R SIG Debian - Apr 2017 - difficulty in Ubuntu 14.04 apt-getting R 3.3.2

Hi:

I have a Dockerfile, which builds an image which installed R 3.3.2 in
Ubuntu 14.04, but building using that Dockerfile seems to have stopped
working and I am unclear why.

I believe the relevant error is:

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-recommended : Depends: r-cran-cluster (>= 1.9.6-2) but it is not going
to be installed
                 Depends: r-cran-rpart (>= 3.1.20) but it is not going to
be installed
                 Depends: r-cran-survival (>= 2.13.2-1) but it is not going
to be installed

Any help in resolving this would be appreciated.

Additional information: while I need R 3.3.2 for historical purposes, when
I substitute 3.3.2 with 3.3.3 in the Dockerfile, the image builds
successfully.

Thanks!

Jen

Dockerfile:

FROM ubuntu:14.04

RUN apt-get update && \
   DEBIAN_FRONTEND="noninteractive" apt-get install -y
--no-install-recommends software-properties-common && \
    apt-add-repository "deb http://cran.r-project.org/bin/linux/ubuntu
trusty/" && \
    apt-get update && \
    DEBIAN_FRONTEND="noninteractive" apt-get install -y --force-yes
--no-install-recommends libcurl3-gnutls libcurl4-gnutls-dev libssl-dev
libssh2-1-dev r-base=3.3.2-1trusty0 r-base-dev=3.3.2-1trusty0
r-recommended=3.3.2-1trusty0 r-base-core=3.3.2-1trusty0

RUN locale-gen en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8

WORKDIR /plugin/

	[[alternative HTML version deleted]]

Try including the files it is telling you are needed, specifically
r-cran-rpart=3.1.20 r-cran-survival=2.13.2-1 r-cran-cluster=1.9.6-2


Thanks,

Sean Southard

On Wed, Apr 19, 2017 at 9:38 AM, Jennifer Lyon <jennifer.s.lyon at
gmail.com>
wrote:
> Hi:
>
> I have a Dockerfile, which builds an image which installed R 3.3.2 in
> Ubuntu 14.04, but building using that Dockerfile seems to have stopped
> working and I am unclear why.
>
> I believe the relevant error is:
>
> 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-recommended : Depends: r-cran-cluster (>= 1.9.6-2) but it is not
going
> to be installed
>                  Depends: r-cran-rpart (>= 3.1.20) but it is not going
to
> be installed
>                  Depends: r-cran-survival (>= 2.13.2-1) but it is not
going
> to be installed
>
> Any help in resolving this would be appreciated.
>
> Additional information: while I need R 3.3.2 for historical purposes, when
> I substitute 3.3.2 with 3.3.3 in the Dockerfile, the image builds
> successfully.
>
> Thanks!
>
> Jen
>
> Dockerfile:
>
> FROM ubuntu:14.04
>
> RUN apt-get update && \
>    DEBIAN_FRONTEND="noninteractive" apt-get install -y
> --no-install-recommends software-properties-common && \
>     apt-add-repository "deb http://cran.r-project.org/bin/linux/ubuntu
> trusty/" && \
>     apt-get update && \
>     DEBIAN_FRONTEND="noninteractive" apt-get install -y
--force-yes
> --no-install-recommends libcurl3-gnutls libcurl4-gnutls-dev libssl-dev
> libssh2-1-dev r-base=3.3.2-1trusty0 r-base-dev=3.3.2-1trusty0
> r-recommended=3.3.2-1trusty0 r-base-core=3.3.2-1trusty0
>
> RUN locale-gen en_US.UTF-8
> ENV LANG en_US.UTF-8
> ENV LANGUAGE en_US:en
> ENV LC_ALL en_US.UTF-8
>
> WORKDIR /plugin/
>
>         [[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 19 April 2017 at 09:38, Jennifer Lyon wrote:
| Hi:
| 
| I have a Dockerfile, which builds an image which installed R 3.3.2 in
| Ubuntu 14.04, but building using that Dockerfile seems to have stopped
| working and I am unclear why.
| 
| I believe the relevant error is:
| 
| 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-recommended : Depends: r-cran-cluster (>= 1.9.6-2) but it is not going
| to be installed
|                  Depends: r-cran-rpart (>= 3.1.20) but it is not going to
| be installed
|                  Depends: r-cran-survival (>= 2.13.2-1) but it is not going
| to be installed
| 
| Any help in resolving this would be appreciated.
| 
| Additional information: while I need R 3.3.2 for historical purposes, when
| I substitute 3.3.2 with 3.3.3 in the Dockerfile, the image builds
| successfully.
| 
| Thanks!
| 
| Jen
| 
| Dockerfile:
| 
| FROM ubuntu:14.04
| 
| RUN apt-get update && \
|    DEBIAN_FRONTEND="noninteractive" apt-get install -y
| --no-install-recommends software-properties-common && \
|     apt-add-repository "deb http://cran.r-project.org/bin/linux/ubuntu
| trusty/" && \
|     apt-get update && \
|     DEBIAN_FRONTEND="noninteractive" apt-get install -y --force-yes
| --no-install-recommends libcurl3-gnutls libcurl4-gnutls-dev libssl-dev
| libssh2-1-dev r-base=3.3.2-1trusty0 r-base-dev=3.3.2-1trusty0
| r-recommended=3.3.2-1trusty0 r-base-core=3.3.2-1trusty0

