Your message dated Wed, 08 Oct 2025 19:34:12 +0000
with message-id <[email protected]>
and subject line Bug#1113054: fixed in iqtree 2.0.7+dfsg-2
has caused the Debian Bug report #1113054,
regarding iqtree: 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.)
--
1113054: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1113054
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: iqtree
Version: 2.0.7+dfsg-1
Severity: serious
User: [email protected]
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
--- End Message ---
--- Begin Message ---
Source: iqtree
Source-Version: 2.0.7+dfsg-2
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
iqtree, 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 iqtree 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: Wed, 08 Oct 2025 20:52:17 +0200
Source: iqtree
Architecture: source
Version: 2.0.7+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1096850 1113054
Changes:
iqtree (2.0.7+dfsg-2) unstable; urgency=medium
.
* Team upload.
* cmake-4.patch: new: bump required cmake to 3.10. (Closes: #1113054)
* gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1096850)
Checksums-Sha1:
09fdd205bc7b19692582fa66d2fdd527ad9780c9 2357 iqtree_2.0.7+dfsg-2.dsc
c7b75704f7fd93895cd1257ef0f9f6e8b52bcf66 21020
iqtree_2.0.7+dfsg-2.debian.tar.xz
Checksums-Sha256:
038cc8594c48a58cbd5a993a52ef003dffb40e4cd1ac9ec70032f9bd982359e1 2357
iqtree_2.0.7+dfsg-2.dsc
6d0d3df522078049c79572dfe6fa1b91851bf8aae2bf9ea3810722b05b739053 21020
iqtree_2.0.7+dfsg-2.debian.tar.xz
Files:
5c11df88b8eb3c0b559674f746d80f37 2357 science optional iqtree_2.0.7+dfsg-2.dsc
c24cdabc01459573b5ffc2c909ae1f49 21020 science optional
iqtree_2.0.7+dfsg-2.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=+Bpc
-----END PGP SIGNATURE-----
pgpT9fQX3471w.pgp
Description: PGP signature
--- End Message ---
