[SOLVED] emerge problems for setuptools after profile change

[jody]

After updating my profile from

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 [23]  default/linux/amd64/23.0/desktop (stable)

to

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  [46]  default/linux/amd64/23.0/split-usr/desktop (stable) *

i did "emerge --ask --update --newuse --deep @world". After several attempts of this which required a number of "USE changes" in the configutaion files, the emerging finally started with more than 500 package to be updated and/or reemerged (but there was a warning "WARNING: One or more updates/rebuilds have been skipped due to a dependency conflict:").

After a few hours, with about 320 package remaining to be emerged, there was a failure with /var/tmp/portage/dev-python/setuptools-70.0.0, the last lines being:

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  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/usr/lib/python3.11/site-packages/setuptools_rust/__init__.py", line 1, in <module>
    from .build import build_rust
  File "/usr/lib/python3.11/site-packages/setuptools_rust/build.py", line 27, in <module>
    from typing_extensions import Literal
ModuleNotFoundError: No module named 'typing_extensions'
 * ERROR: dev-python/setuptools-70.0.0::gentoo failed (compile phase):
 *   Wheel build failed

The package "typing_extensions" is installed:

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$ eix typing-extension
[I] dev-python/typing-extensions
     Available versions:  4.11.0^t ~4.11.0_p20240512^t ~4.12.0_rc1^t ~4.12.0^t ~4.12.1^t ~4.12.2^t {test PYTHON_TARGETS="pypy3 python3_10 python3_11 python3_12 python3_13"}
     Installed versions:  4.11.0^t(10:49:00 PM 06/20/2024)(-test PYTHON_TARGETS="python3_12 -pypy3 -python3_10 -python3_11")
     Homepage:            https://pypi.org/project/typing-extensions/ https://github.com/python/typing_extensions/
     Description:         Backported and Experimental Type Hints for Python 3.7+

When i do emerge --ask --update --newuse --deep --keep-going @world, i get (after the failure of setuptools):

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...
*** Resuming merge...
Calculating dependencies... done!
Dependency resolution took 11.52 s.


 * Messages for package media-libs/mesa-24.0.9:

 * Ignoring USE=vulkan     since VIDEO_CARDS does not contain d3d12, freedreno, intel, radeonsi, or v3d

 * Messages for package dev-python/setuptools-70.0.0:

 * ERROR: dev-python/setuptools-70.0.0::gentoo failed (compile phase):
 *   Wheel build failed
 * 
 * Call stack:
 *     ebuild.sh, line  136:  Called src_compile
 *   environment, line 4115:  Called distutils-r1_src_compile
 *   environment, line 2059:  Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile'
 *   environment, line  859:  Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 3725:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 3231:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 3229:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 1364:  Called distutils-r1_run_phase 'distutils-r1_python_compile'
 *   environment, line 2041:  Called distutils-r1_python_compile
 *   environment, line 1859:  Called distutils_pep517_install '/var/tmp/portage/dev-python/setuptools-70.0.0/work/setuptools-70.0.0-python3_11/install'
 *   environment, line 2387:  Called die
 * The specific snippet of code:
 *       [[ -n ${wheel} ]] || die "No wheel name returned";
 * 
 * If you need support, post the output of `emerge --info '=dev-python/setuptools-70.0.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=dev-python/setuptools-70.0.0::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/dev-python/setuptools-70.0.0/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-python/setuptools-70.0.0/temp/environment'.
 * Working directory: '/var/tmp/portage/dev-python/setuptools-70.0.0/work/setuptools-70.0.0'
 * S: '/var/tmp/portage/dev-python/setuptools-70.0.0/work/setuptools-70.0.0'
 * One or more packages are either masked or have missing dependencies:
 * 
 *   dev-python/typing-extensions[python_targets_python3_10(-),python_targets_python3_11(-)] pulled in by:
 *     (dev-python/setuptools-scm-8.0.4:0/0::gentoo, installed)
 * 
 *   app-admin/system-config-printer pulled in by:
 *     (gnome-base/gnome-control-center-44.3:2/2::gentoo, installed)
 * 
 * The resume list contains packages that are either masked or have
 * unsatisfied dependencies. Please restart/continue the operation
 * manually, or use --skipfirst to skip the first package in the list and
 * any other packages that may be masked or have missing dependencies.
 * 

The failure with setuptools and the problem with typing_extensions prevents me from emerging the remaining 320 packages. (even the options '..skipfirst' and '--keep-going' don't help).

