Use new linker input API

This bumps our minimum bazel version requirement to v3.0.0.
See bazelbuild/bazel#10860.

Also, update some other bazel dependencies we use in our tests.

Updated bazelisk can use GCS as a fallback when github returns an error,
which means we don't have to use a github API token anymore, which were
never available for pull requests anyway.

.github/workflows/tests.yml

@@ -27,6 +27,4 @@ jobs:
       run: sudo apt-get install libcurl4-openssl-dev
 
     - name: Run tests
-      env:
-        BAZELISK_GITHUB_TOKEN: ${{ secrets.BAZELISK_GITHUB_TOKEN }}
       run: tests/run_tests.sh

R/dependencies.bzl

@@ -32,7 +32,7 @@ load(
 r_coverage_dependencies = _r_coverage_dependencies
 
 def r_rules_dependencies():
-    _is_at_least("1.0.0", native.bazel_version)
+    _is_at_least("3.0.0", native.bazel_version)
 
     # TODO: Use bazel-skylib directly instead of replicating functionality when
     # nested workspaces become a reality.  Otherwise, dependencies will need to

R/internal/build.bzl

@@ -80,49 +80,43 @@ def _strip_path_prefixes(iterable, p1, p2):
 
 def _link_info(dep, root_path):
     # Returns libraries to link from a cc_dep, giving preference to PIC.
-
-    linking_context = dep[CcInfo].linking_context
-    libraries_to_link = linking_context.libraries_to_link
-    user_link_flags = linking_context.user_link_flags
     libs = []
     c_so_files = []
-    c_libs_flags = list(user_link_flags)
-    c_libs_flags_short = list(user_link_flags)
-
-    # https://github.com/bazelbuild/bazel/issues/8118
-    # TODO: Simplify when we don't support bazel 0.26.
-    if hasattr(linking_context.libraries_to_link, "to_list"):
-        libraries_to_link = linking_context.libraries_to_link.to_list()
-    else:
-        libraries_to_link = linking_context.libraries_to_link
-
-    for library_to_link in libraries_to_link:
-        if library_to_link.pic_static_library != None:
-            l = library_to_link.pic_static_library
-        elif library_to_link.static_library != None:
-            l = library_to_link.static_library
-        elif library_to_link.interface_library != None:
-            l = library_to_link.interface_library
-        elif library_to_link.dynamic_library != None:
-            l = library_to_link.dynamic_library
-        else:
-            fail("unreachable")
-
-        libs.append(l)
-
-        # dylib is not supported because macOS does not support $ORIGIN in rpath.
-        if l.extension == "so":
-            c_so_files.append(l)
-
-            # We copy the file in srcs and set relative rpath for R CMD INSTALL.
-            c_libs_flags.append(l.basename)
+    c_libs_flags = []
+    c_libs_flags_short = []
 
-            # We use LD_LIBRARY_PATH for R CMD check.
+    linker_inputs = dep[CcInfo].linking_context.linker_inputs.to_list()
+    for linker_input in linker_inputs:
+        for library_to_link in linker_input.libraries:
+            if library_to_link.pic_static_library != None:
+                l = library_to_link.pic_static_library
+            elif library_to_link.static_library != None:
+                l = library_to_link.static_library
+            elif library_to_link.interface_library != None:
+                l = library_to_link.interface_library
+            elif library_to_link.dynamic_library != None:
+                l = library_to_link.dynamic_library
+            else:
+                fail("unreachable")
+
+            libs.append(l)
+
+            # dylib is not supported because macOS does not support $ORIGIN in rpath.
+            if l.extension == "so":
+                c_so_files.append(l)
+
+                # We copy the file in srcs and set relative rpath for R CMD INSTALL.
+                c_libs_flags.append(l.basename)
+
+                # We use LD_LIBRARY_PATH for R CMD check.
+                c_libs_flags_short.append(root_path + l.short_path)
+                continue
+
+            c_libs_flags.append(root_path + l.path)
             c_libs_flags_short.append(root_path + l.short_path)
-            continue
 
-        c_libs_flags.append(root_path + l.path)
-        c_libs_flags_short.append(root_path + l.short_path)
+        c_libs_flags.extend(linker_input.user_link_flags)
+        c_libs_flags_short.extend(linker_input.user_link_flags)
 
     return struct(
         c_libs_flags = c_libs_flags,

README.md

@@ -52,8 +52,7 @@ GRAIL to build 400+ R packages from CRAN and Bioconductor.
 
 The following assumes that you are familiar with how to use Bazel in general.
 
-In order to use the rules, you must have bazel 1.0.0 or later and add the
-following to your WORKSPACE file:
+To begin, you can add the following or equivalent to your WORKSPACE file:
 
 ```python
 # Change master to the git tag you want.
@@ -89,8 +88,10 @@ load("@com_grail_rules_r//R:defs.bzl", "r_package_with_test")
 <a name="configuration"></a>
 ## Configuration
 
-These rules assume that you have R installed on your system (we recommend 3.4.3
-or above), and can be located using the `PATH` environment variable.
+The following software must be installed on your system:
+
+    1. bazel (v3.0.0 or above)
+    2. R (3.4.3 or above; should be locatable using the `PATH` environment variable)
 
 **NOTE**: After re-installing or upgrading R, please reset the registered
 toolchain with `bazel sync --configure` to rebuild your packages with the new

tests/WORKSPACE

@@ -27,23 +27,12 @@ r_rules_dependencies()
 
 r_register_toolchains()
 
-http_archive(
-    name = "com_google_protobuf",
-    sha256 = "d399f651dbdc5f9116a2da199a808c815c0aeeb8d0b46e3213eee5a41263aeff",
-    strip_prefix = "protobuf-3.8.0-rc1",
-    urls = ["https://github.com/protocolbuffers/protobuf/archive/v3.8.0-rc1.tar.gz"],
-)
-
-load("@com_google_protobuf//:protobuf_deps.bzl", "protobuf_deps")
-
-protobuf_deps()
-
 http_archive(
     name = "io_bazel_rules_docker",
-    sha256 = "4521794f0fba2e20f3bf15846ab5e01d5332e587e9ce81629c7f96c793bb7036",
-    strip_prefix = "rules_docker-0.14.4",
+    sha256 = "95d39fd84ff4474babaf190450ee034d958202043e366b9fc38f438c9e6c3334",
+    strip_prefix = "rules_docker-0.16.0",
     urls = [
-        "https://github.com/bazelbuild/rules_docker/releases/download/v0.14.4/rules_docker-v0.14.4.tar.gz",
+        "https://github.com/bazelbuild/rules_docker/releases/download/v0.16.0/rules_docker-v0.16.0.tar.gz",
     ],
 )
 
@@ -58,10 +47,6 @@ load("@io_bazel_rules_docker//repositories:deps.bzl", container_deps = "deps")
 
 container_deps()
 
-load("@io_bazel_rules_docker//repositories:pip_repositories.bzl", "pip_deps")
-
-pip_deps()
-
 load(
     "@io_bazel_rules_docker//container:container.bzl",
     "container_pull",
@@ -101,3 +86,16 @@ r_coverage_dependencies()
 load("@r_coverage_deps_bzl//:r_repositories.bzl", coverage_deps = "r_repositories")
 
 coverage_deps()
+
+http_archive(
+    name = "com_google_protobuf",
+    sha256 = "65e020a42bdab44a66664d34421995829e9e79c60e5adaa08282fd14ca552f57",
+    strip_prefix = "protobuf-3.15.6",
+    urls = [
+        "https://github.com/protocolbuffers/protobuf/archive/v3.15.6.tar.gz",
+    ],
+)
+
+load("@com_google_protobuf//:protobuf_deps.bzl", "protobuf_deps")
+
+protobuf_deps()

tests/run_tests.sh

@@ -24,6 +24,7 @@ source "./setup-bazel.sh"
 # targets. The alternative is to clean the workspace before each test.
 set -x
 "${bazel}" clean
+"${bazel}" version
 "${bazel}" run //binary:binary_sh_test
 bazel-bin/binary/binary_sh_test
 "${bazel}" run //binary:binary_r_test

tests/setup-bazel.sh

@@ -21,7 +21,7 @@ readonly os
 
 # Use bazelisk to catch migration problems.
 # Value of BAZELISK_GITHUB_TOKEN is set as a secret on Travis.
-readonly url="https://github.com/bazelbuild/bazelisk/releases/download/v1.4.0/bazelisk-${os}-amd64"
+readonly url="https://github.com/bazelbuild/bazelisk/releases/download/v1.7.5/bazelisk-${os}-amd64"
 bazel="${TMPDIR:-/tmp}/bazelisk"
 readonly bazel