R SIG Debian - Mar 2016 - Outdated r-base-core when installing on Ubuntu 14.04

Since 14.04 is the Long Term Support version, which also is used by
Linux Mint, it's not really outdated, and a lot of folk, myself
included, use that stream (my machine says Linux Mint 17.1, but I think
that is simply the splash screen). I say stream, because the kernel and
other infrastructure are  being updated, though probably not to the
level Dirk prefers, and I do use other distros for some work. My own
sources.list includes

deb http://cran.stat.sfu.ca/bin/linux/ubuntu trusty/

and R updated fine to 3.2.4 last week with a typical automated prompt
that there were updates available.

So maybe Matt's problem is something else. This was the first time I'd
read about crouton (I run regular Linux distros). Is that getting in the
way somehow?

JN



On 16-03-21 01:35 PM, Dirk Eddelbuettel wrote:
> 
> On 21 March 2016 at 12:10, Matthew Simpson wrote:
> | I have a chromebook with a fresh minimal install of Ubuntu 14.04 running
> | through crouton, and I'm trying to install the latest version of R.
The
> | only thing I have done to the system before trying to install R is
install
> | gedit. When I try to install R I get an unmet dependencies error that
> | complains that the version of r-base-core available isn't new enough.
> | 
> | I followed the instructions at
> | https://cran.r-project.org/bin/linux/ubuntu/README.html to install R.
Here
> | is precisely what I did:
> | 
> | 1) after installing gedit, I added the following two lines to
> | /etc/apt/sources.list
> | 
> | deb http://cran.wustl.edu/bin/linux/ubuntu trusty/
> | deb http://ports.ubuntu.com/ubuntu-ports/ trusty-backports main
restricted
> | universe
> | 
> | (Note: I've tried a couple different R mirrors and it doesn't
affect
> | anything as far as I can
> | tell)
> | 
> | 2) Add Michael Rutter's key with
> | 
> | sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
> | 
> | 3) Update sources and attempt to install R:
> | 
> | sudo apt-get update
> | sudo apt-get install r-base
> | 
> | Here is the full text of the error I get:
> | 
> | sudo apt-get install r-base
> | 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 : Depends: r-base-core (>= 3.2.4-revised-1trusty0) but it is
not
> | going to be installed
> |           Depends: r-recommended (= 3.2.4-revised-1trusty0) but it is not
> | going to be installed
> |           Recommends: r-base-html but it is not going to be installed
> |           Recommends: r-doc-html but it is not going to be installed
> | E: Unable to correct problems, you have held broken packages.
> | 
> | 
> | Using sudo apt-cache showpkg <package> reveals that apt is
attempting to
> | install r-base 3.2.4, but only has access to r-base-core 3.0.2.  It does
> | have access to r-recommended, r-base-html, and r-doc-html all version
3.2.4
> | though.
> 
> Then something is wrong with your apt entries. Check and double check.
> 
> I run wily here (because why would I want to be on an almost two year old
> OS?) and it looks as follows:
> 
> edd at max:~$ apt-cache policy r-base
> r-base:
>   Installed: (none)
>   Candidate: 3.2.4-revised-1wily0
>   Version table:
>      3.2.4-revised-1wily0 0
>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>      3.2.4-1wily 0
>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>      3.2.3-6wily0 0
>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>      3.2.3-4wily0 0
>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>      3.2.3-3wily0 0
>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>      3.2.3-1.wily.0 0
>         500 http://ppa.launchpad.net/edd/misc/ubuntu/ wily/main amd64
Packages
>      3.2.3-1wily1 0
>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>      3.2.3-1wily0 0
>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>      3.2.2-1wily 0
>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>      3.2.2-1 0
>         500 http://archive.ubuntu.com/ubuntu/ wily/universe amd64 Packages
> edd at max:~$ 
> 
> I could have 3.2.2 from the distro -- which makes sense as 15.10 had a
cutoff
> some time last summer -- all the other thanks to Michael rebuilding the
ports
> of why I stick into Debian.
> 
> Dirk
> 
> | 
> | I could probably live with R 3.0.2, but sudo apt-get install r-base=3.0.2
> | yields a similar error complaining that it needs r-recommended 3.0.2, but
> | it won't be installed.
> | 
> | Any help would be appreciated.
> | 
> | Thanks,
> | Matt Simpson
> | 
> | 	[[alternative HTML version deleted]]
> | 
> | _______________________________________________
> | R-SIG-Debian mailing list
> | R-SIG-Debian at r-project.org
> | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>

