From walter.pasiego@gmail.com Tue Feb 05 15:04:46 2013 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 <1U2j8f-002HVD-NS>; Tue, 05 Feb 2013 15:04:45 +0100 Received: from mail-we0-f194.google.com ([74.125.82.194]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1U2j8f-001Gbr-Kr>; Tue, 05 Feb 2013 15:04:45 +0100 Received: by mail-we0-f194.google.com with SMTP id d7so30727wer.9 for ; Tue, 05 Feb 2013 06:04:44 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:x-received:date:message-id:subject:from:to :content-type; bh=3cM2oBUEIWr1ZpFO7D+GYjL31X7bb8mWMdY+RFtXyYU=; b=UmasE8aBLYtoulBzdZiB66ca4rLCg9JiFw5xW4FnVs0jt8wWaLc9GWUIbZhjJFqXpm GUjjTYsm51qqwNR6e8gBKZD7AP0Om+ZxGn+N3sY2t/APa2Ju3GNKNwgYKoTkzy1RPJNl rtj+5o9nbDDAoGqYg3KcZwt48Uvurc1Oc08Ip8bonL7NwdPfKtF3+TGD43K3hr8JYTCD IBSeQ2+iLU+STfWXJNuA0nJXH6XAtQjWVT8X2rLMKD8jRN/Lw8tIDYWt61hZa+dbL4Z+ agVWZHOt+5SeZM9Ggo3TP3nmy9Q0ivqV3T6IFJ2X6JdUJI9kMOduX5XxzAHrRytlLzE1 9hyw== MIME-Version: 1.0 X-Received: by 10.194.172.228 with SMTP id bf4mr42823024wjc.38.1360073084354; Tue, 05 Feb 2013 06:04:44 -0800 (PST) Received: by 10.217.49.67 with HTTP; Tue, 5 Feb 2013 06:04:44 -0800 (PST) Date: Tue, 5 Feb 2013 15:04:44 +0100 Message-ID: From: Walter Pasiego To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=089e013c6c120fbfb904d4fab15c X-Originating-IP: 74.125.82.194 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1360073085-00000B1F-D98A3E14/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000183, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.2 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Problem with GCC 4.6.3 and seq_io.h X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 05 Feb 2013 14:04:46 -0000 --089e013c6c120fbfb904d4fab15c Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Colleagues, I'm starting to play around with SeqAn using the last version available at the svn repo. I'm using Linux with gcc 4.6.3 and Eclipse. So far I succeeded compiling and running an example with the following headers: #include #include #include but as soon as I try another example with: #include the compilers complains with: /src/seqan-trunk/core/include/seqan/store/store_io_sam.h: In function =91bo= ol seqan::operator<(const seqan::CigarElement&, const seqan::CigarElement&)=92: /src/seqan-trunk/core/include/seqan/store/store_io_sam.h:120:96: error: *= =91.=92 cannot appear in a constant-expression* Using the include file (the "musketeer" header file) provokes more errors to shown up. Can anyone please help me and tell if: 1) possibly I am doing something wrong 2) the trunk version of the SeqAn library is still incompatible with gcc 4.?.? 3) there is a workaround? Is there a recommended compiler-version? Many thanks in advance! Walter --089e013c6c120fbfb904d4fab15c Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
Dear Colleagues,
I'm starting to play around with SeqAn using the last versi= on available at the svn repo.
I'm using Linux with gcc 4.6.3 a= nd Eclipse.
So far I succeeded compiling and running an example with the following head= ers:
#include <seqan/basic.h>
#include <seqan/sequence.h>=
#include <seqan/file.h>

but as soon as I try another= example with:
#include <seqan/seq_io.h>

the compilers complains with:=

/src/seqan-trunk/core/include/seqan/store/store_io_sam.h: In functi= on =91bool seqan::operator<(const seqan::CigarElement<TOperation, TCo= unt>&, const seqan::CigarElement<TOperation, TCount>&)=92:=
/src/seqan-trunk/core/include/seqan/store/store_io_sam.h:120:96: error: = =91.=92 cannot appear in a constant-expression

Using the i= nclude file <seqan.h> (the "musketeer" header file) provoke= s more errors to shown up.

Can anyone please help me and tell if:
1) poss= ibly I am doing something wrong
2) the trunk version of the S= eqAn library is still incompatible with gcc 4.?.?
3) there is= a workaround? Is there a recommended compiler-version?

Many thanks in advance!

Walter
--089e013c6c120fbfb904d4fab15c-- From manuel.holtgrewe@fu-berlin.de Tue Feb 05 16:18:42 2013 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 <1U2kIC-002LV2-L2>; Tue, 05 Feb 2013 16:18:40 +0100 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 <1U2kIC-000W2w-ID>; Tue, 05 Feb 2013 16:18:40 +0100 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1U2kIC-001c8U-6N>; Tue, 05 Feb 2013 16:18:40 +0100 Received: from EX02B.campus.fu-berlin.de ([130.133.170.133]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.02.0328.009; Tue, 5 Feb 2013 16:18:39 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] Problem with GCC 4.6.3 and seq_io.h Thread-Index: AQHOA6nTc8NPgJbtlEeJu/bgk+/OpZhrYIDW Message-ID: References: In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_FCCAB9D80C3DAB47B5601C5B0E62872B29437775ex02bcampusfube_" MIME-Version: 1.0 Date: Tue, 05 Feb 2013 16:18:37 +0100 X-Original-Date: Tue, 5 Feb 2013 15:18:37 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1360077520-00000B1F-27008363/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.2 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Problem with GCC 4.6.3 and seq_io.h X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 05 Feb 2013 15:18:42 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B29437775ex02bcampusfube_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear Walter, SeqAn should run with all modern GCC versions. You can see the current nigh= tly build status here: http://cdash.seqan.de/index.php?project=3DSeqAn However, we are currently building with g++-4.6.2 and not the x.3 variant. I will look into this. Cheers, Manuel ________________________________ From: Walter Pasiego [walter.pasiego@gmail.com] Sent: Tuesday, February 05, 2013 3:04 PM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] Problem with GCC 4.6.3 and seq_io.h Dear Colleagues, I'm starting to play around with SeqAn using the last version available at = the svn repo. I'm using Linux with gcc 4.6.3 and Eclipse. So far I succeeded compiling and running an example with the following head= ers: #include #include #include but as soon as I try another example with: #include the compilers complains with: /src/seqan-trunk/core/include/seqan/store/store_io_sam.h: In function =91bo= ol seqan::operator<(const seqan::CigarElement&, const s= eqan::CigarElement&)=92: /src/seqan-trunk/core/include/seqan/store/store_io_sam.h:120:96: error: =91= .=92 cannot appear in a constant-expression Using the include file (the "musketeer" header file) provokes mor= e errors to shown up. Can anyone please help me and tell if: 1) possibly I am doing something wrong 2) the trunk version of the SeqAn library is still incompatible with gcc 4.= ?.? 3) there is a workaround? Is there a recommended compiler-version? Many thanks in advance! Walter --_000_FCCAB9D80C3DAB47B5601C5B0E62872B29437775ex02bcampusfube_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Dear Walter,

SeqAn should run with all modern GCC versions. You can see the current= nightly build status here:


However, we are currently building with g++-4.6.2 and not the = x.3 variant.

I will look into this.

Cheers,
Manuel

From: Walter Pasiego [walter.pasiego@gmai= l.com]
Sent: Tuesday, February 05, 2013 3:04 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Problem with GCC 4.6.3 and seq_io.h

Dear Colleagues,

I'm starting to play around with SeqAn using the last version available at = the svn repo.
I'm using Linux with gcc 4.6.3 and Eclipse.
So far I succeeded compiling and running an example with the following head= ers:
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/file.h>

but as soon as I try another example with:
#include <seqan/seq_io.h>

the compilers complains with:

/src/seqan-trunk/core/include/seqan/store/store_io_sam.h: In function =91bo= ol seqan::operator<(const seqan::CigarElement<TOperation, TCount>&= amp;, const seqan::CigarElement<TOperation, TCount>&)=92:
/src/seqan-trunk/core/include/seqan/store/store_io_sam.h:120:96: error: = =91.=92 cannot appear in a constant-expression

Using the include file <seqan.h> (the "musketeer" header fi= le) provokes more errors to shown up.

Can anyone please help me and tell if:
1) possibly I am doing something wrong
2) the trunk version of the SeqAn library is still incompatible with g= cc 4.?.?
3) there is a workaround? Is there a recommended compiler-version?

Many thanks in advance!

