I’m building a package that has R as a dependency, and calls R via Rpy2; the latter can be installed with pip but R can only be install using conda (AFAIK). I tried to use nbdev to build a conda package, hoping to make life easier for users (to solve the rather complicated installation otherwise). Current status:
-
make pypiworks and the package is hosted on pypi. -
nbdev_conda_packagefails with the following error message, which I wasn’t able to figure out:
(pybrms-dev) adamhaber-s-macbookpro1:pybrms adamhaber$ nbdev_conda_package
No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.11
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.11
INFO:conda_build.variants:Adding in variants from internal_defaults
INFO:conda_build.metadata:Attempting to finalize metadata for pybrms
WARNING: symlink_conda() is deprecated.
WARNING: symlink_conda() is deprecated.
INFO:conda_build.source:Source cache directory is: /Users/adamhaber/miniconda3/conda-bld/src_cache
INFO conda_build.source:download_to_cache(43): Source cache directory is: /Users/adamhaber/miniconda3/conda-bld/src_cache
INFO:conda_build.source:Downloading source to cache: pybrms-0.0.31_1146958652.tar.gz
INFO conda_build.source:download_to_cache(66): Downloading source to cache: pybrms-0.0.31_1146958652.tar.gz
INFO:conda_build.source:Downloading https://files.pythonhosted.org/packages/ef/14/fe18e4febcfd99dc26e851a81b24ddf9737c94e37bb63eff16672833aab9/pybrms-0.0.31.tar.gz
INFO conda_build.source:download_to_cache(80): Downloading https://files.pythonhosted.org/packages/ef/14/fe18e4febcfd99dc26e851a81b24ddf9737c94e37bb63eff16672833aab9/pybrms-0.0.31.tar.gz
INFO:conda_build.source:Success
INFO conda_build.source:download_to_cache(91): Success
Running command python setup.py egg_info
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/tmp/pip-req-build-38lyf6l3/setup.py", line 18, in <module>
assert o in cfg, "missing expected setting: {}".format(o)
AssertionError: missing expected setting: version
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Traceback (most recent call last):
File "/Users/adamhaber/miniconda3/bin/conda-build", line 11, in <module>
sys.exit(main())
File "/Users/adamhaber/miniconda3/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 456, in main
execute(sys.argv[1:])
File "/Users/adamhaber/miniconda3/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 447, in execute
verify=args.verify, variants=args.variants)
File "/Users/adamhaber/miniconda3/lib/python3.6/site-packages/conda_build/api.py", line 208, in build
notest=notest, need_source_download=need_source_download, variants=variants)
File "/Users/adamhaber/miniconda3/lib/python3.6/site-packages/conda_build/build.py", line 2314, in build_tree
notest=notest,
File "/Users/adamhaber/miniconda3/lib/python3.6/site-packages/conda_build/build.py", line 1477, in build
cwd=src_dir, stats=build_stats)
File "/Users/adamhaber/miniconda3/lib/python3.6/site-packages/conda_build/utils.py", line 374, in check_call_env
return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
File "/Users/adamhaber/miniconda3/lib/python3.6/site-packages/conda_build/utils.py", line 354, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/Users/adamhaber/miniconda3/conda-bld/pybrms_1596952201823/work/conda_build.sh']' returned non-zero exit status 1.
