--- Begin Message ---
Package: src:python-seqcluster
Version: 1.2.9+ds-3
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary --with python3,sphinxdoc --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
ln -s /usr/share/javascript/jquery-ui/themes/base/jquery-ui.css
misc/css/jquery-ui.css
dh_auto_configure
I: pybuild base:311: python3.12 setup.py config
running config
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
I: pybuild base:311: /usr/bin/python3 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test
copying test/test_database.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test
copying test/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test
copying test/test_preparedata.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test
copying test/test_cluster.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test
copying test/test_automated_analysis.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
copying seqcluster/make_predictions.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
copying seqcluster/install.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
copying seqcluster/explore_cluster.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
copying seqcluster/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
copying seqcluster/command_line.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
copying seqcluster/create_cluster_info.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
copying seqcluster/stats.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
copying seqcluster/create_report.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
copying seqcluster/collapse.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
copying seqcluster/prepare_data.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
copying seqcluster/make_clusters.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster
creating
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function
copying seqcluster/function/target.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function
copying seqcluster/function/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function
copying seqcluster/function/predictions.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function
copying seqcluster/function/rnafold.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function
copying seqcluster/function/peakdetect.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function
copying seqcluster/function/coral.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function
creating
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/html
copying seqcluster/html/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/html
copying seqcluster/html/HTML.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/html
creating
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/classes.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/annotation.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/do.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/parameters.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/fastq.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/expchart.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/mystats.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/pysen.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/tool.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/read.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/utils.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/barchart.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/logger.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/bayes.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/config.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/table.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/sam2bed.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/multimap.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/peaks.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/stats.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/inputs.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/seqviz.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/thinkbayes.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/parse.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/simulator.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
copying seqcluster/libs/report.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs
creating
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/annotate
copying seqcluster/annotate/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/annotate
copying seqcluster/annotate/coral.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/annotate
creating
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates
copying seqcluster/templates/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates
creating
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/seqbuster
copying seqcluster/seqbuster/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/seqbuster
copying seqcluster/seqbuster/snps.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/seqbuster
copying seqcluster/seqbuster/realign.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/seqbuster
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/db
copying seqcluster/db/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/db
creating
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/detect
copying seqcluster/detect/metacluster.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/detect
copying seqcluster/detect/cluster.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/detect
copying seqcluster/detect/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/detect
copying seqcluster/detect/description.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/detect
creating
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/methods
copying seqcluster/methods/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/methods
running egg_info
creating seqcluster.egg-info
writing seqcluster.egg-info/PKG-INFO
writing dependency_links to seqcluster.egg-info/dependency_links.txt
writing entry points to seqcluster.egg-info/entry_points.txt
writing top-level names to seqcluster.egg-info/top_level.txt
writing manifest file 'seqcluster.egg-info/SOURCES.txt'
reading manifest file 'seqcluster.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'seqcluster.egg-info/SOURCES.txt'
copying seqcluster/templates/cluster ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates
copying seqcluster/templates/info.css ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates
copying seqcluster/templates/main ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates
copying seqcluster/templates/report.rmd ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates
copying seqcluster/templates/style.css ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates
PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bman doc/source
build/man # Manpage generator
Running Sphinx v7.3.7
WARNING: Invalid configuration value found: 'language = None'. Update your
configuration to a valid language code. Falling back to 'en' (English).
making output directory... done
WARNING: html_static_path entry '_static' does not exist
myst v3.0.1: MdParserConfig(commonmark_only=False, gfm_only=False,
enable_extensions=set(), disable_syntax=[], all_links_external=False,
links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'),
ref_domains=None, fence_as_directive=set(), number_code_blocks=[],
title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={},
footnote_transition=True, words_per_minute=200, substitutions={},
linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True,
dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True,
mathjax_classes='tex2jax_process|mathjax_process|math|output_area',
enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
building [mo]: targets for 0 po files that are out of date
writing output...
