From Enrico.Siragusa@fu-berlin.de Tue Feb 03 21:15:35 2015 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 <1YIjsk-003x3r-25>; Tue, 03 Feb 2015 21:15:34 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) with esmtp (envelope-from ) id <1YIjsk-003s8x-0l>; Tue, 03 Feb 2015 21:15:34 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.82) with esmtps (envelope-from ) id <1YIjsj-0031AJ-NX>; Tue, 03 Feb 2015 21:15:33 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0210.002; Tue, 3 Feb 2015 21:15:31 +0100 From: "Siragusa, Enrico" To: SeqAn Development Thread-Topic: post rejected Thread-Index: AQHQPwPKXwaaA9a63kyusEFur4jHlQ== Message-ID: References: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_B620E3661CDE4B2C8866C8A4CA22ACE7fuberlinde_" MIME-Version: 1.0 Date: Tue, 03 Feb 2015 21:15:30 +0100 X-Original-Date: Tue, 3 Feb 2015 20:15:30 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1422994534-000C4EF0-A8A4860D/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,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.4.0 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Cc: "kristianunger@googlemail.com" Subject: [Seqan-dev] Fwd: post rejected 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: Tue, 03 Feb 2015 20:15:35 -0000 --_000_B620E3661CDE4B2C8866C8A4CA22ACE7fuberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Kristian, I assume you are going over the following sequence of commands, as in https= ://github.com/seqan/seqan/blob/master/README.rst#for-the-impatient # mkdir build/Debug # cd build/Debug # cmake ../.. -DCMAKE_BUILD_TYPE=3DDebug # make test_basic Could you please post the full output of cmake? Thanks, Enrico Begin forwarded message: From: "Holtgrewe, Manuel" > To: "Hauswedell, Hannes" >, Rahn, Ren=E9 >, "Siragusa, Enrico" > Subject: FW: post rejected Date: February 2, 2015 at 5:51:49 PM GMT+1 ________________________________ From: Kristian Unger [kristianunger@googlemail.com] Sent: Monday, February 02, 2015 5:17 PM To: seqan-dev-owner@lists.fu-berlin.de Subject: post rejected Hi there I have tried to post the following message: "I am trying to compile seqan following the instructions as given in the RE= ADME.rst. When it comes to the step > make test_basic I get the error > make: *** no role to create =BBtest_basic=AB . I used git clone https://github.com/seqan/seqan to get hold of the source f= iles and I am trying to compile on a Fedora 64 bit system. Can you help me sorting this out, please? Best Kristian" But it was rejected although I am registered with the list. Can you assist? Best Kristian --_000_B620E3661CDE4B2C8866C8A4CA22ACE7fuberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-ID: <0E2FC2AE46F3554D8963E054CA750473@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable
Hi Kristian,

I assume you are going over the following sequence of comma= nds, as in https://github.com/seqan/seqan/blob/master/README.rst#for-the-impatient=

# mkdir build/Debug
# cd build/Debug
# cmake ../.. -DCMAKE_BUILD_TYPE=3DDebug
# make test_basic

Could you please post the full output of cmake?

Thanks,
Enrico

Begin forwarded message:

From: "Holtgrewe, Manuel" <manuel.holtgrewe@fu-= berlin.de>
To: "Hauswedell, Hannes" <Hannes.Hauswedell@= fu-berlin.de>, Rahn, Ren=E9 <rene.maerker@fu-berlin.de>, "Siragusa, Enrico" <Enrico.Siragusa@fu-berlin.de>
Subject: FW: post rejected
Date: February 2, 2015 at 5:51:49 PM GMT+= 1


From: Kristian Unger [kristianunger@googlemail.com= ]
Sent: M= onday, February 02, 2015 5:17 PM
To: seqan-dev-own= er@lists.fu-berlin.de
Subject: post rejected

Hi there

I have tried to post the following message:

"I am trying to compile seq= an following the instructions as given in the README.rst.

When it comes to the step <= /div>

> make test_basic

I get the error

> make: *** no role to create=  =BBtest_basic=AB .

I used git clone https://githu= b.com/seqan/seqan to get hold of the source files and I am trying = to compile on a Fedora 64 bit system.

Can you help me sorting this out= , please?

Best

Kristian"

But it was rejected although I a= m registered with the list. Can you assist?

Best

Kristian

--_000_B620E3661CDE4B2C8866C8A4CA22ACE7fuberlinde_-- From Enrico.Siragusa@fu-berlin.de Wed Feb 04 17:46:41 2015 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YJ366-001W4V-VD>; Wed, 04 Feb 2015 17:46:39 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) with esmtp (envelope-from ) id <1YJ366-000gx4-Td>; Wed, 04 Feb 2015 17:46:38 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.85) with esmtps (envelope-from ) id <1YJ366-0017br-I3>; Wed, 04 Feb 2015 17:46:38 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0210.002; Wed, 4 Feb 2015 17:46:36 +0100 From: "Siragusa, Enrico" To: Kristian Unger Thread-Topic: post rejected Thread-Index: AQHQPwPKXwaaA9a63kyusEFur4jHlZzgoTUAgAAERAA= Message-ID: <9093B62F-F58C-443D-94E1-742DD639FED7@fu-berlin.de> 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_9093B62FF58C443D94E1742DD639FED7fuberlinde_" MIME-Version: 1.0 Date: Wed, 04 Feb 2015 17:46:35 +0100 X-Original-Date: Wed, 4 Feb 2015 16:46:35 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1423068398-000C4EF0-0A29BF3B/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.005696, 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 Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Cc: SeqAn Development Subject: Re: [Seqan-dev] post rejected 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: Wed, 04 Feb 2015 16:46:41 -0000 --_000_9093B62FF58C443D94E1742DD639FED7fuberlinde_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SGksDQoNCkNNYWtlIHJ1bnMgZmluZS4gWW91IGNhbiBnZXQgYSBsaXN0IG9mIHZhbGlkIG1ha2Ug dGFyZ2V0cyB3aXRoOg0KDQojIG1ha2UgaGVscA0KDQpUaGUgdGFyZ2V0IHRlc3RfYmFzaWMgZG9l cyBub3QgZXhpc3QgYW55bW9yZSAtIGFwcGFyZW50bHkgaXQgaGFzIGJlZW4gc3BsaXQgaW4gbWFu eSB0ZXN0X2Jhc2ljX+KApg0KDQpUbyBnZXQgc3RhcnRlZCwgcGxlYXNlIGZvbGxvdyB0aGUgbWFu dWFsOiBodHRwOi8vc2VxYW4ucmVhZHRoZWRvY3Mub3JnLy4NCg0KVGhhbmtzLA0KRW5yaWNvDQoN Ck9uIEZlYiA0LCAyMDE1LCBhdCA1OjMxIFBNLCBLcmlzdGlhbiBVbmdlciA8a3Jpc3RpYW51bmdl ckBnb29nbGVtYWlsLmNvbTxtYWlsdG86a3Jpc3RpYW51bmdlckBnb29nbGVtYWlsLmNvbT4+IHdy b3RlOg0KDQpIaSB0aGVyZSwNCg0KcGxlYXNlIGZpbmRlIHRoZSBvdXRwdXQgb2YgY21ha2UgYmVs b3cuDQoNCkJlc3Qgd2lzaGVzDQoNCktyaXN0aWFuDQoNCi1iYXNoLTQuMiQgIGNtYWtlIC4uLy4u 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2015 17:54:10 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YLaYE-003EV6-CX>; Wed, 11 Feb 2015 17:54:10 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YLaYE-002Pi0-1b>; Wed, 11 Feb 2015 17:54:10 +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 14.03.0224.002; Wed, 11 Feb 2015 17:54:08 +0100 From: =?iso-8859-1?Q?Rahn=2C_Ren=E9?= To: SeqAn Development Thread-Topic: SeqAn-v2.0.0 Thread-Index: AQHQRhta6iBIg9f92kmbHxfDlEBd/g== Message-ID: Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_A25B82860B994A088FF47D971D49F76Bzedatfuberlinde_" MIME-Version: 1.0 Date: Wed, 11 Feb 2015 17:54:08 +0100 X-Original-Date: Wed, 11 Feb 2015 16:54:08 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1423673650-000C4EF0-0B54F1EC/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,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.4.0 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] SeqAn-v2.0.0 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: Wed, 11 Feb 2015 16:54:12 -0000 --_000_A25B82860B994A088FF47D971D49F76Bzedatfuberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear SeqAn-Users and Developers, We are happy to announce the new release of SeqAn 2.0.0. We have many new features and applications for you and improved many parts = in sense of usability, performance and stability. For example, we have improved the usability and the performance of the I/O-= modules. Now BAM-I/O supports parallel read and write operations. We improv= ed automatic read/write operations for compressed file formats, like gzip, = bzip2, etc.. We improved the performance of several data structures like the FMIndex, wh= ich runs now up to 4 times faster than the old version. We extended the library with new features like the X-drop extensions for al= ignments allowing affine gap costs. We added a new realignment module as we= ll as a translation module to translate amino acid alphabet into DNA alphab= et. We implemented many new apps like ANISE and BASIL for insert assembly, Fion= a for read error correction, Yara an enhanced read aligner replacing Masai,= and many many more. With SeqAn 2.0.0 we moved the complete sources to GitHub, which enhances th= e development cycle in a great way. We improved our build system and added = Continous Integration builds with Travis CI. We also updated and improved t= he API documentation (docs.seqan.de) and switched the= tutorials to seqan.readthedocs.org. You can download the new release and the updated apps from www.seqan.de in the downloads section. You can get the complete source= s of the SeqAn 2.0.0 from https://github/seqan/seqan as well. Simply run: git clone -b seqan-v2.0.0 https://github.com/seqan/seqan.git seqan-src and start developing and having fun with SeqAn 2.0.0. A note for SeqAn developers: Many modules are backward compatible with the old release, however, we also= included some API changes to unify and improve the interfaces of some modu= les, like the I/O-modules. If you want to switch to the new release it is l= ikely that you have to slightly adapt your application. You can use the API= documentation (docs.seqan.de) and the tutorials (seq= an.readthedocs.org) to learn more about new i= nterfaces and adapted modules. However, you can also keep track of the las= t stable release and update later if you want. Simply run: git clone -b seqan-v1.4.2 https://github.com/seqan/seqan.git seqan-src to get a fresh clone or just switch to the correct branch within you existi= ng clone: git checkout tags/seqan-v1.4.2 and nothing changes for you. We thank all people involved in the new release for their hard and awesome = work. Enjoy! The SeqAn Team --_000_A25B82860B994A088FF47D971D49F76Bzedatfuberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-ID: Content-Transfer-Encoding: quoted-printable

