--- Begin Message ---
Package: src:shasta
Version: 0.14.0-3
Severity: important
Tags: sid forky ftbfs
User: [email protected]
Usertags: boost1.92
Dear Maintainer,
Boost 1.92 will most likely be the default boost version in the
upcoming Debian 14 (forky) release.
shasta FTBFS with boost 1.92. Note that the FTBFS may not necessarily be
connected to boost - please check the build log for the actual cause.
boost-defaults pointing to 1.92 is available in experimental, so you can
rebuild your package against it to reproduce the failure and test the fix.
Note: This ticket severity will be increased to RC bug when
boost-defaults is switched to 1.92.
If your package depends on versioned boost packages (e.g. libboost1.90-dev),
please switch to the unversioned (default) ones (e.g. libboost-dev), so the
package follows future boost transitions automatically.
Here is the most probably relevant part of the failing build log:
==================== build log ====================
[ 84%] Building CXX object
dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraphDetangle.cpp.o
cd /build/reproducible-path/shasta-0.14.0/obj-x86_64-linux-gnu/dynamicLibrary
&& /usr/bin/x86_64-linux-gnu-g++ -DBOOST_ALLOW_DEPRECATED_HEADERS
-DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.14.0
-DNDEBUG -DSHASTA_PYTHON_API
-I/build/reproducible-path/shasta-0.14.0/dynamicLibrary/../src -g -O2
-ffile-prefix-map=/build/reproducible-path/shasta-0.14.0=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi
-Wunused-parameter -O3 -mcx16 -I/usr/include/python3.14
-I/usr/lib/python3/dist-packages/pybind11/include -MD -MT
dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraphDetangle.cpp.o
-MF
CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraphDetangle.cpp.o.d
-o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraphDetangle.cpp.o
-c /build/reproducible-path/shasta
-0.14.0/src/mode3-AssemblyGraphDetangle.cpp
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp: In member
function âbool
shasta::mode3::AssemblyGraph::detangleVertex(boost::adjacency_list<boost::listS,
boost::listS, boost::bidirectionalS, shasta::mode3::AssemblyGraphVertex,
shasta::mode3::AssemblyGraphEdge>::vertex_descriptor, bool, uint64_t, uint64_t,
bool, double, double)â:
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp:3276:18:
warning: variable âsignificantCountâ set but not used
[-Wunused-but-set-variable=]
3276 | uint64_t significantCount = 0;
| ^~~~~~~~~~~~~~~~
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp: In member
function âbool shasta::mode3::AssemblyGraph::detangleEdge(bool, std::map<long
unsigned int, boost::detail::edge_desc_impl<boost::bidirectional_tag, void*>
>&, std::map<long unsigned int,
boost::detail::edge_desc_impl<boost::bidirectional_tag, void*> >::iterator&,
uint64_t, uint64_t, bool, double, double)â:
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp:3982:18:
warning: variable âsignificantCountâ set but not used
[-Wunused-but-set-variable=]
3982 | uint64_t significantCount = 0;
| ^~~~~~~~~~~~~~~~
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp: In member
function âbool shasta::mode3::AssemblyGraph::detangleShortSuperbubble(bool,
const Superbubbles&, uint64_t, uint64_t, uint64_t, uint64_t, bool, double,
double)â:
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp:4824:14:
warning: variable âsignificantCountâ set but not used
[-Wunused-but-set-variable=]
4824 | uint64_t significantCount = 0;
| ^~~~~~~~~~~~~~~~
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp:4826:14:
warning: variable ânegligibleCountâ set but not used
[-Wunused-but-set-variable=]
4826 | uint64_t negligibleCount = 0;
| ^~~~~~~~~~~~~~~
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp: In member
function âvoid shasta::mode3::AssemblyGraph::PhasingGraph::phase1(bool,
bool)â:
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp:6270:18:
warning: variable âspanningTreeEdgeCountâ set but not used
