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gargoylle_ltk
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PostPosted: Wed Jul 06, 2011 2:19 pm    Post subject: [ FIXED ] glibc-2.13-r3 breaks multiple packages Reply with quote

I just finished upgrading to sys-libs/glibc-2.13-r3 on two systems (both ~amd64). After the upgrade multiple binaries have stopped working (libreoffice-bin for example) and all output the following message when ran:

Code:
Inconsistency detected by ld.so: dl-deps.c: 622: _dl_map_object_deps: Assertion `nlist > 1' failed!


Searching the web I've come across this bug report for upstream glibc:
http://sourceware.org/bugzilla/show_bug.cgi?id=12454

Searching bugs.gentoo.org for this problem has yielded no results.

Any suggestions ?

Just for reference, here is 'emerge --info' on one of the affected systems:
Code:
Portage 2.1.10.4 (default/linux/amd64/10.0/desktop/kde, gcc-4.5.2, glibc-2.13-r3, 2.6.39-gentoo x86_64)
=================================================================
System uname: Linux-2.6.39-gentoo-x86_64-Intel-R-_Core-TM-_i5-2400_CPU_@_3.10GHz-with-gentoo-2.0.3
Timestamp of tree: Wed, 06 Jul 2011 13:00:01 +0000
app-shells/bash:          4.2_p10
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2, 3.2
dev-util/cmake:           2.8.4-r1
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.8.3-r1
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.1-r1
sys-devel/binutils:       2.21.1
sys-devel/gcc:            4.5.2
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 2.6.38 (virtual/os-headers)
sys-libs/glibc:           2.13-r3
Repositories: gentoo
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL AdobeFlash-10 AdobeFlash-10.1 dlj-1.1 google-talkplugin"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=core2 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="ftp://ftp.roedu.net/pub/mirrors/gentoo.org/ http://mirrors.evolva.ro/gentoo/ http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa amd64 apache2 audiofle berkdb bluetooth branding bzip2 cairo caps cdda cddb cdr chi cli consolekit cpudetection cracklib crypt cscope css ctype cups curl cxx dbus declarative djvu dri dts dvb dvd dvdr emboss encode exif expat extras fam ffmpeg firefox flac fontconfig fortran ftp gd gdbm gdu gif git glut gnutls gphoto2 gpm gstreamer gtk gzip iconv imagemagick imap imlib innodb ipod ipv6 jabber jingle jpeg jpeg2k kde kipi kontact lame lcms ldap libnotify libwww lua lzo mad maildir mbox mime mmap mmx mng modules mp3 mp4 mpeg mpi mplayer msn mtp mudflap multilib mysql mysqli nas ncurses nls nptl nptlonly offensive ogg openal opengl openmp pam pango pcntl pcre pdf perl phonon plasma png policykit posix ppds pppd python qt3support qt4 quicktime raw rdesktop readline rss samba scanner sdl semantic-desktop session sharedext smp sockets socks5 speex spell sse sse2 sse3 ssl ssse3 startup-notification subversion suid svg sysfs syslog sysvipc taglib tcpd theora threads tiff truetype udev unicode usb vcd video vim-syntax vnc vorbis webkit x264 xcb xcomposite xine xinerama xml xorg xpm xscreensaver xulrunner xv xvid yahoo zlib" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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="braindump flow karbon kexi kpresenter krita tables words" 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 ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="intel" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS


Last edited by gargoylle_ltk on Thu Jul 07, 2011 1:00 pm; edited 1 time in total
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tomk
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PostPosted: Wed Jul 06, 2011 2:39 pm    Post subject: Re: glibc-2.13-r3 breaks multiple packages Reply with quote

gargoylle_ltk wrote:
Searching bugs.gentoo.org for this problem has yielded no results.

It looks like bug 374107 is the one to watch.
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gargoylle_ltk
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PostPosted: Wed Jul 06, 2011 2:41 pm    Post subject: Re: glibc-2.13-r3 breaks multiple packages Reply with quote

tomk wrote:
gargoylle_ltk wrote:
Searching bugs.gentoo.org for this problem has yielded no results.

It looks like bug 374107 is the one to watch.

Yes, you are correct. I only searched for 'glibc' and 'glibc-2.13-r3'. I'll be watching that report with great interest. Thanks.
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Martux
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PostPosted: Wed Jul 06, 2011 9:58 pm    Post subject: Reply with quote

Can it be downgraded to -r2 easily?
Or will there be a -r4 if fixed officially?
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tr0ll
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PostPosted: Thu Jul 07, 2011 11:25 am    Post subject: Re: glibc-2.13-r3 breaks multiple packages Reply with quote

tomk wrote:
gargoylle_ltk wrote:
Searching bugs.gentoo.org for this problem has yielded no results.

It looks like bug 374107 is the one to watch.


Yes thx following :

Code:
https://bugs.gentoo.org/show_bug.cgi?id=374107#c15


That fixes the issue for me .
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gargoylle_ltk
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PostPosted: Thu Jul 07, 2011 12:59 pm    Post subject: Reply with quote

Yes, I confirm the patch from the bug report fixes this problem.
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padoor
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PostPosted: Thu Jul 07, 2011 1:43 pm    Post subject: Reply with quote

can someone tell me how do i apply the patch?
though none of the packages i use are broken now after glibc-2.13-r3 update yesterday
i would like to apply the patch to my glibc also before i find problems
i need a step by step instructions :(
thanks in advance :)
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molot
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PostPosted: Thu Jul 07, 2011 10:50 pm    Post subject: Reply with quote

padoor wrote:
can someone tell me how do i apply the patch?


