{bio}[intel/2018a] CNVkit v0.9.3, Biopython v1.71, hmmlearn 0.2.0 #6445

boegel · 2018-06-12T12:19:53Z

(created using eb --new-pr)

…on-1.71-intel-2018a-Python-3.6.4.eb, Pysam-0.14.1-intel-2018a-Python-3.6.4.eb, hmmlearn-0.2.0-intel-2018a-Python-3.6.4.eb

boegel · 2018-06-12T12:39:58Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
node2646.swalot.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/c74de535bef020200a1586e1c64b7992 for a full test report.

boegel · 2018-06-12T12:56:58Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
node2056.delcatty.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/95a83dd8221b81c09ac60e824e2a6ba7 for a full test report.

boegel · 2018-06-21T13:47:01Z

Test report by @boegel
FAILED
Build succeeded for 11 out of 13 (4 easyconfigs in this PR)
node3129.skitty.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 2.7.5
See https://gist.github.com/b9dba6d0ebf5bca692069c161fb24ef2 for a full test report.

damianam

lgtm, but as I asked in another PR, did you verify that no other dependencies are downloaded by pip?

boegel · 2018-06-21T15:31:42Z

@damianam That's verified automagically by setting (exts_)download_dep_fail = True in these easyconfigs (cfr. easybuilders/easybuild-easyblocks#1377)

migueldiascosta · 2018-06-25T03:55:12Z

Test report by @migueldiascosta
FAILED
Build succeeded for 7 out of 12 (4 easyconfigs in this PR)
grc-s05 - Linux centos 6.9, Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz, Python 2.6.6
See https://gist.github.com/18278a3ad89675c6386528572892fed2 for a full test report.

migueldiascosta · 2018-06-25T04:27:10Z

missing XZ dependency in Pysam?

migueldiascosta · 2018-06-27T10:30:56Z

Test report by @migueldiascosta
FAILED
Build succeeded for 7 out of 11 (8 easyconfigs in this PR)
grc-s05 - Linux centos 6.9, Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz, Python 2.6.6
See https://gist.github.com/1af748f606fb577477c0adb94fd59011 for a full test report.

boegel · 2018-06-27T11:05:51Z

@migueldiascosta Failure with R is due to changed checksums, cfr. #6446, you'll need to re-download those source tarballs...

Not sure about the issue with Pillow though... Does that ring any bells for you?

migueldiascosta · 2018-06-28T00:46:52Z

@boegel regarding the issue with Pillow, a google search shows a few things about a binutils 2.28 issue, although that doesn't explain why only I seem to have this problem...

boegel · 2018-06-28T07:43:23Z

@migueldiascosta Can you share a full debug log for the failing Pillow? You can obtain it with eb --from-pr 6445 --debug Pillow-5.0.0-intel-2018a-Python-3.6.4.eb .

Also, was LibTIFF/4.0.9-GCCcore-6.4.0 installed with the right binutils version?
Is it an option to try and reinstall that to see if that resolves the issue?

boegel · 2018-06-28T07:46:00Z

@migueldiascosta May be related to the fix in #5945, was LibTIFF installed with that configure option (--enable-ld-version-script) included?

migueldiascosta · 2018-06-28T07:48:18Z

@boegel I did try reinstalling LibTIFF, Pillow still failed although with a slightly different error (different duplicate definition)

at least the second install did have the configure option from #5945

I'll get the full log

migueldiascosta · 2018-06-28T08:42:41Z

full log at https://gist.github.com/migueldiascosta/366d4ae69daf7c08bc44c14ed756f7d6

migueldiascosta · 2018-06-28T09:02:46Z

added the LibTIFF log to the gist

akesandgren · 2019-08-29T06:34:50Z

@boegel Conflicts to be resolved...

akesandgren · 2020-10-16T15:01:08Z

I get

WARNING: Use of 1 unknown easyconfig parameters detected in CNVkit-0.9.3-intel-2018a-Python-3.6.4.eb: full_sanity_check

And so is the tests.

boegelbot · 2020-11-17T09:23:22Z

@boegel: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/367715320
Output from first failing test suite run:

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 809, in test_changed_files_pull_request
    self.check_python_packages(changed_ecs, added_ecs_filenames)
  File "test/easyconfigs/easyconfigs.py", line 646, in check_python_packages
    self.assertFalse(failing_checks, '\n'.join(failing_checks))
AssertionError: 'use_pip' should be set in Biopython-1.71-intel-2018a-Python-3.6.4.eb
sanity_pip_check should be enabled in CNVkit-0.9.3-intel-2018a-Python-3.6.4.eb
'use_pip' should be set in hmmlearn-0.2.0-intel-2018a-Python-3.6.4.eb

