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apt isn't working

antoni
in Beginners

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I'm new to Debian. I've been using Arch for a while. This error occurs on my new RockPro64 when I try to run "apt update": 

Hit:1 http://ports.ubuntu.com focal InRelease
Hit:2 http://ports.ubuntu.com focal-security InRelease
Hit:3 http://ports.ubuntu.com focal-updates InRelease
Hit:4 http://ports.ubuntu.com focal-backports InRelease
Hit:5 https://us.mirrors.fossho.st/armbian/apt focal InRelease
Reading package lists... Error!
E: Problem parsing dependency 21 of gdc-9-x86-64-linux-gnux32:arm64=9.3.0-17ubuntu1~20.04cross1
E: Error occurred while processing gdc-9-x86-64-linux-gnux32 (NewVersion2)
E: Problem with MergeList /var/lib/apt/lists/ports.ubuntu.com_dists_focal-updates_universe_binary-arm64_Packages.lz4
E: The package lists or status file could not be parsed or opened.

 

This error occurs when I try to install or remove any package: 

Reading package lists... Error!
E: Problem parsing dependency 21 of gdc-9-x86-64-linux-gnux32:arm64=9.3.0-17ubuntu1~20.04cross1
E: Error occurred while processing gdc-9-x86-64-linux-gnux32 (NewVersion2)
E: Problem with MergeList /var/lib/apt/lists/ports.ubuntu.com_dists_focal-updates_universe_binary-arm64_Packages.lz4
E: The package lists or status file could not be parsed or opened.

 

I'm concerned about x86_64 in this error message. Am I using the wrong mirrors? Here's "/etc/apt/sources.list" file content: 

deb http://ports.ubuntu.com/ focal main restricted universe multiverse
#deb-src http://ports.ubuntu.com/ focal main restricted universe multiverse

deb http://ports.ubuntu.com/ focal-security main restricted universe multiverse
#deb-src http://ports.ubuntu.com/ focal-security main restricted universe multiverse

deb http://ports.ubuntu.com/ focal-updates main restricted universe multiverse
#deb-src http://ports.ubuntu.com/ focal-updates main restricted universe multiverse

deb http://ports.ubuntu.com/ focal-backports main restricted universe multiverse
#deb-src http://ports.ubuntu.com/ focal-backports main restricted universe multiverse

 

I've already installed openjdk-14-jre, openjdk-14-jre-headless and its dependencies on my system before. without errors. Java doesn't seem to work however. "java --version" command works properly but when I try to run any program then I get SIGSEGV (but I have 4GB of RAM!). I remember that I also got this (SIGSEGV) error before while running apt. Now it always returns this error but before it crashed with "segmentation fault". What's going on?

Solved by antoni

Go to solution
  • Author
48 minutes ago, Igor said:


Files you are requesting doesn't come from Armbian repository. From Ubuntu - there is likely the problem. What have you installed?

 

Just openjdk-14-jre and it's dependencies (openjdk-14-jre, openjdk-14-jre-headless, java-common, ca-certificates-java). What are the correct mirrors I should have in /etc/apt/sources.list?

Just now, antoni said:

Just openjdk-14-jre and it's dependencies (openjdk-14-jre, openjdk-14-jre-headless, java-common, ca-certificates-java). What are the correct mirrors I should have in /etc/apt/sources.list?


From Armbian perspective all this is third party. Try this:
https://www.digitalocean.com/community/tutorials/how-to-install-java-with-apt-on-ubuntu-20-04

  • Author

Java is not my main problem. My main problem is that apt isn't working. Any command (like "apt update", "apt upgrade" or "apt full-upgrade") fails for some reason. Is there any way to fix it?

14 minutes ago, antoni said:

Java is not my main problem. My main problem is that apt isn't working. Any command (like "apt update", "apt upgrade" or "apt full-upgrade") fails for some reason. Is there any way to fix it?


Perhaps DNS problem? Workaround is adding nameserver 1.1.1.1 to /etc/resolv.conf ... or there is some other network issue.

