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I just tried to clone and pip install sgkit in a fresh conda Python 3.7 environment on MacOS using our contributing docs. pip install -r requirements.txt -r requirements-dev.txt fails for me when trying to build numcodecs. It appears that @alimanfoo and @jeromekelleher are familiar with this issue from zarr-developers/numcodecs#210, and that numcodecs wheels are stalled at zarr-developers/numcodecs#70.
I'll just move to GCP for now, but it would be nice to get things working out of the box on MacOS.
Detailed console output
Building wheel for numcodecs (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/local/anaconda3/envs/sgkit/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py'"'"'; __file__='"'"'/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-wheel-gq7ig4o_
cwd: /private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/
Complete output (224 lines):
[numcodecs] setting up Blosc extension
[numcodecs] compiling Blosc extension with SSE2 support
[numcodecs] compiling Blosc extension with AVX2 support
[numcodecs] setting up Zstandard extension
[numcodecs] setting up LZ4 extension
[numcodecs] setting up compat extension
[numcodecs] setting up vlen extension
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/lzma.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/astype.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/gzip.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/bz2.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/version.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/compat.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/checksum32.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/quantize.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/registry.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/pickles.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/fixedscaleoffset.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/zlib.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/delta.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/msgpacks.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/packbits.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/categorize.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/json.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/abc.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
creating build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_categorize.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_registry.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_vlen_utf8.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_gzip.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_delta.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_lzma.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_bz2.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_pickles.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_quantize.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_lz4.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_msgpacks.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_astype.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_packbits.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/common.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_fixedscaleoffset.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_compat.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_zlib.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_json.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_vlen_array.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_zstd.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_vlen_bytes.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_checksum32.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_blosc.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
running build_ext
building 'numcodecs.blosc' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/numcodecs
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/lz4-1.9.1
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zstd-1.4.1
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zstd-1.4.1/common
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zstd-1.4.1/compress
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zstd-1.4.1/decompress
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zstd-1.4.1/dictBuilder
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c numcodecs/blosc.c -o build/temp.macosx-10.9-x86_64-3.7/numcodecs/blosc.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/blosc.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/blosc.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
c-blosc/blosc/blosc.c:445:12: warning: 'LZ4_decompress_fast' is deprecated: This function is deprecated and unsafe. Consider using LZ4_decompress_safe() instead [-Wdeprecated-declarations]
cbytes = LZ4_decompress_fast(input, output, (int)maxout);
^
c-blosc/internal-complibs/lz4-1.9.1/lz4.h:661:1: note: 'LZ4_decompress_fast' has been explicitly marked deprecated here
LZ4_DEPRECATED("This function is deprecated and unsafe. Consider using LZ4_decompress_safe() instead")
^
c-blosc/internal-complibs/lz4-1.9.1/lz4.h:592:52: note: expanded from macro 'LZ4_DEPRECATED'
# define LZ4_DEPRECATED(message) __attribute__((deprecated(message)))
^
c-blosc/blosc/blosc.c:446:14: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
if (cbytes != compressed_length) {
~~~~~~ ^ ~~~~~~~~~~~~~~~~~
c-blosc/blosc/blosc.c:775:38: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'unsigned long' [-Wsign-compare]
if (src_offset < 0 || src_offset > compressedsize - sizeof(int32_t)) {
~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
