Your message dated Tue, 03 Mar 2026 13:20:21 +0000
with message-id <[email protected]>
and subject line Bug#1044832: fixed in fastml 3.11-5
has caused the Debian Bug report #1044832,
regarding fastml: 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.
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--
1044832: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1044832
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: fastml
Version: 3.11-3
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 fastml
> dpkg-buildpackage: info: source version 3.11-3
> 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
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> make -j8 clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> cd libs;make clean
> cd programs;make clean
> make[3]: Entering directory '/<<PKGBUILDDIR>>/libs'
> make[3]: Entering directory '/<<PKGBUILDDIR>>/programs'
> cd fastml && make clean
> cd phylogeny && make clean
> cd gainLoss && make clean
> cd indelCoder && make clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/fastml'
> rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug
> fastml.doubleRep *.o
> make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/gainLoss'
> rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss
> gainLoss.debug gainLoss.doubleRep *.o
> make[4]: Entering directory '/<<PKGBUILDDIR>>/libs/phylogeny'
> rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o
> make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/indelCoder'
> rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a
> indelCoder indelCoder.debug indelCoder.doubleRep *.o
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/indelCoder'
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/fastml'
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/gainLoss'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs'
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/libs/phylogeny'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/libs'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f libs/phylogeny/make.dep \
> programs/fastml/make.dep \
> programs/gainLoss/make.dep \
> programs/indelCoder/make.dep
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_clean
> dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building fastml using existing ./fastml_3.11.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file programs/gainLoss/make.dep,
> use --include-removal to override
> dpkg-source: warning: ignoring deletion of file programs/indelCoder/make.dep,
> use --include-removal to override
> dpkg-source: warning: ignoring deletion of file programs/fastml/make.dep, use
> --include-removal to override
> dpkg-source: warning: ignoring deletion of file libs/phylogeny/#Makefile#,
> use --include-removal to override
> dpkg-source: warning: ignoring deletion of file libs/phylogeny/make.dep, use
> --include-removal to override
> dpkg-source: error: cannot represent change to bin/fastml: binary file
> contents changed
> dpkg-source: error: add bin/fastml in debian/source/include-binaries if you
> want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'bin/fastml' will not be
> represented in diff
> dpkg-source: error: cannot represent change to bin/gainLoss: binary file
> contents changed
> dpkg-source: error: add bin/gainLoss in debian/source/include-binaries if you
> want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'bin/gainLoss' will not be
> represented in diff
> dpkg-source: error: cannot represent change to bin/indelCoder: binary file
> contents changed
> dpkg-source: error: add bin/indelCoder in debian/source/include-binaries if
> you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'bin/indelCoder' will not be
> represented in diff
> dpkg-source: error: cannot represent change to
> libs/phylogeny/tests/checkTreeLikelihoodGivenBranches: binary file contents
> changed
> dpkg-source: error: add libs/phylogeny/tests/checkTreeLikelihoodGivenBranches
> in debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: executable mode 0755 of
> 'libs/phylogeny/tests/checkTreeLikelihoodGivenBranches' will not be
> represented in diff
> dpkg-source: error: cannot represent change to
> libs/phylogeny/tests/doubleRep: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/doubleRep in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: executable mode 0755 of
> 'libs/phylogeny/tests/doubleRep' will not be represented in diff
> dpkg-source: error: cannot represent change to
> libs/phylogeny/tests/given2seqEstimateTheDistBetweenThem: binary file
> contents changed
> dpkg-source: error: add
> libs/phylogeny/tests/given2seqEstimateTheDistBetweenThem in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: executable mode 0755 of
> 'libs/phylogeny/tests/given2seqEstimateTheDistBetweenThem' will not be
> represented in diff
> dpkg-source: error: cannot represent change to
> libs/phylogeny/tests/given2seqEstimateTheDistBetweenThemGamma: binary file
> contents changed
> dpkg-source: error: add
> libs/phylogeny/tests/given2seqEstimateTheDistBetweenThemGamma in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: executable mode 0755 of
> 'libs/phylogeny/tests/given2seqEstimateTheDistBetweenThemGamma' will not be
> represented in diff
> dpkg-source: error: cannot represent change to
> libs/phylogeny/tests/given2seqEstimateTheDistanceK2P: binary file contents
> changed
> dpkg-source: error: add libs/phylogeny/tests/given2seqEstimateTheDistanceK2P
> in debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: executable mode 0755 of
> 'libs/phylogeny/tests/given2seqEstimateTheDistanceK2P' will not be
> represented in diff
> dpkg-source: error: cannot represent change to
> libs/phylogeny/tests/given2seqTheDistBetweenThem-3: binary file contents
> changed
> dpkg-source: error: add libs/phylogeny/tests/given2seqTheDistBetweenThem-3 in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: executable mode 0755 of
> 'libs/phylogeny/tests/given2seqTheDistBetweenThem-3' will not be represented
> in diff
> dpkg-source: error: cannot represent change to
> libs/phylogeny/tests/readTreeWithComments: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/readTreeWithComments in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: executable mode 0755 of
> 'libs/phylogeny/tests/readTreeWithComments' will not be represented in diff
> dpkg-source: error: cannot represent change to
> libs/phylogeny/tests/splitMap_test: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/splitMap_test in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: executable mode 0755 of
> 'libs/phylogeny/tests/splitMap_test' will not be represented in diff
> dpkg-source: error: cannot represent change to
> libs/phylogeny/tests/split_test: binary file contents changed
> dpkg-source: error: add libs/phylogeny/tests/split_test in
> debian/source/include-binaries if you want to store the modified binary in
> the debian tarball
> dpkg-source: warning: executable mode 0755 of
> 'libs/phylogeny/tests/split_test' will not be represented in diff
> 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/fastml_3.11-3_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: fastml
Source-Version: 3.11-5
Done: Santiago Vila <[email protected]>
We believe that the bug you reported is fixed in the latest version of
fastml, 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.
Santiago Vila <[email protected]> (supplier of updated fastml 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: Tue, 03 Mar 2026 13:50:00 +0100
Source: fastml
Architecture: source
Version: 3.11-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Santiago Vila <[email protected]>
Closes: 1044832
Changes:
fastml (3.11-5) unstable; urgency=medium
.
* Team upload.
* Fix clean target. Closes: #1044832.
* Drop "Rules-Requires-Root: no" (default).
* Drop "Priority: optional" (default).
* Update standards-version.
* Simplify and fine-tune salsa-ci.yml.
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