AVRDudeDownloader's extractTarBz2File is incorrect on latest Ubuntu LTS

[fenollp]

Steps to make the bug happen

1. Firmware Update (dialog)
2. Port set to /dev/ttyACM0
3. Clicking "Huge"
4. See error

What was supposed to happen
Firmware upgrade should work.

I managed to work around the problem and this issue should describe how.

Platform (please complete the following information):

• Version: 7.59.1 7621147 (installed via deb, compiled by forking repo + getting CI to generate artefact)
• OS: Ubuntu 24.04.1 LTS
• Robot model (if any): Makelangelo 5 huge

Log file

00:09:56.911 [AWT-EventQueue-0] DEBUG c.m.m.f.FirmwareUploaderPanel - maybe downloading avrdude...
00:09:57.045 [AWT-EventQueue-0] INFO  c.m.m.f.AVRDudeDownloader - download from: http://downloads.arduino.cc/tools/avrdude-6.0.1-arduino2-i686-pc-linux-gnu.tar.bz2
00:09:57.045 [AWT-EventQueue-0] INFO  c.m.m.f.AVRDudeDownloader - temp file: /tmp/download351843625700052922.bz2
00:09:57.213 [AWT-EventQueue-0] INFO  c.m.m.f.AVRDudeDownloader - Extracting tar.bz2 file
00:09:57.464 [AWT-EventQueue-0] INFO  c.m.m.f.AVRDudeDownloader - new path: /home/pete/.makelangelo/avrdude-6.0.1
00:09:57.464 [AWT-EventQueue-0] INFO  c.m.m.f.AVRDudeDownloader - trying path: /home/pete/.makelangelo/avrdude-6.0.1/avrdude
00:09:57.464 [AWT-EventQueue-0] INFO  c.m.m.f.AVRDudeDownloader - trying path: /home/pete/.makelangelo/avrdude-6.0.1/bin/avrdude
00:09:57.464 [AWT-EventQueue-0] DEBUG c.m.m.f.FirmwareUploader - setting install path to /home/pete/.makelangelo/avrdude-6.0.1
00:09:57.464 [AWT-EventQueue-0] DEBUG c.m.m.f.FirmwareUploaderPanel - maybe downloading firmware...
00:09:57.925 [AWT-EventQueue-0] INFO  c.m.m.f.FirmwareDownloader - Latest Release: 2023-11-03-01
00:09:58.563 [AWT-EventQueue-0] INFO  c.m.m.f.FirmwareDownloader - file downloaded ok.
00:09:58.563 [AWT-EventQueue-0] DEBUG c.m.m.f.FirmwareUploaderPanel - finding avrdude file...
00:09:58.563 [AWT-EventQueue-0] INFO  c.m.m.f.FirmwareUploader - Searching for avrdude starting in /home/pete/.makelangelo/avrdude-6.0.1
00:09:58.564 [AWT-EventQueue-0] DEBUG c.m.m.f.FirmwareUploaderPanel - finding conf file...
00:09:58.564 [AWT-EventQueue-0] INFO  c.m.m.f.FirmwareUploader - Searching for avrdude.conf starting in /home/pete/.makelangelo/avrdude-6.0.1
00:09:58.564 [AWT-EventQueue-0] DEBUG c.m.m.f.FirmwareUploaderPanel - setup...
00:09:58.565 [AWT-EventQueue-0] DEBUG c.m.m.f.FirmwareUploader - uploading firmware...
00:09:58.565 [AWT-EventQueue-0] DEBUG c.m.m.f.FirmwareUploader - running command: /home/pete/.makelangelo/avrdude-6.0.1/bin/avrdude -C/home/pete/.makelangelo/avrdude-6.0.1/etc/avrdude.conf -v -V -patmega2560 -cwiring -P/dev/ttyACM0 -b115200 -D -Uflash:w:/home/pete/.makelangelo/firmware-huge.hex:i
00:09:58.569 [AWT-EventQueue-0] DEBUG c.m.m.f.FirmwareUploader - update finished
00:09:58.569 [AWT-EventQueue-0] ERROR c.m.m.f.FirmwareUploaderPanel - upload failed.

