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lasuit
n00b
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Joined: 01 Mar 2011
Posts: 24
Location: London, England

PostPosted: Sat May 02, 2020 9:15 am    Post subject: [Solved] Unable to clear preserved-libs Reply with quote

From about a week about I received the following message after updating:

Code:
!!! existing preserved libs:
>>> package: sys-libs/glibc-2.30-r8
 *  - /lib/ld-2.29.so
 *  - /lib/ld-linux.so.2
 *      used by /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/32/libasan.so.5.0.0 (sys-devel/gcc-9.3.0)
 *      used by /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/32/libgfortran.so.5.0.0 (sys-devel/gcc-9.3.0)
 *      used by /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/32/libstdc++.so.6.0.28 (sys-devel/gcc-9.3.0)
 *  - /lib/libc-2.29.so
 *  - /lib/libc.so.6
 *      used by /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/32/libasan.so.5.0.0 (sys-devel/gcc-9.3.0)
 *      used by /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/32/libatomic.so.1.2.0 (sys-devel/gcc-9.3.0)
 *      used by /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/32/libgcc_s.so.1 (sys-devel/gcc-9.3.0)
 *      used by 8 other files
 *  - /lib/libdl-2.29.so
 *  - /lib/libdl.so.2
 *      used by /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/32/libasan.so.5.0.0 (sys-devel/gcc-9.3.0)
 *      used by /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/32/libgomp.so.1.0.0 (sys-devel/gcc-9.3.0)
 *      used by /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/32/libubsan.so.1.0.0 (sys-devel/gcc-9.3.0)
 *      used by /usr/lib32/libsandbox.so (sys-apps/sandbox-2.13)


I run emerge @preserved-rebuild more than once, but no luck. I've also run "revdep-rebuild" without flags and it says my system is consistent. When I check the gcc setting in eselect it says:
[1] x86_64-pc-linux-gnu-9.3.0 *

and nothing else. Any suggestions have to clear the old libs?


Last edited by lasuit on Tue May 05, 2020 11:30 am; edited 1 time in total
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UlFie
Tux's lil' helper
Tux's lil' helper


Joined: 01 Nov 2011
Posts: 112
Location: Wuppertal

PostPosted: Sat May 02, 2020 2:03 pm    Post subject: Reply with quote

If the tools intended to help you fail, have you tried to reinstall sys-devel/gcc-9.3.0 and sys-apps/sandbox-2.13 (the packages mentioned in the output) manually? You may want to check in /var/log/emerge.log if these packages have been rebuilt after the latest update of glibc. Personally I would very much love to know whether they had been part of a world update that updated glibc, but were erroneously reinstalled before the update of glibc occured as I have experienced a similar issue recently (and currently don't really trust emerge's scheduling algorithm).

Last edited by UlFie on Sun May 03, 2020 12:19 am; edited 1 time in total
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Hu
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Joined: 06 Mar 2007
Posts: 16464

PostPosted: Sat May 02, 2020 4:21 pm    Post subject: Reply with quote

What is the output of emerge --verbose --info sys-libs/glibc sys-devel/gcc:9.3.0 sys-apps/sandbox?
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Anon-E-moose
Watchman
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Joined: 23 May 2008
Posts: 5047
Location: Dallas area

PostPosted: Sat May 02, 2020 5:01 pm    Post subject: Reply with quote

Reinstall glibc.

What does "ls -l /var/lib/portages/preserved_libs_registry" return

ETA:
I say reinstall, because I've seen a similar problem in the last year, where I've had to turn around and recompile the package again because it claims it's depending on the currently installed package. Some screwy condition coming from the emerge section of portage.

