Your message dated Fri, 13 Feb 2026 21:06:45 +0000
with message-id <[email protected]>
and subject line Bug#1127540: fixed in spoa 4.1.5-2
has caused the Debian Bug report #1127540,
regarding spoa: FTBFS: dpkg-gensymbols: error: some symbols or patterns
disappeared in the symbols file: see diff output below
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.)
--
1127540: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1127540
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:spoa
Version: 4.1.5-1
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/202602/
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:spoa, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --no-parallel
dh_autoreconf_clean -O--no-parallel
dh_clean -O--no-parallel
debian/rules binary
dh binary --no-parallel
dh_update_autotools_config -O--no-parallel
dh_autoreconf -O--no-parallel
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -DCMAKE_BUILD_TYPE=Release -Dspoa_build_executable=ON
-Dspoa_build_tests=ON -Dspoa_use_simde_nonvec=ON -Dspoa_use_simde_openmp=ON
-Dspoa_optimize_for_native=OFF
-DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu/cmake/CpuFeatures
-Dspoa_generate_dispatch=ON
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb
PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr
-DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc
-DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON
-DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON
-DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run
-DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles"
-DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu
-DCMAKE_BUILD_TYPE=Release -Dspoa_build_executable=ON -Dspoa_build_tests=ON
-Dspoa_use_simde_nonvec=ON -Dspoa_use_simde_openmp=ON
-Dspoa_optimize_for_native=OFF
-DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu/cmake/CpuFeatures
-Dspoa_generate_dispatch=ON ..
-- The CXX compiler identification is GNU 15.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning (dev) at /usr/share/cmake-4.2/Modules/FetchContent.cmake:1963
(message):
Calling FetchContent_Populate(simde) is deprecated, call
FetchContent_MakeAvailable(simde) instead. Policy CMP0169 can be set to
OLD to allow FetchContent_Populate(simde) to be called directly for now,
but the ability to call it with declared details will be removed completely
in a future version.
Call Stack (most recent call first):
CMakeLists.txt:53 (FetchContent_Populate)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning at /usr/share/cmake-4.2/Modules/FetchContent.cmake:2121 (message):
FETCHCONTENT_FULLY_DISCONNECTED is set to true, which requires the source
directory for dependency simde to already be populated. This generally
means it must not be set to true the first time CMake is run in a build
directory. The following source directory should already be populated, but
it doesn't exist:
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/simde-src
Policy CMP0170 controls enforcement of this requirement.
Call Stack (most recent call first):
/usr/share/cmake-4.2/Modules/FetchContent.cmake:1988:EVAL:1
(__FetchContent_Populate)
/usr/share/cmake-4.2/Modules/FetchContent.cmake:1988 (cmake_language)
CMakeLists.txt:53 (FetchContent_Populate)
-- Configuring done (0.3s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
spoa_build_executable
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -O--no-parallel
cd obj-x86_64-linux-gnu && make -j1 INSTALL="install
--strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
--check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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"Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>
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-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3
-Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -fopenmp-simd -O3
-DNDEBUG -std=c++17 -MD -MT
CMakeFiles/spoa_static.dir/src/sisd_alignment_engine.cpp.o -MF
CMakeFiles/spoa_static.dir/src/sisd_alignment_engine.cpp.o.d -o
CMakeFiles/spoa_static.dir/src/sisd_alignment_engine.cpp.o -c
