Your message dated Fri, 26 Sep 2025 20:35:19 +0000
with message-id <[email protected]>
and subject line Bug#1113116: fixed in libbpp-phyl 2.4.1-12
has caused the Debian Bug report #1113116,
regarding libbpp-phyl: FTBFS with CMake 4
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1113116: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1113116
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: libbpp-phyl
Version: 2.4.1-11
Severity: serious
User: [email protected]
Usertags: cmake-4
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for CMake 4, libbpp-phyl failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
Architecture: any
Version: 2.4.1-11
Maintainer: Debian Med Packaging Team
<[email protected]>
Uploaders: Julien Dutheil <[email protected]>, Andreas Tille
<[email protected]>
Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/libbpp-phyl
Vcs-Git: https://salsa.debian.org/med-team/libbpp-phyl.git
Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), cmake, d-shlibs
(>= 0.106~), libbpp-seq-dev
Package-List:
libbpp-phyl-dev deb libdevel optional arch=any
libbpp-phyl12t64 deb libs optional arch=any
Checksums-Sha1:
fe6808b427b667d4d2609e887dad9f571771a1d2 600392 libbpp-phyl_2.4.1.orig.tar.gz
08131db525d555cdd782da9058da37a683742a12 15220
libbpp-phyl_2.4.1-11.debian.tar.xz
Checksums-Sha256:
e7bf7d4570f756b7773904ffa600ffcd77c965553ddb5cbc252092d1da962ff2 600392
libbpp-phyl_2.4.1.orig.tar.gz
189fb668b1c22181a734ae7ed33d719df1e2769551689019360dc07d9866d13c 15220
libbpp-phyl_2.4.1-11.debian.tar.xz
Files:
05c58ac05a1f7525888df2b04c4a800c 600392 libbpp-phyl_2.4.1.orig.tar.gz
b0690c42d520317f60fddc8533233df6 15220 libbpp-phyl_2.4.1-11.debian.tar.xz
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dpkg-source: warning: cannot verify inline signature for
./libbpp-phyl_2.4.1-11.dsc: no acceptable signature found
dpkg-source: info: extracting libbpp-phyl in
/build/reproducible-path/libbpp-phyl-2.4.1
dpkg-source: info: unpacking libbpp-phyl_2.4.1.orig.tar.gz
dpkg-source: info: unpacking libbpp-phyl_2.4.1-11.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying spelling
dpkg-source: info: applying unforce-cxxflags.patch
dpkg-source: info: applying remove_test_likelihood_nh.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=sbuild
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=sbuild
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -b
dpkg-buildpackage: info: source package libbpp-phyl
dpkg-buildpackage: info: source version 2.4.1-11
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <[email protected]>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb
PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr
-DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc
-DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON
-DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON
-DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run
-DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles"
-DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ..
CMake Error at CMakeLists.txt:8 (cmake_minimum_required):
Compatibility with CMake < 3.5 has been removed from CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
Or, add -DCMAKE_POLICY_VERSION_MINIMUM=3.5 to try configuring anyway.
-- Configuring incomplete, errors occurred!
cd obj-aarch64-linux-gnu && tail -v -n \+0 CMakeCache.txt
==> CMakeCache.txt <==
# This is the CMakeCache file.
# For build in directory:
/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu
# It was generated by CMake: /usr/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
# VALUE is the current value for the KEY.
########################
# EXTERNAL cache entries
########################
//No help, variable specified on the command line.
CMAKE_BUILD_TYPE:UNINITIALIZED=None
//No help, variable specified on the command line.
CMAKE_EXPORT_NO_PACKAGE_REGISTRY:UNINITIALIZED=ON
//No help, variable specified on the command line.
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY:UNINITIALIZED=ON
//Value Computed by CMake.
CMAKE_FIND_PACKAGE_REDIRECTS_DIR:STATIC=/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/CMakeFiles/pkgRedirects
//No help, variable specified on the command line.
CMAKE_FIND_USE_PACKAGE_REGISTRY:UNINITIALIZED=OFF
//No help, variable specified on the command line.
CMAKE_INSTALL_LIBDIR:UNINITIALIZED=lib/aarch64-linux-gnu
//No help, variable specified on the command line.
CMAKE_INSTALL_LOCALSTATEDIR:UNINITIALIZED=/var
//No help, variable specified on the command line.
