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KangchengHou / admix-kit

Toolkit for analyzing genetics data from admixed populations
https://kangchenghou.github.io/admix-kit
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Fail to install admix-kit #23

Closed xiw588 closed 1 year ago

xiw588 commented 1 year ago

Describe the bug I try to install admix-kit following the instructions. I update the cmake first but it turns out to be using the old version, I guess?

To Reproduce cd admix-kit && pip install -e .

Screenshots ERROR: Command errored out with exit status 1: command: /n/sw/eb/apps/centos7/Anaconda3/2020.11/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-_1ohrzxs/tinygwas/setup.py'"'"'; file='"'"'/tmp/pip-install-_1ohrzxs/tinygwas/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 /tmp/pip-wheel-f_9vj7u1 cwd: /tmp/pip-install-_1ohrzxs/tinygwas/ Complete output (39 lines): running bdist_wheel running build running build_ext CMake Error at CMakeLists.txt:1 (cmake_minimum_required): CMake 3.12 or higher is required. You are running version 2.8.12.2

-- Configuring incomplete, errors occurred! Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-_1ohrzxs/tinygwas/setup.py", line 74, in setup( File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/site-packages/setuptools/init.py", line 153, in setup return distutils.core.setup(**attrs) File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/core.py", line 148, in setup dist.run_commands() File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 290, in run self.run_command('build') File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-install-_1ohrzxs/tinygwas/setup.py", line 36, in run self.build_extension(ext) File "/tmp/pip-install-_1ohrzxs/tinygwas/setup.py", line 65, in build_extension subprocess.check_call( File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-_1ohrzxs/tinygwas', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-_1ohrzxs/tinygwas/build/lib.linux-x86_64-3.8', '-DPYTHON_EXECUTABLE=/n/sw/eb/apps/centos7/Anaconda3/2020.11/bin/python', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.

ERROR: Failed building wheel for tinygwas Running setup.py clean for tinygwas Building wheel for pylampld (setup.py) ... error ERROR: Command errored out with exit status 1: command: /n/sw/eb/apps/centos7/Anaconda3/2020.11/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-_1ohrzxs/pylampld/setup.py'"'"'; file='"'"'/tmp/pip-install-_1ohrzxs/pylampld/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 /tmp/pip-wheel-v_wd4m4h cwd: /tmp/pip-install-_1ohrzxs/pylampld/ Complete output (39 lines): running bdist_wheel running build running build_ext CMake Error at CMakeLists.txt:1 (cmake_minimum_required): CMake 3.12 or higher is required. You are running version 2.8.12.2

-- Configuring incomplete, errors occurred! Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-_1ohrzxs/pylampld/setup.py", line 69, in setup( File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/site-packages/setuptools/init.py", line 153, in setup return distutils.core.setup(**attrs) File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/core.py", line 148, in setup dist.run_commands() File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 290, in run self.run_command('build') File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-install-_1ohrzxs/pylampld/setup.py", line 34, in run self.build_extension(ext) File "/tmp/pip-install-_1ohrzxs/pylampld/setup.py", line 62, in build_extension subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-_1ohrzxs/pylampld', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-_1ohrzxs/pylampld/build/lib.linux-x86_64-3.8', '-DPYTHON_EXECUTABLE=/n/sw/eb/apps/centos7/Anaconda3/2020.11/bin/python', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.

ERROR: Failed building wheel for pylampld Running setup.py clean for pylampld Failed to build tinygwas pylampld Installing collected packages: tinygwas, pylampld, admix-kit Running setup.py install for tinygwas ... error ERROR: Command errored out with exit status 1: command: /n/sw/eb/apps/centos7/Anaconda3/2020.11/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-_1ohrzxs/tinygwas/setup.py'"'"'; file='"'"'/tmp/pip-install-_1ohrzxs/tinygwas/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-s0fxgx4d/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /n/home13/xinanwang/.local/include/python3.8/tinygwas cwd: /tmp/pip-install-_1ohrzxs/tinygwas/ Complete output (41 lines): running install running build running build_ext CMake Error at CMakeLists.txt:1 (cmake_minimum_required): CMake 3.12 or higher is required. You are running version 2.8.12.2

-- Configuring incomplete, errors occurred!
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/tmp/pip-install-_1ohrzxs/tinygwas/setup.py", line 74, in <module>
    setup(
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/site-packages/setuptools/__init__.py", line 153, in setup
    return distutils.core.setup(**attrs)
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/site-packages/setuptools/command/install.py", line 61, in run
    return orig.install.run(self)
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/command/install.py", line 545, in run
    self.run_command('build')
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/command/build.py", line 135, in run
    self.run_command(cmd_name)
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/tmp/pip-install-_1ohrzxs/tinygwas/setup.py", line 36, in run
    self.build_extension(ext)
  File "/tmp/pip-install-_1ohrzxs/tinygwas/setup.py", line 65, in build_extension
    subprocess.check_call(
  File "/n/sw/eb/apps/centos7/Anaconda3/2020.11/lib/python3.8/subprocess.py", line 364, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-_1ohrzxs/tinygwas', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-_1ohrzxs/tinygwas/build/lib.linux-x86_64-3.8', '-DPYTHON_EXECUTABLE=/n/sw/eb/apps/centos7/Anaconda3/2020.11/bin/python', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.
----------------------------------------

ERROR: Command errored out with exit status 1: /n/sw/eb/apps/centos7/Anaconda3/2020.11/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-_1ohrzxs/tinygwas/setup.py'"'"'; file='"'"'/tmp/pip-install-_1ohrzxs/tinygwas/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-s0fxgx4d/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /n/home13/xinanwang/.local/include/python3.8/tinygwas Check the logs for full command output.

Additional context Add any other context about the problem here.

xiw588 commented 1 year ago

I checked the version right after updating cmake, it still showed to be cmake version 2.8.12.2

KangchengHou commented 1 year ago

Yes it is the issue of cmake version. The key is to make sure cmake > 3.12 is installed and which cmake shows that. You may try:

  1. find the new version of installed cmake bin and add that to $PATH: export $PATH=$PATH:/path/to/new/cmake
  2. if you are on a computing cluster, do you have something like module load? you may try look at module avail cmake
  3. maybe ask the system administrater for that
xiw588 commented 1 year ago

Hi Kangcheng,

Thank you for our swift response and help! I was unable to run through git clone https://github.com/KangchengHou/admix-kit now. But the error message "ERROR: File "setup.py" not found. Directory cannot be installed in editable mode: /n/home13/XXX" pop up when I tried to run cd admix-kit & pip install -e . I do have setup.py in /n/home13/XXX/admix-kit, and it is allowed to write. Do you know what is wrong there? Thanks!