/<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp
[ 76%] Linking CXX static library lib/libspoa_static.a
/usr/bin/cmake -P CMakeFiles/spoa_static.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/spoa_static.dir/link.txt
--verbose=1
/usr/bin/ar qc lib/libspoa_static.a
CMakeFiles/spoa_static.dir/src/alignment_engine.cpp.o
CMakeFiles/spoa_static.dir/src/graph.cpp.o
CMakeFiles/spoa_static.dir/src/sisd_alignment_engine.cpp.o
/usr/bin/ranlib lib/libspoa_static.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 76%] Built target spoa_static
make -f CMakeFiles/spoa_exe.dir/build.make CMakeFiles/spoa_exe.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends
"Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/spoa_exe.dir/DependInfo.cmake
"--color=" spoa_exe
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/spoa_exe.dir/build.make CMakeFiles/spoa_exe.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 82%] Building CXX object CMakeFiles/spoa_exe.dir/src/main.cpp.o
/usr/bin/c++ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP
-DSIMDE_NO_NATIVE -DSPOA_GENERATE_DISPATCH -DSPOA_USE_SIMDE
-DSTACK_LINE_READER_BUFFER_SIZE=1024 -I/<<PKGBUILDDIR>>/include
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/simde-src -isystem
/usr/include/cpu_features -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2
-Wall -Wextra -pedantic -fopenmp-simd -O3 -DNDEBUG -std=c++17 -MD -MT
CMakeFiles/spoa_exe.dir/src/main.cpp.o -MF
CMakeFiles/spoa_exe.dir/src/main.cpp.o.d -o
CMakeFiles/spoa_exe.dir/src/main.cpp.o -c /<<PKGBUILDDIR>>/src/main.cpp
[ 88%] Linking CXX executable bin/spoa
/usr/bin/cmake -E cmake_link_script CMakeFiles/spoa_exe.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2
-Wall -Wextra -pedantic -fopenmp-simd -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now
-Wl,--dependency-file=CMakeFiles/spoa_exe.dir/link.d
CMakeFiles/spoa_exe.dir/src/main.cpp.o -o bin/spoa
-Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib: lib/libspoa.so.7.0.0 -lz
/usr/lib/x86_64-linux-gnu/libcpu_features.a -ldl
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 88%] Built target spoa_exe
make -f CMakeFiles/spoa_test.dir/build.make CMakeFiles/spoa_test.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends
"Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/spoa_test.dir/DependInfo.cmake
"--color=" spoa_test
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/spoa_test.dir/build.make CMakeFiles/spoa_test.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 94%] Building CXX object CMakeFiles/spoa_test.dir/test/spoa_test.cpp.o
/usr/bin/c++ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP
-DSIMDE_NO_NATIVE -DSPOA_GENERATE_DISPATCH -DSPOA_USE_SIMDE
-DSTACK_LINE_READER_BUFFER_SIZE=1024 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
-I/<<PKGBUILDDIR>>/include
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/simde-src -isystem
/usr/include/cpu_features -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2
-Wall -Wextra -pedantic -fopenmp-simd -O3 -DNDEBUG -std=c++17
-DGTEST_HAS_PTHREAD=1 -MD -MT CMakeFiles/spoa_test.dir/test/spoa_test.cpp.o -MF
CMakeFiles/spoa_test.dir/test/spoa_test.cpp.o.d -o
CMakeFiles/spoa_test.dir/test/spoa_test.cpp.o -c
/<<PKGBUILDDIR>>/test/spoa_test.cpp
[100%] Linking CXX executable bin/spoa_test
/usr/bin/cmake -E cmake_link_script CMakeFiles/spoa_test.dir/link.txt
--verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2
-Wall -Wextra -pedantic -fopenmp-simd -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now
-Wl,--dependency-file=CMakeFiles/spoa_test.dir/link.d
CMakeFiles/spoa_test.dir/test/spoa_test.cpp.o -o bin/spoa_test
-Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib lib/libspoa.so.7.0.0 -lz
/usr/lib/x86_64-linux-gnu/libcpu_features.a -ldl
/usr/lib/x86_64-linux-gnu/libgtest_main.a /usr/lib/x86_64-linux-gnu/libgtest.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[100%] Built target spoa_test
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
`find . -name spoa_test`
Running main() from ./googletest/src/gtest_main.cc
[==========] Running 22 tests from 2 test suites.
[----------] Global test environment set-up.