b'Adding in variants from internal_defaults\nAttempting to finalize metadata for pybrms\nCollecting package metadata (repodata.json): ...working... done\nSolving environment: ...working... done\nCollecting package metadata (repodata.json): ...working... done\nSolving environment: ...working... done\nBUILD START: [\'pybrms-0.0.31-pyr36h39e3cac_0.tar.bz2\']\nCollecting package metadata (repodata.json): ...working... done\nSolving environment: ...working... done\n\n## Package Plan ##\n\n environment location: /Users/adamhaber/miniconda3/conda-bld/pybrms_1596952201823/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold\n\n\nThe following NEW packages will be INSTALLED:\n\n _r-mutex: 1.0.1-anacondar_1 conda-forge\n bwidget: 1.9.14-0 conda-forge\n bzip2: 1.0.8-h0b31af3_2 conda-forge\n c-ares: 1.16.1-haf1e3a3_0 conda-forge\n ca-certificates: 2020.6.20-hecda079_0 conda-forge\n cairo: 1.16.0-ha8983da_1005 conda-forge\n cctools_osx-64: 949.0.1-h5ba7a2e_3 conda-forge\n certifi: 2020.6.20-py36h9f0ad1d_0 conda-forge\n cffi: 1.14.1-py36h6a9c9ac_0 conda-forge\n clang: 10.0.1-default_hf57f61e_1 conda-forge\n clang_osx-64: 10.0.1-h05bbb7f_6 conda-forge\n clangxx: 10.0.1-default_hf57f61e_1 conda-forge\n clangxx_osx-64: 10.0.1-h05bbb7f_6 conda-forge\n compiler-rt: 10.0.1-he6db49b_0 conda-forge\n compiler-rt_osx-64: 10.0.1-h033240e_0 conda-forge\n curl: 7.71.1-hbdca1c0_4 conda-forge\n cycler: 0.10.0-py_2 conda-forge\n cython: 0.29.21-py36h0130604_0 conda-forge\n fontconfig: 2.13.1-h79c0d67_1002 conda-forge\n freetype: 2.10.2-h8da9a1a_0 conda-forge\n fribidi: 1.0.10-h0b31af3_0 conda-forge\n gettext: 0.19.8.1-h46ab8bc_1002 conda-forge\n gfortran_impl_osx-64: 7.5.0-h970e067_1 conda-forge\n gfortran_osx-64: 7.5.0-hb7f2cba_5 conda-forge\n glib: 2.65.0-h577aef8_0 conda-forge\n gmp: 6.2.0-h4a8c4bd_2 conda-forge\n graphite2: 1.3.13-h12caacf_1001 conda-forge\n gsl: 2.6-ha2d443c_0 conda-forge\n harfbuzz: 2.4.0-h1050040_5 conda-forge\n icu: 67.1-h4a8c4bd_0 conda-forge\n isl: 0.22.1-h65ac59c_1 conda-forge\n jinja2: 2.11.2-pyh9f0ad1d_0 conda-forge\n jpeg: 9d-h0b31af3_0 conda-forge\n kiwisolver: 1.2.0-py36h863e41a_0 conda-forge\n krb5: 1.17.1-h14dd6a4_2 conda-forge\n ld64_osx-64: 530-h3c32e8a_3 conda-forge\n libblas: 3.8.0-17_openblas conda-forge\n libcblas: 3.8.0-17_openblas conda-forge\n libclang-cpp10: 10.0.1-default_hf57f61e_1 conda-forge\n libcurl: 7.71.1-he6690cf_4 conda-forge\n libcxx: 10.0.1-h5f48129_0 conda-forge\n libedit: 3.1.20191231-hed1e85f_1 conda-forge\n libev: 4.33-haf1e3a3_0 conda-forge\n libffi: 3.2.1-h4a8c4bd_1007 conda-forge\n libgfortran: 4.0.0-2 conda-forge\n libiconv: 1.15-h0b31af3_1006 conda-forge\n liblapack: 3.8.0-17_openblas conda-forge\n libllvm10: 10.0.1-h009f743_1 conda-forge\n libnghttp2: 1.41.0-h8a08a2b_1 conda-forge\n libopenblas: 0.3.10-openmp_h63d9170_4 conda-forge\n libpng: 1.6.37-hbbe82c9_1 conda-forge\n libssh2: 1.9.0-h39bdce6_5 conda-forge\n libtiff: 4.1.0-h2ae36a8_6 conda-forge\n libwebp-base: 1.1.0-h0b31af3_3 conda-forge\n libxml2: 2.9.10-h7fdee97_2 conda-forge\n llvm-openmp: 10.0.1-h28b9765_0 conda-forge\n llvm-tools: 10.0.1-h1341992_1 conda-forge\n lz4-c: 1.9.2-h4a8c4bd_1 conda-forge\n make: 4.3-h0b31af3_0 conda-forge\n markupsafe: 1.1.1-py36h37b9a7d_1 conda-forge\n matplotlib: 3.1.0-py36_0 conda-forge\n matplotlib-base: 3.1.0-py36habd5b94_0 conda-forge\n mpc: 1.1.0-ha57cd0f_1009 conda-forge\n mpfr: 4.0.2-h65ac59c_1 conda-forge\n ncurses: 6.2-hb1e8313_1 conda-forge\n numpy: 1.11.3-py36hdf140aa_1207 conda-forge\n openssl: 1.1.1g-h0b31af3_1 conda-forge\n packaging: 20.4-pyh9f0ad1d_0 conda-forge\n pandas: 0.23.4-py36h1702cab_1000 conda-forge\n pango: 1.42.4-haa940fe_4 conda-forge\n pcre: 8.44-h4a8c4bd_0 conda-forge\n pip: 20.2.1-py_0 conda-forge\n pixman: 0.38.0-h01d97ff_1003 conda-forge\n pycparser: 2.20-pyh9f0ad1d_2 conda-forge\n pyparsing: 2.4.7-pyh9f0ad1d_0 conda-forge\n pystan: 2.17.1.0-py36h1702cab_1003 conda-forge\n python: 3.6.11-hc38f9c5_2_cpython conda-forge\n python-dateutil: 2.8.1-py_0 