You can carry 10 wood and your hammer with you, drop a workstation at the mouth of your channel, and repair your ship before starting an extended voyage.

You can then dismantle the workstation, pick up the wood and carry it with you. If you take damage during the voyage you can stop by a rock or small island, drop the workstation, repair, pick up the workstation again and continue on your voyage.

If you carry the materials to build a portal with you (and you keep an open portal at your home base) you can drop the work station at your destination and build the portal and connect it to the open portal at your base (make sure that you kill any creatures in range of your portal so they don't destroy it while you aren't there). You can then move anything that isn't metal (or a dragon egg) to and from your home base.

If you make sure that you have room and weight available in your inventory you can stand on the mast of your ship, use your axe to destroy it, recover all the materials that were used in its construction, portal back to your home base, and store the ship components until you are once again ready to sail away. All you need to rebuild the boat is a workstation. No roof required.