pip install nanosv: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 1112: ordinal not in range(128)

[philres]

Hi,

I tried installing nanosv via pip and got the following error:

root@b9549bcea748:/# pip3 install nanosv
Collecting nanosv
  Using cached https://files.pythonhosted.org/packages/42/f8/48ea99c79d98b19b4d91fda2cfdfbd596510ae0a1205a706a31221dfab78/NanoSV-1.2.0.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-mkp3zu0i/nanosv/setup.py", line 16, in <module>
        long_description=readme(),
      File "/tmp/pip-build-mkp3zu0i/nanosv/setup.py", line 10, in readme
        return f.read()
      File "/usr/lib/python3.5/encodings/ascii.py", line 26, in decode
        return codecs.ascii_decode(input, self.errors)[0]
    UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 1112: ordinal not in range(128)
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-mkp3zu0i/nanosv/
You are using pip version 8.1.1, however version 10.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

In case you want to reproduce it, this is the docker image I used:

FROM ubuntu:16.04
MAINTAINER prescheneder

RUN apt-get update \
    && apt-get install --no-install-recommends -y \
        python3 \
        python3-pip \
        python3-dev \
        build-essential \
        git \
        cmake \
        wget \
        libz-dev \
        libncurses-dev \
        libbz2-dev \
        liblzma-dev \
    && pip3 --no-cache-dir install --upgrade \
        setuptools \
        wheel

It is not a problem for me as the following worked, just wanted to let you know.

git clone https://github.com/mroosmalen/nanosv.git \
cd nanosv/ \
touch README.rst \
pip3 install .

Only small hiccup there, was that I had to create the README.rst

Philipp

[philres]

Ok I have to take that back it is a problem, because if I try running NanoSV with data and not only NanoSV -h I get the same error:

$ NanoSV test.bam -o test_nanosv.vcf 
Traceback (most recent call last):
  File "/usr/local/bin/NanoSV", line 11, in <module>
    load_entry_point('NanoSV==1.2.0', 'console_scripts', 'NanoSV')()
  File "/usr/local/lib/python3.5/dist-packages/pkg_resources/__init__.py", line 476, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/usr/local/lib/python3.5/dist-packages/pkg_resources/__init__.py", line 2700, in load_entry_point
    return ep.load()
  File "/usr/local/lib/python3.5/dist-packages/pkg_resources/__init__.py", line 2318, in load
    return self.resolve()
  File "/usr/local/lib/python3.5/dist-packages/pkg_resources/__init__.py", line 2324, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/usr/local/lib/python3.5/dist-packages/nanosv/__init__.py", line 1, in <module>
    from .utils import *
  File "/usr/local/lib/python3.5/dist-packages/nanosv/utils/__init__.py", line 1, in <module>
    from . import coverage
  File "/usr/local/lib/python3.5/dist-packages/nanosv/utils/coverage.py", line 8, in <module>
    import NanoSV
  File "/usr/local/lib/python3.5/dist-packages/nanosv/utils/../NanoSV.py", line 29, in <module>
    cfg.read(args.config)
  File "/usr/lib/python3.5/configparser.py", line 696, in read
    self._read(fp, filename)
  File "/usr/lib/python3.5/configparser.py", line 1012, in _read
    for lineno, line in enumerate(fp, start=1):
  File "/usr/lib/python3.5/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 948: ordinal not in range(128)

[mroosmalen]

This is because of the encoding language.
If you use bash as your shell, you can put these lines in your ~/.bashrc and ~/.profile files

export LC_CTYPE=en_US.UTF-8
export LANG=en_US.UTF-8

[philres]

Hi Mark,

Thanks for the quick reply. For the record, changing the Dockerfile to the following fixed it:

FROM ubuntu:16.04

ENV LC_CTYPE en_US.UTF-8
ENV LANG en_US.UTF-8

RUN apt-get update \
    && apt-get install --no-install-recommends -y \
        language-pack-en \
        python3 \
        python3-pip \
        python3-dev \
        build-essential \
        git \
        cmake \
        wget \
        libz-dev \
        libncurses-dev \
        libbz2-dev \
        liblzma-dev \
    && pip3 --no-cache-dir install --upgrade \
        setuptools \
        wheel

[Asa-Nisi-Masa]

What worked for me was LC_ALL=C.UTF-8 pip3 install nanosv (for a different package)

[Varun-garg]

combining all answers, adding following to Dockerfile worked for me (arch linux)

# this is required for some systems
ENV LC_ALL=C.UTF-8