[-Wunused-but-set-variable=]
6270 | uint64_t spanningTreeEdgeCount = 0;
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraphDetangle.cpp: In
member function âbool
shasta::mode3::AssemblyGraph::detangleSuperbubbleWithReadFollowing(bool, const
Superbubbles&, uint64_t, uint64_t, double, uint64_t, uint64_t)â:
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraphDetangle.cpp:211:18:
warning: variable âiterationâ set but not used [-Wunused-but-set-variable=]
211 | for(uint64_t iteration=0; ; iteration ++) {
| ^~~~~~~~~
In file included from
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp:25:
/usr/include/boost/graph/adj_list_serialize.hpp: In instantiation of âvoid
boost::serialization::load(Archive&, boost::adjacency_list<OEL, VL, D, VP, EP,
GP, EL>&, unsigned int) [with Archive = boost::archive::binary_iarchive; OEL =
boost::listS; VL = boost::listS; D = boost::bidirectionalS; VP =
shasta::mode3::AssemblyGraphVertex; EP = shasta::mode3::AssemblyGraphEdge; GP =
boost::no_property; EL = boost::listS]â:
/usr/include/boost/serialization/split_free.hpp:57:13: required from
âstatic void boost::serialization::free_loader<Archive, T>::invoke(Archive&,
T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T =
boost::adjacency_list<boost::listS, boost::listS, boost::bidirectionalS,
shasta::mode3::AssemblyGraphVertex, shasta::mode3::AssemblyGraphEdge>]â
57 | load(ar, t, v);
| ~~~~^~~~~~~~~~
/usr/include/boost/serialization/split_free.hpp:72:18: required from âvoid
boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive =
boost::archive::binary_iarchive; T = boost::adjacency_list<boost::listS,
boost::listS, boost::bidirectionalS, shasta::mode3::AssemblyGraphVertex,
shasta::mode3::AssemblyGraphEdge>]â
72 | typex::invoke(ar, t, file_version);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/usr/include/boost/graph/adj_list_serialize.hpp:130:41: required from âvoid
boost::serialization::serialize(Archive&, boost::adjacency_list<OEL, VL, D, VP,
EP, GP, EL>&, unsigned int) [with Archive = boost::archive::binary_iarchive;
OEL = boost::listS; VL = boost::listS; D = boost::bidirectionalS; VP =
shasta::mode3::AssemblyGraphVertex; EP = shasta::mode3::AssemblyGraphEdge; GP =
boost::no_property; EL = boost::listS]â
130 | boost::serialization::split_free(ar, graph, file_version);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/boost/serialization/serialization.hpp:109:14: required from
âvoid boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with
Archive = boost::archive::binary_iarchive; T =
boost::adjacency_list<boost::listS, boost::listS, boost::bidirectionalS,
shasta::mode3::AssemblyGraphVertex, shasta::mode3::AssemblyGraphEdge>]â
109 | serialize(ar, t, v);
| ~~~~~~~~~^~~~~~~~~~
/usr/include/boost/archive/detail/iserializer.hpp:189:40: required from
âvoid boost::archive::detail::iserializer<Archive,
T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned
int) const [with Archive = boost::archive::binary_iarchive; T =
boost::adjacency_list<boost::listS, boost::listS, boost::bidirectionalS,
shasta::mode3::AssemblyGraphVertex, shasta::mode3::AssemblyGraphEdge>]â
189 | boost::serialization::serialize_adl(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
190 | boost::serialization::smart_cast_reference<Archive &>(ar),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
191 | * static_cast<T *>(x),
| ~~~~~~~~~~~~~~~~~~~~~~
192 | file_version
| ~~~~~~~~~~~~
193 | );
| ~
/usr/include/boost/archive/detail/iserializer.hpp:122:7: [ skipping 17
instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
122 | class iserializer : public basic_iserializer
| ^~~~~~~~~~~
/usr/include/boost/archive/detail/iserializer.hpp:626:18: required from
âvoid boost::archive::load(Archive&, T&) [with Archive = binary_iarchive; T =
shasta::mode3::AssemblyGraph]â
626 | typex::invoke(ar, t);
| ~~~~~~~~~~~~~^~~~~~~
/usr/include/boost/archive/detail/common_iarchive.hpp:67:22: required from
