spades: fix missing <cstdint> under GCC 14 - #6269
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Summary
Building spades@4.0.0 with GCC 14 fails with e.g.:
id_map.hppusesuint64_tas a default template parameter but never includes<cstdint>-- older GCC pulled it in transitively (via<boost/iterator/iterator_facade.hpp>or one of the other headers it includes), GCC 14's libstdc++ does not.A static scan of the whole
src/tree found 111 files with the same pattern (using fixed-width int types while relying on a transitive include for<cstdint>/<stdint.h>) -- too many to patch file by file, and too easy for the build to hit a new one further along depending on which+tools/+sratargets get compiled. Forcing the header into every translation unit at the compiler level (-include cstdintfor C++,-include stdint.hfor C, since<cstdint>is the C++ wrapper and isn't visible to the plain C compiler) covers all of them at once.Testing
Installed
spades@4.0.0 +sra +tools(all optional projects enabled,SPADES_ENABLE_PROJECTS=all) with%gcc@14.2.0end to end, confirmedspades.py --versionand a real assembly run (contigs.fasta/scaffolds.fasta produced) work.