ERROR: Command errored out with exit status 1 when trying to pip install scrublet

[SanushiD]

ERROR: Command errored out with exit status 1:
command: /opt/conda/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-9vwet5y1/annoy_b86e28e8cccf4119afb50a0b3dd31e21/setup.py'"'"'; file='"'"'/tmp/pip-install-9vwet5y1/annoy_b86e28e8cccf4119afb50a0b3dd31e21/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-u57kxry0
cwd: /tmp/pip-install-9vwet5y1/annoy_b86e28e8cccf4119afb50a0b3dd31e21/
Complete output (14 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/annoy
copying annoy/init.py -> build/lib.linux-x86_64-3.7/annoy
running build_ext
building 'annoy.annoylib' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/src
gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/conda/include/python3.7m -c src/annoymodule.cc -o build/temp.linux-x86_64-3.7/src/annoymodule.o -D_CRT_SECURE_NO_WARNINGS -march=native -O3 -ffast-math -fno-associative-math -DANNOYLIB_MULTITHREADED_BUILD -std=c++14
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
error: command 'gcc' failed with exit status 1

ERROR: Failed building wheel for annoy
Running setup.py clean for annoy
Failed to build annoy
Installing collected packages: numpy, threadpoolctl, six, setuptools, scipy, llvmlite, joblib, scikit-learn, python-dateutil, pyparsing, pillow, numba, kiwisolver, cycler, tifffile, PyWavelets, pytz, pynndescent, networkx, matplotlib, imageio, umap-learn, scikit-image, pandas, cython, annoy, scrublet
Running setup.py install for annoy ... error
ERROR: Command errored out with exit status 1:
command: /opt/conda/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-9vwet5y1/annoy_b86e28e8cccf4119afb50a0b3dd31e21/setup.py'"'"'; file='"'"'/tmp/pip-install-9vwet5y1/annoy_b86e28e8cccf4119afb50a0b3dd31e21/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-am78whzz/install-record.txt --single-version-externally-managed --home /tmp/pip-target-neh7zgs8 --compile --install-headers /tmp/pip-target-neh7zgs8/include/python/annoy
cwd: /tmp/pip-install-9vwet5y1/annoy_b86e28e8cccf4119afb50a0b3dd31e21/
Complete output (14 lines):
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/annoy
copying annoy/init.py -> build/lib.linux-x86_64-3.7/annoy
running build_ext
building 'annoy.annoylib' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/src
gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/conda/include/python3.7m -c src/annoymodule.cc -o build/temp.linux-x86_64-3.7/src/annoymodule.o -D_CRT_SECURE_NO_WARNINGS -march=native -O3 -ffast-math -fno-associative-math -DANNOYLIB_MULTITHREADED_BUILD -std=c++14
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/conda/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-9vwet5y1/annoy_b86e28e8cccf4119afb50a0b3dd31e21/setup.py'"'"'; file='"'"'/tmp/pip-install-9vwet5y1/annoy_b86e28e8cccf4119afb50a0b3dd31e21/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-am78whzz/install-record.txt --single-version-externally-managed --home /tmp/pip-target-neh7zgs8 --compile --install-headers /tmp/pip-target-neh7zgs8/include/python/annoy Check the logs for full command output.
Note: you may need to restart the kernel to use updated packages.

Anyone know how to fix this please?

[trankos]

It looks like you haven't installed the gcc executable. Some python packages require compiling and/or installing additional libraries.

[SanushiD]

Thank you @trankos I have just run pip install gcc7 on my terra bio workspace notebook but I'm still running into the previous error.

[trankos]

Sorry @SanushiD, I was wrong. The missing file is cc1plus, not gcc.
Here there is an explanation. cc1plus is the C++ compiler. I hope this help.