âvoid boost::archive::detail::common_iarchive<Archive>::load_override(T&)
[with T = shasta::mode3::AssemblyGraph; Archive =
boost::archive::binary_iarchive]â
67 | archive::load(* this->This(), t);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:50: required from
âvoid boost::archive::basic_binary_iarchive<Archive>::load_override(T&) [with
T = shasta::mode3::AssemblyGraph; Archive = boost::archive::binary_iarchive]â
76 | this->detail_common_iarchive::load_override(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/archive/binary_iarchive_impl.hpp:58:60: required from
âvoid boost::archive::binary_iarchive_impl<Archive, Elem,
Tr>::load_override(T&) [with T = shasta::mode3::AssemblyGraph; Archive =
boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]â
58 | this->basic_binary_iarchive<Archive>::load_override(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/archive/detail/interface_iarchive.hpp:68:36: required from
âArchive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&)
[with T = shasta::mode3::AssemblyGraph; Archive =
boost::archive::binary_iarchive]â
68 | this->This()->load_override(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp:8067:17:
required from here
8067 | archive >> *this;
| ^~~~
/usr/include/boost/graph/adj_list_serialize.hpp:116:54: error: invalid
conversion from âVertexâ {aka âvoid*â} to
âstd::vector<void*>::size_typeâ {aka âlong unsigned intâ} [-fpermissive]
116 | boost::tie(e, inserted) = add_edge(verts[u], verts[v],
graph);
| ^
| |
| Vertex {aka void*}
In file included from /usr/include/c++/16/vector:68,
from /build/reproducible-path/shasta-0.14.0/src/vector.hpp:4,
from
/build/reproducible-path/shasta-0.14.0/src/MarkerInterval.hpp:10,
from
/build/reproducible-path/shasta-0.14.0/src/mode3-Anchor.hpp:5,
from
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.hpp:6,
from
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp:2:
/usr/include/c++/16/bits/stl_vector.h:1251:28: note: initializing argument 1 of
âconstexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp,
_Alloc>::operator[](size_type) [with _Tp = void*; _Alloc =
std::allocator<void*>; reference = void*&; size_type = long unsigned int]â
1251 | operator[](size_type __n) _GLIBCXX_NOEXCEPT
| ~~~~~~~~~~^~~
/usr/include/boost/graph/adj_list_serialize.hpp:116:64: error: invalid
conversion from âVertexâ {aka âvoid*â} to
âstd::vector<void*>::size_typeâ {aka âlong unsigned intâ} [-fpermissive]
116 | boost::tie(e, inserted) = add_edge(verts[u], verts[v],
graph);
| ^
| |
| Vertex
{aka void*}
/usr/include/c++/16/bits/stl_vector.h:1251:28: note: initializing argument 1 of
âconstexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp,
_Alloc>::operator[](size_type) [with _Tp = void*; _Alloc =
std::allocator<void*>; reference = void*&; size_type = long unsigned int]â
1251 | operator[](size_type __n) _GLIBCXX_NOEXCEPT
| ~~~~~~~~~~^~~
In file included from
/usr/include/boost/archive/detail/interface_oarchive.hpp:24,
from /usr/include/boost/archive/detail/common_oarchive.hpp:22,
from /usr/include/boost/archive/basic_binary_oarchive.hpp:33,
from /usr/include/boost/archive/binary_oarchive_impl.hpp:22,
from /usr/include/boost/archive/binary_oarchive.hpp:21,
from
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp:23:
/usr/include/boost/archive/detail/oserializer.hpp: In instantiation of
âstatic void
boost::archive::detail::save_pointer_type<Archive>::invoke(Archive&, TPtr)
[with TPtr = void*; Archive = boost::archive::binary_oarchive]â:
/usr/include/boost/archive/detail/oserializer.hpp:541:18: required from
âvoid boost::archive::save(Archive&, T&) [with Archive = binary_oarchive; T =
void* const]â
541 | typex::invoke(ar, t);
| ~~~~~~~~~~~~~^~~~~~~
/usr/include/boost/archive/detail/common_oarchive.hpp:71:22: required from
âvoid boost::archive::detail::common_oarchive<Archive>::save_override(T&)
[with T = void* const; Archive = boost::archive::binary_oarchive]â
