMP support 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: Tue, 10 May 2011 07:04:27 -0000 Awesome! Cheers, Fabian On 10/05/11 4:45 PM, Manuel Holtgrewe wrote: > Using the new structure, you have to do this yourself. Currently, > OpenMP is already searched for on the top level structure, so the > OPENMP_FOUND flags are available. However, you have to add the define > yourself in your CMakeLists.txt. With the new structure, you are > mostly responsible for adding dependencies yourself. > > For example: > > cmake_minimum_required (VERSION 2.6) > project (sandbox_weese_apps_razers3) > > if (OPENMP_FOUND) > # We need a configuration header file. First, configure this file, > then > # add the target directory to the inclue path. > configure_file (${CMAKE_CURRENT_SOURCE_DIR}/config.h.in > ${CMAKE_CURRENT_BINARY_DIR}/config.h) > include_directories(${CMAKE_CURRENT_BINARY_DIR}) > > # Enable OpenMP. > set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") > > # Add executable for RazerS 3. > seqan_add_executable (razers3 razers.cpp) > elseif (OPENMP_FOUND) > message(STATUS "Not building RazerS3, since OpenMP could not be > found.") > endif (OPENMP_FOUND) > > Am 10.05.2011 um 08:42 schrieb Fabian Buske: > >> Hi, >> >> After porting my project to the new structure I noticed that the >> OpenMP >> support didn't work properly anymore. >> >> In Xcode you always have to tick the "Enable OpenMP Support" >> checkbox in >> "Project Info/Build" after running the cmake command (which isn't too >> much of a hassle). >> >> For the Makefile version one, however, seems to have to add some flags >> to tell the compiler to do as it is told, i.e. for gcc: >> >> cmake ../.. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-fopenmp" >> >> seems to work. I assumed cmake would take care of this. >> >> Cheers, >> Fabian >> >> -- >> Fabian Buske >> Institute for Molecular Bioscience >> The University of Queensland >> Brisbane, Qld. 4072 Australia >> Phone: (61)-(7)-334-62641 >> >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev -- Fabian Buske Institute for Molecular Bioscience The University of Queensland Brisbane, Qld. 4072 Australia Phone: (61)-(7)-334-62641 From jer15@hermes.cam.ac.uk Fri May 13 19:09:19 2011 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 <1QKvra-0004p3-T5>; Fri, 13 May 2011 19:09:19 +0200 Received: from ppsw-50.csi.cam.ac.uk ([131.111.8.150]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QKvra-0006Gg-Oy>; Fri, 13 May 2011 19:09:18 +0200 X-Cam-AntiVirus: no malware found X-Cam-SpamDetails: not scanned X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from cpc6-dals15-2-0-cust115.hari.cable.virginmedia.com ([82.35.196.116]:58830 helo=[192.168.1.5]) by ppsw-50.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.157]:587) with esmtpsa (PLAIN:jer15) (TLSv1:DHE-RSA-CAMELLIA256-SHA:256) id 1QKvra-0002Kn-r8 (Exim 4.72) for seqan-dev@lists.fu-berlin.de (return-path ); Fri, 13 May 2011 18:09:18 +0100 Message-ID: <4DCD65BD.8090507@mail.cryst.bbk.ac.uk> Date: Fri, 13 May 2011 18:09:17 +0100 From: John Reid User-Agent: Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.17) Gecko/20110424 Lightning/1.0b2 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development Content-Type: multipart/mixed; boundary="------------070908070907020809060209" Sender: "J.E. Reid" X-Originating-IP: 131.111.8.150 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1305306558-00005A17-71DA4C15/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.003143, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: [Seqan-dev] GCC unused-result warnings 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, 13 May 2011 17:09:19 -0000 This is a multi-part message in MIME format. --------------070908070907020809060209 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, I get unused-result warnings with gcc 4.4.3 in the tempFileName() function. Could you apply the attached patch to remove them? Then I'll be able to concentrate on my own warnings.... Thanks, John. --------------070908070907020809060209 Content-Type: text/x-patch; name="unused-result.