[Debian-med-packaging] Bug#1113054: iqtree: FTBFS with CMake 4

roehling at debian.org roehling at debian.org
Sun Aug 31 23:56:20 BST 2025 

Source: iqtree
Version: 2.0.7+dfsg-1
Severity: serious
User: cmake at packages.debian.org
Usertags: cmake-4
Tags: ftbfs, forky, sid

Dear maintainer,

During a test rebuild for CMake 4, iqtree failed to rebuild.

Log Summary:
-------------------------------------------------------------------------------
[...]
Unpacking libopenmpi40:arm64 (5.0.8-5) ...
Selecting previously unselected package openmpi-common.
Preparing to unpack .../125-openmpi-common_5.0.8-5_all.deb ...
Unpacking openmpi-common (5.0.8-5) ...
Selecting previously unselected package zlib1g-dev:arm64.
Preparing to unpack .../126-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ...
Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Selecting previously unselected package openmpi-bin.
Preparing to unpack .../127-openmpi-bin_5.0.8-5_arm64.deb ...
Unpacking openmpi-bin (5.0.8-5) ...
Selecting previously unselected package libopenmpi-dev:arm64.
Preparing to unpack .../128-libopenmpi-dev_5.0.8-5_arm64.deb ...
Unpacking libopenmpi-dev:arm64 (5.0.8-5) ...
Selecting previously unselected package libsprng2.
Preparing to unpack .../129-libsprng2_2.0a-16_arm64.deb ...
Unpacking libsprng2 (2.0a-16) ...
Selecting previously unselected package libsprng2-dev.
Preparing to unpack .../130-libsprng2-dev_2.0a-16_arm64.deb ...
Unpacking libsprng2-dev (2.0a-16) ...
Selecting previously unselected package mpi-default-dev.
Preparing to unpack .../131-mpi-default-dev_1.18_arm64.deb ...
Unpacking mpi-default-dev (1.18) ...
Selecting previously unselected package time.
Preparing to unpack .../132-time_1.9-0.2+b1_arm64.deb ...
Unpacking time (1.9-0.2+b1) ...
Selecting previously unselected package sbuild-build-depends-main-dummy.
Preparing to unpack .../133-sbuild-build-depends-main-dummy_0.invalid.0_arm64.deb ...
Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libexpat1:arm64 (2.7.1-2) ...
Setting up libpipeline1:arm64 (1.5.8-1) ...
Setting up libpciaccess0:arm64 (0.17-3+b3) ...
Setting up libxau6:arm64 (1:1.0.11-1) ...
Setting up libxdmcp6:arm64 (1:1.1.5-1) ...
Setting up time (1.9-0.2+b1) ...
Setting up libkeyutils1:arm64 (1.6.3-6) ...
Setting up libboost1.83-dev:arm64 (1.83.0-4.2) ...
Setting up libxcb1:arm64 (1.17.0-2+b1) ...
Setting up bsdextrautils (2.41.1-1) ...
Setting up libmagic-mgc (1:5.46-5) ...
Setting up libcbor0.10:arm64 (0.10.2-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libxml2-16:arm64 (2.14.5+dfsg-0.2) ...
Setting up libdebhelper-perl (13.26) ...
Setting up libbrotli1:arm64 (1.1.0-2+b7) ...
Setting up libedit2:arm64 (3.1-20250104-1) ...
Setting up libuv1t64:arm64 (1.51.0-2) ...
Setting up libmagic1t64:arm64 (1:5.46-5) ...
Setting up libnghttp2-14:arm64 (1.64.0-1.1+b1) ...
Setting up libibumad3:arm64 (56.1-1) ...
Setting up gettext-base (0.23.1-2+b1) ...
Setting up m4 (1.4.19-8) ...
Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ...
Setting up libibmad5:arm64 (56.1-1) ...
Setting up libcom-err2:arm64 (1.47.2-3+b3) ...
Setting up file (1:5.46-5) ...
Setting up libelf1t64:arm64 (0.192-4) ...
Setting up libkrb5support0:arm64 (1.21.3-5) ...
Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ...
Setting up autotools-dev (20240727.1) ...
Setting up libz3-4:arm64 (4.13.3-1) ...
Setting up libpkgconf3:arm64 (1.8.1-4) ...
Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-4) ...
Setting up libx11-data (2:1.8.12-1) ...
Setting up libjsoncpp26:arm64 (1.9.6-3) ...
Setting up libproc2-0:arm64 (2:4.0.4-9) ...
Setting up libunistring5:arm64 (1.3-2) ...
Setting up libhwloc15:arm64 (2.12.2-1) ...
Setting up autopoint (0.23.1-2) ...
Setting up pkgconf-bin (1.8.1-4) ...
Setting up libncursesw6:arm64 (6.5+20250216-2) ...
Setting up libk5crypto3:arm64 (1.21.3-5) ...
Setting up libltdl7:arm64 (2.5.4-4) ...
Setting up libsasl2-2:arm64 (2.1.28+dfsg1-9) ...
Setting up libgfortran5:arm64 (15.2.0-2) ...
Setting up autoconf (2.72-3.1) ...
Setting up libnghttp3-9:arm64 (1.8.0-1) ...
Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libffi8:arm64 (3.4.8-2) ...
Setting up libnuma1:arm64 (2.0.19-1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.26) ...
Setting up ocl-icd-libopencl1:arm64 (2.3.3-1) ...
Setting up libuchardet0:arm64 (0.0.8-1+b2) ...
Setting up procps (2:4.0.4-9) ...
Setting up libnl-3-200:arm64 (3.7.0-2) ...
Setting up openmpi-common (5.0.8-5) ...
Setting up libtasn1-6:arm64 (4.20.0-2) ...
Setting up libx11-6:arm64 (2:1.8.12-1) ...
Setting up cmake-data (4.1.1-1) ...
Setting up librhash1:arm64 (1.4.6-1) ...
Setting up libkrb5-3:arm64 (1.21.3-5) ...
Setting up libboost-dev:arm64 (1.83.0.2+b2) ...
Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10+b1) ...
Setting up libssh2-1t64:arm64 (1.11.1-1) ...
Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1) ...
Setting up libfuse3-4:arm64 (3.17.4-1) ...
Setting up libfido2-1:arm64 (1.16.0-2) ...
Setting up libdrm-common (2.4.125-2) ...
Setting up libarchive13t64:arm64 (3.7.4-4+b1) ...
Setting up libldap2:arm64 (2.6.10+dfsg-1) ...
Setting up liblocale-gettext-perl (1.07-7+b1) ...
Setting up chrpath (0.18-1) ...
Setting up libsprng2 (2.0a-16) ...
Setting up automake (1:1.17-4) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libgfortran-14-dev:arm64 (14.3.0-5) ...
Setting up libfile-stripnondeterminism-perl (1.14.2-1) ...
Setting up gettext (0.23.1-2+b1) ...
Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-4) ...
Setting up libtool (2.5.4-4) ...
Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10+b1) ...
Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-10+b1) ...
Setting up libxext6:arm64 (2:1.3.4-1+b3) ...
Setting up libidn2-0:arm64 (2.3.8-4) ...
Setting up pkgconf:arm64 (1.8.1-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libnuma-dev:arm64 (2.0.19-1) ...
Setting up libnl-route-3-200:arm64 (3.7.0-2) ...
Setting up libxnvctrl0:arm64 (535.171.04-1+b2) ...
Setting up help2man (1.49.3+b1) ...
Setting up dh-autoreconf (20) ...
Setting up libltdl-dev:arm64 (2.5.4-4) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libllvm17t64:arm64 (1:17.0.6-22+b3) ...
Setting up libp11-kit0:arm64 (0.25.5-3) ...
Setting up libeigen3-dev (3.4.0-5) ...
Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ...
Setting up pkg-config:arm64 (1.8.1-4) ...
Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10+b1) ...
Setting up dh-strip-nondeterminism (1.14.2-1) ...
Setting up libdrm2:arm64 (2.4.125-2) ...
Setting up libnl-3-dev:arm64 (3.7.0-2) ...
Setting up groff-base (1.23.0-9) ...
Setting up libsprng2-dev (2.0a-16) ...
Setting up gfortran-14-aarch64-linux-gnu (14.3.0-5) ...
Setting up libhwloc-dev:arm64 (2.12.2-1) ...
Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b2) ...
Setting up gfortran-14 (14.3.0-5) ...
Setting up libdrm-amdgpu1:arm64 (2.4.125-2) ...
Setting up libgnutls30t64:arm64 (3.8.10-2) ...
Setting up libibverbs1:arm64 (56.1-1) ...
Setting up ibverbs-providers:arm64 (56.1-1) ...
Setting up openssh-client (1:10.0p1-8) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ...
Setting up libhwloc-plugins:arm64 (2.12.2-1) ...
Setting up man-db (2.13.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libnl-route-3-dev:arm64 (3.7.0-2) ...
Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ...
Setting up libevent-dev (2.1.12-stable-10+b1) ...
Setting up librdmacm1t64:arm64 (56.1-1) ...
Setting up libhsakmt1:arm64 (6.2.4+ds-1) ...
Setting up libfabric1:arm64 (2.1.0-1.1) ...
Setting up libcurl4t64:arm64 (8.16.0~rc2-1) ...
Setting up debhelper (13.26) ...
Setting up libibverbs-dev:arm64 (56.1-1) ...
Setting up libhsa-runtime64-1:arm64 (6.1.2-3) ...
Setting up cmake (4.1.1-1) ...
Setting up libamdhip64-5:arm64 (5.7.1-6) ...
Setting up libucx0:arm64 (1.18.1+ds-2+b1) ...
Setting up libopenmpi40:arm64 (5.0.8-5) ...
Setting up openmpi-bin (5.0.8-5) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:arm64 (5.0.8-5) ...
update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode
Setting up mpi-default-dev (1.18) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.41-12) ...