You are pointing to the normal repo.  AFAIK it only keeps _current_ versions
and one cannot, as you do here, request arbitrary older versions.

But take a look at Carl's 'versioned' Rocker containers which may
offer you
want you're after.

  GitHub:  https://github.com/rocker-org/rocker-versioned
  Docker:  https://hub.docker.com/r/rocker/r-ver/

Dirk

| 
| RUN locale-gen en_US.UTF-8
| ENV LANG en_US.UTF-8
| ENV LANGUAGE en_US:en
| ENV LC_ALL en_US.UTF-8
| 
| WORKDIR /plugin/
| 
| 	[[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

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

Thank you, the Rocker containers, or at least what is done in the Rocker
containers is exactly what I need.

Jen

On Wed, Apr 19, 2017 at 9:57 AM, Dirk Eddelbuettel <edd at debian.org>
wrote:
>
> On 19 April 2017 at 09:38, Jennifer Lyon wrote:
> | Hi:
> |
> | I have a Dockerfile, which builds an image which installed R 3.3.2 in
> | Ubuntu 14.04, but building using that Dockerfile seems to have stopped
> | working and I am unclear why.
> |
> | I believe the relevant error is:
> |
> | 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-recommended : Depends: r-cran-cluster (>= 1.9.6-2) but it is not
going
> | to be installed
> |                  Depends: r-cran-rpart (>= 3.1.20) but it is not going
to
> | be installed
> |                  Depends: r-cran-survival (>= 2.13.2-1) but it is not
> going
> | to be installed
> |
> | Any help in resolving this would be appreciated.
> |
> | Additional information: while I need R 3.3.2 for historical purposes,
> when
> | I substitute 3.3.2 with 3.3.3 in the Dockerfile, the image builds
> | successfully.
> |
> | Thanks!
> |
> | Jen
> |
> | Dockerfile:
> |
> | FROM ubuntu:14.04
> |
> | RUN apt-get update && \
> |    DEBIAN_FRONTEND="noninteractive" apt-get install -y
> | --no-install-recommends software-properties-common && \
> |     apt-add-repository "deb
http://cran.r-project.org/bin/linux/ubuntu
> | trusty/" && \
> |     apt-get update && \
> |     DEBIAN_FRONTEND="noninteractive" apt-get install -y
--force-yes
> | --no-install-recommends libcurl3-gnutls libcurl4-gnutls-dev libssl-dev
> | libssh2-1-dev r-base=3.3.2-1trusty0 r-base-dev=3.3.2-1trusty0
> | r-recommended=3.3.2-1trusty0 r-base-core=3.3.2-1trusty0
>
> You are pointing to the normal repo.  AFAIK it only keeps _current_
> versions
> and one cannot, as you do here, request arbitrary older versions.
>
> But take a look at Carl's 'versioned' Rocker containers which
may offer you
> want you're after.
>
>   GitHub:  https://github.com/rocker-org/rocker-versioned
>   Docker:  https://hub.docker.com/r/rocker/r-ver/
>
> Dirk
>
> |
> | RUN locale-gen en_US.UTF-8
> | ENV LANG en_US.UTF-8
> | ENV LANGUAGE en_US:en
> | ENV LC_ALL en_US.UTF-8
> |
> | WORKDIR /plugin/
> |
> |       [[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
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>
	[[alternative HTML version deleted]]

Thank you Dirk for inadvertently fixing my R installation issue in Linux Mint
18.1 that I've been having all week.


