|
|
|
|
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
|