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="unused-result.patch" Index: core/include/seqan/basic/basic_testing.h =================================================================== --- core/include/seqan/basic/basic_testing.h (revision 9403) +++ core/include/seqan/basic/basic_testing.h (working copy) @@ -533,7 +533,7 @@ // There is no mkstemp in MinGW but it does not complain about tmpnam. tmpnam(fileNameBuffer); #else // ifdef PLATFORM_WINDOWS_MINGW - mkstemp(fileNameBuffer); + int _tmp = mkstemp(fileNameBuffer); unlink(fileNameBuffer); #endif // #ifdef PLATFORM_WINDOWS_MINGW StaticData::tempFileNames().push_back(fileNameBuffer); --------------070908070907020809060209-- From manuel.holtgrewe@fu-berlin.de Fri May 13 22:13:52 2011 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 <1QKykA-00037e-Sn>; Fri, 13 May 2011 22:13:50 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1QKykA-0004SN-Qf>; Fri, 13 May 2011 22:13:50 +0200 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.102]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1QKykA-000588-OO>; Fri, 13 May 2011 22:13:50 +0200 Message-Id: <02575D0F-FFBF-4C85-A34D-96EA6C799038@fu-berlin.de> From: Manuel Holtgrewe To: SeqAn Development In-Reply-To: <4DCD65BD.8090507@mail.cryst.bbk.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Content-Transfer-Encoding: quoted-printable Mime-Version: 1.0 (Apple Message framework v936) Date: Fri, 13 May 2011 22:13:50 +0200 References: <4DCD65BD.8090507@mail.cryst.bbk.ac.uk> X-Mailer: Apple Mail (2.936) X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1305317630-00005A17-2F70DAF9/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] GCC unused-result warnings 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, 13 May 2011 20:13:52 -0000 John, I just committed a patch [9638] that hopefully fixes the problem. Are =20= you using the SeqAn CMake scripts and flags to build your programs? I =20= have not seen this warning yet, although we are building with 4.4.5 =20 for the 4.4 series. Bests, Manuel Am 13.05.2011 um 19:09 schrieb John Reid: > Hi, > > I get unused-result warnings with gcc 4.4.3 in the tempFileName() > function. Could you apply the attached patch to remove them? Then I'll > be able to concentrate on my own warnings.... > > Thanks, > John. > --=20 Manuel Holtgrewe manuel.holtgrewe@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 Bioinformatics 14195 Berlin Room 021 From jer15@hermes.cam.ac.uk Sat May 14 09:03:18 2011 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 <1QL8sf-0001Tm-Ks>; Sat, 14 May 2011 09:03:17 +0200 Received: from ppsw-41.csi.cam.ac.uk ([131.111.8.141]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QL8sf-0006Wf-HW>; Sat, 14 May 2011 09:03:17 +0200 X-Cam-AntiVirus: no malware found X-Cam-SpamDetails: not scanned X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from cpc6-dals15-2-0-cust115.hari.cable.virginmedia.com ([82.35.196.116]:36767 helo=[192.168.1.5]) by ppsw-41.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.156]:587) with esmtpsa (PLAIN:jer15) (TLSv1:DHE-RSA-CAMELLIA256-SHA:256) id 1QL8sf-0005kb-Qd (Exim 4.72) for seqan-dev@lists.fu-berlin.de (return-path ); Sat, 14 May 2011 08:03:17 +0100 Message-ID: <4DCE2933.7000809@mail.cryst.bbk.ac.uk> Date: Sat, 14 May 2011 08:03:15 +0100 From: John Reid User-Agent: Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.17) Gecko/20110424 Lightning/1.0b2 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development References: <4DCD65BD.8090507@mail.cryst.bbk.ac.uk> <02575D0F-FFBF-4C85-A34D-96EA6C799038@fu-berlin.de> In-Reply-To: <02575D0F-FFBF-4C85-A34D-96EA6C799038@fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: "J.E. Reid" X-Originating-IP: 131.111.8.141 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1305356597-00005A17-C133B721/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000554, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] GCC unused-result warnings 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: Sat, 14 May 2011 07:03:18 -0000 Manuel, Thanks for that. I'm using boost.build so I guess the default flags are different. I have these flags: -ftemplate-depth-128 -Wno-error -O3 -finline-functions -Wno-inline -Wall -fPIC -Wno-deprecated -Wno-unused -DNDEBUG -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_ENABLE_TESTING=0 Regards, John. On 13/05/11 21:13, Manuel Holtgrewe wrote: > John, > > I just committed a patch [9638] that hopefully fixes the problem. Are > you using the SeqAn CMake scripts and flags to build your programs? I > have not seen this warning yet, although we are building with 4.4.5 > for the 4.4 series. > > Bests, > Manuel > > Am 13.05.2011 um 19:09 schrieb John Reid: > >> Hi, >> >> I get unused-result warnings with gcc 4.4.3 in the tempFileName() >> function. Could you apply the attached patch to remove them? Then I'll >> be able to concentrate on my own warnings.... >> >> Thanks, >> John. >> > From jer15@hermes.cam.ac.uk Sat May 14 09:27:54 2011 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 <1QL9GT-0002L2-Te>; Sat, 14 May 2011 09:27:54 +0200 Received: from ppsw-50.csi.cam.ac.uk ([131.111.8.150]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QL9GT-0001Fn-Oy>; Sat, 14 May 2011 09:27:53 +0200 X-Cam-AntiVirus: no malware found X-Cam-SpamDetails: not scanned X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from cpc6-dals15-2-0-cust115.hari.cable.virginmedia.com ([82.35.196.116]:33855 helo=[192.168.1.5]) by ppsw-50.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.157]:587) with esmtpsa (PLAIN:jer15) (TLSv1:DHE-RSA-CAMELLIA256-SHA:256) id 1QL9GT-0008Ph-r8 (Exim 4.72) for seqan-dev@lists.fu-berlin.de (return-path ); Sat, 14 May 2011 08:27:53 +0100 Message-ID: <4DCE2EF9.8060408@mail.cryst.bbk.ac.uk> Date: Sat, 14 May 2011 08:27:53 +0100 From: John Reid User-Agent: Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.17) Gecko/20110424 Lightning/1.0b2 Thunderbird/3.1.10 MIME-Version: 1.0 To: SeqAn Development References: <4DCD65BD.8090507@mail.cryst.bbk.ac.uk> <02575D0F-FFBF-4C85-A34D-96EA6C799038@fu-berlin.de> In-Reply-To: <02575D0F-FFBF-4C85-A34D-96EA6C799038@fu-berlin.de> Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit Sender: "J.E. Reid" X-Originating-IP: 131.111.8.150 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1305358073-00005A17-A5482A02/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] GCC unused-result warnings 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: Sat, 14 May 2011 07:27:54 -0000 While we're on the subject I also have this warning: /home/john/Dev/ThirdParty/C++/seqan-trunk/core/include/seqan/basic/iterator_interface.h: In function ‘seqan::Container *>::Type & seqan::container( seqan::SimpleType *)’: /home/john/Dev/ThirdParty/C++/seqan-trunk/core/include/seqan/basic/iterator_interface.h:483: instantiated from ‘bool seqan::atBegin(const seqan::SimpleType *&)’ /home/john/Dev/ThirdParty/C++/seqan-trunk/core/include/seqan/modifier/modifier_reverse.h:128: instantiated from ‘void seqan::goNext( seqan::ModifiedIterator *, seqan::ModReverse> &)’ /home/john/Dev/ThirdParty/C++/seqan-trunk/core/include/seqan/modifier/modifier_iterator.h:410: instantiated from ‘const seqan::ModifiedIterator< seqan::SimpleType *, seqan::ModReverse> & seqan::operator++(seqan::ModifiedIterator *, seqan::ModReverse> &)’ src/sandbox/seqan_sandbox_rev_comp_iterator.cpp:28: instantiated from here /home/john/Dev/ThirdParty/C++/seqan-trunk/core/include/seqan/basic/iterator_interface.h:379: warning: reference to local variable ‘me’ returned from the following code in seqan/basic/iterator_interface.h:379: template inline typename Container::Type & container(T me) { // TODO(holtgrew): Default implementation with auto-sequences, remove? SEQAN_CHECKPOINT; return me; } It seems strange to pass the argument by value and return a reference to it. Is this correct? Also why might my code be instantiating a to-be-removed function? Here's my code: #include #include #include #include int main( int argc, char * argv [] ) { using namespace seqan; typedef Dna5 dna_t; typedef String< dna_t > string_t; typedef Iterator< string_t >::Type iterator_t; typedef ModifiedIterator< iterator_t, ModReverse > rev_iterator_t; typedef ModifiedIterator< rev_iterator_t, FunctorComplement< dna_t > > rev_comp_iterator_t; string_t str = "ACGTNAAGGTTCC"; ::std::cout << "Original string: " << str << "\n"; rev_iterator_t rev_begin( end( str ) ); rev_iterator_t rev_end( begin( str ) ); ::std::cout << "Reverse string: " << str; while( rev_begin != rev_end ) { ::std::cout << *rev_begin; ++rev_begin; } ::std::cout << "\n"; return 0; } John. On 13/05/11 21:13, Manuel Holtgrewe wrote: > John, > > I just committed a patch [9638] that hopefully fixes the problem. Are > you using the SeqAn CMake scripts and flags to build your programs? I > have not seen this warning yet, although we are building with 4.4.5 > for the 4.4 series. > > Bests, > Manuel > > Am 13.05.2011 um 19:09 schrieb John Reid: > >> Hi, >> >> I get unused-result warnings with gcc 4.4.3 in the tempFileName() >> function. Could you apply the attached patch to remove them? Then I'll >> be able to concentrate on my own warnings.... >> >> Thanks, >> John. >> > From konrad.rudolph@fu-berlin.de Sat May 14 11:24:00 2011 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 <1QLB4p-0006a6-CO>; Sat, 14 May 2011 11:23:59 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QLB4p-0004eL-AW>; Sat, 14 May 2011 11:23:59 +0200 Received: from dslb-092-078-133-166.pools.arcor-ip.net ([92.78.133.166] helo=[192.168.178.44]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1QLB4p-0000Nq-4I>; Sat, 14 May 2011 11:23:59 +0200 Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 (Apple Message framework v1084) From: Konrad Ludwig Moritz Rudolph In-Reply-To: <4DCE2933.7000809@mail.cryst.bbk.ac.uk> Date: Sat, 14 May 2011 11:23:58 +0200 Content-Transfer-Encoding: quoted-printable Message-Id: <3216B392-6C46-43FE-8B6B-323D3EC90CFE@fu-berlin.de> References: <4DCD65BD.8090507@mail.cryst.bbk.ac.uk> <02575D0F-FFBF-4C85-A34D-96EA6C799038@fu-berlin.de> <4DCE2933.7000809@mail.cryst.bbk.ac.uk> To: SeqAn Development X-Mailer: Apple Mail (2.1084) X-Originating-IP: 92.78.133.166 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1305365039-00005A17-37CE9809/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.001336, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] GCC unused-result warnings 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: Sat, 14 May 2011 09:24:00 -0000 There's a simple fix to hide warnings caused by SeqAn: just include the = SeqAn include headers via the flag `-isystem` instead of `-I`. That is, = append `-isystem PATH/TO/SEQAN` to your CXXFLAGS. Perhaps that helps. Kind regards, Konrad On May 14, 2011, at 9:03, John Reid wrote: > Manuel, >=20 > Thanks for that. I'm using boost.build so I guess the default flags = are different. I have these flags: >=20 > -ftemplate-depth-128 -Wno-error -O3 -finline-functions -Wno-inline = -Wall -fPIC -Wno-deprecated -Wno-unused -DNDEBUG -DSEQAN_ENABLE_DEBUG=3D0 = -DSEQAN_ENABLE_TESTING=3D0 >=20 > Regards, > John. >=20 > On 13/05/11 21:13, Manuel Holtgrewe wrote: >> John, >>=20 >> I just committed a patch [9638] that hopefully fixes the problem. Are = you using the SeqAn CMake scripts and flags to build your programs? I = have not seen this warning yet, although we are building with 4.4.5 for = the 4.4 series. >>=20 >> Bests, >> Manuel >>=20 >> Am 13.05.2011 um 19:09 schrieb John Reid: >>=20 >>> Hi, >>>=20 >>> I get unused-result warnings with gcc 4.4.3 in the tempFileName() >>> function. Could you apply the attached patch to remove them? Then = I'll >>> be able to concentrate on my own warnings.... >>>=20 >>> Thanks, >>> John. >>> >>=20 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From wengl@uci.edu Tue May 17 23:58:09 2011 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 <1QMSHI-0004fD-61>; Tue, 17 May 2011 23:58:08 +0200 Received: from smtp2.es.uci.edu ([128.200.80.32]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QMSHH-0004JA-OO>; Tue, 17 May 2011 23:58:08 +0200 Received: from [128.195.53.171] (dhcp-053171.ics.uci.edu [128.195.53.171]) (authenticated bits=0) by smtp2.es.uci.edu (8.13.8/8.13.8) with ESMTP id p4HLw4Kj015696 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 17 May 2011 14:58:05 -0700 X-UCInetID: wengl Message-ID: <4DD2EFB5.6010004@uci.edu> Date: Tue, 17 May 