ETA2: I notice that all the complaints are about the 32 bit libs, did you do the profile 17.1 update before your problems started appearing?
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lasuit
n00b
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Joined: 01 Mar 2011
Posts: 24
Location: London, England

PostPosted: Sun May 03, 2020 2:56 pm    Post subject: Reply with quote

OK. Here's what I've tried: I've recompiled glibc, sandbox, and gcc.. again. But, still no luck. The output for emerge --verbose --info sys-libs/glibc sys-devel/gcc:9.3.0 sys-apps/sandbox is:

Code:
Portage 2.3.89 (python 3.6.10-final-0, default/linux/amd64/17.0/desktop, gcc-9.3.0, glibc-2.30-r8, 5.4.28-gentoo-x86_64 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-5.4.28-gentoo-x86_64-x86_64-Intel-R-_Core-TM-_i5-4300U_CPU_@_1.90GHz-with-gentoo-2.6
KiB Mem:     3694368 total,   1211304 free
KiB Swap:    4095996 total,   4063996 free
Timestamp of repository gentoo: Sat, 02 May 2020 00:45:02 +0000
Head commit of repository gentoo: 3c9e09cb3f3bf8f03c37de1719f4ace2e25660d4
sh bash 4.4_p23-r1
ld GNU ld (Gentoo 2.33.1 p2) 2.33.1
app-shells/bash:          4.4_p23-r1::gentoo
dev-lang/perl:            5.30.1::gentoo
dev-lang/python:          2.7.18::gentoo, 3.6.10-r2::gentoo, 3.7.7-r2::gentoo, 3.8.2-r2::gentoo
dev-util/cmake:           3.16.5::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.13::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.16.1-r1::gentoo
sys-devel/binutils:       2.33.1-r1::gentoo
sys-devel/gcc:            9.3.0::gentoo
sys-devel/gcc-config:     2.2.1::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 5.4::gentoo (virtual/os-headers)
sys-libs/glibc:           2.30-r8::gentoo
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TWISTED_DISABLE_WRITING_OF_PLUGIN_CACHE="1"
UNINSTALL_IGNORE="/lib/modules/* /var/run /var/lock"
USE="X a52 aac acl acpi alsa amd64 berkdb branding bzip2 cairo cdda cdr cli crypt cups dbus dri dts dvd dvdr elogind emboss encode exif flac fortran gdbm gif gpm gtk iconv icu ipv6 jpeg lcms ldap libnotify libtirpc mad mng mp3 mp4 mpeg multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds qt5 readline sdl seccomp spell split-usr ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xattr xcb xml xv xvid zlib" ABI_X86="64" ADA_TARGET="gnat_2018" 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="karbon sheets words" 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 greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64" 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="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24 ruby25" 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"
USER="art"
USERLAND="GNU"
USE_EXPAND="ABI_MIPS ABI_PPC ABI_RISCV ABI_S390 ABI_X86 ADA_TARGET ALSA_CARDS APACHE2_MODULES APACHE2_MPMS CALLIGRA_FEATURES CAMERAS COLLECTD_PLUGINS CPU_FLAGS_ARM CPU_FLAGS_PPC CPU_FLAGS_X86 CURL_SSL ELIBC ENLIGHTENMENT_MODULES FFTOOLS GPSD_PROTOCOLS GRUB_PLATFORMS INPUT_DEVICES KERNEL L10N LCD_DEVICES LIBREOFFICE_EXTENSIONS LIRC_DEVICES LLVM_TARGETS MONKEYD_PLUGINS NGINX_MODULES_HTTP NGINX_MODULES_MAIL NGINX_MODULES_STREAM OFED_DRIVERS OFFICE_IMPLEMENTATION OPENMPI_FABRICS OPENMPI_OFED_FEATURES OPENMPI_RM PHP_TARGETS POSTGRES_TARGETS PYTHON_SINGLE_TARGET PYTHON_TARGETS QEMU_SOFTMMU_TARGETS QEMU_USER_TARGETS ROS_MESSAGES RUBY_TARGETS SANE_BACKENDS USERLAND UWSGI_PLUGINS VIDEO_CARDS VOICEMAIL_STORAGE XFCE_PLUGINS XTABLES_ADDONS"
USE_EXPAND_HIDDEN="ABI_MIPS ABI_PPC ABI_RISCV ABI_S390 CPU_FLAGS_ARM CPU_FLAGS_PPC ELIBC KERNEL USERLAND"
USE_EXPAND_IMPLICIT="ARCH ELIBC KERNEL USERLAND"
USE_EXPAND_UNPREFIXED="ARCH"
USE_EXPAND_VALUES_ARCH="alpha amd64 amd64-fbsd amd64-linux arm arm64 hppa ia64 m68k m68k-mint mips ppc ppc64 ppc64-linux ppc-aix ppc-macos riscv s390 sh sparc sparc64-solaris sparc-solaris x64-cygwin x64-macos x64-solaris x64-winnt x86 x86-cygwin x86-fbsd x86-linux x86-macos x86-solaris x86-winnt"
USE_EXPAND_VALUES_ELIBC="AIX bionic Cygwin Darwin DragonFly FreeBSD glibc HPUX Interix mingw mintlib musl NetBSD OpenBSD SunOS uclibc Winnt"
USE_EXPAND_VALUES_KERNEL="AIX Darwin FreeBSD freemint HPUX linux NetBSD OpenBSD SunOS Winnt"
USE_EXPAND_VALUES_USERLAND="BSD GNU"
USE_ORDER="env:pkg:conf:defaults:pkginternal:features:repo:env.d"
VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l"
WINDOWID="37748749"
XAUTHORITY="/home/art/.Xauthority"
XDG_CONFIG_DIRS="/etc/xdg"
XDG_DATA_DIRS="/usr/local/share:/usr/share"
XDG_RUNTIME_DIR="/run/user/1000"
XDG_SEAT="seat0"
XDG_SESSION_CLASS="user"
XDG_SESSION_ID="1"
XDG_SESSION_TYPE="x11"
XDG_VTNR="7"
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"
XTERM_LOCALE="en_US.utf8"
XTERM_SHELL="/bin/bash"
XTERM_VERSION="XTerm(351)"

