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Khaito
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PostPosted: Mon Oct 29, 2012 10:48 am    Post subject: Glibc-2.15-r2 error when trying to update system with emerge Reply with quote

I've just recently started looking after a Gentoo server running MediaWiki as an intranet for a client and the OS hadn't been updated in a long time apparently due to emerge breaking. I reinstalled portage fine and got it actually trying to update again but now I've been stuck at glibc-2.15-r2 not updating for a while and it's got me stumped.

I've tried all of the following commands:

Code:
emerge -uDp world
emerge -uDpf world
emerge patch glibc


I went into gcc-config and changed the profile from:
i686-pc-linux-gnu-4.1.2
to
i686-pc-linux-gnu-4.3.4

Tried the following after this:
Code:
emerge patch glibc
emerge -uD --keep-going world
emerge -DuNav world


Still got the same issue.

I then found this post:
http://forums.gentoo.org/viewtopic-t-676655-start-0.html

Where the person was seeing similar error messages in the build.log
../sysdeps/x86_64/memcpy.S:535: Error: suffix or operands invalid for `movnti'

Except the error I'm seeing is:
../sysdeps/i386/i686/fpu/e_logl.S:75: Error: suffix or operands invalid for `fcomip'

And the machine I'm dealing with isn't a 64 bit system, I believe.

But I tried checking out the same things they did:

binutils-config -c
i686-pc-linux-gnu-2.18
binutils-config -l
[1] i686-pc-linux-gnu2.18 *

I don't seem to have an option to change the profile to another one since there only seems to be one.

emerge -info spits out the following:

Code:
Portage 2.1.11.9 (default/linux/x86/10.0, gcc-4.3.4, glibc-2.9_p20081201-r2, 2.6.27-gentoo-r7 i686)
=================================================================
System uname: Linux-2.6.27-gentoo-r7-i686-Pentium_III_-Coppermine-with-gentoo-2.1
Timestamp of tree: Sat, 27 Oct 2012 03:45:01 +0000
app-shells/bash:          4.0_p35
dev-lang/python:          2.5.4-r3, 2.6.4
dev-util/pkgconfig:       0.23
sys-apps/baselayout:      2.1-r1
sys-apps/openrc:          0.9.8.4
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13::<unknown repository>, 2.63-r1
sys-devel/automake:       1.4_p6::<unknown repository>, 1.5::<unknown repository>, 1.6.3::<unknown repository>, 1.7.9-r1::<unknown repository>, 1.8.5-r3::<unknown repository>, 1.9.6-r2::<unknown repository>, 1.10.2, 1.11.1
sys-devel/binutils:       2.18-r3
sys-devel/gcc:            4.1.2, 4.3.4
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.2.6b
sys-devel/make:           3.81::<unknown repository>
sys-kernel/linux-headers: 3.1 (virtual/os-headers)
sys-libs/glibc:           2.9_p20081201-r2
Repositories: gentoo
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="* -@EULA"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=pentium3 -O2 -pipe -msse -mmmx"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-march=pentium3 -O2 -pipe -msse -mmmx"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -march=i686 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -march=i686 -pipe"
GENTOO_MIRRORS="http://gentoo.blueyonder.co.uk/ http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --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.europe.gentoo.org/gentoo-portage"
USE="S3TC X acl acpi admin apache2 apm authdaemond authlib berkdb bundled-adodb bzip2 cairo cli cracklib crypt ctype cups curl curlwrappers cxx diskio dri exif extensions ftp gd gdbm gpm gtk iconv imagemagick ipv6 jpeg jpeg2k latex latin1 lcms maildir math max-idx-128 mng modules mpeg mpm-prefork mudflap mysql mysqli nagios-dns nagios-game nagios-ntp nagios-ping nagios-ssh ncurses nls nptl openmp pam pcre pdf php png pppd quota readline rrdcgi samba sasl sensord session smp snmp sockets spell ssl svg symlink tcl tcpd tiff tk truetype unicode vda vhosts wmf x86 xml xpm xsl zip zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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="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" APACHE2_MPMS="prefork" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" 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" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" 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, USE_PYTHON



