Pacman outputs missing files ,fails to install packages [SOLVED]

MakeMake · 2023-05-06 08:34:35

First post on the forums,
(I apologize in advance if my English is a bit broken, it's not my first language)

Recently i attempted a full system update, (pacman -Syu) which failed with the ambiguous error message:

error: command failed to execute correctly
error: failed to commit transaction (failed to run transaction hooks)
Errors occurred, no packages were upgraded.

During the update i got many missing files warnings, and so assumed these were the source of the error.
Running "pacman -Qk 2>&1 | grep -E ', [1-9][0-9]* missing files' | cut -d':' -f1" got me a list of problematic packages, which in my case is

audit
brltty
btrfs-progs
python-appdirs
python-attrs
python-autocommand
python-automat
python-bottle
python-cffi
python-constantly
python-contourpy

I tried reinstalling them with pacman's overwrite option as is suggested in other posts(i am aware that it is generally not recommended in a well maintained system, but i don't think my system can be considered as such at this point anyways), but got the same warnings
and errors, with the reinstall failing.
The command i ran: "sudo pacman -S python-contourpy -vv --noconfirm --overwrite "*""

Not only these packages but also new ones I am trying to install fail - I tried installing the chromium package and got the same error.
From the pacman troubleshooting page in the wiki I understand that these errors are the result of file conflicts, but how is that the case
when the package was never installed on the system before?

I am currently stuck, without being able to update or install packages,
any assistance would be appreciated

Last edited by MakeMake (2023-05-06 14:50:52)

seth · 2023-05-06 08:45:22

Please don't paraphrase, https://bbs.archlinux.org/viewtopic.php?id=57855
Post your pacman log.

MakeMake · 2023-05-06 09:02:55

Full update command output: (sudo pacman -Syu)

:: Synchronizing package databases...
core is up to date
extra is up to date
community is up to date
multilib is up to date
:: Starting full system upgrade...
:: Replace qemu-virtiofsd with extra/virtiofsd? [Y/n]
resolving dependencies...
looking for conflicting packages...
warning: dependency cycle detected:
warning: python-incremental will be installed before its python-twisted dependency
warning: dependency cycle detected:
warning: libcamera-ipa will be installed before its libcamera dependency