How can i fix this problem?



Here are the required outputs and logs:

the output of `emerge --info '=dev-python/setuptools-70.0.0::gentoo'

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Portage 3.0.63 (python 3.11.9-final-0, default/linux/amd64/23.0/split-usr/desktop, gcc-12, glibc-2.39-r6, 5.10.52-gentoo-dist x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-5.10.52-gentoo-dist-x86_64-Intel-R-_Core-TM-_i5-9300H_CPU_@_2.40GHz-with-glibc2.39
KiB Mem:     7986532 total,    750600 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Thu, 20 Jun 2024 11:00:00 +0000
Head commit of repository gentoo: 341b9bf36b212a4de56cc82c490e3aa4ddcbd480
sh bash 5.1_p16-r11
ld GNU ld (Gentoo 2.39 p6) 2.39.0
app-misc/pax-utils:        1.3.7::gentoo
app-shells/bash:           5.1_p16-r11::gentoo
dev-build/autoconf:        2.13-r7::gentoo, 2.71-r7::gentoo
dev-build/automake:        1.16.5-r2::gentoo
dev-build/cmake:           3.28.5::gentoo
dev-build/libtool:         2.4.7-r4::gentoo
dev-build/make:            4.4.1-r1::gentoo
dev-build/meson:           1.4.0-r1::gentoo
dev-java/java-config:      2.3.3-r1::gentoo
dev-lang/perl:             5.38.2-r3::gentoo
dev-lang/python:           3.9.18::gentoo, 3.10.14_p1-r1::gentoo, 3.11.9-r1::gentoo, 3.12.3-r1::gentoo
dev-lang/rust:             1.77.1::gentoo
sys-apps/baselayout:       2.15::gentoo
sys-apps/openrc:           0.48::gentoo
sys-apps/sandbox:          2.38::gentoo
sys-devel/binutils:        2.39-r5::gentoo, 2.40-r5::gentoo, 2.41-r5::gentoo, 2.42-r1::gentoo
sys-devel/binutils-config: 5.5::gentoo
sys-devel/gcc:             12.3.1_p20230526::gentoo, 13.2.1_p20240210::gentoo
sys-devel/gcc-config:      2.11::gentoo
sys-devel/llvm:            15.0.7::gentoo, 16.0.6::gentoo, 17.0.6::gentoo
sys-kernel/linux-headers:  6.6-r1::gentoo (virtual/os-headers)
sys-libs/glibc:            2.39-r6::gentoo
Repositories:

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

brother-overlay
    location: /var/lib/layman/brother-overlay
    masters: gentoo
    priority: 50
    volatile: True

