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Bug on apt install (permission denied)

Hi everyone,
I’m experiencing a failure (PermissionError: [Errno 13] Permission denied) when installing python3 with apt in a docker container (debian based, e,g, ubuntu:20.04).

Has anyone experienced the same problem?
If so, is there a workaround to permanently fix it?


  • Host: Ubuntu 20.04 on x86-64
  • Docker version: 19.03.13, build 4484c46d9d
  • Guest OSs: ubuntu:18.04, ubuntu:20.04, debian:9
  • Issue-failure: apt install -y python3 fails with permission denied during both build and run phases.
  • Docker info: attached below

To reproduce it is enough to build the following Dockerfile

FROM ubuntu:20.04
RUN apt update && apt install -y python3

When doing docker build . docker fails giving the output attached below.

Instead, if I build the same Dockerfile on Docker for Mac it works successfully.
Similarly python2 can be installed with no problems using apt on the same setting.

docker info output:

 Debug Mode: false

 Containers: 15
  Running: 14
  Paused: 0
  Stopped: 1
 Images: 112
 Server Version: 19.03.11
 Storage Driver: overlay2
  Backing Filesystem: extfs
  Supports d_type: true
  Native Overlay Diff: true
 Logging Driver: json-file
 Cgroup Driver: cgroupfs
  Volume: local
  Network: bridge host ipvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
 Swarm: inactive
 Runtimes: runc
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 7ad184331fa3e55e52b890ea95e65ba581ae3429
 runc version: 
 init version: fec3683
 Security Options:
   Profile: default
 Kernel Version: 5.4.0-48-generic
 Operating System: Ubuntu Core 16
 OSType: linux
 Architecture: x86_64
 CPUs: 24
 Total Memory: 62.86GiB
 Name: *******
 Docker Root Dir: /var/snap/docker/common/var-lib-docker
 Debug Mode: false
 Experimental: false
 Insecure Registries:
 Live Restore Enabled: false

WARNING: No swap limit support

docker build . output:

Sending build context to Docker daemon  359.4MB
Step 1/2 : FROM ubuntu:20.04
 ---> d70eaf7277ea
Step 2/2 : RUN apt update &&     apt install -y python3
 ---> Running in d1653a1b18be

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

Get:1 focal-security InRelease [107 kB]
Get:2 focal InRelease [265 kB]
Get:3 focal-updates InRelease [111 kB]
Get:4 focal-backports InRelease [98.3 kB]
Get:5 focal-security/multiverse amd64 Packages [1170 B]
Get:6 focal-security/main amd64 Packages [438 kB]
Get:7 focal-security/restricted amd64 Packages [85.3 kB]
Get:8 focal-security/universe amd64 Packages [639 kB]
Get:9 focal/multiverse amd64 Packages [177 kB]
Get:10 focal/main amd64 Packages [1275 kB]
Get:11 focal/universe amd64 Packages [11.3 MB]
Get:12 focal/restricted amd64 Packages [33.4 kB]
Get:13 focal-updates/universe amd64 Packages [857 kB]
Get:14 focal-updates/multiverse amd64 Packages [21.6 kB]
Get:15 focal-updates/main amd64 Packages [808 kB]
Get:16 focal-updates/restricted amd64 Packages [107 kB]
Get:17 focal-backports/universe amd64 Packages [4277 B]
Fetched 16.4 MB in 2s (6728 kB/s)
Reading package lists...
Building dependency tree...
Reading state information...
1 package can be upgraded. Run 'apt list --upgradable' to see it.

