[r-packages] installSystemRequirements causes error related to sudo

[dfarnand]

I'm hitting an error when trying to use the installSystemRequirements flag, which I can replicate with the following minimal devcontainer:

{
	"image": "ghcr.io/rocker-org/devcontainer/r-ver:4.5",
	"features": {
		"ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
			"packages": "sf",
			"installSystemRequirements": true
		}
	}
}

It seems to be related to running sudo in the process.

Devcontainer build logs

[2025-08-11T17:21:50.102Z] Dev Containers 0.422.1 in VS Code 1.102.3 (488a1f239235055e34e673291fb8d8c810886f81).
[2025-08-11T17:21:50.102Z] Start: Resolving Remote
[2025-08-11T17:21:50.111Z] Setting up container for folder or workspace: /home/danny/Downloads/devcontainerreprex
[2025-08-11T17:21:50.138Z] Start: Check Docker is running
[2025-08-11T17:21:50.139Z] Start: Run: podman version
[2025-08-11T17:21:50.163Z] Client:       Podman Engine
Version:      4.9.3
API Version:  4.9.3
Go Version:   go1.22.2
Built:        Wed Dec 31 19:00:00 1969
OS/Arch:      linux/amd64
[2025-08-11T17:21:50.166Z] Stop (27 ms): Run: podman version
[2025-08-11T17:21:50.167Z] Stop (29 ms): Check Docker is running
[2025-08-11T17:21:50.167Z] Start: Run: podman volume ls -q
[2025-08-11T17:21:50.200Z] Stop (33 ms): Run: podman volume ls -q
[2025-08-11T17:21:50.201Z] Start: Run: podman ps -q -a --filter label=vsch.local.folder=/home/danny/Downloads/devcontainerreprex --filter label=vsch.quality=stable
[2025-08-11T17:21:50.236Z] Stop (35 ms): Run: podman ps -q -a --filter label=vsch.local.folder=/home/danny/Downloads/devcontainerreprex --filter label=vsch.quality=stable
[2025-08-11T17:21:50.236Z] Start: Run: podman ps -q -a --filter label=devcontainer.local_folder=/home/danny/Downloads/devcontainerreprex --filter label=devcontainer.config_file=/home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json
[2025-08-11T17:21:50.270Z] Stop (34 ms): Run: podman ps -q -a --filter label=devcontainer.local_folder=/home/danny/Downloads/devcontainerreprex --filter label=devcontainer.config_file=/home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json
[2025-08-11T17:21:50.271Z] Start: Run: podman ps -q -a --filter label=devcontainer.local_folder=/home/danny/Downloads/devcontainerreprex
[2025-08-11T17:21:50.305Z] Stop (34 ms): Run: podman ps -q -a --filter label=devcontainer.local_folder=/home/danny/Downloads/devcontainerreprex
[2025-08-11T17:21:50.305Z] Running Dev Containers CLI:   up --user-data-folder /home/danny/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data --docker-path podman --docker-compose-path podman-compose --container-session-data-folder /tmp/devcontainers-4871a4fd-fd9a-4122-adf3-dbec748f04961754932909503 --workspace-folder /home/danny/Downloads/devcontainerreprex --workspace-mount-consistency cached --gpu-availability detect --id-label devcontainer.local_folder=/home/danny/Downloads/devcontainerreprex --id-label devcontainer.config_file=/home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json --log-level debug --log-format json --config /home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json --default-user-env-probe loginInteractiveShell --remove-existing-container --mount type=volume,source=vscode,target=/vscode,external=true --skip-post-create --update-remote-user-uid-default on --mount-workspace-git-root --include-configuration --include-merged-configuration