Walter
--_000_FCCAB9D80C3DAB47B5601C5B0E62872B29437775ex02bcampusfube_-- From manuel.holtgrewe@fu-berlin.de Tue Feb 05 18:12:07 2013 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 <1U2m3v-002SDT-LF>; Tue, 05 Feb 2013 18:12:03 +0100 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 <1U2m3v-0012lj-Hv>; Tue, 05 Feb 2013 18:12:03 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1U2m3v-001sin-58>; Tue, 05 Feb 2013 18:12:03 +0100 Received: from EX02B.campus.fu-berlin.de ([130.133.170.133]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.02.0328.009; Tue, 5 Feb 2013 18:12:02 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] Problem with GCC 4.6.3 and seq_io.h Thread-Index: AQHOA6nTc8NPgJbtlEeJu/bgk+/OpZhrYIDWgAAfmVo= Message-ID: References: , In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_FCCAB9D80C3DAB47B5601C5B0E62872B294377E4ex02bcampusfube_" MIME-Version: 1.0 Date: Tue, 05 Feb 2013 18:12:01 +0100 X-Original-Date: Tue, 5 Feb 2013 17:12:01 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1360084323-00000B1F-C40B3BA2/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.2 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Problem with GCC 4.6.3 and seq_io.h X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 05 Feb 2013 17:12:07 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B294377E4ex02bcampusfube_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear Walter, I just compiled all tests and apps with GCC 4.6.3 and this works. Can you post your whole program here? I assume you followed the instructions here? http://trac.seqan.de/wiki/Tutorial/GettingStarted/LinuxEclipse Cheers, Manuel ________________________________ From: Holtgrewe, Manuel [manuel.holtgrewe@fu-berlin.de] Sent: Tuesday, February 05, 2013 4:18 PM To: SeqAn Development Subject: Re: [Seqan-dev] Problem with GCC 4.6.3 and seq_io.h Dear Walter, SeqAn should run with all modern GCC versions. You can see the current nigh= tly build status here: http://cdash.seqan.de/index.php?project=3DSeqAn However, we are currently building with g++-4.6.2 and not the x.3 variant. I will look into this. Cheers, Manuel ________________________________ From: Walter Pasiego [walter.pasiego@gmail.com] Sent: Tuesday, February 05, 2013 3:04 PM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] Problem with GCC 4.6.3 and seq_io.h Dear Colleagues, I'm starting to play around with SeqAn using the last version available at = the svn repo. I'm using Linux with gcc 4.6.3 and Eclipse. So far I succeeded compiling and running an example with the following head= ers: #include #include #include but as soon as I try another example with: #include the compilers complains with: /src/seqan-trunk/core/include/seqan/store/store_io_sam.h: In function =91bo= ol seqan::operator<(const seqan::CigarElement&, const s= eqan::CigarElement&)=92: /src/seqan-trunk/core/include/seqan/store/store_io_sam.h:120:96: error: =91= .=92 cannot appear in a constant-expression Using the include file (the "musketeer" header file) provokes mor= e errors to shown up. Can anyone please help me and tell if: 1) possibly I am doing something wrong 2) the trunk version of the SeqAn library is still incompatible with gcc 4.= ?.? 3) there is a workaround? Is there a recommended compiler-version? Many thanks in advance! Walter --_000_FCCAB9D80C3DAB47B5601C5B0E62872B294377E4ex02bcampusfube_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Dear Walter,

I just compiled all tests and apps with GCC 4.6.3 and this works.

Can you post your whole program here?

I assume you followed the instructions here?


Cheers,
Manuel

From: Holtgrewe, Manuel [manuel.holtgrewe= @fu-berlin.de]
Sent: Tuesday, February 05, 2013 4:18 PM
To: SeqAn Development
Subject: Re: [Seqan-dev] Problem with GCC 4.6.3 and seq_io.h

Dear Walter,

SeqAn should run with all modern GCC versions. You can see the current= nightly build status here:


However, we are currently building with g++-4.6.2 and not the = x.3 variant.

I will look into this.

Cheers,
Manuel

From: Walter Pasiego [walter.pasiego@gmail.= com]
Sent: Tuesday, February 05, 2013 3:04 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Problem with GCC 4.6.3 and seq_io.h

Dear Colleagues,

I'm starting to play around with SeqAn using the last version available at = the svn repo.
I'm using Linux with gcc 4.6.3 and Eclipse.
So far I succeeded compiling and running an example with the following head= ers:
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/file.h>

but as soon as I try another example with:
#include <seqan/seq_io.h>

the compilers complains with:

/src/seqan-trunk/core/include/seqan/store/store_io_sam.h: In function =91bo= ol seqan::operator<(const seqan::CigarElement<TOperation, TCount>&= amp;, const seqan::CigarElement<TOperation, TCount>&)=92:
/src/seqan-trunk/core/include/seqan/store/store_io_sam.h:120:96: error: = =91.=92 cannot appear in a constant-expression

Using the include file <seqan.h> (the "musketeer" header fi= le) provokes more errors to shown up.

Can anyone please help me and tell if:
1) possibly I am doing something wrong
2) the trunk version of the SeqAn library is still incompatible with g= cc 4.?.?
3) there is a workaround? Is there a recommended compiler-version?

Many thanks in advance!