Probably should add that my machine has Michael's PPA

deb http://ppa.launchpad.net/marutter/rrutter/ubuntu trusty main

as well. That could, of course, be how I got 3.2.4.

If I get a chance later today, I'll try a VirtualBox VM with a clean
Ubuntu 14.04.

JN

On 16-03-21 02:04 PM, ProfJCNash wrote:
> Since 14.04 is the Long Term Support version, which also is used by
> Linux Mint, it's not really outdated, and a lot of folk, myself
> included, use that stream (my machine says Linux Mint 17.1, but I think
> that is simply the splash screen). I say stream, because the kernel and
> other infrastructure are  being updated, though probably not to the
> level Dirk prefers, and I do use other distros for some work. My own
> sources.list includes
> 
> deb http://cran.stat.sfu.ca/bin/linux/ubuntu trusty/
> 
> and R updated fine to 3.2.4 last week with a typical automated prompt
> that there were updates available.
> 
> So maybe Matt's problem is something else. This was the first time
I'd
> read about crouton (I run regular Linux distros). Is that getting in the
> way somehow?
> 
> JN
> 
> 
> 
> On 16-03-21 01:35 PM, Dirk Eddelbuettel wrote:
>>
>> On 21 March 2016 at 12:10, Matthew Simpson wrote:
>> | I have a chromebook with a fresh minimal install of Ubuntu 14.04
running
>> | through crouton, and I'm trying to install the latest version of
R. The
>> | only thing I have done to the system before trying to install R is
install
>> | gedit. When I try to install R I get an unmet dependencies error that
>> | complains that the version of r-base-core available isn't new
enough.
>> | 
>> | I followed the instructions at
>> | https://cran.r-project.org/bin/linux/ubuntu/README.html to install R.
Here
>> | is precisely what I did:
>> | 
>> | 1) after installing gedit, I added the following two lines to
>> | /etc/apt/sources.list
>> | 
>> | deb http://cran.wustl.edu/bin/linux/ubuntu trusty/
>> | deb http://ports.ubuntu.com/ubuntu-ports/ trusty-backports main
restricted
>> | universe
>> | 
>> | (Note: I've tried a couple different R mirrors and it doesn't
affect
>> | anything as far as I can
>> | tell)
>> | 
>> | 2) Add Michael Rutter's key with
>> | 
>> | sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys
E084DAB9
>> | 
>> | 3) Update sources and attempt to install R:
>> | 
>> | sudo apt-get update
>> | sudo apt-get install r-base
>> | 
>> | Here is the full text of the error I get:
>> | 
>> | sudo apt-get install r-base
>> | 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 : Depends: r-base-core (>= 3.2.4-revised-1trusty0) but it
is not
>> | going to be installed
>> |           Depends: r-recommended (= 3.2.4-revised-1trusty0) but it is
not
>> | going to be installed
>> |           Recommends: r-base-html but it is not going to be installed
>> |           Recommends: r-doc-html but it is not going to be installed
>> | E: Unable to correct problems, you have held broken packages.
>> | 
>> | 
>> | Using sudo apt-cache showpkg <package> reveals that apt is
attempting to
>> | install r-base 3.2.4, but only has access to r-base-core 3.0.2.  It
does
>> | have access to r-recommended, r-base-html, and r-doc-html all version
3.2.4
>> | though.
>>
>> Then something is wrong with your apt entries. Check and double check.
>>
>> I run wily here (because why would I want to be on an almost two year
old
>> OS?) and it looks as follows:
>>
>> edd at max:~$ apt-cache policy r-base
>> r-base:
>>   Installed: (none)
>>   Candidate: 3.2.4-revised-1wily0
>>   Version table:
>>      3.2.4-revised-1wily0 0
>>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>>      3.2.4-1wily 0
>>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>>      3.2.3-6wily0 0
>>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>>      3.2.3-4wily0 0
>>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>>      3.2.3-3wily0 0
>>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>>      3.2.3-1.wily.0 0
>>         500 http://ppa.launchpad.net/edd/misc/ubuntu/ wily/main amd64
Packages
>>      3.2.3-1wily1 0
>>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>>      3.2.3-1wily0 0
>>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>>      3.2.2-1wily 0
>>         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
>>      3.2.2-1 0
>>         500 http://archive.ubuntu.com/ubuntu/ wily/universe amd64
Packages
>> edd at max:~$ 
>>
>> I could have 3.2.2 from the distro -- which makes sense as 15.10 had a
cutoff
>> some time last summer -- all the other thanks to Michael rebuilding the
ports
>> of why I stick into Debian.
>>
>> Dirk
>>
>> | 
>> | I could probably live with R 3.0.2, but sudo apt-get install
r-base=3.0.2
>> | yields a similar error complaining that it needs r-recommended 3.0.2,
but
>> | it won't be installed.
>> | 
>> | Any help would be appreciated.
>> | 
>> | Thanks,
>> | Matt Simpson
>> | 
>> | 	[[alternative HTML version deleted]]
>> | 
>> | _______________________________________________
>> | R-SIG-Debian mailing list
>> | R-SIG-Debian at r-project.org
>> | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>>

