Update - another attempt at SPAdes 3.15.5 osx build

[chrisjackson-pellicle]

Yet another attempt to get osx builds working for SPAdes 3.15.5 (see here)

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[chrisjackson-pellicle]

Related: #47860 (comment)

[chrisjackson-pellicle]

test_osx fails. The raw log has the error:

CMake Error at /opt/mambaforge/envs/bioconda/conda-bld/spades_1716806771783/_build_env/share/cmake-3.29/Modules/CMakeTestCCompiler.cmake:67 (message):
The C compiler "/opt/mambaforge/envs/bioconda/conda-bld/spades_1716806771783/_build_env/bin/x86_64-apple-darwin13.4.0-clang" is not able to compile a simple test program. It fails with the following output:

...
...

ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd' for architecture x86_64
clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [CMakeFiles/cmTC_1e4f7.dir/build.make:100: cmTC_1e4f7] Error 1

This is beyond my knowledge level, but:

1. Attempts to build the OSX package on my local Mac using conda build (i.e. not using bioconda-utils build) resulted in a similar "unsupported tapi file type '!tapi-tbd' in YAML file" error.

2. Following the advice here and here, I downloaded MacOSX10.10.sdk and set the CONDA_BUILD_SYSROOT environment variable to point towards it. Running conda build no longer resulted in the "unsupported tapi file type '!tapi-tbd' in YAML file" error; the build continued past this previous error point, although it still failed downstream with errors such as error: no member named 'ldiv' in the global namespace. EDIT - I see that stub libraries (YAML files with extension *.tbd) didn't exist in Apple SDKs until version macOS 10.11 SDK (see here) - hence the lack of "!tapi-tbd" error when using MacOSX10.10.sdk.

From the raw log, it looks like the Bioconda OSX build is using Xcode 14.2 with MacOSX13.1.sdk i.e.CONDA_BUILD_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk and -isysroot /Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.1.sdk. Although is looks like calls to -isysroot are ignored when CONDA_BUILD_SYSROOT is set.

I'm wondering if the Xcode / SDK version is the issue, or whether one of the issues outlined in the accepted answer here could be relevant. @bgruening, any thoughts?

[chrisjackson-pellicle]

...and, after all that, it seems to build fine after removing the conda_build_config.yaml with version constraints on the compilers.

[chrisjackson-pellicle]

@BiocondaBot please add label