Walter
--_000_FCCAB9D80C3DAB47B5601C5B0E62872B294377E4ex02bcampusfube_-- From jer15@hermes.cam.ac.uk Wed Feb 06 23:32:12 2013 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 <1U3DXH-0003rb-8B>; Wed, 06 Feb 2013 23:32:11 +0100 Received: from ppsw-51.csi.cam.ac.uk ([131.111.8.151]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1U3DXH-002fbU-3r>; Wed, 06 Feb 2013 23:32:11 +0100 X-Cam-AntiVirus: no malware found X-Cam-SpamDetails: not scanned X-Cam-ScannerInfo: http://www.ucs.cam.ac.uk/email/scanner/ Received: from cpc6-dals15-2-0-cust115.hari.cable.virginmedia.com ([82.35.196.116]:50914 helo=[192.168.1.16]) by ppsw-51.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.158]:587) with esmtpsa (PLAIN:jer15) (TLSv1:DHE-RSA-CAMELLIA256-SHA:256) id 1U3DXF-00083y-XR (Exim 4.72) for seqan-dev@lists.fu-berlin.de (return-path ); Wed, 06 Feb 2013 22:32:09 +0000 Message-ID: <5112D9E8.2020004@mail.cryst.bbk.ac.uk> Date: Wed, 06 Feb 2013 22:32:08 +0000 From: John Reid User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:17.0) Gecko/20130106 Thunderbird/17.0.2 MIME-Version: 1.0 To: SeqAn Development Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Sender: "J.E. Reid" X-Originating-IP: 131.111.8.151 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1360189931-00000B1F-09220B3C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.117039, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.3 required=5.0 tests=RCVD_IN_DNSWL_MED X-Spam-Checker-Version: SpamAssassin 3.3.2 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Multiple definition problem X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 06 Feb 2013 22:32:12 -0000 Hi, I wonder if the latest svn version is missing some inline definitions. If I have two translation units: #include int main( int argc, char * argv [] ) { return 0; } and #include which I compile and link into an executable I get multiple definition errors: gcc.compile.c++ bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o "/home/john/src/stlfilt/gfilt" -ftemplate-depth-128 -Wno-deprecated -Wno-unused -Wno-error -O3 -finline-functions -Wno-inline -Wall -fPIC -Wno-deprecated -Wno-unused -DBOOST_FILESYSTEM_VERSION=3 -DBOOST_SYSTEM_DYN_LINK=1 -DMS_HAS_VALGRIND -DMYRRH_DISABLE_ASSERTS -DNDEBUG -DPVAL_LOOKUP -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_ENABLE_TESTING=0 -DUSING_GOOGLE_PROFILER -I"." -I"/home/john/Dev/STEME/c++/hmm" -I"/home/john/Dev/STEME/c++/myrrh" -I"/home/john/Dev/myrrh" -I"/home/john/src/boost/boost_1_51_0" -I"/home/john/src/boost/indexing_suite_v2" -I"/home/john/src/seqan/new-trunk/trunk/core/include" -I"/home/john/src/seqan/new-trunk/trunk/extras/include" -I"/usr/local/lib/python2.6/dist-packages/numpy/core/include" -I"include" -c -o "bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o" "sandbox/multiple_defs/translation_unit_1.cpp" gcc.compile.c++ bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o "/home/john/src/stlfilt/gfilt" -ftemplate-depth-128 -Wno-deprecated -Wno-unused -Wno-error -O3 -finline-functions -Wno-inline -Wall -fPIC -Wno-deprecated -Wno-unused -DBOOST_FILESYSTEM_VERSION=3 -DBOOST_SYSTEM_DYN_LINK=1 -DMS_HAS_VALGRIND -DMYRRH_DISABLE_ASSERTS -DNDEBUG -DPVAL_LOOKUP -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_ENABLE_TESTING=0 -DUSING_GOOGLE_PROFILER -I"." -I"/home/john/Dev/STEME/c++/hmm" -I"/home/john/Dev/STEME/c++/myrrh" -I"/home/john/Dev/myrrh" -I"/home/john/src/boost/boost_1_51_0" -I"/home/john/src/boost/indexing_suite_v2" -I"/home/john/src/seqan/new-trunk/trunk/core/include" -I"/home/john/src/seqan/new-trunk/trunk/extras/include" -I"/usr/local/lib/python2.6/dist-packages/numpy/core/include" -I"include" -c -o "bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o" "sandbox/multiple_defs/translation_unit_2.cpp" gcc.link bin/gcc-4.6/release/seqan_multiple_defs "/home/john/src/stlfilt/gfilt" -Wl,-R -Wl,"/home/john/src/boost/boost_1_51_0/bin.v2/libs/regex/build/gcc-4.6/release" -Wl,-R -Wl,"/home/john/src/boost/boost_1_51_0/bin.v2/libs/system/build/gcc-4.6/release" -Wl,-rpath-link -Wl,"/home/john/src/boost/boost_1_51_0/bin.v2/libs/regex/build/gcc-4.6/release" -Wl,-rpath-link -Wl,"/home/john/src/boost/boost_1_51_0/bin.v2/libs/system/build/gcc-4.6/release" -o "bin/gcc-4.6/release/seqan_multiple_defs" -Wl,--start-group "bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o" "bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o" "/home/john/src/boost/boost_1_51_0/bin.v2/libs/regex/build/gcc-4.6/release/libboost_regex.so.1.51.0" "/home/john/src/boost/boost_1_51_0/bin.v2/libs/system/build/gcc-4.6/release/libboost_system.so.1.51.0" -Wl,-Bstatic -Wl,-Bdynamic -lprofiler -lrt -Wl,--end-group bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In function `seqan::ManToolDocPrinter_::print(std::basic_ostream >&, seqan::ToolDoc const&)': translation_unit_2.cpp:(.text+0x820): multiple definition of `seqan::ManToolDocPrinter_::print(ostream &, seqan::ToolDoc const &)' bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0x820): first defined here bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In function `seqan::_indent(int)': translation_unit_2.cpp:(.text+0xcb0): multiple definition of `seqan::_indent(int)' bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0xcb0): first defined here bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In function `seqan::_writeCLIElement(std::basic_ofstream >&, int, std::basic_string, std::allocator > const&, std::basic_string, std::allocator > const&, bool)': translation_unit_2.cpp:(.text+0xd20): multiple definition of `seqan::_writeCLIElement(ofstream &, int, string const &, string const &, bool)' bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0xd20): first defined here bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In function `seqan::_addUsage(seqan::ToolDoc&, seqan::ArgumentParser const&)': translation_unit_2.cpp:(.text+0x1020): multiple definition of `seqan::_addUsage(seqan::ToolDoc &, seqan::ArgumentParser const &)' bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0x1020): first defined here bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In function `seqan::TextToolDocPrinter_::print(std::basic_ostream >&, seqan::ToolDoc const&)': translation_unit_2.cpp:(.text+0x1490): multiple definition of `seqan::TextToolDocPrinter_::print(ostream &, seqan::ToolDoc const &)' bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0x1490): first defined here bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In function `seqan::HtmlToolDocPrinter_::print(std::basic_ostream >&, seqan::ToolDoc const&)': translation_unit_2.cpp:(.text+0x1b10): multiple definition of `seqan::HtmlToolDocPrinter_::print(ostream &, seqan::ToolDoc const &)' bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0x1b10): first defined here collect2: ld returned 1 exit status ...failed updating 1 target... I'm using gcc 4.6.3 with seqan trunk revision 13539. Regards, John. From jer15@hermes.cam.ac.uk Wed Feb 06 23:38:49 2013 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 <1U3Ddf-0004DQ-Jw>; Wed, 06 Feb 2013 23:38:47 +0100 Received: from ppsw-51.csi.cam.ac.uk ([131.111.8.151]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1U3Ddf-002gJ8-E7>; Wed, 06 Feb 2013 23:38:47 +0100 X-Cam-AntiVirus: no malware found X-Cam-SpamDetails: not scanned X-Cam-ScannerInfo: http://www.ucs.cam.ac.uk/email/scanner/ Received: from cpc6-dals15-2-0-cust115.hari.cable.virginmedia.com ([82.35.196.116]:51133 helo=[192.168.1.16]) by ppsw-51.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.158]:587) with esmtpsa (PLAIN:jer15) (TLSv1:DHE-RSA-CAMELLIA256-SHA:256) id 1U3Dde-0000rZ-Wf (Exim 4.72) for seqan-dev@lists.fu-berlin.de (return-path ); Wed, 06 Feb 2013 22:38:46 +0000 Message-ID: <5112DB75.7080304@mail.cryst.bbk.ac.uk> Date: Wed, 06 Feb 2013 22:38:45 +0000 From: John Reid User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:17.0) Gecko/20130106 Thunderbird/17.0.2 MIME-Version: 1.0 To: SeqAn Development References: <5112D9E8.2020004@mail.cryst.bbk.ac.uk> In-Reply-To: <5112D9E8.2020004@mail.cryst.bbk.ac.uk> Content-Type: multipart/mixed; boundary="------------010802090902030200030407" Sender: "J.E. Reid" X-Originating-IP: 131.111.8.151 X-ZEDAT-Hint: A X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1360190327-00000B1F-F11D91DB/3782052108-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.017115, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-1.3 required=5.0 tests=FU_XPURGATE_SUSP, RCVD_IN_DNSWL_MED X-Spam-Checker-Version: SpamAssassin 3.3.2 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Multiple definition problem X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 06 Feb 2013 22:38:49 -0000 This is a multi-part message in MIME format. --------------010802090902030200030407 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit The attached patch seems to fix the problem. John. On 06/02/13 22:32, John Reid wrote: > Hi, > > I wonder if the latest svn version is missing some inline definitions. > If I have two translation units: > > #include > > int > main( int argc, char * argv [] ) { > return 0; > } > > and > > #include > > which I compile and link into an executable I get multiple definition > errors: > > gcc.compile.c++ > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o > > "/home/john/src/stlfilt/gfilt" -ftemplate-depth-128 -Wno-deprecated > -Wno-unused -Wno-error -O3 -finline-functions -Wno-inline -Wall -fPIC > -Wno-deprecated -Wno-unused -DBOOST_FILESYSTEM_VERSION=3 > -DBOOST_SYSTEM_DYN_LINK=1 -DMS_HAS_VALGRIND -DMYRRH_DISABLE_ASSERTS > -DNDEBUG -DPVAL_LOOKUP -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_ENABLE_TESTING=0 > -DUSING_GOOGLE_PROFILER -I"." -I"/home/john/Dev/STEME/c++/hmm" > -I"/home/john/Dev/STEME/c++/myrrh" -I"/home/john/Dev/myrrh" > -I"/home/john/src/boost/boost_1_51_0" > -I"/home/john/src/boost/indexing_suite_v2" > -I"/home/john/src/seqan/new-trunk/trunk/core/include" > -I"/home/john/src/seqan/new-trunk/trunk/extras/include" > -I"/usr/local/lib/python2.6/dist-packages/numpy/core/include" > -I"include" -c -o > "bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o" > "sandbox/multiple_defs/translation_unit_1.cpp" > > gcc.compile.c++ > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o > > "/home/john/src/stlfilt/gfilt" -ftemplate-depth-128 -Wno-deprecated > -Wno-unused -Wno-error -O3 -finline-functions -Wno-inline -Wall -fPIC > -Wno-deprecated -Wno-unused -DBOOST_FILESYSTEM_VERSION=3 > -DBOOST_SYSTEM_DYN_LINK=1 -DMS_HAS_VALGRIND -DMYRRH_DISABLE_ASSERTS > -DNDEBUG -DPVAL_LOOKUP -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_ENABLE_TESTING=0 > -DUSING_GOOGLE_PROFILER -I"." -I"/home/john/Dev/STEME/c++/hmm" > -I"/home/john/Dev/STEME/c++/myrrh" -I"/home/john/Dev/myrrh" > -I"/home/john/src/boost/boost_1_51_0" > -I"/home/john/src/boost/indexing_suite_v2" > -I"/home/john/src/seqan/new-trunk/trunk/core/include" > -I"/home/john/src/seqan/new-trunk/trunk/extras/include" > -I"/usr/local/lib/python2.6/dist-packages/numpy/core/include" > -I"include" -c -o > "bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o" > "sandbox/multiple_defs/translation_unit_2.cpp" > > gcc.link bin/gcc-4.6/release/seqan_multiple_defs > > "/home/john/src/stlfilt/gfilt" -Wl,-R > -Wl,"/home/john/src/boost/boost_1_51_0/bin.v2/libs/regex/build/gcc-4.6/release" > -Wl,-R > -Wl,"/home/john/src/boost/boost_1_51_0/bin.v2/libs/system/build/gcc-4.6/release" > -Wl,-rpath-link > -Wl,"/home/john/src/boost/boost_1_51_0/bin.v2/libs/regex/build/gcc-4.6/release" > -Wl,-rpath-link > -Wl,"/home/john/src/boost/boost_1_51_0/bin.v2/libs/system/build/gcc-4.6/release" > -o "bin/gcc-4.6/release/seqan_multiple_defs" -Wl,--start-group > "bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o" > "bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o" > "/home/john/src/boost/boost_1_51_0/bin.v2/libs/regex/build/gcc-4.6/release/libboost_regex.so.1.51.0" > "/home/john/src/boost/boost_1_51_0/bin.v2/libs/system/build/gcc-4.6/release/libboost_system.so.1.51.0" > -Wl,-Bstatic -Wl,-Bdynamic -lprofiler -lrt -Wl,--end-group > > > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In > function `seqan::ManToolDocPrinter_::print(std::basic_ostream std::char_traits >&, seqan::ToolDoc const&)': > translation_unit_2.cpp:(.text+0x820): multiple definition of > `seqan::ManToolDocPrinter_::print(ostream &, seqan::ToolDoc const &)' > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0x820): > first defined here > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In > function `seqan::_indent(int)': > translation_unit_2.cpp:(.text+0xcb0): multiple definition of > `seqan::_indent(int)' > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0xcb0): > first defined here > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In > function `seqan::_writeCLIElement(std::basic_ofstream std::char_traits >&, int, std::basic_string s, std::allocator > const&, std::basic_string std::char_traits, std::allocator > const&, bool)': > translation_unit_2.cpp:(.text+0xd20): multiple definition of > `seqan::_writeCLIElement(ofstream &, int, string const &, string const > &, bool)' > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0xd20): > first defined here > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In > function `seqan::_addUsage(seqan::ToolDoc&, seqan::ArgumentParser const&)': > translation_unit_2.cpp:(.text+0x1020): multiple definition of > `seqan::_addUsage(seqan::ToolDoc &, seqan::ArgumentParser const &)' > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0x1020): > first defined here > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In > function `seqan::TextToolDocPrinter_::print(std::basic_ostream std::char_traits >&, seqan::ToolDoc const&)': > translation_unit_2.cpp:(.text+0x1490): multiple definition of > `seqan::TextToolDocPrinter_::print(ostream &, seqan::ToolDoc const &)' > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0x1490): > first defined here > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_2.o: In > function `seqan::HtmlToolDocPrinter_::print(std::basic_ostream std::char_traits >&, seqan::ToolDoc const&)': > translation_unit_2.cpp:(.text+0x1b10): multiple definition of > `seqan::HtmlToolDocPrinter_::print(ostream &, seqan::ToolDoc const &)' > bin/gcc-4.6/release/sandbox/multiple_defs/translation_unit_1.o:translation_unit_1.cpp:(.text+0x1b10): > first defined here > collect2: ld returned 1 exit status > ...failed updating 1 target... > > I'm using gcc 4.6.3 with seqan trunk revision 13539. > > Regards, > John. --------------010802090902030200030407 Content-Type: text/x-patch; name="fix-multiple-defs.diff" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="fix-multiple-defs.diff" Index: core/include/seqan/arg_parse/arg_parse_doc.h =================================================================== --- core/include/seqan/arg_parse/arg_parse_doc.h (revision 13539) +++ core/include/seqan/arg_parse/arg_parse_doc.h (working copy) @@ -167,7 +167,7 @@ // Helper Function _addUsage() // ---------------------------------------------------------------------------- -void _addUsage(ToolDoc & toolDoc, ArgumentParser const & me) +inline void _addUsage(ToolDoc & toolDoc, ArgumentParser const & me) { for (unsigned i = 0; i < length(me._usageText); ++i) { Index: core/include/seqan/arg_parse/arg_parse_ctd_support.h =================================================================== --- core/include/seqan/arg_parse/arg_parse_ctd_support.h (revision 13539) +++ core/include/seqan/arg_parse/arg_parse_ctd_support.h (working copy) @@ -182,7 +182,7 @@ // Function _indent() // ---------------------------------------------------------------------------- -std::string _indent(const int currentIndent) +inline std::string _indent(const int currentIndent) { std::string indent = ""; for (int i = 0; i < currentIndent; ++i) @@ -190,7 +190,7 @@ return indent; } -void _writeCLIElement(std::ofstream & ctdfile, int currentIndent, std::string const & optionIdentifier, std::string const & ref_name, bool isList) +inline void _writeCLIElement(std::ofstream & ctdfile, int currentIndent, std::string const & optionIdentifier, std::string const & ref_name, bool isList) { ctdfile << _indent(currentIndent) << " out(stream); @@ -1316,7 +1316,7 @@ stream << "Last update " << doc._date << "\n"; } -void ManToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc) +inline void ManToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc) { std::ostream_iterator out(stream); --------------010802090902030200030407-- From okko73313@gmail.com Tue Feb 12 12:29:14 2013 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 <1U5E2z-003YZw-8p>; Tue, 12 Feb 2013 12:29:13 +0100 Received: from mail-ia0-f179.google.com ([209.85.210.179]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1U5E2z-000HJZ-32>; Tue, 12 Feb 2013 12:29:13 +0100 Received: by mail-ia0-f179.google.com with SMTP id x24so7435478iak.10 for ; Tue, 12 Feb 2013 03:29:10 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:x-received:reply-to:sender:date:x-google-sender-auth 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151147::1360668553-00000B1F-5963E6BC/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000609, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM, FSL_FREEMAIL_1, FSL_FREEMAIL_2,RCVD_IN_DNSWL_LOW,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.2 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] questions about FindPattern X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: k.okonechnikov@gmail.com, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 12 Feb 2013 11:29:14 -0000 Hi! Here is a simple code extract: vector StringUtils::findDnaPattern(const CharString& query, const CharString &source, int minScore) { using namespace seqan; vector results; // Question:Why do we have to copy to be able perform search!? CharString sourceCopy(source); CharString queryCopy(query); Finder directFinder(sourceCopy); Pattern > pattern(queryCopy, SimpleScore(0, -2, -1)); while (seqan::find(directFinder, pattern, minScore)) { while (seqan::findBegin(directFinder, pattern, getScore(pattern))) { // Question: how do I get the score of the alignment? SearchResult r(beginPosition(directFinder), true); results.push_back(r); } } seqan::reverseComplement(queryCopy); Pattern > revPattern(queryCopy, SimpleScore(0, -2, -1)); Finder revFinder(sourceCopy); while (seqan::find(revFinder, revPattern, minScore)) { while (seqan::findBegin(revFinder, revPattern, getScore(revPattern))) { SearchResult r(beginPosition(revFinder), false); results.push_back(r); } } return results; } Questions are the following: 1) How is it possible to instance Pattern and Finder objects using const references? Code doesn't compile if I am not copying the sequences. 2) How can I get the score of the alignment (while iterating over pattern results)? 3) Is there an easier way to search for pattern in reverse complement sequence? Env: Ubuntu 12.04, gcc 4.7, seqan rev 13572 Thanks in advance, Konstantin From rene.maerker@fu-berlin.de Tue Feb 12 17:58:04 2013 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 <1U5JBD-0009im-4S>; Tue, 12 Feb 2013 17:58:03 +0100 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 <1U5JBD-003UdB-2Z>; Tue, 12 Feb 2013 17:58:03 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1U5JBC-003Xhb-OX>; Tue, 12 Feb 2013 17:58:03 +0100 Received: from EX03B.campus.fu-berlin.de ([130.133.170.135]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.02.0328.009; Tue, 12 Feb 2013 17:58:01 +0100 From: =?iso-8859-1?Q?Rahn=2C_Ren=E9?= To: SeqAn Development Thread-Topic: Replacement of the old alignment algorithms Thread-Index: AQHOCUId+XKGg46Y7kGe1RZc+cyWKg== Message-ID: <1E17D2681681D24D9E09E2B9A726C6D4448A4EB1@ex03b.campus.fu-berlin.de> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_1E17D2681681D24D9E09E2B9A726C6D4448A4EB1ex03bcampusfube_" MIME-Version: 1.0 Date: Tue, 12 Feb 2013 17:57:59 +0100 X-Original-Date: Tue, 12 Feb 2013 16:57:59 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1360688283-00000B1F-DF166BFD/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.012061, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.2 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Replacement of the old alignment algorithms X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 12 Feb 2013 16:58:04 -0000 --_000_1E17D2681681D24D9E09E2B9A726C6D4448A4EB1ex03bcampusfube_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear SeqAn developer, as already announced in December 2012, we have now removed the old alignmen= t algorithms from the current trunk version. If you have troubles or find some unexpected behavior, please let me know s= o I can assist you to migrate your code to the new implementation. Kind regards, Ren=E9 Rahn --- Ren=E9 Rahn Ph.D. Student ------------------------------------------------ rene.rahn@fu-berlin.de +49 (0)30 838 75 277 ------------------------------------------------ Algorithmic Bioinformatics (ABI) Department of Informatics Room 018 ------------------------------------------------ Freie Universit=E4t Berlin Takustra=DFe 9 14195 Berlin ------------------------------------------------ --_000_1E17D2681681D24D9E09E2B9A726C6D4448A4EB1ex03bcampusfube_ Content-Type: text/html; charset="iso-8859-1" Content-ID: Content-Transfer-Encoding: quoted-printable Dear SeqAn developer, 