[2025-08-11T17:21:50.306Z] Start: Run: /usr/share/code/code /home/danny/.vscode/extensions/ms-vscode-remote.remote-containers-0.422.1/dist/spec-node/devContainersSpecCLI.js up --user-data-folder /home/danny/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data --docker-path podman --docker-compose-path podman-compose --container-session-data-folder /tmp/devcontainers-4871a4fd-fd9a-4122-adf3-dbec748f04961754932909503 --workspace-folder /home/danny/Downloads/devcontainerreprex --workspace-mount-consistency cached --gpu-availability detect --id-label devcontainer.local_folder=/home/danny/Downloads/devcontainerreprex --id-label devcontainer.config_file=/home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json --log-level debug --log-format json --config /home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json --default-user-env-probe loginInteractiveShell --remove-existing-container --mount type=volume,source=vscode,target=/vscode,external=true --skip-post-create --update-remote-user-uid-default on --mount-workspace-git-root --include-configuration --include-merged-configuration
[2025-08-11T17:21:50.429Z] @devcontainers/cli 0.79.0. Node.js v22.15.1. linux 6.14.0-24-generic x64.
[2025-08-11T17:21:50.429Z] Start: Run: podman buildx version
[2025-08-11T17:21:50.489Z] Stop (60 ms): Run: podman buildx version
[2025-08-11T17:21:50.489Z] buildah 1.33.7
[2025-08-11T17:21:50.489Z] 
[2025-08-11T17:21:50.489Z] Start: Run: podman -v
[2025-08-11T17:21:50.504Z] Stop (15 ms): Run: podman -v
[2025-08-11T17:21:50.504Z] Start: Resolving Remote
[2025-08-11T17:21:50.506Z] Start: Run: git rev-parse --show-cdup
[2025-08-11T17:21:50.510Z] Stop (4 ms): Run: git rev-parse --show-cdup
[2025-08-11T17:21:50.512Z] Start: Run: podman ps -q -a --filter label=devcontainer.local_folder=/home/danny/Downloads/devcontainerreprex --filter label=devcontainer.config_file=/home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json
[2025-08-11T17:21:50.544Z] Stop (32 ms): Run: podman ps -q -a --filter label=devcontainer.local_folder=/home/danny/Downloads/devcontainerreprex --filter label=devcontainer.config_file=/home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json
[2025-08-11T17:21:50.545Z] Start: Run: podman inspect --type image ghcr.io/rocker-org/devcontainer/r-ver:4.5
[2025-08-11T17:21:50.584Z] Stop (39 ms): Run: podman inspect --type image ghcr.io/rocker-org/devcontainer/r-ver:4.5
[2025-08-11T17:21:50.586Z] Resolving Feature dependencies for 'ghcr.io/rocker-org/devcontainer-features/r-packages:1'...
[2025-08-11T17:21:50.586Z] * Processing feature: ghcr.io/rocker-org/devcontainer-features/r-packages:1
[2025-08-11T17:21:50.588Z] Loading 147 extra certificates from /etc/ssl/certs/ca-certificates.crt.
[2025-08-11T17:21:50.661Z] Start: Run: docker-credential-secret get
[2025-08-11T17:21:50.665Z] Stop (4 ms): Run: docker-credential-secret get
[2025-08-11T17:21:50.667Z] Stop (6 ms): Run: docker-credential-secret get
[2025-08-11T17:21:50.801Z] * Processing feature: ghcr.io/devcontainers/features/common-utils
[2025-08-11T17:21:50.880Z] * Processing feature: ghcr.io/rocker-org/devcontainer-features/apt-packages
[2025-08-11T17:21:51.132Z] Files to omit: ''
[2025-08-11T17:21:51.138Z] * Processing feature: ghcr.io/rocker-org/devcontainer-features/r-apt
[2025-08-11T17:21:51.227Z] * Processing feature: ghcr.io/rocker-org/devcontainer-features/r-rig
[2025-08-11T17:21:51.316Z] Soft-dependency 'ghcr.io/rocker-org/devcontainer-features/r-rig' is not required.  Removing from installation order...
[2025-08-11T17:21:51.316Z] Soft-dependency 'ghcr.io/rocker-org/devcontainer-features/r-apt' is not required.  Removing from installation order...
[2025-08-11T17:21:51.316Z] Soft-dependency 'ghcr.io/rocker-org/devcontainer-features/apt-packages' is not required.  Removing from installation order...
[2025-08-11T17:21:51.316Z] Soft-dependency 'ghcr.io/devcontainers/features/common-utils' is not required.  Removing from installation order...
[2025-08-11T17:21:51.321Z] * Fetching feature: r-packages_0_oci
[2025-08-11T17:21:51.415Z] Files to omit: ''
[2025-08-11T17:21:51.417Z] * Fetched feature: r-packages_0_oci version 1.1.0
