[solved] libpthread-stubs : unavailable installed packages

Message

MorgothSauron · Post by **MorgothSauron** » Mon Mar 25, 2024 5:40 pm

Hi,
I'm preparing my system to migrate from profile 17.1 to 23.0.

I decided to run eclean as an extra step and I get the following:

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The following unavailable installed packages were found
            dev-libs/libpthread-stubs-0.4-r1

I get this on my main PC and a VM.

Package dev-libs/libpthread-stubs is not present in any file in /etc/portage and is not part of the world set.

Running revdep-rebuild -i didn't help (nothing to do).

Nothing reported by depclean.

I checked the package page (https://packages.gentoo.org/packages/de ... read-stubs) and only version 0.5 is available, which may explain the eclean message. I also noticed that there is no keyword.

emerge also reports a missing keyword:

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# emerge -pv dev-libs/libpthread-stubs                         

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

Calculating dependencies... done!
Dependency resolution took 1.09 s (backtrack: 0/20).


!!! All ebuilds that could satisfy "dev-libs/libpthread-stubs" have been masked.
!!! One of the following masked packages is required to complete your request:
- dev-libs/libpthread-stubs-0.5::gentoo (masked by: missing keyword)

emerge --info:

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# emerge --info
Portage 3.0.61 (python 3.11.8-final-0, default/linux/amd64/17.1/desktop/plasma, gcc-13, glibc-2.38-r10, 6.8.1-gentoo-x86_64 x86_64)
=================================================================
System uname: Linux-6.8.1-gentoo-x86_64-x86_64-Intel-R-_Core-TM-_i7-9700K_CPU_@_3.60GHz-with-glibc2.38
KiB Mem:    32791196 total,  16733696 free
KiB Swap:    8365052 total,   8365052 free
Timestamp of repository gentoo: Mon, 25 Mar 2024 16:00:00 +0000
Head commit of repository gentoo: 42582d72333ad4e344e636f631a81cdb2445218e
Head commit of repository brave-overlay: 6d6104f378a76db4f214431a3cf9dc2736d8a174

Timestamp of repository steam-overlay: Sun, 24 Mar 2024 09:48:29 +0000
Head commit of repository steam-overlay: 4db06d32f72ef46e43a840483a96d71f239c3bfd

sh bash 5.1_p16-r6
ld GNU ld (Gentoo 2.41 p5) 2.41.0
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:           3.28.3::gentoo
dev-build/libtool:         2.4.7-r3::gentoo
dev-build/make:            4.4.1-r1::gentoo
dev-build/meson:           1.3.2::gentoo
dev-lang/perl:             5.38.2-r2::gentoo
dev-lang/python:           3.11.8_p1::gentoo, 3.12.2_p1::gentoo
dev-lang/rust:             1.75.0-r1::gentoo
sys-apps/baselayout:       2.14-r2::gentoo
sys-apps/openrc:           0.53::gentoo
sys-apps/sandbox:          2.38::gentoo
sys-devel/binutils:        2.41-r5::gentoo
sys-devel/binutils-config: 5.5::gentoo
sys-devel/clang:           17.0.6::gentoo
sys-devel/gcc:             13.2.1_p20240210::gentoo
sys-devel/gcc-config:      2.11::gentoo
sys-devel/lld:             17.0.6::gentoo
sys-devel/llvm:            17.0.6::gentoo
sys-kernel/linux-headers:  6.6::gentoo (virtual/os-headers)
sys-libs/glibc:            2.38-r10::gentoo
Repositories:

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

brave-overlay
    location: /var/db/repos/brave-overlay
    sync-type: git
    sync-uri: https://gitlab.com/jason.oliveira/brave-overlay.git
    masters: gentoo
    volatile: False

steam-overlay
    location: /var/db/repos/steam-overlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/steam-overlay.git
    masters: gentoo
    volatile: False

