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Bug#805299: marked as done (apt: W: Problem unlinking the file security - Clean (21: Is a directory))

Your message dated Wed, 18 Nov 2015 11:27:50 +0100
with message-id <20151118102750.GA2028@crossbow>
and subject line Re: Bug#805299: apt: W: Problem unlinking the file security - Clean (21: Is a directory)
has caused the Debian Bug report #805299,
regarding apt: W: Problem unlinking the file security - Clean (21: Is a directory)
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
805299: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=805299
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: apt
Version: 1.1~exp15
Severity: important

Dear Maintainer,
Dear Maintainer,
I upgraded to the latest apt following some announce or something that
triggered/told me that apt 1.1~exp15 is now in experimental.

Had a look at the changelog and went for it. The upgrade went smoothly
but get the following when updating the index.

Fetched 758 kB in 2min 44s (4,601 B/s)
Reading package lists... Done
Building dependency tree
Reading state information... Done
All packages are up to date.
W: Problem unlinking the file security - Clean (21: Is a directory)

While I can understand this is just a warning, could somebody share to
which package or where it is coming from.

>From the changelog -

* rework errors and warnings around insecure repositories (Closes: 796549)

I am just wondering how security could be an insecure repository though ?

Is this a new bug or am I not understanding correctly.

As an aside, also at times when there is mismatch which the new apt is
supposed to have solved (although reading the relevant bug report
shares a particular use-case, dunno if its relevant to the issue I
face of generic hash-sum mismatches from mirror repos.)

In case of hash-sum mismatches, I usually go to /var/lib/apt/lists,
remove the entire lists, make sure to mkdir security and partial (as
one or the other doesn't get built if I do it without, think it's
partial, haven't checked that atm.)

Anyways, after doing that I have to do an aptitude update for the
index to be rebuilt properly without using the diffs.