[----------] 3 tests from SpoaAlignmentTest
[ RUN ] SpoaAlignmentTest.TypeError
[ OK ] SpoaAlignmentTest.TypeError (0 ms)
[ RUN ] SpoaAlignmentTest.EmptyInput
[ OK ] SpoaAlignmentTest.EmptyInput (0 ms)
[ RUN ] SpoaAlignmentTest.LargeInput
[ OK ] SpoaAlignmentTest.LargeInput (0 ms)
[----------] 3 tests from SpoaAlignmentTest (0 ms total)
[----------] 19 tests from SpoaTest
[ RUN ] SpoaTest.Clear
[ OK ] SpoaTest.Clear (61 ms)
[ RUN ] SpoaTest.Local
[ OK ] SpoaTest.Local (31 ms)
[ RUN ] SpoaTest.LocalAffine
[ OK ] SpoaTest.LocalAffine (45 ms)
[ RUN ] SpoaTest.LocalConvex
[ OK ] SpoaTest.LocalConvex (50 ms)
[ RUN ] SpoaTest.LocalWithQualities
[ OK ] SpoaTest.LocalWithQualities (30 ms)
[ RUN ] SpoaTest.LocalAffineWithQualities
[ OK ] SpoaTest.LocalAffineWithQualities (45 ms)
[ RUN ] SpoaTest.LocalConvexWithQualities
[ OK ] SpoaTest.LocalConvexWithQualities (49 ms)
[ RUN ] SpoaTest.Global
[ OK ] SpoaTest.Global (30 ms)
[ RUN ] SpoaTest.GlobalAffine
[ OK ] SpoaTest.GlobalAffine (43 ms)
[ RUN ] SpoaTest.GlobalConvex
[ OK ] SpoaTest.GlobalConvex (48 ms)
[ RUN ] SpoaTest.GlobalWithQualities
[ OK ] SpoaTest.GlobalWithQualities (30 ms)
[ RUN ] SpoaTest.GlobalAffineWithQualities
[ OK ] SpoaTest.GlobalAffineWithQualities (43 ms)
[ RUN ] SpoaTest.GlobalConvexWithQualities
[ OK ] SpoaTest.GlobalConvexWithQualities (48 ms)
[ RUN ] SpoaTest.SemiGlobal
[ OK ] SpoaTest.SemiGlobal (29 ms)
[ RUN ] SpoaTest.SemiGlobalAffine
[ OK ] SpoaTest.SemiGlobalAffine (44 ms)
[ RUN ] SpoaTest.SemiGlobalConvex
[ OK ] SpoaTest.SemiGlobalConvex (48 ms)
[ RUN ] SpoaTest.SemiGlobalWithQualities
[ OK ] SpoaTest.SemiGlobalWithQualities (29 ms)
[ RUN ] SpoaTest.SemiGlobalAffineWithQualities
[ OK ] SpoaTest.SemiGlobalAffineWithQualities (43 ms)
[ RUN ] SpoaTest.SemiGlobalConvexWithQualities
[ OK ] SpoaTest.SemiGlobalConvexWithQualities (48 ms)
[----------] 19 tests from SpoaTest (803 ms total)
[----------] Global test environment tear-down
[==========] 22 tests from 2 test suites ran. (803 ms total)
[ PASSED ] 22 tests.
