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Gerber, Lauren J

2024-Jul-08 13:07 UTC

[R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest Version of R (R 4.4.1) to Docker Image

Hi All,

I am building a Docker image that uses Ubuntu 22.04 and am having issues
installing the latest version of R (R 4.4.1). The current R version is 4.1.2:
:/# apt-cache policy r-base-core
r-base-core:
  Installed: 4.1.2-1ubuntu2
  Candidate: 4.1.2-1ubuntu2
  Version table:
 *** 4.1.2-1ubuntu2 500
        500 http://archive.ubuntu.com/ubuntu jammy/universe amd64 Packages
        100 /var/lib/dpkg/status

I also checked the Ubuntu version (I am not sure if the ?No LSB modules are
available? is an issue):
:/# lsb_release -a
No LSB modules are available.
Distributor ID:            Ubuntu
Description:                 Ubuntu 22.04.4 LTS
Release:  22.04
Codename:                  jammy

I have tried referring to these instructions listed here:
https://cloud.r-project.org/bin/linux/ubuntu/. Please see below:

When I?m in interactive mode in my Docker container and I try the first line of
suggested code, it results in the following:
:/# apt update -qq
W: GPG error: https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/
InRelease: At least one invalid signature was encountered.
E: The repository 'https://cloud.r-project.org/bin/linux/ubuntu
jammy-cran40/ InRelease' is not signed.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://security.ubuntu.com/ubuntu jammy-security InRelease: At least one invalid
signature was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://archive.ubuntu.com/ubuntu jammy InRelease: At least one invalid signature
was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://archive.ubuntu.com/ubuntu jammy-updates InRelease: At least one invalid
signature was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
https://packages.adoptium.net/artifactory/deb jammy InRelease: At least one
invalid signature was encountered.

I skipped that line and tried the next line:
:/# apt install --no-install-recommends software-properties-common dirmngr
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
dirmngr is already the newest version (2.2.27-3ubuntu2.1).
software-properties-common is already the newest version (0.99.22.9).
0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.

Next, I did this:
:/# wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc |
sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
                ? This returned the public key.

Then, I checked this:
:/# gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
                ? This showed that Michael Rutter?s key had been added (expiring
2027-09-30)

Then I ran this:
:/# add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu
jammy-cran40/<https://cloud.r-project.org/bin/linux/ubuntu%20jammy-cran40/>"
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
Repository: 'deb https://cloud.r-project.org/bin/linux/ubuntu
jammy-cran40/'
Description:
Archive for codename: jammy-cran40/ components:
More info: https://cloud.r-project.org/bin/linux/ubuntu
Adding repository.
Press [ENTER] to continue or Ctrl-c to cancel.

This seemed to be an issue when pressing enter:
Found existing deb entry in
/etc/apt/sources.list.d/archive_uri-https_cloud_r-project_org_bin_linux_ubuntu-jammy.list
Adding deb entry to
/etc/apt/sources.list.d/archive_uri-https_cloud_r-project_org_bin_linux_ubuntu-jammy.list
Found existing deb-src entry in
/etc/apt/sources.list.d/archive_uri-https_cloud_r-project_org_bin_linux_ubuntu-jammy.list
Adding disabled deb-src entry to
/etc/apt/sources.list.d/archive_uri-https_cloud_r-project_org_bin_linux_ubuntu-jammy.list
Get:1 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ InRelease [3626
B]
Get:2 http://security.ubuntu.com/ubuntu jammy-security InRelease [129 kB]
Get:3 https://packages.adoptium.net/artifactory/deb jammy InRelease [7504 B]
Hit:4 http://archive.ubuntu.com/ubuntu jammy InRelease
Get:5 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [128 kB]
Err:1 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ InRelease
  At least one invalid signature was encountered.
Err:2 http://security.ubuntu.com/ubuntu jammy-security InRelease
  At least one invalid signature was encountered.
Err:3 https://packages.adoptium.net/artifactory/deb jammy InRelease
  At least one invalid signature was encountered.
Err:4 http://archive.ubuntu.com/ubuntu jammy InRelease
  At least one invalid signature was encountered.
Err:5 http://archive.ubuntu.com/ubuntu jammy-updates InRelease
  At least one invalid signature was encountered.
Reading package lists... Done
W: GPG error: https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/
InRelease: At least one invalid signature was encountered.
E: The repository 'https://cloud.r-project.org/bin/linux/ubuntu
jammy-cran40/ InRelease' is not signed.
N: Updating from such a repository can't be done securely, and is therefore
disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration
details.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://security.ubuntu.com/ubuntu jammy-security InRelease: At least one invalid
signature was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
https://packages.adoptium.net/artifactory/deb jammy InRelease: At least one
invalid signature was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://archive.ubuntu.com/ubuntu jammy InRelease: At least one invalid signature
was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://archive.ubuntu.com/ubuntu jammy-updates InRelease: At least one invalid
signature was encountered.

Then, I tried this:
:/# apt install --no-install-recommends r-base
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Suggested packages:
  elpa-ess r-doc-info | r-doc-pdf
Recommended packages:
  r-base-html
The following NEW packages will be installed:
  r-base
0 upgraded, 1 newly installed, 0 to remove and 4 not upgraded.
Need to get 9288 B of archives.
After this operation, 63.5 kB of additional disk space will be used.
E: You don't have enough free space in /var/cache/apt/archives/.

It seems there is an issue with Ubuntu 22.04 and the signature verification, as
well as a space issue in /var/cache/apt/archives/.

I am not sure how to resolve these issues when building my Docker image.

Would you please advise?

Thank you.

Br,
Lauren

	[[alternative HTML version deleted]]

Dirk Eddelbuettel

2024-Jul-08 14:52 UTC

head link

[R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest Version of R (R 4.4.1) to Docker Image

Lauren,

Glad you made it over here. I am still 'away' but will be back soon at
which
point I can re-run the sample scripts I use all the time for r2u setups on
Ubuntu (part of which involves getting R itself).
>From your previous email (to me) I gathered that one issue may be thesigning key, how to install that key changed between Ubuntu 20.04 and 22.04
but we do have scripted solutions.
>From your new email here I see that it ends on
   E: You don't have enough free space in /var/cache/apt/archives/.

That is a HARD error message. You are asking your computer to install a
(large) package (name 'r-base' and its dependencies).  Maybe start with

   sudo apt install --no-install-recommends r-base-core

You can precede it with 'apt-cache policy r-base-core' (as I had
mentioned
before) to see whether you have the right repo and version available.

Overall, I think you are very close in the somewhat technical quest of adding
the CRAN/R repo to another container.

Good luck,  Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

m@rcobi@@chette m@iii@g oii icioud@com

2024-Jul-08 16:37 UTC

head link

[R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest Version of R (R 4.4.1) to Docker Image

Lauren, here?s my Dockerfile I use to build r-base from the repos, it builds on
both Arm64 (Mac with Apple M2 chip) and Amd64 (AWS m5.4xlarge instance running
Ubuntu 24.04). I rebuilt the docker image this morning and it builds fine with R
4.4.1

The last RUN is for installing a bit of custom configuration as well as the base
of Bio Conductor.

Hope this helps (I also have a Dockerfile for building from source if you care
to have the minimal footprint in your images).


FROM ubuntu:22.04

USER root

ENV DEBIAN_FRONTEND noninteractive

## Configure Ubuntu for R install
RUN apt-get update \
    && apt install -y --no-install-recommends \
    software-properties-common \
    dirmngr \
    gnupg2 \
    wget \
    build-essential \
    libcurl4-openssl-dev \
    libxml2-dev \
    && wget -q -O -
https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
    | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc  \
    && add-apt-repository -y "ppa:marutter/rrutter4.0"

## Install R
RUN apt-get update -y \
    && apt-get install -y r-base\
    && apt-get clean \
    && apt-get purge \
    && rm -rf /var/lib/apt/lists/* /tmp/*

## Configure parallel options to use max CPUs by default and install BioC
RUN /usr/bin/R -e 'options(Ncpus = parallel::detectCores())'\
    -e 'install.packages("BiocManager")' \
    -e 'BiocManager::install()'



From: R-SIG-Debian <r-sig-debian-bounces at r-project.org> on behalf of
Gerber, Lauren J <lauren.gerber at helsinki.fi>
Date: Monday, July 8, 2024 at 6:08?AM
To: r-sig-debian at r-project.org <r-sig-debian at r-project.org>
Subject: [R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest
Version of R (R 4.4.1) to Docker Image
Hi All,

I am building a Docker image that uses Ubuntu 22.04 and am having issues
installing the latest version of R (R 4.4.1). The current R version is 4.1.2:
:/# apt-cache policy r-base-core
r-base-core:
  Installed: 4.1.2-1ubuntu2
  Candidate: 4.1.2-1ubuntu2
  Version table:
 *** 4.1.2-1ubuntu2 500
        500 http://archive.ubuntu.com/ubuntu jammy/universe amd64 Packages
        100 /var/lib/dpkg/status

I also checked the Ubuntu version (I am not sure if the ?No LSB modules are
available? is an issue):
:/# lsb_release -a
No LSB modules are available.
Distributor ID:            Ubuntu
Description:                 Ubuntu 22.04.4 LTS
Release:  22.04
Codename:                  jammy

I have tried referring to these instructions listed here:
https://cloud.r-project.org/bin/linux/ubuntu/. Please see below:

When I?m in interactive mode in my Docker container and I try the first line of
suggested code, it results in the following:
:/# apt update -qq
W: GPG error: https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/
InRelease: At least one invalid signature was encountered.
E: The repository 'https://cloud.r-project.org/bin/linux/ubuntu
jammy-cran40/ InRelease' is not signed.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://security.ubuntu.com/ubuntu jammy-security InRelease: At least one invalid
signature was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://archive.ubuntu.com/ubuntu jammy InRelease: At least one invalid signature
was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://archive.ubuntu.com/ubuntu jammy-updates InRelease: At least one invalid
signature was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
https://packages.adoptium.net/artifactory/deb jammy InRelease: At least one
invalid signature was encountered.