I followed the R-CRAN page<https://cran.r-project.org/> on installing from
the Debian repositry and I've always used this
link<https://cran.ma.imperial.ac.uk/>, which has served me well. Until
this week after upgrading my Mint machine. Running from the terminal, I was
getting all this shit (not exact output, but similar):


The repository 'http://cran.ma.imperial.ac.uk/bin/linux/debian stable main
Release' does not have a Release file.


W: GPG error: https://cran.ma.imperial.ac.uk/ Release: The following signatures
couldn't be verified because

the public key is not available: NO_PUBKEY 51716619E084DAB9

W: http://dl.google.com/linux/chrome/deb/dists/stable/Release.gpg: Signature by

key 4CCA1EAF950CEE4AB83976DCA040830F7FAC5991 uses weak digest algorithm (SHA1)

This had never happened to me before in six years of downloading and installing
R onto several Linux distros on various of my machines. It was spitting these
same errors with other UK mirrors such as this
one<https://www.stats.bris.ac.uk/R/>. Implementing all the keys made no
damned difference.

Now, I know that Mint and Ubuntu both come from Debian parentage, so - again
from the R-CRAN page but for Ubuntu - I spun the wheel using your
repositry<http://deb-src%20http://cran.r-project.org/bin/linux/ubuntu%20trusty/>:

