Your message dated Sat, 27 Sep 2025 18:49:04 +0000
with message-id <[email protected]>
and subject line Bug#1096367: fixed in bifrost 1.3.1-2
has caused the Debian Bug report #1096367,
regarding bifrost: ftbfs with GCC-15
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.)
--
1096367: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1096367
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:bifrost
Version: 1.3.1-1
Severity: important
Tags: sid forky
User: [email protected]
Usertags: ftbfs-gcc-15
[This bug is NOT targeted to the upcoming trixie release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.
The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/bifrost_1.3.1-1_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.
To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other Common build failures are new warnings resulting in build failures
with -Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-15/porting_to.html
[...]
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu &&
/usr/bin/cmake -E cmake_depends "Unix Makefiles"
/build/reproducible-path/bifrost-1.3.1
/build/reproducible-path/bifrost-1.3.1/src
/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu
/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src
/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake
"--color="
make[3]: Entering directory
'/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu &&
/usr/bin/cmake -E cmake_depends "Unix Makefiles"
/build/reproducible-path/bifrost-1.3.1
/build/reproducible-path/bifrost-1.3.1/src
/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu
/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src
/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src/CMakeFiles/bifrost_dynamic.dir/DependInfo.cmake
"--color="
make[3]: Leaving directory
'/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
make -f src/CMakeFiles/bifrost_static.dir/build.make
src/CMakeFiles/bifrost_static.dir/build
make[3]: Leaving directory
'/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
make -f src/CMakeFiles/bifrost_dynamic.dir/build.make
src/CMakeFiles/bifrost_dynamic.dir/build
make[3]: Entering directory
'/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
make[3]: Entering directory
'/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
[ 12%] Building CXX object
src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o
[ 12%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o
[ 12%] Building CXX object
src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o
[ 12%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o
[ 15%] Building CXX object src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o
[ 18%] Building CXX object src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
-ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-std=c++11 -fPIC -O3 -MD -MT
src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -MF
CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o.d -o
CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -c
/build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
-ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-std=c++11 -O3 -MD -MT
src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -MF
CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o.d -o
CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -c
/build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
-ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o
-MF CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o.d -o
CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -c
/build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
-ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-std=c++11 -fPIC -O3 -MD -MT
src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -MF
CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o.d -o
CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -c
/build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
-ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -MF
CMakeFiles/bifrost_static.dir/BitContainer.cpp.o.d -o
CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -c
/build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
-ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o -MF
CMakeFiles/bifrost_static.dir/ColorSet.cpp.o.d -o
CMakeFiles/bifrost_static.dir/ColorSet.cpp.o -c
/build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp
[ 25%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
[ 25%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
-ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF
CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o
CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c
/build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
-ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o
-MF CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o.d -o
CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -c
/build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp
In file included from
/build/reproducible-path/bifrost-1.3.1/src/DataManager.hpp:10,
from
/build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.hpp:10,
from /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:2:
/build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc: In copy constructor
‘DataStorage<Unitig_data_t>::DataStorage(const DataStorage<Unitig_data_t>&)’:
/build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:81:69: error: ‘const
class DataStorage<Unitig_data_t>’ has no member named ‘sz_link’
[-Wtemplate-body]
81 | for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] =
o.sz_link[i].load();
|
^~~~~~~
In file included from
/build/reproducible-path/bifrost-1.3.1/src/DataManager.hpp:10,
from
/build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.hpp:10,
from /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:2:
/build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc: In copy constructor
‘DataStorage<Unitig_data_t>::DataStorage(const DataStorage<Unitig_data_t>&)’:
/build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:81:69: error: ‘const
class DataStorage<Unitig_data_t>’ has no member named ‘sz_link’
[-Wtemplate-body]
81 | for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] =
o.sz_link[i].load();
|
^~~~~~~
[ 28%] Building CXX object
src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
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src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o -MF
CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o.d -o
CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o -c
/build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp
[ 31%] Building CXX object
src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
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src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o -MF
CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o.d -o
CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o -c
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src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
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CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o.d -o
CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -c
/build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp
[ 37%] Building CXX object src/CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
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CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o.d -o
CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o -c
/build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.cpp
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src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o
cd /build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS
-I/build/reproducible-path/bifrost-1.3.1/src -g -O2
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src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -MF
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/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32
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/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS
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make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:82:
src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o] Error 1
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'/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:147: src/CMakeFiles/bifrost_dynamic.dir/all]
Error 2
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make[2]: *** [CMakeFiles/Makefile2:115: src/CMakeFiles/bifrost_static.dir/all]
Error 2
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'/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:139: all] Error 2
make[1]: Leaving directory
'/build/reproducible-path/bifrost-1.3.1/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install
--strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: bifrost
Source-Version: 1.3.1-2
Done: Sergio Durigan Junior <[email protected]>
We believe that the bug you reported is fixed in the latest version of
bifrost, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Sergio Durigan Junior <[email protected]> (supplier of updated bifrost
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 27 Sep 2025 14:33:42 -0400
Source: bifrost
Architecture: source
Version: 1.3.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Sergio Durigan Junior <[email protected]>
Closes: 1096367
Changes:
bifrost (1.3.1-2) unstable; urgency=medium
.
* Team upload.
* d/p/0002-Fix-compilation-error-with-custom-unitig-data.patch:
Fix FTBFS with GCC 15. (Closes: #1096367)
* d/bifrost.examples: Remove bugs file.
Checksums-Sha1:
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