Your message dated Mon, 20 Oct 2025 06:04:15 +0000
with message-id <[email protected]>
and subject line Bug#1113291: fixed in mmseqs2 18-8cc5c+ds-1
has caused the Debian Bug report #1113291,
regarding mmseqs2: 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.)
--
1113291: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1113291
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: mmseqs2
Version: 15-6f452+ds-2
Severity: serious
User: [email protected]
Usertags: cmake-4
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for CMake 4, mmseqs2 failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
Files:
f072939874061057828878e97a85c92e 6770980 mmseqs2_15-6f452+ds.orig.tar.xz
fdb34d0ef47202ac056418b248817ffb 6548600 mmseqs2_15-6f452+ds-2.debian.tar.xz
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dpkg-source: warning: cannot verify inline signature for
./mmseqs2_15-6f452+ds-2.dsc: no acceptable signature found
dpkg-source: info: extracting mmseqs2 in
/build/reproducible-path/mmseqs2-15-6f452+ds
dpkg-source: info: unpacking mmseqs2_15-6f452+ds.orig.tar.xz
dpkg-source: info: unpacking mmseqs2_15-6f452+ds-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_tests.patch
dpkg-source: info: applying fix_util_installation.patch
dpkg-source: info: applying use_system_gzstream.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 mmseqs2
dpkg-buildpackage: info: source version 15-6f452+ds-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <[email protected]>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/mmseqs2-15-6f452+ds'
dh_auto_clean
rm -Rf build-*
make[1]: Leaving directory '/build/reproducible-path/mmseqs2-15-6f452+ds'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure-arch
make[1]: Entering directory '/build/reproducible-path/mmseqs2-15-6f452+ds'
dh_auto_configure -- -DUSE_SYSTEM_ZSTD=1 -DVERSION_OVERRIDE=15-6f452+ds-2
-DNATIVE_ARCH=0
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
-DUSE_SYSTEM_ZSTD=1 -DVERSION_OVERRIDE=15-6f452\+ds-2 -DNATIVE_ARCH=0 ..
CMake Error at CMakeLists.txt:1 (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/mmseqs2-15-6f452+ds/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/mmseqs2-15-6f452+ds/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
//No help, variable specified on the command line.
NATIVE_ARCH:UNINITIALIZED=0
//No help, variable specified on the command line.
USE_SYSTEM_ZSTD:UNINITIALIZED=1
//No help, variable specified on the command line.
VERSION_OVERRIDE:UNINITIALIZED=15-6f452+ds-2
########################
# INTERNAL cache entries
########################
//This is the directory where this CMakeCache.txt was created
CMAKE_CACHEFILE_DIR:INTERNAL=/build/reproducible-path/mmseqs2-15-6f452+ds/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/mmseqs2-15-6f452+ds
//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
-DUSE_SYSTEM_ZSTD=1 -DVERSION_OVERRIDE=15-6f452\+ds-2 -DNATIVE_ARCH=0 ..
returned exit code 1
make[1]: *** [debian/rules:31: override_dh_auto_configure-arch] Error 2
make[1]: Leaving directory '/build/reproducible-path/mmseqs2-15-6f452+ds'
make: *** [debian/rules:20: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-08-30T08:00:02Z
-------------------------------------------------------------------------------
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/2404369/
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/154134/
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: mmseqs2
Source-Version: 18-8cc5c+ds-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
mmseqs2, 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.
Andreas Tille <[email protected]> (supplier of updated mmseqs2 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: Sun, 19 Oct 2025 21:28:28 +0200
Source: mmseqs2
Architecture: source
Version: 18-8cc5c+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1113291
Changes:
mmseqs2 (18-8cc5c+ds-1) unstable; urgency=medium
.
* Team upload.
.
[ Michael R. Crusoe ]
* d/control: simplify architecture specification by using the
provisions from the architecture-properties package.
* d/salsi-ci.yml: skip i386 build, add link to salsa-ci docs.
.
[ Andreas Tille ]
* Fix build with CMake 4
Closes: #1113291
* d/watch: version=5
* New upstream version
* Standards-Version: 4.7.2 (routine-update)
* debputy lint --auto-fix (routine-update)
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