Your message dated Wed, 23 Aug 2023 20:50:01 +0000
with message-id <e1qyunh-0028qi...@fasolo.debian.org>
and subject line Bug#1042046: fixed in pyranges 0.0.111+ds-5
has caused the Debian Bug report #1042046,
regarding pyranges: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i
python{version} -p 3.11 returned exit code 13
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1042046: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1042046
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: pyranges
Version: 0.0.111+ds-4
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20230724 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_build
> I: pybuild base:240: /usr/bin/python3 setup.py build
> echo 'Generating corresponding files ...'
> Generating corresponding files ...
> cat debian/missing-sources/test_sorted.sam| samtools view -Sb - >
> tests/test_data/test_sorted.bam
> cat debian/missing-sources/control.sam| samtools view -Sb - >
> pyranges/example_data/control.bam
> samtools index tests/test_data/test_sorted.bam
> tests/test_data/test_sorted.bam.bai
> samtools index pyranges/example_data/control.bam
> pyranges/example_data/control.bam.bai
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild pybuild:307: cp -av /<<PKGBUILDDIR>>/tests/*.bed
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av
> /<<PKGBUILDDIR>>/tests/test_data
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av
> /<<PKGBUILDDIR>>/tests/data
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av
> /<<PKGBUILDDIR>>/pyranges/example_data
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges
> '/<<PKGBUILDDIR>>/tests/chip_10.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/chip_10.bed'
> '/<<PKGBUILDDIR>>/tests/f1.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/f1.bed'
> '/<<PKGBUILDDIR>>/tests/f2.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/f2.bed'
> '/<<PKGBUILDDIR>>/tests/test_data' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_data'
> '/<<PKGBUILDDIR>>/tests/test_data/ensembl.gtf' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/ensembl.gtf'
> '/<<PKGBUILDDIR>>/tests/test_data/gencode.gff3' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/gencode.gff3'
> '/<<PKGBUILDDIR>>/tests/test_data/ucsc_df_to_parse.txt' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/ucsc_df_to_parse.txt'
> '/<<PKGBUILDDIR>>/tests/test_data/test_sorted.bam' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/test_sorted.bam'
> '/<<PKGBUILDDIR>>/tests/test_data/test_sorted.bam.bai' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/test_sorted.bam.bai'
> '/<<PKGBUILDDIR>>/tests/data' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/data'
> '/<<PKGBUILDDIR>>/tests/data/test_data.py' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/data/test_data.py'
> '/<<PKGBUILDDIR>>/pyranges/example_data/exons.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/exons.bed'
> '/<<PKGBUILDDIR>>/pyranges/example_data/ensembl.gtf' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ensembl.gtf'
> '/<<PKGBUILDDIR>>/pyranges/example_data/ucsc_human.bed.gz' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ucsc_human.bed.gz'
> '/<<PKGBUILDDIR>>/pyranges/example_data/chipseq_background.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chipseq_background.bed'
> '/<<PKGBUILDDIR>>/pyranges/example_data/f2.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/f2.bed'
> '/<<PKGBUILDDIR>>/pyranges/example_data/bw.bw' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/bw.bw'
> '/<<PKGBUILDDIR>>/pyranges/example_data/f1.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/f1.bed'
> '/<<PKGBUILDDIR>>/pyranges/example_data/cpg.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/cpg.bed'
> '/<<PKGBUILDDIR>>/pyranges/example_data/lamina.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/lamina.bed'
> '/<<PKGBUILDDIR>>/pyranges/example_data/gencode_human.gtf.gz' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/gencode_human.gtf.gz'
> '/<<PKGBUILDDIR>>/pyranges/example_data/chipseq.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chipseq.bed'
> '/<<PKGBUILDDIR>>/pyranges/example_data/aorta.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/aorta.bed'
> '/<<PKGBUILDDIR>>/pyranges/example_data/ensembl_human.gtf.gz' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ensembl_human.gtf.gz'
> '/<<PKGBUILDDIR>>/pyranges/example_data/chromsizes.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chromsizes.bed'
> '/<<PKGBUILDDIR>>/pyranges/example_data/aorta2.bed' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/aorta2.bed'
> '/<<PKGBUILDDIR>>/pyranges/example_data/control.bam' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/control.bam'
> '/<<PKGBUILDDIR>>/pyranges/example_data/control.bam.bai' ->
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/control.bam.bai'
> I: pybuild base:240: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build; python3.11 -m pytest
> -n 8
> ============================= test session starts
> ==============================
> platform linux -- Python 3.11.4, pytest-7.4.0, pluggy-1.2.0
> rootdir: /<<PKGBUILDDIR>>
> plugins: xdist-3.3.1, hypothesis-6.82.0
> created: 8/8 workers
> 8 workers [531 items]
>
> ........................................................................ [
> 13%]
> ........................................................................ [
> 27%]
> ........................................................................ [
> 40%]
> ........................................................................ [
> 54%]
> ........................................................................ [
> 67%]
> ........................................................................ [
> 81%]
> ........................................................................ [
> 94%]
> ....................F......
