Ubuntu

upgrade error after installing R

Asked by Salman Ullah Siddiqui on 2020-08-09

I installed R after that i am facing following issues in upgrading

(base) salmansiddiqui@salmansiddiqui-Latitude-E5440:~$ sudo apt update
Hit:1 http://security.ubuntu.com/ubuntu bionic-security InRelease
Hit:2 http://sa.archive.ubuntu.com/ubuntu bionic InRelease
Hit:3 http://sa.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:4 http://sa.archive.ubuntu.com/ubuntu bionic-backports InRelease
Hit:6 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease
Hit:5 https://packages.cloud.google.com/apt kubernetes-xenial InRelease
Reading package lists... Done
Building dependency tree
Reading state information... Done
2 packages can be upgraded. Run 'apt list --upgradable' to see them.
(base) salmansiddiqui@salmansiddiqui-Latitude-E5440:~$ sudo apt upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages were automatically installed and are no longer required:
  cdbs dh-translations intltool jq libfile-which-perl libjq1 libonig4 python3-scour scour
Use 'sudo apt autoremove' to remove them.
The following packages will be upgraded:
  r-base-html r-doc-html
2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
20 not fully installed or removed.
Need to get 660 kB of archives.
After this operation, 71.7 kB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ r-base-html 3.6.3-1bionic [89.7 kB]
Get:2 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ r-doc-html 3.6.3-1bionic [570 kB]
Fetched 660 kB in 1s (812 kB/s)
debconf: DbDriver "config": /var/cache/debconf/config.dat is locked by another process: Resource temporarily unavailable
(Reading database ... 230273 files and directories currently installed.)
Preparing to unpack .../r-base-html_3.6.3-1bionic_all.deb ...
Unpacking r-base-html (3.6.3-1bionic) over (3.4.4-1ubuntu1) ...
Preparing to unpack .../r-doc-html_3.6.3-1bionic_all.deb ...
Unpacking r-doc-html (3.6.3-1bionic) over (3.4.4-1ubuntu1) ...
Setting up r-base-core (3.6.3-1bionic) ...
debconf: DbDriver "config": /var/cache/debconf/config.dat is locked by another process: Resource temporarily unavailable
dpkg: error processing package r-base-core (--configure):
installed r-base-core package post-installation script subprocess returned error exit status 1
dpkg: dependency problems prevent configuration of r-cran-class:
r-cran-class depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-class depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-class (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-kernsmooth:
r-cran-kernsmooth depends on r-base-core; however:
Package r-base-core is not configured yet.

dpkg: error processing package r-cran-kernsmooth (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-nnet:
r-cran-nnet depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-nnet depends on r-api-3.5; however:
No apport report written because the error message indicates its a followup error from a previous failure.
                                                                                                          No apport report written because the error message indicates its a followup error from a previous failure.
                                            No apport report written because MaxReports is reached already

Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-nnet (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-base-dev:
r-base-dev depends on r-base-core (>= 3.6.3-1bionic); however:
Package r-base-core is not configured yet.

dpkg: error processing package r-base-dev (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-mgcv:
r-cran-mgcv depends on r-base-core; however:
Package r-base-core is not configured yet.

No apport report written because MaxReports is reached already
                                                              No apport report written because MaxReports is reached already
                                                                                                                            No apport report written because MaxReports is reached already
                  dpkg: error processing package r-cran-mgcv (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-rpart:
r-cran-rpart depends on r-base-core (>= 3.6.1-3bionic); however:
  Package r-base-core is not configured yet.
r-cran-rpart depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-rpart (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-base-html:
r-base-html depends on r-base-core; however:
Package r-base-core is not configured yet.

dpkg: error processing package r-base-html (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-spatial:
r-cran-spatial depends on r-base-core (>= 3.5.0-1bionic); however:
  Package r-base-core is not No apport report written because MaxReports is reached already
                                                                                           No apport report written because MaxReports is reached already
                                                                                                                                                         No apport report written because MaxReports is reached already
                                               configured yet.
r-cran-spatial depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-spatial (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-base:
r-base depends on r-base-core (>= 3.6.3-1bionic); however:
Package r-base-core is not configured yet.

