All of a sudden, I'm having issues install packages. For example,
> install.packages("bayestestR")
Error: dbus: Call failed: Failed to activate service 'org.r_project.linux1': timed out (service_start_timeout=25000ms)
> install.packages("deming")
Error: dbus: Call failed: Launch helper exited with unknown return code 1
>
If I run with verbose=TRUE or use a different repo, I get the same behavior.
Has anyone else had this problem?
Here's my system info:
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] stats graphics datasets grDevices utils methods base
other attached packages:
[1] devtools_2.4.5 usethis_2.2.2 default_1.0.0
loaded via a namespace (and not attached):
[1] miniUI_0.1.1.1 compiler_4.3.1 crayon_1.5.2 promises_1.2.1
[5] Rcpp_1.0.11 bspm_0.5.1 stringr_1.5.0 callr_3.7.3
[9] later_1.3.1 fastmap_1.1.1 mime_0.12 R6_2.5.1
[13] htmlwidgets_1.6.1 profvis_0.3.8 shiny_1.7.5 rlang_1.1.1
[17] cachem_1.0.8 stringi_1.7.12 httpuv_1.6.11 fs_1.6.3
[21] pkgload_1.3.3 memoise_2.0.1 cli_3.6.1 magrittr_2.0.3
[25] ps_1.7.5 digest_0.6.33 processx_3.8.2 xtable_1.8-4
[29] remotes_2.4.2.1 lifecycle_1.0.3 prettyunits_1.2.0 vctrs_0.6.3
[33] glue_1.6.2 urlchecker_1.0.1 sessioninfo_1.2.2 pkgbuild_1.4.2
[37] purrr_1.0.1 tools_4.3.1 ellipsis_0.3.2 htmltools_0.5.6.1
>
Looking at my /var/log/syslog file indicated it was a gpg key issue.
The following signatures couldn't be verified because the public key is not available: NO_PUBKEY BAC6F0C353D04109
As a result, I used the first part of the instructions for setting up R on an ubuntu computer here: (https://cran.r-project.org/bin/linux/ubuntu/)
Briefly
# update indices
sudo apt update -qq
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr
# add the signing key (by Michael Rutter) for these repos
# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9
This seemed to fix the problem.