Your message dated Sun, 22 Feb 2026 16:18:43 +0000
with message-id <[email protected]>
and subject line Bug#1113067: fixed in kallisto 0.51.1+dfsg-1
has caused the Debian Bug report #1113067,
regarding kallisto: 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.)
--
1113067: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1113067
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: kallisto
Version: 0.48.0+dfsg-4
Severity: serious
User: [email protected]
Usertags: cmake-4
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for CMake 4, kallisto failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
Checksums-Sha256:
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kallisto_0.48.0+dfsg.orig.tar.xz
f0fa8ca0d2bb8ce6210e2c7725547397adc0e8520e3703889289524308e9b298 7116
kallisto_0.48.0+dfsg-4.debian.tar.xz
Files:
fcce4ec57b434469d66837f75030998e 1085076 kallisto_0.48.0+dfsg.orig.tar.xz
8e5675599154f7503ab32dff51b39063 7116 kallisto_0.48.0+dfsg-4.debian.tar.xz
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dpkg-source: warning: cannot verify inline signature for
./kallisto_0.48.0+dfsg-4.dsc: no acceptable signature found
dpkg-source: info: extracting kallisto in
/build/reproducible-path/kallisto-0.48.0+dfsg
dpkg-source: info: unpacking kallisto_0.48.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking kallisto_0.48.0+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_htslib.patch
dpkg-source: info: applying spelling
dpkg-source: info: applying htslib1.3
dpkg-source: info: applying gcc11.patch
dpkg-source: info: applying disable-failing-bustools-test.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 kallisto
dpkg-buildpackage: info: source version 0.48.0+dfsg-4
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
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg'
dh_auto_configure -- -DDEBIAN_BUILD=1 -DLINK=shared -DBUILD_FUNCTESTING=1
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
-DDEBIAN_BUILD=1 -DLINK=shared -DBUILD_FUNCTESTING=1 ..
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/kallisto-0.48.0+dfsg/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.
BUILD_FUNCTESTING:UNINITIALIZED=1
//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/kallisto-0.48.0+dfsg/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.
DEBIAN_BUILD:UNINITIALIZED=1
//No help, variable specified on the command line.
FETCHCONTENT_FULLY_DISCONNECTED:UNINITIALIZED=ON
//No help, variable specified on the command line.
LINK:UNINITIALIZED=shared
########################
# INTERNAL cache entries
########################
//This is the directory where this CMakeCache.txt was created
CMAKE_CACHEFILE_DIR:INTERNAL=/build/reproducible-path/kallisto-0.48.0+dfsg/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/kallisto-0.48.0+dfsg
//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
-DDEBIAN_BUILD=1 -DLINK=shared -DBUILD_FUNCTESTING=1 .. returned exit code 1
make[1]: *** [debian/rules:15: override_dh_auto_configure] Error 2
make[1]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg'
make: *** [debian/rules:12: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-08-29T23:21:27Z
-------------------------------------------------------------------------------
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/2394621/
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/153228/
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: kallisto
Source-Version: 0.51.1+dfsg-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
kallisto, 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 kallisto 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, 22 Feb 2026 17:01:24 +0100
Source: kallisto
Architecture: source
Version: 0.51.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1047324 1057131 1113067
Changes:
kallisto (0.51.1+dfsg-1) unstable; urgency=medium
.
[ Andreas Tille ]
* New upstream version
* Standards-Version: 4.7.3
* Add support for loongarch64 in d/control
Closes: #1057131
* Remove patch Check_busOptions.seq_length_before_accessing.patch that is
missing from debian/patches/series.
* Fix build with CMake 4
Closes: #1113067
* d/watch: version=5
* Cleanup properly after build time test + fix clean target
Closes: #1047324
* debputy lint --auto-fix (routine-update)
* Try hard to get bifrost build with recent gcc
* bifrost: Add default values for MAX_KMER_SIZE and MAX_GMER_SIZE
* Fix typo in bifrost
* Do not build in parallel
.
[ Michael R. Crusoe ]
* d/control: simplify architecture specifications by using provisions
from the architecture-properties package.
* d/rules: change dh_auto_test rule from an override to an
execute_after to remove the need to check DEB_BUILD_OPTIONS.
* Upstream has forked bifrost, use their copy instead.
* d/rules: need cmake option needed: USE_BAM.
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