[Debian-med-packaging] Bug#1037879: unifrac-tools: ftbfs with GCC-13

[Matthias Klose]

Package: src:unifrac-tools
Version: 1.2-2
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/unifrac-tools_1.2-2_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

[...]
  279 | int32_t BPTree::parent(uint32_t i) const {
      |         ^~~~~~
tree.cpp:279:24: error: ‘uint32_t’ was not declared in this scope
  279 | int32_t BPTree::parent(uint32_t i) const {
      |                        ^~~~~~~~
tree.cpp:279:24: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
tree.cpp:283:9: error: ‘int32_t su::BPTree::enclose’ is not a static data member of ‘class su::BPTree’
  283 | int32_t BPTree::enclose(uint32_t i) const {
      |         ^~~~~~
tree.cpp:283:25: error: ‘uint32_t’ was not declared in this scope
  283 | int32_t BPTree::enclose(uint32_t i) const {
      |                         ^~~~~~~~
tree.cpp:283:25: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
tree.cpp:290:9: error: ‘int32_t su::BPTree::bwd’ is not a static data member of ‘class su::BPTree’
  290 | int32_t BPTree::bwd(uint32_t i, int d) const {
      |         ^~~~~~
tree.cpp:290:21: error: ‘uint32_t’ was not declared in this scope
  290 | int32_t BPTree::bwd(uint32_t i, int d) const {
      |                     ^~~~~~~~
tree.cpp:290:21: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
tree.cpp:290:33: error: expected primary-expression before ‘int’
  290 | int32_t BPTree::bwd(uint32_t i, int d) const {
      |                                 ^~~
tree.cpp:290:38: error: expression list treated as compound expression in initializer [-fpermissive]
  290 | int32_t BPTree::bwd(uint32_t i, int d) const {
      |                                      ^
tree.cpp: In member function ‘void su::BPTree::newick_to_bp(std::string)’:
tree.cpp:350:5: error: ‘nparens’ was not declared in this scope; did you mean ‘parent’?
  350 |     nparens = structure.size();
      |     ^~~~~~~
      |     parent
tree.cpp: In member function ‘void su::BPTree::structure_to_openclose()’:
tree.cpp:365:22: error: invalid types ‘int[unsigned int]’ for array subscript
  365 |             openclose[i] = open_idx;
      |                      ^
tree.cpp:366:22: error: invalid types ‘int[unsigned int]’ for array subscript
  366 |             openclose[open_idx] = i;
      |                      ^
tree.cpp: In function ‘std::string& rtrim(std::string&)’:
tree.cpp:374:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
  374 |             std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
      |                       ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from tree.hpp:13:
/usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here
 1126 |     ptr_fun(_Result (*__x)(_Arg))
      |     ^~~~~~~
tree.cpp: In member function ‘void su::BPTree::newick_to_metadata(std::string)’:
tree.cpp:412:24: error: ‘open’ was not declared in this scope; did you mean ‘popen’?
  412 |             open_idx = open(structure_idx);
      |                        ^~~~
      |                        popen
tree.cpp: At global scope:
tree.cpp:491:13: error: ‘uint32_t’ was not declared in this scope
  491 | std::vector<uint32_t> BPTree::get_openclose() {
      |             ^~~~~~~~
tree.cpp:491:13: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
tree.cpp:491:21: error: template argument 1 is invalid
  491 | std::vector<uint32_t> BPTree::get_openclose() {
      |                     ^
tree.cpp:491:21: error: template argument 2 is invalid
make[3]: *** [Makefile:129: tree.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:9: api] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" PREFIX=/<<PKGBUILDDIR>>/debian/tmp/usr returned exit code 2
make[1]: *** [debian/rules:15: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2