Package: src:snakemake
Version: 7.32.4-6
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
find . -name '__pycache__' | xargs -r rm -r
rm -rf .snakemake snakemake.egg-info
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --with python3,sphinxdoc --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
[... snipped ...]
reading sources... [ 13%] executing/grouping
reading sources... [ 16%] executing/interoperability
reading sources... [ 18%] executing/monitoring
reading sources... [ 21%] executor_tutorial/azure_aks
reading sources... [ 24%] executor_tutorial/azure_batch
reading sources... [ 26%] executor_tutorial/flux
reading sources... [ 29%] executor_tutorial/google_lifesciences
reading sources... [ 32%] executor_tutorial/tutorial
reading sources... [ 34%] getting_started/installation
reading sources... [ 37%] index
reading sources... [ 39%] project_info/authors
reading sources... [ 42%] project_info/citations
reading sources... [ 45%] project_info/contributing
reading sources... [ 47%] project_info/faq
reading sources... [ 50%] project_info/history
reading sources... [ 53%] project_info/license
reading sources... [ 55%] project_info/more_resources
reading sources... [ 58%] snakefiles/best_practices
reading sources... [ 61%] snakefiles/configuration
reading sources... [ 63%] snakefiles/deployment
reading sources... [ 66%] snakefiles/foreign_wms
reading sources... [ 68%] snakefiles/modularization
reading sources... [ 71%] snakefiles/remote_files
reading sources... [ 74%] snakefiles/reporting
reading sources... [ 76%] snakefiles/rules
reading sources... [ 79%] snakefiles/testing
reading sources... [ 82%] snakefiles/utils
reading sources... [ 84%] snakefiles/writing_snakefiles
reading sources... [ 87%] tutorial/additional_features
reading sources... [ 89%] tutorial/advanced
reading sources... [ 92%] tutorial/basics
reading sources... [ 95%] tutorial/setup
reading sources... [ 97%] tutorial/short
reading sources... [100%] tutorial/tutorial
/<<PKGBUILDDIR>>/docs/executing/cli.rst:174: CRITICAL: Title level inconsistent:
Use templating in profiles
~~~~~~~~~~~~~~~~~~~~~~~~~~ [docutils]
/<<PKGBUILDDIR>>/docs/executing/cli.rst:227: ERROR: Unknown directive type
"argparse".
.. argparse::
:module: snakemake
:func: get_argument_parser
:prog: snakemake
All command line options can be printed by calling ``snakemake -h``.
[docutils]
/<<PKGBUILDDIR>>/docs/executing/cli.rst:111: WARNING: duplicate label profiles,
other instance in /<<PKGBUILDDIR>>/docs/executing/cli.rst
[autosectionlabel.executing/cli]
/<<PKGBUILDDIR>>/docs/executing/cloud.rst:233: WARNING: duplicate label machine
types, other instance in /<<PKGBUILDDIR>>/docs/executing/cloud.rst
[autosectionlabel.executing/cloud]
/<<PKGBUILDDIR>>/docs/executing/cloud.rst:490: WARNING: duplicate label
execution, other instance in /<<PKGBUILDDIR>>/docs/executing/cloud.rst
[autosectionlabel.executing/cloud]
/<<PKGBUILDDIR>>/docs/executing/cluster.rst:13: WARNING: Title overline too
short.
--------------
Executing on SLURM clusters
-------------- [docutils]
/<<PKGBUILDDIR>>/docs/executing/monitoring.rst:5: WARNING: duplicate label
monitoring, other instance in /<<PKGBUILDDIR>>/docs/executing/monitoring.rst
[autosectionlabel.executing/monitoring]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_aks.rst:184: ERROR: Unexpected
indentation. [docutils]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst:47: WARNING: Title
underline too short.
Create an Azure Storage Account and upload example data
::::::::::::::::::::::::::::::::::::::::::::::: [docutils]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst:47: WARNING: Title
underline too short.
Create an Azure Storage Account and upload example data
::::::::::::::::::::::::::::::::::::::::::::::: [docutils]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst:119: WARNING: Title
underline too short.
Azure Blob Storage Warning:
::::::::::::::::::: [docutils]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst:119: WARNING: Title
underline too short.
Azure Blob Storage Warning:
::::::::::::::::::: [docutils]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst:367: WARNING: Title
underline too short.
Defining a Start Task
::::: [docutils]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst:367: WARNING: Title
underline too short.
