error in update Subprocess failed. Error: RPM failed: Command exited with status 1.

English Install/Boot/Login
1

During update with YAST of my laptop using KDE I get these three errors:

Subprocess failed. Error: RPM failed: Command exited with status 1.History:
 - error: unpacking of archive failed on file /var/lib/dkms/dkms_dbversion: cpio: File from package already exists as a directory in system
   error: dkms-2.6.1-bp154.1.30.noarch: install failed
   error: dkms-2.3-bp153.1.17.noarch: erase skipped
   
   Subprocess failed. Error: RPM failed: Command exited with status 1.
History:
 - error: unpacking of archive failed on file /var/lib/dict/words: cpio: File from package already exists as a directory in system
   error: words-2015.02.15-bp154.1.46.noarch: install failed
   error: words-2015.02.15-bp153.1.15.noarch: erase skipped


   Subprocess failed. Error: RPM failed: Command exited with status 1.
History:
 - error: unpacking of archive failed on file /var/lib/misc/Makefile: cpio: File from package already exists as a directory in system
   error: glibc-extra-2.31-150300.41.1.x86_64: install failed
   error: glibc-extra-2.31-7.30.x86_64: erase skipped

how can I solve?

2

Update from what to what? Previous version in each case is from Leap 15.3 and new version is from Leap 15.4 (OK, glibc updates are shared between 15.3 and 15.4).

3

Post:

zypper lr -d
4

the update was yast>software management>package>all packages>update if a new version is available.
in yast>software management I can see that twords and dkms comes from main repository

here is:

