[Debichem-devel] Bug#1037671: gemmi: ftbfs with GCC-13

[Matthias Klose]

Package: src:gemmi
Version: 0.5.7+ds-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/gemmi_0.5.7+ds-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

[...]
      |                               ^
      |                               ;
/<<PKGBUILDDIR>>/include/gemmi/cifdoc.hpp: At global scope:
/<<PKGBUILDDIR>>/include/gemmi/cifdoc.hpp:45:8: error: ‘uint8_t’ does not name a type
   45 | inline uint8_t char_table(char c) {
      |        ^~~~~~~
/<<PKGBUILDDIR>>/include/gemmi/cifdoc.hpp:22:1: note: ‘uint8_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
   21 | #include <unordered_set>
  +++ |+#include <cstdint>
   22 | #include <vector>
/<<PKGBUILDDIR>>/include/gemmi/cifdoc.hpp: In lambda function:
/<<PKGBUILDDIR>>/include/gemmi/cifdoc.hpp:1093:59: error: ‘char_table’ was not declared in this scope
 1093 |   if (std::all_of(v.begin(), v.end(), [](char c) { return char_table(c) == 1; })
      |                                                           ^~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/gemmi/cifdoc.hpp:9,
                 from /<<PKGBUILDDIR>>/python/cif.cpp:3:
/<<PKGBUILDDIR>>/include/gemmi/atox.hpp: In function ‘bool gemmi::is_space(char)’:
/<<PKGBUILDDIR>>/include/gemmi/atox.hpp:23:21: error: ‘uint8_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’?
   23 |   static const std::uint8_t table[256] = { // 1 for 9-13 and 32
      |                     ^~~~~~~
      |                     wint_t
/<<PKGBUILDDIR>>/include/gemmi/atox.hpp:33:10: error: ‘table’ was not declared in this scope; did you mean ‘mutable’?
   33 |   return table[(std::uint8_t)c] != 0;
      |          ^~~~~
      |          mutable
/<<PKGBUILDDIR>>/include/gemmi/atox.hpp:33:22: error: ‘uint8_t’ is not a member of ‘std’; did you mean ‘wint_t’?
   33 |   return table[(std::uint8_t)c] != 0;
      |                      ^~~~~~~
      |                      wint_t
/<<PKGBUILDDIR>>/include/gemmi/atox.hpp:33:30: error: expected ‘]’ before ‘c’
   33 |   return table[(std::uint8_t)c] != 0;
      |                              ^
      |                              ]
/<<PKGBUILDDIR>>/include/gemmi/atox.hpp:33:30: error: expected ‘;’ before ‘c’
   33 |   return table[(std::uint8_t)c] != 0;
      |                              ^
      |                              ;
/<<PKGBUILDDIR>>/include/gemmi/atox.hpp:33:31: error: expected ‘;’ before ‘]’ token
   33 |   return table[(std::uint8_t)c] != 0;
      |                               ^
      |                               ;
/<<PKGBUILDDIR>>/include/gemmi/cifdoc.hpp: At global scope:
/<<PKGBUILDDIR>>/include/gemmi/cifdoc.hpp:45:8: error: ‘uint8_t’ does not name a type
   45 | inline uint8_t char_table(char c) {
      |        ^~~~~~~
/<<PKGBUILDDIR>>/include/gemmi/cifdoc.hpp:22:1: note: ‘uint8_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
   21 | #include <unordered_set>
  +++ |+#include <cstdint>
   22 | #include <vector>
/<<PKGBUILDDIR>>/include/gemmi/cifdoc.hpp: In lambda function:
/<<PKGBUILDDIR>>/include/gemmi/cifdoc.hpp:1093:59: error: ‘char_table’ was not declared in this scope
 1093 |   if (std::all_of(v.begin(), v.end(), [](char c) { return char_table(c) == 1; })
      |                                                           ^~~~~~~~~~
make[3]: *** [CMakeFiles/py.dir/build.make:93: CMakeFiles/py.dir/python/gemmi.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [CMakeFiles/input.dir/build.make:79: CMakeFiles/input.dir/src/input.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:136: CMakeFiles/input.dir/all] Error 2
make[3]: *** [CMakeFiles/py.dir/build.make:149: CMakeFiles/py.dir/python/cif.cpp.o] Error 1
make[3]: *** [CMakeFiles/py.dir/build.make:135: CMakeFiles/py.dir/python/chemcomp.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 17%] Built target output
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:1346: CMakeFiles/py.dir/all] Error 2
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:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2