Basic linux
& Docker

Lecture 20

Dr. Colin Rundel

Duke VCM



vcm.duke.edu

Getting Started

Connecting

rundel@tbBook [~]$ ssh cr173@vcm-47003.vm.duke.edu
The authenticity of host 'vcm-47003.vm.duke.edu (67.159.69.176)' can't be established.
ED25519 key fingerprint is SHA256:fSZfURPpnL4M+0bWv6S3jMYtalAeKZWSLH6DR+sxOe0.
This key is not known by any other names.
Are you sure you want to continue connecting (yes/no/[fingerprint])? 
Warning: Permanently added 'vcm-47003.vm.duke.edu' (ED25519) to the list of known hosts.
cr173@vcm-47003.vm.duke.edu's password:
Welcome to Ubuntu 24.04.2 LTS (GNU/Linux 6.8.0-56-generic x86_64)

 * Documentation:  https://help.ubuntu.com
 * Management:     https://landscape.canonical.com
 * Support:        https://ubuntu.com/pro

 System information as of Thu Mar 27 10:11:09 AM EDT 2025

  System load:    0.55              Processes:             193
  Usage of /home: 2.1% of 17.93GB   Users logged in:       0
  Memory usage:   18%               IPv4 address for eth0: 67.159.69.176
  Swap usage:     0%

 * Strictly confined Kubernetes makes edge and IoT secure. Learn how MicroK8s
   just raised the bar for easy, resilient and secure K8s cluster deployment.

   https://ubuntu.com/engage/secure-kubernetes-at-the-edge

Expanded Security Maintenance for Applications is enabled.

0 updates can be applied immediately.



The programs included with the Ubuntu system are free software;
the exact distribution terms for each program are described in the
individual files in /usr/share/doc/*/copyright.

Ubuntu comes with ABSOLUTELY NO WARRANTY, to the extent permitted by
applicable law.

Determining Distribution

cr173@vcm-47003:~$ cat /etc/os-release
PRETTY_NAME="Ubuntu 24.04.2 LTS"
NAME="Ubuntu"
VERSION_ID="24.04"
VERSION="24.04.2 LTS (Noble Numbat)"
VERSION_CODENAME=noble
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=noble
LOGO=ubuntu-logo
cr173@germain [~]$ cat /etc/os-release
NAME="Fedora Linux"
VERSION="40 (Server Edition)"
ID=fedora
VERSION_ID=40
VERSION_CODENAME=""
PLATFORM_ID="platform:f40"
PRETTY_NAME="Fedora Linux 40 (Server Edition)"
ANSI_COLOR="0;38;2;60;110;180"
LOGO=fedora-logo-icon
CPE_NAME="cpe:/o:fedoraproject:fedora:40"
HOME_URL="https://fedoraproject.org/"
DOCUMENTATION_URL="https://docs.fedoraproject.org/en-US/fedora/f40/system-administrators-guide/"
SUPPORT_URL="https://ask.fedoraproject.org/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Fedora"
REDHAT_BUGZILLA_PRODUCT_VERSION=40
REDHAT_SUPPORT_PRODUCT="Fedora"
REDHAT_SUPPORT_PRODUCT_VERSION=40
SUPPORT_END=2025-05-13
VARIANT="Server Edition"
VARIANT_ID=server

System Details

Filesystem Hierarchy Standard

cr173@vcm-47003:~$ tree -d -L 1 /
/
├── bin -> usr/bin
├── bin.usr-is-merged
├── boot
├── cdrom
├── dev
├── etc
├── home
├── lib -> usr/lib
├── lib64 -> usr/lib64
├── lib.usr-is-merged
├── media
├── mnt
├── opt
├── proc
├── root
├── run
├── sbin -> usr/sbin
├── sbin.usr-is-merged
├── snap
├── srv
├── sys
├── tmp
├── usr
└── var

25 directories
cr173@algebra2 [~]$ tree -d -L 1 /usr
/usr
├── bin
├── games
├── include
├── lib
├── lib64
├── libexec
├── local
├── sbin
├── share
└── src

11 directories




Some common folders:

  • /bin/ & /usr/bin/ - executeables

  • /etc/ - configuration files

  • /lib*/ & /usr/lib*/ - Static and shared libraries

  • /usr/include/ - header files

  • /home/ - home directories

  • /var/ - logs

  • /tmp/ - temporary files

Installing packages with apt (Ubuntu, Debian, etc.)

Update the package list

cr173@vcm-47003:~$ apt update
Reading package lists... Done
E: Could not open lock file /var/lib/apt/lists/lock - open (13: Permission denied)
E: Unable to lock directory /var/lib/apt/lists/
W: Problem unlinking the file /var/cache/apt/pkgcache.bin - RemoveCaches (13: Permission denied)
W: Problem unlinking the file /var/cache/apt/srcpkgcache.bin - RemoveCaches (13: Permission denied)```