[2025-08-11T17:21:51.422Z] Start: Run: podman buildx build --load --build-context dev_containers_feature_content_source=/tmp/devcontainercli-danny/container-features/0.79.0-1754932910585 --build-arg _DEV_CONTAINERS_BASE_IMAGE=ghcr.io/rocker-org/devcontainer/r-ver:4.5 --build-arg _DEV_CONTAINERS_IMAGE_USER=root --build-arg _DEV_CONTAINERS_FEATURE_CONTENT_SOURCE=dev_container_feature_content_temp --target dev_containers_target_stage -f /tmp/devcontainercli-danny/container-features/0.79.0-1754932910585/Dockerfile.extended -t vsc-devcontainerreprex-381dd2da2f27302bd98e36305f07858a146ae899b3c2558dcafe054511b7dccf-features /home/danny/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data/empty-folder
[2025-08-11T17:21:51.449Z] [1/2] STEP 1/4: FROM ghcr.io/rocker-org/devcontainer/r-ver:4.5 AS dev_containers_feature_content_normalize
[2025-08-11T17:21:51.469Z] [1/2] STEP 2/4: USER root
[2025-08-11T17:21:51.470Z] --> Using cache aae03b7d7a67c605446dcdb108b0661a66d4570608c790e67d751816863c615b
--> aae03b7d7a67
[2025-08-11T17:21:51.476Z] [1/2] STEP 3/4: COPY --from=dev_containers_feature_content_source devcontainer-features.builtin.env /tmp/build-features/
[2025-08-11T17:21:51.565Z] --> Using cache db25f0373d0af4f54c8727f4262de348ce2d368dcf85993e40b0f2d87a359357
--> db25f0373d0a
[2025-08-11T17:21:51.571Z] [1/2] STEP 4/4: RUN chmod -R 0755 /tmp/build-features/
[2025-08-11T17:21:51.573Z] --> Using cache 60fe435984cf764e146d12c6622f06a622320adfef33d621408cc8b86e804298
--> 60fe435984cf
[2025-08-11T17:21:51.577Z] [2/2] STEP 1/9: FROM ghcr.io/rocker-org/devcontainer/r-ver:4.5 AS dev_containers_target_stage
[2025-08-11T17:21:51.585Z] [2/2] STEP 2/9: USER root
[2025-08-11T17:21:51.586Z] --> Using cache aae03b7d7a67c605446dcdb108b0661a66d4570608c790e67d751816863c615b
--> aae03b7d7a67
[2025-08-11T17:21:51.591Z] [2/2] STEP 3/9: RUN mkdir -p /tmp/dev-container-features
[2025-08-11T17:21:51.593Z] --> Using cache b9e6ec1ae1760b7b335c3f24312b8c04d962defd32df7e990294065c2f786a58
--> b9e6ec1ae176
[2025-08-11T17:21:51.598Z] [2/2] STEP 4/9: COPY --from=dev_containers_feature_content_normalize /tmp/build-features/ /tmp/dev-container-features
[2025-08-11T17:21:51.689Z] --> Using cache a369471e36301b4c765cbe1e5fd2bc72916b760bc47f74a59d1626ef658774d7
--> a369471e3630
[2025-08-11T17:21:51.694Z] [2/2] STEP 5/9: RUN echo "_CONTAINER_USER_HOME=$( (command -v getent >/dev/null 2>&1 && getent passwd 'root' || grep -E '^root|^[^:]*:[^:]*:root:' /etc/passwd || true) | cut -d: -f6)" >> /tmp/dev-container-features/devcontainer-features.builtin.env && echo "_REMOTE_USER_HOME=$( (command -v getent >/dev/null 2>&1 && getent passwd 'rstudio' || grep -E '^rstudio|^[^:]*:[^:]*:rstudio:' /etc/passwd || true) | cut -d: -f6)" >> /tmp/dev-container-features/devcontainer-features.builtin.env
[2025-08-11T17:21:51.695Z] --> Using cache e73825da1327ba2b1abaf07a4f45eda2d03d24b8e6d6b89ce460de78aed4c735
--> e73825da1327
[2025-08-11T17:21:51.700Z] [2/2] STEP 6/9: RUN --mount=type=bind,from=dev_containers_feature_content_source,source=r-packages_0,target=/tmp/build-features-src/r-packages_0,z     cp -ar /tmp/build-features-src/r-packages_0 /tmp/dev-container-features  && chmod -R 0755 /tmp/dev-container-features/r-packages_0  && cd /tmp/dev-container-features/r-packages_0  && chmod +x ./devcontainer-features-install.sh  && ./devcontainer-features-install.sh  && rm -rf /tmp/dev-container-features/r-packages_0
[2025-08-11T17:21:51.909Z] ===========================================================================
Feature       : R packages (via pak)
Description   : Installs R packages via the pak R package's function. R must be already installed.
Id            : ghcr.io/rocker-org/devcontainer-features/r-packages
Version       : 1.1.0
Documentation : https://github.com/rocker-org/devcontainer-features/tree/main/src/r-packages
Options       :
    PACKAGES="sf"
    PAKVERSION="auto"
    ADDITIONALREPOSITORIES=""
    INSTALLSYSTEMREQUIREMENTS="true"
    CRANMIRROR=""