Defining a Start Task
::::: [docutils]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst:386: WARNING: Title
underline too short.
Autoscaling and Task Distribution
::::: [docutils]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst:386: WARNING: Title
underline too short.
Autoscaling and Task Distribution
::::: [docutils]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst:28: WARNING: duplicate
label setup, other instance in
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_aks.rst
[autosectionlabel.executor_tutorial/azure_batch]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst:163: WARNING: duplicate
label running the workflow, other instance in
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_aks.rst
[autosectionlabel.executor_tutorial/azure_batch]
/<<PKGBUILDDIR>>/docs/executor_tutorial/flux.rst:13: WARNING: duplicate label
setup, other instance in
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst
[autosectionlabel.executor_tutorial/flux]
/<<PKGBUILDDIR>>/docs/executor_tutorial/google_lifesciences.rst:13: WARNING:
duplicate label setup, other instance in
/<<PKGBUILDDIR>>/docs/executor_tutorial/flux.rst
[autosectionlabel.executor_tutorial/google_lifesciences]
/<<PKGBUILDDIR>>/docs/index.rst:5: WARNING: Duplicate explicit target name:
"bioconda". [docutils]
/<<PKGBUILDDIR>>/docs/index.rst:: WARNING: duplicate label execution, other
instance in /<<PKGBUILDDIR>>/docs/executing/cloud.rst
/<<PKGBUILDDIR>>/docs/index.rst:64: WARNING: duplicate label resources, other
instance in /<<PKGBUILDDIR>>/docs/executor_tutorial/flux.rst
[autosectionlabel.index]
/<<PKGBUILDDIR>>/docs/project_info/faq.rst:5: WARNING: Duplicate explicit
target name: "here". [docutils]
/<<PKGBUILDDIR>>/docs/project_info/faq.rst:5: WARNING: Duplicate explicit
target name: "here". [docutils]
/<<PKGBUILDDIR>>/docs/project_info/faq.rst:5: WARNING: Duplicate explicit
target name: "here". [docutils]
/<<PKGBUILDDIR>>/docs/project_info/faq.rst:5: WARNING: Duplicate explicit
target name: "here". [docutils]
/<<PKGBUILDDIR>>/docs/project_info/faq.rst:5: WARNING: Duplicate explicit
target name: "here". [docutils]
/<<PKGBUILDDIR>>/docs/project_info/faq.rst:688: WARNING: Title underline too
short.
How can I avoid system /tmp to be used when combining singularity and conda?
------------------------------------------------------ [docutils]
/<<PKGBUILDDIR>>/docs/project_info/faq.rst:688: WARNING: Title underline too
short.
How can I avoid system /tmp to be used when combining singularity and conda?
------------------------------------------------------ [docutils]
/<<PKGBUILDDIR>>/docs/snakefiles/best_practices.rst:5: WARNING: Duplicate
explicit target name: "here". [docutils]
/<<PKGBUILDDIR>>/docs/snakefiles/configuration.rst:55: WARNING: malformed
hyperlink target. [docutils]
/<<PKGBUILDDIR>>/docs/snakefiles/configuration.rst:5: WARNING: duplicate label
configuration, other instance in /<<PKGBUILDDIR>>/docs/executing/cloud.rst
[autosectionlabel.snakefiles/configuration]
/<<PKGBUILDDIR>>/docs/snakefiles/configuration.rst:77: WARNING: duplicate label
environment variables, other instance in
/<<PKGBUILDDIR>>/docs/executing/cloud.rst
[autosectionlabel.snakefiles/configuration]
/<<PKGBUILDDIR>>/docs/snakefiles/modularization.rst:7: WARNING: Duplicate
explicit target name: "cwl". [docutils]
/<<PKGBUILDDIR>>/docs/snakefiles/remote_files.rst:653: WARNING: Inline literal
start-string without end-string. [docutils]
/<<PKGBUILDDIR>>/docs/snakefiles/reporting.rst:5: WARNING: Duplicate explicit
target name: "here". [docutils]
/<<PKGBUILDDIR>>/docs/snakefiles/reporting.rst:5: WARNING: Duplicate explicit
target name: "here". [docutils]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:5: WARNING: Duplicate explicit
target name: "humanfriendly package". [docutils]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:5: WARNING: Duplicate explicit
target name: "here". [docutils]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:1262: WARNING: malformed hyperlink
target. [docutils]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:330: WARNING: duplicate label
