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When I try skype --secondary, I get:

Gtk-Message: Failed to load module "overlay-scrollbar"
Gtk-Message: Failed to load module "unity-gtk-module"

With sudo nautilus I get:

(nautilus:15683): Gtk-WARNING **: Failed to register client: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name org.gnome.SessionManager was not provided by any .service files

And I also get some other GTK+ warnings when installing for example VMware or other programs.

I get these errors, but everything works just fine, but I want to know why is this happening and how can I resolve this.

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Most of these are not errors, they are warnings or messages. The issues are, more often than not, minor programming mistakes or dependence on deprecated APIs etc.

You should not care about these, as long as the applications are working as expected. Unless if you are a developer of course.

In your Nautilus example, however, this is not even a real issue, the warning informs you that the current user does not have a D-Bus session, which is to be expected, if you are running it as root. Don't use sudo to run graphical applications, use PolicyKit instead:

pkexec nautilus
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  • pkexec needs to be configured first to launch graphical applications. You would usually use gksudo or at least sudo -H instead.
    – Byte Commander ♦
    Oct 26, 2015 at 13:57
  • gksudo (the original) is AFAIK deprecated. And the new gksu is using PolicyKit as its backend.
    – meskobalazs
    Oct 26, 2015 at 14:18
  • All true, but I think anyone with GTK experience will admit that GTK is, at times, overly verbose with non-issues that should probably be silenced.
    – EntangledLoops
    Feb 6, 2017 at 21:53

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