=================================================================
                        Package Settings
=================================================================

sys-libs/glibc-2.30-r8::gentoo was built with the following:
USE="(crypt) multiarch (multilib) ssp (static-libs) -audit -caps (-cet) -compile-locales -custom-cflags -doc -gd -headers-only -nscd -profile (-selinux) -suid -systemtap -test (-vanilla)" ABI_X86="(64)"
CFLAGS="-march=native -pipe -O2"
CXXFLAGS="-march=native -pipe -O2"
FEATURES="binpkg-logs sandbox multilib-strict unmerge-logs unmerge-orphans strict userpriv usersync buildpkg ebuild-locks pid-sandbox fixlafiles news network-sandbox binpkg-docompress ipc-sandbox usersandbox unknown-features-warn userfetch protect-owned parallel-fetch distlocks config-protect-if-modified xattr assume-digests binpkg-dostrip preserve-libs merge-sync qa-unresolved-soname-deps sfperms"


sys-devel/gcc-9.3.0::gentoo was built with the following:
USE="(cxx) fortran (multilib) nls nptl openmp pch (pie) sanitize ssp vtv (-ada) (-altivec) -d -debug -doc (-fixed-point) -go -graphite (-hardened) (-jit) (-libssp) -lto -objc -objc++ -objc-gc -pgo -systemtap -test -vanilla" ABI_X86="(64)"
CFLAGS="-march=native -pipe -O2"
CXXFLAGS="-march=native -pipe -O2"
FEATURES="buildpkg qa-unresolved-soname-deps sfperms xattr binpkg-dostrip multilib-strict userfetch ebuild-locks preserve-libs sandbox usersandbox strict binpkg-logs distlocks unknown-features-warn parallel-fetch merge-sync binpkg-docompress pid-sandbox userpriv unmerge-orphans protect-owned ipc-sandbox config-protect-if-modified usersync fixlafiles unmerge-logs assume-digests news network-sandbox"


sys-apps/sandbox-2.13::gentoo was built with the following:
USE="" ABI_X86="(32) (64) (-x32)"


The output of ls -l /var/lib/portage/preserved_libs_registrry is:

Code:
-rw-rw---- 1 root portage 214 May  3 15:34 /var/lib/portage/preserved_libs_registry


Also this install was done in Jaunuary 2020, so no old profiles
My profile is:

Code:
  [5]   default/linux/amd64/17.0/desktop (stable) *


Any other thoughts? There seems to be something weird with the sandbox build saying (32), but also (-x32). I have no lib32 or /usr/lib32 symlinks, but I do have a regular lib32 directory.
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fturco
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Joined: 08 Dec 2010
Posts: 1184
Location: Italy