resources, other instance in /<<PKGBUILDDIR>>/docs/index.rst
[autosectionlabel.snakefiles/rules]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:1396: WARNING: duplicate label job
properties, other instance in /<<PKGBUILDDIR>>/docs/executing/cluster.rst
[autosectionlabel.snakefiles/rules]
/<<PKGBUILDDIR>>/docs/tutorial/additional_features.rst:73: WARNING: duplicate
label modularization, other instance in
/<<PKGBUILDDIR>>/docs/snakefiles/modularization.rst
[autosectionlabel.tutorial/additional_features]
/<<PKGBUILDDIR>>/docs/tutorial/additional_features.rst:198: WARNING: duplicate
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/<<PKGBUILDDIR>>/docs/executing/cluster.rst
[autosectionlabel.tutorial/additional_features]
/<<PKGBUILDDIR>>/docs/tutorial/advanced.rst:82: WARNING: duplicate label
exercise, other instance in
/<<PKGBUILDDIR>>/docs/tutorial/additional_features.rst
[autosectionlabel.tutorial/advanced]
/<<PKGBUILDDIR>>/docs/tutorial/advanced.rst:177: WARNING: duplicate label
exercise, other instance in /<<PKGBUILDDIR>>/docs/tutorial/advanced.rst
[autosectionlabel.tutorial/advanced]
/<<PKGBUILDDIR>>/docs/tutorial/advanced.rst:213: WARNING: duplicate label
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[autosectionlabel.tutorial/advanced]
/<<PKGBUILDDIR>>/docs/tutorial/advanced.rst:250: WARNING: duplicate label
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[autosectionlabel.tutorial/advanced]
/<<PKGBUILDDIR>>/docs/tutorial/advanced.rst:304: WARNING: duplicate label
exercise, other instance in /<<PKGBUILDDIR>>/docs/tutorial/advanced.rst
[autosectionlabel.tutorial/advanced]
/<<PKGBUILDDIR>>/docs/tutorial/basics.rst:303: WARNING: duplicate label
exercise, other instance in /<<PKGBUILDDIR>>/docs/tutorial/advanced.rst
[autosectionlabel.tutorial/basics]
/<<PKGBUILDDIR>>/docs/tutorial/basics.rst:381: WARNING: duplicate label
exercise, other instance in /<<PKGBUILDDIR>>/docs/tutorial/basics.rst
[autosectionlabel.tutorial/basics]
/<<PKGBUILDDIR>>/docs/tutorial/basics.rst:492: WARNING: duplicate label
exercise, other instance in /<<PKGBUILDDIR>>/docs/tutorial/basics.rst
[autosectionlabel.tutorial/basics]
/<<PKGBUILDDIR>>/docs/tutorial/basics.rst:500: WARNING: duplicate label
summary, other instance in /<<PKGBUILDDIR>>/docs/tutorial/advanced.rst
[autosectionlabel.tutorial/basics]
/<<PKGBUILDDIR>>/docs/tutorial/setup.rst:5: WARNING: duplicate label setup,
other instance in
/<<PKGBUILDDIR>>/docs/executor_tutorial/google_lifesciences.rst
[autosectionlabel.tutorial/setup]
/<<PKGBUILDDIR>>/docs/tutorial/short.rst:344: WARNING: duplicate label threads,
other instance in /<<PKGBUILDDIR>>/docs/snakefiles/rules.rst
[autosectionlabel.tutorial/short]
/<<PKGBUILDDIR>>/docs/tutorial/short.rst:376: WARNING: duplicate label step 2,
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[autosectionlabel.tutorial/short]
/<<PKGBUILDDIR>>/docs/tutorial/short.rst:396: WARNING: duplicate label step 3,
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[autosectionlabel.tutorial/short]
/<<PKGBUILDDIR>>/docs/tutorial/short.rst:416: WARNING: duplicate label step 4,
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[autosectionlabel.tutorial/short]
/<<PKGBUILDDIR>>/docs/tutorial/short.rst:435: WARNING: duplicate label step 5,
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[autosectionlabel.tutorial/short]
/<<PKGBUILDDIR>>/docs/tutorial/short.rst:457: WARNING: duplicate label step 6,
other instance in /<<PKGBUILDDIR>>/docs/tutorial/short.rst
[autosectionlabel.tutorial/short]
/<<PKGBUILDDIR>>/docs/tutorial/short.rst:476: WARNING: duplicate label step 7,
other instance in /<<PKGBUILDDIR>>/docs/tutorial/short.rst
[autosectionlabel.tutorial/short]
/<<PKGBUILDDIR>>/docs/tutorial/short.rst:492: WARNING: duplicate label step 8,
other instance in /<<PKGBUILDDIR>>/docs/tutorial/short.rst
[autosectionlabel.tutorial/short]
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets...
copying downloadable files... [ 50%] tests/test_report/custom-stylesheet.css
copying downloadable files... [100%]
tests/test_report/expected-results/report.html
copying static files...
