search

bxlab / bx-python

Tools for manipulating biological data, particularly multiple sequence alignments
MIT License
145 stars 53 forks source link

Build errors on osx-arm64 (bioconda) #98

Closed corneliusroemer closed 2 months ago

corneliusroemer commented 2 months ago

I'm trying to get the latest bx-python v0.12 into bioconda (the pypi path changed so autobump didn't make a PR).

On osx-arm64, I'm getting build errors:

11:29:13 BIOCONDA INFO (ERR)   building 'bx.bitset' extension
11:29:13 BIOCONDA INFO (ERR)   creating build/temp.macosx-11.0-arm64-cpython-311
11:29:13 BIOCONDA INFO (ERR)   creating build/temp.macosx-11.0-arm64-cpython-311/lib
11:29:13 BIOCONDA INFO (ERR)   creating build/temp.macosx-11.0-arm64-cpython-311/lib/bx
11:29:13 BIOCONDA INFO (ERR)   creating build/temp.macosx-11.0-arm64-cpython-311/src
11:29:13 BIOCONDA INFO (ERR)   creating build/temp.macosx-11.0-arm64-cpython-311/src/kent
11:29:15 BIOCONDA INFO (ERR)   building 'bx.seq._nib' extension
11:29:15 BIOCONDA INFO (ERR)   creating build/temp.macosx-11.0-arm64-cpython-311/lib/bx/seq
11:29:16 BIOCONDA INFO (ERR)   building 'bx.seq._twobit' extension
11:29:16 BIOCONDA INFO (ERR)   lib/bx/_seqmapping.c:3608:15: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations]
11:29:16 BIOCONDA INFO (ERR)     __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 54, __pyx_L1_error)
11:29:16 BIOCONDA INFO (ERR)                 ^
11:29:16 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11/abstract.h:353:1: note: 'PyObject_AsWriteBuffer' has been explicitly marked deprecated here
11:29:16 BIOCONDA INFO (ERR)   Py_DEPRECATED(3.0)
11:29:16 BIOCONDA INFO (ERR)   ^
11:29:16 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11/pyport.h:336:54: note: expanded from macro 'Py_DEPRECATED'
11:29:16 BIOCONDA INFO (ERR)   #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
11:29:16 BIOCONDA INFO (ERR)                                                        ^
11:29:16 BIOCONDA INFO (ERR)   lib/bx/_seqmapping.c:3868:15: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations]
11:29:16 BIOCONDA INFO (ERR)     __pyx_t_7 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 77, __pyx_L1_error)
11:29:16 BIOCONDA INFO (ERR)                 ^
11:29:16 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11/abstract.h:353:1: note: 'PyObject_AsWriteBuffer' has been explicitly marked deprecated here
11:29:16 BIOCONDA INFO (ERR)   Py_DEPRECATED(3.0)
11:29:16 BIOCONDA INFO (ERR)   ^
11:29:16 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11/pyport.h:336:54: note: expanded from macro 'Py_DEPRECATED'
11:29:16 BIOCONDA INFO (ERR)   #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
11:29:16 BIOCONDA INFO (ERR)                                                        ^
11:29:16 BIOCONDA INFO (ERR)   lib/bx/_seqmapping.c:5306:15: warning: 'PyObject_AsReadBuffer' is deprecated [-Wdeprecated-declarations]
11:29:16 BIOCONDA INFO (ERR)     __pyx_t_1 = PyObject_AsReadBuffer(__pyx_v_src, ((void const **)(&__pyx_v_s_buf)), (&__pyx_v_s_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 134, __pyx_L1_error)
11:29:16 BIOCONDA INFO (ERR)                 ^
11:29:16 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11/abstract.h:342:1: note: 'PyObject_AsReadBuffer' has been explicitly marked deprecated here
11:29:16 BIOCONDA INFO (ERR)   Py_DEPRECATED(3.0)
11:29:16 BIOCONDA INFO (ERR)   ^
11:29:16 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11/pyport.h:336:54: note: expanded from macro 'Py_DEPRECATED'
11:29:16 BIOCONDA INFO (ERR)   #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
11:29:16 BIOCONDA INFO (ERR)                                                        ^
11:29:16 BIOCONDA INFO (ERR)   lib/bx/_seqmapping.c:5386:15: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations]
11:29:16 BIOCONDA INFO (ERR)     __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 139, __pyx_L1_error)
11:29:16 BIOCONDA INFO (ERR)                 ^
11:29:16 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11/abstract.h:353:1: note: 'PyObject_AsWriteBuffer' has been explicitly marked deprecated here
11:29:16 BIOCONDA INFO (ERR)   Py_DEPRECATED(3.0)
11:29:16 BIOCONDA INFO (ERR)   ^
11:29:16 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11/pyport.h:336:54: note: expanded from macro 'Py_DEPRECATED'
11:29:16 BIOCONDA INFO (ERR)   #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
11:29:16 BIOCONDA INFO (ERR)                                                        ^
11:29:17 BIOCONDA INFO (ERR)   4 warnings generated.
