m@rcobi@@chette m@iii@g oii icioud@com
2024-Jul-08 16:37 UTC
[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]] _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian [[alternative HTML version deleted]]
Dirk Eddelbuettel
2024-Jul-08 18:56 UTC
[R-sig-Debian] Issues with Ubuntu 22.04 and Installing the Latest Version of R (R 4.4.1) to Docker Image
On 8 July 2024 at 16:37, marcoblanchette at icloud.com wrote: | 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 That's very kind but recall that Lauren wants _a pre-made binary_ of R. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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