Writing evaluated template result to
/<<PKGBUILDDIR>>/docs/_build/html/_static/documentation_options.js
Writing evaluated template result to
/<<PKGBUILDDIR>>/docs/_build/html/_static/basic.css
Writing evaluated template result to
/<<PKGBUILDDIR>>/docs/_build/html/_static/language_data.js
Writing evaluated template result to
/<<PKGBUILDDIR>>/docs/_build/html/_static/js/versions.js
copying static files: done
copying extra files...
copying extra files: done
copying assets: done
writing output... [ 3%] executing/caching
writing output... [ 5%] executing/cli
writing output... [ 8%] executing/cloud
writing output... [ 11%] executing/cluster
writing output... [ 13%] executing/grouping
writing output... [ 16%] executing/interoperability
writing output... [ 18%] executing/monitoring
writing output... [ 21%] executor_tutorial/azure_aks
writing output... [ 24%] executor_tutorial/azure_batch
writing output... [ 26%] executor_tutorial/flux
writing output... [ 29%] executor_tutorial/google_lifesciences
writing output... [ 32%] executor_tutorial/tutorial
writing output... [ 34%] getting_started/installation
writing output... [ 37%] index
writing output... [ 39%] project_info/authors
writing output... [ 42%] project_info/citations
writing output... [ 45%] project_info/contributing
writing output... [ 47%] project_info/faq
writing output... [ 50%] project_info/history
writing output... [ 53%] project_info/license
writing output... [ 55%] project_info/more_resources
writing output... [ 58%] snakefiles/best_practices
writing output... [ 61%] snakefiles/configuration
writing output... [ 63%] snakefiles/deployment
writing output... [ 66%] snakefiles/foreign_wms
writing output... [ 68%] snakefiles/modularization
writing output... [ 71%] snakefiles/remote_files
writing output... [ 74%] snakefiles/reporting
writing output... [ 76%] snakefiles/rules
writing output... [ 79%] snakefiles/testing
writing output... [ 82%] snakefiles/utils
writing output... [ 84%] snakefiles/writing_snakefiles
writing output... [ 87%] tutorial/additional_features
writing output... [ 89%] tutorial/advanced
writing output... [ 92%] tutorial/basics
writing output... [ 95%] tutorial/setup
writing output... [ 97%] tutorial/short
writing output... [100%] tutorial/tutorial
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/executing/cluster.rst:65: WARNING: undefined label:
'snakefiles-mpi' [ref.ref]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/executor_tutorial/azure_batch.rst:266: WARNING: Lexing
literal_block '# required env variables\nexport
AZ_BLOB_PREFIX=snakemake-tutorial\nexport
AZ_BATCH_ACCOUNT_URL="${batch_account_url}"\nexport
AZ_BATCH_ACCOUNT_KEY="${az_batch_account_key}"\nexport
AZ_BLOB_ACCOUNT_URL="${storage_account_url_with_sas}"\n\n# optional environment
variables with defaults listed\n\n# network and identity\n# export
BATCH_POOL_SUBNET_ID=\n# export BATCH_MANAGED_IDENTITY_RESOURCE_ID=\n# export
BATCH_MANAGED_IDENTITY_CLIENT_ID=\n\n# if unset, default is "classic"\n# export
BATCH_NODE_COMMUNICATION_SIMPLIFIED=true\n\n# don\'t recommend changing\n#
export BATCH_POOL_IMAGE_PUBLISHER=microsoft-azure-batch\n# export
BATCH_POOL_IMAGE_OFFER=ubuntu-server-container\n# export
BATCH_POOL_IMAGE_SKU=20-04-lts\n# export
BATCH_POOL_RESOURCE_FILE_PREFIX=resource-files\n\n# export
BATCH_POOL_VM_CONTAINER_IMAGE=ubuntu\n# export
BATCH_POOL_VM_NODE_AGENT_SKU_ID="batch.node.ubuntu 20.04"\n\n# can be used
to add a startup task to the batch nodes formatted as an sas url to a bash
script\n# export BATCH_NODE_START_TASK_SAS_URL=\n\n# can be useful to alter
task distribution across nodes\n\n# export BATCH_POOL_VM_SIZE=Standard_D2_v3\n#
export BATCH_NODE_FILL_TYPE=spread\n# export BATCH_POOL_NODE_COUNT=1\n# export
BATCH_TASKS_PER_NODE=1\n\n# container registry configuration to pull container
image from custom registry\n# export BATCH_CONTAINER_REGISTRY_URL=\n# export