as already announced in December 2012, we have now removed the old ali= gnment algorithms from the current trunk version. 
If you have troubles or find some unexpected behavior, please let me k= now so I can assist you to migrate your code to the new implementation.

Kind regards,

Ren=E9 Rahn

---

Ren=E9 Rahn
Ph.D. Student
------------------------------------------------
rene.rahn@fu-berlin.de
+49 (0)30 838 75 277
------------------------------------------------
Algorithmic Bioinformatics (ABI)
Department of Informatics 
Room  018
------------------------------------------------
Freie Universit=E4t Berlin
Takustra=DFe 9 
14195 Berlin
------------------------------------------------




--_000_1E17D2681681D24D9E09E2B9A726C6D4448A4EB1ex03bcampusfube_-- From nzshjamil@yahoo.com Thu Feb 28 15:26:39 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UB4RS-003lNr-35>; Thu, 28 Feb 2013 15:26:38 +0100 Received: from nm8-vm0.bullet.mail.bf1.yahoo.com ([98.139.213.95]) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with smtp (envelope-from ) id <1UB4RR-002XBz-Oc>; Thu, 28 Feb 2013 15:26:38 +0100 Received: from [98.139.212.152] by nm8.bullet.mail.bf1.yahoo.com with NNFMP; 28 Feb 2013 14:26:35 -0000 Received: from [98.139.212.238] by tm9.bullet.mail.bf1.yahoo.com with NNFMP; 28 Feb 2013 14:26:35 -0000 Received: from [127.0.0.1] by omp1047.mail.bf1.yahoo.com with NNFMP; 28 Feb 2013 14:26:35 -0000 X-Yahoo-Newman-Property: ymail-3 X-Yahoo-Newman-Id: 746259.6407.bm@omp1047.mail.bf1.yahoo.com Received: (qmail 87265 invoked by uid 60001); 28 Feb 2013 14:26:35 -0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=yahoo.com; s=s1024; t=1362061595; bh=cVDe5PB9uksSwZ6hSg31/p00brw5rqv+PvsjTb3vL1I=; h=X-YMail-OSG:Received:X-Rocket-MIMEInfo:X-Mailer:Message-ID:Date:From:Reply-To:Subject:To:MIME-Version:Content-Type; b=fYMdGy43RqAhS8371qJifd08eehP6yqJQ6KhWhq7juuAJ0MsEegD1yTlIiI/cqr0sKLkm6Xm03V6ZNWtZwLEhUgTxz7X3A1HXMVrdpIR6xSpazXwPJ/K/QdFI58Hm0xsx5jp/5k653Od3A/kBqvFB+bMB/CjlKTd2G7gXxSb3nU= DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=X-YMail-OSG:Received:X-Rocket-MIMEInfo:X-Mailer:Message-ID:Date:From:Reply-To:Subject:To:MIME-Version:Content-Type; b=kuFYFaYL/Xe0ZzZtisq80OhG4yVq4AvRMeZ2uCtGkLjuiTPL0Q8vFPayNNwwAsNMvDDDozMk5fdYdEIRwNb9XFUQFwco6RoXqpd7Zd8sIwZ74jZO3K29cK5JcoVty+JxuQcX+nb+bAs62UuYTHOgHwx9mTldfC1urkD+tMmIlMk=; X-YMail-OSG: GQljPMcVM1nHQ3ToK0Zwl0ji292xt5fvBAfi.gEl89rdd.I jG9W2KUE75KJtFd5NHQ1ScwnBeFytkhwOGsWutEXJUYC_WICnqVZbbVKvsVY ptJYOqu_eBF28ifw3Kvn8Owts_kEra5i4sD3zk560dy.JaO6x4PIXmg.fLKC FM0eFo9Nwm_eevPFAJfum4GTzNsgHaogBrd0Nrhg3ohuRYuCfFwqD6xF0559 8qv3sDbnzsJmZdx80oM1_zgRodW0vFrAECRXfSGjfaCzBImufT.zKZOU3PrB 9V9twZvbXifYfAJeY5T.xdWRSsS4JJb73NeEdMWYVR5Xj22.biRiFZkdESOK 3P1Y0SLUHwBBPYqcWmeN9IwUDd4NcJS5pEZPUdlNkguOXrbooDuSsIk.SSb1 Od9X0_i6QW1xHI1tChuBaq0qzWG4I8tHdZbX8620T3.OB09cQpJ2Ov8KzM6C uhduYOJLbxaUR9QaiaMmwaP2Fj0VEbQcN5o_YanQIZfitdwtx7dK79fcuJg- - Received: from [182.185.127.162] by web160706.mail.bf1.yahoo.com via HTTP; Thu, 28 Feb 2013 06:26:35 PST X-Rocket-MIMEInfo: 001.001, aGVsbG8saSBoYXZlIHByb2JsZW0gd2hlbiBpbmNsdWRpbmcgc2VxQW4gbGlicmFyeSB0byBEZXYgYysrID8_P3BsZWFzZSBoZWxwIG1lIGluIGluY2x1ZGluZyB0aGlzIGxpYnJhcnk_Pz8gYWN0dWFsbHkgb3VyIHByb2plY3QgaXMgZGVzaWduaW5nIHNvZnR3YXJlIGZvciBNUFNBKG11bHRpcGxlIHByb3RlaW4gc2VxdWVuY2UgYWxpZ25tZW50KS4uLnRoYXRzd2h5IHdlIGFyZSBpbnRlcnN0ZWQgaW4gdXNpbmcgc2VxYW4gbGlicmFyeT8_Pz95b3UgaGF2ZSBhbnkgc29sdXRpb24gZm9yIHRoaXMgcHJvYmxlbSABMAEBAQE- X-Mailer: YahooMailWebService/0.8.135.514 Message-ID: <1362061595.86170.YahooMailNeo@web160706.mail.bf1.yahoo.com> Date: Thu, 28 Feb 2013 06:26:35 -0800 (PST) From: Nazish Jamil To: "seqan-dev@lists.fu-berlin.de" MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="-2109272776-46016797-1362061595=:86170" X-Originating-IP: 98.139.213.95 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1362061598-00000B1F-EAFD4649/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.500041, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=1.5 required=5.0 tests=FREEMAIL_FROM, FSL_FREEMAIL_1, FSL_FREEMAIL_2, FU_BOGO_UNSURE, HTML_MESSAGE, RCVD_IN_DNSWL_NONE, T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.2 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: x Subject: [Seqan-dev] having problem in including seqan library to dev c++ X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: Nazish Jamil , SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 28 Feb 2013 14:26:39 -0000 ---2109272776-46016797-1362061595=:86170 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable hello,i have problem when including seqAn library to Dev c++ ???please help= me in including this library??? actually our project is designing software= for MPSA(multiple protein sequence alignment)...thatswhy we are intersted = in using seqan library????you have any solution for this problem or suggest= any other IDE for seqan=A0=0A=A0thanks=A0 ---2109272776-46016797-1362061595=:86170 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
hello,i have pro= blem when including seqAn library to Dev c++ ???please help me in including= this library??? actually our project is designing software for MPSA(multip= le protein sequence alignment)...thatswhy we are intersted in using seqan l= ibrary????you have any solution for this problem or suggest any other IDE f= or seqan 
 thanks 
---2109272776-46016797-1362061595=:86170-- From nzshjamil@yahoo.com Thu Feb 28 15:43:54 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UB4i8-003miS-Sc>; Thu, 28 Feb 2013 15:43:52 +0100 Received: from nm33-vm7.bullet.mail.bf1.yahoo.com ([72.30.239.207]) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UB4i7-002b7f-OG>; Thu, 28 Feb 2013 15:43:52 +0100 Received: from [98.139.212.144] by nm33.bullet.mail.bf1.yahoo.com with NNFMP; 28 Feb 2013 14:43:49 -0000 Received: from [98.139.212.207] by tm1.bullet.mail.bf1.yahoo.com with NNFMP; 28 Feb 2013 14:43:49 -0000 Received: from [127.0.0.1] by omp1016.mail.bf1.yahoo.com with NNFMP; 28 Feb 2013 14:43:49 -0000 X-Yahoo-Newman-Property: ymail-3 X-Yahoo-Newman-Id: 425541.46337.bm@omp1016.mail.bf1.yahoo.com Received: (qmail 86821 invoked by uid 60001); 28 Feb 2013 14:43:49 -0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=yahoo.com; s=s1024; t=1362062629; bh=YPvLrC4ucqPc6cMAW7uUV9GZ40dkvAwJkgedcErM8To=; h=X-YMail-OSG:Received:X-Rocket-MIMEInfo:X-Mailer:References:Message-ID:Date:From:Reply-To:Subject:To:MIME-Version:Content-Type; b=eTzDgonEB4j0gIYO9xSdQE6cpGpHWYOHhHKmYFODtBATxmEOwAx6AfO+scFX63J1KOxPR5tMCeK/XcVNX2oW9dumGr06UbtZOkAd3GmLjPsdE0UQvHGI5J4lbuMcdbEKojt6JkU9ExgTSp+sSJKhdQ/ldpERU+d+IdI3tCq3OgY= DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=X-YMail-OSG:Received:X-Rocket-MIMEInfo:X-Mailer:References:Message-ID:Date:From:Reply-To:Subject:To:MIME-Version:Content-Type; b=RIduQv54jr10msirgA1z2w/8tvOFoxqWrsfpplmXRomrnWLoWzcQ3nNeZuNaa7CwU5W1J84LwidJ4ITo486el88asJor7dx2YCcxnoF0wFi8mXOuEySndPuFIJOrBVtDPv/v4QQtHCKMk2GKjuTIeiuHZi6TWgMtnZne9DeGWfI=; X-YMail-OSG: M8QBi0EVM1mxcV4Aj0IefJojn_ckYEhIpvpf3HixqNQkY5h zeIow0DkJ0BVvtSCXFr5K0cn010SSlxbWlkr.p8cJ4J14fAmzwv66PNEvgnP GLgp4ElfXHiIM.SPakdTKsVR54ORhu.x.IPUOR52TES80vI7Ga8l3PyqxO45 Hx_k5lAILduQvAe_l98rxmBHn987j_lxDGAerrt4b4ihjbR3XDi_VQDIVBHC i0tHdaTA5SdLhu.eDkN4LibgbL8daRfquDIKBSWgi2vxU8XteI9EWxVDzSSs iZabTj54AYl7Sbc2DaQcjU4cLEP099INFQqvuy0LSJK66FjS1fzVCPj76VTd a_ky6mtvXB3MRwQOQr_3aYVDJXGEeQ.MCwfNu71eyZhC1waq.UsSmUsfxY42 NnLonyzMjwiq1dEBdujDXpxOoKRmOIUkzyILRV9bdTwNcD5cAOKnzTzeOd8g aiBGPGJouSTd5AgbFoilzzVpCgSgHM7CCUUDn_QzeupZI.a3JAcJbryNfmQ- - Received: from [182.185.127.162] by web160705.mail.bf1.yahoo.com via HTTP; Thu, 28 Feb 2013 06:43:49 PST X-Rocket-MIMEInfo: 001.001, aGVsbG8saSBoYXZlIHByb2JsZW0gd2hlbiBpbmNsdWRpbmcgc2VxQW7CoGxpYnJhcnnCoHRvIERldiBjKysgPz8_cGxlYXNlIGhlbHAgbWUgaW4gaW5jbHVkaW5nIHRoaXMgbGlicmFyeT8_PyBhY3R1YWxseSBvdXIgcHJvamVjdCBpcyBkZXNpZ25pbmcgc29mdHdhcmUgZm9yIE1QU0EobXVsdGlwbGUgcHJvdGVpbiBzZXF1ZW5jZSBhbGlnbm1lbnQpLi4udGhhdHN3aHkgd2UgYXJlIGludGVyc3RlZCBpbiB1c2luZyBzZXFhbiBsaWJyYXJ5Pz8_P3lvdSBoYXZlIGFueSBzb2x1dGlvbiBmb3IgdGhpcyBwcm9ibGUBMAEBAQE- X-Mailer: YahooMailWebService/0.8.135.514 References: Message-ID: <1362062629.53755.YahooMailNeo@web160705.mail.bf1.yahoo.com> Date: Thu, 28 Feb 2013 06:43:49 -0800 (PST) From: Nazish Jamil To: "seqan-dev@lists.fu-berlin.de" MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="-630955406-325487221-1362062629=:53755" X-Originating-IP: 72.30.239.207 X-ZEDAT-Hint: A X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1362062632-00000B1F-3BE1F0F4/3805019453-0/0-1 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.492295, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=2.5 required=5.0 tests=FREEMAIL_FROM, FSL_FREEMAIL_1, FSL_FREEMAIL_2,FU_BOGO_UNSURE,FU_XPURGATE_SUSP,HTML_MESSAGE, RCVD_IN_DNSWL_NONE,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.2 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: xx Subject: [Seqan-dev] problem X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: Nazish Jamil , SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 28 Feb 2013 14:43:54 -0000 ---630955406-325487221-1362062629=:53755 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable hello,i have problem when including seqAn=A0library=A0to Dev c++ ???please = help me in including this library??? actually our project is designing soft= ware for MPSA(multiple protein sequence alignment)...thatswhy we are inters= ted in using seqan library????you have any solution for this problem or sug= gest any other IDE for seqan=A0=0A=A0thanks=A0 ---630955406-325487221-1362062629=:53755 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
hello,i have pro= blem when including seqAn library to Dev c++ ???please help me in including this li= brary??? actually our project is designing software for MPSA(multiple prote= in sequence alignment)...thatswhy we are intersted in using seqan library??= ??you have any solution for this problem or suggest any other IDE for seqan=  
 thanks 
=
---630955406-325487221-1362062629=:53755-- From rene.maerker@fu-berlin.de Thu Feb 28 15:46:27 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UB4kc-003muT-6D>; Thu, 28 Feb 2013 15:46:26 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) with esmtp (envelope-from ) id <1UB4kc-003CsA-46>; Thu, 28 Feb 2013 15:46:26 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) with esmtp (envelope-from ) id <1UB4kb-001uVe-Oq>; Thu, 28 Feb 2013 15:46:26 +0100 Received: from EX03A.campus.fu-berlin.de ([130.133.170.134]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0123.003; Thu, 28 Feb 2013 15:46:23 +0100 From: =?iso-8859-1?Q?Rahn=2C_Ren=E9?= To: Nazish Jamil , SeqAn Development Thread-Topic: [Seqan-dev] having problem in including seqan library to dev c++ Thread-Index: AQHOFb+lhsXKaW+bwUes6El3XmACQJiPSH0A Message-ID: <0E0C86E7-EC43-4665-9DFB-1BBFA6C4AD11@fu-berlin.de> References: <1362061595.86170.YahooMailNeo@web160706.mail.bf1.yahoo.com> In-Reply-To: <1362061595.86170.YahooMailNeo@web160706.mail.bf1.yahoo.com> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_0E0C86E7EC4346659DFB1BBFA6C4AD11fuberlinde_" MIME-Version: 1.0 Date: Thu, 28 Feb 2013 15:46:22 +0100 X-Original-Date: Thu, 28 Feb 2013 14:46:22 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1362062786-00000B1F-18CDB233/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.349771, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.2 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] having problem in including seqan library to dev c++ X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 28 Feb 2013 14:46:27 -0000 --_000_0E0C86E7EC4346659DFB1BBFA6C4AD11fuberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Nazish, I also tried Dev c++ once, but couldn't find appropriate support within the= cmake system for this IDE so I let it go. As far as I remember KDevelop se= ems to work and if you are working on a windows machine, we strongly recomm= end to use visual studio (the express version is free of charge). If you ar= e working on a mac os, we recommend to use Xcode. Personally, I work with E= clipse which runs smooth on all systems as long as you have enough RAM (min= imum should be 4 GB). You can find more support on the website: http://trac.seqan.de/wiki/Tutoria= l/GettingStarted. Note, that eclipse on windows works just fine but is a little bit more comp= licated to set up. On the wiki page linked above you'll also find some instructions of how to = bind our library in to your project, so you can use your own build system i= f you want. Please, let us know if we can be of any more help. Kind regards, Ren=E9 Rahn On Feb 28, 2013, at 3:26 PM, Nazish Jamil wrote: hello,i have problem when including seqAn library to Dev c++ ???please help= me in including this library??? actually our project is designing software= for MPSA(multiple protein sequence alignment)...thatswhy we are intersted = in using seqan library????you have any solution for this problem or suggest= any other IDE for seqan thanks _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev --- Ren=E9 Rahn Ph.D. Student ------------------------------------------------ rene.rahn@fu-berlin.de +49 (0)30 838 75 277 ------------------------------------------------ Algorithmic Bioinformatics (ABI) Department of Informatics Room 018 ------------------------------------------------ Freie Universit=E4t Berlin Takustra=DFe 9 14195 Berlin ------------------------------------------------ --_000_0E0C86E7EC4346659DFB1BBFA6C4AD11fuberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-ID: Content-Transfer-Encoding: quoted-printable Dear Nazish,

