Re: [R-sig-Debian] Fwd: Re: r-base installation fails on Ubuntu 14.04

[Dirk Eddelbuettel]

On 23 March 2016 at 13:50, Alex M wrote:
| He was suggesting to upgrade to 15.10 if you needed the newer fortran
| for some reason (or other newer things only in backports or not even there).

Yup.

Which from 14.04 requires upgrades to 14.10, then 15.04, then 15.10.  In
short may _right now_ also just wait for 16.04 LTS.

| I also mostly run LTS versions of Ubuntu, especially in my research
| group where I manage our cloud/servers. Which also matches the computer
| cluster available to me. That said I also stick to the stock packages
| for all the basic underlying libraries like fortran. If for some reason
| I need super new stuff to run a specific tool/analysis that's when I
| spin up a custom VM/Docker to create such an environment.

If you must keep on a version it can also help to __build you own backports__
which by being built locally will match your packages.  Explaining how to do
that is beyond the scope of this thread which failed over much simpler things.

Dirk

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

___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] Fwd: Re: r-base installation fails on Ubuntu 14.04

[Alex M]

He was suggesting to upgrade to 15.10 if you needed the newer fortran
for some reason (or other newer things only in backports or not even there).

I also mostly run LTS versions of Ubuntu, especially in my research
group where I manage our cloud/servers. Which also matches the computer
cluster available to me. That said I also stick to the stock packages
for all the basic underlying libraries like fortran. If for some reason
I need super new stuff to run a specific tool/analysis that's when I
spin up a custom VM/Docker to create such an environment.

In this case I can understand, 14.04 came from the hardware vendor, so
it makes sense to stick with that for now given the support from the
company for drivers (hopefully they will also support 16.04). In which
case, yes roll back your backported fortran to use the version Ubuntu
originally supplied.

Thanks,
Alex

On 03/23/2016 01:33 PM, Barnet Wagman wrote:
> 
> 
> 
>  Forwarded Message 
> Subject:  Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04
> Date: Wed, 23 Mar 2016 13:07:44 -0700
> From: Barnet Wagman 
> To:   Dirk Eddelbuettel 
> 
> 
> 
>> Lastly, and please don't take this the wrong way: I think I am helping way
>> more people like you who for one reason or other insist on older / frozen
>> system like 14.04 but then desire newer software.  Simply running _current_
>> Ubuntu and upgrading every six months is IMHO much easier.
> 
> Are suggesting upgrading to Ubuntu 15 or just running apt-get upgrade or
> apt-get dist-upgrade (which I've done).  Ubuntu 14.04 is the latest LTS
> version, which is probably why a lot of people are not going to 15.
> 
> 
> PS Inadvertently sent this to Dirk instead of list.  Sorry.
> 
> 

>

___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

[R-sig-Debian] Fwd: Re: r-base installation fails on Ubuntu 14.04

[Barnet Wagman]

 Forwarded Message 
Subject:Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04
Date:   Wed, 23 Mar 2016 13:07:44 -0700
From:   Barnet Wagman 
To: Dirk Eddelbuettel 



> Lastly, and please don't take this the wrong way: I think I am helping way
> more people like you who for one reason or other insist on older / frozen
> system like 14.04 but then desire newer software.  Simply running _current_
> Ubuntu and upgrading every six months is IMHO much easier.

Are suggesting upgrading to Ubuntu 15 or just running apt-get upgrade or
apt-get dist-upgrade (which I've done).  Ubuntu 14.04 is the latest LTS
version, which is probably why a lot of people are not going to 15.


PS Inadvertently sent this to Dirk instead of list.  Sorry.




[[alternative HTML version deleted]]

___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[ProfJCNash]

Apologies for my bit of that. I thought I'd only got the top.
Fumble fingers!

JN

On 16-03-23 03:14 PM, Dirk Eddelbuettel wrote:
> 
> Folks,
> 
> Could we PLEASE stop replies on 100kb logs without cutting the quoted part?
> 
> I learned my lesson; I'll never post a log again. Whatever happened to list
> etiquette?
> 
> Dirk
>

___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Dirk Eddelbuettel]

On 23 March 2016 at 12:35, Barnet Wagman wrote:
| One of the dependency problems I'm having is:
| 
| gfortran-4.8 : Depends: gcc-4.8-base (= 4.8.2-19ubuntu1) but 
| 4.8.4-2ubuntu1~14.04.1 is installed.
| 
| I'm not sure how to  interpret this.  Does this mean that the gfortran 
| installed is too recent?  If so, does R really require an older version 
| of gfortran, or is this related to the way the r-base-core package is 
| specified?

That is more promising and probably related to the liblapack/libblas issue!
With a bit of 'apt-cache policy' on these you may be able to find where they
are from; and you need the ones that R wants into order to use R.

Sometimes you get by specifying both as in

  $ sudo apt-get install gfortran-4.8 gcc-4.8-base

ie asking for both to be (re-)installed.  That may point to another package,
and you may have to recurse once or twice more.  As Alex correctly pointed
out, this is quite possibly due to the other backports.

I "own" Docker setup involving Ubuntu 12.04 and 14.04, but rarely add
anything besides CRAN in those (by design more minimal) setups.

Lastly, and please don't take this the wrong way: I think I am helping way
more people like you who for one reason or other insist on older / frozen
system like 14.04 but then desire newer software.  Simply running _current_
Ubuntu and upgrading every six months is IMHO much easier.  I've been doing
it for a decade on lots of machines across home and different workplaces.
YMMV, but it may be worth considering to just upgrade.  gcc and g++ 5.2 are
much nicer anyway :)

Dirk

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

___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Barnet Wagman]

One of the dependency problems I'm having is:

gfortran-4.8 : Depends: gcc-4.8-base (= 4.8.2-19ubuntu1) but 
4.8.4-2ubuntu1~14.04.1 is installed.


I'm not sure how to  interpret this.  Does this mean that the gfortran 
installed is too recent?  If so, does R really require an older version 
of gfortran, or is this related to the way the r-base-core package is 
specified?


___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Dirk Eddelbuettel]

On 23 March 2016 at 11:38, Barnet Wagman wrote:
| It's a Dell XPS 13.
| 
| Obviously I don't understand what's in libcmanager0.  I wonder if I can 
| safely replace it.  I'm a bit uneasy about replacing things Dell 
| installed.  I gather there are some specialized drivers for the monitor 
| on this system.

i)  Apply common sense

ii) If that fails do 'apt-cache show libcmanager0'.

It sounds like a system library so it is unlikely to interfere with your
lapack/blas issue which is almost surely only affecting R (and possibly
Octave, Scilab, some Python libs etc pp).

'apt-cache rdepends libcmanager0' will show you who depends on libcmanager0.

Dirk

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

___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Dirk Eddelbuettel]

Folks,

Could we PLEASE stop replies on 100kb logs without cutting the quoted part?

I learned my lesson; I'll never post a log again. Whatever happened to list
etiquette?

Dirk

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

___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Dirk Eddelbuettel]

On 23 March 2016 at 10:53, Barnet Wagman wrote:
| I've never used docker and installing it appears to require changing 
| kernels which I'd rather not do.

I never suggested you install docker.  

I used Docker to demonstrate to you that the repos are fine. Your system is
not.  Several people told you so by now.
 
| Is there any other way to get useful information?
| FYI I've tried installing r-base-core and got the same errors listed in 
| my first email.

I did not suggest to randomly re-install, hoping it would solve the issues.

So here is a simple suggestion one short of reinstalling, I hope this is not
too complicated for you:

i)   Comment out ALL entries for apt apart from those for Ubuntu, and CRAN.
 Keep mate if you must; it should not matter but we cannot know.

ii)  apt-get update

iii) apt-get install r-base-core

and look at each error message and the packages it involves. Maybe remove
those packages.  Exercise caution, do not remove anything mission critical.

For most of us the last step is not necessarily required as we mostly manage
to make sense of the error messages.  They may be cryptic, but they also
contain important information.  Use it to your advantage.

