From 878d695448f08584e0b90a88fb60614e4c346d6e Mon Sep 17 00:00:00 2001 From: Carl Boettiger Date: Tue, 11 Nov 2014 21:20:06 -0800 Subject: [PATCH 1/6] boilerplate for r-base image documentation Still needs a proper "how to use this image" section; this just fills in the license, logo, wikipedia summary etc --- r-base/README-short.txt | 1 + r-base/README.md | 54 ++++++++++++++++++++++++++++++++++++++++ r-base/content.md | 31 +++++++++++++++++++++++ r-base/license.md | 2 ++ r-base/logo.png | Bin 0 -> 13580 bytes 5 files changed, 88 insertions(+) create mode 100644 r-base/README-short.txt create mode 100644 r-base/README.md create mode 100644 r-base/content.md create mode 100644 r-base/license.md create mode 100644 r-base/logo.png diff --git a/r-base/README-short.txt b/r-base/README-short.txt new file mode 100644 index 000000000..197415303 --- /dev/null +++ b/r-base/README-short.txt @@ -0,0 +1 @@ +R is a free software environment for statistical computing and graphics. diff --git a/r-base/README.md b/r-base/README.md new file mode 100644 index 000000000..f81cbbd63 --- /dev/null +++ b/r-base/README.md @@ -0,0 +1,54 @@ +# Supported tags and respective `Dockerfile` links + +- [`3.1.1` (*3.1/Dockerfile*)](https://github.com/docker-library/gcc/blob/ba6f069df8e6c838d0465b09215e96f8d5d65269/4.6/Dockerfile) + +For more information about this image and its history, please see the [relevant +manifest file +(`library/r-base`)](https://github.com/docker-library/official-images/blob/master/library/r-base) +in the [`docker-library/official-images` GitHub +repo](https://github.com/docker-library/official-images). + +# What is R? + +R is a free software programming language and software environment for statistical computing and graphics. The R language is widely used among statisticians and data miners for developing statistical software and data analysis. Polls and surveys of data miners are showing R's popularity has increased substantially in recent years. + +R is an implementation of the S programming language combined with lexical scoping semantics inspired by Scheme. S was created by John Chambers while at Bell Labs. R was created by Ross Ihaka and Robert Gentleman at the University of Auckland, New Zealand, and is currently developed by the R Development Core Team, of which Chambers is a member. R is named partly after the first names of the first two R authors and partly as a play on the name of S. + +R is a GNU project. The source code for the R software environment is written primarily in C, Fortran, and R. R is freely available under the GNU General Public License, and pre-compiled binary versions are provided for various operating systems. R uses a command line interface; however, several graphical user interfaces are available for use with R. + +> [wikipedia.org/wiki/R_(programming_language)](http://en.wikipedia.org/wiki/R_(programming_language)) + +![logo](https://raw.githubusercontent.com/docker-library/docs/master/r-base/logo.png) + +# How to use this image + + + + + +# License + +View [license information](https://github.com/rocker-org/rocker/blob/master/LICENSE) +for the software contained in this image. + +# User Feedback + +## Issues + +If you have any problems with or questions about this image, please contact us + through a [GitHub issue](https://github.com/rocker-org/rocker/issues). + +You can also reach many of the official image maintainers on Twitter: [@cboettig](http://twitter.com/cboettig) and [@eddelbuettel](http://twitter.com/eddelbuettel). + + +## Contributing + +You are invited to contribute new features, fixes, or updates, large or small; +we are always thrilled to receive pull requests, and do our best to process them +as fast as we can. + +Before you start to code, we recommend discussing your plans +through a [GitHub issue](https://github.com/rocker-org/rocker/issues), especially for more ambitious +contributions. This gives other contributors a chance to point you in the right +direction, give you feedback on your design, and help you find out if someone +else is