building [man]: all manpages
updating environment: [new config] 14 added, 0 changed, 0 removed
reading sources... [ 7%] citation
reading sources... [ 14%] classes
reading sources... [ 21%] collapse
reading sources... [ 29%] documentation
reading sources... [ 36%] example_pipeline
reading sources... [ 43%] getting_started
reading sources... [ 50%] index
reading sources... [ 57%] installation
reading sources... [ 64%] literature
reading sources... [ 71%] mirna_annotation
reading sources... [ 79%] multi_mapped
reading sources... [ 86%] outputs
reading sources... [ 93%] presentations
reading sources... [100%] tools
/<<PKGBUILDDIR>>/doc/source/classes.rst:8: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.sequence_unique
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:12: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.cluster_info_obj
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:16: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.sequence
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:20: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.position
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:24: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.annotation
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:28: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.dbannotation
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:32: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.cluster
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:36: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.bedaligned
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:40: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.mergealigned
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/collapse.rst:4: WARNING: Title overline too short.
***************
Collapse fastq(.gz) files
***************
/<<PKGBUILDDIR>>/doc/source/documentation.rst:8: ERROR: Unknown directive type
"automodule".
.. automodule:: seqcluster.prepare_data
:members:
:undoc-members:
:private-members:
/<<PKGBUILDDIR>>/doc/source/documentation.rst:13: ERROR: Unknown directive type
"automodule".
.. automodule:: seqcluster.make_clusters
:members:
:undoc-members:
:private-members:
/<<PKGBUILDDIR>>/doc/source/example_pipeline.rst:3: WARNING: Title overline too
short.
***************
Examples of small RNA analysis
***************
/<<PKGBUILDDIR>>/doc/source/example_pipeline.rst:8: WARNING: Title underline
too short.
miRQC data
-------
/<<PKGBUILDDIR>>/doc/source/getting_started.rst:189: WARNING: Bullet list ends
without a blank line; unexpected unindent.
/<<PKGBUILDDIR>>/doc/source/getting_started.rst:194: WARNING: Block quote ends
without a blank line; unexpected unindent.
/<<PKGBUILDDIR>>/doc/source/index.rst:14: WARNING: Title underline too short.
Welcome to seqbuster/seqcluster's documentation!
=====================================
/<<PKGBUILDDIR>>/doc/source/installation.rst:53: WARNING: Title underline too
short.
Tools dependecies for a full small RNA pipeline
---------
/<<PKGBUILDDIR>>/doc/source/installation.rst:53: WARNING: Title underline too
short.
Tools dependecies for a full small RNA pipeline
---------
/<<PKGBUILDDIR>>/doc/source/installation.rst:66: WARNING: Bullet list ends
without a blank line; unexpected unindent.
/<<PKGBUILDDIR>>/doc/source/installation.rst:98: WARNING: Duplicate explicit target name:
"bcbio".
/<<PKGBUILDDIR>>/doc/source/installation.rst:12: ERROR: Duplicate target name, cannot be
used as a unique reference: "bcbio".
/<<PKGBUILDDIR>>/doc/source/installation.rst:61: ERROR: Duplicate target name, cannot be
used as a unique reference: "bcbio".
/<<PKGBUILDDIR>>/doc/source/installation.rst:71: ERROR: Duplicate target name, cannot be
used as a unique reference: "bcbio".
/<<PKGBUILDDIR>>/doc/source/literature.rst:1: WARNING: malformed hyperlink
target.
/<<PKGBUILDDIR>>/doc/source/literature.rst:4: WARNING: Title overline too short.
***************
Relevant papers about isomiRs and other novel small RNAs with functional
relevance
***************
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:4: WARNING: Title overline too
short.
***************
miRNA annotation
***************
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:6: WARNING: Duplicate explicit target
name: "here".
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:138: WARNING: Literal block
expected; none found.
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:142: WARNING: Inline emphasis
start-string without end-string.
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:144: WARNING: Inline emphasis
start-string without end-string.
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:146: WARNING: Inline emphasis
start-string without end-string.
/<<PKGBUILDDIR>>/doc/source/multi_mapped.rst:4: WARNING: Title overline too
short.
***************
Handling multi-mapped reads
***************
/<<PKGBUILDDIR>>/doc/source/presentations.rst:1: WARNING: malformed hyperlink
target.
/<<PKGBUILDDIR>>/doc/source/tools.rst:4: WARNING: Title overline too short.
***************
Tools for downstream analysis
***************
/<<PKGBUILDDIR>>/doc/source/tools.rst:28: WARNING: Title underline too short.
