Bug#727799: apt-get not marking manual correctly and apt-mark showmanual also wrong
Package: apt
Version: 0.9.9.1~ubuntu3
Severity: normal
Dear Maintainer,
*** Please consider answering these questions, where appropriate ***
I first noticed this when I typed apt-mark showmanual. It shows a lot of stuff like xserver and so on that I didn't install
manually. I also looked at a StackOverflow thread "Generating list of manually installed packages and querying individual packages" where several people commented on the same situation and one of them said there seems to be a bug in Ubuntu. I think this bug is actually in Debian. I have been told that the manual status is drawn from /var/lib/apt/extended_states and that does not show the vast majority of the stuff that's showing up.
In that same thread someone provided a python script using apt_pkg which runs on /var/lib/extended_states directly and it shows only like 5 packages versus the dozens or maybe even hundreds using showmanual.
However only 5 packages also didn't seem right, and when I installed a couple packages manually, they didn't get added to /var/lib/extended_states at all (as either automatic or manual). The packages were pudb and reportbug. There are other places online where people have commented on the same thing which I can add later if you want, but they don't provide any insight into why.
I also tried installing packages with aptitude rather than apt-get and the same thing happened.
These packages (pudb and reportbug) do show up correctly in the dpkg log at /var/lib/dpkg/status
-- Package-specific info:
-- apt-config dump --
APT "";
APT::Architecture "amd64";
APT::Build-Essential "";
APT::Build-Essential:: "build-essential";
APT::Install-Recommends "1";
APT::Install-Suggests "0";
APT::Authentication "";
APT::Authentication::TrustCDROM "true";
APT::NeverAutoRemove "";
APT::NeverAutoRemove:: "^firmware-linux.*";
APT::NeverAutoRemove:: "^linux-firmware$";
APT::NeverAutoRemove:: "^kfreebsd-image.*";
APT::NeverAutoRemove:: "^gnumach$";
APT::NeverAutoRemove:: "^gnumach-image.*";
APT::NeverAutoRemove:: "^linux-image-3.11.0-12-generic$";
APT::NeverAutoRemove:: "^linux-image-extra-3.11.0-12-generic$";
APT::NeverAutoRemove:: "^linux-signed-image-3.11.0-12-generic$";
APT::NeverAutoRemove:: "^linux-backports-modules-.*-3.11.0-12-generic$";
APT::NeverAutoRemove:: "^linux-headers-3.11.0-12-generic$";
APT::NeverAutoRemove:: "^linux-tools-3.11.0-12-generic$";
APT::NeverAutoRemove:: "^linux-image-3.8.0-31-generic$";
APT::NeverAutoRemove:: "^linux-image-extra-3.8.0-31-generic$";
APT::NeverAutoRemove:: "^linux-signed-image-3.8.0-31-generic$";
APT::NeverAutoRemove:: "^linux-backports-modules-.*-3.8.0-31-generic$";
APT::NeverAutoRemove:: "^linux-headers-3.8.0-31-generic$";
APT::NeverAutoRemove:: "^linux-tools-3.8.0-31-generic$";
APT::Never-MarkAuto-Sections "";
APT::Never-MarkAuto-Sections:: "metapackages";
APT::Never-MarkAuto-Sections:: "restricted/metapackages";
APT::Never-MarkAuto-Sections:: "universe/metapackages";
APT::Never-MarkAuto-Sections:: "multiverse/metapackages";
APT::Never-MarkAuto-Sections:: "oldlibs";
APT::Never-MarkAuto-Sections:: "restricted/oldlibs";
APT::Never-MarkAuto-Sections:: "universe/oldlibs";
APT::Never-MarkAuto-Sections:: "multiverse/oldlibs";
APT::Periodic "";
APT::Periodic::Update-Package-Lists "1";
APT::Periodic::Download-Upgradeable-Packages "0";
APT::Periodic::AutocleanInterval "0";
APT::Periodic::Unattended-Upgrade "0";
APT::Update "";
APT::Update::Post-Invoke-Success "";
APT::Update::Post-Invoke-Success:: "touch /var/lib/apt/periodic/update-success-stamp 2>/dev/null || true";
