r-pak: use metadata checks

BioArchLinux/r-pak/PKGBUILD

@@ -1,52 +1,70 @@
-# Maintainer: sukanka <su975853527@gmail.com>
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: sukanka <su975853527@gmail.com>
+# Contributor: peippo <christoph+aur@christophfink.com>
 
 _pkgname=pak
 _pkgver=0.7.1
 pkgname=r-${_pkgname,,}
-pkgver=0.7.1
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Another Approach to Package Installation'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Another Approach to Package Installation"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
-)
-optdepends=(
   r-callr
   r-cli
-  r-covr
   r-curl
   r-desc
-  r-digest
-  r-distro
   r-filelock
-  r-gitcreds
-  r-glue
   r-jsonlite
-  r-mockery
-  r-pingr
+  r-lpsolve
   r-pkgbuild
   r-pkgcache
   r-pkgdepends
   r-pkgsearch
-  r-prettyunits
   r-processx
   r-ps
-  r-rprojroot
+  r-r6
+  r-zip
+)
+checkdepends=(
+  r-mockery
+  r-testthat
+)
+optdepends=(
+  r-covr
+  r-gitcreds
+  r-glue
+  r-mockery
+  r-pingr
   r-rstudioapi
   r-testthat
   r-withr
 )
-source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('e7e70605cead736ea15b0e10c0aea14c90ff7c3d36afa10142fd8f6a14711965')
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "system-libs.patch")
+md5sums=('9eddae8f9345c4e5ad3a9692be09e6f8'
+         '29b1470e2d25f82ebeafc02fe3b2594a')
+b2sums=('2b5daa9c7c8e97907030933ede18e37a0f879dccfeebab7825b8475639663f757571a37d918e8ba4e724c0e34b8399b51e7ba8ca708acae87eef2291f279ed38'
+        'b422c6a23d6850831433fdcf3e81684189bdaea1735fcc85edeff3202fe084f4167876949ff9ddfd5654cb2ce202ed005800a217dfe9bb12fb8240456880b4f1')
+
+prepare() {
+  # devendor R dependencies
+  patch -Np1 -i system-libs.patch
+}
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-pak/lilac.py

@@ -1,12 +1,33 @@
 #!/usr/bin/env python3
 from lilaclib import *
 
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+import shutil, tarfile
+from tempfile import NamedTemporaryFile
+
 def pre_build():
-    for line in edit_file('PKGBUILD'):
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+    # Get the names of dependencies in embedded library
+    deps = []
+    newver = _G.newver.rsplit("#", 1)[0]
+    with tarfile.open(f"pak_{newver}.tar.gz", "r:gz") as tar:
+        prefix = "pak/src/library/"
+        for member in tar.getmembers():
+            name = member.name
+            if not name.startswith(prefix) or not member.isdir():
+                continue
+            name = name[len(prefix):]
+            if "/" not in name:
+                deps.append(name)
+
+    r_pre_build(
+        _G,
+        expect_needscompilation = True,
+        extra_r_depends = deps,
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-pak/lilac.yaml

@@ -1,9 +1,29 @@
 build_prefix: extra-x86_64
 maintainers:
-  - github: sukanka
-    email: su975853527@gmail.com
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-callr
+- r-cli
+- r-curl
+- r-desc
+- r-filelock
+- r-jsonlite
+- r-lpsolve
+- r-pkgbuild
+- r-pkgcache
+- r-pkgdepends
+- r-pkgsearch
+- r-processx
+- r-ps
+- r-r6
+- r-zip
+repo_makedepends:
+- r-mockery
+- r-testthat
 update_on:
-  - regex: pak_([\d._-]+).tar.gz
-    source: regex
-    url: https://cran.r-project.org/package=pak
-  - alias: r
+- source: rpkgs
+  pkgname: pak
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-pak/system-libs.patch

