Fix some tests

grailbio · Mar 20, 2024 · 20cfa77 · 20cfa77
1 parent ee170a7
commit 20cfa77
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Showing 14 changed files with 51 additions and 95 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -8,6 +8,7 @@ on:
 
 jobs:
   test:
+    name: Test
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -63,5 +64,5 @@ jobs:
       uses: actions/upload-artifact@v4
       if: ${{ always() }}
       with:
-        name: archive-debug-artifacts
+        name: archive-debug-artifacts-${{ matrix.os }}-${{ matrix.bazel_version }}-${{ matrix.r_version }}
         path: /tmp/debug-artifacts/*
diff --git a/tests/BUILD b/tests/BUILD
@@ -114,10 +114,10 @@ r_toolchain(
 toolchain(
     name = "toolchain-linux",
     exec_compatible_with = [
-        "@bazel_tools//platforms:linux",
+        "@platforms//os:linux",
     ],
     target_compatible_with = [
-        "@bazel_tools//platforms:linux",
+        "@platforms//os:linux",
     ],
     toolchain = ":r-toolchain-linux",
     toolchain_type = "@rules_r//R:toolchain_type",
@@ -127,10 +127,10 @@ toolchain(
 toolchain(
     name = "toolchain-darwin",
     exec_compatible_with = [
-        "@bazel_tools//platforms:osx",
+        "@platforms//os:osx",
     ],
     target_compatible_with = [
-        "@bazel_tools//platforms:osx",
+        "@platforms//os:osx",
     ],
     toolchain = ":r-toolchain-darwin",
     toolchain_type = "@rules_r//R:toolchain_type",

diff --git a/tests/coverage/all_instrumented_C.xml b/tests/coverage/all_instrumented_C.xml
@@ -1,17 +1,18 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<coverage line-rate="1" branch-rate="0" lines-covered="31" lines-valid="31" branches-covered="0" branches-valid="0" complexity="0" version="3.5.1" timestamp="1960-01-01 00:00:00">
+<!DOCTYPE coverage SYSTEM "https://raw.githubusercontent.com/cobertura/cobertura/master/cobertura/src/site/htdocs/xml/coverage-04.dtd">
+<coverage line-rate="1" branch-rate="0" lines-covered="23" lines-valid="23" branches-covered="0" branches-valid="0" complexity="0" version="3.6.4" timestamp="1960-01-01 00:00:00">
   <sources/>
   <packages>
     <package name="NULL" line-rate="1" branch-rate="0" complexity="0">
       <classes>
         <class name="fn.R" filename="external/workspaceroot/R/fn.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="hello" signature="" line-rate="1" branch-rate="0">
+            <method name="hello" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="1" branch="false"/>
               </lines>
             </method>
-            <method name="helloC" signature="" line-rate="1" branch-rate="0">
+            <method name="helloC" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="20" hits="1" branch="false"/>
               </lines>
@@ -30,7 +31,7 @@
         </class>
         <class name="fn.R" filename="packages/exampleA/R/fn.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="exampleA" signature="" line-rate="1" branch-rate="0">
+            <method name="exampleA" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="2" branch="false"/>
               </lines>
@@ -42,7 +43,7 @@
         </class>
         <class name="fn.R" filename="packages/exampleB/R/fn.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="exampleB" signature="" line-rate="1" branch-rate="0">
+            <method name="exampleB" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="2" branch="false"/>
               </lines>
@@ -54,7 +55,7 @@
         </class>
         <class name="fn.R" filename="packages/exampleC/R/fn.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="exampleC" signature="" line-rate="1" branch-rate="0">
+            <method name="exampleC" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="1" branch="false"/>
               </lines>
@@ -66,12 +67,12 @@
         </class>
         <class name="rcpp.R" filename="packages/exampleC/R/rcpp.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="rcppHello" signature="" line-rate="1" branch-rate="0">
+            <method name="rcppHello" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="2" branch="false"/>
               </lines>
             </method>
-            <method name="rcppHelloWrapped" signature="" line-rate="1" branch-rate="0">
+            <method name="rcppHelloWrapped" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="20" hits="2" branch="false"/>
               </lines>
@@ -106,24 +107,6 @@
             <line number="19" hits="1" branch="false"/>
           </lines>
         </class>
-        <class name="getCharacter.c" filename="packages/exampleC/src/lib/getCharacter.c" line-rate="1" branch-rate="0" complexity="0">
-          <methods/>
-          <lines>
-            <line number="17" hits="1" branch="false"/>
-          </lines>
-        </class>
-        <class name="rcpp.cc" filename="packages/exampleC/src/lib/rcpp.cc" line-rate="1" branch-rate="0" complexity="0">
-          <methods/>
-          <lines>
-            <line number="20" hits="4" branch="false"/>
-            <line number="21" hits="4" branch="false"/>
-            <line number="28" hits="4" branch="false"/>
-            <line number="33" hits="2" branch="false"/>
-            <line number="40" hits="2" branch="false"/>
-            <line number="41" hits="2" branch="false"/>
-            <line number="42" hits="2" branch="false"/>
-          </lines>
-        </class>
         <class name="rcpp.cc" filename="packages/exampleC/src/rcpp.cc" line-rate="1" branch-rate="0" complexity="0">
           <methods/>
           <lines>

diff --git a/tests/coverage/all_instrumented_D.xml b/tests/coverage/all_instrumented_D.xml
@@ -1,12 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<coverage line-rate="1" branch-rate="0" lines-covered="4" lines-valid="4" branches-covered="0" branches-valid="0" complexity="0" version="3.5.1" timestamp="1960-01-01 00:00:00">
+<!DOCTYPE coverage SYSTEM "https://raw.githubusercontent.com/cobertura/cobertura/master/cobertura/src/site/htdocs/xml/coverage-04.dtd">
+<coverage line-rate="1" branch-rate="0" lines-covered="4" lines-valid="4" branches-covered="0" branches-valid="0" complexity="0" version="3.6.4" timestamp="1960-01-01 00:00:00">
   <sources/>
   <packages>
     <package name="NULL" line-rate="1" branch-rate="0" complexity="0">
       <classes>
         <class name="proto.R" filename="packages/exampleD/R/proto.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="proto" signature="" line-rate="1" branch-rate="0">
+            <method name="proto" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="1" branch="false"/>
                 <line number="17" hits="1" branch="false"/>

diff --git a/tests/coverage/coverage_test.sh b/tests/coverage/coverage_test.sh
@@ -112,8 +112,7 @@ echo "=== Testing custom toolchain ==="
 echo "Checking coverage results with the LLVM toolchain:"
 toolchain_args=(
   "--extra_toolchains=//:toolchain-${os}"
-  "--extra_toolchains=@llvm_toolchain//:cc-toolchain-x86_64-${os}"
-  "--incompatible_enable_cc_toolchain_resolution"
+  "--extra_toolchains=@llvm_toolchain//:cc-toolchain-${bzl_arch}-${os}"
   "--toolchain_resolution_debug=rules_r"
 )
 "${bazel}" coverage "${bazel_test_opts[@]}" "${toolchain_args[@]}" //...

diff --git a/tests/coverage/custom_toolchain_C.xml b/tests/coverage/custom_toolchain_C.xml
@@ -1,12 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<coverage line-rate="1" branch-rate="0" lines-covered="19" lines-valid="19" branches-covered="0" branches-valid="0" complexity="0" version="3.5.1" timestamp="1960-01-01 00:00:00">
+<!DOCTYPE coverage SYSTEM "https://raw.githubusercontent.com/cobertura/cobertura/master/cobertura/src/site/htdocs/xml/coverage-04.dtd">
+<coverage line-rate="1" branch-rate="0" lines-covered="19" lines-valid="19" branches-covered="0" branches-valid="0" complexity="0" version="3.6.4" timestamp="1960-01-01 00:00:00">
   <sources/>
   <packages>
     <package name="NULL" line-rate="1" branch-rate="0" complexity="0">
       <classes>
         <class name="fn.R" filename="packages/exampleC/R/fn.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="exampleC" signature="" line-rate="1" branch-rate="0">
+            <method name="exampleC" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="1" branch="false"/>
               </lines>
@@ -18,12 +19,12 @@
         </class>
         <class name="rcpp.R" filename="packages/exampleC/R/rcpp.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="rcppHello" signature="" line-rate="1" branch-rate="0">
+            <method name="rcppHello" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="2" branch="false"/>
               </lines>
             </method>
-            <method name="rcppHelloWrapped" signature="" line-rate="1" branch-rate="0">
+            <method name="rcppHelloWrapped" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="20" hits="2" branch="false"/>
               </lines>

diff --git a/tests/coverage/custom_toolchain_D.xml b/tests/coverage/custom_toolchain_D.xml
@@ -1,12 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<coverage line-rate="1" branch-rate="0" lines-covered="4" lines-valid="4" branches-covered="0" branches-valid="0" complexity="0" version="3.5.1" timestamp="1960-01-01 00:00:00">
+<!DOCTYPE coverage SYSTEM "https://raw.githubusercontent.com/cobertura/cobertura/master/cobertura/src/site/htdocs/xml/coverage-04.dtd">
+<coverage line-rate="1" branch-rate="0" lines-covered="4" lines-valid="4" branches-covered="0" branches-valid="0" complexity="0" version="3.6.4" timestamp="1960-01-01 00:00:00">
   <sources/>
   <packages>
     <package name="NULL" line-rate="1" branch-rate="0" complexity="0">
       <classes>
         <class name="proto.R" filename="packages/exampleD/R/proto.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="proto" signature="" line-rate="1" branch-rate="0">
+            <method name="proto" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="1" branch="false"/>
                 <line number="17" hits="1" branch="false"/>

diff --git a/tests/coverage/default_instrumented.xml b/tests/coverage/default_instrumented.xml
@@ -1,12 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<coverage line-rate="1" branch-rate="0" lines-covered="26" lines-valid="26" branches-covered="0" branches-valid="0" complexity="0" version="3.5.1" timestamp="1960-01-01 00:00:00">
+<!DOCTYPE coverage SYSTEM "https://raw.githubusercontent.com/cobertura/cobertura/master/cobertura/src/site/htdocs/xml/coverage-04.dtd">
+<coverage line-rate="1" branch-rate="0" lines-covered="18" lines-valid="18" branches-covered="0" branches-valid="0" complexity="0" version="3.6.4" timestamp="1960-01-01 00:00:00">
   <sources/>
   <packages>
     <package name="NULL" line-rate="1" branch-rate="0" complexity="0">
       <classes>
         <class name="fn.R" filename="packages/exampleC/R/fn.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="exampleC" signature="" line-rate="1" branch-rate="0">
+            <method name="exampleC" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="1" branch="false"/>
               </lines>
@@ -18,12 +19,12 @@
         </class>
         <class name="rcpp.R" filename="packages/exampleC/R/rcpp.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="rcppHello" signature="" line-rate="1" branch-rate="0">
+            <method name="rcppHello" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="2" branch="false"/>
               </lines>
             </method>
-            <method name="rcppHelloWrapped" signature="" line-rate="1" branch-rate="0">
+            <method name="rcppHelloWrapped" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="20" hits="2" branch="false"/>
               </lines>
@@ -58,24 +59,6 @@
             <line number="19" hits="1" branch="false"/>
           </lines>
         </class>
-        <class name="getCharacter.c" filename="packages/exampleC/src/lib/getCharacter.c" line-rate="1" branch-rate="0" complexity="0">
-          <methods/>
-          <lines>
-            <line number="17" hits="1" branch="false"/>
-          </lines>
-        </class>
-        <class name="rcpp.cc" filename="packages/exampleC/src/lib/rcpp.cc" line-rate="1" branch-rate="0" complexity="0">
-          <methods/>
-          <lines>
-            <line number="20" hits="4" branch="false"/>
-            <line number="21" hits="4" branch="false"/>
-            <line number="28" hits="4" branch="false"/>
-            <line number="33" hits="2" branch="false"/>
-            <line number="40" hits="2" branch="false"/>
-            <line number="41" hits="2" branch="false"/>
-            <line number="42" hits="2" branch="false"/>
-          </lines>
-        </class>
         <class name="rcpp.cc" filename="packages/exampleC/src/rcpp.cc" line-rate="1" branch-rate="0" complexity="0">
           <methods/>
           <lines>

diff --git a/tests/coverage/workspace_instrumented_C.xml b/tests/coverage/workspace_instrumented_C.xml
@@ -1,12 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<coverage line-rate="1" branch-rate="0" lines-covered="28" lines-valid="28" branches-covered="0" branches-valid="0" complexity="0" version="3.5.1" timestamp="1960-01-01 00:00:00">
+<!DOCTYPE coverage SYSTEM "https://raw.githubusercontent.com/cobertura/cobertura/master/cobertura/src/site/htdocs/xml/coverage-04.dtd">
+<coverage line-rate="1" branch-rate="0" lines-covered="20" lines-valid="20" branches-covered="0" branches-valid="0" complexity="0" version="3.6.4" timestamp="1960-01-01 00:00:00">
   <sources/>
   <packages>
     <package name="NULL" line-rate="1" branch-rate="0" complexity="0">
       <classes>
         <class name="fn.R" filename="packages/exampleA/R/fn.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="exampleA" signature="" line-rate="1" branch-rate="0">
+            <method name="exampleA" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="2" branch="false"/>
               </lines>
@@ -18,7 +19,7 @@
         </class>
         <class name="fn.R" filename="packages/exampleB/R/fn.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="exampleB" signature="" line-rate="1" branch-rate="0">
+            <method name="exampleB" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="2" branch="false"/>
               </lines>
@@ -30,7 +31,7 @@
         </class>
         <class name="fn.R" filename="packages/exampleC/R/fn.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="exampleC" signature="" line-rate="1" branch-rate="0">
+            <method name="exampleC" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="1" branch="false"/>
               </lines>
@@ -42,12 +43,12 @@
         </class>
         <class name="rcpp.R" filename="packages/exampleC/R/rcpp.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="rcppHello" signature="" line-rate="1" branch-rate="0">
+            <method name="rcppHello" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="2" branch="false"/>
               </lines>
             </method>
-            <method name="rcppHelloWrapped" signature="" line-rate="1" branch-rate="0">
+            <method name="rcppHelloWrapped" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="20" hits="2" branch="false"/>
               </lines>
@@ -82,24 +83,6 @@
             <line number="19" hits="1" branch="false"/>
           </lines>
         </class>
-        <class name="getCharacter.c" filename="packages/exampleC/src/lib/getCharacter.c" line-rate="1" branch-rate="0" complexity="0">
-          <methods/>
-          <lines>
-            <line number="17" hits="1" branch="false"/>
-          </lines>
-        </class>
-        <class name="rcpp.cc" filename="packages/exampleC/src/lib/rcpp.cc" line-rate="1" branch-rate="0" complexity="0">
-          <methods/>
-          <lines>
-            <line number="20" hits="4" branch="false"/>
-            <line number="21" hits="4" branch="false"/>
-            <line number="28" hits="4" branch="false"/>
-            <line number="33" hits="2" branch="false"/>
-            <line number="40" hits="2" branch="false"/>
-            <line number="41" hits="2" branch="false"/>
-            <line number="42" hits="2" branch="false"/>
-          </lines>
-        </class>
         <class name="rcpp.cc" filename="packages/exampleC/src/rcpp.cc" line-rate="1" branch-rate="0" complexity="0">
           <methods/>
           <lines>

diff --git a/tests/coverage/workspace_instrumented_D.xml b/tests/coverage/workspace_instrumented_D.xml
@@ -1,12 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<coverage line-rate="1" branch-rate="0" lines-covered="4" lines-valid="4" branches-covered="0" branches-valid="0" complexity="0" version="3.5.1" timestamp="1960-01-01 00:00:00">
+<!DOCTYPE coverage SYSTEM "https://raw.githubusercontent.com/cobertura/cobertura/master/cobertura/src/site/htdocs/xml/coverage-04.dtd">
+<coverage line-rate="1" branch-rate="0" lines-covered="4" lines-valid="4" branches-covered="0" branches-valid="0" complexity="0" version="3.6.4" timestamp="1960-01-01 00:00:00">
   <sources/>
   <packages>
     <package name="NULL" line-rate="1" branch-rate="0" complexity="0">
       <classes>
         <class name="proto.R" filename="packages/exampleD/R/proto.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="proto" signature="" line-rate="1" branch-rate="0">
+            <method name="proto" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="1" branch="false"/>
                 <line number="17" hits="1" branch="false"/>

diff --git a/tests/coverage/workspaceroot.xml b/tests/coverage/workspaceroot.xml
@@ -1,17 +1,18 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<coverage line-rate="1" branch-rate="0" lines-covered="3" lines-valid="3" branches-covered="0" branches-valid="0" complexity="0" version="3.5.1" timestamp="1960-01-01 00:00:00">
+<!DOCTYPE coverage SYSTEM "https://raw.githubusercontent.com/cobertura/cobertura/master/cobertura/src/site/htdocs/xml/coverage-04.dtd">
+<coverage line-rate="1" branch-rate="0" lines-covered="3" lines-valid="3" branches-covered="0" branches-valid="0" complexity="0" version="3.6.4" timestamp="1960-01-01 00:00:00">
   <sources/>
   <packages>
     <package name="NULL" line-rate="1" branch-rate="0" complexity="0">
       <classes>
         <class name="fn.R" filename="external/workspaceroot/R/fn.R" line-rate="1" branch-rate="0" complexity="0">
           <methods>
-            <method name="hello" signature="" line-rate="1" branch-rate="0">
+            <method name="hello" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="16" hits="1" branch="false"/>
               </lines>
             </method>
-            <method name="helloC" signature="" line-rate="1" branch-rate="0">
+            <method name="helloC" signature="" line-rate="1" branch-rate="0" complexity="0">
               <lines>
                 <line number="20" hits="1" branch="false"/>
               </lines>

diff --git a/tests/cran/Makevars.gnu b/tests/cran/Makevars.gnu
@@ -46,5 +46,7 @@ CPPFLAGS += "-Wno-builtin-macro-redefined" \
   "-ffile-prefix-map=_EXEC_ROOT_=" \
   "-no-canonical-prefixes" \
 
+LDFLAGS += -fuse-ld=lld
+
 # Following flags should be enabled if switching to gcc:
 # CPPFLAGS += -fno-canonical-system-headers