-- 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::Sandbox "";
APT::Sandbox::User "_apt";
APT::Authentication "";
APT::Authentication::TrustCDROM "true";
APT::NeverAutoRemove "";
APT::NeverAutoRemove:: "^firmware-linux.*";
APT::NeverAutoRemove:: "^linux-firmware$";
APT::NeverAutoRemove:: "^linux-image-4\.2\.0-1-amd64$";
APT::NeverAutoRemove:: "^linux-headers-4\.2\.0-1-amd64$";
APT::NeverAutoRemove:: "^linux-image-extra-4\.2\.0-1-amd64$";
APT::NeverAutoRemove:: "^linux-signed-image-4\.2\.0-1-amd64$";
APT::NeverAutoRemove:: "^kfreebsd-image-4\.2\.0-1-amd64$";
APT::NeverAutoRemove:: "^kfreebsd-headers-4\.2\.0-1-amd64$";
APT::NeverAutoRemove:: "^gnumach-image-4\.2\.0-1-amd64$";
APT::NeverAutoRemove:: "^.*-modules-4\.2\.0-1-amd64$";
APT::NeverAutoRemove:: "^.*-kernel-4\.2\.0-1-amd64$";
APT::NeverAutoRemove:: "^linux-backports-modules-.*-4\.2\.0-1-amd64$";
APT::NeverAutoRemove:: "^linux-tools-4\.2\.0-1-amd64$";
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::Update "";
APT::Update::Post-Invoke-Success "";
APT::Update::Post-Invoke-Success:: "test -x /usr/bin/apt-show-versions
|| exit 0 ; apt-show-versions -i";
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::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 "";
APT::Update::Post-Invoke:: "[ ! -x /usr/bin/debtags ] || debtags
update || true";
APT::Architectures "";
APT::Architectures:: "amd64";
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::xz "";
APT::Compressor::xz::Name "xz";
APT::Compressor::xz::Extension ".xz";
APT::Compressor::xz::Binary "xz";
APT::Compressor::xz::Cost "3";
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 "4";
APT::Compressor::bzip2::CompressArg "";
APT::Compressor::bzip2::CompressArg:: "-9";
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 "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";
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::dpkg "/usr/bin/dpkg";
Dir::Bin::bzip2 "/bin/bzip2";
Dir::Bin::xz "/usr/bin/xz";
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::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$";
Acquire "";
Acquire::AllowInsecureRepositories "1";
Acquire::AllowDowngradeToInsecureRepositories "0";
Acquire::cdrom "";
Acquire::cdrom::mount "/media/cdrom";
Acquire::IndexTargets "";
Acquire::IndexTargets::deb "";
Acquire::IndexTargets::deb::Packages "";
Acquire::IndexTargets::deb::Packages::MetaKey
"$(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::Languages "";
Acquire::Languages:: "en";
Acquire::Languages:: "none";
DPkg "";
DPkg::Pre-Install-Pkgs "";
DPkg::Pre-Install-Pkgs:: "/usr/sbin/apt-listbugs apt";
DPkg::Pre-Install-Pkgs:: "adequate --help >/dev/null 2>&1 || exit 0;
exec adequate --user nobody --apt-preinst";
DPkg::Pre-Install-Pkgs:: "/usr/bin/apt-listchanges --apt || test $? -ne 10";
DPkg::Pre-Install-Pkgs:: "/usr/sbin/dpkg-preconfigure --apt || true";
DPkg::Tools "";
DPkg::Tools::Options "";
DPkg::Tools::Options::/usr/sbin/apt-listbugs "";
DPkg::Tools::Options::/usr/sbin/apt-listbugs::Version "3";
DPkg::Tools::Options::/usr/sbin/apt-listbugs::InfoFD "20";
DPkg::Tools::Options::adequate "";
DPkg::Tools::Options::adequate::Version "2";
DPkg::Tools::Options::/usr/bin/apt-listchanges "";
DPkg::Tools::Options::/usr/bin/apt-listchanges::Version "2";
DPkg::Post-Invoke "";
DPkg::Post-Invoke:: "adequate --help >/dev/null 2>&1 || exit 0;
DEBIAN_FRONTEND=readline exec adequate --debconf --user nobody
--pending";
DPkg::Post-Invoke:: "/usr/bin/test -e
/usr/share/dbus-1/system-services/org.freedesktop.PackageKit.service
&& /usr/bin/test -S /var/run/dbus/system_bus_socket && /usr/bin/gdbus
call --system --dest org.freedesktop.PackageKit --object-path
/org/freedesktop/PackageKit --timeout 4 --method
org.freedesktop.PackageKit.StateHasChanged cache-update > /dev/null;
/bin/echo > /dev/null";
DPkg::Post-Invoke:: "test -x /usr/lib/needrestart/apt-pinvoke &&
/usr/lib/needrestart/apt-pinvoke || true";
AptListbugs "";
AptListbugs::Severities "critical,grave,serious";
Adequate "";
Adequate::Enabled "true";
Unattended-Upgrade "";
Unattended-Upgrade::Origins-Pattern "";
Unattended-Upgrade::Origins-Pattern::
"origin=Debian,codename=${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::DPkg "";
Binary::apt::DPkg::Progress-Fancy "1";
Binary::apt::Acquire "";
Binary::apt::Acquire::AllowInsecureRepositories "0";
CommandLine "";
CommandLine::AsString "apt-config dump";

-- /etc/apt/preferences --

Package: *
Pin: release testing
Pin-Priority: 600

Package: *
Pin: release experimental
Pin-Priority: 1

Package: *
Pin: release unstable
Pin-Priority: 1

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

#### testing #########
deb http://httpredir.debian.org/debian/ testing main contrib non-free
deb-src http://httpredir.debian.org/debian testing main contrib non-free

 #### unstable #########
deb http://httpredir.debian.org/debian unstable main contrib non-free
deb-src http://httpredir.debian.org/debian unstable main contrib

