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Bug#908734: apt: Apt gets messed up after I enable contrib and non-free repositories

Package: apt
Version: 1.4.8
Severity: normal

Dear Maintainer,

*** Reporter, please consider answering these questions, where appropriate ***

   * What led up to the situation?
I edited the sources list to add contrib and non -free after main in the
sources
   * What exactly did you do (or not do) that was effective (or
I wanted to enable non-free and contrib repositories to install a missing
firmware intel microcode, the absence of which was causing system problems.
     ineffective)?
   * What was the outcome of this action?
There is a message from apt after I try apt update
   * What outcome did you expect instead?
Normal outcome, adding and removing repositories in Debian or changing them,
has always been problematic. No graphical interface like yast in opensuse or
easily adding and removing with yum and dnf like in Fedora or even the
graphical interface that Debian has now which is the same as that of Ubuntu,
also causes the same problem.

Here is the error message
W: http://debian.lagis.at/debian/dists/stretch-updates/InRelease: The key(s) in
the keyring /etc/apt/trusted.gpg are ignored as the file is not readable by
user '_apt' executing apt-key.
W: http://debian.lagis.at/debian/dists/stretch/Release.gpg: The key(s) in the
keyring /etc/apt/trusted.gpg are ignored as the file is not readable by user
'_apt' executing apt-key.


*** End of the template - remove these template lines ***



-- Package-specific info:

-- apt-config dump --

APT "";
APT::Architecture "amd64";
APT::Build-Essential "";
APT::Build-Essential:: "build-essential";
APT::Install-Recommends "true";
APT::Install-Suggests "0";
APT::Sandbox "";
APT::Sandbox::User "_apt";
APT::Authentication "";
APT::Authentication::TrustCDROM "true";
APT::NeverAutoRemove "";
APT::NeverAutoRemove:: "^firmware-linux.*";
APT::NeverAutoRemove:: "^linux-firmware$";
APT::NeverAutoRemove:: "^linux-image-4\.9\.0-7-amd64$";
APT::NeverAutoRemove:: "^linux-image-4\.9\.0-8-amd64$";
APT::NeverAutoRemove:: "^linux-headers-4\.9\.0-7-amd64$";
APT::NeverAutoRemove:: "^linux-headers-4\.9\.0-8-amd64$";
APT::NeverAutoRemove:: "^linux-image-extra-4\.9\.0-7-amd64$";
APT::NeverAutoRemove:: "^linux-image-extra-4\.9\.0-8-amd64$";
APT::NeverAutoRemove:: "^linux-signed-image-4\.9\.0-7-amd64$";
APT::NeverAutoRemove:: "^linux-signed-image-4\.9\.0-8-amd64$";
APT::NeverAutoRemove:: "^kfreebsd-image-4\.9\.0-7-amd64$";
APT::NeverAutoRemove:: "^kfreebsd-image-4\.9\.0-8-amd64$";
APT::NeverAutoRemove:: "^kfreebsd-headers-4\.9\.0-7-amd64$";
APT::NeverAutoRemove:: "^kfreebsd-headers-4\.9\.0-8-amd64$";
APT::NeverAutoRemove:: "^gnumach-image-4\.9\.0-7-amd64$";
APT::NeverAutoRemove:: "^gnumach-image-4\.9\.0-8-amd64$";
APT::NeverAutoRemove:: "^.*-modules-4\.9\.0-7-amd64$";
APT::NeverAutoRemove:: "^.*-modules-4\.9\.0-8-amd64$";
APT::NeverAutoRemove:: "^.*-kernel-4\.9\.0-7-amd64$";
APT::NeverAutoRemove:: "^.*-kernel-4\.9\.0-8-amd64$";
APT::NeverAutoRemove:: "^linux-backports-modules-.*-4\.9\.0-7-amd64$";
APT::NeverAutoRemove:: "^linux-backports-modules-.*-4\.9\.0-8-amd64$";
APT::NeverAutoRemove:: "^linux-tools-4\.9\.0-7-amd64$";
APT::NeverAutoRemove:: "^linux-tools-4\.9\.0-8-amd64$";
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::Periodic "";
APT::Periodic::Update-Package-Lists "1";
APT::Periodic::Unattended-Upgrade "1";
APT::Update "";
APT::Update::Post-Invoke-Success "";
APT::Update::Post-Invoke-Success:: "/usr/bin/test -e /usr/share/dbus-1/system-
services/org.freedesktop.PackageKit.service && /usr/bin/test -S
/var/run/dbus/system_bus_socket && /usr/bin/gdbus call --system --dest
org.freedesktop.PackageKit --object-path /org/freedesktop/PackageKit --timeout
4 --method org.freedesktop.PackageKit.StateHasChanged cache-update > /dev/null;
/bin/echo > /dev/null";
APT::Update::Post-Invoke-Success:: "if /usr/bin/test -w /var/cache/app-info -a
-e /usr/bin/appstreamcli; then appstreamcli refresh-cache > /dev/null; fi";
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/cdrom";
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]+$";
Dir::Ignore-Files-Silently:: "\.ucf-[a-z]+$";
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-$(LANGUAGE)";
Acquire::IndexTargets::deb::DEP-11 "";
Acquire::IndexTargets::deb::DEP-11::MetaKey
"$(COMPONENT)/dep11/Components-$(NATIVE_ARCHITECTURE).yml";
Acquire::IndexTargets::deb::DEP-11::ShortDescription
"Components-$(NATIVE_ARCHITECTURE)";
Acquire::IndexTargets::deb::DEP-11::Description "$(RELEASE)/$(COMPONENT)
$(NATIVE_ARCHITECTURE) DEP-11 Metadata";
Acquire::IndexTargets::deb::DEP-11::KeepCompressed "true";
Acquire::IndexTargets::deb::DEP-11::KeepCompressedAs "gz";
Acquire::IndexTargets::deb::DEP-11-icons "";
Acquire::IndexTargets::deb::DEP-11-icons::MetaKey
"$(COMPONENT)/dep11/icons-64x64.tar";
Acquire::IndexTargets::deb::DEP-11-icons::ShortDescription "icons-64x64";
Acquire::IndexTargets::deb::DEP-11-icons::Description "$(RELEASE)/$(COMPONENT)
DEP-11 64x64 Icons";
Acquire::IndexTargets::deb::DEP-11-icons::KeepCompressed "true";
Acquire::IndexTargets::deb::DEP-11-icons::KeepCompressedAs "gz";
Acquire::IndexTargets::deb::DEP-11-icons::DefaultEnabled "true";
Acquire::IndexTargets::deb::DEP-11-icons-hidpi "";
Acquire::IndexTargets::deb::DEP-11-icons-hidpi::MetaKey
"$(COMPONENT)/dep11/icons-128x128.tar";
Acquire::IndexTargets::deb::DEP-11-icons-hidpi::ShortDescription
"icons-128x128";
Acquire::IndexTargets::deb::DEP-11-icons-hidpi::Description
"$(RELEASE)/$(COMPONENT) DEP-11 128x128 Icons";
Acquire::IndexTargets::deb::DEP-11-icons-hidpi::KeepCompressed "true";
Acquire::IndexTargets::deb::DEP-11-icons-hidpi::KeepCompressedAs "gz";
Acquire::IndexTargets::deb::DEP-11-icons-hidpi::DefaultEnabled "false";
Acquire::IndexTargets::deb-src "";
Acquire::IndexTargets::deb-src::Sources "";
Acquire::IndexTargets::deb-src::Sources::MetaKey "$(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 "$(RELEASE) Sources";
Acquire::IndexTargets::deb-src::Sources::Optional "0";
Acquire::Changelogs "";
Acquire::Changelogs::URI "";
Acquire::Changelogs::URI::Origin "";
Acquire::Changelogs::URI::Origin::Debian "http://metadata.ftp-
master.debian.org/changelogs/@CHANGEPATH@_changelog";
Acquire::Changelogs::URI::Origin::Tanglu
"http://metadata.tanglu.org/changelogs/@CHANGEPATH@_changelog";;
Acquire::Changelogs::URI::Origin::Ubuntu
"http://changelogs.ubuntu.com/changelogs/pool/@CHANGEPATH@/changelog";;
Acquire::Changelogs::URI::Origin::Ultimedia
"http://packages.ultimediaos.com/changelogs/pool/@CHANGEPATH@/changelog.txt";;
Acquire::Changelogs::AlwaysOnline "";
Acquire::Changelogs::AlwaysOnline::Origin "";
Acquire::Changelogs::AlwaysOnline::Origin::Ubuntu "1";
Acquire::Languages "";
Acquire::Languages:: "en";
Acquire::Languages:: "none";
Acquire::CompressionTypes "";
Acquire::CompressionTypes::xz "xz";
Acquire::CompressionTypes::bz2 "bzip2";
Acquire::CompressionTypes::lzma "lzma";
Acquire::CompressionTypes::gz "gzip";
Acquire::CompressionTypes::lz4 "lz4";
DPkg "";
DPkg::Post-Invoke "";
DPkg::Post-Invoke:: "/usr/bin/test -e /usr/share/dbus-1/system-
services/org.freedesktop.PackageKit.service && /usr/bin/test -S
/var/run/dbus/system_bus_socket && /usr/bin/gdbus call --system --dest
org.freedesktop.PackageKit --object-path /org/freedesktop/PackageKit --timeout
4 --method org.freedesktop.PackageKit.StateHasChanged cache-update > /dev/null;
/bin/echo > /dev/null";
DPkg::Pre-Install-Pkgs "";
DPkg::Pre-Install-Pkgs:: "/usr/sbin/dpkg-preconfigure --apt || true";
Unattended-Upgrade "";
Unattended-Upgrade::Origins-Pattern "";
Unattended-Upgrade::Origins-Pattern::
"origin=Debian,codename=${distro_codename},label=Debian-Security";
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 --