No apport report written because MaxReports is reached already
                                                              dpkg: error processing package r-base (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-mass:
r-cran-mass depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-mass depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-mass (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-survival:
r-cran-survival depends on r-base-core; however:
Package r-base-core is not configured yet.

dpkg: error processing package r-cran-survival (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-cluster:
r-cran-cluster depends on r-base-core (>= 3.6.1-3bionic); however:
  Package r-base-core is nNo apport report written because MaxReports is reached already
                                                                                        No apport report written because MaxReports is reached already
                                                                                                                                                      ot configured yet.
r-cran-cluster depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-cluster (--configure):
dependency problems - leaving unconfigured
Setting up r-doc-html (3.6.3-1bionic) ...
dpkg: dependency problems prevent configuration of r-cran-boot:
r-cran-boot depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-boot depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-boot (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-recommended:
r-recommended depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-recommended depends on r-cran-boot (>= 1.2.19); however:
  Package r-cran-boot is not configured yet.
r-recommended depends on r-cran-cluster (>= 1.9.6-2); however:
  Package r-cran-cluster is not configured yet.
r-recommended depends on r-cran-kernsmooth (>= 2.2.14); however:
  Package r-cran-kernsmooth is not configured yet.
r-recommended depends on r-cran-mgcv (>=No apport report written because MaxReports is reached already
                                                                                                       No apport report written because MaxReports is reached already
                                                                                                                                                                     No apport report written because MaxReports is reached already
                                                           No apport report written because MaxReports is reached already
                                                                                                                         No apport report written because MaxReports is reached already
               No apport report written because MaxReports is reached already
                                                                             No apport report written because MaxReports is reached already
                                                                                                                                            1.1.5); however:
  Package r-cran-mgcv is not configured yet.
r-recommended depends on r-cran-rpart (>= 3.1.20); however:
  Package r-cran-rpart is not configured yet.
r-recommended depends on r-cran-survival (>= 2.13.2-1); however:
  Package r-cran-survival is not configured yet.
r-recommended depends on r-cran-mass; however:
  Package r-cran-mass is not configured yet.
r-recommended depends on r-cran-class; however:
  Package r-cran-class is not configured yet.
r-recommended depends on r-cran-nnet; however:
  Package r-cran-nnet is not configured yet.
r-recommended depends on r-cran-spatial; however:
  Package r-cran-spatial is not configured yet.

dpkg: error processing package r-recommended (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-codetools:
r-cran-codetools depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-codetools depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-codetools (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-matrix:
r-cran-matrix depends on r-base-core (>= 3.6.1-3bionic); however:
  Package r-base-core is not configured yet.
r-cran-matrix depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-matrix (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-lattice:
r-cran-lattice depends on r-base-core; however:
Package r-base-core is not configured yet.

dpkg: error processing package r-cran-lattice (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-nlme:
r-cran-nlme depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-nlme depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.
r-cran-nlme depends on r-cran-lattice (>= 0.12-11.1); however:
  Package r-cran-lattice is not configured yet.

