Some "compiling from source" emulators crashing

[NowArrivingHere]

I am also having issues with both np2pi and Commander Genius crashing while the installation script is running. I will place my relevant log files and error messages below.

Raspberry Pi 3B (not overclocked)
RetroPie 4.2.16
RetroPie installed on top of Raspbian
2.4A power supply

np2pi:

Could not successfully install NEC PC-9801 emulator
/home/pi/RetroPie-Setup/tmp/build/np2pi/np2pi/bin/np2 not found

Log file: https://pastebin.com/3q1Uk7Ad

Commander Genius (shows as installed because it worked months ago, but updating currently fails and this has left cgenius unable to run):

Could not successfully install Commander Genius - Modern Interpreter for the Commander Keen Games (Vorticon and Galaxy Games)
/home/pi/RetroPie-Setup/tmp/build/cgeneius/vfsroot/games not found

Log file: https://pastebin.com/7Dn0hGnQ

EDIT: Thank you BuZz! np2pi installation is now working for me.

[darknior]

Thanks @BuZz i have update NP2PI and LR-Hatari without any problem.
Do you write to not use lr-hatari because the original hatari emulator is better like ever ?

I always have my problem with RETROARCH :(

You are real for the SHADER directory, it was root access i don't know why ? I have change it for pi.
But now it is my retroarch.cfg it don't like and crash the update :(

install -m644 docs/retroarch-cg2glsl.6 /opt/retropie/emulators/retroarch/share/man/man6
install -m644 media/retroarch.svg /opt/retropie/emulators/retroarch/share/pixmaps
« /home/pi/RetroPie-Setup/tmp/build/retroarch/retroarch.cfg » -> « /opt/retropie/emulators/retroarch/retroarch.cfg »
/home/pi
/opt/retropie/emulators/retroarch /home/pi

= = = = = = = = = = = = = = = = = = = = =
Configuring 'retroarch' : RetroArch - frontend to the libretro emulator cores - required by all lr-* emulators
= = = = = = = = = = = = = = = = = = = = =

error: bad index file sha1 signature
fatal: index file corrupt
fatal: Reference has invalid format: 'refs/remotes/origin/rpi
'
error: bad index file sha1 signature
fatal: index file corrupt
error: bad index file sha1 signature
fatal: index file corrupt
Copying new default configuration to /opt/retropie/configs/all/retroarch.cfg.rp-dist
/home/pi
Error running 'git pull' - returned 1
Error running 'git submodule update --init --recursive' - returned 1

Log ended at: jeudi 24 août 2017, 14:44:20 (UTC+0200)
Total running time: 0 hours, 7 mins, 8 secs

I try many things but nothing works for me :(
I read there you write to remove the CONFIG dir and install again RETROARCH but it is impossible, i work so many days on my configs ...
https://retropie.org.uk/forum/topic/9147/default-all-retroarch-cfg

I have try to remove the retroarch.cfg and expect it will create a new one but it crash too :(
Maybe if some one can share his file with me, i will use it to update and after i will update settings with mine.

Thanks