GW - cannot execute binary macos x86_64

[kcleal]

A strange issue has appeared when trying to compile GW for osx x86_64:

#51426

The binary gets built but the tests fail - the binary can not be executed. The issue also now affects the previous version of GW which previously compiled on bioconda without issue. Not sure what is causing it, or how to try and fix it. I added some debug commands, e.g. file, otool and nm. The output confirms the binary is not a Mach o file.

https://dev.azure.com/bioconda/bioconda-recipes/_build/results?buildId=72081&view=logs&j=1b052f1d-4456-52f0-9d43-71c4c5bd734d&t=34540139-28f3-5244-2e84-5ff07800d4d9

This is the output which is probably most informative:

BIOCONDA INFO (OUT) x86_64-apple-darwin13.4.0-clang++ -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gw-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_LIBCPP_DISABLE_AVAILABILITY -Wall -std=c++17 -fno-common -fwrapv -fno-omit-frame-pointer -O3 -DNDEBUG -g -D OSX -stdlib=libc++ -arch x86_64 -fvisibility=hidden -mmacosx-version-min=11 -Wno-deprecated-declarations -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$BUILD_PREFIX/include -I./lib/skia -I./lib/libBigWig -I./include -I.  -I./src -I/usr/local/include  -c -o src/drawing.o src/drawing.cpp
18:21:25 BIOCONDA INFO (OUT) x86_64-apple-darwin13.4.0-clang++ -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gw-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_LIBCPP_DISABLE_AVAILABILITY -Wall -std=c++17 -fno-common -fwrapv -fno-omit-frame-pointer -O3 -DNDEBUG -g -D OSX -stdlib=libc++ -arch x86_64 -fvisibility=hidden -mmacosx-version-min=11 -Wno-deprecated-declarations -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$BUILD_PREFIX/include -I./lib/skia -I./lib/libBigWig -I./include -I.  -I./src -I/usr/local/include  -c -o src/glfw_keys.o src/glfw_keys.cpp
18:21:25 BIOCONDA INFO (OUT) x86_64-apple-darwin13.4.0-clang++ -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gw-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_LIBCPP_DISABLE_AVAILABILITY -Wall -std=c++17 -fno-common -fwrapv -fno-omit-frame-pointer -O3 -DNDEBUG -g -D OSX -stdlib=libc++ -arch x86_64 -fvisibility=hidden -mmacosx-version-min=11 -Wno-deprecated-declarations -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$BUILD_PREFIX/include -I./lib/skia -I./lib/libBigWig -I./include -I.  -I./src -I/usr/local/include  -c -o src/hts_funcs.o src/hts_funcs.cpp
18:21:25 BIOCONDA INFO (OUT) x86_64-apple-darwin13.4.0-clang++ -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gw-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_LIBCPP_DISABLE_AVAILABILITY -Wall -std=c++17 -fno-common -fwrapv -fno-omit-frame-pointer -O3 -DNDEBUG -g -D OSX -stdlib=libc++ -arch x86_64 -fvisibility=hidden -mmacosx-version-min=11 -Wno-deprecated-declarations -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$BUILD_PREFIX/include -I./lib/skia -I./lib/libBigWig -I./include -I.  -I./src -I/usr/local/include  -c -o src/ideogram.o src/ideogram.cpp


18:22:29 BIOCONDA INFO (ERR) ++ which gw
18:22:29 BIOCONDA INFO (ERR) + file /opt/mambaforge/envs/bioconda/conda-bld/gw_1729275387348/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/gw
18:22:29 BIOCONDA INFO (ERR) ++ which gw
18:22:29 BIOCONDA INFO (ERR) + otool -L /opt/mambaforge/envs/bioconda/conda-bld/gw_1729275387348/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/gw
18:22:30 BIOCONDA INFO (ERR) ++ which gw
18:22:30 BIOCONDA INFO (ERR) + nm /opt/mambaforge/envs/bioconda/conda-bld/gw_1729275387348/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/gw
18:22:30 BIOCONDA INFO (ERR) + gw --version
18:22:30 BIOCONDA INFO (ERR) /opt/mambaforge/envs/bioconda/conda-bld/gw_1729275387348/test_tmp/run_test.sh: line 10: /opt/mambaforge/envs/bioconda/conda-bld/gw_1729275387348/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/gw: cannot execute binary file
18:22:31 BIOCONDA INFO (ERR) WARNING: Tests failed for gw-1.1.0-h553a77b_1.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken
18:22:31 BIOCONDA INFO (OUT) export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gw_1729275387348/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
18:22:31 BIOCONDA INFO (OUT) export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/gw_1729275387348/test_tmp
18:22:31 BIOCONDA INFO (OUT) $PREFIX/bin/gw
18:22:31 BIOCONDA INFO (OUT) -rwxr-xr-x  2 runner  wheel    13M Oct 18 18:21 $PREFIX/bin/gw
18:22:31 BIOCONDA INFO (ERR) TESTS FAILED: gw-1.1.0-h553a77b_1.tar.bz2
18:22:31 BIOCONDA INFO (OUT) Darwin Mac-1729273363556.local 23.6.0 Darwin Kernel Version 23.6.0: Wed Jul 31 20:48:44 PDT 2024; root:xnu-10063.141.1.700.5~1/RELEASE_X86_64 x86_64
18:22:31 BIOCONDA INFO (OUT) $PREFIX/bin/gw: data
18:22:31 BIOCONDA INFO (OUT) $PREFIX/bin/gw: is not an object file
18:22:43 BIOCONDA ERROR COMMAND FAILED (exited with 1): /opt/mambaforge/envs/bioconda/bin/conda-build --override-channels --no-anaconda-upload -c conda-forge -c bioconda -e /opt/mambaforge/envs/bioconda/conda_build_config.yaml -e /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml recipes/gw/meta.yaml

18:22:43 BIOCONDA ERROR BUILD FAILED recipes/gw
18:22:43 BIOCONDA INFO (COMMAND) conda build purge

There are conflicting mmacosx-version-min flags set, but other than that I can't see an issue with the compilation. Do you think this could be the issue?

Any help would be much appreciated.