I can:
Code:

mkdir -p /etc/portage/patches/sys-libs/glibc-2.13-r3
cd /etc/portage/patches/sys-libs/glibc-2.13-r3
wget "https://bugs.gentoo.org/attachment.cgi?id=279269&action=diff&context=patch&collapsed=&headers=1&format=raw" ian.patch
emerge glibc


Just make sure I got wget's line right. Writing from memory.
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padoor
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PostPosted: Fri Jul 08, 2011 2:21 am    Post subject: Reply with quote

Code:
localhost ramaswamy # mkdir -p /etc/portage/patches/sys-libs/glibc-2.13-r3
localhost ramaswamy # cd /etc/portage/patches/sys-libs/glibc-2.13-r3
localhost glibc-2.13-r3 # wget "https://bugs.gentoo.org/attachment.cgi?id=279269&action=diff&context=patch&collapsed=&headers=1&format=raw" ian.patch
--2011-07-08 07:35:46--  https://bugs.gentoo.org/attachment.cgi?id=279269&action=diff&context=patch&collapsed=&headers=1&format=raw
Resolving bugs.gentoo.org... 94.100.119.165
Connecting to bugs.gentoo.org|94.100.119.165|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: `attachment.cgi?id=279269&action=diff&context=patch&collapsed=&headers=1&format=raw'

    [ <=>                                   ] 4,323       --.-K/s   in 0.001s 

2011-07-08 07:35:49 (4.82 MB/s) - `attachment.cgi?id=279269&action=diff&context=patch&collapsed=&headers=1&format=raw' saved [4323]

--2011-07-08 07:35:49--  http://ian.patch/
Resolving ian.patch... 92.242.132.8
Connecting to ian.patch|92.242.132.8|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 915 [text/html]
Saving to: `index.html'

100%[======================================>] 915         --.-K/s   in 0s     

2011-07-08 07:35:50 (28.7 MB/s) - `index.html' saved [915/915]

FINISHED --2011-07-08 07:35:50--
Downloaded: 2 files, 5.1K in 0.001s (5.64 MB/s)
localhost glibc-2.13-r3 # emerge glibc -av

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

Calculating dependencies... done!
[ebuild   R    ] sys-libs/glibc-2.13-r3  USE="nls -debug -gd -glibc-omitfp (-hardened) (-multilib) -profile (-selinux) -vanilla" 0 kB

Total: 1 package (1 reinstall), Size of downloads: 0 kB

Would you like to merge these packages? [Yes/No]

Code:
[D] sys-libs/glibc
     Available versions:  (2.2) (~)2.9_p20081201-r3!s 2.10.1-r1!s 2.11.3!s (~)2.12.1-r3!s 2.12.2!s (~)2.13-r2!s **2.14!s
   {crosscompile_opts_headers-only debug gd glibc-omitfp hardened multilib nls profile selinux vanilla}
     Installed versions:  2.13-r3(2.2)!s(10:26:10 07/06/11)(nls -crosscompile_opts_headers-only -debug -gd -glibc-omitfp -hardened -multilib -profile -selinux -vanilla)
     Homepage:            http://www.gnu.org/software/libc/libc.html
     Description:         GNU libc6 (also called glibc2) C library



emerge glibc -av shows same as already installed version except for the crosscompile part
is it what is expected with the patch ?
if things are ok i will proceed

Wed Jul 6 10:30:18 2011 >>> sys-libs/glibc-2.13-r3
merge time: 3 hours, 25 minutes and 14 seconds.

takes about 4 hrs for me.
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molot
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PostPosted: Fri Jul 08, 2011 6:43 am    Post subject: Reply with quote

Well it is the same version, the same ebuild. When your emerge starts, you will see long list of Gentoo patches. Just under it, you should get list of user patches. Well, actually a list of one user patch. So just make sure it is there and Ctrl+C if not (I strongly suggest making it under X for easier scrolling).

Should look like that:
Code:

>>> Unpacking source...         
make -j4 -s glibc-test           
 * Checking gcc for __thread support ...                                     [ ok ]
 * Checking kernel version (2.6.39 >= 2.6.9) ...                             [ ok ]
 * Checking linux-headers version (2.6.38 >= 2.6.9) ...                      [ ok ]
>>> Unpacking glibc-2.13.tar.bz2 to /var/tmp/portage/sys-libs/glibc-2.13-r3/work   
>>> Unpacking glibc-ports-2.13.tar.bz2 to /var/tmp/portage/sys-libs/glibc-2.13-r3/work/glibc-2.13                                     
>>> Unpacking glibc-2.13-patches-7.tar.bz2 to /var/tmp/portage/sys-libs/glibc-2.13-r3/work                                             
 * Applying Gentoo Glibc Patchset 2.13-7 ...                                       
 *   0020_all_glibc-tweak-rfc1918-lookup.patch ...                           [ ok ]
 *   0030_all_glibc-respect-env-CPPFLAGS.patch ...                           [ ok ]
 *   0043_all_glibc-2.12-broken-tls-init.patch ...                           [ ok ]
 *   0045_all_glibc-2.13-canonical-getaddrinfo.patch ...                     [ ok ]
 *   0046_all_glibc-2.13-dso-init-fini-order.patch ...                       [ ok ]
 *   0050_all_glibc-2.13-ldso-prelink-segv.patch ...                         [ ok ]
 *   0055_all_glibc-2.12-static-shared-getpagesize.patch ...                 [ ok ]
 *   0060_all_glibc-2.13-static-memmove-ssse3.patch ...                      [ ok ]
 *   0061_all_glibc-2.13-static-memset.patch ...                             [ ok ]
 *   0085_all_glibc-disable-ldconfig.patch ...                               [ ok ]
 *   1005_all_glibc-sigaction.patch ...                                      [ ok ]
 *   1010_all_glibc-queue-header-updates.patch ...                           [ ok ]
 *   1020_all_glibc-longjmp-chk-hidden-fortify.patch ...                     [ ok ]
 *   1030_all_glibc-manual-no-perl.patch ...                                 [ ok ]
 *   1040_all_2.3.3-localedef-fix-trampoline.patch ...                       [ ok ]
 *   1055_all_glibc-resolv-dynamic.patch ...                                 [ ok ]
 *   1060_all_glibc-localedef-mmap.patch ...                                 [ ok ]
 *   1070_all_glibc-fadvise64_64.patch ...                                   [ ok ]
 *   1075_all_glibc-section-comments.patch ...                               [ ok ]
 *   1080_all_glibc-no-inline-gmon.patch ...                                 [ ok ]
 *   1085_all_glibc-2.9-check_native-headers.patch ...                       [ ok ]
 *   1090_all_glibc-2.3.6-fix-pr631.patch ...                                [ ok ]
 *   1095_all_glibc-2.9-assume-pipe2.patch ...                               [ ok ]
 *   1100_all_glibc-2.3.3-china.patch ...                                    [ ok ]
 *   1103_all_glibc-new-valencian-locale.patch ...                           [ ok ]
 *   1120_all_glibc-2.11-longjmp-chk-fallback.patch ...                      [ ok ]
 *   1130_all_glibc-2.4-undefine-__i686.patch ...                            [ ok ]
 *   1160_all_glibc-2.8-nscd-one-fork.patch ...                              [ ok ]
 *   1502_all_hppa-glibc-2.13-F_GET-SETPIPE_SZ.patch ...                     [ ok ]
 *   1508_all_glibc-2.13-hppa-DEFAULT_STACK_PERMS.patch ...                  [ ok ]
 *   1509_all_glibc-2.11-hppa-SOCK_CLOEXEC.patch ...                         [ ok ]
 *   1530_all_glibc-m68k-sys-user.patch ...                                  [ ok ]
 *   3000_all_2.3.6-dl_execstack-PaX-support.patch ...                       [ ok ]
 *   3010_all_2.3.3_pre20040117-pt_pax.patch ...                             [ ok ]
 *   3020_all_glibc-tests-sandbox-libdl-paths.patch ...                      [ ok ]
 *   5063_all_glibc-dont-build-timezone.patch ...                            [ ok ]
 *   6018_all_alpha-glibc-2.8-cache-shape.patch ...                          [ ok ]
 *   6019_all_alpha-glibc-2.13-longjmp-chk.patch ...                         [ ok ]
 *   6020_all_alpha-fix-gcc-4.1-warnings.patch ...                           [ ok ]
 *   6021_all_alpha-glibc-2.13-ptr-mangle.patch ...                          [ ok ]
 *   6023_all_alpha-glibc-2.13-statfs64.patch ...                            [ ok ]
 *   6026_all_alpha-fix-rtld-fPIC.patch ...                                  [ ok ]
 *   6027_all_alpha-glibc-2.13-F_GET-SETPIPE_SZ.patch ...                    [ ok ]
 *   6028_all_alpha-glibc-2.13-statfs.f_flags.patch ...                      [ ok ]
 *   6029_all_alpha-glibc-2.13-DEFAULT_STACK_PERMS.patch ...                 [ ok ]
 *   6030_all_alpha-glibc-2.13-hidden-libm.patch ...                         [ ok ]
 *   6031_all_alpha-glibc-2.12-epoll_create1.patch ...                       [ ok ]
 *   6032_all_alpha-syscall-6.patch ...                                      [ ok ]
 *   6120_all_ppc-glibc-2.9-atomic.patch ...                                 [ ok ]
 *   6130_all_ppc-glibc-2.11-cell-vector.patch ...                           [ ok ]
 *   6145_all_powerpc64-glibc-2.13-syscall.patch ...                         [ ok ]
 *   6146_all_ppc-glibc-2.13-vsx-toc-O3.patch ...                            [ ok ]
 *   6220_all_glibc-2.4-arm-cirrus-ep93xx-maverick-crunch-fpu.patch ...      [ ok ]
 *   6230_all_arm-glibc-hardened.patch ...                                   [ ok ]
 *   6240_all_glibc-2.8-nptl-lowlevellock.patch ...                          [ ok ]
 *   6532_all_sparc64-tls-cross-test.patch ...                               [ ok ]
 *   6605_all_glibc-2.4-fpu-cw-mips.patch ...                                [ ok ]
 *   6610_all_glibc-r10k-workarounds.patch ...                               [ ok ]
 * Done with patching
 * Applying user patches from /etc/portage/patches/sys-libs/glibc-2.13-r3 ...
 *   ian.patch ...        [ ok ]
 * Done with patching
 * Using GNU config files from /usr/share/gnuconfig
 *   Updating scripts/config.sub                                             [ ok ]
 *   Updating scripts/config.guess                                           [ ok ]
>>> Source unpacked in /var/tmp/portage/sys-libs/glibc-2.13-r3/work
>>> Compiling source in /var/tmp/portage/sys-libs/glibc-2.13-r3/work/glibc-2.13 ...