11:29:17 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -bundle -undefined dynamic_lookup -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 build/temp.macosx-11.0-arm64-cpython-311/lib/bx/_seqmapping.o -o build/lib.macosx-11.0-arm64-cpython-311/bx/_seqmapping.cpython-311-darwin.so
11:29:17 BIOCONDA INFO (ERR)   building 'bx.misc.bgzf' extension
11:29:17 BIOCONDA INFO (ERR)   creating build/temp.macosx-11.0-arm64-cpython-311/lib/bx/misc
11:29:17 BIOCONDA INFO (ERR)   creating build/temp.macosx-11.0-arm64-cpython-311/src/samtools
11:29:17 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 -Isrc/samtools -I/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11 -c lib/bx/misc/bgzf.c -o build/temp.macosx-11.0-arm64-cpython-311/lib/bx/misc/bgzf.o
11:29:17 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 -Isrc/samtools -I/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11 -c src/samtools/bgzf.c -o build/temp.macosx-11.0-arm64-cpython-311/src/samtools/bgzf.o
11:29:17 BIOCONDA INFO (ERR)   src/samtools/bgzf.c:247:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 139 to -117 [-Wconstant-conversion]
11:29:17 BIOCONDA INFO (ERR)       buffer[1] = GZIP_ID2;
11:29:17 BIOCONDA INFO (ERR)                 ~ ^~~~~~~~
11:29:17 BIOCONDA INFO (ERR)   src/samtools/bgzf.c:255:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 255 to -1 [-Wconstant-conversion]
11:29:17 BIOCONDA INFO (ERR)       buffer[9] = OS_UNKNOWN;
11:29:17 BIOCONDA INFO (ERR)                 ~ ^~~~~~~~~~
11:29:17 BIOCONDA INFO (ERR)   src/samtools/bgzf.c:603:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
11:29:17 BIOCONDA INFO (ERR)                           int count, block_length = deflate_block(fp, 0);
11:29:17 BIOCONDA INFO (ERR)                               ^
11:29:17 BIOCONDA INFO (ERR)   src/samtools/bgzf.c:44:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
11:29:17 BIOCONDA INFO (ERR)   KHASH_MAP_INIT_INT64(cache, cache_t)
11:29:17 BIOCONDA INFO (ERR)   ^
11:29:17 BIOCONDA INFO (ERR)   src/samtools/khash.h:468:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
11:29:17 BIOCONDA INFO (ERR)           KHASH_INIT(name, uint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
11:29:17 BIOCONDA INFO (ERR)           ^
11:29:17 BIOCONDA INFO (ERR)   src/samtools/khash.h:140:21: note: expanded from macro 'KHASH_INIT'
11:29:17 BIOCONDA INFO (ERR)           static inline void kh_clear_##name(kh_##name##_t *h)                            \
11:29:17 BIOCONDA INFO (ERR)                              ^
11:29:17 BIOCONDA INFO (ERR)   <scratch space>:75:1: note: expanded from here
11:29:17 BIOCONDA INFO (ERR)   kh_clear_cache
11:29:17 BIOCONDA INFO (ERR)   ^
11:29:17 BIOCONDA INFO (ERR)   4 warnings generated.
11:29:17 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -bundle -undefined dynamic_lookup -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 build/temp.macosx-11.0-arm64-cpython-311/lib/bx/misc/bgzf.o build/temp.macosx-11.0-arm64-cpython-311/src/samtools/bgzf.o -lz -o build/lib.macosx-11.0-arm64-cpython-311/bx/misc/bgzf.cpython-311-darwin.so
11:29:17 BIOCONDA INFO (ERR)   building 'bx.intervals.cluster' extension
11:29:17 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 -Isrc -I/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11 -c lib/bx/intervals/cluster.c -o build/temp.macosx-11.0-arm64-cpython-311/lib/bx/intervals/cluster.o
11:29:18 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 -Isrc -I/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11 -c src/cluster.c -o build/temp.macosx-11.0-arm64-cpython-311/src/cluster.o
11:29:18 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -bundle -undefined dynamic_lookup -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 build/temp.macosx-11.0-arm64-cpython-311/lib/bx/intervals/cluster.o build/temp.macosx-11.0-arm64-cpython-311/src/cluster.o -o build/lib.macosx-11.0-arm64-cpython-311/bx/intervals/cluster.cpython-311-darwin.so
11:29:18 BIOCONDA INFO (ERR)   building 'bx.pwm._position_weight_matrix' extension
11:29:18 BIOCONDA INFO (ERR)   creating build/temp.macosx-11.0-arm64-cpython-311/lib/bx/pwm
11:29:18 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 -Isrc -I/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11 -c lib/bx/pwm/_position_weight_matrix.c -o build/temp.macosx-11.0-arm64-cpython-311/lib/bx/pwm/_position_weight_matrix.o
11:29:18 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 -Isrc -I/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11 -c src/pwm_utils.c -o build/temp.macosx-11.0-arm64-cpython-311/src/pwm_utils.o