Dear SeqAn-Users and Developers,


We are happy to announce the new release of SeqAn 2.0.0. 

We have many new features and applications for you a= nd improved many parts in sense of usability, performance and stability.

For example, we have improved the usability and the = performance of the I/O-modules. Now BAM-I/O supports parallel read and write operations. We improved automatic read/write operations for compressed file formats, like <= b class=3D""> gzip, bzip2, etc..

We improved the performance of several data structur= es like the FMIndex, which runs now up to 4 times faste= r than the old version.

We extended the library with new features like the <= b class=3D""> X-drop extensions for alignments allowing affine gap = costs. We added a new realignment module as well as a translation= module to translate amino acid alphabet into DNA alphabet.

We implemented many new apps like ANIS= E and BASIL for insert assembly, Fiona for read error correction, Yara a= n enhanced read aligner replacing Masai, and many many more.

With SeqAn 2.0.0 we moved the comp= lete sources to GitHub, which enhances the development cycle in a great w= ay. We improved our build system and added Continous Integration builds with Travis CI. We also upda= ted and improved the API documentation (docs.seqan.de) and switched the tutorials to seqan.rea= dthedocs.org.

You can download the new release and the updated app= s from www.seqan.de in the down= loads section. You can get the complete sources of the SeqAn 2.0.0 from https://github/seqan/seqan as well.

Simply run:

git clone -b seqan= -v2.0.0 https://github.com/seqan/seqan.git seqan-src 

and start developing and having fun with SeqAn 2.0.0.


A note for SeqAn developers: 

Many modules are backward compatible with the old re= lease, however, we also included some API changes to unify and improve the = interfaces of some modules, like the I/O-modules. If you want to switch to = the new release it is likely that you have to slightly adapt your application. You can use the API documenta= tion (docs.seqan.de) and th= e tutorials (seqan.read= thedocs.org) to learn more about new interfaces and adapted modules.  However, you can also keep track of = the last stable release and update later if you want.=

Simply run:

git clone -b seqan= -v1.4.2 https://github.com/seqan/seqan.git seqan-src

to get a fresh clone or just switch to the correct b= ranch within you existing clone:

git checkout tags/= seqan-v1.4.2

and nothing changes for you.


We thank all people involved in the new release for = their hard and awesome work.

Enjoy!

