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#1 2019-02-20 09:49:51

kelnoky
Member
Registered: 2007-11-20
Posts: 134

/var failed to mount once, pacman packages corrupted now?

Hey guys, when I booted yesterday, I got an error about one of my drives not responding properly and thus the system didn't boot. I ran a fsck on the drive, it fixed a bunch of errors (too many to recount, mostly it was time mismatches and some lost inodes) and everything worked again when I tried to boot again. However, now I get this when I want to -Syu:

william% up
[sudo] password for kelnoky: 
:: Synchronising package databases...
 core                     133.8 KiB  1537K/s 00:00 [###] 100%
 extra                   1710.4 KiB  7.05M/s 00:00 [###] 100%
 community                  4.8 MiB  14.8M/s 00:00 [###] 100%
 multilib                 175.8 KiB  1430K/s 00:00 [###] 100%
:: Starting full system upgrade...
error: could not open file /var/lib/pacman/local/haskell-dbus-1.2.4-1/desc: No such file or directory
error: could not open file /var/lib/pacman/local/haskell-xml-conduit-1.8.0.1-33/desc: No such file or directory
warning: zeitgeist: local (1.0+1+g1bcc8585-2) is newer than extra (1.0.1-1)
resolving dependencies...
error: could not open file /var/lib/pacman/local/haskell-blaze-html-0.9.1.1-15/desc: No such file or directory
error: could not open file /var/lib/pacman/local/haskell-lens-4.17-31/desc: No such file or directory
error: could not open file /var/lib/pacman/local/haskell-vector-algorithms-0.8.0.1-7/desc: No such file or directory
looking for conflicting packages...
warning: could not fully load metadata for package haskell-dbus-1.2.4-1
error: failed to prepare transaction (invalid or corrupted package)
william [up] ~                                     19-02-20 10:24am
william%

What do I do here?

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#2 2019-02-20 10:11:23

loqs
Member
Registered: 2014-03-06
Posts: 17,493

Re: /var failed to mount once, pacman packages corrupted now?

# pacman -Qkk &> pacman.check #then post the contents of pacman.check

If it will not fit in a post please use a pastebin.

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#3 2019-02-20 10:16:20

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 21,842

Re: /var failed to mount once, pacman packages corrupted now?

For the literal error, just touch the files it mentions.

However you shouldn't just handwave "had to fsck and fixed a bunch of errors, literally too many to recount". Why were the errors there in the first place? Is your disk dying? run a long smart test on the affected drive and post the result, preferably you'd do that before any further writes to the drive.

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#4 2019-02-20 19:24:50

kelnoky
Member
Registered: 2007-11-20
Posts: 134

Re: /var failed to mount once, pacman packages corrupted now?

There have been some disturbing sounds that are probably harddrive related. They have been going on for more than half a year by now so I just got used to them after smart tests didn't show anything when the sounds began. I am running a long test now though, it's a big drive, so it will take until tomorrow.

Here is the output of -Qkk: https://bpaste.net/show/621b318d9bc8

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#5 2019-02-20 19:32:54

loqs
Member
Registered: 2014-03-06
Posts: 17,493

Re: /var failed to mount once, pacman packages corrupted now?

The output from pacman -Qkk looks fine (assuming you forgot to run the command as root) the issue seems limited to the desc files pacman listed.
I would still wait for the S.M.A.R.T. test result to be sure.

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#6 2019-02-21 17:44:13

kelnoky
Member
Registered: 2007-11-20
Posts: 134

Re: /var failed to mount once, pacman packages corrupted now?

So this is the result of the long smartctl test:

