Try running it same as the Geany version from the command line, ex: $ echo "Some PHP Code Here" | php_beautifier -s4 -l "..." or $ cat "some-code-file.php" | php_beautifier -s4 -l "..."
done. Both the commands work fine in terminal.
What platform are you on? Version of Geany, version of GTK and Glib, from help->debug messages? Look for error messages in help->debug messages.
Xubuntu 12.10, Geany 1.22, GTK 2.24.13
Those are the error messages in Help>Debug:
11:03:17: Geany WARNING : php_beautifier -s4 -l "ArrayNested() NewLines(before=if:switch:while:for:foreach:function:T_CLASS:return:break,after=T_COMMENT) IndentStyles(style=k&r)": PHP Strict Standards: Non-static method Console_Getopt::readPHPArgv() should not be called statically in /usr/bin/php_beautifier on line 70 PHP Strict Standards: Non-static method Console_Getopt::getopt() should not be called statically in /usr/bin/php_beautifier on line 84 PHP Strict Standards: Non-static method Console_Getopt::doGetopt() should not be called statically in /usr/share/php/Console/Getopt.php on line 92 PHP Strict Standards: Non-static method PEAR::isError() should not be called statically in /usr/share/php/Console/Getopt.php on line 109 PHP Strict Standards: Non-static method Console_Getopt::_parseShortOption() should not be called statically in /usr/share/php/Console/Getopt.php on line 166 PHP Strict Standards: Non-static method PEAR::isError() should not be called statically in /usr/share/php/Console/Getopt.php on line 167 PHP Strict Standards: Non-static method Console_Getopt::_parseShortOption() should not be called statically in /usr/share/php/Console/Getopt.php on line 166 PHP Strict Standards: Non-static method Console_Getopt::_isShortOpt() should not be called statically in /usr/share/php/Console/Getopt.php on line 220 PHP Strict Standards: Non-static method Console_Getopt::_isLongOpt() should not be called statically in /usr/share/php/Console/Getopt.php on line 221 PHP Strict Standards: Non-static method PEAR::isError() should not be called statically in /usr/share/php/Console/Getopt.php on line 167 PHP Strict Standards: Non-static method PEAR::isError() should not be called statically in /usr/bin/php_beautifier on line 85
Those same messages are also shown in terminal but all works however!