It seems there's no way of getting the product from a canning machine using buildcraft wooden pipes. This is a real pain if you want to automate the canning of biofuel, since the product can't stack! I know that inter-mod support is not something that most mod developers deal with, but I'm sure it's just a matter of rearranging some data value to make it work? It would be amazing if this could be made possible in the next release. Thanks!
[Question]BuildCraft with canning machines
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I am also having this problem. It seems that regardless of the side you try to pipe in/out of, it always puts items in this order:
1) the item to be canned (top)
2) the battery (left)
3) the output slot (right)
4) the empty can slot (bottom)