If none of this works reinstall cleanly and mess with fewer PPAs. I tend to
have one or two active besides CRAN and never had issues over several years
of running several Ubuntu machines at work and home.

Good luck, Dirk

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

___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Barnet Wagman]

It's a Dell XPS 13.

Obviously I don't understand what's in libcmanager0.  I wonder if I can 
safely replace it.  I'm a bit uneasy about replacing things Dell 
installed.  I gather there are some specialized drivers for the monitor 
on this system.


On 03/23/2016 11:34 AM, Alex M wrote:

That could do it
http://packages.ubuntu.com/trusty-backports/libcgmanager0

Seems to be libc related, which is a pretty core library to much of the
whole system.

Hmm, which model Dell? We just got a Dell 5000 series with Ubuntu, I
have not checked with my boss if there was R installation issues.

Thanks,
Alex

On 03/23/2016 11:22 AM, Barnet Wagman wrote:

Synaptic can show the origin of packages.

The only thing I see from a backport is

 libcmanager0

I don't think this is relevant to R.  Or is it.

The only thing I've got installed from a ppa is mate (a desktop).  I
don't see anything related to mate that is related to R.

FYI the ubunu I'm using came preinstalled from Dell (on a notebook;
usually I install linux myself).

On 03/23/2016 10:35 AM, Alex M wrote

I can make a few suggestions to help you hunt for the issue. This kind
of error is often caused by conflicting packages from proposed,
backports, ppas, or other 3rd party repos. If for some reason you have a
dependency installed from one of those sources that is newer than what R
on cran was built against (stock ubuntu 14.04) then you will hit a conflict.

Simply removing backports from your repos will not solve the problem.
You actually have to roll back the version of any packages you install
from backports.

For ppas, there's a really cool tool out there call ppa-purge which will
roll back anything installed from a specific ppa. For backports you're
going to have to do it by hand. Maybe there's a nice dpkg way to list
all packages you installed from backports?

Thanks,
Alex

On 03/23/2016 10:23 AM, Dirk Eddelbuettel wrote:

On 23 March 2016 at 09:35, Barnet Wagman wrote:
| I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu
| 14.04 system.  According to
| https://cran.r-project.org/bin/linux/ubuntu/README (and many other sources),
| R is available for this version of Ubuntu (which is a stable version).
|
| I currently have
|
| deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/
|
| in sources.list.  I've tried this with and without
|
| deb https://  mirrors.rit.edu/ubuntu trusty-backports main
| restricted universe

Is the space an error for the email, or do you really have it there?

| I've tried installing using apt-get , aptitude, and synaptic. (I have,
| of course, run apt-get update.) All hit problems they cannot resolve
| (listed below).
|
| I'd appreciate any thoughts on this.  I've installed R on many linux
| distributions in the past (suse, redhat, debian, most recently
| elementary os) and never run into anything like this before.   (I'm
| getting desperate enough to consider building R from src, but as I
| recall getting the right libraries installed isn't that easy).

We (somewhat obviously) know that "all systems are green" because so many
automated processes (think Travis CI) depend on it.  Ditto with say Docker
autobuilds.  And as it is so easy to document, a quick and dirty (as I didn't
bother with keys inside the container) check using Docker.  Below is a quick
log from a shell inside an Emacs session (hence the command echos).

In essence I do just these few steps:

- start a Docker session with Ubuntu 14.04
- add an entry for CRAN to apt's config
- apt-get update
- apt-get install (with proper switches to override interactive use and 
warnings)
- start R

and we see R 3.2.4 as expected.  I only used r-base-core and not r-base here
to keep the download smaller but it should really work the same way.

If your system 'balks' you have to figure why/what something conflicts and
resolve those.   Show us the details.  Some of us may know.

Dirk


edd@max:~$ docker run --rm -ti ubuntu:trusty ## basic 14.04
]0;root@8776f0c1263e: /root@8776f0c1263e:/# export PS1="> "# nicer here
export PS1="> "

echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" > 
/etc/apt/sources.list.d/cran.list

.list.d/cran.list

apt-get update

apt-get update
Ign http://cran.rstudio.com trusty/ InRelease
Get:1 http://cran.rstudio.com trusty/ Release.gpg [473 B]
Get:2 http://cran.rstudio.com trusty/ Release [3703 B]
Ign http://archive.ubuntu.com trusty InRelease
Get:3 http://archive.ubuntu.com trusty-updates InRelease [65.9 kB]
Ign http://cran.rstudio.com trusty/ Release
Get:4 http://cran.rstudio.com trusty/ Packages [153 kB]
Get:5 http://archive.ubuntu.com trusty-security InRelease [65.9 kB]
Hit http://archive.ubuntu.com trusty Release.gpg
Get:6 http://archive.ubuntu.com trusty-updates/main Sources [340 kB]
Get:7 http://archive.ubuntu.com trusty-updates/restricted Sources [5217 B]
Get:8 http://archive.ubuntu.com trusty-updates/universe Sources [190 kB]
Get:9 http://archive.ubuntu.com trusty-updates/main amd64 Packages 

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Barnet Wagman]

Good thought but no, everything is 64.

On 03/23/2016 11:29 AM, ProfJCNash wrote:

Possibly off the wall and a long shot, but is pre-installed Linux
perhaps 32 bit, while the R attempt is 64?

JN

On 16-03-23 02:22 PM, Barnet Wagman wrote:

Synaptic can show the origin of packages.

The only thing I see from a backport is

 libcmanager0

I don't think this is relevant to R.  Or is it.

The only thing I've got installed from a ppa is mate (a desktop).  I
don't see anything related to mate that is related to R.

FYI the ubunu I'm using came preinstalled from Dell (on a notebook;
usually I install linux myself).

On 03/23/2016 10:35 AM, Alex M wrote

I can make a few suggestions to help you hunt for the issue. This kind
of error is often caused by conflicting packages from proposed,
backports, ppas, or other 3rd party repos. If for some reason you have a
dependency installed from one of those sources that is newer than what R
on cran was built against (stock ubuntu 14.04) then you will hit a conflict.

Simply removing backports from your repos will not solve the problem.
You actually have to roll back the version of any packages you install
from backports.

For ppas, there's a really cool tool out there call ppa-purge which will
roll back anything installed from a specific ppa. For backports you're
going to have to do it by hand. Maybe there's a nice dpkg way to list
all packages you installed from backports?

Thanks,
Alex

On 03/23/2016 10:23 AM, Dirk Eddelbuettel wrote:

On 23 March 2016 at 09:35, Barnet Wagman wrote:
| I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu
| 14.04 system.  According to
| https://cran.r-project.org/bin/linux/ubuntu/README (and many other sources),
| R is available for this version of Ubuntu (which is a stable version).
|
| I currently have
|
| deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/
|
| in sources.list.  I've tried this with and without
|
| deb https://  mirrors.rit.edu/ubuntu trusty-backports main
| restricted universe

Is the space an error for the email, or do you really have it there?

| I've tried installing using apt-get , aptitude, and synaptic. (I have,
| of course, run apt-get update.) All hit problems they cannot resolve
| (listed below).
|
| I'd appreciate any thoughts on this.  I've installed R on many linux
| distributions in the past (suse, redhat, debian, most recently
| elementary os) and never run into anything like this before.   (I'm
| getting desperate enough to consider building R from src, but as I
| recall getting the right libraries installed isn't that easy).

We (somewhat obviously) know that "all systems are green" because so many
automated processes (think Travis CI) depend on it.  Ditto with say Docker
autobuilds.  And as it is so easy to document, a quick and dirty (as I didn't
bother with keys inside the container) check using Docker.  Below is a quick
log from a shell inside an Emacs session (hence the command echos).

In essence I do just these few steps:

- start a Docker session with Ubuntu 14.04
- add an entry for CRAN to apt's config
- apt-get update
- apt-get install (with proper switches to override interactive use and 
warnings)
- start R

and we see R 3.2.4 as expected.  I only used r-base-core and not r-base here
to keep the download smaller but it should really work the same way.