    NOTCRAN="false"
===========================================================================
[2025-08-11T17:21:51.916Z] Install R packages...
[2025-08-11T17:21:51.917Z] /tmp/r-packages /tmp/dev-container-features/r-packages_0
[2025-08-11T17:21:52.191Z] pak is already installed. Skip pak installation...
[2025-08-11T17:21:52.194Z] find: ‘/var/lib/apt/lists/*’: No such file or directory
[2025-08-11T17:21:52.194Z] Running apt-get update...
[2025-08-11T17:21:52.256Z] Get:1 http://security.ubuntu.com/ubuntu noble-security InRelease [126 kB]
[2025-08-11T17:21:52.377Z] Get:2 http://security.ubuntu.com/ubuntu noble-security/restricted amd64 Packages [1,975 kB]
[2025-08-11T17:21:52.387Z] Get:3 http://archive.ubuntu.com/ubuntu noble InRelease [256 kB]
[2025-08-11T17:21:52.591Z] Get:4 http://security.ubuntu.com/ubuntu noble-security/main amd64 Packages [1,326 kB]
[2025-08-11T17:21:52.693Z] Get:5 http://security.ubuntu.com/ubuntu noble-security/universe amd64 Packages [1,134 kB]
[2025-08-11T17:21:52.767Z] Get:6 http://security.ubuntu.com/ubuntu noble-security/multiverse amd64 Packages [23.0 kB]
[2025-08-11T17:21:52.865Z] Get:7 http://archive.ubuntu.com/ubuntu noble-updates InRelease [126 kB]
[2025-08-11T17:21:52.970Z] Get:8 http://archive.ubuntu.com/ubuntu noble-backports InRelease [126 kB]
[2025-08-11T17:21:53.078Z] Get:9 http://archive.ubuntu.com/ubuntu noble/restricted amd64 Packages [117 kB]
[2025-08-11T17:21:53.106Z] Get:10 http://archive.ubuntu.com/ubuntu noble/main amd64 Packages [1,808 kB]
[2025-08-11T17:21:53.345Z] Get:11 http://archive.ubuntu.com/ubuntu noble/universe amd64 Packages [19.3 MB]
[2025-08-11T17:21:54.477Z] Get:12 http://archive.ubuntu.com/ubuntu noble/multiverse amd64 Packages [331 kB]
[2025-08-11T17:21:54.493Z] Get:13 http://archive.ubuntu.com/ubuntu noble-updates/multiverse amd64 Packages [45.2 kB]
[2025-08-11T17:21:54.497Z] Get:14 http://archive.ubuntu.com/ubuntu noble-updates/main amd64 Packages [1,666 kB]
[2025-08-11T17:21:54.601Z] Get:15 http://archive.ubuntu.com/ubuntu noble-updates/restricted amd64 Packages [2,092 kB]
[2025-08-11T17:21:54.717Z] Get:16 http://archive.ubuntu.com/ubuntu noble-updates/universe amd64 Packages [1,454 kB]
[2025-08-11T17:21:54.792Z] Get:17 http://archive.ubuntu.com/ubuntu noble-backports/universe amd64 Packages [33.9 kB]
Get:18 http://archive.ubuntu.com/ubuntu noble-backports/main amd64 Packages [48.8 kB]
[2025-08-11T17:21:55.275Z] Fetched 32.0 MB in 3s (10.5 MB/s)
Reading package lists...
[2025-08-11T17:21:56.055Z] 
[2025-08-11T17:21:56.351Z] > pak::repo_add(); pak::pak(trimws(unlist(strsplit('sf', ',')))); pak::cache_clean()
[2025-08-11T17:21:57.748Z] 
[2025-08-11T17:21:58.369Z] ✔ Updated metadata database: 4.06 MB in 8 files.
[2025-08-11T17:21:58.370Z] 
[2025-08-11T17:21:58.370Z] ℹ Updating metadata database
[2025-08-11T17:22:01.390Z] ✔ Updating metadata database ... done
[2025-08-11T17:22:01.390Z] 
[2025-08-11T17:22:01.722Z]  
[2025-08-11T17:22:01.726Z] → Will install 8 packages.
[2025-08-11T17:22:01.736Z] → Will download 8 packages with unknown size.
[2025-08-11T17:22:01.752Z] + classInt   0.4-11 [dl]
+ DBI        1.2.3  [dl]
+ e1071      1.7-16 [dl]
+ proxy      0.4-27 [dl]
+ s2         1.1.9  [dl] + ✖ libabsl-dev, ✖ cmake, ✔ libssl-dev
+ sf         1.0-21 [dl] + ✖ libgdal-dev, ✖ gdal-bin, ✖ libgeos-dev, ✖ libproj-dev, ✖ libsqlite3-dev
+ units      0.8-7  [dl] + ✖ libudunits2-dev
+ wk         0.9.4  [dl]
[2025-08-11T17:22:01.757Z] → Will install 8 system packages:
[2025-08-11T17:22:01.758Z] + cmake            - s2   
+ gdal-bin         - sf   
+ libabsl-dev      - s2   
+ libgdal-dev      - sf   
+ libgeos-dev      - sf   
+ libproj-dev      - sf   
+ libsqlite3-dev   - sf   
+ libudunits2-dev  - units
[2025-08-11T17:22:01.806Z] ℹ Getting 8 pkgs with unknown sizes
[2025-08-11T17:22:02.227Z] ✔ Got e1071 1.7-16 (x86_64-pc-linux-gnu-ubuntu-24.04) (596.57 kB)