I skipped that line and tried the next line:
:/# apt install --no-install-recommends software-properties-common dirmngr
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
dirmngr is already the newest version (2.2.27-3ubuntu2.1).
software-properties-common is already the newest version (0.99.22.9).
0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.

Next, I did this:
:/# wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc |
sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
                ? This returned the public key.

Then, I checked this:
:/# gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
                ? This showed that Michael Rutter?s key had been added (expiring
2027-09-30)

Then I ran this:
:/# add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu
jammy-cran40/<https://cloud.r-project.org/bin/linux/ubuntu%20jammy-cran40/>"
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
WARNING:root:system-image-cli failed, using defaults: [Errno 20] Not a
directory: 'system-image-cli'
Repository: 'deb https://cloud.r-project.org/bin/linux/ubuntu
jammy-cran40/'
Description:
Archive for codename: jammy-cran40/ components:
More info: https://cloud.r-project.org/bin/linux/ubuntu
Adding repository.
Press [ENTER] to continue or Ctrl-c to cancel.

This seemed to be an issue when pressing enter:
Found existing deb entry in
/etc/apt/sources.list.d/archive_uri-https_cloud_r-project_org_bin_linux_ubuntu-jammy.list
Adding deb entry to
/etc/apt/sources.list.d/archive_uri-https_cloud_r-project_org_bin_linux_ubuntu-jammy.list
Found existing deb-src entry in
/etc/apt/sources.list.d/archive_uri-https_cloud_r-project_org_bin_linux_ubuntu-jammy.list
Adding disabled deb-src entry to
/etc/apt/sources.list.d/archive_uri-https_cloud_r-project_org_bin_linux_ubuntu-jammy.list
Get:1 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ InRelease [3626
B]
Get:2 http://security.ubuntu.com/ubuntu jammy-security InRelease [129 kB]
Get:3 https://packages.adoptium.net/artifactory/deb jammy InRelease [7504 B]
Hit:4 http://archive.ubuntu.com/ubuntu jammy InRelease
Get:5 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [128 kB]
Err:1 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ InRelease
  At least one invalid signature was encountered.
Err:2 http://security.ubuntu.com/ubuntu jammy-security InRelease
  At least one invalid signature was encountered.
Err:3 https://packages.adoptium.net/artifactory/deb jammy InRelease
  At least one invalid signature was encountered.
Err:4 http://archive.ubuntu.com/ubuntu jammy InRelease
  At least one invalid signature was encountered.
Err:5 http://archive.ubuntu.com/ubuntu jammy-updates InRelease
  At least one invalid signature was encountered.
Reading package lists... Done
W: GPG error: https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/
InRelease: At least one invalid signature was encountered.
E: The repository 'https://cloud.r-project.org/bin/linux/ubuntu
jammy-cran40/ InRelease' is not signed.
N: Updating from such a repository can't be done securely, and is therefore
disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration
details.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://security.ubuntu.com/ubuntu jammy-security InRelease: At least one invalid
signature was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
https://packages.adoptium.net/artifactory/deb jammy InRelease: At least one
invalid signature was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://archive.ubuntu.com/ubuntu jammy InRelease: At least one invalid signature
was encountered.
W: An error occurred during the signature verification. The repository is not
updated and the previous index files will be used. GPG error:
http://archive.ubuntu.com/ubuntu jammy-updates InRelease: At least one invalid
signature was encountered.

Then, I tried this:
:/# apt install --no-install-recommends r-base
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Suggested packages:
  elpa-ess r-doc-info | r-doc-pdf
Recommended packages:
  r-base-html
The following NEW packages will be installed:
  r-base
0 upgraded, 1 newly installed, 0 to remove and 4 not upgraded.
Need to get 9288 B of archives.
After this operation, 63.5 kB of additional disk space will be used.
E: You don't have enough free space in /var/cache/apt/archives/.

It seems there is an issue with Ubuntu 22.04 and the signature verification, as
well as a space issue in /var/cache/apt/archives/.

I am not sure how to resolve these issues when building my Docker image.

Would you please advise?

Thank you.

Br,
Lauren

        [[alternative HTML version deleted]]

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