This vignette discusses different options for installing the TileDB R package.
The TileDB R package is released via the Comprehensive R Archive Network, or CRAN. CRAN generally provides binaries for the two most widely operating systems, Windows and macOS. So issueing the command
will, on those two operating system, default to
type="binary"
and install a ready-to-run binary
package.
On other operating systems such as Linux, or by explicitly selecting
type="source" on Windows or macOS, an installation from source is attempted when using
install.packages(“tiledb”)`.
On Linux or macOS, this invokes the standard R build process which
will rely on configure
. If pkg-config
is
found, it is used to query the system about a possible TileDB
installation. If one is found, it used. Otherwise, on all three main
operating systems a prebuilt archive with the TileDB Embedded library is
downloaded from GitHub and unpacked. Each build of the R package will
have one matching build of TileDB Embedded associated with it via file
the tools/tiledbVersion.txt
specifying a version and
release commit sha1. These two values are used to find the corresponding
binary artifacts from a release at GitHub.
The location of an existing installed version of TileDB Embedded can
also be provided to the configure
script which supplies an
argument --with-tiledb=PATH
. So on the command-line, one
could say
to pass the configure
argument on. From within R, the
equivalent command is
Lastly, one can also override the default download location
(otherwise inferred via tools/tiledbVersion.txt
. The
configure
script supports an option
--with-download=URL
so the two calls become,
respectively
and
Using for example the current condaforge/mambaforge
container from the conda-forge project,
we can do
mamba install -y r-tiledb # installs R, tiledb and deps without extra prompt
# ...several lines of installation detail omitted
R
# ... several lines of R startup output omitted
> library(tiledb)
which installs R, the tiledb package and all respective dependencies.
Builds of the TileDB package could also be provided via Docker containers. At present, no official TileDB R containers are provided by TileDB. However, the discussion of installation from source above describes how to create such containers.
This note described several installation options for the TileDB R package.