CMAKE_INSTALL_PREFIX:UNINITIALIZED=/usr
//No help, variable specified on the command line.
CMAKE_INSTALL_RUNSTATEDIR:UNINITIALIZED=/run
//No help, variable specified on the command line.
CMAKE_INSTALL_SYSCONFDIR:UNINITIALIZED=/etc
//No help, variable specified on the command line.
CMAKE_SKIP_INSTALL_ALL_DEPENDENCY:UNINITIALIZED=ON
//No help, variable specified on the command line.
CMAKE_VERBOSE_MAKEFILE:UNINITIALIZED=ON
//No help, variable specified on the command line.
FETCHCONTENT_FULLY_DISCONNECTED:UNINITIALIZED=ON
########################
# INTERNAL cache entries
########################
//This is the directory where this CMakeCache.txt was created
CMAKE_CACHEFILE_DIR:INTERNAL=/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu
//Major version of cmake used to create the current loaded cache
CMAKE_CACHE_MAJOR_VERSION:INTERNAL=4
//Minor version of cmake used to create the current loaded cache
CMAKE_CACHE_MINOR_VERSION:INTERNAL=1
//Patch version of cmake used to create the current loaded cache
CMAKE_CACHE_PATCH_VERSION:INTERNAL=1
//Path to CMake executable.
CMAKE_COMMAND:INTERNAL=/usr/bin/cmake
//Path to cpack program executable.
CMAKE_CPACK_COMMAND:INTERNAL=/usr/bin/cpack
//Path to ctest program executable.
CMAKE_CTEST_COMMAND:INTERNAL=/usr/bin/ctest
//Name of external makefile project generator.
CMAKE_EXTRA_GENERATOR:INTERNAL=
//Name of generator.
CMAKE_GENERATOR:INTERNAL=Unix Makefiles
//Generator instance identifier.
CMAKE_GENERATOR_INSTANCE:INTERNAL=
//Name of generator platform.
CMAKE_GENERATOR_PLATFORM:INTERNAL=
//Name of generator toolset.
CMAKE_GENERATOR_TOOLSET:INTERNAL=
//Source directory with the top level CMakeLists.txt file for this
// project
CMAKE_HOME_DIRECTORY:INTERNAL=/build/reproducible-path/libbpp-phyl-2.4.1
//Name of CMakeLists files to read
CMAKE_LIST_FILE_NAME:INTERNAL=CMakeLists.txt
//number of local generators
CMAKE_NUMBER_OF_MAKEFILES:INTERNAL=1
//Path to CMake installation.
CMAKE_ROOT:INTERNAL=/usr/share/cmake-4.1
dh_auto_configure: error: cd obj-aarch64-linux-gnu &&
DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake
-DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None
-DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var
-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON
-DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run
-DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles"
-DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ..
returned exit code 1
make: *** [debian/rules:8: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-08-30T03:26:45Z
-------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/2399569/
The most likely cause of build failures is the removed backwards compatibility
for
CMake versions earlier than 3.5. You can find additional information in my
debian-devel announcement:
https://lists.debian.org/debian-devel/2025/04/msg00310.html
About the archive rebuild: The build was made on debusine.debian.net,
using sbuild.
You can find the build task here:
https://debusine.debian.net/work-request/153691/
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,
Timo
--- End Message ---
--- Begin Message ---
Source: libbpp-phyl
Source-Version: 2.4.1-12
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libbpp-phyl, 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.
Étienne Mollier <[email protected]> (supplier of updated libbpp-phyl 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: Fri, 26 Sep 2025 21:44:17 +0200
Source: libbpp-phyl
Architecture: source
Version: 2.4.1-12
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1113116
Changes:
libbpp-phyl (2.4.1-12) unstable; urgency=medium
.
* Team upload.
* cmake-4.patch: new: bump cmake minimum to 3.10. (Closes: #1113116)
* d/control: declare compliance to standards version 4.7.2.
* d/control: remove redundant Rules-Requires-Root: no.
* d/watch: convert to v5 Github template.
* d/copyright: remove the old FSF address.
* d/*lintian-overrides: remove now unused t64 override.
* d/s/lintian-overrides: glob d/control line number.
This fixes mismatches caused by variability in the d/control file.
* d/*lintian-overrides: override conflicts-with-version.
This overrides is necessary in the context of the t64 transition.
Checksums-Sha1:
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Files:
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