The SeqAn Team

--_000_A25B82860B994A088FF47D971D49F76Bzedatfuberlinde_-- From gusevfe@gmail.com Wed Feb 11 18:12:43 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YLaq9-002c0S-P3>; Wed, 11 Feb 2015 18:12:41 +0100 Received: from mail-ie0-f179.google.com ([209.85.223.179]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YLaq9-002ztG-FC>; Wed, 11 Feb 2015 18:12:41 +0100 Received: by iecar1 with SMTP id ar1so5584822iec.0 for ; Wed, 11 Feb 2015 09:12:38 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:from:date:message-id:subject:to :content-type; bh=5L6cnW1WAnbGit95WoKlLDwBk8G6JWgXkCQupmesKRU=; b=ybIVrkFjGN2RcbjRkIcJCPPdo23rNPdXFhfW8goQ0zm8CdEYS0adadP8BnfRVN2ML+ q01JKXc8WiJ4/H6kK2bPpCr+zQ9pOcHyYml9qRUoiO4Np3jf7zs22/vdRKos/e/D/cvk 2LgKt3AQ0WMQ1G8wj4L2NVB8Zo3e/TMM3fw/ak3DeMqecQF6Vydl6RLEAKMwrrbFFroy znlkdD9ijr/Xizht3yYzEtXMmJWJc9eXLCDEgWuJytGBgpin3zQ6Dw6Fl4OGCbpXOeoC gg+mhAuV/S0dq+PvBXLEP3FbFNHIO3rSOxgn1ldJPFR3HLmCDAilTF0e3letbKuStB3d Bzvg== X-Received: by 10.107.47.22 with SMTP id j22mr40963569ioo.16.1423674758643; Wed, 11 Feb 2015 09:12:38 -0800 (PST) MIME-Version: 1.0 Received: by 10.36.122.6 with HTTP; Wed, 11 Feb 2015 09:11:58 -0800 (PST) In-Reply-To: References: From: Fedor Gusev Date: Wed, 11 Feb 2015 20:11:58 +0300 Message-ID: To: SeqAn Development Content-Type: multipart/alternative; boundary=001a11c1664843c640050ed31c2f X-Originating-IP: 209.85.223.179 X-ZEDAT-Hint: A X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1423674761-000C4EF0-1E193D1B/1/4500350045 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000032, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.3 required=5.0 tests=FREEMAIL_FROM, FU_XPURGATE_SUSP, HTML_MESSAGE,RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] SeqAn-v2.0.0 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: Wed, 11 Feb 2015 17:12:43 -0000 --001a11c1664843c640050ed31c2f Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Great news! I've run into a problem though :( If you download a package from from http://packages.seqan.de/seqan-library/seqan-library-2.0.0.tar.bz2 and define SEQAN_HAS_ZLIB, then #include "zipstream/zutil.h" has effect. But the file is missing from the package, yet present in github repo. Is this intended? On Wed, Feb 11, 2015 at 7:54 PM, Rahn, Ren=C3=A9 wrote: > Dear SeqAn-Users and Developers, > > > We are happy to announce the new release of *SeqAn 2.0.0.* > > We have many new features and applications for you and improved many part= s > in sense of usability, performance and stability. > > For example, we have improved the usability and the performance of the > I/O-modules. Now *BAM-I/O* supports *parallel read *and *write* > operations. We improved automatic *read/write* operations for compressed > file formats, like * gzip*, *bzip2*, etc.. > > We improved the performance of several data structures like the *FMIndex*= , > which runs now up to *4 times faster* than the old version. > > We extended the library with new features like the * X-drop* extensions > for *alignments* allowing affine gap costs. We added a new *realignment > module *as well as a *translation module * to translate amino acid > alphabet into DNA alphabet. > > We implemented many new apps like *ANISE* and* BASIL* for insert > assembly, *Fiona* for read error correction, *Yara* an enhanced read > aligner replacing *Masai*, and many many more. > > With *SeqAn 2.0.0 *we moved the complete sources to *GitHub*, which > enhances the development cycle in a great way. We improved our build syst= em > and added *Continous Integration *builds with Travis CI. We also updated > and * improved* the *API documentation *(docs.seqan.de) and switched the > tutorials to *seqan.readthedocs.org *. > > You can download the new release and the updated apps from * www.seqan.de > * in the downloads section. You can get the complete > sources of the *SeqAn 2.0.0* from* https://github/seqan/seqan > * as well. > > Simply run: > > git clone -b seqan-v2.0.0 https://github.com/seqan/seqan.git seqan-src > > and start developing and having fun with *SeqAn 2.0.0*. > > > A note for SeqAn developers: > > Many modules are backward compatible with the old release, however, we > also included some API changes to unify and improve the interfaces of som= e > modules, like the I/O-modules. If you want to switch to the new release i= t > is likely that you have to slightly adapt your application. You can use t= he > API documentation (docs.seqan.de) and the tutorials (seqan.readthedocs.or= g) > to learn more about new interfaces and adapted modules. However, you can > also keep track of the last stable release and update later if you want. > > Simply run: > > git clone -b seqan-v1.4.2 https://github.com/seqan/seqan.git seqan-src > > to get a fresh clone or just switch to the correct branch within you > existing clone: > > git checkout tags/seqan-v1.4.2 > > and nothing changes for you. > > > We thank all people involved in the new release for their hard and > awesome work. > > Enjoy! > > The SeqAn Team > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > --=20 Kind regards, Fedor Gusev. --001a11c1664843c640050ed31c2f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Great news!

I've run into a problem= though :(
If you download a package from from=C2=A0http://pa= ckages.seqan.de/seqan-library/seqan-library-2.0.0.tar.bz2 and define=C2= =A0SEQAN_HAS_ZLIB, then=C2=A0
#include "zipstream/zutil.h&qu= ot;
has effect. But the file is missing from the package, yet pre= sent in github repo. Is this intended?

On Wed, Feb 11, 2015 at 7:54 PM, Rahn, Ren= =C3=A9 <rene.maerker@fu-berlin.de> wrote:

Dear SeqAn-Users and Developers,


We are happy to announce the new release of SeqAn= 2.0.0.=C2=A0

We have many new features and applications for you a= nd improved many parts in sense of usability, performance and stability.

For example, we have improved the usability and the = performance of the I/O-modules. Now BAM-I/O supports parallel read and write operations. W= e improved automatic read/write operations for compressed file formats, like gzip, bzip2, etc..

We improved the performance of several data structur= es like the FMIndex, which runs now up to 4 times faster than the old ver= sion.

We extended the library with new features like the <= b> X-drop extensions for alignments allowing affine gap costs. We a= dded a new realignment module as well as a translation module to translate amino acid alphabet into DNA alphabet.

We implemented many new apps like ANISE and BASIL for insert assembly, Fiona for read error correction, Yara an enhanced read aligne= r replacing Masai, and many many more.

With SeqAn 2.0.0 we moved the complete source= s to GitHub, which enhances the development cycle in a great way. We impr= oved our build system and added Continous Integration builds with Travis CI. We also updated and improved the API documentation (docs.seqan.de) and switched the tutorials to seqan.readthe= docs.org.

You can download the new release and the updated app= s from www.seqan.de in t= he downloads section. You can get the complete sources of the SeqAn 2.0.0 from https://github/seqan/seqan as well.

Simply run:

git clone -b seqan-v2.0.0 https://github.com/seqan/seqan.git seqan-src=C2=A0

and start developing and having fun with SeqAn 2.= 0.0.


A note for SeqAn developers:=C2=A0

Many modules are backward compatible with the old re= lease, however, we also included some API changes to unify and improve the = interfaces of some modules, like the I/O-modules. If you want to switch to = the new release it is likely that you have to slightly adapt your application. You can use the API documenta= tion (docs.seqan.de)= and the tutorials (seqan.readthedocs.org) to learn more about new interfaces and adapted modules.=C2=A0 However, you can also keep track of = the last stable release and update later if you want.

Simply run:

git clone -b seqan-v1.4.2 https://github.com/seqan/seqan.git seqan-src

to get a fresh clone or just switch to the correct b= ranch within you existing clone:

git checkout tags/seqan-v1.4.= 2

and nothing changes for you.


We thank all people involved in the new release for = their hard and awesome work.

Enjoy!

