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Uhm weird as im able to compile it on linux without problem.
Have you run a apt-get upgrade/update for gcc etc ?
Not sure if it will help but it might help :p.
Btw what linux distro are you using ?
I'm myself quite a linux noob. but i got it compiling and running without to much trouble.
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I'd try deleting all MCServer sources and checking them out afresh. If you did some changes and later updated, there could have been conflicts which would be marked in the file and thus the files won't compile.
Or if you don't want to clean out everything, try "svn status" and see what it gives. If there's a conflict, you need to solve it before compiling.
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I had deleted everything and redid the svn update as I do every time I modify something. SO that's ruled out by default. Like I said I'm switching distros, so we'll see how it works once I switch. I think Fedora has been going the wrong direction since they decided to stick with GNOME 3, instead of going to MATE or xfce, for the default install.
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Seems like the squirrel vm is causing too much trouble. I'm definitely gonna remove it. In the meantime, you can open the GNUmakefile and add -fpermissive to CXXFLAGS in the release section, that should temporarily fix the compilation.