edlib requirement caused install hiccup
betteridiot opened this issue · 2 comments
Describe the bug
On a minimal install of badread
within a Windows Subsystem for Linux build of Ubuntu 18.04 64-bit, the installation of edlib
via the requirments.txt
can cause an issue if the machine does not have the most up-to-date version of build-essentials
installed. View #2 for all output
To reproduce
(base) $ conda create -n badread python=3.6 --no-default-packages && conda activate badread
(badread) $ pip install git+https://github.com/rrwick/Badread.git
Collecting git+https://github.com/rrwick/Badread.git
Cloning https://github.com/rrwick/Badread.git to /tmp/pip-req-build-6sj3au9h
Collecting edlib (from Badread==0.1.3)
Downloading https://files.pythonhosted.org/packages/33/04/0dd73c02c0a5148754a6144df9a7b5dd55ccdbb1b17481bbc89b0193c544/edlib-1.2.4.tar.gz (54kB)
100% |████████████████████████████████| 61kB 1.3MB/s
Collecting numpy (from Badread==0.1.3)
Downloading https://files.pythonhosted.org/packages/35/d5/4f8410ac303e690144f0a0603c4b8fd3b986feb2749c435f7cdbb288f17e/numpy-1.16.2-cp36-cp36m-manylinux1_x86_64.whl (17.3MB)
100% |████████████████████████████████| 17.3MB 1.4MB/s
Collecting scipy (from Badread==0.1.3)
Downloading https://files.pythonhosted.org/packages/7f/5f/c48860704092933bf1c4c1574a8de1ffd16bf4fde8bab190d747598844b2/scipy-1.2.1-cp36-cp36m-manylinux1_x86_64.whl (24.8MB)
100% |████████████████████████████████| 24.8MB 795kB/s
Building wheels for collected packages: Badread, edlib
Building wheel for Badread (setup.py) ... done
Stored in directory: /tmp/pip-ephem-wheel-cache-p2cgzrv1/wheels/db/38/bd/d192f5ff0b1d97bab8a1b7478730232764f120170c8a730e57
Building wheel for edlib (setup.py) ... error
Complete output from command /root/miniconda3/envs/badread/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-926py29e/edlib/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-jd40pj7t --python-tag cp36:
running bdist_wheel
running build
running build_ext
building 'edlib' extension
creating build
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/edlib
creating build/temp.linux-x86_64-3.6/edlib/src
gcc -pthread -B /root/miniconda3/envs/badread/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iedlib/include -I/root/miniconda3/envs/badread/include/python3.6m -c edlib.bycython.cpp -o build/temp.linux-x86_64-3.6/edlib.bycython.o -O3 -std=c++11
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
Failed building wheel for edlib
Running setup.py clean for edlib
Successfully built Badread
Failed to build edlib
Installing collected packages: edlib, numpy, scipy, Badread
Running setup.py install for edlib ... error
Complete output from command /root/miniconda3/envs/badread/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-926py29e/edlib/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-b2nec6ur/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_ext
building 'edlib' extension
creating build
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/edlib
creating build/temp.linux-x86_64-3.6/edlib/src
gcc -pthread -B /root/miniconda3/envs/badread/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iedlib/include -I/root/miniconda3/envs/badread/include/python3.6m -c edlib.bycython.cpp -o build/temp.linux-x86_64-3.6/edlib.bycython.o -O3 -std=c++11
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/root/miniconda3/envs/badread/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-926py29e/edlib/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-b2nec6ur/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-926py29e/edlib/
System info
- Windows Subsystem for Linux
- OS: Ubuntu 18.04.2 LTS (Bionic Beaver)
- Python version: Python 3.6.7
Suggested Actions
Add a FAQ page to your Wiki and prescribe updating build-essentials
before install. This might be able to preempt this problem in the future
Thanks! It's easy to forget that not everyone has compilers set up on their machine 😄
I've added an Installation issues page to the wiki and linked to it in the installation section of the README. This page covers installing compilers for common OSs (and pip issues to address #4).
Thank you. This addresses my concern here.