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-rw-r--r--lib/spack/docs/build_systems/rpackage.rst71
-rw-r--r--lib/spack/spack/build_systems/r.py36
-rw-r--r--lib/spack/spack/cmd/create.py24
3 files changed, 125 insertions, 6 deletions
diff --git a/lib/spack/docs/build_systems/rpackage.rst b/lib/spack/docs/build_systems/rpackage.rst
index 486fd95b69..a375b5328c 100644
--- a/lib/spack/docs/build_systems/rpackage.rst
+++ b/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
-(second line), or both depending on what you feel is most appropriate.
+The first line is a short description (title) and the second line is a long
+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
diff --git a/lib/spack/spack/build_systems/r.py b/lib/spack/spack/build_systems/r.py
index f713706882..f8553c476b 100644
--- a/lib/spack/spack/build_systems/r.py
+++ b/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 []
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py
index 71d34a7ebb..6eaab4a07d 100644
--- a/lib/spack/spack/cmd/create.py
+++ b/lib/spack/spack/cmd/create.py
@@ -328,14 +328,34 @@ class RPackageTemplate(PackageTemplate):
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):