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 make -j2 make[1]: Entering directory '/<<PKGBUILDDIR>>' make all-recursive make[2]: Entering directory '/<<PKGBUILDDIR>>' Making all in src make[3]: Entering directory '/<<PKGBUILDDIR>>/src' 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 ivar.o ivar.cpp 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_consensus_pileup.o call_consensus_pileup.cpp Using built-in specs. COLLECT_GCC=x86_64-linux-gnu-g++ Using built-in specs. 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=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>>=.' 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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 /usr/include/c++/16/backward /usr/lib/gcc/x86_64-linux-gnu/16/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. Compiler executable checksum: 0604b665ce86504fe98d703b76bd556f Compiler executable checksum: 0604b665ce86504fe98d703b76bd556f COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' 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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' 'alignment.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 alignment.cpp -quiet -dumpbase alignment.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/ccmXsL7t.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 /usr/include/c++/16/backward /usr/lib/gcc/x86_64-linux-gnu/16/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include 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>>=.' 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'-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_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_consensus_pileup.' 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 suffix_tree.o suffix_tree.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>>=.' 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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' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/bin/x86_64-linux-gnu-as -v -I . -I .. --gdwarf-5 --64 -o alignment.o /tmp/ccmXsL7t.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' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'alignment.' 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 trim_primer_quality.o trim_primer_quality.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' 'trim_primer_quality.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 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.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/ccNykahs.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 /usr/include/c++/16/backward /usr/lib/gcc/x86_64-linux-gnu/16/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include 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' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /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 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' '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: . .. /usr/include/c++/16 /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 /usr/include/x86_64-linux-gnu /usr/include 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 /usr/include/c++/16/backward /usr/lib/gcc/x86_64-linux-gnu/16/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include 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: . .. /usr/include/c++/16 /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 /usr/include/x86_64-linux-gnu /usr/include End of search list. Compiler executable checksum: 0604b665ce86504fe98d703b76bd556f 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 --------------------------------------------------------------------------------