> [100%]
> =================================== FAILURES
> ===================================
> _________________________________ test_getitem
> _________________________________
> [gw3] linux -- Python 3.11.4 /usr/bin/python3.11
>
> @settings(
> > max_examples=max_examples,
> deadline=deadline,
> suppress_health_check=HealthCheck.all())
> E hypothesis.errors.FailedHealthCheck: Tests run under @given should
> return None, but test_getitem returned Empty PyRanges instead.
> E See https://hypothesis.readthedocs.io/en/latest/healthchecks.html for
> more information about this. If you want to disable just this health check,
> add HealthCheck.return_value to the suppress_health_check settings for this
> test.
>
> tests/test_unary.py:290: FailedHealthCheck
> ---------------------------------- Hypothesis
> ----------------------------------
> You can add @seed(38673206842016826684023353536273025751) to this test or run
> pytest with --hypothesis-seed=38673206842016826684023353536273025751 to
> reproduce this failure.
> =============================== warnings summary
> ===============================
> tests/conftest.py:83
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/conftest.py:83:
> DeprecationWarning: invalid escape sequence '\s'
> sep="\s+",
>
> pyranges/__init__.py:18
> pyranges/__init__.py:18
> pyranges/__init__.py:18
> pyranges/__init__.py:18
> pyranges/__init__.py:18
> pyranges/__init__.py:18
> pyranges/__init__.py:18
> pyranges/__init__.py:18
> pyranges/__init__.py:18
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/__init__.py:18:
> DeprecationWarning: pkg_resources is deprecated as an API. See
> https://setuptools.pypa.io/en/latest/pkg_resources.html
> import pkg_resources
>
> tests/test_binary.py:118
> tests/test_binary.py:118
> tests/test_binary.py:118
> tests/test_binary.py:118
> tests/test_binary.py:118
> tests/test_binary.py:118
> tests/test_binary.py:118
> tests/test_binary.py:118
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:118:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_binary.py:139
> tests/test_binary.py:139
> tests/test_binary.py:139
> tests/test_binary.py:139
> tests/test_binary.py:139
> tests/test_binary.py:139
> tests/test_binary.py:139
> tests/test_binary.py:139
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:139:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_binary.py:160
> tests/test_binary.py:160
> tests/test_binary.py:160
> tests/test_binary.py:160
> tests/test_binary.py:160
> tests/test_binary.py:160
> tests/test_binary.py:160
> tests/test_binary.py:160
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:160:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_binary.py:187
> tests/test_binary.py:187
> tests/test_binary.py:187
> tests/test_binary.py:187
> tests/test_binary.py:187
> tests/test_binary.py:187
> tests/test_binary.py:187
> tests/test_binary.py:187
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:187:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_binary.py:212
> tests/test_binary.py:212
> tests/test_binary.py:212
> tests/test_binary.py:212
> tests/test_binary.py:212
> tests/test_binary.py:212
> tests/test_binary.py:212
> tests/test_binary.py:212
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:212:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_binary.py:291
> tests/test_binary.py:291
> tests/test_binary.py:291
> tests/test_binary.py:291
> tests/test_binary.py:291
> tests/test_binary.py:291
> tests/test_binary.py:291
> tests/test_binary.py:291
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:291:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_binary.py:329
> tests/test_binary.py:329
> tests/test_binary.py:329
> tests/test_binary.py:329
> tests/test_binary.py:329
> tests/test_binary.py:329
> tests/test_binary.py:329
> tests/test_binary.py:329
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:329:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_binary.py:368
> tests/test_binary.py:368
> tests/test_binary.py:368
> tests/test_binary.py:368
> tests/test_binary.py:368
> tests/test_binary.py:368
> tests/test_binary.py:368
> tests/test_binary.py:368
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:368:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_binary.py:392
