easybuild-easyconfigs {bio}[foss/2020b] Trinity 2.12.0

(created using eb --new-pr)

May 04 '21 19:05 fizwit

@fizwit: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/811181124 Output from first failing test suite run:

Failed to determine merge base (ec: 1, output: ''), falling back to specifying target branch develop
Failed to determine merge base (ec: 1, output: ''), falling back to specifying target branch develop

List of added easyconfig files in this PR:
	Trinity-2.12.0-foss-2020b-Python-3.8.6.eb
======================================================================
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 156, in test_conflicts
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
    EasyConfigTest.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 460, 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 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: Jellyfish/2.3.0-foss-2020b (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 140, in test_dep_graph
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
    EasyConfigTest.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 460, 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 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: Jellyfish/2.3.0-foss-2020b (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 538, in test_dep_versions_per_toolchain_generation
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
    EasyConfigTest.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 460, 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 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: Jellyfish/2.3.0-foss-2020b (no easyconfig file or existing module found)'

======================================================================
FAIL: test_changed_files_pull_request (test.easyconfigs.easyconfigs.EasyConfigTest)
Specific checks only done for the (easyconfig) files that were changed in a pull request.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 986, in test_changed_files_pull_request
    self.check_python_packages(changed_ecs, added_ecs_filenames)
  File "test/easyconfigs/easyconfigs.py", line 800, in check_python_packages
    self.fail('\n'.join(failing_checks))
AssertionError: '-Python-%(pyver)s' should no longer be included in versionsuffix in Trinity-2.12.0-foss-2020b-Python-3.8.6.eb

----------------------------------------------------------------------
Ran 12075 tests in 436.631s

FAILED (failures=1, errors=3)
ERROR: Not all tests were successful.

bleep, bloop, I'm just a bot (boegelbot v20200716.01) Please talk to my owner @boegel if you notice you me acting stupid), or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

May 07 '21 12:05 boegelbot

@fizwit: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/820945412 Output from first failing test suite run:

FAIL: test__parse_easyconfig_Trinity-2.12.0-foss-2020b-Python-3.8.6.eb (test.easyconfigs.easyconfigs.EasyConfigTest)
Test for parsing of easyconfig Trinity-2.12.0-foss-2020b-Python-3.8.6.eb
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 1247, in innertest
    template_easyconfig_test(self, spec_path)
  File "test/easyconfigs/easyconfigs.py", line 1122, in template_easyconfig_test
    self.assertTrue(res, error_msg)
AssertionError: Invalid checksum for patch file trinityrnaseq-v2.12.0_bamsifter.patch in Trinity-2.12.0-foss-2020b-Python-3.8.6.eb: 97262400f851905f055a921543aead9d3252d610a05ee44e7831b2ab64ff5e2b

======================================================================
FAIL: test_changed_files_pull_request (test.easyconfigs.easyconfigs.EasyConfigTest)
Specific checks only done for the (easyconfig) files that were changed in a pull request.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 986, in test_changed_files_pull_request
    self.check_python_packages(changed_ecs, added_ecs_filenames)
  File "test/easyconfigs/easyconfigs.py", line 800, in check_python_packages
    self.fail('\n'.join(failing_checks))
AssertionError: '-Python-%(pyver)s' should no longer be included in versionsuffix in Trinity-2.12.0-foss-2020b-Python-3.8.6.eb

======================================================================
FAIL: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 604, in test_dep_versions_per_toolchain_generation
    self.assertFalse(multi_dep_vars, error_msg)
AssertionError: No multi-variant deps found for '^.*-(?P<tc_gen>20[2-9][0-9][ab]).*\.eb$' easyconfigs:

found 2 variants of 'ant' dependency in easyconfigs using '2020b' toolchain generation
* version: 1.10.8; versionsuffix: -Java-11 as dep for set(['Trinity-2.12.0-foss-2020b.eb', 'Trinity-2.12.0-foss-2020b-Python-3.8.6.eb'])
* version: 1.10.9; versionsuffix: -Java-11 as dep for set(['OpenCV-4.5.1-foss-2020b-contrib.eb', 'OpenCV-4.5.1-fosscuda-2020b-contrib.eb'])


----------------------------------------------------------------------
Ran 12083 tests in 406.939s

FAILED (failures=3)
ERROR: Not all tests were successful.

bleep, bloop, I'm just a bot (boegelbot v20200716.01) Please talk to my owner @boegel if you notice you me acting stupid), or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

May 07 '21 16:05 boegelbot

@fizwit: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/3055155183 Output from first failing test suite run:

FAIL: test__parse_easyconfig_Trinity-2.12.0-foss-2020b-Python-3.8.6.eb (test.easyconfigs.easyconfigs.EasyConfigTest)
Test for easyconfig Trinity-2.12.0-foss-2020b-Python-3.8.6.eb
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 1481, in innertest
    template_easyconfig_test(self, spec_path)
  File "test/easyconfigs/easyconfigs.py", line 1352, in template_easyconfig_test
    self.assertTrue(res, error_msg)
AssertionError: Invalid checksum for patch file trinityrnaseq-v2.12.0_bamsifter.patch in Trinity-2.12.0-foss-2020b-Python-3.8.6.eb: 97262400f851905f055a921543aead9d3252d610a05ee44e7831b2ab64ff5e2b

======================================================================
FAIL: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 864, in test_dep_versions_per_toolchain_generation
    self.assertFalse(multi_dep_vars, error_msg)
AssertionError: No multi-variant deps found for '^.*-(?P<tc_gen>20(1[89]|[2-9][0-9])[ab]).*\.eb$' easyconfigs:

found 2 variants of 'ant' dependency in easyconfigs using '2020b' toolchain generation
* version: 1.10.8; versionsuffix: -Java-11 as dep for set(['Trinity-2.12.0-foss-2020b-Python-3.8.6.eb'])
* version: 1.10.9; versionsuffix: -Java-11 as dep for set(['OpenCV-4.5.1-foss-2020b-contrib.eb', 'OpenCV-4.5.1-fosscuda-2020b-contrib.eb', 'Trinity-2.12.0-foss-2020b.eb'])


======================================================================
FAIL: test_pr_python_packages (test.easyconfigs.easyconfigs.EasyConfigTest)
Several checks for easyconfigs that install (bundles of) Python packages.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 1058, in test_pr_python_packages
    self.fail('\n'.join(failing_checks))
AssertionError: '-Python-%(pyver)s' should no longer be included in versionsuffix in Trinity-2.12.0-foss-2020b-Python-3.8.6.eb

----------------------------------------------------------------------
Ran 15352 tests in 758.843s

FAILED (failures=3)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01) Please talk to my owner @boegel if you notice you me acting stupid), or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

Sep 14 '22 19:09 boegelbot

closing this since foss/2020b is deprecated, see https://docs.easybuild.io/policies/toolchains

Jan 13 '24 19:01 boegel

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{bio}[foss/2020b] Trinity 2.12.0

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