 

Or perhaps remove /var/lib/apt/list 
https://www.linuxquestions.org/questions/ubuntu-63/how-to-fix-corrupted-apt-get-4175603435/

  • Author
9 minutes ago, Igor said:


Perhaps DNS problem? Workaround is adding nameserver 1.1.1.1 to /etc/resolv.conf ... or there is some other network issue.

 

No. It didn't change anything. I managed to fix "apt update" by clearing /var/lib/apt/lists/ directory. However "apt upgrade still don't work. It gives me such an error: 

Preconfiguring packages ...
(Reading database ... 84586 files and directories currently installed.)
Preparing to unpack .../0-libc6-dev_2.31-0ubuntu9.1_arm64.deb ...
Unpacking libc6-dev:arm64 (2.31-0ubuntu9.1) over (2.31-0ubuntu9) ...
dpkg-deb (subprocess): decompressing archive member: lzma error: compressed data is corrupt
dpkg-deb: error: <decompress> subprocess returned error exit status 2
dpkg: error processing archive /tmp/apt-dpkg-install-ewJj1L/0-libc6-dev_2.31-0ubuntu9.1_arm64.deb (--unpack):
 cannot copy extracted data for './usr/lib/aarch64-linux-gnu/libm.a' to '/usr/lib/aarch64-linux-gnu/libm.a.dpkg-new': unexpected end of file or stream
Preparing to unpack .../1-libc-dev-bin_2.31-0ubuntu9.1_arm64.deb ...
Unpacking libc-dev-bin (2.31-0ubuntu9.1) over (2.31-0ubuntu9) ...
Preparing to unpack .../2-linux-libc-dev_5.4.0-54.60_arm64.deb ...
Unpacking linux-libc-dev:arm64 (5.4.0-54.60) over (5.4.0-42.46) ...
dpkg-deb (subprocess): decompressing archive member: lzma error: compressed data is corrupt
dpkg-deb: error: <decompress> subprocess returned error exit status 2
dpkg: error processing archive /tmp/apt-dpkg-install-ewJj1L/2-linux-libc-dev_5.4.0-54.60_arm64.deb (--unpack):
 cannot copy extracted data for './usr/include/linux/input-event-codes.h' to '/usr/include/linux/input-event-codes.h.dpkg-new': unexpected end of file or stream
Preparing to unpack .../3-libgcc1_1%3a10.2.0-5ubuntu1~20.04_arm64.deb ...
Unpacking libgcc1 (1:10.2.0-5ubuntu1~20.04) over (1:10-20200411-0ubuntu1) ...
Preparing to unpack .../4-libubsan1_10.2.0-5ubuntu1~20.04_arm64.deb ...
Unpacking libubsan1:arm64 (10.2.0-5ubuntu1~20.04) over (10-20200411-0ubuntu1) ...
Preparing to unpack .../5-libtsan0_10.2.0-5ubuntu1~20.04_arm64.deb ...
Unpacking libtsan0:arm64 (10.2.0-5ubuntu1~20.04) over (10-20200411-0ubuntu1) ...
Preparing to unpack .../6-liblsan0_10.2.0-5ubuntu1~20.04_arm64.deb ...
Unpacking liblsan0:arm64 (10.2.0-5ubuntu1~20.04) over (10-20200411-0ubuntu1) ...
Preparing to unpack .../7-libitm1_10.2.0-5ubuntu1~20.04_arm64.deb ...
Unpacking libitm1:arm64 (10.2.0-5ubuntu1~20.04) over (10-20200411-0ubuntu1) ...
Preparing to unpack .../8-libgomp1_10.2.0-5ubuntu1~20.04_arm64.deb ...
Unpacking libgomp1:arm64 (10.2.0-5ubuntu1~20.04) over (10-20200411-0ubuntu1) ...
Preparing to unpack .../9-gcc-10-base_10.2.0-5ubuntu1~20.04_arm64.deb ...
Unpacking gcc-10-base:arm64 (10.2.0-5ubuntu1~20.04) over (10-20200411-0ubuntu1) ...
Errors were encountered while processing:
 /tmp/apt-dpkg-install-ewJj1L/0-libc6-dev_2.31-0ubuntu9.1_arm64.deb
 /tmp/apt-dpkg-install-ewJj1L/2-linux-libc-dev_5.4.0-54.60_arm64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

 

  • Author

+ Now "apt update" sommetimes crash on reading package lists... 