Thanks for the replies.

Crouton does get in the way of installing arbitrary linux distros - in
particular the only ubuntu distros that are fully supported are precise and
trusty (12.04 and 14.04). Others have gotten vivid and wily to work with
some effort. I found a reasonably detailed guide for vivid, so I'm
currently installing it on the machine. We'll see how it goes. Once it's
done installing, I'll recheck apt entries and try adding Michael's PPA
&
some different R mirriors in vivid (if I get it working) and trusty and
report back.

It may be significant that my chromebook has an ARM processor. I don't know
about the details of how this works, but perhaps some pieces of the R
install haven't been ported to the appropriate architecture?

Matt

On Mon, Mar 21, 2016 at 1:04 PM, ProfJCNash <profjcnash at gmail.com>
wrote:
> Since 14.04 is the Long Term Support version, which also is used by
> Linux Mint, it's not really outdated, and a lot of folk, myself
> included, use that stream (my machine says Linux Mint 17.1, but I think
> that is simply the splash screen). I say stream, because the kernel and
> other infrastructure are  being updated, though probably not to the
> level Dirk prefers, and I do use other distros for some work. My own
> sources.list includes
>
> deb http://cran.stat.sfu.ca/bin/linux/ubuntu trusty/
>
> and R updated fine to 3.2.4 last week with a typical automated prompt
> that there were updates available.
>
> So maybe Matt's problem is something else. This was the first time
I'd
> read about crouton (I run regular Linux distros). Is that getting in the
> way somehow?
>
> JN
>
>
>
> On 16-03-21 01:35 PM, Dirk Eddelbuettel wrote:
> >
> > On 21 March 2016 at 12:10, Matthew Simpson wrote:
> > | I have a chromebook with a fresh minimal install of Ubuntu 14.04
> running
> > | through crouton, and I'm trying to install the latest version of
R. The
> > | only thing I have done to the system before trying to install R is
> install
> > | gedit. When I try to install R I get an unmet dependencies error
that
> > | complains that the version of r-base-core available isn't new
enough.
> > |
> > | I followed the instructions at
> > | https://cran.r-project.org/bin/linux/ubuntu/README.html to install
R.
> Here
> > | is precisely what I did:
> > |
> > | 1) after installing gedit, I added the following two lines to
> > | /etc/apt/sources.list
> > |
> > | deb http://cran.wustl.edu/bin/linux/ubuntu trusty/
> > | deb http://ports.ubuntu.com/ubuntu-ports/ trusty-backports main
> restricted
> > | universe
> > |
> > | (Note: I've tried a couple different R mirrors and it
doesn't affect
> > | anything as far as I can
> > | tell)
> > |
> > | 2) Add Michael Rutter's key with
> > |
> > | sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys
E084DAB9
> > |
> > | 3) Update sources and attempt to install R:
> > |
> > | sudo apt-get update
> > | sudo apt-get install r-base
> > |
> > | Here is the full text of the error I get:
> > |
> > | sudo apt-get install r-base
> > | 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 : Depends: r-base-core (>= 3.2.4-revised-1trusty0) but it
is
> not
> > | going to be installed
> > |           Depends: r-recommended (= 3.2.4-revised-1trusty0) but it
is
> not
> > | going to be installed
