R cannot install packages in Fedora 38

Ask Fedora
,
1

When I try to install packages for R I get the following error with dbus:

$ R
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

>  install.packages("car")

Available system packages...

Install system packages...
[SKIPPED] R-CRAN-lattice-0.21.8-1.fc38.copr5814828.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-dplyr-1.1.2-1.fc38.copr5826104.x86_64.rpm: Already downloaded 
[SKIPPED] R-CRAN-munsell-0.5.0-3.fc38.copr5815607.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-SparseM-1.81-1.fc38.copr5812258.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-generics-0.1.3-1.fc38.copr5812201.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-backports-1.4.1-1.fc38.copr5812120.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-magrittr-2.0.3-1.fc38.copr5812133.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-fansi-1.0.4-1.fc38.copr5812149.x86_64.rpm: Already downloaded 
[SKIPPED] R-CRAN-pillar-1.9.0-1.fc38.copr5819458.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-broom-1.0.5-1.fc38.copr6058644.noarch.rpm: Already downloaded 
[SKIPPED] R-CRAN-pbkrtest-0.5.2-1.fc38.copr5833696.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-nnet-7.3.19-1.fc38.copr5871776.x86_64.rpm: Already downloaded 
[SKIPPED] R-CRAN-R6-2.5.1-1.fc38.copr5812135.noarch.rpm: Already downloaded    
[SKIPPED] R-CRAN-tibble-3.2.1-1.fc38.copr5821162.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-colorspace-2.1.0-1.fc38.copr5812150.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-farver-2.1.1-1.fc38.copr5812193.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-tidyr-1.3.0-1.fc38.copr5826999.x86_64.rpm: Already downloaded 
[SKIPPED] R-CRAN-RColorBrewer-1.1.3-1.fc38.copr5812145.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-nlme-3.1.163-1.fc38.copr6261982.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-stringi-1.7.12-1.fc38.copr5812147.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-vctrs-0.6.3-1.fc38.copr6083656.x86_64.rpm: Already downloaded 
[SKIPPED] R-CRAN-stringr-1.5.0-1.fc38.copr5819451.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-ellipsis-0.3.2-1.fc38.copr5815610.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-boot-1.3.28.1-1.fc38.copr5814823.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-tidyselect-1.2.0-1.fc38.copr5819454.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-viridisLite-0.4.2-1.fc38.copr5868842.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-lme4-1.1.34-1.fc38.copr6142201.x86_64.rpm: Already downloaded 
[SKIPPED] R-CRAN-rlang-1.1.1-1.fc38.copr5859944.x86_64.rpm: Already downloaded 
[SKIPPED] R-CRAN-MASS-7.3.60-1.fc38.copr5874691.x86_64.rpm: Already downloaded 
[SKIPPED] R-CRAN-cli-3.6.1-1.fc38.copr5812158.x86_64.rpm: Already downloaded   
[SKIPPED] R-CRAN-Matrix-1.6.1-1.fc38.copr6276379.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-minqa-1.2.5-1.fc38.copr5815611.x86_64.rpm: Already downloaded 
[SKIPPED] R-CRAN-survival-3.5.7-1.fc38.copr6276404.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-abind-1.4.5-3.fc38.copr5812119.noarch.rpm: Already downloaded 
[SKIPPED] R-CRAN-glue-1.6.2-1.fc38.copr5812116.x86_64.rpm: Already downloaded  
[SKIPPED] R-CRAN-mgcv-1.9.0-1.fc38.copr6163110.x86_64.rpm: Already downloaded  
[SKIPPED] R-CRAN-nloptr-2.0.3-1.fc38.copr5831161.x86_64.rpm: Already downloaded
[SKIPPED] R-CRAN-purrr-1.0.2-1.fc38.copr6264939.x86_64.rpm: Already downloaded 
[SKIPPED] R-CRAN-MatrixModels-0.5.2-1.fc38.copr6159751.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-numDeriv-2016.8.1.1-3.fc38.copr5812231.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-scales-1.2.1-1.fc38.copr5817798.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-lifecycle-1.0.3-1.fc38.copr5816294.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-withr-2.5.0-1.fc38.copr5812126.noarch.rpm: Already downloaded 
[SKIPPED] R-CRAN-Rcpp-1.0.11-1.fc38.copr6148288.x86_64.rpm: Already downloaded 
[SKIPPED] R-CRAN-car-3.1.2-1.fc38.copr5834305.noarch.rpm: Already downloaded   
[SKIPPED] R-CRAN-utf8-1.2.3-1.fc38.copr5812151.x86_64.rpm: Already downloaded  
[SKIPPED] R-CRAN-carData-3.0.5-1.fc38.copr5812168.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-labeling-0.4.2-1.fc38.copr5812144.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-pkgconfig-2.0.3-3.fc38.copr5812134.noarch.rpm: Already downloaded
[SKIPPED] R-CRAN-quantreg-5.97-1.fc38.copr6319331.x86_64.rpm: Already downloaded
[SKIPPED] R-littler-0.3.18-4.fc38.x86_64.rpm: Already downloaded               
Error: dbus: Call failed: Transaction test error:  package R-CRAN-rlang-1.1.1-1.fc38.copr5859944.x86_64 does not verify: Header V4 RSA/SHA256 Signature, key ID 1a3b4456: NOTTRUSTED  package R-CRAN-glue-1.6.2-1.fc38.copr5812116.x86_64 does not verify: Header V4 RSA/SHA256 Signature, key ID 1a3b4456: NOTTRUSTED  package R-CRAN-cli-3.6.1-1.fc38.copr5812158.x86_64 does not verify: Header V4 RSA/SHA256 Signature, key ID 1a3b4456: NOTTRUSTED  package R-CRAN-lifecycle-1.0.3-1.fc38.copr5816294.noarch does not verify: Header V4 RSA/SHA256 Signature, key ID 1a3b4456: NOTTRUSTED  package R-CRAN-vctrs-0.6.3-1.fc38.copr6083656.x86_64 does not verify: Header V4 RSA/SHA256 Signature, key ID 1a3b4456: NOTTRUSTED  package R-CRAN-magrittr-2.0.3-1.fc38.copr5812133.x86_64 does not verify: Header V4 RSA/SHA256 Signature, key ID 1a3b4456: NOTTRUSTED  package R-CRAN-MASS-7.3.60-1.fc38.copr5874691.x86_64 does not verify: Header V4 RSA/SHA256 Signature, key ID 1a3b4456: NOTTRUSTED  package R-CRAN-lattice-0.21.