BATCH_CONTAINER_REGISTRY_USER=\n# export
BATCH_CONTAINER_REGISTRY_PASS=\n\nsnakemake \\\n --jobs 3 \\\n -rpf
--verbose --default-remote-prefix $AZ_BLOB_PREFIX \\\n --use-conda \\\n
--default-remote-provider AzBlob \\\n --envvars AZ_BLOB_ACCOUNT_URL \\\n
--az-batch \\\n --container-image snakemake/snakemake \\\n
--az-batch-account-url $AZ_BATCH_ACCOUNT_URL' as "console" resulted in an error
at token: "'". Retrying in relaxed mode. [misc.highlighting_failure]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:45: WARNING: undefined label: 'changelog'
[ref.ref]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
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generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/snakefiles/best_practices.rst:22: WARNING: undefined
label: 'snakefiles_tabular_configuration' [ref.ref]
/<<PKGBUILDDIR>>/docs/snakefiles/best_practices.rst:22: WARNING: undefined
label: 'snakefiles_peps' [ref.ref]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/snakefiles/configuration.rst:35: WARNING: undefined
label: 'api_reference_snakemake' [ref.ref]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/snakefiles/foreign_wms.rst:30: WARNING: undefined label:
'snakefiles-local-rule' [ref.ref]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:316: WARNING: undefined label:
'user_manual-snakemake_options' [ref.ref]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:412: WARNING: undefined label:
'user_manual-snakemake_options' [ref.ref]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:433: WARNING: undefined label:
'resources_remote_execution' [ref.ref]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:441: WARNING: undefined label:
'resources_remote_execution' [ref.ref]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:1108: WARNING: undefined label:
'snakefiles_external-scripts' [ref.ref]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:1296: WARNING: undefined label:
'snakefiles_input-functions' [ref.ref]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:1368: WARNING: undefined label:
'snakefiles_ensure' [ref.ref]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:1957: WARNING: undefined label:
'job-grouping' [ref.ref]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:1957: WARNING: undefined label:
'job-grouping' [ref.ref]
/<<PKGBUILDDIR>>/docs/snakefiles/rules.rst:2420: WARNING: Pygments lexer name
'jinja2' is not known
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/snakefiles/utils.rst:7: WARNING: undefined label:
'utils-api' [ref.ref]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/tutorial/basics.rst:394: WARNING: undefined label: '..
_snakefiles-rules' [ref.ref]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
/<<PKGBUILDDIR>>/docs/index.rst:134: WARNING: toctree contains reference to
document 'project_info/history' that doesn't have a title: no link will be
generated [toc.no_title]
generating indices... genindex /<<PKGBUILDDIR>>/docs/index.rst:134: WARNING:
toctree contains reference to document 'project_info/history' that doesn't have
a title: no link will be generated [toc.no_title]
done
highlighting module code...
writing additional pages... search /<<PKGBUILDDIR>>/docs/index.rst:134:
WARNING: toctree contains reference to document 'project_info/history' that
doesn't have a title: no link will be generated [toc.no_title]
done
copying images... [ 14%] executor_tutorial/workflow/upload-google-storage.png
copying images... [ 29%] executor_tutorial/workflow/quals.svg
copying images... [ 43%] executor_tutorial/workflow/results-google-storage.png
copying images... [ 57%] project_info/img/idea.png
copying images... [ 71%] snakefiles/images/snakemake-notebook-demo.gif
copying images... [ 86%] tutorial/workflow/dag_index.png
copying images... [100%] tutorial/workflow/dag_call.png
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 122 warnings.
The HTML pages are in _build/html.
