[R-sig-Debian] Having both R-current and R-devel installed on Ubuntu

Liviu Andronic landronimirc at gmail.com
Sun Aug 30 09:38:53 CEST 2015


On Sat, Aug 29, 2015 at 5:44 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
> There is an easier way.
>
> Install docker, either via the docker.io package or (as I do now) via the apt
> repo docker.com offers.  I maintain two images
>
>    rocker/drd         "Daily R-devel" -- a little smaller, deletes build deps
>
>    rocker/r-devel     r-devel builds
>
> you can use 'as is'.
>
I tried this, but I'm new to the docker world. I managed to:
docker run hello-world

without issues, as well as:
docker pull rocker/r-devel

But what next? I am unable to:
docker run rocker/r-devel

either as root or as user. I checked teh wiki
(https://github.com/rocker-org/rocker/wiki), but it doesn't seem to
provide instructions for absolute novices.

Regards,
Liviu


> Or you can use the script you mentioned. I mostly do the latter.
>
> Dirk
>
> | Liviu
> |
> |
> | On Wed, Aug 8, 2012 at 11:22 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
> | >
> | > Hi Søren,
> | >
> | > On 8 August 2012 at 20:38, Søren Højsgaard wrote:
> | > | Dear List,
> | > |
> | > | Having used R on Windows for years, I have recently installed Ubuntu as a virtual machine. I admit that I am quite new to the linux world.
> | >
> | > Good :)  It's even better once you "host" on Linux as Linux is generally
> | > better with limited resources.
> | >
> | > | Installing R (current version = 2.15.1) went smoothly, but I would like to have both the current version of R and R-devel installed. I've searched the net for info on doing this but so far without luck.
> | >
> | > I hope you found the README on CRAN to get you the prebuilt version. That is
> | > the way many of us find most convenient to get "r-release" up and going.
> | >
> | > | Can anyone help me getting this up and running?
> | > |
> | > | A related question: How do I upgrade the current version of R to the patched versions?
> | >
> | > R-devel and R-patched can only be had from source, and not from a .deb
> | > because I never reorganised the packaging to allow for multiple versions.
> | >
> | > But because CRAN makes us check against R-devel, it is of use to have it.  So
> | > I keep a svn checkout and every few weeks build locally via a little script
> | > which carries over a few of the configuration choices I make for the Debian /
> | > Ubuntu package (plus memory debugging from when Doug and I were chasing
> | > something).  Followed by 'make install', this puts R into /usr/local/lib/R-devel
> | > which is then completely off the PATH and does not affect normal R.
> | >
> | > I then use this via a second script ~/bin/R-devel.sh which calls it. Also
> | > below.
> | >
> | > Hope this helps, Dirk
> | >
> | >
> | > ## --snip here ------------------------------------------------------------------------------
> | > ## ~/bin/build-R-devel
> | >
> | > #!/bin/sh
> | >
> | > cd ~/svn/r-devel
> | >
> | > # R_PAPERSIZE=letter                            \
> | > # R_BATCHSAVE="--no-save --no-restore"          \
> | > # R_BROWSER=xdg-open                            \
> | > # PAGER=/usr/bin/pager                          \
> | > # PERL=/usr/bin/perl                            \
> | > # R_UNZIPCMD=/usr/bin/unzip                     \
> | > # R_ZIPCMD=/usr/bin/zip                         \
> | > # R_PRINTCMD=/usr/bin/lpr                               \
> | > # LIBnn=lib                                     \
> | > # AWK=/usr/bin/awk                                \
> | > # CC="ccache gcc"                                       \
> | > # CFLAGS="-ggdb -pipe -std=gnu99 -Wall -pedantic -DTESTING_WRITE_BARRIER" \
> | > # CXX="ccache g++"                              \
> | > # CXXFLAGS="-ggdb -std=c++0x -pipe -Wall -pedantic" \
> | > # FC="ccache gfortran"                          \
> | > # FCFLAGS="-ggdb -pipe -Wall -pedantic"         \
> | > # F77="ccache gfortran"                         \
> | > # FFLAGS="-ggdb -pipe -Wall -pedantic"          \
> | > # MAKE="make -j4"                                       \
> | > # ./configure                                   \
> | > #     --prefix=/usr/local/lib/R-devel           \
> | > #     --enable-R-shlib                          \
> | > #     --enable-strict-barrier                   \
> | > #     --with-blas                               \
> | > #     --with-lapack                             \
> | > #     --with-readline                           \
> | > #     --without-recommended-packages
> | >
> | > R_PAPERSIZE=letter                              \
> | > R_BATCHSAVE="--no-save --no-restore"            \
> | > R_BROWSER=xdg-open                              \
> | > PAGER=/usr/bin/pager                            \
> | > PERL=/usr/bin/perl                              \
> | > R_UNZIPCMD=/usr/bin/unzip                       \
> | > R_ZIPCMD=/usr/bin/zip                           \
> | > R_PRINTCMD=/usr/bin/lpr                         \
> | > LIBnn=lib                                       \
> | > AWK=/usr/bin/awk                                \
> | > CC="ccache gcc"                                 \
> | > CFLAGS="-ggdb -pipe -std=gnu99 -Wall -pedantic" \
> | > CXX="ccache g++"                                \
> | > CXXFLAGS="-ggdb -pipe -Wall -pedantic"          \
> | > FC="ccache gfortran"                            \
> | > F77="ccache gfortran"                           \
> | > MAKE="make -j4"                                 \
> | > ./configure                                     \
> | >     --prefix=/usr/local/lib/R-devel             \
> | >     --enable-R-shlib                            \
> | >     --with-blas                                 \
> | >     --with-lapack                               \
> | >     --with-readline                             \
> | >     --without-recommended-packages
> | >
> | > #CC="clang -O3"                                  \
> | > #CXX="clang++ -03"                              \
> | >
> | >
> | > #make svnonly
> | > make
> | >
> | > echo "*** Done -- now run 'make install'"
> | >
> | >
> | >
> | >
> | > ## --snip here ------------------------------------------------------------------------------
> | > ## ~/bin/R-devel.sh
> | >
> | > #!/bin/bash
> | >
> | > export R_LIBS_SITE=${R_LIBS_SITE-'/usr/lib/R-devel/lib/R/library:/usr/local/lib/R/site-library:/usr/lib/R/site-library::/usr/lib/R/library'}
> | > export PATH="/usr/local/lib/R-devel/bin:$PATH"
> | > R "$@"
> | >
> | > --
> | > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
> | >
> | > _______________________________________________
> | > R-SIG-Debian mailing list
> | > R-SIG-Debian at r-project.org
> | > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
> |
> |
> |
> | --
> | Do you think you know what math is?
> | http://www.ideasroadshow.com/issues/ian-stewart-2013-08-02
> | Or what it means to be intelligent?
> | http://www.ideasroadshow.com/issues/john-duncan-2013-08-30
> | Think again:
> | http://www.ideasroadshow.com/library
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org



-- 
Do you think you know what math is?
http://www.ideasroadshow.com/issues/ian-stewart-2013-08-02
Or what it means to be intelligent?
http://www.ideasroadshow.com/issues/john-duncan-2013-08-30
Think again:
http://www.ideasroadshow.com/library



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