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Bug 717786 - Gentoo Prefix bootstrap fails on Stage 3 due to circular dependencies (sys-apps/gawk-5.1.0 pulls virtual/libcrypt-1:0/1::gentoo)
Summary: Gentoo Prefix bootstrap fails on Stage 3 due to circular dependencies (sys-ap...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo/Alt
Classification: Unclassified
Component: Prefix Support (show other bugs)
Hardware: All Linux
: Normal normal
Assignee: Gentoo Prefix
URL:
Whiteboard:
Keywords:
: 717816 (view as bug list)
Depends on:
Blocks:
 
Reported: 2020-04-17 04:00 UTC by Sammy Pfeiffer
Modified: 2020-05-12 10:17 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments

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Description Sammy Pfeiffer 2020-04-17 04:00:08 UTC
Since 16/04/2020 Gentoo Prefix (on amd64 and x86) has stopped bootstrapping on Stage 3, when doing:

USE=-acl -berkdb -fortran -gdbm -git -libcxx -nls -pcre -ssl -python -qmanifest -qtegrity bootstrap clang internal-glib prefix-stack PKG=sys-apps/gawk


By getting:

* Error: circular dependencies:
(virtual/libcrypt-1:0/1::gentoo, ebuild scheduled for merge) depends on
(sys-libs/glibc-2.30-r8:2.2/2.2::gentoo, ebuild scheduled for merge) (runtime)
(dev-lang/python-3.6.10-r1:3.6/3.6m::gentoo, ebuild scheduled for merge) (buildtime)
(virtual/libcrypt-1:0/1::gentoo, ebuild scheduled for merge) (buildtime_slot_op)


Full log of Stage 3: https://dev.azure.com/12719821/e566c963-8f77-4f01-b7bc-ae2d91b1334f/_apis/build/builds/1717/logs/41

Docker image to find yourself in exactly this state:
docker pull awesomebytes/gentoo_prefix_ci_stage3:1717
docker run -it awesomebytes/gentoo_prefix_ci_stage3:1717 /bin/bash
Comment 1 Sammy Pfeiffer 2020-04-21 23:53:39 UTC
The build is still broken at the same point (so unfortunately this is not a temporary issue as has happened a few other times).

I tried to apply the suggested:

2020-04-21T16:25:30.7011411Z The following USE changes are necessary to proceed:
2020-04-21T16:25:30.7011820Z  (see "package.use" in the portage(5) man page for more details)
2020-04-21T16:25:30.7012500Z # required by sys-apps/portage-2.3.99-r1::gentoo[python_targets_python3_6,-build]
2020-04-21T16:25:30.7013190Z # required by app-admin/perl-cleaner-2.28::gentoo
2020-04-21T16:25:30.7013799Z # required by dev-lang/perl-5.30.2::gentoo
2020-04-21T16:25:30.7014406Z # required by perl-core/File-Temp-0.230.900::gentoo
2020-04-21T16:25:30.7015060Z # required by virtual/perl-File-Temp-0.230.900::gentoo
2020-04-21T16:25:30.7015672Z >=dev-lang/python-3.6.10-r1:3.6 ssl

(By adding it to $EPREFIX/tmp/etc/portage/package.use, and I also tried $EPREFIX/etc/portage/package.use just in case)

But as the command itself:

USE=-acl -berkdb -fortran -gdbm -git -libcxx -nls -pcre -ssl -python -qmanifest -qtegrity bootstrap clang internal-glib prefix-stack PKG=sys-apps/gawk

Contains "-ssl" it didn't help.

I lack the knowledge on what is going on at that point of the bootstrap to know what makes sense to do. There is no ssl at that point and it must be for a reason, so just trying to bootstrap with ssl is probably not going to work.