If your system 'balks' you have to figure why/what something conflicts and
resolve those.   Show us the details.  Some of us may know.

Dirk


edd@max:~$ docker run --rm -ti ubuntu:trusty ## basic 14.04
]0;root@8776f0c1263e: /root@8776f0c1263e:/# export PS1="> "# nicer here
export PS1="> "

echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" > 
/etc/apt/sources.list.d/cran.list

.list.d/cran.list

apt-get update

apt-get update
Ign http://cran.rstudio.com trusty/ InRelease
Get:1 http://cran.rstudio.com trusty/ Release.gpg [473 B]
Get:2 http://cran.rstudio.com trusty/ Release [3703 B]
Ign http://archive.ubuntu.com trusty InRelease
Get:3 http://archive.ubuntu.com trusty-updates InRelease [65.9 kB]
Ign http://cran.rstudio.com trusty/ Release
Get:4 http://cran.rstudio.com trusty/ Packages [153 kB]
Get:5 http://archive.ubuntu.com trusty-security InRelease [65.9 kB]
Hit http://archive.ubuntu.com trusty Release.gpg
Get:6 http://archive.ubuntu.com trusty-updates/main Sources [340 kB]
Get:7 http://archive.ubuntu.com trusty-updates/restricted Sources [5217 B]
Get:8 http://archive.ubuntu.com trusty-updates/universe Sources [190 kB]
Get:9 http://archive.ubuntu.com trusty-updates/main amd64 Packages [930 kB]
Get:10 http://archive.ubuntu.com trusty-updates/restricted amd64 Packages [23.5 
kB]
Get:11 http://archive.ubuntu.com trusty-updates/universe amd64 Packages [460 kB]
Hit http://archive.ubuntu.com trusty Release
Get:12 http://archive.ubuntu.com trusty-security/main Sources [138 kB]
Get:13 http://archive.ubuntu.com trusty-security/restricted Sources [3920 B]
Get:14 http://archive.ubuntu.com 

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Alex M]

That could do it
http://packages.ubuntu.com/trusty-backports/libcgmanager0

Seems to be libc related, which is a pretty core library to much of the
whole system.

Hmm, which model Dell? We just got a Dell 5000 series with Ubuntu, I
have not checked with my boss if there was R installation issues.

Thanks,
Alex

On 03/23/2016 11:22 AM, Barnet Wagman wrote:
> Synaptic can show the origin of packages.
> 
> The only thing I see from a backport is
> 
> libcmanager0
> 
> I don't think this is relevant to R.  Or is it.
> 
> The only thing I've got installed from a ppa is mate (a desktop).  I 
> don't see anything related to mate that is related to R.
> 
> FYI the ubunu I'm using came preinstalled from Dell (on a notebook; 
> usually I install linux myself).
> 
> On 03/23/2016 10:35 AM, Alex M wrote
>> I can make a few suggestions to help you hunt for the issue. This kind
>> of error is often caused by conflicting packages from proposed,
>> backports, ppas, or other 3rd party repos. If for some reason you have a
>> dependency installed from one of those sources that is newer than what R
>> on cran was built against (stock ubuntu 14.04) then you will hit a conflict.
>>
>> Simply removing backports from your repos will not solve the problem.
>> You actually have to roll back the version of any packages you install
>> from backports.
>>
>> For ppas, there's a really cool tool out there call ppa-purge which will
>> roll back anything installed from a specific ppa. For backports you're
>> going to have to do it by hand. Maybe there's a nice dpkg way to list
>> all packages you installed from backports?
>>
>> Thanks,
>> Alex
>>
>> On 03/23/2016 10:23 AM, Dirk Eddelbuettel wrote:
>>> On 23 March 2016 at 09:35, Barnet Wagman wrote:
>>> | I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu
>>> | 14.04 system.  According to
>>> | https://cran.r-project.org/bin/linux/ubuntu/README (and many other 
>>> sources),
>>> | R is available for this version of Ubuntu (which is a stable version).
>>> |
>>> | I currently have
>>> |
>>> | deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/
>>> |
>>> | in sources.list.  I've tried this with and without
>>> |
>>> | deb https://  mirrors.rit.edu/ubuntu trusty-backports main
>>> | restricted universe
>>>
>>> Is the space an error for the email, or do you really have it there?
>>>
>>> | I've tried installing using apt-get , aptitude, and synaptic. (I have,
>>> | of course, run apt-get update.) All hit problems they cannot resolve
>>> | (listed below).
>>> |
>>> | I'd appreciate any thoughts on this.  I've installed R on many linux
>>> | distributions in the past (suse, redhat, debian, most recently
>>> | elementary os) and never run into anything like this before.   (I'm
>>> | getting desperate enough to consider building R from src, but as I
>>> | recall getting the right libraries installed isn't that easy).
>>>
>>> We (somewhat obviously) know that "all systems are green" because so many
>>> automated processes (think Travis CI) depend on it.  Ditto with say Docker
>>> autobuilds.  And as it is so easy to document, a quick and dirty (as I 
>>> didn't
>>> bother with keys inside the container) check using Docker.  Below is a quick
>>> log from a shell inside an Emacs session (hence the command echos).
>>>
>>> In essence I do just these few steps:
>>>
>>> - start a Docker session with Ubuntu 14.04
>>> - add an entry for CRAN to apt's config
>>> - apt-get update
>>> - apt-get install (with proper switches to override interactive use and 
>>> warnings)
>>> - start R
>>>
>>> and we see R 3.2.4 as expected.  I only used r-base-core and not r-base here
>>> to keep the download smaller but it should really work the same way.
>>>
>>> If your system 'balks' you have to figure why/what something conflicts and
>>> resolve those.   Show us the details.  Some of us may know.
>>>
>>> Dirk
>>>
>>>
>>> edd@max:~$ docker run --rm -ti ubuntu:trusty ## basic 14.04
>>> ]0;root@8776f0c1263e: /root@8776f0c1263e:/# export PS1="> "# nicer 
>>> here
>>> export PS1="> "
 echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" > 
 /etc/apt/sources.list.d/cran.list
>>> .list.d/cran.list
 apt-get update
>>> apt-get update
>>> Ign http://cran.rstudio.com trusty/ InRelease
>>> Get:1 http://cran.rstudio.com trusty/ Release.gpg [473 B]
>>> Get:2 http://cran.rstudio.com trusty/ Release [3703 B]
>>> Ign http://archive.ubuntu.com trusty InRelease
>>> Get:3 http://archive.ubuntu.com trusty-updates InRelease [65.9 kB]
>>> Ign http://cran.rstudio.com trusty/ Release
>>> Get:4 http://cran.rstudio.com trusty/ Packages [153 kB]
>>> Get:5 http://archive.ubuntu.com trusty-security InRelease [65.9 kB]
>>> Hit http://archive.ubuntu.com trusty Release.gpg
>>> Get:6 http://archive.ubuntu.com trusty-updates/main Sources [340 kB]
>>> Get:7 http://archive.ubuntu.com trusty-updates/restricted Sources [5217 B]
>>> Get:8 http://archive.ubuntu.com trusty-updates/universe 

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Alex M]

I doubt it since apt autofills that part of the package request
typically and CRAN mirrors do provide both.