Interesting row is that with ian.patch

Good luck!
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padoor
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PostPosted: Fri Jul 08, 2011 7:12 am    Post subject: Reply with quote

Code:
>>> Verifying ebuild manifests

>>> Emerging (1 of 1) sys-libs/glibc-2.13-r3
 * glibc-2.13.tar.bz2 RMD160 SHA1 SHA256 size ;-) ...                    [ ok ]
 * glibc-ports-2.13.tar.bz2 RMD160 SHA1 SHA256 size ;-) ...              [ ok ]
 * glibc-2.13-patches-7.tar.bz2 RMD160 SHA1 SHA256 size ;-) ...          [ ok ]
 * Package:    sys-libs/glibc-2.13-r3
 * Repository: gentoo
 * Maintainer: toolchain@gentoo.org
 * USE:        elibc_glibc kernel_linux nls userland_GNU x86
 * FEATURES:   ccache sandbox
make -j1 -s glibc-test
make -j1 -s glibc-test
>>> Unpacking source...
make -j1 -s glibc-test
 * Checking gcc for __thread support ...                                 [ ok ]
 * Checking kernel version (2.6.39 >= 2.6.9) ...                         [ ok ]
 * Checking linux-headers version (2.6.38 >= 2.6.9) ...                  [ ok ]
>>> Unpacking glibc-2.13.tar.bz2 to /var/tmp/portage/sys-libs/glibc-2.13-r3/work

>>> Unpacking glibc-ports-2.13.tar.bz2 to /var/tmp/portage/sys-libs/glibc-2.13-r3/work/glibc-2.13
>>> Unpacking glibc-2.13-patches-7.tar.bz2 to /var/tmp/portage/sys-libs/glibc-2.13-r3/work
 * Applying Gentoo Glibc Patchset 2.13-7 ...
 *   0020_all_glibc-tweak-rfc1918-lookup.patch ...                       [ ok ]
 *   0030_all_glibc-respect-env-CPPFLAGS.patch ...                       [ ok ]
 *   0043_all_glibc-2.12-broken-tls-init.patch ...                       [ ok ]
 *   0045_all_glibc-2.13-canonical-getaddrinfo.patch ...                 [ ok ]
 *   0046_all_glibc-2.13-dso-init-fini-order.patch ...                   [ ok ]
 *   0050_all_glibc-2.13-ldso-prelink-segv.patch ...                     [ ok ]
 *   0055_all_glibc-2.12-static-shared-getpagesize.patch ...             [ ok ]
 *   0060_all_glibc-2.13-static-memmove-ssse3.patch ...                  [ ok ]
 *   0061_all_glibc-2.13-static-memset.patch ...                         [ ok ]
 *   0085_all_glibc-disable-ldconfig.patch ...                           [ ok ]
 *   1005_all_glibc-sigaction.patch ...                                  [ ok ]
 *   1010_all_glibc-queue-header-updates.patch ...                       [ ok ]
 *   1020_all_glibc-longjmp-chk-hidden-fortify.patch ...                 [ ok ]
 *   1030_all_glibc-manual-no-perl.patch ...                             [ ok ]
 *   1040_all_2.3.3-localedef-fix-trampoline.patch ...                   [ ok ]
 *   1055_all_glibc-resolv-dynamic.patch ...                             [ ok ]
 *   1060_all_glibc-localedef-mmap.patch ...                             [ ok ]
 *   1070_all_glibc-fadvise64_64.patch ...                               [ ok ]
 *   1075_all_glibc-section-comments.patch ...                           [ ok ]
 *   1080_all_glibc-no-inline-gmon.patch ...                             [ ok ]
 *   1085_all_glibc-2.9-check_native-headers.patch ...                   [ ok ]
 *   1090_all_glibc-2.3.6-fix-pr631.patch ...                            [ ok ]
 *   1095_all_glibc-2.9-assume-pipe2.patch ...                           [ ok ]
 *   1100_all_glibc-2.3.3-china.patch ...                                [ ok ]
 *   1103_all_glibc-new-valencian-locale.patch ...                       [ ok ]
 *   1120_all_glibc-2.11-longjmp-chk-fallback.patch ...                  [ ok ]
 *   1130_all_glibc-2.4-undefine-__i686.patch ...                        [ ok ]
 *   1160_all_glibc-2.8-nscd-one-fork.patch ...                          [ ok ]
 *   1502_all_hppa-glibc-2.13-F_GET-SETPIPE_SZ.patch ...                 [ ok ]
 *   1508_all_glibc-2.13-hppa-DEFAULT_STACK_PERMS.patch ...              [ ok ]
 *   1509_all_glibc-2.11-hppa-SOCK_CLOEXEC.patch ...                     [ ok ]
 *   1530_all_glibc-m68k-sys-user.patch ...                              [ ok ]
 *   3000_all_2.3.6-dl_execstack-PaX-support.patch ...                   [ ok ]
 *   3010_all_2.3.3_pre20040117-pt_pax.patch ...                         [ ok ]
 *   3020_all_glibc-tests-sandbox-libdl-paths.patch ...                  [ ok ]
 *   5063_all_glibc-dont-build-timezone.patch ...                        [ ok ]
 *   6018_all_alpha-glibc-2.8-cache-shape.patch ...                      [ ok ]
 *   6019_all_alpha-glibc-2.13-longjmp-chk.patch ...                     [ ok ]
 *   6020_all_alpha-fix-gcc-4.1-warnings.patch ...                       [ ok ]
 *   6021_all_alpha-glibc-2.13-ptr-mangle.patch ...                      [ ok ]
 *   6023_all_alpha-glibc-2.13-statfs64.patch ...                        [ ok ]
 *   6026_all_alpha-fix-rtld-fPIC.patch ...                              [ ok ]
 *   6027_all_alpha-glibc-2.13-F_GET-SETPIPE_SZ.patch ...                [ ok ]
 *   6028_all_alpha-glibc-2.13-statfs.f_flags.patch ...                  [ ok ]
 *   6029_all_alpha-glibc-2.13-DEFAULT_STACK_PERMS.patch ...             [ ok ]
 *   6030_all_alpha-glibc-2.13-hidden-libm.patch ...                     [ ok ]
 *   6031_all_alpha-glibc-2.12-epoll_create1.patch ...                   [ ok ]
 *   6032_all_alpha-syscall-6.patch ...                                  [ ok ]
 *   6120_all_ppc-glibc-2.9-atomic.patch ...                             [ ok ]
 *   6130_all_ppc-glibc-2.11-cell-vector.patch ...                       [ ok ]
 *   6145_all_powerpc64-glibc-2.13-syscall.patch ...                     [ ok ]
 *   6146_all_ppc-glibc-2.13-vsx-toc-O3.patch ...                        [ ok ]
 *   6220_all_glibc-2.4-arm-cirrus-ep93xx-maverick-crunch-fpu.patch ...  [ ok ]
 *   6230_all_arm-glibc-hardened.patch ...                               [ ok ]
 *   6240_all_glibc-2.8-nptl-lowlevellock.patch ...                      [ ok ]
 *   6532_all_sparc64-tls-cross-test.patch ...                           [ ok ]
 *   6605_all_glibc-2.4-fpu-cw-mips.patch ...                            [ ok ]
 *   6610_all_glibc-r10k-workarounds.patch ...                           [ ok ]
 * Done with patching
 * Applying user patches from /etc/portage/patches/sys-libs/glibc-2.13-r3 ...
 * Done with patching
 * Using GNU config files from /usr/share/gnuconfig
 *   Updating scripts/config.sub                                         [ ok ]
 *   Updating scripts/config.guess                                       [ ok ]
>>> Source unpacked in /var/tmp/portage/sys-libs/glibc-2.13-r3/work
>>> Compiling source in /var/tmp/portage/sys-libs/glibc-2.13-r3/work/glibc-2.13 ...
make -j1 -s glibc-test