And the last chunk of the build.log for glibc is:

Code:
i686-pc-linux-gnu-gcc  ../sysdeps/i386/i686/fpu/e_logl.S -c -U_FORTIFY_SOURCE -U_FORTIFY_SOURCE -D__NO_MATH_INLINES -D__LIBC_INTERNAL_MATH_INLINES -I../include -I/var/tmp/portage/sys-libs/glibc-2.15-r2/work/build-default-i686-pc-linux-gnu-nptl/math -I/var/tmp/portage/sys-libs/glibc-2.15-r2/work/build-default-i686-pc-linux-gnu-nptl -I../sysdeps/i386/elf -I../nptl/sysdeps/unix/sysv/linux/i386/i686 -I../sysdeps/unix/sysv/linux/i386/i686 -I../nptl/sysdeps/unix/sysv/linux/i386 -I../sysdeps/unix/sysv/linux/i386 -I../nptl/sysdeps/unix/sysv/linux -I../nptl/sysdeps/pthread -I../sysdeps/pthread -I../ports/sysdeps/unix/sysv/linux -I../sysdeps/unix/sysv/linux -I../sysdeps/gnu -I../sysdeps/unix/common -I../sysdeps/unix/mman -I../sysdeps/unix/inet -I../sysdeps/unix/sysv/i386 -I../nptl/sysdeps/unix/sysv -I../ports/sysdeps/unix/sysv -I../sysdeps/unix/sysv -I../sysdeps/unix/i386 -I../nptl/sysdeps/unix -I../ports/sysdeps/unix -I../sysdeps/unix -I../sysdeps/posix -I../sysdeps/i386/i686/fpu -I../nptl/sysdeps/i386/i686 -I../sysdeps/i386/i686 -I../sysdeps/i386/i486 -I../nptl/sysdeps/i386/i486 -I../sysdeps/i386/fpu -I../nptl/sysdeps/i386 -I../sysdeps/i386 -I../sysdeps/wordsize-32 -I../sysdeps/ieee754/ldbl-96 -I../sysdeps/ieee754/dbl-64 -I../sysdeps/ieee754/flt-32 -I../sysdeps/ieee754 -I../sysdeps/generic/elf -I../sysdeps/generic -I../nptl -I../ports  -I.. -I../libio -I. -nostdinc -isystem /usr/lib/gcc/i686-pc-linux-gnu/4.3.4/include -isystem /usr/lib/gcc/i686-pc-linux-gnu/4.3.4/include-fixed -isystem /usr/include -D_LIBC_REENTRANT -include ../include/libc-symbols.h   -DNOT_IN_libc=1 -DIS_IN_libm=1    -DASSEMBLER  -DGAS_SYNTAX  -Wa,--noexecstack  -Wa,--noexecstack  -Wa,-mtune=i686 -o /var/tmp/portage/sys-libs/glibc-2.15-r2/work/build-default-i686-pc-linux-gnu-nptl/math/e_logl.o -MD -MP -MF /var/tmp/portage/sys-libs/glibc-2.15-r2/work/build-default-i686-pc-linux-gnu-nptl/math/e_logl.o.dt -MT /var/tmp/portage/sys-libs/glibc-2.15-r2/work/build-default-i686-pc-linux-gnu-nptl/math/e_logl.o
../sysdeps/i386/i686/fpu/e_logl.S: Assembler messages:
../sysdeps/i386/i686/fpu/e_logl.S:49: Error: suffix or operands invalid for `fcomip'
../sysdeps/i386/i686/fpu/e_logl.S:75: Error: suffix or operands invalid for `fcomip'
make[2]: *** [/var/tmp/portage/sys-libs/glibc-2.15-r2/work/build-default-i686-pc-linux-gnu-nptl/math/e_logl.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory `/var/tmp/portage/sys-libs/glibc-2.15-r2/work/glibc-2.15/math'
make[1]: *** [math/others] Error 2
make[1]: Leaving directory `/var/tmp/portage/sys-libs/glibc-2.15-r2/work/glibc-2.15'
make: *** [all] Error 2
emake failed
 * ERROR: sys-libs/glibc-2.15-r2 failed (compile phase):
 *   make for default failed
 *
 * Call stack:
 *           ebuild.sh, line   85:  Called src_compile
 *         environment, line 3543:  Called eblit-run 'src_compile'
 *         environment, line  922:  Called eblit-glibc-src_compile
 *   src_compile.eblit, line  221:  Called toolchain-glibc_src_compile
 *   src_compile.eblit, line  132:  Called die
 * The specific snippet of code:
 *         emake || die "make for ${ABI} failed"
 *
 * If you need support, post the output of `emerge --info '=sys-libs/glibc-2.15-r2'`,
 * the complete build log and the output of `emerge -pqv '=sys-libs/glibc-2.15-r2'`.
 * The complete build log is located at '/var/tmp/portage/sys-libs/glibc-2.15-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sys-libs/glibc-2.15-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/sys-libs/glibc-2.15-r2/work/build-default-i686-pc-linux-gnu-nptl'
 * S: '/var/tmp/portage/sys-libs/glibc-2.15-r2/work/glibc-2.15'