APT::Update::Post-Invoke-Success:: "[ ! -f /var/run/dbus/system_bus_socket ] || /usr/bin/dbus-send --system --dest=org.debian.apt --type=signal /org/debian/apt org.debian.apt.CacheChanged || true";
APT::Archives "";
APT::Archives::MaxAge "30";
APT::Archives::MinAge "2";
APT::Archives::MaxSize "500";
APT::Changelogs "";
APT::Changelogs::Server "http://changelogs.ubuntu.com/changelogs";;
APT::Architectures "";
APT::Architectures:: "amd64";
APT::Architectures:: "i386";
APT::Compressor "";
APT::Compressor::. "";
APT::Compressor::.::Name ".";
APT::Compressor::.::Extension "";
APT::Compressor::.::Binary "";
APT::Compressor::.::Cost "1";
APT::Compressor::gzip "";
APT::Compressor::gzip::Name "gzip";
APT::Compressor::gzip::Extension ".gz";
APT::Compressor::gzip::Binary "gzip";
APT::Compressor::gzip::Cost "2";
APT::Compressor::gzip::CompressArg "";
APT::Compressor::gzip::CompressArg:: "-9n";
APT::Compressor::gzip::UncompressArg "";
APT::Compressor::gzip::UncompressArg:: "-d";
APT::Compressor::bzip2 "";
APT::Compressor::bzip2::Name "bzip2";
APT::Compressor::bzip2::Extension ".bz2";
APT::Compressor::bzip2::Binary "bzip2";
APT::Compressor::bzip2::Cost "3";
APT::Compressor::bzip2::CompressArg "";
APT::Compressor::bzip2::CompressArg:: "-9";
APT::Compressor::bzip2::UncompressArg "";
APT::Compressor::bzip2::UncompressArg:: "-d";
APT::Compressor::xz "";
APT::Compressor::xz::Name "xz";
APT::Compressor::xz::Extension ".xz";
APT::Compressor::xz::Binary "xz";
APT::Compressor::xz::Cost "4";
APT::Compressor::xz::CompressArg "";
APT::Compressor::xz::CompressArg:: "-6";
APT::Compressor::xz::UncompressArg "";
APT::Compressor::xz::UncompressArg:: "-d";
APT::Compressor::lzma "";
APT::Compressor::lzma::Name "lzma";
APT::Compressor::lzma::Extension ".lzma";
APT::Compressor::lzma::Binary "xz";
APT::Compressor::lzma::Cost "5";
APT::Compressor::lzma::CompressArg "";
APT::Compressor::lzma::CompressArg:: "--format=lzma";
APT::Compressor::lzma::CompressArg:: "-9";
APT::Compressor::lzma::UncompressArg "";
APT::Compressor::lzma::UncompressArg:: "--format=lzma";
APT::Compressor::lzma::UncompressArg:: "-d";
APT::Compressor::::Name "";
APT::Compressor::::Extension ".";
APT::Compressor::::Binary "";
APT::Compressor::::Cost "100";
APT::Compressor::::CompressArg "";
APT::Compressor::::CompressArg:: "-9";
APT::Compressor::::UncompressArg "";
APT::Compressor::::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::vendorlist "vendors.list";
Dir::Etc::vendorparts "vendors.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::dpkg "/usr/bin/dpkg";
Dir::Bin::bzip2 "/bin/bzip2";
Dir::Bin::xz "/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::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$";
Acquire "";
Acquire::cdrom "";
Acquire::cdrom::mount "/media/cdrom/";
Acquire::Languages "";
Acquire::Languages:: "en";
Acquire::Languages:: "none";
Aptitude "";
Aptitude::Get-Root-Command "sudo:/usr/bin/sudo";
Aptitude::Keep-Unused-Pattern "^linux-image.*$ | ^linux-restricted-modules.*$ | ^linux-ubuntu-modules.*$";
Unattended-Upgrade "";
Unattended-Upgrade::Allowed-Origins "";
Unattended-Upgrade::Allowed-Origins:: "${distro_id}:${distro_codename}-security";
DPkg "";
DPkg::Pre-Install-Pkgs "";
DPkg::Pre-Install-Pkgs:: "/usr/sbin/dpkg-preconfigure --apt || true";
DPkg::Post-Invoke "";
DPkg::Post-Invoke:: "if [ -d /var/lib/update-notifier ]; then touch /var/lib/update-notifier/dpkg-run-stamp; fi; if [ -e /var/lib/update-notifier/updates-available ]; then echo > /var/lib/update-notifier/updates-available; fi ";
CommandLine "";
CommandLine::AsString "apt-config dump";
