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Title: Possible failure to preserve libraries
Author: Sam James <sam@gentoo.org>
Author: Hank Leininger <hlein@korelogic.com>
Posted: 2021-09-29
Revision: 1
News-Item-Format: 2.0
Display-If-Installed: sys-apps/portage
We have observed in some cases corruption of Portage's internal database
(VDB), where the libraries provided by a package are not recorded. This
can break the "preserve-libs" functionality, and thus in rare cases
break your system during much later updates (even if you do not use
"preseved-libs" now, but decide to switch it on later).
The underlying problem occurs usually when glibc has been upgraded to a
new major version, but pax-utils has not yet been upgraded to a version
compatible with it (but at that moment stays undetected).
The full technical details and investigation can be found on a Wiki page
[0] and on Bugzilla [1]. Changes have been made to prevent this happening
again both within Portage [7] (with possibly more to come [2]) and within the
glibc and pax-utils ebuilds [3][4].
To detect whether a system is affected, emerge the
app-portage/recover-broken-vdb package:
```
$ emerge --ask --verbose --oneshot app-portage/recover-broken-vdb
```
which provides two tools: recover-broken-vdb-find-broken.sh and
recover-broken-vdb.
Then run recover-broken-vdb-find-broken.sh:
```
$ recover-broken-vdb-find-broken.sh | tee broken_vdb_packages
```
This check should be run on all Gentoo systems. It is only necessary
to run this as a one-off, as changes have been made to prevent such
problems occurring in future.
If you have any output, read on.
Fixing a broken system is not always straightforward. It is strongly
recommended to take a backup of your full system before proceeding,
as well as a copy of /var/db/pkg (the VDB):
1. A tool has been developed [5] to attempt to fix the consistency
of the Portage database. Using this tool to modify the VDB is NOT
mandatory (read the full news item before proceeding) - you can skip
to Step 2 if you wish, but fixing the integrity of the VDB
makes it as safe as reasonably possible to proceed with
rebuilding packages.
Run:
```
# Take a backup of /var/db/pkg before proceeding, such as by doing:
$ cp -a /var/db/pkg /var/db/pkg.orig
# And then:
$ emerge --ask --verbose --oneshot --noreplace \
app-portage/recover-broken-vdb
$ recover-broken-vdb
# The tool will output to a random temporary directory.
# Inspect the results, and then update the real /var/db/pkg/
# by doing either:
$ recover-broken-vdb --output /var/db/pkg
# Or, manually copying the new files from the temporary directory tree
# into your real /var/db/pkg/ directory tree.
```
2. Attempt to rebuild the affected packages, first upgrading
app-misc/pax-utils to the latest version:
```
$ emerge --ask --verbose --oneshot ">=app-misc/pax-utils-1.3.3"
$ emerge --ask --verbose --oneshot --usepkg=n $(grep -v '#' broken_vdb_packages)
```
Given that there are possible other side-effects of the corruption/bug,
it is strongly recommended that if any corruption is detected, all
packages on the system should be rebuilt, after following the above
steps:
```
$ emerge --ask --emptytree --usepkg=n @world
```
Note that binary packages may need to be discarded given they may
contain corrupt metadata.
Please see the wiki [0] for a full description of the background
of this problem and handling corner cases such as e.g. already
being affected by system breakage [6] as a result of the bug.
[0] https://wiki.gentoo.org/wiki/Project:Toolchain/Corrupt_VDB_ELF_files
[1] https://bugs.gentoo.org/811462
[2] https://github.com/gentoo/portage/pull/744
[3] https://bugs.gentoo.org/811462#c6
[4] https://bugs.gentoo.org/811462#c7
[5] https://github.com/thesamesam/recover-broken-vdb
[6] https://wiki.gentoo.org/wiki/Fix_my_Gentoo
[7] https://gitweb.gentoo.org/proj/portage.git/commit/?id=83af7270fafbd7b1eed0031a5e06836ad1edf06d
|
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