Your message dated Thu, 25 Sep 2025 20:26:11 +0000
with message-id <[email protected]>
and subject line Bug#1097555: fixed in pbcopper 2.3.0+dfsg-3
has caused the Debian Bug report #1097555,
regarding pbcopper: 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.)
--
1097555: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097555
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:pbcopper
Version: 2.3.0+dfsg-2
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/pbcopper_2.3.0+dfsg-2_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
[...]
../meson.build:2: WARNING: Keyword argument "default_options" defined multiple
times.
WARNING: This will be an error in Meson 2.0.
Project name: pbcopper
Project version: 2.3.0
C compiler for the host machine: cc (gcc 15.0.1 "cc (Debian 15-20250213-1)
15.0.1 20250213 (experimental) [master r15-7502-g26baa2c09b3]")
C linker for the host machine: cc ld.bfd 2.44
C++ compiler for the host machine: c++ (gcc 15.0.1 "c++ (Debian 15-20250213-1)
15.0.1 20250213 (experimental) [master r15-7502-g26baa2c09b3]")
C++ linker for the host machine: c++ ld.bfd 2.44
Host machine cpu family: x86_64
Host machine cpu: x86_64
Compiler for C++ supports arguments -Wduplicated-cond: YES
Compiler for C++ supports arguments -Wduplicated-branches: YES
Compiler for C++ supports arguments -Wlogical-op: YES
Compiler for C++ supports arguments -Wrestrict: YES
Compiler for C++ supports arguments -Wdouble-promotion: YES
Compiler for C++ supports arguments -Wshadow: YES
Compiler for C++ supports arguments -Wformat=1: YES
Compiler for C supports arguments -Wc++-compat: YES
Compiler for C supports arguments -Wno-unused-parameter: YES
Compiler for C supports arguments -Wno-unused-variable: YES
Compiler for C supports arguments -Wno-sign-compare: YES
Compiler for C supports arguments -Wno-unused-but-set-variable: YES
Compiler for C supports arguments -msse4.1: YES
Run-time dependency threads found: YES
Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1
Run-time dependency Boost found: YES 1.83.0 (/usr/include)
Configuring PbcopperVersion.cpp using configuration
Configuring LibraryVersion.h using configuration
Program tools/check-formatting found: YES
(/build/reproducible-path/pbcopper-2.3.0+dfsg/tools/check-formatting)
Run-time dependency GTest found: YES 1.15.0
Configuring PbcopperTestData.h using configuration
Build targets in project: 5
pbcopper 2.3.0
User defined options
buildtype : plain
libdir : lib/x86_64-linux-gnu
localstatedir : /var
prefix : /usr
python.bytecompile: -1
sysconfdir : /etc
wrap_mode : nodownload
Found ninja-1.12.1 at /usr/bin/ninja
dh_auto_build -O--builddirectory=build
cd build && LC_ALL=C.UTF-8 ninja -j8 -v
[1/182] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in
src/LibraryGitHash.h 2.3.0 /build/reproducible-path/pbcopper-2.3.0+dfsg/src
@COPPER_GIT_SHA1@ '(.*)' git describe --always '--dirty=*'
[2/182] /usr/bin/meson --internal vcstagger
../src/utility/PbcopperGitHash.cpp.in src/utility/PbcopperGitHash.cpp 2.3.0
/build/reproducible-path/pbcopper-2.3.0+dfsg/src/utility @COPPER_GIT_SHA1@
'(.*)' git describe --always '--dirty=*'
[3/182] c++ -Isrc/libpbcopper.so.2.3.0.p -Isrc -I../src -Iinclude -I../include
-Isrc/utility -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1
-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -g -O2
-ffile-prefix-map=/build/reproducible-path/pbcopper-2.3.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fPIC -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches
-Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
src/libpbcopper.so.2.3.0.p/meson-generated_.._utility_PbcopperGitHash.cpp.o -MF
src/libpbcopper.so.2.3.0.p/meson-generated_.._utility_PbcopperGitHash.cpp.o.d
-o src/libpbcopper.so.2.3.0.p/meson-generated_.._utility_PbcopperGitHash.cpp.o
-c src/utility/PbcopperGitHash.cpp
[4/182] c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include
-I../tests/include -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1
-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -g -O2
-ffile-prefix-map=/build/reproducible-path/pbcopper-2.3.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fPIC -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
-pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches
-Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
tests/pbcopper_test.p/src_algorithm_test_LSHIndex.cpp.o -MF
tests/pbcopper_test.p/src_algorithm_test_LSHIndex.cpp.o.d -o
tests/pbcopper_test.p/src_algorithm_test_LSHIndex.cpp.o -c
../tests/src/algorithm/test_LSHIndex.cpp
FAILED: tests/pbcopper_test.p/src_algorithm_test_LSHIndex.cpp.o
c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include
-I../tests/include -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1
-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -g -O2
-ffile-prefix-map=/build/reproducible-path/pbcopper-2.3.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fPIC -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
-pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches
-Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
tests/pbcopper_test.p/src_algorithm_test_LSHIndex.cpp.o -MF
tests/pbcopper_test.p/src_algorithm_test_LSHIndex.cpp.o.d -o
tests/pbcopper_test.p/src_algorithm_test_LSHIndex.cpp.o -c
../tests/src/algorithm/test_LSHIndex.cpp
In file included from ../tests/src/algorithm/test_LSHIndex.cpp:2:
../include/pbcopper/algorithm/LSHIndex.h: In static member function ‘static
PacBio::Algorithm::LSHIndex<KeyT, IdT> PacBio::Algorithm::LSHIndex<KeyT,
IdT>::CloneLike(const PacBio::Algorithm::LSHIndex<KeyT, IdT>&)’:
../include/pbcopper/algorithm/LSHIndex.h:232:32: error: ‘const class
PacBio::Algorithm::LSHIndex<KeyT, IdT>’ has no member named ‘isBottomKOnly__’;
did you mean ‘isBottomKOnly_’? [-Wtemplate-body]
232 | res.isBottomKOnly_ = o.isBottomKOnly__;
| ^~~~~~~~~~~~~~~
| isBottomKOnly_
[5/182] c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include
-I../tests/include -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1
-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -g -O2