william% sudo smartctl -a /dev/sdc
[sudo] password for kelnoky: 
smartctl 7.0 2018-12-30 r4883 [x86_64-linux-4.20.10-arch1-1-ARCH] (local build)
Copyright (C) 2002-18, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     Seagate Surveillance
Device Model:     ST4000VX000-1F4168
Serial Number:    Z303D6E4
LU WWN Device Id: 5 000c50 07aadc1da
Firmware Version: CV13
User Capacity:    4,000,787,030,016 bytes [4.00 TB]
Sector Sizes:     512 bytes logical, 4096 bytes physical
Rotation Rate:    5900 rpm
Form Factor:      3.5 inches
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   ACS-2, ACS-3 T13/2161-D revision 3b
SATA Version is:  SATA 3.1, 6.0 Gb/s (current: 6.0 Gb/s)
Local Time is:    Thu Feb 21 18:42:40 2019 CET
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:  (0x82)	Offline data collection activity
					was completed without error.
					Auto Offline Data Collection: Enabled.
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: 		(   97) seconds.
Offline data collection
capabilities: 			 (0x7b) SMART execute Offline immediate.
					Auto Offline data collection on/off support.
					Suspend Offline collection upon new
					command.
					Offline surface scan supported.
					Self-test supported.
					Conveyance Self-test supported.
					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: 	 (   1) minutes.
Extended self-test routine
recommended polling time: 	 ( 482) minutes.
Conveyance self-test routine
recommended polling time: 	 (   2) minutes.
SCT capabilities: 	       (0x10b9)	SCT Status supported.
					SCT Error Recovery Control supported.
					SCT Feature Control supported.
					SCT Data Table supported.

SMART Attributes Data Structure revision number: 10
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE
  1 Raw_Read_Error_Rate     0x000f   115   100   006    Pre-fail  Always       -       85652016
  3 Spin_Up_Time            0x0003   097   093   000    Pre-fail  Always       -       0
  4 Start_Stop_Count        0x0032   100   100   020    Old_age   Always       -       276
  5 Reallocated_Sector_Ct   0x0033   100   100   010    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x000f   100   253   030    Pre-fail  Always       -       209702
  9 Power_On_Hours          0x0032   093   093   000    Old_age   Always       -       6625
 10 Spin_Retry_Count        0x0013   100   100   097    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   098   098   020    Old_age   Always       -       2050
184 End-to-End_Error        0x0032   100   100   099    Old_age   Always       -       0
187 Reported_Uncorrect      0x0032   100   100   000    Old_age   Always       -       0
188 Command_Timeout         0x0032   100   100   000    Old_age   Always       -       0
189 High_Fly_Writes         0x003a   100   100   000    Old_age   Always       -       0
190 Airflow_Temperature_Cel 0x0022   054   047   045    Old_age   Always       -       46 (Min/Max 45/48)
191 G-Sense_Error_Rate      0x0032   100   100   000    Old_age   Always       -       0
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       183
193 Load_Cycle_Count        0x0032   099   099   000    Old_age   Always       -       2404
194 Temperature_Celsius     0x0022   046   053   000    Old_age   Always       -       46 (0 19 0 0 0)
197 Current_Pending_Sector  0x0012   100   100   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0010   100   100   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x003e   200   200   000    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%      6624         -
# 2  Extended offline    Interrupted (host reset)      00%      6617         -
# 3  Extended offline    Interrupted (host reset)      00%      6609         -
# 4  Extended offline    Interrupted (host reset)      00%      6606         -
# 5  Short offline       Completed without error       00%      6600         -
# 6  Extended offline    Aborted by host               90%      6600         -
# 7  Short offline       Completed without error       00%      5498         -
# 8  Short offline       Completed without error       00%      4964         -
# 9  Short offline       Interrupted (host reset)      10%      1673         -

SMART Selective self-test log data structure revision number 1
 SPAN  MIN_LBA  MAX_LBA  CURRENT_TEST_STATUS
    1        0        0  Not_testing
    2        0        0  Not_testing
    3        0        0  Not_testing
    4        0        0  Not_testing
    5        0        0  Not_testing
Selective self-test flags (0x0):
  After scanning selected spans, do NOT read-scan remainder of disk.
If Selective self-test is pending on power-up, resume after 0 minute delay.

It looks good, doesn't it? Maybe the failure to mount /var was just a one time thing and the bad sounds are coming from a different drive (I have 4).

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#7 2019-02-21 17:48:02

loqs
Member
Registered: 2014-03-06
Posts: 17,493

Re: /var failed to mount once, pacman packages corrupted now?

It could well be from a different drive the smartctl output looks fine to me.

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#8 2019-02-21 23:58:58

kelnoky
Member
Registered: 2007-11-20
Posts: 134

Re: /var failed to mount once, pacman packages corrupted now?