dpkg: error processing package r-cran-nlme (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-foreign:
r-cran-foreign depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-foreign depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-foreign (--configure):
dependency problems - leaving unconfigured
Errors were encountered while processing:
r-base-core
r-cran-class
r-cran-kernsmooth
r-cran-nnet
r-base-dev
r-cran-mgcv
r-cran-rpart
r-base-html
r-cran-spatial
r-base
r-cran-mass
r-cran-survival
r-cran-cluster
r-cran-boot
r-recommended
r-cran-codetools
r-cran-matrix
r-cran-lattice
r-cran-nlme
r-cran-foreign
E: Sub-process /usr/bin/dpkg returned an error code (1)
(base) salmansiddiqui@salmansiddiqui-Latitude-E5440:~$ uname -a
Linux salmansiddiqui-Latitude-E5440 5.4.0-42-generic #46~18.04.1-Ubuntu SMP Fri Jul 10 07:21:24 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
(base) salmansiddiqui@salmansiddiqui-Latitude-E5440:~$ lsb_release -crid
Distributor ID: Ubuntu
Description: Ubuntu 18.04.5 LTS
Release: 18.04
Codename: bionic
(base) salmansiddiqui@salmansiddiqui-Latitude-E5440:~$ sudo dpkg --audit
The following packages have been unpacked but not yet configured.
They must be configured using dpkg --configure or the configure
menu option in dselect for them to work:
r-base GNU R statistical computation and graphics system
r-base-dev GNU R installation of auxiliary GNU R packages
r-base-html GNU R html docs for statistical computing system function
r-cran-boot GNU R package for bootstrapping functions from Davison an
r-cran-class GNU R package for classification
r-cran-cluster GNU R package for cluster analysis by Rousseeuw et al
r-cran-codetools GNU R package providing code analysis tools
r-cran-foreign GNU R package to read/write data from other stat. systems
r-cran-kernsmooth GNU R package "Functions for Kernel Smoothing Supporting
r-cran-lattice GNU R package "Trellis Graphics for R"
r-cran-mass GNU R package of Venables and Ripley's MASS
r-cran-matrix GNU R package of classes for dense and sparse matrices
r-cran-mgcv GNU R package "Mixed GAM Computation Vehicle with
r-cran-nlme GNU R package for (non-)linear mixed effects models
r-cran-nnet GNU R package for feed-forward neural networks
r-cran-rpart GNU R package for recursive partitioning and regression t
r-cran-spatial GNU R package for spatial statistics
r-cran-survival GNU R package "Survival Analysis"
r-recommended GNU R collection of recommended packages [metapackage]

The following packages are only half configured, probably due to problems
configuring them the first time. The configuration should be retried using
dpkg --configure <package> or the configure menu option in dselect:
r-base-core GNU R core of statistical computation and graphics system

(base) salmansiddiqui@salmansiddiqui-Latitude-E5440:~$ sudo dpkg --configure -a
Setting up r-base-core (3.6.3-1bionic) ...
debconf: DbDriver "config": /var/cache/debconf/config.dat is locked by another process: Resource temporarily unavailable
dpkg: error processing package r-base-core (--configure):
installed r-base-core package post-installation script subprocess returned error exit status 1
dpkg: dependency problems prevent configuration of r-cran-class:
r-cran-class depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-class depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-mgcv (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-rpart:
r-cran-rpart depends on r-base-core (>= 3.6.1-3bionic); however:
  Package r-base-core is not configured yet.
r-cran-rpart depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-base (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-mass:
r-cran-mass depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-mass depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-cluster (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-boot:
r-cran-boot depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-boot depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-foreign (--configure):
dependency problems - leaving unconfigured
Errors were encountered while processing:
r-base-core
r-cran-class
r-cran-kernsmooth
r-cran-nnet
r-base-dev
r-cran-mgcv
r-cran-rpart
r-base-html
r-cran-spatial
r-base
r-cran-mass
r-cran-survival
r-cran-cluster
r-cran-boot
r-recommended
r-cran-codetools
r-cran-matrix
r-cran-lattice
r-cran-nlme
r-cran-foreign
(base) salmansiddiqui@salmansiddiqui-Latitude-E5440:~$ sudo apt install -f
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
  cdbs dh-translations intltool jq libfile-which-perl libjq1 libonig4 python3-scour scour
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
20 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
debconf: DbDriver "config": /var/cache/debconf/config.dat is locked by another process: Resource temporarily unavailable
Setting up r-base-core (3.6.3-1bionic) ...
debconf: DbDriver "config": /var/cache/debconf/config.dat is locked by another process: Resource temporarily unavailable
dpkg: error processing package r-base-core (--configure):
installed r-base-core package post-installation script subprocess returned error exit status 1
dpkg: dependency problems prevent configuration of r-cran-class:
r-cran-class depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-class depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-nnet (--configure):
dependency problems - leaving unconfigured
No apport report written because MaxReports is reached already
dpkg: dependency problems prevent configuration of r-base-dev:
r-base-dev depends on r-base-core (>= 3.6.3-1bionic); however:
Package r-base-core is not configured yet.

