Hi all,
I wanted to try nighres via Docker container but receive an error when building the Docker image (see below). I’m not sure what the problem is or whether I am doing something wrong. Can someone please help?
Thanks!
Best wishes,
Livia
docker build . -t nighres
[+] Building 42.3s (9/16)
=> [internal] load build definition from Dockerfile 0.1s
=> => transferring dockerfile: 86B 0.0s
=> [internal] load .dockerignore 0.1s
=> => transferring context: 2B 0.0s
=> [internal] load metadata for docker.io/library/ubuntu:16.04 2.2s
=> [ 1/11] FROM docker.io/library/ubuntu:16.04@sha256:e74994b7a9ec8e2129cfc6a871f3236940006ed31091de355578492ed140a39c 0.0s
=> CACHED https://github.com/krallin/tini/releases/download/v0.6.0/tini 0.0s
=> [internal] load build context 0.1s
=> => transferring context: 20.34kB 0.1s
=> CACHED [ 2/11] RUN apt-get update && apt-get -y install sudo && sudo apt-get update -qq && apt-get install -y python3 python3-pip 0.0s
=> CACHED [ 3/11] RUN ln -svT “/usr/lib/jvm/java-8-openjdk-$(dpkg --print-architecture)” /docker-java-home 0.0s
=> ERROR [ 4/11] RUN sudo apt-get install -y jcc && python3 -m pip install --upgrade pip wheel J 39.8s
[ 4/11] RUN sudo apt-get install -y jcc && python3 -m pip install --upgrade pip wheel JCC urllib3 && python3 -m pip install jupyter nilearn sklearn nose matplotlib scipy psutil:
#7 4.367 Reading package lists…
#7 5.749 Building dependency tree…
#7 5.908 Reading state information…
#7 6.062 The following additional packages will be installed:
#7 6.062 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib python
#7 6.062 python-minimal python2.7 python2.7-minimal
#7 6.063 Suggested packages:
#7 6.063 python-doc python-tk python2.7-doc binfmt-support
#7 6.064 The following NEW packages will be installed:
#7 6.065 jcc libpython-stdlib libpython2.7-minimal libpython2.7-stdlib python
#7 6.065 python-minimal python2.7 python2.7-minimal
#7 6.717 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded.
#7 6.717 Need to get 4044 kB of archives.
#7 6.717 After this operation, 17.6 MB of additional disk space will be used.
#7 6.717 Get:1 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpython2.7-minimal amd64 2.7.12-1ubuntu016.04.18 [338 kB]16.04.18 [1260 kB]
#7 6.989 Get:2 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 python2.7-minimal amd64 2.7.12-1ubuntu0
#7 7.249 Get:3 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-minimal amd64 2.7.12-116.04 [28.1 kB]16.04.18 [1883 kB]
#7 7.252 Get:4 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpython2.7-stdlib amd64 2.7.12-1ubuntu0
#7 7.528 Get:5 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 python2.7 amd64 2.7.12-1ubuntu016.04.18 [224 kB]16.04 [7768 B]
#7 7.563 Get:6 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpython-stdlib amd64 2.7.12-1
#7 7.567 Get:7 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 python amd64 2.7.12-116.04 [137 kB]16.04.18_amd64.deb …
#7 7.576 Get:8 http://archive.ubuntu.com/ubuntu xenial/universe amd64 jcc amd64 2.21-1.1 [166 kB]
#7 7.868 debconf: delaying package configuration, since apt-utils is not installed
#7 7.922 Fetched 4044 kB in 1s (2968 kB/s)
#7 7.974 Selecting previously unselected package libpython2.7-minimal:amd64.
(Reading database … 19878 files and directories currently installed.)
#7 8.128 Preparing to unpack …/libpython2.7-minimal_2.7.12-1ubuntu0
#7 8.132 Unpacking libpython2.7-minimal:amd64 (2.7.12-1ubuntu016.04.18) …16.04.18_amd64.deb …
#7 8.300 Selecting previously unselected package python2.7-minimal.
#7 8.301 Preparing to unpack …/python2.7-minimal_2.7.12-1ubuntu0
#7 8.313 Unpacking python2.7-minimal (2.7.12-1ubuntu016.04.18) …16.04_amd64.deb …
#7 8.471 Selecting previously unselected package python-minimal.
#7 8.473 Preparing to unpack …/python-minimal_2.7.12-1
#7 8.476 Unpacking python-minimal (2.7.12-116.04) …16.04.18_amd64.deb …
#7 8.516 Selecting previously unselected package libpython2.7-stdlib:amd64.
#7 8.517 Preparing to unpack …/libpython2.7-stdlib_2.7.12-1ubuntu0
#7 8.520 Unpacking libpython2.7-stdlib:amd64 (2.7.12-1ubuntu016.04.18) …16.04.18_amd64.deb …
#7 8.872 Selecting previously unselected package python2.7.