Thanks,
Alex

On 03/23/2016 11:29 AM, ProfJCNash wrote:
> Possibly off the wall and a long shot, but is pre-installed Linux
> perhaps 32 bit, while the R attempt is 64?
> 
> JN
> 
> On 16-03-23 02:22 PM, Barnet Wagman wrote:
>> Synaptic can show the origin of packages.
>>
>> The only thing I see from a backport is
>>
>> libcmanager0
>>
>> I don't think this is relevant to R.  Or is it.
>>
>> The only thing I've got installed from a ppa is mate (a desktop).  I 
>> don't see anything related to mate that is related to R.
>>
>> FYI the ubunu I'm using came preinstalled from Dell (on a notebook; 
>> usually I install linux myself).
>>
>> On 03/23/2016 10:35 AM, Alex M wrote
>>> I can make a few suggestions to help you hunt for the issue. This kind
>>> of error is often caused by conflicting packages from proposed,
>>> backports, ppas, or other 3rd party repos. If for some reason you have a
>>> dependency installed from one of those sources that is newer than what R
>>> on cran was built against (stock ubuntu 14.04) then you will hit a conflict.
>>>
>>> Simply removing backports from your repos will not solve the problem.
>>> You actually have to roll back the version of any packages you install
>>> from backports.
>>>
>>> For ppas, there's a really cool tool out there call ppa-purge which will
>>> roll back anything installed from a specific ppa. For backports you're
>>> going to have to do it by hand. Maybe there's a nice dpkg way to list
>>> all packages you installed from backports?
>>>
>>> Thanks,
>>> Alex
>>>
>>> On 03/23/2016 10:23 AM, Dirk Eddelbuettel wrote:
 On 23 March 2016 at 09:35, Barnet Wagman wrote:
 | I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu
 | 14.04 system.  According to
 | https://cran.r-project.org/bin/linux/ubuntu/README (and many other 
 sources),
 | R is available for this version of Ubuntu (which is a stable version).
 |
 | I currently have
 |
 | deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/
 |
 | in sources.list.  I've tried this with and without
 |
 | deb https://  mirrors.rit.edu/ubuntu trusty-backports main
 | restricted universe

 Is the space an error for the email, or do you really have it there?

 | I've tried installing using apt-get , aptitude, and synaptic. (I have,
 | of course, run apt-get update.) All hit problems they cannot resolve
 | (listed below).
 |
 | I'd appreciate any thoughts on this.  I've installed R on many linux
 | distributions in the past (suse, redhat, debian, most recently
 | elementary os) and never run into anything like this before.   (I'm
 | getting desperate enough to consider building R from src, but as I
 | recall getting the right libraries installed isn't that easy).

 We (somewhat obviously) know that "all systems are green" because so many
 automated processes (think Travis CI) depend on it.  Ditto with say Docker
 autobuilds.  And as it is so easy to document, a quick and dirty (as I 
 didn't
 bother with keys inside the container) check using Docker.  Below is a 
 quick
 log from a shell inside an Emacs session (hence the command echos).

 In essence I do just these few steps:

 - start a Docker session with Ubuntu 14.04
 - add an entry for CRAN to apt's config
 - apt-get update
 - apt-get install (with proper switches to override interactive use and 
 warnings)
 - start R

 and we see R 3.2.4 as expected.  I only used r-base-core and not r-base 
 here
 to keep the download smaller but it should really work the same way.

 If your system 'balks' you have to figure why/what something conflicts and
 resolve those.   Show us the details.  Some of us may know.

 Dirk


 edd@max:~$ docker run --rm -ti ubuntu:trusty ## basic 14.04
 ]0;root@8776f0c1263e: /root@8776f0c1263e:/# export PS1="> "# nicer 
 here
 export PS1="> "
> echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" > 
> /etc/apt/sources.list.d/cran.list
 .list.d/cran.list
> apt-get update
 apt-get update
 Ign http://cran.rstudio.com trusty/ InRelease
 Get:1 http://cran.rstudio.com trusty/ Release.gpg [473 B]
 Get:2 http://cran.rstudio.com trusty/ Release [3703 B]
 Ign http://archive.ubuntu.com trusty InRelease
 Get:3 http://archive.ubuntu.com trusty-updates InRelease [65.9 kB]
 Ign http://cran.rstudio.com trusty/ Release
 Get:4 http://cran.rstudio.com trusty/ Packages [153 kB]
 Get:5 http://archive.ubuntu.com trusty-security InRelease [65.9 kB]
 Hit http://archive.ubuntu.com trusty Release.gpg
 Get:6 http://archive.ubuntu.com trusty-updates/main Sources [340 kB]
 Get:7 http://archive.ubuntu.com 

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Barnet Wagman]

Problems are showing up with libgfortran3 and liblapack3.
Results of apt-cache policy are below.  FYI no part of R is currently 
installed on my system.  Thanks.


root@bwud:/etc/apt# apt-get install r-base-core

...

The following packages have unmet dependencies:
 r-base-core : Depends: libgfortran3 (>= 4.3) but it is not going to be 
installed

   Depends: liblapack3 but it is not going to be installed or
liblapack.so.3
   Recommends: r-recommended but it is not going to be 
installed

   Recommends: r-base-dev but it is not going to be installed


root@bwud:/etc/apt# apt-cache policy libgfortran3
libgfortran3:
  Installed: (none)
  Candidate: 4.8.2-19ubuntu1
  Version table:
 4.8.2-19ubuntu1 0
500 http://archive.ubuntu.com/ubuntu/ trusty/main amd64 Packages

root@bwud:/etc/apt# apt-cache policy liblapack3
liblapack3:
  Installed: (none)
  Candidate: 3.5.0-2ubuntu1
  Version table:
 3.5.0-2ubuntu1 0
500 http://archive.ubuntu.com/ubuntu/ trusty/main amd64 Packages


On 03/23/2016 11:06 AM, Dirk Eddelbuettel wrote:

On 23 March 2016 at 10:35, Alex M wrote:
| I can make a few suggestions to help you hunt for the issue. This kind
| of error is often caused by conflicting packages from proposed,
| backports, ppas, or other 3rd party repos. If for some reason you have a
| dependency installed from one of those sources that is newer than what R
| on cran was built against (stock ubuntu 14.04) then you will hit a conflict.
|
| Simply removing backports from your repos will not solve the problem.
| You actually have to roll back the version of any packages you install
| from backports.
|
| For ppas, there's a really cool tool out there call ppa-purge which will
| roll back anything installed from a specific ppa. For backports you're
| going to have to do it by hand. Maybe there's a nice dpkg way to list
| all packages you installed from backports?

+1

And that is what I was referring to with 'show us your error messages'.  If
something 'blocks', do a 'apt-cache policy nameofthatpackage' to see where it
came from.  Worst case, uninstall components (carefully) as suggested here.
By removing R and pieces you should not be able to brick your system.

PPAs are great, but they are /not/ tested against each other as the distro
core is.

Dirk



___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[ProfJCNash]

Possibly off the wall and a long shot, but is pre-installed Linux
perhaps 32 bit, while the R attempt is 64?