# 

# deb cdrom:[Official Debian GNU/Linux Live 9.5.0 gnome 2018-07-14T18:02]/ stretch main contrib non-free

# deb cdrom:[Official Debian GNU/Linux Live 9.5.0 gnome 2018-07-14T18:02]/ stretch main contrib non-free

deb http://debian.lagis.at/debian/ stretch main contrib non-free
deb-src http://debian.lagis.at/debian/ stretch main contrib non-free

deb http://debian.lagis.at/debian/ stretch/updates main contrib non-free
deb-src http://debian.lagis.at/debian/ stretch/updates main contrib non-free

# stretch-updates, previously known as 'volatile'
deb http://debian.lagis.at/debian/ stretch-updates main contrib non-free
deb-src http://debian.lagis.at/debian/ stretch-updates main contrib non-free

-- /etc/apt/sources.list.d/base.list --

# deb-src http://deb.debian.org/debian/ stretch main

-- /etc/apt/sources.list.d/base.list.save --

deb http://deb.debian.org/debian/ stretch main
#deb-src http://deb.debian.org/debian/ stretch main

-- System Information:
Debian Release: 9.5
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.9.0-8-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages apt depends on:
ii  adduser                 3.115
ii  debian-archive-keyring  2017.5
ii  gpgv                    2.1.18-8~deb9u2
ii  init-system-helpers     1.48
ii  libapt-pkg5.0           1.4.8
ii  libc6                   2.24-11+deb9u3
ii  libgcc1                 1:6.3.0-18+deb9u1
ii  libstdc++6              6.3.0-18+deb9u1

Versions of packages apt recommends:
ii  gnupg  2.1.18-8~deb9u2

Versions of packages apt suggests:
pn  apt-doc         <none>
pn  dpkg-dev        <none>
pn  powermgmt-base  <none>
pn  python-apt      <none>
ii  synaptic        0.84.2

-- no debconf information
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