I tried!
Comment 2 Nuno Alexandre 2020-04-29 01:27:16 UTC
For now, comment out virtual/libcrypt from dev-lang/python:3.6 ebuild

emerge dev-lang/python:3.6

put virtual/libcrypt back in dev-lang/python:3.6

emerge dev-lang/python:3.6

It's ugly... but will work ;)
Comment 3 Sammy Pfeiffer 2020-05-03 02:27:52 UTC
@Nuno I've tried your workaround but it doesn't work for me as dev-lang/python-3.6 complains that it needs the SSL USE key. Which is explicitly disabled at that point of the bootstrap. The output I get is:

>>> Creating Manifest for /tmp/gentoo/var/db/repos/gentoo/dev-lang/python
USE=-acl -berkdb -fortran -gdbm -git -libcxx -nls -pcre -ssl -python -qmanifest -qtegrity bootstrap clang internal-glib prefix-stack PKG=dev-lang/python
WARNING: One or more repositories have been ignored due to duplicate
  profiles/repo_name entries:

  /tmp/gentoo/, gentoo, /tmp/gentoo/var/db/repos/gentoo overrides
    /tmp/gentoo/tmp/var/db/repos/gentoo

  All profiles/repo_name entries must be unique in order to avoid having
  duplicates ignored. Set PORTAGE_REPO_DUPLICATE_WARN="0" in
  /etc/portage/make.conf if you would like to disable this warning.



