[Debian-med-packaging] Bug#1037655: filtlong: ftbfs with GCC-13

[Matthias Klose]

Package: src:filtlong
Version: 0.2.1-3
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/filtlong_0.2.1-3_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

[...]
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/kmers.cpp:107:13: error: ‘reverse_kmer’ was not declared in this scope
  107 |             reverse_kmer = starting_kmer_to_bits_reverse(sequence);
      |             ^~~~~~~~~~~~
src/kmers.cpp:107:28: error: ‘starting_kmer_to_bits_reverse’ was not declared in this scope
  107 |             reverse_kmer = starting_kmer_to_bits_reverse(sequence);
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/kmers.cpp:109:21: error: ‘void*’ is not a pointer-to-object type
  109 |             (this->*add_kmer)(forward_kmer);
      |                     ^~~~~~~~
src/kmers.cpp:110:21: error: ‘void*’ is not a pointer-to-object type
  110 |             (this->*add_kmer)(reverse_kmer);
      |                     ^~~~~~~~
src/kmers.cpp:114:33: error: ‘base_to_bits_forward’ was not declared in this scope
  114 |                 forward_kmer |= base_to_bits_forward(sequence[i]);
      |                                 ^~~~~~~~~~~~~~~~~~~~
src/kmers.cpp:117:33: error: ‘base_to_bits_reverse’ was not declared in this scope
  117 |                 reverse_kmer |= base_to_bits_reverse(sequence[i]);
      |                                 ^~~~~~~~~~~~~~~~~~~~
src/kmers.cpp:119:25: error: ‘void*’ is not a pointer-to-object type
  119 |                 (this->*add_kmer)(forward_kmer);
      |                         ^~~~~~~~
src/kmers.cpp:120:25: error: ‘void*’ is not a pointer-to-object type
  120 |                 (this->*add_kmer)(reverse_kmer);
      |                         ^~~~~~~~
src/kmers.cpp: At global scope:
src/kmers.cpp:137:6: error: variable or field ‘add_kmer_require_one_copy’ declared void
  137 | void Kmers::add_kmer_require_one_copy(uint32_t kmer) {
      |      ^~~~~
src/kmers.cpp:137:39: error: ‘uint32_t’ was not declared in this scope
  137 | void Kmers::add_kmer_require_one_copy(uint32_t kmer) {
      |                                       ^~~~~~~~
src/kmers.cpp:137:39: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
src/kmers.cpp:142:6: error: variable or field ‘add_kmer_require_multiple_copies’ declared void
  142 | void Kmers::add_kmer_require_multiple_copies(uint32_t kmer) {
      |      ^~~~~
src/kmers.cpp:142:46: error: ‘uint32_t’ was not declared in this scope
  142 | void Kmers::add_kmer_require_multiple_copies(uint32_t kmer) {
      |                                              ^~~~~~~~
src/kmers.cpp:142:46: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
src/kmers.cpp:170:6: error: ‘bool Kmers::is_kmer_present’ is not a static data member of ‘class Kmers’
  170 | bool Kmers::is_kmer_present(uint32_t kmer) {
      |      ^~~~~
src/kmers.cpp:170:29: error: ‘uint32_t’ was not declared in this scope
  170 | bool Kmers::is_kmer_present(uint32_t kmer) {
      |                             ^~~~~~~~
src/kmers.cpp:170:29: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
src/kmers.cpp:176:1: error: ‘uint32_t’ does not name a type
  176 | uint32_t Kmers::base_to_bits_forward(char base) {
      | ^~~~~~~~
src/kmers.cpp:176:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
src/kmers.cpp:199:1: error: ‘uint32_t’ does not name a type
  199 | uint32_t Kmers::base_to_bits_reverse(char base) {
      | ^~~~~~~~
src/kmers.cpp:199:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
src/kmers.cpp:222:1: error: ‘uint32_t’ does not name a type
  222 | uint32_t Kmers::starting_kmer_to_bits_forward(char * sequence) {
      | ^~~~~~~~
src/kmers.cpp:222:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
src/kmers.cpp:232:1: error: ‘uint32_t’ does not name a type
  232 | uint32_t Kmers::starting_kmer_to_bits_reverse(char * sequence) {
      | ^~~~~~~~
src/kmers.cpp:232:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
make[2]: *** [Makefile:49: src/kmers.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" returned exit code 2
make[1]: *** [debian/rules:10: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:7: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2