working on the same thing. diff --git a/r-base/content.md b/r-base/content.md new file mode 100644 index 000000000..e8824e247 --- /dev/null +++ b/r-base/content.md @@ -0,0 +1,31 @@ +# What is R? + +R is a free software programming language and software environment for statistical computing and graphics. The R language is widely used among statisticians and data miners for developing statistical software and data analysis. Polls and surveys of data miners are showing R's popularity has increased substantially in recent years. + +R is an implementation of the S programming language combined with lexical scoping semantics inspired by Scheme. S was created by John Chambers while at Bell Labs. R was created by Ross Ihaka and Robert Gentleman at the University of Auckland, New Zealand, and is currently developed by the R Development Core Team, of which Chambers is a member. R is named partly after the first names of the first two R authors and partly as a play on the name of S. + +R is a GNU project. The source code for the R software environment is written primarily in C, Fortran, and R. R is freely available under the GNU General Public License, and pre-compiled binary versions are provided for various operating systems. R uses a command line interface; however, several graphical user interfaces are available for use with R. + +> [wikipedia.org/wiki/R_(programming_language)](http://en.wikipedia.org/wiki/R_(programming_language)) + +%%LOGO%% + +# How to use this image + +## Start an R instance + +The most straightforward way to use this image is to use a gcc container as both +the build and runtime environment. In your `Dockerfile`, writing something along +the lines of the following will compile and run your project: + + FROM r-base:latest + COPY . /usr/src/myscripts + WORKDIR /usr/src/myscripts + CMD ["Rscript -e myscript.R"] + +Then, build and run the Docker image: + + docker build -t my-r-app . + docker run -it --rm --name my-running-app my-r-app + + diff --git a/r-base/license.md b/r-base/license.md new file mode 100644 index 000000000..d9d2e12e5 --- /dev/null +++ b/r-base/license.md @@ -0,0 +1,2 @@ +View [license information](https://github.com/rocker-org/rocker/blob/master/LICENSE) +for the software contained in this image. diff --git a/r-base/logo.png b/r-base/logo.png new file mode 100644 index 0000000000000000000000000000000000000000..c17a0174b626e602eb5e88d04f5c50ae4f73983c GIT binary patch literal 13580 zcmZX52T&7V)bE0T0YO3$f`Wk3LNipU0#Sj49#D#Oq=R&jCM}>KO?pR4KtwvB7p02y z-a#qSoAmze|9vxW=FPk8va{LT$!71l=lse|sJf~G1=(FP001aZiqA0M@in+BLkPkD zw0^-l;DN|ePDKs?%A#&vm=J^K1TGi_Bv9PPxCWlEm?>gZ0Kkg_0Q|84a0b5QzX||u z2mn|&1^|g90HAkFtJ9DIFOZljDLezN|NHygm>&ziLh7if>jD6L=l|^l7w^$403cL@ zdM2m!b_(C%8E2sF#@W#CxN_d%g-cPwO~!~!l$&>TbmZ_-LRpA}VqvSUG412q0j?5E zNSbn%tfzFdmwaA>%x@&yZbKVR?Ci+P+3$5Hn0KYD=)S=89p4f5J=qG*T=i3xMPj_KC4#duFGX7ZZOZ9a9~s{-6#t2|p|)kc9+5 zhgKU7SMH3nbU5krCn_i?JThz$la@9pdKnB&bAjXHFb@mk1Sy`v*|AWhBAg0|g@!vp zi6E@#0_&7y<-CfDiu`=e%>HBdV{<`<;qrrAfewf$f)&M>nm|kzgVjJErUh%*P0}F~ zsh~(y*J1p;Z>cF=atJ9vsszYhf0M;qyrQfZnWEv0yz{aB&!0a91qEV}q^x%KF>cF3KjTz(ThMJxG4jCd0y16}DM8?9)*#1u1xr4*Xqg||DVL<`BX(wYP0-#7* zf2|5*(mwohRm;zM@&ux+q9msf=n$}G=4yAaI+$bGpTU>d4H)Ytn82JEZT6FQzV1s` z-^sENz=tQiSl_>^fG$Xr)ccKw$3syuR!?J*?M}S7HkeSy-1(g3o94@-gd$cfHi^m3 z)-aY$0Af!(UtL<_N2;Sit(S-UA^3#=zL+iZsK;nZV*O()W=TpN3k; 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The R language is widely used among statisticians and data miners for developing statistical software and data analysis. Polls and surveys of data miners are showing R's popularity has increased substantially in recent years. +R is a system for statistical computation and graphics. It consists of a +language plus a run-time environment with graphics, a debugger, access to +certain system functions, and the ability to run programs stored in script +files. -R is an implementation of the S programming language combined with lexical scoping semantics inspired by Scheme. S was created by John Chambers while at Bell Labs. R was created by Ross Ihaka and Robert Gentleman