[2025-08-11T17:22:02.256Z] ✔ Got DBI 1.2.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (916.93 kB)
[2025-08-11T17:22:02.268Z] ✔ Got proxy 0.4-27 (x86_64-pc-linux-gnu-ubuntu-24.04) (175.47 kB)
[2025-08-11T17:22:02.356Z] ✔ Got classInt 0.4-11 (x86_64-pc-linux-gnu-ubuntu-24.04) (496.56 kB)
[2025-08-11T17:22:02.405Z] ✔ Got units 0.8-7 (x86_64-pc-linux-gnu-ubuntu-24.04) (467.34 kB)
[2025-08-11T17:22:02.545Z] ✔ Got wk 0.9.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.73 MB)
[2025-08-11T17:22:02.642Z] ✔ Got s2 1.1.9 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.21 MB)
[2025-08-11T17:22:02.927Z] ✔ Got sf 1.0-21 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.08 MB)
[2025-08-11T17:22:02.954Z] ℹ Installing system requirements
[2025-08-11T17:22:02.958Z] ℹ Executing `sudo sh -c apt-get -y update`
[2025-08-11T17:22:05.627Z] Error: 
! error in pak subprocess
Caused by error in `processx::run(sh, cmdline, stdout_callback = callback, stderr_to_stdout = TRUE)`:
! System command 'sudo' failed
---
Exit status: 1
Stdout & stderr:
sudo: The "no new privileges" flag is set, which prevents sudo from running as root.
sudo: If sudo is running in a container, you may need to adjust the container configuration to disable the flag.
---
Backtrace:
1. pak::pak(trimws(unlist(strsplit("sf", ","))))
2. pak::pkg_install(pkg, ...)
3. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
4. err$throw(res$error)
---
Subprocess backtrace:
 1. base::withCallingHandlers(cli_message = function(msg) { …
 2. get("pkg_install_do_plan", asNamespace("pak"))(...)
 3. proposal$install_sysreqs()
 4. pkgdepends:::sysreqs_install(cmds, config)
 5. base::lapply(cmds, function(cmd) { …
 6. local FUN(X[[i]], ...)
 7. processx::run(sh, cmdline, stdout_callback = callback, stderr_to_stdout = …
 8. base::throw(new_process_error(res, call = sys.call(), echo = echo, …
 9. | base::signalCondition(cond)
10. global (function (e) …
Execution halted
[2025-08-11T17:22:05.659Z] ERROR: Feature "R packages (via pak)" (ghcr.io/rocker-org/devcontainer-features/r-packages) failed to install! Look at the documentation at https://github.com/rocker-org/devcontainer-features/tree/main/src/r-packages for help troubleshooting this error.
[2025-08-11T17:22:05.761Z] Error: building at STEP "RUN --mount=type=bind,from=dev_containers_feature_content_source,source=r-packages_0,target=/tmp/build-features-src/r-packages_0,z cp -ar /tmp/build-features-src/r-packages_0 /tmp/dev-container-features  && chmod -R 0755 /tmp/dev-container-features/r-packages_0  && cd /tmp/dev-container-features/r-packages_0  && chmod +x ./devcontainer-features-install.sh  && ./devcontainer-features-install.sh  && rm -rf /tmp/dev-container-features/r-packages_0": while running runtime: exit status 1
[2025-08-11T17:22:05.765Z] Stop (14343 ms): Run: podman buildx build --load --build-context dev_containers_feature_content_source=/tmp/devcontainercli-danny/container-features/0.79.0-1754932910585 --build-arg _DEV_CONTAINERS_BASE_IMAGE=ghcr.io/rocker-org/devcontainer/r-ver:4.5 --build-arg _DEV_CONTAINERS_IMAGE_USER=root --build-arg _DEV_CONTAINERS_FEATURE_CONTENT_SOURCE=dev_container_feature_content_temp --target dev_containers_target_stage -f /tmp/devcontainercli-danny/container-features/0.79.0-1754932910585/Dockerfile.extended -t vsc-devcontainerreprex-381dd2da2f27302bd98e36305f07858a146ae899b3c2558dcafe054511b7dccf-features /home/danny/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data/empty-folder