The SeqAn Team


_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev




--
Kind regards,
Fedor Gusev.
--001a11c1664843c640050ed31c2f-- From rene.maerker@fu-berlin.de Wed Feb 11 18:43:29 2015 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YLbJv-002e2Q-9m>; Wed, 11 Feb 2015 18:43:27 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YLbJv-003TD6-8h>; Wed, 11 Feb 2015 18:43:27 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YLbJu-002Vlr-S1>; Wed, 11 Feb 2015 18:43:27 +0100 Received: from EX03B.campus.fu-berlin.de ([130.133.170.135]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0224.002; Wed, 11 Feb 2015 18:43:25 +0100 From: =?utf-8?B?UmFobiwgUmVuw6k=?= To: SeqAn Development Thread-Topic: [Seqan-dev] SeqAn-v2.0.0 Thread-Index: AQHQRhta6iBIg9f92kmbHxfDlEBd/pzrnrUAgAAIvYA= Message-ID: <47A2B937-D00B-4915-A85F-C7D6E005A648@zedat.fu-berlin.de> References: In-Reply-To: Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_47A2B937D00B4915A85FC7D6E005A648zedatfuberlinde_" MIME-Version: 1.0 Date: Wed, 11 Feb 2015 18:43:24 +0100 X-Original-Date: Wed, 11 Feb 2015 17:43:24 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1423676607-000C4EF0-49ADA139/0/0 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,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.4.0 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] SeqAn-v2.0.0 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn 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d3M6IDI7IiBjbGFzcz0iIj48Zm9udCBmYWNlPSJDb3VyaWVyIE5ldyIgY2xhc3M9IiI+MTQxOTUg QmVybGluPC9mb250PjwvZGl2Pg0KPGRpdiBzdHlsZT0ib3JwaGFuczogMjsgd2lkb3dzOiAyOyIg Y2xhc3M9IiI+PGZvbnQgZmFjZT0iQ291cmllciBOZXciIGNsYXNzPSIiPi0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tPC9mb250PjwvZGl2Pg0KPC9kaXY+DQo8L2Rpdj4NCjxiciBjbGFz cz0iIj4NCjwvZGl2Pg0KPC9ib2R5Pg0KPC9odG1sPg0K --_000_47A2B937D00B4915A85FC7D6E005A648zedatfuberlinde_-- From daniel.bartha@gmail.com Thu Feb 19 00:44:43 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YOEIL-000LAy-Ae>; Thu, 19 Feb 2015 00:44:41 +0100 Received: from mail-we0-f170.google.com ([74.125.82.170]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YOEIL-003xGO-6w>; Thu, 19 Feb 2015 00:44:41 +0100 Received: by wesx3 with SMTP id x3so4200584wes.7 for ; Wed, 18 Feb 2015 15:44:39 -0800 (PST) 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X-purgate-type: clean X-purgate-ID: 151147::1424303081-000C4EF0-FB0D98EB/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.492753, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] seqan 2 system_condition problems on windows 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: Wed, 18 Feb 2015 23:44:43 -0000 --047d7b86d8b2202452050f656746 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Everyone, I'm trying to work with seqan 2 on windows. This is pain-in-the-ass as usual, but now there is something that grinds my nervs, and has to do with the lib self. Here my program, simply stolen from the docs: #include #include #include using namespace seqan; int main() { CharString id; Dna5String seq; CharString qual; SeqFileIn seqFileIn("E:/some.fastq"); readRecord(id, seq, qual, seqFileIn); } Not that big deal. But somehow I get a list of undefined references in the 'system_condition.h'. See the error log below. Do anyone have an idea, where the problem is? I assume that its either seqan or the compilation parameters, since the code itself is primitive. Regards: Daniel 00:20:19: Starting: "C:\Qt\Tools\mingw491_32\bin\mingw32-make.exe" C:/Qt/Tools/mingw491_32/bin/mingw32-make -f Makefile.Release mingw32-make[1]: Entering directory 'E:/dev/build-console_1-Desktop_Qt_5_4_0_MinGW_32bit-Release' g++ -c -pipe -fno-keep-inline-dllexport -O2 -frtti -Wall -Wextra -fexceptions -mthreads -I..\console_1 -I"C:\seqan-library-2.0.0\include" -I"." -I"C:\Qt\5.4\mingw491_32\mkspecs\win32-g++" -o release\main.o ..\console_1\main.cpp In file included from C:\seqan-library-2.0.0\include/seqan/parallel.h:56:0, from C:\seqan-library-2.0.0\include/seqan/modifier.h:48, from C:\seqan-library-2.0.0\include/seqan/file.h:59, from C:\seqan-library-2.0.0\include/seqan/stream.h:62, from C:\seqan-library-2.0.0\include/seqan/seq_io.h:45, from ..\console_1\main.cpp:3: C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In constructor 'seqan::Condition::Condition(seqan::CriticalSection&)': C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:57:47: error: 'InitializeConditionVariable' was not declared in this scope InitializeConditionVariable(&data_cond); ^ C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In destructor 'seqan::Condition::~Condition()': C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:62:44: error: 'WakeAllConditionVariable' was not declared in this scope WakeAllConditionVariable(&data_cond); ^ C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In function 'void seqan::waitFor(seqan::Condition&)': C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:98:92: error: 'SleepConditionVariableCS' was not declared in this scope BOOL success =3D SleepConditionVariableCS(&cond.data_cond, &cond.csPtr->data_cs, INFINITE); ^ C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In function 'void seqan::waitFor(seqan::Condition&, long int, bool&)': C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:112:98: error: 'SleepConditionVariableCS' was not declared in this scope inProgress =3D (SleepConditionVariableCS(&cond.data_cond, &cond.csPtr->data_cs, timeoutMilliSec) =3D=3D 0); ^ C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In function 'void seqan::signal(seqan::Condition&)': C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:137:45: error: 'WakeAllConditionVariable' was not declared in this scope WakeAllConditionVariable(&cond.data_cond); ^ In file included from C:\seqan-library-2.0.0\include/seqan/basic/basic_debug.h:52:0, from C:\seqan-library-2.0.0\include/seqan/basic.h:49, from C:\seqan-library-2.0.0\include/seqan/sequence.h:51, from ..\console_1\main.cpp:2: C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h: In instantiation of 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 =3D lo= ng unsigned int; T2 =3D long int]': C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h:1014:77: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 =3D long unsigned int; T= 2 =3D long int]' C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:114:9: required from here C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h:955:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (!(value1 =3D=3D value2)) ^ In file included from C:\seqan-library-2.0.0\include/seqan/basic.h:61:0, from C:\seqan-library-2.0.0\include/seqan/sequence.h:51, from ..\console_1\main.cpp:2: C:\seqan-library-2.0.0\include/seqan/basic/basic_exception.h: At global scope: C:\seqan-library-2.0.0\include/seqan/basic/basic_exception.h:358:37: warning: 'seqan::_globalExceptionHandler' defined but not used [-Wunused-variable] static const std::terminate_handler _globalExceptionHandler =3D std::set_terminate(globalExceptionHandler); ^ Makefile.Release:485: recipe for target 'release/main.o' failed mingw32-make[1]: *** [release/main.o] Error 1 mingw32-make[1]: Leaving directory 'E:/dev/build-console_1-Desktop_Qt_5_4_0_MinGW_32bit-Release' makefile:34: recipe for target 'release' failed mingw32-make: *** [release] Error 2 00:20:22: The process "C:\Qt\Tools\mingw491_32\bin\mingw32-make.exe" exited with code 2. Error while building/deploying project console_1 (kit: Desktop Qt 5.4.0 MinGW 32bit) When executing step "Make" 00:20:22: Elapsed time: 00:03. Live long and prosper Bartha D=C3=A1niel --047d7b86d8b2202452050f656746 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Everyone,

I'm trying to work with seqan 2 on= windows. This is pain-in-the-ass as usual, but now there is something that= grinds my nervs, and has to do with the lib self.

Here my program, = simply stolen from the docs:

#include <iostream>
#include <seqan=
/sequence.h>
#include <seqan=
/seq_io.h>
using namespac=
e seqan;

int main()
{
    CharString id;
    Dna5String seq;
    CharString qual;

    SeqFileIn seqFileIn("E:/some.fa=
stq");
    readRecord(=
id=
, seq, qual, seqFileIn);
}=C2=A0

Not that big deal. But somehow I get a list of undef= ined references in the 'system_condition.h'. See the error log belo= w. Do anyone have an idea, where the problem is? I assume that its either s= eqan or the compilation parameters, since the code itself is primitive.
=
Regards: Daniel

00:20:19: Starting: "C:\Qt\Tools\mingw491_= 32\bin\mingw32-make.exe"

C= :/Qt/Tools/mingw491_32/bin/mingw32-make -f Makefile.Release

m= ingw32-make[1]: Entering directory 'E:/dev/build-console_1-Desktop_Qt_5= _4_0_MinGW_32bit-Release'

g= ++ -c -pipe -fno-keep-inline-dllexport -O2 -frtti -Wall -Wextra -fexception= s -mthreads -I..\console_1 -I"C:\seqan-library-2.0.0\include" -I= "." -I"C:\Qt\5.4\mingw491_32\mkspecs\win32-g++" -o rele= ase\main.o ..\console_1\main.cpp

In file included from C:\seqan-library-2.0.0\include/seqan/parallel.h:56:0= ,

from C:\seqan-library-2.0.0\include/seqan/modifier.h:48,<= /font>

from C:\seqan-library-2.0.0\include/seqan/file.h:59,

from C:\seqan-library-2.0.0\include/seqan/stream.h:62,

from C:\seqan-library-2.0.0\include/seqan/seq_io.h:45,

from ..\console_1\main.cpp:3:

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In constru= ctor 'seqan::Condition::Condition(seqan::CriticalSection&)':

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:57:47: erro= r: 'InitializeConditionVariable' was not declared in this scope

InitializeConditionVariable(&data_cond);

^

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In destruc= tor 'seqan::Condition::~Condition()':

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:62:44: erro= r: 'WakeAllConditionVariable' was not declared in this scope=

WakeAllConditionVariable(&data_cond);

