Closed joel-roediger closed 2 years ago
Hi,
The problem does appear to be that your machine doesn't have a version of gcc installed. However, gcc lives at a lower level then conda, so you'll need to install it separately. If you tell me what OS you are using, I can point you in the right direction on how to do that.
Thanks Max. I am using OSX 11.3.1.
Running xcode-select --install
should get gcc where it needs to be. You will need to restart your terminal once the install is complete. If that doesn't work for some reason, let me know.
Doesn't seem to work.
(kcwidrp) bash-3.2$ xcode-select --install
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
I assume you wanted me to run the command from my kcwidrp environment?
I would try to use the Software Update tool in System Preferences to update the Command Line Tools (if memory serves, I had to do that a while ago). There is a chance that your computer won't see that there's an update available, in which case you can run sudo rm -rf /Library/Developer/CommandLineTools
to remove the old installation, and run the xcode-select --install
command to get a fresh install of the newest version.
To make sure I understand, you want me to:
(1) Run the Software Update tool and then re-run pip install kcwidrp
.
(2) If that doesn't work, run sudo rm -rf /Library/Developer/CommandLineTools
, xcode-select --install
and then pip install kcwidrp
.
Is that correct?
To make sure I understand, you want me to: (1) Run the Software Update tool and then re-run
pip install kcwidrp
. (2) If that doesn't work, runsudo rm -rf /Library/Developer/CommandLineTools
,xcode-select --install
and thenpip install kcwidrp
.Is that correct?
Yup
Sorry for the delay, Max. I tried (1) and got a different error this time:
Building wheels for collected packages: psutil
Building wheel for psutil (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Users/roedigerj/anaconda3/envs/kcwidrp/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/2y/kz8n0qgx3yx44wyh7z30f09r0000gq/T/pip-install-h_d6om69/psutil_eab016ee13ca457e83a60b2554a166ab/setup.py'"'"'; __file__='"'"'/private/var/folders/2y/kz8n0qgx3yx44wyh7z30f09r0000gq/T/pip-install-h_d6om69/psutil_eab016ee13ca457e83a60b2554a166ab/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/2y/kz8n0qgx3yx44wyh7z30f09r0000gq/T/pip-wheel-rzkw_jxf
cwd: /private/var/folders/2y/kz8n0qgx3yx44wyh7z30f09r0000gq/T/pip-install-h_d6om69/psutil_eab016ee13ca457e83a60b2554a166ab/
Complete output (54 lines):
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/psutil
copying psutil/_pswindows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_common.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psosx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psbsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psaix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pslinux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_compat.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psposix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pssunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
creating build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_contracts.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_connections.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/runner.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_unicode.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_misc.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_posix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_linux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_sunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_aix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_process.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_bsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_system.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_osx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_memleaks.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_windows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__main__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_testutils.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
running build_ext
building 'psutil._psutil_osx' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/psutil
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch/osx
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}-${PKG_VERSION} -fdebug-prefix-map=/Users/roedigerj/anaconda3/envs/kcwidrp=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=573 -DPSUTIL_OSX=1 -I/Users/roedigerj/anaconda3/envs/kcwidrp/include/python3.7m -c psutil/_psutil_common.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_common.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/roedigerj/anaconda3/envs/kcwidrp=/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/roedigerj/anaconda3/envs/kcwidrp/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=573 -DPSUTIL_OSX=1 -I/Users/roedigerj/anaconda3/envs/kcwidrp/include/python3.7m -c psutil/_psutil_posix.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_posix.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
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}-${PKG_VERSION} -fdebug-prefix-map=/Users/roedigerj/anaconda3/envs/kcwidrp=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=573 -DPSUTIL_OSX=1 -I/Users/roedigerj/anaconda3/envs/kcwidrp/include/python3.7m -c psutil/_psutil_osx.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_osx.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/roedigerj/anaconda3/envs/kcwidrp=/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/roedigerj/anaconda3/envs/kcwidrp/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=573 -DPSUTIL_OSX=1 -I/Users/roedigerj/anaconda3/envs/kcwidrp/include/python3.7m -c psutil/arch/osx/process_info.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/arch/osx/process_info.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/roedigerj/anaconda3/envs/kcwidrp/lib -L/Users/roedigerj/anaconda3/envs/kcwidrp/lib -flto -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/roedigerj/anaconda3/envs/kcwidrp/lib -L/Users/roedigerj/anaconda3/envs/kcwidrp/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/roedigerj/anaconda3/envs/kcwidrp/lib -L/Users/roedigerj/anaconda3/envs/kcwidrp/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_common.o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_posix.o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_osx.o build/temp.macosx-10.9-x86_64-3.7/psutil/arch/osx/process_info.o -o build/lib.macosx-10.9-x86_64-3.7/psutil/_psutil_osx.cpython-37m-darwin.so -framework CoreFoundation -framework IOKit
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd' for architecture x86_64
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
ERROR: Failed building wheel for psutil
Running setup.py clean for psutil
Failed to build psutil
Installing collected packages: psutil, phantomjs, pandas, ccdproc, bokeh, kcwidrp
Attempting uninstall: psutil
Found existing installation: psutil 5.8.0
Uninstalling psutil-5.8.0:
Successfully uninstalled psutil-5.8.0
Running setup.py install for psutil ... error
ERROR: Command errored out with exit status 1:
