Possible solution to R installation problemst for Linux Mint 19 users

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Possible solution to R installation problemst for Linux Mint 19 users

R help mailing list-2
Hello!

If you're a newly-minted (pun _fully_ intended) user of Linux Mint 19
("Tara") and you find you're having issues installing R (as I just have),
please read on as I may have a solution for you.

To set out the context, the problem looks like this:

You (naturally) consult the relevant webpage at cran.r-project.org for your
Linux Mint system (ubuntu) and add the pub key (I've always used Michael
Rutter's). On my last Linux Mint system (18.2), I was using the following
repositories

deb http://cran.ma.imperial.ac.uk/bin/linux/ubuntu xenial/
deb-src http://cran.ma.imperial.ac.uk/bin/linux/ubuntu xenial/

which worked fine for me. Unfortunately on my new Linux Mint 19 system:

clive@climate:~$ sudo apt-get update
clive@climate:~$ sudo apt-get upgrade
clive@climate:~$ sudo apt-get install r-base r-base-core r-base-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies.
 r-base-core : Depends: libcurl3 (>= 7.28.0) but it is not going to be
installed
               Depends: libpng12-0 (>= 1.2.13-4) but it is not installable
               Depends: libreadline6 (>= 6.0) but it is not installable
E: Unable to correct problems, you have held broken packages.

No matter how many legitimate bash calls I made, such as

sudo dpkg --configure -a # NOT CURRENTLY WORKING PROPERLY AT PRESENT - THE
LINUX TEAM ARE ONTO THIS, APPARENTLY
sudo apt-get -f install
sudo apt-get --fix-broken install r-base r-base-core r-base-dev

nothing worked: I would simply get variations of the same error.

It turns out the solution is to switch away from -xenial- to *-artful-* (a
repository I've never used before and which appears to be the newest of all
the Ubuntu repositories), so that

deb http://cran.ma.imperial.ac.uk/bin/linux/ubuntu artful/
deb-src http://cran.ma.imperial.ac.uk/bin/linux/ubuntu artful/

(or whichever is your favourite mirror).

Then:

clive@climate:~$ sudo apt-get install r-base r-base-core r-base-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
  cdbs dh-translations jq libfile-which-perl libjq1 libonig4 python3-scour
r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
r-cran-kernsmooth
  r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme
r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended scour
Suggested packages:
  devscripts ess r-doc-info | r-doc-pdf r-mathlib r-base-html
gir1.2-rsvg-2.0
Recommended packages:
  r-base-html r-doc-html
The following NEW packages will be installed
  cdbs dh-translations jq libfile-which-perl libjq1 libonig4 python3-scour
r-base r-base-core r-base-dev r-cran-boot r-cran-class r-cran-cluster
r-cran-codetools
  r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix
r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial
r-cran-survival
  r-recommended scour
0 to upgrade, 27 to newly install, 0 to remove and 3 not to upgrade.
Need to get 39.5 MB of archives.
After this operation, 59.9 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://ftp.snt.utwente.nl/pub/os/linux/ubuntu bionic/universe amd64
libonig4 amd64 6.7.0-1 [119 kB]

[...]

Setting up r-base (3.4.4-1ubuntu1) ...
clive@climate:~$ R

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> plot(rnorm(1000)) # GRAPHIC DULY PRODUCED WITH NO ISSUES!
> q()
Save workspace image? [y/n/c]: n
clive@climate:~$

*Volia!* (Okay, so it doesn't install R 3.5.1 - the latest version - but
that should eventually correct itself with future updates.)

So, if you're having the same R installation problems I've just had after
migrating to Linux Mint 19, this should work for you. Good luck. :)


--
Clive Nicholas

"My colleagues in the social sciences talk a great deal about methodology.
I prefer to call it style." -- Freeman J. Dyson

        [[alternative HTML version deleted]]

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Re: Possible solution to R installation problemst for Linux Mint 19 users

Jeff Newmiller
Each Mint version builds from an Ubuntu version. I don't use Mint. but this [1] web page tells me you should be pulling from a Bionic repo. Artful may work for you now, but in general it is risky to mix distribution revisions.

Note that this informative discussion should have occurred on the R-sig-debian mailing list, as it involves the intersection of R and debian derivatives, and is not about the R language as this mailing list is.