dpkg: error processing package r-cran-mgcv (--configure):
dependency problems - leaving unconfigured
No apport report written because MaxReports is reached already
                                                              No apport report written because MaxReports is reached already
                                                                                                                            dpkg: dependency problems prevent configuration of r-cran-rpart:
r-cran-rpart depends on r-base-core (>= 3.6.1-3bionic); however:
  Package r-base-core is not configured yet.
r-cran-rpart depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-base-html (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of r-cran-spatial:
r-cran-spatial depends on r-base-core (>= 3.5.0-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-spatial depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  PackagNo apport report written because MaxReports is reached already
                                                                      No apport report written because MaxReports is reached already
                                                                                                                                    No apport report written because MaxReports is reached already
                          e r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-mass (--configure):
dependency problems - leaving unconfigured
No apport report written because MaxReports is reached already
                                                              No apport report written because MaxReports is reached already
                                                                                                                            dpkg: dependency problems prevent configuration of r-cran-survival:
r-cran-survival depends on r-base-core; however:
  Package r-base-core is not configured yet.

dpkg: error processing package r-cran-cluster (--configure):
dependency problems - leaving unconfigured
No apport report written because MaxReports is reached already
                                                              dpkg: dependency problems prevent configuration of r-cran-boot:
r-cran-boot depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-boot depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-boot (--configure):
dependency problems - leaving unconfigured
No apport report written because MaxReports is reached already
                                                              dpkg: dependency problems prevent configuration of r-recommended:
r-recommended depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-recommended depends on r-cran-boot (>= 1.2.19); however:
  Package r-cran-boot is not configured yet.
r-recommended depends on r-cran-cluster (>= 1.9.6-2); however:
  Package r-cran-cluster is not configured yet.
r-recommended depends on r-cran-kernsmooth (>= 2.2.14); however:
  Package r-cran-kernsmooth is not configured yet.
r-recommended depends on r-cran-mgcv (>= 1.1.5); however:
  Package r-cran-mgcv is not configured yet.
r-recommended depends on r-cran-rpart (>= 3.1.20); however:
  Package r-cran-rpart is not configured yet.
r-recommended depends on r-cran-survival (>= 2.13.2-1); however:
  Package r-cran-survival is not configured yet.
r-recommended depends on r-cran-mass; however:
  Package r-cran-mass is not configured yet.
r-recommended depends on r-cran-class; however:
  Package r-cran-class is not configured yet.
r-recommended depends on r-cran-nnet; however:
  Package r-cran-nnet is not configured yet.
r-recommended depends on r-cran-spatial; however:
  Package r-cran-spatial is not configured yet.

dpkg: error processing package r-recommended (--configure):
dependency problems - leaving unconfigured
No apport report written because MaxReports is reached already
                                                              No apport report written because MaxReports is reached already
                                                                                                                            dpkg: dependency problems prevent configuration of r-cran-codetools:
r-cran-codetools depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-codetools depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-matrix (--configure):
dependency problems - leaving unconfigured
No apport report written because MaxReports is reached already
dpkg: dependency problems prevent configuration of r-cran-lattice:
r-cran-lattice depends on r-base-core; however:
Package r-base-core is not configured yet.

dpkg: error processing package r-cran-lattice (--configure):
dependency problems - leaving unconfigured
No apport report written because MaxReports is reached already
                                                              dpkg: dependency problems prevent configuration of r-cran-nlme:
r-cran-nlme depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-nlme depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.
r-cran-nlme depends on r-cran-lattice (>= 0.12-11.1); however:
  Package r-cran-lattice is not configured yet.

dpkg: error processing package r-cran-nlme (--configure):
dependency problems - leaving unconfigured
No apport report written because MaxReports is reached already
                                                              dpkg: dependency problems prevent configuration of r-cran-foreign:
r-cran-foreign depends on r-base-core (>= 3.6.3-1bionic); however:
  Package r-base-core is not configured yet.
r-cran-foreign depends on r-api-3.5; however:
  Package r-api-3.5 is not installed.
  Package r-base-core which provides r-api-3.5 is not configured yet.