Command-lines
-----------
/<<PKGBUILDDIR>>/doc/source/tools.rst:28: WARNING: Title underline too short.
Command-lines
-----------
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
writing... seqcluster.1 { installation citation getting_started outputs
example_pipeline mirna_annotation collapse multi_mapped tools literature
presentations documentation classes } done
build succeeded, 39 warnings.
The manual pages are in build/man.
PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml doc/source
build/html # HTML generator
Running Sphinx v7.3.7
WARNING: Invalid configuration value found: 'language = None'. Update your
configuration to a valid language code. Falling back to 'en' (English).
making output directory... done
WARNING: html_static_path entry '_static' does not exist
myst v3.0.1: MdParserConfig(commonmark_only=False, gfm_only=False,
enable_extensions=set(), disable_syntax=[], all_links_external=False,
links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'),
ref_domains=None, fence_as_directive=set(), number_code_blocks=[],
title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={},
footnote_transition=True, words_per_minute=200, substitutions={},
linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True,
dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True,
mathjax_classes='tex2jax_process|mathjax_process|math|output_area',
enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 14 source files that are out of date
updating environment: [new config] 14 added, 0 changed, 0 removed
reading sources... [ 7%] citation
reading sources... [ 14%] classes
reading sources... [ 21%] collapse
reading sources... [ 29%] documentation
reading sources... [ 36%] example_pipeline
reading sources... [ 43%] getting_started
reading sources... [ 50%] index
reading sources... [ 57%] installation
reading sources... [ 64%] literature
reading sources... [ 71%] mirna_annotation
reading sources... [ 79%] multi_mapped
reading sources... [ 86%] outputs
reading sources... [ 93%] presentations
reading sources... [100%] tools
/<<PKGBUILDDIR>>/doc/source/classes.rst:8: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.sequence_unique
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:12: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.cluster_info_obj
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:16: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.sequence
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:20: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.position
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:24: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.annotation
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:28: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.dbannotation
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:32: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.cluster
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:36: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.bedaligned
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/classes.rst:40: ERROR: Unknown directive type
"autoclass".
.. autoclass:: seqcluster.libs.classes.mergealigned
:members:
:undoc-members:
/<<PKGBUILDDIR>>/doc/source/collapse.rst:4: WARNING: Title overline too short.
***************
Collapse fastq(.gz) files
***************
/<<PKGBUILDDIR>>/doc/source/documentation.rst:8: ERROR: Unknown directive type
"automodule".
.. automodule:: seqcluster.prepare_data
:members:
:undoc-members:
:private-members:
/<<PKGBUILDDIR>>/doc/source/documentation.rst:13: ERROR: Unknown directive type
"automodule".
.. automodule:: seqcluster.make_clusters
:members:
:undoc-members:
:private-members:
/<<PKGBUILDDIR>>/doc/source/example_pipeline.rst:3: WARNING: Title overline too
short.
***************
Examples of small RNA analysis
***************
/<<PKGBUILDDIR>>/doc/source/example_pipeline.rst:8: WARNING: Title underline
too short.
miRQC data
-------
/<<PKGBUILDDIR>>/doc/source/getting_started.rst:189: WARNING: Bullet list ends
without a blank line; unexpected unindent.
/<<PKGBUILDDIR>>/doc/source/getting_started.rst:194: WARNING: Block quote ends
without a blank line; unexpected unindent.
/<<PKGBUILDDIR>>/doc/source/index.rst:14: WARNING: Title underline too short.
Welcome to seqbuster/seqcluster's documentation!
=====================================
/<<PKGBUILDDIR>>/doc/source/installation.rst:53: WARNING: Title underline too
short.
Tools dependecies for a full small RNA pipeline
---------
/<<PKGBUILDDIR>>/doc/source/installation.rst:53: WARNING: Title underline too
short.
Tools dependecies for a full small RNA pipeline
---------
/<<PKGBUILDDIR>>/doc/source/installation.rst:66: WARNING: Bullet list ends
without a blank line; unexpected unindent.
/<<PKGBUILDDIR>>/doc/source/installation.rst:98: WARNING: Duplicate explicit target name:
"bcbio".
