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#1 2022-03-30 23:56:25

Jack Lagas
Member
Registered: 2021-11-20
Posts: 8

Issue Installing New Packages with pacman

I'm currently having issues installing programs via pacman and I get an error that says

 "warning: warning given when extracting /usr/bin/<program name> (Can't create '/usr/bin/<program name>')"

for everything I try to install.
Here's the full output of the command sudo pacman -S docker:

warning: docker-1:20.10.14-1 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...

Packages (1) docker-1:20.10.14-1

Total Installed Size:  156.90 MiB
Net Upgrade Size:        0.00 MiB

:: Proceed with installation? [Y/n] 
(1/1) checking keys in keyring                     [#############] 100%
(1/1) checking package integrity                   [#############] 100%
(1/1) loading package files                        [#############] 100%
(1/1) checking for file conflicts                  [#############] 100%
(1/1) checking available disk space                [#############] 100%
warning: could not get file information for usr/bin/docker
warning: could not get file information for usr/bin/docker-init
warning: could not get file information for usr/bin/docker-proxy
warning: could not get file information for usr/bin/dockerd
:: Processing package changes...
error: cannot remove file '/usr/bin/': Operation not permitted
(1/1) reinstalling docker                          [#############] 100%
warning: warning given when extracting /usr/bin/docker (Can't create '/usr/bin/docker')
warning: warning given when extracting /usr/bin/docker-init (Can't create '/usr/bin/docker-init')
warning: warning given when extracting /usr/bin/docker-proxy (Can't create '/usr/bin/docker-proxy')
warning: warning given when extracting /usr/bin/dockerd (Can't create '/usr/bin/dockerd')
ldconfig: File /usr/lib/libudev.so.6 is empty, not checked.
:: Running post-transaction hooks...
(1/4) Creating system user accounts...
(2/4) Reloading system manager configuration...
(3/4) Reloading device manager configuration...
(4/4) Arming ConditionNeedsUpdate...

Last edited by Jack Lagas (2022-03-31 00:43:45)

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#2 2022-03-31 00:14:14

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 25,081

Re: Issue Installing New Packages with pacman

You appear to have various forms of file corruption. What are the permissions on /usr/bin/ ? Post/wrap your outputs in code tags 

stat /bin /usr/bin
pacman -Qkk > /dev/null

is this still a Manjaro install?

Last edited by V1del (2022-03-31 00:16:34)

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#3 2022-03-31 00:20:06

Jack Lagas
Member
Registered: 2021-11-20
Posts: 8

Re: Issue Installing New Packages with pacman

Here's the output for stat /usr/bin:

  File: /usr/bin
  Size: 69632     	Blocks: 144        IO Block: 4096   directory
Device: 254,0	Inode: 262153      Links: 5
Access: (0755/drwxr-xr-x)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2022-03-30 22:56:34.259323716 +0000
Modify: 2022-03-06 17:41:08.437477188 +0000
Change: 2022-03-06 17:41:08.500810538 +0000
 Birth: 2021-12-27 13:10:32.457695715 +0000

The output for pacman -Qkk > /dev/null is really long but here's a snippet from it:

warning: yarn: /usr/bin/yarn (Modification time mismatch)
warning: yarn: /usr/bin/yarnpkg (Modification time mismatch)
warning: yay: /usr/bin/yay (Modification time mismatch)
warning: yay: /usr/bin/yay (Size mismatch)
warning: yay: /usr/bin/yay (MD5 checksum mismatch)
warning: yay: /usr/bin/yay (SHA256 checksum mismatch)
warning: zstd: /usr/bin/pzstd (Modification time mismatch)
warning: zstd: /usr/bin/pzstd (Size mismatch)
warning: zstd: /usr/bin/pzstd (MD5 checksum mismatch)
warning: zstd: /usr/bin/pzstd (SHA256 checksum mismatch)
warning: zstd: /usr/bin/unzstd (Modification time mismatch)
warning: zstd: /usr/bin/zstd (Modification time mismatch)
warning: zstd: /usr/bin/zstd (MD5 checksum mismatch)
warning: zstd: /usr/bin/zstd (SHA256 checksum mismatch)
warning: zstd: /usr/bin/zstdcat (Modification time mismatch)
warning: zstd: /usr/bin/zstdgrep (Modification time mismatch)
warning: zstd: /usr/bin/zstdless (Modification time mismatch)
warning: zstd: /usr/bin/zstdmt (Modification time mismatch)

The rest of the output looked like this for but for all the other files but I can get the rest if it's helpful.
Also this is a different computer from my Manjaro machine and has only every had this current Arch install on it.

Last edited by Jack Lagas (2022-03-31 00:42:44)

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#4 2022-03-31 00:35:25

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 25,081

Re: Issue Installing New Packages with pacman

Wrap outputs in [ code ] [ /code ] tags without the spaces, and edit all your posts accordingly

File corruption all around, boot a live disk, run 

smartctl -t long /dev/$yourdiskdevice$
#...Wait for the mentioned time to elapse
smartctl -a /dev/$yourdiskdevice$

if you don't want to/can't wait for the test to actually complete post just the output of smartctl -a.

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#5 2022-03-31 00:46:22

loqs
Member
Registered: 2014-03-06
Posts: 18,828

Re: Issue Installing New Packages with pacman

Please also check kernel messages.  Was the root filesystem remounted readonly due to detected issues?  That could explain why the binaries could not be written.

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#6 2022-03-31 00:46:34

Jack Lagas
Member
Registered: 2021-11-20
Posts: 8

Re: Issue Installing New Packages with pacman

Alright thanks for the advice I don't have time to do that right now unfortunately but I'm probably gonna switch to a more server focused os soon anyways so I'll probably just do that instead. Thank you for the help though.