 *             ABI:   default
 *          CBUILD:   i686-pc-linux-gnu
 *           CHOST:   i686-pc-linux-gnu
 *         CTARGET:   i686-pc-linux-gnu
 *      CBUILD_OPT:   
 *     CTARGET_OPT:   
 *              CC:   i686-pc-linux-gnu-gcc
 *          CFLAGS:   -march=pentium4 -pipe -O2 -fno-strict-aliasing
 *       Manual CC:   i686-pc-linux-gnu-gcc

 * Configuring GLIBC for nptl
/var/tmp/portage/sys-libs/glibc-2.13-r3/work/glibc-2.13/configure --disable-stackguard-randomization --enable-old-ssp-compat --enable-add-ons=nptl,c_stubs,libidn,ports --enable-kernel=2.6.9 --without-selinux --without-cvs --enable-bind-now --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --disable-profile --without-gd --with-headers=/usr/include --prefix=/usr --libdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --libexecdir=/usr/lib/misc/glibc
checking build system type... i686-pc-linux-gnu


in my case it is not mentioning ian patch as your shown list
i am not sure it is doing as in your case
i have cancelled it at that
Code:
done > /var/tmp/portage/sys-libs/glibc-2.13-r3/work/build-default-i686-pc-linux-gnu-nptl/sysd-syscallsT
^C

Exiting on signal 2
sandbox:stop  caught signal 2 in pid 9114
sandbox:stop  signal already caught and busy still cleaning up!
make: *** [all] Interrupt

/usr/portage/sys-libs/glibc/glibc-2.13-r3.ebuild: src_compile aborted; exiting.



i don't see why i did not get the ian patch line.
is it only for 64bit system ?
i run x86 32b system
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Last edited by padoor on Fri Jul 08, 2011 7:18 am; edited 1 time in total
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Martux
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PostPosted: Fri Jul 08, 2011 7:16 am    Post subject: Reply with quote

Is this the recommended way of patching anything? I mean if I ever download a patch from bugzilla and want to apply it, do I just create the directory under "/etc/portage/patches" and remerge the package?
That patch worked for me, too.
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padoor
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PostPosted: Fri Jul 08, 2011 7:21 am    Post subject: Reply with quote

i am also interested in the answer to the post just above of Martux :)
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molot
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PostPosted: Fri Jul 08, 2011 9:25 am    Post subject: Reply with quote

@padoor - Try doing the same and tell me if you got the same results:
Code:


molot ~ # cd /etc/portage/patches/
molot patches # tree
.
└── sys-libs
    └── glibc-2.13-r3
        └── ian.patch