-- (no /etc/apt/preferences present) --
-- /etc/apt/sources.list --
# deb cdrom:[Kubuntu 12.10 _Quantal Quetzal_ - Release amd64 (20121017.1)]/ quantal main multiverse restricted universe
# See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
# newer versions of the distribution.
deb http://us.archive.ubuntu.com/ubuntu/ saucy main restricted
deb-src http://us.archive.ubuntu.com/ubuntu/ saucy universe main restricted multiverse #Added by software-properties
## Major bug fix updates produced after the final release of the
## distribution.
deb http://us.archive.ubuntu.com/ubuntu/ saucy-updates main restricted
deb-src http://us.archive.ubuntu.com/ubuntu/ saucy-updates universe main restricted multiverse #Added by software-properties
## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
deb http://us.archive.ubuntu.com/ubuntu/ saucy universe
deb http://us.archive.ubuntu.com/ubuntu/ saucy-updates universe
## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team, and may not be under a free licence. Please satisfy yourself as to
## your rights to use the software. Also, please note that software in
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
deb http://us.archive.ubuntu.com/ubuntu/ saucy multiverse
deb http://us.archive.ubuntu.com/ubuntu/ saucy-updates multiverse
## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.
deb http://us.archive.ubuntu.com/ubuntu/ saucy-backports main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ saucy-backports main restricted universe multiverse #Added by software-properties
deb http://security.ubuntu.com/ubuntu saucy-security main restricted
deb-src http://security.ubuntu.com/ubuntu saucy-security universe main restricted multiverse #Added by software-properties
deb http://security.ubuntu.com/ubuntu saucy-security universe
deb http://security.ubuntu.com/ubuntu saucy-security multiverse
## Uncomment the following two lines to add software from Canonical's
## 'partner' repository.
## This software is not part of Ubuntu, but is offered by Canonical and the
## respective vendors as a service to Ubuntu users.
# deb http://archive.canonical.com/ubuntu quantal partner
# deb-src http://archive.canonical.com/ubuntu quantal partner
## This software is not part of Ubuntu, but is offered by third-party
## developers who want to ship their latest software.
deb http://extras.ubuntu.com/ubuntu saucy main
deb-src http://extras.ubuntu.com/ubuntu saucy main
-- System Information:
Debian Release: wheezy/sid
APT prefers saucy-updates
APT policy: (500, 'saucy-updates'), (500, 'saucy-security'), (500, 'saucy'), (100, 'saucy-backports')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 3.11.0-12-generic (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages apt depends on:
ii gnupg 1.4.14-1ubuntu2
ii libapt-pkg4.12 0.9.9.1~ubuntu3
ii libc6 2.17-93ubuntu4
ii libgcc1 1:4.8.1-10ubuntu8
ii libstdc++6 4.8.1-10ubuntu8
ii ubuntu-keyring 2012.05.19
apt recommends no packages.
Versions of packages apt suggests:
pn apt-doc <none>
ii aptitude 0.6.8.2-1ubuntu2
ii dpkg-dev 1.16.12ubuntu1
ii python-apt 0.8.9.1ubuntu1
ii xz-utils 5.1.1alpha+20120614-2ubuntu1
-- no debconf information
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