c-blosc/blosc/blosc.c:995:19: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'unsigned long' [-Wsign-compare]
if (blocksize > BLOSC_MAX_BLOCKSIZE) {
~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~
c-blosc/blosc/blosc.c:1451:53: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
if (context->blocksize <= 0 || context->blocksize > destsize ||
~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~
c-blosc/blosc/blosc.c:1452:26: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'unsigned long' [-Wsign-compare]
context->blocksize > BLOSC_MAX_BLOCKSIZE || context->typesize <= 0 ||
~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~
c-blosc/blosc/blosc.c:1617:57: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'unsigned long' [-Wsign-compare]
if (blocksize <= 0 || blocksize > nbytes || blocksize > BLOSC_MAX_BLOCKSIZE ||
~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~
7 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/bitshuffle-generic.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/bitshuffle-generic.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/shuffle.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/shuffle.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
In file included from c-blosc/blosc/shuffle.c:11:
c-blosc/blosc/shuffle-generic.h:32:13: warning: unused function 'shuffle_generic_inline' [-Wunused-function]
static void shuffle_generic_inline(const size_t type_size,
^
c-blosc/blosc/shuffle-generic.h:61:13: warning: unused function 'unshuffle_generic_inline' [-Wunused-function]
static void unshuffle_generic_inline(const size_t type_size,
^
2 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/fastcopy.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/fastcopy.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
c-blosc/blosc/fastcopy.c:143:30: warning: unused function 'copy_32_bytes_aligned' [-Wunused-function]
static inline unsigned char *copy_32_bytes_aligned(unsigned char *out, const unsigned char *from) {
^
1 warning generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/blosclz.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/blosclz.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
c-blosc/blosc/blosclz.c:219:35: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if (_mm256_movemask_epi8(cmp) != 0xFFFFFFFF) {
~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~
c-blosc/blosc/blosclz.c:323:35: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if (_mm256_movemask_epi8(cmp) != 0xFFFFFFFF) {
~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~
c-blosc/blosc/blosclz.c:101:17: warning: unused function 'get_run' [-Wunused-function]
static uint8_t *get_run(uint8_t *ip, const uint8_t *ip_bound, const uint8_t *ref) {
^
c-blosc/blosc/blosclz.c:129:17: warning: unused function 'get_run_16' [-Wunused-function]
static uint8_t *get_run_16(uint8_t *ip, const uint8_t *ip_bound, const uint8_t *ref) {
^
4 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/shuffle-generic.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/shuffle-generic.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/lz4-1.9.1/lz4hc.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/lz4-1.9.1/lz4hc.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/lz4-1.9.1/lz4.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/lz4-1.9.1/lz4.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/snappy-1.1.1/snappy-stubs-internal.cc -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1/snappy-stubs-internal.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/snappy-1.1.1/snappy-c.cc -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1/snappy-c.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/snappy-1.1.1/snappy-sinksource.cc -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1/snappy-sinksource.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/snappy-1.1.1/snappy.cc -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1/snappy.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
c-blosc/internal-complibs/snappy-1.1.1/snappy.cc:1013:33: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare]
if (curr_iov_index_ + 1 >= output_iov_count_) {
~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~
c-blosc/internal-complibs/snappy-1.1.1/snappy.cc:1095:35: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare]
if (curr_iov_index_ + 1 >= output_iov_count_) {
~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~
2 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/zlib-1.2.8/inflate.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8/inflate.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/zlib-1.2.8/compress.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8/compress.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/zlib-1.2.8/deflate.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8/deflate.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/zlib-1.2.8/gzread.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8/gzread.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
c-blosc/internal-complibs/zlib-1.2.8/gzread.c:30:15: error: implicit declaration of function 'read' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
ret = read(state->fd, buf + *have, len - *have);
^
c-blosc/internal-complibs/zlib-1.2.8/gzread.c:30:15: note: did you mean 'fread'?
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdio.h:158:9: note: 'fread' declared here
size_t fread(void * __restrict __ptr, size_t __size, size_t __nitems, FILE * __restrict __stream);
^
c-blosc/internal-complibs/zlib-1.2.8/gzread.c:591:11: error: implicit declaration of function 'close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
ret = close(state->fd);
^
2 errors generated.
