[Debian-med-packaging] Bug#1037749: libwfa2: ftbfs with GCC-13

Wed Jun 14 10:27:32 BST 2023

Package: src:libwfa2
Version: 2.3.3-1
Severity: normal
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-13

[This bug is targeted to the upcoming trixie release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.

The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/libwfa2_2.3.3-1_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 13, either set CC=gcc-13 CXX=g++-13 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-13/porting_to.html

[...]
                 from /<<PKGBUILDDIR>>/bindings/cpp/../../wavefront/wavefront_align.h:34,
                 from /<<PKGBUILDDIR>>/bindings/cpp/WFAligner.cpp:35:
/<<PKGBUILDDIR>>/./system/mm_stack.h:50:3: error: ‘uint64_t’ does not name a type
   50 |   uint64_t segment_size;          // Memory segment size (bytes)
      |   ^~~~~~~~
/<<PKGBUILDDIR>>/./system/mm_stack.h:1:1: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
  +++ |+#include <cstdint>
    1 | /*
/<<PKGBUILDDIR>>/./system/mm_stack.h:52:3: error: ‘uint64_t’ does not name a type
   52 |   uint64_t current_segment_idx;   // Current segment being used (serving memory)
      |   ^~~~~~~~
/<<PKGBUILDDIR>>/./system/mm_stack.h:52:3: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
/<<PKGBUILDDIR>>/./system/mm_stack.h:63:11: error: ‘uint64_t’ does not name a type
   63 |     const uint64_t segment_size);
      |           ^~~~~~~~
/<<PKGBUILDDIR>>/./system/mm_stack.h:63:11: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
/<<PKGBUILDDIR>>/./system/mm_stack.h:74:11: error: ‘uint64_t’ does not name a type
   74 |     const uint64_t num_bytes,
      |           ^~~~~~~~
/<<PKGBUILDDIR>>/./system/mm_stack.h:74:11: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
/<<PKGBUILDDIR>>/./system/mm_stack.h:76:11: error: ‘uint64_t’ does not name a type
   76 |     const uint64_t align_bytes);
      |           ^~~~~~~~
/<<PKGBUILDDIR>>/./system/mm_stack.h:76:11: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
/<<PKGBUILDDIR>>/bindings/cpp/WFAligner.cpp:209:11: error: ‘uint64_t’ does not name a type
  209 |     const uint64_t maxMemoryResident,
      |           ^~~~~~~~
/<<PKGBUILDDIR>>/bindings/cpp/WFAligner.cpp:36:1: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
   35 |   #include "../../wavefront/wavefront_align.h"
  +++ |+#include <cstdint>
   36 | }
/<<PKGBUILDDIR>>/bindings/cpp/WFAligner.cpp:210:11: error: ‘uint64_t’ does not name a type
  210 |     const uint64_t maxMemoryAbort) {
      |           ^~~~~~~~
/<<PKGBUILDDIR>>/bindings/cpp/WFAligner.cpp:210:11: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
[ 85%] Building C object CMakeFiles/wfa2_static.dir/utils/sequence_buffer.c.o
/usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/<<PKGBUILDDIR>>/. -I/<<PKGBUILDDIR>>/wavefront -I/<<PKGBUILDDIR>>/utils -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/wfa2_static.dir/utils/sequence_buffer.c.o -MF CMakeFiles/wfa2_static.dir/utils/sequence_buffer.c.o.d -o CMakeFiles/wfa2_static.dir/utils/sequence_buffer.c.o -c /<<PKGBUILDDIR>>/utils/sequence_buffer.c
make[3]: *** [CMakeFiles/wfa2cpp_static.dir/build.make:79: CMakeFiles/wfa2cpp_static.dir/bindings/cpp/WFAligner.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:144: CMakeFiles/wfa2cpp_static.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
[ 86%] Building C object CMakeFiles/wfa2_static.dir/utils/vector.c.o
/usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/<<PKGBUILDDIR>>/. -I/<<PKGBUILDDIR>>/wavefront -I/<<PKGBUILDDIR>>/utils -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/wfa2_static.dir/utils/vector.c.o -MF CMakeFiles/wfa2_static.dir/utils/vector.c.o.d -o CMakeFiles/wfa2_static.dir/utils/vector.c.o -c /<<PKGBUILDDIR>>/utils/vector.c
[ 88%] Building C object CMakeFiles/wfa2_static.dir/utils/commons.c.o
/usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/<<PKGBUILDDIR>>/. -I/<<PKGBUILDDIR>>/wavefront -I/<<PKGBUILDDIR>>/utils -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/wfa2_static.dir/utils/commons.c.o -MF CMakeFiles/wfa2_static.dir/utils/commons.c.o.d -o CMakeFiles/wfa2_static.dir/utils/commons.c.o -c /<<PKGBUILDDIR>>/utils/commons.c
[ 89%] Building C object CMakeFiles/wfa2_static.dir/utils/heatmap.c.o
/usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/<<PKGBUILDDIR>>/. -I/<<PKGBUILDDIR>>/wavefront -I/<<PKGBUILDDIR>>/utils -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/wfa2_static.dir/utils/heatmap.c.o -MF CMakeFiles/wfa2_static.dir/utils/heatmap.c.o.d -o CMakeFiles/wfa2_static.dir/utils/heatmap.c.o -c /<<PKGBUILDDIR>>/utils/heatmap.c
[ 90%] Building C object CMakeFiles/wfa2_static.dir/utils/string_padded.c.o
/usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/<<PKGBUILDDIR>>/. -I/<<PKGBUILDDIR>>/wavefront -I/<<PKGBUILDDIR>>/utils -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/wfa2_static.dir/utils/string_padded.c.o -MF CMakeFiles/wfa2_static.dir/utils/string_padded.c.o.d -o CMakeFiles/wfa2_static.dir/utils/string_padded.c.o -c /<<PKGBUILDDIR>>/utils/string_padded.c
[ 91%] Building C object CMakeFiles/wfa2_static.dir/alignment/affine2p_penalties.c.o
/usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/<<PKGBUILDDIR>>/. -I/<<PKGBUILDDIR>>/wavefront -I/<<PKGBUILDDIR>>/utils -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/wfa2_static.dir/alignment/affine2p_penalties.c.o -MF CMakeFiles/wfa2_static.dir/alignment/affine2p_penalties.c.o.d -o CMakeFiles/wfa2_static.dir/alignment/affine2p_penalties.c.o -c /<<PKGBUILDDIR>>/alignment/affine2p_penalties.c
[ 92%] Building C object CMakeFiles/wfa2_static.dir/alignment/affine_penalties.c.o
/usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/<<PKGBUILDDIR>>/. -I/<<PKGBUILDDIR>>/wavefront -I/<<PKGBUILDDIR>>/utils -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/wfa2_static.dir/alignment/affine_penalties.c.o -MF CMakeFiles/wfa2_static.dir/alignment/affine_penalties.c.o.d -o CMakeFiles/wfa2_static.dir/alignment/affine_penalties.c.o -c /<<PKGBUILDDIR>>/alignment/affine_penalties.c
[ 94%] Building C object CMakeFiles/wfa2_static.dir/alignment/cigar.c.o
/usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/<<PKGBUILDDIR>>/. -I/<<PKGBUILDDIR>>/wavefront -I/<<PKGBUILDDIR>>/utils -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/wfa2_static.dir/alignment/cigar.c.o -MF CMakeFiles/wfa2_static.dir/alignment/cigar.c.o.d -o CMakeFiles/wfa2_static.dir/alignment/cigar.c.o -c /<<PKGBUILDDIR>>/alignment/cigar.c
[ 95%] Building C object CMakeFiles/wfa2_static.dir/alignment/score_matrix.c.o
/usr/bin/cc -DVERSION=\"v2.3\" -DWFA2LIB_VERSION=\"v2.3\" -I/<<PKGBUILDDIR>>/. -I/<<PKGBUILDDIR>>/wavefront -I/<<PKGBUILDDIR>>/utils -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/wfa2_static.dir/alignment/score_matrix.c.o -MF CMakeFiles/wfa2_static.dir/alignment/score_matrix.c.o.d -o CMakeFiles/wfa2_static.dir/alignment/score_matrix.c.o -c /<<PKGBUILDDIR>>/alignment/score_matrix.c
[ 96%] Linking C static library libwfa2.a
/usr/bin/cmake -P CMakeFiles/wfa2_static.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/wfa2_static.dir/link.txt --verbose=1
/usr/bin/ar qc libwfa2.a CMakeFiles/wfa2_static.dir/wavefront/wavefront_align.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_aligner.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_attributes.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_backtrace_buffer.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_backtrace.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_backtrace_offload.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_bialign.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_bialigner.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_components.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_compute_affine2p.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_compute_affine.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_compute.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_compute_edit.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_compute_linear.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_debug.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_display.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_extend.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_heuristic.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_pcigar.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_penalties.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_plot.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_slab.c.o CMakeFiles/wfa2_static.dir/wavefront/wavefront_unialign.c.o CMakeFiles/wfa2_static.dir/system/mm_stack.c.o CMakeFiles/wfa2_static.dir/system/mm_allocator.c.o CMakeFiles/wfa2_static.dir/system/profiler_counter.c.o CMakeFiles/wfa2_static.dir/system/profiler_timer.c.o CMakeFiles/wfa2_static.dir/utils/bitmap.c.o CMakeFiles/wfa2_static.dir/utils/dna_text.c.o CMakeFiles/wfa2_static.dir/utils/sequence_buffer.c.o CMakeFiles/wfa2_static.dir/utils/vector.c.o CMakeFiles/wfa2_static.dir/utils/commons.c.o CMakeFiles/wfa2_static.dir/utils/heatmap.c.o CMakeFiles/wfa2_static.dir/utils/string_padded.c.o CMakeFiles/wfa2_static.dir/alignment/affine2p_penalties.c.o CMakeFiles/wfa2_static.dir/alignment/affine_penalties.c.o CMakeFiles/wfa2_static.dir/alignment/cigar.c.o CMakeFiles/wfa2_static.dir/alignment/score_matrix.c.o
/usr/bin/ranlib libwfa2.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 96%] Built target wfa2_static
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:149: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2