To be honest, I do not yet know what is the problem with your install.
So, in order to help you, I need some more info.
Your fpc.cfg should contain something like:
# begin fpcup do not remove x86_64-linux
#cross compile settings dependent on both target OS and target CPU
#IFDEF FPC_CROSSCOMPILING
#IFDEF CPUX86_64
#IFDEF LINUX
# Inserted by fpcup 22-10-2016 13:44:41
-FDC:\NewPascal\cross\bin\x86_64-linux\
-XPx86_64-linux-
-Tlinux
-FlC:\NewPascal\cross\lib\x86_64-linux\
-Xr/usr/lib
#ENDIF
#ENDIF
#ENDIF
# end fpcup do not remove
So, when you choose Linux 64 bit, these settings point FPC towards the right binutils and libraries.
binutils: C:\NewPascal\cross\bin\x86_64-linux
libs: C:\NewPascal\cross\lib\x86_64-linux
Also, you should have a directory C:\NewPascal\fpc\units\x86_64-linux, filled with all kinds of packages.
Correct ?
OK @DonAlfredo - I think I know what the problem was, and it was (as expected) my fault.
Here's how I messed up - it may be useful to you to solve other folk's problems.
1. I installed NewPascal with cross-compilers for Linux 32/64 as per instructions
2. I opened an existing project which had been created with my previous fpc/laz distribution and found it wouldn't cross-compile. (mistake #1)
(this was my error - I should have tested with a new clean empty Application in NewPascal)
3. In order to 'fix' things, I ran fpcup in update mode to the NewPascal folder. I now know this was a stupid thing to do because it must have messed up the NewPascal environment by deleting the linux fpc/units and God knows what else. (mistake #2)
4. I then (belatedly) tested using Create New Application in NewPascal for Win64, Linux32 and Linux64. It didn't work of course and I blamed the distribution. (mistake #3)
Now I see that I made 2 fatal assumptions:
1. Ignoring an existing projects environment (lpi file?) when testing a new environment
2. Trying to 'fix it myself' using fpcup, and then
compounding the error by not telling you I'd done it when asking for help.
BTW in order to cross-compile to linux 32/64, every lpr file needs the lines you posted. It doesn't work otherwise. Perhaps you could put that on the web page.
$IFDEF LINUX}
{$IFDEF FPC_CROSSCOMPILING}
{$linklib libc_nonshared.a}
{$IFDEF CPUARM}
// if we have a GUI, uncomment
// {$linklib GLESv2}
{$ENDIF}
{$ENDIF}
{$ENDIF}
All works well now, and the 'NewPascal initiative' is a credit to your ingenuity and hard work.
Perhaps the only good thing to come from this is perhaps to warn NewPascal users NOT to:
1. Test cross-compiling using an existing project (or delete the lpi file before trying it)
2. Attempt to update using fpcup unless you know what you're doing (I didn't!)
Thanks for your patience, and I am now loving the 'NewPascal environment'