 #### experimental #########
deb http://httpredir.debian.org/debian experimental main contrib
deb-src http://httpredir.debian.org/debian experimental main contrib

-- System Information:
Debian Release: stretch/sid
  APT prefers testing
  APT policy: (600, 'testing'), (1, 'experimental'), (1, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.2.0-1-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=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                 3.113+nmu3
ii  debian-archive-keyring  2014.3
ii  gnupg                   1.4.19-6
ii  gnupg2                  2.1.9-1
ii  gpgv                    1.4.19-6
ii  libapt-pkg5.0           1.1~exp15
ii  libc6                   2.21-0experimental2
ii  libgcc1                 1:5.2.1-23
ii  libstdc++6              5.2.1-23

apt recommends no packages.

Versions of packages apt suggests:
ii  apt-doc     1.1~exp15
ii  aptitude    0.7.4-1
ii  dpkg-dev    1.18.3
ii  python-apt  1.1.0~alpha3+b1
ii  synaptic    0.82

-- no debconf information


-- 
          Regards,
          Shirish Agarwal  शिरीष अग्रवाल
  My quotes in this email licensed under CC 3.0
http://creativecommons.org/licenses/by-nc/3.0/
http://flossexperiences.wordpress.com
EB80 462B 08E1 A0DE A73A  2C2F 9F3D C7A4 E1C4 D2D8

--- End Message ---
--- Begin Message --- 
On Mon, Nov 16, 2015 at 06:24:04PM +0000, shirish शिरीष wrote:
> In case of hash-sum mismatches, I usually go to /var/lib/apt/lists,
> remove the entire lists, make sure to mkdir security and partial (as
> one or the other doesn't get built if I do it without, think it's
> partial, haven't checked that atm.)

The error message isn't talking about "security" as a concept, but about
a file (which turns out to be a directory) called "security" which as
you say in the quoted paragraph you have created yourself. So, trivial
fix for your problem: Do not create that directory. APT doesn't use it
and as this is a private directory no other application could be using
it either. So, yes, apt doesn't create a 'security' directory on its
own, but just because it doesn't need it – and actually wants to have it
gone.

Also, do not create a "partial" directory. APT does that by itself if it
is missing. You don't even have to create the parent directory "lists".
Not even the parent parent directory "apt". If for some reason apt isn't
creating them on it its own if it has to report it as a bug. That isn't
the first "bug" which is actually caused by a user fiddling with
internal state they shouldn't fiddle with if they don't know what they
are doing.


Its indeed ~exp15 which 'introduces' this warning, but just because
I made it so that a warning is shown if apt can't delete something it
wanted to be gone – so it was always tried, it just never said anything
about it that it failed.

We could talk about why apt is showing such a warning given that this is
a harmless empty directory in the wrong place, but that directory
doesn't belong there and in a future version we might us directories for
something and suddently a directory being there could be no longer
harmless. There was a time an '*_InRelease' file would be ignored in
that directory (well, until it got deleted by the cleanup which now
complains). Now its an important file which if it didn't get deleted if
it has no reason to stay would cause apt to believe in an incorrect
state. Maybe next week there will be a need for a security directory.
Who knows…

So, in theory we could make apt go on a 'rampage' and just silently
delete directories in there as well, but I don't see much benefit in it
for now, so we don't for the moment. The point is: We could do it
because this directory contains only apt-stuff. Doing stuff in it and
complaining that apt kills it is like complaining about that you
modified another persons /home directory to your liking, but she keeps
changing it back to her liking.

btw: I have a bit of sympathy for a different mountpoint, so I will see
how to ignore lost+found in this, but there isn't all too much point in
it as there is nothing on this mountpoint which would make sense to
recover – or at least its a million times easier to delete all files and
let apt start fresh with an 'apt update' than trying to make a partly
broken state work again (mainly as recovery usually only gives you back
content, but in the case of lists/ the file metadata like filename,
modification time and such stuff is what you really need to be correct).


Best regards

David Kalnischkies

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