Your message dated Sat, 16 May 2026 10:23:18 +0000
with message-id <[email protected]>
and subject line Released with 13.5
has caused the Debian Bug report #1135228,
regarding trixie-pu: package toil/8.0.0-5+deb13u1
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1135228: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1135228
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: release.debian.org
Severity: normal
Tags: trixie
X-Debbugs-Cc: [email protected], [email protected]
Control: affects -1 + src:toil
User: [email protected]
Usertags: pu
[ Reason ]
Fix FTBFS Bug #1108056. Some tests fail on single-CPU systems.
[ Impact ]
Anybody trying to build the package on a single-CPU system will unexpectedly
find that the package does not build.
[ Tests ]
I've checked that the package builds ok again on the systems where it used to
fail.
[ Risks ]
Very low. No real code changes. Only some tests are disabled, and only
when it's detected that they would fail.
[ Checklist ]
[X] *all* changes are documented in the d/changelog
[X] I reviewed all changes and I approve them
[X] attach debdiff against the package in (old)stable
[X] the issue is verified as fixed in unstable
[ Changes ]
See changelog.
[ Other info ]
I've already uploaded the package.
diff -Nru toil-8.0.0/debian/changelog toil-8.0.0/debian/changelog
--- toil-8.0.0/debian/changelog 2025-04-09 13:42:27.000000000 +0200
+++ toil-8.0.0/debian/changelog 2026-04-29 20:30:00.000000000 +0200
@@ -1,3 +1,11 @@
+toil (8.0.0-5+deb13u1) trixie; urgency=medium
+
+ * Team upload.
+ * Conditionally skip tests requiring more CPUs than available.
+ Closes: #1108056.
+
+ -- Santiago Vila <[email protected]> Wed, 29 Apr 2026 20:30:00 +0200
+
toil (8.0.0-5) unstable; urgency=medium
* d/rules: skip flaky testServices. Closes: #1101085
diff -Nru toil-8.0.0/debian/patches/conditionally-skip-tests.patch
toil-8.0.0/debian/patches/conditionally-skip-tests.patch
--- toil-8.0.0/debian/patches/conditionally-skip-tests.patch 1970-01-01
01:00:00.000000000 +0100
+++ toil-8.0.0/debian/patches/conditionally-skip-tests.patch 2026-04-29
18:14:00.000000000 +0200
@@ -0,0 +1,73 @@
+From: Santiago Vila <[email protected]>
+Subject: Conditionally skip tests requiring more CPUs than available
+Bug-Debian: https://bugs.debian.org/1108056
+Forwarded: https://github.com/DataBiosphere/toil/issues/5482
+
+--- a/src/toil/test/batchSystems/batchSystemTest.py
++++ b/src/toil/test/batchSystems/batchSystemTest.py
+@@ -24,6 +24,8 @@
+ from fractions import Fraction
+ from unittest import skipIf
+
++import pytest
++
+ from toil.batchSystems.abstractBatchSystem import (
+ AbstractBatchSystem,
+ BatchSystemSupport,
+@@ -505,6 +507,10 @@
+ _, maxValue = getCounters(counterPath)
+ self.assertEqual(maxValue, self.cpuCount // coresPerJob)
+
++ @pytest.mark.skipif(
++ SingleMachineBatchSystem.numCores < 2,
++ reason="Need at least two cores to run this test",
++ )
+ def test_omp_threads(self):
+ """
+ Test if the OMP_NUM_THREADS env var is set correctly based on
jobs.cores.
+--- a/src/toil/test/docs/scriptsTest.py
++++ b/src/toil/test/docs/scriptsTest.py
+@@ -68,6 +68,10 @@
+ n = re.search(pattern, outerr)
+ self.assertNotEqual(n, None,
f"Pattern:\n{expectedPattern}\nOutput:\n{outerr}")
+
++ @pytest.mark.skipif(
++ os.cpu_count() < 2,
++ reason="Need at least two cores to run this test",
++ )
+ def testStats(self):
+ # This script asks for 4 cores but we might need to run the tests in
only 3.
+ self.checkExitCode("tutorial_stats.py", ["--scale=0.5"])
+--- a/src/toil/test/src/promisedRequirementTest.py
++++ b/src/toil/test/src/promisedRequirementTest.py
+@@ -16,6 +16,8 @@
+ import os
+ import time
+
++import pytest
++
+ import toil.test.batchSystems.batchSystemTest as batchSystemTest
+ from toil.batchSystems.mesos.test import MesosTestSupport
+ from toil.job import Job, PromisedRequirement
+@@ -127,6 +129,10 @@
+ assert (minValue, maxValue) == (0, 0)
+ return counterPath
+
++ @pytest.mark.skipif(
++ os.cpu_count() < 2,
++ reason="Need at least two cores to run this test",
++ )
+ def testPromisesWithJobStoreFileObjects(self, caching=True):
+ """
+ Check whether FileID objects are being pickled properly when used
as return
+@@ -153,6 +159,10 @@
+ F1, self.getOptions(self._createTempDir("testFiles"),
caching=caching)
+ )
+
++ @pytest.mark.skipif(
++ os.cpu_count() < 2,
++ reason="Need at least two cores to run this test",
++ )
+ def testPromisesWithNonCachingFileStore(self):
+ self.testPromisesWithJobStoreFileObjects(caching=False)
+
diff -Nru toil-8.0.0/debian/patches/series toil-8.0.0/debian/patches/series
--- toil-8.0.0/debian/patches/series 2025-03-17 19:11:04.000000000 +0100
+++ toil-8.0.0/debian/patches/series 2026-04-29 18:00:00.000000000 +0200
@@ -11,3 +11,4 @@
accept_debian_packaged_docker_version.patch
allow_newer_requests
soften-psutil
+conditionally-skip-tests.patch
--- End Message ---
--- Begin Message ---
Package: release.debian.org
Version: 13.5
This update has been released as part of Debian 13.5.
--- End Message ---
