Weird situation where pacman thinks I have no packages installed

Right!

sudo paccache -rvk 1 && sudo paccache -ruvk 0

may be a better option.

yes, but it said that the files.list file is empty

Update: Guys I think I fixed it!
although pacman -Syu returns

[root@vadym-swiftsf31442 ~]# pacman -Syu
:: Synchronizing package databases...
 endeavouros is up to date
 core-testing is up to date
 core is up to date
 extra-testing is up to date
 extra                                                                                8.3 MiB  5.01 MiB/s 00:02 [------------------------------------------------------------------] 100%
 multilib-testing is up to date
 multilib is up to date
 home_bespokesynth_Arch                                                            1770.0   B  8.96 KiB/s 00:00 [------------------------------------------------------------------] 100%
:: Starting full system upgrade...
resolving dependencies...
looking for conflicting packages...

Package (1)       Old Version  New Version  Net Change  Download Size

extra/python-rsa  4.9-2        4.9-3          0.00 MiB       0.06 MiB

Total Download Size:   0.06 MiB
Total Installed Size:  0.30 MiB
Net Upgrade Size:      0.00 MiB

:: Proceed with installation? [Y/n]
:: Retrieving packages...
 python-rsa-4.9-3-any                                                                60.7 KiB   607 KiB/s 00:00 [------------------------------------------------------------------] 100%
(1/1) checking keys in keyring                                                                                  [------------------------------------------------------------------] 100%
(1/1) checking package integrity                                                                                [------------------------------------------------------------------] 100%
(1/1) loading package files                                                                                     [------------------------------------------------------------------] 100%
(1/1) checking for file conflicts                                                                               [------------------------------------------------------------------] 100%
(1/1) checking available disk space                                                                             [------------------------------------------------------------------] 100%
warning: could not get file information for usr/bin/pyrsa-decrypt
warning: could not get file information for usr/bin/pyrsa-encrypt
warning: could not get file information for usr/bin/pyrsa-keygen
warning: could not get file information for usr/bin/pyrsa-priv2pub
warning: could not get file information for usr/bin/pyrsa-sign
warning: could not get file information for usr/bin/pyrsa-verify
warning: could not get file information for usr/lib/python3.11/site-packages/rsa-4.9-py3.11.egg-info/
warning: could not get file information for usr/lib/python3.11/site-packages/rsa-4.9-py3.11.egg-info/PKG-INFO
warning: could not get file information for usr/lib/python3.11/site-packages/rsa-4.9-py3.11.egg-info/SOURCES.txt
warning: could not get file information for usr/lib/python3.11/site-packages/rsa-4.9-py3.11.egg-info/dependency_links.txt
warning: could not get file information for usr/lib/python3.11/site-packages/rsa-4.9-py3.11.egg-info/entry_points.txt
warning: could not get file information for usr/lib/python3.11/site-packages/rsa-4.9-py3.11.egg-info/requires.txt
warning: could not get file information for usr/lib/python3.11/site-packages/rsa-4.9-py3.11.egg-info/top_level.txt
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__init__.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/__init__.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/__init__.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/asn1.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/asn1.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/cli.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/cli.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/common.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/common.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/core.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/core.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/key.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/key.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/parallel.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/parallel.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/pem.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/pem.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/pkcs1.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/pkcs1.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/pkcs1_v2.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/pkcs1_v2.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/prime.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/prime.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/randnum.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/randnum.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/transform.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/transform.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/util.cpython-311.opt-1.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/__pycache__/util.cpython-311.pyc
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/asn1.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/cli.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/common.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/core.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/key.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/parallel.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/pem.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/pkcs1.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/pkcs1_v2.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/prime.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/py.typed
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/randnum.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/transform.py
warning: could not get file information for usr/lib/python3.11/site-packages/rsa/util.py
warning: could not get file information for usr/share/licenses/python-rsa/
warning: could not get file information for usr/share/licenses/python-rsa/LICENSE
:: Processing package changes...
(1/1) upgrading python-rsa                                                                                      [------------------------------------------------------------------] 100%
:: Running post-transaction hooks...
(1/2) Arming ConditionNeedsUpdate...
(2/2) Checking which packages need to be rebuilt
[root@vadym-swiftsf31442 ~]#

And pacman -Qk returns
(Log file is too big for this and Pastebin)

How do I fix these warnings?

