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I was able to compile one module, but when I tried to compile the problematic module, there is no output:

josh@josh-desktop:~/Desktop/BlitzMax/bin$ ./bmk makemods leadwerks.bankex
Archiving:bankex.debug.linux.x86.a
ar: creating /home/josh/Desktop/BlitzMax/mod/leadwerks.mod/bankex.mod/bankex.debug.linux.x86.a
Archiving:bankex.release.linux.x86.a
ar: creating /home/josh/Desktop/BlitzMax/mod/leadwerks.mod/bankex.mod/bankex.release.linux.x86.a
josh@josh-desktop:~/Desktop/BlitzMax/bin$ ./bmk makemods leadwerks.apptiming
josh@josh-desktop:~/Desktop/BlitzMax/bin$

Here is the source to leadwerks.apptiming:
Import leadwerks.mathex



Rem

bbdoc: Leadwerks.AppTiming

End Rem

Module leadwerks.apptiming



Private



Global GAMETIME_UPS

Global GAMETIME_UPDATES

Global GAMETIME_VALUE

Global GAMETIME_PAUSESTART=0

Global GAMETIME_SPEED#=1.0

Global GAMETIME_DESIREDGAMELOOPTIME#=1000.0/60.0

Global GAMETIME_LASTUPDATETIME=0

Global GAMETIME_LASTUPSTIME



Public



Rem

bbdoc:

End Rem

Global AppTimeSmoothing#=4.0



Rem

bbdoc: 

End Rem

Global AppTimeUPS#=60.0



Rem

bbdoc: 

End Rem

Function UpdateAppTime()

	GAMETIME_DESIREDGAMELOOPTIME=1000.0/AppTimeUPS



	time=MilliSecs()



	If GAMETIME_LASTUPDATETIME=0

		GAMETIME_SPEED#=1.0

		GAMETIME_LASTUPDATETIME=time

		GAMETIME_VALUE=time

		GAMETIME_LASTUPSTIME=time

		'Return GAMETIME_VALUE

	Else

		GAMETIME_ELAPSED=time-GAMETIME_LASTUPDATETIME

		'If GAMETIME_ELAPSED<0 Notify GAMETIME_LASTUPDATETIME+", "+time

		If GAMETIME_ELAPSED=0 GAMETIME_ELAPSED=1	

		GAMETIME_SPEED=Curve(Float(GAMETIME_ELAPSED)/Float(GAMETIME_DESIREDGAMELOOPTIME),GAMETIME_SPEED,AppTimeSmoothing)'((Float(GAMETIME_ELAPSED)/Float(GAMETIME_DESIREDGAMELOOPTIME))+GAMETIME_SPEED)/2.0

		'If GAMETIME_SPEED>4.0 GAMETIME_SPEED=4.0

		GAMETIME_VALUE=GAMETIME_VALUE+GAMETIME_ELAPSED

		GAMETIME_LASTUPDATETIME=time

		'programlog "Gamespeed (internal): "+GAMETIME_SPEED

		'Return GAMETIME_VALUE

	EndIf

	

	GAMETIME_UPDATES:+1

	If GAMETIME_VALUE-GAMETIME_LASTUPSTIME>=1000

		GAMETIME_LASTUPSTIME=GAMETIME_VALUE

		GAMETIME_UPS=GAMETIME_UPDATES

		GAMETIME_UPDATES=0

	EndIf

	

EndFunction



Rem

bbdoc:

End Rem

Function UPS:Int()

	Return GAMETIME_UPS

EndFunction



Rem

bbdoc: 

End Rem

Function AppTime()

	Return GAMETIME_VALUE

EndFunction



Rem

bbdoc:

End Rem

Function PauseApp:Int()

	If GAMETIME_PAUSESTART>0 Return False

	GAMETIME_PAUSESTART=MilliSecs()

	Return True

EndFunction



Rem

bbdoc:

End Rem

Function AppPaused:Int()

	If GAMETIME_PAUSESTART>0

		Return True

	Else

		Return False

	EndIf

EndFunction



Rem

bbdoc: 

End Rem

Function ResumeApp()

	If GAMETIME_PAUSESTART=0 Return

	If GAMETIME_LASTUPDATETIME

		elapsed=MilliSecs()-GAMETIME_PAUSESTART

		GAMETIME_LASTUPDATETIME:+elapsed

	EndIf

	GAMETIME_PAUSESTART=0

EndFunction



Rem

bbdoc: 

End Rem

Function AppSpeed#()

	Return GAMETIME_SPEED

EndFunction



Rem

bbdoc: 

End Rem

'Function UPS#()

'	Return AppTimeUPS/GAMETIME_SPEED

'EndFunction


I commented out the Module line and attempted to compile apptiming.bmx in the IDE, and received this error:
Building AppTiming
Compiling:AppTiming.bmx
flat assembler version 1.64
3 passes, 7193 bytes.
Linking:AppTiming.debug
/usr/bin/ld: warning: libstdc++.so.6, needed by /usr/lib/libGLU.so, may conflict with libstdc++.so.5

Process complete