XKCD 149 - Sandwich

Update the package list

cr173@vcm-47003:~$ sudo apt update
[sudo] password for cr173: 
Hit:1 http://archive.linux.duke.edu/ubuntu focal InRelease
Get:2 http://archive.linux.duke.edu/ubuntu focal-updates InRelease [114 kB]
Hit:3 https://falcon-dl.oit.duke.edu/ubuntu focal InRelease
Get:4 http://archive.linux.duke.edu/ubuntu focal-backports InRelease [108 kB]
Get:5 http://archive.linux.duke.edu/ubuntu focal-security InRelease [114 kB]
Get:6 http://archive.linux.duke.edu/ubuntu focal-updates/main amd64 Packages [1,711 kB]
Get:7 http://archive.linux.duke.edu/ubuntu focal-updates/main i386 Packages [628 kB]
Get:8 http://archive.linux.duke.edu/ubuntu focal-updates/main Translation-en [320 kB]
Get:9 http://archive.linux.duke.edu/ubuntu focal-updates/restricted amd64 Packages [917 kB]
Get:10 http://archive.linux.duke.edu/ubuntu focal-updates/restricted Translation-en [131 kB]
Get:11 http://archive.linux.duke.edu/ubuntu focal-updates/universe amd64 Packages [916 kB]
Get:12 http://archive.linux.duke.edu/ubuntu focal-updates/universe i386 Packages [676 kB]
Get:13 http://archive.linux.duke.edu/ubuntu focal-updates/universe Translation-en [204 kB]
Get:14 http://archive.linux.duke.edu/ubuntu focal-updates/universe amd64 c-n-f Metadata [20.4 kB]
Get:15 http://archive.linux.duke.edu/ubuntu focal-security/main i386 Packages [416 kB]
Get:16 http://archive.linux.duke.edu/ubuntu focal-security/main amd64 Packages [1,383 kB]
Get:17 http://archive.linux.duke.edu/ubuntu focal-security/main Translation-en [239 kB]
Get:18 http://archive.linux.duke.edu/ubuntu focal-security/restricted amd64 Packages [859 kB]
Get:19 http://archive.linux.duke.edu/ubuntu focal-security/restricted Translation-en [122 kB]
Get:20 http://archive.linux.duke.edu/ubuntu focal-security/universe i386 Packages [547 kB]
Get:21 http://archive.linux.duke.edu/ubuntu focal-security/universe amd64 Packages [696 kB]
Get:22 http://archive.linux.duke.edu/ubuntu focal-security/universe Translation-en [122 kB]
Get:23 http://archive.linux.duke.edu/ubuntu focal-security/universe amd64 c-n-f Metadata [14.1 kB]
Fetched 10.3 MB in 3s (4,100 kB/s)
Reading package lists... Done
Building dependency tree
Reading state information... Done
1 package can be upgraded. Run 'apt list --upgradable' to see it.

Installing R

cr173@vcm-47003:~$ sudo apt install r-base
[sudo] password for cr173:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
  build-essential bzip2-doc cpp cpp-9 dpkg-dev fakeroot fontconfig fontconfig-config fonts-dejavu-core g++ g++-9 gcc gcc-9 gcc-9-base gfortran gfortran-9 icu-devtools
  libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libasan5 libatomic1 libauthen-sasl-perl libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0
  libdata-dump-perl libdatrie1 libdpkg-perl libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libencode-locale-perl libfakeroot libfile-basedir-perl
  libfile-desktopentry-perl libfile-fcntllock-perl libfile-listing-perl libfile-mimeinfo-perl libfont-afm-perl libfontconfig1 libfontenc1 libgcc-9-dev libgfortran-9-dev
  libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libharfbuzz0b libhtml-form-perl libhtml-format-perl
  libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6
  libicu-dev libio-html-perl libio-socket-ssl-perl libio-stringy-perl libipc-system-simple-perl libisl22 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
  libjpeg8-dev liblapack-dev liblapack3 libllvm12 liblsan0 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzma-dev libmailtools-perl libmpc3 libmpfr6 libncurses-dev
  libncurses5-dev libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1
  libpciaccess0 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpixman-1-0 libpng-dev libpng-tools libquadmath0
  libreadline-dev libsensors-config libsensors5 libsm6 libstdc++-9-dev libtcl8.6 libthai-data libthai0 libtie-ixhash-perl libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl
  libtsan0 libubsan1 liburi-perl libvulkan1 libwayland-client0 libwebp6 libwww-perl libwww-robotrules-perl libx11-protocol-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0
  libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxfixes3 libxft2 libxi6
  libxinerama1 libxkbfile1 libxml-parser-perl libxml-twig-perl libxml-xpathengine-perl libxmu6 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxv1
  libxxf86dga1 libxxf86vm1 make mesa-vulkan-drivers perl-openssl-defaults pkg-config r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools
  r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html
  r-recommended unzip x11-common x11-utils x11-xserver-utils xdg-utils zip zlib1g-dev
Suggested packages:
  cpp-doc gcc-9-locales debian-keyring g++-multilib g++-9-multilib gcc-9-doc gcc-multilib autoconf automake libtool flex bison gdb gcc-doc gcc-9-multilib gfortran-multilib
  gfortran-doc gfortran-9-multilib gfortran-9-doc libcoarrays-dev libdigest-hmac-perl libgssapi-perl liblapack-doc bzr icu-doc libcrypt-ssleay-perl liblzma-doc ncurses-doc
  readline-doc lm-sensors libstdc++-9-doc tcl8.6 tk8.6 libauthen-ntlm-perl libunicode-map8-perl libunicode-string-perl xml-twig-tools make-doc elpa-ess r-doc-info | r-doc-pdf
  r-mathlib texlive-base texlive-latex-base texlive-plain-generic texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texlive-latex-recommended texlive-latex-extra
  texinfo mozilla | www-browser mesa-utils nickle cairo-5c xorg-docs-core
The following NEW packages will be installed:
  build-essential bzip2-doc cpp cpp-9 dpkg-dev fakeroot fontconfig fontconfig-config fonts-dejavu-core g++ g++-9 gcc gcc-9 gcc-9-base gfortran gfortran-9 icu-devtools
  libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libasan5 libatomic1 libauthen-sasl-perl libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0
  libdata-dump-perl libdatrie1 libdpkg-perl libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libencode-locale-perl libfakeroot libfile-basedir-perl
  libfile-desktopentry-perl libfile-fcntllock-perl libfile-listing-perl libfile-mimeinfo-perl libfont-afm-perl libfontconfig1 libfontenc1 libgcc-9-dev libgfortran-9-dev
  libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libharfbuzz0b libhtml-form-perl libhtml-format-perl
  libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6
  libicu-dev libio-html-perl libio-socket-ssl-perl libio-stringy-perl libipc-system-simple-perl libisl22 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
  libjpeg8-dev liblapack-dev liblapack3 libllvm12 liblsan0 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzma-dev libmailtools-perl libmpc3 libmpfr6 libncurses-dev
  libncurses5-dev libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1
  libpciaccess0 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpixman-1-0 libpng-dev libpng-tools libquadmath0
  libreadline-dev libsensors-config libsensors5 libsm6 libstdc++-9-dev libtcl8.6 libthai-data libthai0 libtie-ixhash-perl libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl
  libtsan0 libubsan1 liburi-perl libvulkan1 libwayland-client0 libwebp6 libwww-perl libwww-robotrules-perl libx11-protocol-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0
  libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxfixes3 libxft2 libxi6
  libxinerama1 libxkbfile1 libxml-parser-perl libxml-twig-perl libxml-xpathengine-perl libxmu6 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxv1
  libxxf86dga1 libxxf86vm1 make mesa-vulkan-drivers perl-openssl-defaults pkg-config r-base r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster
  r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
  r-doc-html r-recommended unzip x11-common x11-utils x11-xserver-utils xdg-utils zip zlib1g-dev
0 upgraded, 202 newly installed, 0 to remove and 0 not upgraded.
Need to get 158 MB of archives.
After this operation, 914 MB of additional disk space will be used.
Do you want to continue? [Y/n]