dpkg: error processing package r-cran-foreign (--configure):
dependency problems - leaving unconfigured
No apport report written because MaxReports is reached already
Errors were encountered while processing:
r-base-core
r-cran-class
r-cran-kernsmooth
r-cran-nnet
r-base-dev
r-cran-mgcv
r-cran-rpart
r-base-html
r-cran-spatial
r-base
r-cran-mass
r-cran-survival
r-cran-cluster
r-cran-boot
r-recommended
r-cran-codetools
r-cran-matrix
r-cran-lattice
r-cran-nlme
r-cran-foreign
E: Sub-process /usr/bin/dpkg returned an error code (1)

Question information

Language:: English Edit question

Status:: Answered

For:: Ubuntu Edit question

Assignee:: No assignee Edit question

Last query:: 2020-08-09

Last reply:: 2020-08-11

Link existing bug

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actionparsnip (andrew-woodhead666) said on 2020-08-09:

I suggest you contact the repository maintainer of the repository you added. The files you want are in the default Ubuntu repositories so why add anything? You can use apt on a default install and the packages will install without issues.

If you remove the 3rd party source, remove the R packages you have installed then run:

sudo apt clean

You should then be able to install the application from the Canonical sources.

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Manfred Hampl (m-hampl) said on 2020-08-10:

debconf: DbDriver "config": /var/cache/debconf/config.dat is locked by another process: Resource temporarily unavailable

Ubuntu's package management system makes sure that only one package management program runs at a certain moment in time to avoid concurrent update (imagine, in one window you install a package that depends on presence of another package, but in a second window you uninstall that package at the same time).

Apparently there is a stalled package installation program running in the background, now preventing all further updates.

To clean-up that situation try the commands

sudo fuser --verbose --kill -SIGTERM /var/cache/debconf/config.dat
sudo dpkg --configure -a

and report the results.

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Salman Ullah Siddiqui (salman079) said on 2020-08-11:

Actually i uninstalled the R as asked earlier.
Now i ran the above commands and this is the output
i will install R again and see the result

(base) salmansiddiqui@salmansiddiqui-Latitude-E5440:~$ sudo fuser --verbose --kill -SIGTERM /var/cache/debconf/config.dat
[sudo] password for salmansiddiqui:
Sorry, try again.
[sudo] password for salmansiddiqui:
USER PID ACCESS COMMAND
/var/cache/debconf/config.dat:
root 7831 F.... frontend
(base) salmansiddiqui@salmansiddiqui-Latitude-E5440:~$ sudo fuser --verbose --kill -SIGTERM /var/cache/debconf/config.dat
(base) salmansiddiqui@salmansiddiqui-Latitude-E5440:~$ sudo dpkg --configure -a
Setting up r-base-core (3.6.3-1bionic) ...

Creating config file /etc/R/Renviron with new version
Setting up r-cran-kernsmooth (2.23-17-1cran1.1804.0) ...
Setting up r-cran-nnet (7.3-14-1.1804.0) ...
Setting up r-base-dev (3.6.3-1bionic) ...
Setting up r-cran-spatial (7.3-11-2cranArtful0~ubuntu18.04.1~ppa1) ...
Setting up r-cran-mass (7.3-51.6-1.1804.0) ...
Setting up r-cran-cluster (2.1.0-2bionic0) ...
Setting up r-cran-boot (1.3-25-2.1804.0) ...
Setting up r-cran-codetools (0.2-16-2.1804.0) ...
Setting up r-cran-lattice (0.20-41-1cran1bionic0) ...
Setting up r-cran-nlme (3.1.147-1.1804.0) ...
Setting up r-cran-foreign (0.8.76-1.1804.0) ...
Setting up r-cran-class (7.3-17-1.1804.0) ...
Setting up r-cran-matrix (1.2-18-1bionic0) ...
Setting up r-cran-mgcv (1.8-31-1cran1bionic0) ...
Setting up r-cran-survival (3.1-12-1cran1.1804.0) ...
Setting up r-cran-rpart (4.1-15-2bionic0) ...
Setting up r-recommended (3.6.3-1bionic) ...

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actionparsnip (andrew-woodhead666) said on 2020-08-11:

Looks good. Are you able to use the application now?

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Salman Ullah Siddiqui (salman079) said on 2020-10-14:

what is this???

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Manfred Hampl (m-hampl) said on 2020-10-14:

Comment #5 is spam. Just ignore it.

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upgrade error after installing R

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