Packages (377) a52dec-0.8.0-1 appstream-0.16.2-1 appstream-qt-0.16.2-1 archlinux-keyring-20230504-1 argon2-20190702-5 audacity-1:3.3.1-2 audit-3.1.1-1 avahi-0.8+22+gfd482a7-4 avogadrolibs-1.97.0-7
avogadrolibs-qt5-1.97.0-7 babl-0.1.104-1 binutils-2.40-5 blender-17:3.5.1-3 boost-1.81.0-5 boost-libs-1.81.0-5 botan-3.0.0-1 botan2-2.19.3-1 brltty-6.5-4 brotli-1.0.9-12
btrfs-progs-6.3-2 cantor-23.04.0-2 capstone-4.0.2-7 clang-15.0.7-9 coreutils-9.3-1 criu-3.17.1-2 crun-1.8.3-2 cuda-12.1.1-3 dav1d-1.2.0-1 dbus-python-1.2.18-5 device-mapper-2.03.21-1
dolphin-23.04.0-3 dtc-1.7.0-4 edk2-aarch64-202302-1 edk2-arm-202302-1 edk2-ovmf-202302-1 esbuild-0.17.18-1 falkon-23.04.0-2 ffmpeg-2:6.0-5 ffmpeg4.4-4.4.3-2
firefox-developer-edition-113.0b9-1 firewalld-1.3.2-1 freecad-0.20.2-6 fzf-0.40.0-1 gcc-13.1.1-1 gcc-libs-13.1.1-1 gcc12-12.2.1-1 gcc12-libs-12.2.1-1 gdb-13.1-3 gdb-common-13.1-3
git-2.40.1-1 glib2-2.76.2-1 glibc-2.37-3 glusterfs-1:11.0-1 gobject-introspection-runtime-1.76.1-2 gpgme-1.20.0-2 gpm-1.20.7.r38.ge82d1a6-5 graphviz-8.0.5-2 gspell-1.12.1-1
gst-plugins-bad-1.22.2-1 gst-plugins-bad-libs-1.22.2-1 gst-plugins-base-1.22.2-1 gst-plugins-base-libs-1.22.2-1 gst-plugins-good-1.22.2-1 gstreamer-1.22.2-1 gvim-9.0.1420-2
harfbuzz-7.2.0-1 harfbuzz-icu-7.2.0-1 hivex-1.3.21-8 hwdata-0.370-1 imagemagick-7.1.1.8-1 imath-3.1.7-2 imlib2-1.11.1-1 inkscape-1.2.2-5 iproute2-6.3.0-1 iso-codes-4.15.0-1
jdk-openjdk-20.0.1.u9-3 jre-openjdk-20.0.1.u9-3 jre-openjdk-headless-20.0.1.u9-3 jxrlib-0.2.4-2 kajongg-23.04.0-2 kdenlive-23.04.0-2 keepassxc-2.7.4-2 keyutils-1.6.3-2 kig-23.04.0-2
kopeninghours-23.04.0-2 krita-5.1.5-6 ldb-2:2.7.2-2 lensfun-1:0.3.3-2 less-1:633-1 level-zero-loader-1.9.4-1 lib32-gcc-libs-13.1.1-1 lib32-glib2-2.76.2-1 lib32-glibc-2.37-3
lib32-harfbuzz-7.2.0-1 lib32-libgpg-error-1.47-1 lib32-libxfixes-6.0.1-1 lib32-libxml2-2.10.4-4 lib32-mesa-23.0.3-1 lib32-sqlite-3.41.2-1 lib32-systemd-253.4-1 lib32-xz-5.4.3-1
lib32-zstd-1.5.5-1 libaccounts-glib-1.26-2 libadwaita-1:1.3.2-1 libblockdev-2.28-2 libbytesize-2.7-2 libcamera-0.0.5-1 libcamera-ipa-0.0.5-1 libcap-ng-0.8.3-2 libftdi-1.5-5
libgexiv2-0.14.0-4 libgirepository-1.76.1-2 libguestfs-1.48.6-5 libheif-1.16.1-1 libieee1284-0.2.11-15 libimobiledevice-1.3.0-7 libixion-0.17.0-5 liblouis-3.25.0-2 libmsym-0.2.3-8
libmtp-1.1.21-1 libmwaw-0.3.22-1 libnewt-0.52.23-2 libopenmpt-0.7.0-1 liborcus-0.17.2-5 libpackagekit-glib-1.2.6-2 libpcap-1.10.4-1 libpipewire-1:0.3.70-2 libplist-2.2.0-7
libproxy-0.4.18-3 libreoffice-still-7.4.6-2 libseccomp-2.5.4-2 libsignon-glib-2.1-6 libsmbios-2.4.3-6 libsoup3-3.4.2-1 libspeechd-0.11.4-2 libssh-0.10.5-1 libteam-1.31-8
libtool-2.4.7+4+g1ec8fa28-3 libupnp-1.14.17-1 libvirt-python-1:9.2.0-2 libwbclient-4.18.2-2 libwpg-0.3.4-1 libxi-1.8.1-1 libxml2-2.10.4-4 libxslt-1.1.37-3 lilv-0.24.20-2
