R

Installation

The TileDB-Rpackage has is available on CRAN which provides binaries for Windows and macOS which can be installed via install.packages("tiledb"). On Linux this result in installation from source. For all operating systems, one can also clone the repository and create a compressed tarfile to check and install as described in the R manual, or install directly from Github. We also describe installing releases from Github as shown below.

# -- from CRAN
install.packages("tiledb")

# -- alternatively, from GitHub
# if not yet installed, install the 'remotes' package
if (requireNamespace("remotes") == FALSE) install.packages("remotes")
remotes::install_github("TileDB-Inc/TileDB-R", ref = remotes::github_release())

# -- once installed, check via
tiledb::tiledb_version()
#> major minor patch
#>     1     7     5

If the TileDB library is installed in a custom location, you need to pass the explicit path:

remotes::install_github("TileDB-Inc/TileDB-R", 
    ref = remotes::github_release(),
    args="--configure-args='--with-tiledb=/path/to/tiledb'")

To build the latest development version of TileDB-R:

remotes::install_github("TileDB-Inc/TileDB-R")

install_github will delete all temporary files upon failure. To debug build failures, clone this repository locally and build a compressed tarfile to check and install, or run the commanddevtools::install("/path/to/TileDB-R").

If you are using the TileDB Conda package, you may need to explicitly add the conda path after activating the environment with conda activate tiledb.

$ export CPATH=$CONDA_PREFIX/include
$ export LIBRARY_PATH=$CONDA_PREFIX/lib
$ export LD_LIBRARY_PATH=$CONDA_PREFIX/lib

Developer Documentation

Instructions for setting up a RStudio development environment, building, and testing the TileDB-R package are located in the developer documentation wiki.

Troubleshooting

If you experience issues when installing devtools, see these instructions. If the problem persists, you can install devtools with conda by running:

conda install -c conda-forge r-devtools