Additional context
I encountered a few issues:

First: extracting tar.bz2 drops chmod and symlinks

AVRDudeDownloader on my distro ended up with unusable files:

• unexecutable avrdude_bin
• some files were empty

     .makelangelo λ t avrdude-6.0.1
[4.0K]  avrdude-6.0.1/
├── [4.0K]  bin/
│   ├── [ 108]  avrdude*
│   ├── [368K]  avrdude_bin*
│   └── [1.3K]  libusb-config*
├── [4.0K]  etc/
│   └── [453K]  avrdude.conf
├── [4.0K]  include/
│   ├── [4.0K]  libusb-1.0/
│   │   └── [ 67K]  libusb.h
│   └── [8.6K]  usb.h
└── [4.0K]  lib/
    ├── [  19]  libusb-0.1.so.4 -> libusb-0.1.so.4.4.4*
    ├── [   0]  libusb-0.1.so.4.4.4*
    ├── [116K]  libusb-1.0.a
    ├── [1017]  libusb-1.0.la*
    ├── [  19]  libusb-1.0.so -> libusb-1.0.so.0.1.0*
    ├── [  19]  libusb-1.0.so.0 -> libusb-1.0.so.0.1.0*
    ├── [102K]  libusb-1.0.so.0.1.0*
    ├── [ 15K]  libusb.a
    ├── [1.1K]  libusb.la*
    ├── [  19]  libusb.so -> libusb-0.1.so.4.4.4*
    └── [4.0K]  pkgconfig/
        ├── [ 386]  libusb-1.0.pc
        └── [ 363]  libusb.pc

7 directories, 18 files

My fix:

cd ~/.makelangelo
we http://downloads.arduino.cc/tools/avrdude-6.0.1-arduino2-i686-pc-linux-gnu.tar.bz2
rm -rf avrdude-6.0.1
tar --dereference --extract --file avrdude-6.0.1-arduino2-i686-pc-linux-gnu.tar.bz2

Note --dereference to follow symlinks. This ends up with usable files:

  2s .makelangelo λ t avrdude-6.0.1
[4.0K]  avrdude-6.0.1/
├── [4.0K]  bin/
│   ├── [ 108]  avrdude*
│   ├── [368K]  avrdude_bin*
│   └── [1.3K]  libusb-config*
├── [4.0K]  etc/
│   └── [453K]  avrdude.conf
├── [4.0K]  include/
│   ├── [4.0K]  libusb-1.0/
│   │   └── [ 67K]  libusb.h
│   └── [8.6K]  usb.h
└── [4.0K]  lib/
    ├── [  19]  libusb-0.1.so.4 -> libusb-0.1.so.4.4.4*
    ├── [ 22K]  libusb-0.1.so.4.4.4*
    ├── [116K]  libusb-1.0.a
    ├── [1017]  libusb-1.0.la*
    ├── [  19]  libusb-1.0.so -> libusb-1.0.so.0.1.0*
    ├── [  19]  libusb-1.0.so.0 -> libusb-1.0.so.0.1.0*
    ├── [102K]  libusb-1.0.so.0.1.0*
    ├── [ 15K]  libusb.a
    ├── [1.1K]  libusb.la*
    ├── [  19]  libusb.so -> libusb-0.1.so.4.4.4*
    └── [4.0K]  pkgconfig/
        ├── [ 386]  libusb-1.0.pc
        └── [ 363]  libusb.pc

7 directories, 18 files

Second: missing libtinfo5 (32bit)

     .makelangelo λ /home/pete/.makelangelo/avrdude-6.0.1/bin/avrdude -C/home/pete/.makelangelo/avrdude-6.0.1/etc/avrdude.conf -v -V -patmega2560 -cwiring -P/dev/ttyACM0 -b115200 -D -Uflash:w:/home/pete/.makelangelo/firmware-huge.hex:i
/home/pete/.makelangelo/avrdude-6.0.1/bin/avrdude: error while loading shared libraries: libtinfo.so.5: cannot open shared object file: No such file or directory

Turns out it's replaced by libtinfo6 on latest Ubuntu LTS. I found debs at https://www.ubuntuupdates.org/package/core/focal/universe/updates/libtinfo5
I initially installed the 64bit version but avrdude is a 32bit executable. Maybe it's possible to switch to an amd64 version? I didn't look.