pla@pla4ST:~> zypper lr -d
#  | Alias                                        | Name                                                                 
                       | Enabled | GPG Check | Refresh | Priority | Type     | URI                                       
                                      | Service
---+----------------------------------------------+----------------------------------------------------------------------
-----------------------+---------+-----------+---------+----------+----------+-------------------------------------------
--------------------------------------+--------
 1 | 15.2                                         | Tuxedo leap 15.4                                                     
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | https://rpm.tuxedocomputers.com/opensuse/1
5.4/                                  |  
 2 | ftp.gwdg.de-openSUSE_Leap_$releasever        | Packman direct-gwdg                                                  
                       | No      | ----      | ----    |   99     | rpm-md   | http://ftp.gwdg.de/pub/linux/misc/packman/
suse/openSUSE_Leap_15.4/              |  
 3 | openSUSE-Leap-${releasever}-1                | openSUSE-Leap-15.4-1                                                 
                       | No      | ----      | ----    |   99     | NONE     | hd:/?device=/dev/disk/by-id/usb-Verbatim_S
TORE_N_GO_07211470C205FE48-0:0-part2  |  
 4 | openSUSE_Factory                             | suse-network:/telephony(skype)                                       
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | https://download.opensuse.org/repositories
/network:/telephony/15.4/             |  
 5 | openSUSE_Factory_1                           | suse-/server:/messaging(telegram)                                    
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | https://download.opensuse.org/repositories
/server:/messaging/15.4/              |  
 6 | openSUSE_Leap_${releasever}                  | suse-/mozilla(firefox)                                               
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | https://download.opensuse.org/repositories
/mozilla/openSUSE_Leap_15.4/          |  
 8 | openSUSE_Leap_${releasever}_2                | suse-/security(ike-scan)                                             
                       | No      | ----      | ----    |   99     | NONE     | https://download.opensuse.org/repositories
/security/openSUSE_Leap_15.4/         |  
 9 | openSUSE_Leap_${releasever}_3                | suse-science(openSCAD)                                               
                       | No      | ----      | ----    |   99     | NONE     | http://download.opensuse.org/repositories/
science/openSUSE_Leap_15.4/           |  
10 | openSUSE_Leap_${releasever}_4                | suse-Emulators:/Wine(Wine)                                           
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://download.opensuse.org/repositories/
Emulators:/Wine/15.4/                 |  
11 | openSUSE_Leap_${releasever}_5                | suse-GNOME:/Apps                                                     
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://download.opensuse.org/repositories/
GNOME:/Apps/15.4/                     |  
12 | openSUSE_Leap_${releasever}_6                | suse-M17N:/fonts                                                     
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://download.opensuse.org/repositories/
M17N:/fonts/15.4/                     |  
13 | openSUSE_Leap_${releasever}_7                | suse-LibreOffice:/7.2                                                
                       | No      | ----      | ----    |   99     | NONE     | https://download.opensuse.org/repositories
/LibreOffice:/7.2/openSUSE_Leap_15.4/ |  
14 | openSUSE_Leap_${releasever}_8                | suse-network:/im(signal)                                             
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | https://download.opensuse.org/repositories
/network:/im:/signal/15.4/            |  
15 | openSUSE_Leap_${releasever}_9                | suse-home:/edogawa(KIM kde service menu)                             
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | https://download.opensuse.org/repositories
/home:/edogawa/15.4/                  |  
 7 | openSUSE_Leap_${releasever}_10               | suse-/graphics(paint)                                                
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | https://download.opensuse.org/repositories
/graphics/15.4/                       |  
16 | openSUSE_Leap_15.2                           | suse-TUXEDO                                                          
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://download.opensuse.org/repositories/
isv:/TUXEDO/15.4/                     |  
17 | opensuse-guide.org-openSUSE_Leap_$releasever | Libdvdcss Repository                                                 
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://opensuse-guide.org/repo/openSUSE_Le
ap_15.4/                              |  
18 | packman-halifax                              | packman direct-halifax                                               
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | ftp://ftp.halifax.rwth-aachen.de/packman/s
use/openSUSE_Leap_15.4/               |  
19 | repo-backports-debug-update                  | Update repository with updates for openSUSE Leap debuginfo packages f
rom openSUSE Backports | No      | ----      | ----    |   99     | NONE     | http://download.opensuse.org/update/leap/1
5.4/backports_debug/                  |  
20 | repo-backports-update                        | Update repository of openSUSE Backports                              
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://download.opensuse.org/update/leap/1
5.4/backports/                        |  
21 | repo-debug                                   | Debug Repository                                                     
                       | No      | ----      | ----    |   99     | NONE     | http://download.opensuse.org/debug/distrib
ution/leap/15.4/repo/oss/             |  
22 | repo-debug-non-oss                           | Debug Repository (Non-OSS)                                           
                       | No      | ----      | ----    |   99     | NONE     | http://download.opensuse.org/debug/distrib
ution/leap/15.4/repo/non-oss/         |  
23 | repo-debug-update                            | Update Repository (Debug)                                            
                       | No      | ----      | ----    |   99     | NONE     | http://download.opensuse.org/debug/update/
leap/15.4/oss/                        |  
24 | repo-debug-update-non-oss                    | Update Repository (Debug, Non-OSS)                                   
                       | No      | ----      | ----    |   99     | NONE     | http://download.opensuse.org/debug/update/
leap/15.4/non-oss/                    |  
25 | repo-non-oss                                 | Non-OSS Repository                                                   
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://download.opensuse.org/distribution/
leap/15.4/repo/non-oss/               |  
26 | repo-oss                                     | Main Repository                                                      
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://download.opensuse.org/distribution/
leap/15.4/repo/oss/                   |  
27 | repo-sle-debug-update                        | Update repository with debuginfo for updates from SUSE Linux Enterpri
se 15                  | No      | ----      | ----    |   99     | NONE     | http://download.opensuse.org/debug/update/
leap/15.4/sle/                        |  
28 | repo-sle-update                              | Update repository with updates from SUSE Linux Enterprise 15         
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://download.opensuse.org/update/leap/1
5.4/sle/                              |  
29 | repo-source                                  | Source Repository                                                    
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://download.opensuse.org/source/distri
bution/leap/15.4/repo/oss/            |  
30 | repo-update                                  | Main Update Repository                                               
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://download.opensuse.org/update/leap/1
5.4/oss/                              |  
31 | repo-update-non-oss                          | Update Repository (Non-Oss)                                          
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://download.opensuse.org/update/leap/1
5.4/non-oss/                          |  
32 | repositoryST                                 | z-LOCAL-repository(zoom-ipscan)                                      
                       | Yes     | ( p) Yes  | Yes     |   99     | plaindir | dir:/dati/impo-conf/repositoryST          
                                      |  
33 | suse-devel:languages:gogocryptfs             | suse-devel:/languages:/go(gocryptfs)                                 
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | https://download.opensuse.org/repositories
/devel:/languages:/go/15.4/           |  
34 | suse-home:obs_mhogomchungusirikali_crypto    | suse-home:/obs_mhogomchungu(sirikali crypto)                         
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | https://download.opensuse.org/repositories
/home:/obs_mhogomchungu/15.4/         |  
35 | x86_64                                       | google(chrome)                                                       
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | http://dl.google.com/linux/chrome/rpm/stab
le/x86_64/                            |  
36 | x86_64_1                                     | brave(web browser)                                                   
                       | Yes     | (r ) Yes  | Yes     |   99     | rpm-md   | https://brave-browser-rpm-release.s3.brave
.com/x86_64/                          |  
pla@pla4ST:~> ^C
pla@pla4ST:~>
5

Was this an Upgrade from Leap 15.3 to Leap 15.4?

Because:

LANG=C zypper se -s dkms
Loading repository data...
Reading installed packages...

