Liviu Andronic
2015-Aug-29 15:14 UTC
[R-sig-Debian] Having both R-current and R-devel installed on Ubuntu
Hi Dirk, I too would need to get R-devel on my Ubuntu box (alongside an existing R installation) to check my packages, especially given the mayhem that awaits us when the new `R CMD check --as-cran` goes live. ( http://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html ) I was wondering if the script that you posted on r-sig-debian a couple years back was still valid. More however, I'd like to know if you ever considered/worked on putting this script into proper 'debian' packaging instructions? If such existed, it would be easy enough to mirror the R repo on Launchpad and then provide daily builds of r-devel on a PPA (in view of independent installation from stable R packages). Any ideas on this? Regards, Liviu On Wed, Aug 8, 2012 at 11:22 PM, Dirk Eddelbuettel <edd at debian.org> wrote:> > Hi S?ren, > > On 8 August 2012 at 20:38, S?ren H?jsgaard 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
Dirk Eddelbuettel
2015-Aug-29 15:44 UTC
[R-sig-Debian] Having both R-current and R-devel installed on Ubuntu
On 29 August 2015 at 17:14, Liviu Andronic wrote:
| Hi Dirk,
| I too would need to get R-devel on my Ubuntu box (alongside an
| existing R installation) to check my packages, especially given the
| mayhem that awaits us when the new `R CMD check --as-cran` goes live.
| ( http://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html )
|
| I was wondering if the script that you posted on r-sig-debian a couple
| years back was still valid. More however, I'd like to know if you ever
Yes. I update R-devel about weekly as I too need to check my packages.
| considered/worked on putting this script into proper 'debian'
| packaging instructions? If such existed, it would be easy enough to
I think about it a bit, but I just do not have the time and bandwith to
i) completely rewrite debian/* for the r-base package
ii) to become accomodating of two R interpreters
iii) in a way that is seemless and does not introduce bugs in the transition
| mirror the R repo on Launchpad and then provide daily builds of
| r-devel on a PPA (in view of independent installation from stable R
| packages).
|
| Any ideas on this? Regards,
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'.
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 S?ren,
| >
| > On 8 August 2012 at 20:38, S?ren H?jsgaard 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
Liviu Andronic
2015-Aug-30 07:38 UTC
[R-sig-Debian] Having both R-current and R-devel installed on Ubuntu
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 S?ren, > | > > | > On 8 August 2012 at 20:38, S?ren H?jsgaard 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