deps: fix aarch64 and macOS builds - #232
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onecode cast line types and string pointers to a concrete i8, the same c_char width bug that broke lib_wfa2 on aarch64. Pinning onecode in fastga-rs and sweepga as well collapses the duplicate copies, so one build of each remains.
wfmash-rs forced Homebrew GCC on macOS even when CC and CXX were already set. Under conda that GCC cannot parse the Xcode SDK headers. Its vendored atomic_queue.h also used the template keyword with no argument list, which clang 19 rejects.
AndreaGuarracino
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No repo tested aarch64-linux, which is why the c_char bugs in lib_wfa2 and onecode reached a release. macos-latest is arm64 but c_char is signed there, so those casts compiled fine and only bioconda's linux-aarch64 job caught them.
Found by the new linux-aarch64 CI job: fastga-rs cast 'g' to a concrete i8 when calling onecode's oneGoto.
syng passed *mut i8 to syng_ffi, which takes c_char. That is u8 on aarch64-linux, so the build failed there while x86-64 and macOS were fine. syng.rs:3081 already used the c_char form; the rest now match.
char is signed on x86-64 and unsigned on aarch64. syng assumes signed, and on aarch64 syngBWTadvanceRank reached a negative node and aborted the test suite. The flag is a no-op where char is already signed.
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Fixes the three platforms that v0.5.1 still could not build. linux-64 already passes on bioconda.
linux-aarch64.
onecodecast line types and string pointers to a concretei8, the samec_charwidth bug as lib_wfa2:i8on x86-64,u8on aarch64-linux. 19 type errors. Fixed upstream in onecode-rs5fa1e93.osx-64.
wfmash-rsforced Homebrew GCC even whenCCandCXXwere already set. Under conda that GCC cannot parse the Xcode SDK headers and fails withunknown type name 'FILE'. The environment now wins.osx-arm64. With no Homebrew GCC it fell back to clang 19, which rejects
Base::template do_pop_any(...)in the vendoredatomic_queue.h, since there is no template argument list. GCC accepts it. Removed in 4 places.onecodeandfastga-rswere pinned in several crates and every copy gets compiled, so all were bumped. The lock file now holds one copy each of onecode, fastga-rs, wfmash-rs, lib_wfa2 and sweepga.572 tests pass.