2 directories, 1 file
molot patches # head sys-libs/glibc-2.13-r3/ian.patch
--- a/elf/dl-deps.c
+++ b/elf/dl-deps.c
@@ -617,61 +617,64 @@ Filters not supported with LD_TRACE_PRELINKING"));
        map->l_searchlist.r_list[i]->l_reserved = 0;
     }
 
-  /* Now determine the order in which the initialization has to happen.  */
+  /* Sort the initializer list to take dependencies into account.  The binary
+     itself will always be initialize last.  */
   memcpy (l_initfini, map->l_searchlist.r_list,
molot patches #
If not, maybe your patch is in wrong directory? Or maybe I misspelled wget line and what you downloaded is html version instead of raw one?

@both you up - As far as I know it's only testing way, and stable one is to create an ebuild in portage overlay, or make a bugreport so that your patch can became official. But I would like an official answer just as you do!
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Martux
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PostPosted: Fri Jul 08, 2011 10:13 am    Post subject: Reply with quote

@molot: You mean testing as in ~arch? That would be handy, as my whole system is that :)
This is a very convenient way of applying patches.
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p04ty
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PostPosted: Fri Jul 08, 2011 11:03 am    Post subject: Reply with quote

Anyone could please paste a patch for easier work? I can't save it properly from commandline wget.

Edit: my system does not want to use a file from /etc/portage/patches/sys-libs/glibc-2.13-r3. Why?


Last edited by p04ty on Fri Jul 08, 2011 11:10 am; edited 1 time in total
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spy20
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PostPosted: Fri Jul 08, 2011 11:08 am    Post subject: Reply with quote

Sorry but I don't understand how I can apply the patch

I download this.
Then I tried emerge glibc or emerge mono
But I have already the same error.

I also tried this with the prefix EPATCH=directory_of_patch emerge package

Nothing works.
Thanks in advance for advices
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molot
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PostPosted: Fri Jul 08, 2011 11:20 am    Post subject: Reply with quote

https://bugs.gentoo.org/attachment.cgi?id=279269&action=diff&context=patch&collapsed=&headers=1&format=raw

But now it starts with
Code:

--- file_not_specified_in_diff   
+++ file_not_specified_in_diff   
And that's bad.
Version that worked for me is:
Code:

--- a/elf/dl-deps.c
+++ b/elf/dl-deps.c
@@ -617,61 +617,64 @@ Filters not supported with LD_TRACE_PRELINKING"));
    map->l_searchlist.r_list[i]->l_reserved = 0;
     }
 
-  /* Now determine the order in which the initialization has to happen.  */
+  /* Sort the initializer list to take dependencies into account.  The binary
+     itself will always be initialize last.  */
   memcpy (l_initfini, map->l_searchlist.r_list,
      nlist * sizeof (struct link_map *));
-
-  /* We can skip looking for the binary itself which is at the front
-     of the search list.  */
-  assert (nlist > 1);
-  i = 1;
-  bool seen[nlist];
-  memset (seen, false, nlist * sizeof (seen[0]));
-  while (1)
+  if (__builtin_expect (nlist > 1, 1))
     {
-      /* Keep track of which object we looked at this round.  */
-      seen[i] = true;
-      struct link_map *thisp = l_initfini[i];
-
-      /* Find the last object in the list for which the current one is
-    a dependency and move the current object behind the object
-    with the dependency.  */
-      unsigned int k = nlist - 1;
-      while (k > i)
+      /* We can skip looking for the binary itself which is at the front
+    of the search list.  */
+      i = 1;
+      bool seen[nlist];
+      memset (seen, false, nlist * sizeof (seen[0]));
+      while (1)
    {
-     struct link_map **runp = l_initfini[k]->l_initfini;
-     if (runp != NULL)
-       /* Look through the dependencies of the object.  */
-       while (*runp != NULL)
-         if (__builtin_expect (*runp++ == thisp, 0))
-      {
-        /* Move the current object to the back past the last
-           object with it as the dependency.  */
-        memmove (&l_initfini[i], &l_initfini[i + 1],
-            (k - i) * sizeof (l_initfini[0]));
-        l_initfini[k] = thisp;
-
-        if (seen[i + 1])
+     /* Keep track of which object we looked at this round.  */
+     seen[i] = true;
+     struct link_map *thisp = l_initfini[i];
+
+     /* Find the last object in the list for which the current one is
+        a dependency and move the current object behind the object
+        with the dependency.  */
+     unsigned int k = nlist - 1;
+     while (k > i)
+       {
+         struct link_map **runp = l_initfini[k]->l_initfini;
+         if (runp != NULL)
+      /* Look through the dependencies of the object.  */
+      while (*runp != NULL)
+        if (__builtin_expect (*runp++ == thisp, 0))
           {
-            ++i;
-            goto next_clear;
+            /* Move the current object to the back past the last
+          object with it as the dependency.  */
+            memmove (&l_initfini[i], &l_initfini[i + 1],
+                (k - i) * sizeof (l_initfini[0]));
+            l_initfini[k] = thisp;
+
+            if (seen[i + 1])
+         {
+           ++i;
+           goto next_clear;
+         }
+
+            memmove (&seen[i], &seen[i + 1],
+                (k - i) * sizeof (seen[0]));
+            seen[k] = true;
+
+            goto next;
           }
 