Removing R

cr173@vcm-47003:~$ sudo apt remove r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
  fontconfig fontconfig-config fonts-dejavu-core gfortran gfortran-9 icu-devtools libblas-dev libblas3 libbz2-dev libcairo2 libdatrie1 libdrm-amdgpu1 libdrm-intel1
  libdrm-nouveau2 libdrm-radeon1 libfile-basedir-perl libfile-desktopentry-perl libfile-mimeinfo-perl libfontconfig1 libfontenc1 libgfortran-9-dev libgfortran5 libgl1
  libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgraphite2-3 libharfbuzz0b libice6 libicu-dev libio-stringy-perl libipc-system-simple-perl libjbig0 libjpeg-dev
  libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libllvm12 liblzma-dev libncurses-dev libncurses5-dev libnet-dbus-perl libpango-1.0-0
  libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3
  libpcrecpp0v5 libpixman-1-0 libpng-dev libpng-tools libreadline-dev libsensors-config libsensors5 libsm6 libtcl8.6 libthai-data libthai0 libtie-ixhash-perl libtiff5 libtk8.6
  libvulkan1 libwayland-client0 libwebp6 libx11-protocol-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0
  libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxfixes3 libxft2 libxi6 libxinerama1 libxkbfile1 libxml-parser-perl libxml-twig-perl
  libxml-xpathengine-perl libxmu6 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 mesa-vulkan-drivers pkg-config r-base-core
  r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
  r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended unzip x11-common x11-utils x11-xserver-utils xdg-utils zip zlib1g-dev
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
  r-base
0 upgraded, 0 newly installed, 1 to remove and 1 not upgraded.
After this operation, 62.5 kB disk space will be freed.

and all of its dependencies

cr173@vcm-47003:~$ sudo apt autoremove
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
  fontconfig fontconfig-config fonts-dejavu-core gfortran gfortran-9 icu-devtools libblas-dev libblas3 libbz2-dev libcairo2 libdatrie1 libdrm-amdgpu1 libdrm-intel1
  libdrm-nouveau2 libdrm-radeon1 libfile-basedir-perl libfile-desktopentry-perl libfile-mimeinfo-perl libfontconfig1 libfontenc1 libgfortran-9-dev libgfortran5 libgl1
  libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgraphite2-3 libharfbuzz0b libice6 libicu-dev libio-stringy-perl libipc-system-simple-perl libjbig0 libjpeg-dev
  libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libllvm12 liblzma-dev libncurses-dev libncurses5-dev libnet-dbus-perl libpango-1.0-0
  libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3
  libpcrecpp0v5 libpixman-1-0 libpng-dev libpng-tools libreadline-dev libsensors-config libsensors5 libsm6 libtcl8.6 libthai-data libthai0 libtie-ixhash-perl libtiff5 libtk8.6
  libvulkan1 libwayland-client0 libwebp6 libx11-protocol-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0
  libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxfixes3 libxft2 libxi6 libxinerama1 libxkbfile1 libxml-parser-perl libxml-twig-perl
  libxml-xpathengine-perl libxmu6 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 mesa-vulkan-drivers pkg-config r-base-core
  r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
  r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended unzip x11-common x11-utils x11-xserver-utils xdg-utils zip zlib1g-dev
0 upgraded, 0 newly installed, 140 to remove and 1 not upgraded.
After this operation, 749 MB disk space will be freed.
Do you want to continue? [Y/n]

Updating & Upgrading

cr173@vcm-47003:~$ sudo apt update
Hit:1 http://archive.linux.duke.edu/ubuntu focal InRelease
Hit:2 http://archive.linux.duke.edu/ubuntu focal-updates InRelease
Hit:3 http://archive.linux.duke.edu/ubuntu focal-backports InRelease
Hit:4 http://archive.linux.duke.edu/ubuntu focal-security InRelease
Hit:5 https://falcon-dl.oit.duke.edu/ubuntu focal InRelease
Reading package lists... Done
Building dependency tree
Reading state information... Done
1 package can be upgraded. Run 'apt list --upgradable' to see it.
cr173@vcm-47003:~$ sudo apt upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages will be upgraded:
  libfribidi0
1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1 standard security update
Need to get 24.2 kB of archives.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n]

Aside - Conflicts

...
update-initramfs: deferring update (trigger activated)
amd64-microcode: microcode will be updated at next boot
Setting up intel-microcode (3.20180807a.0ubuntu0.18.04.1) ...
update-initramfs: deferring update (trigger activated)
intel-microcode: microcode will be updated at next boot
Setting up kmod (24-1ubuntu3.1) ...

*Configuration file '/etc/modprobe.d/blacklist.conf'
* ==> Modified (by you or by a script) since installation.
* ==> Package distributor has shipped an updated version.
*   What would you like to do about it ?  Your options are:
*    Y or I  : install the package maintainer's version
*    N or O  : keep your currently-installed version
*      D     : show the differences between the versions
*      Z     : start a shell to examine the situation
* The default action is to keep your current version.
**** blacklist.conf (Y/I/N/O/D/Z) [default=N] ?
Setting up initramfs-tools-core (0.130ubuntu3.6) ...
Setting up linux-headers-4.15.0-43-generic (4.15.0-43.46) ...
Setting up initramfs-tools (0.130ubuntu3.6) ...

...