----------------------------------------------------------------------
Ran 10939 tests in 916.701s

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

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migueldiascosta · 2020-12-11T05:33:18Z

Test report by @migueldiascosta
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
sms - Linux centos linux 7.6.1810, x86_64, AMD EPYC 7601 32-Core Processor (zen), Python 2.7.5
See https://gist.github.com/d8014dc3dd078b0aed0713163c46c895 for a full test report.

migueldiascosta · 2020-12-11T08:20:48Z

@boegel I think my old failing tests can be ignored, I don't seem to be able to reproduce them even in that old CentOS 6 cluster

…asyconfigs + enhance sanity check for Biopython

boegel · 2020-12-11T10:20:21Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node2707.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/055720f0bf081b0007c4ca0a5088d96e for a full test report.

boegel · 2020-12-11T10:32:10Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3129.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/6d82d485ea495e1d2b9cc1f51568abed for a full test report.

akesandgren

LGTM

akesandgren · 2020-12-11T14:45:08Z

Test report by @akesandgren
SUCCESS
Build succeeded for 8 out of 8 (3 easyconfigs in total)
b-an04.hpc2n.umu.se - Linux ubuntu 16.04, x86_64, Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, Python 2.7.12
See https://gist.github.com/20ee9c162464caae987f1479495c6710 for a full test report.

akesandgren · 2020-12-11T14:51:33Z

Going in, thanks @boegel!

adding easyconfigs: CNVkit-0.9.3-intel-2018a-Python-3.6.4.eb, Biopyth…

f37f12e

…on-1.71-intel-2018a-Python-3.6.4.eb, Pysam-0.14.1-intel-2018a-Python-3.6.4.eb, hmmlearn-0.2.0-intel-2018a-Python-3.6.4.eb

boegel added the update label Jun 12, 2018

add patch file for CNVkit 0.9.3

2c36ec6

boegel added this to the 3.6.2 milestone Jun 12, 2018

boegel requested a review from wpoely86 June 13, 2018 16:08

damianam reviewed Jun 21, 2018

View reviewed changes

boegel added 2 commits June 27, 2018 11:27

Merge branch 'develop' into 20180612141944_new_pr_CNVkit093

4954386

add missing XZ dep for Pysam 0.14.*

0980700

boegel modified the milestones: 3.6.2, next release Jul 6, 2018

boegel modified the milestones: 3.7.0, next release Sep 22, 2018

boegel modified the milestones: 3.7.1, next release Oct 10, 2018

boegel modified the milestones: 3.8.0, 3.8.1 Dec 14, 2018

boegel modified the milestones: 3.8.1, 3.x Jan 19, 2019

boegel modified the milestones: 3.x, 4.x Feb 20, 2020

Merge branch 'develop' into 20180612141944_new_pr_CNVkit093

9a302cc

boegel added 3 commits October 18, 2020 11:54

Merge branch 'develop' into 20180612141944_new_pr_CNVkit093

d01a919

use PythonBundle for CNVkit

c177d0a

Merge branch 'develop' into 20180612141944_new_pr_CNVkit093

6670a42

boegel changed the title ~~{bio}[intel/2018a] CNVkit v0.9.3, Biopython v1.71, Pysam v0.14.1, ...~~ {bio}[intel/2018a] CNVkit v0.9.3, Biopython v1.71, hmmlearn 0.2.0 Nov 17, 2020

Merge branch 'develop' into 20180612141944_new_pr_CNVkit093

ac333d0

boegel added 3 commits December 11, 2020 10:21

add missing use_pip/sanity_pip_check in hmmlearn, CNVkit, Biopython e…

e6cf4c0

…asyconfigs + enhance sanity check for Biopython

fix Python shebangs in CNVkit scripts + add sanity check command

2807395

use https in Biopython/CNVkit easyconfigs

61046cd

akesandgren approved these changes Dec 11, 2020

View reviewed changes

akesandgren merged commit 3c57b62 into easybuilders:develop Dec 11, 2020

boegel deleted the 20180612141944_new_pr_CNVkit093 branch December 11, 2020 15:04

boegel modified the milestones: 4.x, next release (4.3.3?) Dec 11, 2020

{bio}[intel/2018a] CNVkit v0.9.3, Biopython v1.71, hmmlearn 0.2.0 #6445

{bio}[intel/2018a] CNVkit v0.9.3, Biopython v1.71, hmmlearn 0.2.0 #6445

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