JN

On 16-03-23 02:22 PM, Barnet Wagman wrote:
> Synaptic can show the origin of packages.
> 
> The only thing I see from a backport is
> 
> libcmanager0
> 
> I don't think this is relevant to R.  Or is it.
> 
> The only thing I've got installed from a ppa is mate (a desktop).  I 
> don't see anything related to mate that is related to R.
> 
> FYI the ubunu I'm using came preinstalled from Dell (on a notebook; 
> usually I install linux myself).
> 
> On 03/23/2016 10:35 AM, Alex M wrote
>> I can make a few suggestions to help you hunt for the issue. This kind
>> of error is often caused by conflicting packages from proposed,
>> backports, ppas, or other 3rd party repos. If for some reason you have a
>> dependency installed from one of those sources that is newer than what R
>> on cran was built against (stock ubuntu 14.04) then you will hit a conflict.
>>
>> Simply removing backports from your repos will not solve the problem.
>> You actually have to roll back the version of any packages you install
>> from backports.
>>
>> For ppas, there's a really cool tool out there call ppa-purge which will
>> roll back anything installed from a specific ppa. For backports you're
>> going to have to do it by hand. Maybe there's a nice dpkg way to list
>> all packages you installed from backports?
>>
>> Thanks,
>> Alex
>>
>> On 03/23/2016 10:23 AM, Dirk Eddelbuettel wrote:
>>> On 23 March 2016 at 09:35, Barnet Wagman wrote:
>>> | I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu
>>> | 14.04 system.  According to
>>> | https://cran.r-project.org/bin/linux/ubuntu/README (and many other 
>>> sources),
>>> | R is available for this version of Ubuntu (which is a stable version).
>>> |
>>> | I currently have
>>> |
>>> | deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/
>>> |
>>> | in sources.list.  I've tried this with and without
>>> |
>>> | deb https://  mirrors.rit.edu/ubuntu trusty-backports main
>>> | restricted universe
>>>
>>> Is the space an error for the email, or do you really have it there?
>>>
>>> | I've tried installing using apt-get , aptitude, and synaptic. (I have,
>>> | of course, run apt-get update.) All hit problems they cannot resolve
>>> | (listed below).
>>> |
>>> | I'd appreciate any thoughts on this.  I've installed R on many linux
>>> | distributions in the past (suse, redhat, debian, most recently
>>> | elementary os) and never run into anything like this before.   (I'm
>>> | getting desperate enough to consider building R from src, but as I
>>> | recall getting the right libraries installed isn't that easy).
>>>
>>> We (somewhat obviously) know that "all systems are green" because so many
>>> automated processes (think Travis CI) depend on it.  Ditto with say Docker
>>> autobuilds.  And as it is so easy to document, a quick and dirty (as I 
>>> didn't
>>> bother with keys inside the container) check using Docker.  Below is a quick
>>> log from a shell inside an Emacs session (hence the command echos).
>>>
>>> In essence I do just these few steps:
>>>
>>> - start a Docker session with Ubuntu 14.04
>>> - add an entry for CRAN to apt's config
>>> - apt-get update
>>> - apt-get install (with proper switches to override interactive use and 
>>> warnings)
>>> - start R
>>>
>>> and we see R 3.2.4 as expected.  I only used r-base-core and not r-base here
>>> to keep the download smaller but it should really work the same way.
>>>
>>> If your system 'balks' you have to figure why/what something conflicts and
>>> resolve those.   Show us the details.  Some of us may know.
>>>
>>> Dirk
>>>
>>>
>>> edd@max:~$ docker run --rm -ti ubuntu:trusty ## basic 14.04
>>> ]0;root@8776f0c1263e: /root@8776f0c1263e:/# export PS1="> "# nicer 
>>> here
>>> export PS1="> "
 echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" > 
 /etc/apt/sources.list.d/cran.list
>>> .list.d/cran.list
 apt-get update
>>> apt-get update
>>> Ign http://cran.rstudio.com trusty/ InRelease
>>> Get:1 http://cran.rstudio.com trusty/ Release.gpg [473 B]
>>> Get:2 http://cran.rstudio.com trusty/ Release [3703 B]
>>> Ign http://archive.ubuntu.com trusty InRelease
>>> Get:3 http://archive.ubuntu.com trusty-updates InRelease [65.9 kB]
>>> Ign http://cran.rstudio.com trusty/ Release
>>> Get:4 http://cran.rstudio.com trusty/ Packages [153 kB]
>>> Get:5 http://archive.ubuntu.com trusty-security InRelease [65.9 kB]
>>> Hit http://archive.ubuntu.com trusty Release.gpg
>>> Get:6 http://archive.ubuntu.com trusty-updates/main Sources [340 kB]
>>> Get:7 http://archive.ubuntu.com trusty-updates/restricted Sources [5217 B]
>>> Get:8 http://archive.ubuntu.com trusty-updates/universe Sources [190 kB]
>>> Get:9 http://archive.ubuntu.com trusty-updates/main amd64 Packages [930 kB]
>>> Get:10 http://archive.ubuntu.com trusty-updates/restricted amd64 Packages 
>>> [23.5 kB]
>>> Get:11 

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Barnet Wagman]

Synaptic can show the origin of packages.

The only thing I see from a backport is

libcmanager0

I don't think this is relevant to R.  Or is it.

The only thing I've got installed from a ppa is mate (a desktop).  I 
don't see anything related to mate that is related to R.

FYI the ubunu I'm using came preinstalled from Dell (on a notebook; 
usually I install linux myself).

On 03/23/2016 10:35 AM, Alex M wrote
> I can make a few suggestions to help you hunt for the issue. This kind
> of error is often caused by conflicting packages from proposed,
> backports, ppas, or other 3rd party repos. If for some reason you have a
> dependency installed from one of those sources that is newer than what R
> on cran was built against (stock ubuntu 14.04) then you will hit a conflict.
>
> Simply removing backports from your repos will not solve the problem.
> You actually have to roll back the version of any packages you install
> from backports.
>
> For ppas, there's a really cool tool out there call ppa-purge which will
> roll back anything installed from a specific ppa. For backports you're
> going to have to do it by hand. Maybe there's a nice dpkg way to list
> all packages you installed from backports?
>
> Thanks,
> Alex
>
> On 03/23/2016 10:23 AM, Dirk Eddelbuettel wrote:
>> On 23 March 2016 at 09:35, Barnet Wagman wrote:
>> | I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu
>> | 14.04 system.  According to
>> | https://cran.r-project.org/bin/linux/ubuntu/README (and many other 
>> sources),
>> | R is available for this version of Ubuntu (which is a stable version).
>> |
>> | I currently have
>> |
>> | deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/
>> |
>> | in sources.list.  I've tried this with and without
>> |
>> | deb https://  mirrors.rit.edu/ubuntu trusty-backports main
>> | restricted universe
>>
>> Is the space an error for the email, or do you really have it there?
>>
>> | I've tried installing using apt-get , aptitude, and synaptic. (I have,
>> | of course, run apt-get update.) All hit problems they cannot resolve
>> | (listed below).
>> |
>> | I'd appreciate any thoughts on this.  I've installed R on many linux
>> | distributions in the past (suse, redhat, debian, most recently
>> | elementary os) and never run into anything like this before.   (I'm
>> | getting desperate enough to consider building R from src, but as I
>> | recall getting the right libraries installed isn't that easy).
>>
>> We (somewhat obviously) know that "all systems are green" because so many
>> automated processes (think Travis CI) depend on it.  Ditto with say Docker
>> autobuilds.  And as it is so easy to document, a quick and dirty (as I didn't
>> bother with keys inside the container) check using Docker.  Below is a quick
>> log from a shell inside an Emacs session (hence the command echos).
>>
>> In essence I do just these few steps:
>>
>> - start a Docker session with Ubuntu 14.04
>> - add an entry for CRAN to apt's config
>> - apt-get update
>> - apt-get install (with proper switches to override interactive use and 
>> warnings)
>> - start R
>>
>> and we see R 3.2.4 as expected.  I only used r-base-core and not r-base here
>> to keep the download smaller but it should really work the same way.
>>
>> If your system 'balks' you have to figure why/what something conflicts and
>> resolve those.   Show us the details.  Some of us may know.
>>
>> Dirk
>>
>>
>> edd@max:~$ docker run --rm -ti ubuntu:trusty ## basic 14.04
>> ]0;root@8776f0c1263e: /root@8776f0c1263e:/# export PS1="> "# nicer here
>> export PS1="> "
>>> echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" > 
>>> /etc/apt/sources.list.d/cran.list
>> .list.d/cran.list
>>> apt-get update
>> apt-get update
>> Ign http://cran.rstudio.com trusty/ InRelease
>> Get:1 http://cran.rstudio.com trusty/ Release.gpg [473 B]
>> Get:2 http://cran.rstudio.com trusty/ Release [3703 B]
>> Ign http://archive.ubuntu.com trusty InRelease
>> Get:3 http://archive.ubuntu.com trusty-updates InRelease [65.9 kB]
>> Ign http://cran.rstudio.com trusty/ Release
>> Get:4 http://cran.rstudio.com trusty/ Packages [153 kB]
>> Get:5 http://archive.ubuntu.com trusty-security InRelease [65.9 kB]
>> Hit http://archive.ubuntu.com trusty Release.gpg
>> Get:6 http://archive.ubuntu.com trusty-updates/main Sources [340 kB]
>> Get:7 http://archive.ubuntu.com trusty-updates/restricted Sources [5217 B]
>> Get:8 http://archive.ubuntu.com trusty-updates/universe Sources [190 kB]
>> Get:9 http://archive.ubuntu.com trusty-updates/main amd64 Packages [930 kB]
>> Get:10 http://archive.ubuntu.com trusty-updates/restricted amd64 Packages 
>> [23.5 kB]
>> Get:11 http://archive.ubuntu.com trusty-updates/universe amd64 Packages [460 
>> kB]
>> Hit http://archive.ubuntu.com trusty Release
>> Get:12 http://archive.ubuntu.com trusty-security/main Sources [138 kB]
>> Get:13 http://archive.ubuntu.com trusty-security/restricted Sources [3920 B]
>> Get:14 

