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Bug 558528

Summary: Migration to git breaked portage sync on Yandex mirror
Product: Mirrors Reporter: Sergey S. Starikoff <Ikonta>
Component: Server ProblemAssignee: Mirror Admins <mirror-admin>
Status: RESOLVED DUPLICATE    
Severity: normal CC: alexander
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---

Description Sergey S. Starikoff 2015-08-24 06:55:28 UTC
During today's world update I've got the following error message:

# emerge -uDN world

These are the packages that would be merged, in order:

Calculating dependencies... done!
… (some package list)
Would you like to merge these packages? [Yes/No] y

>>> Verifying ebuild manifests
!!! A file is not listed in the Manifest: '/usr/portage/gentoo/dev-perl/Net-SSLeay/Net-SSLeay-1.650.0.ebuild'

The directory:
# ls -l /usr/portage/gentoo/dev-perl/Net-SSLeay/
итого 20
-rw-r--r-- 1 portage portage 15712 апр  5 05:31 ChangeLog
-rw-r--r-- 1 portage portage  1506 авг 23 22:01 Manifest
-rw-r--r-- 1 portage portage   360 авг  9 23:34 metadata.xml
-rw-r--r-- 1 portage portage   987 авг  9 23:34 Net-SSLeay-1.650.0.ebuild
-rw-r--r-- 1 portage portage   989 авг 23 22:01 Net-SSLeay-1.650.0-r1.ebuild

Manifest:
# cat  /usr/portage/gentoo/dev-perl/Net-SSLeay/Manifest 
DIST Net-SSLeay-1.65.tar.gz 384413 SHA256 2fb1371120b85f018944d95736c107163f04ba56b6029c0709a2c3d6247b9c06 SHA512 e347ac7cc5ee22b9785953a5318d35fa3a2d5a21a2e726f49c74621d2dad9ea68373e208068dcd60d8a8d5ab027ae6e32fc0b671995d1645a14c2934eb5a884f WHIRLPOOL 15f38b5a026734f7a074b290979f3e346dfea125d02d8f63e7f5c163de7a4514456d3948ade61b74a53173e27aa221b9142736a98b9d6631c61f0239e6f0833b
EBUILD Net-SSLeay-1.650.0-r1.ebuild 989 SHA256 1d24a91001864b24f9a981878f34578764478134deb8adea8301e89f3ac93c13 SHA512 5da86941e1e03cf1dff5170ac9e31e032c6cb5c2d88ef7ed24d41917034c897e3bcd5ca95ef4e635b5ccf683912582058cf98d5bbf87d4c8756ea9fc515da4fe WHIRLPOOL 8f4291dd91d49222e08ec9f92148f761abf46598f01b81d881e5f446d26fd47939a1d5a188b2210bc05abac638e2897a76a44869bc9e3e98c3ef2844cb2b22a6
MISC ChangeLog 15712 SHA256 ec106adcc3fea4133d601cff2e724f611b0e04cefa7d7938dc4715f1fdfef059 SHA512 5e22c74a8bd35c92a0fff19318126cdaa370f1023e4b3abe6bdb259dd1f483fce9c04cf1b402f41d88a7fa9da7cd3031ecbb9fe7ea6456472af28f88fdce32f4 WHIRLPOOL 198aa66c6bca80d08af54160244f1be1adb5e809cffd8da65e029b4bcb659f474eeee72b94345b8e51499d40ecaa077e9d907c86dfeea4bccdeb73eb93d94f1f
MISC metadata.xml 360 SHA256 48e579c4e66afcb8446fa9c00fa4ee3bfbac51dc1d31b4b9a7541eabab810cd8 SHA512 fd34357b99c21dd5b6bcb18ba5125317de4d176268ef8166b3203926889c7306a2de079af073460fbd22e48b99108432100790ac6da0d03672b76b7657f01127 WHIRLPOOL 007a9ad3829d11fa7946da71edce49947c3b2f6ddf6573f2521901b1958b23c20c5784e8d43f97c0a60ec91fc4f8d96be44c496d2ee74643f61a3f24920bcb56

Changelog doesn't describe last update (Net-SSLeay-1.650.0-r1.ebuild commit), but Manifest contains it's digest, but previous (last described in Changelog) is not listed.
Comment 1 Sergey S. Starikoff 2015-08-24 07:52:32 UTC
Completing update (cleaning obsolete distfiles) showed some more similiar errors:
# eclean-dist 
 * Building file list for distfiles cleaning...
 * A file is not listed in the Manifest: '/usr/portage/gentoo/gnome-base/gnome-settings-daemon/gnome-settings-daemon-3.14.2.ebuild'
 * Missing digest for '/usr/portage/gentoo/dev-python/pypy-bin/pypy-bin-2.3.1-r2.ebuild'
 * A file is not listed in the Manifest: '/usr/portage/gentoo/www-client/chromium/chromium-45.0.2454.15-r1.ebuild'
 * A file is not listed in the Manifest: '/usr/portage/gentoo/media-gfx/eog-plugins/eog-plugins-3.14.1.ebuild'
 * Missing digest for '/usr/portage/gentoo/gnome-base/gnome-settings-daemon/gnome-settings-daemon-3.14.2.ebuild'
 * Missing digest for '/usr/portage/gentoo/media-gfx/eog-plugins/eog-plugins-3.14.1.ebuild'
 * A file is not listed in the Manifest: '/usr/portage/gentoo/app-misc/tracker/tracker-1.2.5.ebuild'
 * A file is not listed in the Manifest: '/usr/portage/gentoo/dev-python/pypy/pypy-2.3.1-r2.ebuild'
 * Missing digest for '/usr/portage/gentoo/app-misc/tracker/tracker-1.2.5.ebuild'
 * Missing digest for '/usr/portage/gentoo/www-client/chromium/chromium-45.0.2454.15-r1.ebuild'
 * Missing digest for '/usr/portage/gentoo/www-client/chromium/chromium-45.0.2454.15.ebuild'
 * Missing digest for '/usr/portage/gentoo/dev-python/pypy/pypy-2.3.1-r2.ebuild'
 * Cleaning distfiles...
…
Comment 2 Alexander Tsoy 2015-08-24 09:41:44 UTC
Something wrong with the mirror you are using?