`find . -name spoa | grep bin` test/data/sample.fastq.gz
>Consensus LN:i:496
AATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTTTACACGCGCAACCAAGGATTTCGG
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--no-parallel
dh_prep -O--no-parallel
dh_auto_install -O--no-parallel
cd obj-x86_64-linux-gnu && make -j1 install
DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install
--strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
--check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing:
/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libspoa.so.7.0.0
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libspoa.so
-- Installing:
/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libspoa_static.a
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/spoa
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/spoa/spoa.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/spoa/graph.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/spoa/alignment_engine.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/spoa/version.hpp
-- Installing:
/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/spoa/spoaTargets.cmake
-- Installing:
/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/spoa/spoaTargets-release.cmake
-- Installing:
/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/spoa/spoaConfig.cmake
-- Installing:
/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/spoa/spoaConfigVersion.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/spoa
-- Set non-toolchain portion of runtime path of
"/<<PKGBUILDDIR>>/debian/tmp/usr/bin/spoa" to ""
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
d-shlibmove --commit \
--multiarch \
--devunversioned \
--exclude-la \
--exclude-a \
--movedev debian/tmp/usr/include/spoa usr/include \
--movedev debian/tmp/usr/lib/x86_64-linux-gnu/cmake
/usr/lib/x86_64-linux-gnu \
debian/tmp/usr/lib/*/*.so
Library package automatic movement utility
set -e
install -d -m 755 debian/libspoa-dev/usr/lib/x86_64-linux-gnu
install -d -m 755 debian/libspoa7.0.0/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/libspoa.so
debian/libspoa-dev/usr/lib/x86_64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libspoa.so.7.0.0
debian/libspoa7.0.0/usr/lib/x86_64-linux-gnu
PKGDEV=libspoa-dev
PKGSHL=libspoa7.0.0
install -d -m 755 debian/libspoa-dev/usr/include
mv debian/tmp/usr/include/spoa debian/libspoa-dev/usr/include
install -d -m 755 debian/libspoa-dev//usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/cmake
debian/libspoa-dev//usr/lib/x86_64-linux-gnu
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -O--no-parallel
dh_installchangelogs -O--no-parallel
dh_installexamples -O--no-parallel
dh_installman -O--no-parallel
dh_installsystemduser -O--no-parallel
dh_perl -O--no-parallel
dh_link -O--no-parallel
dh_strip_nondeterminism -O--no-parallel
dh_compress -O--no-parallel
dh_fixperms -O--no-parallel
dh_missing -O--no-parallel
dh_dwz -a -O--no-parallel
dh_strip -a -O--no-parallel
dh_makeshlibs -a -O--no-parallel
dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see
diff output below
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols
file: see diff output below
dpkg-gensymbols: warning: debian/libspoa7.0.0/DEBIAN/symbols does not match
completely debian/libspoa7.0.0.symbols.amd64
--- debian/libspoa7.0.0.symbols.amd64 (libspoa7.0.0_4.1.5-1_amd64)
+++ dpkg-gensymbolsAg564Y 2026-02-09 15:48:45.403228786 +0000
@@ -28,8 +28,8 @@
GetXCR0Eax@Base 4.0.7
StackLineReader_Initialize@Base 4.0.7
StackLineReader_NextLine@Base 4.0.7
-
(optional)_ZGVN6cereal6detail12StaticObjectINS0_18PolymorphicCastersEE8instanceE@Base
4.0.5
-
(optional)_ZGVZN6cereal6detail12StaticObjectINS0_18PolymorphicCastersEE6createEvE1t@Base
