[Debian-med-packaging] Bug#1031473: freebayes: FTBFS: Variant.h:36:10: fatal error: wavefront/wfa.hpp: No such file or directory

[Andreas Henriksson]

Control: reassign -1 libvcflib-dev 1.0.7+dfsg-1
Control: retitle -1 libvcflib-dev lacks dependency on libwfa2-dev
Control: affects -1 freebayes


Hello,

On Fri, Feb 17, 2023 at 08:01:41AM +0100, Lucas Nussbaum wrote:
> Source: freebayes
> Version: 1.3.6-2
> Severity: serious
> Justification: FTBFS
> Tags: bookworm sid ftbfs
> User: lucas at debian.org
> Usertags: ftbfs-20230216 ftbfs-bookworm
> 
> Hi,
> 
> During a rebuild of all packages in sid, your package failed to build
> on amd64.
> 
> 
> Relevant part (hopefully):
> > c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp
> > In file included from ../src/AlleleParser.h:32,
> >                  from ../src/DataLikelihood.h:20,
> >                  from ../src/DataLikelihood.cpp:1:
> > /usr/include/vcflib/Variant.h:36:10: fatal error: wavefront/wfa.hpp: No such file or directory
> >    36 | #include "wavefront/wfa.hpp"
> >       |          ^~~~~~~~~~~~~~~~~~~
> > compilation terminated.
[...]


Note than it's not freebayes that includes "wavefront/wfa.hpp", but
vcflib.

Given that vcflib has had a recent new upload to unstable that makes me
think this is actually a problem in vcflib. The new vcflib version has
not yet migrated to testing, so reassigning this to add a(n additional)
blocker for that to happen and prevent the problem from affecting
testing.

I notiled that libvcflib-dev does *not* have a dependency on libwfa2-dev
(which has wavefront/wfa.hpp). Maybe this is the bug itself.

There could possibly be additional problems like cflags (and libs) not
propagating properly up the chain. There seems to be no .pc (pkgconfig)
file included in libwfa2-dev. Not sure how the needed
"-I/usr/include/wfa2lib/" are supposed to be propagated up, but lets
first fix the dependency issue and then I'll leave potential additional
problems as an excercise for the maintainer(s) to figure out while
testing their new package.

Please consider adding a simple compile test as an autopkgtest,
which would help you catch missing dependencies in the -dev packages.
For example see:
https://sources.debian.org/src/util-linux/2.38.1-5/debian/tests/libmount-dev/

Regards,
Andreas Henriksson