-ffile-prefix-map=/build/reproducible-path/pbcopper-2.3.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fPIC -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
-pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches
-Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
tests/pbcopper_test.p/src_align_test_EdlibAlign.cpp.o -MF
tests/pbcopper_test.p/src_align_test_EdlibAlign.cpp.o.d -o
tests/pbcopper_test.p/src_align_test_EdlibAlign.cpp.o -c
../tests/src/align/test_EdlibAlign.cpp
[6/182] c++ -Isrc/libpbcopper.so.2.3.0.p -Isrc -I../src -Iinclude -I../include
-Isrc/utility -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1
-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -g -O2
-ffile-prefix-map=/build/reproducible-path/pbcopper-2.3.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fPIC -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches
-Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
src/libpbcopper.so.2.3.0.p/LibraryInfo.cpp.o -MF
src/libpbcopper.so.2.3.0.p/LibraryInfo.cpp.o.d -o
src/libpbcopper.so.2.3.0.p/LibraryInfo.cpp.o -c ../src/LibraryInfo.cpp
[7/182] c++ -Isrc/libpbcopper.so.2.3.0.p -Isrc -I../src -Iinclude -I../include
-Isrc/utility -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1
-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -g -O2
-ffile-prefix-map=/build/reproducible-path/pbcopper-2.3.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fPIC -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches
-Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
src/libpbcopper.so.2.3.0.p/algorithm_Heteroduplex.cpp.o -MF
src/libpbcopper.so.2.3.0.p/algorithm_Heteroduplex.cpp.o.d -o
src/libpbcopper.so.2.3.0.p/algorithm_Heteroduplex.cpp.o -c
../src/algorithm/Heteroduplex.cpp
[8/182] c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include
-I../tests/include -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1
-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -g -O2
-ffile-prefix-map=/build/reproducible-path/pbcopper-2.3.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fPIC -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
-pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches
-Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
tests/pbcopper_test.p/src_align_test_BandedChainAlign.cpp.o -MF
tests/pbcopper_test.p/src_align_test_BandedChainAlign.cpp.o.d -o
tests/pbcopper_test.p/src_align_test_BandedChainAlign.cpp.o -c
../tests/src/align/test_BandedChainAlign.cpp
[9/182] c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include
-I../tests/include -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1
-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -g -O2
-ffile-prefix-map=/build/reproducible-path/pbcopper-2.3.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fPIC -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
-pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches
-Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
tests/pbcopper_test.p/src_algorithm_test_Heteroduplex.cpp.o -MF
tests/pbcopper_test.p/src_algorithm_test_Heteroduplex.cpp.o.d -o
tests/pbcopper_test.p/src_algorithm_test_Heteroduplex.cpp.o -c
../tests/src/algorithm/test_Heteroduplex.cpp
[10/182] c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include
-I../tests/include -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1
-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -g -O2
-ffile-prefix-map=/build/reproducible-path/pbcopper-2.3.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fPIC -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
-pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches
-Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
tests/pbcopper_test.p/src_algorithm_test_KMerIndex.cpp.o -MF
tests/pbcopper_test.p/src_algorithm_test_KMerIndex.cpp.o.d -o
tests/pbcopper_test.p/src_algorithm_test_KMerIndex.cpp.o -c
../tests/src/algorithm/test_KMerIndex.cpp
[11/182] c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include
-I../tests/include -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1
-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -g -O2
-ffile-prefix-map=/build/reproducible-path/pbcopper-2.3.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fPIC -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
-pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches
-Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
tests/pbcopper_test.p/src_align_test_Alignment.cpp.o -MF
tests/pbcopper_test.p/src_align_test_Alignment.cpp.o.d -o
tests/pbcopper_test.p/src_align_test_Alignment.cpp.o -c
../tests/src/align/test_Alignment.cpp
ninja: build stopped: subcommand failed.
dh_auto_build: error: cd build && LC_ALL=C.UTF-8 ninja -j8 -v returned exit
code 1
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: pbcopper
Source-Version: 2.3.0+dfsg-3
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
pbcopper, 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.
Étienne Mollier <[email protected]> (supplier of updated pbcopper 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: Thu, 25 Sep 2025 21:14:18 +0200
Source: pbcopper
Architecture: source
Version: 2.3.0+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1097555
Changes:
pbcopper (2.3.0+dfsg-3) unstable; urgency=medium
.
* Team upload.
.
[ Michael R. Crusoe ]
* d/control: simplify architecture specifications by using provisions
from the architecture-properties package.
* d/salsi-ci.yml: skip i386 build, add link to salsa-ci docs.
.
[ Étienne Mollier ]
* gcc-15: new patch: fix build failure with gcc-15. (Closes: #1097555)
* d/control: build depends on pkgconf.
* d/patches/*: normalize Last-Update timestamp.
* d/watch: upgrade to version 5 watch file.
* d/control: remove redundant Rules-Requires-Root: no.
* d/control: declare compliance to standards version 4.7.2.
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Files:
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pbcopper_2.3.0+dfsg-3.dsc
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