BUG: clang-9: error: -Wl,-export_dynamic: 'linker' input unused (OSX)

[xhochy]

• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of pandas.

• (optional) I have confirmed this bug exists on the master branch of pandas.

---

conda environment

conda create -n pandas-compile-test compilers numpy cython

  binutils-meta      conda-forge/osx-64::binutils-meta-1.0.4-0
  c-compiler         conda-forge/osx-64::c-compiler-1.0.4-h1239861_0
  ca-certificates    conda-forge/osx-64::ca-certificates-2020.4.5.1-hecc5488_0
  cctools            conda-forge/osx-64::cctools-927.0.2-h5ba7a2e_4
  certifi            conda-forge/osx-64::certifi-2020.4.5.1-py38h32f6830_0
  clang              conda-forge/osx-64::clang-9.0.1-default_hf57f61e_0
  clang_osx-64       conda-forge/osx-64::clang_osx-64-9.0.1-h05bbb7f_0
  clangxx            conda-forge/osx-64::clangxx-9.0.1-default_hf57f61e_0
  clangxx_osx-64     conda-forge/osx-64::clangxx_osx-64-9.0.1-h05bbb7f_0
  compiler-rt        conda-forge/osx-64::compiler-rt-9.0.1-h6a512c6_3
  compiler-rt_osx-64 conda-forge/noarch::compiler-rt_osx-64-9.0.1-h99342c6_3
  compilers          conda-forge/osx-64::compilers-1.0.4-0
  cxx-compiler       conda-forge/osx-64::cxx-compiler-1.0.4-h707564b_0
  cython             conda-forge/osx-64::cython-0.29.16-py38hc84c608_0
  fortran-compiler   conda-forge/osx-64::fortran-compiler-1.0.4-he991be0_0
  gfortran_impl_osx~ conda-forge/osx-64::gfortran_impl_osx-64-7.3.0-hf4212f2_2
  gfortran_osx-64    conda-forge/osx-64::gfortran_osx-64-7.3.0-h22b1bf0_9
  gmp                conda-forge/osx-64::gmp-6.2.0-h4a8c4bd_2
  isl                conda-forge/osx-64::isl-0.19-0
  ld64               conda-forge/osx-64::ld64-450.3-h3c32e8a_4
  libblas            conda-forge/osx-64::libblas-3.8.0-16_openblas
  libcblas           conda-forge/osx-64::libcblas-3.8.0-16_openblas
  libcxx             conda-forge/osx-64::libcxx-9.0.1-1
  libffi             conda-forge/osx-64::libffi-3.2.1-h4a8c4bd_1007
  libgfortran        conda-forge/osx-64::libgfortran-4.0.0-2
  libiconv           conda-forge/osx-64::libiconv-1.15-h0b31af3_1006
  liblapack          conda-forge/osx-64::liblapack-3.8.0-16_openblas
  libllvm9           conda-forge/osx-64::libllvm9-9.0.1-ha1b3eb9_0
  libopenblas        conda-forge/osx-64::libopenblas-0.3.9-h3d69b6c_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-9.0.1-h28b9765_2
  mpc                conda-forge/osx-64::mpc-1.1.0-h4160ff4_1006
  mpfr               conda-forge/osx-64::mpfr-4.0.2-h44b798e_0
  ncurses            conda-forge/osx-64::ncurses-6.1-h0a44026_1002
  numpy              conda-forge/osx-64::numpy-1.18.1-py38h1f821a2_1
  openssl            conda-forge/osx-64::openssl-1.1.1f-h0b31af3_0
  pip                conda-forge/noarch::pip-20.0.2-py_2
  python             conda-forge/osx-64::python-3.8.2-hd5f0129_5_cpython
  python_abi         conda-forge/osx-64::python_abi-3.8-1_cp38
  readline           conda-forge/osx-64::readline-8.0-hcfe32e1_0
  setuptools         conda-forge/osx-64::setuptools-46.1.3-py38h32f6830_0
  sqlite             conda-forge/osx-64::sqlite-3.30.1-h93121df_0
  tapi               conda-forge/osx-64::tapi-1000.10.8-ha1b3eb9_4
  tk                 conda-forge/osx-64::tk-8.6.10-hbbe82c9_0
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  xz                 conda-forge/osx-64::xz-5.2.4-h0b31af3_1002
  zlib               conda-forge/osx-64::zlib-1.2.11-h0b31af3_1006

Error message:

clang-9: error: -Wl,-export_dynamic: 'linker' input unused [-Werror,-Wunused-command-line-argument]