$ rsync --list-only rsync://rsync.gentoo.org/gentoo-portage/dev-perl/Net-SSLeay/
Welcome to starling.gentoo.org / rsync.gentoo.org

Server Address : 81.91.253.252, 2a01:90:200:10::1a
Contact Name   : mirror-admin@gentoo.org
Hardware       : 2 x Intel(R) Xeon(R) CPU E5649 @ 2.53GHz, 3959MB RAM
Sponsor        : Qube Managed Services Limited, Zurich, Switzerland, EU

Please note: common gentoo-netiquette says you should not sync more
than once a day.  Users who abuse the rsync.gentoo.org rotation
may be added to a temporary ban list.

MOTD autogenerated by update-rsync-motd on Thu Jul 24 06:39:12 UTC 2014

drwxr-xr-x            184 2015/08/24 12:07:35 .
-rw-r--r--         15,712 2015/04/05 05:31:08 ChangeLog
-rw-r--r--          1,506 2015/08/23 22:01:02 Manifest
-rw-r--r--            989 2015/08/23 22:01:02 Net-SSLeay-1.650.0-r1.ebuild
-rw-r--r--            360 2015/08/09 23:34:51 metadata.xml
Comment 3 Alexander Tsoy 2015-08-24 10:02:53 UTC
Well.. I can confirm the problem on yandex mirrors (they already fixed it). Our mirror has been synced from it this morning. Note the mtime of files ".lastsync" and "Archive-Update-in-Progress-kruimel.snt.utwente.nl":

$ rsync --list-only rsync://mirror.xxxxx.xxx/gentoo-portage/dev-perl/Net-SSLeay/
drwxr-xr-x              7 2015/08/24 06:37:48 .
-rw-r--r--         15,712 2015/04/05 05:31:08 ChangeLog
-rw-r--r--          1,506 2015/08/23 22:01:02 Manifest
-rw-r--r--            989 2015/08/23 22:01:02 Net-SSLeay-1.650.0-r1.ebuild
-rw-r--r--            987 2015/08/09 23:34:51 Net-SSLeay-1.650.0.ebuild
-rw-r--r--            360 2015/08/09 23:34:51 metadata.xml
$ rsync --list-only rsync://mirror.xxxxx.xxx/gentoo-portage/
drwxrwxr-x            176 2015/08/24 07:02:21 .
-rw-r--r--             67 2015/08/13 04:31:01 .gitignore
-rw-r--r--             29 2015/08/24 07:02:21 .lastsync
-rw-r--r--             29 2015/08/24 07:01:00 .mirror.yandex.ru
-r--r--r--              1 2015/08/23 18:00:01 Archive-Update-in-Progress-kruimel.snt.utwente.nl
...
...
Comment 4 Sergey S. Starikoff 2015-08-24 10:33:40 UTC
(In reply to Alexander Tsoy from comment #3)
> Well.. I can confirm the problem on yandex mirrors (they already fixed it).

Yes it is.
Excuse me for this miss. I've used Yandex mirror, single sync today about 1 hour before bug report.
Comment 5 Sergey S. Starikoff 2015-08-25 06:36:26 UTC
It was temporary issue with Yandex mirror.
Today's sync confirmed fix.
Comment 6 Sergey S. Starikoff 2015-09-07 10:56:27 UTC
Today's sync (from rsync://mirror.yandex.ru/gentoo-portage/) showed the following error:
# eclean-dist 
 * Building file list for distfiles cleaning...
 * Missing digest for '/usr/portage/gentoo/app-emulation/qemu/qemu-2.4.0.ebuild'

Previous week sync also showed some error.
So, something wrong in this mirror's sync procedure.
Comment 7 Sergey S. Starikoff 2015-09-25 22:07:01 UTC
Last (already yesterday's) sync produced the following error:

 * A file is not listed in the Manifest: '/usr/portage/gentoo/dev-php/pecl-yaml/pecl-yaml-1.1.1-r1.ebuild'

15 and 22 September's snapshot (emerge-webrsyc) syncs were OK.
Comment 8 Sergey S. Starikoff 2015-10-19 11:00:41 UTC
For now seems to be fixed.
Comment 9 Sergey S. Starikoff 2015-10-23 17:46:41 UTC
Not fixed.
For ordinar sync (using emerge --sync instead of emerge-webrsync) foday I've got the following error:

 * Building file list for distfiles cleaning...
 * Missing digest for '/usr/portage/gentoo/net-misc/bfgminer/bfgminer-5.4.0.ebuild'
 * Missing digest for '/usr/portage/gentoo/net-misc/bfgminer/bfgminer-4.10.4.ebuild'
Comment 10 Sergey S. Starikoff 2015-10-26 12:01:03 UTC
Today's emerge-webrsync (using yesterday's snapshot) showed the following error:
# eclean-dist 
 * Building file list for distfiles cleaning...
 * Missing digest for '/usr/portage/gentoo/sci-geosciences/opencpn-plugin-logbookkonni/opencpn-plugin-logbookkonni-1.2018-r1.ebuild'
Comment 11 Sergey S. Starikoff 2015-11-17 10:13:38 UTC
Looking a very like diplicate of bug #565694

*** This bug has been marked as a duplicate of bug 565694 ***