Broken Glibc-2.19-r1 Upgrade

Anything that pertains to Entropy, Equo or Sulfur

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rdnetto
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Broken Glibc-2.19-r1 Upgrade

Post by rdnetto » Thu Jan 29, 2015 19:10

Hi,
I upgraded glibc to 2.19-r1 via portage earlier this week (when the Ghost vulnerability was announced), and everything seemed to work fine. (I also ran spmsync after this, so entropy knew about the new version.) However, when I tried running equo upgrade today, which included an entropy package for the same version of glibc, the result was a broken system. Entropy failed with an error message (below), and the result was a root file system with no libc (/lib/libc.so.6 was a broken symlink), which broke pretty much everything.

I've since fixed my system by reverting to before I upgraded libc with Portage (using btrfs snapshots), but I'd like to know what/if I did something wrong, and also to give a heads up to anyone who did the same thing as me (since this problem seems to be reproducible).

Thanks in advance.

Code: Select all

╠  +++ >>>  (2/123) sys-libs/glibc-2.19-r1
╠    ## Unpacking: sys-libs:glibc-2.19-r1.3d9e8a5dd28c6a5abbd68aacf4895b8e05f7afa3~0.tbz2
╠    ## Package phase: setup
╠    ## Package phase: preinstall
sed: can't read /var/tmp/portage/sys-libs/glibc-2.19-r1/image//etc/host.conf: No such file or directory
 * Defaulting /etc/host.conf:multi to on
/var/tmp/entropy/sys-libs/glibc-2.19-r1/uKZ3u1/portage/sys-libs/glibc-2.19-r1/temp/environment: line 2281: pushd: /var/tmp/portage/sys-libs/glibc-2.19-r1/image//lib64: No such file or directory
/var/tmp/entropy/sys-libs/glibc-2.19-r1/uKZ3u1/portage/sys-libs/glibc-2.19-r1/temp/environment: line 2296: ./ld-*.so: No such file or directory
 * ERROR: sys-libs/glibc-2.19-r1::gentoo failed (preinst phase):
 *   simple run test (/usr/bin/cal) failed
 * 
 * Call stack:
 *     ebuild.sh, line   93:  Called pkg_preinst
 *   environment, line 3046:  Called eblit-run 'pkg_preinst'
 *   environment, line 1160:  Called eblit-glibc-pkg_preinst
 *   environment, line  995:  Called glibc_sanity_check
 *   environment, line 2296:  Called die
 * The specific snippet of code:
 *           ./ld-*.so --library-path . ${x} > /dev/null || die "simple run test (${x}) failed";
 * 
 * If you need support, post the output of `emerge --info '=sys-libs/glibc-2.19-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sys-libs/glibc-2.19-r1::gentoo'`.
 * The complete build log is located at '/var/tmp/entropy/sys-libs/glibc-2.19-r1/uKZ3u1/portage/sys-libs/glibc-2.19-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/entropy/sys-libs/glibc-2.19-r1/uKZ3u1/portage/sys-libs/glibc-2.19-r1/temp/environment'.
 * Working directory: '/'
 * S: '/var/tmp/entropy/sys-libs/glibc-2.19-r1/uKZ3u1/portage/sys-libs/glibc-2.19-r1/work/glibc-2.19'
☛    ## QA: Cannot run phase preinstall, Phase terminated with exit status: 1. Please report it.
╠    ## Installing package: sys-libs/glibc-2.19-r1
╠    ## [GNU libc6 (also called glibc2) C library]
☛    ## Protecting config file: /etc/locale.gen
╠    ## Updating installed packages repository: sys-libs/glibc-2.19-r1
╠    ## Cleaning previously installed application data.
☛    ## Protecting: /usr/lib/debug/.build-id/ec/6fe63e88ce15cc19d78dbc52838d8cd5929a4e, library needed by:
☛    :: media-libs/libprojectm-2.1.0-r1
[redacted for brevity]
☛    ## Collision found during removal of:
☛    ## /etc/locale.gen
☛    :: Removing library: /usr/lib/debug/.build-id/ec/6fe63e88ce15cc19d78dbc52838d8cd5929a4e [libpthread.so.0, 2]
☛    :: Removing library: /usr/lib/debug/.build-id/dc/bfcbf6fad7bafbf027500b5bc5fa9e18fc2d03 [librt.so.1, 2]
☛    :: Removing library: /usr/lib/debug/.build-id/db/b122a8cba0edc89c551ed11e4f5078c3692427 [libresolv.so.2, 1]
☛    :: Removing library: /usr/lib/debug/.build-id/a1/fbf115e48256956fdeeb430ff79e6725aed372 [libcrypt.so.1, 1]
☛    :: Removing library: /usr/lib/debug/.build-id/96/852959036afe466da57cea6ef0ff2901a6e314 [libnsl.so.1, 1]
☛    :: Removing library: /usr/lib/debug/.build-id/8e/459e08812aee8188e179281fe20748d014b5c2 [librt.so.1, 1]
☛    :: Removing library: /usr/lib/debug/.build-id/75/e977722425d58218f978a9b9d9e7f41f4b847c [libresolv.so.2, 2]
☛    :: Removing library: /usr/lib/debug/.build-id/71/a3a355fae73e3813d422907f9d083c0fae9e12 [libdl.so.2, 2]
☛    :: Removing library: /usr/lib/debug/.build-id/6a/46914c66c9a27363ce5c72311f156eeab680eb [libc.so.6, 1]
☛    :: Removing library: /usr/lib/debug/.build-id/5b/af310d3f829409bb88385d7f447f2c20a70930 [libpthread.so.0, 1]
☛    :: Removing library: /usr/lib/debug/.build-id/40/df0410e2c638432180d4fccf2fe95a72790853 [libm.so.6, 1]
☛    :: Removing library: /usr/lib/debug/.build-id/39/5293978c5c1d50e6f08a687bae843cb3b53a46 [ld-linux-x86-64.so.2, 2]
☛    :: Removing library: /usr/lib/debug/.build-id/34/227c8306c8cb62a2fb89cce7ee61d2af6bb89b [libdl.so.2, 1]
☛    :: Removing library: /usr/lib/debug/.build-id/2b/dbd2d485d5816dfc27dcf1e7ca42358795d97f [libnsl.so.1, 2]
☛    :: Removing library: /usr/lib/debug/.build-id/2a/5cf51df685601a04ca19bd584327cf3cef49d5 [libc.so.6, 2]
☛    :: Removing library: /usr/lib/debug/.build-id/22/6b5bb7b85c8b922546d252bfd3764f8f0dbcd0 [libutil.so.1, 2]
☛    :: Removing library: /usr/lib/debug/.build-id/1d/f53fc2724cdefba10b48895ec736f02bbcb023 [libcrypt.so.1, 2]
☛    :: Removing library: /usr/lib/debug/.build-id/1d/6d69ef1fb4c14b4e1e334ce0861159e40f963b [libanl.so.1, 2]
☛    :: Removing library: /usr/lib/debug/.build-id/1c/b5eee8f887a1aafe31aa1df193ff2959dbbcf8 [libm.so.6, 2]
☛    :: Removing library: /usr/lib/debug/.build-id/15/66c3d695d0b56294e42b400da0d9629932486c [libutil.so.1, 1]
☛    :: Removing library: /usr/lib/debug/.build-id/13/f6c6f9f888bb85d77007a7dab1d8e58645b8e1 [ld-linux.so.2, 1]
☢    ## An error occurred. Action aborted.


joost
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Re: Broken Glibc-2.19-r1 Upgrade

Post by joost » Fri Jan 30, 2015 20:21

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rdnetto
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Re: Broken Glibc-2.19-r1 Upgrade

Post by rdnetto » Fri Jan 30, 2015 20:25

The post there says "Ignore it for now. the installation should be fine.". However, this is definitely not the case for the scenario I described (upgrading from a portage version of glibc) - the resulting system is completely broken as it has no libc.

joost
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Re: Broken Glibc-2.19-r1 Upgrade

Post by joost » Fri Jan 30, 2015 20:33

Switching between glibc like that could certainly break the system. On a pure Entropy systems there is also a warn thrown about a test failing, that can be ignored.
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rdnetto
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Re: Broken Glibc-2.19-r1 Upgrade

Post by rdnetto » Fri Jan 30, 2015 20:40

joost wrote:Switching between glibc like that could certainly break the system. On a pure Entropy systems there is also a warn thrown about a test failing, that can be ignored.
The thing I'm trying to understand is why it broke. Both entropy and portage were working with the same version of glibc, and installing that version through either one worked fine - it was only the horizontal change from portage to entropy that broke it. Additionally, all of the libraries listed at the end of the log were deleted incorrectly. Surely that indicates some kind of bug in entropy?

joost
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Re: Broken Glibc-2.19-r1 Upgrade

Post by joost » Fri Jan 30, 2015 20:44

Guess why mixing Portage and Entropy isn't supported. To a certain level you can do some minor changes but pulling some crucial stuff in the mix like glibc is playing with fire and you just got burned.

Why it went wrong? I have no idea. I hope you have a good snapshot to revert to.
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