linux-6.3.1.arch1-1 linux-api-headers-6.3-1 linux-firmware-20230404.2e92a49f-1 linux-firmware-whence-20230404.2e92a49f-1 linux-headers-6.3.1.arch1-1 llvm-libs-15.0.7-3 log4cplus-2.1.0-1
lvm2-2.03.21-1 med-openmpi-4.1.1-4 mesa-23.0.3-1 miniupnpc-2.2.4-2 mlt-7.14.0-8 mpfr-4.2.0.p4-1 net-snmp-5.9.1-6 nftables-1:1.0.7-2 ninja-1.11.1-3 noto-fonts-20230501-1 npm-8.19.2-2
nvidia-530.41.03-9 nyx-2.1.0-6 onetbb-2021.8.0-3 openbabel-3.1.1-7 opencolorio-2.2.1-6 openimageio-2.4.10.0-2 openjdk-doc-20.0.1.u9-3 openresolv-3.13.1-1 openshadinglanguage-1.12.12.0-1
openvdb-10.0.1-4 packagekit-1.2.6-2 pahole-1:1.25-4 pciutils-3.10.0-1 pipewire-1:0.3.70-2 protobuf-21.12-2 pybind11-2.10.4-3 pyside2-5.15.9-5 pyside2-tools-5.15.9-5 pystring-1.1.4-1
python-3.11.3-1 python-appdirs-1.4.4-8 python-attrs-22.2.0-3 python-autocommand-2.2.2-4 python-automat-22.10.0-3 python-bottle-0.12.25-3 python-cachecontrol-1:0.12.11-2
python-cairo-1.23.0-4 python-capng-0.8.3-2 python-cffi-1.15.1-3 python-chardet-5.1.0-3 python-click-8.1.3-3 python-constantly-15.1.0-13 python-contourpy-1.0.7-3
python-cryptography-40.0.2-1 python-cssselect-1.2.0-3 python-cycler-0.11.0-3 python-dateutil-2.8.2-5 python-distro-1.8.0-3 python-docopt-0.6.2-12 python-fasteners-0.18-2
python-fastjsonschema-2.16.3-4 python-feedparser-6.0.10-3 python-fonttools-4.39.3-3 python-gitdb-1:4.0.10-2 python-gitpython-3.1.31-2 python-gobject-3.44.1-3 python-gpgme-1.20.0-2
python-html2text-2020.1.16-9 python-hyperlink-21.0.0-5 python-idna-3.4-3 python-incremental-22.10.0-3 python-inflect-6.0.4-2 python-jaraco.context-4.3.0-3 python-jaraco.functools-3.6.0-3
python-jaraco.text-3.11.1-3 python-jinja-1:3.1.2-4 python-kiwisolver-1.4.4-4 python-lockfile-0.12.2-12 python-lxml-4.9.2-3 python-markdown-3.4.3-2 python-markupsafe-2.1.2-3
python-matplotlib-3.7.1-4 python-more-itertools-9.1.1-4 python-msgpack-1.0.4-2 python-numpy-1.24.3-2 python-ordered-set-4.1.0-4 python-packaging-23.0-3 python-pillow-9.5.0-2
python-pip-23.1.2-1 python-pivy-0.6.8-2 python-platformdirs-3.5.0-2 python-ply-3.11-12 python-protobuf-21.12-2 python-psutil-5.9.5-1 python-pycparser-2.21-5 python-pydantic-1.10.7-4
python-pygments-2.15.1-1 python-pyjwt-2.6.0-2 python-pynacl-1.4.0-6 python-pyparsing-3.0.9-3 python-pyqt5-5.15.9-2 python-pyqt5-sip-12.12.1-2 python-pysocks-1.7.1-8 python-qtpy-2.3.1-2
python-requests-2.28.2-4 python-setuptools-1:67.7.0-1 python-sgmllib3k-1.0.0-5 python-shiboken2-5.15.9-5 python-six-1.16.0-8 python-smmap-1:5.0.0-4 python-stem-1.8.1-2 python-tomli-2.0.1-3
python-tqdm-4.65.0-3 python-trove-classifiers-2023.4.22-1 python-twisted-22.10.0-3 python-typing_extensions-4.5.0-4 python-urllib3-1.26.15-1 python-urwid-2.1.2.r56.gabc098c-1
