From alex@biotec.tu-dresden.de Fri Jul 04 11:32:19 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1X2zqr-0004nl-AA>; Fri, 04 Jul 2014 11:32:17 +0200 Received: from mailserver.biotec.tu-dresden.de ([141.30.193.4]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1X2zqr-002ufH-8z>; Fri, 04 Jul 2014 11:32:17 +0200 Received: from [192.168.194.134] (bioinfws32.biotec.tu-dresden.de [192.168.194.134]) (using TLSv1 with cipher DHE-RSA-AES128-SHA (128/128 bits)) (No client certificate requested) by mailserver.biotec.tu-dresden.de (Postfix) with ESMTPSA id 0E395C13903 for ; Fri, 4 Jul 2014 11:32:16 +0200 (CEST) Message-ID: <53B67479.3020901@biotec.tu-dresden.de> Date: Fri, 04 Jul 2014 11:31:37 +0200 From: Alex Mestiashvili User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Icedove/24.5.0 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: 141.30.193.4 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1404466337-0009B030-C5144797/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-2.3 required=5.0 tests=RCVD_IN_DNSWL_MED X-Spam-Checker-Version: SpamAssassin 3.4.0 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] help needed to build tophat with seqan >=1.4 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 04 Jul 2014 09:32:19 -0000 Dear SeqAn Developers, We distribute SeqAn in Debian and recently packaged SeqAn version 1.4. However after switching to the new version, tophat [0] fails to build. Here are the build errors which we couldn't solve: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=733352#45 It would be really great if you would give us a hint. Debianized tophat lives here: http://anonscm.debian.org/gitweb/?p=debian-med/tophat.git Thank you, Alex [0] http://ccb.jhu.edu/software/tophat/index.shtml Please also CC to 733352@bugs.debian.org From manuel.holtgrewe@fu-berlin.de Sun Jul 06 13:35:42 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1X3kjI-002smC-Ji>; Sun, 06 Jul 2014 13:35:36 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1X3kjI-002Wrs-IT>; Sun, 06 Jul 2014 13:35:36 +0200 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1X3kjI-003inN-5m>; Sun, 06 Jul 2014 13:35:36 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.03.0195.001; Sun, 6 Jul 2014 13:35:34 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] help needed to build tophat with seqan >=1.4 Thread-Index: AQHPl2rduzk+YsQY5EitHEgkNZ6geJuS7Yeh Message-ID: References: <53B67479.3020901@biotec.tu-dresden.de> In-Reply-To: <53B67479.3020901@biotec.tu-dresden.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Content-Type: multipart/mixed; boundary="_002_FCCAB9D80C3DAB47B5601C5B0E62872B961F8869ex02acampusfube_" MIME-Version: 1.0 Date: Sun, 06 Jul 2014 13:35:34 +0200 X-Original-Date: Sun, 6 Jul 2014 11:35:34 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1404646536-0009B030-01A3CE04/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.4.0 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] help needed to build tophat with seqan >=1.4 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 06 Jul 2014 11:35:42 -0000 --_002_FCCAB9D80C3DAB47B5601C5B0E62872B961F8869ex02acampusfube_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Alex,=0A= =0A= attached is a patch that circumvents the problems in TopHat with SeqAn 1.4.= 1.=0A= =0A= I had problems building tophat from your git repository so I had to hack th= e Makefiles a bit.=0A= =0A= Do not hesitate to send another email in case the problem remains.=0A= =0A= HTH,=0A= Manuel=0A= ________________________________________=0A= From: Alex Mestiashvili [alex@biotec.tu-dresden.de]=0A= Sent: Friday, July 04, 2014 11:31 AM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] help needed to build tophat with seqan >=3D1.4=0A= =0A= Dear SeqAn Developers,=0A= =0A= We distribute SeqAn in Debian and recently packaged SeqAn version 1.4.