This is, what I get by test-running the installed lyx 2.0.5-1
with 
wolfgang@wolfgang:/mnt/sda/home/wolfgang/lyx-2.0.5.1$ ./src/lyx &
[1] 15863
wolfgang@wolfgang:/mnt/sda/home/wolfgang/lyx-2.0.5.1$ LyXRC.cpp (1130): 
Ignoring unknown flag `zipped=native' for format `dia'.
LyXRC.cpp (1130): Ignoring unknown flag `zipped=native' for format `odg'.
Warning: Die Konfigurationsdatei konnte nicht gelesen werden
= configuration file could not be read
----------------------------------------
Fehler beim Lesen der Konfigurationsdatei
preferences.
Bitte prüfen Sie Ihre Installation.
check your installation

Checking config.log gives me a number of 
result: no
outputs, the second one being:

configure:4744: checking whether we are cross compiling
configure:4752: gcc -o conftest    conftest.c  >&5
configure:4756: $? = 0
configure:4763: ./conftest
configure:4767: $? = 0
configure:4782: result: no
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
How would I go ahead to track down the error in reading the config file?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>


Wolfgang

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