conda-forge\n python_abi: 3.6-1_cp36m conda-forge\n pytz: 2020.1-pyh9f0ad1d_0 conda-forge\n r: 3.6-r36_1004 conda-forge\n r-base: 3.6.3-hc30ca75_3 conda-forge\n r-boot: 1.3_25-r36h6115d3f_1 conda-forge\n r-class: 7.3_17-r36h17f1fa6_1 conda-forge\n r-cluster: 2.1.0-r36h384270c_3 conda-forge\n r-codetools: 0.2_16-r36h6115d3f_1002 conda-forge\n r-foreign: 0.8_76-r36h17f1fa6_1 conda-forge\n r-kernsmooth: 2.23_17-r36h3830744_1 conda-forge\n r-lattice: 0.20_41-r36h17f1fa6_2 conda-forge\n r-mass: 7.3_51.6-r36h17f1fa6_2 conda-forge\n r-matrix: 1.2_18-r36h26f5615_3 conda-forge\n r-mgcv: 1.8_31-r36h26f5615_1 conda-forge\n r-nlme: 3.1_148-r36h384270c_0 conda-forge\n r-nnet: 7.3_14-r36h17f1fa6_1 conda-forge\n r-recommended: 3.6-r36_1004 conda-forge\n r-rpart: 4.1_15-r36h17f1fa6_2 conda-forge\n r-spatial: 7.3_12-r36h17f1fa6_1 conda-forge\n r-survival: 3.2_3-r36h17f1fa6_0 conda-forge\n readline: 8.0-h0678c8f_2 conda-forge\n rpy2: 3.3.2-py36r36h255dfe6_0 conda-forge\n setuptools: 49.2.1-py36h9f0ad1d_0 conda-forge\n simplegeneric: 0.8.1-py_1 conda-forge\n six: 1.15.0-pyh9f0ad1d_0 conda-forge\n sqlite: 3.32.3-h93121df_1 conda-forge\n tapi: 1000.10.8-h879752b_4 conda-forge\n tk: 8.6.10-hbbe82c9_0 conda-forge\n tktable: 2.10-h008db23_3 conda-forge\n tornado: 6.0.4-py36h37b9a7d_1 conda-forge\n tzlocal: 2.1-pyh9f0ad1d_0 conda-forge\n wheel: 0.34.2-py_1 conda-forge\n xz: 5.2.5-h0b31af3_1 conda-forge\n zlib: 1.2.11-h0b31af3_1006 conda-forge\n zstd: 1.4.5-h0384e3a_2 conda-forge\n\nPreparing transaction: ...working... done\nVerifying transaction: ...working... done\nExecuting transaction: ...working... done\nCollecting package metadata (repodata.json): ...working... done\nSolving environment: ...working... done\nSource cache directory is: /Users/adamhaber/miniconda3/conda-bld/src_cache\nDownloading source to cache: pybrms-0.0.31_1146958652.tar.gz\nDownloading https://files.pythonhosted.org/packages/ef/14/fe18e4febcfd99dc26e851a81b24ddf9737c94e37bb63eff16672833aab9/pybrms-0.0.31.tar.gz\nSuccess\nExtracting download\nsource tree in: /Users/adamhaber/miniconda3/conda-bld/pybrms_1596952201823/work\nexport PREFIX=/Users/adamhaber/miniconda3/conda-bld/pybrms_1596952201823/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold\nexport BUILD_PREFIX=/Users/adamhaber/miniconda3/conda-bld/pybrms_1596952201823/_build_env\nexport SRC_DIR=/Users/adamhaber/miniconda3/conda-bld/pybrms_1596952201823/work\nINFO: activate_clang_osx-64.sh made the following environmental changes:\n+AR=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-ar\n+AS=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-as\n+CC=x86_64-apple-darwin13.4.0-clang\n+CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I$PREFIX/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix\n+CHECKSYMS=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-checksyms\n+CLANG=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-clang\n+CODESIGN_ALLOCATE=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-codesign_allocate\n+CONDA_BUILD_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk\n+CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9\n+DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -I$PREFIX/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix\n+HOST=x86_64-apple-darwin13.4.0\n+INDR=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-indr\n+INSTALL_NAME_TOOL=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-install_name_tool\n+LD=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-ld\n+LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib\n+LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib\n+LIBTOOL=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-libtool\n+LIPO=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-lipo\n+NM=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-nm\n+NMEDIT=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-nmedit\n+OTOOL=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-otool\n+PAGESTUFF=