at the University of Auckland, New Zealand, and is currently developed by the R Development Core Team, of which Chambers is a member. R is named partly after the first names of the first two R authors and partly as a play on the name of S. +The R language is widely used among statisticians and data miners for +developing statistical software and data analysis. Polls and surveys of data +miners are showing R's popularity has increased substantially in recent +years. -R is a GNU project. The source code for the R software environment is written primarily in C, Fortran, and R. R is freely available under the GNU General Public License, and pre-compiled binary versions are provided for various operating systems. R uses a command line interface; however, several graphical user interfaces are available for use with R. +R is an implementation of the S programming language combined with lexical +scoping semantics inspired by Scheme. S was created by John Chambers while at +Bell Labs. R was created by Ross Ihaka and Robert Gentleman at the University +of Auckland, New Zealand, and is currently developed by the R Development +Core Team, of which Chambers is a member. R is named partly after the first +names of the first two R authors and partly as a play on the name of S. +R is a GNU project. The source code for the R software environment is written +primarily in C, Fortran, and R. R is freely available under the GNU General +Public License, and pre-compiled binary versions are provided for various +operating systems. R uses a command line interface; however, several +graphical user interfaces are available for use with R. + +> [R FAQ](http://cran.r-project.org/doc/FAQ/R-FAQ.html#What-is-R_003f) > [wikipedia.org/wiki/R_(programming_language)](http://en.wikipedia.org/wiki/R_(programming_language)) ![logo](https://raw.githubusercontent.com/docker-library/docs/master/r-base/logo.png) # How to use this image - - +R can be used interactively, as well as in scripts via Rscript +front-end. Both modes are supported by the container. + # License -View [license information](https://github.com/rocker-org/rocker/blob/master/LICENSE) +View [GPL 2 license information](https://github.com/rocker-org/rocker/blob/master/LICENSE) for the software contained in this image. # User Feedback ## Issues -If you have any problems with or questions about this image, please contact us - through a [GitHub issue](https://github.com/rocker-org/rocker/issues). +If you have any problems with or questions about this image, please contact +us through a [GitHub issue](https://github.com/rocker-org/rocker/issues). -You can also reach many of the official image maintainers on Twitter: [@cboettig](http://twitter.com/cboettig) and [@eddelbuettel](http://twitter.com/eddelbuettel). +You can also reach us by email via email at `rocker-maintainers@eddelbuettel.com`. ## Contributing @@ -47,8 +67,8 @@ You are invited to contribute new features, fixes, or updates, large or small; we are always thrilled to receive pull requests, and do our best to process them as fast as we can. -Before you start to code, we recommend discussing your plans -through a [GitHub issue](https://github.com/rocker-org/rocker/issues), especially for more ambitious -contributions. This gives other contributors a chance to point you in the right -direction, give you feedback on your design, and help you find out if someone -else is working on the same thing. +Before you start to code, we recommend discussing your plans through a +[GitHub issue](https://github.com/rocker-org/rocker/issues), especially for +more ambitious contributions. This gives other contributors a chance to point +you in the right direction, give you feedback on your design, and help you +find out if someone else is working on the same thing. diff --git a/r-base/content.md b/r-base/content.md index e8824e247..7a3d6945e 100644 --- a/r-base/content.md +++ b/r-base/content.md @@ -1,11 +1,31 @@ # What is R? -R is a free software programming language and software environment for statistical computing and graphics. The R language is widely used among statisticians and data miners for developing statistical software and data analysis. Polls and surveys of data miners are showing R's popularity has increased substantially in recent years. +# What is R? -R is an implementation of the S programming language combined with lexical scoping semantics inspired by Scheme. S was created by John Chambers while at Bell Labs. R was created by Ross Ihaka and Robert Gentleman at the University of Auckland, New Zealand, and is currently developed by the R Development Core Team, of which Chambers is a member. R is named partly after the first names of the first two R authors and partly as a play on the name of S. +R is a system for statistical computation and graphics. It consists of a +language plus a run-time environment with graphics, a debugger, access to +certain system functions, and the ability to run programs stored in script +files. -R is a GNU project. The source code for the R software environment is written primarily in C, Fortran, and R. R is freely available under the GNU General Public License, and pre-compiled binary versions are provided for various operating systems. R uses a command line interface; however, several graphical user interfaces are available for use with R. +The R language is widely used among statisticians and data miners for +developing statistical software and data analysis. Polls and surveys of data +miners are showing R's popularity has increased substantially in recent +years. +R is an implementation of the S programming language combined with lexical +scoping semantics inspired by Scheme. S was created by John Chambers while at +Bell Labs. R was created by Ross Ihaka and Robert Gentleman at the University +of Auckland, New Zealand, and is currently developed by the R Development +Core Team, of which Chambers is a member. R is named partly after the first +names of the first two R authors and partly as a play on the name of S. + +R is a GNU project. The source code for the R software environment is written +primarily in C, Fortran, and R. R is freely available under the GNU General +Public License, and pre-compiled binary versions are provided for various +operating systems. R uses a command line interface; however, several +graphical user interfaces are available for use with R. + +> [R FAQ](http://cran.r-project.org/doc/FAQ/R-FAQ.html#What-is-R_003f) > [wikipedia.org/wiki/R_(programming_language)](http://en.wikipedia.org/wiki/R_(programming_language)) %%LOGO%% @@ -14,18 +34,23 @@ R is a GNU project. The source code for the R software environment is written pr ## Start an R instance -The most straightforward way to use this image is to use a gcc container as both +The most straightforward way to use this image is to use a container as both the build and runtime environment. In your `Dockerfile`, writing something along the lines of the following will compile and run your project: FROM r-base:latest - COPY . /usr/src/myscripts - WORKDIR /usr/src/myscripts + COPY . /usr/local/src/myscripts + WORKDIR /usr/local/src/myscripts CMD ["Rscript -e myscript.R"] Then, build and run the Docker image: docker build -t my-r-app . + docker run -it --rm --name my-running-app my-r-app +Lauch R directory for interactive work: + + docker run -ti --rm rocker/r-base /usr/bin/R + diff --git a/r-base/license.md b/r-base/license.md index d9d2e12e5..ce5e45ec1 100644 --- a/r-base/license.md +++ b/r-base/license.md @@ -1,2 +1,2 @@ -View [license information](https://github.com/rocker-org/rocker/blob/master/LICENSE) +View [the GPL 2 license information](https://github.com/rocker-org/rocker/blob/master/LICENSE) for the software contained in this image. From bfcce19c7e6018868b0689cfcdba33f73b318f92 Mon Sep 17 00:00:00 2001 From: Carl Boettiger Date: Tue, 18 Nov 2014 15:40:59 -0800 Subject: [PATCH 3/6] add a few more realistic examples of use cases --- r-base/README.md | 41 ++++++++++++++++++++++++++++++++++++++--- r-base/content.md | 41 ++++++++++++++++++++++++++++++----------- 2 files changed, 68 insertions(+), 14 deletions(-) diff --git a/r-base/README.md b/r-base/README.md index 5eca8d80f..ef6eec866 100644 --- a/r-base/README.md +++ b/r-base/README.md @@ -41,9 +41,44 @@ graphical user interfaces are available for use with R. # How to use this image -R can be used interactively, as well as in scripts via Rscript -front-end. Both modes are supported by the container. - +## Interactive R ## + +Launch R directly for interactive work: + + docker run -ti --rm r-base /usr/bin/R + +## Batch mode ## + +Link the working directory to run R batch commands. We recommend specifying a non-root user when linking a volume to the container to avoid permission changes, as illustrated here: + + docker run -ti --rm -v $(pwd):/home/docker -w /home/docker -u docker r-base R CMD check . + +Alternatively, just run a bash session on the container first. This allows a user to run batch commands and also edit and run scripts: + + docker run -ti --rm r-base /usr/bin/bash + vim.tiny myscript.R + +Write the script in the container, exit `vim` and run `Rscript` + + Rscript myscript.R + + +## Dockerfiles ## + +Use `r-base` as a base for your own Dockerfiles. For instance, something along the lines of the following will compile and run your project: + + FROM r-base:latest + COPY . /usr/local/src/myscripts + WORKDIR /usr/local/src/myscripts + CMD ["Rscript -e myscript.R"] + +Build your image with the command: + + docker build -t myscript /path/to/Dockerfile + +Running this container with no command will execute the script. Alternatively, a user could run this container in interactive or batch mode as described above, instead of linking volumes. + +Further documentation and example use cases can be found at the [rocker-org](https://github.com/rocker-org/rocker/wiki) project wiki. # License diff --git a/r-base/content.md b/r-base/content.md index 7a3d6945e..d1a1d8f11 100644 --- a/r-base/content.md +++ b/r-base/content.md @@ -32,25 +32,44 @@ graphical user interfaces are available for use with R. # How to use this image -## Start an R instance +## Interactive R ## -The most straightforward way to use this image is to use a container as both -the build and runtime environment. In your `Dockerfile`, writing something along -the lines of the following will compile and run your project: +Launch R directly for interactive work: + + docker run -ti --rm r-base /usr/bin/R + +## Batch mode ## + +Link the working directory to run R batch commands. We recommend specifying a non-root user when linking a volume to the container to avoid permission changes, as illustrated here: + + docker run -ti --rm -v $(pwd):/home/docker -w /home/docker -u docker r-base R CMD check . + +Alternatively, just run a bash session on the container first. This allows a user to run batch commands and also edit and run scripts: + + docker run -ti --rm r-base /usr/bin/bash + vim.tiny myscript.R + +Write the script in the container, exit `vim` and run `Rscript` + + Rscript myscript.R + + +## Dockerfiles ## + +Use `r-base` as a base for your own Dockerfiles. For instance, something along the lines of the following will compile and run your project: FROM r-base:latest COPY . /usr/local/src/myscripts WORKDIR /usr/local/src/myscripts CMD ["Rscript -e myscript.R"] -Then, build and run the Docker image: +Build your image with the command: - docker build -t my-r-app . - - docker run -it --rm --name my-running-app my-r-app + docker build -t myscript /path/to/Dockerfile -Lauch R directory for interactive work: - - docker run -ti --rm rocker/r-base /usr/bin/R +Running this container with no command will execute the script. Alternatively, a user could run this container in interactive or batch mode as described above, instead of linking volumes. + +Further documentation and example use cases can be found at the [rocker-org](https://github.com/rocker-org/rocker/wiki) project wiki. + From 07de1a32c7fea1224c4fb73707cba7ed18e8e643 Mon Sep 17 00:00:00 2001 From: Carl Boettiger Date: Wed, 19 Nov 2014 11:33:44 -0800 Subject: [PATCH 4/6] use the new default