S | Name | Type    | Version          | Arch   | Repository
--+------+---------+------------------+--------+----------------
  | dkms | package | 2.6.1-bp154.1.30 | noarch | Main Repository

Only 1 dkms package and you:

6

this was onli an update, but yes, about one month ago I did an upgrade from 15.3 to 15.4

7

So post:

zypper se -s dkms

or

zypper se -s glibc-extra
8

I would do:

rpm -e --nodeps dkms-2.3-bp153.1.17 words-2015.02.15-bp153.1.15 glibc-extra-2.31-7.30
zypper in dkms words glibc-extra
zypper up
zypper dup

The last I might answer N to for proceeding, depending on whether zypper succeeded to install the 15.4 versions of dkms, words and glibc-extra without errors. rpm -e --nodeps is a pretty common method of working past “cpio: File from package already exists as a directory in system”, a too often recent problem rpm can’t deal with directly.

9

here is:

pla@pla4ST:~> zypper se -s dkmsRepository 'suse-GNOME:/Apps' is out-of-date. You can run 'zypper refresh' as root to update it.
Repository 'suse-network:/im(signal)' is out-of-date. You can run 'zypper refresh' as root to update it.
Loading repository data...
Reading installed packages...


S  | Name          | Type       | Version          | Arch   | Repository
---+---------------+------------+------------------+--------+------------------
i+ | dkms          | package    | 2.3-bp153.1.17   | noarch | (System Packages)
v  | dkms          | package    | 2.6.1-bp154.1.30 | noarch | Main Repository
   | dkms          | srcpackage | 2.6.1-bp154.1.30 | noarch | Source Repository
   | dkms-bbswitch | package    | 0.8-lp151.3.1    | noarch | Tuxedo leap 15.4
   | r8168-dkms    | package    | 8.040.00-10.57   | noarch | Tuxedo leap 15.4
pla@pla4ST:~> 

pla@pla4ST:~> zypper se -s glibc-extraRepository 'suse-GNOME:/Apps' is out-of-date. You can run 'zypper refresh' as root to update it.
Repository 'suse-network:/im(signal)' is out-of-date. You can run 'zypper refresh' as root to update it.
Loading repository data...
Reading installed packages...


S  | Name        | Type    | Version          | Arch   | Repository
---+-------------+---------+------------------+--------+-------------------------------------------------------------
i+ | glibc-extra | package | 2.31-7.30        | x86_64 | (System Packages)
v  | glibc-extra | package | 2.31-150300.41.1 | x86_64 | Update repository with updates from SUSE Linux Enterprise 15
v  | glibc-extra | package | 2.31-150300.37.1 | x86_64 | Update repository with updates from SUSE Linux Enterprise 15
v  | glibc-extra | package | 2.31-150300.31.2 | x86_64 | Update repository with updates from SUSE Linux Enterprise 15
v  | glibc-extra | package | 2.31-150300.26.5 | x86_64 | Update repository with updates from SUSE Linux Enterprise 15
v  | glibc-extra | package | 2.31-150300.20.7 | x86_64 | Main Repository
pla@pla4ST:~>
10

it seems it is gone well:

pla@pla4ST:~> rpm -e --nodeps dkms-2.3-bp153.1.17 words-2015.02.15-bp153.1.15 glibc-extra-2.31-7.30error: can't create transaction lock on /usr/lib/sysimage/rpm/.rpm.lock (Permission denied)
pla@pla4ST:~> su -
Password: 
pla4ST:~ # rpm -e --nodeps dkms-2.3-bp153.1.17 words-2015.02.15-bp153.1.15 glibc-extra-2.31-7.30
rm: cannot remove '/var/lib/systemd/migrated/dkms': No such file or directory
pla4ST:~ # 

pla4ST:~ # zypper in dkms words glibc-extraRetrieving repository 'suse-GNOME:/Apps' metadata .................................................................[done]
Building repository 'suse-GNOME:/Apps' cache ......................................................................[done]
Retrieving repository 'suse-network:/im(signal)' metadata .........................................................[done]
Building repository 'suse-network:/im(signal)' cache ..............................................................[done]
Loading repository data...
Reading installed packages...
Resolving package dependencies...


