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hey there is a new version out and the old ebuild works! 
 
This obsoletes #23525.

g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/X11R6/include -I/usr/qt/3/include
-I/usr/include/qt -I/usr/X11R6/include/qt -I../openbabel -DUNIX
-DRINGHOME="\"/usr/share/xdrawchem/\"" -DXDC_SERVER=\"herger.ibb.gatech.edu\" 
-g -c -o xruler.o `test -f 'xruler.cpp' || echo './'`xruler.cpp
moc ./application.h -o application.moc.cpp
moc: invalid option -- o
moc 1.1.0
Usage:
moc [OPTIONS]... [FILE]...
-V --version            Show program version and exit.
-h --help               Show usage and exit.
-r --recursively        Add files in direstories given as an argument
                        recursively.
-f --fullinfo           Show titles (eg from id3tags) instead of names in the
                        menu (default).
-s --shortinfo          Show file names in the menu (opposite to -f).
-m --musicdir           Go to your music directory after start (requires such
                        entry in the config file).
-e --errors             Show errors in streams.
-n --no-errors          Do not show errors in streams (opposite to -e).
-p --priority N         Set the priority to a given value.
-l --dont-play          Don't start playing files added as command line
                        arguments.
-R --repeat             Turn on repeat.
-E --no-repeat          Turn off repeat.
make[2]: *** [application.moc.cpp] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory
`/var/tmp/portage/xdrawchem-1.7.3/work/xdrawchem-1.7.3/xdrawchem'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/var/tmp/portage/xdrawchem-1.7.3/work/xdrawchem-1.7.3'
make: *** [all] Error 2

!!! ERROR: app-sci/xdrawchem-1.7.3 failed.
!!! Function src_compile, Line 20, Exitcode 2
!!! (no error message)

it fails for me :/ Any idea why/how? :)

You seem to have a different version of Qt. 
 
On my system the current version of Qt is 3.1.2-r4 
 
# moc -v 
Qt Meta Object Compiler version 26 (Qt 3.1.2) 
 
 

Sorry I am kinda blind these days. 
Rob, you have installed media-sound/moc, which interferes with moc from Qt - try 
 
# which moc 
/usr/qt/3/bin/moc 
 
The above is what I get with no media-sound/moc installed. 
Hermann 
 

oh fun. well spotted.

*thinks*

Is there a Gentoo standard procedure for conflicting binary names? 
Hermann 

Not as such no, as the paths are different. Not sure how to tell the makefile
where moc is either :/ Any ideas? Maybe tweak the path. Seems a bit hacky.

Created an attachment (id=14520) [details]
this ebuild makes use of QTDIR to ensure the correct moc binary is executed

Commited :) Many thanks.