/<<PKGBUILDDIR>>/doc/source/installation.rst:12: ERROR: Duplicate target name, cannot be
used as a unique reference: "bcbio".
/<<PKGBUILDDIR>>/doc/source/installation.rst:61: ERROR: Duplicate target name, cannot be
used as a unique reference: "bcbio".
/<<PKGBUILDDIR>>/doc/source/installation.rst:71: ERROR: Duplicate target name, cannot be
used as a unique reference: "bcbio".
/<<PKGBUILDDIR>>/doc/source/literature.rst:1: WARNING: malformed hyperlink
target.
/<<PKGBUILDDIR>>/doc/source/literature.rst:4: WARNING: Title overline too short.
***************
Relevant papers about isomiRs and other novel small RNAs with functional
relevance
***************
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:4: WARNING: Title overline too
short.
***************
miRNA annotation
***************
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:6: WARNING: Duplicate explicit target
name: "here".
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:138: WARNING: Literal block
expected; none found.
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:142: WARNING: Inline emphasis
start-string without end-string.
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:144: WARNING: Inline emphasis
start-string without end-string.
/<<PKGBUILDDIR>>/doc/source/mirna_annotation.rst:146: WARNING: Inline emphasis
start-string without end-string.
/<<PKGBUILDDIR>>/doc/source/multi_mapped.rst:4: WARNING: Title overline too
short.
***************
Handling multi-mapped reads
***************
/<<PKGBUILDDIR>>/doc/source/presentations.rst:1: WARNING: malformed hyperlink
target.
/<<PKGBUILDDIR>>/doc/source/tools.rst:4: WARNING: Title overline too short.
***************
Tools for downstream analysis
***************
/<<PKGBUILDDIR>>/doc/source/tools.rst:28: WARNING: Title underline too short.
Command-lines
-----------
/<<PKGBUILDDIR>>/doc/source/tools.rst:28: WARNING: Title underline too short.
Command-lines
-----------
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... copying static files... done
copying extra files... done
done
writing output... [ 7%] citation
writing output... [ 14%] classes
writing output... [ 21%] collapse
writing output... [ 29%] documentation
writing output... [ 36%] example_pipeline
writing output... [ 43%] getting_started
writing output... [ 50%] index
writing output... [ 57%] installation
writing output... [ 64%] literature
writing output... [ 71%] mirna_annotation
writing output... [ 79%] multi_mapped
writing output... [ 86%] outputs
writing output... [ 93%] presentations
writing output... [100%] tools
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
/<<PKGBUILDDIR>>/doc/source/index.rst:22: WARNING: toctree contains reference
to document 'presentations' that doesn't have a title: no link will be generated
generating indices... genindex /<<PKGBUILDDIR>>/doc/source/index.rst:22:
WARNING: toctree contains reference to document 'presentations' that doesn't have a title:
no link will be generated
done
writing additional pages... search /<<PKGBUILDDIR>>/doc/source/index.rst:22:
WARNING: toctree contains reference to document 'presentations' that doesn't have a title:
no link will be generated
done
copying images... [ 50%] seqcluster.png
copying images... [100%] logo.png
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 56 warnings.
The HTML pages are in build/html.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo -n "PWD:" /<<PKGBUILDDIR>>
PWD: /<<PKGBUILDDIR>>ln -sf /<<PKGBUILDDIR>>/data
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build
dh_auto_install
I: pybuild base:311: /usr/bin/python3 setup.py install --root
/<<PKGBUILDDIR>>/debian/python3-seqcluster
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66:
SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html
for details.
********************************************************************************
!!
