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Bug#855891: upgrade removes packages



Package: apt
Version: 1.0.9.8.4
Severity: important

I upgraded a jessie system to stretch last night, using the usual
dpkg --configure -a && dpkg --audit && apt-get upgrade && apt-get
dist-upgrade sequence.

During the upgrade step, ifupdown (among others) was removed:

  Commandline: apt-get upgrade
  […]
  Remove: libuuid-perl:amd64 (0.05-1+b1), ifupdown:amd64
  (0.8.13~bpo8+1), libperl4-corelibs-perl:amd64 (0.003-1),
  python-bson:amd64 (2.7.2-1), libasprintf0c2:amd64 (0.19.3-2),
  python-pymongo:amd64 (2.7.2-1)

I consider this a pretty bad policy violation, but I can't rule out
that I haven't made a mistake, so not making this RC for now… please
feel free to change.

This bug report was composed in reaction to
https://lists.debian.org/msgid-search/20170222121627.qjbhg7bitu4le4b7@crossbow

Please note that the backports.org version was installed, not sure
that's of any relevance though. Unfortunately, I had installed the
backport just shortly before the upgrade, in an attempt to get
a feature (systemd --user) to work on jessie, which required this
upgrade of ifupdown, and there exists no dpkg.status backup with the
backports.org version just before the upgrade.

However, libperl4-corelibs-perl was also removed during the
"upgrade", and that exists in the previous dpkg.status backup:

  Package: libperl4-corelibs-perl
  Status: install ok installed
  Version: 0.003-1

and also in the apt.extended_states backup:

  Package: libperl4-corelibs-perl
  Architecture: amd64
  Auto-Installed: 1

and in the aptitude.pkgstates backup, although aptitude was not used
in any of this:

  Package: libperl4-corelibs-perl
  Architecture: amd64
  Unseen: no
  State: 1
  Dselect-State: 1
  Remove-Reason: 0

> A good idea might also be to write down the result of "grep ^Date
> /var/lib/apt/lists/*Release" somewhere to have an easier time of
> getting the same mirror state out of snapshot if we need that.

debian_dists_jessie_Release:Date: Sat, 14 Jan 2017 11:03:32 UTC
debian-security_dists_jessie_updates_InRelease:Date: Mon, 20 Feb 2017 19:21:05 UTC
debian_dists_jessie-updates_InRelease:Date: Tue, 21 Feb 2017 14:31:12 UTC
debian_dists_jessie-backports_InRelease:Date: Tue, 21 Feb 2017 14:31:12 UTC

> I would suggest to report a bug with all the details you collected
> [and all those the bugscript wants to collect] as its hard to
> reproduce otherwise

Here's the bugscript output, though run (manually) after the stretch upgrade of
course:

-- apt-config dump --

APT "";
APT::Architecture "amd64";
APT::Build-Essential "";
APT::Build-Essential:: "build-essential";
APT::Install-Recommends "false";
APT::Install-Suggests "0";
APT::Sandbox "";
APT::Sandbox::User "_apt";
APT::NeverAutoRemove "";
APT::NeverAutoRemove:: "^firmware-linux.*";
APT::NeverAutoRemove:: "^linux-firmware$";
APT::NeverAutoRemove:: "^linux-image-3\.16\.0-4-amd64$";
APT::NeverAutoRemove:: "^linux-image-4\.9\.0-1-amd64$";
APT::NeverAutoRemove:: "^linux-headers-3\.16\.0-4-amd64$";
APT::NeverAutoRemove:: "^linux-headers-4\.9\.0-1-amd64$";
APT::NeverAutoRemove:: "^linux-image-extra-3\.16\.0-4-amd64$";
APT::NeverAutoRemove:: "^linux-image-extra-4\.9\.0-1-amd64$";
APT::NeverAutoRemove:: "^linux-signed-image-3\.16\.0-4-amd64$";
APT::NeverAutoRemove:: "^linux-signed-image-4\.9\.0-1-amd64$";
APT::NeverAutoRemove:: "^kfreebsd-image-3\.16\.0-4-amd64$";
APT::NeverAutoRemove:: "^kfreebsd-image-4\.9\.0-1-amd64$";
APT::NeverAutoRemove:: "^kfreebsd-headers-3\.16\.0-4-amd64$";
APT::NeverAutoRemove:: "^kfreebsd-headers-4\.9\.0-1-amd64$";
APT::NeverAutoRemove:: "^gnumach-image-3\.16\.0-4-amd64$";
APT::NeverAutoRemove:: "^gnumach-image-4\.9\.0-1-amd64$";
APT::NeverAutoRemove:: "^.*-modules-3\.16\.0-4-amd64$";
APT::NeverAutoRemove:: "^.*-modules-4\.9\.0-1-amd64$";
APT::NeverAutoRemove:: "^.*-kernel-3\.16\.0-4-amd64$";
APT::NeverAutoRemove:: "^.*-kernel-4\.9\.0-1-amd64$";
APT::NeverAutoRemove:: "^linux-backports-modules-.*-3\.16\.0-4-amd64$";
APT::NeverAutoRemove:: "^linux-backports-modules-.*-4\.9\.0-1-amd64$";
APT::NeverAutoRemove:: "^linux-tools-3\.16\.0-4-amd64$";
APT::NeverAutoRemove:: "^linux-tools-4\.9\.0-1-amd64$";
APT::NeverAutoRemove:: "^postgresql-";
APT::VersionedKernelPackages "";
APT::VersionedKernelPackages:: "linux-image";
APT::VersionedKernelPackages:: "linux-headers";
APT::VersionedKernelPackages:: "linux-image-extra";
APT::VersionedKernelPackages:: "linux-signed-image";
APT::VersionedKernelPackages:: "kfreebsd-image";
APT::VersionedKernelPackages:: "kfreebsd-headers";
APT::VersionedKernelPackages:: "gnumach-image";
APT::VersionedKernelPackages:: ".*-modules";
APT::VersionedKernelPackages:: ".*-kernel";
APT::VersionedKernelPackages:: "linux-backports-modules-.*";
APT::VersionedKernelPackages:: "linux-tools";
APT::Never-MarkAuto-Sections "";
APT::Never-MarkAuto-Sections:: "metapackages";
APT::Never-MarkAuto-Sections:: "contrib/metapackages";
APT::Never-MarkAuto-Sections:: "non-free/metapackages";
APT::Never-MarkAuto-Sections:: "restricted/metapackages";
APT::Never-MarkAuto-Sections:: "universe/metapackages";
APT::Never-MarkAuto-Sections:: "multiverse/metapackages";
APT::Move-Autobit-Sections "";
APT::Move-Autobit-Sections:: "oldlibs";
APT::Move-Autobit-Sections:: "contrib/oldlibs";
APT::Move-Autobit-Sections:: "non-free/oldlibs";
APT::Move-Autobit-Sections:: "restricted/oldlibs";
APT::Move-Autobit-Sections:: "universe/oldlibs";
APT::Move-Autobit-Sections:: "multiverse/oldlibs";
APT::Get "";
APT::Get::Purge "false";
APT::Get::AutomaticRemove "true";
APT::Architectures "";
APT::Architectures:: "amd64";
APT::Compressor "";
APT::Compressor::. "";
APT::Compressor::.::Name ".";
APT::Compressor::.::Extension "";
APT::Compressor::.::Binary "";
APT::Compressor::.::Cost "0";
APT::Compressor::lz4 "";
APT::Compressor::lz4::Name "lz4";
APT::Compressor::lz4::Extension ".lz4";
APT::Compressor::lz4::Binary "false";
APT::Compressor::lz4::Cost "50";
APT::Compressor::gzip "";
APT::Compressor::gzip::Name "gzip";
APT::Compressor::gzip::Extension ".gz";
APT::Compressor::gzip::Binary "gzip";
APT::Compressor::gzip::Cost "100";
APT::Compressor::gzip::CompressArg "";
APT::Compressor::gzip::CompressArg:: "-6n";
APT::Compressor::gzip::UncompressArg "";
APT::Compressor::gzip::UncompressArg:: "-d";
APT::Compressor::xz "";
APT::Compressor::xz::Name "xz";
APT::Compressor::xz::Extension ".xz";
APT::Compressor::xz::Binary "xz";
APT::Compressor::xz::Cost "200";
APT::Compressor::xz::CompressArg "";
APT::Compressor::xz::CompressArg:: "-6";
APT::Compressor::xz::UncompressArg "";
APT::Compressor::xz::UncompressArg:: "-d";
APT::Compressor::bzip2 "";
APT::Compressor::bzip2::Name "bzip2";
APT::Compressor::bzip2::Extension ".bz2";
APT::Compressor::bzip2::Binary "bzip2";
APT::Compressor::bzip2::Cost "300";
APT::Compressor::bzip2::CompressArg "";
APT::Compressor::bzip2::CompressArg:: "-6";
APT::Compressor::bzip2::UncompressArg "";
APT::Compressor::bzip2::UncompressArg:: "-d";
APT::Compressor::lzma "";
APT::Compressor::lzma::Name "lzma";
APT::Compressor::lzma::Extension ".lzma";
APT::Compressor::lzma::Binary "xz";
APT::Compressor::lzma::Cost "400";
APT::Compressor::lzma::CompressArg "";
APT::Compressor::lzma::CompressArg:: "--format=lzma";
APT::Compressor::lzma::CompressArg:: "-6";
APT::Compressor::lzma::UncompressArg "";
APT::Compressor::lzma::UncompressArg:: "--format=lzma";
APT::Compressor::lzma::UncompressArg:: "-d";
Dir "/";
Dir::State "var/lib/apt";
Dir::State::lists "lists/";
Dir::State::cdroms "cdroms.list";
Dir::State::mirrors "mirrors/";
Dir::State::extended_states "extended_states";
Dir::State::status "/var/lib/dpkg/status";
Dir::Cache "var/cache/apt";
Dir::Cache::archives "archives/";
Dir::Cache::srcpkgcache "srcpkgcache.bin";
Dir::Cache::pkgcache "pkgcache.bin";
Dir::Etc "etc/apt";
Dir::Etc::sourcelist "sources.list";
Dir::Etc::sourceparts "sources.list.d";
Dir::Etc::main "apt.conf";
Dir::Etc::netrc "auth.conf";
Dir::Etc::parts "apt.conf.d";
Dir::Etc::preferences "preferences";
Dir::Etc::preferencesparts "preferences.d";
Dir::Etc::trusted "trusted.gpg";
Dir::Etc::trustedparts "trusted.gpg.d";
Dir::Bin "";
Dir::Bin::methods "/usr/lib/apt/methods";
Dir::Bin::solvers "";
Dir::Bin::solvers:: "/usr/lib/apt/solvers";
Dir::Bin::planners "";
Dir::Bin::planners:: "/usr/lib/apt/planners";
Dir::Bin::dpkg "/usr/bin/dpkg";
Dir::Bin::gzip "/bin/gzip";
Dir::Bin::bzip2 "/bin/bzip2";
Dir::Bin::xz "/usr/bin/xz";
Dir::Bin::lz4 "/usr/bin/lz4";
Dir::Bin::lzma "/usr/bin/xz";
Dir::Media "";
Dir::Media::MountPath "/media/apt";
Dir::Log "var/log/apt";
Dir::Log::Terminal "term.log";
Dir::Log::History "history.log";
Dir::Log::Planner "eipp.log.xz";
Dir::Ignore-Files-Silently "";
Dir::Ignore-Files-Silently:: "~$";
Dir::Ignore-Files-Silently:: "\.disabled$";
Dir::Ignore-Files-Silently:: "\.bak$";
Dir::Ignore-Files-Silently:: "\.dpkg-[a-z]+$";
Dir::Ignore-Files-Silently:: "\.save$";
Dir::Ignore-Files-Silently:: "\.orig$";
Dir::Ignore-Files-Silently:: "\.distUpgrade$";
Acquire "";
Acquire::AllowInsecureRepositories "0";
Acquire::AllowWeakRepositories "0";
Acquire::AllowDowngradeToInsecureRepositories "0";
Acquire::cdrom "";
Acquire::cdrom::mount "/media/cdrom/";
Acquire::IndexTargets "";
Acquire::IndexTargets::deb "";
Acquire::IndexTargets::deb::Packages "";
Acquire::IndexTargets::deb::Packages::MetaKey "$(COMPONENT)/binary-$(ARCHITECTURE)/Packages";
Acquire::IndexTargets::deb::Packages::flatMetaKey "Packages";
Acquire::IndexTargets::deb::Packages::ShortDescription "Packages";
Acquire::IndexTargets::deb::Packages::Description "$(RELEASE)/$(COMPONENT) $(ARCHITECTURE) Packages";
Acquire::IndexTargets::deb::Packages::flatDescription "$(RELEASE) Packages";
Acquire::IndexTargets::deb::Packages::Optional "0";
Acquire::IndexTargets::deb::Translations "";
Acquire::IndexTargets::deb::Translations::MetaKey "$(COMPONENT)/i18n/Translation-$(LANGUAGE)";
Acquire::IndexTargets::deb::Translations::flatMetaKey "$(LANGUAGE)";
Acquire::IndexTargets::deb::Translations::ShortDescription "Translation-$(LANGUAGE)";
Acquire::IndexTargets::deb::Translations::Description "$(RELEASE)/$(COMPONENT) Translation-$(LANGUAGE)";
Acquire::IndexTargets::deb::Translations::flatDescription "$(RELEASE) Translation-$(LANGUAGE)";
Acquire::IndexTargets::deb-src "";
Acquire::IndexTargets::deb-src::Sources "";
Acquire::IndexTargets::deb-src::Sources::MetaKey "$(COMPONENT)/source/Sources";
Acquire::IndexTargets::deb-src::Sources::flatMetaKey "Sources";
Acquire::IndexTargets::deb-src::Sources::ShortDescription "Sources";
Acquire::IndexTargets::deb-src::Sources::Description "$(RELEASE)/$(COMPONENT) Sources";
Acquire::IndexTargets::deb-src::Sources::flatDescription "$(RELEASE) Sources";
Acquire::IndexTargets::deb-src::Sources::Optional "0";
Acquire::Changelogs "";
Acquire::Changelogs::URI "";
Acquire::Changelogs::URI::Origin "";
Acquire::Changelogs::URI::Origin::Debian "http://metadata.ftp-master.debian.org/changelogs/@CHANGEPATH@_changelog";;
Acquire::Changelogs::URI::Origin::Tanglu "http://metadata.tanglu.org/changelogs/@CHANGEPATH@_changelog";;
Acquire::Changelogs::URI::Origin::Ubuntu "http://changelogs.ubuntu.com/changelogs/pool/@CHANGEPATH@/changelog";;
Acquire::Changelogs::URI::Origin::Ultimedia "http://packages.ultimediaos.com/changelogs/pool/@CHANGEPATH@/changelog.txt";;
Acquire::Changelogs::AlwaysOnline "";
Acquire::Changelogs::AlwaysOnline::Origin "";
Acquire::Changelogs::AlwaysOnline::Origin::Ubuntu "1";
Acquire::PDiffs "false";
Acquire::Languages "";
Acquire::Languages:: "en_NZ";
Acquire::Languages:: "en";
Acquire::Languages:: "none";
Acquire::CompressionTypes "";
Acquire::CompressionTypes::xz "xz";
Acquire::CompressionTypes::bz2 "bzip2";
Acquire::CompressionTypes::lzma "lzma";
Acquire::CompressionTypes::gz "gzip";
Acquire::CompressionTypes::lz4 "lz4";
DPkg "";
DPkg::Pre-Install-Pkgs "";
DPkg::Pre-Install-Pkgs:: "/usr/bin/apt-listchanges --apt || test $? -lt 10";
DPkg::Pre-Install-Pkgs:: "/usr/sbin/dpkg-preconfigure --apt || true";
DPkg::Tools "";
DPkg::Tools::Options "";
DPkg::Tools::Options::/usr/bin/apt-listchanges "";
DPkg::Tools::Options::/usr/bin/apt-listchanges::Version "2";
DPkg::Tools::Options::/usr/bin/apt-listchanges::InfoFD "20";
Binary "apt-config";
Binary::apt "";
Binary::apt::APT "";
Binary::apt::APT::Color "1";
Binary::apt::APT::Cache "";
Binary::apt::APT::Cache::Show "";
Binary::apt::APT::Cache::Show::Version "2";
Binary::apt::APT::Cache::AllVersions "0";
Binary::apt::APT::Cache::ShowVirtuals "1";
Binary::apt::APT::Cache::Search "";
Binary::apt::APT::Cache::Search::Version "2";
Binary::apt::APT::Cache::ShowDependencyType "1";
Binary::apt::APT::Cache::ShowVersion "1";
Binary::apt::APT::Get "";
Binary::apt::APT::Get::Upgrade-Allow-New "1";
Binary::apt::APT::Cmd "";
Binary::apt::APT::Cmd::Show-Update-Stats "1";
Binary::apt::APT::Keep-Downloaded-Packages "0";
Binary::apt::DPkg "";
Binary::apt::DPkg::Progress-Fancy "1";
Binary::apt-get "";
Binary::apt-get::Acquire "";
Binary::apt-get::Acquire::AllowInsecureRepositories "1";
CommandLine "";
CommandLine::AsString "apt-config dump";

-- (no /etc/apt/preferences present) --


-- (no /etc/apt/preferences.d/* present) --


-- /etc/apt/sources.list --

# Ansible managed: /home/madduck/sa/ansible/playbooks/apt/sourceslist.j2 modified
# on 2015-11-25 14:46:25 by madduck on fishbowl
#
# Put local repository definitions into /etc/apt/sources.list.d/local-*
#

# repository: debian
deb     http://ftp.uni-erlangen.de/debian stretch main

# repository: debian-security
deb     http://security.debian.org/debian-security stretch/updates main

# repository: madduck
deb     http://debian.madduck.net/repo stretch main

-- 
 .''`.   martin f. krafft <madduck@d.o> @martinkrafft
: :'  :  proud Debian developer
`. `'`   http://people.debian.org/~madduck
  `-  Debian - when you have better things to do than fixing systems

Attachment: digital_signature_gpg.asc
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