Output of pip install -e ~/Development/pandas --no-deps --no-use-pep517 -vvv:

Non-user install because site-packages writeableCreated temporary directory: /private/var/folders/3r/k0d_q3hs2mb2_jxfh_9hjyqr0000gn/T/pip-ephem-wheel-cache-ehxkyhsg
Created temporary directory: /private/var/folders/3r/k0d_q3hs2mb2_jxfh_9hjyqr0000gn/T/pip-req-tracker-waeimcjv
Initialized build tracking at /private/var/folders/3r/k0d_q3hs2mb2_jxfh_9hjyqr0000gn/T/pip-req-tracker-waeimcjv
Created build tracker: /private/var/folders/3r/k0d_q3hs2mb2_jxfh_9hjyqr0000gn/T/pip-req-tracker-waeimcjv
Entered build tracker: /private/var/folders/3r/k0d_q3hs2mb2_jxfh_9hjyqr0000gn/T/pip-req-tracker-waeimcjv
Created temporary directory: /private/var/folders/3r/k0d_q3hs2mb2_jxfh_9hjyqr0000gn/T/pip-install-5lvoa7_h
Obtaining file:///Users/uwe/Development/pandas
  Added file:///Users/uwe/Development/pandas to build tracker '/private/var/folders/3r/k0d_q3hs2mb2_jxfh_9hjyqr0000gn/T/pip-req-tracker-waeimcjv'
    Running setup.py (path:/Users/uwe/Development/pandas/setup.py) egg_info for package from file:///Users/uwe/Development/pandas
    Running command python setup.py egg_info
    Compiling pandas/_libs/hashing.pyx because it depends on /Users/uwe/miniconda3/envs/pandas-compile-test/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling pandas/_libs/reshape.pyx because it depends on /Users/uwe/miniconda3/envs/pandas-compile-test/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling pandas/_libs/window/indexers.pyx because it depends on /Users/uwe/miniconda3/envs/pandas-compile-test/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd.
    [1/3] Cythonizing pandas/_libs/hashing.pyx
    [2/3] Cythonizing pandas/_libs/reshape.pyx
    [3/3] Cythonizing pandas/_libs/window/indexers.pyx
    running egg_info
    writing pandas.egg-info/PKG-INFO
    writing dependency_links to pandas.egg-info/dependency_links.txt
    writing entry points to pandas.egg-info/entry_points.txt
    writing requirements to pandas.egg-info/requires.txt
    writing top-level names to pandas.egg-info/top_level.txt
    reading manifest file 'pandas.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    no previously-included directories found matching 'doc/build'
    warning: no previously-included files matching '*.pyd' found anywhere in distribution
    warning: no previously-included files matching '*~' found anywhere in distribution
    warning: no previously-included files matching '.DS_Store' found anywhere in distribution
    warning: no previously-included files matching '#*' found anywhere in distribution
    writing manifest file 'pandas.egg-info/SOURCES.txt'
  Source in /Users/uwe/Development/pandas has version 1.1.0.dev0+1122.g01f73100d.dirty, which satisfies requirement pandas==1.1.0.dev0+1122.g01f73100d.dirty from file:///Users/uwe/Development/pandas
  Removed pandas==1.1.0.dev0+1122.g01f73100d.dirty from file:///Users/uwe/Development/pandas from build tracker '/private/var/folders/3r/k0d_q3hs2mb2_jxfh_9hjyqr0000gn/T/pip-req-tracker-waeimcjv'
Installing collected packages: pandas
  Running setup.py develop for pandas
    Running command /Users/uwe/miniconda3/envs/pandas-compile-test/bin/python3.8 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/uwe/Development/pandas/setup.py'"'"'; __file__='"'"'/Users/uwe/Development/pandas/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
    running develop
    running egg_info
    writing pandas.egg-info/PKG-INFO
    writing dependency_links to pandas.egg-info/dependency_links.txt
    writing entry points to pandas.egg-info/entry_points.txt
    writing requirements to pandas.egg-info/requires.txt
    writing top-level names to pandas.egg-info/top_level.txt
    reading manifest file 'pandas.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    no previously-included directories found matching 'doc/build'
    warning: no previously-included files matching '*.pyd' found anywhere in distribution
    warning: no previously-included files matching '*~' found anywhere in distribution
    warning: no previously-included files matching '.DS_Store' found anywhere in distribution
    warning: no previously-included files matching '#*' found anywhere in distribution
    writing manifest file 'pandas.egg-info/SOURCES.txt'
    running build_ext
    building 'pandas._libs.algos' extension
    x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/uwe/miniconda3/envs/pandas-compile-test=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/uwe/miniconda3/envs/pandas-compile-test/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/uwe/miniconda3/envs/pandas-compile-test/include -DNPY_NO_DEPRECATED_API=0 -I./pandas/_libs -Ipandas/_libs/src/klib -I/Users/uwe/miniconda3/envs/pandas-compile-test/lib/python3.8/site-packages/numpy/core/include -I/Users/uwe/miniconda3/envs/pandas-compile-test/include/python3.8 -c pandas/_libs/algos.c -o build/temp.macosx-10.9-x86_64-3.8/pandas/_libs/algos.o -Werror
    clang-9: error: -Wl,-export_dynamic: 'linker' input unused [-Werror,-Wunused-command-line-argument]
    error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
Cleaning up...
Removed build tracker: '/private/var/folders/3r/k0d_q3hs2mb2_jxfh_9hjyqr0000gn/T/pip-req-tracker-waeimcjv'
ERROR: Command errored out with exit status 1: /Users/uwe/miniconda3/envs/pandas-compile-test/bin/python3.8 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/uwe/Development/pandas/setup.py'"'"'; __file__='"'"'/Users/uwe/Development/pandas/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.