Package Details

cr173@vcm-47003:~$ apt show r-base
Package: r-base
Version: 3.6.3-2
Priority: optional
Section: universe/math
Origin: Ubuntu
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Original-Maintainer: Dirk Eddelbuettel <edd@debian.org>
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 62.5 kB
Depends: r-base-core (>= 3.6.3-2), r-recommended (= 3.6.3-2)
Recommends: r-base-html, r-doc-html
Suggests: elpa-ess, r-doc-info | r-doc-pdf
Homepage: http://www.r-project.org/
Download-Size: 9,308 B
APT-Manual-Installed: yes
APT-Sources: http://archive.linux.duke.edu/ubuntu focal/universe amd64 Packages
Description: GNU R statistical computation and graphics system
 R is a system for statistical computation and graphics.  It consists
 of a language plus a run-time environment with graphics, a debugger,
 access to certain system functions, and the ability to run programs
 stored in script files.
...

Package Contents

To list the files installed by a package,

cr173@vcm-47003:~$ dpkg -L r-base
/.
/usr
/usr/share
/usr/share/doc
/usr/share/doc/r-base
/usr/share/doc/r-base/README.Debian
/usr/share/doc/r-base/copyright
/usr/share/doc/r-base/changelog.Debian.gz


or if you want to find which package created a file,

cr173@vcm-47003:~$ dpkg -S /usr/bin/R
r-base-core: /usr/bin/R

Package Manager Comparison

Ubuntu / Debian RHEL Fedora Requires root
Install apt install yum install dnf install Yes
Install Local dpkg -i pkg.deb yum install pkg.rpm dnf install pkg.rpm Yes
Remove apt remove yum remove dnf remove Yes
Update apt update yum check-update dnf check-update Yes
Upgrade apt upgrade
apt full-upgrade		 yum upgrade dnf upgrade Yes
Clean Deps. apt autoremove yum autoremove dnf autoremove Yes
Reinstall apt install --reinstall yum reinstall dnf reinstall Yes
Details. apt show yum info dnf info No
Dependencies apt show yum deplist dnf repoquery
--requires		 No
Pkg -> Files dpkg -L rpm -qf rpm -qf No
Files -> Pkg dpkg -S rpm -ql rpm -ql or
dnf repoquery -l		 No

A bit about libraries

System libraries

These are shared common components that are used by a variety of software on a linux system. For the most part they are a collection of compiled code (typically C / C++) that are stored in a single file.

  • Allows for code reuse

  • Allows for multiple (concurrent) versions

  • Avoids reinventing the wheel

  • Installed in /lib, /usr/lib, /usr/local/lib, etc.

  • Two flavors: static (.a) and dynamic / shared (.so)

libcurl

cr173@vcm-47003:~$ ls -la /usr/lib/x86_64-linux-gnu/libcurl*
-rw-r--r-- 1 root root 1057632 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl.a
lrwxrwxrwx 1 root root      19 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.3 -> libcurl-gnutls.so.4
lrwxrwxrwx 1 root root      23 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4 -> libcurl-gnutls.so.4.5.0
-rw-r--r-- 1 root root  510408 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4.5.0
-rw-r--r-- 1 root root     951 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl.la
lrwxrwxrwx 1 root root      16 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl.so -> libcurl.so.4.5.0
lrwxrwxrwx 1 root root      16 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl.so.4 -> libcurl.so.4.5.0
-rw-r--r-- 1 root root  518600 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl.so.4.5.0

Getting what you want

The following is a basic heuristic of library package naming schemes for the two primary distro families, there are exceptions and edge cases.

These are the names that would then be used with something like apt install or yum install respectively.


Debian Redhat
Dynamic library (.so) lib{name} {name}
Headers lib{name}-dev {name}-devel
Static library (.a) lib{name}-dev {name}-static
Documentation lib{name}-doc {name}-devel

Troubleshooting dynamic libraries

cr173@vcm-47003:~$ ldd /usr/lib/x86_64-linux-gnu/libcurl.so
    linux-vdso.so.1 (0x00007ffd98176000)
    libnghttp2.so.14 => /usr/lib/x86_64-linux-gnu/libnghttp2.so.14 (0x00007f1e3dc60000)
    libidn2.so.0 => /usr/lib/x86_64-linux-gnu/libidn2.so.0 (0x00007f1e3da43000)
    librtmp.so.1 => /usr/lib/x86_64-linux-gnu/librtmp.so.1 (0x00007f1e3d827000)
    libpsl.so.5 => /usr/lib/x86_64-linux-gnu/libpsl.so.5 (0x00007f1e3d619000)
    libssl.so.1.1 => /usr/lib/x86_64-linux-gnu/libssl.so.1.1 (0x00007f1e3d3af000)
    libcrypto.so.1.1 => /usr/lib/x86_64-linux-gnu/libcrypto.so.1.1 (0x00007f1e3cf37000)
    libgssapi_krb5.so.2 => /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x00007f1e3ccec000)
    libldap_r-2.4.so.2 => /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2 (0x00007f1e3ca9a000)
    liblber-2.4.so.2 => /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2 (0x00007f1e3c88c000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f1e3c66f000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f1e3c450000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f1e3c05f000)
    libunistring.so.2 => /usr/lib/x86_64-linux-gnu/libunistring.so.2 (0x00007f1e3bce1000)
    libgnutls.so.30 => /usr/lib/x86_64-linux-gnu/libgnutls.so.30 (0x00007f1e3b97c000)
    libhogweed.so.4 => /usr/lib/x86_64-linux-gnu/libhogweed.so.4 (0x00007f1e3b748000)
    libnettle.so.6 => /usr/lib/x86_64-linux-gnu/libnettle.so.6 (0x00007f1e3b512000)
    libgmp.so.10 => /usr/lib/x86_64-linux-gnu/libgmp.so.10 (0x00007f1e3b291000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f1e3b08d000)
    libkrb5.so.3 => /usr/lib/x86_64-linux-gnu/libkrb5.so.3 (0x00007f1e3adb7000)
    libk5crypto.so.3 => /usr/lib/x86_64-linux-gnu/libk5crypto.so.3 (0x00007f1e3ab85000)
    libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x00007f1e3a981000)
    libkrb5support.so.0 => /usr/lib/x86_64-linux-gnu/libkrb5support.so.0 (0x00007f1e3a776000)
    libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007f1e3a55b000)
    libsasl2.so.2 => /usr/lib/x86_64-linux-gnu/libsasl2.so.2 (0x00007f1e3a340000)
    libgssapi.so.3 => /usr/lib/x86_64-linux-gnu/libgssapi.so.3 (0x00007f1e3a0ff000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f1e3e104000)
    libp11-kit.so.0 => /usr/lib/x86_64-linux-gnu/libp11-kit.so.0 (0x00007f1e39dd0000)
    libtasn1.so.6 => /usr/lib/x86_64-linux-gnu/libtasn1.so.6 (0x00007f1e39bbd000)
    libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 (0x00007f1e399b9000)
    libheimntlm.so.0 => /usr/lib/x86_64-linux-gnu/libheimntlm.so.0 (0x00007f1e397b0000)
    libkrb5.so.26 => /usr/lib/x86_64-linux-gnu/libkrb5.so.26 (0x00007f1e39523000)
    libasn1.so.8 => /usr/lib/x86_64-linux-gnu/libasn1.so.8 (0x00007f1e39281000)
    libhcrypto.so.4 => /usr/lib/x86_64-linux-gnu/libhcrypto.so.4 (0x00007f1e3904b000)
    libroken.so.18 => /usr/lib/x86_64-linux-gnu/libroken.so.18 (0x00007f1e38e35000)
    libffi.so.6 => /usr/lib/x86_64-linux-gnu/libffi.so.6 (0x00007f1e38c2d000)
    libwind.so.0 => /usr/lib/x86_64-linux-gnu/libwind.so.0 (0x00007f1e38a04000)
    libheimbase.so.1 => /usr/lib/x86_64-linux-gnu/libheimbase.so.1 (0x00007f1e387f5000)
    libhx509.so.5 => /usr/lib/x86_64-linux-gnu/libhx509.so.5 (0x00007f1e385ab000)
    libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 (0x00007f1e382a2000)
    libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1 (0x00007f1e3806a000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f1e37ccc000)

