[Seqan-dev] google test incompatibility (was: CMake issue)

[Peter Robinson <Peter.Robinson@jax.org>]

Thanks, I have now gotten that to run. I am trying to integrate a CMake file for SeqAn and google's gtest in order to prepare for a larger project.

I am getting the following error (abbreviated) when I try to make the tests.

error: ambiguous overload for ‘operator<<’ (operand types are ‘std::ostream {aka std::basic_ostream<char>}’ and ‘const seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >’)
   *os << value;

I am trying this out on my GitHub page (https://github.com/pnrobinson/GTT), in case anybody wants to see the gory details.

I realise that seqan has its own unit testing framework, but I would love to use gtest -- is there any workaround?
thanks Peter


Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
10 Discovery Drive
Farmington, CT 06032
860.837.2095 t | 860.990.3130 m
peter.robinson@jax.org
www.jax.org
Robinson lab: https://robinsongroup.github.io/
New Book: Computational Exome and Genome Analysis
The Jackson Laboratory: Leading the search for tomorrow's cures

________________________________________
From: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
Sent: Monday, December 11, 2017 6:20 AM
To: seqan-dev@lists.fu-berlin.de
Cc: Peter Robinson
Subject: Re: [Seqan-dev] CMake issue

Am Samstag, 9. Dezember 2017, 16:01:37 schrieb Peter Robinson:
> Hi everybody,
>
> I am trying to use SeqAn in a new project, and am running into issues with
> CMake.
>
> I am running an up-to-date Ubuntu system and installed seqan like this
>
> $sudo apt install seqan-dev

Hi Nick,

the package is now called libseqan2-dev because of Debian naming rules (that
are shared by Ubuntu), but you need at least Ubuntu 17.04.

> According to this (
>
> http://seqan.readthedocs.io/en/master/Infrastructure/Use/Install.html#infra-> use-install
>

We need to update this to reflect the new package name!


> ) and this (
>
> http://seqan.readthedocs.io/en/master/Infrastructure/Use/FindSeqAnCMake.html
>
> )
>
> the installation procedure should put a file called seqan-config.cmake  into
> a system path that CMake would find.
>
> However, apparently no such file gets installed, and CMake produces an error
> message that I pasted into the bottom of this mail.

The new package should install the cmake file; please let us know if it
doesn't.

Best regards,
Hannes
--
Hannes Hauswedell

Scientific staff & PhD candidate
Freie Universität Berlin / Max Planck Institute for Molecular Genetics

address     Institut für Informatik
            Takustraße 9
            Room 019
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e-mail      hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]
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