> tests/test_binary.py:392
> tests/test_binary.py:392
> tests/test_binary.py:392
> tests/test_binary.py:392
> tests/test_binary.py:392
> tests/test_binary.py:392
> tests/test_binary.py:392
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:392:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_binary.py:426
> tests/test_binary.py:426
> tests/test_binary.py:426
> tests/test_binary.py:426
> tests/test_binary.py:426
> tests/test_binary.py:426
> tests/test_binary.py:426
> tests/test_binary.py:426
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:426:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_binary.py:516
> tests/test_binary.py:516
> tests/test_binary.py:516
> tests/test_binary.py:516
> tests/test_binary.py:516
> tests/test_binary.py:516
> tests/test_binary.py:516
> tests/test_binary.py:516
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:516:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_binary.py:579
> tests/test_binary.py:579
> tests/test_binary.py:579
> tests/test_binary.py:579
> tests/test_binary.py:579
> tests/test_binary.py:579
> tests/test_binary.py:579
> tests/test_binary.py:579
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:579:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_do_not_error.py:46
> tests/test_do_not_error.py:46
> tests/test_do_not_error.py:46
> tests/test_do_not_error.py:46
> tests/test_do_not_error.py:46
> tests/test_do_not_error.py:46
> tests/test_do_not_error.py:46
> tests/test_do_not_error.py:46
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_do_not_error.py:46:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_unary.py:35
> tests/test_unary.py:35
> tests/test_unary.py:35
> tests/test_unary.py:35
> tests/test_unary.py:35
> tests/test_unary.py:35
> tests/test_unary.py:35
> tests/test_unary.py:35
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:35:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_unary.py:100
> tests/test_unary.py:100
> tests/test_unary.py:100
> tests/test_unary.py:100
> tests/test_unary.py:100
> tests/test_unary.py:100
> tests/test_unary.py:100
> tests/test_unary.py:100
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:100:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_unary.py:164
> tests/test_unary.py:164
> tests/test_unary.py:164
> tests/test_unary.py:164
> tests/test_unary.py:164
> tests/test_unary.py:164
> tests/test_unary.py:164
> tests/test_unary.py:164
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:164:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_unary.py:206
> tests/test_unary.py:206
> tests/test_unary.py:206
> tests/test_unary.py:206
> tests/test_unary.py:206
> tests/test_unary.py:206
> tests/test_unary.py:206
> tests/test_unary.py:206
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:206:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_unary.py:235
> tests/test_unary.py:235
> tests/test_unary.py:235
> tests/test_unary.py:235
> tests/test_unary.py:235
> tests/test_unary.py:235
> tests/test_unary.py:235
> tests/test_unary.py:235
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:235:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_unary.py:274
> tests/test_unary.py:274
> tests/test_unary.py:274
> tests/test_unary.py:274
> tests/test_unary.py:274
> tests/test_unary.py:274
> tests/test_unary.py:274
> tests/test_unary.py:274
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:274:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_unary.py:292
> tests/test_unary.py:292
> tests/test_unary.py:292
> tests/test_unary.py:292
> tests/test_unary.py:292
> tests/test_unary.py:292
> tests/test_unary.py:292
> tests/test_unary.py:292
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:292:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> tests/test_unary.py:317
> tests/test_unary.py:317
> tests/test_unary.py:317
> tests/test_unary.py:317
> tests/test_unary.py:317
> tests/test_unary.py:317
> tests/test_unary.py:317
> tests/test_unary.py:317
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:317:
> HypothesisDeprecationWarning: `Healthcheck.all()` is deprecated; use
> `list(HealthCheck)` instead.
> The `hypothesis codemod` command-line tool can automatically refactor
> your code to fix this warning.
