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jwezel
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Joined: 29 Jan 2003
Posts: 58
Location: Birr, Switzerland

PostPosted: Tue Jan 28, 2014 8:21 pm    Post subject: My /var/db/pkg is slowly getting corrupted! Reply with quote

I'm facing a severe problem with my /var/db/pkg. It's slowly getting corrupted by obj entries where the last number has a u suffix which causes emerge to issue error messages:

Here is list of such entries, created with
Code:
find -name CONTENTS | xargs grep ' [0-9][0-9]*u$'
:

Code:
./media-gfx/graphite2-1.2.1/CONTENTS:obj /usr/lib64/libgraphite2.so.3.0.1 6e5abbf10be2dbcd1b6285d8598966ac 1364654715u
./sys-libs/zlib-1.2.8-r1/CONTENTS:obj /lib64/libz.so.1.2.8 d417a14a2082fc028b1e98a5b0317f59 1383753221u
./sys-libs/libcap-2.22/CONTENTS:obj /lib64/libcap.so.2.22 bd79b3f7b7999c8d20bfe99d6e35fb36 1359810637u
./sys-libs/libcap-2.22/CONTENTS:obj /sbin/setcap e2bb3e1c96e938f4ff1a8c0261140e08 1359810637u
./sys-libs/libcap-2.22/CONTENTS:obj /sbin/getcap 70b88e645013607376e64e37b514bfd1 1359810637u
./sys-libs/libcap-2.22/CONTENTS:obj /sbin/getpcaps d93ced968a756d3527ddf77eb9bf5936 1359810637u
./sys-libs/libcap-2.22/CONTENTS:obj /sbin/capsh 357f1b08f5f72fb566fbbced0b377162 1359810637u
./sys-libs/ncurses-5.9-r2/CONTENTS:obj /lib64/libncursesw.so.5.9 504920ce39899d1d5872b636762e040c 1359194555u
./sys-libs/ncurses-5.9-r2/CONTENTS:obj /lib64/libncurses.so.5.9 a6ed2099fb60c5dd903596be6c7eed74 1359194555u
./sys-libs/libutempter-1.1.6-r1/CONTENTS:obj /usr/lib64/libutempter.so.1.1.6 07cf69a438b45a787c8f54be536b1fc6 1381936407u
./sys-libs/libutempter-1.1.6-r1/CONTENTS:obj /usr/lib64/misc/utempter/utempter a6ec9b3d887fe3032961dd27d405014a 1381936407u
./sys-libs/readline-6.2_p1/CONTENTS:obj /lib64/libreadline.so.6.2 17f7f6d2cef2b73911387ed113cc2b0d 1355116923u
./sys-libs/e2fsprogs-libs-1.42.7/CONTENTS:obj /lib64/libss.so.2.0 ef96527bb1e8129cd02ec9e027a9795f 1367075317u
./sys-libs/e2fsprogs-libs-1.42.7/CONTENTS:obj /lib64/libcom_err.so.2.1 44fc38a170f39b6bfb39761b90083002 1367075317u
./sys-libs/pam-1.1.6-r2/CONTENTS:obj /lib64/libpam.so.0.83.1 636d6c876553b8fec3d46b7ea8452247 1359984671u
./sys-libs/pam-1.1.6-r2/CONTENTS:obj /lib64/libpam_misc.so.0.82.0 9df9001a32b926355c322173594384e5 1359984671u
./sys-libs/pam-1.1.6-r2/CONTENTS:obj /sbin/pam_tally b1016090a25c6cfc08c8d819a20f1f58 1359984672u
./sys-libs/pam-1.1.6-r2/CONTENTS:obj /sbin/pam_tally2 66133dd7703e169b08ee8912e32e7650 1359984672u
