difficulty in Ubuntu 14.04 apt-getting R 3.3.2
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
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