PostPosted: Sun May 03, 2020 3:05 pm    Post subject: Reply with quote

lasuit wrote:
Also this install was done in Jaunuary 2020, so no old profiles
My profile is:

Code:
  [5]   default/linux/amd64/17.0/desktop (stable) *

Your profile is old. Profile 17.1 has been marked as stable since 2019-06-05:
https://gentoo.org/support/news-items/2019-06-05-amd64-17-1-profiles-are-now-stable.html
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Anon-E-moose
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Joined: 23 May 2008
Posts: 5047
Location: Dallas area

PostPosted: Sun May 03, 2020 3:21 pm    Post subject: Reply with quote

You could change profile, but that's not what's causing your problem.

At this point I'm tempted to tell you to remove /var/lib/portage/preserved_libs_registry and do an emerge pretend world to see what happens.

You could view the file "less /var/lib/portage/preserved_libs_registry" to see what's in it.
_________________
PRIME x570-pro, 3700x, RX 550 - 5.8 zen kernel
Acer E5-575 (laptop), i3-7100u - i965 - 5.5 zen kernel
---both---
gcc 9.3.0, profile 17.1 (no-pie) amd64-no-multilib, eudev, openrc, openbox

The New OTW
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lasuit
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Joined: 01 Mar 2011
Posts: 24
Location: London, England

PostPosted: Mon May 04, 2020 12:27 pm    Post subject: Reply with quote

I've made a small amount of "progress." When I was looking through the lib32 directory I found a dangling symlink. It was libm.so.6. There was an identical one in lib64 that went to libm.2.30.so. So, I deleted the dead one in lib32 and did an "emerge @preserved-rebuild." The result was that the warnings of preserved libs went away, but now I have a new problem, gcc-9.3.0 breaks in the compile phase.

When looking at the build.log I find this: "/usr/x86_64-pc-linux-gnu/bin/ld: cannot find crti.o: No such file or directory
collect2: error: ld returned 1 exit status"

I'm not sure which package should have the "crti.o" file, but would be happy to get some guidance.

Also output from emerge --info =sys-devel/gcc-9.3.0::gentoo shows:
Code:

sys-devel/gcc-9.3.0::gentoo was built with the following:
USE="(cxx) fortran (multilib) nls nptl openmp pch (pie) sanitize ssp vtv (-ada) (-altivec) -d -debug -doc (-fixed-point) -go -graphite (-hardened) (-jit) (-libssp) -lto -objc -objc++ -objc-gc -pgo -systemtap -test -vanilla" ABI_X86="(64)"
CFLAGS="-march=native -pipe -O2"
CXXFLAGS="-march=native -pipe -O2"
FEATURES="unmerge-orphans buildpkg unmerge-logs xattr parallel-fetch news strict fixlafiles protect-owned assume-digests usersandbox binpkg-logs usersync binpkg-dostrip binpkg-docompress userfetch distlocks sandbox pid-sandbox sfperms config-protect-if-modified network-sandbox ipc-sandbox preserve-libs unknown-features-warn multilib-strict ebuild-locks userpriv merge-sync qa-unresolved-soname-deps"


Thanks for your help.
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Anon-E-moose
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Joined: 23 May 2008
Posts: 5047
Location: Dallas area

PostPosted: Mon May 04, 2020 12:32 pm    Post subject: Reply with quote

crti.o comes from glibc.

If you have separate /usr/lib and /usr/lib64 then see if it is in the wrong place (look in both for it)
_________________
PRIME x570-pro, 3700x, RX 550 - 5.8 zen kernel
Acer E5-575 (laptop), i3-7100u - i965 - 5.5 zen kernel
---both---
gcc 9.3.0, profile 17.1 (no-pie) amd64-no-multilib, eudev, openrc, openbox

The New OTW
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lasuit
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Joined: 01 Mar 2011
Posts: 24
Location: London, England

PostPosted: Tue May 05, 2020 11:30 am    Post subject: Reply with quote

Finally! It's fixed. Thank you Anon-E-moose! After cleaning the broken symlink and then your suggestion about glibc, I first recompiled glibc, then recompiled gcc and now everything is clean.
Thanks again.
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