I can upload the full build.log if need be, just let me know.


Any help would be greatly appreciated as I'm more of a RedHat/MacOSX girl than a Gentoo one. :?
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Last edited by Khaito on Mon Oct 29, 2012 12:16 pm; edited 1 time in total
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Veldrin
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PostPosted: Mon Oct 29, 2012 11:01 am    Post subject: Reply with quote

Quote:
I've just recently started looking after a Gentoo server running MediaWiki as an intranet for a client and the OS hadn't been updated in a long time apparently due to emerge breaking. I reinstalled portage fine and got it actually trying to update again but now I've been stuck at glibc-2.15-r2 not updating for a while and it's got me stumped.
Gentoo is a rolling distro - not upgrade for a long time leads to problems. Maybe this can be fixed.
Quote:
But I tried checking out the same things they did:

Code:
binutils-config -c
i686-pc-linux-gnu-2.18
binutils-config -l
[1] i686-pc-linux-gnu2.18 *


I don't seem to have an option to change the profile to another one since there only seems to be one.

You showed the version, but did not actually reassign it. Please run the same commands as the other thread suggests
Code:
binutils-config 1
source /etc/profile
emerge glibc


if it does not work, I am tempted to ask you to rebuild/upgrade the entire toolchain (glibc, gcc, binutils, linux-headers).
Which then again could force you to upgrade the kernel.



V.
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Khaito
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PostPosted: Mon Oct 29, 2012 11:13 am    Post subject: Reply with quote

I ran source /etc/profile then I realised it was for a different problem so didn't try emerge glibc but I'll go do that just now.

Thanks for the reply. :)
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PostPosted: Mon Oct 29, 2012 12:10 pm    Post subject: Reply with quote

After running

Code:
binutils-config -l
binutils-config 1
source /etc/profile
emerge glibc


I got the following fail:

Code:
../sysdeps/i386/i686/fpu/e_logl.S: Assembler messages:
../sysdeps/i386/i686/fpu/e_logl.S:49: Error: suffix or operands invalid for `fcomip'
../sysdeps/i386/i686/fpu/e_logl.S:75: Error: suffix or operands invalid for `fcomip'
make[2]: *** [/var/tmp/portage/sys-libs/glibc-2.15-r3/work/build-default-i686-pc-linux-gnu-nptl/math/e_logl.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory `/var/tmp/portage/sys-libs/glibc-2.15-r3/work/glibc-2.15/math'
make[1]: *** [math/others] Error 2
make[1]: Leaving directory `/var/tmp/portage/sys-libs/glibc-2.15-r3/work/glibc-2.15'
make: *** [all] Error 2
emake failed
 * ERROR: sys-libs/glibc-2.15-r3 failed (compile phase):
 *   make for default failed
 *
 * Call stack:
 *           ebuild.sh, line   85:  Called src_compile
 *         environment, line 3543:  Called eblit-run 'src_compile'
 *         environment, line  922:  Called eblit-glibc-src_compile
 *   src_compile.eblit, line  221:  Called toolchain-glibc_src_compile
 *   src_compile.eblit, line  132:  Called die
 * The specific snippet of code:
 *         emake || die "make for ${ABI} failed"
 *
 * If you need support, post the output of `emerge --info '=sys-libs/glibc-2.15-r3'`,
 * the complete build log and the output of `emerge -pqv '=sys-libs/glibc-2.15-r3'`.
 * The complete build log is located at '/var/tmp/portage/sys-libs/glibc-2.15-r3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sys-libs/glibc-2.15-r3/temp/environment'.
 * Working directory: '/var/tmp/portage/sys-libs/glibc-2.15-r3/work/build-default-i686-pc-linux-gnu-nptl'
 * S: '/var/tmp/portage/sys-libs/glibc-2.15-r3/work/glibc-2.15'