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#7 2022-03-31 00:59:44

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 25,081

Re: Issue Installing New Packages with pacman

If your HW is dying then you can switch to whatever OS you want it will still be dying, best check/rule that out before going through the hassle of setting up another install and then have that fail in the same/similar ways

Last edited by V1del (2022-03-31 01:00:49)

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#8 2022-03-31 01:07:21

Jack Lagas
Member
Registered: 2021-11-20
Posts: 8

Re: Issue Installing New Packages with pacman

I ran the smartctl -a command on my install disk and got this result:

smartctl 7.2 2020-12-30 r5155 [x86_64-linux-5.16.8-arch1-1] (local build)
Copyright (C) 2002-20, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     WD Blue / Red / Green SSDs
Device Model:     WDC  WDS100T2B0B-00YS70
Serial Number:    21360N800465
LU WWN Device Id: 5 001b44 8bc8fcbd8
Firmware Version: 415020WD
User Capacity:    1,000,204,886,016 bytes [1.00 TB]
Sector Size:      512 bytes logical/physical
Rotation Rate:    Solid State Device
Form Factor:      M.2
TRIM Command:     Available, deterministic, zeroed
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   ACS-4 T13/BSR INCITS 529 revision 5
SATA Version is:  SATA 3.3, 6.0 Gb/s (current: 6.0 Gb/s)
Local Time is:    Thu Mar 31 01:05:16 2022 UTC
SMART support is: Available - device has SMART capability.
SMART support is: Enabled

=== START OF READ SMART DATA SECTION ===
SMART overall-health self-assessment test result: PASSED

General SMART Values:
Offline data collection status:  (0x00) Offline data collection activity
                                        was never started.
                                        Auto Offline Data Collection: Disabled.
Self-test execution status:      (   0) The previous self-test routine completed
                                        without error or no self-test has ever
                                        been run.
Total time to complete Offline
data collection:                (    0) seconds.
Offline data collection
capabilities:                    (0x11) SMART execute Offline immediate.
                                        No Auto Offline data collection support.
                                        Suspend Offline collection upon new
                                        command.
                                        No Offline surface scan supported.
                                        Self-test supported.
                                        No Conveyance Self-test supported.
                                        No Selective Self-test supported.
SMART capabilities:            (0x0003) Saves SMART data before entering
                                        power-saving mode.
                                        Supports SMART auto save timer.
Error logging capability:        (0x01) Error logging supported.
                                        General Purpose Logging supported.
Short self-test routine
recommended polling time:        (   2) minutes.
Extended self-test routine
recommended polling time:        (  10) minutes.

SMART Attributes Data Structure revision number: 4
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE
  5 Reallocated_Sector_Ct   0x0032   100   100   ---    Old_age   Always       -       0
  9 Power_On_Hours          0x0032   100   100   ---    Old_age   Always       -       2251
 12 Power_Cycle_Count       0x0032   100   100   ---    Old_age   Always       -       4
165 Block_Erase_Count       0x0032   100   100   ---    Old_age   Always       -       25166095
166 Minimum_PE_Cycles_TLC   0x0032   100   100   ---    Old_age   Always       -       0
167 Max_Bad_Blocks_per_Die  0x0032   100   100   ---    Old_age   Always       -       39
168 Maximum_PE_Cycles_TLC   0x0032   100   100   ---    Old_age   Always       -       1
169 Total_Bad_Blocks        0x0032   100   100   ---    Old_age   Always       -       313
170 Grown_Bad_Blocks        0x0032   100   100   ---    Old_age   Always       -       0
171 Program_Fail_Count      0x0032   100   100   ---    Old_age   Always       -       0
172 Erase_Fail_Count        0x0032   100   100   ---    Old_age   Always       -       0
173 Average_PE_Cycles_TLC   0x0032   100   100   ---    Old_age   Always       -       0
174 Unexpected_Power_Loss   0x0032   100   100   ---    Old_age   Always       -       0
184 End-to-End_Error        0x0032   100   100   ---    Old_age   Always       -       0
187 Reported_Uncorrect      0x0032   100   100   ---    Old_age   Always       -       0
188 Command_Timeout         0x0032   100   100   ---    Old_age   Always       -       0
194 Temperature_Celsius     0x0022   062   042   ---    Old_age   Always       -       38 (Min/Max 19/42)
199 UDMA_CRC_Error_Count    0x0032   100   100   ---    Old_age   Always       -       0
230 Media_Wearout_Indicator 0x0032   001   001   ---    Old_age   Always       -       0x003600000036
232 Available_Reservd_Space 0x0033   100   100   004    Pre-fail  Always       -       100
233 NAND_GB_Written_TLC     0x0032   100   100   ---    Old_age   Always       -       410
234 NAND_GB_Written_SLC     0x0032   100   100   ---    Old_age   Always       -       4044
241 Host_Writes_GiB         0x0030   253   253   ---    Old_age   Offline      -       3746
242 Host_Reads_GiB          0x0030   253   253   ---    Old_age   Offline      -       74
244 Temp_Throttle_Status    0x0032   000   100   ---    Old_age   Always       -       0

SMART Error Log Version: 1
No Errors Logged

SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Extended offline    Completed without error       00%      2250         -

Selective Self-tests/Logging not supported

Not sure if i did it correct though.

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#9 2022-03-31 07:03:48

seth
Member
From: Don't DM me only for attention
Registered: 2012-09-03
Posts: 73,844

Re: Issue Installing New Packages with pacman

Doesn't look critical besides maybe

169 Total_Bad_Blocks        0x0032   100   100   ---    Old_age   Always       -       313

did the system crash during an update? Otherwise I'd be careful around data trimming - the FS corruption is there and came from *something*.

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