Hit:1 http://ports.ubuntu.com focal InRelease
Hit:2 http://ports.ubuntu.com focal-security InRelease
Hit:3 http://ports.ubuntu.com focal-updates InRelease
Hit:4 http://ports.ubuntu.com focal-backports InRelease
Get:5 https://uk.mirrors.fossho.st/armbian/apt focal InRelease [18.2 kB]
Fetched 18.2 kB in 2s (10.2 kB/s)   
Segmentation faultsts... 79%

  

Hit:1 http://ports.ubuntu.com focal InRelease
Hit:2 http://ports.ubuntu.com focal-security InRelease
Hit:3 http://ports.ubuntu.com focal-updates InRelease
Hit:4 http://ports.ubuntu.com focal-backports InRelease
Get:5 https://mirrors.dotsrc.org/armbian-apt focal InRelease [18.2 kB]
Fetched 18.2 kB in 2s (11.0 kB/s)                     
Segmentation faultsts... 44%

 

  • Author
15 minutes ago, Igor said:


I never crashed APT to such degree so I am running out of ideas. Perhaps other will have it ...

 

Can you start from a clean image?

 

I would rather not do it because I have already configured a lot, but I think I will have to... I get tons of bugs. Tons of weird bugs. Including my first kernel oops:

  

dpkg-deb: error: <decompress> subprocess returned error exit status 2
dpkg: error processing archive /tmp/apt-dpkg-install-KeRyGj/121-linux-dtb-current-rockchip64_20.08.21_arm64.deb (--unpack):
 cannot copy extracted data for './boot/dtb-5.8.17-rockchip64/amlogic/meson-gxbb-vega-s95-meta.dtb' to '/boot/dtb-5.8.17-rockchip64/amlogic/meson-gxbb-vega-s95-meta.dtb.dpkg-new': unexpected end of 
file or stream
Preparing to unpack .../122-linux-focal-root-current-rockpro64_20.08.17_arm64.deb ...
dpkg-divert: error: parsing file '/var/lib/dpkg/status' near line 1259 package 'console-setup':
 missing 'Version' field
Unpacking linux-focal-root-current-rockpro64 (20.08.17) over (20.08.1) ...
dpkg-deb (subprocess): decompressing archive member: lzma error: compressed data is corrupt
dpkg-deb: error: <decompress> subprocess returned error exit status 2
dpkg: error processing archive /tmp/apt-dpkg-install-KeRyGj/122-linux-focal-root-current-rockpro64_20.08.17_arm64.deb (--unpack):
 cannot copy extracted data for './usr/lib/nand-sata-install/a13/bootloader/linux/u-boot.bin' to '/usr/lib/nand-sata-install/a13/bootloader/linux/u-boot.bin.dpkg-new': unexpected end of file or stre
am
dpkg-deb (subprocess): decompressing archive member: lzma error: compressed data is corrupt
dpkg-deb: error: <decompress> subprocess returned error exit status 2
dpkg: error processing archive /tmp/apt-dpkg-install-KeRyGj/123-linux-image-current-rockchip64_20.08.21_arm64.deb (--unpack):
 dpkg-deb --control subprocess returned error exit status 2
Preparing to unpack .../124-linux-libc-dev_5.4.0-54.60_arm64.deb ...
Unpacking linux-libc-dev:arm64 (5.4.0-54.60) over (5.4.0-42.46) ...
dpkg: error processing archive /tmp/apt-dpkg-install-KeRyGj/124-linux-libc-dev_5.4.0-54.60_arm64.deb (--unpack):
 corrupted filesystem tarfile in package archive: invalid tar header checksum
dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)
Preparing to unpack .../125-linux-u-boot-rockpro64-current_20.08.13_arm64.deb ...
Unpacking linux-u-boot-rockpro64-current (20.08.13) over (20.08.1) ...