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=skylake -O2 -pipe -mavx"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
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/apache2-php8.2/ext-active/ /etc/php/cgi-php8.1/ext-active/ /etc/php/cgi-php8.2/ext-active/ /etc/php/cli-php8.1/ext-active/ /etc/php/cli-php8.2/ext-active/ /etc/php/fpm-php8.1/ext-active/ /etc/php/fpm-php8.2/ext-active/ /etc/php/phpdbg-php8.1/ext-active/ /etc/php/phpdbg-php8.2/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"
CXXFLAGS="-march=skylake -O2 -pipe -mavx"
DISTDIR="/var/cache/distfiles"
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="-O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync merge-wait multilib-strict network-sandbox news parallel-fetch pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="https://mirror.eu.oneandone.net/linux/distributions/gentoo/gentoo/ http://mirror.netcologne.de/gentoo/ rsync://mirror.netcologne.de/gentoo/ https://ftp.halifax.rwth-aachen.de/gentoo/ ftp://ftp.halifax.rwth-aachen.de/gentoo/ rsync://ftp.halifax.rwth-aachen.de/gentoo/ https://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ rsync://ftp-stud.hs-esslingen.de/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs"
LEX="flex"
MAKEOPTS="-j2"
PKGDIR="/var/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/tmp"
PYTHONPATH="/home/jody/progs/multi_spc_QHG3/useful_stuff:/home/jody/progs/multi_spc_QHG3/useful_stuff:"
SHELL="/bin/bash"
USE="X a52 aac acl acpi alsa amd64 apache2 bash-completion bluetooth branding bzip2 cairo cdda cdr cet cgi crypt cups cxx dbus dri dts dvd dvdr elogind emacs encode exif ffmpeg fftw flac gd gdbm gif gimp glut gnome gnuplot gpm gsl gtk gui gzip hdf5 iconv icu imagemagick ipv6 java jpeg jpeg2k kf6compat lapack latex lcms libnotify libtirpc mad mng mp3 mp4 mpeg mplayer multilib ncurses netcdf networkmanager nls ogg opengl openmp pam pango pcre pdf php png policykit postgres ppds python qt5 readline sdl seccomp session sound spell split-usr sqlite ssl startup-notification subversion svg tcl test-rust threads tiff tk truetype udev udisks unicode upower usb vorbis vulkan wxwidgets x264 xattr xcb xemacs xft xml xv xvid zip 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="mmx mmxext sse sse2" 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" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="libinput synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-2" POSTGRES_TARGETS="postgres15" PYTHON_SINGLE_TARGET="python3_12" PYTHON_TARGETS="python3_12" RUBY_TARGETS="ruby31 ruby32" VIDEO_CARDS="nouveau" 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, EMERGE_DEFAULT_OPTS, 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, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS

The output of emerge -pqv '=dev-python/setuptools-70.0.0::gentoo':

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[ebuild     U ] dev-python/setuptools-70.0.0 [69.5.1-r1] USE="-test" PYTHON_TARGETS="python3_10 python3_11 python3_12* (-pypy3) (-python3_13)" 
[ebuild     U ] dev-python/setuptools-scm-8.1.0 [8.0.4] USE="-test" PYTHON_TARGETS="python3_10 python3_11 python3_12* (-pypy3) (-python3_13)" 

The build log for setuptools is here https://pastebin.com/dgwSyWj6

[fedeliallalinea]

The package "typing_extensions" is installed:

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$ eix typing-extension
[I] dev-python/typing-extensions
     Available versions:  4.11.0^t ~4.11.0_p20240512^t ~4.12.0_rc1^t ~4.12.0^t ~4.12.1^t ~4.12.2^t {test PYTHON_TARGETS="pypy3 python3_10 python3_11 python3_12 python3_13"}
     Installed versions:  4.11.0^t(10:49:00 PM 06/20/2024)(-test PYTHON_TARGETS="python3_12 -pypy3 -python3_10 -python3_11")
     Homepage:            https://pypi.org/project/typing-extensions/ https://github.com/python/typing_extensions/
     Description:         Backported and Experimental Type Hints for Python 3.7+

True but without python_targets_python3_11 support.
It seems your update to python3_12 target is not clean, try to run an emerge -UD @world.

[logrusx]

After updating my profile from

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 [23]  default/linux/amd64/23.0/desktop (stable)

to

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  [46]  default/linux/amd64/23.0/split-usr/desktop (stable) *

Is that supported at all? Did you mean you updated from 17.1? If the upper line is meant to mean 17.1 then it's all right, but it it wasn't, I don't think you can do that, at least not without manual intervention.