./sys-libs/pam-1.1.6-r2/CONTENTS:obj /sbin/mkhomedir_helper 6f889fa93b5602465a954e6a43eaf7b0 1359984672u
./sys-libs/glibc-2.17/CONTENTS:obj /lib32/libpthread-2.17.so 965590f0f3347fe401346ef1bcf1c7a8 1389543211u
./sys-libs/glibc-2.17/CONTENTS:obj /lib32/libm-2.17.so 1a1557add4780bf8bfaa32910a840636 1389543201u
./sys-libs/glibc-2.17/CONTENTS:obj /lib32/libc-2.17.so 5d5f118c49e156b4f5c4e9b5a02be01a 1389543201u
./sys-libs/glibc-2.17/CONTENTS:obj /lib32/libcrypt-2.17.so 9808e9e8076c9dd08236a21ded2658e0 1389543201u
./sys-libs/glibc-2.17/CONTENTS:obj /lib32/ld-2.17.so 4f781510b8f1ac39bcaf30d1aee4940e 1389543201u
./sys-libs/glibc-2.17/CONTENTS:obj /lib32/libdl-2.17.so 8fcc6922a19a076097fd5de75a666b53 1389543201u
./sys-libs/glibc-2.17/CONTENTS:obj /lib32/libresolv-2.17.so 8693738215d164475dddc073901fcb89 1389543201u
./sys-libs/glibc-2.17/CONTENTS:obj /lib32/librt-2.17.so 4320d0486cf901478a301728e36ee099 1389543201u
./sys-libs/glibc-2.17/CONTENTS:obj /lib64/libpthread-2.17.so 3017b301b72b46f93bdfef7444142a73 1389543211u
./sys-libs/glibc-2.17/CONTENTS:obj /lib64/libutil-2.17.so 9432d63b9a3b929a8eb113b5f5f888e7 1389543211u
./sys-libs/glibc-2.17/CONTENTS:obj /lib64/libm-2.17.so d9e2fee2fc81f23ef318632024ba7619 1389543210u
./sys-libs/glibc-2.17/CONTENTS:obj /lib64/libc-2.17.so 630a4929f8d3e2b3b9dbe495627d64b0 1389543211u
./sys-libs/glibc-2.17/CONTENTS:obj /lib64/libcrypt-2.17.so ec5c93a3f463a1994338d7c1155da505 1389543210u
./sys-libs/glibc-2.17/CONTENTS:obj /lib64/ld-2.17.so cdca8068ffda10f49554782c85b1cb22 1389543206u
./sys-libs/glibc-2.17/CONTENTS:obj /lib64/libdl-2.17.so bc27a588119998857b2449403bd403ac 1389543210u
./sys-libs/glibc-2.17/CONTENTS:obj /lib64/libresolv-2.17.so 858914650e3f7b48b9abff0611a6390d 1389543210u
./sys-libs/glibc-2.17/CONTENTS:obj /lib64/librt-2.17.so 9321cde24a1bcc949e383b9426c974b5 1389543211u
./sys-libs/glibc-2.17/CONTENTS:obj /lib64/libnsl-2.17.so 34b1857409752d227b2402a01e20673a 1389543211u
./sys-libs/glibc-2.17/CONTENTS:obj /usr/lib64/misc/glibc/getconf/XBS5_LP64_OFF64 6cb35791a54c67dbea15e0672d35d39e 1389543210u
./sys-libs/glibc-2.17/CONTENTS:obj /usr/lib64/misc/glibc/getconf/POSIX_V7_LP64_OFF64 6cb35791a54c67dbea15e0672d35d39e 1389543210u
./sys-libs/glibc-2.17/CONTENTS:obj /usr/lib64/misc/glibc/getconf/POSIX_V6_LP64_OFF64 6cb35791a54c67dbea15e0672d35d39e 1389543210u
./net-wireless/bluedevil-1.3.2/CONTENTS:obj /usr/lib64/kde4/libexec/bluedevil-authorize 5403c7c95491f689b67968ba825bdd43 1390657116u
