On 2/4/25 22:17, Orion Poplawski wrote:
I'm working on updating libmamba to 2.0.X [1] but hitting the following
error:
cd /home/orion/fedora/libmamba/libmamba-2.0.6-build/mamba-2.0.6/redhat-
linux-build/libmambapy && /usr/lib64/ccache/g++ -DFMT_SHARED -
DMAMBA_USE_INSTALL_PREFIX_AS_BASE -DSPDLOG_FMT_EXTERNAL -
DSPDLOG_FWRITE_UNLOCKED -Dbindings_EXPORTS -I/home/orion/fedora/
libmamba/libmamba-2.0.6-build/mamba-2.0.6/libmambapy/src/libmambapy/
bindings -I/home/orion/fedora/libmamba/libmamba-2.0.6-build/mamba-2.0.6/
libmamba/include -isystem /usr/include/python3.13 -isystem /usr/share -
O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -
pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-
D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/
redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/
redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-
unwind-tables -fstack-clash-protection -fcf-protection -mtls-
dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g
-DNDEBUG -fPIC -fvisibility=hidden -Wall -Wextra -Wshadow -Wnon-virtual-
dtor -Wold-style-cast -Wcast-align -Wunused -Woverloaded-virtual -
Wpedantic -Wconversion -Wsign-conversion -Wnull-dereference -Wdouble-
promotion -Wformat=2 -Wunreachable-code -Wuninitialized -Werror -
Wmisleading-indentation -Wduplicated-cond -Wduplicated-branches -
Wlogical-op -Wuseless-cast -Wno-error=deprecated-declarations -MD -MT
libmambapy/CMakeFiles/bindings.dir/src/libmambapy/bindings/legacy.cpp.o
-MF CMakeFiles/bindings.dir/src/libmambapy/bindings/legacy.cpp.o.d -o
CMakeFiles/bindings.dir/src/libmambapy/bindings/legacy.cpp.o -c /home/
orion/fedora/libmamba/libmamba-2.0.6-build/mamba-2.0.6/libmambapy/src/
libmambapy/bindings/legacy.cpp
/home/orion/fedora/libmamba/libmamba-2.0.6-build/mamba-2.0.6/libmambapy/
src/libmambapy/bindings/legacy.cpp: In lambda function:
/home/orion/fedora/libmamba/libmamba-2.0.6-build/mamba-2.0.6/libmambapy/
src/libmambapy/bindings/legacy.cpp:557:47: warning:
‘mamba::expected_t<std::__cxx11::basic_string<char> >
mamba::SubdirData::cache_path() const’ is deprecated: since version 2.0
use ``valid_solv_cache`` or ``valid_json_cache`` instead [-Wdeprecated-
declarations]
557 | return extract(self.cache_path());
| ~~~~~~~~~~~~~~~^~
In file included from /home/orion/fedora/libmamba/libmamba-2.0.6-build/
mamba-2.0.6/libmambapy/src/libmambapy/bindings/legacy.cpp:30:
/home/orion/fedora/libmamba/libmamba-2.0.6-build/mamba-2.0.6/libmamba/
include/mamba/core/subdirdata.hpp:135:33: note: declared here
135 | expected_t<std::string> cache_path() const;
| ^~~~~~~~~~
In file included from /usr/include/pybind11/attr.h:14,
from /usr/include/pybind11/detail/class.h:12,
from /usr/include/pybind11/pybind11.h:12,
from /usr/include/pybind11/functional.h:14,
from /home/orion/fedora/libmamba/libmamba-2.0.6-build/
mamba-2.0.6/libmambapy/src/libmambapy/bindings/legacy.cpp:11:
In function
‘pybind11::detail::collect_arguments<(pybind11::return_value_policy)1,
std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >&,
pybind11::detail::accessor<pybind11::detail::accessor_policies::str_attr>, pybind11::arg_v, void>(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, pybind11::detail::accessor<pybind11::detail::accessor_policies::str_attr>&&, pybind11::arg_v&&)pybind11::detail::unpacking_collector<(pybind11::return_value_policy)1>’,
inlined from
‘pybind11::detail::object_api<pybind11::detail::accessor<pybind11::detail::accessor_policies::str_attr> >::operator()<(pybind11::return_value_policy)1, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, pybind11::detail::accessor<pybind11::detail::accessor_policies::str_attr>, pybind11::arg_v>(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, pybind11::detail::accessor<pybind11::detail::accessor_policies::str_attr>&&, pybind11::arg_v&&) constpybind11::object’ at /usr/include/pybind11/cast.h:1823:45,
