[Debian-med-packaging] Bug#1078976: fast5: FTBFS against HDF5 1.14 - Needs -DH5_USE_110_API

[Gilles Filippini]

Source: fast5
Version: 0.6.5-7
Severity: important

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Hi,

The fast5 package fails to build from source in a test rebuild
against hdf5 1.14 currently in experimental:

x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection 
- -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I../include -I../src -I/usr/include/python3.12 -c fast5/fast5.cpp -o build/temp.linux-x86_64-cpython-312/fast5/fast5.o -std
=c++11 -Wall -Wextra -Wpedantic -isystem /usr/include/hdf5/serial
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
In file included from ../include/fast5.hpp:27,
                 from fast5/fast5.cpp:1292:
../include/fast5/hdf5_tools.hpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > hdf5_tools::File::get_attr_list(const std::string&) const’:
../include/fast5/hdf5_tools.hpp:2110:27: error: no matching function for call to ‘hdf5_tools::detail::Util::wrap(herr_t (&)(hid_t, H5O_info2_t*, unsigned int), hid_t&, H5O_info2_t*) const’
 2110 |         detail::Util::wrap(H5Oget_info, id_holder.id, &info);
      |         ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/fast5/hdf5_tools.hpp:244:5: note: candidate: ‘template<class Function, class ... Args> static typename std::result_of<_Functor(_ArgTypes ...)>::type hdf5_tools::detail::Util::wrap(Function&&, Args&& ...)’
  244 |     wrap(Function && f, Args && ...args)
      |     ^~~~
../include/fast5/hdf5_tools.hpp:244:5: note:   template argument deduction/substitution failed:
../include/fast5/hdf5_tools.hpp: In substitution of ‘template<class Function, class ... Args> static typename std::result_of<_Functor(_ArgTypes ...)>::type hdf5_tools::detail::Util::wrap(Function&&, Args&& ...) [with Function = int (&)(long int, H5O_info2_t*, unsigned int); Args = {long int&, H5O_info2_t*}]’:
../include/fast5/hdf5_tools.hpp:2110:27:   required from here
 2110 |         detail::Util::wrap(H5Oget_info, id_holder.id, &info);
      |         ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/fast5/hdf5_tools.hpp:244:5: error: no type named ‘type’ in ‘struct std::result_of<int (&(long int&, H5O_info2_t*))(long int, H5O_info2_t*, unsigned int)>’
  244 |     wrap(Function && f, Args && ...args)
      |     ^~~~


Adding -DH5_USE_110_API to CPPFLAGS fixes the issue.

Best,
_g.


- -- System Information:
Debian Release: 12.0
Architecture: amd64 (x86_64)

Kernel: Linux 6.1.0-21-amd64 (SMP w/12 CPU threads; PREEMPT)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

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