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

[Andreas Tille]

Hi,

I've commited packaging for freebayes 1.1.0 to Git (Git repository
became a mess which is caused by the fact that I had some local packages
during freeze since new Build-Depends where needed and I failed to keep
repositories in sync).

The htslib issue remains the same but I have no idea how to fix it.

Kind regards

    Andreas.

----- Forwarded message from Adrian Bunk <bunk at debian.org> -----

Date: Fri, 30 Jun 2017 19:09:10 +0300
From: Adrian Bunk <bunk at debian.org>
To: Debian Bug Tracking System <submit at bugs.debian.org>
Subject: Bug#866646: freebayes FTBFS with libhts-dev 1.4.1-2
X-Debian-PR-Message: report 866646
X-Debian-PR-Package: src:freebayes
X-Debian-PR-Keywords: 
X-Debian-PR-Source: freebayes

Source: freebayes
Version: 1.0.2-1
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/freebayes.html

...
g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I/usr/include/bamtools -I../ttmath -I/usr/include/vcflib -I/usr/include/intervaltree `pkg-config --cflags libsmithwaterman` -ldisorder -c freebayes.cpp
In file included from /usr/include/htslib/tbx.h:30:0,
                 from /usr/include/tabix.hpp:5,
                 from /usr/include/vcflib/Variant.h:18,
                 from AlleleParser.h:31,
                 from freebayes.cpp:28:
/usr/include/htslib/hts.h:140:5: error: 'json' redeclared as different kind of symbol
     json,
     ^~~~
In file included from freebayes.cpp:26:0:
Allele.h:99:19: note: previous declaration 'std::__cxx11::string json(Allele*&)'
     friend string json(Allele* &allele);
                   ^~~~
Makefile:92: recipe for target 'freebayes.o' failed
make[2]: *** [freebayes.o] Error 1
make[2]: Leaving directory '/build/1st/freebayes-1.0.2/src'
Makefile:2: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/build/1st/freebayes-1.0.2'
dh_auto_build: make -j1 returned exit code 2
debian/rules:4: recipe for target 'build' failed
make: *** [build] Error 2

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----- End forwarded message -----

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