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There was a potential fix for this I was exploring but since have not have time to test where by running the server standalone and by that I mean making a copy of starbound and placing that somewhere else for and configuring it solely for server use, then method one may not conflict with the install you are playing the game with.
(I don't have much hope though as assets loaded and in use seem to be the issue)
However I did see some benift form method ones flaw that being any previous characters you have created prior to starting the dedicated server executable are not phsyically delted or broken! they are simply hidden from the character menu while the server is running, viewing the logs shows that the assets from mods where in use which were not being found... ironicly probably because of what I said above.
That said it MAY be possible to use this to your advantage by using the now FREE character slot\slot's to make fresh charcaters for use on your presistant universe server (dedicated server) then when you close the dedicated server executable those should techincally now be hidden and your previous ones restored as that is what happend on my system can you confirm it?
Note
I am pondering about adding a Method Three! Starbound Dedicated Server does NOT actually require steam to function and since Steam allows you to login on more than one device simutaniously one could come to the decision that all this path linking and work arounds are pointless :)... If one is to host it dedicated on a seperate machine, you can actually install Steam on your Server Machine! and copy your existing starbound over to the new steam install and verify it. (it will find the exsting files and not download anything but I bet you knew that already)
Then create a workshop collection if you not already done so which contains all the stuff you need on the server bare in mind just about every single UI mod or visual mod is client sided ;) your now second steam login will download and update those and starbound for you! best part is will be completely seperate to your gaming machines install of starbound and workshop no more conflicts will happen.
So for now i will try and see if i can get the copy and run bat file to work
any ideas?
so what i did was trying to figure out how to copy just the content of the folders and not the folders themself
ones i found that i had to problem that all files are called contents.pak and it would just overwrite eachother, so i had to rename them
not being the best at batch files i went searching for a way to rename them to contents_(original subfolder name)
however being a noob at batch i couldn't figure that out, so my solution.... just use the nearest damned solution i could come up with
then i found out i could print the file size behind it instead
this seemed to me the most reliable way to do it since i highly doubt (thought it is posible) that you ever run in to 2 mods that are the exact same size up to the byte
so yea, thats my solution for now, feel free to clean up my mess xD
However if I was going to resort too a script to copy and rename I'd use a PowerShell script for the extra flexibility.
The good thing is you can create a service out of the PowerShell script and have it run when the date changes on a file. I'm not sure exactly from memory too explain how but I do know that the PowerShell shell is tightly tied into Windows where just about any variable will work.
Though if you want something more reliable which you can also use over the network I suggest this http://www.cobiansoft.com/cobianbackup.htm
Sure it's not a "2016" program but you will not be disappointed! It can do file lookup and rename so for what you want to do it can. You can rename a file on destination path and prefix or affix filenames aswell including sequencing same name files if you rather.
As stated it can do differential copies so only runs when schedule detects a change in the file and it can run over ftp and local network storage ;), it's FREE did I say FREE haha.
but when i make it load the pak files instead of the folders like i did i get this
and that time it does work, i can craft the items fine and place them and everything works fine
Complete Re-Write of the 1st post, and added a new method which 100% works every time when used properly.
Steam Guide Coming Soon
My only problem with this myself initially was "what if the workshop updates files while the server is running?"
Perhaps you know the answer. Does it work fine? Do you get errors? Are the files write-locked while the server is loaded?
Personally I don't think they're locked and they're also not loaded in once at the start and that's that -- I deleted the mod folder while the server was running at one point and immediately started getting errors out of the wazoo.
I run mine locally for a persistent shared universe for lan play and I usually let it update before I start it.
However for more serious hosting you would have thr query and remote connect enabled for a console so you would just have a moderator restart it.