{bio}[foss/2020b] PPanGGOLiN v1.1.136 + dependencies

[deniskristak]

adding easyconfigs: PPanGGOLiN-1.1.136-foss-2020b.eb, ARAGORN-1.2.41-foss-2020b.eb, Infernal-1.1.4-foss-2020b.eb, genoPlotR-0.8.11-foss-2020b.eb, rpy2-3.4.5-foss-2020b.eb and patches: PPanGGOLiN-1.1.136_new_compiler_compatibility.patch

[deniskristak]

@boegel please take a look at aragorn easyconfig line 28 if we can do anything about that

[boegel]

@deniskristak Can you take a look at how painful it would to move this to the foss/2021b toolchain, so we can just add genoPlotR as an extension to R 4.1.2?

I need to add a couple of other extensions to R anyway, I'll include genoPlotR straight away as well...

[boegel]

Since this only depends on R, we should probably just add this as an extension to R itself?

I would prefer doing that only for the latest R version we have though (4.1.2 with foss/2021b)...

[boegel]

@deniskristak I've added genoPlotR to R 4.1.2 in #14433

[boegel]

Do any of these support --help or --version, or similar?
If so, please add a sanity check command for some (or all) of them.

If you do all, introduce a local variable local_bins = ['bin/cm%s' % x for x in ['align', ...]]

[boegel]

Why are these commented out?

[deniskristak]

i had to figure out how to do this properly, because the above didnt prevent tests from running (and failing)...its updated now

[boegel]

@deniskristak Trivial code style issue to fix:

$ eb --from-pr 14399 --check-style
== Temporary log file in case of crash /tmp/eb-1lh0xz7p/easybuild-r4cb77p0.log

Running style check on 5 easyconfig(s)...

[PASS] /tmp/eb-1lh0xz7p/files_pr14399/a/ARAGORN/ARAGORN-1.2.41-foss-2020b.eb
[PASS] /tmp/eb-1lh0xz7p/files_pr14399/g/genoPlotR/genoPlotR-0.8.11-foss-2020b.eb
[PASS] /tmp/eb-1lh0xz7p/files_pr14399/i/Infernal/Infernal-1.1.4-foss-2020b.eb
/tmp/eb-1lh0xz7p/files_pr14399/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2020b.eb:49:121: E501 line too long (131 > 120 characters)
[FAIL] /tmp/eb-1lh0xz7p/files_pr14399/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2020b.eb
[PASS] /tmp/eb-1lh0xz7p/files_pr14399/r/rpy2/rpy2-3.4.5-foss-2020b.eb

[boegelbot]

@deniskristak: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/1508484726
Output from first failing test suite run:

Merge base for develop and HEAD: 770a7b8a9c620bc6afbfffad28d6c9e969b1ccb3
======================================================================
Merge base for develop and HEAD: 770a7b8a9c620bc6afbfffad28d6c9e969b1ccb3
FAIL: test_pr_python_packages (test.easyconfigs.easyconfigs.EasyConfigTest)

Several checks for easyconfigs that install (bundles of) Python packages.
List of added easyconfig files in this PR:
----------------------------------------------------------------------
	ARAGORN-1.2.41-foss-2020b.eb
Traceback (most recent call last):
	genoPlotR-0.8.11-foss-2020b.eb
  File "test/easyconfigs/easyconfigs.py", line 981, in test_pr_python_packages
	Infernal-1.1.4-foss-2020b.eb
    self.fail('\n'.join(failing_checks))
	PPanGGOLiN-1.1.136-foss-2020b.eb
AssertionError: '*download_dep_fail' should not be set in PPanGGOLiN-1.1.136-foss-2020b.eb since PythonBundle easyblock is used
	rpy2-3.4.5-foss-2020b.eb

----------------------------------------------------------------------
Ran 13712 tests in 517.245s

FAILED (failures=1)
ERROR: Not all tests were successful

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[boegel]

@deniskristak I think this can be closed, superseded by #14449?