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+#MISSING: 4.1.5-1#
(optional)_ZGVN6cereal6detail12StaticObjectINS0_18PolymorphicCastersEE8instanceE@Base
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+#MISSING: 4.1.5-1#
(optional)_ZGVZN6cereal6detail12StaticObjectINS0_18PolymorphicCastersEE6createEvE1t@Base
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_ZN4spoa15AlignmentEngine6CreateENS_13AlignmentTypeEaaa@Base 4.0.5
_ZN4spoa15AlignmentEngine6CreateENS_13AlignmentTypeEaaaa@Base 4.0.5
@@ -120,10 +120,10 @@
_ZN4spoa5GraphD1Ev@Base 1.1.3
_ZN4spoa5GraphD2Ev@Base 1.1.3
_ZN4spoa7VersionB5cxx11Ev@Base 4.1.4
-
(optional)_ZN6cereal6detail12StaticObjectINS0_18PolymorphicCastersEE6createEv@Base
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-
(optional)_ZN6cereal6detail12StaticObjectINS0_18PolymorphicCastersEE8instanceE@Base
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- (optional)_ZN6cereal6detail18PolymorphicCastersD1Ev@Base 4.0.5
- (optional)_ZN6cereal6detail18PolymorphicCastersD2Ev@Base 4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZN6cereal6detail12StaticObjectINS0_18PolymorphicCastersEE6createEv@Base
4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZN6cereal6detail12StaticObjectINS0_18PolymorphicCastersEE8instanceE@Base
4.0.5
+#MISSING: 4.1.5-1# (optional)_ZN6cereal6detail18PolymorphicCastersD1Ev@Base
4.0.5
+#MISSING: 4.1.5-1# (optional)_ZN6cereal6detail18PolymorphicCastersD2Ev@Base
4.0.5
_ZNK4spoa15AlignmentEngine23WorstCaseAlignmentScoreEll@Base 4.0.5
_ZNK4spoa5Graph15ExtractSubgraphEPKNS0_4NodeES3_@Base 4.0.5
_ZNK4spoa5Graph15UpdateAlignmentERKSt6vectorIPKNS0_4NodeESaIS4_EEPS1_ISt4pairIiiESaISA_EE@Base
4.0.5
@@ -134,48 +134,50 @@
_ZNK4spoa5Graph8PrintDotERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base
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-
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4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZNSt10_HashtableISt10type_indexSt4pairIKS0_St13unordered_mapIS0_St6vectorIPKN6cereal6detail17PolymorphicCasterESaIS9_EESt4hashIS0_ESt8equal_toIS0_ESaIS1_IS2_SB_EEEESaISJ_ENSt8__detail10_Select1stESF_SD_NSL_18_Mod_range_hashingENSL_20_Default_ranged_hashENSL_20_Prime_rehash_policyENSL_17_Hashtable_traitsILb0ELb0ELb1EEEE5clearEv@Base
4.0.5
(optional)_ZNSt10_HashtableIjjSaIjENSt8__detail9_IdentityESt8equal_toIjESt4hashIjENS1_18_Mod_range_hashingENS1_20_Default_ranged_hashENS1_20_Prime_rehash_policyENS1_17_Hashtable_traitsILb0ELb1ELb1EEEE15_M_emplace_uniqIJRKjEEESt4pairINS1_14_Node_iteratorIjLb1ELb0EEEbEDpOT_@Base
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4.1.4
_ZNSt13_Bvector_baseISaIbEE13_M_deallocateEv@Base 1.1.3
-
(optional)_ZNSt5dequeIPKN4spoa5Graph4NodeESaIS4_EE16_M_push_back_auxIJRKS4_EEEvDpOT_@Base
4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZNSt5dequeIPKN4spoa5Graph4NodeESaIS4_EE16_M_push_back_auxIJRKS4_EEEvDpOT_@Base
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(optional)_ZNSt5dequeIPKN4spoa5Graph4NodeESaIS4_EE17_M_reallocate_mapEmb@Base
4.1.5
-
(optional)_ZNSt5dequeIPN4spoa5Graph4NodeESaIS3_EE16_M_push_back_auxIJRKS3_EEEvDpOT_@Base
4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZNSt5dequeIPN4spoa5Graph4NodeESaIS3_EE16_M_push_back_auxIJRKS3_EEEvDpOT_@Base
4.0.5
_ZNSt5dequeIPN4spoa5Graph4NodeESaIS3_EE17_M_reallocate_mapEmb@Base 4.0.5
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(optional)_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_appendIJRS5_EEEvDpOT_@Base
4.1.4
-
(optional)_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base
1.1.3
-
_ZNSt6vectorIPKN4spoa5Graph4NodeESaIS4_EE14_M_fill_insertEN9__gnu_cxx17__normal_iteratorIPS4_S6_EEmRKS4_@Base
4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base
1.1.3