export | grep FLAGS:

CFLAGS='-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/uwe/miniconda3/envs/pandas-compile-test/include'
CONDA_BACKUP_LDFLAGS=' -Wl,-rpath,/Users/uwe/miniconda3/envs/pandas-compile-test/lib -L/Users/uwe/miniconda3/envs/pandas-compile-test/lib'
CPPFLAGS='-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/uwe/miniconda3/envs/pandas-compile-test/include'
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 /Users/uwe/miniconda3/envs/pandas-compile-test/include'
DEBUG_CFLAGS='-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem /Users/uwe/miniconda3/envs/pandas-compile-test/include'
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 /Users/uwe/miniconda3/envs/pandas-compile-test/include'
DEBUG_FFLAGS='-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/uwe/miniconda3/envs/pandas-compile-test/include -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments'
DEBUG_FORTRANFLAGS='-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/uwe/miniconda3/envs/pandas-compile-test/include -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments'
FFLAGS='-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/uwe/miniconda3/envs/pandas-compile-test/include'
FORTRANFLAGS='-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/uwe/miniconda3/envs/pandas-compile-test/include'
LDFLAGS=' -Wl,-rpath,/Users/uwe/miniconda3/envs/pandas-compile-test/lib -L/Users/uwe/miniconda3/envs/pandas-compile-test/lib'
LDFLAGS_LD='-pie -headerpad_max_install_names -dead_strip_dylibs -rpath /Users/uwe/miniconda3/envs/pandas-compile-test/lib -L/Users/uwe/miniconda3/envs/pandas-compile-test/lib'
XPC_FLAGS=0x0

Seems like this is not the first issue in response to #32163, there is also e.g. #33224

[xhochy]

This is probably down somewhere in the packaged Python/distutils code but instead of fixing this, I'd rather see #33315 tackled.

[WillAyd]

I am unable to reproduce this on macOS - can you check this is still relevant?

conda list

packages in environment at /Users/williamayd/miniconda3/envs/pandas-compile-test:

Name Version Build Channel

c-compiler 1.1.2 hc929b4f_0 conda-forge
ca-certificates 2020.11.8 h033912b_0 conda-forge
cctools 949.0.1 h8821f95_16 conda-forge
cctools_osx-64 949.0.1 h8e49ea9_16 conda-forge
certifi 2020.11.8 py39h6e9494a_0 conda-forge
clang 11.0.0 1 conda-forge
clang-11 11.0.0 default_h000dee7_1 conda-forge
clang_osx-64 11.0.0 hb91bd55_5 conda-forge
clangxx 11.0.0 default_hf57f61e_1 conda-forge
clangxx_osx-64 11.0.0 h7e1b574_5 conda-forge
compiler-rt 11.0.0 h01488ec_2 conda-forge
compiler-rt_osx-64 11.0.0 hd3c4e95_2 conda-forge
compilers 1.1.2 h694c41f_0 conda-forge
cxx-compiler 1.1.2 h9a9d8cb_0 conda-forge
cython 0.29.21 py39h13a702c_1 conda-forge
fortran-compiler 1.1.2 hcc3dc05_0 conda-forge
gfortran_impl_osx-64 7.5.0 h34a0dec_13 conda-forge
gfortran_osx-64 7.5.0 h1174d25_10 conda-forge
gmp 6.2.0 h2e338ed_4 conda-forge
isl 0.22.1 hb1e8313_2 conda-forge
ld64 530 h755cc8a_16 conda-forge
ld64_osx-64 530 h66d9e41_16 conda-forge
ldid 2.1.2 h7660a38_2 conda-forge
libblas 3.9.0 2_openblas conda-forge
libcblas 3.9.0 2_openblas conda-forge
libclang-cpp11 11.0.0 default_h000dee7_1 conda-forge
libcxx 11.0.0 h439d374_0 conda-forge
libffi 3.2.1 hb1e8313_1007 conda-forge
libgfortran 4.0.0 h50e675f_13 conda-forge
libgfortran-devel_osx-64 7.5.0 h50e675f_13 conda-forge
libgfortran4 7.5.0 h50e675f_13 conda-forge
libiconv 1.16 haf1e3a3_0 conda-forge
liblapack 3.9.0 2_openblas conda-forge
libllvm11 11.0.0 hf85e3d2_0 conda-forge
libopenblas 0.3.12 openmp_h63d9170_1 conda-forge
llvm-openmp 11.0.0 h73239a0_1 conda-forge
llvm-tools 11.0.0 hf85e3d2_0 conda-forge
mpc 1.1.0 ha57cd0f_1009 conda-forge
mpfr 4.0.2 h72d8aaf_1 conda-forge
ncurses 6.2 h2e338ed_4 conda-forge
numpy 1.19.4 py39hd3e5478_1 conda-forge
openssl 1.1.1h haf1e3a3_0 conda-forge
pandas 1.2.0.dev0+831.gcd9c56e2c.dirty dev_0
pip 20.2.4 py_0 conda-forge
python 3.9.0 ha017127_4_cpython conda-forge
python-dateutil 2.8.1 pypi_0 pypi
python_abi 3.9 1_cp39 conda-forge
pytz 2020.4 pypi_0 pypi
readline 8.0 h0678c8f_2 conda-forge
setuptools 49.6.0 py39h2c36a5b_2 conda-forge
six 1.15.0 pypi_0 pypi
sqlite 3.33.0 h960bd1c_1 conda-forge
tapi 1100.0.11 h9ce4665_0 conda-forge
tk 8.6.10 hb0a8c7a_1 conda-forge
tzdata 2020d h516909a_0 conda-forge
wheel 0.35.1 pyh9f0ad1d_0 conda-forge
xz 5.2.5 haf1e3a3_1 conda-forge
zlib 1.2.11 h7795811_1010 conda-forge

[xhochy]

Yes, this still happens:

git clone https://github.com/pandas-dev/pandas
cd pandas
mamba env create -n pandas-compile-test
mamba install -n pandas-compile-test c-compiler
# Only activate at the end to get the correct environment flags
conda activate pandas-compile-test

This then leads to

% python setup.py build_ext
Compiling pandas/_libs/algos.pyx because it changed.
…
Compiling pandas/io/sas/sas.pyx because it changed.
[ 1/40] Cythonizing pandas/_libs/algos.pyx
…
[40/40] Cythonizing pandas/io/sas/sas.pyx
running build_ext
building 'pandas._libs.algos' extension
creating build
creating build/temp.macosx-10.9-x86_64-3.8
creating build/temp.macosx-10.9-x86_64-3.8/pandas
creating build/temp.macosx-10.9-x86_64-3.8/pandas/_libs
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/uwe/miniconda3/envs/pandas-compile-testd=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/uwe/miniconda3/envs/pandas-compile-testd/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/uwe/miniconda3/envs/pandas-compile-testd/include -DNPY_NO_DEPRECATED_API=0 -I./pandas/_libs -Ipandas/_libs/src/klib -I/Users/uwe/miniconda3/envs/pandas-compile-testd/lib/python3.8/site-packages/numpy/core/include -I/Users/uwe/miniconda3/envs/pandas-compile-testd/include/python3.8 -c pandas/_libs/algos.c -o build/temp.macosx-10.9-x86_64-3.8/pandas/_libs/algos.o -Werror -Wno-error=deprecated-declarations -Wno-error=unreachable-code
clang-10: error: -Wl,-export_dynamic: 'linker' input unused [-Werror,-Wunused-command-line-argument]
error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1

Note that I'm using mamba instead of conda in the above commands as I'm impatient, you should get the same result by only using conda.