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ackalker opened this issue Jul 23, 2020 · 10 comments
Open

"switch_alt_group: Assertion `curpkgd' failed." when uninstalling a package #312

ackalker opened this issue Jul 23, 2020 · 10 comments

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@ackalker
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ackalker commented Jul 23, 2020 •
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On Void Linux x86_64 (GLibc), xbps-0.59.1_2, today I hit this assertion when trying to uninstall some packages which are no longer in the repo.

Captured output of what I did:

# xbps-remove -fR ConsoleKit2 advancescan archivemount chirp-daily conkeror libprotobuf-lite18 libtk-img lunzip php-zmq pm-utils python-crypto python-websockify python3-PyQt4 statifier

Name               Action    Version           New version            Download size
ConsoleKit2        remove    1.2.1_2           -                      - 
cgmanager          remove    0.42_1            -                      - 
libcgmanager       remove    0.42_1            -                      - 
libnih             remove    1.0.3_5           -                      - 
advancescan        remove    1.18_1            -                      - 
archivemount       remove    0.8.7_1           -                      - 
chirp-daily        remove    20170714_1        -                      - 
pygtk              remove    2.24.0_14         -                      - 
python-gobject2    remove    2.28.7_2          -                      - 
python-pyserial    remove    3.4_3             -                      - 
libxml2-python     remove    2.9.10_2          -                      - 
conkeror           remove    1.0.3_1           -                      - 
libprotobuf-lite18 remove    3.7.1_1           -                      - 
libtk-img          remove    1.4.6_1           -                      - 
lunzip             remove    1.9_1             -                      - 
php-zmq            remove    1.1.3_1           -                      - 
zeromq             remove    4.3.2_1           -                      - 
pm-utils           remove    1.4.1_8           -                      - 
python-crypto      remove    2.6.1_9           -                      - 
python-websockify  remove    0.8.0_1           -                      - 
python3-PyQt4      remove    4.12.1_3          -                      - 
qt                 remove    4.8.7_29          -                      - 
python3-sip        remove    4.19.19_2         -                      - 
statifier          remove    1.7.4_1           -                      - 

Size freed on disk:             77MB
Space available on disk:        29GB

Do you want to continue? [Y/n] 
Removing `ConsoleKit2-1.2.1_2' ...
Removed `ConsoleKit2-1.2.1_2' successfully.
Removing `cgmanager-0.42_1' ...
Removed `cgmanager-0.42_1' successfully.
Removing `libcgmanager-0.42_1' ...
Removed `libcgmanager-0.42_1' successfully.
Removing `libnih-1.0.3_5' ...
Removed `libnih-1.0.3_5' successfully.
Removing `advancescan-1.18_1' ...
Removed `advancescan-1.18_1' successfully.
Removing `archivemount-0.8.7_1' ...
Removed `archivemount-0.8.7_1' successfully.
Removing `chirp-daily-20170714_1' ...
Updating MIME database...
Removed `chirp-daily-20170714_1' successfully.
Removing `pygtk-2.24.0_14' ...
Removing byte-compiled python2.7 code for module gtk-2.0/gtk...
Updating ldconfig(8) cache...
Removed `pygtk-2.24.0_14' successfully.
Removing `python-gobject2-2.28.7_2' ...
Removing byte-compiled python2.7 code for module glib...
Removing byte-compiled python2.7 code for module gobject...
Removing byte-compiled python2.7 code for module gtk-2.0...
Removing byte-compiled python2.7 code for module pygtk.py...
Updating ldconfig(8) cache...
Removed `python-gobject2-2.28.7_2' successfully.
Removing `python-pyserial-3.4_3' ...
Removing byte-compiled python2.7 code for module serial...
Updating ldconfig(8) cache...
python-pyserial-3.4_3: unregistered 'pyserial' alternatives group
Removed `python-pyserial-3.4_3' successfully.
Removing `libxml2-python-2.9.10_2' ...
Removing byte-compiled python2.7 code for module drv_libxml2.py...
Removing byte-compiled python2.7 code for module libxml2.py...
Updating ldconfig(8) cache...
Removed `libxml2-python-2.9.10_2' successfully.
Removing `conkeror-1.0.3_1' ...
Updating MIME database...
Removed `conkeror-1.0.3_1' successfully.
Removing `libprotobuf-lite18-3.7.1_1' ...
Removed `libprotobuf-lite18-3.7.1_1' successfully.
Removing `libtk-img-1.4.6_1' ...
Removed `libtk-img-1.4.6_1' successfully.
Removing `lunzip-1.9_1' ...
Removed `lunzip-1.9_1' successfully.
Removing `php-zmq-1.1.3_1' ...
Removed `php-zmq-1.1.3_1' successfully.
Removing `zeromq-4.3.2_1' ...
Removed `zeromq-4.3.2_1' successfully.
Removing `pm-utils-1.4.1_8' ...
Removed `pm-utils-1.4.1_8' successfully.
Removing `python-crypto-2.6.1_9' ...
Removing byte-compiled python2.7 code for module Crypto...
Updating ldconfig(8) cache...
Removed `python-crypto-2.6.1_9' successfully.
Removing `python-websockify-0.8.0_1' ...
Removed `python-websockify-0.8.0_1' successfully.
Removing `python3-PyQt4-4.12.1_3' ...
Removing 'pyqt4' alternatives group symlink: pyuic4
python3-PyQt4-4.12.1_3: unregistered 'pyqt4' alternatives group
xbps-remove: package_alternatives.c:319: switch_alt_group: Assertion `curpkgd' failed.
Aborted