inlined from ‘deprecated(std::basic_string_view<char,
std::char_traits<char> >, std::basic_string_view<char,
std::char_traits<char> >)’ at /home/orion/fedora/libmamba/
libmamba-2.0.6-build/mamba-2.0.6/libmambapy/src/libmambapy/bindings/
legacy.cpp:52:26:
/usr/include/pybind11/cast.h:1812:67: error: ‘SR.32262’ may be used
uninitialized [-Werror=maybe-uninitialized]
1812 | return
unpacking_collector<policy>(std::forward<Args>(args)...);
|
^
/usr/include/pybind11/cast.h: In function
‘deprecated(std::basic_string_view<char, std::char_traits<char> >,
std::basic_string_view<char, std::char_traits<char> >)’:
/usr/include/pybind11/cast.h:1823:45: note: ‘SR.32262’ was declared here
1823 | return
detail::collect_arguments<policy>(std::forward<Args>(args)...).call(derived().ptr());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc1plus: all warnings being treated as errors
gmake[2]: *** [libmambapy/CMakeFiles/bindings.dir/build.make:96:
libmambapy/CMakeFiles/bindings.dir/src/libmambapy/bindings/legacy.cpp.o]
Error 1
I'm guessing 'SR.32262' is some kind of temporary variable. libmamba
has taken the (perhaps admirable?) step of compiling with -Werror so it
fails.
The pybind11/cast.h function is:
/// Collect all arguments, including keywords and unpacking (only
instantiated when needed)
template <return_value_policy policy,
typename... Args,
typename = enable_if_t<!args_are_all_positional<Args...>()>>
unpacking_collector<policy> collect_arguments(Args &&...args) {
// Following argument order rules for generalized unpacking
according to PEP 448
static_assert(constexpr_last<is_positional, Args...>()
< constexpr_first<is_keyword_or_ds, Args...>()
&& constexpr_last<is_s_unpacking, Args...>()
< constexpr_first<is_ds_unpacking,
Args...>(),
"Invalid function call: positional args must precede
keywords and ** unpacking; "
"* unpacking must precede ** unpacking");
return unpacking_collector<policy>(std::forward<Args>(args)...);
}
and it error on the return line.
libmambapy/bindings/legacy.cpp:52:26: is
warnings.attr("warn")(total_message,
builtins.attr("DeprecationWarning"), py::arg("stacklevel") = 2);
This is all way above me - hopefully some C++ expert can chime in here.
[1] - https://src.fedoraproject.org/rpms/libmamba/pull-request/2
I think we definitely have something strange going on here, though
wether it is in pybind11, or libmamba I cannot tell. If I disable
-Werror and go on to build the deps, I start to see python abort() in
one of the tests for conda.
The stack strace starts with:
tests/core/test_solve.py::test_force_remove_1[libmamba] Fatal Python
error: Aborted
Thread 0x00007fc1cd12e6c0 (most recent call first):
File "/usr/lib64/python3.13/socket.py", line 295 in accept
File "/usr/lib/python3.13/site-packages/pytest_rerunfailures.py",
line 440 in run_server
File "/usr/lib64/python3.13/threading.py", line 992 in run
File "/usr/lib64/python3.13/threading.py", line 1041 in _bootstrap_inner
File "/usr/lib64/python3.13/threading.py", line 1012 in _bootstrap
Current thread 0x00007fc2374bfbc0 (most recent call first):
File
"/usr/lib/python3.13/site-packages/conda_libmamba_solver/solver.py",
line 891 in _conda_spec_to_libmamba_spec
File
"/usr/lib/python3.13/site-packages/conda_libmamba_solver/solver.py",
line 409 in _specs_to_request_jobs
File
"/usr/lib/python3.13/site-packages/conda_libmamba_solver/solver.py",
line 356 in _solve_attempt
File
"/usr/lib/python3.13/site-packages/conda_libmamba_solver/solver.py",
line 307 in _solving_loop
...