+------------------------------------------------------------------------------+
| Check architectures                          Fri, 29 Aug 2025 22:41:46 +0000 |
+------------------------------------------------------------------------------+

E: dsc: arm64 not in arch list or does not match any arch wildcards: amd64 hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386 -- skipping

+------------------------------------------------------------------------------+
| Cleanup                                      Fri, 29 Aug 2025 22:41:48 +0000 |
+------------------------------------------------------------------------------+

Purging /build/reproducible-path
Not cleaning session: cloned chroot in use
E: dsc: arm64 not in arch list or does not match any arch wildcards: amd64 hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386 -- skipping

+------------------------------------------------------------------------------+
| Summary                                      Fri, 29 Aug 2025 22:41:51 +0000 |
+------------------------------------------------------------------------------+

Build Architecture: arm64
Build Type: binary
Build-Space: n/a
Build-Time: 0
Distribution: sid
Fail-Stage: arch-check
Host Architecture: arm64
Install-Time: 39
Job: /tmp/debusine-fetch-exec-upload-w7yqwpva/iqtree_2.0.7+dfsg-1.dsc
Machine Architecture: arm64
Package: iqtree
Package-Time: 0
Source-Version: 2.0.7+dfsg-1
Space: n/a
Status: skipped
Version: 2.0.7+dfsg-1
--------------------------------------------------------------------------------
Finished at 2025-08-29T22:40:30Z
Build needed 00:00:00, no disk space

-------------------------------------------------------------------------------

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/2394219/

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/153182/

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

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