./net-wireless/bluedevil-1.3.2/CONTENTS:obj /usr/lib64/kde4/libexec/bluedevil-requestconfirmation 5beab87f5397e10dfdb4a81cf9a6da8f 1390657116u
./net-wireless/bluedevil-1.3.2/CONTENTS:obj /usr/lib64/kde4/libexec/bluedevil-confirmmodechange 5844224d52ad2e89bf47db687949f20b 1390657116u
./net-wireless/bluedevil-1.3.2/CONTENTS:obj /usr/lib64/kde4/libexec/bluedevil-requestpin ad9be830e2e2d162a9b0d8b5ee193c95 1390657116u
./sys-auth/polkit-kde-agent-0.99.0-r1/CONTENTS:obj /usr/lib64/kde4/libexec/polkit-kde-authentication-agent-1 198ce66fc51875e855fbaf1808dac5fe 1365870798u
./sys-auth/polkit-0.112/CONTENTS:obj /usr/lib64/libpolkit-agent-1.so.0.0.0 5afeef673f30174bbdebc2318fd5b251 1380123266u
./sys-auth/polkit-0.112/CONTENTS:obj /usr/lib64/libpolkit-gobject-1.so.0.0.0 373f1e4d3d085853b355c31c03d3c501 1380123266u
./sys-auth/polkit-0.112/CONTENTS:obj /usr/lib/polkit-1/polkitd 2d02100713d8d3f2dc57c41f7f7752d5 1380123266u
./sys-auth/polkit-0.112/CONTENTS:obj /usr/lib/polkit-1/polkit-agent-helper-1 4f7bd1fecadfd72412b444c337646eb9 1380123266u
./sys-auth/polkit-qt-0.103.0/CONTENTS:obj /usr/lib64/libpolkit-qt-agent-1.so.1.103.0 7ba7bf377ccfa20851d3deebf5bce179 1357614019u
./sys-auth/polkit-qt-0.103.0/CONTENTS:obj /usr/lib64/libpolkit-qt-core-1.so.1.103.0 b8776fc514db4f23488112a40ff26600 1357614019u
./sys-auth/consolekit-0.4.6/CONTENTS:obj /usr/lib/ConsoleKit/ck-get-x11-display-device 8572180c1a8e7b0957bd807a04525486 1379318011u
./sys-auth/consolekit-0.4.6/CONTENTS:obj /usr/lib/ConsoleKit/udev-acl 63880a43fd51c2334a92fbe73767f30a 1379318011u
./sys-auth/consolekit-0.4.6/CONTENTS:obj /usr/lib/ConsoleKit/ck-get-x11-server-pid 0bddf0030ee021bec4641b44aae2d592 1379318011u
./sys-auth/consolekit-0.4.6/CONTENTS:obj /usr/lib/ConsoleKit/ck-collect-session-info 10750a1791d79613e50d8e93e0f5deb2 1379318011u
./app-accessibility/at-spi2-core-2.8.0/CONTENTS:obj /usr/lib64/libatspi.so.0.0.1 a6ab82cdf024ec9d6d185670a03e68b8 1386179335u
./app-accessibility/at-spi2-atk-2.8.1/CONTENTS:obj /usr/lib64/libatk-bridge-2.0.so.0.0.0 79e7fdf97c4a09f1d1ee17c318611dc1 1386179456u
./dev-cpp/clucene-2.3.3.4-r5/CONTENTS:obj /usr/lib64/libclucene-core.so.2.3.3.4 d6a7f8a64c6bbdbad800dee4cd08a93c 1374068026u
./dev-cpp/clucene-2.3.3.4-r5/CONTENTS:obj /usr/lib64/libclucene-contribs-lib.so.2.3.3.4 49595c7538357584f5673220a358baf9 1374068025u
./dev-cpp/clucene-2.3.3.4-r5/CONTENTS:obj /usr/lib64/libclucene-shared.so.2.3.3.4 4310cfc2b2774a77aaeb5ebb006eba3e 1374068025u