>>> Failed to emerge sys-libs/glibc-2.15-r3, Log file:

>>>  '/var/tmp/portage/sys-libs/glibc-2.15-r3/temp/build.log'

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PostPosted: Mon Oct 29, 2012 12:54 pm    Post subject: Reply with quote

Veldrin wrote:
if it does not work, I am tempted to ask you to rebuild/upgrade the entire toolchain (glibc, gcc, binutils, linux-headers).
Which then again could force you to upgrade the kernel.


Is there a simple way to update the whole toolchain? Or is it just a case of running emerge against each one? Updating the kernel isn't something I'm against doing either.

I'm thinking it might be simpler to just install a fresh linux OS on another HD and migrate the MediaWiki + SQL DB over to it and wipe the old one but need to document the current installation's setup first.
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PostPosted: Mon Oct 29, 2012 3:23 pm    Post subject: Reply with quote

one technique would to be to try to upgrade to an intermediate level. If you can't get the newest version of gcc/glibc/binutils to compile, to may be able to get a newer - but not newest verison to compile and install (same with with dependencies). You can "mask off" the newer version temporarily by adding them to /etc/portage/package.mask, or (if your portage is too old), specify the desired version (and the version of dependencies) directly on the command line (emerge '<=sys-libs/glibc-2.12 <=sys-devel/gcc-4.5 ...), Then using the newer verison, repeat the process incrementally until you've got the newest versions.
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PostPosted: Mon Oct 29, 2012 3:49 pm    Post subject: Reply with quote

salahx wrote:
one technique would to be to try to upgrade to an intermediate level. If you can't get the newest version of gcc/glibc/binutils to compile, to may be able to get a newer - but not newest verison to compile and install (same with with dependencies). You can "mask off" the newer version temporarily by adding them to /etc/portage/package.mask, or (if your portage is too old), specify the desired version (and the version of dependencies) directly on the command line (emerge '<=sys-libs/glibc-2.12 <=sys-devel/gcc-4.5 ...), Then using the newer verison, repeat the process incrementally until you've got the newest versions.


Thanks, that sounds like a good plan. I'll give it a shot. I got GCC updated okay, I'm away to try binutils and then will give glibc another shot, if it still doesn't update I'll try both options you suggested. :)
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PostPosted: Mon Oct 29, 2012 6:47 pm    Post subject: Reply with quote

I think I'm having the exactly same problem. But my system was updated recently (a couple of months or so) instead of sitting around being neglected. I'm going to update gcc/binutils and see whether doing so makes any difference.
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PostPosted: Tue Oct 30, 2012 3:51 am    Post subject: Reply with quote

It turned out that my case was different from the original poster; "/etc/make.profile" (to be exact, it was "/etc/portage/make.conf") was pointing to a wrong profile. After I corrected it, I was able to emerge glibc without a problem.
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someone0012
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PostPosted: Fri Nov 02, 2012 9:36 pm    Post subject: Reply with quote

I too ran into same error when updating a negleted system. Emerging binutils then glibc corrected the problem for me at least.
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PostPosted: Mon Nov 05, 2012 2:22 pm    Post subject: Reply with quote

Got glibc updated. :)

Same as the above post, ran emerge gcc, switched the newest profile, source /etc/profile, emerge binutils, source /etc/profile and then ran emerge glibc again and it updated to latest version. Thanks for the help! :)
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