I believe this is not an error related to R, but more with the package dbus.

1 Like
2

It looks more like the the copr repository hasn’t updated the package signature.
Try refreshing copr repo or wait until the repository has updated the packages.

latest R-CRAN-rlang from COPR seems to be 1.1.1-1.copr6279308 but yours is trying to download 1.1.1-1.fc38.copr5859944.

1 Like
3

How can I syncronize both versions without downgrading the version of R-CoprManager?

4 
$ dnf info R-CoprManager

Installed Packages
Name         : R-CoprManager
Version      : 0.5.5
Release      : 1.fc38.copr6331124
Architecture : noarch
Size         : 113 k
Source       : R-CoprManager-0.5.5-1.fc38.copr6331124.src.rpm
Repository   : @System
From repo    : copr:copr.fedorainfracloud.org:iucar:cran
Summary      : Package Manager for the 'cran2copr' Project
URL          : https://github.com/Enchufa2/bspm
License      : MIT
Description  : Enables binary package installations in Fedora systems based on
             : the 'cran2copr' project. Provides a installation function that
             : talks over D-Bus to a systemd service that manages package
             : installations via DNF.
5

I decided to get started with RStudio yesterday and ran into the same problem as soon as I tried installing an R-package through R-CoprManager. Hope the package signature will be updated soon as compiling from source is a pain on my laptop.
Not sure if the different package versions that martrs mentioned might be the root of the problem, but my fresh install also tried to install R-CRAN-rlang-1.1.1-1.fc38.copr5859944.x86_64