11:29:18 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -bundle -undefined dynamic_lookup -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 build/temp.macosx-11.0-arm64-cpython-311/lib/bx/pwm/_position_weight_matrix.o build/temp.macosx-11.0-arm64-cpython-311/src/pwm_utils.o -o build/lib.macosx-11.0-arm64-cpython-311/bx/pwm/_position_weight_matrix.cpython-311-darwin.so
11:29:18 BIOCONDA INFO (ERR)   building 'bx.motif._pwm' extension
11:29:18 BIOCONDA INFO (ERR)   creating build/temp.macosx-11.0-arm64-cpython-311/lib/bx/motif
11:29:18 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 -I/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include -I/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11 -c lib/bx/motif/_pwm.c -o build/temp.macosx-11.0-arm64-cpython-311/lib/bx/motif/_pwm.o
11:29:18 BIOCONDA INFO (ERR)   In file included from lib/bx/motif/_pwm.c:1240:
11:29:18 BIOCONDA INFO (ERR)   In file included from /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
11:29:18 BIOCONDA INFO (ERR)   In file included from /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
11:29:18 BIOCONDA INFO (ERR)   In file included from /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948:
11:29:18 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
11:29:18 BIOCONDA INFO (ERR)   #warning "Using deprecated NumPy API, disable it with " \
11:29:18 BIOCONDA INFO (ERR)    ^
11:29:18 BIOCONDA INFO (ERR)   In file included from lib/bx/motif/_pwm.c:1240:
11:29:18 BIOCONDA INFO (ERR)   In file included from /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
11:29:18 BIOCONDA INFO (ERR)   In file included from /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:21:
11:29:18 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/__multiarray_api.h:1477:1: warning: unused function '_import_array' [-Wunused-function]
11:29:18 BIOCONDA INFO (ERR)   _import_array(void)
11:29:18 BIOCONDA INFO (ERR)   ^
11:29:18 BIOCONDA INFO (ERR)   2 warnings generated.
11:29:18 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -bundle -undefined dynamic_lookup -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 build/temp.macosx-11.0-arm64-cpython-311/lib/bx/motif/_pwm.o -o build/lib.macosx-11.0-arm64-cpython-311/bx/motif/_pwm.cpython-311-darwin.so
11:29:18 BIOCONDA INFO (ERR)   building 'bx.arrays.array_tree' extension
11:29:18 BIOCONDA INFO (ERR)   creating build/temp.macosx-11.0-arm64-cpython-311/lib/bx/arrays
11:29:18 BIOCONDA INFO (ERR)   arm64-apple-darwin20.0.0-clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -fPIC -O2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -arch arm64 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work=/usr/local/src/conda/bx-python-0.12.0 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -mmacosx-version-min=11.0 -I/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include -I/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.11 -c lib/bx/arrays/array_tree.c -o build/temp.macosx-11.0-arm64-cpython-311/lib/bx/arrays/array_tree.o
11:29:18 BIOCONDA INFO (ERR)   In file included from lib/bx/arrays/array_tree.c:1249:
11:29:18 BIOCONDA INFO (ERR)   In file included from /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
11:29:18 BIOCONDA INFO (ERR)   In file included from /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
11:29:18 BIOCONDA INFO (ERR)   In file included from /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948:
11:29:18 BIOCONDA INFO (ERR)   /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
11:29:18 BIOCONDA INFO (ERR)   #warning "Using deprecated NumPy API, disable it with " \
11:29:18 BIOCONDA INFO (ERR)    ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:4772:13: error: call to undeclared function 'PyDataType_ELSIZE'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyDataType_ELSIZE(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:4806:13: error: call to undeclared function 'PyDataType_ALIGNMENT'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyDataType_ALIGNMENT(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:4844:15: error: call to undeclared function 'PyDataType_FIELDS'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_t_1 = PyDataType_FIELDS(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)                 ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:4844:13: error: incompatible integer to pointer conversion assigning to 'PyObject *' (aka 'struct _object *') from 'int' [-Wint-conversion]