Python management

cr173@vcm-47003:~$ pip install torch
Command 'pip' not found, but can be installed with:

apt install python3-pip
Please ask your administrator.
cr173@vcm-47003:~$ sudo apt install python3-pip
[sudo] password for cr173:
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
The following additional packages will be installed:
  build-essential bzip2 cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu dpkg-dev fakeroot g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13 gcc-13-base
  gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu javascript-common libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libasan8 libatomic1 libcc1-0 libdpkg-perl
  libexpat1-dev libfakeroot libfile-fcntllock-perl libgcc-13-dev libgomp1 libhwasan0 libisl23 libitm1 libjs-jquery libjs-sphinxdoc libjs-underscore liblsan0 libmpc3 libpython3-dev
  libpython3.12-dev libquadmath0 libstdc++-13-dev libtsan2 libubsan1 lto-disabled-list make python3-dev python3-wheel python3.12-dev zlib1g-dev
Suggested packages:
  bzip2-doc cpp-doc gcc-13-locales cpp-13-doc debian-keyring g++-multilib g++-13-multilib gcc-13-doc gcc-multilib autoconf automake libtool flex bison gdb gcc-doc gcc-13-multilib
  gdb-x86-64-linux-gnu apache2 | lighttpd | httpd bzr libstdc++-13-doc make-doc
The following NEW packages will be installed:
  build-essential bzip2 cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu dpkg-dev fakeroot g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13 gcc-13-base
  gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu javascript-common libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libasan8 libatomic1 libcc1-0 libdpkg-perl
  libexpat1-dev libfakeroot libfile-fcntllock-perl libgcc-13-dev libgomp1 libhwasan0 libisl23 libitm1 libjs-jquery libjs-sphinxdoc libjs-underscore liblsan0 libmpc3 libpython3-dev
  libpython3.12-dev libquadmath0 libstdc++-13-dev libtsan2 libubsan1 lto-disabled-list make python3-dev python3-pip python3-wheel python3.12-dev zlib1g-dev
0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded.
Need to get 72.6 MB of archives.
After this operation, 251 MB of additional disk space will be used.
Do you want to continue? [Y/n]

Package manager vs pip

cr173@vcm-47003:~$ sudo apt install python3-numpy
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
The following additional packages will be installed:
  libblas3 libgfortran5 liblapack3
Suggested packages:
  gfortran python3-pytest
The following NEW packages will be installed:
  libblas3 libgfortran5 liblapack3 python3-numpy
0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
Need to get 8,238 kB of archives.
After this operation, 35.2 MB of additional disk space will be used.
Do you want to continue? [Y/n]

pip install & PEP 668

cr173@vcm-47003:~$ sudo pip install numpy --upgrade
sudo pip install numpy --upgrade
error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try apt install
    python3-xyz, where xyz is the package you are trying to
    install.
    
    If you wish to install a non-Debian-packaged Python package,
    create a virtual environment using python3 -m venv path/to/venv.
    Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make
    sure you have python3-full installed.
    
    If you wish to install a non-Debian packaged Python application,
    it may be easiest to use pipx install xyz, which will manage a
    virtual environment for you. Make sure you have pipx installed.
    
    See /usr/share/doc/python3.12/README.venv for more information.

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.
cr173@vcm-47003:~$ sudo pip install numpy --upgrade --break-system-packages --ignore-installed
Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (1.26.4)
Collecting numpy
  Downloading numpy-2.2.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.0/62.0 kB 2.5 MB/s eta 0:00:00
Downloading numpy-2.2.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.1/16.1 MB 116.8 MB/s eta 0:00:00
Installing collected packages: numpy
Successfully installed numpy-2.2.4
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv

Outdated python libraries

cr173@vcm-47003:~$ sudo pip list --outdated
Package          Version        Latest      Type
---------------- -------------- ----------- -----
ansible          9.2.0          11.4.0      wheel
ansible-core     2.16.3         2.18.4      wheel
apache-libcloud  3.4.1          3.8.0       wheel
argcomplete      3.1.4          3.6.1       wheel
attrs            23.2.0         25.3.0      wheel
Automat          22.10.0        24.8.1      wheel
Babel            2.10.3         2.17.0      wheel
bcrypt           3.2.2          4.3.0       wheel
blinker          1.7.0          1.9.0       wheel
boto3            1.34.46        1.37.22     wheel
botocore         1.34.46        1.37.22     wheel
certifi          2023.11.17     2025.1.31   wheel
click            8.1.6          8.1.8       wheel
configobj        5.0.8          5.0.9       wheel
cryptography     41.0.7         44.0.2      wheel
dbus-python      1.3.2          1.4.0       sdist
dnspython        2.6.1          2.7.0       wheel
httplib2         0.20.4         0.22.0      wheel
idna             3.6            3.10        wheel
incremental      22.10.0        24.7.2      wheel
Jinja2           3.1.2          3.1.6       wheel
jsonpointer      2.0            3.0.0       wheel
jsonschema       4.10.3         4.23.0      wheel
launchpadlib     1.11.0         2.1.0       wheel
lazr.uri         1.0.6          1.0.7       wheel
MarkupSafe       2.1.5          3.0.2       wheel
netaddr          0.8.0          1.3.0       wheel
numpy            1.26.4         2.2.4       wheel
packaging        24.0           24.2        wheel
pip              24.0           25.0.1      wheel
pyasn1           0.4.8          0.6.1       wheel
pyasn1-modules   0.2.8          0.4.1       wheel
Pygments         2.17.2         2.19.1      wheel
PyGObject        3.48.2         3.52.3      sdist
PyJWT            2.7.0          2.10.1      wheel
pykerberos       1.1.14         1.2.4       sdist
pyOpenSSL        23.2.0         25.0.0      wheel
pyparsing        3.1.1          3.2.3       wheel
python-dateutil  2.8.2          2.9.0.post0 wheel
python-debian    0.1.49+ubuntu2 1.0.1       wheel
pytz             2024.1         2025.2      wheel
pywinrm          0.4.3          0.5.0       wheel
PyYAML           6.0.1          6.0.2       wheel
requests         2.31.0         2.32.3      wheel
requests-ntlm    1.1.0          1.3.0       wheel
resolvelib       1.0.1          1.1.0       wheel
rich             13.7.1         13.9.4      wheel
s3transfer       0.10.1         0.11.4      wheel
service-identity 24.1.0         24.2.0      wheel
setuptools       68.1.2         78.1.0      wheel
simplejson       3.19.2         3.20.1      wheel
six              1.16.0         1.17.0      wheel
Twisted          24.3.0         24.11.0     wheel
urllib3          2.0.7          2.3.0       wheel
wadllib          1.3.6          2.0.0       wheel
wheel            0.42.0         0.45.1      wheel
xmltodict        0.13.0         0.14.2      wheel
zope.interface   6.1            7.2         wheel

Docker

Docker

Docker can package an application and its dependencies in a virtual container that can run on any Linux, Windows, or macOS computer. This enables the application to run in a variety of locations, such as on-premises, in the public or private cloud. When running on Linux, Docker uses the resource isolation features of the Linux kernel (such as cgroups and kernel namespaces) and a union-capable file system to allow containers to run within a single Linux instance, avoiding the overhead of starting and maintaining virtual machines.

From Wikipedia

Installation - Ubuntu / Debian

# Remove system packages
sudo apt-get remove docker docker-engine docker.io containerd runc

# Utililty Packages
sudo apt-get update
sudo apt-get install \
   ca-certificates \
   curl \
   gnupg \
   lsb-release

# Add apt repo signing key
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg

# Add apt repo
echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu \
  $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
   
# Install Docker
sudo apt-get update
sudo apt-get install docker-ce docker-ce-cli containerd.io

Troubleshooting - daemon

$ sudo docker run hello-world
docker: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?.
See 'docker run --help'.


This occurs when the docker daemon (service) is not running, this can be fixed by enabling & starting the docker service / daemon,


# Make sure the daemon runs automatically in the future
sudo systemctl enable docker
Synchronizing state of docker.service with SysV service script with /usr/lib/systemd/systemd-sysv-install.
Executing: /usr/lib/systemd/systemd-sysv-install enable docker
# Start the daemon
sudo systemctl start docker

Success

sudo docker run hello-world
Unable to find image 'hello-world:latest' locally
latest: Pulling from library/hello-world
1b930d010525: Pull complete 
Digest: sha256:2557e3c07ed1e38f26e389462d03ed943586f744621577a99efb77324b0fe535
Status: Downloaded newer image for hello-world:latest

Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (amd64)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://hub.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/get-started/

Troubleshooting - permissions

docker run hello-world
docker: Got permission denied while trying to connect to the Docker daemon socket at 
unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.39/containers/create: 
dial unix /var/run/docker.sock: connect: permission denied.
See 'docker run --help'.

You must either be root or be a member of the docker group to use docker. Currently, your VM may or may not have a docker group and your account is likely not a member. If you get tired of typing sudo + your password there is an easy fix,

# Make sure the docker group exists
sudo groupadd docker

# Add your user to the docker group
sudo usermod -aG docker $USER

# Check memberships
groups
# If docker is not listed you should log out and log back in

Success

docker run hello-world
Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (amd64)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://hub.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/get-started/

Getting Started

Getting images

docker pull ubuntu
Using default tag: latest
latest: Pulling from library/ubuntu
5a7813e071bf: Pull complete 
Digest: sha256:72297848456d5d37d1262630108ab308d3e9ec7ed1c3286a32fe09856619a782
Status: Downloaded newer image for ubuntu:latest
docker.io/library/ubuntu:latest


docker images
REPOSITORY    TAG       IMAGE ID       CREATED        SIZE
ubuntu        latest    a04dc4851cbc   8 weeks ago    78.1MB
hello-world   latest    74cc54e27dc4   2 months ago   10.1kB

Tags (Versions)

docker pull ubuntu:24.10
24.10: Pulling from library/ubuntu
31734b193a81: Pull complete 
Digest: sha256:102bc1874fdb136fc2d218473f03cf84135cb7496fefdb9c026c0f553cfe1b6d
Status: Downloaded newer image for ubuntu:24.10
docker.io/library/ubuntu:24.10
docker pull ubuntu:24.04
24.04: Pulling from library/ubuntu
Digest: sha256:72297848456d5d37d1262630108ab308d3e9ec7ed1c3286a32fe09856619a782
Status: Downloaded newer image for ubuntu:24.04
docker.io/library/ubuntu:24.04
docker images
REPOSITORY    TAG       IMAGE ID       CREATED        SIZE
ubuntu        24.04     a04dc4851cbc   8 weeks ago    78.1MB
ubuntu        latest    a04dc4851cbc   8 weeks ago    78.1MB
hello-world   latest    74cc54e27dc4   2 months ago   10.1kB
ubuntu        24.10     e40b6e31bd8c   4 months ago   80.1MB