I also tried Dev c++ once, but couldn't find appropriate suppo= rt within the cmake system for this IDE so I let it go. As far as I remembe= r KDevelop seems to work and if you are working on a windows machine, we st= rongly recommend to use visual studio (the express version is free of charge). If you are working on a mac os, we rec= ommend to use Xcode. Personally, I work with Eclipse which runs smooth on a= ll systems as long as you have enough RAM (minimum should be 4 GB).
You can find more support on the website: http://trac.seqan.de/wiki/Tutorial/G= ettingStarted.
Note, that eclipse on windows works just fine but is a little bit more= complicated to set up.
On the wiki page linked above you'll also find some instructions of ho= w to bind our library in to your project, so you can use your own build sys= tem if you want.

Please, let us know if we can be of any more help.

Kind regards,

Ren=E9 Rahn

On Feb 28, 2013, at 3:26 PM, Nazish Jamil wrote:

hello,i have problem when including seqAn library to Dev c++ ?= ??please help me in including this library??? actually our project is desig= ning software for MPSA(multiple protein sequence alignment)...thatswhy we a= re intersted in using seqan library????you have any solution for this problem or suggest any other IDE for seqan = ;
 thanks 
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev


---

Ren=E9 Rahn
Ph.D. Student
------------------------------------------------
rene.rahn@fu-berlin.de
+49 (0)30 838 75 277
------------------------------------------------
Algorithmic Bioinformatics (ABI)
Department of Informatics 
Room  018
------------------------------------------------
Freie Universit=E4t Berlin
Takustra=DFe 9 
14195 Berlin
------------------------------------------------