Huh, now however I am faced with different errors. I touched all the files pacman said didn't exist and I am getting this: 

william% up
[sudo] password for kelnoky: 
:: Synchronising package databases...
 core                                          133.3 KiB  1550K/s 00:00 [#################
 extra                                        1709.1 KiB  8.18M/s 00:00 [#################
 community                                       4.8 MiB  12.7M/s 00:00 [#################
 multilib is up to date
:: Starting full system upgrade...
warning: zeitgeist: local (1.0+1+g1bcc8585-2) is newer than extra (1.0.1-1)
resolving dependencies...
looking for conflicting packages...

Packages (37) cabal-install-2.4.0.0-49  curl-7.64.0-9  gpgme-1.12.0-2  graphene-1.8.4-1
              haskell-conduit-extra-1.3.1-1  haskell-dbus-1.2.4-2
              haskell-http-4000.3.12-120  haskell-resolv-0.1.1.1-20
              haskell-xml-conduit-1.8.0.1-34  lib32-libcap-2.26-1
              lib32-libgpg-error-1.35-1  lib32-systemd-241.7-1  libfontenc-1.1.4-1
              libunrar-1:5.7.2-1  linux-4.20.11.arch1-1  linux-headers-4.20.11.arch1-1
              linux-lts-4.19.24-1  lua-socket-20190219-1  lua52-socket-20190219-1
              nvidia-415.27-8  opera-58.0.3135.68-1  python-websocket-client-0.54.0-2
              quassel-client-0.13.1-1  systemd-241.7-2  systemd-libs-241.7-2
              systemd-sysvcompat-241.7-2  unrar-1:5.7.2-1  vulkan-headers-1:1.1.100-1
              weechat-2.4-1  xmobar-0.29.4-25  xorg-xev-1.2.3-1  xorg-xhost-1.0.8-1
              xorg-xlsatoms-1.1.3-1  xorg-xmodmap-1.0.10-1  xorg-xrdb-1.2.0-1
              xorg-xvinfo-1.1.4-1  youtube-dl-2019.02.18-1

Total Download Size:    98.59 MiB
Total Installed Size:  637.41 MiB
Net Upgrade Size:        7.46 MiB

:: Proceed with installation? [Y/n] y
:: Retrieving packages...
 linux-4.20.11.arch1-1-x...    70.4 MiB  23.1M/s 00:03 [############################] 100%
 linux-headers-4.20.11.a...    16.9 MiB  24.0M/s 00:01 [############################] 100%
 nvidia-415.27-8-x86_64        11.3 MiB  24.1M/s 00:00 [############################] 100%
(37/37) checking keys in keyring                       [############################] 100%
(37/37) checking package integrity                     [############################] 100%
(37/37) loading package files                          [############################] 100%
(37/37) checking for file conflicts                        [###############################] 100%
error: could not open file /var/lib/pacman/local/haskell-blaze-html-0.9.1.1-15/files: No such file or directory
error: could not open file /var/lib/pacman/local/haskell-lens-4.17-31/files: No such file or directory
error: could not open file /var/lib/pacman/local/haskell-vector-algorithms-0.8.0.1-7/files: No such file or directory
error: failed to commit transaction (conflicting files)
haskell-resolv: /usr/lib/ghc-8.6.3/site-local/resolv-0.1.1.1/Compat.dyn_hi exists in filesystem
haskell-resolv: /usr/lib/ghc-8.6.3/site-local/resolv-0.1.1.1/Network/DNS.dyn_hi exists in filesystem
haskell-resolv: /usr/lib/ghc-8.6.3/site-local/resolv-0.1.1.1/Network/DNS/FFI.dyn_hi exists in filesystem
haskell-resolv: /usr/lib/ghc-8.6.3/site-local/resolv-0.1.1.1/Network/DNS/Message.dyn_hi exists in filesystem
haskell-resolv: /usr/lib/libHSresolv-0.1.1.1-F3KQTQkIJ8EHTF6KWEEwzf-ghc8.6.3.so exists in filesystem
haskell-resolv: /usr/share/haskell/register/haskell-resolv.sh exists in filesystem
haskell-resolv: /usr/share/haskell/unregister/haskell-resolv.sh exists in filesystem
haskell-xml-conduit: /usr/lib/ghc-8.6.3/site-local/xml-conduit-1.8.0.1/Text/XML.dyn_hi exists in filesystem
haskell-xml-conduit: /usr/lib/ghc-8.6.3/site-local/xml-conduit-1.8.0.1/Text/XML/Cursor.dyn_hi exists in filesystem
haskell-xml-conduit: /usr/lib/ghc-8.6.3/site-local/xml-conduit-1.8.0.1/Text/XML/Cursor/Generic.dyn_hi exists in filesystem
haskell-xml-conduit: /usr/lib/ghc-8.6.3/site-local/xml-conduit-1.8.0.1/Text/XML/Stream/Parse.dyn_hi exists in filesystem
haskell-xml-conduit: /usr/lib/ghc-8.6.3/site-local/xml-conduit-1.8.0.1/Text/XML/Stream/Render.dyn_hi exists in filesystem
haskell-xml-conduit: /usr/lib/ghc-8.6.3/site-local/xml-conduit-1.8.0.1/Text/XML/Stream/Token.dyn_hi exists in filesystem
haskell-xml-conduit: /usr/lib/ghc-8.6.3/site-local/xml-conduit-1.8.0.1/Text/XML/Unresolved.dyn_hi exists in filesystem
haskell-xml-conduit: /usr/share/haskell/register/haskell-xml-conduit.sh exists in filesystem
haskell-xml-conduit: /usr/share/haskell/unregister/haskell-xml-conduit.sh exists in filesystem
haskell-xml-conduit: /usr/share/licenses/haskell-xml-conduit/LICENSE exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Client.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Generation.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Internal/Address.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Internal/Message.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Internal/Types.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Internal/Wire.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Introspection.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Introspection/Parse.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Introspection/Render.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Introspection/Types.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Socket.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/TH.dyn_hi exists in filesystem
haskell-dbus: /usr/lib/ghc-8.6.3/site-local/dbus-1.2.4/DBus/Transport.dyn_hi exists in filesystem
haskell-dbus: /usr/share/haskell/register/haskell-dbus.sh exists in filesystem
haskell-dbus: /usr/share/haskell/unregister/haskell-dbus.sh exists in filesystem
Errors occurred, no packages were upgraded.