[2025-08-11T17:22:05.765Z] Error: Command failed: podman buildx build --load --build-context dev_containers_feature_content_source=/tmp/devcontainercli-danny/container-features/0.79.0-1754932910585 --build-arg _DEV_CONTAINERS_BASE_IMAGE=ghcr.io/rocker-org/devcontainer/r-ver:4.5 --build-arg _DEV_CONTAINERS_IMAGE_USER=root --build-arg _DEV_CONTAINERS_FEATURE_CONTENT_SOURCE=dev_container_feature_content_temp --target dev_containers_target_stage -f /tmp/devcontainercli-danny/container-features/0.79.0-1754932910585/Dockerfile.extended -t vsc-devcontainerreprex-381dd2da2f27302bd98e36305f07858a146ae899b3c2558dcafe054511b7dccf-features /home/danny/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data/empty-folder
[2025-08-11T17:22:05.765Z]     at D6 (/home/danny/.vscode/extensions/ms-vscode-remote.remote-containers-0.422.1/dist/spec-node/devContainersSpecCLI.js:467:1253)
[2025-08-11T17:22:05.765Z]     at ax (/home/danny/.vscode/extensions/ms-vscode-remote.remote-containers-0.422.1/dist/spec-node/devContainersSpecCLI.js:467:997)
[2025-08-11T17:22:05.765Z]     at async H6 (/home/danny/.vscode/extensions/ms-vscode-remote.remote-containers-0.422.1/dist/spec-node/devContainersSpecCLI.js:484:3842)
[2025-08-11T17:22:05.765Z]     at async BC (/home/danny/.vscode/extensions/ms-vscode-remote.remote-containers-0.422.1/dist/spec-node/devContainersSpecCLI.js:484:4957)
[2025-08-11T17:22:05.766Z]     at async d7 (/home/danny/.vscode/extensions/ms-vscode-remote.remote-containers-0.422.1/dist/spec-node/devContainersSpecCLI.js:665:202)
[2025-08-11T17:22:05.766Z]     at async f7 (/home/danny/.vscode/extensions/ms-vscode-remote.remote-containers-0.422.1/dist/spec-node/devContainersSpecCLI.js:664:14804)
[2025-08-11T17:22:05.766Z]     at async /home/danny/.vscode/extensions/ms-vscode-remote.remote-containers-0.422.1/dist/spec-node/devContainersSpecCLI.js:484:1188
[2025-08-11T17:22:05.771Z] Stop (15465 ms): Run: /usr/share/code/code /home/danny/.vscode/extensions/ms-vscode-remote.remote-containers-0.422.1/dist/spec-node/devContainersSpecCLI.js up --user-data-folder /home/danny/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data --docker-path podman --docker-compose-path podman-compose --container-session-data-folder /tmp/devcontainers-4871a4fd-fd9a-4122-adf3-dbec748f04961754932909503 --workspace-folder /home/danny/Downloads/devcontainerreprex --workspace-mount-consistency cached --gpu-availability detect --id-label devcontainer.local_folder=/home/danny/Downloads/devcontainerreprex --id-label devcontainer.config_file=/home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json --log-level debug --log-format json --config /home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json --default-user-env-probe loginInteractiveShell --remove-existing-container --mount type=volume,source=vscode,target=/vscode,external=true --skip-post-create --update-remote-user-uid-default on --mount-workspace-git-root --include-configuration --include-merged-configuration
[2025-08-11T17:22:05.771Z] Exit code 1
[2025-08-11T17:22:05.775Z] Command failed: /usr/share/code/code /home/danny/.vscode/extensions/ms-vscode-remote.remote-containers-0.422.1/dist/spec-node/devContainersSpecCLI.js up --user-data-folder /home/danny/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data --docker-path podman --docker-compose-path podman-compose --container-session-data-folder /tmp/devcontainers-4871a4fd-fd9a-4122-adf3-dbec748f04961754932909503 --workspace-folder /home/danny/Downloads/devcontainerreprex --workspace-mount-consistency cached --gpu-availability detect --id-label devcontainer.local_folder=/home/danny/Downloads/devcontainerreprex --id-label devcontainer.config_file=/home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json --log-level debug --log-format json --config /home/danny/Downloads/devcontainerreprex/.devcontainer/devcontainer.json --default-user-env-probe loginInteractiveShell --remove-existing-container --mount type=volume,source=vscode,target=/vscode,external=true --skip-post-create --update-remote-user-uid-default on --mount-workspace-git-root --include-configuration --include-merged-configuration
[2025-08-11T17:22:05.775Z] Exit code 1

