More R package support.

ognibuild/buildsystem.py

@@ -27,6 +27,7 @@ from . import shebang_binary, UnidentifiedError
 from .outputs import (
     BinaryOutput,
     PythonPackageOutput,
+    RPackageOutput,
 )
 from .requirements import (
     BinaryRequirement,
@@ -34,6 +35,7 @@ from .requirements import (
     PerlModuleRequirement,
     NodePackageRequirement,
     CargoCrateRequirement,
+    RPackageRequirement,
 )
 from .fix_build import run_with_build_fixers
 
@@ -456,16 +458,41 @@ class R(BuildSystem):
         return "%s(%r)" % (type(self).__name__, self.path)
 
     def build(self, session, resolver, fixers):
+        pass
+
+    def dist(self, session, resolver, fixers, quiet=False):
         run_with_build_fixers(session, ["R", "CMD", "build", "."], fixers)
 
+    def install(self, session, resolver, fixers, install_target):
+        run_with_build_fixers(session, ["R", "CMD", "INSTALL", "."], fixers)
+
     def test(self, session, resolver, fixers):
-        run_with_build_fixers(session, ["R", "CMD", "test", "."], fixers)
+        run_with_build_fixers(session, ["R", "CMD", "check", "."], fixers)
 
     @classmethod
     def probe(cls, path):
         if os.path.exists(os.path.join(path, 'DESCRIPTION')):
             return cls(path)
 
+    def _read_description(self):
+        path = os.path.join(self.path, 'DESCRIPTION')
+        from email.parser import BytesParser
+        with open(path, 'rb') as f:
+            return BytesParser().parse(f)
+
+    def get_declared_dependencies(self, session, fixers=None):
+        description = self._read_description()
+        if 'Suggests' in description:
+            suggests = [s.strip() for s in description['Suggests'].split(',') if s.strip()]
+            for s in suggests:
+                # TODO(jelmer): Look at version
+                yield "build", RPackageRequirement.from_str(s)
+
+    def get_declared_outputs(self, session, fixers=None):
+        description = self._read_description()
+        if 'Package' in description:
+            yield RPackageOutput(description['Package'])
+
 
 class Meson(BuildSystem):
 

ognibuild/outputs.py

@@ -46,3 +46,15 @@ class PythonPackageOutput(UpstreamOutput):
             self.name,
             self.python_version,
         )
+
+
+class RPackageOutput(UpstreamOutput):
+    def __init__(self, name):
+        super(RPackageOutput, self).__init__("r-package")
+        self.name = name
+
+    def __str__(self):
+        return "R package: %s" % self.name
+
+    def __repr__(self):
+        return "%s(%r)" % (type(self).__name__, self.name)

ognibuild/requirements.py

@@ -17,6 +17,7 @@
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
 
 import posixpath
+import re
 import subprocess
 from typing import Optional, List, Tuple, Set
 
@@ -249,6 +250,30 @@ class RPackageRequirement(Requirement):
         self.package = package
         self.minimum_version = minimum_version
 
+    def __repr__(self):
+        return "%s(%r, minimum_version=%r)" % (
+            type(self).__name__,
+            self.package,
+            self.minimum_version,
+        )
+
+    def __str__(self):
+        if self.minimum_version:
+            return "R package: %s (>= %s)" % (self.package, self.minimum_version)
+        else:
+            return "R package: %s" % (self.package,)
+
+    @classmethod
+    def from_str(cls, text):
+        # TODO(jelmer): More complex parser
+        m = re.fullmatch(r'(.*) \(>= (.*)\)', text)
+        if m:
+            return cls(m.group(1), m.group(2))
+        m = re.fullmatch(r'([^ ]+)', text)
+        if m:
+            return cls(m.group(1))
+        raise ValueError(text)
+
 
 class LibraryRequirement(Requirement):
 

ognibuild/resolver/__init__.py

@@ -76,8 +76,8 @@ class CPANResolver(Resolver):
             raise UnsatisfiedRequirements(missing)
 
 
-class CRANResolver(Resolver):
+class RResolver(Resolver):
-    def __init__(self, session, repos='"http://cran.r-project.org'):
+    def __init__(self, session, repos):
         self.session = session
         self.repos = repos
 
@@ -114,6 +114,19 @@ class CRANResolver(Resolver):
             raise UnsatisfiedRequirements(missing)
 
 
+class CRANResolver(RResolver):
+
+    def __init__(self, session):
+        super(CRANResolver, self).__init__(session, 'http://cran.r-project.org')
+
+
+class BioconductorResolver(RResolver):
+
+    def __init__(self, session):
+        super(BioconductorResolver, self).__init__(
+            session, 'https://hedgehog.fhcrc.org/bioconductor')
+
+
 class HackageResolver(Resolver):
     def __init__(self, session):
         self.session = session
@@ -307,6 +320,7 @@ NATIVE_RESOLVER_CLS = [
     GoResolver,
     HackageResolver,
     CRANResolver,
+    BioconductorResolver,
     ]