--_000_0E0C86E7EC4346659DFB1BBFA6C4AD11fuberlinde_-- From nzshjamil@yahoo.com Thu Feb 28 15:57:33 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UB4vL-003o6M-QS>; Thu, 28 Feb 2013 15:57:31 +0100 Received: from nm13.bullet.mail.bf1.yahoo.com ([98.139.212.172]) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with smtp (envelope-from ) id <1UB4vL-002dyv-78>; Thu, 28 Feb 2013 15:57:31 +0100 Received: from [98.139.215.142] by nm13.bullet.mail.bf1.yahoo.com with NNFMP; 28 Feb 2013 14:57:29 -0000 Received: from [98.139.212.245] by tm13.bullet.mail.bf1.yahoo.com with NNFMP; 28 Feb 2013 14:57:29 -0000 Received: from [127.0.0.1] by omp1054.mail.bf1.yahoo.com with NNFMP; 28 Feb 2013 14:57:29 -0000 X-Yahoo-Newman-Property: ymail-3 X-Yahoo-Newman-Id: 12894.18434.bm@omp1054.mail.bf1.yahoo.com Received: (qmail 74671 invoked by uid 60001); 28 Feb 2013 14:57:28 -0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=yahoo.com; s=s1024; t=1362063448; bh=Dk2IStQ740xaPr1oPZK1PVJbEDcTuiElz8tZaxtGQ5I=; h=X-YMail-OSG:Received:X-Rocket-MIMEInfo:X-Mailer:References:Message-ID:Date:From:Reply-To:Subject:To:In-Reply-To:MIME-Version:Content-Type; b=xbAe5+wff7Wd0ywlbydMFnVcCdH8SYzSrMjJM1WTX3SrxDyaPepkiXQQybWfc7mTS9x8c0lYcUKzran1KwqQrdWR3wUVMSpd13d3frdKgn+KEpRMerrgJa23Yl3vJmCtsjqYClPp0bf6aFHeMDcuzm0xAIdz1p2jjBPuWw62fx4= DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=X-YMail-OSG:Received:X-Rocket-MIMEInfo:X-Mailer:References:Message-ID:Date:From:Reply-To:Subject:To:In-Reply-To:MIME-Version:Content-Type; b=r6H3y6xszscjmhhCASKxK54NGZOtz3k+AHdJmsr0PF4CPa/dRdp+PbdyDm5lEmdwo6k5F/JLgIALd5/korc1R5n4AOoMS3rhxIKWGJi9tEH3Neu8Ie+u0zoiqp9pXPmQ5AbPlZVZLar25PpezrjUQT/oXgtjqNGr4YTHrNFYKfw=; X-YMail-OSG: 5q7sqEoVM1nlFKtIkc8ujtWoXxw91muH99GJ0i4ilHSRaCq B33ZJA08OrUQxDcbCnwD0d_L35EAJnTxMI8FivNanJ2qlzWAHJbdQn1LWTnp FqhzH.F4mYO9aOxnXN0lQxGK2z6tA9GSS.g9C2yxWs.03luwOMlge0unJWfk 2C4vu0NIk_NMugH0U_7sgcP.cgBgtGPVmmGXGtCzUM7_cmPY5QnhZCx_3Cre DbiFzwVBqzgK_wmCvW3VLqqdWBHYjxaNiIUjgqCyo8xXn3gwUTyaMOo05iP. KcpfBUpP8oaWa7Cy12aqSK0mG32d.LMZEmMpuReY15T.5PmlakcVkvpWGAG_ H.6.Okxj.c2b7nPNxvk7CMlaVoBPzU37VJRZLs47I7h2AJ6feFooOedgvLmp ntVoUjDj2nrj9ZSVwblG77lPUR6LmCPPYKSkH7QpzGT_TNwgi71rnapxNjj2 f3_r5kS43jQwGWaHk0smFBqZNUiXRsHbuKs8YNo3fTHpIf_11DY4Q7V_eRMc 3_BXGqmLSmCawBHWiOzebNNxWU511_8NgOzMleA6zvk7h84IwVnwFdhPYGnz oZltLZUxjr_obhj6lPD73q6oHCdSWMzesa.bG3dp06wDDx8JBlb.JoLhcGpA - Received: from [182.185.127.162] by web160704.mail.bf1.yahoo.com via HTTP; Thu, 28 Feb 2013 06:57:28 PST X-Rocket-MIMEInfo: 001.001, RGVhcsKgUmFobiwgUmVuw6kKCgpUaGFuayB5b3Ugc28gbXVjaCBhbmQgc28gbmljZSBvZiB5b3UgdGhhdCB5b3UgaGVscCBtZS4gb2sgLGkgYW0gdXNpbmcgd2luZG93cy4uLmkgYWxzbyB0cmllZCBlY2xpcHNlIGJ1dCBpIGRvbnQgdW5kZXJzdGFuZC4uLi5vayBpZiBpIGFnYWluIGluc3RhbGwgZWNsaXBzZSBob3cgY2FuIGkgaW5jbHVkZSBzZXFhbiA_Pz8_aW0gaW50ZXJzZXRlZCBpbiB1c2luZyBjL2MrK0lERS4KdGhhbmtzCgoKX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX18KIEZyb206ICJSYWgBMAEBAQE- X-Mailer: YahooMailWebService/0.8.135.514 References: <1362061595.86170.YahooMailNeo@web160706.mail.bf1.yahoo.com> <0E0C86E7-EC43-4665-9DFB-1BBFA6C4AD11@fu-berlin.de> Message-ID: <1362063448.74587.YahooMailNeo@web160704.mail.bf1.yahoo.com> Date: Thu, 28 Feb 2013 06:57:28 -0800 (PST) From: Nazish Jamil To: =?iso-8859-1?Q?Rahn=2C_Ren=E9?= , SeqAn Development In-Reply-To: <0E0C86E7-EC43-4665-9DFB-1BBFA6C4AD11@fu-berlin.de> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="-672873354-1414168698-1362063448=:74587" X-Originating-IP: 98.139.212.172 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1362063451-00000B1F-203B3749/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.216586, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=FREEMAIL_FROM, FSL_FREEMAIL_1, FSL_FREEMAIL_2,HTML_MESSAGE,RCVD_IN_DNSWL_NONE,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.2 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] having problem in including seqan library to dev c++ X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: Nazish Jamil , SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 28 Feb 2013 14:57:33 -0000 ---672873354-1414168698-1362063448=:74587 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear=A0Rahn, Ren=E9=0A=0A=0AThank you so much and so nice of you that you h= elp me. ok ,i am using windows...i also tried eclipse but i dont understand= ....ok if i again install eclipse how can i include seqan ????im interseted= in using c/c++IDE.=0Athanks=0A=0A=0A________________________________=0A Fr= om: "Rahn, Ren=E9" =0ATo: Nazish Jamil ; SeqAn Development =0ASent: Thu= rsday, February 28, 2013 7:46 PM=0ASubject: Re: [Seqan-dev] having problem = in including seqan library to dev c++=0A =0A=0ADear Nazish, =0A=0AI also tr= ied Dev c++ once, but couldn't find appropriate support within the cmake sy= stem for this IDE so I let it go. As far as I remember KDevelop seems to wo= rk and if you are working on a windows machine, we strongly recommend to us= e visual studio (the express version is free of charge). If you are working= on a mac os, we recommend to use Xcode. Personally, I work with Eclipse wh= ich runs smooth on all systems as long as you have enough RAM (minimum shou= ld be 4 GB).=0AYou can find more support on the website:=A0http://trac.seqa= n.de/wiki/Tutorial/GettingStarted.=0ANote, that eclipse on windows works ju= st fine but is a little bit more complicated to set up.=0AOn the wiki page = linked above you'll also find some instructions of how to bind our library = in to your project, so you can use your own build system if you want.=0A=0A= Please, let us know if we can be of any more help.=0A=0AKind regards,=0A=0A= Ren=E9 Rahn=0A=0A=0AOn Feb 28, 2013, at 3:26 PM, Nazish Jamil wrote:=0A=0Ah= ello,i have problem when including seqAn library to Dev c++ ???please help = me in including this library??? actually our project is designing software = for MPSA(multiple protein sequence alignment)...thatswhy we are intersted i= n using seqan library????you have any solution for this problem or suggest = any other IDE for seqan=A0=0A>=A0thanks=A0=0A______________________________= _________________=0A>seqan-dev mailing list=0A>seqan-dev@lists.fu-berlin.de= =0A>https://lists.fu-berlin.de/listinfo/seqan-dev=0A>=0A=0A=0A---=0A=0ARen= =E9 Rahn=0APh.D. Student=0A------------------------------------------------= =0Arene.rahn@fu-berlin.de=0A+49 (0)30 838 75 277=0A------------------------= ------------------------=0AAlgorithmic Bioinformatics (ABI)=0ADepartment of= Informatics=A0=0ARoom =A0018=0A-------------------------------------------= -----=0AFreie Universit=E4t Berlin=0ATakustra=DFe 9=A0=0A14195 Berlin=0A---= --------------------------------------------- ---672873354-1414168698-1362063448=:74587 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear = Rahn, Ren=E9


Thank you so much and so nice of you that you he= lp me. ok ,i am using windows...i also tried eclipse but i dont understand.= ...ok if i again install eclipse how can i include seqan ????im interseted = in using c/c++IDE.
thanks

From: "Rahn, Ren=E9" <rene.maerker@= fu-berlin.de>
To: N= azish Jamil <nzshjamil@yahoo.com>; SeqAn Development <seqan-dev@li= sts.fu-berlin.de>
Sent: Thursday, February 28, 2013 7:46 PM
Subject: Re: [Seqan-dev] having problem in including se= qan library to dev c++

=0A
= =0A=0A =0A=0A
=0ADear Nazish,=0A

=0A
=0A
I also tried = Dev c++ once, but couldn't find appropriate support within the cmake system= for this IDE so I let it go. As far as I remember KDevelop seems to work a= nd if you are working on a windows machine, we strongly recommend to use vi= sual studio (the=0A express version is free of charge). If you are working = on a mac os, we recommend to use Xcode. Personally, I work with Eclipse whi= ch runs smooth on all systems as long as you have enough RAM (minimum shoul= d be 4 GB).
=0A
You can find more support on the website: htt= p://trac.seqan.de/wiki/Tutorial/GettingStarted.
=0A
Note, that ecl= ipse on windows works just fine but is a little bit more complicated to set= up.
=0A
On the wiki page linked above you'll also find some instr= uctions of how to bind our library in to your project, so you can use your = own build system if you want.
=0A

=0A
=0A
Please, let= us know if we can be of any more help.
=0A

=0A
=0A
K= ind regards,
=0A

=0A
=0A
Ren=E9 Rahn
=0A
=0A=

=0A
=0A
=0A
=0A
On Feb 28, 2013, at 3:26 PM, Nazi= sh Jamil wrote:
=0A
=0A
=0A
=0A
=0A
hello,i have problem when i= ncluding seqAn library to Dev c++ ???please help me in including this libra= ry??? actually our project is designing software for MPSA(multiple protein = sequence alignment)...thatswhy we are intersted in using seqan library????y= ou=0A have any solution for this problem or suggest any other IDE for seqan=  
=0A
 thanks 
=0A
=0A
=0A__________= _____________________________________
=0Aseqan-dev mailing list
=0Aseqan-dev@lists.fu-be= rlin.de
=0Ahttps://lists.fu-berlin.de/listinfo/seqan-dev
=0A=0A
=0A
=0A
=0A
=0A= =0A
=0A=0A
=0A=0A
=0A
=0A

=0A---
=0A

=0A<= /div>=0A
Ren=E9 Rahn
=0A
Ph.D. Student
=0A
-------= -----------------------------------------
=0A=0A
+49 (0)30 8= 38 75 277
=0A
------------------------------------------------=0A
Algorithmic Bioinformatics (ABI)
=0A
Department of Infor= matics 
=0A
Room  018
=0A
---------------------= ---------------------------
=0A
Freie Universit=E4t Berlin
= =0A
Takustra=DFe 9 
=0A
14195 Berlin
=0A
-------= -----------------------------------------
=0A
=0A
=0A=
=0A
=0A=0A
=0A<= br class=3D"yiv906931486Apple-interchange-newline">=0A
=0A
=0A=0A
=0A
=0A
=0A=0A


