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RPackage docs: use cloud.r-project.org (#12471)

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42
lib/spack/docs/build_systems/rpackage.rst
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@ -42,7 +42,11 @@ If it isn't on CRAN, try Bioconductor, another common R repository.
For the purposes of this tutorial, we will be walking through
`r-caret <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/r-caret/package.py>`_
as an example. If you search for "CRAN caret", you will quickly find what
you are looking for at https://cran.r-project.org/web/packages/caret/index.html.
you are looking for at https://cran.r-project.org/package=caret.
https://cran.r-project.org is the main CRAN website. However, CRAN also
has a https://cloud.r-project.org site that automatically redirects to
`mirrors around the world <https://cloud.r-project.org/mirrors.html>`_.
For stability and performance reasons, we will use https://cloud.r-project.org/package=caret.
If you search for "Package source", you will find the download URL for
the latest release. Use this URL with ``spack create`` to create a new
package.
@ -93,8 +97,8 @@ If you look at the bottom of the page, you'll see:
Please use the canonical form https://CRAN.R-project.org/package=caret to link to this page.
Please uphold the wishes of the CRAN admins and use
https://CRAN.R-project.org/package=caret as the homepage instead of
https://cran.r-project.org/web/packages/caret/index.html. The latter may
https://cloud.r-project.org/package=caret as the homepage instead of
https://cloud.r-project.org/web/packages/caret/index.html. The latter may
change without notice.
^^^
@ -109,12 +113,12 @@ List URL
^^^^^^^^
CRAN maintains a single webpage containing the latest release of every
single package: https://cran.r-project.org/src/contrib/
single package: https://cloud.r-project.org/src/contrib/
Of course, as soon as a new release comes out, the version you were using
in your package is no longer available at that URL. It is moved to an
archive directory. If you search for "Old sources", you will find:
https://cran.r-project.org/src/contrib/Archive/caret
https://cloud.r-project.org/src/contrib/Archive/caret
If you only specify the URL for the latest release, your package will
no longer be able to fetch that version as soon as a new release comes
@ -138,12 +142,12 @@ every R package needs this, the ``RPackage`` base class contains:
Take a close look at the homepage for ``caret``. If you look at the
"Depends" section, you'll notice that ``caret`` depends on "R (≥ 2.10)".
"Depends" section, you'll notice that ``caret`` depends on "R (≥ 3.2.0)".
You should add this to your package like so:
.. code-block:: python
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r@3.2.0:', type=('build', 'run'))
^^^^^^^^^^^^^^
@ -162,7 +166,7 @@ and list all of their dependencies in the following sections:
As far as Spack is concerned, all 3 of these dependency types
correspond to ``type=('build', 'run')``, so you don't have to worry
about them. If you are curious what they mean,
about the details. If you are curious what they mean,
https://github.com/spack/spack/issues/2951 has a pretty good summary:
``Depends`` is required and will cause those R packages to be *attached*,
@ -193,6 +197,14 @@ R packages already have enough dependencies as it is, and adding
optional dependencies can really slow down the concretization
process. They can also introduce circular dependencies.
A fifth rarely used section is:
* Enhances
This means that the package can be used as an optional dependency
for another package. Again, these packages should **NOT** be listed
as dependencies.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Core, recommended, and non-core packages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -208,8 +220,8 @@ If you look at the ``caret`` homepage, you'll notice a few dependencies
that don't have a link to the package, like ``methods``, ``stats``, and
``utils``. These packages are part of the core R distribution and are
tied to the R version installed. You can basically consider these to be
"R itself". These are so essential to R so it would not make sense that
they could be updated via CRAN. If so, you would basically get a different
"R itself". These are so essential to R that it would not make sense for
them to be updated via CRAN. If you did, you would basically get a different
version of R. Thus, they're updated when R is updated.
You can find a list of these core libraries at:
@ -265,7 +277,7 @@ Non-R dependencies
Some packages depend on non-R libraries for linking. Check out the
`r-stringi <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/r-stringi/package.py>`_
package for an example: https://CRAN.R-project.org/package=stringi.
package for an example: https://cloud.r-project.org/package=stringi.
If you search for the text "SystemRequirements", you will see:
ICU4C (>= 52, optional)
@ -344,3 +356,11 @@ External documentation
For more information on installing R packages, see:
https://stat.ethz.ch/R-manual/R-devel/library/utils/html/INSTALL.html
For more information on writing R packages, see:
https://cloud.r-project.org/doc/manuals/r-release/R-exts.html
In particular,
https://cloud.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies
has a great explanation of the difference between Depends, Imports,
and LinkingTo.