Update: did some cleaning
Before cleaning

$ df -h
Filesystem      Size  Used Avail Use% Mounted on
/dev/nvme0n1p2  225G  200G   14G  94% /

After cleaning Pacman cache

$ df -h
Filesystem      Size  Used Avail Use% Mounted on
/dev/nvme0n1p2  225G  176G   38G  83% /

After running BleachBit

$ df -h
Filesystem      Size  Used Avail Use% Mounted on
/dev/nvme0n1p2  225G  173G   41G  82% /
sudo pacman -S widelands wpewebkit wpewebkit-docs xalan-c xerces-c xiphos xtrabackup yaz zabbix-agent zabbix-agent2 zabbix-proxy zabbix-web-service zim-tools znc zxing-cpp

still same warnings (when I run pacman -Qk), what do I do?

The exact same or similiar? In other words, is the last warning about that same package? I suspect that the log you posted was truncated since it started with “w”.

What does this return:

sudo pacman -Qk | grep -vi Warning | grep -v "0 missing files" | grep -v swiftsf3 | awk -F ':' '{print $1}' | awk NF=NF RS= OFS=" "

I ran

sudo pacman -Qk | grep -vi Warning | grep -v "0 missing files" | grep -v swiftsf3 | awk -F ':' '{print $1}' | awk NF=NF RS= OFS=" " | tee output.txt

The contents of output.txt are:

