I'm building nautilus with meson and flatpak and with ccache uninstalled.
Seems when ccache is not installed in the system this errors happens when linking in nautilus:
[202/202] Linking target test/test-eel-string-rtrim-punctuation
[1/188] Compiling c object 'subprojects/libgd/libgd/gd@sta/gd-entry-focus-hack.c.o'
FAILED: subprojects/libgd/libgd/gd@sta/gd-entry-focus-hack.c.o 
ccache cc  '-Isubprojects/libgd/libgd/gd@sta' '-Isubprojects/libgd/libgd' '-I../../../../../Projects/nautilus/subprojects/libgd/libgd' '-Isubprojects/libgd' '-I../../../../../Projects/nautilus/subprojects/libgd' '-I/usr/include/at-spi2-atk/2.0' '-I/usr/include/at-spi-2.0' '-I/usr/include/dbus-1.0' '-I/usr/lib/dbus-1.0/include' '-I/usr/include/gtk-3.0' '-I/usr/include/gio-unix-2.0/' '-I/usr/include/pango-1.0' '-I/usr/include/atk-1.0' '-I/usr/include/cairo' '-I/usr/include/pixman-1' '-I/usr/include/freetype2' '-I/usr/include/harfbuzz' '-I/usr/include/gdk-pixbuf-2.0' '-I/usr/include/libpng16' '-I/usr/include/glib-2.0' '-I/usr/lib/glib-2.0/include' '-fdiagnostics-color=always' '-pipe' '-Wall' '-Winvalid-pch' '-O0' '-g' '-Wno-deprecated-declarations' '-Wno-deprecated-declarations' '-Og' '-fPIC' '-pthread' '-DLIBGD_GTK_HACKS=1' '-DLIBGD__VIEW_COMMON=1' '-DLIBGD_MAIN_ICON_VIEW=1' '-DLIBGD_MAIN_LIST_VIEW=1' '-DLIBGD_MAIN_VIEW=1' '-DLIBGD_TAGGED_ENTRY=1' '-DG_LOG_DOMAIN="libgd"' '-DG_DISABLE_DEPRECATED' '-MMD' '-MQ' 'subprojects/libgd/libgd/gd@sta/gd-entry-focus-hack.c.o' '-MF' 'subprojects/libgd/libgd/gd@sta/gd-entry-focus-hack.c.o.d' -o 'subprojects/libgd/libgd/gd@sta/gd-entry-focus-hack.c.o' -c ../../../../../Projects/nautilus/subprojects/libgd/libgd/gd-entry-focus-hack.c
ccache: error: /home/csoriano/.ccache/ccache.conf: No such file or directory

Once installed ccache it works fine.
I'm not sure what can be, and after discussing in #flatpak channel couldn't figure it out since ccache is optional in meson (it does ccache --version for checking) and builder does --ccache with flatpak-builder, but I guess that shouldn't change things.