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Dirk Eddelbuettel]

On 23 March 2016 at 10:35, Alex M wrote:
| I can make a few suggestions to help you hunt for the issue. This kind
| of error is often caused by conflicting packages from proposed,
| backports, ppas, or other 3rd party repos. If for some reason you have a
| dependency installed from one of those sources that is newer than what R
| on cran was built against (stock ubuntu 14.04) then you will hit a conflict.
| 
| Simply removing backports from your repos will not solve the problem.
| You actually have to roll back the version of any packages you install
| from backports.
| 
| For ppas, there's a really cool tool out there call ppa-purge which will
| roll back anything installed from a specific ppa. For backports you're
| going to have to do it by hand. Maybe there's a nice dpkg way to list
| all packages you installed from backports?

+1

And that is what I was referring to with 'show us your error messages'.  If
something 'blocks', do a 'apt-cache policy nameofthatpackage' to see where it
came from.  Worst case, uninstall components (carefully) as suggested here.
By removing R and pieces you should not be able to brick your system.

PPAs are great, but they are /not/ tested against each other as the distro
core is.

Dirk

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

___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Alex M]

On 03/23/2016 10:53 AM, Barnet Wagman wrote:
> 
> 
> On 03/23/2016 10:23 AM, Dirk Eddelbuettel wrote:
>> On 23 March 2016 at 09:35, Barnet Wagman wrote:
>> | I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu
>> | 14.04 system.  According to
>> | https://cran.r-project.org/bin/linux/ubuntu/README (and many other
>> sources),
>> | R is available for this version of Ubuntu (which is a stable version).
>> |
>> | I currently have
>> |
>> | deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/
>> |
>> | in sources.list.  I've tried this with and without
>> |
>> | deb https://  mirrors.rit.edu/ubuntu trusty-backports main
>> | restricted universe
>>
>> Is the space an error for the email, or do you really have it there?
> Error in the email: sorry about that.
> 
> I've never used docker and installing it appears to require changing
> kernels which I'd rather not do.
> 
> Is there any other way to get useful information?
> FYI I've tried installing r-base-core and got the same errors listed in
> my first email.
> 
> thanks
> 

You can also use a full VM to test instead of docker. Vagrant would be
the easiest way to go down that route.

It's starting to sound like you've got some backports that are the issue.

Thanks,
Alex

___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Barnet Wagman]

On 03/23/2016 10:23 AM, Dirk Eddelbuettel wrote:

On 23 March 2016 at 09:35, Barnet Wagman wrote:
| I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu
| 14.04 system.  According to
| https://cran.r-project.org/bin/linux/ubuntu/README (and many other sources),
| R is available for this version of Ubuntu (which is a stable version).
|
| I currently have
|
| deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/
|
| in sources.list.  I've tried this with and without
|
| deb https://  mirrors.rit.edu/ubuntu trusty-backports main
| restricted universe

Is the space an error for the email, or do you really have it there?

Error in the email: sorry about that.

I've never used docker and installing it appears to require changing 
kernels which I'd rather not do.


Is there any other way to get useful information?
FYI I've tried installing r-base-core and got the same errors listed in 
my first email.


thanks

___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Alex M]

I can make a few suggestions to help you hunt for the issue. This kind
of error is often caused by conflicting packages from proposed,
backports, ppas, or other 3rd party repos. If for some reason you have a
dependency installed from one of those sources that is newer than what R
on cran was built against (stock ubuntu 14.04) then you will hit a conflict.

Simply removing backports from your repos will not solve the problem.
You actually have to roll back the version of any packages you install
from backports.

For ppas, there's a really cool tool out there call ppa-purge which will
roll back anything installed from a specific ppa. For backports you're
going to have to do it by hand. Maybe there's a nice dpkg way to list
all packages you installed from backports?

Thanks,
Alex

On 03/23/2016 10:23 AM, Dirk Eddelbuettel wrote:
> 
> On 23 March 2016 at 09:35, Barnet Wagman wrote:
> | I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu 
> | 14.04 system.  According to 
> | https://cran.r-project.org/bin/linux/ubuntu/README (and many other sources),
> | R is available for this version of Ubuntu (which is a stable version).
> | 
> | I currently have
> | 
> | deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/
> | 
> | in sources.list.  I've tried this with and without
> | 
> | deb https://  mirrors.rit.edu/ubuntu trusty-backports main
> | restricted universe
> 
> Is the space an error for the email, or do you really have it there?
> 
> | I've tried installing using apt-get , aptitude, and synaptic. (I have, 
> | of course, run apt-get update.) All hit problems they cannot resolve 
> | (listed below).
> | 
> | I'd appreciate any thoughts on this.  I've installed R on many linux 
> | distributions in the past (suse, redhat, debian, most recently 
> | elementary os) and never run into anything like this before.   (I'm 
> | getting desperate enough to consider building R from src, but as I 
> | recall getting the right libraries installed isn't that easy).
> 
> We (somewhat obviously) know that "all systems are green" because so many
> automated processes (think Travis CI) depend on it.  Ditto with say Docker
> autobuilds.  And as it is so easy to document, a quick and dirty (as I didn't
> bother with keys inside the container) check using Docker.  Below is a quick
> log from a shell inside an Emacs session (hence the command echos).
> 
> In essence I do just these few steps:
> 
> - start a Docker session with Ubuntu 14.04
> - add an entry for CRAN to apt's config
> - apt-get update
> - apt-get install (with proper switches to override interactive use and 
> warnings)
> - start R
> 
> and we see R 3.2.4 as expected.  I only used r-base-core and not r-base here
> to keep the download smaller but it should really work the same way.
> 
> If your system 'balks' you have to figure why/what something conflicts and
> resolve those.   Show us the details.  Some of us may know.
> 
> Dirk
> 
> 
> edd@max:~$ docker run --rm -ti ubuntu:trusty ## basic 14.04
> ]0;root@8776f0c1263e: /root@8776f0c1263e:/# export PS1="> "# nicer here
> export PS1="> "
>> echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" > 
>> /etc/apt/sources.list.d/cran.list
> .list.d/cran.list
>> apt-get update
> apt-get update
> Ign http://cran.rstudio.com trusty/ InRelease
> Get:1 http://cran.rstudio.com trusty/ Release.gpg [473 B]
> Get:2 http://cran.rstudio.com trusty/ Release [3703 B]
> Ign http://archive.ubuntu.com trusty InRelease
> Get:3 http://archive.ubuntu.com trusty-updates InRelease [65.9 kB]
> Ign http://cran.rstudio.com trusty/ Release
> Get:4 http://cran.rstudio.com trusty/ Packages [153 kB]
> Get:5 http://archive.ubuntu.com trusty-security InRelease [65.9 kB]
> Hit http://archive.ubuntu.com trusty Release.gpg
> Get:6 http://archive.ubuntu.com trusty-updates/main Sources [340 kB]
> Get:7 http://archive.ubuntu.com trusty-updates/restricted Sources [5217 B]
> Get:8 http://archive.ubuntu.com trusty-updates/universe Sources [190 kB]
> Get:9 http://archive.ubuntu.com trusty-updates/main amd64 Packages [930 kB]
> Get:10 http://archive.ubuntu.com trusty-updates/restricted amd64 Packages 
> [23.5 kB]
> Get:11 http://archive.ubuntu.com trusty-updates/universe amd64 Packages [460 
> kB]
> Hit http://archive.ubuntu.com trusty Release
> Get:12 http://archive.ubuntu.com trusty-security/main Sources [138 kB]
> Get:13 http://archive.ubuntu.com trusty-security/restricted Sources [3920 B]
> Get:14 http://archive.ubuntu.com trusty-security/universe Sources [39.2 kB]
> Get:15 http://archive.ubuntu.com trusty-security/main amd64 Packages [555 kB]
> Get:16 http://archive.ubuntu.com trusty-security/restricted amd64 Packages 
> [20.2 kB]
> Get:17 http://archive.ubuntu.com trusty-security/universe amd64 Packages [163 
> kB]
> Get:18 http://archive.ubuntu.com trusty/main Sources [1335 kB]
> Get:19 http://archive.ubuntu.com trusty/restricted Sources [5335 B]
> Get:20 http://archive.ubuntu.com trusty/universe Sources 

