[SOLVED] Arch update fails with file conflicts

CollieJim · 10-15-2014, 05:52 AM

Hi,

When I tried to update today, I was asked if I wanted to replace java-common with extra/java-runtime-common. The update failed. It did not matter whether I accepted the default or said n to the request.

What do I need to do to get rid of the file conflicts? Besides the brute-force option of manually deleting the named files?

Code:

216 16:09:53 / # pacman -Syu
:: Synchronizing package databases...
 core                     116.7 KiB   110K/s 00:01 [######################] 100%
 extra                   1767.0 KiB   218K/s 00:08 [######################] 100%
error: failed retrieving file 'community.db' from mirror.us.leaseweb.net : Recv failure: Connection reset by peer
 community                  2.3 MiB   147K/s 00:16 [######################] 100%
error: failed retrieving file 'multilib.db' from mirror.us.leaseweb.net : Recv failure: Connection reset by peer
 multilib                 118.7 KiB  81.3K/s 00:01 [######################] 100%
 gnome15 is up to date
:: Starting full system upgrade...
:: Replace java-common with extra/java-runtime-common? [Y/n] 
resolving dependencies...
looking for inter-conflicts...

Packages (66): bash-4.3.030-1  bluez-5.24-1  boost-libs-1.56.0-2
               cups-filters-1.0.61-1  dhcpcd-6.5.0-1  digikam-4.2.0-3
               ffmpeg-1:2.4.2-1  foomatic-db-3:20141011-1
               foomatic-db-engine-3:20141011-1  gegl-0.2.0-13
               gimp-help-en_gb-2.8.2-3  gnutls-3.3.9-1  imagemagick-6.8.9.8-1
               java-common-1-8 [removal]  java-environment-common-2-1
               java-runtime-common-2-1  jdk7-openjdk-7.u65_2.5.2-3
               jemalloc-3.6.0-1  jre7-openjdk-7.u65_2.5.2-3
               jre7-openjdk-headless-7.u65_2.5.2-3  k3b-2.0.2-11
               kde-gtk-config-2.2.1-2  kdebase-runtime-4.14.1-4
               kdelibs-4.14.1-2  kdiff3-0.9.98-2  lib32-libtasn1-4.2-1
               lib32-mesa-10.3.1-1  lib32-mesa-dri-10.3.1-1
               lib32-mesa-libgl-10.3.1-1  lib32-mpg123-1.21.0-1
               lib32-pcre-8.36-1  lib32-xz-5.0.7-1  libdvdnav-5.0.1-1
               libibus-1.5.9-3  libkface-4.2.0-3  libkfbapi-1.0-2
               libkgeomap-4.2.0-3  libkpeople-0.2.2-2  libktorrent-1.3.1-3
               libldap-2.4.40-1  libmariadbclient-10.0.14-2  libogg-1.3.2-1
               libtiff-4.0.3-5  linux-3.16.4-1  lirc-utils-1:0.9.1.a-5
               man-pages-3.74-1  mariadb-10.0.14-2  mariadb-clients-10.0.14-2
               mesa-10.3.1-1  mesa-dri-10.3.1-1  mesa-libgl-10.3.1-1
               mono-3.10.0-1  mpg123-1.21.0-1  nfs-utils-1.3.1-1
               nvidia-utils-343.22-1  pcre-8.36-1  polkit-kde-0.99.0-5
               protobuf-2.6.0-2  protobuf-c-1.0.2-1  python-3.4.2-1
               python2-pillow-2.6.0-1  qscintilla-2.8.4-2
               speech-dispatcher-0.8.1-1  sudo-1.8.11.p1-1  syslinux-6.03-1
               telepathy-kde-common-internals-0.8.1-3

Total Download Size:    361.18 MiB
Total Installed Size:   1095.89 MiB
Net Upgrade Size:       -3.69 MiB