[numcodecs] command 'gcc' failed with exit status 1
Traceback (most recent call last):
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/unixccompiler.py", line 118, in _compile
extra_postargs)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/ccompiler.py", line 910, in spawn
spawn(cmd, dry_run=self.dry_run)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/spawn.py", line 36, in spawn
_spawn_posix(cmd, search_path, dry_run=dry_run)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/spawn.py", line 159, in _spawn_posix
% (cmd, exit_status))
distutils.errors.DistutilsExecError: command 'gcc' failed with exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py", line 286, in build_extension
build_ext.build_extension(self, ext)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/command/build_ext.py", line 534, in build_extension
depends=ext.depends)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/ccompiler.py", line 574, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/unixccompiler.py", line 120, in _compile
raise CompileError(msg)
distutils.errors.CompileError: command 'gcc' failed with exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py", line 362, in <module>
run_setup(with_extensions)
File "/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py", line 355, in run_setup
license='MIT',
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/site-packages/setuptools/__init__.py", line 163, in setup
return distutils.core.setup(**attrs)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 223, in run
self.run_command('build')
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py", line 279, in run
build_ext.run(self)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/command/build_ext.py", line 340, in run
self.build_extensions()
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/command/build_ext.py", line 449, in build_extensions
self._build_extensions_serial()
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/command/build_ext.py", line 474, in _build_extensions_serial
self.build_extension(ext)
File "/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py", line 289, in build_extension
raise BuildFailed()
__main__.BuildFailed
----------------------------------------
ERROR: Failed building wheel for numcodecs
Running setup.py clean for numcodecs
Successfully built zarr pyyaml toolz asciitree
Failed to build numcodecs
DEPRECATION: Could not build wheels for numcodecs which do not use PEP 517. pip will fall back to legacy 'setup.py install' for these. pip 21.0 will remove support for this functionality. A possible replacement is to fix the wheel build issue reported above. You can find discussion regarding this at https://github.com/pypa/pip/issues/8368.
Installing collected packages: numpy, six, python-dateutil, pytz, pandas, xarray, pyyaml, toolz, dask, scipy, llvmlite, numba, asciitree, monotonic, fasteners, numcodecs, zarr, idna, urllib3, chardet, requests, coverage, codecov, nodeenv, appdirs, distlib, filelock, zipp, importlib-metadata, virtualenv, identify, toml, cfgv, pre-commit, pyparsing, packaging, iniconfig, more-itertools, pluggy, attrs, py, pytest, pytest-cov, pytest-datadir, sortedcontainers, hypothesis, patsy, statsmodels, alabaster, sphinxcontrib-qthelp, sphinxcontrib-serializinghtml, imagesize, sphinxcontrib-jsmath, Pygments, sphinxcontrib-devhelp, MarkupSafe, Jinja2, sphinxcontrib-htmlhelp, docutils, babel, sphinxcontrib-applehelp, snowballstemmer, sphinx, sphinx-rtd-theme
Running setup.py install for numcodecs ... error
ERROR: Command errored out with exit status 1:
command: /usr/local/anaconda3/envs/sgkit/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py'"'"'; __file__='"'"'/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-record-luj7ziku/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/anaconda3/envs/sgkit/include/python3.7m/numcodecs
cwd: /private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/
Complete output (226 lines):
[numcodecs] setting up Blosc extension
[numcodecs] compiling Blosc extension with SSE2 support
[numcodecs] compiling Blosc extension with AVX2 support
[numcodecs] setting up Zstandard extension
[numcodecs] setting up LZ4 extension
[numcodecs] setting up compat extension
[numcodecs] setting up vlen extension
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/lzma.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/astype.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/gzip.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/bz2.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/version.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/compat.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/checksum32.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/quantize.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/registry.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/pickles.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/fixedscaleoffset.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/zlib.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/delta.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/msgpacks.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/packbits.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/categorize.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/json.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
copying ./numcodecs/abc.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs
creating build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_categorize.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_registry.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_vlen_utf8.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_gzip.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_delta.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_lzma.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_bz2.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_pickles.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_quantize.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_lz4.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_msgpacks.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_astype.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_packbits.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/common.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_fixedscaleoffset.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_compat.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_zlib.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_json.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_vlen_array.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_zstd.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_vlen_bytes.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_checksum32.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
