LilyPondTool's PDF viewer solves this problem by automatically closing
the file when compiling.
In Windows, you can also use taskkill.exe to close the pdf before the
compilation
http://commandwindows.com/taskkill.htm
Here is the little script (lily.bat ) i use to run lilypond.
%%%%%%%%%%%%%%%%%%%%%
@echo off
cd /D "%~dp1"
taskkill /FI "WINDOWTITLE eq %~n1.pdf*" > null
cls
echo.
echo --------------------------------
echo.
lilypond "%~nx1"
if exist "%~n1.pdf" start "" "%~n1.pdf"
echo.
echo -------------------------------
echo.
pause >nul
%%%%%%%%%%%%%%%%%%%%%%%%%%%
I think something equivalent can be made in linux.
Gilles
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