CMD in the example use --- r-base/README.md | 2 +- r-base/content.md | 4 +--- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/r-base/README.md b/r-base/README.md index ef6eec866..8f4818967 100644 --- a/r-base/README.md +++ b/r-base/README.md @@ -45,7 +45,7 @@ graphical user interfaces are available for use with R. Launch R directly for interactive work: - docker run -ti --rm r-base /usr/bin/R + docker run -ti --rm r-base ## Batch mode ## diff --git a/r-base/content.md b/r-base/content.md index d1a1d8f11..305e8fc89 100644 --- a/r-base/content.md +++ b/r-base/content.md @@ -1,7 +1,5 @@ # What is R? -# What is R? - R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script @@ -36,7 +34,7 @@ graphical user interfaces are available for use with R. Launch R directly for interactive work: - docker run -ti --rm r-base /usr/bin/R + docker run -ti --rm r-base ## Batch mode ## From 841f34355a86174c7ecf137f4945236fb3b1eeb0 Mon Sep 17 00:00:00 2001 From: Carl Boettiger Date: Wed, 19 Nov 2014 12:52:03 -0800 Subject: [PATCH 5/6] update Dockerfile links --- r-base/README.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/r-base/README.md b/r-base/README.md index 8f4818967..11695d90a 100644 --- a/r-base/README.md +++ b/r-base/README.md @@ -1,12 +1,11 @@ # Supported tags and respective `Dockerfile` links -- [`3.1.1` (*3.1/Dockerfile*)](https://github.com/docker-library/gcc/blob/ba6f069df8e6c838d0465b09215e96f8d5d65269/4.6/Dockerfile) +- [`3.1.2` (*3.1.2/Dockerfile*)](https://github.com/rocker-org/rocker/blob/105fca2b42051c5cd0894da31839c99a9b7de320/debian/r-base/Dockerfile) For more information about this image and its history, please see the -[relevant manifest file (`library/r-base`)](https://github.com/docker-library/official-images/blob/master/library/r-base) -in the -[`docker-library/official-images` GitHub repo](https://github.com/docker-library/official-images). - +[relevant manifest file (`library/r-base`)](https://github.com/rocker-org/official-images/blob/master/library/r-base) +and the +[`rocker-org/rocker` GitHub repo](https://github.com/rocker-org/rocker). # What is R? From 99469ac7da07ffbd6af82952397bd13c4bf912a9 Mon Sep 17 00:00:00 2001 From: Carl Boettiger Date: Mon, 1 Dec 2014 21:35:59 -0800 Subject: [PATCH 6/6] Add license link and correct CMD example as suggested by @tianon --- r-base/README.md | 5 ++--- r-base/content.md | 2 +- r-base/license.md | 4 ++-- 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/r-base/README.md b/r-base/README.md index 11695d90a..77e9d78b1 100644 --- a/r-base/README.md +++ b/r-base/README.md @@ -69,7 +69,7 @@ Use `r-base` as a base for your own Dockerfiles. For instance, something along t FROM r-base:latest COPY . /usr/local/src/myscripts WORKDIR /usr/local/src/myscripts - CMD ["Rscript -e myscript.R"] + CMD ["Rscript", "myscript.R"] Build your image with the command: @@ -82,8 +82,7 @@ Further documentation and example use cases can be found at the [rocker-org](htt # License -View [GPL 2 license information](https://github.com/rocker-org/rocker/blob/master/LICENSE) -for the software contained in this image. +View [R-project license information](http://www.r-project.org/Licenses/) for the software contained in this image. # User Feedback diff --git a/r-base/content.md b/r-base/content.md index 305e8fc89..78b660bc8 100644 --- a/r-base/content.md +++ b/r-base/content.md @@ -59,7 +59,7 @@ Use `r-base` as a base for your own Dockerfiles. For instance, something along t FROM r-base:latest COPY . /usr/local/src/myscripts WORKDIR /usr/local/src/myscripts - CMD ["Rscript -e myscript.R"] + CMD ["Rscript", "myscript.R"] Build your image with the command: diff --git a/r-base/license.md b/r-base/license.md index ce5e45ec1..3eef07d01 100644 --- a/r-base/license.md +++ b/r-base/license.md @@ -1,2 +1,2 @@ -View [the GPL 2 license information](https://github.com/rocker-org/rocker/blob/master/LICENSE) -for the software contained in this image. +View [R-project license information](http://www.r-project.org/Licenses/) for the software contained in this image. +