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## Overview This vignette discusses different options for installing the TileDB R package. ### CRAN #### Binaries 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 ``` r install.packages("tiledb")
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
R CMD INSTALL --configure-args='--with-tiledb=/some/path' tiledb_*.tar.gz
to pass the configure
argument on. From within R, the equivalent
command is
install.packages("tiledb", repos=NULL, configure.args="--with-tiledb=/some/path")
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
R CMD INSTALL --configure-args='--with-download=https://some.where.net/file.tgz' tiledb_*.tar.gz
and
install.packages("tiledb_0.11.0.tar.gz", repos=NULL, configure.args="--with-download=https://some.where.net/file.tgz")
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.
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