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/var/portage/cache/distfiles"
EMERGE_DEFAULT_OPTS="--ask --jobs 3 --load-average 6"
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=native -O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live clean-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 strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://gentoo.mirrors.ovh.net/gentoo-distfiles/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LEX="flex"
MAKEOPTS="-j8"
PKGDIR="/var/portage/cache/binpkgs"
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/portage/tmpfs"
SHELL="/bin/zsh"
USE="X a52 aac acl acpi activities alsa amd64 bzip2 cairo cdda cdr cli crypt cryptsetup cups dbus declarative dri dts dvd dvdr elogind encode exif flac fortran gdbm gif gpm gtk gui iconv icu ipv6 jpeg jumbo-build kde kwallet lcms libnotify libtirpc luks1_default mad mng mp3 mp4 mpeg multilib ncurses nls ogg opengl openmp pam pango pcre pdf pipewire plasma png policykit ppds pulseaudio qml qt5 readline savedconfig screencast sdl seccomp semantic-desktop sound spell split-usr ssl startup-notification svg sysv-utils test-rust tiff truetype udev udisks unicode upower usb verify-sig vorbis vulkan wayland widgets wxwidgets x264 xattr xcb xft xml xv xvid zlib" ABI_X86="64" ADA_TARGET="gcc_12" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_anon authn_dbm authn_file authz_dbm authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir env expires ext_filter file_cache filter headers include info log_config logio 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="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 ntrip navcom oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tsip tripmate tnt ublox" INPUT_DEVICES="libinput" KERNEL="linux" L10N="en" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-1" POSTGRES_TARGETS="postgres15" PYTHON_SINGLE_TARGET="python3_11" PYTHON_TARGETS="python3_11" QEMU_SOFTMMU_TARGETS="x86_64 aarch64" QEMU_USER_TARGETS="x86_64" RUBY_TARGETS="ruby31" SANE_BACKENDS="net" VIDEO_CARDS="amdgpu radeonsi" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipp2p iface geoip fuzzy condition tarpit sysrq proto logmark ipmark dhcpmac delude chaos account"
Unset:  ADDR2LINE, AR, 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, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS

My understanding is that dev-libs/libpthread-stubs is installed as a dependecy for x11-libs/libxcb, which is in turn a dependency for firefox.

The only thing that seems to do the trick is to accept all keywords (**) for this package.

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# ACCEPT_KEYWORDS="**" emerge -pv dev-libs/libpthread-stubs

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

Calculating dependencies... done!
Dependency resolution took 4.22 s (backtrack: 0/20).

[ebuild     U  ] dev-libs/libpthread-stubs-0.5::gentoo [0.4-r1::gentoo] ABI_X86="(64) -32 (-x32)" 56 KiB

Total: 1 package (1 upgrade), Size of downloads: 56 KiB

However, I'm not sure if this is the right thing to do because I never had to specify keyword for this package. Of course, I would only add a line for the package to package.accept_keywords to accept all keywords.

Should I simply update portage configuration to accept all keywords for the package and be happy with it ?

Thanks.

Post by Hu » Mon Mar 25, 2024 5:50 pm

No. How did you determine that libxcb needs this? As I read the ebuild, that is only true for Darwin, and you appear to be on Linux. What is the output of emerge --pretend --verbose x11-libs/libxcb ; emerge --pretend --verbose --depclean dev-libs/libpthread-stubs?

MorgothSauron · Post by **MorgothSauron** » Mon Mar 25, 2024 6:08 pm

Hu wrote:No. How did you determine that libxcb needs this? As I read the ebuild, that is only true for Darwin, and you appear to be on Linux. What is the output of emerge --pretend --verbose x11-libs/libxcb ; emerge --pretend --verbose --depclean dev-libs/libpthread-stubs?

emerge --pretend --verbose x11-libs/libxcb:

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# emerge --pretend --verbose x11-libs/libxcb

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

Calculating dependencies... done!
Dependency resolution took 1.77 s (backtrack: 0/20).