I think the relevant section is this:

[2025-08-11T17:22:02.954Z] ℹ Installing system requirements
[2025-08-11T17:22:02.958Z] ℹ Executing `sudo sh -c apt-get -y update`
[2025-08-11T17:22:05.627Z] Error: 
! error in pak subprocess
Caused by error in `processx::run(sh, cmdline, stdout_callback = callback, stderr_to_stdout = TRUE)`:
! System command 'sudo' failed
---
Exit status: 1
Stdout & stderr:
sudo: The "no new privileges" flag is set, which prevents sudo from running as root.
sudo: If sudo is running in a container, you may need to adjust the container configuration to disable the flag.
---
Backtrace:
1. pak::pak(trimws(unlist(strsplit("sf", ","))))
2. pak::pkg_install(pkg, ...)
3. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
4. err$throw(res$error)
---
Subprocess backtrace:
 1. base::withCallingHandlers(cli_message = function(msg) { …
 2. get("pkg_install_do_plan", asNamespace("pak"))(...)
 3. proposal$install_sysreqs()
 4. pkgdepends:::sysreqs_install(cmds, config)
 5. base::lapply(cmds, function(cmd) { …
 6. local FUN(X[[i]], ...)
 7. processx::run(sh, cmdline, stdout_callback = callback, stderr_to_stdout = …
 8. base::throw(new_process_error(res, call = sys.call(), echo = echo, …
 9. | base::signalCondition(cond)
10. global (function (e) …
Execution halted

