[Debian-med-packaging] Bug#1116921: tombo: FTBFS with the nocheck build profile
Santiago Vila
sanvila at debian.org
Tue Sep 30 15:55:32 BST 2025
Package: src:tombo
Version: 1.5.1-7
Severity: important
Tags: forky sid ftbfs
User: debian-qa at lists.debian.org
Usertags: ftbfs-nocheck-profile
Dear maintainer:
During a rebuild of all packages in unstable using the nocheck build profile,
your package failed to build.
Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202509/
A wiki page discussing how to reproduce bugs in this category and
possible solutions is available here:
https://wiki.debian.org/qa.debian.org/FTBFS/Nocheck
(It's a wiki, so you are welcome to contribute)
[ Note: This is RC, but I will wait at least two weeks before raising
the severities, there are a lot of gcc-15 and CMake 4 bugs open now ].
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:tombo, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py clean
************************************************************
INSTALLATION ERROR:
Need to install numpy before tombo installation.
This is required in order to get maximum efficincy from cython code optimizations.
To install run:
$ pip install numpy
************************************************************
debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f tombo/_c_dynamic_programming.cpp tombo/_c_helper.cpp
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
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py config
************************************************************
INSTALLATION ERROR:
Need to install numpy before tombo installation.
This is required in order to get maximum efficincy from cython code optimizations.
To install run:
$ pip install numpy
************************************************************
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3 setup.py build
************************************************************
INSTALLATION ERROR:
Need to install numpy before tombo installation.
This is required in order to get maximum efficincy from cython code optimizations.
To install run:
$ pip install numpy
************************************************************
debian/rules execute_after_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
sphinx-build -N -bhtml docs docs/build
Running Sphinx v8.2.3
WARNING: Calling get_html_theme_path is deprecated. If you are calling it to define html_theme_path, you are safe to remove that code.
loading translations [en]... done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 11 source files that are out of date
updating environment: [new config] 11 added, 0 changed, 0 removed
reading sources... [ 9%] examples
reading sources... [ 18%] filtering
reading sources... [ 27%] index
reading sources... [ 36%] model_training
reading sources... [ 45%] modified_base_detection
reading sources... [ 55%] plotting
reading sources... [ 64%] resquiggle
reading sources... [ 73%] rna
reading sources... [ 82%] text_output
reading sources... [ 91%] tombo
reading sources... [100%] tutorials
WARNING: autodoc: failed to import module 'tombo'; the following exception was raised:
['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'tombo'\n"] [autodoc.import_object]
WARNING: autodoc: failed to import module 'resquiggle' from module 'tombo'; the following exception was raised:
['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'tombo'\n"] [autodoc.import_object]
WARNING: autodoc: failed to import module 'tombo_helper' from module 'tombo'; the following exception was raised:
['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'tombo'\n"] [autodoc.import_object]
WARNING: autodoc: failed to import module 'tombo_stats' from module 'tombo'; the following exception was raised:
['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'tombo'\n"] [autodoc.import_object]
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets...
copying static files...
Writing evaluated template result to /<<PKGBUILDDIR>>/docs/build/_static/basic.css
Writing evaluated template result to /<<PKGBUILDDIR>>/docs/build/_static/language_data.js
Writing evaluated template result to /<<PKGBUILDDIR>>/docs/build/_static/documentation_options.js
Writing evaluated template result to /<<PKGBUILDDIR>>/docs/build/_static/js/versions.js
copying static files: done
copying extra files...
copying extra files: done
copying assets: done
writing output... [ 9%] examples
writing output... [ 18%] filtering
writing output... [ 27%] index
writing output... [ 36%] model_training
writing output... [ 45%] modified_base_detection
writing output... [ 55%] plotting
writing output... [ 64%] resquiggle
writing output... [ 73%] rna
writing output... [ 82%] text_output
writing output... [ 91%] tombo
writing output... [100%] tutorials
generating indices... genindex done
highlighting module code...
writing additional pages... search done
copying images... [ 4%] _images/testing_method_comparison.png
copying images... [ 9%] _images/alt_density_est.png
copying images... [ 13%] _images/old_correction_plot.png
copying images... [ 17%] _images/outlier_robust_llr.gif
copying images... [ 22%] _images/dampened_fraction.png
copying images... [ 26%] _images/single_samp.png
copying images... [ 30%] _images/sample_comp.png
copying images... [ 35%] _images/model_comp.png
copying images... [ 39%] _images/alt_model_comp.png
copying images... [ 43%] _images/boxplot.png
copying images... [ 48%] _images/quantile.png
copying images... [ 52%] _images/density.png
copying images... [ 57%] _images/pre_read_5mC.png
copying images... [ 61%] _images/per_read_do_novo.png
copying images... [ 65%] _images/stat_dist.png
copying images... [ 70%] _images/kmer_levels.png
copying images... [ 74%] _images/roc.png
copying images... [ 78%] _images/per_read_stat_dist.png
copying images... [ 83%] _images/begin_half_z_scores.png
copying images... [ 87%] _images/begin_forward_pass.png
copying images... [ 91%] _images/adaptive_half_z_scores.png
copying images... [ 96%] _images/adaptive_forward_pass.png
copying images... [100%] _images/stat_dist_null.png
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 5 warnings.
The HTML pages are in docs/build.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh: command-omitted: The call to "dh_auto_test -O--buildsystem=pybuild" was omitted due to "DEB_BUILD_OPTIONS=nocheck"
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
dh_prep -O--buildsystem=pybuild
dh_auto_install -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/tmp
************************************************************
INSTALLATION ERROR:
Need to install numpy before tombo installation.
This is required in order to get maximum efficincy from cython code optimizations.
To install run:
$ pip install numpy
************************************************************
dh_install -O--buildsystem=pybuild
dh_install: warning: Cannot find (any matches for) "usr" (tried in ., debian/tmp)
dh_install: warning: tombo missing files: usr
dh_install: error: missing files, aborting
make: *** [debian/rules:9: binary] Error 255
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
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