Bug#1143665: marked as done (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])

Debian Bug Tracking System Thu, 13 Aug 2026 02:35:29 -0700

Your message dated Thu, 13 Aug 2026 09:34:13 +0000
with message-id <[email protected]>
and subject line Bug#1143665: fixed in ivar 1.4.4+dfsg-3
has caused the Debian Bug report #1143665,
regarding 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]
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.)


-- 
1143665: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1143665
Debian Bug Tracking System
Contact [email protected] with problems

--- Begin Message ---

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
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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
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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
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configure: creating ./config.status
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config.status: creating src/Makefile
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In file included from call_variants.h:13,
                 from call_variants.cpp:1:
In copy constructor âconstexpr allele::allele(const allele&)â,
    inlined from âconstexpr _Tp* std::construct_at(_Tp*, _Args&& ...) [with 
_Tp = allele; _Args = {const allele&}]â at 
/usr/include/c++/16/bits/stl_construct.h:110:9,
    inlined from âstatic constexpr void 
std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, 
_Up*, _Args&& ...) [with _Up = allele; _Args = {const allele&}; _Tp = 
allele]â at /usr/include/c++/16/bits/alloc_traits.h:716:21,
    inlined from âconstexpr void std::vector<_Tp, 
_Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const allele&}; _Tp = 
allele; _Alloc = std::allocator<allele>]â at 
/usr/include/c++/16/bits/vector.tcc:594:26,
    inlined from âconstexpr void std::vector<_Tp, _Alloc>::push_back(const 
value_type&) [with _Tp = allele; _Alloc = std::allocator<allele>]â at 
/usr/include/c++/16/bits/stl_vector.h:1417:21,
    inlined from âint call_variants_from_plup(std::istream&, std::string, 
uint8_t, double, uint32_t, std::string, std::string, bool)â at 
call_variants.cpp:131:19:
allele_functions.h:9:8: error: â*(const __vector(2) unsigned int*)((char*)&a 
+ offsetof(allele, allele::beg))â may be used uninitialized 
[-Werror=maybe-uninitialized]
    9 | struct allele {
      |        ^~~~~~
call_variants.cpp: In function âint call_variants_from_plup(std::istream&, 
std::string, uint8_t, double, uint32_t, std::string, std::string, bool)â:
call_variants.cpp:126:14: note: âaâ declared here
  126 |       allele a;
      |              ^
In copy constructor âconstexpr allele::allele(const allele&)â,
    inlined from âconstexpr _Tp* std::construct_at(_Tp*, _Args&& ...) [with 
_Tp = allele; _Args = {const allele&}]â at 
/usr/include/c++/16/bits/stl_construct.h:110:9,
    inlined from âstatic constexpr void 
std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, 
_Up*, _Args&& ...) [with _Up = allele; _Args = {const allele&}; _Tp = 
allele]â at /usr/include/c++/16/bits/alloc_traits.h:716:21,
    inlined from âconstexpr void std::vector<_Tp, 
_Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const allele&}; _Tp = 
allele; _Alloc = std::allocator<allele>]â at 
/usr/include/c++/16/bits/vector.tcc:594:26,
    inlined from âconstexpr void std::vector<_Tp, _Alloc>::push_back(const 
value_type&) [with _Tp = allele; _Alloc = std::allocator<allele>]â at 
/usr/include/c++/16/bits/stl_vector.h:1417:21,
    inlined from âint call_variants_from_plup(std::istream&, std::string, 
uint8_t, double, uint32_t, std::string, std::string, bool)â at 
call_variants.cpp:131:19:
allele_functions.h:9:8: error: âa.allele::tmp_mean_qualâ may be used 
uninitialized [-Werror=maybe-uninitialized]
    9 | struct allele {
      |        ^~~~~~
call_variants.cpp: In function âint call_variants_from_plup(std::istream&, 
std::string, uint8_t, double, uint32_t, std::string, std::string, bool)â:
call_variants.cpp:126:14: note: âaâ 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
--------------------------------------------------------------------------------

--- End Message ---

--- Begin Message ---

Source: ivar
Source-Version: 1.4.4+dfsg-3
Done: Andreas Tille <[email protected]>

We believe that the bug you reported is fixed in the latest version of
ivar, 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.
Andreas Tille <[email protected]> (supplier of updated ivar 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, 13 Aug 2026 11:00:09 +0200
Source: ivar
Architecture: source
Version: 1.4.4+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1143665
Changes:
 ivar (1.4.4+dfsg-3) unstable; urgency=medium
 .
   * d/watch: version=5
   * d/rules: Add -std=c++17
     Closes: #1143665
   * Standards-Version: 4.7.4 (routine-update)
   * Reflow Uploaders field (cme)
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--- End Message ---

Bug#1143665: marked as done (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])

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Bug#1143665: marked as done (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])