Best Regards,
Georgi

[sam_]

After updating my profile from

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 [23]  default/linux/amd64/23.0/desktop (stable)

to

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  [46]  default/linux/amd64/23.0/split-usr/desktop (stable) *

Is that supported at all?

Best Regards,
Georgi

No. split-usr -> merged-usr can be done via a tool, merged-usr -> split-usr requires using a custom stage built with catalyst or similar.

Cleaned up the double post --Banana

[logrusx]

After updating my profile from

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 [23]  default/linux/amd64/23.0/desktop (stable)

to

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  [46]  default/linux/amd64/23.0/split-usr/desktop (stable) *

Is that supported at all?

Best Regards,
Georgi

No.

I thought so, that's why I redacted my post to explicitly ask if OP didn't make a mistake and mistype 17.1 as 23. You were very quick to answer :-)

Best Regards,
Georgi

[Hu]

To elaborate on the basis for logrusx's question (and as a recap for the OP):

• default/linux/amd64/17.1/desktop (which logrusx suspects was used, but OP did not mention) is implicitly split-usr
• default/linux/amd64/23.0/desktop (which OP says was the old profile) is implicitly merged-usr, because it does not say split-usr
• default/linux/amd64/23.0/split-usr/desktop (which OP says is the new profile) is explicitly split-usr.

Thus, if we accept OP's post as written, then OP switched from an (implicitly) merged-usr profile to an (explicitly) split-usr profile. Everyone posting in the thread so far agrees that switching merged-usr -> split-usr won't work. Hence, if logrusx's guess is correct, OP is trying something normal, and we need to understand what went wrong. If logrusx is wrong and OP's post is correct as originally written, then OP is doing something that we know cannot work, and we need to unwind the change.

[eschwartz]

Eek! I thought I fixed this.

There's a complex interplay with plugin extension points. Setuptools-rust used to break due to dev-python/semantic-version for the same reason but I PRed a workaround upstream. I thought that typing-extensions was only needed at mypy time but it appears I overlooked it, and that needs a fix as well.

I'll have to fix that again.

[eschwartz]

See https://bugs.gentoo.org/933553 for the previous breakage.

[eschwartz]

Rechecking, the problem is that setuptools-rust is very outdated on your system. Possibly because, it's only ever a build dep of other packages so it never got updated?

The only solution is to uninstall it or upgrade it first -- currently discussing with people, how we can try to automatically resolve this for people.

The answer might be !! blockers -- that would at least tell you the only viable solution is to depclean setuptools-rust.

[jody]

@logrusx, @georgi: You are right - my previous profile has probably been

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  [5]   default/linux/amd64/17.1/desktop 

I remember that if first set it to

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 [23]  default/linux/amd64/23.0/desktop (stable)

but then i got a complaint that i can not change from "split" to "merged", so i changed it to

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[46]  default/linux/amd64/23.0/split-usr/desktop (stable) *

@fedeliallalinea: the command "emerge -UD @world" didn't succeed - it failed because if un met requirements.

@eschwartz: i unmerged both dev-python/setuptools and dev-python/setuptools-rust, and then emerged both again. This seemed to have worked - the emerging of setuptools caused no error this time. Thanks!

I now continue the emerging of the remaining 320 packages and see whether i run into another problem...

EDIT: the emerging of @world almost ran through - i was left with

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[ebuild     U  ] app-text/evince-45.0 [44.3]
[ebuild  N     ] net-libs/webkit-gtk-2.44.1-r410  USE="X gstreamer introspection jumbo-build lcms pdf (seccomp) spell (-aqua) -avif -examples -gamepad -jpegxl -keyring -systemd -wayland" 
[ebuild     U  ] gnome-base/gnome-settings-daemon-45.1 [44.1]
[ebuild     U  ] gnome-base/gnome-control-center-45.3 [44.3]

All of these failrd to compile, but the cause is probably something else.
As far as i am concerned, the issue (setuptools) is solved. Thanks again.