clive at climate ~ $ sudo apt-key adv --keyserver keyserver.ubuntu.com
--recv-keys E084DAB9
[sudo] password for clive:
Executing: /tmp/tmp.31XeOMQKnK/gpg.1.sh --keyserver
keyserver.ubuntu.com
--recv-keys
E084DAB9
gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com
gpg: key E084DAB9: public key "Michael Rutter <marutter at
gmail.com>" imported
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)
clive at climate ~ $ sudo apt-get update
Ign:1 http://www.mirrorservice.org/sites/packages.linuxmint.com/packages serena
InRelease
Hit:2 http://ubuntu.mirrors.uk2.net/ubuntu xenial InRelease
Hit:3 http://www.mirrorservice.org/sites/packages.linuxmint.com/packages serena
Release
Hit:4 http://ubuntu.mirrors.uk2.net/ubuntu xenial-updates InRelease
Hit:5 http://ubuntu.mirrors.uk2.net/ubuntu xenial-backports InRelease
Hit:6 http://security.ubuntu.com/ubuntu xenial-security InRelease
Hit:7 http://archive.canonical.com/ubuntu xenial InRelease
Ign:8 http://cran.r-project.org/bin/linux/ubuntu trusty/ InRelease
Hit:9 http://cran.r-project.org/bin/linux/ubuntu trusty/ Release
Get:10 http://cran.r-project.org/bin/linux/ubuntu trusty/ Release.gpg [473 B]
Hit:12 https://repo.skype.com/deb stable InRelease
Ign:13 http://dl.google.com/linux/chrome/deb stable InRelease
Hit:14 http://dl.google.com/linux/chrome/deb stable Release
Fetched 473 B in 5s (88 B/s)
Reading package lists... Done
clive at climate ~ $ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages will be upgraded:
  distro-info-data firefox firefox-locale-en libfreetype6 libfreetype6:i386
  libfreetype6-dev r-base-core r-base-dev
8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 70.0 MB of archives.
After this operation, 815 kB disk space will be freed.
Do you want to continue? [Y/n] y
WARNING: The following packages cannot be authenticated!
  r-base-core r-base-dev
Install these packages without verification? [y/N] y
Get:1 http://ubuntu.mirrors.uk2.net/ubuntu xenial-updates/main amd64
distro-info-data all 0.28ubuntu0.3 [4048 B]
Get:2 http://www.mirrorservice.org/sites/packages.linuxmint.com/packages
serena/upstream amd64 firefox amd64 53.0+linuxmint1+serena [46.5 MB]
Get:3 http://ubuntu.mirrors.uk2.net/ubuntu xenial-updates/main amd64
libfreetype6-dev amd64 2.6.1-0.1ubuntu2.2 [955 kB]
Get:4 http://cran.r-project.org/bin/linux/ubuntu trusty/ r-base-core
3.3.3-1trusty0 [21.1 MB]
Get:5 http://ubuntu.mirrors.uk2.net/ubuntu xenial-updates/main i386 libfreetype6
i386 2.6.1-0.1ubuntu2.2 [330 kB]
Get:6 http://ubuntu.mirrors.uk2.net/ubuntu xenial-updates/main amd64
libfreetype6 amd64 2.6.1-0.1ubuntu2.2 [315 kB]
Get:7 http://www.mirrorservice.org/sites/packages.linuxmint.com/packages
serena/upstream amd64 firefox-locale-en amd64 53.0+linuxmint1+serena [769 kB]
Get:8 http://cran.r-project.org/bin/linux/ubuntu trusty/ r-base-dev
3.3.3-1trusty0 [4408 B]
Fetched 70.0 MB in 37s (1879 kB/s)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = "en_GB:en",
LC_ALL = (unset),
LANG = "mate.desktop"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
locale: Cannot set LC_CTYPE to default locale: No such file or directory
locale: Cannot set LC_MESSAGES to default locale: No such file or directory
locale: Cannot set LC_ALL to default locale: No such file or directory
(Reading database ... 359338 files and directories currently installed.)
Preparing to unpack .../distro-info-data_0.28ubuntu0.3_all.deb ...
Unpacking distro-info-data (0.28ubuntu0.3) over (0.28ubuntu0.2) ...
Setting up distro-info-data (0.28ubuntu0.3) ...
(Reading database ... 359338 files and directories currently installed.)
Preparing to unpack .../libfreetype6-dev_2.6.1-0.1ubuntu2.2_amd64.deb ...
Unpacking libfreetype6-dev:amd64 (2.6.1-0.1ubuntu2.2) over (2.6.1-0.1ubuntu2.1)
...
Preparing to unpack .../libfreetype6_2.6.1-0.1ubuntu2.2_amd64.deb ...
De-configuring libfreetype6:i386 (2.6.1-0.1ubuntu2.1) ...
Unpacking libfreetype6:amd64 (2.6.1-0.1ubuntu2.2) over (2.6.1-0.1ubuntu2.1) ...
Preparing to unpack .../libfreetype6_2.6.1-0.1ubuntu2.2_i386.deb ...
Unpacking libfreetype6:i386 (2.6.1-0.1ubuntu2.2) over (2.6.1-0.1ubuntu2.1) ...
Preparing to unpack .../firefox_53.0+linuxmint1+serena_amd64.deb ...
Unpacking firefox (53.0+linuxmint1+serena) over (52.0.2+linuxmint1+serena) ...
Preparing to unpack .../firefox-locale-en_53.0+linuxmint1+serena_amd64.deb ...
Unpacking firefox-locale-en (53.0+linuxmint1+serena) over
(52.0.2+linuxmint1+serena) ...
Preparing to unpack .../r-base-core_3.3.3-1trusty0_amd64.deb ...
Unpacking r-base-core (3.3.3-1trusty0) over (3.2.3-4) ...
Preparing to unpack .../r-base-dev_3.3.3-1trusty0_all.deb ...
Unpacking r-base-dev (3.3.3-1trusty0) over (3.2.3-4) ...
Processing triggers for doc-base (0.10.7) ...
Processing 1 changed doc-base file...
Registering documents with scrollkeeper...
Processing triggers for man-db (2.7.5-1) ...
Processing triggers for libc-bin (2.23-0ubuntu7) ...
Processing triggers for desktop-file-utils (0.22-1ubuntu5.1) ...
Processing triggers for mime-support (3.59ubuntu1) ...
Processing triggers for mintsystem (8.3.0) ...
Processing triggers for hicolor-icon-theme (0.15-0ubuntu1) ...
Processing triggers for tex-common (6.04) ...
locale: Cannot set LC_CTYPE to default locale: No such file or directory
locale: Cannot set LC_MESSAGES to default locale: No such file or directory
locale: Cannot set LC_ALL to default locale: No such file or directory
Running mktexlsr. This may take some time... done.
Processing triggers for install-info (6.1.0.dfsg.1-5) ...
Setting up libfreetype6:amd64 (2.6.1-0.1ubuntu2.2) ...
Setting up libfreetype6:i386 (2.6.1-0.1ubuntu2.2) ...
Setting up libfreetype6-dev:amd64 (2.6.1-0.1ubuntu2.2) ...
Setting up firefox (53.0+linuxmint1+serena) ...
Please restart all running instances of firefox, or you will experience
problems.
Setting up firefox-locale-en (53.0+linuxmint1+serena) ...
Setting up r-base-core (3.3.3-1trusty0) ...
Installing new version of config file /etc/R/repositories ...
Installing new version of config file /etc/R/Makeconf ...
Installing new version of config file /etc/R/ldpaths ...
Preserving user changes to /usr/share/bash-completion/completions/R (renamed
from /etc/bash_completion.d/R)...
locale: Cannot set LC_CTYPE to default locale: No such file or directory
locale: Cannot set LC_MESSAGES to default locale: No such file or directory
locale: Cannot set LC_ALL to default locale: No such file or directory
Replacing config file /etc/R/Renviron with new version
Setting up r-base-dev (3.3.3-1trusty0) ...
Processing triggers for libc-bin (2.23-0ubuntu7) ...

