Your message dated Fri, 13 Feb 2026 21:17:34 +0200
with message-id <aY94zvoljR_t-vu0@localhost>
and subject line Re: Bug#1125660: toppic: FTBFS: clang++: error: linker command
failed with exit code 1 (use -v to see invocation)
has caused the Debian Bug report #1125660,
regarding toppic: FTBFS: clang++: error: linker command failed with exit code 1
(use -v to see invocation)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1125660: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1125660
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:toppic
Version: 1.8.0+repack1-1
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202601/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:toppic, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0: undefined
reference to `std::vector<int, std::allocator<int> > const
onnx::ParseData<int>(onnx::TensorProto const*)'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0: undefined
reference to `onnx::MakeAttribute(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&, long const&)'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0: undefined
reference to `std::vector<float, std::allocator<float> > const
onnx::ParseData<float>(onnx::TensorProto const*)'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0: undefined
reference to `std::vector<long, std::allocator<long> > const
onnx::ParseData<long>(onnx::TensorProto const*)'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0: undefined
reference to `onnx::MakeAttribute(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&, onnx::TensorProto
const&)'
clang++: error: linker command failed with exit code 1 (use -v to see
invocation)
ctrum_set.cpp.o CMakeFiles/topfd.dir/src/ms/spec/support_peak.cpp.o
CMakeFiles/topfd.dir/src/ms/spec/theo_peak.cpp.o
CMakeFiles/topfd.dir/src/ms/mzml/mzml_ms_group.cpp.o
CMakeFiles/topfd.dir/src/ms/mzml/mzml_ms_group_reader.cpp.o
CMakeFiles/topfd.dir/src/ms/mzml/mzml_ms_json_writer.cpp.o
CMakeFiles/topfd.dir/src/ms/mzml/mzml_ms_sql_writer.cpp.o
CMakeFiles/topfd.dir/src/ms/mzml/mzml_profile.cpp.o
CMakeFiles/topfd.dir/src/ms/mzml/pw_ms_reader.cpp.o -o bin/topfd
-lboost_chrono -lboost_filesystem -lboost_program_options -lboost_iostreams
-lboost_thread -lxerces-c -lsqlite3
/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.12 -lz
/usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0
/usr/lib/x86_64-linux-gnu/libonnx.so.1
make[3]: *** [CMakeFiles/topfd.dir/build.make:2482: bin/topfd] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:148: CMakeFiles/topfd.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
On Thu, Jan 15, 2026 at 04:54:44PM +0000, Santiago Vila wrote:
> Package: src:toppic
> Version: 1.8.0+repack1-1
> Severity: serious
> Tags: ftbfs forky sid
>...
> --------------------------------------------------------------------------------
> [...]
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0: undefined
> reference to `std::vector<int, std::allocator<int> > const
> onnx::ParseData<int>(onnx::TensorProto const*)'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0: undefined
> reference to `onnx::MakeAttribute(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&, long const&)'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0: undefined
> reference to `std::vector<float, std::allocator<float> > const
> onnx::ParseData<float>(onnx::TensorProto const*)'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0: undefined
> reference to `std::vector<long, std::allocator<long> > const
> onnx::ParseData<long>(onnx::TensorProto const*)'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0: undefined
> reference to `onnx::MakeAttribute(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&, onnx::TensorProto
> const&)'
> clang++: error: linker command failed with exit code 1 (use -v to see
> invocation)
> ctrum_set.cpp.o CMakeFiles/topfd.dir/src/ms/spec/support_peak.cpp.o
> CMakeFiles/topfd.dir/src/ms/spec/theo_peak.cpp.o
> CMakeFiles/topfd.dir/src/ms/mzml/mzml_ms_group.cpp.o
> CMakeFiles/topfd.dir/src/ms/mzml/mzml_ms_group_reader.cpp.o
> CMakeFiles/topfd.dir/src/ms/mzml/mzml_ms_json_writer.cpp.o
> CMakeFiles/topfd.dir/src/ms/mzml/mzml_ms_sql_writer.cpp.o
> CMakeFiles/topfd.dir/src/ms/mzml/mzml_profile.cpp.o
> CMakeFiles/topfd.dir/src/ms/mzml/pw_ms_reader.cpp.o -o bin/topfd
> -lboost_chrono -lboost_filesystem -lboost_program_options -lboost_iostreams
> -lboost_thread -lxerces-c -lsqlite3
> /usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.12 -lz
> /usr/lib/x86_64-linux-gnu/libonnxruntime.so.1.21.0
> /usr/lib/x86_64-linux-gnu/libonnx.so.1
> make[3]: *** [CMakeFiles/topfd.dir/build.make:2482: bin/topfd] Error 1
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make[2]: *** [CMakeFiles/Makefile2:148: CMakeFiles/topfd.dir/all] Error 2
> make[2]: *** Waiting for unfinished jobs....
> --------------------------------------------------------------------------------
toppic does build now, this was likely an issue related to the
onnxruntime transition and not specific to toppic.
cu
Adrian
--- End Message ---
