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#1 2023-02-13 09:47:00

dartfira
Member
Registered: 2010-08-23
Posts: 104

File exists in filesystem

Hello all, I'm banging my head against that problem since that:
https://bbs.archlinux.org/viewtopic.php?id=279654&p=3

I recently switched from KDE to GNOME, for the first was really slow, during that change I managed to reinstall some KDE Apps, resulting in a lot of that "file exists" errors, here is one:

LANG=C sudo pacman -S kdenlive
[sudo] password for dartie: 
resolving dependencies...
looking for conflicting packages...

Packages (70) accounts-qml-module-0.7-4  attica-5.102.0-1
              breeze-icons-5.102.0-1  convertlit-1.8-11
              ebook-tools-0.2.2-7
              kaccounts-integration-22.12.2-1
              karchive-5.102.0-1  kauth-5.102.0-1
              kbookmarks-5.102.0-1  kcmutils-5.102.0-1
              kcodecs-5.102.0-1  kcompletion-5.102.0-1
              kconfig-5.102.0-1  kconfigwidgets-5.102.0-1
              kcoreaddons-5.102.0-1  kcrash-5.102.0-1
              kdbusaddons-5.102.0-1  kdeclarative-5.102.0-1
              kded-5.102.0-1  kfilemetadata-5.102.0-1
              kglobalaccel-5.102.0-1  kguiaddons-5.102.0-1
              ki18n-5.102.0-1  kiconthemes-5.102.0-1
              kio-5.102.0-1  kirigami2-5.102.0-1
              kitemviews-5.102.0-1  kjobwidgets-5.102.0-1
              knewstuff-5.102.0-1  knotifications-5.102.0-1
              knotifyconfig-5.102.0-1  kpackage-5.102.0-1
              kservice-5.102.0-1  ktextwidgets-5.102.0-1
              kwallet-5.102.0-1  kwidgetsaddons-5.102.0-1
              kwindowsystem-5.102.0-1  kxmlgui-5.102.0-1
              libaccounts-glib-1.26-1  libaccounts-qt-1.16-3
              libdbusmenu-qt5-0.9.3+16.04.20160218-6
              libebur128-1.2.6-1  libzip-1.9.2-1
              media-player-info-24-2  mlt-7.12.0-2
              polkit-qt5-0.114.0-1  poppler-qt5-23.02.0-1
              purpose-5.102.0-1  qca-qt5-2.3.5-2
              qt5-graphicaleffects-5.15.8-1
              qt5-location-5.15.8+kde+r3-1
              qt5-multimedia-5.15.8+kde+r2-1
              qt5-networkauth-5.15.8-1
              qt5-quickcontrols-5.15.8-1
              qt5-quickcontrols2-5.15.8+kde+r7-1
              qt5-speech-5.15.8+kde+r1-1
              qt5-svg-5.15.8+kde+r8-1
              qt5-webchannel-5.15.8+kde+r3-1
              qt5-webengine-5.15.12-2  qt5-x11extras-5.15.8-1
              re2-1:20230201-1
              signon-kwallet-extension-22.12.2-1
              signon-plugin-oauth2-0.25-1
              signon-ui-0.17+20171022-3  signond-8.61-1
              snappy-1.1.9-2  solid-5.102.0-1  sonnet-5.102.0-1
              syndication-5.102.0-1  kdenlive-22.12.2-1

Total Installed Size:  447.22 MiB

:: Proceed with installation? [Y/n] y
(70/70) checking keys in keyring                   [######] 100%
(70/70) checking package integrity                 [######] 100%
(70/70) loading package files                      [######] 100%
(70/70) checking for file conflicts                [######] 100%
error: failed to commit transaction (conflicting files)
kwallet: /usr/lib/libkwalletbackend5.so.5 exists in filesystem
libzip: /usr/lib/libzip.so.5 exists in filesystem
kaccounts-integration: /usr/lib/libkaccounts.so.2 exists in filesystem
purpose: /usr/lib/libReviewboardHelpers.so.5 exists in filesystem
Errors occurred, no packages were upgraded.

Then i remove that files manually and I can install the packages, but then again I noticed that that's not the first time libzip.so.5 comes up with that problem, so again i remove kdenlive by "pacman -Rs kdenlive"
and again tried to reinstall, same problem again:
error: failed to commit transaction (conflicting files)

kwallet: /usr/lib/libkwalletbackend5.so.5 exists in filesystem
libzip: /usr/lib/libzip.so.5 exists in filesystem
kaccounts-integration: /usr/lib/libkaccounts.so.2 exists in filesystem
purpose: /usr/lib/libReviewboardHelpers.so.5 exists in filesystem
Errors occurred, no packages were upgraded.