^

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In functio= n 'void seqan::waitFor(seqan::Condition&)':

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:98:92: erro= r: 'SleepConditionVariableCS' was not declared in this scope=

BOOL success =3D SleepConditionVariableCS(&cond.data_cond, &c= ond.csPtr->data_cs, INFINITE);

= ^

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In functio= n 'void seqan::waitFor(seqan::Condition&, long int, bool&)'= :

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:112:98: err= or: 'SleepConditionVariableCS' was not declared in this scope

inProgress =3D (SleepConditionVariableCS(&cond.data_cond, &co= nd.csPtr->data_cs, timeoutMilliSec) =3D=3D 0);

= ^

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In functio= n 'void seqan::signal(seqan::Condition&)':

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:137:45: err= or: 'WakeAllConditionVariable' was not declared in this scope

WakeAllConditionVariable(&cond.data_cond);

^

In file included from C:\seqan-library-2.0.0\include/seqan/basic/basic_deb= ug.h:52:0,

from C:\seqan-library-2.0.0\include/seqan/basic.h:49,

from C:\seqan-library-2.0.0\include/seqan/sequence.h:51,<= /font>

from ..\console_1\main.cpp:2:

C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h: In instant= iation of 'bool seqan::ClassTest::testEqual(const char*, int, const T1&= amp;, const char*, const T2&, const char*, const char*, ...) [with T1 = =3D long unsigned int; T2 =3D long int]':

C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h:1014:77: = required from 'bool seqan::ClassTest::testEqual(const char*, int, const= T1&, const char*, const T2&, const char*) [with T1 =3D long unsign= ed int; T2 =3D long int]'

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:114:9: re= quired from here

C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h:955:18: war= ning: comparison between signed and unsigned integer expressions [-Wsign-co= mpare]

if (!(value1 =3D=3D value2))

^

In file included from C:\seqan-library-2.0.0\include/seqan/basic.h:61:0,

from C:\seqan-library-2.0.0\include/seqan/sequence.h:51,<= /font>

from ..\console_1\main.cpp:2:

C:\seqan-library-2.0.0\include/seqan/basic/basic_exception.h: At global sc= ope:

C:\seqan-library-2.0.0\include/seqan/basic/basic_exception.h:358:37: warni= ng: 'seqan::_globalExceptionHandler' defined but not used [-Wunused= -variable]

static const std::terminate_handler _globalExceptionHandler =3D std::set_= terminate(globalExceptionHandler);

^

M= akefile.Release:485: recipe for target 'release/main.o' failed

mingw32-make[1]: *** [release/main.o] Error 1

m= ingw32-make[1]: Leaving directory 'E:/dev/build-console_1-Desktop_Qt_5_= 4_0_MinGW_32bit-Release'

m= akefile:34: recipe for target 'release' failed

mingw32-make: *** [release] Error 2

= 00:20:22: The process "C:\Qt\Tools\mingw491_32\bin\mi= ngw32-make.exe" exited with code 2.

Error while building/deploying project console_1 (kit: Desktop Qt 5.4.0 Mi= nGW 32bit)

When executing step "Make"

00:20:22: Elapsed time: 00:03.