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  file libexpat1 libmagic-mgc libmagic1 libmpdec2 libpython3-stdlib
  libpython3.8-minimal libpython3.8-stdlib libreadline8 libsqlite3-0 libssl1.1
  mime-support python3-minimal python3.8 python3.8-minimal readline-common
Suggested packages:
  python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binutils
  binfmt-support readline-doc
The following NEW packages will be installed:
  file libexpat1 libmagic-mgc libmagic1 libmpdec2 libpython3-stdlib
  libpython3.8-minimal libpython3.8-stdlib libreadline8 libsqlite3-0 libssl1.1
  mime-support python3 python3-minimal python3.8 python3.8-minimal
  readline-common xz-utils
0 upgraded, 18 newly installed, 0 to remove and 1 not upgraded.
Need to get 7372 kB of archives.
After this operation, 32.7 MB of additional disk space will be used.
Get:1 focal/main amd64 libssl1.1 amd64 1.1.1f-1ubuntu2 [1318 kB]
Get:2 focal-updates/main amd64 libpython3.8-minimal amd64 3.8.5-1~20.04 [714 kB]
Get:3 focal/main amd64 libexpat1 amd64 2.2.9-1build1 [73.3 kB]
Get:4 focal-updates/main amd64 python3.8-minimal amd64 3.8.5-1~20.04 [1898 kB]
Get:5 focal/main amd64 python3-minimal amd64 3.8.2-0ubuntu2 [23.6 kB]
Get:6 focal/main amd64 mime-support all 3.64ubuntu1 [30.6 kB]
Get:7 focal/main amd64 libmpdec2 amd64 2.4.2-3 [81.1 kB]
Get:8 focal/main amd64 readline-common all 8.0-4 [53.5 kB]
Get:9 focal/main amd64 libreadline8 amd64 8.0-4 [131 kB]
Get:10 focal-updates/main amd64 libsqlite3-0 amd64 3.31.1-4ubuntu0.2 [549 kB]
Get:11 focal-updates/main amd64 libpython3.8-stdlib amd64 3.8.5-1~20.04 [1671 kB]
Get:12 focal-updates/main amd64 python3.8 amd64 3.8.5-1~20.04 [373 kB]
Get:13 focal/main amd64 libpython3-stdlib amd64 3.8.2-0ubuntu2 [7068 B]
Get:14 focal/main amd64 python3 amd64 3.8.2-0ubuntu2 [47.6 kB]
Get:15 focal/main amd64 libmagic-mgc amd64 1:5.38-4 [218 kB]
Get:16 focal/main amd64 libmagic1 amd64 1:5.38-4 [75.9 kB]
Get:17 focal/main amd64 file amd64 1:5.38-4 [23.3 kB]
Get:18 focal-updates/main amd64 xz-utils amd64 5.2.4-1ubuntu1 [82.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 7372 kB in 1s (9815 kB/s)
Selecting previously unselected package libssl1.1:amd64.
(Reading database ... 4121 files and directories currently installed.)
Preparing to unpack .../libssl1.1_1.1.1f-1ubuntu2_amd64.deb ...
Unpacking libssl1.1:amd64 (1.1.1f-1ubuntu2) ...
Selecting previously unselected package libpython3.8-minimal:amd64.
Preparing to unpack .../libpython3.8-minimal_3.8.5-1~20.04_amd64.deb ...
Unpacking libpython3.8-minimal:amd64 (3.8.5-1~20.04) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.2.9-1build1_amd64.deb ...
Unpacking libexpat1:amd64 (2.2.9-1build1) ...
Selecting previously unselected package python3.8-minimal.
Preparing to unpack .../python3.8-minimal_3.8.5-1~20.04_amd64.deb ...
Unpacking python3.8-minimal (3.8.5-1~20.04) ...
Setting up libssl1.1:amd64 (1.1.1f-1ubuntu2) ...
debconf: unable to initialize frontend: Dialog
debconf: (TERM is not set, so the dialog frontend is not usable.)
debconf: falling back to frontend: Readline
debconf: unable to initialize frontend: Readline
debconf: (Can't locate Term/ in @INC (you may need to install the Term::ReadLine module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/share/perl5/Debconf/FrontEnd/ line 7.)
debconf: falling back to frontend: Teletype
Setting up libpython3.8-minimal:amd64 (3.8.5-1~20.04) ...
Setting up libexpat1:amd64 (2.2.9-1build1) ...
Setting up python3.8-minimal (3.8.5-1~20.04) ...
Traceback (most recent call last):
  File "/usr/lib/python3.8/", line 218, in <module>
  File "/usr/lib/python3.8/", line 209, in main
    compile(filename, doraise=True)
  File "/usr/lib/python3.8/", line 172, in compile
    importlib._bootstrap_external._write_atomic(cfile, bytecode, mode)
  File "<frozen importlib._bootstrap_external>", line 126, in _write_atomic
PermissionError: [Errno 13] Permission denied: '/usr/lib/python3.8/__pycache__/__future__.cpython-38.pyc.140554240003856'
dpkg: error processing package python3.8-minimal (--configure):
 installed python3.8-minimal package post-installation script subprocess returned error exit status 1
Errors were encountered while processing:
E: Sub-process /usr/bin/dpkg returned an error code (1)
The command '/bin/sh -c apt update && apt install -y python3' returned a non-zero code: 100

This Dockerfile builds fine on my machine (Debian Buster). When did you pull the ubuntu:20.04 image? Maybe you should update it?
To get rid of the “apt does not have a stable CLI interface.” warnings you could use apt-get, but I don’t think this is related to your error.

sudo apt-get update –fix-missing. and.
sudo dpkg –configure -a. and.
sudo apt-get install -f. the problem of a broken package still exist the solution is to edit the dpkg status file manually. …
Unlock the dpkg – (message /var/lib/dpkg/lock)
sudo fuser -vki /var/lib/dpkg/lock.
sudo dpkg –configure -a. For 12.04 and newer: