Merge pull request #2754 from MRtrix3/configure_isystem

configure: revert to -isystem rather than -idirafter

.github/workflows/checks.yml

@@ -27,7 +27,7 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install clang libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev 
+         sudo apt-get install clang libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev python3-distutils
 
     - name: configure
       run: ./configure -assert || { cat configure.log; false; }
@@ -41,6 +41,8 @@ jobs:
     - name: binary tests
       run: ./run_tests binaries || { cat testing_binaries.log; false; }
 
+    - name: check command documentation
+      run: ./docs/generate_user_docs.sh && git diff --exit-code docs/
 
 
 
@@ -103,9 +105,6 @@ jobs:
     - name: binary tests
       run: ./run_tests binaries || { cat testing_binaries.log; false; }
 
-    - name: check command documentation
-      run: ./docs/generate_user_docs.sh && git diff --exit-code docs/
-
 
 
 

configure

@@ -572,7 +572,7 @@ def get_flags (default=None, env=None, pkg_config_flags=None):
       flags = []
       for flag in shlex.split (execute ([ 'pkg-config' ] + pkg_config_flags.split(), RunError)[1]):
         if flag.startswith ('-I'):
-          flags += [ '-idirafter', flag[2:] ]
+          flags += [ '-isystem', flag[2:] ]
         else:
           flags += [ flag ]
       return flags
@@ -1318,7 +1318,7 @@ int main() { Foo f; }
         if entry[0] != '$' and not entry == '-I.':
           entry = entry.replace('\"','').replace("'",'')
           if entry.startswith('-I'):
-            qt_cflags += [ '-idirafter', entry[2:] ]
+            qt_cflags += [ '-isystem', entry[2:] ]
           else:
             qt_cflags += [ entry ]