{bio}[GCC/9.3.0] SRA-Toolkit v2.10.8 #11161

mboisson · 2020-08-25T19:20:02Z

(created using eb --new-pr)

mboisson · 2020-08-25T19:22:57Z

This is a version of SRA-Toolkit which uses HDF5.Serial, since there really is nothing MPI about this software.

mboisson · 2020-08-25T19:32:30Z

It requires this PR #11155

boegelbot · 2020-08-25T20:25:55Z

@mboisson: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/224209125
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 148, in test_conflicts
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 121, 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: HDF5.Serial/1.10.6-GCC-9.3.0 (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 132, in test_dep_graph
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 121, 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: HDF5.Serial/1.10.6-GCC-9.3.0 (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 430, in test_dep_versions_per_toolchain_generation
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 121, 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: HDF5.Serial/1.10.6-GCC-9.3.0 (no easyconfig file or existing module found)'

======================================================================
ERROR: test_sanity_check_paths (test.easyconfigs.easyconfigs.EasyConfigTest)
Make sure specified sanity check paths adher to the requirements.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 493, in test_sanity_check_paths
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 121, 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: HDF5.Serial/1.10.6-GCC-9.3.0 (no easyconfig file or existing module found)'

----------------------------------------------------------------------
Ran 10298 tests in 420.090s

FAILED (errors=4)
ERROR: Not all tests were successful.

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Please talk to my owner @boegel if you notice you me acting stupid),
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zao · 2020-09-01T08:42:18Z

Test report by @zao
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in this PR)
freja - Linux Ubuntu 20.04, x86_64, Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz, Python 3.8.2
See https://gist.github.com/a775ad61161a2a8b8dbfef74637c0bc5 for a full test report.

zao · 2020-09-01T08:45:09Z

Environment variable for HDF5.Serial is EBROOTHDF5SERIAL, --with-hdf5-prefix=$EBROOTHDF5 is erroneous.

verdurin · 2020-11-02T15:27:44Z

@mboisson any thoughts on the most recent comment from @zao ?

mboisson · 2020-11-02T15:30:11Z

@zao good catch.I missed that because we rename the HDF5.Serial -> HDF5, and HDF5 -> HDF5-mpi. locally. Will fix the PR and adjust our hooks accordingly.

boegelbot · 2020-11-02T16:23:26Z

@mboisson: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/341987556
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 148, in test_conflicts
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 121, 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: HDF5.Serial/1.10.6-GCC-9.3.0 (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 132, in test_dep_graph
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 121, 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: HDF5.Serial/1.10.6-GCC-9.3.0 (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 439, in test_dep_versions_per_toolchain_generation
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 121, 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: HDF5.Serial/1.10.6-GCC-9.3.0 (no easyconfig file or existing module found)'

======================================================================
ERROR: test_sanity_check_paths (test.easyconfigs.easyconfigs.EasyConfigTest)
Make sure specified sanity check paths adher to the requirements.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 502, in test_sanity_check_paths
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 121, 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: HDF5.Serial/1.10.6-GCC-9.3.0 (no easyconfig file or existing module found)'

----------------------------------------------------------------------
Ran 10812 tests in 495.756s

FAILED (errors=4)
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.

boegelbot · 2022-10-13T18:01:14Z

@mboisson: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/3244311782
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 326, in test_conflicts
    self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False),
  File "test/easyconfigs/easyconfigs.py", line 278, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 216, 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.Serial/1.10.6-GCC-9.3.0 (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 313, in test_dep_graph
    dep_graph(fn, self.ordered_specs)
  File "test/easyconfigs/easyconfigs.py", line 278, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 216, 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.Serial/1.10.6-GCC-9.3.0 (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 837, in test_dep_versions_per_toolchain_generation
    for ec in self.ordered_specs:
  File "test/easyconfigs/easyconfigs.py", line 278, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 216, 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.Serial/1.10.6-GCC-9.3.0 (no easyconfig file or existing module found)'

----------------------------------------------------------------------
Ran 15483 tests in 791.966s

FAILED (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.

boegel · 2024-01-14T08:45:39Z

closing this since GCC/9.3.0 is deprecated, see https://docs.easybuild.io/policies/toolchains

adding easyconfigs: SRA-Toolkit-2.10.8-GCC-9.3.0.eb

dde974e

lexming added the enhancement label Sep 15, 2020

lexming added this to the 4.x milestone Sep 15, 2020

replaced EBROOTHDF5 by EBROOTHDF5SERIAL

f29ea70

mboisson closed this Oct 13, 2022

mboisson reopened this Oct 13, 2022

boegel closed this Jan 14, 2024

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{bio}[GCC/9.3.0] SRA-Toolkit v2.10.8 #11161

{bio}[GCC/9.3.0] SRA-Toolkit v2.10.8 #11161

mboisson commented Aug 25, 2020

mboisson commented Aug 25, 2020

mboisson commented Aug 25, 2020

boegelbot commented Aug 25, 2020

zao commented Sep 1, 2020

zao commented Sep 1, 2020

verdurin commented Nov 2, 2020

mboisson commented Nov 2, 2020

boegelbot commented Nov 2, 2020

boegelbot commented Oct 13, 2022

boegel commented Jan 14, 2024

{bio}[GCC/9.3.0] SRA-Toolkit v2.10.8 #11161

{bio}[GCC/9.3.0] SRA-Toolkit v2.10.8 #11161

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mboisson commented Aug 25, 2020

mboisson commented Aug 25, 2020

mboisson commented Aug 25, 2020

boegelbot commented Aug 25, 2020

zao commented Sep 1, 2020

zao commented Sep 1, 2020

verdurin commented Nov 2, 2020

mboisson commented Nov 2, 2020

boegelbot commented Nov 2, 2020

boegelbot commented Oct 13, 2022

boegel commented Jan 14, 2024