@@ -0,0 +1,17 @@
+diff --git a/pak/src/Makevars.in b/pak/src/Makevars.in
+index c6c73fd..f012da3 100644
+--- a/pak/src/Makevars.in
++++ b/pak/src/Makevars.in
+@@ -7,10 +7,7 @@ clean:
+ 	@echo Nothing to clean.
+ 
+ mylibs:
+-	@unset SHLIB R_PACKAGE_NAME R_INSTALL_PKG MAKEFLAGS \
+-		R_DEFAULT_PACKAGES && \
+-	"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" --vanilla \
+-		"install-embedded.R" --build=$(BUILD_PLATFORM) \
+-		--target=$(TARGET_PLATFORM) 2>&1 | grep -v "^\\*"
++	ln -s /usr/lib/R/library $(R_PACKAGE_DIR)
++	touch DONE
+ 
+ .PHONY: all mylibs clean

lilac-extensions/lilac_r_utils.py

@@ -32,6 +32,10 @@ def r_update_pkgver_and_pkgrel(newver: str):
     if oldrel is None:
         raise Exception("pkgrel is not defined")
 
+def _r_name_to_arch(r_pkg_name: str) -> str:
+    """Converts R package name to the corresponding Arch package"""
+    return f"r-{r_pkg_name.lower()}"
+
 class Description:
     """Metadata from the DESCRIPTION file, package names are converted to Arch format"""
 
@@ -87,10 +91,6 @@ class Description:
 
         return {field.decode(encoding): value.decode(encoding) for field, value in rawdata.items()}
 
-    def _r_name_to_arch(self, r_pkg_name: str) -> str:
-        """Converts R package name to the corresponding Arch package"""
-        return f"r-{r_pkg_name.lower()}"
-
     def _parse_deps(self, field: str) -> list:
         """Parse a field that contains a list of dependencies"""
         if field not in self.desc:
@@ -102,7 +102,7 @@ class Description:
                 dep = dep[:i]
             dep = dep.strip()
             if dep != "R" and len(dep) > 0:
-                ret.append(self._r_name_to_arch(dep))
+                ret.append(_r_name_to_arch(dep))
         return ret
 
 class Pkgbuild:
@@ -236,12 +236,14 @@ class CheckConfig:
         expect_needscompilation: bool = None,
         expect_systemrequirements: str = None,
         expect_title: str = None,
+        extra_r_depends: list = [],
         ignore_fortran_files: bool = False,
     ):
         self.expect_license = expect_license
         self.expect_needscompilation = expect_needscompilation
         self.expect_systemrequirements = expect_systemrequirements
         self.expect_title = expect_title
+        self.extra_r_depends = extra_r_depends
         self.ignore_fortran_files = ignore_fortran_files
 
 def check_default_pkgs(pkg: Pkgbuild, desc: Description, cfg: CheckConfig):
@@ -255,10 +257,12 @@ def check_default_pkgs(pkg: Pkgbuild, desc: Description, cfg: CheckConfig):
 
 def check_depends(pkg: Pkgbuild, desc: Description, cfg: CheckConfig):
     implicit_r_dep = explicit_r_dep = False
+    expected_depends = set(desc.depends + desc.imports)
+    expected_depends.update((_r_name_to_arch(dep) for dep in cfg.extra_r_depends))
     errors = []
     for dep in pkg.depends:
         if dep.startswith("r-"):
-            if (dep not in desc.depends) and (dep not in desc.imports):
+            if dep not in expected_depends:
                 errors.append(f"Unnecessary dependency: {dep}")
             else:
                 implicit_r_dep = True
@@ -266,7 +270,7 @@ def check_depends(pkg: Pkgbuild, desc: Description, cfg: CheckConfig):
             explicit_r_dep = True
 
     not_missing = True
-    for dep in desc.depends + desc.imports:
+    for dep in expected_depends:
         if (dep not in cfg.default_r_pkgs) and (dep not in pkg.depends):
             not_missing = False
             errors.append(f"Missing dependency: {dep}")
@@ -398,7 +402,7 @@ def r_check_pkgbuild(newver: str, cfg: CheckConfig):
     pkgbuild = Pkgbuild()
     cfg.default_r_pkgs = get_default_r_pkgs()
     errors = []
-    with tarfile.open(f"{pkgbuild._pkgname}_{newver}.tar.gz", "r") as tar:
+    with tarfile.open(f"{pkgbuild._pkgname}_{newver}.tar.gz", "r:gz") as tar:
         description = Description(tar, pkgbuild._pkgname)
         cfg.tar = tar