389-ds-base aegisub agda ansible-core aqbanking aspell attica5 audiofile avfs baloo5 benchmark biblesync blender bluedevil bluez-libs bluez-qt5 bluez-utils breezy brltty-udev-generic btrfs-progs bullet-dp capnproto chafa chromium coffeescript couchdb cryfs crypto++ cuda cuda-tools cutefish-settings d-spy deepin-anything deepin-anything-arch deepin-appearance deepin-application-manager deepin-editor deepin-file-manager deepin-grand-search deepin-qt-dbus-factory deepin-qt5integration deepin-system-monitor deepin-util-dfm deepin-wloutput-daemon devhelp dino docopt docparser dovecot dovecot-fts-xapian dtkcore dtkgui dtkwidget egl-wayland eglexternalplatform electron22 electron23 electron24 enchant eos-qogir-icons eos-translations extra-cmake-modules fcft feedbackd ffms2 fishui flatpak-builder fltk folks frameworkintegration5 freerdp freetds fwbuilder gcc12 gcc12-libs gdal geary gentium-plus-font geoip-database geos gflags gmime3 gnome-builder gnome-text-editor gnucash gnuplot gnustep-base grafana grafana-zabbix grub gsettings-qt gst-plugin-gtk gtksourceview5 gumbo-parser gvfs harfbuzz-cairo harfbuzz-docs harfbuzz-utils haskell-attoparsec-aeson haskell-cpphs haskell-data-hash haskell-edit-distance haskell-equivalence haskell-fsnotify haskell-gitrev haskell-hakyll haskell-hinotify haskell-http-conduit haskell-lifted-async haskell-lrucache haskell-microlens haskell-microlens-ghc haskell-microlens-mtl haskell-microlens-th haskell-murmur-hash haskell-open-browser haskell-parallel haskell-peano haskell-polyparse haskell-shakespeare haskell-stmonadtrans haskell-time-locale-compat haskell-utility-ht haskell-vector-hashtables icu imv intel-oneapi-openmp js91 jsonrpc-glib jxrlib kactivities-stats5 kactivities5 karchive5 kauth5 kbibtex kbookmarks5 kcalendarcore5 kcmutils5 kcodecs5 kcompletion5 kconfig5 kconfigwidgets5 kcontacts5 kcoreaddons5 kcrash5 kdb kdbusaddons5 kdeclarative5 kdelibs4support kdeplasma-addons kdesu5 kdiff3 kdnssd5 kdsingleapplication kemoticons kfilemetadata5 kglobalaccel5 kguiaddons5 kholidays5 khtml ki18n5 kiconthemes5 kidletime5 kio5 kirigami2 kitemmodels5 kitemviews5 kjobwidgets5 kjs knewstuff5 knotifications5 knotifyconfig5 konsole kpackage5 kparts5 kpeople5 kpty5 kross krunner5 kscreen kservice5 ktexteditor5 ktextwidgets5 kunitconversion5 kwallet5 kwayland-integration kwayland5 kwidgetsaddons5 kwindowsystem5 kxmlgui5 lib32-clang lib32-harfbuzz-cairo lib32-harfbuzz-icu lib32-icu lib32-lcms2 lib32-libxml2 lib32-opencl-clover-mesa lib32-opencl-rusticl-mesa lib32-spirv-llvm-translator lib32-spirv-tools lib32-vulkan-intel lib32-vulkan-mesa-layers lib32-vulkan-swrast lib32-vulkan-virtio libcerf libchardet libclc libcue libcutefish libdatovka libdbi libdex libfido2 libfishsound libfreexl libgeotiff libgit2-glib libgpiod libgpod libgrss libgxps libiptcdata libkiwix libnsgif libofx liboggz libpanel libperconaserverclient libprocps libqtxdg libreoffice-fresh-sdk librime librttopo libsidplayfp libsignal-protocol-c libspatialite libspelling libspelling-docs libunrar libxml2 libxml2-docs libytnef libzim licenses linux-firmware linux-headers llvm14 llvm14-libs lshw lua51-cassowary lua51-cldr lua51-cliargs lua51-compat53 lua51-cosmo lua51-expat lua51-filesystem lua51-fluent lua51-linenoise lua51-loadkit lua51-lpeg lua51-luaepnf lua51-luarepl lua51-luautf8 lua51-penlight lua51-sec lua51-socket lua51-vstruct lua51-zlib luajit lucene++ lxc lzlib maim mapnik marisa materialx mathjax modemmanager-qt5 mongo-c-driver mpd ncmpcpp networkmanager-qt5 nuspell nvidia-utils okteta openblas opencl-clover-mesa opencl-nvidia opencl-rusticl-mesa openipmi openldap openmw openrct2 opensearch-alerting-plugin opensearch-analysis-kuromoji-plugin opensearch-analysis-nori-plugin opensearch-analysis-smartcn-plugin opensearch-analysis-stempel-plugin opensearch-analysis-ukrainian-plugin opensearch-anomaly-detection-plugin opensearch-asynchronous-search-plugin opensearch-cross-cluster-replication-plugin opensearch-dashboards-alerting-plugin opensearch-dashboards-anomaly-detection-plugin opensearch-dashboards-gantt-chart-plugin opensearch-dashboards-index-management-plugin opensearch-dashboards-maps-plugin opensearch-dashboards-notifications-plugin opensearch-dashboards-observability-plugin opensearch-dashboards-reports-plugin opensearch-discovery-azure-classic-plugin opensearch-discovery-ec2-plugin opensearch-geospatial-plugin opensearch-index-management-plugin opensearch-ingest-attachment-plugin opensearch-job-scheduler-plugin opensearch-knn-plugin opensearch-mapper-annotated-text-plugin opensearch-mapper-murmur3-plugin opensearch-mapper-size-plugin