71 | archive::save(* this->This(), t);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/usr/include/boost/archive/basic_binary_oarchive.hpp:80:50: required from
âvoid boost::archive::basic_binary_oarchive<Archive>::save_override(const T&)
[with T = void*; Archive = boost::archive::binary_oarchive]â
80 | this->detail_common_oarchive::save_override(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/archive/binary_oarchive_impl.hpp:59:60: required from
âvoid boost::archive::binary_oarchive_impl<Archive, Elem,
Tr>::save_override(T&) [with T = void* const; Archive =
boost::archive::binary_oarchive; Elem = char; Tr = std::char_traits<char>]â
59 | this->basic_binary_oarchive<Archive>::save_override(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/archive/detail/interface_oarchive.hpp:71:36: required from
âArchive&
boost::archive::detail::interface_oarchive<Archive>::operator<<(const T&) [with
T = void*; Archive = boost::archive::binary_oarchive]â
71 | this->This()->save_override(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/serialization/nvp.hpp:48:8: [ skipping 35 instantiation
contexts, use -ftemplate-backtrace-limit=0 to disable ]
48 | ar << t.const_value();
| ~~~^~~~~~~~~~~~~~~~~~
/usr/include/boost/archive/detail/oserializer.hpp:541:18: required from
âvoid boost::archive::save(Archive&, T&) [with Archive = binary_oarchive; T =
const shasta::mode3::AssemblyGraph]â
541 | typex::invoke(ar, t);
| ~~~~~~~~~~~~~^~~~~~~
/usr/include/boost/archive/detail/common_oarchive.hpp:71:22: required from
âvoid boost::archive::detail::common_oarchive<Archive>::save_override(T&)
[with T = const shasta::mode3::AssemblyGraph; Archive =
boost::archive::binary_oarchive]â
71 | archive::save(* this->This(), t);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/usr/include/boost/archive/basic_binary_oarchive.hpp:80:50: required from
âvoid boost::archive::basic_binary_oarchive<Archive>::save_override(const T&)
[with T = shasta::mode3::AssemblyGraph; Archive =
boost::archive::binary_oarchive]â
80 | this->detail_common_oarchive::save_override(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/archive/binary_oarchive_impl.hpp:59:60: required from
âvoid boost::archive::binary_oarchive_impl<Archive, Elem,
Tr>::save_override(T&) [with T = const shasta::mode3::AssemblyGraph; Archive =
boost::archive::binary_oarchive; Elem = char; Tr = std::char_traits<char>]â
59 | this->basic_binary_oarchive<Archive>::save_override(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/archive/detail/interface_oarchive.hpp:71:36: required from
âArchive&
boost::archive::detail::interface_oarchive<Archive>::operator<<(const T&) [with
T = shasta::mode3::AssemblyGraph; Archive = boost::archive::binary_oarchive]â
71 | this->This()->save_override(t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/shasta-0.14.0/src/mode3-AssemblyGraph.cpp:8059:17:
required from here
8059 | archive << *this;
| ^~~~
/usr/include/boost/archive/detail/oserializer.hpp:482:18: error: âvoid*â is
not a pointer-to-object type
482 | save(ar, * t);
| ^~~
make[3]: ***
[dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make:1650:
dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o]
Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory
'/build/reproducible-path/shasta-0.14.0/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:132:
dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/all] Error 2
make[2]: Leaving directory
'/build/reproducible-path/shasta-0.14.0/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:139: all] Error 2
make[1]: Leaving directory
'/build/reproducible-path/shasta-0.14.0/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 INSTALL="install
--strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:15: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
==================== end of build log =============
Thanks,
Anton Gladky
--- End Message ---
pgpd0J4HgqByo.pgp