=0A= However after switching to the new version, tophat [0] fails to build.=0A= Here are the build errors which we couldn't solve:=0A= =0A= https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=3D733352#45=0A= =0A= It would be really great if you would give us a hint.=0A= =0A= Debianized tophat lives here:=0A= http://anonscm.debian.org/gitweb/?p=3Ddebian-med/tophat.git=0A= =0A= Thank you,=0A= Alex=0A= =0A= [0] http://ccb.jhu.edu/software/tophat/index.shtml=0A= =0A= Please also CC to 733352@bugs.debian.org=0A= =0A= _______________________________________________=0A= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A= --_002_FCCAB9D80C3DAB47B5601C5B0E62872B961F8869ex02acampusfube_ Content-Type: text/x-patch; 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Mon, 07 Jul 2014 14:07:28 +0200 Received: from mailserver.biotec.tu-dresden.de ([141.30.193.4]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1X47hg-000etR-NI>; Mon, 07 Jul 2014 14:07:28 +0200 Received: from [192.168.194.134] (bioinfws32.biotec.tu-dresden.de [192.168.194.134]) (using TLSv1 with cipher DHE-RSA-AES128-SHA (128/128 bits)) (No client certificate requested) by mailserver.biotec.tu-dresden.de (Postfix) with ESMTPSA id 7ACC2C0015B for ; Mon, 7 Jul 2014 14:07:27 +0200 (CEST) Message-ID: <53BA8D54.7030102@biotec.tu-dresden.de> Date: Mon, 07 Jul 2014 14:06:44 +0200 From: Alex Mestiashvili User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Icedove/24.5.0 MIME-Version: 1.0 To: SeqAn Development References: <53B67479.3020901@biotec.tu-dresden.de> In-Reply-To: Content-Type: multipart/alternative; boundary="------------020203080101060607000802" X-Originating-IP: 141.30.193.4 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1404734848-0009B030-26E17B27/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-2.3 required=5.0 tests=HTML_MESSAGE, RCVD_IN_DNSWL_MED X-Spam-Checker-Version: SpamAssassin 3.4.0 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] help needed to build tophat with seqan >=1.4 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 07 Jul 2014 12:07:30 -0000 This is a multi-part message in MIME format. --------------020203080101060607000802 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear Manuel, Thank you a lot! I could successfully compile the latest version of tophat with the patch. Awesome! Best regards, Alex On 07/06/2014 01:35 PM, Holtgrewe, Manuel wrote: > Hi Alex, > > attached is a patch that circumvents the problems in TopHat with SeqAn 1.4.1. > > I had problems building tophat from your git repository so I had to hack the Makefiles a bit. > > Do not hesitate to send another email in case the problem remains. > > HTH, > Manuel > ________________________________________ > From: Alex Mestiashvili [alex@biotec.tu-dresden.de] > Sent: Friday, July 04, 2014 11:31 AM > To: seqan-dev@lists.fu-berlin.de > Subject: [Seqan-dev] help needed to build tophat with seqan >=1.4 > > Dear SeqAn Developers, > > We distribute SeqAn in Debian and recently packaged SeqAn version 1.4. > However after switching to the new version, tophat [0] fails to build. > Here are the build errors which we couldn't solve: > > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=733352#45 > > It would be really great if you would give us a hint. > > Debianized tophat lives here: > http://anonscm.debian.org/gitweb/?p=debian-med/tophat.git > > Thank you, > Alex > > [0] http://ccb.jhu.edu/software/tophat/index.shtml > > Please also CC to 733352@bugs.debian.org > > _______________________________________________ > 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 --------------020203080101060607000802 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Dear Manuel,

