Improve R package creation (#21861)

* Improve R package creation

This PR adds the `list_url` attribute to CRAN R packages when using
`spack create`. It also adds the `git` attribute to R Bioconductor
packages upon creation.

* Switch over to using cran/bioc attributes

The cran/bioc entries are set to have the '=' line up with homepage
entry, but homepage does not need to exist in the package file. If it
does not, that could affect the alignment.

* Do not have to split bioc

* Edit R package documentation

Explain Bioconductor packages and add `cran` and `bioc` attributes.

* Update lib/spack/docs/build_systems/rpackage.rst

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update lib/spack/docs/build_systems/rpackage.rst

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Simplify the cran attribute

The version can be faked so that the cran attribute is simply equal to
the CRAN package name.

* Edit the docs to reflect new `cran` attribute format

* Use the first element of self.versions() for url

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

lib/spack/docs/build_systems/rpackage.rst

@@ -79,12 +79,14 @@ Description
 The first thing you'll need to add to your new package is a description.
 The top of the homepage for ``caret`` lists the following description:
 
-   caret: Classification and Regression Training
+   Classification and Regression Training
 
    Misc functions for training and plotting classification and regression models.
 
-You can either use the short description (first line), long description
+The first line is a short description (title) and the second line is a long
-(second line), or both depending on what you feel is most appropriate.
+description. In this case the description is only one line but often the
+description is several lines. Spack makes use of both short and long
+descriptions and convention is to use both when creating an R  package.
 
 ^^^^^^^^
 Homepage
@@ -124,6 +126,67 @@ 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
 out. To get around this, add the archive directory as a ``list_url``.
 
+^^^^^^^^^^^^^^^^^^^^^
+Bioconductor packages
+^^^^^^^^^^^^^^^^^^^^^
+
+Bioconductor packages are set up in a similar way to CRAN packages, but there
+are some very important distinctions. Bioconductor packages can be found at:
+https://bioconductor.org/. Bioconductor packages are R packages and so follow
+the same packaging scheme as CRAN packages. What is different is that
+Bioconductor itself is versioned and released. This scheme, using the
+Bioconductor package installer, allows further specification of the minimum
+version of R as well as further restrictions on the dependencies between
+packages than what is possible with the native R packaging system. Spack can
+not replicate these extra features and thus Bioconductor packages in Spack need
+to be managed as a group during updates in order to maintain package
+consistency with Bioconductor itself.
+
+Another key difference is that, while previous versions of packages are
+available, they are not available from a site that can be programmatically set,
+thus a ``list_url`` attribute can not be used. However, each package is also
+available in a git repository, with branches corresponding to each Bioconductor
+release. Thus, it is always possible to retrieve the version of any package
+corresponding to a Bioconductor release simply by fetching the branch that
+corresponds to the Bioconductor release of the package repository. For this
+reason, spack Bioconductor R packages use the git repository, with the commit
+of the respective branch used in the ``version()`` attribute of the package.
+
+^^^^^^^^^^^^^^^^^^^^^^^^
+cran and bioc attributes
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+Much like the ``pypi`` attribute for python packages, due to the fact that R
+packages are obtained from specific repositories, it is possible to set up shortcut
+attributes that can be used to set ``homepage``, ``url``, ``list_url``, and
+``git``. For example, the following ``cran`` attribute:
+
+.. code-block:: python
+
+   cran = 'caret'
+
+is equivalent to:
+
+.. code-block:: python
+
+   homepage = 'https://cloud.r-project.org/package=caret'
+   url      = 'https://cloud.r-project.org/src/contrib/caret_6.0-86.tar.gz'
+   list_url = 'https://cloud.r-project.org/src/contrib/Archive/caret'
+
+Likewise, the following ``bioc`` attribute:
+
+.. code-block:: python
+
+   bioc = 'BiocVersion'
+
+is equivalent to:
+
+.. code-block:: python
+
+   homepage = 'https://bioconductor.org/packages/BiocVersion/'
+   git      = 'https://git.bioconductor.org/packages/BiocVersion'
+
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 Build system dependencies
 ^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -156,7 +219,7 @@ R dependencies
 R packages are often small and follow the classic Unix philosophy
 of doing one thing well. They are modular and usually depend on
 several other packages. You may find a single package with over a
-hundred dependencies. Luckily, CRAN packages are well-documented
+hundred dependencies. Luckily, R packages are well-documented
 and list all of their dependencies in the following sections:
 
 * Depends

lib/spack/spack/build_systems/r.py

@@ -25,6 +25,14 @@ class RPackage(PackageBase):
     """
     phases = ['install']
 
+    # package attributes that can be expanded to set the homepage, url,
+    # list_url, and git values
+    # For CRAN packages
+    cran = None
+
+    # For Bioconductor packages
+    bioc = None
+
     maintainers = ['glennpj']
 
     #: This attribute is used in UI queries that need to know the build
@@ -33,6 +41,34 @@ class RPackage(PackageBase):
 
     extends('r')
 
+    @property
+    def homepage(self):
+        if self.cran:
+            return 'https://cloud.r-project.org/package=' + self.cran
+        elif self.bioc:
+            return 'https://bioconductor.org/packages/' + self.bioc
+
+    @property
+    def url(self):
+        if self.cran:
+            return (
+                'https://cloud.r-project.org/src/contrib/'
+                + self.cran + '_' + str(list(self.versions)[0]) + '.tar.gz'
+            )
+
+    @property
+    def list_url(self):
+        if self.cran:
+            return (
+                'https://cloud.r-project.org/src/contrib/Archive/'
+                + self.cran + '/'
+            )
+
+    @property
+    def git(self):
+        if self.bioc:
+            return 'https://git.bioconductor.org/packages/' + self.bioc
+
     def configure_args(self):
         """Arguments to pass to install via ``--configure-args``."""
         return []

lib/spack/spack/cmd/create.py

@@ -328,14 +328,34 @@ def configure_args(self):
         args = []
         return args"""
 
-    def __init__(self, name, *args, **kwargs):
+    def __init__(self, name, url, *args, **kwargs):
         # If the user provided `--name r-rcpp`, don't rename it r-r-rcpp
         if not name.startswith('r-'):
             # Make it more obvious that we are renaming the package
             tty.msg("Changing package name from {0} to r-{0}".format(name))
             name = 'r-{0}'.format(name)
 
-        super(RPackageTemplate, self).__init__(name, *args, **kwargs)
+        r_name = parse_name(url)
+
+        cran = re.search(
+            r'(?:r-project)[^/]+/src' + '/([^/]+)' * 2,
+            url
+        )
+
+        if cran:
+            url = r_name
+            self.url_line = '    cran     = "{url}"'
+
+        bioc = re.search(
+            r'(?:bioconductor)[^/]+/packages' + '/([^/]+)' * 5,
+            url
+        )
+
+        if bioc:
+            self.url_line = '    url      = "{0}"\n'\
+                '    bioc     = "{1}"'.format(url, r_name)
+
+        super(RPackageTemplate, self).__init__(name, url, *args, **kwargs)
 
 
 class PerlmakePackageTemplate(PackageTemplate):