I've subsequently installed r-base as well.

Well, I'll certainly know next time, you can be damned sure of that. Thanks
for your inadvertent help: you're an absolute lifesaver. But, seriously,
what an absolute nonsense.

Yours with thanks,
Clive Nicholas
<https://cran.r-project.org/>
________________________________
From: R-SIG-Debian <r-sig-debian-bounces at r-project.org> on behalf of
Dirk Eddelbuettel <edd at debian.org>
Sent: 19 April 2017 15:57
To: Jennifer Lyon
Cc: r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] difficulty in Ubuntu 14.04 apt-getting R 3.3.2


On 19 April 2017 at 09:38, Jennifer Lyon wrote:
| Hi:
|
| I have a Dockerfile, which builds an image which installed R 3.3.2 in
| Ubuntu 14.04, but building using that Dockerfile seems to have stopped
| working and I am unclear why.
|
| I believe the relevant error is:
|
| 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-recommended : Depends: r-cran-cluster (>= 1.9.6-2) but it is not going
| to be installed
|                  Depends: r-cran-rpart (>= 3.1.20) but it is not going to
| be installed
|                  Depends: r-cran-survival (>= 2.13.2-1) but it is not going
| to be installed
|
| Any help in resolving this would be appreciated.
|
| Additional information: while I need R 3.3.2 for historical purposes, when
| I substitute 3.3.2 with 3.3.3 in the Dockerfile, the image builds
| successfully.
|
| Thanks!
|
| Jen
|
| Dockerfile:
|
| FROM ubuntu:14.04
|
| RUN apt-get update && \
|    DEBIAN_FRONTEND="noninteractive" apt-get install -y
| --no-install-recommends software-properties-common && \
|     apt-add-repository "deb http://cran.r-project.org/bin/linux/ubuntu
| trusty/" && \
|     apt-get update && \
|     DEBIAN_FRONTEND="noninteractive" apt-get install -y --force-yes
| --no-install-recommends libcurl3-gnutls libcurl4-gnutls-dev libssl-dev
| libssh2-1-dev r-base=3.3.2-1trusty0 r-base-dev=3.3.2-1trusty0
| r-recommended=3.3.2-1trusty0 r-base-core=3.3.2-1trusty0

You are pointing to the normal repo.  AFAIK it only keeps _current_ versions
and one cannot, as you do here, request arbitrary older versions.

But take a look at Carl's 'versioned' Rocker containers which may
offer you
want you're after.

  GitHub:  https://github.com/rocker-org/rocker-versioned
[https://avatars2.githubusercontent.com/u/9100160?v=3&s=400]<https://github.com/rocker-org/rocker-versioned>

GitHub - rocker-org/rocker-versioned: Run earlier versions
...<https://github.com/rocker-org/rocker-versioned>
github.com
This repository provides alternate stack to r-base, rocker/rstudio,
rocker/hadleyverse series, with an emphasis on reproducibility. Compared to
those images, this stack:



  Docker:  https://hub.docker.com/r/rocker/r-ver/
r-ver - hub.docker.com<https://hub.docker.com/r/rocker/r-ver/>
hub.docker.com
This repository provides alternate stack to r-base, rocker/rstudio,
rocker/hadleyverse series, with an emphasis on reproducibility. Compared to
those images, this stack:




Dirk

|
| RUN locale-gen en_US.UTF-8
| ENV LANG en_US.UTF-8
| ENV LANGUAGE en_US:en
| ENV LC_ALL en_US.UTF-8
|
| WORKDIR /plugin/
|
|        [[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

--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Dirk Eddelbuettel<http://dirk.eddelbuettel.com/>
dirk.eddelbuettel.com
Welcome. I contribute to several open source efforts, mostly Debian and R.
Besides looking after a number of Debian packages, I ...




_______________________________________________
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]]