command: /Users/roedigerj/anaconda3/envs/kcwidrp/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/2y/kz8n0qgx3yx44wyh7z30f09r0000gq/T/pip-install-h_d6om69/psutil_eab016ee13ca457e83a60b2554a166ab/setup.py'"'"'; __file__='"'"'/private/var/folders/2y/kz8n0qgx3yx44wyh7z30f09r0000gq/T/pip-install-h_d6om69/psutil_eab016ee13ca457e83a60b2554a166ab/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/2y/kz8n0qgx3yx44wyh7z30f09r0000gq/T/pip-record-pkqizsqx/install-record.txt --single-version-externally-managed --compile --install-headers /Users/roedigerj/anaconda3/envs/kcwidrp/include/python3.7m/psutil
cwd: /private/var/folders/2y/kz8n0qgx3yx44wyh7z30f09r0000gq/T/pip-install-h_d6om69/psutil_eab016ee13ca457e83a60b2554a166ab/
Complete output (54 lines):
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/psutil
copying psutil/_pswindows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_common.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psosx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psbsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psaix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pslinux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_compat.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psposix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pssunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
creating build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_contracts.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_connections.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/runner.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_unicode.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_misc.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_posix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_linux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_sunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_aix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_process.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_bsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_system.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_osx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_memleaks.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_windows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__main__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_testutils.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
running build_ext
building 'psutil._psutil_osx' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/psutil
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch/osx
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}-${PKG_VERSION} -fdebug-prefix-map=/Users/roedigerj/anaconda3/envs/kcwidrp=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=573 -DPSUTIL_OSX=1 -I/Users/roedigerj/anaconda3/envs/kcwidrp/include/python3.7m -c psutil/_psutil_common.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_common.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/roedigerj/anaconda3/envs/kcwidrp=/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/roedigerj/anaconda3/envs/kcwidrp/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=573 -DPSUTIL_OSX=1 -I/Users/roedigerj/anaconda3/envs/kcwidrp/include/python3.7m -c psutil/_psutil_posix.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_posix.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
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}-${PKG_VERSION} -fdebug-prefix-map=/Users/roedigerj/anaconda3/envs/kcwidrp=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=573 -DPSUTIL_OSX=1 -I/Users/roedigerj/anaconda3/envs/kcwidrp/include/python3.7m -c psutil/_psutil_osx.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_osx.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/roedigerj/anaconda3/envs/kcwidrp=/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/roedigerj/anaconda3/envs/kcwidrp/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=573 -DPSUTIL_OSX=1 -I/Users/roedigerj/anaconda3/envs/kcwidrp/include/python3.7m -c psutil/arch/osx/process_info.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/arch/osx/process_info.o
clang-10: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/roedigerj/anaconda3/envs/kcwidrp/lib -L/Users/roedigerj/anaconda3/envs/kcwidrp/lib -flto -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/roedigerj/anaconda3/envs/kcwidrp/lib -L/Users/roedigerj/anaconda3/envs/kcwidrp/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/roedigerj/anaconda3/envs/kcwidrp/lib -L/Users/roedigerj/anaconda3/envs/kcwidrp/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/roedigerj/anaconda3/envs/kcwidrp/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_common.o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_posix.o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_osx.o build/temp.macosx-10.9-x86_64-3.7/psutil/arch/osx/process_info.o -o build/lib.macosx-10.9-x86_64-3.7/psutil/_psutil_osx.cpython-37m-darwin.so -framework CoreFoundation -framework IOKit
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd' for architecture x86_64
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
----------------------------------------
Rolling back uninstall of psutil
Moving to /Users/roedigerj/anaconda3/envs/kcwidrp/lib/python3.7/site-packages/psutil-5.8.0.dist-info/
from /Users/roedigerj/anaconda3/envs/kcwidrp/lib/python3.7/site-packages/~sutil-5.8.0.dist-info
Moving to /Users/roedigerj/anaconda3/envs/kcwidrp/lib/python3.7/site-packages/psutil/
from /Users/roedigerj/anaconda3/envs/kcwidrp/lib/python3.7/site-packages/~sutil
ERROR: Command errored out with exit status 1: /Users/roedigerj/anaconda3/envs/kcwidrp/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/2y/kz8n0qgx3yx44wyh7z30f09r0000gq/T/pip-install-h_d6om69/psutil_eab016ee13ca457e83a60b2554a166ab/setup.py'"'"'; __file__='"'"'/private/var/folders/2y/kz8n0qgx3yx44wyh7z30f09r0000gq/T/pip-install-h_d6om69/psutil_eab016ee13ca457e83a60b2554a166ab/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/2y/kz8n0qgx3yx44wyh7z30f09r0000gq/T/pip-record-pkqizsqx/install-record.txt --single-version-externally-managed --compile --install-headers /Users/roedigerj/anaconda3/envs/kcwidrp/include/python3.7m/psutil Check the logs for full command output.
Now the problem appears to be with x86_64-apple-darwin13.4.0-clang
?
At this point, I'd recommend looking for help with the psutil
folks (https://github.com/giampaolo/psutil). Once you manage to get that installed, hopefully the DRP will install cleanly.
UPDATE
I was able to complete the installation by setting my CC and CXX environment variables to the locations of gcc and clang within my installation of the Command Line Tools package. What gave me this idea was this line from the terminal output above:
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd' for architecture x86_64 clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
Hello,
I am attempting to install kcwidrp manually (because doing so with the YML file wasn't working) and am encountering an error while executing the command "pip install kcwidrp". The error can be traced to the part where wheels are built for the packages bokeh, ccdproc, and psutil. Here is the terminal output:
Could the problem be that my environment lacks the gcc compiler? I have tried finding one through the conda installer but with no luck so far.
Regards, Joel