python-validate-pyproject-0.12.2-3 python-wheel-0.40.0-3 python-yaml-6.0-3 python-zope-interface-6.0-3 qca-qt5-2.3.6-2 qemu-audio-alsa-8.0.0-1 qemu-audio-dbus-8.0.0-1
qemu-audio-jack-8.0.0-1 qemu-audio-oss-8.0.0-1 qemu-audio-pa-8.0.0-1 qemu-audio-sdl-8.0.0-1 qemu-audio-spice-8.0.0-1 qemu-block-curl-8.0.0-1 qemu-block-dmg-8.0.0-1
qemu-block-gluster-8.0.0-1 qemu-block-iscsi-8.0.0-1 qemu-block-nfs-8.0.0-1 qemu-block-ssh-8.0.0-1 qemu-chardev-baum-8.0.0-1 qemu-chardev-spice-8.0.0-1 qemu-common-8.0.0-1 qemu-docs-8.0.0-1
qemu-full-8.0.0-1 qemu-hw-display-qxl-8.0.0-1 qemu-hw-display-virtio-gpu-8.0.0-1 qemu-hw-display-virtio-gpu-gl-8.0.0-1 qemu-hw-display-virtio-gpu-pci-8.0.0-1
qemu-hw-display-virtio-gpu-pci-gl-8.0.0-1 qemu-hw-display-virtio-vga-8.0.0-1 qemu-hw-display-virtio-vga-gl-8.0.0-1 qemu-hw-s390x-virtio-gpu-ccw-8.0.0-1 qemu-hw-usb-host-8.0.0-1
qemu-hw-usb-redirect-8.0.0-1 qemu-hw-usb-smartcard-8.0.0-1 qemu-img-8.0.0-1 qemu-pr-helper-8.0.0-1 qemu-system-aarch64-8.0.0-1 qemu-system-alpha-8.0.0-1 qemu-system-alpha-firmware-8.0.0-1
qemu-system-arm-8.0.0-1 qemu-system-arm-firmware-8.0.0-1 qemu-system-avr-8.0.0-1 qemu-system-cris-8.0.0-1 qemu-system-hppa-8.0.0-1 qemu-system-hppa-firmware-8.0.0-1
qemu-system-loongarch64-8.0.0-1 qemu-system-m68k-8.0.0-1 qemu-system-microblaze-8.0.0-1 qemu-system-microblaze-firmware-8.0.0-1 qemu-system-mips-8.0.0-1 qemu-system-nios2-8.0.0-1
qemu-system-or1k-8.0.0-1 qemu-system-ppc-8.0.0-1 qemu-system-ppc-firmware-8.0.0-1 qemu-system-riscv-8.0.0-1 qemu-system-riscv-firmware-8.0.0-1 qemu-system-rx-8.0.0-1
qemu-system-s390x-8.0.0-1 qemu-system-s390x-firmware-8.0.0-1 qemu-system-sh4-8.0.0-1 qemu-system-sparc-8.0.0-1 qemu-system-sparc-firmware-8.0.0-1 qemu-system-tricore-8.0.0-1
qemu-system-x86-8.0.0-1 qemu-system-x86-firmware-8.0.0-1 qemu-system-xtensa-8.0.0-1 qemu-tests-8.0.0-1 qemu-tools-8.0.0-1 qemu-ui-curses-8.0.0-1 qemu-ui-dbus-8.0.0-1
qemu-ui-egl-headless-8.0.0-1 qemu-ui-gtk-8.0.0-1 qemu-ui-opengl-8.0.0-1 qemu-ui-sdl-8.0.0-1 qemu-ui-spice-app-8.0.0-1 qemu-ui-spice-core-8.0.0-1 qemu-user-8.0.0-1
qemu-vhost-user-gpu-8.0.0-1 qemu-virtiofsd-7.2.1-1 [removal] qgpgme-1.20.0-2 qt5-declarative-5.15.9+kde+r25-1 qt5-quickcontrols2-5.15.9+kde+r6-1 qt5-svg-5.15.9+kde+r8-1 rmlint-2.10.1-4
rust-1:1.69.0-3 samba-4.18.2-2 smbclient-4.18.2-2 systemd-253.4-1 systemd-libs-253.4-1 systemd-sysvcompat-253.4-1 talloc-2.4.0-3 tdb-1.4.8-2 tevent-1:0.14.1-2
thin-provisioning-tools-1.0.4-1 torbrowser-launcher-0.3.6-2 tracker3-3.5.1-1 twolame-0.4.0-3 util-linux-2.38.1-4 util-linux-libs-2.38.1-4 vamp-plugin-sdk-2.10.0-2 vid.stab-1.1.1-1
vim-runtime-9.0.1420-2 virt-install-4.1.0-2 virt-manager-4.1.0-2 virtiofsd-1.6.0-2 volume_key-0.3.12-8 vtk-9.2.6-5 vulkan-headers-1:1.3.248-1 xcb-proto-1.15.2-3
xdg-desktop-portal-1.16.0-2 xorg-xdpyinfo-1.3.4-1 xorg-xinput-1.6.4-1 xz-5.4.3-1 zbar-0.23.90-2 zstd-1.5.5-1

