Re: Any idea how to fix freebayes? [Was: Bug#866646: freebayes FTBFS with libhts-dev 1.4.1-2]
Hi Fabian,
On Mon, Sep 04, 2017 at 12:47:05PM +0200, Fabian Klötzl wrote:
> On 02.09.2017 14:54, Andreas Tille wrote:
> > The htslib issue remains the same but I have no idea how to fix it.
>
> The problem is that Allele.h defines a friend function called `json`
> residing in global namespace. However, hts.h already defined a value of
> an enum with the same name, thus the symbols clash. Basically, a
>
> sed -i 's/json/to_json/' src/Allele.*
>
> will fix the issue (also one call in Sample.cpp:267). However, in the
> long term hts should stop exporting such generic names. C++ invented
> namespaces and `enum class` exactly to avoid these problems. As htslib
> is pure C, they should prefix their symbols, as everyone else does it.
Fully ACK. Would you volunteer to create an issue in htslib bug tracker.
> Btw, I had to add -std=c++11 for a successful build.
Seems you have build the package locally. Would you mind pushing your
changes to Git?
Kind regards and thanks for the hints in any case
Andreas.
--
http://fam-tille.de
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