[R-sig-Debian] difficulty in Ubuntu 14.04 apt-getting R 3.3.2

CLIVE NICHOLAS clivenicholas at hotmail.com
Fri Apr 21 21:37:27 CEST 2017 

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 ...




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