+#MISSING: 4.1.5-1#
_ZNSt6vectorIPKN4spoa5Graph4NodeESaIS4_EE14_M_fill_insertEN9__gnu_cxx17__normal_iteratorIPS4_S6_EEmRKS4_@Base
4.0.5
(optional)_ZNSt6vectorIPN4spoa5Graph4EdgeESaIS3_EE17_M_realloc_appendIJS3_EEEvDpOT_@Base
4.1.4
-
(optional)_ZNSt6vectorIPN4spoa5Graph4EdgeESaIS3_EE17_M_realloc_insertIJS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_@Base
4.0.5
-
(optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EE12emplace_backIJRS3_EEEvDpOT_@Base
4.0.5
-
(optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EE12emplace_backIJS3_EEEvDpOT_@Base
4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorIPN4spoa5Graph4EdgeESaIS3_EE17_M_realloc_insertIJS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_@Base
4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EE12emplace_backIJRS3_EEEvDpOT_@Base
4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EE12emplace_backIJS3_EEEvDpOT_@Base
4.0.5
(optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EE17_M_realloc_appendIJRKS3_EEEvDpOT_@Base
4.1.4
-
(optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EE17_M_realloc_appendIJRS3_EEEvDpOT_@Base
4.1.4
-
(optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EE17_M_realloc_insertIJRKS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_@Base
4.0.5
- (optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EED1Ev@Base 4.1.4
- (optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EED2Ev@Base 4.1.4
-
(optional)_ZNSt6vectorISt10unique_ptrIN4spoa5Graph4EdgeESt14default_deleteIS3_EESaIS6_EE17_M_realloc_insertIJPS3_EEEvN9__gnu_cxx17__normal_iteratorIPS6_S8_EEDpOT_@Base
4.0.7
-
(optional)_ZNSt6vectorISt10unique_ptrIN4spoa5Graph4NodeESt14default_deleteIS3_EESaIS6_EE17_M_realloc_insertIJPS3_EEEvN9__gnu_cxx17__normal_iteratorIPS6_S8_EEDpOT_@Base
4.0.5
- (optional)_ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJRjiEEEvDpOT_@Base
4.0.5
- (optional)_ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJijEEEvDpOT_@Base
3.0.0
- (optional)_ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJjiEEEvDpOT_@Base
3.4.0
- (optional)_ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJjjEEEvDpOT_@Base
3.0.0
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EE17_M_realloc_appendIJRS3_EEEvDpOT_@Base
4.1.4
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EE17_M_realloc_insertIJRKS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_@Base
4.0.5
+#MISSING: 4.1.5-1# (optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EED1Ev@Base
4.1.4
+#MISSING: 4.1.5-1# (optional)_ZNSt6vectorIPN4spoa5Graph4NodeESaIS3_EED2Ev@Base
4.1.4
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorISt10unique_ptrIN4spoa5Graph4EdgeESt14default_deleteIS3_EESaIS6_EE17_M_realloc_insertIJPS3_EEEvN9__gnu_cxx17__normal_iteratorIPS6_S8_EEDpOT_@Base
4.0.7
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorISt10unique_ptrIN4spoa5Graph4NodeESt14default_deleteIS3_EESaIS6_EE17_M_realloc_insertIJPS3_EEEvN9__gnu_cxx17__normal_iteratorIPS6_S8_EEDpOT_@Base
4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJRjiEEEvDpOT_@Base
4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJijEEEvDpOT_@Base 3.0.0
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJjiEEEvDpOT_@Base 3.4.0
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJjjEEEvDpOT_@Base 3.0.0
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE17_M_realloc_appendIJRjiEEEvDpOT_@Base
4.1.4
-
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE17_M_realloc_appendIJijEEEvDpOT_@Base
4.1.4
-
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE17_M_realloc_appendIJjjEEEvDpOT_@Base
4.1.4
-
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE17_M_realloc_insertIJRjiEEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base
4.1.4
-