Fix:

we http://security.ubuntu.com/ubuntu/pool/universe/n/ncurses/libtinfo5_6.2-0ubuntu2.1_i386.deb
sudo dpkg -i libtinfo5_6.2-0ubuntu2.1_i386.deb
sudo apt --fix-broken install # Add missing 32bit packages (libc, ...)
sudo dpkg -i libtinfo5_6.2-0ubuntu2.1_i386.deb
ln -s /usr/lib/i386-linux-gnu/libtinfo.so.5 avrdude-6.0.1/lib/libtinfo.so.5 # Simplest way to add our installed lib to $LD_LIBRARY_PATH

  25s .makelangelo λ l avrdude-6.0.1/lib/libtinfo.so.5
lrwxrwxrwx 1 pete pete 37 Nov 13 00:31 avrdude-6.0.1/lib/libtinfo.so.5 -> /usr/lib/i386-linux-gnu/libtinfo.so.5

Lastly: executable requires sudo rights

Running the avrdude command I had this error:

avrdude: ser_open(): can't open device "/dev/ttyACM0": Permission denied

Also, in the middle of this I had deleted the hex file so repeated the whole process just to hopefully re-generate it. It seems to have worked OK.

     .makelangelo λ sha256sum firmware-huge.hex 
a75bc6122f404b6dbab4238d133d5f96b8ce5e0c83f987389488488e387c46da  firmware-huge.hex

Finally:

  2s .makelangelo λ sudo /home/pete/.makelangelo/avrdude-6.0.1/bin/avrdude -C/home/pete/.makelangelo/avrdude-6.0.1/etc/avrdude.conf -v -V -patmega2560 -cwiring -P/dev/ttyACM0 -b115200 -D -Uflash:w:/home/pete/.makelangelo/firmware-huge.hex:i

avrdude: Version 6.0.1, compiled on Mar 19 2015 at 11:53:10
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "/home/pete/.makelangelo/avrdude-6.0.1/etc/avrdude.conf"
         User configuration file is "/root/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping

         Using Port                    : /dev/ttyACM0
         Using Programmer              : wiring
         Overriding Baud Rate          : 115200
         AVR Part                      : ATmega2560
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
           flash         65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

         Programmer Type : Wiring
         Description     : Wiring
         Programmer Model: AVRISP
         Hardware Version: 15
         Firmware Version Master : 2.10
         Vtarget         : 0.0 V
         SCK period      : 173.7 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.01s

avrdude: Device signature = 0x1e9801
avrdude: safemode: lfuse reads as FF
avrdude: safemode: hfuse reads as D8
avrdude: safemode: efuse reads as FF
avrdude: reading input file "/home/pete/.makelangelo/firmware-huge.hex"
avrdude: writing flash (96406 bytes):

Writing | ################################################## | 100% 15.44s

avrdude: 96406 bytes of flash written

avrdude: safemode: lfuse reads as FF
avrdude: safemode: hfuse reads as D8
avrdude: safemode: efuse reads as FF
avrdude: safemode: Fuses OK (H:FF, E:D8, L:FF)

avrdude done.  Thank you.

  19s .makelangelo λ 

Then I had to init or reload EEPROM and the Configuration screen showed the huge minX/minY numbers mentioned at the end of https://mcr.dozuki.com/Guide/2.+Makelangelo+5+to+HUGE+upgrade/41?lang=en

---

Now I have no idea how to patch this Java repo, plus I used many of my Bash aliases here hoping you'll infer their meaning.
So I guess that's the best help I can be for this to get fixed or for others to work around this issue...

I hope this helps!