Hopefully I'll be able to provide more info on request.
@ackalker
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ackalker commented Jul 23, 2020 •
edited
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Running xbps-alternatives -l after the above leads to another assertion:

$ xbps-alternatives -l
awk
 - gawk (current)
  - awk:/usr/bin/gawk
  - awk.1:/usr/share/man/man1/gawk.1
babel
 - python3-Babel (current)
  - pybabel:/usr/bin/pybabel3
bc
 - bc (current)
  - bc:/usr/bin/gnu-bc
  - bc.1:/usr/share/man/man1/gnu-bc.1
chardet
 - python-chardet (current)
  - chardetect:/usr/bin/chardetect2
 - python3-chardet
  - chardetect:/usr/bin/chardetect3
coverage
 - python-coverage (current)
  - coverage:/usr/bin/coverage2
crond
 - dcron (current)
  - crond:/etc/sv/dcron
  - crond:/usr/bin/dcrond
  - crontab:/usr/bin/dcrontab
  - crontab.1:/usr/share/man/man1/dcrontab.1
  - crond.8:/usr/share/man/man8/dcrond.8
cython
 - python3-Cython (current)
  - cygdb:/usr/bin/cygdb3
  - cython:/usr/bin/cython3
  - cythonize:/usr/bin/cythonize3
dc
 - bc (current)
  - dc:/usr/bin/gnu-dc
  - dc.1:/usr/share/man/man1/gnu-dc.1
docutils
 - python3-docutils (current)
  - rst2html:/usr/bin/rst2html.py3
  - rst2html4:/usr/bin/rst2html4.py3
  - rst2html5:/usr/bin/rst2html5.py3
  - rst2latex:/usr/bin/rst2latex.py3
  - rst2man:/usr/bin/rst2man.py3
  - rst2odt:/usr/bin/rst2odt.py3
  - rst2odt_prepstyles:/usr/bin/rst2odt_prepstyles.py3
  - rst2pseudoxml:/usr/bin/rst2pseudoxml.py3
  - rst2s5:/usr/bin/rst2s5.py3
  - rst2xetex:/usr/bin/rst2xetex.py3
  - rst2xml:/usr/bin/rst2xml.py3
  - rstpep2html:/usr/bin/rstpep2html.py3
find
 - findutils (current)
  - find:/usr/bin/gfind
  - find.1:/usr/share/man/man1/gfind.1
gntp
 - python-gntp (current)
  - gntp:/usr/bin/gntp2
hostname
 - coreutils (current)
  - hostname:/usr/bin/hostname-coreutils
  - hostname.1:/usr/share/man/man1/hostname-coreutils.1
 - net-tools
  - hostname:/usr/bin/net-tools-hostname
  - /usr/share/man/man1/hostname.1:/usr/share/man/man8/net-tools-hostname.1
ifconfig
 - net-tools (current)
  - ifconfig:/usr/bin/net-tools-ifconfig
  - /usr/share/man/man1/ifconfig.1:/usr/share/man/man8/net-tools-ifconfig.8
iptables
 - iptables (current)
  - ip6tables:/usr/bin/xtables-legacy-multi
  - ip6tables-restore:/usr/bin/xtables-legacy-multi
  - ip6tables-save:/usr/bin/xtables-legacy-multi
  - iptables:/usr/bin/xtables-legacy-multi
  - iptables-restore:/usr/bin/xtables-legacy-multi
  - iptables-save:/usr/bin/xtables-legacy-multi
java
 - openjdk8 (current)
  - /usr/bin/java:/usr/lib/jvm/java-1.8-openjdk/bin/java
  - /usr/bin/jjs:/usr/lib/jvm/java-1.8-openjdk/bin/jjs
  - /usr/bin/keytool:/usr/lib/jvm/java-1.8-openjdk/bin/keytool
  - /usr/bin/orbd:/usr/lib/jvm/java-1.8-openjdk/bin/orbd
  - /usr/bin/pack200:/usr/lib/jvm/java-1.8-openjdk/bin/pack200
  - /usr/bin/policytool:/usr/lib/jvm/java-1.8-openjdk/bin/policytool
  - /usr/bin/rmid:/usr/lib/jvm/java-1.8-openjdk/bin/rmid
  - /usr/bin/rmiregistry:/usr/lib/jvm/java-1.8-openjdk/bin/rmiregistry
  - /usr/bin/servertool:/usr/lib/jvm/java-1.8-openjdk/bin/servertool