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Dirk Eddelbuettel]

On 23 March 2016 at 09:35, Barnet Wagman wrote:
| I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu 
| 14.04 system.  According to 
| https://cran.r-project.org/bin/linux/ubuntu/README (and many other sources),
| R is available for this version of Ubuntu (which is a stable version).
| 
| I currently have
| 
| deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/
| 
| in sources.list.  I've tried this with and without
| 
| deb https://  mirrors.rit.edu/ubuntu trusty-backports main
| restricted universe

Is the space an error for the email, or do you really have it there?

| I've tried installing using apt-get , aptitude, and synaptic. (I have, 
| of course, run apt-get update.) All hit problems they cannot resolve 
| (listed below).
| 
| I'd appreciate any thoughts on this.  I've installed R on many linux 
| distributions in the past (suse, redhat, debian, most recently 
| elementary os) and never run into anything like this before.   (I'm 
| getting desperate enough to consider building R from src, but as I 
| recall getting the right libraries installed isn't that easy).

We (somewhat obviously) know that "all systems are green" because so many
automated processes (think Travis CI) depend on it.  Ditto with say Docker
autobuilds.  And as it is so easy to document, a quick and dirty (as I didn't
bother with keys inside the container) check using Docker.  Below is a quick
log from a shell inside an Emacs session (hence the command echos).

In essence I do just these few steps:

- start a Docker session with Ubuntu 14.04
- add an entry for CRAN to apt's config
- apt-get update
- apt-get install (with proper switches to override interactive use and 
warnings)
- start R

and we see R 3.2.4 as expected.  I only used r-base-core and not r-base here
to keep the download smaller but it should really work the same way.

If your system 'balks' you have to figure why/what something conflicts and
resolve those.   Show us the details.  Some of us may know.

Dirk


edd@max:~$ docker run --rm -ti ubuntu:trusty ## basic 14.04
]0;root@8776f0c1263e: /root@8776f0c1263e:/# export PS1="> "# nicer here
export PS1="> "
> echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" > 
> /etc/apt/sources.list.d/cran.list
.list.d/cran.list
> apt-get update
apt-get update
Ign http://cran.rstudio.com trusty/ InRelease
Get:1 http://cran.rstudio.com trusty/ Release.gpg [473 B]
Get:2 http://cran.rstudio.com trusty/ Release [3703 B]
Ign http://archive.ubuntu.com trusty InRelease
Get:3 http://archive.ubuntu.com trusty-updates InRelease [65.9 kB]
Ign http://cran.rstudio.com trusty/ Release
Get:4 http://cran.rstudio.com trusty/ Packages [153 kB]
Get:5 http://archive.ubuntu.com trusty-security InRelease [65.9 kB]
Hit http://archive.ubuntu.com trusty Release.gpg
Get:6 http://archive.ubuntu.com trusty-updates/main Sources [340 kB]
Get:7 http://archive.ubuntu.com trusty-updates/restricted Sources [5217 B]
Get:8 http://archive.ubuntu.com trusty-updates/universe Sources [190 kB]
Get:9 http://archive.ubuntu.com trusty-updates/main amd64 Packages [930 kB]
Get:10 http://archive.ubuntu.com trusty-updates/restricted amd64 Packages [23.5 
kB]
Get:11 http://archive.ubuntu.com trusty-updates/universe amd64 Packages [460 kB]
Hit http://archive.ubuntu.com trusty Release
Get:12 http://archive.ubuntu.com trusty-security/main Sources [138 kB]
Get:13 http://archive.ubuntu.com trusty-security/restricted Sources [3920 B]
Get:14 http://archive.ubuntu.com trusty-security/universe Sources [39.2 kB]
Get:15 http://archive.ubuntu.com trusty-security/main amd64 Packages [555 kB]
Get:16 http://archive.ubuntu.com trusty-security/restricted amd64 Packages 
[20.2 kB]
Get:17 http://archive.ubuntu.com trusty-security/universe amd64 Packages [163 
kB]
Get:18 http://archive.ubuntu.com trusty/main Sources [1335 kB]
Get:19 http://archive.ubuntu.com trusty/restricted Sources [5335 B]
Get:20 http://archive.ubuntu.com trusty/universe Sources [7926 kB]
Get:21 http://archive.ubuntu.com trusty/main amd64 Packages [1743 kB]
Get:22 http://archive.ubuntu.com trusty/restricted amd64 Packages [16.0 kB]
Get:23 http://archive.ubuntu.com trusty/universe amd64 Packages [7589 kB]
Fetched 21.8 MB in 1min 19s (274 kB/s)
Reading package lists... Done
W: GPG error: http://cran.rstudio.com trusty/ Release: The following signatures 
couldn't be verified because the public key is not available: NO_PUBKEY 
51716619E084DAB9
> apt-get install -y --force=yes r-base-core   
apt-get install -y --force=yes r-base-core   
E: Command line option --force=yes is not understood
> apt-get install -y --force-yes r-base-core   
apt-get install -y --force-yes r-base-core   
Reading package lists... Done
Building dependency tree   
Reading state information... Done
The following extra packages will be installed:
  autoconf automake autotools-dev binutils bsdmainutils build-essential
  ca-certificates cdbs cpp cpp-4.8 curl debhelper dh-apparmor dh-translations
  

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Barnet Wagman]

My system is amd64 (intel i5-5200U) so the processor can't be the problem.

thanks

On 03/23/2016 10:13 AM, Matthew Simpson wrote:
I just essentially the same question on this mailing list and the 
problem ended up being that my cpu's architecture was not supported by 
the ubuntu releases (or any releases for that matter). I had to build 
R from source, but it wasn't much headache.


The Ubuntu releases only support i386 and amd64 --- i.e. 32 bit & 64 
bit intel and amd cpus and not, e.g., the arm cpus that are becoming 
more common in lower end laptops. On Debian there is an armel release, 
but not an armhf release --- so if your cpu is armel you could switch 
to Debian to avoid having to build from source.


Matt



___
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Re: [R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Matthew Simpson]

I just essentially the same question on this mailing list and the problem
ended up being that my cpu's architecture was not supported by the ubuntu
releases (or any releases for that matter). I had to build R from source,
but it wasn't much headache.

The Ubuntu releases only support i386 and amd64 --- i.e. 32 bit & 64 bit
intel and amd cpus and not, e.g., the arm cpus that are becoming more
common in lower end laptops. On Debian there is an armel release, but not
an armhf release --- so if your cpu is armel you could switch to Debian to
avoid having to build from source.