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-pagestuff\n+RANLIB=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-ranlib\n+REDO_PREBINDING=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-redo_prebinding\n+SEGEDIT=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-segedit\n+SEG_ADDR_TABLE=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-seg_addr_table\n+SEG_HACK=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-seg_hack\n+SIZE=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-size\n+STRINGS=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-strings\n+STRIP=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-strip\n+_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0\nINFO: activate_clangxx_osx-64.sh made the following environmental changes:\n+CLANGXX=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-clang++\n+CXX=x86_64-apple-darwin13.4.0-clang++\n+CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -I$PREFIX/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix\n+DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra -I$PREFIX/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix\nINFO: deactivate_clangxx_osx-64.sh made the following environmental changes:\n-CLANGXX=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-clang++\n-CXX=x86_64-apple-darwin13.4.0-clang++\n-CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -I$PREFIX/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix\n-DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra -I$PREFIX/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix\nINFO: deactivate_clang_osx-64.sh made the following environmental changes:\n-AR=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-ar\n-AS=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-as\n-CC=x86_64-apple-darwin13.4.0-clang\n-CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I$PREFIX/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix\n-CHECKSYMS=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-checksyms\n-CLANG=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-clang\n-CODESIGN_ALLOCATE=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-codesign_allocate\n-CONDA_BUILD_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk\n-CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9\n-DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -I$PREFIX/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix\n-INDR=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-indr\n-INSTALL_NAME_TOOL=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-install_name_tool\n-LD=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-ld\n-LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib\n-LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib\n-LIBTOOL=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-libtool\n-LIPO=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-lipo\n-NM=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-nm\n-NMEDIT=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-nmedit\n-OTOOL=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-otool\n-PAGESTUFF=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-pagestuff\n-RANLIB=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-ranlib\n-REDO_PREBINDING=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-redo_prebinding\n-SEGEDIT=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-segedit\n-SEG_ADDR_TABLE=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-seg_addr_table\n-SEG_HACK=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-seg_hack\n-SIZE=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-size\n-STRINGS=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-strings\n-STRIP=/Users/adamhaber/miniconda3/bin/x86_64-apple-darwin13.4.0-strip\n-_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0\nINFO: activate-gfortran_osx-64.sh made the following environmental changes:\n+DEBUG_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pybrms-0.0.31 