Your message dated Wed, 27 Nov 2024 20:49:17 +0000
with message-id <[email protected]>
and subject line Bug#1049071: fixed in tombo 1.5.1-7
has caused the Debian Bug report #1049071,
regarding tombo: Fails to build source after successful build
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
1049071: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1049071
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: tombo
Version: 1.5.1-4
Severity: minor
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: [email protected]
Usertags: qa-doublebuild
Hi,
This package fails to build a source package after a successful build
(dpkg-buildpackage ; dpkg-buildpackage -S).
This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.
More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/SourceAfterBuild
Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env
> -us -uc -rfakeroot -S
> -----------------------------------------------------------------------------------------------------------------
>
> dpkg-buildpackage: info: source package tombo
> dpkg-buildpackage: info: source version 1.5.1-4
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <[email protected]>
> dpkg-source --before-build .
> debian/rules clean
> dh clean --with python3,sphinxdoc --buildsystem=pybuild
> dh_auto_clean -O--buildsystem=pybuild
> I: pybuild base:275: python3.11 setup.py clean
> running clean
> removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build' (and everything
> under it)
> 'build/bdist.linux-x86_64' does not exist -- can't clean it
> 'build/scripts-3.11' does not exist -- can't clean it
> dh_autoreconf_clean -O--buildsystem=pybuild
> dh_clean -O--buildsystem=pybuild
> dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building tombo using existing ./tombo_1.5.1.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/environment.pickle: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/environment.pickle in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/examples.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/examples.doctree in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/filtering.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/filtering.doctree in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/index.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/index.doctree in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/model_training.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/model_training.doctree in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/modified_base_detection.doctree: binary file contents
> changed
> dpkg-source: error: add docs/build/.doctrees/modified_base_detection.doctree
> in debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/plotting.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/plotting.doctree in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/resquiggle.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/resquiggle.doctree in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/rna.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/rna.doctree in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/text_output.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/text_output.doctree in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/tombo.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/tombo.doctree in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/.doctrees/tutorials.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/tutorials.doctree in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/adaptive_forward_pass.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/adaptive_forward_pass.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/adaptive_half_z_scores.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/adaptive_half_z_scores.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/alt_density_est.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/alt_density_est.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/alt_model_comp.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/alt_model_comp.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/begin_forward_pass.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/begin_forward_pass.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/begin_half_z_scores.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/begin_half_z_scores.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/boxplot.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/boxplot.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/dampened_fraction.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/dampened_fraction.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/density.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/density.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/kmer_levels.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/kmer_levels.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/model_comp.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/model_comp.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/old_correction_plot.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/old_correction_plot.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/outlier_robust_llr.gif: binary file contents changed
> dpkg-source: error: add docs/build/_images/outlier_robust_llr.gif in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/per_read_do_novo.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/per_read_do_novo.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/per_read_stat_dist.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/per_read_stat_dist.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/pre_read_5mC.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/pre_read_5mC.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/quantile.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/quantile.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/roc.png:
> binary file contents changed
> dpkg-source: error: add docs/build/_images/roc.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/sample_comp.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/sample_comp.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/single_samp.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/single_samp.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/stat_dist.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/stat_dist.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/stat_dist_null.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/stat_dist_null.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_images/testing_method_comparison.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/testing_method_comparison.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: file tombo-1.5.1/docs/build/_static/basic.css has no
> final newline (either original or modified version)
> dpkg-source: warning: file
> tombo-1.5.1/docs/build/_static/documentation_options.js has no final newline
> (either original or modified version)
> dpkg-source: error: cannot represent change to docs/build/_static/file.png:
> binary file contents changed
> dpkg-source: error: add docs/build/_static/file.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/Lato-Bold.ttf: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Bold.ttf in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/Lato-Bold.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Bold.woff2 in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/Lato-BoldItalic.ttf: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-BoldItalic.ttf in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/Lato-BoldItalic.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-BoldItalic.woff2 in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/Lato-Italic.ttf: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Italic.ttf in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/Lato-Italic.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Italic.woff2 in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/Lato-Regular.ttf: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Regular.ttf in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/Lato-Regular.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Regular.woff2 in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/RobotoSlab-Bold.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/RobotoSlab-Bold.woff2 in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/RobotoSlab-Regular.woff2: binary file contents
> changed
> dpkg-source: error: add docs/build/_static/fonts/RobotoSlab-Regular.woff2 in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/fontawesome-webfont.eot: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/fontawesome-webfont.eot in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/fontawesome-webfont.ttf: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/fontawesome-webfont.ttf in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/fontawesome-webfont.woff: binary file contents
> changed
> dpkg-source: error: add docs/build/_static/fonts/fontawesome-webfont.woff in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to
> docs/build/_static/fonts/fontawesome-webfont.woff2: binary file contents
> changed
> dpkg-source: error: add docs/build/_static/fonts/fontawesome-webfont.woff2 in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/minus.png:
> binary file contents changed
> dpkg-source: error: add docs/build/_static/minus.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/plus.png:
> binary file contents changed
> dpkg-source: error: add docs/build/_static/plus.png in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: file tombo-1.5.1/docs/build/_static/pygments.css has no
> final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/examples.html has no final
> newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/filtering.html has no final
> newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/genindex.html has no final
> newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/index.html has no final
> newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/model_training.html has no
> final newline (either original or modified version)
> dpkg-source: warning: file
> tombo-1.5.1/docs/build/modified_base_detection.html has no final newline
> (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/objects.inv has no final
> newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/plotting.html has no final
> newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/resquiggle.html has no
> final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/rna.html has no final
> newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/search.html has no final
> newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/searchindex.js has no final
> newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/text_output.html has no
> final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/tombo.html has no final
> newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/tutorials.html has no final
> newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/ont_tombo.egg-info/SOURCES.txt has no
> final newline (either original or modified version)
> dpkg-source: error: unrepresentable changes to source
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 1
>
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage
> --sanitize-env -us -uc -rfakeroot -S' failed to run.
The full build log is available from:
http://qa-logs.debian.net/2023/08/13/tombo_1.5.1-4_unstable.log
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: tombo
Source-Version: 1.5.1-7
Done: Ananthu C V <[email protected]>
We believe that the bug you reported is fixed in the latest version of
tombo, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Ananthu C V <[email protected]> (supplier of updated tombo package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 28 Nov 2024 01:40:55 +0530
Source: tombo
Architecture: source
Version: 1.5.1-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Ananthu C V <[email protected]>
Closes: 1049071 1083801 1087117
Changes:
tombo (1.5.1-7) unstable; urgency=medium
.
* Team upload
* Use execute_after hooks instead of overriding targets
* Remove built doc files from debian source tree after they are installed
* Make sure to clean built files before next build (Closes: #1049071)
* Add patch to use importlib instead of deprecated pkg_resources
(Closes: #1083801)
* Correct patch header metadata
* Add patch to drop distutils usage
* Apply wrap-and-sort
* Fix installed file permissions
* Add patch to remove badges from built docs
* Add patch to fix invalid escape sequence syntax warnings
(Closes: #1087117)
* Bump Standards-Version to 4.7.0 (no changes needed)
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