11:29:18 BIOCONDA INFO (ERR)     __pyx_t_1 = PyDataType_FIELDS(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:4886:15: error: call to undeclared function 'PyDataType_NAMES'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_t_1 = PyDataType_NAMES(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)                 ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:4886:13: error: incompatible integer to pointer conversion assigning to 'PyObject *' (aka 'struct _object *') from 'int' [-Wint-conversion]
11:29:18 BIOCONDA INFO (ERR)     __pyx_t_1 = PyDataType_NAMES(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:4924:13: error: call to undeclared function 'PyDataType_SUBARRAY'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyDataType_SUBARRAY(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:4924:11: error: incompatible integer to pointer conversion assigning to 'PyArray_ArrayDescr *' (aka 'struct _arr_descr *') from 'int' [-Wint-conversion]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyDataType_SUBARRAY(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)             ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:4958:13: error: call to undeclared function 'PyDataType_FLAGS'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyDataType_FLAGS(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:4992:13: error: call to undeclared function 'PyArray_MultiIter_NUMITER'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyArray_MultiIter_NUMITER(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:5026:13: error: call to undeclared function 'PyArray_MultiIter_SIZE'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyArray_MultiIter_SIZE(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:5060:13: error: call to undeclared function 'PyArray_MultiIter_INDEX'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyArray_MultiIter_INDEX(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:5094:13: error: call to undeclared function 'PyArray_MultiIter_NDIM'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyArray_MultiIter_NDIM(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:5128:13: error: call to undeclared function 'PyArray_MultiIter_DIMS'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyArray_MultiIter_DIMS(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:5128:11: error: incompatible integer to pointer conversion assigning to 'npy_intp *' (aka 'long *') from 'int' [-Wint-conversion]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyArray_MultiIter_DIMS(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)             ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:5162:13: error: call to undeclared function 'PyArray_MultiIter_ITERS'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyArray_MultiIter_ITERS(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)               ^
11:29:18 BIOCONDA INFO (ERR)   lib/bx/arrays/array_tree.c:5162:11: error: incompatible integer to pointer conversion assigning to 'void **' from 'int' [-Wint-conversion]
11:29:18 BIOCONDA INFO (ERR)     __pyx_r = PyArray_MultiIter_ITERS(__pyx_v_self);
11:29:18 BIOCONDA INFO (ERR)             ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11:29:18 BIOCONDA INFO (ERR)   1 warning and 17 errors generated.
11:29:18 BIOCONDA INFO (ERR)   error: command '/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_build_env/bin/arm64-apple-darwin20.0.0-clang' failed with exit code 1
11:29:19 BIOCONDA INFO (ERR)   error: subprocess-exited-with-error
11:29:19 BIOCONDA INFO (ERR) 
11:29:19 BIOCONDA INFO (ERR)   × Building wheel for bx-python (pyproject.toml) did not run successfully.
11:29:19 BIOCONDA INFO (ERR)   │ exit code: 1
11:29:19 BIOCONDA INFO (ERR)   ╰─> See above for output.
11:29:19 BIOCONDA INFO (ERR) 
11:29:19 BIOCONDA INFO (ERR)   note: This error originates from a subprocess, and is likely not a problem with pip.
11:29:19 BIOCONDA INFO (ERR)   full command: /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmpx6vna78n
11:29:19 BIOCONDA INFO (ERR)   cwd: /opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720956510234/work
11:29:19 BIOCONDA INFO (ERR)   ERROR: Failed building wheel for bx-python
11:29:19 BIOCONDA INFO (ERR) ERROR: Could not build wheels for bx-python, which is required to install pyproject.toml-based projects

Could you have a look and see whether this is an issue with bx-python itself or the bioconda-recipe?

Here's the PR: https://github.com/bioconda/bioconda-recipes/pull/49231

corneliusroemer commented 2 months ago

Ah I think I've found the issue, you now require numpy >=1.25 for python >=3.9

nsoranzo commented 2 months ago

Fixed in https://github.com/bioconda/bioconda-recipes/pull/49231 .