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE17_M_realloc_insertIJijEEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base
4.1.4
-
_ZNSt6vectorIiSaIiEE14_M_fill_insertEN9__gnu_cxx17__normal_iteratorIPiS1_EEmRKi@Base
1.1.3
- (optional)_ZNSt6vectorIiSaIiEED1Ev@Base 4.1.4
- (optional)_ZNSt6vectorIiSaIiEED2Ev@Base 4.1.4
- (optional)_ZNSt6vectorIjSaIjEE12emplace_backIJjEEEvDpOT_@Base 3.4.0
-
_ZNSt6vectorIjSaIjEE14_M_fill_insertEN9__gnu_cxx17__normal_iteratorIPjS1_EEmRKj@Base
1.1.3
- (optional)_ZNSt6vectorIjSaIjEE17_M_realloc_appendIJiEEEvDpOT_@Base 4.1.4
- (optional)_ZNSt6vectorIjSaIjEE17_M_realloc_appendIJjEEEvDpOT_@Base 4.1.4
-
(optional)_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_@Base
4.0.5
- (optional)_ZNSt6vectorIjSaIjEED1Ev@Base 4.1.4
- (optional)_ZNSt6vectorIjSaIjEED2Ev@Base 4.1.4
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE17_M_realloc_appendIJijEEEvDpOT_@Base
4.1.4
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE17_M_realloc_appendIJjjEEEvDpOT_@Base
4.1.4
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE17_M_realloc_insertIJRjiEEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base
4.1.4
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorISt4pairIiiESaIS1_EE17_M_realloc_insertIJijEEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base
4.1.4
+ _ZNSt6vectorIiSaIiEE14_M_fill_appendEmRKi@Base 4.1.5-1
+#MISSING: 4.1.5-1#
_ZNSt6vectorIiSaIiEE14_M_fill_insertEN9__gnu_cxx17__normal_iteratorIPiS1_EEmRKi@Base
1.1.3
+#MISSING: 4.1.5-1# (optional)_ZNSt6vectorIiSaIiEED1Ev@Base 4.1.4
+#MISSING: 4.1.5-1# (optional)_ZNSt6vectorIiSaIiEED2Ev@Base 4.1.4
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorIjSaIjEE12emplace_backIJjEEEvDpOT_@Base 3.4.0
+ _ZNSt6vectorIjSaIjEE14_M_fill_appendEmRKj@Base 4.1.5-1
+#MISSING: 4.1.5-1#
_ZNSt6vectorIjSaIjEE14_M_fill_insertEN9__gnu_cxx17__normal_iteratorIPjS1_EEmRKj@Base
1.1.3
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorIjSaIjEE17_M_realloc_appendIJiEEEvDpOT_@Base 4.1.4
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorIjSaIjEE17_M_realloc_appendIJjEEEvDpOT_@Base 4.1.4
+#MISSING: 4.1.5-1#
(optional)_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_@Base
4.0.5
+#MISSING: 4.1.5-1# (optional)_ZNSt6vectorIjSaIjEED1Ev@Base 4.1.4
+#MISSING: 4.1.5-1# (optional)_ZNSt6vectorIjSaIjEED2Ev@Base 4.1.4
_ZTIN4spoa15AlignmentEngineE@Base 1.1.3
_ZTIN4spoa19SimdAlignmentEngineILNS_12ArchitectureE0EEE@Base 4.0.5
_ZTIN4spoa19SimdAlignmentEngineILNS_12ArchitectureE1EEE@Base 4.0.5
@@ -191,4 +193,4 @@
_ZTVN4spoa19SimdAlignmentEngineILNS_12ArchitectureE1EEE@Base 4.0.5
_ZTVN4spoa19SimdAlignmentEngineILNS_12ArchitectureE2EEE@Base 4.0.5
_ZTVN4spoa19SisdAlignmentEngineE@Base 1.1.3
-
(optional)_ZZN6cereal6detail12StaticObjectINS0_18PolymorphicCastersEE6createEvE1t@Base
4.0.5
+#MISSING: 4.1.5-1#
(optional)_ZZN6cereal6detail12StaticObjectINS0_18PolymorphicCastersEE6createEvE1t@Base
4.0.5
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:24: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: spoa
Source-Version: 4.1.5-2
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
spoa, 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 spoa 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: Fri, 13 Feb 2026 20:55:42 +0100
Source: spoa
Architecture: source
Version: 4.1.5-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1127540
Changes:
spoa (4.1.5-2) unstable; urgency=medium
.
* d/*symbols*: mark most (all?) leaked compiler symbols as (optional).
(Closes: #1127540)
* d/control: drop redundant Priority: optional.
* d/control: declare compliance to standards version 4.7.3.
Checksums-Sha1:
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Files:
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