Emerge displays error messages like:

Code:
!!! Parse error in '/var/db/pkg/x11-drivers/nvidia-drivers-331.38/CONTENTS'
!!!   line 3: Unrecognized CONTENTS entry
!!!   line 4: Unrecognized CONTENTS entry
!!!   line 5: Unrecognized CONTENTS entry
!!!   line 6: Unrecognized CONTENTS entry
!!!   line 7: Unrecognized CONTENTS entry
!!!   line 8: Unrecognized CONTENTS entry
!!!   line 9: Unrecognized CONTENTS entry
!!!   line 10: Unrecognized CONTENTS entry
!!!   line 51: Unrecognized CONTENTS entry
!!!   line 70: Unrecognized CONTENTS entry
!!!   line 78: Unrecognized CONTENTS entry
!!!   line 85: Unrecognized CONTENTS entry
!!! Parse error in '/var/db/pkg/dev-libs/libatasmart-0.19-r1/CONTENTS'
!!!   line 6: Unrecognized CONTENTS entry


There are over 3800 of these entries. On another system it started too, there are only 8 such entries there.

emerge --info:

Code:
Portage 2.2.7 (default/linux/amd64/13.0/desktop/kde, gcc-4.7.3, glibc-2.17, 3.10.7-gentoo x86_64)
=================================================================
System uname: Linux-3.10.7-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_E8400_@_3.00GHz-with-gentoo-2.2
KiB Mem:     4053836 total,    203836 free
KiB Swap:     995992 total,    738020 free
Timestamp of tree: Sat, 25 Jan 2014 12:15:01 +0000
ld GNU ld (GNU Binutils) 2.23.2
ccache version 3.1.9 [disabled]
app-shells/bash:          4.2_p45
dev-java/java-config:     2.1.12-r1
dev-lang/python:          2.7.5-r3, 3.3.3
dev-util/ccache:          3.1.9-r3
dev-util/cmake:           2.8.11.2
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6, 1.12.6, 1.13.4
sys-devel/binutils:       2.23.2
sys-devel/gcc:            4.7.3-r1
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.9 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -O2 -pipe -w"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/portage /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=core2 -O2 -pipe -w"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--autounmask y --autounmask-write y --quiet-build y -j3 --load-average=3"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync metadata-transfer news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="ftp://gentoo.inode.at/source/ ftp://ftp.snt.utwente.nl/pub/os/linux/gentoo ftp://mirror.switch.ch/mirror/gentoo/"
LANG="C"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync.nl.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa amd64 berkdb bindist bluetooth branding bzip2 cairo cdda cdr cli consolekit cpudetection cracklib crypt cups cxx dbus declarative dri dts dvd dvdr emboss encode exif fam firefox flac fortran g3dvl gallium gdbm gif gpm gtk iconv ipv6 jpeg kde kipi lcms ldap libnotify mad mmx mmxext mng modules mp3 mp4 mpeg multilib ncurses nls nptl nvidia nvram nvtt ogg opengl openmp pam pango pcre pdf phonon plasma png policykit ppds qt3support qt4 readline sdl semantic-desktop session spell sse sse2 sse3 sse4 sse41 sse4_1 ssl ssse3 startup-notification svg tcpd tiff truetype udev udisks unicode upower usb video virtuoso vorbis wxwidgets x264 xcb xcomposite xinerama xml xscreensaver xv xvid xvmc zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en de" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON


I think every emerge sync adds more of those entries. What is happening?
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augury
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PostPosted: Tue Jan 28, 2014 8:45 pm    Post subject: Reply with quote

If I was forced at gun point to identify a pattern: it looks like all of those files have symbolic links . . . NO WAIT ...they are executable? DOH!
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PostPosted: Tue Jan 28, 2014 9:04 pm    Post subject: Reply with quote

Personally I would remove acl from the USE flags. Minus acl. (I might take unmerge-orphans out of the features, too, and use portageq for this function).

How old is build? What file system are you using?
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PostPosted: Tue Jan 28, 2014 10:47 pm    Post subject: Reply with quote

Hmm, its strange you have this problem on two different machines. I never saw these before.

Could you check the portage installation?
Code:
equery check portage


When you remerge a package, are the same files affected?

Which python is currently active?
Code:
eselect python list


"emerge --sync" should (imo) not touch the package-db. Can you proof that? (Copy db and diff against the db after a sync.)

Have you noticed any pattern for which files get a bogus entry?
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PostPosted: Wed Jan 29, 2014 12:27 pm    Post subject: Reply with quote

lagalopex wrote:
Hmm, its strange you have this problem on two different machines. I never saw these before.

Could you check the portage installation?
Code:
equery check portage


No corruptions on both machines.

Quote:
When you remerge a package, are the same files affected?