-        memmove (&seen[i], &seen[i + 1], (k - i) * sizeof (seen[0]));
-        seen[k] = true;
+         --k;
+       }
 
-        goto next;
-      }
+     if (++i == nlist)
+       break;
+   next_clear:
+     memset (&seen[i], false, (nlist - i) * sizeof (seen[0]));
 
-     --k;
+   next:;
    }
-
-      if (++i == nlist)
-   break;
-    next_clear:
-      memset (&seen[i], false, (nlist - i) * sizeof (seen[0]));
-
-    next:;
     }
 
   /* Terminate the list of dependencies.  */
--- a/elf/dl-fini.c
+++ b/elf/dl-fini.c
@@ -33,9 +33,12 @@ internal_function
 _dl_sort_fini (struct link_map *l, struct link_map **maps, size_t nmaps,
           char *used, Lmid_t ns)
 {
+  /* A list of one element need not be sorted.  */
+  if (nmaps == 1)
+    return;
+
   /* We can skip looking for the binary itself which is at the front
      of the search list for the main namespace.  */
-  assert (nmaps > 1);
   unsigned int i = ns == LM_ID_BASE;
   bool seen[nmaps];
   memset (seen, false, nmaps * sizeof (seen[0]));
@@ -195,9 +198,8 @@ _dl_fini (void)
       assert (ns == LM_ID_BASE || i == nloaded || i == nloaded - 1);
       nmaps = i;
 
-      if (nmaps > 1)
-   /* Now we have to do the sorting.  */
-   _dl_sort_fini (GL(dl_ns)[ns]._ns_loaded, maps, nmaps, NULL, ns);
+      /* Now we have to do the sorting.  */
+      _dl_sort_fini (GL(dl_ns)[ns]._ns_loaded, maps, nmaps, NULL, ns);
 
       /* We do not rely on the linked list of loaded object anymore from
     this point on.  We have our own list here (maps).  The various


And my make.conf for reference purposes:
Code:

CFLAGS="-O2 -pipe -msse3 -march=athlon64"
CXXFLAGS="-O2 -pipe  -msse3 -march=athlon64"
MAKEOPTS="-j4"

# WARNING: Changing your CHOST is not something that should be done lightly.
# Please consult http://www.gentoo.org/doc/en/change-chost.xml before changing.
CHOST="x86_64-pc-linux-gnu"
# These are the USE flags that were used in addition to what is provided by the
# profile used for building.
USE="3dnow 3dnowext 64bit 7zip X X509 a52 aac aalib acpi addition alsa apache2
     apm apng arts aspell atm audiofile bash-completion boundschecking
     branding cairo calendar cdb cdparanoia cdr cgi consolekit cpudetection
     cscope css cuda curl curlwrappers cvs daemon dbus declarative
     device-mapper dga dovecot-sasl dri dso dv dvb dvd dvdr emerald encode
     enscript exif exiscan-acl extras fam fastcgi fbcon ffmpeg fftw firefox
     firefox3 flac flash fontconfig fontforge ftp gcj gd gif gimp gnuplot
     gnutls gpm hash icu imap ipv6 jabber java java6 javascript jpeg kde latex
     libmpeg2 libsamplerate lm_sensors lzo mad magic mikmod mime mng mp2 mp3
     mp3rtp mp3tunes mp4 mp4live mpeg mpeg2 mpi mplayer multitarget mysql
     netware network nforce2 nptl nptlonly nsplugin objc objc++ odbc openal
     opengl openvpn pch pdf pdo php plasma player png policykit posix postgres
     powerkadu python qt-dbus qt3support qt4 rar raw reiser4 reiserfs rss
     samba sasl scanner screen sdl secure-delete semantic-desktop sensord
     simplexml smp spell sql sse3 svg svgz syslog theora threads threadsafe
     threadsonly tidy tiff truetype unicode usb utils v4l2 vcd vcdinfo vcdx
     vhosts video vim vim-syntax webkit x264 xcomposite xinerama xml xmlrpc
     xsl zip -berkdb -faac -gnome -gnome-keyring -gnome-print -mysqli -postfix
     -spamassassin"

ACCEPT_KEYWORDS="~amd64"
ACCEPT_LICENSE="*"
# Private section
vga="nvidia"
VGA="nvidia"                                                                                                                                                                                                                                 
INPUT_DEVICES="keyboard mouse"                                                                                                                                                                                                               
VIDEO_CARDS="nvidia v4l v4l2"                                                                                                                                                                                                               
FEATURES="parallel-fetch" # ccache"                                                                                                                                                                                                         
ALSA_CARDS="hda-intel hdsp hdspm"                                                                                                                                                                                                           
PORTDIR_OVERLAY="/usr/local/portage"                                                                                                                                                                                                         
LINGUAS="pl en en_GB en_US"                                                                                                                                                                                                                 
PHP_TARGETS="php5-3 php5-2"                       


@Martux - I like that way too. However when I was messing with patches (especially for ROOT - damn you CERN) I always did my best to send an ebuild to my friends. I don't know if this way would work for them, they don't have ACCEPT_KEYWORDS="~amd64" in make.conf but I never tested it. Ebuilds was just more consistent way and allowed me to append numbers to "my" patches. "My" in parenthesis as I only selected them and maybe sometimes kicked around a bit to make them work, nothing more. But who I am to tell you, you are veteran here so I bet if anything you should teach me!
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Last edited by molot on Fri Jul 08, 2011 11:36 am; edited 1 time in total
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PostPosted: Fri Jul 08, 2011 11:33 am    Post subject: Reply with quote