Thank you a lot! I could successfully compile the latest version of tophat with the patch.
Awesome!

Best regards,
Alex


On 07/06/2014 01:35 PM, Holtgrewe, Manuel wrote:
Hi Alex,

attached is a patch that circumvents the problems in TopHat with SeqAn 1.4.1.

I had problems building tophat from your git repository so I had to hack the Makefiles a bit.

Do not hesitate to send another email in case the problem remains.

HTH,
Manuel
________________________________________
From: Alex Mestiashvili [alex@biotec.tu-dresden.de]
Sent: Friday, July 04, 2014 11:31 AM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] help needed to build tophat with seqan >=1.4

Dear SeqAn Developers,

We distribute SeqAn in Debian and recently packaged SeqAn version 1.4.
However after switching to the new version, tophat [0] fails to build.
Here are the build errors which we couldn't solve:

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=733352#45

It would be really great if you would give us a hint.

Debianized tophat lives here:
http://anonscm.debian.org/gitweb/?p=debian-med/tophat.git

Thank you,
Alex

[0] http://ccb.jhu.edu/software/tophat/index.shtml

Please also CC to 733352@bugs.debian.org

_______________________________________________
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

--------------020203080101060607000802-- From manuel.holtgrewe@fu-berlin.de Thu Jul 10 19:04:32 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1X5Hlm-000NgY-EW>; Thu, 10 Jul 2014 19:04:30 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1X5Hlm-001Xoy-D4>; Thu, 10 Jul 2014 19:04:30 +0200 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1X5Hlm-000McL-3t>; Thu, 10 Jul 2014 19:04:30 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0195.001; Thu, 10 Jul 2014 19:04:29 +0200 From: "Holtgrewe, Manuel" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: Completing migrating to GitHub Thread-Index: Ac+cYFY/RNx5oK15R5S1jnuVCSkNzA== Message-ID: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_FCCAB9D80C3DAB47B5601C5B0E62872B961FB810ex02acampusfube_" MIME-Version: 1.0 Date: Thu, 10 Jul 2014 19:04:27 +0200 X-Original-Date: Thu, 10 Jul 2014 17:04:27 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1405011870-00000941-F1E3464A/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.003182, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.4.0 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Completing migrating to GitHub X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 10 Jul 2014 17:04:32 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B961FB810ex02acampusfube_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear SeqAn Users, Short version: The new SVN trunk is https://github.com/seqan/seqan/branches= /master (no login required). As you all know, main development now happens on GitHub. So far, we have pr= ovided a mirror of the "master" branch at svn.seqan.de. We plan to switch o= ff svn.seqan.de in the near future (in 2 months at the end of August). Ther= e regularly were problems with automatically copying patches from Git to Su= bversion. However, the nice folks over at GitHub provide a Subversion interface to al= l GitHub repositories, so you can simply use one of the following URLs via = Subversion. You will have to create a fresh SVN checkout but you should not= have any problems beside that. https://github.com/seqan/seqan/branches/master -- This is equivalent to the current SeqAn SVN trunk. It is a stable versio= n and only bug fixes are applied here until the next SeqAn release. https://github.com/seqan/seqan/branches/develop -- The current development branch for SeqAn. Actual development happens in = feature branches so it is more stable than the SVN trunk two years ago when= all development happened in the SeqAn trunk. However, the branch contains = the latest and greatest new SeqAn code and features. Or, if you wish, you can also directly use git for getting SeqAn. A short G= it tutorial for Subversion users can be found here, for example: http://git= .or.cz/course/svn.html Do not hesitate to ask any questions you might have. Cheers, Manuel --_000_FCCAB9D80C3DAB47B5601C5B0E62872B961FB810ex02acampusfube_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear SeqAn Users,

Short version: The new SVN trunk is https://github.com/seqan/seqan/branches/master (no login required).<= br>
As you all know, main development now happens on GitHub. So far, we have pr= ovided a mirror of the "master" branch at svn.seqan.de. We plan t= o switch off svn.seqan.de in the near future (in 2 months at the end of Aug= ust). There regularly were problems with automatically copying patches from Git to Subversion.

However, the nice folks over at GitHub provide a Subversion interface to al= l GitHub repositories, so you can simply use one of the following URLs via = Subversion. You will have to create a fresh SVN checkout but you should not= have any problems beside that.

https://github.com/se= qan/seqan/branches/master
-- This is equivalent to the current SeqAn SVN trunk. It is a stable versio= n and only bug fixes are applied here until the next SeqAn release.

https://github.com/se= qan/seqan/branches/develop
-- The current development branch for SeqAn. Actual development happens in = feature branches so it is more stable than the SVN trunk two years ago when= all development happened in the SeqAn trunk. However, the branch contains = the latest and greatest new SeqAn code and features.

Or, if you wish, you can also directly use git for getting SeqAn. A short G= it tutorial for Subversion users can be found here, for example: http:= //git.or.cz/course/svn.html

Do not hesitate to ask any questions you might have.

Cheers,
Manuel
--_000_FCCAB9D80C3DAB47B5601C5B0E62872B961FB810ex02acampusfube_-- From alex@biotec.tu-dresden.de Sun Jul 20 19:40:21 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1X8v5w-003gLx-It>; Sun, 20 Jul 2014 19:40:20 +0200 Received: from mailserver.biotec.tu-dresden.de ([141.30.193.4]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1X8v5w-000YjA-GA>; Sun, 20 Jul 2014 19:40:20 +0200 Received: from [10.0.1.254] (drsd-4db3cd87.pool.mediaWays.net [77.179.205.135]) (using TLSv1 with cipher DHE-RSA-AES128-SHA (128/128 bits)) (No client certificate requested) by mailserver.biotec.tu-dresden.de (Postfix) with ESMTPSA id 17AA4C13820 for ; Sun, 20 Jul 2014 19:40:19 +0200 (CEST) Message-ID: <53CBFEFE.3000800@biotec.tu-dresden.de> Date: Sun, 20 Jul 2014 19:40:14 +0200 From: Alex Mestiashvili User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Icedove/24.5.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Originating-IP: 141.30.193.4 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1405878020-00000941-C6D48DAA/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-2.3 required=5.0 tests=RCVD_IN_DNSWL_MED X-Spam-Checker-Version: SpamAssassin 3.4.0 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] tophat with seqan 1.4.1 fails to build on mips/mipsel X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: alex@biotec.tu-dresden.de, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 20 Jul 2014 17:40:22 -0000 Hi All, there is another problem with seqan 1.4.1 and tophat - it fails to build on mips and mipsel architectures: --- | make[3]: Entering directory '/«BUILDDIR»/tophat-2.0.12+dfsg/src' | g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o reads.o reads.cpp | In file included from /usr/include/seqan/file.h:56:0, | from /usr/include/seqan/score/score_matrix.h:40, | from /usr/include/seqan/score.h:48, | from /usr/include/seqan/find.h:45, | from reads.cpp:21: | /usr/include/seqan/file/file_generated_forwards.h:927:66: error: invalid abstract return type 'seqan::FileFormat' | template inline FileFormat guessFileFormat(TFile & file, TData & data); // "seqan-1.3.1/seqan/file/file_format_guess.h"(65) | ^ | In file included from /usr/include/seqan/file.h:84:0, | from /usr/include/seqan/score/score_matrix.h:40, | from /usr/include/seqan/score.h:48, | from /usr/include/seqan/find.h:45, | from reads.cpp:21: | /usr/include/seqan/file/file_format.h:143:8: note: because the following virtual functions are pure within 'seqan::FileFormat': | struct FileFormat | ^ | /usr/include/seqan/file/file_format.h:154:2: note: virtual void* seqan::FileFormat::formatID_() const | formatID_() const = 0; | ^ | /usr/include/seqan/file/file_format.h:157:2: note: virtual void seqan::FileFormat::read_(TFile&, TData&) const | read_(TFile & file, TData & data) const = 0; | ^ | /usr/include/seqan/file/file_format.h:159:2: note: virtual void seqan::FileFormat::read_(TFile&, TData&, seqan::FileFormat::TSize) const | read_(TFile & file, TData & data, TSize limit) const = 0; | ^ | /usr/include/seqan/file/file_format.h:162:2: note: virtual void seqan::FileFormat::readMeta_(TFile&, TMeta&) const | readMeta_(TFile & file, TMeta & meta) const = 0; | ^ | /usr/include/seqan/file/file_format.h:165:2: note: virtual void seqan::FileFormat::goNext_(TFile&) const | goNext_(TFile & file) const = 0; | ^ | /usr/include/seqan/file/file_format.h:168:2: note: virtual seqan::FileFormat::TSize seqan::FileFormat::length_(TFile&) const | length_(TFile & file) const = 0; | ^ | /usr/include/seqan/file/file_format.h:171:2: note: virtual void seqan::FileFormat::write_(TFile&, TData&) const | write_(TFile & file, TData & data) const = 0; | ^ | /usr/include/seqan/file/file_format.h:173:2: note: virtual void seqan::FileFormat::write_(TFile&, TData&, TMeta&) const | write_(TFile & file, TData & data, TMeta & meta) const = 0; | ^ | make[3]: *** [reads.o] Error 1 help would be greatly appreciated. Here are the full build logs: https://buildd.debian.org/status/fetch.php?pkg=tophat&arch=mipsel&ver=2.0.12%2Bdfsg-1&stamp=1404743513 https://buildd.debian.org/status/fetch.php?pkg=tophat&arch=mips&ver=2.0.12%2Bdfsg-1&stamp=1404739146 Thank you, Alex