self.initialize_options()
running build
running build_py
running egg_info
writing seqcluster.egg-info/PKG-INFO
writing dependency_links to seqcluster.egg-info/dependency_links.txt
writing entry points to seqcluster.egg-info/entry_points.txt
writing top-level names to seqcluster.egg-info/top_level.txt
reading manifest file 'seqcluster.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'seqcluster.egg-info/SOURCES.txt'
running install_lib
creating /<<PKGBUILDDIR>>/debian/python3-seqcluster
creating /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr
creating /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib
creating /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test/test_database.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test/__init__.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test/test_preparedata.py
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test/test_cluster.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/test
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test/test_automated_analysis.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/test
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/make_predictions.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function/target.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function/__init__.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function/predictions.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function/rnafold.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function/peakdetect.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/function/coral.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/html
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/html/__init__.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/html
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/html/HTML.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/html
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/classes.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/annotation.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/do.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/parameters.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/fastq.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/expchart.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/mystats.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/pysen.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/tool.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/__init__.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/read.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/utils.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/barchart.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/logger.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/bayes.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/config.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/table.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/sam2bed.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/multimap.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/peaks.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/stats.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/inputs.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/seqviz.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/thinkbayes.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/parse.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/simulator.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/libs/report.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/install.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/explore_cluster.py
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/__init__.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/annotate
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/annotate/__init__.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/annotate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/annotate/coral.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/annotate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/command_line.py
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/templates
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates/info.css
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/templates
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates/__init__.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/templates
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates/style.css ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/templates
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates/report.rmd ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/templates
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates/main
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/templates
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/templates/cluster
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/templates
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/seqbuster
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/seqbuster/__init__.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/seqbuster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/seqbuster/snps.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/seqbuster
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/seqbuster/realign.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/seqbuster
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/create_cluster_info.py
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/stats.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/create_report.py
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/db
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/db/__init__.py
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/db
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/collapse.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/prepare_data.py
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/detect
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/detect/metacluster.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/detect
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/detect/cluster.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/detect
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/detect/__init__.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/detect
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/detect/description.py
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/detect
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/make_clusters.py
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/methods
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/seqcluster/methods/__init__.py ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/methods
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/1
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/1/maps.fa
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/1
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/1/maps.html
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/1
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/1/maps.tsv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/1
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/1/info.css
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/1
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/1/maps.png
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/1
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/info.css
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/4
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/4/maps.fa
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/4
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/4/maps.html
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/4
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/4/maps.tsv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/4
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/4/info.css
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/4
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/4/maps.png
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/4
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/3
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/3/maps.fa
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/3
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/3/maps.html
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/3
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/3/maps.tsv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/3
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/3/info.css
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/3
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/3/maps.png
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/3
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/5
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/5/maps.fa
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/5
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/5/maps.html
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/5
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/5/maps.tsv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/5
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/5/info.css
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/5
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/5/maps.png
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/5
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/2
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/2/maps.fa
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/2
