[Debian-med-packaging] Bug#1143665: ivar: FTBFS: allele_functions.h:9:8: error: '*(const __vector(2) unsigned int*)((char*)&a + offsetof(allele, allele::beg))' may be used uninitialized [-Werror=maybe-uninitialized]
Santiago Vila
sanvila at debian.org
Wed Aug 5 12:24:07 BST 2026
Package: src:ivar
Version: 1.4.4+dfsg-2
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/202608/
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:ivar, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
autoreconf: export WARNINGS=
autoreconf: Entering directory '.'
autoreconf: configure.ac: no obvious need to run autopoint
autoreconf: running: aclocal --force
autoreconf: configure.ac: tracing
autoreconf: configure.ac: not using Libtool
autoreconf: configure.ac: not using Intltool
autoreconf: configure.ac: not using Gtkdoc
autoreconf: configure.ac: no need to run autopoint (confirmed)
autoreconf: running: /usr/bin/autoconf --force
autoreconf: running: /usr/bin/autoheader --force
autoreconf: running: automake --add-missing --copy --force-missing
configure.ac:12: installing './compile'
configure.ac:58: installing './config.guess'
configure.ac:58: installing './config.sub'
configure.ac:6: installing './install-sh'
configure.ac:6: installing './missing'
src/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
autoreconf: configure.ac: not running make: --make not given
autoreconf: Leaving directory '.'
dh_auto_configure
./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking xargs -n works... yes
checking whether UID '995' is supported by ustar format... yes
checking whether GID '995' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking for gawk... (cached) mawk
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether x86_64-linux-gnu-g++ accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of x86_64-linux-gnu-g++... none
checking for gcc... x86_64-linux-gnu-gcc
checking whether the compiler supports GNU C... yes
checking whether x86_64-linux-gnu-gcc accepts -g... yes
checking for x86_64-linux-gnu-gcc option to enable C23 features... none needed
checking whether x86_64-linux-gnu-gcc understands -c and -o together... yes
checking dependency style of x86_64-linux-gnu-gcc... none
checking how to run the C preprocessor... x86_64-linux-gnu-gcc -E
checking for main in -lhts... no
checking for main in -lpthread... no
checking for main in -lz... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for unistd.h... (cached) yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99 or later... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking whether malloc (0) returns nonnull... no
checking whether realloc (0, 0) returns nonnull... no
checking for memmove... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: executing depfiles commands
dh_auto_build
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Making all in src
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Configured with: ../src/configure -v --with-pkgversion='Debi [too-long-redacted] n --enable-link-serialization=3
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 16.1.0 (Debian 16.1.0-3)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
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GNU C++20 (Debian 16.1.0-3) version 16.1.0 (x86_64-linux-gnu)
compiled by GNU C version 16.1.0, GMP version 6.3.0, MPFR version 4.2.2, MPC version 1.3.1, isl version isl-0.28-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/16"
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ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/include-fixed/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
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End of search list.
Compiler executable checksum: 0604b665ce86504fe98d703b76bd556f
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/usr/bin/x86_64-linux-gnu-as -v -I . -I .. --gdwarf-5 --64 -o trim_primer_quality.o /tmp/ccNykahs.s
GNU assembler version 2.47 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.47
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LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/16/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'trim_primer_quality.'
x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp
Using built-in specs.
COLLECT_GCC=x86_64-linux-gnu-g++
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debi [too-long-redacted] n --enable-link-serialization=3
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 16.1.0 (Debian 16.1.0-3)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
/usr/libexec/gcc/x86_64-linux-gnu/16/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccYjcA3P.s
GNU C++20 (Debian 16.1.0-3) version 16.1.0 (x86_64-linux-gnu)
compiled by GNU C version 16.1.0, GMP version 6.3.0, MPFR version 4.2.2, MPC version 1.3.1, isl version isl-0.28-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/16"
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/include-fixed/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
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/usr/include/x86_64-linux-gnu/c++/16
/usr/include/c++/16/backward
/usr/lib/gcc/x86_64-linux-gnu/16/include
/usr/local/include
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End of search list.
Compiler executable checksum: 0604b665ce86504fe98d703b76bd556f
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
/usr/bin/x86_64-linux-gnu-as -v -I . -I .. --gdwarf-5 --64 -o suffix_tree.o /tmp/ccFsbFru.s
GNU assembler version 2.47 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.47
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/16/:/usr/libexec/gcc/x86_64-linux-gnu/16/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/16/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/16/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'suffix_tree.'
x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp
Using built-in specs.
COLLECT_GCC=x86_64-linux-gnu-g++
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debi [too-long-redacted] n --enable-link-serialization=3
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 16.1.0 (Debian 16.1.0-3)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
/usr/libexec/gcc/x86_64-linux-gnu/16/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccTXK1bA.s
GNU C++20 (Debian 16.1.0-3) version 16.1.0 (x86_64-linux-gnu)
compiled by GNU C version 16.1.0, GMP version 6.3.0, MPFR version 4.2.2, MPC version 1.3.1, isl version isl-0.28-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/16"
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/include-fixed/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/16
/usr/include/x86_64-linux-gnu/c++/16
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End of search list.