Matt

On Wed, Mar 23, 2016 at 11:35 AM, Barnet Wagman  wrote:

> I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu
> 14.04 system.  According to
> https://cran.r-project.org/bin/linux/ubuntu/README (and many other
> sources),
> R is available for this version of Ubuntu (which is a stable version).
>
> I currently have
>
> deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/
>
> in sources.list.  I've tried this with and without
>
> deb https://  mirrors.rit.edu/ubuntu trusty-backports main
> restricted universe
>
> I've tried installing using apt-get , aptitude, and synaptic. (I have,
> of course, run apt-get update.) All hit problems they cannot resolve
> (listed below).
>
> I'd appreciate any thoughts on this.  I've installed R on many linux
> distributions in the past (suse, redhat, debian, most recently
> elementary os) and never run into anything like this before.   (I'm
> getting desperate enough to consider building R from src, but as I
> recall getting the right libraries installed isn't that easy).
>
> Using apt-get install, I get the error message:
>
> 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
>   r-base-dev : Depends: r-base-core (>= 3.2.4-revised-1trusty0) but
> it is not going to be installed
>Depends: gfortran but it is not going to be installed
>Depends: liblapack-dev but it is not going to be
> installed or
> libatlas-base-dev but it is not installable
> E: Unable to correct problems, you have held broken packages.
>
> Using aptitude:
>
> root@bwud:/home/moi# aptitude install r-base
> The following NEW packages will be installed:
>cdbs{a} dh-translations{a} gfortran{a} gfortran-4.8{ab}
> libblas-dev{a} libblas3{a} libbz2-dev{a} libgfortran-4.8-dev{ab}
> libgfortran3{ab}
>libjpeg-dev{a} libjpeg-turbo8-dev{a} libjpeg8-dev{a}
> liblapack-dev{a} liblapack3{a} liblzma-dev{a} libncurses5-dev{a}
> libpcre3-dev{a}
>libpcrecpp0{a} libpng12-dev{a} libreadline-dev{a}
> libreadline6-dev{a} libtinfo-dev{a} python-scour{a} r-base
> r-base-core{a} r-base-dev{a}
>r-base-html{a} r-cran-boot{a} r-cran-class{a} r-cran-cluster{a}
> r-cran-codetools{a} r-cran-foreign{a} r-cran-kernsmooth{a}
>r-cran-lattice{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a}
> r-cran-nlme{a} r-cran-nnet{a} r-cran-rpart{a} r-cran-spatial{a}
>r-cran-survival{a} r-doc-html{a} r-recommended{a} zlib1g-dev{a}
> 0 packages upgraded, 45 newly installed, 0 to remove and 0 not
> upgraded.
> Need to get 47.8 MB of archives. After unpacking 105 MB will be used.
> The following packages have unmet dependencies:
>   gfortran-4.8 : Depends: gcc-4.8-base (= 4.8.2-19ubuntu1) but
> 4.8.4-2ubuntu1~14.04.1 is installed.
>  Depends: gcc-4.8 (= 4.8.2-19ubuntu1) but
> 4.8.4-2ubuntu1~14.04.1 is installed.
>   libgfortran3 : Depends: gcc-4.8-base (= 4.8.2-19ubuntu1) but
> 4.8.4-2ubuntu1~14.04.1 is installed.
>   libgfortran-4.8-dev : Depends: gcc-4.8-base (= 4.8.2-19ubuntu1)
> but 4.8.4-2ubuntu1~14.04.1 is installed.
> Depends: libgcc-4.8-dev (= 4.8.2-19ubuntu1)
> but 4.8.4-2ubuntu1~14.04.1 is installed.
> The following actions will resolve these dependencies:
>
>Keep the following packages at their current version:
> 1)  gfortran [Not Installed]
> 2)  gfortran-4.8 [Not Installed]
> 3)  libgfortran-4.8-dev [Not Installed]
> 4)  libgfortran3 [Not Installed]
> 5)  liblapack-dev [Not Installed]
> 6)  liblapack3 [Not Installed]
> 7)  r-base [Not Installed]
> 8)  r-base-core [Not 

[R-sig-Debian] r-base installation fails on Ubuntu 14.04

[Barnet Wagman]

I am unable to install R on an up to date (i.e. apt upgraded) Ubuntu 
14.04 system.  According to 
https://cran.r-project.org/bin/linux/ubuntu/README (and many other sources),
R is available for this version of Ubuntu (which is a stable version).

I currently have

deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu trusty/

in sources.list.  I've tried this with and without

deb https://  mirrors.rit.edu/ubuntu trusty-backports main
restricted universe

I've tried installing using apt-get , aptitude, and synaptic. (I have, 
of course, run apt-get update.) All hit problems they cannot resolve 
(listed below).

I'd appreciate any thoughts on this.  I've installed R on many linux 
distributions in the past (suse, redhat, debian, most recently 
elementary os) and never run into anything like this before.   (I'm 
getting desperate enough to consider building R from src, but as I 
recall getting the right libraries installed isn't that easy).

Using apt-get install, I get the error message:

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
  r-base-dev : Depends: r-base-core (>= 3.2.4-revised-1trusty0) but
it is not going to be installed
   Depends: gfortran but it is not going to be installed
   Depends: liblapack-dev but it is not going to be
installed or
libatlas-base-dev but it is not installable
E: Unable to correct problems, you have held broken packages.

Using aptitude:

root@bwud:/home/moi# aptitude install r-base
The following NEW packages will be installed:
   cdbs{a} dh-translations{a} gfortran{a} gfortran-4.8{ab}
libblas-dev{a} libblas3{a} libbz2-dev{a} libgfortran-4.8-dev{ab}
libgfortran3{ab}
   libjpeg-dev{a} libjpeg-turbo8-dev{a} libjpeg8-dev{a}
liblapack-dev{a} liblapack3{a} liblzma-dev{a} libncurses5-dev{a}
libpcre3-dev{a}
   libpcrecpp0{a} libpng12-dev{a} libreadline-dev{a}
libreadline6-dev{a} libtinfo-dev{a} python-scour{a} r-base
r-base-core{a} r-base-dev{a}
   r-base-html{a} r-cran-boot{a} r-cran-class{a} r-cran-cluster{a}
r-cran-codetools{a} r-cran-foreign{a} r-cran-kernsmooth{a}
   r-cran-lattice{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a}
r-cran-nlme{a} r-cran-nnet{a} r-cran-rpart{a} r-cran-spatial{a}
   r-cran-survival{a} r-doc-html{a} r-recommended{a} zlib1g-dev{a}
0 packages upgraded, 45 newly installed, 0 to remove and 0 not upgraded.
Need to get 47.8 MB of archives. After unpacking 105 MB will be used.
The following packages have unmet dependencies:
  gfortran-4.8 : Depends: gcc-4.8-base (= 4.8.2-19ubuntu1) but
4.8.4-2ubuntu1~14.04.1 is installed.
 Depends: gcc-4.8 (= 4.8.2-19ubuntu1) but
4.8.4-2ubuntu1~14.04.1 is installed.
  libgfortran3 : Depends: gcc-4.8-base (= 4.8.2-19ubuntu1) but
4.8.4-2ubuntu1~14.04.1 is installed.
  libgfortran-4.8-dev : Depends: gcc-4.8-base (= 4.8.2-19ubuntu1)
but 4.8.4-2ubuntu1~14.04.1 is installed.
Depends: libgcc-4.8-dev (= 4.8.2-19ubuntu1)
but 4.8.4-2ubuntu1~14.04.1 is installed.
The following actions will resolve these dependencies:

   Keep the following packages at their current version:
1)  gfortran [Not Installed]
2)  gfortran-4.8 [Not Installed]
3)  libgfortran-4.8-dev [Not Installed]
4)  libgfortran3 [Not Installed]
5)  liblapack-dev [Not Installed]
6)  liblapack3 [Not Installed]
7)  r-base [Not Installed]
8)  r-base-core [Not Installed]
9)  r-base-dev [Not Installed]
10) r-base-html [Not Installed]
11) r-cran-boot [Not Installed]
12) r-cran-class [Not Installed]
13) r-cran-cluster [Not Installed]
14) r-cran-codetools [Not Installed]
15) r-cran-foreign [Not Installed]
16) r-cran-kernsmooth [Not Installed]
17) r-cran-lattice [Not Installed]
18) r-cran-mass [Not Installed]
19) r-cran-matrix [Not Installed]
20) r-cran-mgcv [Not Installed]
21) r-cran-nlme [Not Installed]
22) r-cran-nnet [Not Installed]
23) r-cran-rpart [Not Installed]
24) r-cran-spatial [Not Installed]
25) r-cran-survival [Not Installed]
26) r-recommended [Not Installed]



Accept this solution? [Y/n/q/?] Y
No packages will