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Update ms2rescore-rs to 0.4.1 #53247

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merged 7 commits into from
Jan 20, 2025

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RalfG
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@RalfG RalfG commented Jan 15, 2025

Fixes and supersedes #49308 and #53125.


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RalfG commented Jan 20, 2025

The macOS x64 tests are failing to compile a low-level dependency on the libz-sys Rust package:

11:21:35 BIOCONDA INFO (ERR)   make: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
11:21:35 BIOCONDA INFO (ERR)   In file included from /opt/mambaforge/envs/bioconda/conda-bld/ms2rescore-rs_1737112454133/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/libz-sys-1.1.21/src/zlib-ng/zutil.c:7:
11:21:35 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/ms2rescore-rs_1737112454133/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/libz-sys-1.1.21/src/zlib-ng/zutil_p.h:22:20: error: call to undeclared library function 'aligned_alloc' with type 'void *(unsigned long, unsigned long)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:21:35 BIOCONDA INFO (ERR)      22 |     return (void *)aligned_alloc(64, size);  /* Defined in C11 */
11:21:35 BIOCONDA INFO (ERR)         |                    ^
11:21:35 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/ms2rescore-rs_1737112454133/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/libz-sys-1.1.21/src/zlib-ng/zutil_p.h:22:20: note: include the header <stdlib.h> or explicitly provide a declaration for 'aligned_alloc'
11:21:35 BIOCONDA INFO (ERR)   1 error generated.
11:21:35 BIOCONDA INFO (ERR)   make[2]: *** [CMakeFiles/zlib.dir/build.make:457: CMakeFiles/zlib.dir/zutil.c.o] Error 1
11:21:35 BIOCONDA INFO (ERR)   make[1]: *** [CMakeFiles/Makefile2:87: CMakeFiles/zlib.dir/all] Error 2
11:21:35 BIOCONDA INFO (ERR)   make: *** [Makefile:156: all] Error 2
11:21:35 BIOCONDA INFO (ERR)   thread 'main' panicked at /opt/mambaforge/envs/bioconda/conda-bld/ms2rescore-rs_1737112454133/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/cmake-0.1.52/src/lib.rs:1115:5:

I tried several things:

  • Adding clangdev as build dependency
  • Adding libcxx as build dependency
  • Adding -std=c11 to CFLAGS (led to compile errors in other Rust packages)
  • Adding -std=c17 to CFLAGS (no change)
  • Moving zlib from host to build dependencies

But none worked. Skipping builds for macOS x64 for now...


Potentially relevant: https://stackoverflow.com/questions/29247065/compiler-cant-find-aligned-alloc-function

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RalfG commented Jan 20, 2025

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Jan 20, 2025
@martin-g martin-g merged commit 1eece33 into bioconda:master Jan 20, 2025
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