[Debian-med-packaging] Bug#866646: Any idea how to fix freebayes? [Was: Bug#866646: freebayes FTBFS with libhts-dev 1.4.1-2]

[Fabian Klötzl]

Hi Andreas,

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.

Btw, I had to add -std=c++11 for a successful build.

Best,
Fabian