Other sources

DockerHub is not the only source of images - their are many other possible hosts and all you need to provide is a URL along with the image name.

docker pull ghcr.io/sta663-sp25/sta663-base:latest
latest: Pulling from sta663-sp25/sta663-base
5a7813e071bf: Already exists 
8b4eecc45940: Pull complete 
8a0564787037: Pull complete 
3696d23a471e: Pull complete 
23672a6cfd33: Pull complete 
942334ec7964: Pull complete 
423b2646039f: Pull complete 
68b5b1f45ce3: Pull complete 
4f4fb700ef54: Pull complete 
2b80b363e49e: Pull complete 
5e022bd8982c: Pull complete 
7ebaab8841b3: Pull complete 
5af20e6ba13b: Pull complete 
824e38cc86cc: Pull complete 
b12348c1e7d6: Pull complete 
5dd53c23776c: Pull complete 
196321479ae8: Pull complete 
6da941aca655: Pull complete 
17404b9cf4a9: Pull complete 
Digest: sha256:22b2c0de05a032aae1f7a5c76bc711836fed7c2792758b1f713875fa42804871
Status: Downloaded newer image for ghcr.io/sta663-sp25/sta663-base:latest
ghcr.io/sta663-sp25/sta663-base:latest

docker images
REPOSITORY                        TAG       IMAGE ID       CREATED        SIZE
ghcr.io/sta663-sp25/sta663-base   latest    0b725e0ad9c9   3 weeks ago    7.75GB
ubuntu                            24.04     a04dc4851cbc   8 weeks ago    78.1MB
ubuntu                            latest    a04dc4851cbc   8 weeks ago    78.1MB
hello-world                       latest    74cc54e27dc4   2 months ago   10.1kB
ubuntu                            24.10     e40b6e31bd8c   4 months ago   80.1MB

Running a container

docker run --rm ubuntu cat /etc/os-release
PRETTY_NAME="Ubuntu 24.04.1 LTS"
NAME="Ubuntu"
VERSION_ID="24.04"
VERSION="24.04.1 LTS (Noble Numbat)"
VERSION_CODENAME=noble
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=noble
LOGO=ubuntu-logo
docker run --rm ubuntu:24.10 cat /etc/os-release
PRETTY_NAME="Ubuntu 24.10"
NAME="Ubuntu"
VERSION_ID="24.10"
VERSION="24.10 (Oracular Oriole)"
VERSION_CODENAME=oracular
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=oracular
LOGO=ubuntu-logo

docker run --rm fedora:latest cat /etc/os-release
Unable to find image 'fedora:latest' locally
latest: Pulling from library/fedora
0c5a86865c5d: Pull complete 
Digest: sha256:3ec60eb34fa1a095c0c34dd37cead9fd38afb62612d43892fcf1d3425c32bc1e
Status: Downloaded newer image for fedora:latest
NAME="Fedora Linux"
VERSION="41 (Container Image)"
RELEASE_TYPE=stable
ID=fedora
VERSION_ID=41
VERSION_CODENAME=""
PLATFORM_ID="platform:f41"
PRETTY_NAME="Fedora Linux 41 (Container Image)"
ANSI_COLOR="0;38;2;60;110;180"
LOGO=fedora-logo-icon
CPE_NAME="cpe:/o:fedoraproject:fedora:41"
DEFAULT_HOSTNAME="fedora"
HOME_URL="https://fedoraproject.org/"
DOCUMENTATION_URL="https://docs.fedoraproject.org/en-US/fedora/f41/system-administrators-guide/"
SUPPORT_URL="https://ask.fedoraproject.org/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Fedora"
REDHAT_BUGZILLA_PRODUCT_VERSION=41
REDHAT_SUPPORT_PRODUCT="Fedora"
REDHAT_SUPPORT_PRODUCT_VERSION=41
SUPPORT_END=2025-05-13
VARIANT="Container Image"
VARIANT_ID=container

docker run common options


docker run [OPTIONS] IMAGE[:TAG|@DIGEST] [COMMAND] [ARG...]


Option Description
--name Give your container a name
--rm Automatically remove the container when it exits
-i -t Allow for interaction with container (STDIN & tty specifically)
-p host:cont Publish a container’s port
-v host:cont Share filesystems
-e "VAR=VAL" Define environmental variables

Other useful commands

command Description
docker pull NAME[:TAG] Pull docker image (usually from DockerHub)
docker images List docker images
docker rmi IMAGE Remove an image
docker container ls [--all] List (all) docker containers
docker rm CONTAINER Remove a container
docker stop CONTAINER Stop a running container
docker start CONTAINER Start a stopped container
docker attach CONTAINER Attach to a running container
docker exec CONTAINER CMD Runs a new command in a running container
docker commit CONTAINER REPO[:TAG] Create an image from a container
docker rename CONTAINER NAME Rename a container

rocker

+ = Rocker

The rocker project provides a collection of containers suited for different needs. find a base image to extend or images with popular software and optimized libraries pre-installed. Get the latest version or a reproducibly fixed environment.

Docker + Python

docker pull python:latest
latest: Pulling from library/python
7cd785773db4: Pull complete 
091eb8249475: Pull complete 
255774e0027b: Pull complete 
353e14e5cc47: Pull complete 
70847531e23d: Pull complete 
af0b544b1a82: Pull complete 
379f06e37dbb: Pull complete 
Digest: sha256:8c55c44b9e81d537f8404d0000b7331863d134db87c1385dd0ec7fefff656495
Status: Downloaded newer image for python:latest
docker.io/library/python:latest
docker run --rm python:latest python -V
Python 3.13.2
docker run --rm python:latest pip install numpy
Collecting numpy
  Downloading numpy-2.2.4-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Downloading numpy-2.2.4-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.1/16.1 MB 77.0 MB/s eta 0:00:00
Installing collected packages: numpy
Successfully installed numpy-2.2.4
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.