:: Proceed with installation? [Y/n] 
:: Retrieving packages ...
 bash-4.3.030-1-x86_64   1237.5 KiB   148K/s 00:08 [######################] 100%
 dhcpcd-6.5.0-1-x86_64    132.3 KiB  35.2K/s 00:04 [######################] 100%
 pcre-8.36-1-x86_64       903.6 KiB   143K/s 00:06 [######################] 100%
...
 lib32-mpg123-1.21.0...   115.5 KiB   105K/s 00:01 [######################] 100%
 lib32-pcre-8.36-1-x...   322.9 KiB  42.0K/s 00:08 [######################] 100%
 lib32-xz-5.0.7-1-x86_64   72.1 KiB  18.0K/s 00:04 [######################] 100%
(65/65) checking keys in keyring                   [######################] 100%
(65/65) checking package integrity                 [######################] 100%
(65/65) loading package files                      [######################] 100%
(65/65) checking for file conflicts                [######################] 100%
error: failed to commit transaction (conflicting files)
java-runtime-common: /usr/bin/java exists in filesystem
java-runtime-common: /usr/bin/keytool exists in filesystem
java-runtime-common: /usr/bin/orbd exists in filesystem
java-runtime-common: /usr/bin/pack200 exists in filesystem
java-runtime-common: /usr/bin/policytool exists in filesystem
java-runtime-common: /usr/bin/rmid exists in filesystem
java-runtime-common: /usr/bin/rmiregistry exists in filesystem
java-runtime-common: /usr/bin/servertool exists in filesystem
java-runtime-common: /usr/bin/tnameserv exists in filesystem
java-runtime-common: /usr/bin/unpack200 exists in filesystem
java-runtime-common: /usr/lib/jvm/default exists in filesystem
java-runtime-common: /usr/lib/jvm/default-runtime exists in filesystem
java-environment-common: /usr/bin/appletviewer exists in filesystem
java-environment-common: /usr/bin/extcheck exists in filesystem
java-environment-common: /usr/bin/idlj exists in filesystem
java-environment-common: /usr/bin/jar exists in filesystem
java-environment-common: /usr/bin/jarsigner exists in filesystem
java-environment-common: /usr/bin/javac exists in filesystem
java-environment-common: /usr/bin/javadoc exists in filesystem
java-environment-common: /usr/bin/javah exists in filesystem
java-environment-common: /usr/bin/javap exists in filesystem
java-environment-common: /usr/bin/jcmd exists in filesystem
java-environment-common: /usr/bin/jconsole exists in filesystem
java-environment-common: /usr/bin/jdb exists in filesystem
java-environment-common: /usr/bin/jhat exists in filesystem
java-environment-common: /usr/bin/jinfo exists in filesystem
java-environment-common: /usr/bin/jmap exists in filesystem
java-environment-common: /usr/bin/jps exists in filesystem
java-environment-common: /usr/bin/jrunscript exists in filesystem
java-environment-common: /usr/bin/jsadebugd exists in filesystem
java-environment-common: /usr/bin/jstack exists in filesystem
java-environment-common: /usr/bin/jstat exists in filesystem
java-environment-common: /usr/bin/jstatd exists in filesystem
java-environment-common: /usr/bin/native2ascii exists in filesystem
java-environment-common: /usr/bin/rmic exists in filesystem
java-environment-common: /usr/bin/schemagen exists in filesystem
java-environment-common: /usr/bin/serialver exists in filesystem
java-environment-common: /usr/bin/wsgen exists in filesystem
java-environment-common: /usr/bin/wsimport exists in filesystem
java-environment-common: /usr/bin/xjc exists in filesystem
Errors occurred, no packages were upgraded.
217 17:02:02 / #

syg00 · 10-15-2014, 06:29 AM

Arch uses their news service to warn of upcoming potential breakages, and circumvention.
Pays to stay on top of that prior to updating.

ondoho · 10-15-2014, 01:07 PM

...in other words: can you read? => www.archlinux.org

CollieJim · 10-16-2014, 07:43 AM

Yes, but that requires opening my eyes...
I was not aware that sometimes manual intervention would be required. Thanks for providing the link.

I appear to have tied myself in a knot. I forced a delete of java-common when I was trying to get the update to work. Now when I try to follow the instructions at the link, I find that java-common is not installed, and I do not have an 'archlinux-java' command.

Code:

pacman -Sydd --asdeps java-runtime-common

still fails, but with only about half the conflicting files.

Code:

# pacman -Q java-common
error: package 'java-common' was not found
# archlinux-java unset
bash: archlinux-java: command not found
# pacman -S java-common
error: target not found: java-common
# pacman -Sydd --asdeps java-runtime-common
:: Synchronizing package databases...
 core                     116.7 KiB   110K/s 00:01 [######################] 100%
 extra                   1774.0 KiB   186K/s 00:10 [######################] 100%
 community                  2.3 MiB   218K/s 00:11 [######################] 100%
 multilib                 118.9 KiB   108K/s 00:01 [######################] 100%
 gnome15 is up to date
looking for inter-conflicts...

Packages (1): java-runtime-common-2-1

Total Installed Size:   0.01 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%
error: failed to commit transaction (conflicting files)
java-runtime-common: /usr/bin/java exists in filesystem
java-runtime-common: /usr/bin/keytool exists in filesystem
java-runtime-common: /usr/bin/orbd exists in filesystem
java-runtime-common: /usr/bin/pack200 exists in filesystem
java-runtime-common: /usr/bin/policytool exists in filesystem
java-runtime-common: /usr/bin/rmid exists in filesystem
java-runtime-common: /usr/bin/rmiregistry exists in filesystem
java-runtime-common: /usr/bin/servertool exists in filesystem
java-runtime-common: /usr/bin/tnameserv exists in filesystem
java-runtime-common: /usr/bin/unpack200 exists in filesystem
java-runtime-common: /usr/lib/jvm/default exists in filesystem
java-runtime-common: /usr/lib/jvm/default-runtime exists in filesystem
Errors occurred, no packages were upgraded.

bstaletic · 10-16-2014, 09:17 AM

Try downgrading java-common package using -Suu and pacman's cache. That is if you haven't recently cleard everythihng from pacman's cache.

CollieJim · 10-16-2014, 09:16 PM

Thanks for the help.

I probably did not do it right -

Code:

pacman -Suu java-common

said java-common not found, but

Code:

pacman -U /var/cache/pacman/pkg/java-common-1-8-any.pkg.tar.zx

worked and I was able to proceed.

The update appeared successful, but now thunderbird and firefox hang...
I'm sure I have a backup around here somewhere.....

ondoho · 10-17-2014, 10:45 AM

Quote:

Originally Posted by CollieJim

Yes, but that requires opening my eyes...
I was not aware that sometimes manual intervention would be required. Thanks for providing the link.

and thank you for having enough self-confidence and/or sense of humour to not be pissed off by my remark.
so many people here seem to lack both.

CollieJim · 10-19-2014, 12:40 AM

A sense of humor is a required dependency! Tact and organisation are two words that normally do not apply to me, so it rarely affects me when I'm the target. I continually need to remind myself, when posting a problem, to *check the logs first*. To which I now add the Arch news service.

Cheers

ondoho · 10-19-2014, 04:35 AM

to understand archlinux you really have to understand how much they rely on the community channels to keep it working.

...it happened to me, too. once. ever since, when an update doesn't work as expected, that's the first place i look.