It's a bug. I looked for an open issue a while back and had no luck myself. It won;t affect your map though. Just annoying. 

I submitted it as an issue on Github just in case. 

The "View" -> "Show X brushes" (hint, skip, clip, etc) system was broken in TB2 RC4. This is the same code makes clip brushes semitransparent. It's fixed in git / will be fixed in the next RC. 

Probably a long shot if anyone knows this one-

In Hexen 2, water brushes (or rather, any brushes that are rendered underwater), have this really ugly warping effect. It basically arbitrarily warps the vertices of the underwater geometry around in a wavy fashion, which is a neat idea, but it makes clipping errors and texture stretching.

As far as I know, the variable for this is called r_waterwarp 1. I tried turning this off in the console (r_waterwarp 0), and in autoexec.cfg, but it claims "Unknown command".

I'm a little confused because I tried a couple other vars from the console commands, like "r_transwater 0" should remove transparency on water, but it also claims "Unknown command"

Here are (supposedly) the H2 console commands

https://www.quakewiki.net/archives/console/commands/hexen_2.html

Would anyone know why they don't work? I'm using glh2.exe, from Steam 

Ah, ok. Thanks for clearing that up, ericw! 

I'm pretty sure I've used Pak Explorer via Wine before, but can't get it to work any more. Any recommendations? I'm using Linux Mint 64 bit. 

I think the preferred .pak tool is Pakscape, which I've used with Wine in a Linux distro before. Maybe try that? 

If you just want to rip stuff out of a pak file and are comfortable with Python, I made this module a while back: https://github.com/neogeographica/expak 

damage_inc: Thanks, that did the trick!

Johnny Law: Thanks for the link. I'm not comfortable with any programming/coding language, but I'd like to be. Made a note of this; I might try to use it later just as a learning experience. 

All righty. :-) BTW if you do install that module, it also installs a command-line utility http://expak.readthedocs.io/en/latest/simple_expak.html so you don't need to write any Python code to do simple things with it. 

Noted, thanks very much! :) 

Here are shots of the 'clipping' with Hexen 2's water warping effect (which I assume, to be related to "r_waterwarp 1")

https://i.imgur.com/Pn1jag1.png

https://i.imgur.com/2AS3Dei.png

As you can see it warps around the tris of any underwater geometry. I'm not sure if this was in Quake (Quake 2?) also, but I'd like to disable it. "r_waterwarp 0" in console returns "Unknown command" but I am fairly sure that's the right variable

If no one ends up knowing about this one though then I'll have to live with it :-) 

this ugly warp effect and the fact that r_waterwarp is ignored are both problems in GLQuake as well. It's fixed in a lot of modern quake ports but perhaps not in the Hexen 2 port you are using? 

What does Port mean in this context? I'm using vanilla Hexen II, well, glh2.exe. Back in the day (when I had my disk) I remember there was just a "h2.exe" but the Steam version only comes with glh2.exe 

"Port" as in source port, modified engines made by the community.
http://uhexen2.sourceforge.net is the Hexen 2 one I know of. 

I'll have to patch that then, looks like they fixed a lot, thanks : )

I've run into another water-related problem and I'm very confused now. It seems that if your map has leaks, then VIS will not run, and water will look weird -- That is, it will look weirder than it is normally supposed to look. It will be 100% opaque instead of transparent, and you can see other parts of the level if you look into the water... Pictures work better here:

https://i.imgur.com/cDSzy8L.png
https://i.imgur.com/iZaaPXK.png
https://i.imgur.com/8tq80zP.png

The water is definitely not supposed to look that way. It's 'supposed' to look like this:

https://i.imgur.com/2AS3Dei.png

A note -- whenever the water appeared opaque like that, that was an indication that my map had leaks. I was fairly sure I didn't have any... but I slowly 'chunked off' entire parts of the map with giant wall chunks, and deleting any lights, etc that would've been outside the map, to try and find where the leak was. I eventually enclosed the entire map with new, giant brushes, enclosing the large map to a single hallway -- made a test water brush, and it still didn't look right (which means VIS isn't running, I guess)

I thought, then, maybe my map file is corrupt, and I made a new map. Single room, 6 sides, 1 light, 1 playerstart, no leaks, little barrier in the corner with 1 water brush inside ... that's the room pictures in the first three screenshots. Water STILL looks incorrect. What is happening here?