---672873354-1414168698-1362063448=:74587-- From rene.maerker@fu-berlin.de Thu Feb 28 16:33:33 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UB5UC-003zGT-C9>; Thu, 28 Feb 2013 16:33:32 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) with esmtp (envelope-from ) id <1UB5UC-003URb-9g>; Thu, 28 Feb 2013 16:33:32 +0100 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) with esmtp (envelope-from ) id <1UB5UB-0020ok-U0>; Thu, 28 Feb 2013 16:33:32 +0100 Received: from EX03A.campus.fu-berlin.de ([130.133.170.134]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.03.0123.003; Thu, 28 Feb 2013 16:33:29 +0100 From: =?iso-8859-1?Q?Rahn=2C_Ren=E9?= To: Nazish Jamil Thread-Topic: [Seqan-dev] having problem in including seqan library to dev c++ Thread-Index: AQHOFb+lhsXKaW+bwUes6El3XmACQA== Message-ID: <77D9E3F9-1290-453E-81A8-8A0FF7BFD1EA@fu-berlin.de> References: <1362063448.74587.YahooMailNeo@web160704.mail.bf1.yahoo.com> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_77D9E3F91290453E81A88A0FF7BFD1EAfuberlinde_" MIME-Version: 1.0 Date: Thu, 28 Feb 2013 16:33:28 +0100 X-Original-Date: Thu, 28 Feb 2013 15:33:28 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: A X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1362065612-00000B1F-76F8556D/3805051148-0/0-19 X-Bogosity: Ham, tests=bogofilter, spamicity=0.046189, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-49.0 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP, HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.2 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: Cc: SeqAn Development Subject: [Seqan-dev] Fwd: having problem in including seqan library to dev c++ X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 28 Feb 2013 15:33:33 -0000 --_000_77D9E3F91290453E81A88A0FF7BFD1EAfuberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Nazish, 1. Install MinGW by following the installation instructions here: http://ww= w.mingw.org/wiki/Getting_Started. 2. Make sure you have no parallel cygwin installation, because cmake does n= ot allow any sh.exe in the PATH environment. (Is still an open issue in cma= ke)! Anyway if you really need cygwin installation use the path fix batch file = in "util/mingw/mingw_path_fix" to temporarily remove the cygwin path from w= ithin the terminal session you are currently in. It is important to start e= clipse from within this terminal session, so that the PATH is fixed for thi= s session. This is a little workaround we added for MinGW/Cygwin user. Note= , that cygwin is at the moment not supported as a build system within the w= indows environment. Regardless of this, you should be able to run with nati= ve cygwin compilers within a cygwin bash. But than you also could just run = a linux :). 3. Download the latest eclipse build from their homepage. Note, that there = are known issues with the 64 bit version of eclipse regarding the console o= utput (it is slow :) ). But this will be probably fixed by the next major r= elease of CDT?! If you have installed eclipse-cdt than you just need to ad= d the svn plugin within eclipse. Go to help-> install new software -> select update site of your eclipse bui= ld (probably indigo). In the Dialog box below search for svn and check Sub= versive SVN Team Provider (Incubation). Confirm all questions and wait for = install to be finished. Restart eclipse as prompted and go to project view 'svn repository explorin= g'. Wait for install to be finished and restart eclipse. Add a new resource= (fill in the svn trunk address of seqan) within the svn repository perspec= tive. Checkout Seqan trunk. Wait until it is finished. 4. From here on you just can follow the steps described here: http://trac.s= eqan.de/wiki/Tutorial/GettingStarted/LinuxEclipse#AFirstBuild These steps are only necessary if you plan to work within SeqAn. However,if= you have your own project and you want to just use our library, then you o= nly have to link against the seqan library. How you can do that is describe= d here: http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwnBuildSy= stem Try these steps and let me know if it worked out. Kind regards, Ren=E9 Begin forwarded message: From: Nazish Jamil > Subject: Re: [Seqan-dev] having problem in including seqan library to dev c= ++ Date: February 28, 2013 3:57:28 PM GMT+01:00 To: Rahn, Ren=E9 >, "SeqAn Development" > Reply-To: Nazish Jamil > Dear Rahn, Ren=E9 Thank you so much and so nice of you that you help me. ok ,i am using windo= ws...i also tried eclipse but i dont understand....ok if i again install ec= lipse how can i include seqan ????im interseted in using c/c++IDE. thanks ________________________________ From: "Rahn, Ren=E9" > To: Nazish Jamil >; SeqAn D= evelopment > Sent: Thursday, February 28, 2013 7:46 PM Subject: Re: [Seqan-dev] having problem in including seqan library to dev c= ++ Dear Nazish, I also tried Dev c++ once, but couldn't find appropriate support within the= cmake system for this IDE so I let it go. As far as I remember KDevelop se= ems to work and if you are working on a windows machine, we strongly recomm= end to use visual studio (the express version is free of charge). If you ar= e working on a mac os, we recommend to use Xcode. Personally, I work with E= clipse which runs smooth on all systems as long as you have enough RAM (min= imum should be 4 GB). You can find more support on the website: http://trac.seqan.de/wiki/Tutoria= l/GettingStarted. Note, that eclipse on windows works just fine but is a little bit more comp= licated to set up. On the wiki page linked above you'll also find some instructions of how to = bind our library in to your project, so you can use your own build system i= f you want. Please, let us know if we can be of any more help. Kind regards, Ren=E9 Rahn On Feb 28, 2013, at 3:26 PM, Nazish Jamil wrote: hello,i have problem when including seqAn library to Dev c++ ???please help= me in including this library??? actually our project is designing software= for MPSA(multiple protein sequence alignment)...thatswhy we are intersted = in using seqan library????you have any solution for this problem or suggest= any other IDE for seqan thanks _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev --- Ren=E9 Rahn Ph.D. Student ------------------------------------------------ rene.rahn@fu-berlin.de +49 (0)30 838 75 277 ------------------------------------------------ Algorithmic Bioinformatics (ABI) Department of Informatics Room 018 ------------------------------------------------ Freie Universit=E4t Berlin Takustra=DFe 9 14195 Berlin ------------------------------------------------ --- Ren=E9 Rahn Ph.D. Student ------------------------------------------------ rene.rahn@fu-berlin.de +49 (0)30 838 75 277 ------------------------------------------------ Algorithmic Bioinformatics (ABI) Department of Informatics Room 018 ------------------------------------------------ Freie Universit=E4t Berlin Takustra=DFe 9 14195 Berlin ------------------------------------------------ --_000_77D9E3F91290453E81A88A0FF7BFD1EAfuberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-ID: <74AD2B19BC34D6469E7F5C36586FAACB@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable Dear Nazish,

1. Install MinGW by following the installation instructions here: = ;http://www.mingw.org= /wiki/Getting_Started. 
2. Make sure you have no parallel cygwin installation, because cmake d= oes not allow any sh.exe in the PATH environment. (Is still an open issue i= n cmake)!
 Anyway if you really need cygwin installation use the path fix b= atch file in "util/mingw/mingw_path_fix" to temporarily remove th= e cygwin path from within the terminal session you are currently in. It is = important to start eclipse from within this terminal session, so that the PATH is fixed for this session. This is a little work= around we added for MinGW/Cygwin user. Note, that cygwin is at the moment n= ot supported as a build system within the windows environment. Regardless o= f this, you should be able to run with native cygwin compilers within a cygwin bash. But than you also could= just run a linux :).
3. Download the latest eclipse build from their homepage. Note, that t= here are known issues with the 64 bit version of eclipse regarding the cons= ole output (it is slow :) ). But this will be probably fixed by the next ma= jor release of CDT?!  If you have installed eclipse-cdt than you just need to add the svn plugin within ecli= pse. 
Go to help-> install new software -> select update site of your = eclipse build (probably indigo). In the Dialog box below search for svn and= check  Subversive SVN Team Provider (Incubation). Confirm all qu= estions and wait for install to be finished. 
Restart eclipse as prompted and go to project view 'svn repository exp= loring'. Wait for install to be finished and restart eclipse. Add= a new resource (fill in the svn trunk address of seqan) within the svn rep= ository perspective. Checkout Seqan trunk. Wait until it is finished.
4. From here on you just can follow the steps described here: http://trac.seqan.de/wiki/Tutorial/GettingStarted/LinuxEclipse#AFi= rstBuild

These steps are only necessary if you plan to work within SeqAn. Howev= er,if you have your own project and you want to just use our library, then = you only have to link against the seqan library. How you can do that is des= cribed here: http://trac.seqan.de/wiki/BuildManual/Integratio= nWithYourOwnBuildSystem

Try these steps and let me know if it worked out.

Kind regards,

Ren=E9


Begin forwarded message:

From: Nazis= h Jamil <nzshjamil@yahoo.com&= gt;
Subject: Re= : [Seqan-dev] having problem in including seqan library to dev c++<= /b>
Date: Febru= ary 28, 2013 3:57:28 PM GMT+01:00
To: Rahn,= Ren=E9 <rene.maerker@fu-be= rlin.de>, "SeqAn Development" <seqan-dev@lists.fu-berlin.de>
Reply-To: Nazis= h Jamil <nzshjamil@yahoo.com&= gt;

Dear Rahn, Ren=E9


Thank you so much and so nice of you that you help me. ok ,i am using windo= ws...i also tried eclipse but i dont understand....ok if i again install ec= lipse how can i include seqan ????im interseted in using c/c++IDE.<= /div>
thanks

From: "Rahn, Ren=E9&qu= ot; <rene.maerker@fu-berlin= .de>
To: Nazish Jamil <nzshjamil@yahoo.com>; SeqAn Develo= pment <seqan-dev@lists.f= u-berlin.de>
Sent: Thursday, February 2= 8, 2013 7:46 PM
Subject: Re: [Seqan-dev] h= aving problem in including seqan library to dev c++

Dear Nazish,

I also tried Dev c++ once, but couldn't find appropriate suppo= rt within the cmake system for this IDE so I let it go. As far as I remembe= r KDevelop seems to work and if you are working on a windows machine, we st= rongly recommend to use visual studio (the express version is free of charge). If you are working on a mac os, we rec= ommend to use Xcode. Personally, I work with Eclipse which runs smooth on a= ll systems as long as you have enough RAM (minimum should be 4 GB).
You can find more support on the website: http://trac.seqan.de/wiki/Tutorial/G= ettingStarted.
Note, that eclipse on windows works just fine but is a little bit more= complicated to set up.
On the wiki page linked above you'll also find some instructions of ho= w to bind our library in to your project, so you can use your own build sys= tem if you want.

Please, let us know if we can be of any more help.

Kind regards,

Ren=E9 Rahn

On Feb 28, 2013, at 3:26 PM, Nazish Jamil wrote:

hello,i have problem when including seqAn library to Dev c++ ?= ??please help me in including this library??? actually our project is desig= ning software for MPSA(multiple protein sequence alignment)...thatswhy we a= re intersted in using seqan library????you have any solution for this problem or suggest any other IDE for seqan = ;
 thanks 
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu= -berlin.de
https://lists.fu-= berlin.de/listinfo/seqan-dev






---

Ren=E9 Rahn
Ph.D. Student
------------------------------------------------
rene.rahn@fu-berlin.de
+49 (0)30 838 75 277
------------------------------------------------
Algorithmic Bioinformatics (ABI)
Department of Informatics 
Room  018
------------------------------------------------
Freie Universit=E4t Berlin
Takustra=DFe 9 
14195 Berlin
------------------------------------------------




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