#7 8.874 Preparing to unpack …/python2.7_2.7.12-1ubuntu0
#7 8.876 Unpacking python2.7 (2.7.12-1ubuntu016.04.18) …16.04_amd64.deb …
#7 8.919 Selecting previously unselected package libpython-stdlib:amd64.
#7 8.921 Preparing to unpack …/libpython-stdlib_2.7.12-1
#7 8.923 Unpacking libpython-stdlib:amd64 (2.7.12-116.04) …16.04.18) …
#7 8.942 Processing triggers for mime-support (3.59ubuntu1) …
#7 8.992 Setting up libpython2.7-minimal:amd64 (2.7.12-1ubuntu0
#7 9.004 Setting up python2.7-minimal (2.7.12-1ubuntu016.04.18) …16.04) …
#7 9.377 Linking and byte-compiling packages for runtime python2.7…
#7 9.394 Setting up python-minimal (2.7.12-1
#7 9.478 Selecting previously unselected package python.
(Reading database … 20625 files and directories currently installed.)
#7 9.491 Preparing to unpack …/python_2.7.12-116.04_amd64.deb …16.04) …
#7 9.503 Unpacking python (2.7.12-1
#7 9.565 Selecting previously unselected package jcc.
#7 9.567 Preparing to unpack …/jcc_2.21-1.1_amd64.deb …
#7 9.570 Unpacking jcc (2.21-1.1) …
#7 9.636 Setting up libpython2.7-stdlib:amd64 (2.7.12-1ubuntu016.04.18) …16.04.18) …
#7 9.643 Setting up python2.7 (2.7.12-1ubuntu0
#7 10.62 Setting up libpython-stdlib:amd64 (2.7.12-116.04) …16.04) …
#7 10.62 Setting up python (2.7.12-1
#7 10.64 Setting up jcc (2.21-1.1) …
#7 12.81 Collecting pip
#7 13.01 Downloading https://files.pythonhosted.org/packages/fe/ef/60d7ba03b5c442309ef42e7d69959f73aacccd0d86008362a681c4698e83/pip-21.0.1-py3-none-any.whl (1.5MB)
#7 13.66 Collecting wheel
#7 13.71 Downloading https://files.pythonhosted.org/packages/65/63/39d04c74222770ed1589c0eaba06c05891801219272420b40311cd60c880/wheel-0.36.2-py2.py3-none-any.whl
#7 13.74 Collecting JCC
#7 14.29 Downloading https://files.pythonhosted.org/packages/b6/38/4dd526bbf12ce20a750e958aa09b0097fc792ccc75fa3a15f1523db82ccb/JCC-3.9.tar.gz (186kB)
#7 17.81 Collecting urllib3
#7 17.97 Downloading https://files.pythonhosted.org/packages/09/c6/d3e3abe5b4f4f16cf0dfc9240ab7ce10c2baa0e268989a4e3ec19e90c84e/urllib3-1.26.4-py2.py3-none-any.whl (153kB)
#7 18.05 Building wheels for collected packages: JCC
#7 18.05 Running setup.py bdist_wheel for JCC: started
#7 38.03 Running setup.py bdist_wheel for JCC: finished with status ‘done’
#7 38.04 Stored in directory: /root/.cache/pip/wheels/16/49/4c/6eb12fce9e7329940f358c1415523670fd542bc32e1a55bcd0
#7 38.07 Successfully built JCC
#7 38.07 Installing collected packages: pip, wheel, JCC, urllib3
#7 38.07 Found existing installation: pip 8.1.1
#7 38.11 Not uninstalling pip at /usr/lib/python3/dist-packages, outside environment /usr
#7 39.14 Found existing installation: wheel 0.29.0
#7 39.14 Not uninstalling wheel at /usr/lib/python3/dist-packages, outside environment /usr
#7 39.34 Successfully installed JCC-3.9 pip-21.0.1 urllib3-1.26.4 wheel-0.36.2
#7 39.66 Traceback (most recent call last):
#7 39.66 File “/usr/lib/python3.5/runpy.py”, line 184, in _run_module_as_main
#7 39.66 “main”, mod_spec)
#7 39.66 File “/usr/lib/python3.5/runpy.py”, line 85, in _run_code
#7 39.66 exec(code, run_globals)
#7 39.66 File “/usr/local/lib/python3.5/dist-packages/pip/main.py”, line 21, in
#7 39.66 from pip._internal.cli.main import main as _main
#7 39.66 File “/usr/local/lib/python3.5/dist-packages/pip/_internal/cli/main.py”, line 60
#7 39.66 sys.stderr.write(f"ERROR: {exc}")
#7 39.66 ^
#7 39.66 SyntaxError: invalid syntax
executor failed running [/bin/sh -c sudo apt-get install -y jcc && python3 -m pip install --upgrade pip wheel JCC urllib3 && python3 -m pip install jupyter nilearn sklearn nose matplotlib scipy psutil]: exit code: 1