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

Calculating dependencies  . ... done!
[ebuild  N     ] app-arch/bzip2-1.0.8-r1:0/1::gentoo  USE="(split-usr) -static -static-libs" 792 KiB
[ebuild  N     ] sys-devel/gnuconfig-20190912::gentoo  58 KiB
[ebuild  N     ] app-arch/bzip2-1.0.8-r1:0/1::gentoo  USE="(split-usr) -static -static-libs" 0 KiB
[ebuild  N     ] sys-apps/sed-4.8::gentoo  USE="-acl -nls (-selinux) -static" 0 KiB
[ebuild  N     ] app-arch/gzip-1.10::gentoo  USE="-pic -static" 0 KiB
[ebuild  N     ] app-arch/tar-1.32::gentoo  USE="-acl -minimal -nls (-selinux) -static -xattr" 0 KiB
[ebuild  N     ] sys-libs/timezone-data-2020a::gentoo  USE="-leaps-timezone -nls" 640 KiB
[ebuild  N     ] virtual/libiconv-0-r2::gentoo  0 KiB
[ebuild  N     ] dev-lang/python-exec-2.4.6-r1:2::gentoo  PYTHON_TARGETS="(pypy3) (python2_7) (python3_6) (python3_7) (python3_8)" 86 KiB
[ebuild  N     ] app-misc/c_rehash-1.7-r1::gentoo  5 KiB
[ebuild  N     ] dev-libs/libffi-3.3-r1:0/7::gentoo  USE="-debug -pax_kernel -static-libs -test -test-bhaible" 0 KiB
[ebuild  N     ] app-misc/mime-types-9::gentoo  16 KiB
[ebuild  N     ] sys-devel/autoconf-wrapper-13-r1::gentoo  0 KiB
[ebuild  N     ] dev-lang/python-exec-2.4.6-r1:2::gentoo  PYTHON_TARGETS="(pypy3) (python2_7) (python3_6) (python3_7) (python3_8)" 0 KiB
[ebuild  N     ] sys-devel/automake-wrapper-11::gentoo  0 KiB
[ebuild  N     ] app-portage/portage-utils-0.86::gentoo  USE="openmp -libressl -nls -qmanifest -qtegrity -static" 1733 KiB
[ebuild  N     ] app-misc/mime-types-9::gentoo  0 KiB
[ebuild  N     ] virtual/libintl-0-r2::gentoo  0 KiB
[ebuild  N     ] dev-util/pkgconf-1.6.3:0/3::gentoo  USE="pkg-config -test" 0 KiB
[ebuild  N     ] virtual/libintl-0-r2::gentoo  0 KiB
[ebuild  N     ] sys-libs/zlib-1.2.11-r2:0/1::gentoo  USE="(split-usr) -minizip -static-libs" 0 KiB
[ebuild  N     ] virtual/libcrypt-1:0/1::gentoo  USE="static-libs" 0 KiB
[ebuild  N     ] sys-apps/coreutils-8.32-r1::gentoo  USE="(split-usr) -acl -caps -gmp -hostname -kill -multicall -nls (-selinux) -static -test -vanilla -xattr" 0 KiB
[ebuild  N     ] app-arch/xz-utils-5.2.5::gentoo  USE="extra-filters (split-usr) threads -nls -static-libs" 0 KiB
[ebuild  N     ] sys-apps/file-5.38-r1::gentoo  USE="bzip2 zlib -lzma -python -static-libs" PYTHON_TARGETS="python2_7 python3_6 -python3_7 -python3_8" 911 KiB
[ebuild  N     ] virtual/os-headers-0-r2::gentoo  0 KiB
[ebuild  N     ] dev-libs/popt-1.16-r2::gentoo  USE="-nls -static-libs" 687 KiB
[ebuild  N     ] dev-libs/libunistring-0.9.10:0/2::gentoo  USE="-doc -static-libs" 3658 KiB
[ebuild  N     ] dev-libs/libltdl-2.4.6::gentoo  USE="-static-libs" 951 KiB
[ebuild  N     ] virtual/pkgconfig-1::gentoo  0 KiB
[ebuild  N     ] sys-apps/util-linux-2.35.1-r2::gentoo  USE="cramfs logger ncurses readline (split-usr) suid unicode -audit -build -caps -cryptsetup -fdformat -hardlink -kill -nls (-pam) -python (-selinux) -slang -static-libs -su (-systemd) -test -tty-helpers -udev" PYTHON_TARGETS="python3_6 -python3_7 -python3_8" 5018 KiB
[ebuild  N     ] net-misc/rsync-3.1.3::gentoo  USE="iconv ipv6 -acl -examples -static -stunnel -xattr" 885 KiB
[ebuild  N     ] sys-apps/file-5.38-r1::gentoo  USE="bzip2 zlib -lzma -python -static-libs" PYTHON_TARGETS="python2_7 python3_6 -python3_7 -python3_8" 0 KiB
[ebuild  N     ] app-admin/eselect-1.4.16::gentoo  USE="-doc -emacs -vim-syntax" 175 KiB
[ebuild  N     ] app-admin/eselect-1.4.16::gentoo  USE="-doc -emacs -vim-syntax" 0 KiB
[ebuild  N     ] app-eselect/eselect-python-20190417::gentoo  46 KiB
[ebuild  N     ] app-eselect/eselect-python-20190417::gentoo  0 KiB
[ebuild  N     ] dev-lang/perl-5.30.2:0/5.30::gentoo  USE="-berkdb -debug -doc -gdbm -ithreads" 12207 KiB
[ebuild  N     ] virtual/perl-Test-Harness-3.420.0-r2::gentoo  0 KiB
