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Old kernel is broken when emerging glibc-2.23-r4
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TheMachinesTeacher
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Joined: 09 Sep 2017
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PostPosted: Sun Sep 10, 2017 5:30 am    Post subject: Old kernel is broken when emerging glibc-2.23-r4 Reply with quote

I am unable to emerge anything that is dependent on glibc. I have just installed gentoo for the first time, so I may have missed something, but I have followed the handbooks directions twice now (I started over once).

The "old kernel" is the current stable version which is 4.12.5. In hopes that a new kernel would fix this problem, I tried out 4.13.0, but got the same nondescript error.

It states that syscall(<bignum>) will break and references https://bugs.gentoo.org/279260, which has a similar problem on an older kernel and glibc, but the recommended solutions do not work.

I am on Ryzen 1600X x86_64. As emerge has requested, here are the notable logs:

emerge --info =sys-libs/glibc-2.23-r4
Code:

Portage 2.3.6 (python 2.7.12-final-0, default/linux/amd64/13.0, gcc-5.4.0, uclibc-ng-1.0.25, 4.5.2-aufs-r1 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.5.2-aufs-r1-x86_64-AMD_Ryzen_5_1600X_Six-Core_Processor-with-gentoo-2.3
KiB Mem:    16379372 total,  14104904 free
KiB Swap:     524284 total,    524284 free
Timestamp of repository gentoo: Sat, 09 Sep 2017 00:45:01 +0000
sh bash 4.3_p48-r1
ld GNU ld (Gentoo 2.28.1 p1.0) 2.28.1
app-shells/bash:          4.3_p48-r1::gentoo
dev-lang/perl:            5.24.1-r2::gentoo
dev-lang/python:          2.7.12::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.28::gentoo
sys-apps/sandbox:         2.10-r3::gentoo
sys-devel/autoconf:       2.69::gentoo
sys-devel/automake:       1.15-r2::gentoo
sys-devel/binutils:       2.28.1::gentoo
sys-devel/gcc:            5.4.0-r3::gentoo
sys-devel/gcc-config:     1.7.3::gentoo
sys-devel/libtool:        2.4.6-r3::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.4::gentoo (virtual/os-headers)
sys-libs/uclibc-ng:       1.0.25::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-gentoo-linux-uclibc"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-gentoo-linux-uclibc"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j7"
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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X acl alsa amd64 berkdb bindist bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mmx modules multilib ncurses nls nptl openmp pcre readline seccomp session sse sse2 ssl tcpd unicode usb xattr 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" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_4" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby22" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa 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:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS


emerge -pqv '=sys-libs/glibc-2.23-r4::gentoo'
Code:

[ebuild  N    ] sys-libs/timezone-data-2017a  USE="nls -leaps_timezone"
[ebuild  N    ] sys-libs/glibc-2.23-r4  USE="(multilib) rpc -audit -caps -debug -gd (-hardened) -nscd -profile (-selinux) -suid -systemtap -vanilla"
[uninstall    ] dev-libs/libintl-0.19.7  USE="threads -static-libs" ABI_X86="(64) -32 (-x32)"
[blocks b     ] sys-libs/glibc ("sys-libs/glibc" is blocking dev-libs/libintl-0.19.7)
[uninstall    ] dev-libs/libiconv-1.14-r1  USE="static-libs" ABI_X86="(64) -32 (-x32)"
[blocks b     ] sys-libs/glibc ("sys-libs/glibc" is blocking dev-libs/libiconv-1.14-r1)

Could this error occur because of the blocking? If so, please point me in the right direction to learn how to resolve this.

cat /var/temp/portage/sys-libs/glibc-2.23-r4/temp/build.log
Code:

#[32;01m * #[39;49;00mPackage:    sys-libs/glibc-2.23-r4
#[32;01m * #[39;49;00mRepository: gentoo
#[32;01m * #[39;49;00mMaintainer: toolchain@gentoo.org
#[32;01m * #[39;49;00mUSE:        abi_x86_64 amd64 elibc_glibc kernel_linux multilib rpc userland_GNU
#[32;01m * #[39;49;00mFEATURES:   preserve-libs sandbox userpriv usersandbox
make -j7 -s glibc-test
make -j7 -s glibc-test
 #[31;01m*#[0m Your old kernel is broken.  You need to update it to
 #[31;01m*#[0m a newer version as syscall(<bignum>) will break.
 #[31;01m*#[0m http://bugs.gentoo.org/279260
 #[31;01m*#[0m ERROR: sys-libs/glibc-2.23-r4::gentoo failed (pretend phase):
 #[31;01m*#[0m   keeping your system alive, say thank you
 #[31;01m*#[0m
 #[31;01m*#[0m Call stack:
 #[31;01m*#[0m                ebuild.sh, line 115:  Called pkg_pretend
 #[31;01m*#[0m                ebuild.sh, line 348:  Called toolchain-glibc_pkg_pretend
 #[31;01m*#[0m   toolchain-glibc.eclass, line 517:  Called die
 #[31;01m*#[0m The specific snippet of code:
 #[31;01m*#[0m            die "keeping your system alive, say thank you"
 #[31;01m*#[0m
 #[31;01m*#[0m If you need support, post the output of `emerge --info '=sys-libs/glibc-2.23-r4::gentoo'`,
 #[31;01m*#[0m the complete build log and the output of `emerge -pqv '=sys-libs/glibc-2.23-r4::gentoo'`.
 #[31;01m*#[0m The complete build log is located at '/var/tmp/portage/sys-libs/glibc-2.23-r4/temp/build.log'.
 #[31;01m*#[0m The ebuild environment file is located at '/var/tmp/portage/sys-libs/glibc-2.23-r4/temp/die.env'.
 #[31;01m*#[0m Working directory: '/var/tmp/portage/sys-libs/glibc-2.23-r4/homedir'
 #[31;01m*#[0m S: '/var/tmp/portage/sys-libs/glibc-2.23-r4/work/glibc-2.23'