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments\n+DEBUG_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pybrms-0.0.31 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments\n+F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran\n+F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran\n+F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran\n+FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran\n+FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pybrms-0.0.31 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix\n+FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pybrms-0.0.31 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix\n+GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran\nINFO: activate_clang_osx-64.sh made the following environmental changes:\n+AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar\n+AS=$PREFIX/bin/x86_64-apple-darwin13.4.0-as\n+CC=x86_64-apple-darwin13.4.0-clang\n+CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pybrms-0.0.31 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix\n+CHECKSYMS=$PREFIX/bin/x86_64-apple-darwin13.4.0-checksyms\n+CLANG=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang\n+CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib\n+CMAKE_PREFIX_PATH=:$PREFIX\n+CONDA_BUILD_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk\n+CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem $PREFIX/include\n+DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pybrms-0.0.31 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix\n+INDR=$PREFIX/bin/x86_64-apple-darwin13.4.0-indr\n+INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool\n+LD=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld\n+LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib\n+LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib\n+LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool\n+LIPO=$PREFIX/bin/x86_64-apple-darwin13.4.0-lipo\n+NM=$PREFIX/bin/x86_64-apple-darwin13.4.0-nm\n+NMEDIT=$PREFIX/bin/x86_64-apple-darwin13.4.0-nmedit\n+OTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-otool\n+PAGESTUFF=$PREFIX/bin/x86_64-apple-darwin13.4.0-pagestuff\n+RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib\n+REDO_PREBINDING=$PREFIX/bin/x86_64-apple-darwin13.4.0-redo_prebinding\n+SEGEDIT=$PREFIX/bin/x86_64-apple-darwin13.4.0-segedit\n+SEG_ADDR_TABLE=$PREFIX/bin/x86_64-apple-darwin13.4.0-seg_addr_table\n+SEG_HACK=$PREFIX/bin/x86_64-apple-darwin13.4.0-seg_hack\n+SIZE=$PREFIX/bin/x86_64-apple-darwin13.4.0-size\n+STRINGS=$PREFIX/bin/x86_64-apple-darwin13.4.0-strings\n+STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip\n+_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0\n+host_alias=x86_64-apple-darwin13.4.0\nINFO: activate_clangxx_osx-64.sh made the following environmental changes:\n+CLANGXX=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang++\n+CXX=x86_64-apple-darwin13.4.0-clang++\n+CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pybrms-0.0.31 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix\n+DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pybrms-0.0.31 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix\nUsing pip 20.2.1 from $PREFIX/lib/python3.6/site-packages/pip (python 3.6)\nNon-user install because user site-packages disabled\nIgnoring indexes: https://pypi.org/simple\nCreated temporary directory: /private/tmp/pip-ephem-wheel-cache-h83x0qe5\nCreated temporary directory: /private/tmp/pip-req-tracker-ftqx3vym\nInitialized build tracking at /private/tmp/pip-req-tracker-ftqx3vym\nCreated build tracker: /private/tmp/pip-req-tracker-ftqx3vym\nEntered build tracker: /private/tmp/pip-req-tracker-ftqx3vym\nCreated temporary directory: /private/tmp/pip-install-crilr3dv\nProcessing $SRC_DIR\n Created temporary directory: /private/tmp/pip-req-build-38lyf6l3\n Added file://$SRC_DIR to build tracker \'/private/tmp/pip-req-tracker-ftqx3vym\'\n Running setup.py (path:/private/tmp/pip-req-build-38lyf6l3/setup.py) egg_info for package from file://$SRC_DIR\n Created temporary directory: /private/tmp/pip-pip-egg-info-9w81no2f\nException information:\nTraceback (most recent call last):\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 216, in _main\n status = self.run(options, args)\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/cli/req_command.py", line 182, in wrapper\n return func(self, options, args)\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 325, in run\n reqs, check_supported_wheels=not options.target_dir\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/resolution/legacy/resolver.py", line 183, in resolve\n discovered_reqs.extend(self._resolve_one(requirement_set, req))\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/resolution/legacy/resolver.py", line 388, in _resolve_one\n abstract_dist = self._get_abstract_dist_for(req_to_install)\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/resolution/legacy/resolver.py", line 340, in _get_abstract_dist_for\n abstract_dist = self.preparer.prepare_linked_requirement(req)\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 483, in prepare_linked_requirement\n req, self.req_tracker, self.finder, self.build_isolation,\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 91, in _get_prepared_distribution\n abstract_dist.prepare_distribution_metadata(finder, build_isolation)\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/distributions/sdist.py", line 40, in prepare_distribution_metadata\n self.req.prepare_metadata()\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/req/req_install.py", line 554, in prepare_metadata\n self.metadata_directory = self._generate_metadata()\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/req/req_install.py", line 534, in _generate_metadata\n details=self.name or "from {}".format(self.link)\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/operations/build/metadata_legacy.py", line 73, in generate_metadata\n command_desc=\'python setup.py egg_info\',\n File "$PREFIX/lib/python3.6/site-packages/pip/_internal/utils/subprocess.py", line 242, in call_subprocess\n raise InstallationError(exc_msg)\npip._internal.exceptions.InstallationError: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.\nRemoved file://$SRC_DIR from build tracker \'/private/tmp/pip-req-tracker-ftqx3vym\'\nRemoved build tracker: \'/private/tmp/pip-req-tracker-ftqx3vym\'\n'
Build failed.
Traceback (most recent call last):
File "/Users/adamhaber/.local/bin/nbdev_conda_package", line 8, in <module>
sys.exit(nbdev_conda_package())
File "/Users/adamhaber/miniconda3/envs/pybrms-dev/lib/python3.6/site-packages/fastscript/core.py", line 76, in _f
func(**args.__dict__)
File "/Users/adamhaber/.local/lib/python3.6/site-packages/nbdev/cli.py", line 318, in nbdev_conda_package
if 'anaconda upload' not in res:
UnboundLocalError: local variable 'res' referenced before assignment
This seemed like a version related issue, so I verified that I have version in settings.ini, and that if I run the following code (from setup.py):
from packaging.version import parse
from configparser import ConfigParser
import setuptools
assert parse(setuptools.__version__) >= parse("36.2")
# note: all settings are in settings.ini; edit there, not here
config = ConfigParser(delimiters=["="])
config.read("settings.ini")
cfg = config["DEFAULT"]
cfg_keys = "version description keywords author author_email".split()
expected = (
cfg_keys
+ "lib_name user branch license status min_python audience language".split()
)
for o in expected:
assert o in cfg, "missing expected setting: {}".format(o)
The assertion doesn’t fail. It is as if the setup.py that is being run by nbdev_conda_package doesn’t find settings.ini (or finds one without version, since it doesn’t fail on config.read) whereas the “regular” setup.py does find it.
I also tried make clean and make dist and then nbdev_conda_package, but got the same error.
Any help would be much appreciated!