So I added a print to that:
def _conda_spec_to_libmamba_spec(self, spec: MatchSpec) ->
LibmambaMatchSpec:
print(f'_conda_spec_to_libmamba_spec: parsing {str(spec)}',
file=sys.stderr)
return LibmambaMatchSpec.parse(str(spec))
and I see:
_conda_spec_to_libmamba_spec: parsing numpy 1.7.1 py27_0
which seems pretty innocuous. If I then run in gdb I see:
#4 0x00007ffff440b0c2 in std::__glibcxx_assert_fail
(file=file@entry=0x7fff87946368 "/usr/include/c++/15/string_view",
line=line@entry=260,
function=function@entry=0x7fff87946f80 "constexpr const
std::basic_string_view<_CharT, _Traits>::value_type&
std::basic_string_view<_CharT, _Traits>::operator[](size_type) const
[with _CharT = char; _Traits = std::char_traits<char>; const_r"...,
condition=condition@entry=0x7fff8793d827 "__pos < this->_M_len")
at ../../../../../libstdc++-v3/src/c++11/assert_fail.cc:41
41 abort();
(gdb) up
#5 0x00007fff87615b75 in std::basic_string_view<char,
std::char_traits<char> >::operator[](unsigned long) const [clone
.part.0] [clone .lto_priv.0] [clone .lto_priv.0] (__pos=<optimized out>,
this=<optimized out>, this=<optimized out>, __pos=<optimized out>) at
/usr/include/c++/15/string_view:260
260 __glibcxx_assert(__pos < this->_M_len);
(gdb) up
#6 0x00007fff876198fe in std::basic_string_view<char,
std::char_traits<char> >::operator[] (this=<optimized out>,
__pos=<optimized out>, this=<optimized out>,
__pos=<optimized out>) at /usr/include/c++/15/bits/basic_string.h:410
410 __throw_length_error(__N(__s));
(gdb) up
#7 mamba::specs::MatchSpec::parse (
str='\000' <repeats 112 times>,
"\360\266\377\377\377\177\000\000\001\000\000\000\000\000\000\000*",
'\000' <repeats 15 times>,
"\020\267\377\377\377\177\000\000\001\000\000\000\000\000\000\000*",
'\000' <repeats 39 times>...) at
/usr/src/debug/libmamba-2.0.6-2.fc43.x86_64/libmamba/src/specs/match_spec.cpp:508
508 if (const auto idx = str.find('#'); idx !=
std::string::npos && str[idx - 1] == ' ')
at which point I seem to have garbage.
505 auto MatchSpec::parse(std::string_view str) ->
expected_parse_t<MatchSpec>
506 {
507 // Remove comments, i.e. everything after ` #` (space
included)
508 if (const auto idx = str.find('#'); idx !=
std::string::npos && str[idx - 1] == ' ')
509 {
510 str = str.substr(0, idx);
511 }
(gdb) up
#8 0x00007fff87b2e57b in
pybind11::detail::argument_loader<std::basic_string_view<char,
std::char_traits<char> >
>::call_impl<tl::expected<mamba::specs::MatchSpec,
mamba::specs::ParseError>, tl::expected<mamba::specs::MatchSpec,
mamba::specs::ParseError> (*&)(std::basic_string_view<char,
std::char_traits<char> >), 0ul,
pybind11::detail::void_type>(tl::expected<mamba::specs::MatchSpec,
mamba::specs::ParseError> (*&)(std::basic_string_view<char,
std::char_traits<char> >), std::integer_sequence<unsigned long, 0ul>,
pybind11::detail::void_type&&) && (this=0x7fffffffb910, f=<optimized
out>) at /usr/include/pybind11/cast.h:1631
1631 return
std::forward<Func>(f)(cast_op<Args>(std::move(std::get<Is>(argcasters)))...);
(gdb) print *this
$5 = {static kwargs_pos = -1, static args_pos = -1, static arg_names =
{text = "{str}"}, argcasters = std::tuple containing = {
[0] =
{<pybind11::detail::string_caster<std::basic_string_view<char,
std::char_traits<char> >, true>> = {value = "numpy 1.7.1 py27_0"}, <No
data fields>}}}
valgrind doesn't show any issues that I can see.
Well, it doesn't appear to gcc 15 related as I can reproduce the same
issue in F41.
--
Orion Poplawski
he/him/his - surely the least important thing about me
IT Systems Manager 720-772-5637
NWRA, Boulder/CoRA Office FAX: 303-415-9702
3380 Mitchell Lane or...@nwra.com
Boulder, CO 80301 https://www.nwra.com/
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