This is almost what it shows me when it fails, minus the weird character encoding information at the start of the line.

If you think it will be helpful, I am happy to provide /var/temp/portage/sys-libs/glibc-2.23-r4/temp/die.env, but since it is huge, I have omitted it.

This error happens when I try to run any of these commands:
Code:

emerge --ask --update --deep --with-bdeps=y --newuse @world
emerge --ask --update --deep --with-bdeps=y --newuse sys-kernel/gentoo-sources
emerge --ask gnome-base/gnome


So any ideas on what I can do to fix this?
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charles17
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Joined: 02 Mar 2008
Posts: 2379

PostPosted: Sun Sep 10, 2017 8:50 am    Post subject: Re: Old kernel is broken when emerging glibc-2.23-r4 Reply with quote

TheMachinesTeacher wrote:
The "old kernel" is the current stable version which is 4.12.5. ...

You should be able to verify the kernel version doing uname -r. Does it say 4.12.5?


TheMachinesTeacher wrote:
emerge --info =sys-libs/glibc-2.23-r4
Code:

Portage 2.3.6 (python 2.7.12-final-0, default/linux/amd64/13.0, gcc-5.4.0, uclibc-ng-1.0.25, 4.5.2-aufs-r1 x86_64)
=================================================================
                         System Settings
=================================================================

There it says kernel version is 4.5.2-aufs-r1 ...
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NeddySeagoon
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Posts: 38874
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PostPosted: Sun Sep 10, 2017 10:08 am    Post subject: Reply with quote

TheMachinesTeacher,

From the kernel version, 4.5.2-aufs-r1, it looks like you are chrooted from a live CD/DVD or your running kernel was copied from one.
4.5.2 is a very old kernel and the aufs part of the version shows that it contains a union filesystem that allows a read only filesysysem, such as a CD/DVD, to appear read/write by usung a section of RAM to keep the changes.

You may have omitted to mount /boot for later kernel installs.

However it happened, you are not using the kernel you think you are.
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NeddySeagoon

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TheMachinesTeacher
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Joined: 09 Sep 2017
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PostPosted: Sun Sep 10, 2017 4:27 pm    Post subject: Reply with quote

Well when I posted that information I was using a livecd because my gentoo installation does not have a desktop environment, so I could not use copy-paste or graphically browse the internet. I can boot into the installation however, and when I run uname -r it says
Code:

4.12.5-gentoo


When I run the commands that I stated cause issue, I get the same problem. I do see what you mean though about it being 4.5.2-aufs-r1 in my original post, but when I run the command again, it says

Code:

Portage 2.3.6 (python2.7.12-final-0, default/linux/amd64/13.0, gcc-5.4.0, uclibc-ng-1.0.25, 4.12.5-gentoo x86_64)

when I run emerge --info =sys-libs/glibc-2.23-r4

This problem persists outside of the livecd environment.
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Hu
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PostPosted: Sun Sep 10, 2017 4:29 pm    Post subject: Reply with quote

It looks strange to me that OP is using a uclibc-ng based system and trying to install, not upgrade/replace, glibc.

OP: from where did you get the environment you are using? uclibc-ng is uncommon on desktop systems and is probably not what you want. Your CHOST is consistent with using uclibc, which is good, but I'd be a bit surprised if you can usefully install glibc on this system even if you got past the immediate problem.
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TheMachinesTeacher
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PostPosted: Sun Sep 10, 2017 6:06 pm    Post subject: Reply with quote

Wow super quick reply! Thank you.

Good point! I did not realize that uclibc-ng was a poor choice for a desktop environment. When I was going through the handbook, I did not know which stage tarball to choose and the one that had uclibc-ng seemed like the right one since I don't want systemd, nomultilib, nor just x32 (although I am just assuming x32 means 32bit, which I realize now that could be wrong).

I think I will try the installation again as it makes sense that I would have this problem if I used the uclibc-ng tarball. Thank you. I will report back if this does in fact solve the problem.
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Hu
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PostPosted: Sun Sep 10, 2017 8:58 pm    Post subject: Reply with quote

If that solves the problem, then in my opinion, the glibc/uclibc ebuilds need mutual blockers (or perhaps mutual masks, since we have dedicated profiles for each). Since it makes no sense to co-install them, the package manager should've prevented you from attempting it.
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TheMachinesTeacher
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PostPosted: Mon Sep 11, 2017 1:59 am    Post subject: Reply with quote

Selecting a tarball without uclibc-ng did solve the problem. Thank you all for the quick help and support.
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