Docker /bin/sh: 1: : not found miniconda3

Question

When I try to build the following Dockerfile with the command line docker build -t my-image-name .

FROM continuumio/miniconda3
EXPOSE 8880

# Set working directory
WORKDIR /my-workingdir

# Add scripts to docker workdir
ADD Dockerfile .
ADD environment.yml .
ADD all-my-python-files.py .

# Update & installation of linux packages
RUN apt-get update -y && \
    apt-get install -y libgl1-mesa-glx apt-utils && \
    apt-get install -y openssh-server && \
    apt-get install -y net-tools
# Conda update and creation of environment
RUN conda update conda \
    && conda env create -f environment.yml \
# Activation of environment
    && echo "source activate environment" > ~/.bashrc

# Mount volumes
VOLUME /my-workingdir/Input

CMD ["python" , "execute_given_python_file.py"]

I get an error at the time of building it: /bin/sh: 1: : not found I am building an image in a macOS Hihg Sierra Version 10.13.6 but when I build the image in a linux CentOS environment (Inside another Docker container), the Dockerfile runs perfectly. The Docker version I am using on the mac is

Client:
- Version: 18.06.1-ce
- API version: 1.38
Server:
- Engine:
- Version: 18.06.1-ce
- API version: 1.38 (minimum version 1.12)

I have tried the following:

Reinstall Docker on the mac
apt-get update (without the -y)
sudo apt-get update
Do not update
Do not create the conda environment
Do not CMD

But i still get errors. How can the issue be solved?

UPDATE: The last lines before the error message appears during the building of the image are:

Get:6 http://security.debian.org/debian-security stretch/updates/main amd64 Packages [490 kB] Get:7 http://deb.debian.org/debian stretch-updates/main amd64 Packages [5476 B] Get:8 http://deb.debian.org/debian stretch/main amd64 Packages [9500 kB] Fetched 10.3 MB in 2s (4564 kB/s) Reading package lists... /bin/sh: 1: : not found

Docker returns a non-zero code: 127

In order to replicate the error, I am including a python script and a yml environment.

Python script all-my-python-files.py tested during an error:

# Name of file: all-my-python-files.py
import openpyxl
import requests
import datetime as dt
import time 
from pandas.io.json import json_normalize
import argparse
import os
import pandas as pd
print("At this point, libraries should be imported")
print("End of python script")

The environment.yml file is:

name: environment
channels:
  - statiskit
  - anaconda
  - conda-forge
  - defaults
dependencies:
  - asn1crypto=0.24.0
  # For space the following line are not separated into single lines:

- cffi=1.11.5 - chardet=3.0.4 - cryptography=2.3.1 - et_xmlfile=1.0.1 - idna=2.7 - jdcal=1.4 - openpyxl=2.5.5 - pycparser=2.18 - pyopenssl=18.0.0 - pysocks=1.6.8 - requests=2.19.1 - urllib3=1.23 - ca-certificates=2018.8.24 - openssl=1.0.2p - time=1.7 - blas=1.0 - certifi=2018.8.24 - intel-openmp=2018.0.3 - libedit=3.1.20170329 - libffi=3.2.1 # - libgfortran=3.0.1 # Not running in linux - mkl=2018.0.3 - mkl_fft=1.0.4 - mkl_random=1.0.1 - ncurses=6.1 - numpy=1.15.1 - numpy-base=1.15.1 - pandas=0.23.4 - pip=10.0.1 - python=3.7.0 - python-dateutil=2.7.3 - pytz=2018.5 - readline=7.0 - setuptools=40.2.0 - six=1.11.0 - sqlite=3.24.0 - tk=8.6.8 - wheel=0.31.1 - xz=5.2.4 - zlib=1.2.11 # - libcxx=4.0.1 # Not running in linux # - libcxxabi=4.0.1 # Not running in linux - pip: - datetime==4.2 - zope.interface==4.5.0 prefix: /Users/Elias/miniconda3/envs/xlshp

You may want to check if the line returns are unix like or windows like and change them (probably in your python files) — Jorge Lavín
The log lines are linux-like. In fact, the python files work well when I build the image on a CentOS linux system. I have included the last lines before the error in the post. — eliasmaxil
Whether log output is "linux-like" isn't what we care about. We care about whether the file has CRLF newlines or LF newlines. If you try to run a script with CRLF newlines with an interpreter that only recognizes LF newlines, every line has a CR -- an invisible character -- on the end that makes your commands invalid. — Charles Duffy
That said, putting a set -x; at the top of any RUN command that's failing is a good place to start. (Thus, RUN set -x; apt-get update -y, or RUN set -x; conda update conda). — Charles Duffy
...also, in general, dealing with .bashrc for services in general is a code smell. .bashrc is intended to be used to configure interactive shells, and is only guaranteed to be invoked for interactive shells (and not all interactive shells, but just the ones that aren't login shells). When you use it to configure a noninteractive service, you're Doing It Wrong. — Charles Duffy

eliasmaxil eliasmaxil · Accepted Answer · 2018-09-12T21:25:46

As @Charler Duffy mentioned, the issue was related with the invisible end of lines in the script. Somehow, writing the code in the following way solved the problem:

RUN apt-get update
RUN apt-get install -y libgl1-mesa-glx apt-utils openssh-server net-tools
# Conda update and creation of environment
RUN conda update conda && \
    conda env create -f environment.yml && \
    # Activation of environment and correction of bash
    echo "source activate xlshp_env" > ~/.bash

So when all the linux packages were installed in the same line, the Dockerfile could build the image.

Docker /bin/sh: 1: : not found miniconda3

1 Answers