Atom crashes when opening the "select file" modal

[zarelit]

Describe the bug
Atom crashes when opening a "save file", "open file" modal with an error printed in the journal. I did a bisection and it looks like it has been introduced in e8e569c

To Reproduce
Steps to reproduce the behavior:

1. Open atom
2. Create a new file
3. Try to save file

OR

1. Open atom
2. File -> Add Project Folder...

Expected behavior
Modal opens.

Additional context
The error printed in the journal. There might be some noise but there is an error in libglib-2.0.so.0.6200.4 and a core dump

Jul 06 19:50:06 playa kernel: traps: atom[21060] trap int3 ip:7f9a7fe29c75 sp:7ffe01f194a0 error:0 in libglib-2.0.so.0.6200.4[7f9a7fdf0000+80000]
Jul 06 19:50:06 playa systemd[1]: Started Process Core Dump (PID 21332/UID 0).
Jul 06 19:50:06 playa xsession[2285]: /nix/store/mynp9jqx52adr2q4klxlrh1fgzwgd0j0-atom-1.42.0/bin/.atom-wrapped: line 192: 21060 Trace/breakpoint trap   (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1
Jul 06 19:50:06 playa xsession[2285]: Fontconfig warning: "/etc/fonts/fonts.conf", line 86: unknown element "blank"
Jul 06 19:50:06 playa xsession[2285]: ** Message: 19:48:47.454: Remote error from secret service: org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.secrets was not provided by any .service files
Jul 06 19:50:06 playa xsession[2285]: ** Message: 19:48:47.455: Remote error from secret service: org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.secrets was not provided by any .service files
Jul 06 19:50:06 playa xsession[2285]: ** Message: 19:48:47.456: Remote error from secret service: org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.secrets was not provided by any .service files
Jul 06 19:50:06 playa xsession[2285]: ** Message: 19:48:47.458: Remote error from secret service: org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.secrets was not provided by any .service files
Jul 06 19:50:06 playa xsession[2285]: ** Message: 19:48:47.459: Remote error from secret service: org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.secrets was not provided by any .service files
Jul 06 19:50:06 playa xsession[2285]: (atom:21060): GLib-GIO-ERROR **: 19:50:06.312: No GSettings schemas are installed on the system
Jul 06 19:50:06 playa xsession[2285]: qt.qpa.xcb: QXcbConnection: XCB error: 3 (BadWindow), sequence: 51831, resource id: 138412033, major code: 15 (QueryTree), minor code: 0
Jul 06 19:50:06 playa xsession[2285]: qt.qpa.xcb: QXcbConnection: XCB error: 3 (BadWindow), sequence: 51835, resource id: 138412033, major code: 18 (ChangeProperty), minor code: 0
Jul 06 19:50:07 playa systemd-coredump[21333]: Process 21060 (atom) of user 1000 dumped core

This is the bisection log:

git bisect start
# bad: [a1b8dae54aedcae9acc0618abc08ad9fe13fdc37] alt-ergo: 2.3.0 → 2.3.1
git bisect bad a1b8dae54aedcae9acc0618abc08ad9fe13fdc37
# good: [db75eb4257161252246ee02deaf2dd91149714f1] Merge pull request #82741 from hercules-ci/backport-20.03-80102
git bisect good db75eb4257161252246ee02deaf2dd91149714f1
# bad: [97f65b2de9c30a3376bb17f6085a74f5eddfb04c] Merge pull request #82848 from aanderse/zhf/rsyslog
git bisect bad 97f65b2de9c30a3376bb17f6085a74f5eddfb04c
# bad: [ec0923f9830bc5ce68b5067fd68ba95a7942cc06] Merge pull request #82676 from veprbl/pr/texlive_2019_final_20.03
git bisect bad ec0923f9830bc5ce68b5067fd68ba95a7942cc06
# bad: [26a5a71da51626302dd27ffccfd71dd1865fcd28] tomcat8: 8.5.42 -> 8.5.51
git bisect bad 26a5a71da51626302dd27ffccfd71dd1865fcd28
# bad: [a0adbb1bdb92561b525dfc7dd3bfff880c5d956e] libarchive: 3.4.1 -> 3.4.2
git bisect bad a0adbb1bdb92561b525dfc7dd3bfff880c5d956e
# bad: [0c3057c59dd407a5e6b3c1a1a423d544961ea922] Merge pull request #81266 from Frostman/20.03-go-1.14
git bisect bad 0c3057c59dd407a5e6b3c1a1a423d544961ea922
# good: [e378b239f6c94d0e1e49f1f9bf2646b347a205d4] grafana: switch to latest go
git bisect good e378b239f6c94d0e1e49f1f9bf2646b347a205d4
# bad: [e8e569ce79897885fe9f59dd164413f9b7298c4c] wrapGAppsHook: Fix #78803
git bisect bad e8e569ce79897885fe9f59dd164413f9b7298c4c
# good: [e78f26b977155d091345c033d807658651bbd372] Merge branch 'release-20.03' into staging-20.03
git bisect good e78f26b977155d091345c033d807658651bbd372
# first bad commit: [e8e569ce79897885fe9f59dd164413f9b7298c4c] wrapGAppsHook: Fix #78803