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/2/maps.html
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/2
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/2/maps.tsv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/2
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/2/info.css
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/2
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/2/maps.png
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/2
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/index.html
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/6
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/6/maps.html
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/6
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/6/maps.tsv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/6
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/6/info.css
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/6
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples_report/html/6/maps.png
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples_report/html/6
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/pipeline_example
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/pipeline_example/mirqc
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/pipeline_example/mirqc/run.sh
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/pipeline_example/mirqc
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/pipeline_example/mirqc/mirqc_bcbio.csv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/pipeline_example/mirqc
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/pipeline_example/mirqc/download.sh
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/pipeline_example/mirqc
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/pipeline_example/mirqc/template.yaml
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/pipeline_example/mirqc
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/pipeline_example/mirqc/non_mirqc_bcbio.csv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/pipeline_example/mirqc
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/bwt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/bwt/ref.fa ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/bwt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/bwt/ref.fa.fai ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/bwt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/bwt/ref.2.bt2 ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/bwt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/bwt/ref.3.bt2 ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/bwt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/bwt/ref.1.bt2 ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/bwt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/bwt/ref.rev.2.bt2 ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/bwt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/bwt/ref.rev.1.bt2 ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/bwt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/bwt/ref.4.bt2 ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/bwt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/s2.fasta ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/primary_tss
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/primary_tss/saini_hg17.txt.csv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/primary_tss
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/primary_tss/corcoran_hg18.txt.csv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/primary_tss
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/primary_tss/marson_hg17.txt.csv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/primary_tss
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/primary_tss/landgraf_hg17.txt.csv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/primary_tss
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/primary_tss/fujita_hg17.txt.csv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/primary_tss
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/primary_tss/mirstart_2010_prediction.txt.csv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/primary_tss
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/primary_tss/chien_hg19.txt.csv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/primary_tss
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/primary_tss/ozsolak_hg18.txt.csv
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/primary_tss
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/primary_tss/hua_hg19-SP5-global_mir_promoter.bed
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/primary_tss
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/genome.fa.fai
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes/star
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/star/SAindex
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes/star
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/star/chrName.txt
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes/star
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/star/chrLength.txt ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes/star
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/star/chrStart.txt ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes/star
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/star/SA ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes/star
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/star/chrNameLength.txt
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes/star
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/star/genomeParameters.txt
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes/star
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/star/Genome
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes/star
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/Log.out ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/genome.fa ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/genomes/regions.bed
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/genomes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/s1.fasta ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/function
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/function/test_input.txt
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/function
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/function/run.sh
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/function
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/2_clusters_2_seqs_shared
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/miraligner
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/miraligner/run.sh ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/miraligner
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/miraligner/sim_isomir.fa
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/miraligner
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/miraligner/sim_mut.fa
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/miraligner
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/miraligner/hsa.gff3
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/miraligner
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/miraligner/sim_isomir.sam
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/miraligner
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/miraligner/hairpin.fa
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/miraligner
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/miraligner/miRNA.str
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/miraligner
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/miraligner/sim_isomir.fastq
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/miraligner
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/5_clusters_1_sequences
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/collapse
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/collapse/collapse
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/collapse/collapse/Cell_S3_trimmed.fastq
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/collapse/collapse
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/collapse/collapse/Cell_S2_trimmed.fastq
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/collapse/collapse
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/collapse/collapse/Cell_S4_trimmed.fa
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/collapse/collapse
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/collapse/config
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/collapse
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/simulated
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/simulated/run.sh ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/simulated
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/simulated/origin.fa
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/simulated
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/2_clusters_differents
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/umis
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/umis/sample.fastq ->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/umis
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/cluster/run.sh
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/cluster
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/cluster/ann_reduced.gtf
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/cluster
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/cluster/seqs_map.bam
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/cluster
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/cluster/seqs_set.fa
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/cluster