Total Installed Size: 12297.17 MiB
Net Upgrade Size: 275.14 MiB

:: Proceed with installation? [Y/n]
(376/376) checking keys in keyring [#############################################################################] 100%
(376/376) checking package integrity [#############################################################################] 100%
(376/376) loading package files [#############################################################################] 100%
(376/376) checking for file conflicts [#############################################################################] 100%
(377/377) checking available disk space [#############################################################################] 100%
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:: Running pre-transaction hooks...
(1/2) Checking Arch News with Informant ...
There are 10 unread news items! Use informant to read them.
:: informant: Run `informant read` before re-running your pacman command
error: command failed to execute correctly
error: failed to commit transaction (failed to run transaction hooks)
Errors occurred, no packages were upgraded.

I hope that helps.

skunktrader · 2023-05-06 09:04:01

How recently did you run pacman -Syu?

Ninja'd by OP. Can be deleted

Last edited by skunktrader (2023-05-06 09:04:56)

MakeMake · 2023-05-06 09:14:07

I ran the command around half an hour ago

Raynman · 2023-05-06 09:43:15

:: Running pre-transaction hooks...
(1/2) Checking Arch News with Informant ...
There are 10 unread news items! Use informant to read them.
:: informant: Run `informant read` before re-running your pacman command

So it wasn't an "ambiguous error message", but you cut off the specifics.

The python warnings may just disappear after upgrading.

Fuxino · 2023-05-06 09:52:06

Please use code tags to post command outputs.

MakeMake wrote:

:: informant: Run `informant read` before re-running your pacman command
error: command failed to execute correctly
error: failed to commit transaction (failed to run transaction hooks)

It says there why the upgrade failed and also what to do before re-running the pacman command. The warnings are unrelated and they mean that those files are missing. If they're still there after upgrading the system try reinstalling those packages.

MakeMake · 2023-05-06 14:49:47

Yes! informant was indeed the problem. I ran the command before my failed update attempt, but apparently it requires
root permissions to run properly. I executed

sudo informant read

and then upgraded, and it worked as expected. Thanks everyone for pointing that out for me. Marking as solved.

Arch Linux

#1 2023-05-06 08:34:35

Pacman outputs missing files ,fails to install packages [SOLVED]

#2 2023-05-06 08:45:22

Re: Pacman outputs missing files ,fails to install packages [SOLVED]

#3 2023-05-06 09:02:55

Re: Pacman outputs missing files ,fails to install packages [SOLVED]

#4 2023-05-06 09:04:01

Re: Pacman outputs missing files ,fails to install packages [SOLVED]

#5 2023-05-06 09:14:07

Re: Pacman outputs missing files ,fails to install packages [SOLVED]

#6 2023-05-06 09:43:15

Re: Pacman outputs missing files ,fails to install packages [SOLVED]

#7 2023-05-06 09:52:06

Re: Pacman outputs missing files ,fails to install packages [SOLVED]

#8 2023-05-06 14:49:47

Re: Pacman outputs missing files ,fails to install packages [SOLVED]

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