Merge pull request #328 from boegel/2023.06_2021a_R-4.1.0

{2023.06}[foss/2021a] R v4.1.0

.github/workflows/test_eessi.yml

@@ -30,6 +30,7 @@ jobs:
         - eessi-2023.06-eb-4.8.0-system.yml
         - eessi-2023.06-eb-4.8.0-2021b.yml
         - eessi-2023.06-eb-4.8.1-system.yml
+        - eessi-2023.06-eb-4.8.1-2021a.yml
         - eessi-2023.06-eb-4.8.1-2021b.yml
         - eessi-2023.06-eb-4.8.1-2022a.yml
     steps:

eb_hooks.py

@@ -277,6 +277,32 @@ def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs):
         self.cfg['testopts'] = "|| echo ignoring failing tests" 
 
 
+def pre_single_extension_hook(ext, *args, **kwargs):
+    """Main pre-configure hook: trigger custom functions based on software name."""
+    if ext.name in PRE_SINGLE_EXTENSION_HOOKS:
+        PRE_SINGLE_EXTENSION_HOOKS[ext.name](ext, *args, **kwargs)
+
+
+def pre_single_extension_testthat(ext, *args, **kwargs):
+    """
+    Pre-extension hook for testthat R package, to fix build on top of recent glibc.
+    """
+    if ext.name == 'testthat' and LooseVersion(ext.version) < LooseVersion('3.1.0'):
+        # use constant value instead of SIGSTKSZ for stack size,
+        # cfr. https://github.com/r-lib/testthat/issues/1373 + https://github.com/r-lib/testthat/pull/1403
+        ext.cfg['preinstallopts'] = "sed -i 's/SIGSTKSZ/32768/g' inst/include/testthat/vendor/catch.h && "
+
+
+def pre_single_extension_isoband(ext, *args, **kwargs):
+    """
+    Pre-extension hook for isoband R package, to fix build on top of recent glibc.
+    """
+    if ext.name == 'isoband' and LooseVersion(ext.version) < LooseVersion('0.2.5'):
+        # use constant value instead of SIGSTKSZ for stack size in vendored testthat included in isoband sources,
+        # cfr. https://github.com/r-lib/isoband/commit/6984e6ce8d977f06e0b5ff73f5d88e5c9a44c027
+        ext.cfg['preinstallopts'] = "sed -i 's/SIGSTKSZ/32768/g' src/testthat/vendor/catch.h && "
+
+
 def pre_test_hook_ignore_failing_tests_FFTWMPI(self, *args, **kwargs):
     """
     Pre-test hook for FFTW.MPI: skip failing tests for FFTW.MPI 3.3.10 on neoverse_v1
@@ -286,6 +312,7 @@ def pre_test_hook_ignore_failing_tests_FFTWMPI(self, *args, **kwargs):
     if self.name == 'FFTW.MPI' and self.version == '3.3.10' and cpu_target == CPU_TARGET_NEOVERSE_V1:
         self.cfg['testopts'] = "|| echo ignoring failing tests"
 
+
 PARSE_HOOKS = {
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
@@ -309,3 +336,8 @@ def pre_test_hook_ignore_failing_tests_FFTWMPI(self, *args, **kwargs):
     'SciPy-bundle': pre_test_hook_ignore_failing_tests_SciPybundle,
     'FFTW.MPI': pre_test_hook_ignore_failing_tests_FFTWMPI,
 }
+
+PRE_SINGLE_EXTENSION_HOOKS = {
+    'isoband': pre_single_extension_isoband,
+    'testthat': pre_single_extension_testthat,
+}

eessi-2023.06-eb-4.8.1-2021a.yml

@@ -0,0 +1,7 @@
+easyconfigs:
+  - Xvfb-1.20.11-GCCcore-10.3.0.eb:
+       # fix permission issues for xvfb-run script,
+       # see https://github.com/easybuilders/easybuild-easyconfigs/pull/18834
+       options:
+         from-pr: 18834
+  - R-4.1.0-foss-2021a.eb