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February 24, 2022 07:15
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Malis pip installation error on Windows workstation (required for CNNectome Janelia project)
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| (CNNectome) C:\Users\CryoEM\Documents\GitHub\OpenOrganelle\CNNectome>pip install malis[malis_loss]@git+https://github.com/neptunes5thmoon/malis.git@fix_setup | |
| Collecting malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup | |
| Cloning https://github.com/neptunes5thmoon/malis.git (to revision fix_setup) to c:\users\cryoem\appdata\local\temp\pip-install-835bihd5\malis_d558e69fd2aa477b8a3ada5875704cf7 | |
| Running command git clone -q https://github.com/neptunes5thmoon/malis.git 'C:\Users\CryoEM\AppData\Local\Temp\pip-install-835bihd5\malis_d558e69fd2aa477b8a3ada5875704cf7' | |
| Running command git checkout -b fix_setup --track origin/fix_setup | |
| branch 'fix_setup' set up to track 'origin/fix_setup'. | |
| Switched to a new branch 'fix_setup' | |
| Resolved https://github.com/neptunes5thmoon/malis.git to commit 2a54eed480edc8b0e9948f24b1193a58c5714d2d | |
| WARNING: malis 1.0 does not provide the extra 'malis_loss' | |
| Requirement already satisfied: cython in c:\users\cryoem\.conda\envs\cnnectome\lib\site-packages (from malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup) (0.29.28) | |
| Requirement already satisfied: numpy in c:\users\cryoem\.conda\envs\cnnectome\lib\site-packages (from malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup) (1.19.5) | |
| Requirement already satisfied: h5py in c:\users\cryoem\.conda\envs\cnnectome\lib\site-packages (from malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup) (3.1.0) | |
| Requirement already satisfied: scipy in c:\users\cryoem\.conda\envs\cnnectome\lib\site-packages (from malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup) (1.5.4) | |
| Requirement already satisfied: cached-property in c:\users\cryoem\.conda\envs\cnnectome\lib\site-packages (from h5py->malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup) (1.5.2) | |
| Building wheels for collected packages: malis | |
| Building wheel for malis (setup.py) ... error | |
| ERROR: Command errored out with exit status 1: | |
| command: 'C:\Users\CryoEM\.conda\envs\CNNectome\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\CryoEM\\AppData\\Local\\Temp\\pip-install-835bihd5\\malis_d558e69fd2aa477b8a3ada5875704cf7\\setup.py'"'"'; __file__='"'"'C:\\Users\\CryoEM\\AppData\\Local\\Temp\\pip-install-835bihd5\\malis_d558e69fd2aa477b8a3ada5875704cf7\\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 'C:\Users\CryoEM\AppData\Local\Temp\pip-wheel-9ykghi5l' | |
| cwd: C:\Users\CryoEM\AppData\Local\Temp\pip-install-835bihd5\malis_d558e69fd2aa477b8a3ada5875704cf7\ | |
| Complete output (16 lines): | |
| running bdist_wheel | |
| running build | |
| running build_py | |
| creating build | |
| creating build\lib.win-amd64-3.6 | |
| creating build\lib.win-amd64-3.6\malis | |
| copying malis\malis_loss.py -> build\lib.win-amd64-3.6\malis | |
| copying malis\setup.py -> build\lib.win-amd64-3.6\malis | |
| copying malis\test_malis.py -> build\lib.win-amd64-3.6\malis | |
| copying malis\__init__.py -> build\lib.win-amd64-3.6\malis | |
| running build_ext | |
| cythoning malis/malis.pyx to malis\malis.cpp | |
| C:\Users\CryoEM\.conda\envs\CNNectome\lib\site-packages\Cython\Compiler\Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: C:\Users\CryoEM\AppData\Local\Temp\pip-install-835bihd5\malis_d558e69fd2aa477b8a3ada5875704cf7\malis\malis.pyx | |
| tree = Parsing.p_module(s, pxd, full_module_name) | |
| building 'malis.malis' extension | |
| error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/ | |
| ---------------------------------------- | |
| ERROR: Failed building wheel for malis | |
| Running setup.py clean for malis | |
| Failed to build malis | |
| Installing collected packages: malis | |
| Running setup.py install for malis ... error | |
| ERROR: Command errored out with exit status 1: | |
| command: 'C:\Users\CryoEM\.conda\envs\CNNectome\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\CryoEM\\AppData\\Local\\Temp\\pip-install-835bihd5\\malis_d558e69fd2aa477b8a3ada5875704cf7\\setup.py'"'"'; __file__='"'"'C:\\Users\\CryoEM\\AppData\\Local\\Temp\\pip-install-835bihd5\\malis_d558e69fd2aa477b8a3ada5875704cf7\\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 'C:\Users\CryoEM\AppData\Local\Temp\pip-record-4ajy1cd2\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\CryoEM\.conda\envs\CNNectome\Include\malis' | |
| cwd: C:\Users\CryoEM\AppData\Local\Temp\pip-install-835bihd5\malis_d558e69fd2aa477b8a3ada5875704cf7\ | |
| Complete output (14 lines): | |
| running install | |
| running build | |
| running build_py | |
| creating build | |
| creating build\lib.win-amd64-3.6 | |
| creating build\lib.win-amd64-3.6\malis | |