[eitsupi]

Thanks for rasing that.

Are you using podman? If so, could it be a podman issue?
Given that the pak hasn't been updated in months, it's unlikely that this is a sudden issue.
Did it work before?

[dfarnand]

Thanks for your reply!

I am using podman, and I just successfully built on a different machine that uses docker, so podman-related for sure.

It was working before, but unfortunately its been a few weeks and while I don't remember changing anything about my system (except for routine updates), I can't say for sure. Unhelpful, I know!

Also worth mentioning my current workaround is to explicitly install the dependencies with the apt-packages feature.

{
	"image": "ghcr.io/rocker-org/devcontainer/r-ver:4.5",
	"features": {
		"ghcr.io/rocker-org/devcontainer-features/apt-packages:1": {
			"packages": "libabsl-dev cmake libssl-dev libgdal-dev gdal-bin libgeos-dev libproj-dev libsqlite3-dev libudunits2-dev"
		},
		"ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
			"packages": "sf",
			"installSystemRequirements": false
		}
	}
}

Since this works fine, some aspect of how r-packages (or pak itself I guess) runs apt differently than apt-packages combined with podman seems to be the issue. Fortunately the workaround is easy, with only the cost of a slightly more cluttered json file!

[eitsupi]

Installing R packages via pak requires sudo because it is done by the remote user (non-root in this case), but the apt-packages Feature does not use sudo because the root user installs the packages.

I suspect that the issue is caused by an update to podman or your podman configuration on your system, and I don't think there's anything we can do here.

Anyway, isn't this something specific to this Feature, but rather a general issue with the use of sudo on containers?
I recommend asking the wider podman community.