  - /usr/bin/tnameserv:/usr/lib/jvm/java-1.8-openjdk/bin/tnameserv
  - /usr/bin/unpack200:/usr/lib/jvm/java-1.8-openjdk/bin/unpack200
 - openjdk8-jre
  - /usr/bin/java:/usr/lib/jvm/java-1.8-openjdk/jre/bin/java
  - /usr/bin/jjs:/usr/lib/jvm/java-1.8-openjdk/jre/bin/jjs
  - /usr/bin/keytool:/usr/lib/jvm/java-1.8-openjdk/jre/bin/keytool
  - /usr/bin/orbd:/usr/lib/jvm/java-1.8-openjdk/jre/bin/orbd
  - /usr/bin/pack200:/usr/lib/jvm/java-1.8-openjdk/jre/bin/pack200
  - /usr/bin/policytool:/usr/lib/jvm/java-1.8-openjdk/jre/bin/policytool
  - /usr/bin/rmid:/usr/lib/jvm/java-1.8-openjdk/jre/bin/rmid
  - /usr/bin/rmiregistry:/usr/lib/jvm/java-1.8-openjdk/jre/bin/rmiregistry
  - /usr/bin/servertool:/usr/lib/jvm/java-1.8-openjdk/jre/bin/servertool
  - /usr/bin/tnameserv:/usr/lib/jvm/java-1.8-openjdk/jre/bin/tnameserv
  - /usr/bin/unpack200:/usr/lib/jvm/java-1.8-openjdk/jre/bin/unpack200
jdk
 - openjdk8 (current)
  - /usr/bin/appletviewer:/usr/lib/jvm/java-1.8-openjdk/bin/appletviewer
  - /usr/bin/extcheck:/usr/lib/jvm/java-1.8-openjdk/bin/extcheck
  - /usr/bin/idlj:/usr/lib/jvm/java-1.8-openjdk/bin/idlj
  - /usr/bin/jar:/usr/lib/jvm/java-1.8-openjdk/bin/jar
  - /usr/bin/jarsigner:/usr/lib/jvm/java-1.8-openjdk/bin/jarsigner
  - /usr/bin/java:/usr/lib/jvm/java-1.8-openjdk/bin/java
  - /usr/bin/java-rmi.cgi:/usr/lib/jvm/java-1.8-openjdk/bin/java-rmi.cgi
  - /usr/bin/javac:/usr/lib/jvm/java-1.8-openjdk/bin/javac
  - /usr/bin/javadoc:/usr/lib/jvm/java-1.8-openjdk/bin/javadoc
  - /usr/bin/javah:/usr/lib/jvm/java-1.8-openjdk/bin/javah
  - /usr/bin/javap:/usr/lib/jvm/java-1.8-openjdk/bin/javap
  - /usr/bin/jcmd:/usr/lib/jvm/java-1.8-openjdk/bin/jcmd
  - /usr/bin/jconsole:/usr/lib/jvm/java-1.8-openjdk/bin/jconsole
  - /usr/bin/jdb:/usr/lib/jvm/java-1.8-openjdk/bin/jdb
  - /usr/bin/jdeps:/usr/lib/jvm/java-1.8-openjdk/bin/jdeps
  - /usr/bin/jhat:/usr/lib/jvm/java-1.8-openjdk/bin/jhat
  - /usr/bin/jinfo:/usr/lib/jvm/java-1.8-openjdk/bin/jinfo
  - /usr/bin/jjs:/usr/lib/jvm/java-1.8-openjdk/bin/jjs
  - /usr/bin/jmap:/usr/lib/jvm/java-1.8-openjdk/bin/jmap
  - /usr/bin/jps:/usr/lib/jvm/java-1.8-openjdk/bin/jps
  - /usr/bin/jrunscript:/usr/lib/jvm/java-1.8-openjdk/bin/jrunscript
  - /usr/bin/jsadebugd:/usr/lib/jvm/java-1.8-openjdk/bin/jsadebugd
  - /usr/bin/jstack:/usr/lib/jvm/java-1.8-openjdk/bin/jstack
  - /usr/bin/jstat:/usr/lib/jvm/java-1.8-openjdk/bin/jstat
  - /usr/bin/jstatd:/usr/lib/jvm/java-1.8-openjdk/bin/jstatd
  - /usr/bin/keytool:/usr/lib/jvm/java-1.8-openjdk/bin/keytool
  - /usr/bin/native2ascii:/usr/lib/jvm/java-1.8-openjdk/bin/native2ascii
  - /usr/bin/orbd:/usr/lib/jvm/java-1.8-openjdk/bin/orbd
  - /usr/bin/pack200:/usr/lib/jvm/java-1.8-openjdk/bin/pack200
  - /usr/bin/policytool:/usr/lib/jvm/java-1.8-openjdk/bin/policytool
  - /usr/bin/rmic:/usr/lib/jvm/java-1.8-openjdk/bin/rmic
  - /usr/bin/rmid:/usr/lib/jvm/java-1.8-openjdk/bin/rmid
  - /usr/bin/rmiregistry:/usr/lib/jvm/java-1.8-openjdk/bin/rmiregistry
  - /usr/bin/schemagen:/usr/lib/jvm/java-1.8-openjdk/bin/schemagen
  - /usr/bin/serialver:/usr/lib/jvm/java-1.8-openjdk/bin/serialver
  - /usr/bin/servertool:/usr/lib/jvm/java-1.8-openjdk/bin/servertool
  - /usr/bin/tnameserv:/usr/lib/jvm/java-1.8-openjdk/bin/tnameserv
  - /usr/bin/unpack200:/usr/lib/jvm/java-1.8-openjdk/bin/unpack200
  - /usr/bin/wsgen:/usr/lib/jvm/java-1.8-openjdk/bin/wsgen
  - /usr/bin/wsimport:/usr/lib/jvm/java-1.8-openjdk/bin/wsimport
  - /usr/bin/xjc:/usr/lib/jvm/java-1.8-openjdk/bin/xjc
locate
 - findutils (current)
logger
 - util-linux (current)
  - logger:/usr/bin/util-linux-logger
  - logger.1:/usr/share/man/man1/util-linux-logger.1
lua
 - lua52 (current)
  - lua:/usr/bin/lua5.2
  - luac:/usr/bin/luac5.2
  - lua.1:/usr/share/man/man1/lua5.2.1
  - luac.1:/usr/share/man/man1/luac5.2.1
  - lua:/usr/share/doc/lua5.2
 - lua51
  - lua:/usr/bin/lua5.1
  - luac:/usr/bin/luac5.1
  - lua.1:/usr/share/man/man1/lua5.1.1
  - luac.1:/usr/share/man/man1/luac5.1.1
  - lua:/usr/share/doc/lua5.1
 - lua53
  - lua:/usr/bin/lua5.3
  - luac:/usr/bin/luac5.3
  - lua.1:/usr/share/man/man1/lua5.3.1
  - luac.1:/usr/share/man/man1/luac5.3.1
  - lua:/usr/share/doc/lua5.3
mail
 - mailx (current)
  - mail.rc:/etc/mailx.rc
  - mail:/usr/bin/mailx
  - mail.1:/usr/share/man/man1/mailx.1
man
 - mdocml (current)
  - man:/usr/bin/mandoc
  - whatis:/usr/bin/mandoc
  - apropos:/usr/bin/mandoc
  - man.1:/usr/share/man/man1/mandoc-man.1
  - whatis.1:/usr/share/man/man1/mandoc-whatis.1
  - apropos.1:/usr/share/man/man1/mandoc-apropos.1
markdown
 - python-Markdown (current)
  - markdown_py:/usr/bin/markdown_py2
mkpasswd
 - expect (current)
  - mkpasswd:/usr/bin/expect-mkpasswd
  - mkpasswd.1:/usr/share/man/man1/expect-mkpasswd.1
nc
 - netcat (current)
  - nc:/usr/bin/gnetcat
  - nc.1:/usr/share/man/man1/gnetcat.1
 - openbsd-netcat
  - nc:/usr/bin/openbsd-nc
  - nc.1:/usr/share/man/man1/openbsd-nc.1
 - nmap
  - nc:/usr/bin/ncat
  - nc.1:/usr/share/man/man1/ncat.1
ntpd
 - chrony (current)
  - ntpd:/usr/bin/chronyd
  - ntpd.8:/usr/share/man/man8/chronyd.8
  - ntpd:/etc/sv/chronyd
numpy
 - python-numpy (current)
  - f2py:/usr/bin/f2py2
 - python3-numpy
  - f2py:/usr/bin/f2py3
pinentry
 - pinentry (current)
  - pinentry:/usr/bin/pinentry-curses
 - pinentry-gtk
  - pinentry:/usr/bin/pinentry-gtk-2
ping
 - iputils (current)
  - ping:/usr/bin/iputils-ping
  - ping.8:/usr/share/man/man8/iputils-ping.8
ping6
 - iputils (current)
  - ping6:/usr/bin/iputils-ping
  - ping6.8:/usr/share/man/man8/iputils-ping.8
pip
 - python3-pip (current)
  - pip:/usr/bin/pip3
 - python-pip
  - pip:/usr/bin/pip2
pkg-config
 - pkg-config (current)
  - pkg-config:/usr/bin/pkg-config.pkg-config
  - pkg-config.1:/usr/share/man/man1/pkg-config.1.pkg-config
  - pkg.m4:/usr/share/aclocal/pkg.m4.pkg-config
 - pkgconf
  - pkg-config:/usr/bin/pkgconf
  - pkg-config.1:/usr/share/man/man1/pkgconf.1
  - pkg.m4:/usr/share/aclocal/pkg.m4.pkgconf
pygments
 - python3-Pygments (current)
  - pygmentize:/usr/bin/pygmentize3
pyqt4
 - python3-PyQt4 (current)
  - pyuic4:/usr/bin/python3-pyuic4
 - python-PyQt4
xbps-alternatives: main.c:152: list_alternatives: Assertion `pkgd' failed.
Aborted

Running xbps-pkdb -a results in:

# xbps-pkgdb -a
ConsoleKit2: cannot read /var/db/xbps/.ConsoleKit2-files.plist, ignoring...
conkeror: cannot read /var/db/xbps/.conkeror-files.plist, ignoring...
cgmanager: cannot read /var/db/xbps/.cgmanager-files.plist, ignoring...
chirp-daily: cannot read /var/db/xbps/.chirp-daily-files.plist, ignoring...
advancescan: cannot read /var/db/xbps/.advancescan-files.plist, ignoring...
archivemount: cannot read /var/db/xbps/.archivemount-files.plist, ignoring...
libcgmanager: cannot read /var/db/xbps/.libcgmanager-files.plist, ignoring...
libnih: cannot read /var/db/xbps/.libnih-files.plist, ignoring...
libprotobuf-lite18: cannot read /var/db/xbps/.libprotobuf-lite18-files.plist, ignoring...
libtk-img: cannot read /var/db/xbps/.libtk-img-files.plist, ignoring...
libxml2-python: cannot read /var/db/xbps/.libxml2-python-files.plist, ignoring...
lunzip: cannot read /var/db/xbps/.lunzip-files.plist, ignoring...
php-zmq: cannot read /var/db/xbps/.php-zmq-files.plist, ignoring...
pm-utils: cannot read /var/db/xbps/.pm-utils-files.plist, ignoring...
python-gobject2: cannot read /var/db/xbps/.python-gobject2-files.plist, ignoring...
pygtk: cannot read /var/db/xbps/.pygtk-files.plist, ignoring...
python-websockify: cannot read /var/db/xbps/.python-websockify-files.plist, ignoring...
python-pyserial: cannot read /var/db/xbps/.python-pyserial-files.plist, ignoring...
python-crypto: cannot read /var/db/xbps/.python-crypto-files.plist, ignoring...
ERROR: python3-PyQt4: alternatives group pyqt4 symlink /usr/bin/pyuic4: No such file or directory
zeromq: cannot read /var/db/xbps/.zeromq-files.plist, ignoring...

@ackalker
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xbps-pkgdb -a doesn't appear to fix these problems; running it a second time results in identical output.

@ericonr
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ericonr commented Jul 23, 2020 

Removing 'pyqt4' alternatives group symlink: pyuic4
python3-PyQt4-4.12.1_3: unregistered 'pyqt4' alternatives group
xbps-remove: package_alternatives.c:319: switch_alt_group: Assertion `curpkgd' failed.
Aborted

It either erroneously called switch_alt_group or that function should know how to deal with cases like this. I will try to reproduce this one.

I believe (but you're better off waiting for someone who understand XBPS better) you might be able to finish uninstalling these packages if you force reinstall them (assuming they are still in your cache), then remove them again. But perhaps leave the PyQt4 package alone. Also, you should probably make a copy of your database if you decide to mess with this stuff, it's in /var/db/xbps/pkgdb*.

@ackalker
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ackalker commented Jul 24, 2020 •
edited
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Thanks for your suggestions.
I have forcibly reinstalled python3-PyQt4 from my cache using xdowngrade from the xtools package (without doing this I couldn't install anything anyway, as xbps-install would complain about python3-PyQt4 package being broken), and successfully uninstalled all other packages in my original list except for this one.
Sadly the problem persists, trying to uninstall python3-PyQt4 produces the same error. At least xbps-pkgdb -a now no longer complains about files for the other packages.

@ericonr
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ericonr commented Jul 24, 2020

Could you share your pkgdb? I believe it would help with diagnosing your issue.

@ackalker
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ackalker commented Feb 20, 2021 •
edited
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@ericonr I'm sorry for the very long delay answering your question.
I'm still experiencing problems with xbps-alternatives -l erroring out.

I have created a repository on Github with the contents of my /var/db/xbps directory as of today, I hope this can be of some use.

@ackalker
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ackalker commented Feb 20, 2021 •
edited
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From some digging in the XBPS source (sadly I've lost my notes about it), I have a hunch that the problem is somehow related to a situation where the _XBPS_ALTERNATIVES_ key/dict is left with references to non-existent packages. I think this can happen when:

  • some update to package X in a remote repository removes its alternatives
  • the user first syncs remote repositories, without touching package X
  • the user then uninstalls package X

@Chocimier
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As a kludge, any of following works:

  • cd $(mktemp -d) && xbps-create -n python-PyQt4-1_1 -s pyqt4 -A noarch . && xbps-rindex -a *.xbps && xbps-install python-PyQt4 -R . && xbps-remove python3-PyQt4 && xbps-remove python-PyQt4
  • backup /var/db/xbps/pkgdb-0.38.plist, then remove python-PyQt4 entry from _XBPS_ALTERNATIVES_, then remove python3-PyQt4

Proper fix is unlikely to appear soon.

@Vagabond
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I can confirm the second approach worked. I removed both the key and dict for pyqt4 and xbps tools started working again.

@Chocimier
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Problem occurs in following way:

  • update package from version defining alternatives to newer one that do not define, using xbps < 0.58 (fixed by lib/package_alternatives.c: prune obsolete alternatives groups #179). After that step, _XBPS_ALTERNATIVES_ in pkgdb lists packages it shoudn't.
  • remove that package
  • attempt to remove other package, such that previously removed package is selected as alternatives provider. Observe crash.

Draft of crash fix is sent in #457.

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@Vagabond @ackalker @Chocimier @ericonr