Question 290390 in Ubuntu Question posted in
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Ubuntu – Can't install packages in R anymore: dbus error

Suddenly, I can’t install any more packages in R using install.packages. For any package I want to install (including random characters), I get the following error message:

> install.packages('tensorA')
Error in install.packages : dbus: Call failed: Traceback (most recent call last):  File "/usr/lib/python3/dist-packages/dbus/service.py", line 658, in _message_cb    (candidate_method, parent_method) = _method_lookup(self, method_name, interface_name)  File "/usr/lib/python3/dist-packages/dbus/service.py", line 248, in _method_lookup    raise UnknownMethodException('%s is not a valid method of interface %s' % (method_name, dbus_interface))dbus.exceptions.UnknownMethodException: org.freedesktop.DBus.Error.UnknownMethod: Unknown method: available is not a valid method of interface org.r_project.linux1.PackageManager

That’s my session info:

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 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/liblapack.so.3;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Berlin
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods  
[7] base     

loaded via a namespace (and not attached):
[1] compiler_4.3.2  cli_3.6.1       tools_4.3.2     rstudioapi_0.14
[5] bspm_0.5.1      rlang_1.1.0

Any tip appreciated!

Tags:

2

Answers


  1. 0

    The operation is trying to contact the bspm service (which appears to be a helper service that uses the OS package manager – dnf, apt, pacman etc. – to install R packages). This happens to be done via D-Bus, but the error message is not actually related to D-Bus; it comes from bspm itself.

    The message says that R attempted to call the available() function, which doesn’t exist in the service. According to Git commit logs, this function was added in version 0.3.10.1 of bspm.

    Use busctl status org.r_project.linux1.PackageManager (with or without --user, I’m not sure) to find the process (PID and command line) that currently provides this service. It’s likely that bspm was upgraded but an old version is still running; kill the process and let it restart automatically.

    (It’s also possible that you somehow have two versions of bspm – R is trying to use 0.5.1 which expects the available() method to be available, but D-Bus is set up to automatically start a much older version.)

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  2. 0

    Make sure that bspm is installed via sudo — the error is indicative of it not being the case.

    The bspm docs state

    Then, you should install bspm as a system package to be able to use it as a regular user. Download the latest version from CRAN or GitHub and proceed with the installation (note sudo):

    $ sudo R CMD INSTALL bspm_[version].tar.gz

    The error message is a little confusing, and can happen if you say, upgrade bspm via a normal installation and thereby ‘drop’ the system level aspect.

    You can also call the helper function bspm::shadowed_packages() to see if you accidentally installed a second copy of bspm in the .libPaths().

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