[1] https://linuxmint.com/download_all.php



On July 21, 2018 5:50:02 PM PDT, Clive Nicholas via R-help <[hidden email]> wrote:

>Hello!
>
>If you're a newly-minted (pun _fully_ intended) user of Linux Mint 19
>("Tara") and you find you're having issues installing R (as I just
>have),
>please read on as I may have a solution for you.
>
>To set out the context, the problem looks like this:
>
>You (naturally) consult the relevant webpage at cran.r-project.org for
>your
>Linux Mint system (ubuntu) and add the pub key (I've always used
>Michael
>Rutter's). On my last Linux Mint system (18.2), I was using the
>following
>repositories
>
>deb http://cran.ma.imperial.ac.uk/bin/linux/ubuntu xenial/
>deb-src http://cran.ma.imperial.ac.uk/bin/linux/ubuntu xenial/
>
>which worked fine for me. Unfortunately on my new Linux Mint 19 system:
>
>clive@climate:~$ sudo apt-get update
>clive@climate:~$ sudo apt-get upgrade
>clive@climate:~$ sudo apt-get install r-base r-base-core r-base-dev
>Reading package lists... Done
>Building dependency tree
>Reading state information... Done
>Some packages could not be installed. This may mean that you have
>requested an impossible situation or if you are using the unstable
>distribution that some required packages have not yet been created
>or been moved out of Incoming.
>The following information may help to resolve the situation:
>
>The following packages have unmet dependencies.
> r-base-core : Depends: libcurl3 (>= 7.28.0) but it is not going to be
>installed
>            Depends: libpng12-0 (>= 1.2.13-4) but it is not installable
>               Depends: libreadline6 (>= 6.0) but it is not installable
>E: Unable to correct problems, you have held broken packages.
>
>No matter how many legitimate bash calls I made, such as
>
>sudo dpkg --configure -a # NOT CURRENTLY WORKING PROPERLY AT PRESENT -
>THE
>LINUX TEAM ARE ONTO THIS, APPARENTLY
>sudo apt-get -f install
>sudo apt-get --fix-broken install r-base r-base-core r-base-dev
>
>nothing worked: I would simply get variations of the same error.
>
>It turns out the solution is to switch away from -xenial- to *-artful-*
>(a
>repository I've never used before and which appears to be the newest of
>all
>the Ubuntu repositories), so that
>
>deb http://cran.ma.imperial.ac.uk/bin/linux/ubuntu artful/
>deb-src http://cran.ma.imperial.ac.uk/bin/linux/ubuntu artful/
>
>(or whichever is your favourite mirror).
>
>Then:
>
>clive@climate:~$ sudo apt-get install r-base r-base-core r-base-dev
>Reading package lists... Done
>Building dependency tree
>Reading state information... Done
>The following additional packages will be installed:
>cdbs dh-translations jq libfile-which-perl libjq1 libonig4
>python3-scour
>r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
>r-cran-kernsmooth
>  r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme
>r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended
>scour
>Suggested packages:
>  devscripts ess r-doc-info | r-doc-pdf r-mathlib r-base-html
>gir1.2-rsvg-2.0
>Recommended packages:
>  r-base-html r-doc-html
>The following NEW packages will be installed
>cdbs dh-translations jq libfile-which-perl libjq1 libonig4
>python3-scour
>r-base r-base-core r-base-dev r-cran-boot r-cran-class r-cran-cluster
>r-cran-codetools
>r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass
>r-cran-matrix
>r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial
>r-cran-survival
>  r-recommended scour
>0 to upgrade, 27 to newly install, 0 to remove and 3 not to upgrade.
>Need to get 39.5 MB of archives.
>After this operation, 59.9 MB of additional disk space will be used.
>Do you want to continue? [Y/n] y
>Get:1 http://ftp.snt.utwente.nl/pub/os/linux/ubuntu bionic/universe
>amd64
>libonig4 amd64 6.7.0-1 [119 kB]
>
>[...]
>
>Setting up r-base (3.4.4-1ubuntu1) ...
>clive@climate:~$ R
>
>R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
>Copyright (C) 2018 The R Foundation for Statistical Computing
>Platform: x86_64-pc-linux-gnu (64-bit)
>
>R is free software and comes with ABSOLUTELY NO WARRANTY.
>You are welcome to redistribute it under certain conditions.
>Type 'license()' or 'licence()' for distribution details.
>
>  Natural language support but running in an English locale
>
>R is a collaborative project with many contributors.
>Type 'contributors()' for more information and
>'citation()' on how to cite R or R packages in publications.
>
>Type 'demo()' for some demos, 'help()' for on-line help, or
>'help.start()' for an HTML browser interface to help.
>Type 'q()' to quit R.
>
>> plot(rnorm(1000)) # GRAPHIC DULY PRODUCED WITH NO ISSUES!
>> q()
>Save workspace image? [y/n/c]: n
>clive@climate:~$
>
>*Volia!* (Okay, so it doesn't install R 3.5.1 - the latest version -
>but
>that should eventually correct itself with future updates.)
>
>So, if you're having the same R installation problems I've just had
>after
>migrating to Linux Mint 19, this should work for you. Good luck. :)

--
Sent from my phone. Please excuse my brevity.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.