I'm thinking that's something broken inside my system and I'd like to resolve it and not reinstalling from the scratch, any advice?

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#2 2023-02-13 09:58:17

seth
Member
Registered: 2012-09-03
Posts: 51,056

Re: File exists in filesystem

stat /usr/lib/libzip.so.5
lsattr /usr/lib/libzip.so.5
mount

If the file isn't immutable, it's probably a filesystem error what could be the FS (btrfs, zfs?) or the disk…

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#3 2023-02-13 15:38:16

dartfira
Member
Registered: 2010-08-23
Posts: 104

Re: File exists in filesystem

It's Ext4 the FS

stat /usr/lib/libzip.so.5

  File: /usr/lib/libzip.so.5 -> libzip.so.5.4
  Size: 13        	Blocks: 0          IO Block: 4096   symbolic link
Device: 254,2	Inode: 527746      Links: 1
Access: (0777/lrwxrwxrwx)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2023-02-13 10:56:06.931853545 +0100
Modify: 2023-02-13 10:26:25.682955896 +0100
Change: 2023-02-13 10:26:25.682955896 +0100
 Birth: 2023-02-13 10:26:25.682955896 +0100

lsattr /usr/lib/libzip.so.5

lsattr: Operation not supported While reading flags on /usr/lib/libzip.so.5

mount

...
/dev/mapper/root on / type ext4 (rw,relatime,stripe=32)
...

Last edited by dartfira (2023-02-13 15:44:05)

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#4 2023-02-13 17:31:50

seth
Member
Registered: 2012-09-03
Posts: 51,056

Re: File exists in filesystem

pacman -Qs libzip
pacman -Qo /usr/lib/libzip.so.5 /usr/lib/libzip.so.5.4

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#5 2023-02-13 19:11:02

dartfira
Member
Registered: 2010-08-23
Posts: 104

Re: File exists in filesystem

libzip is not currently installed on my system, so -Qs gives no response while
pacman -Qo /usr/lib/libzip.so.5 /usr/lib/libzip.so.5.4

error: No package owns /usr/lib/libzip.so.5
error: No package owns /usr/lib/libzip.so.5.4

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#6 2023-02-13 19:45:29

seth
Member
Registered: 2012-09-03
Posts: 51,056

Re: File exists in filesystem

That explains the collision, but not why the files are there.

i remove kdenlive by "pacman -Rs kdenlive" and again tried to reinstall, same problem

Removing the current libzip would leave /usr/lib/libzip.so.5.4 (only delete libzip.so.5.5) behind, but not /usr/lib/libzip.so.5 and I also don't see how the latter would be re-linked to the former.

Remove both, re-install libzip, remove libzip and then check the file status again.
Then try to install libzip again.

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#7 2023-02-14 19:32:07

dartfira
Member
Registered: 2010-08-23
Posts: 104

Re: File exists in filesystem

Ok done, same problem again.

LANG=C pacman -Qo /usr/lib/libzip.so.5 /usr/lib/libzip.so.5.4
error: No package owns /usr/lib/libzip.so.5
error: No package owns /usr/lib/libzip.so.5.4
LANG=C sudo pacman -S libzip
resolving dependencies...
looking for conflicting packages...

Packages (1) libzip-1.9.2-1

Total Installed Size:  0.43 MiB

:: Proceed with installation? [Y/n] y
(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%
error: failed to commit transaction (conflicting files)
libzip: /usr/lib/libzip.so.5 exists in filesystem
Errors occurred, no packages were upgraded.

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#8 2023-02-14 20:09:04

seth
Member
Registered: 2012-09-03
Posts: 51,056

Re: File exists in filesystem

When seth wrote:

check the file status again

seth meant "stat", pacman isn't helpful here, because even "pacman -Qo /etc/gnarf" will tell you that nothing owns this file, despite chances for it to exist on your system are neglectable.

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#9 2023-02-15 19:24:17

dartfira
Member
Registered: 2010-08-23
Posts: 104

Re: File exists in filesystem

Ah ok, so that's it

stat /usr/lib/libzip.so.5

  File: /usr/lib/libzip.so.5 -> libzip.so.5.4
  Size: 13        	Blocks: 0          IO Block: 4096   symbolic link
Device: 254,2	Inode: 527746      Links: 1
Access: (0777/lrwxrwxrwx)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2023-02-15 10:29:44.947252531 +0100
Modify: 2023-02-14 20:28:43.222902971 +0100
Change: 2023-02-14 20:28:43.222902971 +0100
 Birth: 2023-02-14 20:28:43.222902971 +0100

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#10 2023-02-15 22:11:34

seth
Member
Registered: 2012-09-03
Posts: 51,056

Re: File exists in filesystem

There's stale symlink to a dated version of libzip, but how removing libzip 5.5 can result in this condition is beyond me.
You did previously remove those files (both!), ensure that they were removed, installed libzip-1.9.2-1, uninstalled it and the consequence are those files?
Post your pacman log.