It's all related to those three packages obviously. I don't really wanna use --force willy-nilly. I did pacman -Qo on a few files and it seems none of these files is owned by any package? That confuses me kinda:

william% sudo pacman -Qo /usr/lib/ghc-8.6.3/site-local/resolv-0.1.1.1/Compat.dyn_hi 
error: could not open file /var/lib/pacman/local/haskell-blaze-html-0.9.1.1-15/files: No such file or directory
error: could not open file /var/lib/pacman/local/haskell-lens-4.17-31/files: No such file or directory
error: could not open file /var/lib/pacman/local/haskell-vector-algorithms-0.8.0.1-7/files: No such file or directory
error: No package owns /usr/lib/ghc-8.6.3/site-local/resolv-0.1.1.1/Compat.dyn_hi
william [sudo pacman -Qo /usr/lib/ghc-8.6.3/site-local/resolv-0.1.1.1/Compat.dyn_hi] ~                       19-02-22 12:54am
william% sudo pacman -Qo /usr/share/haskell/register/haskell-xml-conduit.sh
error: could not open file /var/lib/pacman/local/haskell-blaze-html-0.9.1.1-15/files: No such file or directory
error: could not open file /var/lib/pacman/local/haskell-lens-4.17-31/files: No such file or directory
error: could not open file /var/lib/pacman/local/haskell-vector-algorithms-0.8.0.1-7/files: No such file or directory
error: No package owns /usr/share/haskell/register/haskell-xml-conduit.sh
william [sudo pacman -Qo /usr/share/haskell/register/haskell-xml-conduit.sh] ~                               19-02-22 12:57am
william% sudo pacman -Qo /usr/lib/libHSresolv-0.1.1.1-F3KQTQkIJ8EHTF6KWEEwzf-ghc8.6.3.so
error: could not open file /var/lib/pacman/local/haskell-blaze-html-0.9.1.1-15/files: No such file or directory
error: could not open file /var/lib/pacman/local/haskell-lens-4.17-31/files: No such file or directory
error: could not open file /var/lib/pacman/local/haskell-vector-algorithms-0.8.0.1-7/files: No such file or directory
error: No package owns /usr/lib/libHSresolv-0.1.1.1-F3KQTQkIJ8EHTF6KWEEwzf-ghc8.6.3.so

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