The following 3 NEW packages are going to be installed:
  dkms glibc-extra words


3 new packages to install.
Overall download size: 847.2 KiB. Already cached: 0 B. After the operation, additional 3.3 MiB will be used.
Continue? [y/n/v/...? shows all options] (y): y
Retrieving package dkms-2.6.1-bp154.1.30.noarch                                     (1/3),  74.1 KiB (200.1 KiB unpacked)
Retrieving: dkms-2.6.1-bp154.1.30.noarch.rpm ......................................................................[done]
Retrieving package words-2015.02.15-bp154.1.46.noarch                               (2/3), 708.5 KiB (  3.1 MiB unpacked)
Retrieving: words-2015.02.15-bp154.1.46.noarch.rpm ................................................................[done]
Retrieving package glibc-extra-2.31-150300.41.1.x86_64                              (3/3),  64.6 KiB ( 27.7 KiB unpacked)
Retrieving: glibc-extra-2.31-150300.41.1.x86_64.rpm ...............................................................[done]


Checking for file conflicts: ......................................................................................[done]
(1/3) Installing: dkms-2.6.1-bp154.1.30.noarch ....................................................................[done]
Updating /etc/sysconfig/words ...
(2/3) Installing: words-2015.02.15-bp154.1.46.noarch ..............................................................[done]
(3/3) Installing: glibc-extra-2.31-150300.41.1.x86_64 .............................................................[done]
pla4ST:~ # 




pla4ST:~ # zypper upLoading repository data...
Reading installed packages...


The following 3 items are locked and will not be changed by any action:
 Available:
  PackageKit aws-vault plasma-pass


The following 60 package updates will NOT be installed:
  alee-fonts cantarell-fonts dcraw dcraw-lang dejavu-fonts efont-unicode-bitmap-fonts ffmpeg-4 gdk-pixbuf-loader-libheif
  gimp-help gnome-shell-extension-onboard google-caladea-fonts google-carlito-fonts google-droid-fonts
  google-poppins-fonts google-roboto-fonts intlfonts-arabic-bitmap-fonts intlfonts-chinese-big-bitmap-fonts
  intlfonts-chinese-bitmap-fonts intlfonts-euro-bitmap-fonts intlfonts-japanese-big-bitmap-fonts
  intlfonts-japanese-bitmap-fonts khmeros-fonts libavcodec58_134 libavdevice58_13 libavfilter7_110 libavformat58_76
  libavresample4_0 libavutil56_70 libgexiv2-2 libgsm1 libgts-0_7-5 libheif1 libjbig2 libjpeg8 liblqr-1-0 libmtp-udev
  libmtp9 libnewt0_52 libopenjpeg1 libpostproc55_9 libpotrace0 libraw20 libspeex1 libspeexdsp1 libsrtp2-1
  libswresample3_9 libswscale5_9 libturbojpeg0 mypaint-brushes nautilus-share nautilus-share-lang onboard onboard-data
  onboard-lang patterns-fonts-fonts patterns-fonts-fonts_opt pavucontrol pavucontrol-lang raleway-fonts xkeyboard-config
Nothing to do.
pla4ST:~ # 

pla4ST:~ # zypper dupLoading repository data...
Reading installed packages...
Warning: You are about to do a distribution upgrade with all enabled repositories. Make sure these repositories are compatible before you continue. See 'man zypper' for more information about this command.
Computing distribution upgrade...


Problem: problem with the installed QGnomePlatform-0.8.4-lp154.18.1.x86_64
 Solution 1: install QGnomePlatform-0.5-150400.7.5.x86_64 from vendor SUSE LLC <https://www.suse.com/>
  replacing QGnomePlatform-0.8.4-lp154.18.1.x86_64 from vendor obs://build.opensuse.org/GNOME
 Solution 2: keep obsolete QGnomePlatform-0.8.4-lp154.18.1.x86_64


Choose from above solutions by number or cancel [1/2/c/d/?] (c): 1
Resolving dependencies...
Computing distribution upgrade...


The following 3 items are locked and will not be changed by any action:
 Available:
  PackageKit aws-vault plasma-pass


The following 29 packages are going to be downgraded:
  QGnomePlatform adobe-sourcecodepro-fonts adobe-sourcesanspro-fonts adobe-sourceserifpro-fonts alee-fonts
  baekmuk-bitmap-fonts baekmuk-ttf-fonts cantarell-fonts dejavu-fonts efont-unicode-bitmap-fonts google-caladea-fonts
  google-carlito-fonts google-droid-fonts google-opensans-fonts google-poppins-fonts google-roboto-fonts
  google-roboto-slab-fonts hack-fonts inter-fonts intlfonts-arabic-bitmap-fonts intlfonts-chinese-big-bitmap-fonts
  intlfonts-chinese-bitmap-fonts intlfonts-euro-bitmap-fonts intlfonts-japanese-big-bitmap-fonts
  intlfonts-japanese-bitmap-fonts khmeros-fonts liberation-fonts raleway-fonts stix-fonts


The following package is going to change vendor:
  QGnomePlatform  obs://build.opensuse.org/GNOME -> SUSE LLC <https://www.suse.com/>


29 packages to downgrade, 1 to change vendor.
Overall download size: 71.4 MiB. Already cached: 0 B. After the operation, 157.9 KiB will be freed.
Continue? [y/n/v/...? shows all options] (y): y