Notify maintainers
@worldofpeace

Metadata

• system: "x86_64-linux"
• host os: Linux 5.4.49, NixOS, 20.03.2447.afa9ca61924 (Markhor)
• multi-user?: yes
• sandbox: yes
• version: nix-env (Nix) 2.3.6
• channels(zarel): "nixpkgs-20.09pre232692.7db146538e4"
• channels(root): "nixos-20.03.2447.afa9ca61924"
• nixpkgs: /home/zarel/.nix-defexpr/channels/nixpkgs

Maintainer information:

# a list of nixpkgs attributes affected by the problem
attribute: atom

[jtojnar]

That commit caused a regression but that should have been fixed by e544e03

What is the content of atom/electron file? There should be gtk's gsettings-schemas in XDG_DATA_DIRS.

[zarelit]

@jtojnar thank you for your help!

in the XDG_DATA_DIRS looks like there is no gsettings-schemas:

[zarel@playa:~/code/nixpkgs]$ echo $XDG_DATA_DIRS | tr ':' "\n" | grep -i setting

[zarel@playa:~/code/nixpkgs]$ echo $XDG_DATA_DIRS | tr ':' "\n" | grep -i schema

[zarel@playa:~/code/nixpkgs]$ echo $XDG_DATA_DIRS | tr ':' "\n" | grep -i gtk

I don't understand what is the atom/electron file you're referring to, where can I find it?

[jtojnar]

I meant that you should check /bin/atom in the atom package.

But now I looked into it and the issue is that Atom does not use the generic builder, which all setup hooks depend on, but does its own thing:

nixpkgs/pkgs/applications/editors/atom/default.nix

Lines 44 to 73 in 7403a99

	buildCommand = ''
	mkdir -p $out/usr/
	ar p $src data.tar.xz | tar -C $out -xJ ./usr
	sed -i -e "s|Exec=.*$|Exec=$out/bin/${pname}|" $out/usr/share/applications/${pname}.desktop
	mv $out/usr/* $out/
	rm -r $out/share/lintian
	rm -r $out/usr/
	sed -i "s/${pname})/.${pname}-wrapped)/" $out/bin/${pname}
	fixupPhase
	share=$out/share/${pname}
	patchelf --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
	--set-rpath "${atomEnv.libPath}:$share" \
	$share/atom
	patchelf --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
	--set-rpath "${atomEnv.libPath}" \
	$share/resources/app/apm/bin/node
	patchelf --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
	$share/resources/app.asar.unpacked/node_modules/symbols-view/vendor/ctags-linux
	dugite=$share/resources/app.asar.unpacked/node_modules/dugite
	rm -f $dugite/git/bin/git
	ln -s ${pkgs.git}/bin/git $dugite/git/bin/git
	rm -f $dugite/git/libexec/git-core/git
	ln -s ${pkgs.git}/bin/git $dugite/git/libexec/git-core/git
	find $share -name "*.node" -exec patchelf --set-rpath "${atomEnv.libPath}:$share" {} \;
	'';

In particular, it does not run preFixupPhases, which is necessary for wrapGAppsHook to work.

cc Atom maintainers @offlinehacker @NeQuissimus @ysndr