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/cluster/seqs_set.ma
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/cluster
creating
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/map_snp
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/map_snp/hsa_toy.gff3
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/map_snp
copying
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/map_snp/dbsnp_toy.vcf
->
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples/map_snp
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/seqs_set.ma
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data/examples/seqcluster.json
-> /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/data/examples
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/test/test_database.py
to test_database.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/test/__init__.py
to __init__.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/test/test_preparedata.py
to test_preparedata.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/test/test_cluster.py
to test_cluster.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/test/test_automated_analysis.py
to test_automated_analysis.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/make_predictions.py
to make_predictions.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function/target.py
to target.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function/__init__.py
to __init__.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function/predictions.py
to predictions.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function/rnafold.py
to rnafold.cpython-312.pyc
/usr/lib/python3.12/dist-packages/seqcluster/function/rnafold.py:18:
SyntaxWarning: invalid escape sequence '\('
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function/peakdetect.py
to peakdetect.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/function/coral.py
to coral.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/html/__init__.py
to __init__.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/html/HTML.py
to HTML.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/classes.py
to classes.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/annotation.py
to annotation.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/do.py
to do.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/parameters.py
to parameters.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/fastq.py
to fastq.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/expchart.py
to expchart.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/mystats.py
to mystats.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/pysen.py
to pysen.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/tool.py
to tool.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/__init__.py
to __init__.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/read.py
to read.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/utils.py
to utils.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/barchart.py
to barchart.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/logger.py
to logger.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/bayes.py
to bayes.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/config.py
to config.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/table.py
to table.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/sam2bed.py
to sam2bed.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/multimap.py
to multimap.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/peaks.py
to peaks.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/stats.py
to stats.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/inputs.py
to inputs.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/seqviz.py
to seqviz.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/thinkbayes.py
to thinkbayes.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/parse.py
to parse.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/simulator.py
to simulator.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/libs/report.py
to report.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/install.py
to install.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/explore_cluster.py
to explore_cluster.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/__init__.py
to __init__.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/annotate/__init__.py
to __init__.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/annotate/coral.py
to coral.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/command_line.py
to command_line.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/templates/__init__.py
to __init__.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/seqbuster/__init__.py
to __init__.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/seqbuster/snps.py
to snps.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/seqbuster/realign.py
to realign.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/create_cluster_info.py
to create_cluster_info.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/stats.py
to stats.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/create_report.py
to create_report.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/db/__init__.py
to __init__.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/collapse.py
to collapse.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/prepare_data.py
to prepare_data.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/detect/metacluster.py
to metacluster.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/detect/cluster.py
to cluster.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/detect/__init__.py
to __init__.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/detect/description.py
to description.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/make_clusters.py
to make_clusters.cpython-312.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster/methods/__init__.py
to __init__.cpython-312.pyc
running install_egg_info
Copying seqcluster.egg-info to
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/lib/python3.12/dist-packages/seqcluster-1.2.9.egg-info
Skipping SOURCES.txt
running install_scripts
Installing seqcluster script to
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/bin
Installing seqcluster_install script to
/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/bin
sed -i '1s/$/ -d/' /<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/bin/seqcluster
PYBUILD_SYSTEM=custom \
PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/bin:$PATH ; \
cd {build_dir}; export PYTHONPATH=$(pwd):$(build_dir); {interpreter} -m
nose2 \
-q" dh_auto_test
/bin/sh: 3: build_dir: not found
I: pybuild pybuild:308: cp -av /<<PKGBUILDDIR>>/data
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build || true
cp: '/<<PKGBUILDDIR>>/data' and
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/data' are the same file
I: pybuild base:311: cd /<<PKGBUILDDIR>>; export
PATH=/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
; cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build; export
PYTHONPATH=/<<PKGBUILDDIR>>:; python3.12 -m nose2 -q
/usr/lib/python3/dist-packages/Bio/pairwise2.py:278:
BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend
to remove it in a future release of Biopython. As an alternative, please
consider using Bio.Align.PairwiseAligner as a replacement, and contact the
Biopython developers if you still need the Bio.pairwise2 module.
warnings.warn(
/usr/lib/python3/dist-packages/Bio/pairwise2.py:278:
BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend
to remove it in a future release of Biopython. As an alternative, please
consider using Bio.Align.PairwiseAligner as a replacement, and contact the
Biopython developers if you still need the Bio.pairwise2 module.
warnings.warn(
/<<PKGBUILDDIR>>/seqcluster/function/rnafold.py:18: SyntaxWarning: invalid
escape sequence '\('
out = float(re.search(' \((.+)\)', line).group(1))
[32m07/23/2024 03:12:52 AM INFO[0m: Run cluster[0m
[32m07/23/2024 03:12:52 AM INFO[0m: Checking parameters and files[0m
[32m07/23/2024 03:12:52 AM INFO[0m: Output dir will be: test_out_res[0m
[32m07/23/2024 03:12:52 AM INFO[0m: Clean bam file with highly repetitive reads
with low counts. sum(counts)/n_hits > 1%[0m
[32m07/23/2024 03:12:52 AM INFO[0m: Using
../../data/examples/cluster/seqs_map_rmlw.bam file[0m
[32m07/23/2024 03:12:52 AM INFO[0m: Total genome with sequences: 0.774092 [0m
[32m07/23/2024 03:12:52 AM INFO[0m: Parsing matrix file[0m
[32m07/23/2024 03:12:52 AM INFO[0m: counts after: 27393689[0m
[32m07/23/2024 03:12:52 AM INFO[0m: # sequences after: 2139[0m
[32m07/23/2024 03:12:52 AM INFO[0m: Cleaning bam file[0m
[32m07/23/2024 03:12:52 AM INFO[0m: counts after: 27390481[0m
[32m07/23/2024 03:12:52 AM INFO[0m: # sequences after: 2112[0m
[32m07/23/2024 03:12:52 AM INFO[0m: Parsing aligned file[0m
[32m07/23/2024 03:12:52 AM INFO[0m: Merging sequences[0m
[32m07/23/2024 03:12:52 AM INFO[0m: Creating clusters[0m
[32m07/23/2024 03:12:53 AM INFO[0m: 234 Clusters read[0m
[32m07/23/2024 03:12:53 AM INFO[0m: Creating meta-clusters based on shared
sequences: 2112[0m
0% | |
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[32m07/23/2024 03:12:53 AM INFO[0m: 4 metaclusters from 2106 sequences[0m
[32m07/23/2024 03:12:53 AM INFO[0m: 4 clusters found[0m
[32m07/23/2024 03:12:53 AM INFO[0m: counts after: 27390481[0m
[32m07/23/2024 03:12:53 AM INFO[0m: # sequences after: 2112[0m
[32m07/23/2024 03:12:53 AM INFO[0m: Solving multi-mapping events in the
network of clusters[0m
[32m07/23/2024 03:12:53 AM INFO[0m: Number of loci: 234[0m
0% | |
Probably this will fail, you need bcbio-nextgen for many installation functions.
