I'm trying to play the Linux PixelJunk shooter release and, after completing two levels (that is, two spots on the map screen), I've spent enough time that, if I simply haven't reached some kind of checkpoint, it's a major design flaw in the game.

I couldn't find any explicit save command and, when I restarted the game, all my progress was lost.

Does anyone know how to solve this issue or do I have to grab a copy of VirtualBox and use the "save machine state" functionality in a manner similar to an emulator's savestate feature?

I have the same problem (Linux too - no saves), which is a pity because my kids enjoy playing the game... but they don't want to redo the same levels !

Have you found out a way to fix this problem ?

Not yet. I've been far too busy (first with coursework and tracking down bugs reported in my own creations, now with holiday preparations).

I'll let you know when I find a solution. (I say "when" because, even if it's just a set of instructions for getting the Windows version working flawlessly in PlayOnLinux, I will find one.)

Pixeljunk shooter will save your progress, if you start it with root rights.

The savegame-file is then in /root/.local/share/PJShooter. I tried to get it to work without root rights, but had no luck.

When you copy the savegame-file to /"your username"/.local/share/PJShooter/ and change the access privileges, so that everyone can read and write it, then the game will load the savegame, but immediately delete the savegame-file.
That means when you close the game and start it again, you have to start from the very beginning.

Then i changed the access privileges of the folder "PJShooter" in /"your username"/.local/share/PJShooter/ so that you can`t create oder delete any files. Now the game will not delete your savegame-file, but it also will not save any further progress.

Ugh. Well, at least we know more about the problem. When I'm not so burned out from trying symlink-based trickery, I'll have to run it in strace and see if I can figure out what it actually wants.

Same problem here. It does not create a save file when I complete a stage. And starting the game with root rights does not help.

Also it won't save all settings. The game starts every time in windowed mode even though I have played it in full screen.

I already reported it back when I opened this thread. Never received a fix.

As for your solution, it works beautifully and now I can finally stop procrastinating playing this. (Given how many games I own, I was putting off installing the Windows version of this in Wine)

I've hex-edited things before, so I'm a bit surprised I didn't think to investigate this avenue. I guess I was just too fixated on the strace output.

Just in case anyone using GNU/Linux now is reading this thread:
This was fixed ... when installing the game it will automatically use:
    ~/.local/share/PJShooter
as config directory, so no hexeditor necessary.

But if using a more recent GNU/Linux distro (like Kubuntu 20.10), one may get an error:
    <PATH>/PixelJunk_Shooter_incl_cfg/game/CaveShooter: symbol lookup error:
    /lib/i386-linux-gnu/libxcb-dri3.so.0: undefined symbol: xcb_get_reply_fds
and one should use the system lib ... so in 'start.sh' the line:
    ./"Shooter.sh"
should be changed in:
    LD_PRELOAD='/usr/$LIB/libstdc++.so.6' LIBGL_DRI3_DISABLE=1 ./"Shooter.sh"
So the game can start.

One should note that:
   o The game starts as a tiny stamp (on a 4k screen) but after changing settings by
      un-marking window, it will start in fullscreen mode looking good.
   o Controller F310 works perfectly with intuitive defaults:
      Keyboard and Controller are freely assignable - and Defaults (F310) intuitive:
        A (green) - Select
        B (red)     - Back/Escape
        Start         - Pause Menu
        ~
        LS           - movement of ship
        RS           - aiming
        LB|LT       - using hook/capture
        RB|RT     - shooting/fire (holding for larger rockets)