There is no "* Applying user patches from /etc/portage/patches/sys-libs/glibc-2.13-r3 ... " line on my system. Why?
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PostPosted: Fri Jul 08, 2011 11:38 am    Post subject: Reply with quote

Give me tree of your /etc/portage, head of your patch file and content of your make.conf and then I may try to figure it out.
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PostPosted: Fri Jul 08, 2011 11:57 am    Post subject: Reply with quote

Damn, the tree was chmod 664 not 774.
But after fixing permissions I get error:

Code:
 * Failed Patch: glibc-2.13-r3.patch !
 *  ( /etc/portage/patches/sys-libs/glibc-2.13-r3/glibc-2.13-r3.patch )
 *
 * Include in your bugreport the contents of:
 *
 *   /var/tmp/portage/sys-libs/glibc-2.13-r3/temp/glibc-2.13-r3.patch.out
 * ERROR: sys-libs/glibc-2.13-r3 failed (unpack phase):
 *   Failed Patch: glibc-2.13-r3.patch!
 *
 * Call stack:
 *          ebuild.sh, line   56:  Called src_unpack
 *        environment, line 3649:  Called eblit-run 'src_unpack'
 *        environment, line 1078:  Called eblit-glibc-src_unpack
 *   src_unpack.eblit, line  155:  Called toolchain-glibc_src_unpack
 *   src_unpack.eblit, line  147:  Called epatch_user
 *        environment, line 1921:  Called epatch
 *        environment, line 1903:  Called die
 * The specific snippet of code:
 *               die "Failed Patch: ${patchname}!";
 *
 * If you need support, post the output of 'emerge --info =sys-libs/glibc-2.13-r3',
 * the complete build log and the output of 'emerge -pqv =sys-libs/glibc-2.13-r3'.
 * The complete build log is located at '/var/tmp/portage/sys-libs/glibc-2.13-r3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sys-libs/glibc-2.13-r3/temp/environment'.
 * S: '/var/tmp/portage/sys-libs/glibc-2.13-r3/work/glibc-2.13'
 *
 * The following package has failed to build or install:
 *
 *  (sys-libs/glibc-2.13-r3::gentoo, ebuild scheduled for merge), Log file:
 *   '/var/tmp/portage/sys-libs/glibc-2.13-r3/temp/build.log'


patch.out

Code:
head /etc/portage/patches/sys-libs/glibc-2.13-r3/glibc-2.13-r3.patch
--- a/elf/dl-deps.c
+++ b/elf/dl-deps.c
@@ -617,61 +617,64 @@ Filters not supported with LD_TRACE_PRELINKING"));
    map->l_searchlist.r_list[i]->l_reserved = 0;
     }
 
-  /* Now determine the order in which the initialization has to happen.  */
+  /* Sort the initializer list to take dependencies into account.  The binary
+     itself will always be initialize last.  */
   memcpy (l_initfini, map->l_searchlist.r_list,



Edit:
OK, after countless number of trials seems that patching was succesfully made, reemerging glibc now.

The patch file which gave no error: http://pastebin.com/FvYmHrXS


Last edited by p04ty on Fri Jul 08, 2011 12:04 pm; edited 1 time in total
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PostPosted: Fri Jul 08, 2011 12:04 pm    Post subject: Reply with quote

@molot:
Personally, I try to avoid fiddling with ebuilds as much as possible. In other words, probably I won't be able to do it. I became Veteran here by simply asking a lot of question when something was not working. Back 2005-2006 that was quite often :lol:
I didn't even know that you can apply patches within the ebuild directly. Most of the time when something is really not working, someone on bugzilla has an ebuild there already.
Regards,

Marcus

PS: OT: your avatar looks like a blood sucking german flag... I really hope you don't see "us" that way? ;)
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PostPosted: Fri Jul 08, 2011 12:19 pm    Post subject: Reply with quote

Martux wrote:
@molot:
Personally, I try to avoid fiddling with ebuilds as much as possible. In other words, probably I won't be able to do it. I became Veteran here by simply asking a lot of question when something was not working. Back 2005-2006 that was quite often :lol:
See when and guess why I registered :P

Martux wrote:
I didn't even know that you can apply patches within the ebuild directly.
Not directly. I hosted them online. Old times like an year or two ago when I was running a home server ;)

Martux wrote:
PS: OT: your avatar looks like a blood sucking german flag... I really hope you don't see "us" that way? ;)
My avatar is a kite. Damn KITE. Colorful thing meant to fly high and give joy!
I need to take a photo of one of my current kites. Maybe that traditional delta one will do it?
Regards
Molot

@p04ty - I simply don't know. Maybe cleaning your distfiles and portage tmp would help? Like rm -rf /var/tmp/portage/* /usr/portage/distfiles/*
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PostPosted: Fri Jul 08, 2011 12:29 pm    Post subject: Reply with quote

OK, thx, it works now with the patch: http://pastebin.com/FvYmHrXS
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PostPosted: Fri Jul 08, 2011 12:35 pm    Post subject: Reply with quote

p04ty wrote:
OK, thx, it works now with the patch: http://pastebin.com/FvYmHrXS
Isn't that the very same patch I pasted here in a [ code ] block few posts above?..
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