opensearch-ml-commons-plugin opensearch-neural-search-plugin opensearch-notifications-plugin opensearch-observability-plugin opensearch-performance-analyzer-plugin opensearch-reports-scheduler-plugin opensearch-repository-azure-plugin opensearch-repository-gcs-plugin opensearch-repository-hdfs-plugin opensearch-repository-s3-plugin opensearch-security-plugin opensearch-sql-plugin opensearch-store-smb-plugin opensearch-transport-nio-plugin opensp openttd optipng pandoc-crossref pandoc-plot percona-server percona-server-clients performous perl-dbd-mysql perl-dbi phoc phosh phosh-mobile-settings php-apache php-cgi php-dblib php-embed php-enchant php-gd php-legacy php-legacy-apache php-legacy-cgi php-legacy-dblib php-legacy-embed php-legacy-enchant php-legacy-fpm php-legacy-gd php-legacy-odbc php-legacy-pgsql php-legacy-phpdbg php-legacy-pspell php-legacy-snmp php-legacy-sodium php-legacy-sqlite php-legacy-tidy php-legacy-xsl php-odbc php-pgsql php-phpdbg php-pspell php-snmp php-sodium php-tidy php-xsl plasma-framework5 plasma-wayland-session podofo-0.9 poedit postfix postfix-cdb postgresql postgresql-docs postgresql-old-upgrade prison5 proj purpose5 python-absl python-apsw python-astor python-astunparse python-bleach python-brotli python-brotlicffi python-cachetools python-css-parser python-fastbencode python-faust-cchardet python-feedparser python-flatbuffers python-gast03 python-gnupg python-google-auth python-google-auth-oauthlib python-grpcio python-h11 python-h5py python-html2text python-html5-parser python-httpx python-idna python-inflate64 python-keras python-keras-applications python-keras-preprocessing python-ldap python-mechanize python-merge3 python-ml-dtypes python-multivolumefile python-oauthlib python-pandas python-paramiko python-pasta python-patiencediff python-pdftotext python-py7zr python-pybcj python-pycapnp python-pycryptodome python-pydot python-pyicu python-pyparsing python-pyppmd python-pyqt6-webengine python-pyzstd python-requests-oauthlib python-scipy python-setuptools python-sniffio python-sword python-tensorboard_plugin_wit python-tensorflow-estimator python-tensorflow-opt python-texttable python-ujson python-unrardll python-virtualenv python-websockets python-wrapt python-xxhash qhull qpdf qt5-xcb-private-headers qt6-positioning qt6-webchannel qt6-webengine r rime-bopomofo rime-cangjie rime-essay rime-prelude rime-stroke rime-terra-pinyin rocm-llvm rspamd samba scribus sdl2_image sgml-common sile slop socat solid5 sonic-visualiser sonnet5 squeekboard startdde strawberry surge-xt-common surge-xt-standalone sword syndication5 syntax-highlighting5 sysprof systemd tectonic tensorboard tensorflow-opt threadweaver5 thunderbird-i18n-af thunderbird-i18n-ar thunderbird-i18n-ast thunderbird-i18n-be thunderbird-i18n-bg thunderbird-i18n-br thunderbird-i18n-ca thunderbird-i18n-cak thunderbird-i18n-cs thunderbird-i18n-cy thunderbird-i18n-da thunderbird-i18n-de thunderbird-i18n-dsb thunderbird-i18n-el thunderbird-i18n-en-gb thunderbird-i18n-en-us thunderbird-i18n-es-ar thunderbird-i18n-es-es thunderbird-i18n-et thunderbird-i18n-eu thunderbird-i18n-fi thunderbird-i18n-fr thunderbird-i18n-fy-nl thunderbird-i18n-ga-ie thunderbird-i18n-gd thunderbird-i18n-gl thunderbird-i18n-he thunderbird-i18n-hr thunderbird-i18n-hsb thunderbird-i18n-hu thunderbird-i18n-hy-am thunderbird-i18n-id thunderbird-i18n-is thunderbird-i18n-it thunderbird-i18n-ja thunderbird-i18n-ka thunderbird-i18n-kab thunderbird-i18n-kk thunderbird-i18n-ko thunderbird-i18n-lt thunderbird-i18n-ms thunderbird-i18n-nb-no thunderbird-i18n-nl thunderbird-i18n-nn-no thunderbird-i18n-pa-in thunderbird-i18n-pl thunderbird-i18n-pt-br thunderbird-i18n-pt-pt thunderbird-i18n-rm thunderbird-i18n-ro thunderbird-i18n-ru thunderbird-i18n-sk thunderbird-i18n-sl thunderbird-i18n-sq thunderbird-i18n-sr thunderbird-i18n-sv-se thunderbird-i18n-th thunderbird-i18n-tr thunderbird-i18n-uk thunderbird-i18n-uz thunderbird-i18n-vi thunderbird-i18n-zh-cn thunderbird-i18n-zh-tw tidy tinycdb totem-pl-parser tracker3-docs tracker3-miners udisks2-qt5 unarchiver unshield vim-runtime vivaldi vmaf vte-docs vte3 vte4 vulkan-intel vulkan-mesa-layers vulkan-swrast vulkan-virtio webkit2gtk webkit2gtk-4.1 webkit2gtk-4.1-docs webkit2gtk-docs webkitgtk-6.0 webkitgtk-6.0-docs zabbix-server

That is a huge list. I am wondering if your package list had packages you didn’t really have installed.

You have two choices. You can reinstall that list of packages or you can assume they shouldn’t be there and you can remove them.

Reinstalling them is probably the safer option.

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