{lang}[foss/2021.07] R v4.1.1

[branfosj]

(created using eb --new-pr)

• {data}[gompi/2021.07] GDAL v3.3.2, netCDF v4.8.1, HDF5 v1.12.1 w/ Python 3.9.6 #13977
• I've added in ncdf4, rather than having it as a separate ec
• Bioconductor 3.14 should be released in a month, so that will follow then

[SebastianAchilles]

#13977 adds GDAL v3.3.2

[boegelbot]

@branfosj: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/1264931152
Output from first failing test suite run:

======================================================================
ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 296, in test_conflicts
    self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False),
  File "test/easyconfigs/easyconfigs.py", line 254, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 206, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: HDF5/1.12.1-foss-2021.07, GDAL/3.3.2-foss-2021.07 (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_graph (test.easyconfigs.easyconfigs.EasyConfigTest)
Unit test that builds a full dependency graph.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 283, in test_dep_graph
    dep_graph(fn, self.ordered_specs)
  File "test/easyconfigs/easyconfigs.py", line 254, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 206, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: HDF5/1.12.1-foss-2021.07, GDAL/3.3.2-foss-2021.07 (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 737, in test_dep_versions_per_toolchain_generation
    for ec in self.ordered_specs:
  File "test/easyconfigs/easyconfigs.py", line 254, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 206, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: HDF5/1.12.1-foss-2021.07, GDAL/3.3.2-foss-2021.07 (no easyconfig file or existing module found)'

----------------------------------------------------------------------
Ran 13367 tests in 772.237s

FAILED (errors=3)
Merge base for develop and HEAD: d7b8416c02e0a769eed9857a9afced9e3c6a7a97
Merge base for develop and HEAD: d7b8416c02e0a769eed9857a9afced9e3c6a7a97

List of added easyconfig files in this PR:
	R-4.1.1-foss-2021.07.eb
ERROR: Not all tests were successful

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[branfosj]

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u08b.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/96cada19f8b2b36e1564ad2eed1abe3f for a full test report.

[SebastianAchilles]

Test report by @SebastianAchilles
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
rocky8-eb - Linux rocky linux 8.4, x86_64, Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz (broadwell), Python 3.6.8
See https://gist.github.com/3e73a6e891986b07f9a8737bad3dd0b2 for a full test report.

[boegel]

R 4.1.2 will be released on Nov 1st, not sure if we should hold on for that?

[branfosj]

Bioconductor 3.14 is being released next Wednesday. I think this is sufficiently old that the best option is to close this and go with R 4.1.2 and Bioconductor 3.14 at the start of November instead. This would have the bonus of matching release date of all the R and Bioconductor libraries from about the same time, which is generally better.

[branfosj]

R 4.1.2 and Bioconductor 3.14 will be released soon. So I am closing this PR and we'll go with fresh PRs for those two.