sbml-5.19.0 build error with gcc 13.3.0 on JURECA

Summary

Summary	Spack package build failure
Package info	sbml-5.19.0
System	JURECA
Related

Steps to reproduce the issue

$ spack -d install --fresh --test root

Error message

Error message

/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-sbml-5.19.0-6wgp2zr7t6llqulghtddg7s4ifdm3ya7/spack-src/src/sbml/xml/XMLErrorL
og.cpp:103:24: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  103 | struct Delete : public unary_function
      |                        ^~~~~~~~~~~~~~
In file included from /p/software/fs/jurecadc/stages/2025/software/GCCcore/13.3.0/include/c++/13.3.0/functional:49,
                 from /p/usersoftware/ebrains-sw-stack/ebrains-24.04/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-sbml-5.19.0-6wgp2zr7t6llqulghtddg7s4ifdm3ya7/spack-src/src/sbml/xml/XMLErrorLog.cpp:43:
/p/software/fs/jurecadc/stages/2025/software/GCCcore/13.3.0/include/c++/13.3.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-sbml-5.19.0-6wgp2zr7t6llqulghtddg7s4ifdm3ya7/spack-src/src/sbml/xml/XMLOutputStream.cpp: In member function 'void XMLOutputStream::writeComment(const std::string&, const std::string&, bool)':
/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-sbml-5.19.0-6wgp2zr7t6llqulghtddg7s4ifdm3ya7/spack-src/src/sbml/xml/XMLOutputStream.cpp:997:44: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 5 and 15 [-Wformat-truncation=]
  997 |     snprintf(formattedDateAndTime, 17, "%d-%02d-%02d %02d:%02d",
      |                                            ^~~~
In member function 'void XMLOutputStream::writeComment(const std::string&, const std::string&, bool)',
    inlined from 'void XMLOutputStream::writeComment(const std::string&, const std::string&, bool)' at /p/usersoftware/ebrains-sw-stack/ebrains-24.04/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-sbml-5.19.0-6wgp2zr7t6llqulghtddg7s4ifdm3ya7/spack-src/src/sbml/xml/XMLOutputStream.cpp:973:1:
/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-sbml-5.19.0-6wgp2zr7t6llqulghtddg7s4ifdm3ya7/spack-src/src/sbml/xml/XMLOutputStream.cpp:997:40: note: directive argument in the range [-2147483647, 2147483647]
  997 |     snprintf(formattedDateAndTime, 17, "%d-%02d-%02d %02d:%02d",
      |                                        ^~~~~~~~~~~~~~~~~~~~~~~~
/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-sbml-5.19.0-6wgp2zr7t6llqulghtddg7s4ifdm3ya7/spack-src/src/sbml/xml/XMLOutputStream.cpp:997:13: note: 'snprintf' output between 14 and 60 bytes into a destination of size 17
  997 |     snprintf(formattedDateAndTime, 17, "%d-%02d-%02d %02d:%02d",
      |     ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  998 |             now->tm_year+1900, now->tm_mon+1, now->tm_mday,
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  999 |             now->tm_hour, now->tm_min);
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~
/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-sbml-5.19.0-6wgp2zr7t6llqulghtddg7s4ifdm3ya7/spack-src/src/sbml/xml/LibXMLParser.cpp: In member function 'virtual bool LibXMLParser::parseNext()':
/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-sbml-5.19.0-6wgp2zr7t6llqulghtddg7s4ifdm3ya7/spack-src/src/sbml/xml/LibXMLParser.cpp:427:46: error: invalid conversion from 'const xmlError*' {aka 'const _xmlError*'} to 'xmlErrorPtr' {aka '_xmlError*'} [-fpermissive]
  427 |     xmlErrorPtr libxmlError = xmlGetLastError();
      |                               ~~~~~~~~~~~~~~~^~
      |                                              |
      |                                              const xmlError* {aka const _xmlError*}
make[2]: *** [src/CMakeFiles/sbml-static.dir/build.make:5497: src/CMakeFiles/sbml-static.dir/sbml/xml/LibXMLParser.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-sbml-5.19.0-6wgp2zr7t6llqulghtddg7s4ifdm3ya7/spac
k-build-6wgp2zr'
make[1]: *** [CMakeFiles/Makefile2:263: src/CMakeFiles/sbml-static.dir/all] Error 2
make[1]: Leaving directory '/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-sbml-5.19.0-6wgp2zr7t6llqulghtddg7s4ifdm3ya7/spack-build-6wgp2zr'
make: *** [Makefile:159: all] Error 2

Information on your system

Additional information

• spack-build-out.txt

added build-error label

changed title from sblm-5.19.0 build error with gcc 13.3.0 on JURECA to sbml-5.19.0 build error with gcc 13.3.0 on JURECA

mentioned in issue #88

That's a syntax error in the upstream code base — a pointer-to-const-type is assigned to a pointer-to-type; not sure why older compilers didn't complain about that. We pull it in via r-sbtabvfgen which is a top-level ESD package → @elmath do you know the maintainers?