['cluster', '-m', '../../data/examples/cluster/seqs_set.ma', '-a',
'../../data/examples/cluster/seqs_map.bam', '--gtf',
'../../data/examples/cluster/ann_reduced.gtf', '-r',
'../../data/genomes/genome.fa', '-o', 'test_out_res']
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/bin/seqcluster", line 33, in
<module>
sys.exit(load_entry_point('seqcluster==1.2.9', 'console_scripts',
'seqcluster')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/seqcluster/command_line.py", line 28, in main
cluster(kwargs["args"])
File "/<<PKGBUILDDIR>>/seqcluster/make_clusters.py", line 76, in cluster
clusLred = _cleaning(clusL, args.dir_out)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/seqcluster/make_clusters.py", line 294, in _cleaning
clus_obj = reduceloci(clusL, path)
^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/seqcluster/detect/metacluster.py", line 70, in
reduceloci
filtered, n_cluster = _iter_loci(c, clus_obj.clus, (clus_obj.loci,
clus_obj.seq), filtered, n_cluster)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/seqcluster/detect/metacluster.py", line 148, in
_iter_loci
loci_similarity = _calculate_similarity(loci)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/seqcluster/detect/metacluster.py", line 207, in
_calculate_similarity
[ma.update({(idc, idc2): _common(set1, _get_seqs(c[idc2]), idc, idc2)}) for
idc2 in c if idc != idc2 and (idc2, idc) not in ma]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/seqcluster/detect/metacluster.py", line 227, in _common
is_gt = up_threshold(pct, t * 1.0, parameters.similar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/seqcluster/libs/mystats.py", line 11, in up_threshold
elif stat.binom_test(x, s, p) > 0.01:
^^^^^^^^^^^^^^^
AttributeError: module 'scipy.stats' has no attribute 'binom_test'. Did you
mean: 'binomtest'?
======================================================================
ERROR: test_srnaseq_cluster
(test.test_automated_analysis.AutomatedAnalysisTest.test_srnaseq_cluster)
Run cluster analysis
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build/test/test_automated_analysis.py",
line 79, in test_srnaseq_cluster
subprocess.check_call(cl)
File "/usr/lib/python3.12/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['seqcluster', 'cluster', '-m',
'../../data/examples/cluster/seqs_set.ma', '-a',
'../../data/examples/cluster/seqs_map.bam', '--gtf',
'../../data/examples/cluster/ann_reduced.gtf', '-r',
'../../data/genomes/genome.fa', '-o', 'test_out_res']' returned non-zero exit
status 1.
----------------------------------------------------------------------
Ran 6 tests in 2.367s
FAILED (errors=1)
seqcluster cluster -m ../../data/examples/cluster/seqs_set.ma -a
../../data/examples/cluster/seqs_map.bam --gtf
../../data/examples/cluster/ann_reduced.gtf -r ../../data/genomes/genome.fa -o
test_out_res
seqcluster seqbuster --sps hsa --hairpin
../../data/examples/miraligner/hairpin.fa --mirna
../../data/examples/miraligner/miRNA.str --gtf
../../data/examples/miraligner/hsa.gff3 -o test_out_mirs_fasta --miraligner
../../data/examples/miraligner/sim_isomir.fa
E: pybuild pybuild:389: test: plugin custom failed with: exit code=1: cd /<<PKGBUILDDIR>>; export
PATH=/<<PKGBUILDDIR>>/debian/python3-seqcluster/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
; cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_seqcluster/build; export
PYTHONPATH=/<<PKGBUILDDIR>>:; python3.12 -m nose2 -q
dh_auto_test: error: pybuild --test --test-nose2 -i python{version} -p 3.12
returned exit code 13
make[1]: *** [debian/rules:39: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:8: 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/202407/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large 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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
--- End Message ---
pgp5IrvnIg8H4.pgp
