Your message dated Fri, 26 Sep 2025 20:35:26 +0000
with message-id <[email protected]>
and subject line Bug#1113117: fixed in libbpp-phyl-omics 2.4.1-8
has caused the Debian Bug report #1113117,
regarding libbpp-phyl-omics: 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.)
--
1113117: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1113117
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: libbpp-phyl-omics
Version: 2.4.1-7
Severity: serious
User: [email protected]
Usertags: cmake-4
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for CMake 4, libbpp-phyl-omics failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
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-omics
Vcs-Git: https://salsa.debian.org/med-team/libbpp-phyl-omics.git
Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), cmake, d-shlibs
(>= 0.106~), libbpp-phyl-dev, libbpp-seq-omics-dev
Package-List:
libbpp-phyl-omics-dev deb libdevel optional arch=any
libbpp-phyl-omics3t64 deb libs optional arch=any
Checksums-Sha1:
b3132c35963eec7890514c1766b6c13f5c661a31 48482
libbpp-phyl-omics_2.4.1.orig.tar.gz
f07d9e671ce92f33785fb09e6e422cb040048cb4 10632
libbpp-phyl-omics_2.4.1-7.debian.tar.xz
Checksums-Sha256:
fb0908422e59c71065db874e68d5c71acddf66d8a51776f7e04a5f8d5f0f6577 48482
libbpp-phyl-omics_2.4.1.orig.tar.gz
4d614b594eaf300295bc8917f4ef099983f308d8cf0cd94e1c7c5bf80e9cafcd 10632
libbpp-phyl-omics_2.4.1-7.debian.tar.xz
Files:
7c1c1d06e0c0ff61ddecc7fcc4064f51 48482 libbpp-phyl-omics_2.4.1.orig.tar.gz
729df38076498102b04f2079f46081db 10632 libbpp-phyl-omics_2.4.1-7.debian.tar.xz
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dpkg-source: warning: cannot verify inline signature for
./libbpp-phyl-omics_2.4.1-7.dsc: no acceptable signature found
dpkg-source: info: extracting libbpp-phyl-omics in
/build/reproducible-path/libbpp-phyl-omics-2.4.1
dpkg-source: info: unpacking libbpp-phyl-omics_2.4.1.orig.tar.gz
dpkg-source: info: unpacking libbpp-phyl-omics_2.4.1-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying unforce-cxxflags.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-omics
dpkg-buildpackage: info: source version 2.4.1-7
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-omics-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-omics-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-omics-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-omics-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 2025-08-30T03:26:38Z
-------------------------------------------------------------------------------
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/2399568/
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/153692/
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-omics
Source-Version: 2.4.1-8
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libbpp-phyl-omics, 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-omics
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 21:58:45 +0200
Source: libbpp-phyl-omics
Architecture: source
Version: 2.4.1-8
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1113117
Changes:
libbpp-phyl-omics (2.4.1-8) unstable; urgency=medium
.
* Team upload.
* cmake-4.patch: new: bump minimum cmake to 3.10. (Closes: #1113117)
* 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 unused t64 override.
* d/*lintian-overrides: add conflicts-with-version override.
* d/s/lintian-overrides: glob d/control line number.
This addresses mismatches due to variability in d/control file.
* d/control: declare compliance to standards version 4.7.2.
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Files:
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libbpp-phyl-omics_2.4.1-8.dsc
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