Build finished. The HTML pages are in _build/html.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/docs'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
. /etc/profile.d/modules.sh && PYBUILD_SYSTEM=custom dh_auto_test
I: pybuild pybuild:308: chmod +x /<<PKGBUILDDIR>>/bin/snakemake; cp -r
/<<PKGBUILDDIR>>/bin /<<PKGBUILDDIR>>/tests
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_snakemake/build
I: pybuild base:311: python3.13 -m pytest -o faulthandler_timeout=60 -v
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_snakemake/build/tests/test*.py -k 'not
test_cwl and not test_cwl_singularity and not test_url_include and not
test_wrapper and not test_issue1083 and not test_github_issue78 and not
test_container and not test_singularity and not test_singularity_conda and not
test_convert_to_cwl and not test_report and not test_report_zip and not
test_archive and not test_jupyter_notebook and not test_conda and not
test_upstream_conda and not test_conda_custom_prefix and not test_script and
not test_issue635 and not test_issue1093 and not test_default_resources and not
test_default_remote and not test_remote and not test_output_file_cache_remote
and not test_tibanna and not test_module_complex and not test_module_complex2
and not test_module_with_script and not test_module_report and not
test_modules_meta_wrapper and not test_tes and not test_deploy_script and not
test_deploy_hashing and n
ot test_peppy and not test_modules_peppy and not test_report_display_code and
not test_wrapper_local_git_prefix and not test_github_issue1396 and not
test_az_batch_executor and not test_modules_prefix and not test_ancient and not
test_github_issue1062 and not test_symlink_time_handling and not
test_env_modules and not test_github_issue1460 and not
test_rule_inheritance_globals and not test_prebuilt_conda_script and not
test_persistent_dict and not test_issue328'
============================= test session starts ==============================
platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 --
/usr/bin/python3.13
cachedir: .pytest_cache
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_snakemake/build
configfile: pyproject.toml
plugins: mock-3.14.0, typeguard-4.4.1, requests_mock-1.12.1
collecting ... collected 395 items / 92 deselected / 303 selected
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[ 13%]
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[ 30%]
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Timeout (0:01:00)!
Thread 0x00007fb78effd6c0 (most recent call first):
File "/usr/lib/python3.13/selectors.py", line 452 in select
File "/usr/lib/python3.13/asyncio/base_events.py", line 2002 in _run_once
File "/usr/lib/python3.13/asyncio/base_events.py", line 683 in run_forever
File "/usr/lib/python3.13/asyncio/base_events.py", line 712 in
run_until_complete
File "/usr/lib/python3.13/asyncio/runners.py", line 118 in run
File "/usr/lib/python3.13/asyncio/runners.py", line 195 in run
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_snakemake/build/snakemake/executors/__init__.py",
line 886 in _wait_thread
File "/usr/lib/python3.13/threading.py", line 992 in run
File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner
File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap
Thread 0x00007fb7a9ffb6c0 (most recent call first):
File "/usr/lib/python3.13/contextlib.py", line 115 in __init__
File Segmentation fault
E: pybuild pybuild:389: test: plugin custom failed with: exit code=139:
python3.13 -m pytest -o faulthandler_timeout=60 -v
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_snakemake/build/tests/test*.py -k 'not
test_cwl and not test_cwl_singularity and not test_url_include and not
test_wrapper and not test_issue1083 and not test_github_issue78 and not
test_container and not test_singularity and not test_singularity_conda and not
test_convert_to_cwl and not test_report and not test_report_zip and not
test_archive and not test_jupyter_notebook and not test_conda and not
test_upstream_conda and not test_conda_custom_prefix and not test_script and
not test_issue635 and not test_issue1093 and not test_default_resources and not
test_default_remote and not test_remote and not test_output_file_cache_remote
and not test_tibanna and not test_module_complex and not test_module_complex2
and not test_module_with_script and not test_module_report and not
test_modules_meta_wrapper and not test_tes and not t
est_deploy_script and not test_deploy_hashing and not test_peppy and not
test_modules_peppy and not test_report_display_code and not
test_wrapper_local_git_prefix and not test_github_issue1396 and not
test_az_batch_executor and not test_modules_prefix and not test_ancient and not
test_github_issue1062 and not test_symlink_time_handling and not
test_env_modules and not test_github_issue1460 and not
test_rule_inheritance_globals and not test_prebuilt_conda_script and not
test_persistent_dict and not test_issue328'
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13
returned exit code 13
make[1]: *** [debian/rules:60: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:47: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202502/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:snakemake, so that this is still
visible in the BTS web page for this package.
Thanks.
