GNOME is no longer running at bootup

Yesterday, I did a system update with pamac. One of the apps would not update (see footnote) so I removed all orphans (in the GUI), thinking I’d run out of disk space as I have on another computer. I had to repeat this a few times before the orphans were all gone. I also did some cleanup ('pamac clean --keep 3" and “pamac clean --build-files”). Then I suspended overnight. Today I returned and could not enter my password. The login screen looked ok but when I typed there was a sort of cursor flash but no characters appeared. I also could not shutdown because the only option under Power was Suspend. So I forced shutdown by holding the power button for a while.

On restart, I only have a console and can type commands but not start up GNOME (I don’t know how to).

I think I removed something that GNOME needs that was registered as an orphan.

Can I get a list of what was removed (pamac history??) and reinstall, or is there another way to repair GNOME?

The alternative is to reinstall everything but I first need to backup /home as I don’t trust my latest backup. I tried mounting an external WD Passport drive that was formatted to work on Windows and Linux (fdisk shows it as HFS/NTFS/exFAT). When I mount it, the mount is owned by root, and when I “rsync -a” to that, all the files are owned by root and have full permissions (-rwxrwxrwx) so it’s not a good sync. Maybe it’s because of the way it’s formatted?

Footnote: the app that wouldn’t update was cisco packttracer which I later remembered I’d set up for a course, so I just removed it. Didn’t think it would cause this much trouble :frowning:

Hi @johnsgp,

I’d recommend following this guide:

Hope it helps!

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Microsoft filesystems do not support POSIX file ownership and permissions. By consequence, these are only virtual, and they are set at mount time, through the mount options.

It is a very bad idea to try and back up to a Microsoft filesystem, exactly because all of the POSIX permission-related information will be lost.


Just a suggestion to keep it simple:
you can run the backup of your /home as root - but not with rsync.
Use tar instead - it creates an archive, a single file, the contents of which are not affected by the capabilities and permissions of the underlying file system.


It is possible to look into the logfiles, to find what you did remove. Then it may be best to reinstall these. (Or rollback with timeshift) :footprints:

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Yes. It prints to pacmans log.

grep -i removed /var/log/pacman.log
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Hi @Mirdarthos, thanks for this tip but I don’t think it applies as I did not interrupt the update. It completed successfully.

Hi @cscs - this is exactly what I needed. I got hold of the list of deleted programs and reinstalled them, and all is well again! I don’t know which one(s) were the important ones but clearly, removing orphans is not safe. I will approach it with caution in future. I issued this command to fix it but probably didn’t need all of these. I don’t recommend this as a solution for anyone else: I’m only including it here in case someone notices what got deleted and has a look into why fundamentals get deleted as orphans by pamac.

sudo pamac install endeavour opencolorio python-jsonschema perl-locale-codes wayland-protocols gtk-vnc python-wheel jemalloc qt6-5compat shared-color-targets alsa-card-profiles libindicator-gtk3 autoconf pugixml ldns lib32-libvisual libconfig python-jaraco.test python-appdirs yq mbedtls quazip-qt5 perl-mozilla-ca python-anytree unpaper python-async-timeout cmake libisofs geocode-glib pkgfile kitty-terminfo libgit2 kdsoap-ws-discovery-client wireguard-tools lib32-readline perl-config-general perl-filesys-df intltool python-pytest pastebinit python-pysmbc gendesk perl-list-moreutils perl-set-intspan perl-pdf-builder libvips perl-gtk3-simplelist debugedit perl-log-log4perl cython gradience lib32-attr perl-pdf-api2 bison python-pyopencl xorg-server-xvfb rest python-installer python-nspektr foomatic-db-engine dotnet-runtime yarn portmidi libidl2 electron squashfuse perl-graphics-tiff appstream-glib python-toml python-pybluez liblouis python-pydrive kitty-shell-integration perl-image-sane libusb-compat python-setuptools-scm gdb perl-date-calc lib32-gtk3 python-build lib32-smpeg automake gdm lua52 kjs gptfdisk perl-data-uuid vala itstool meson python-mock dkms electron25 python-cssutils python-poetry-core python-distro gsl lib32-pcre js102 python-mako python-pytools python-svglib pkgconf pyopencl-headers perl-exception-class python-argcomplete perl-bit-vector source-highlight perl-xml-libxml lib32-libepoxy libvisual python-lark-parser re2 yaml-cpp perl-font-ttf glew make python-tqdm faudio perl-dbi minizip-ng python-pyproject-hooks ninja python-pbr python-material-color-utilities python-pyrsistent perl-extutils-depends jsoncpp tinyxml smpeg python-pluggy rhash perl-extutils-pkgconfig gdb-common http-parser python-anyascii kdsoap-qt6 perl-test-requires dnssec-anchors libwrap python-jsonschema-specifications python-iniconfig perl-list-moreutils-xs python-yapsy pystring lib32-libnsl cfitsio python-xmltodict gtk-doc libcgif python-tomlkit perl-exporter-tiny patch cppdap lib32-colord glib2-docs python-numpy perl-alien-libxml2 python-regex python-cssselect2 python-referencing perl-devel-stacktrace perl-class-data-inheritable perl-io-string perl-carp-clan lib32-lcms2 docbook-xsl python-reportlab opencl-headers cblas docbook-xml perl-alien-build python-tinycss2 python-rpds-py perl-ffi-checklib perl-path-tiny perl-file-chdir python-webencodings perl-capture-tiny

There were a few more removals which would not reinstall, so I removed them from the list:

webkit2gtk-5.0 lib32-libwrap nodejs-nativefier lib32-faudio js91 js78 openssl-1.0 lib32-openssl-1.0 gnome-shell-extension-material-shell libsidplay

A few things to point out
endeavor is not a package in repos or aur.
Also … do not use sudo with pamac.

Never has been, especially if you arent careful to mark packages as explicit, etc.
In the past pamac removed packages using recursive cascade which could be a problem, but i think that was reversed a long time ago.
Always check the package list first before removing.

pacman -Qdt

~ I dont need any of these ~

sudo pacman -Rns $(pacman -Qdtq)
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Thanks @Aragorn, I know that using a Windows FS is not a good idea, but I explicitly formatted the drive for general use when I bought it years ago (or so I thought), so my confusion is why fdisk says it’s type HPFS/NTFS/exFAT (I left out the ‘P’ yesterday). Stranger yet, when I mounted from the console (sudo mount /dev/sdc1 /run/media/xyz), then rsync works as I previously described, but when I mount using Nautilus, the permissions are preserved perfectly.

However, I’ll use the tarball method instead. I just need to decide what to backup. I think it’s /home, /etc and /opt, or maybe just /home is enough, since I’m planning to switch from Manjaro GNOME to Manjaro i3wm.

I think after reinstalling Manjaro, I will switch to mostly using pacman.

fdisk -l gives just the general type, not what file system it actually is

If you want to know what file system is on the disk, use:
lsblk -f
for instance

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