Re: [Seqan-dev] Some SeqAn problems

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Dear Jose,

I think this is a problem with the MacPorts install.

We are planning to publish some improvements of the build system such that it will be easier to keep the MacPorts builds up to date.

For now, may I ask you to do a SVN checkout of http://svn.seqan.de/seqan/trunk/ and use the include headers from there? It should be enough to check out the core/include and extras/include folders and make both available in your include path.

Please report any further problems to this list. I will get back to you in a more timely fashion than with this email.

Sorry for any inconvenience,

Manuel

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From: José Iguelmar Miranda [jose.ig.miranda@gmail.com]
Sent: Thursday, November 01, 2012 2:36 AM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Some SeqAn problems

Hi:

First and foremost, my best congratulations for this wonderful C++ library. SeqAn is an awesome contribution to sequence analysis. You guys are great!

I installed SeqAn in my MBP-intel using MacPorts. Almost everything runs smooth. But I am stuck with some problems:

1. In the tutorial PairwiseSequenceAlignment I got problems with the use of LocalAlignmentEnumerator, Banded alignment (two last parms values) and globalAlignmentScore. The compiler error msg is "xxx was not declared in this scope." Indeed, I double checked the headers and the ones corresponding to these statements aren't available in the includes (/opt/local/include/seqan/).

2. The same happens with FMIndex (was not declared in this scope).

3. In the graph tutorial, the same happens with assignVertexMap (was not declared in this scope).

Searching your sources, I could find the headers for these statements. Would it be a problem with the MacPorts installation?

Best regards.

Jose I Miranda.