Which python is currently active?
Code:
eselect python list


2.7 on both machines

Quote:
"emerge --sync" should (imo) not touch the package-db. Can you proof that? (Copy db and diff against the db after a sync.)[


A sha1sum did not report any differences after a eix-sync (that's what I use here).

Question remains, when is /var/db/pkg updated and by which command and by which code. Reading the forums, it almost seems to be a trade secret.

Quote:
Have you noticed any pattern for which files get a bogus entry?


On the first machine, they were all created on the very last emerge -uND @world on January 25. Python 3.3.3 was among the packages merged.

On the second machine, the bogus entries were created on the second last emerge -uND @world on January 18 (last was on 25). Python 2.7.5 was among the packages merged.

Part of the emerge script is a run of python-updater:

Code:
#!/bin/bash

export LD_PRELOAD=/usr/lib/libtcmalloc.so
export MAKEOPTS='-j3'

eix-sync -q

EMERGE="emerge
        --jobs 3
        --load-average 3
        --nospinner
        --update
        --newuse
        --deep
        --keep-going
        --autounmask y
        --autounmask-write y
        world"

main() {
        # Try again in case package masking or use-flags have been changed
        $EMERGE || (cfg-update --update --automatic-only; $EMERGE) || exit 1
        python-updater
        emerge --depclean
        revdep-rebuild --ignore
        cfg-update --update --automatic-only
        prelink --all
        qcheck -auB
        eclean distfiles
}

main > /tmp/emerge-update.log 2> /tmp/emerge-update.err


The case on the second machine would mean that this happened only once (the last emerge apparently did not add more bogus entries). Maybe the emerge of Python was involved in the mess-up, but it's strange since on one machine it was Python 3.3.3 and on the other it was 2.7.5, and on both machines 2.7 is the active one.

What's much more disturbing is that many packages on the one machine got corrupted which were not part of the emerge.

Since the numbers look OK appart from the u-suffix (is it to mark an unsigned number or something?), I could edit them away, if I knew it would not hurt portage.
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PostPosted: Wed Jan 29, 2014 12:52 pm    Post subject: Reply with quote

Well I just did what I said last, to edit away those u-suffixes. The command was:

Code:
find /var/db/pkg -name CONTENTS | xargs grep -l ' [0-9][0-9]*u$' | xargs sed -i.old 's/ \([0-9][0-9]*\)u$/\1/'


A test with an emerge that failed before the edit succeeded now. So I guess it's safe to do so.

The question, however, remains: how on earth could this happen?
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PostPosted: Wed Jan 29, 2014 2:19 pm    Post subject: Reply with quote

jwezel wrote:
Question remains, when is /var/db/pkg updated and by which command and by which code. Reading the forums, it almost seems to be a trade secret.

It is the db where every file owned by that package is recorded. (Used for unmerge of a package, detect file collisions, find the package owning a specific file etc)

Imo it should just be created/changed/deleted when emerging/updating/unmerging the corresponding package.


jwezel wrote:
Well I just did what I said last, to edit away those u-suffixes. The command was:

Code:
find /var/db/pkg -name CONTENTS | xargs grep -l ' [0-9][0-9]*u$' | xargs sed -i.old 's/ \([0-9][0-9]*\)u$/\1/'

Did you miss one space in the sed command? Wouldnt this be enough:
Code:
sed -i.bak 's/ \([0-9]\+\)u$/ \1/g' /var/db/pkg/*/*/CONTENTS



Have you merged a package that was affected before? Did the 'u's return?

Its really strange you hit this twice but nobody else :?
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jwezel
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Joined: 29 Jan 2003
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PostPosted: Wed Jan 29, 2014 4:25 pm    Post subject: Reply with quote

Quote:
Did you miss one space in the sed command? Wouldnt this be enough:
Code:
sed -i.bak 's/ \([0-9]\+\)u$/ \1/g' /var/db/pkg/*/*/CONTENTS


Yep, one space didn't make it. I wasn't sure what sed does when no edits take place, so I resorted to a find/grep with resulting in only those files with issues.

Quote:
Have you merged a package that was affected before? Did the 'u's return?


As I said, an emerge of a package that couldn't be emerged before because of emerge complaining could be emerged after the correction. There was no u-suffix anymore. Let's hope it stays like that.
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