Bug 924613 – sci-libs/pcl-1.12.1-r2 stable rebuild for new dev-libs/boost-1.84.0-r3 stable fails

• Product: Gentoo Linux
• Status: RESOLVED DUPLICATE

[Description CaptainBlood 2024-02-15 00:50:39 UTC]

Created attachment 885002 [details]
ebuild log

emerge --info sci-libs/pcl
Portage 3.0.61 (python 3.11.8-final-0, default/linux/amd64/17.1, gcc-13, glibc-2.38-r10, 6.7.4-gentoo-std x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-6.7.4-gentoo-std-x86_64-Intel-R-_Core-TM-_i3-6100_CPU_@_3.70GHz-with-glibc2.38
KiB Mem:     3933672 total,   1260532 free
KiB Swap:   65535996 total,  65534704 free
Timestamp of repository gentoo: Wed, 14 Feb 2024 23:15:01 +0000
Head commit of repository gentoo: 8ba2bff67eee79c0342063107fc910f7d92a643e
sh bash 5.1_p16-r6
ld GNU ld (Gentoo 2.41 p4) 2.41.0
distcc 3.4 x86_64-pc-linux-gnu [disabled]
app-misc/pax-utils:        1.3.7::gentoo
app-shells/bash:           5.1_p16-r6::gentoo
dev-build/autoconf:        2.13-r8::gentoo, 2.71-r6::gentoo
dev-build/automake:        1.16.5-r2::gentoo
dev-build/cmake:           3.27.9::gentoo
dev-build/libtool:         2.4.7-r1::gentoo
dev-build/make:            4.4.1-r1::gentoo
dev-build/meson:           1.3.1-r1::gentoo
dev-java/java-config:      2.3.3-r1::gentoo
dev-lang/perl:             5.38.2-r1::gentoo
dev-lang/python:           2.7.18_p16-r2::gentoo, 3.10.13_p3::gentoo, 3.11.8_p1::gentoo
dev-lang/rust:             1.76.0::pg_overlay
sys-apps/baselayout:       2.14-r2::gentoo
sys-apps/openrc:           0.53::gentoo
sys-apps/sandbox:          2.38::gentoo
sys-devel/binutils:        2.41-r3::gentoo
sys-devel/binutils-config: 5.5::gentoo
sys-devel/clang:           15.0.7-r3::gentoo, 16.0.6::gentoo, 17.0.6::gentoo
sys-devel/gcc:             10.5.0::gentoo, 11.4.1_p20231214::gentoo, 12.3.1_p20240112::gentoo, 13.2.1_p20240113-r1::gentoo
sys-devel/gcc-config:      2.11::gentoo
sys-devel/lld:             15.0.7::gentoo, 17.0.6::gentoo
sys-devel/llvm:            15.0.7-r3::gentoo, 16.0.6::gentoo, 17.0.6::gentoo
sys-kernel/linux-headers:  6.7::gentoo (virtual/os-headers)
sys-libs/glibc:            2.38-r10::gentoo
Repositories:


gentoo
    location: /var/db/repos/gentoo
    sync-type: rsync
    sync-uri: rsync://rsync.europe.gentoo.org/gentoo-portage
    priority: -1000
    volatile: False
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-metamanifest: yes
    sync-rsync-extra-opts: 
    sync-rsync-verify-max-age: 24

local
    location: /var/db/repos/local
    masters: gentoo
    priority: 10000
    volatile: False

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
AR="gcc-ar"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -mtune=native -O2 -pipe -Wa,-mbranches-within-32B-boundaries "
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.9/conf"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php8.1/ext-active/ /etc/php/cgi-php8.1/ext-active/ /etc/php/cli-php8.1/ext-active/ /etc/php/fpm-php8.1/ext-active/ /etc/php/phpdbg-php8.1/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=core2 -mtune=native -O2 -pipe -Wa,-mbranches-within-32B-boundaries "
DISTDIR="/var/cache/distfiles"
EMERGE_DEFAULT_OPTS="--alert y 			--alphabetical 			--ask-enter-invalid 			--autounmask y  			--autounmask-only n  			--autounmask-unrestricted-atoms y  			--autounmask-write y              --complete-graph y  			--misspell-suggestions n 			--noconfmem 		--nospinner  			--tree 			--with-bdeps y"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR XDG_STATE_HOME"
FCFLAGS="-march=core2 -mtune=native -O2 -pipe -Wa,-mbranches-within-32B-boundaries "
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live compress-build-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms split-elog strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-march=core2 -mtune=native -O2 -pipe -Wa,-mbranches-within-32B-boundaries "
GENTOO_MIRRORS="http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/     http://ftp.halifax.rwth-aachen.de/gentoo/     http://ftp.free.fr/mirrors/ftp.gentoo.org/     http://mirrors.soeasyto.com/distfiles.gentoo.org/     http://gentoo.mirrors.ovh.net/gentoo-distfiles/     http://mirror.eu.oneandone.net/linux/distributions/gentoo/gentoo/     http://mirror.leaseweb.com/gentoo/     http://www.mirrorservice.org/sites/distfiles.gentoo.org/     http://ftp.belnet.be/pub/rsync.gentoo.org/gentoo/     http://mirror.bytemark.co.uk/gentoo/"
LANG="fr_FR.utf8"
LDFLAGS="-Wl,-O1 -Wl,-fuse-ld=bfd "
LEX="flex"
LINGUAS="fr"
MAKEOPTS="-j1 -l1"
NM="gcc-nm"
PKGDIR="/var/cache/binpkgs"
PORTAGE_COMPRESS="lzma"
PORTAGE_COMPRESS_FLAGS="-9"
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"
RANLIB="gcc-ranlib"
SHELL="/bin/bash"
USE="amd64 asm custom-cflags emacs eselect-ldso fortran gentoo-vm gtk-doc minimal ocamlopt split-usr test-rust verify-sig" ABI_X86="64" ALSA_CARDS="hda-intel" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="libinput" KERNEL="linux" L10N="fr" LUA_SINGLE_TARGET="lua5-4" LUA_TARGETS="lua5-4" PHP_TARGETS="php8-1" PYTHON_SINGLE_TARGET="python3_11" PYTHON_TARGETS="python3_11" QEMU_USER_TARGETS="aarch64" RUBY_TARGETS="ruby31" VIDEO_CARDS="intel"
Unset:  ADDR2LINE, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS

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

sci-libs/pcl-1.12.1-r2::gentoo was built with the following:
USE="(-cuda) -doc opengl -openni openni2 -pcap -png -qhull qt5 -test -tutorials usb vtk" ABI_X86="(64)" CPU_FLAGS_X86="sse"
CFLAGS="-march=core2 -mtune=native -O2 -flto -fuse-linker-plugin -fno-fat-lto-objects -pipe -Wa,-mbranches-within-32B-boundaries"
CXXFLAGS="-march=core2 -mtune=native -O2 -flto -fuse-linker-plugin -fno-fat-lto-objects -pipe -Wa,-mbranches-within-32B-boundaries"
FEATURES="merge-sync assume-digests usersync config-protect-if-modified userfetch pid-sandbox binpkg-multi-instance split-elog unknown-features-warn usersandbox binpkg-docompress pkgdir-index-trusted unmerge-logs buildpkg binpkg-logs binpkg-dostrip multilib-strict parallel-fetch ipc-sandbox strict userpriv distlocks sfperms unmerge-orphans compress-build-logs protect-owned qa-unresolved-soname-deps network-sandbox buildpkg-live ebuild-locks fixlafiles sandbox news preserve-libs"

[Comment 1 CaptainBlood 2024-02-17 12:53:05 UTC]

Title edited because unsure if new boost is source of failure along with being source of rebuild:

!!! existing preserved libs:
>>> package: dev-libs/boost-1.84.0-r3
 *  - /usr/lib64/libboost_atomic.so.1.82.0
 *      used by /usr/bin/pcl_add_gaussian_noise (sci-libs/pcl-1.12.1-r2)
 *      used by /usr/bin/pcl_boundary_estimation (sci-libs/pcl-1.12.1-r2)
 *      used by /usr/bin/pcl_cluster_extraction (sci-libs/pcl-1.12.1-r2)
 *      used by 141 other files
 *  - /usr/lib64/libboost_filesystem.so.1.82.0
 *      used by /usr/bin/0ad (games-strategy/0ad-0.0.26_alpha-r1)
 *      used by /usr/bin/pcl_add_gaussian_noise (sci-libs/pcl-1.12.1-r2)
 *      used by /usr/bin/pcl_boundary_estimation (sci-libs/pcl-1.12.1-r2)
 *      used by 142 other files
 *  - /usr/lib64/libboost_iostreams.so.1.82.0
 *      used by /usr/bin/pcl_add_gaussian_noise (sci-libs/pcl-1.12.1-r2)
 *      used by /usr/bin/pcl_boundary_estimation (sci-libs/pcl-1.12.1-r2)
 *      used by /usr/bin/pcl_cluster_extraction (sci-libs/pcl-1.12.1-r2)
 *      used by 87 other files
 *  - /usr/lib64/libboost_system.so.1.82.0
 *      used by /usr/bin/0ad (games-strategy/0ad-0.0.26_alpha-r1)
 *      used by /usr/bin/pcl_outofcore_print (sci-libs/pcl-1.12.1-r2)
 *      used by /usr/bin/pcl_outofcore_process (sci-libs/pcl-1.12.1-r2)
 *      used by 56 other files
Use emerge @preserved-rebuild to rebuild packages using these libraries

[Comment 2 Bill Prendergast 2024-02-17 20:31:12 UTC]

The "pcl-1.13.1-boost-1.84.patch" (included for sci-libs/pcl-1.13.1) will also fix sci-libs/pcl-1.12.1-r2

One can add as a custom patch by dropping the patch into /etc/portage/patches/sci-libs/pcl-1.12.1-r2

[Comment 3 CaptainBlood 2024-02-18 14:10:17 UTC]

Currently testing under root account:

mkdir --parents /etc/portage/patches/sci-libs/pcl-1.12.1-r2
cp /var/db/repos/gentoo/sci-libs/pcl/files/pcl-1.13.1-boost-1.84.patch /etc/portage/patches/sci-libs/pcl-1.12.1-r2
emerge -1 sci-libs/pcl

[Comment 4 Andreas Sturmlechner 2024-02-18 15:02:22 UTC]

*** This bug has been marked as a duplicate of bug 921289 ***