If you've a stale libzip.so.5.4 flying around, ldconfig might have autogenerated the symlink.

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#11 2023-02-16 14:31:34

dartfira
Member
Registered: 2010-08-23
Posts: 104

Re: File exists in filesystem

I made a mistake during the last command, I didn't remove the other file, doing this made the second installation working fine.

Thank for your support, is there a way to check all the files who could have this problem?

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#12 2023-02-16 14:42:38

seth
Member
Registered: 2012-09-03
Posts: 51,056

Re: File exists in filesystem

libraries that have a major.minor but no minor or unversioned .so

foo.so.1.2 will get you foo.so.1 & foo.so
foo.so.1 & foo.so.1.2 will still get you foo.so

for name in *.so.*; do [ -e "${name%.so.*}.so" ] || echo $name; done

Is kinda suspicious and you should look at it, but DON'T JUST BLINDLY DELETE THOSE!!

Also pacman told you which libraries it doesn't like for file collisions, so take a look at them.

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#13 2023-02-27 11:22:14

DaniAndTheWeb
Member
Registered: 2021-12-04
Posts: 3

Re: File exists in filesystem

I've been having the same problem on my desktop PC for a week. Some packages suddenly start breaking and I'm unable to the errors. I even tried reinstalling arch from scratch two times already but the problem keeps coming back. I searched all the weekend for how to troubleshoot the problem but I can't find the reason since the filesystem also seems fine.
On my laptop I have a similar arch installation but there I've never seen this problem.

Last edited by DaniAndTheWeb (2023-02-27 11:24:31)

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#14 2023-02-27 11:25:51

Scimmia
Fellow
Registered: 2012-09-01
Posts: 11,544

Re: File exists in filesystem

DaniAndTheWeb wrote:

I've been having the same problem on my desktop PC for a week. Some packages suddenly start breaking and I'm unable to the errors. I even tried reinstalling arch from scratch two times already but the problem keeps coming back. I searched all the weekend for how to troubleshoot the problem but I can't find the reason since the filesystem also seems fine.
On my laptop I have a similar arch installation but there I've never seen this problem.

What problem, exactly?

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#15 2023-02-27 11:38:56

DaniAndTheWeb
Member
Registered: 2021-12-04
Posts: 3

Re: File exists in filesystem

The conflicting files error on pacman. The problem is that the error seems to start randomly on packages that I haven't even touched.

Last edited by DaniAndTheWeb (2023-02-27 11:39:13)

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#16 2023-02-27 12:00:29

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 21,672

Re: File exists in filesystem

You should open a new thread. If this routinely happens with random packages then either your disk is on it's last legs or you are randomly installing stuff pacman would provide outside of pacman. Did you ever run pip or npm as root? You might want to start your own thread and post some output for which packages this happens, to check the HW install smartmontools, run

smartctl -t long /dev/sdX

where /dev/sdX is your harddisk giving you problems, wait for the mentioned time to elapse and then post

smartctl -a /dev/sdX

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#17 2023-02-27 12:32:10

Scimmia
Fellow
Registered: 2012-09-01
Posts: 11,544

Re: File exists in filesystem

DaniAndTheWeb wrote:

The conflicting files error on pacman. The problem is that the error seems to start randomly on packages that I haven't even touched.

Don't do that. Post exact errors, always.

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#18 2023-03-01 12:03:28

DaniAndTheWeb
Member
Registered: 2021-12-04
Posts: 3

Re: File exists in filesystem

V1del wrote:

You should open a new thread. If this routinely happens with random packages then either your disk is on it's last legs or you are randomly installing stuff pacman would provide outside of pacman. Did you ever run pip or npm as root? You might want to start your own thread and post some output for which packages this happens, to check the HW install smartmontools, run

smartctl -t long /dev/sdX

where /dev/sdX is your harddisk giving you problems, wait for the mentioned time to elapse and then post

smartctl -a /dev/sdX

Thanks for the help but at the end it seems like for me it's been caused by a strange bios error that messed up some settings. After resetting and updating the bios and having reinstalled the broken packages it seems like I'm not having the issue anymore.

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