[ebuild   R    ] x11-libs/libxcb-1.16-r1:0/1.12::gentoo  USE="xkb -doc (-selinux) -test" ABI_X86="32 (64) (-x32)" 0 KiB

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

#

emerge --pretend --verbose --depclean dev-libs/libpthread-stubs:

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# emerge --pretend --verbose --depclean dev-libs/libpthread-stubs

Calculating dependencies... done!
  dev-libs/libpthread-stubs-0.4-r1 pulled in by:
    www-client/brave-bin-1.64.109 requires dev-libs/libpthread-stubs

>>> No packages selected for removal by depclean
Packages installed:   1439
Packages in world:    152
Packages in system:   49
Required packages:    1439
Number to remove:     0

#

I totally misinterpreted the ouptut of equery and missed the 'Darwin' part

I forgot to provide that information in my post, sorry. It is a dependency for www-client/brave-bin apparently ...

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# equery d libpthread-stubs                                      
 * These packages depend on libpthread-stubs:
www-client/brave-bin-1.64.109 (dev-libs/libpthread-stubs)
x11-libs/libxcb-1.16-r1 (elibc_Darwin ? dev-libs/libpthread-stubs)

The ebuild for brave confirms that dev-libs/libpthread-stubs is a dependency

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...
DESCRIPTION="Brave Web Browser"
HOMEPAGE="https://brave.com"
SRC_URI="https://github.com/brave/brave-browser/releases/download/v${PV}/brave-browser-${PV}-linux-amd64.zip -> ${P}.zip"

LICENSE="MPL-2.0"
SLOT="0"
KEYWORDS="amd64"
IUSE="keyring"

# gconf is deprecated.
# DEPEND="gnome-base/gconf:2"
RDEPEND="
	${DEPEND}
	dev-libs/libpthread-stubs
	x11-libs/libxcb
...

My guess is that dev-libs/libpthread-stubs was installed a while ago with version 0.4 when I installed brave-bin for the first time. It is not complaining because the ebuild doesn't require a specific version.

Edit: There is an issue for this in the brave-bin git repo: https://gitlab.com/jason.oliveira/brave ... /issues/23

Post by Hu » Mon Mar 25, 2024 7:01 pm

That seems right. Additionally, it looks like libpthread-stubs-0.4 was dropped, and there was no need to keyword 0.5-r1 for Linux, because nothing in ::gentoo requires it for Linux. libxcb is the only consumer, and then only on Darwin. It is not uncommon for packages that are only consumed by an out-of-tree package to be broken by in-tree maintenance, as Brave-on-Linux was here.

Since this package appears to be empty on Linux, keywording it is probably safe, if you cannot remove brave or switch to a version of brave with a corrected dependency.

MorgothSauron · Post by **MorgothSauron** » Mon Mar 25, 2024 7:18 pm

For now I updated /etc/portage/package.accept_keywords:

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dev-libs/libpthread-stubs **

emerge only updated that package.

I will keep an eye on the GitLab issue I referenced and see if the issue if fixed or not. I will decide later what I do with Brave.

Thank you.

Erdie · Post by **Erdie** » Thu May 02, 2024 5:18 pm

Great to see this here because I had the same issue and fixed it in the same way. But I did not know if this was a good decision.

What I think is quite wired: If I uninstall libprthread-stubs completly while brave is installed, Brave seems to work flawless anyway. It looks like it does not really need this or maybe I did not find the function where this lib is used and cause a crash when trying to execue it?

MorgothSauron · Post by **MorgothSauron** » Mon May 06, 2024 2:54 pm

Erdie wrote:Great to see this here because I had the same issue and fixed it in the same way. But I did not know if this was a good decision.

What I think is quite wired: If I uninstall libprthread-stubs completly while brave is installed, Brave seems to work flawless anyway. It looks like it does not really need this or maybe I did not find the function where this lib is used and cause a crash when trying to execue it?

I think this is because libprthread-stubs is just a "dummy" package that doesn't install anything.

As other pointed out, that dependency only make sense for macOS/Darwin.

In my case I didn't have any issue installing this package. I'm waiting for the Brave package to be updated to remove this dependency (https://gitlab.com/jason.oliveira/brave ... /issues/23)