2011 14:59:17 -0700 From: Lingjie Weng User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9.2.14) Gecko/20110223 Thunderbird/3.1.8 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 128.200.80.32 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1305669488-00005A17-F7C0F487/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.030885, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD X-Mailman-Approved-At: Wed, 18 May 2011 00:00:14 +0200 Subject: [Seqan-dev] memory issue when calling function in seqan 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: Tue, 17 May 2011 21:58:09 -0000 Dear Seqan team, I am interested in our Seqan C++ library, it is really helpful. But I got some problem when try to use the function "globalAlignment(Align & align_,Score const &, MyersBitVector" in seqan/align/align.myers.h file. I was trying to call this function in my project, I called it in this way (got those code from /demos/alignment.cpp) : typedef String TSequence; TSequence seq1 = "atcgaatgcgga"; TSequence seq2 = "actcgttgca"; Score score(0, -1, -1, -2); Align align; resize(rows(align), 2); assignSource(row(align, 0), seq1); assignSource(row(align, 1), seq2); ::std::cout << "Score = " << globalAlignment(align, score, MyersBitVector()) << ::std::endl; I found you have internally clean up the memory in the function "globalAlignment ()". My question is how could clean up the memory I allocated for initialization, for example, Tsequence, align... When I am using it for millions of reads alignment, the memory keeps increasing, which turns out to be a big issue to me. Do you have any idea how to release memory properly? I really appreciate if you could show me how to fix it. I am looking forward to your reply. Thanks, Lingjie PhD student University of California, Irvine From manuel.holtgrewe@fu-berlin.de Wed May 18 00:15:44 2011 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 <1QMSYH-0005NM-Sf>; Wed, 18 May 2011 00:15:41 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1QMSYH-0001Vj-Qs>; Wed, 18 May 2011 00:15:41 +0200 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.102]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1QMSYH-00072w-Mg>; Wed, 18 May 2011 00:15:41 +0200 Message-Id: From: Manuel Holtgrewe To: SeqAn Development In-Reply-To: <4DD2EFB5.6010004@uci.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Content-Transfer-Encoding: quoted-printable Mime-Version: 1.0 (Apple Message framework v936) Date: Wed, 18 May 2011 00:15:41 +0200 References: <4DD2EFB5.6010004@uci.edu> X-Mailer: Apple Mail (2.936) X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1305670541-00005A17-EC5D8774/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000477, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] memory issue when calling function in seqan 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: Tue, 17 May 2011 22:15:44 -0000 Lingjie, can you submit a minimal demo program that compiles and shows your =20 error? Please compile it on your computer and run it under valgrind =20 [1,2] and make sure that a memory leak is reported. I just replaced "MyersHirschberg" with "MyersBitVector" in the demos/=20 alignment.cpp file, compiled it and ran it through valgrind. Valgrind =20= [1,2] reported no memory leaks, so it is very unlikely that this =20 function produces leaks per se in the current trunk version. If it turns out that your memory leak is in another position, valgrind =20= is a very useful and versatile tool to find such leaks. You will find =20= many high-quality tutorials on the internet. There are known leaks with the last release version when using SeqAn =20 Strings of non-POD types (i.e. objects that allocate memory and where =20= the destructor has to be called in order to free memory) that is fixed =20= in the current trunk version. A workaround here, is to upgrade to the =20= trunk version or use std::vector<> objects. Also, the SeqAn Map =20 specialization based on skiplists is known to leak memory. Use another =20= specialization or std::map<,> directly. What SeqAn version are you using? The last release version? May I =20 recommend you to