I should reiterate that this wasn't happening before, and water looked transparent and looked totally correct (aside from the vertex manipulation warpy effect of the engine). I'm baffled as to how this could still be messed up on a brand new map? 

Screenshots 2 and 3 look like a map that were QBSP'ed and VIS'ed without transparent water support - the vis data is culling stuff beneath the water surface when the player is above, because it thinks you can't see under the surface, but the engine is using transparency so you can see through and it looks glitchy.

The fix is to run QBSP with transparent water support. I'm not sure which tools you are using but check the docs for a "-transwater" command or something like ythat. If your tools don't have it my quake compiling suite does by default: http://ericwa.github.io/ericw-tools/ ; it supports hexen 2 with the -hexen2 flag added to qbsp.

but I slowly 'chunked off' entire parts of the map with giant wall chunks, and deleting any lights, etc that would've been outside the map, to try and find where the leak was.
This works but there are easier ways; TrenchBroom and JACK can load the pts file which should draw a path that goes through the leak. I think you can also load the leak in the engine with the "pointfile" command (in Quake at least). 

"I'm not sure which tools you are using but check the docs for a "-transwater" command or something like ythat. If your tools don't have it my quake compiling suite does by default: http://ericwa.github.io/ericw-tools/ ; it supports hexen 2 with the -hexen2 flag added to qbsp. "

To be honest, I'm not sure. I'm using that editor called BSP and - I had used it before long ago on my old computer, but when I tried to install it more recently on my new computer, I had forgotten how I got it all set up to actually work (error messages, missing files etc), and couldn't get it to run. So I just copied the entire folder over from my old computer on a flash drive. The point being that I'm not sure if the compile tools were downloaded separately or what, can't remember, but they are Bat files called Fast.bat, Full.bat, Leaktest.bat, Novis.bat, Relight.bat, Super.bat. I only have a general idea of how it all works and I usually just run Full.bat and then copy the created .bsp to my H2 folder to test it ingame.

The weird thing about the compiler not supporting transparent water is that...well... it WAS, before. I have no idea why it isn't now. In fact, "r_transwater" isn't even a valid command in the H2 console, and I'm unsure of where I could've accidentally turned off a setting like this, since the build files are just Bats that I run from a drop-down from the editor. :[

The easiest thing for me to try first (I only thought of this now), is to re-copy over my BSP editor files, so I'll try that first. 

I suggest using Necros' compiler GUI and Ericw's tools instead of those batch files that came with BSP. You will just have Nercos' GUI running in the background and alt tab to it when you want to compile.

The GUI is the easiest way to compile maps and it's extremely customizable. I recommend reading the entire web page before using it:

https://shoresofnis.wordpress.com/utilities/ne_q1spcompilinggui/ 

GUI program wants these. I have them, but nowhere that I put them it seems to like?

I tried:

same directory as Compiling GUI
directory of .map file (source)
directory of .bsp (output)
directory of the utils (qbsp, vis, light)
system32
sysWOW64

(I needed these dlls before for using bsputil, but putting them in the same folder as bsputil solved that) 

Disregard that, sorry. This was a problem of 32- 64- mismatching. The DLLs I have mentioned in the above post, are 32-bit, because other tools that required them were 32-bit. My OS is 64 so I downloaded 64-bit of eric's tools, thus it didn't recognize the DLLs existing. Whoops. :) 

..And for some good news..

https://i.imgur.com/qX21b3a.png

The water transparency is correct again now! The GUI+eric's compilers worked out

Thanks, guys.
I KNEW there wasn't a leak, man!

I have no idea why transparency suddenly disabled itself in the pre-packaged qbsp.exe/vis.exe/light.exe that came with my "BSP" Editor, and I will probably never find out either. The next thing is probably to download Hammer of Thyrion but I think I'll work on the map for a while first. :) 

Glad you got it working. take a look at *waterskip in the qbsp readme of eric's tools. if you put that texture on every surface but the top of the water - it really helps with weird water effects. 

Hmm, I used TexMex to add a *WATERSKIP texture to my wad and put it on all the water brush surfaces, aside from the top surfaces - but I still get the wavy vertices for any underwater geometry. Maybe a Hexen 2 specific problem? Or is there something else I need to do?

They worked, though, in the sense that it was still water in-game, and they were invisible - that is, the sides of adjacent water brushes were invisible - but they were actually invisible before, also. 

The "wavy" water is a in-engine feature. Not related to textures.