copying ./numcodecs/tests/test_blosc.py -> build/lib.macosx-10.9-x86_64-3.7/numcodecs/tests
running build_ext
building 'numcodecs.blosc' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/numcodecs
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/lz4-1.9.1
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zstd-1.4.1
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zstd-1.4.1/common
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zstd-1.4.1/compress
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zstd-1.4.1/decompress
creating build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zstd-1.4.1/dictBuilder
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c numcodecs/blosc.c -o build/temp.macosx-10.9-x86_64-3.7/numcodecs/blosc.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/blosc.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/blosc.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
c-blosc/blosc/blosc.c:445:12: warning: 'LZ4_decompress_fast' is deprecated: This function is deprecated and unsafe. Consider using LZ4_decompress_safe() instead [-Wdeprecated-declarations]
cbytes = LZ4_decompress_fast(input, output, (int)maxout);
^
c-blosc/internal-complibs/lz4-1.9.1/lz4.h:661:1: note: 'LZ4_decompress_fast' has been explicitly marked deprecated here
LZ4_DEPRECATED("This function is deprecated and unsafe. Consider using LZ4_decompress_safe() instead")
^
c-blosc/internal-complibs/lz4-1.9.1/lz4.h:592:52: note: expanded from macro 'LZ4_DEPRECATED'
# define LZ4_DEPRECATED(message) __attribute__((deprecated(message)))
^
c-blosc/blosc/blosc.c:446:14: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
if (cbytes != compressed_length) {
~~~~~~ ^ ~~~~~~~~~~~~~~~~~
c-blosc/blosc/blosc.c:775:38: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'unsigned long' [-Wsign-compare]
if (src_offset < 0 || src_offset > compressedsize - sizeof(int32_t)) {
~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
c-blosc/blosc/blosc.c:995:19: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'unsigned long' [-Wsign-compare]
if (blocksize > BLOSC_MAX_BLOCKSIZE) {
~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~
c-blosc/blosc/blosc.c:1451:53: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
if (context->blocksize <= 0 || context->blocksize > destsize ||
~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~
c-blosc/blosc/blosc.c:1452:26: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'unsigned long' [-Wsign-compare]
context->blocksize > BLOSC_MAX_BLOCKSIZE || context->typesize <= 0 ||
~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~
c-blosc/blosc/blosc.c:1617:57: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'unsigned long' [-Wsign-compare]
if (blocksize <= 0 || blocksize > nbytes || blocksize > BLOSC_MAX_BLOCKSIZE ||
~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~
7 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/bitshuffle-generic.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/bitshuffle-generic.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/shuffle.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/shuffle.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
In file included from c-blosc/blosc/shuffle.c:11:
c-blosc/blosc/shuffle-generic.h:32:13: warning: unused function 'shuffle_generic_inline' [-Wunused-function]
static void shuffle_generic_inline(const size_t type_size,
^
c-blosc/blosc/shuffle-generic.h:61:13: warning: unused function 'unshuffle_generic_inline' [-Wunused-function]
static void unshuffle_generic_inline(const size_t type_size,
^
2 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/fastcopy.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/fastcopy.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
c-blosc/blosc/fastcopy.c:143:30: warning: unused function 'copy_32_bytes_aligned' [-Wunused-function]
static inline unsigned char *copy_32_bytes_aligned(unsigned char *out, const unsigned char *from) {
^
1 warning generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/blosclz.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/blosclz.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
c-blosc/blosc/blosclz.c:219:35: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if (_mm256_movemask_epi8(cmp) != 0xFFFFFFFF) {
~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~
c-blosc/blosc/blosclz.c:323:35: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if (_mm256_movemask_epi8(cmp) != 0xFFFFFFFF) {
~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~
c-blosc/blosc/blosclz.c:101:17: warning: unused function 'get_run' [-Wunused-function]
static uint8_t *get_run(uint8_t *ip, const uint8_t *ip_bound, const uint8_t *ref) {
^
c-blosc/blosc/blosclz.c:129:17: warning: unused function 'get_run_16' [-Wunused-function]
static uint8_t *get_run_16(uint8_t *ip, const uint8_t *ip_bound, const uint8_t *ref) {
^
4 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/blosc/shuffle-generic.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/blosc/shuffle-generic.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/lz4-1.9.1/lz4hc.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/lz4-1.9.1/lz4hc.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/lz4-1.9.1/lz4.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/lz4-1.9.1/lz4.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/snappy-1.1.1/snappy-stubs-internal.cc -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1/snappy-stubs-internal.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/snappy-1.1.1/snappy-c.cc -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1/snappy-c.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/snappy-1.1.1/snappy-sinksource.cc -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1/snappy-sinksource.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/snappy-1.1.1/snappy.cc -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1/snappy.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