Message from syslogd@localhost at Nov 20 17:26:45 ...
 kernel:[  398.570141] Internal error: Oops: 96000004 [#1] PREEMPT SMP

Message from syslogd@localhost at Nov 20 17:26:45 ...
 kernel:[  398.592784] Code: b4001313 b94022e2 b94010a0 11000400 (f8626a62) 
dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)

  

Hit:1 http://ports.ubuntu.com focal InRelease
Hit:2 http://ports.ubuntu.com focal-security InRelease
Hit:3 http://ports.ubuntu.com focal-updates InRelease
Hit:4 http://ports.ubuntu.com focal-backports InRelease
Get:5 https://minio.k-space.ee/armbian/apt focal InRelease [18.2 kB]
Fetched 18.2 kB in 2s (10.5 kB/s)   

Message from syslogd@localhost at Nov 20 17:27:40 ...
 kernel:[  453.966558] Internal error: Oops: 96000004 [#2] PREEMPT SMP

Message from syslogd@localhost at Nov 20 17:27:40 ...
 kernel:[  453.987767] Code: f94033f7 f84a0efa eb17035f 54000340 (b8570340) 
Segmentation fault

 

18 minutes ago, antoni said:

I would rather not do it because I have already configured a lot, but I think I will have to... I get tons of bugs. Tons of weird bugs. Including my first kernel oops:


Get another SD card and try ... from what you are reporting, we can't rule our hardware related issues.

 

Where we can help little. Also one quick tip is to slightly clock down CPU and set governor to ondemand or performance. 

  • Author

Ekh... I flashed this image again and... This same... I just logged via SSH, ran only 2 commands "apt update" and "apt upgrade", and here I have new error:

  

.
.
.
Preparing to unpack .../135-mutter_3.36.6-1ubuntu0.20.04.2_arm64.deb ...
Unpacking mutter (3.36.6-1ubuntu0.20.04.2) over (3.36.4-0ubuntu0.20.04.2) ...
Errors were encountered while processing:
 /tmp/apt-dpkg-install-mIEip0/098-firefox_83.0+build2-0ubuntu0.20.04.1_arm64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

 

  • Author
24 minutes ago, Igor said:


Get another SD card and try ... from what you are reporting, we can't rule our hardware related issues.

 

Where we can help little. Also one quick tip is to slightly clock down CPU and set governor to ondemand or performance. 

 

It's set to ondemand by default.

45 minutes ago, antoni said:

Ekh... I flashed this image again and... This same... I just logged via SSH, ran only 2 commands "apt update" and "apt upgrade", and here I have new error:


I couldn't recreate this problem by using the same image:
https://armbian.tnahosting.net/dl/rockpro64/archive/Armbian_20.08.1_Rockpro64_focal_current_5.8.6_desktop.img.xz

 

apt update

apt upgrade

finishes normally.

You have either broken SD card or broken board.

  • Author

One of my previous errors: 

[...]
Unpacking linux-libc-dev:arm64 (5.4.0-54.60) over (5.4.0-42.46) ...
dpkg: error processing archive /tmp/apt-dpkg-install-KeRyGj/124-linux-libc-dev_5.4.0-54.60_arm64.deb (--unpack):
 corrupted filesystem tarfile in package archive: invalid tar header checksum       <=================================
dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)
[...]

 

This could also be a problem with the internet connection. However, the broken SD card would explain kernel oops and so frequent SIGSEGV when running various programs. I don't think I have a broken board, that would explain SIGSEGVs, but it wouldn't explain so frequent invalid tar header checksums that leaded apt to failure. Obviously, that would be the worst scenario.

  • Author
  • Solution

Ok, I bought better SD card and now everything works great. Tank you!

Edited by antoni
thanks

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