Installation fails on MacOS 10.15 #134

hammer · 2020-08-22T20:26:31Z

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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jeromekelleher · 2020-08-24T09:29:13Z

Yes, this exact issue is one of the key motivations for making the dependencies for sgkit as clear and simple as possible. It's a real pain.

tomwhite · 2020-08-24T09:54:50Z

Until numcodecs wheels are available we could avoid numcodecs 0.6.4 (like napari/napari#666), or remove the explicit zarr dependency. The latter is a problem since we added it for read_vcfzarr, and our IO readers all generally use zarr as an intermediate format, so it's not something we can (or want to) avoid.

tomwhite · 2020-11-16T18:47:19Z

Can we close this now?

hammer · 2020-11-16T18:50:58Z

Yes!

hammer changed the title ~~Installation fails on MacOS~~ Installation fails on MacOS 10.15 and Ubuntu 18.04 Aug 22, 2020

hammer changed the title ~~Installation fails on MacOS 10.15 and Ubuntu 18.04~~ Installation fails on MacOS 10.15 Aug 22, 2020

ravwojdyla mentioned this issue Aug 24, 2020

Mergify not merging #138

Closed

jeromekelleher mentioned this issue Aug 27, 2020

Can't install precommit toolchain on OSX #141

Closed

hammer mentioned this issue Aug 31, 2020

Build wheels on github actions zarr-developers/numcodecs#224

Merged

hammer closed this as completed Nov 16, 2020

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Installation fails on MacOS 10.15 #134

Installation fails on MacOS 10.15 #134

hammer commented Aug 22, 2020 •

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jeromekelleher commented Aug 24, 2020

tomwhite commented Aug 24, 2020

tomwhite commented Nov 16, 2020

hammer commented Nov 16, 2020

Installation fails on MacOS 10.15 #134

Installation fails on MacOS 10.15 #134

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hammer commented Aug 22, 2020 • edited Loading

jeromekelleher commented Aug 24, 2020

tomwhite commented Aug 24, 2020

tomwhite commented Nov 16, 2020

hammer commented Nov 16, 2020

hammer commented Aug 22, 2020 •

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