| copying malis\malis_loss.py -> build\lib.win-amd64-3.6\malis | |
| copying malis\setup.py -> build\lib.win-amd64-3.6\malis | |
| copying malis\test_malis.py -> build\lib.win-amd64-3.6\malis | |
| copying malis\__init__.py -> build\lib.win-amd64-3.6\malis | |
| running build_ext | |
| skipping 'malis\malis.cpp' Cython extension (up-to-date) | |
| building 'malis.malis' extension | |
| error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/ | |
| ---------------------------------------- | |
| ERROR: Command errored out with exit status 1: 'C:\Users\CryoEM\.conda\envs\CNNectome\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\CryoEM\\AppData\\Local\\Temp\\pip-install-835bihd5\\malis_d558e69fd2aa477b8a3ada5875704cf7\\setup.py'"'"'; __file__='"'"'C:\\Users\\CryoEM\\AppData\\Local\\Temp\\pip-install-835bihd5\\malis_d558e69fd2aa477b8a3ada5875704cf7\\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 'C:\Users\CryoEM\AppData\Local\Temp\pip-record-4ajy1cd2\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\CryoEM\.conda\envs\CNNectome\Include\malis' Check the logs for full command output. | |
| (CNNectome) C:\Users\CryoEM\Documents\GitHub\OpenOrganelle\CNNectome> |
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2022-03-03
Downloaded and installed Microsoft C++ Build Tools as required. New error on pip installation of malis. Looks like boost is not installed (or not installed correctly) on this computer.
(base) C:\Users\CryoEM>conda info --envs
conda environments:
base * C:\ProgramData\Anaconda3
CNNectome C:\Users\CryoEM.conda\envs\CNNectome
(base) C:\Users\CryoEM>conda activate CNNectome
(CNNectome) C:\Users\CryoEM>which pip
/c/Users/CryoEM/.conda/envs/CNNectome/Scripts/pip
(CNNectome) C:\Users\CryoEM>pip install malis[malis_loss]@git+https://github.com/neptunes5thmoon/malis.git@fix_setup
Collecting malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup
Cloning https://github.com/neptunes5thmoon/malis.git (to revision fix_setup) to c:\users\cryoem\appdata\local\temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727
Running command git clone -q https://github.com/neptunes5thmoon/malis.git 'C:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727'
Running command git checkout -b fix_setup --track origin/fix_setup
branch 'fix_setup' set up to track 'origin/fix_setup'.
Switched to a new branch 'fix_setup'
Resolved https://github.com/neptunes5thmoon/malis.git to commit 2a54eed480edc8b0e9948f24b1193a58c5714d2d
WARNING: malis 1.0 does not provide the extra 'malis_loss'
Requirement already satisfied: cython in c:\users\cryoem.conda\envs\cnnectome\lib\site-packages (from malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup) (0.29.28)
Requirement already satisfied: numpy in c:\users\cryoem.conda\envs\cnnectome\lib\site-packages (from malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup) (1.19.5)
Requirement already satisfied: h5py in c:\users\cryoem.conda\envs\cnnectome\lib\site-packages (from malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup) (3.1.0)
Requirement already satisfied: scipy in c:\users\cryoem.conda\envs\cnnectome\lib\site-packages (from malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup) (1.5.4)
Requirement already satisfied: cached-property in c:\users\cryoem.conda\envs\cnnectome\lib\site-packages (from h5py->malis[malis_loss]@ git+https://github.com/neptunes5thmoon/malis.git@fix_setup) (1.5.2)
Building wheels for collected packages: malis
Building wheel for malis (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: 'C:\Users\CryoEM.conda\envs\CNNectome\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727\setup.py'"'"'; file='"'"'C:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727\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 'C:\Users\CryoEM\AppData\Local\Temp\pip-wheel-0gnyt6wt'
cwd: C:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727
Complete output (29 lines):
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-3.6
creating build\lib.win-amd64-3.6\malis
copying malis\malis_loss.py -> build\lib.win-amd64-3.6\malis
copying malis\setup.py -> build\lib.win-amd64-3.6\malis
copying malis\test_malis.py -> build\lib.win-amd64-3.6\malis
copying malis_init_.py -> build\lib.win-amd64-3.6\malis
running build_ext
cythoning malis/malis.pyx to malis\malis.cpp
C:\Users\CryoEM.conda\envs\CNNectome\lib\site-packages\Cython\Compiler\Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: C:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727\malis\malis.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
building 'malis.malis' extension
creating build\temp.win-amd64-3.6
creating build\temp.win-amd64-3.6\Release
creating build\temp.win-amd64-3.6\Release\malis
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30133\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -IC:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727\malis -IC:\Users\CryoEM.conda\envs\CNNectome -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\lib\site-packages\numpy\core\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30133\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\cppwinrt" /EHsc /Tpmalis\malis.cpp /Fobuild\temp.win-amd64-3.6\Release\malis\malis.obj -std=c++11 -w
cl : Command line warning D9025 : overriding '/W3' with '/w'
cl : Command line warning D9002 : ignoring unknown option '-std=c++11'
malis.cpp
C:\Users\CryoEM.conda\envs\CNNectome\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30133\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -IC:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727\malis -IC:\Users\CryoEM.conda\envs\CNNectome -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\lib\site-packages\numpy\core\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30133\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\cppwinrt" /EHsc /Tpmalis/malis_cpp.cpp /Fobuild\temp.win-amd64-3.6\Release\malis/malis_cpp.obj -std=c++11 -w
cl : Command line warning D9025 : overriding '/W3' with '/w'
cl : Command line warning D9002 : ignoring unknown option '-std=c++11'
malis_cpp.cpp
malis/malis_cpp.cpp(4): fatal error C1083: Cannot open include file: 'boost/pending/disjoint_sets.hpp': No such file or directory
error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30133\bin\HostX86\x64\cl.exe' failed with exit status 2
ERROR: Failed building wheel for malis
Running setup.py clean for malis
Failed to build malis
Installing collected packages: malis
Running setup.py install for malis ... error
ERROR: Command errored out with exit status 1:
command: 'C:\Users\CryoEM.conda\envs\CNNectome\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727\setup.py'"'"'; file='"'"'C:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727\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 'C:\Users\CryoEM\AppData\Local\Temp\pip-record-4ypry3s0\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\CryoEM.conda\envs\CNNectome\Include\malis'
cwd: C:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727
Complete output (27 lines):
running install
running build
running build_py
creating build
creating build\lib.win-amd64-3.6
creating build\lib.win-amd64-3.6\malis
copying malis\malis_loss.py -> build\lib.win-amd64-3.6\malis
copying malis\setup.py -> build\lib.win-amd64-3.6\malis
copying malis\test_malis.py -> build\lib.win-amd64-3.6\malis
copying malis_init_.py -> build\lib.win-amd64-3.6\malis
running build_ext
skipping 'malis\malis.cpp' Cython extension (up-to-date)
building 'malis.malis' extension
creating build\temp.win-amd64-3.6
creating build\temp.win-amd64-3.6\Release
creating build\temp.win-amd64-3.6\Release\malis
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30133\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -IC:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727\malis -IC:\Users\CryoEM.conda\envs\CNNectome -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\lib\site-packages\numpy\core\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30133\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\cppwinrt" /EHsc /Tpmalis\malis.cpp /Fobuild\temp.win-amd64-3.6\Release\malis\malis.obj -std=c++11 -w
cl : Command line warning D9025 : overriding '/W3' with '/w'
cl : Command line warning D9002 : ignoring unknown option '-std=c++11'
malis.cpp
C:\Users\CryoEM.conda\envs\CNNectome\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30133\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -IC:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727\malis -IC:\Users\CryoEM.conda\envs\CNNectome -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\include -IC:\Users\CryoEM.conda\envs\CNNectome\lib\site-packages\numpy\core\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30133\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\cppwinrt" /EHsc /Tpmalis/malis_cpp.cpp /Fobuild\temp.win-amd64-3.6\Release\malis/malis_cpp.obj -std=c++11 -w
cl : Command line warning D9025 : overriding '/W3' with '/w'
cl : Command line warning D9002 : ignoring unknown option '-std=c++11'
malis_cpp.cpp
malis/malis_cpp.cpp(4): fatal error C1083: Cannot open include file: 'boost/pending/disjoint_sets.hpp': No such file or directory
error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30133\bin\HostX86\x64\cl.exe' failed with exit status 2
----------------------------------------
ERROR: Command errored out with exit status 1: 'C:\Users\CryoEM.conda\envs\CNNectome\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727\setup.py'"'"'; file='"'"'C:\Users\CryoEM\AppData\Local\Temp\pip-install-zpir3mr_\malis_7e6c75081b78406890519a8b3f35f727\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 'C:\Users\CryoEM\AppData\Local\Temp\pip-record-4ypry3s0\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\CryoEM.conda\envs\CNNectome\Include\malis' Check the logs for full command output.
(CNNectome) C:\Users\CryoEM>