Live long and prosper
Bartha D= =C3=A1niel

--047d7b86d8b2202452050f656746-- From Enrico.Siragusa@fu-berlin.de Thu Feb 19 01:01:35 2015 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YOEYf-000MAk-D1>; Thu, 19 Feb 2015 01:01:33 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YOEYf-0001Mk-BT>; Thu, 19 Feb 2015 01:01:33 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YOEYe-001Sfm-Tb>; Thu, 19 Feb 2015 01:01:33 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0224.002; Thu, 19 Feb 2015 01:01:32 +0100 From: "Siragusa, Enrico" To: SeqAn Development Thread-Topic: [Seqan-dev] seqan 2 system_condition problems on windows Thread-Index: AQHQS9UGUVJriF1X3ES5lmKuBh9OXpz3Bf8A Message-ID: <4A5541EC-E88C-41C6-BA44-963B7625B5EE@fu-berlin.de> 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_4A5541ECE88C41C6BA44963B7625B5EEfuberlinde_" MIME-Version: 1.0 Date: Thu, 19 Feb 2015 01:01:30 +0100 X-Original-Date: Thu, 19 Feb 2015 00:01:30 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: XA X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1424304093-000C4EF0-96C0CDA2/1/4508628044 X-Bogosity: Ham, tests=bogofilter, spamicity=0.438087, version=1.2.4 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 3.4.0 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] seqan 2 system_condition problems on windows X-BeenThere: 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<1YOV6z-00231z-Co>; Thu, 19 Feb 2015 18:42:05 +0100 Received: from mail-wg0-f51.google.com ([74.125.82.51]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YOV6z-003HoR-98>; Thu, 19 Feb 2015 18:42:05 +0100 Received: by mail-wg0-f51.google.com with SMTP id y19so8622739wgg.10 for ; Thu, 19 Feb 2015 09:42:03 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=JxSiqvdhtqaVcbaPPXKrFRlsqBi4HuT7YbC24HpU2W0=; b=GGNtP2iJOQPuY32eAXe/353N/A52iM37rE7KYX3rFOiS8HRbnD+663lU5q142lEwhb nTo9qD65ATjr+lZ7AMBlFFNAF6bvLdLKluk14wSEM7UpnybFlqeOpEjPZLFPITKlqaqY /75t5HkP9YNDVF8qmi+/lgbczRYZB/3arigh36V24V7ERutOv6LGjQ6NJEQanDn0GdUS iv3ymXMa00B5xtWhi+JkdHu2zqBOTbhaB213kqKPZnRTHptPvmB8dkiBuiK80Zf0OOXi bUtT4eHJ2rMkJut+QVgWpJTwsykEEB0YzCGa5+Jd0C0R6ZcoYVd6qJL/ufI+ocMg7tft AKnw== MIME-Version: 1.0 X-Received: by 10.194.240.164 with SMTP id wb4mr11206175wjc.66.1424367723830; Thu, 19 Feb 2015 09:42:03 -0800 (PST) Received: by 10.180.45.45 with HTTP; Thu, 19 Feb 2015 09:42:03 -0800 (PST) In-Reply-To: <4A5541EC-E88C-41C6-BA44-963B7625B5EE@fu-berlin.de> References: <4A5541EC-E88C-41C6-BA44-963B7625B5EE@fu-berlin.de> Date: Thu, 19 Feb 2015 18:42:03 +0100 Message-ID: From: =?UTF-8?Q?Bartha_D=C3=A1niel?= To: SeqAn Development Content-Type: multipart/alternative; boundary=089e01419fbe356234050f7474c1 X-Originating-IP: 74.125.82.51 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1424367725-000C4EF0-DBAE8727/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.391474, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] seqan 2 system_condition problems on windows 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, 19 Feb 2015 17:42:07 -0000 --089e01419fbe356234050f7474c1 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Enrico, thanks for the hint. That is not so simple, since Qt is also essential for my plans, and that works best with mingw. I will try it with something else.. Regards: Daniel Live long and prosper Bartha D=C3=A1niel MTA-VMRI, 2014 2015-02-19 1:01 GMT+01:00 Siragusa, Enrico : > Hi Daniel, > > We decided to drop mingw. > > See https://github.com/seqan/seqan/blob/master/README.rst#prerequisites > for a list of supported platform. > > I would suggest Visual Studio 12 on Windows=E2=80=A6 > > Enrico > > On Feb 19, 2015, at 12:44 AM, Bartha D=C3=A1niel > wrote: > > Hi Everyone, > > I'm trying to work with seqan 2 on windows. This is pain-in-the-ass as > usual, but now there is something that grinds my nervs, and has to do wit= h > the lib self. > > Here my program, simply stolen from the docs: > > #include > > #include > > #include > > using namespace seqan; > > > int main() > > { > > CharString id; > > Dna5String seq; > > CharString qual; > > > SeqFileIn seqFileIn("E:/some.fastq"); > > readRecord(id, seq, qual, seqFileIn); > > } > > Not that big deal. But somehow I get a list of undefined references in th= e > 'system_condition.h'. See the error log below. Do anyone have an idea, > where the problem is? I assume that its either seqan or the compilation > parameters, since the code itself is primitive. > > Regards: Daniel > > 00:20:19: Starting: "C:\Qt\Tools\mingw491_32\bin\mingw32-make.exe" > C:/Qt/Tools/mingw491_32/bin/mingw32-make -f Makefile.Release > mingw32-make[1]: Entering directory > 'E:/dev/build-console_1-Desktop_Qt_5_4_0_MinGW_32bit-Release' > g++ -c -pipe -fno-keep-inline-dllexport -O2 -frtti -Wall -Wextra > -fexceptions -mthreads -I..\console_1 -I"C:\seqan-library-2.0.0\include" > -I"." -I"C:\Qt\5.4\mingw491_32\mkspecs\win32-g++" -o release\main.o > ..\console_1\main.cpp > In file included from C:\seqan-library-2.0.0\include/seqan/parallel.h:56:= 0, > from C:\seqan-library-2.0.0\include/seqan/modifier.h:48, > from C:\seqan-library-2.0.0\include/seqan/file.h:59, > from C:\seqan-library-2.0.0\include/seqan/stream.h:62, > from C:\seqan-library-2.0.0\include/seqan/seq_io.h:45, > from ..\console_1\main.cpp:3: > C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In > constructor 'seqan::Condition::Condition(seqan::CriticalSection&)': > C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:57:47: > error: 'InitializeConditionVariable' was not declared in this scope > InitializeConditionVariable(&data_cond); > ^ > C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In > destructor 'seqan::Condition::~Condition()': > C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:62:44: > error: 'WakeAllConditionVariable' was not declared in this scope > WakeAllConditionVariable(&data_cond); > ^ > C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In > function 'void seqan::waitFor(seqan::Condition&)': > C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:98:92: > error: 'SleepConditionVariableCS' was not declared in this scope > BOOL success =3D SleepConditionVariableCS(&cond.data_cond, > &cond.csPtr->data_cs, INFINITE); > ^ > C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In > function 'void seqan::waitFor(seqan::Condition&, long int, bool&)': > C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:112:98: > error: 'SleepConditionVariableCS' was not declared in this scope > inProgress =3D (SleepConditionVariableCS(&cond.data_cond, > &cond.csPtr->data_cs, timeoutMilliSec) =3D=3D 0); > ^ > C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In > function 'void seqan::signal(seqan::Condition&)': > C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:137:45: > error: 'WakeAllConditionVariable' was not declared in this scope > WakeAllConditionVariable(&cond.data_cond); > ^ > In file included from > C:\seqan-library-2.0.0\include/seqan/basic/basic_debug.h:52:0, > from C:\seqan-library-2.0.0\include/seqan/basic.h:49, > from C:\seqan-library-2.0.0\include/seqan/sequence.h:51, > from ..\console_1\main.cpp:2: > C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h: In > instantiation of 'bool seqan::ClassTest::testEqual(const char*, int, cons= t > T1&, const char*, const T2&, const char*, const char*, ...) [with T1 =3D = long > unsigned int; T2 =3D long int]': > C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h:1014:77: > required from 'bool seqan::ClassTest::testEqual(const char*, int, const > T1&, const char*, const T2&, const char*) [with T1 =3D long unsigned int;= T2 > =3D long int]' > C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:114:9: > required from here > C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h:955:18: > warning: comparison between signed and unsigned integer expressions > [-Wsign-compare] > if (!(value1 =3D=3D value2)) > ^ > In file included from C:\seqan-library-2.0.0\include/seqan/basic.h:61:0, > from C:\seqan-library-2.0.0\include/seqan/sequence.h:51, > from ..\console_1\main.cpp:2: > C:\seqan-library-2.0.0\include/seqan/basic/basic_exception.h: At global > scope: > C:\seqan-library-2.0.0\include/seqan/basic/basic_exception.h:358:37: > warning: 'seqan::_globalExceptionHandler' defined but not used > [-Wunused-variable] > static const std::terminate_handler _globalExceptionHandler =3D > std::set_terminate(globalExceptionHandler); > ^ > Makefile.Release:485: recipe for target 'release/main.o' failed > mingw32-make[1]: *** [release/main.o] Error 1 > mingw32-make[1]: Leaving directory > 'E:/dev/build-console_1-Desktop_Qt_5_4_0_MinGW_32bit-Release' > makefile:34: recipe for target 'release' failed > mingw32-make: *** [release] Error 2 > 00:20:22: The process "C:\Qt\Tools\mingw491_32\bin\mingw32-make.exe" > exited with code 2. > Error while building/deploying project console_1 (kit: Desktop Qt 5.4.0 > MinGW 32bit) > When executing step "Make" > 00:20:22: Elapsed time: 00:03. > > > > Live long and prosper > Bartha D=C3=A1niel > > _______________________________________________ > 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 > > --089e01419fbe356234050f7474c1 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Enrico,

thanks for the hint. That is not so simp= le, since Qt is also essential for my plans, and that works best with mingw= . I will try it with something else..

Regards:

Daniel

Live long and prosper
Bartha D=C3=A1niel
MTA-VMRI, 2014<= /div>

2015-02-19 1:01 GMT+01:00 Siragusa, Enrico <= span dir=3D"ltr"><Enrico.Siragusa@fu-berlin.de>:
Hi Daniel,

We decided to drop mingw.


I would suggest Visual Studio 12 on Windows=E2=80=A6

Enrico

On Feb 19, 2015, at 12:44 AM, Bartha D=C3=A1niel <daniel.bartha@gmail.com>= wrote:

Hi Everyone,

I'm trying to work with seqan 2 on windows. This is pain-in-the-ass as = usual, but now there is something that grinds my nervs, and has to do with = the lib self.

Here my program, simply stolen from the docs:

#include <iostr=
eam>
#include <seqan=
/sequence.h>
#include <seqan=
/seq_io.h>
using namespac=
e seqan;

int main()
{
    CharString id;
    Dna5String seq;
    CharString qual;

    SeqFileIn seqFileIn("E:/some.fastq");
    readRecord=
(id, seq, qual, seqFileIn);
}=C2=A0



Not that big deal. But somehow I get a list of undefined references in the =
'system_condition.h'. See the error log below. Do anyone have an id=
ea, where the problem is? I assume that its either seqan or the compilation=
 parameters, since the code itself is primitive.



Regards: Daniel




00:20:19: Starting: "C:\Qt\Tools\mingw491_32\bin\mingw32-make.exe&q=
uot;



C:/Qt/Tools/mingw491_32/bi=
n/mingw32-make -f Makefile.Release


mingw32-make[1]: Entering =
directory 'E:/dev/build-console_1-Desktop_Qt_5_4_0_MinGW_32bit-Release&=
#39;


g++ -c -pipe -fno-keep-inl=
ine-dllexport -O2 -frtti -Wall -Wextra -fexceptions -mthreads -I..\console_=
1 -I"C:\seqan-library-2.0.0\include" -I"." -I"C:\Q=
t\5.4\mingw491_32\mkspecs\win32-g++"
 -o release\main.o ..\console_1\main.cpp


In file included from C:\seqan-library-2.0.0\include/seqan/parallel.h:56=
:0,


from C:\seqan-library-2.0.0\include/seqan/modifier.h:48,

from C:\seqan-library-2.0.0\include/seqan/file.h:59,


from C:\seqan-library-2.0.0\include/seqan/stream.h:62,

from C:\seqan-library-2.0.0\include/seqan/seq_io.h:45,

from ..\console_1\main.cpp:3:


C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In const=
ructor 'seqan::Condition::Condition(seqan::CriticalSection&)':<=
/font>


C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:57:47: er=
ror: 'InitializeConditionVariable' was not declared in this scope


InitializeConditionVariable(&data_cond);


^


C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In destr=
uctor 'seqan::Condition::~Condition()':


C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:62:44: er=
ror: 'WakeAllConditionVariable' was not declared in this scope


WakeAllConditionVariable(&data_cond);


^


C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In funct=
ion 'void seqan::waitFor(seqan::Condition&)':

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:98:92: er=
ror: 'SleepConditionVariableCS' was not declared in this scope


BOOL success =3D SleepConditionVariableCS(&cond.data_cond, &cond=
.csPtr->data_cs, INFINITE);


^


C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In funct=
ion 'void seqan::waitFor(seqan::Condition&, long int, bool&)=
9;:


C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:112:98: e=
rror: 'SleepConditionVariableCS' was not declared in this scope


inProgress =3D (SleepConditionVariableCS(&cond.data_cond, &cond.=
csPtr->data_cs, timeoutMilliSec) =3D=3D 0);


^


C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In funct=
ion 'void seqan::signal(seqan::Condition&)':

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:137:45: e=
rror: 'WakeAllConditionVariable' was not declared in this scope


WakeAllConditionVariable(&cond.data_cond);


^


In file included from C:\seqan-library-2.0.0\include/seqan/basic/basic_d=
ebug.h:52:0,


from C:\seqan-library-2.0.0\include/seqan/basic.h:49,

from C:\seqan-library-2.0.0\include/seqan/sequence.h:51,

from ..\console_1\main.cpp:2:


C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h: In insta=
ntiation of 'bool seqan::ClassTest::testEqual(const char*, int, const T=
1&, const char*,
 const T2&, const char*, const char*, ...) [with T1 =3D long unsigned i=
nt; T2 =3D long int]':


C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h:1014:77: =
required from 'bool seqan::ClassTest::testEqual(const char*, int, const=
 T1&, const char*,
 const T2&, const char*) [with T1 =3D long unsigned int; T2 =3D long in=
t]'


C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:114:9: re=
quired from here


C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h:955:18: w=
arning: comparison between signed and unsigned integer expressions [-Wsign-=
compare]


if (!(value1 =3D=3D value2))


^


In file included from C:\seqan-library-2.0.0\include/seqan/basic.h:61:0,=



from C:\seqan-library-2.0.0\include/seqan/sequence.h:51,

from ..\console_1\main.cpp:2:


C:\seqan-library-2.0.0\include/seqan/basic/basic_exception.h: At global =
scope:


C:\seqan-library-2.0.0\include/seqan/basic/basic_exception.h:358:37: war=
ning: 'seqan::_globalExceptionHandler' defined but not used [-Wunus=
ed-variable]


static const std::terminate_handler _globalExceptionHandler =3D std::set=
_terminate(globalExceptionHandler);


^


Makefile.Release:485: reci=
pe for target 'release/main.o' failed


mingw32-make[1]: *** [release/main.o] Error 1


mingw32-make[1]: Leaving d=
irectory 'E:/dev/build-console_1-Desktop_Qt_5_4_0_MinGW_32bit-Release&#=
39;


makefile:34: recipe for ta=
rget 'release' failed


mingw32-make: *** [release] Error 2


00:20:22: The process "C:\Qt\Tools\mingw491_32\bin\=
mingw32-make.exe" exited with code 2.


Error while building/deploying project console_1 (kit: Desktop Qt 5.4.0 =
MinGW 32bit)


When executing step "Make"


00:20:22: Elapsed time: 00:03.














Live long and prosper



Bartha D=C3=A1niel













_______________________________________________

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.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev


--089e01419fbe356234050f7474c1-- From hlk.dogan@gmail.com Fri Feb 20 08:25:22 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YOhxg-003lKW-Mq>; Fri, 20 Feb 2015 08:25:20 +0100 Received: from mail-ob0-f178.google.com ([209.85.214.178]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YOhxg-0013Dw-HI>; Fri, 20 Feb 2015 08:25:20 +0100 Received: by mail-ob0-f178.google.com with SMTP id uz6so22526447obc.9 for ; Thu, 19 Feb 2015 23:25:17 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=ekWqysHzGbanB7pVbjVnhb/fGc4ecnt40e/TNJd4JC4=; b=nRqk5M+EnNCsuy3RxcCnZMeiaP5An1hon3D6ooQFSMQPCTvkGjVCEY8LceF+8kdMy2 2dZ15a3zP4cGA1EgfBvLTErHgyXKH7OP8ANSR2ivBP9tZZNuXKkHPhIOv0ndvyitf6Z5 xFpCVXV0AYc72OfsPxPFpMDX09VBjNl6zweIREivjdJ9fjE/VhvYu4maH958LMuAHyWi oH9N6rD7l+qKBODKMhmErZt7K0SEUYBAE0AC2TJw/X7X26c4fb12p1KOX6AemsXzs9f3 0cMvk9PBNK/9NfNVhb7ZHyFFHrG0iWkvCDWlpyr9fXiXYfun7Z67C3trEBNwKz8Pacb0 uYDg== MIME-Version: 1.0 X-Received: by 10.60.94.70 with SMTP id da6mr5624693oeb.48.1424417117698; Thu, 19 Feb 2015 23:25:17 -0800 (PST) Received: by 10.182.27.175 with HTTP; Thu, 19 Feb 2015 23:25:17 -0800 (PST) Date: Fri, 20 Feb 2015 01:25:17 -0600 Message-ID: From: Haluk Dogan To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=089e012287c04fff9b050f7ff4ef X-Originating-IP: 209.85.214.178 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1424417120-000C4EF0-F3E6BBA8/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.080683, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] printing String 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, 20 Feb 2015 07:25:22 -0000 --089e012287c04fff9b050f7ff4ef Content-Type: text/plain; charset=UTF-8 Hi, I have "*use of undeclared identifier 'directionIterator'" *error while printing a String object. My gcc version is 4.9. Is the problem on my side? The full error output is in the following: *seqan-src/include/seqan/sequence/string_base.h:2009:60: error: use of undeclared identifier 'directionIterator'* * typename DirectionIterator::Type it = directionIterator(target, Output());* * ^* *~/git/seqan-src/demos/seqan_dev/test.cpp:37:15: note: in instantiation of function template specialization 'seqan::operator<<, seqan::SimpleType,* * seqan::Alloc >' requested here* * std::cout << dnaSeq << std::endl;* Thank you. -- HD --089e012287c04fff9b050f7ff4ef Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,

I have "us= e of undeclared identifier 'directionIterator'"=C2=A0error= while printing a String<Dna> object. My gcc version is 4.9. Is the p= roblem on my side?

The full error output is= in the following:

seqan-src/include/seqan/sequence/string_b= ase.h:2009:60: error: use o= f undeclared identifier 'directionIterator'

=C2=A0 =C2=A0 typename DirectionIterator&= lt;TStream, Output>::Type it =3D directionIterator(target, Output());

=C2=A0=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 ^

~/git/seqan-src/demos/seqan_dev/test.cpp:= 37:15: note: in instantiati= on of function template specialization 'seqan::operator<<<std:= :__1::basic_ostream<char>, seqan::SimpleType<unsigned char, seqan:= :Dna_>,

=C2=A0 =C2=A0 =C2=A0 seqan::Alloc<void= > >' requested here

=C2=A0 =C2=A0 std::cout << dnaSeq &= lt;< std::endl;

Thank you.
--
HD
--089e012287c04fff9b050f7ff4ef-- From manuel.holtgrewe@fu-berlin.de Fri Feb 20 09:36:57 2015 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YOj4x-0043gC-Uc>; Fri, 20 Feb 2015 09:36:56 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YOj4x-002V7f-TY>; Fri, 20 Feb 2015 09:36:55 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YOj4x-001Hcc-JP>; Fri, 20 Feb 2015 09:36:55 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0224.002; Fri, 20 Feb 2015 09:36:54 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] printing String Thread-Index: AQHQTN5rH8DweT15HUGIx3l5Sk4CuJz5NvO2 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_FCCAB9D80C3DAB47B5601C5B0E62872B96290A1Dex02acampusfube_" MIME-Version: 1.0 Date: Fri, 20 Feb 2015 09:36:53 +0100 X-Original-Date: Fri, 20 Feb 2015 08:36:53 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1424421415-000C4EF0-964D00C6/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000059, 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 Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] printing String 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, 20 Feb 2015 08:36:57 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B96290A1Dex02acampusfube_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Haluk, Make sure to include . Cheers, Manuel ________________________________ From: Haluk Dogan [hlk.dogan@gmail.com] Sent: Friday, February 20, 2015 8:25 AM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] printing String Hi, I have "use of undeclared identifier 'directionIterator'" error while print= ing a String object. My gcc version is 4.9. Is the problem on my side? The full error output is in the following: seqan-src/include/seqan/sequence/string_base.h:2009:60: error: use of undec= lared identifier 'directionIterator' typename DirectionIterator::Type it =3D directionItera= tor(target, Output()); ^ ~/git/seqan-src/demos/seqan_dev/test.cpp:37:15: note: in instantiation of f= unction template specialization 'seqan::operator<<, seqan::SimpleType, seqan::Alloc >' requested here std::cout << dnaSeq << std::endl; Thank you. -- HD --_000_FCCAB9D80C3DAB47B5601C5B0E62872B96290A1Dex02acampusfube_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Haluk,

Make sure to include <seqan/stream.h>.

Cheers,
Manuel

From: Haluk Dogan [hlk.dogan@gmail.com] Sent: Friday, February 20, 2015 8:25 AM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] printing String<Dna>

Hi,

I have "use of undeclared identifier 'directi= onIterator'" error while printing a String<Dna> object.= My gcc version is 4.9. Is the problem on my side?

The full error output is in the following:

seqan-src/include/seqan/sequence/string_b= ase.h:2009:60: error: use of undeclared id= entifier 'directionIterator'

    typename DirectionIterator&= lt;TStream, Output>::Type it =3D directionIterator(target, Output());

           =                      = ;                     &nb= sp;     ^

~/git/seqan-src/demos/seqan_dev/test.cpp:= 37:15: note: in instantiation of function= template specialization 'seqan::operator<<<std::__1::basic_ostrea= m<char>, seqan::SimpleType<unsigned char, seqan::Dna_>,<= /b>

      seqan::Alloc<void= > >' requested here

    std::cout << dnaSeq &= lt;< std::endl;

Thank you.
--
HD
--_000_FCCAB9D80C3DAB47B5601C5B0E62872B96290A1Dex02acampusfube_-- From hlk.dogan@gmail.com Fri Feb 20 14:46:11 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YOnuD-000fSW-3x>; Fri, 20 Feb 2015 14:46:09 +0100 Received: from mail-ob0-f182.google.com ([209.85.214.182]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YOnuC-002Klz-V2>; Fri, 20 Feb 2015 14:46:09 +0100 Received: by mail-ob0-f182.google.com with SMTP id nt9so23565602obb.13 for ; Fri, 20 Feb 2015 05:46:06 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=0Mx55dHyy9THlDpDklzpnDJprMTNtns3dRhrRZ3C1Tw=; b=QJsoLQhRR9KMjcHvKq8gx4aF6ecV18IsrIHzVoh0gIRV+Ft1MUzO2ZJefjmeMpgZrA +z62RK92qZnpfCefV6kEWhTC4uKu583bpkZSUQjC0EjBUdWYHxmV6jvWBDlq+p3G0huu QDfxELU2mPLEO8PSZy4T7Ji2jj4w6PM0TqqpFkZzql44M6uNFQD+sHgZUT83sVqAdZ+K 8jVLvXuh9o9W4hyoBQ/3qQPozZ37U35q9uQuf4HBH3fyBDxKfF5o9tjUdD1TIIPjsmV1 UeqYsap5uxGhOJDUY5kfV967BHk6Q80o6GPXMdIwcCvzy6fkRSU/soIQWD2Kr2uWWH7i Nkog== MIME-Version: 1.0 X-Received: by 10.60.198.228 with SMTP id jf4mr6059854oec.32.1424439966312; Fri, 20 Feb 2015 05:46:06 -0800 (PST) Received: by 10.182.27.175 with HTTP; Fri, 20 Feb 2015 05:46:06 -0800 (PST) In-Reply-To: References: Date: Fri, 20 Feb 2015 07:46:06 -0600 Message-ID: From: Haluk Dogan To: SeqAn Development Content-Type: multipart/alternative; boundary=001a113472b2322ed9050f854689 X-Originating-IP: 209.85.214.182 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1424439969-000C4EF0-9F5ECA8A/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000119, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] printing String 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, 20 Feb 2015 13:46:11 -0000 --001a113472b2322ed9050f854689 Content-Type: text/plain; charset=UTF-8 I see. It worked now. I copied the whole code from Sequences tutorial. stream.h is missing in the tutorial. Thank you. On Fri, Feb 20, 2015 at 2:36 AM, Holtgrewe, Manuel < manuel.holtgrewe@fu-berlin.de> wrote: > Dear Haluk, > > Make sure to include . > > Cheers, > Manuel > > ------------------------------ > *From:* Haluk Dogan [hlk.dogan@gmail.com] > *Sent:* Friday, February 20, 2015 8:25 AM > *To:* seqan-dev@lists.fu-berlin.de > *Subject:* [Seqan-dev] printing String > > Hi, > > I have "*use of undeclared identifier 'directionIterator'" *error while > printing a String object. My gcc version is 4.9. Is the problem on my > side? > > The full error output is in the following: > > *seqan-src/include/seqan/sequence/string_base.h:2009:60: error: use of > undeclared identifier 'directionIterator'* > > * typename DirectionIterator::Type it = > directionIterator(target, Output());* > > * ^* > > *~/git/seqan-src/demos/seqan_dev/test.cpp:37:15: note: in instantiation of > function template specialization > 'seqan::operator<<, > seqan::SimpleType,* > > * seqan::Alloc >' requested here* > > * std::cout << dnaSeq << std::endl;* > Thank you. > -- > HD > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > -- HD --001a113472b2322ed9050f854689 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I see. It worked now. I copied the whole code from Sequenc= es tutorial. stream.h is missing in the tutorial.

Thank = you.

O= n Fri, Feb 20, 2015 at 2:36 AM, Holtgrewe, Manuel <manuel.holt= grewe@fu-berlin.de> wrote:
Dear Haluk,

Make sure to include <seqan/stream.h>.

Cheers,
Manuel

Fro= m: Haluk Dogan [hlk.dogan@gmail.com]
Sent: Friday, February 20, 2015 8:25 AM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] printing String<Dna>

Hi,

I have "use of undeclared identifier 'directionItera= tor'"=C2=A0error while printing a String<Dna> object. My= gcc version is 4.9. Is the problem on my side?

The full error output is in the following:

seqan-src/include/seqan/sequence/string_base.h:2009:60: error: use of undeclared identifier 'directio= nIterator'

=C2=A0 =C2=A0 typename DirectionIterator<TStream, Output>= ::Type it =3D directionIterator(target, Output());

=C2=A0=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ^=

~/git/seqan-src/demos/seqan_dev/test.cpp:37:15: note: in instantiation of function template specializati= on 'seqan::operator<<<std::__1::basic_ostream<char>, seq= an::SimpleType<unsigned char, seqan::Dna_>,

=C2=A0 =C2=A0 =C2=A0 seqan::Alloc<void> >' request= ed here

=C2=A0 =C2=A0 std::cout << dnaSeq << std::endl;=

Thank you.
--
HD

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HD
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