swolock / scrublet

Detect doublets in single-cell RNA-seq data
MIT License
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Installation issue #33

Open coralzhang opened 3 years ago

coralzhang commented 3 years ago

Hi I have been trying to install Scurblet on a Ubuntu system, but keep having issue with the annoy package. Similar issues seem to persist for me on a Windows machine. Could any one please help? Thank you!

Collecting annoy Using cached annoy-1.17.0.tar.gz (646 kB) Building wheels for collected packages: annoy Building wheel for annoy (setup.py) ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3.8 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-sy8ildii/annoy_2e810ff0c07b4e659c0864ad78457d65/setup.py'"'"'; file='"'"'/tmp/pip-install-sy8ildii/annoy_2e810ff0c07b4e659c0864ad78457d65/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 /tmp/pip-wheel-3qzotfhp cwd: /tmp/pip-install-sy8ildii/annoy_2e810ff0c07b4e659c0864ad78457d65/ Complete output (19 lines): /home/woelk/.local/lib/python3.8/site-packages/setuptools/init.py:148: SetuptoolsDeprecationWarning: setup_requires is deprecated. Supply build dependencies using PEP 517 pyproject.toml build-requires. warnings.warn( running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.8 creating build/lib.linux-x86_64-3.8/annoy copying annoy/init.py -> build/lib.linux-x86_64-3.8/annoy running build_ext building 'annoy.annoylib' extension creating build/temp.linux-x86_64-3.8 creating build/temp.linux-x86_64-3.8/src /usr/bin/gcc-8 -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c src/annoymodule.cc -o build/temp.linux-x86_64-3.8/src/annoymodule.o -D_CRT_SECURE_NO_WARNINGS -march=native -O3 -ffast-math -fno-associative-math -DANNOYLIB_MULTITHREADED_BUILD -std=c++14 src/annoymodule.cc:17:10: fatal error: Python.h: No such file or directory

include "Python.h"

^~~~~~ compilation terminated. error: command '/usr/bin/gcc-8' failed with exit status 1

ERROR: Failed building wheel for annoy Running setup.py clean for annoy Failed to build annoy Installing collected packages: annoy Running setup.py install for annoy ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3.8 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-sy8ildii/annoy_2e810ff0c07b4e659c0864ad78457d65/setup.py'"'"'; file='"'"'/tmp/pip-install-sy8ildii/annoy_2e810ff0c07b4e659c0864ad78457d65/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 /tmp/pip-record-bved_ku2/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/woelk/.local/include/python3.8/annoy cwd: /tmp/pip-install-sy8ildii/annoy_2e810ff0c07b4e659c0864ad78457d65/ Complete output (21 lines): /home/woelk/.local/lib/python3.8/site-packages/setuptools/init.py:148: SetuptoolsDeprecationWarning: setup_requires is deprecated. Supply build dependencies using PEP 517 pyproject.toml build-requires. warnings.warn( running install /home/woelk/.local/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib.linux-x86_64-3.8 creating build/lib.linux-x86_64-3.8/annoy copying annoy/init.py -> build/lib.linux-x86_64-3.8/annoy running build_ext building 'annoy.annoylib' extension creating build/temp.linux-x86_64-3.8 creating build/temp.linux-x86_64-3.8/src /usr/bin/gcc-8 -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c src/annoymodule.cc -o build/temp.linux-x86_64-3.8/src/annoymodule.o -D_CRT_SECURE_NO_WARNINGS -march=native -O3 -ffast-math -fno-associative-math -DANNOYLIB_MULTITHREADED_BUILD -std=c++14 src/annoymodule.cc:17:10: fatal error: Python.h: No such file or directory

include "Python.h"

^~~~~~ compilation terminated. error: command '/usr/bin/gcc-8' failed with exit status 1

ERROR: Command errored out with exit status 1: /usr/bin/python3.8 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-sy8ildii/annoy_2e810ff0c07b4e659c0864ad78457d65/setup.py'"'"'; file='"'"'/tmp/pip-install-sy8ildii/annoy_2e810ff0c07b4e659c0864ad78457d65/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 /tmp/pip-record-bved_ku2/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/woelk/.local/include/python3.8/annoy Check the logs for full command output. WARNING: You are using pip version 21.2.4; however, version 21.3.1 is available. You should consider upgrading via the '/usr/bin/python3.8 -m pip install --upgrade pip' command.

cornhundred commented 1 year ago

I'm seeing a similar issue