c-blosc/internal-complibs/snappy-1.1.1/snappy.cc:1013:33: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare]
if (curr_iov_index_ + 1 >= output_iov_count_) {
~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~
c-blosc/internal-complibs/snappy-1.1.1/snappy.cc:1095:35: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare]
if (curr_iov_index_ + 1 >= output_iov_count_) {
~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~
2 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/zlib-1.2.8/inflate.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8/inflate.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/zlib-1.2.8/compress.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8/compress.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/zlib-1.2.8/deflate.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8/deflate.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -I/usr/local/anaconda3/envs/sgkit/include -arch x86_64 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.9.1 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.4.1 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.4.1/compress -Ic-blosc/internal-complibs/zstd-1.4.1/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.1/decompress -Ic-blosc/internal-complibs/zstd-1.4.1/legacy -Ic-blosc/internal-complibs/zstd-1.4.1/common -Ic-blosc/internal-complibs/zstd-1.4.1/dll -Ic-blosc/internal-complibs/zstd-1.4.1/deprecated -I/usr/local/anaconda3/envs/sgkit/include/python3.7m -c c-blosc/internal-complibs/zlib-1.2.8/gzread.c -o build/temp.macosx-10.9-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8/gzread.o -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED
c-blosc/internal-complibs/zlib-1.2.8/gzread.c:30:15: error: implicit declaration of function 'read' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
ret = read(state->fd, buf + *have, len - *have);
^
c-blosc/internal-complibs/zlib-1.2.8/gzread.c:30:15: note: did you mean 'fread'?
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdio.h:158:9: note: 'fread' declared here
size_t fread(void * __restrict __ptr, size_t __size, size_t __nitems, FILE * __restrict __stream);
^
c-blosc/internal-complibs/zlib-1.2.8/gzread.c:591:11: error: implicit declaration of function 'close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
ret = close(state->fd);
^
2 errors generated.
[numcodecs] command 'gcc' failed with exit status 1
Traceback (most recent call last):
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/unixccompiler.py", line 118, in _compile
extra_postargs)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/ccompiler.py", line 910, in spawn
spawn(cmd, dry_run=self.dry_run)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/spawn.py", line 36, in spawn
_spawn_posix(cmd, search_path, dry_run=dry_run)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/spawn.py", line 159, in _spawn_posix
% (cmd, exit_status))
distutils.errors.DistutilsExecError: command 'gcc' failed with exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py", line 286, in build_extension
build_ext.build_extension(self, ext)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/command/build_ext.py", line 534, in build_extension
depends=ext.depends)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/ccompiler.py", line 574, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/unixccompiler.py", line 120, in _compile
raise CompileError(msg)
distutils.errors.CompileError: command 'gcc' failed with exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py", line 362, in <module>
run_setup(with_extensions)
File "/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py", line 355, in run_setup
license='MIT',
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/site-packages/setuptools/__init__.py", line 163, in setup
return distutils.core.setup(**attrs)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/site-packages/setuptools/command/install.py", line 61, in run
return orig.install.run(self)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/command/install.py", line 545, in run
self.run_command('build')
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py", line 279, in run
build_ext.run(self)
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/command/build_ext.py", line 340, in run
self.build_extensions()
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/command/build_ext.py", line 449, in build_extensions
self._build_extensions_serial()
File "/usr/local/anaconda3/envs/sgkit/lib/python3.7/distutils/command/build_ext.py", line 474, in _build_extensions_serial
self.build_extension(ext)
File "/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py", line 289, in build_extension
raise BuildFailed()
__main__.BuildFailed
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/anaconda3/envs/sgkit/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py'"'"'; __file__='"'"'/private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-install-sveaklyg/numcodecs/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/tz/1_mlmz691xz8kkjx6x2s2l340000gn/T/pip-record-luj7ziku/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/anaconda3/envs/sgkit/include/python3.7m/numcodecs Check the logs for full command output.
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Issue metadata
Issue description
I just tried to clone and pip install
sgkit
in a fresh conda Python 3.7 environment on MacOS using our contributing docs.pip install -r requirements.txt -r requirements-dev.txt
fails for me when trying to buildnumcodecs
. It appears that @alimanfoo and @jeromekelleher are familiar with this issue from zarr-developers/numcodecs#210, and thatnumcodecs
wheels are stalled at zarr-developers/numcodecs#70.I'll just move to GCP for now, but it would be nice to get things working out of the box on MacOS.
Detailed console output
The text was updated successfully, but these errors were encountered: