I get the same error if I run the commands you gave to me. I am on Windows btw, so I just ran the *.bat versions. I think it is caused by a dependency from Applied Energistics to Rotary Craft, here is the error:
warning: [options] bootstrap class path not set in conjunction with -source 1.6
E:\SVNs\NuclearControl\build\sources\java\shedar\mods\ic2\nuclearcontrol\crossmod\appeng\TileEntityNetworkLink.java:96: error: cannot access AdvancedShaftPowerReceiver
ItemStack is = chest.getInternalInventory().getStackInSlot(0);
class file for Reika.RotaryCraft.API.Power.AdvancedShaftPowerReceiver not found
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
The ^ is pointing to the dot between chest and getInternalInventory. Looks to me like Applied Energistics would require the mentioned class from rotarycraft to be loaded.