[notice] A new release of pip is available: 24.3.1 -> 25.0.1
[notice] To update, run: pip install --upgrade pip

Interactive usage

For interactive use we use the -it (or -i -t) flags,

docker run -it python:latest
Python 3.13.2 (main, Mar 18 2025, 03:30:45) [GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> 
docker run -it python:latest  bash
root@0200ab573e93:/# 


docker ps
CONTAINER ID   IMAGE     COMMAND   CREATED   STATUS    PORTS     NAMES
docker ps --all
CONTAINER ID   IMAGE           COMMAND     CREATED          STATUS                      PORTS     NAMES
fa52839a6bb0   python:latest   "bash"      4 seconds ago    Exited (0) 2 seconds ago              elated_pare
41de571bce2d   python:latest   "python3"   12 seconds ago   Exited (0) 10 seconds ago             zealous_knuth

Building a container interactively

docker run python:latest
root@e45df4642247:/# pip install numpy pandas seaborn
Collecting numpy
  Downloading numpy-2.2.4-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Collecting pandas
  Downloading pandas-2.2.3-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
Collecting seaborn
  Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting python-dateutil>=2.8.2 (from pandas)
  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas)
  Downloading pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas)
  Downloading tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting matplotlib!=3.6.1,>=3.4 (from seaborn)
  Downloading matplotlib-3.10.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting contourpy>=1.0.1 (from matplotlib!=3.6.1,>=3.4->seaborn)
  Downloading contourpy-1.3.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.4 kB)
Collecting cycler>=0.10 (from matplotlib!=3.6.1,>=3.4->seaborn)
  Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib!=3.6.1,>=3.4->seaborn)
  Downloading fonttools-4.56.0-cp313-cp313-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (101 kB)
Collecting kiwisolver>=1.3.1 (from matplotlib!=3.6.1,>=3.4->seaborn)
  Downloading kiwisolver-1.4.8-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.2 kB)
Collecting packaging>=20.0 (from matplotlib!=3.6.1,>=3.4->seaborn)
  Downloading packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pillow>=8 (from matplotlib!=3.6.1,>=3.4->seaborn)
  Downloading pillow-11.1.0-cp313-cp313-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
Collecting pyparsing>=2.3.1 (from matplotlib!=3.6.1,>=3.4->seaborn)
  Downloading pyparsing-3.2.3-py3-none-any.whl.metadata (5.0 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas)
  Downloading six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Downloading numpy-2.2.4-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.1/16.1 MB 93.9 MB/s eta 0:00:00
Downloading pandas-2.2.3-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.7/12.7 MB 120.1 MB/s eta 0:00:00
Downloading seaborn-0.13.2-py3-none-any.whl (294 kB)
Downloading matplotlib-3.10.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.6/8.6 MB 110.9 MB/s eta 0:00:00
Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Downloading pytz-2025.2-py2.py3-none-any.whl (509 kB)
Downloading tzdata-2025.2-py2.py3-none-any.whl (347 kB)
Downloading contourpy-1.3.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (322 kB)
Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Downloading fonttools-4.56.0-cp313-cp313-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.8/4.8 MB 64.6 MB/s eta 0:00:00
Downloading kiwisolver-1.4.8-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.5/1.5 MB 83.2 MB/s eta 0:00:00
Downloading packaging-24.2-py3-none-any.whl (65 kB)
Downloading pillow-11.1.0-cp313-cp313-manylinux_2_28_x86_64.whl (4.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 95.8 MB/s eta 0:00:00
Downloading pyparsing-3.2.3-py3-none-any.whl (111 kB)
Downloading six-1.17.0-py2.py3-none-any.whl (11 kB)
Installing collected packages: pytz, tzdata, six, pyparsing, pillow, packaging, numpy, kiwisolver, fonttools, cycler, python-dateutil, contourpy, pandas, matplotlib, seaborn
Successfully installed contourpy-1.3.1 cycler-0.12.1 fonttools-4.56.0 kiwisolver-1.4.8 matplotlib-3.10.1 numpy-2.2.4 packaging-24.2 pandas-2.2.3 pillow-11.1.0 pyparsing-3.2.3 python-dateutil-2.9.0.post0 pytz-2025.2 seaborn-0.13.2 six-1.17.0 tzdata-2025.2
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.

[notice] A new release of pip is available: 24.3.1 -> 25.0.1
[notice] To update, run: pip install --upgrade pip

Container -> Image

docker ps --all
CONTAINER ID   IMAGE           COMMAND     CREATED              STATUS                     PORTS     NAMES
e45df4642247   python:latest   "bash"      About a minute ago   Exited (0) 4 seconds ago             python-test
fa52839a6bb0   python:latest   "bash"      6 minutes ago        Exited (0) 6 minutes ago             elated_pare
41de571bce2d   python:latest   "python3"   6 minutes ago        Exited (0) 6 minutes ago             zealous_knuth
docker commit python-test python-test:latest
sha256:a69a3249750f888838192869a29cc035403c7cbe70a4c9be98fa1f6e3c2a9546
docker images
REPOSITORY                        TAG       IMAGE ID       CREATED          SIZE
python-test                       latest    a69a3249750f   33 seconds ago   1.3GB
ghcr.io/sta663-sp25/sta663-base   latest    0b725e0ad9c9   3 weeks ago      7.75GB
python                            latest    e6c8fe2e1108   7 weeks ago      1.02GB
ubuntu                            24.04     a04dc4851cbc   8 weeks ago      78.1MB
ubuntu                            latest    a04dc4851cbc   8 weeks ago      78.1MB
hello-world                       latest    74cc54e27dc4   2 months ago     10.1kB
ubuntu                            24.10     e40b6e31bd8c   4 months ago     80.1MB
fedora                            latest    aa6787b90fe6   4 months ago     158MB

Using the image

docker run --rm -it python-test:latest
root@ee76fcc4451f:/# python
Python 3.13.2 (main, Mar 18 2025, 03:30:45) [GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.__version__
'2.2.4'
>>> import seaborn as sns
>>> sns.__version__
'0.13.2'
>>> import seaborn as sns
>>> sns.__version__
'0.13.2'
>>> import pandas as pd
>>> pd.__version__
'2.2.3'