v2.8.0

Setting Up New or Additional Languages

Environment editor provides flexibility to set up your computation environment. After you select a starter environment, you can add additional languages to your capsule.

If you are building a bi or multi-language capsule:

  • Use a base Ubuntu (18.04 or 16.04) environment, if you are not using a pre-installed language.

  • Start from an environment with the proprietary language if you are using one, for example Matlab.

  • Select an environment with GPU access, these will be labeled as such, or will reference CUDA or a deep learning framework, if you are using GPU.

Installing a Language Using Package Managers

The following are all available as apt-get packages:

  • build-essential for the C/C++ toolchain (gcc/g++, make, etc.);

  • r-base for R (note: r-base-dev will help you install R packages, we recommend adding a MRAN snapshot for installing archived R packages, see more detail below);

  • octave for Octave;

  • python-pip for Python 2 and the pip installer;

  • python3-pip for Python 3 and the pip3 installer;

  • perl for Perl (add cpanm if needed);

  • luajit for Lua (add luarocks if needed);

  • default-jdk for Java;

  • gfortran for Fortran.

Once you add R or python, the commands Rscript or python will become available, respectively.

Adding R Language

Installing R in a non-R environment, or updating to the most recent version

While Code Ocean's environments are based on a recent version of Ubuntu (18.04 code name "Bionic Beaver" or just "Bionic"), the version of R it included is 3.4.4. To get newer versions of R to install on Code Ocean:

  1. In the environment editor, click the gear icon next to apt-get. This will open the apt-get configuration window.

  2. In Additional sources, copy and paste deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ (for R 3.6) or deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/ (for R 4.0). This tells apt-get to search for packages on the R project's own repository.

  3. In GPG Keys, copy and paste E298A3A825C0D65DFD57CBB651716619E084DAB9. This is a piece of information provided by the R project to guarantee the authenticity of the repository.

4. Click Save.

5. Navigate back to the environment editor.

6. Add r-base as an apt-get dependency, this step is crucial.

Note: the various R installer options will show up automatically, which you can immediately add packages to.

Using MRAN Snapshots to Install Archived R Packages

When you are installing R packages through CRAN, you may find packages failing to install, reporting that a dependency relies on a very new version of R.

You need to specify an MRAN snapshot for the CRAN installer in the environment.

  1. Add the R packages to the CRAN installer.

2. Click the gear icon next to R (CRAN) and add a date in the following form:

This will direct the CRAN installer to use an older index of packages, instead of the most recent one. A good default is to go with the release date of the next major version of R, which is the latest point in time when all of the packages in the index must have supported the one that preceded it.

A few useful snapshots:

Notes:

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