> suppress_health_check=HealthCheck.all())
>
> .pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py: 18000 warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:349:
> FutureWarning: In a future version of pandas all arguments of DataFrame.drop
> except for the argument 'labels' will be keyword-only.
> bedtools_df = bedtools_df.drop("Chromosome2", 1)
>
> .pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py: 18000 warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:544:
> FutureWarning: In a future version of pandas all arguments of DataFrame.drop
> except for the argument 'labels' will be keyword-only.
> bedtools_df = bedtools_df.drop("Chromosome2", 1)
>
> .pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py: 11940 warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/pyranges.py:2503:
> FutureWarning: is_monotonic is deprecated and will be removed in a future
> version. Use is_monotonic_increasing instead.
> if not result.__IX__.is_monotonic:
>
> .pybuild/cpython3_3.11_pyranges/build/tests/test_genomicfeatures.py: 119
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_genomicfeatures.py:40:
> DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will
> attempt to set the values inplace instead of always setting a new array. To
> retain the old behavior, use either `df[df.columns[i]] = newvals` or, if
> columns are non-unique, `df.isetitem(i, newvals)`
> x.loc[:, "Start"] = x.Start.astype(int)
>
> .pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 2000 warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:119:
> FutureWarning: The squeeze argument has been deprecated and will be removed
> in a future version. Append .squeeze("columns") to the call to squeeze.
>
>
> bedtools_df = pd.read_csv(
>
> .pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 2000 warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:193:
> DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will
> attempt to set the values inplace instead of always setting a new array. To
> retain the old behavior, use either `df[df.columns[i]] = newvals` or, if
> columns are non-unique, `df.isetitem(i, newvals)`
> expected.loc[:, "Cluster"] = expected.Cluster.astype(np.int32)
>
> .pybuild/cpython3_3.11_pyranges/build/tests/test_concat.py::test_concat_stranded_unstranded
> .pybuild/cpython3_3.11_pyranges/build/tests/test_concat.py::test_concat_unstranded_stranded
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/methods/concat.py:47:
> DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will
> attempt to set the values inplace instead of always setting a new array. To
> retain the old behavior, use either `df[df.columns[i]] = newvals` or, if
> columns are non-unique, `df.isetitem(i, newvals)`
> v.loc[:, "Strand"] = type_v.cat.add_categories(["."])
>
> .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same
> .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same
> .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same
> .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same
> .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same
> .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/pyranges/multioverlap.py:155:
> DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will
> attempt to set the values inplace instead of always setting a new array. To
> retain the old behavior, use either `df[df.columns[i]] = newvals` or, if
> columns are non-unique, `df.isetitem(i, newvals)`
> df.loc[:, names] = df[names].astype(np.int32)
>
> .pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 1000 warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:251:
> FutureWarning: The squeeze argument has been deprecated and will be removed
> in a future version. Append .squeeze("columns") to the call to squeeze.
>
>
> bedtools_df = pd.read_csv(
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info
> ============================
> FAILED tests/test_unary.py::test_getitem -
> hypothesis.errors.FailedHealthChec...
> ========== 1 failed, 530 passed, 53245 warnings in 3159.08s (0:52:39)
> ==========
> E: pybuild pybuild:388: test: plugin distutils failed with: exit code=1: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pyranges/build; python3.11 -m pytest
> -n 8
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11
> returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2023/07/24/pyranges_0.0.111+ds-4_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230724;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230724&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: pyranges
Source-Version: 0.0.111+ds-5
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
pyranges, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1042...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated pyranges package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 23 Aug 2023 19:54:31 +0200
Source: pyranges
Architecture: source
Version: 0.0.111+ds-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1042046
Changes:
pyranges (0.0.111+ds-5) unstable; urgency=medium
.
* healthcheck-all.patch: new: fix test failure.
The test failure seems to be caused by a call to an obsoleted method
in a decorator describing the properties of the affected test.
(Closes: #1042046)
* d/control: add myself to uploaders.
* d/rules: use execute_after_dh_* targets in place of overrides.
* d/clean: remove remnants of *.bam* test data.
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pyranges_0.0.111+ds-5.debian.tar.xz
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