Creating a Conda Package from an R Package¶

Overview¶

To create a package with Conda, you first need to make a new release and tag in the github repo of the R package you would like to create into a Conda Package.

For more information on best practices in R package creation, review this documentation.

Before creating the release on github, please check for proper dependencies listed in the files NAMESPACE and DESCRIPTION.

These files should have the same list of dependencies, and the version numbers for dependencies can be specified in the DESCRIPTION file. The DESCRIPTION file must be edited manually, while the NAMESPACE file should not be edited manually, but rather created automatically using the document() function.

The DESCRIPTION file must also be correctly formatted. For more information, see the following website.

Download the R package release from Github¶

To download the most recent release from the most recent tag on Github, activate Conda then use Conda skeleton to pull the correct URL. In the example below, replace $githubURL with the URL to your R package's github repo.

conda activate 

conda skeleton cran $githubURL

A folder is then created for the downloaded release. Ror example running the following:

conda skeleton cran https://github.com/NIDAP-Community/DSPWorkflow

Creates the folder

r-dspworkflow

Within this newly created folder is a file named meta.yaml. You will need to edit this file to include the channels and edit any information on the the package version number or dependency version numbers.

Here is an example of the top of the meta.yaml file with the channels section added:

{% set version = '0.9.5.2' %}

{% set posix = 'm2-' if win else '' %}
{% set native = 'm2w64-' if win else '' %}

package:
  name: r-dspworkflow
  version: {{ version|replace("-", "_") }}

channels:
  - conda-forge
  - bioconda
  - default
  - file://rstudio-files/RH/ccbr-projects/Conda_package_tutorial/local_channel/channel

source:

  git_url: https://github.com/NIDAP-Community/DSPWorkflow
  git_tag: 0.9.5

build:
  merge_build_host: True  # [win]
  # If this is a new build for the same version, increment the build number.
  number: 0
  # no skip

  # This is required to make R link correctly on Linux.
  rpaths:
    - lib/R/lib/
    - lib/

    # Suggests: testthat (== 3.1.4)
requirements:
  build:
    - {{ posix }}filesystem        # [win]
    - {{ posix }}git
    - {{ posix }}zip               # [win]

Here is an example of the sections for specifying dependency versions from the meta.yaml file:

  host:
    - r-base =4.1.3=h2f963a2_5
    - bioconductor-biobase =2.54.0=r41hc0cfd56_2
    - bioconductor-biocgenerics =0.40.0=r41hdfd78af_0
    - bioconductor-geomxtools =3.1.1=r41hdfd78af_0
    - bioconductor-nanostringnctools =1.2.0
    - bioconductor-spatialdecon =1.4.3
    - bioconductor-complexheatmap =2.10.0=r41hdfd78af_0
    - r-cowplot =1.1.1=r41hc72bb7e_1
    - r-dplyr =1.0.9=r41h7525677_0
    - r-ggforce =0.3.4=r41h7525677_0
    - r-ggplot2 =3.3.6=r41hc72bb7e_1
    - r-gridextra =2.3=r41hc72bb7e_1004
    - r-gtable =0.3.0=r41hc72bb7e_3
    - r-knitr =1.40=r41hc72bb7e_1
    - r-patchwork =1.1.2=r41hc72bb7e_1
    - r-reshape2 =1.4.4=r41h7525677_2
    - r-scales =1.2.1=r41hc72bb7e_1
    - r-tibble =3.1.8=r41h06615bd_1
    - r-tidyr =1.2.1=r41h7525677_1
    - r-umap =0.2.9.0=r41h7525677_1
    - r-rtsne =0.16=r41h37cf8d7_1
    - r-magrittr =2.0.3=r41h06615bd_1
    - r-rlang =1.1.0=r41h38f115c_0

  run:
    - r-base =4.1.3=h2f963a2_5
    - bioconductor-biobase =2.54.0=r41hc0cfd56_2
    - bioconductor-biocgenerics =0.40.0=r41hdfd78af_0
    - bioconductor-geomxtools =3.1.1=r41hdfd78af_0
    - bioconductor-nanostringnctools =1.2.0
    - bioconductor-spatialdecon =1.4.3
    - bioconductor-complexheatmap =2.10.0=r41hdfd78af_0
    - r-cowplot =1.1.1=r41hc72bb7e_1
    - r-dplyr =1.0.9=r41h7525677_0
    - r-ggforce =0.3.4=r41h7525677_0
    - r-ggplot2 =3.3.6=r41hc72bb7e_1
    - r-gridextra =2.3=r41hc72bb7e_1004
    - r-gtable =0.3.0=r41hc72bb7e_3
    - r-knitr =1.40=r41hc72bb7e_1
    - r-patchwork =1.1.2=r41hc72bb7e_1
    - r-reshape2 =1.4.4=r41h7525677_2
    - r-scales =1.2.1=r41hc72bb7e_1
    - r-tibble =3.1.8=r41h06615bd_1
    - r-tidyr =1.2.1=r41h7525677_1
    - r-umap =0.2.9.0=r41h7525677_1
    - r-rtsne =0.16=r41h37cf8d7_1
    - r-magrittr =2.0.3=r41h06615bd_1
    - r-rlang =1.1.0=r41h38f115c_0

In the above example, each of the dependencies has been assigned a conda build string, so that when conda builds a conda package, it will only use that specific build of the dependency from the listed conda channels. The above example is very restrictive, the dependencies can also be listed in the "meta.yaml" file to be more open--it will choose a conda build string that fits in with the other resolved dependency build strings based on what is available in the channels.

Also note that the "host" section matches the "run" section.

Here is some examples of a more open setup for these dependencies:

  host:
    - r-base >=4.1.3
    - bioconductor-biobase >=2.54.0
    - bioconductor-biocgenerics >=0.40.0
    - bioconductor-geomxtools >=3.1.1
    - bioconductor-nanostringnctools >=1.2.0
    - bioconductor-spatialdecon =1.4.3
    - bioconductor-complexheatmap >=2.10.0
    - r-cowplot >=1.1.1
    - r-dplyr >=1.0.9
    - r-ggforce >=0.3.4
    - r-ggplot2 >=3.3.6
    - r-gridextra >=2.3
    - r-gtable >=0.3.0
    - r-knitr >=1.40
    - r-patchwork >=1.1.2
    - r-reshape2 >=1.4.4
    - r-scales >=1.2.1
    - r-tibble >=3.1.8
    - r-tidyr >=1.2.1
    - r-umap >=0.2.9.0
    - r-rtsne >=0.16
    - r-magrittr >=2.0.3
    - r-rlang >=1.1.0

Build the Conda package¶

When the meta.yaml has been prepared, you can now build the Conda package. To do so, run the command, replacing

$r-package with the name of the R package folder that was created after running conda skeleton (the folder where the meta.yaml is located).
$build_log_name.log with the name for the log file, such as the date, time, and initials.

conda-build $r-package 2>&1|tee $build_log_name.log

Example

conda-build r-dspworkflow 2>&1|tee 05_12_23_330_nc.log

The log file will list how conda has built the package, including what dependencies version numbers and corresponding build strings were used to resolve the conda environment. These dependencies are what we specified in the "meta.yaml" file. The log file will be useful troubleshooting a failed build.

Be aware, the build can take anywhere from several minutes to an hour to complete, depending on the size of the package and the number of dependencies.

The conda package will be built as a tar.bz2 file.