[Debian-med-packaging] Bug#1004516: cwltool breaks toil autopkgtest: No such file or directory: '/home/debci/tmp/tmpgxz5j85g'
Paul Gevers
elbrus at debian.org
Sat Jan 29 18:41:25 GMT 2022
Source: cwltool, toil
Control: found -1 cwltool/3.1.20220119140128-2
Control: found -1 toil/5.6.0-2
Severity: serious
Tags: sid bookworm
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of cwltool the autopkgtest of toil fails in testing
when that autopkgtest is run with the binary packages of cwltool from
unstable. It passes when run with only packages from testing. In tabular
form:
pass fail
cwltool from testing 3.1.20220119140128-2
toil from testing 5.6.0-2
versioned deps [0] from testing from unstable
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of cwltool to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[0] You can see what packages were added from the second line of the log
file quoted below. The migration software adds source package from
unstable to the list if they are needed to install packages from
cwltool/3.1.20220119140128-2. I.e. due to versioned dependencies or
breaks/conflicts.
[1] https://qa.debian.org/excuses.php?package=cwltool
https://ci.debian.net/data/autopkgtest/testing/amd64/t/toil/18793124/log.gz
=================================== FAILURES
===================================
_______________ FileJobStoreTest.testEmptyFileStoreIDIsReadable
________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/jobStores/fileJobStore.py",
line 489, in read_file
os.link(jobStoreFilePath, local_path)
FileExistsError: [Errno 17] File exists:
'/tmp/autopkgtest-lxc.85mlkjg3/downtmp/build.vip/src/jobstore-test-07ead108-dcba-43a6-9148-1858e1cd24c6/files/no-job/file-db26c7b57ee84f5597ddbf2a60af46e7/stream'
-> '/home/debci/tmp/tmpgxz5j85g'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py",
line 1039, in testEmptyFileStoreIDIsReadable
self.jobstore_initialized.read_file(id, path)
File "/usr/lib/python3/dist-packages/toil/jobStores/fileJobStore.py",
line 498, in read_file
os.link(jobStoreFilePath, local_path)
OSError: [Errno 18] Invalid cross-device link:
'/tmp/autopkgtest-lxc.85mlkjg3/downtmp/build.vip/src/jobstore-test-07ead108-dcba-43a6-9148-1858e1cd24c6/files/no-job/file-db26c7b57ee84f5597ddbf2a60af46e7/stream'
-> '/home/debci/tmp/tmpgxz5j85g'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py",
line 1042, in testEmptyFileStoreIDIsReadable
os.unlink(path)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/debci/tmp/tmpgxz5j85g'
---------------------------- Captured stdout setup
-----------------------------
[TEST]
toil.test.jobStores.jobStoreTest.FileJobStoreTest:testEmptyFileStoreIDIsReadable
(Jan 29 2022 03:14:35:362865 PST)
------------------------------ Captured log call
-------------------------------
INFO toil.test:__init__.py:109 Setting up
toil.test.jobStores.jobStoreTest.FileJobStoreTest.testEmptyFileStoreIDIsReadable
...
DEBUG toil.jobStores.fileJobStore:fileJobStore.py:74 Path to job
store directory is
'/tmp/autopkgtest-lxc.85mlkjg3/downtmp/build.vip/src/jobstore-test-07ead108-dcba-43a6-9148-1858e1cd24c6'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:183 The
workflow ID is: '38228cb7-9d17-4058-b812-cd5f00e89fc6'
DEBUG toil.jobStores.fileJobStore:fileJobStore.py:74 Path to job
store directory is
'/tmp/autopkgtest-lxc.85mlkjg3/downtmp/build.vip/src/jobstore-test-07ead108-dcba-43a6-9148-1858e1cd24c6'.
INFO toil.test:__init__.py:114 Tore down
toil.test.jobStores.jobStoreTest.FileJobStoreTest.testEmptyFileStoreIDIsReadable
- generated xml file:
/tmp/autopkgtest-lxc.85mlkjg3/downtmp/run-unit-tests-artifacts/toil-tests-junit.xml
-
=========================== short test summary info
============================
SKIPPED [6]
../../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:153:
Install Toil with the 'kubernetes' extra to include this test.
SKIPPED [6]
../../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:153:
Install py-tes to include this test
SKIPPED [122]
../../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:153:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py:998:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [2]
../../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py:377:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py:1038:
Need at least four cores to run this test
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:942:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1015:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:780:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:896:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:799:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [53]
../../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:153:
Install Toil with the 'google' extra to include this test.
SKIPPED [44]
../../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:153:
Skipping docker test.
SKIPPED [8]
../../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:153:
Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test.
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py:502:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py:531:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py:600:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/provisioners/aws/awsProvisionerTest.py:50:
Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test.
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/provisioners/aws/awsProvisionerTest.py:58:
Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test.
SKIPPED [2]
../../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:153:
Install Toil with the 'server' extra to include this test.
SKIPPED [12]
../../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:153:
Install Mesos (and Toil with the 'mesos' extra) to include this test.
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py:35:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py:51:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py:96:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py:127:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [2]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:118:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [2]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:168:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:623:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:453:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:421:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:437:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:1096:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:399:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:903:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:792:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:803:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:1149:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:1142:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:911:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:926:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:84:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py:79:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [2]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py:56:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [2]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py:76:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [2]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py:137:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [2]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py:114:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [2]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py:40:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [2]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py:107:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobTest.py:373:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobTest.py:265:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobTest.py:287:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobTest.py:152:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: Skipped
because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/jobTest.py:122:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py:48:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:37:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:53:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:123:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/regularLogTest.py:56:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/regularLogTest.py:84:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/regularLogTest.py:74:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/restartDAGTest.py:43:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/restartDAGTest.py:47:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py:41:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py:48:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py:120:
Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test.
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py:319:
Skipping docker test.
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py:331:
Skipping docker test.
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py:270:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py:164:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py:231:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/wdl/toilwdlTest.py:323:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/wdl/toilwdlTest.py:113:
Skipping docker test.
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/wdl/toilwdlTest.py:266:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/wdl/toilwdlTest.py:280:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/wdl/toilwdlTest.py:294:
Skipped because TOIL_TEST_QUICK is "True"
SKIPPED [1]
../../../../../usr/lib/python3/dist-packages/toil/test/wdl/toilwdlTest.py:308:
Skipped because TOIL_TEST_QUICK is "True"
=== 1 failed, 228 passed, 331 skipped, 217 deselected in 1447.83s
(0:24:07) ====
autopkgtest [03:37:28]: test run-unit-tests
-------------- next part --------------
A non-text attachment was scrubbed...
Name: OpenPGP_signature
Type: application/pgp-signature
Size: 495 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20220129/03ad4b17/attachment-0001.sig>
More information about the Debian-med-packaging
mailing list