> > |           Recommends: r-base-html but it is not going to be
installed
> > |           Recommends: r-doc-html but it is not going to be installed
> > | E: Unable to correct problems, you have held broken packages.
> > |
> > |
> > | Using sudo apt-cache showpkg <package> reveals that apt is
attempting
> to
> > | install r-base 3.2.4, but only has access to r-base-core 3.0.2.  It
> does
> > | have access to r-recommended, r-base-html, and r-doc-html all
version
> 3.2.4
> > | though.
> >
> > Then something is wrong with your apt entries. Check and double check.
> >
> > I run wily here (because why would I want to be on an almost two year
old
> > OS?) and it looks as follows:
> >
> > edd at max:~$ apt-cache policy r-base
> > r-base:
> >   Installed: (none)
> >   Candidate: 3.2.4-revised-1wily0
> >   Version table:
> >      3.2.4-revised-1wily0 0
> >         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
> >      3.2.4-1wily 0
> >         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
> >      3.2.3-6wily0 0
> >         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
> >      3.2.3-4wily0 0
> >         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
> >      3.2.3-3wily0 0
> >         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
> >      3.2.3-1.wily.0 0
> >         500 http://ppa.launchpad.net/edd/misc/ubuntu/ wily/main amd64
> Packages
> >      3.2.3-1wily1 0
> >         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
> >      3.2.3-1wily0 0
> >         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
> >      3.2.2-1wily 0
> >         500 http://cran.rstudio.com/bin/linux/ubuntu/ wily/ Packages
> >      3.2.2-1 0
> >         500 http://archive.ubuntu.com/ubuntu/ wily/universe amd64
> Packages
> > edd at max:~$
> >
> > I could have 3.2.2 from the distro -- which makes sense as 15.10 had a
> cutoff
> > some time last summer -- all the other thanks to Michael rebuilding
the
> ports
> > of why I stick into Debian.
> >
> > Dirk
> >
> > |
> > | I could probably live with R 3.0.2, but sudo apt-get install
> r-base=3.0.2
> > | yields a similar error complaining that it needs r-recommended
3.0.2,
> but
> > | it won't be installed.
> > |
> > | Any help would be appreciated.
> > |
> > | Thanks,
> > | Matt Simpson
> > |
> > |     [[alternative HTML version deleted]]
> > |
> > | _______________________________________________
> > | R-SIG-Debian mailing list
> > | R-SIG-Debian at r-project.org
> > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
> >
>
	[[alternative HTML version deleted]]

On 21 March 2016 at 13:18, Matthew Simpson wrote:
| It may be significant that my chromebook has an ARM processor. I don't
know
| about the details of how this works, but perhaps some pieces of the R install
| haven't been ported to the appropriate architecture?

Bahh. I am clearly not awake.  Should have realized that.

That is why you had r-doc-html, r-recommended, ... etc which are binary=all.
On CRAN you will /only/ find i386 and amd64.  On the Ubuntu PPAs you /may/
find arm builds as Ubuntu supports them for their tablet plans etc pp.

As such, the Dockerfile I sent you is more relevant than the CRAN README.

Good luck, Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org