try out the trunk version and check whether the =20 problem persists? Bests, Manuel [1] http://www.valgrind.org [2] http://lh3lh3.users.sourceforge.net/memdebug.shtml Am 17.05.2011 um 23:59 schrieb Lingjie Weng: > Dear Seqan team, > > I am interested in our Seqan C++ library, it is really helpful. But I > got some problem when try to use the function > "globalAlignment(Align & align_,Score Simple> const &, MyersBitVector" in seqan/align/align.myers.h file. > > I was trying to call this function in my project, I called it in this > way (got those code from /demos/alignment.cpp) : > > typedef String TSequence; > TSequence seq1 =3D "atcgaatgcgga"; > TSequence seq2 =3D "actcgttgca"; > Score score(0, -1, -1, -2); > Align align; > resize(rows(align), 2); > assignSource(row(align, 0), seq1); > assignSource(row(align, 1), seq2); > ::std::cout << "Score =3D " << globalAlignment(align, score, > MyersBitVector()) << ::std::endl; > > I found you have internally clean up the memory in the function > "globalAlignment ()". My question is how could clean up the memory I > allocated for initialization, for example, Tsequence, align... > > When I am using it for millions of reads alignment, the memory keeps > increasing, which turns out to be a big issue to me. Do you have any > idea how to release memory properly? I really appreciate if you could > show me how to fix it. > > I am looking forward to your reply. > > > Thanks, > Lingjie > > PhD student > University of California, Irvine > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --=20 Manuel Holtgrewe manuel.holtgrewe@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 Bioinformatics 14195 Berlin Room 021 From wengl@uci.edu Wed May 18 00:41:47 2011 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 <1QMSxW-0006LQ-Ch>; Wed, 18 May 2011 00:41:46 +0200 Received: from smtp2.es.uci.edu ([128.200.80.32]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QMSxV-0008DJ-Un>; Wed, 18 May 2011 00:41:46 +0200 Received: from [128.195.53.171] (dhcp-053171.ics.uci.edu [128.195.53.171]) (authenticated bits=0) by smtp2.es.uci.edu (8.13.8/8.13.8) with ESMTP id p4HMfhDg021226 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 17 May 2011 15:41:44 -0700 X-UCInetID: wengl Message-ID: <4DD2F9F0.8060708@uci.edu> Date: Tue, 17 May 2011 15:42:56 -0700 From: Lingjie Weng User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9.2.14) Gecko/20110223 Thunderbird/3.1.8 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 128.200.80.32 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1305672106-00005A17-DD2593CF/3356026812-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.045615, version=1.2.2 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=1.8 required=5.0 tests=FU_XPURGATE_SUSP, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] memory issue when calling function in seqan 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: Tue, 17 May 2011 22:41:47 -0000 Dear Seqan team, I am interested in our Seqan C++ library, it is really helpful. But I got some problem when try to use the function "globalAlignment(Align & align_,Score const &, MyersBitVector" in seqan/align/align.myers.h file. I was trying to call this function in my project, I called it in this way (got those code from /demos/alignment.cpp) : typedef String TSequence; TSequence seq1 = "atcgaatgcgga"; TSequence seq2 = "actcgttgca"; Score score(0, -1, -1, -2); Align align; resize(rows(align), 2); assignSource(row(align, 0), seq1); assignSource(row(align, 1), seq2); ::std::cout << "Score = " << globalAlignment(align, score, MyersBitVector()) << ::std::endl; I found you have internally clean up the memory in the function "globalAlignment ()". My question is how could clean up the memory I allocated for initialization, for example, Tsequence, align... When I am using it for millions of reads alignment, the memory keeps increasing, which turns out to be a big issue to me. Do you have any idea how to release memory properly? I really appreciate if you could show me how to fix it. I am looking forward to your reply. Thanks, Lingjie Weng PhD student University of California, Irvine