Compiler executable checksum: 0604b665ce86504fe98d703b76bd556f
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
/usr/bin/x86_64-linux-gnu-as -v -I . -I .. --gdwarf-5 --64 -o remove_reads_from_amplicon.o /tmp/ccYjcA3P.s
GNU assembler version 2.47 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.47
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/16/:/usr/libexec/gcc/x86_64-linux-gnu/16/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/16/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/16/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'remove_reads_from_amplicon.'
x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp
Using built-in specs.
COLLECT_GCC=x86_64-linux-gnu-g++
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debi [too-long-redacted] n --enable-link-serialization=3
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 16.1.0 (Debian 16.1.0-3)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
/usr/libexec/gcc/x86_64-linux-gnu/16/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/cc3jwbNl.s
GNU C++20 (Debian 16.1.0-3) version 16.1.0 (x86_64-linux-gnu)
compiled by GNU C version 16.1.0, GMP version 6.3.0, MPFR version 4.2.2, MPC version 1.3.1, isl version isl-0.28-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/16"
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/include-fixed/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/16/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
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..
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/usr/include/x86_64-linux-gnu
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End of search list.
Compiler executable checksum: 0604b665ce86504fe98d703b76bd556f
In file included from call_variants.h:13,
from call_variants.cpp:1:
In copy constructor ‘constexpr allele::allele(const allele&)’,
inlined from ‘constexpr _Tp* std::construct_at(_Tp*, _Args&& ...) [with _Tp = allele; _Args = {const allele&}]’ at /usr/include/c++/16/bits/stl_construct.h:110:9,
inlined from ‘static constexpr void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = allele; _Args = {const allele&}; _Tp = allele]’ at /usr/include/c++/16/bits/alloc_traits.h:716:21,
inlined from ‘constexpr void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const allele&}; _Tp = allele; _Alloc = std::allocator<allele>]’ at /usr/include/c++/16/bits/vector.tcc:594:26,
inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = allele; _Alloc = std::allocator<allele>]’ at /usr/include/c++/16/bits/stl_vector.h:1417:21,
inlined from ‘int call_variants_from_plup(std::istream&, std::string, uint8_t, double, uint32_t, std::string, std::string, bool)’ at call_variants.cpp:131:19:
allele_functions.h:9:8: error: ‘*(const __vector(2) unsigned int*)((char*)&a + offsetof(allele, allele::beg))’ may be used uninitialized [-Werror=maybe-uninitialized]
9 | struct allele {
| ^~~~~~
call_variants.cpp: In function ‘int call_variants_from_plup(std::istream&, std::string, uint8_t, double, uint32_t, std::string, std::string, bool)’:
call_variants.cpp:126:14: note: ‘a’ declared here
126 | allele a;
| ^
In copy constructor ‘constexpr allele::allele(const allele&)’,
inlined from ‘constexpr _Tp* std::construct_at(_Tp*, _Args&& ...) [with _Tp = allele; _Args = {const allele&}]’ at /usr/include/c++/16/bits/stl_construct.h:110:9,
inlined from ‘static constexpr void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = allele; _Args = {const allele&}; _Tp = allele]’ at /usr/include/c++/16/bits/alloc_traits.h:716:21,
inlined from ‘constexpr void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const allele&}; _Tp = allele; _Alloc = std::allocator<allele>]’ at /usr/include/c++/16/bits/vector.tcc:594:26,
inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = allele; _Alloc = std::allocator<allele>]’ at /usr/include/c++/16/bits/stl_vector.h:1417:21,
inlined from ‘int call_variants_from_plup(std::istream&, std::string, uint8_t, double, uint32_t, std::string, std::string, bool)’ at call_variants.cpp:131:19:
allele_functions.h:9:8: error: ‘a.allele::tmp_mean_qual’ may be used uninitialized [-Werror=maybe-uninitialized]
9 | struct allele {
| ^~~~~~
call_variants.cpp: In function ‘int call_variants_from_plup(std::istream&, std::string, uint8_t, double, uint32_t, std::string, std::string, bool)’:
call_variants.cpp:126:14: note: ‘a’ declared here
126 | allele a;
| ^
cc1plus: all warnings being treated as errors
make[3]: *** [Makefile:402: call_variants.o] Error 1
make[3]: *** Waiting for unfinished jobs....
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
/usr/bin/x86_64-linux-gnu-as -v -I . -I .. --gdwarf-5 --64 -o primer_bed.o /tmp/cc3jwbNl.s
GNU assembler version 2.47 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.47
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/16/:/usr/libexec/gcc/x86_64-linux-gnu/16/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/16/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/16/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/16/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'primer_bed.'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:377: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:318: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j2 returned exit code 2
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
--------------------------------------------------------------------------------
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