[ebuild  N     ] virtual/perl-Data-Dumper-2.174.0::gentoo  0 KiB
[ebuild  N     ] perl-core/File-Temp-0.230.900::gentoo  74 KiB
[ebuild  N     ] virtual/perl-File-Temp-0.230.900::gentoo  0 KiB
[ebuild  N     ] sys-kernel/linux-headers-5.6::gentoo  USE="-headers-only" 0 KiB
[ebuild  N     ] virtual/os-headers-0-r2::gentoo  0 KiB
[ebuild  N     ] sys-devel/autoconf-2.69-r5:2.69::gentoo  USE="-emacs" 1438 KiB
[ebuild  N     ] sys-apps/help2man-1.47.15::gentoo  USE="-nls" 199 KiB
[ebuild  N     ] net-dns/libidn2-2.3.0:0/2::gentoo  USE="-static-libs" 2115 KiB
[ebuild  N     ] sys-devel/automake-1.16.2:1.16::gentoo  USE="-test" 1510 KiB
[ebuild  N     ] sys-devel/libtool-2.4.6-r6:2::gentoo  USE="-vanilla" 0 KiB
[ebuild  N     ] dev-libs/expat-2.2.9::gentoo  USE="(split-usr) unicode -examples -static-libs" 413 KiB
[ebuild  N     ] dev-libs/expat-2.2.9::gentoo  USE="(split-usr) unicode -examples -static-libs" 0 KiB
[ebuild  N     ] sys-libs/libseccomp-2.4.3::gentoo  USE="-static-libs" 585 KiB
[ebuild  N     ] app-misc/pax-utils-1.2.6::gentoo  USE="seccomp -caps -debug -python" PYTHON_SINGLE_TARGET="python3_6 -python3_7 -python3_8" 665 KiB
[ebuild  N     ] sys-apps/sandbox-2.18::gentoo  418 KiB
[ebuild  N     ] dev-lang/python-3.9.0_alpha6:3.9::gentoo  USE="ipv6 ncurses readline xml -bluetooth -build -examples -gdbm -hardened -libressl -sqlite -ssl -test -tk -wininst" 17785 KiB
[ebuild  N     ] sys-apps/debianutils-4.9.1::gentoo  USE="installkernel -static" 154 KiB
[ebuild  N     ] sys-kernel/installkernel-gentoo-2::gentoo  3 KiB
[ebuild  N     ] dev-libs/openssl-1.1.1g:0/1.1::gentoo  USE="asm zlib -bindist -rfc3779 -sctp -sslv3 -static-libs -test -tls-heartbeat -vanilla" CPU_FLAGS_X86="(sse2)" 9572 KiB
[ebuild  N     ] dev-lang/python-3.6.10-r2:3.6/3.6m::gentoo  USE="ipv6 ncurses readline ssl (threads) xml -bluetooth -build -examples -gdbm -hardened -libressl -sqlite -test -tk -wininst" 16 KiB
[ebuild  N     ] app-misc/ca-certificates-20190110.3.43::gentoo  USE="-cacert" 23154 KiB
[ebuild  N     ] sys-libs/glibc-2.31-r2:2.2::gentoo  USE="(crypt) multiarch ssp (static-libs) -audit -caps (-cet) -compile-locales -custom-cflags -doc -gd -headers-only (-multilib) -nscd -profile (-selinux) -static-pie -suid -systemtap -test (-vanilla)" 0 KiB
[ebuild  N     ] virtual/libcrypt-1:0/1::gentoo  USE="static-libs" 0 KiB
[ebuild  N     ] sys-apps/util-linux-2.35.1-r2::gentoo  USE="cramfs logger ncurses readline (split-usr) suid unicode -audit -build -caps -cryptsetup -fdformat -hardlink -kill -nls (-pam) -python (-selinux) -slang -static-libs -su (-systemd) -test -tty-helpers -udev" PYTHON_TARGETS="python3_6 -python3_7 -python3_8" 0 KiB
[ebuild  N     ] sys-apps/portage-2.3.99-r2::gentoo  USE="(ipc) -apidoc -build -doc -gentoo-dev (-native-extensions) -rsync-verify (-selinux) -xattr" PYTHON_TARGETS="python3_6 -pypy3 -python3_7 -python3_8" 1028 KiB
[ebuild  N     ] app-admin/perl-cleaner-2.28::gentoo  8 KiB

Total: 65 packages (65 new), Size of downloads: 86987 KiB

The following USE changes are necessary to proceed:
 (see "package.use" in the portage(5) man page for more details)
# required by sys-apps/portage-2.3.99-r2::gentoo[python_targets_python3_6,-build]
# required by app-admin/perl-cleaner-2.28::gentoo
# required by dev-lang/perl-5.30.2::gentoo
# required by perl-core/File-Temp-0.230.900::gentoo
# required by virtual/perl-File-Temp-0.230.900::gentoo
>=dev-lang/python-3.6.10-r2:3.6 ssl



Thanks for the reply though. I hope someone with a better understanding than me has some time to look into this soon :)
Comment 4 Benda Xu gentoo-dev 2020-05-05 11:42:08 UTC
*** Bug 717816 has been marked as a duplicate of this bug. ***
Comment 5 Larry the Git Cow gentoo-dev 2020-05-11 06:59:27 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/proj/prefix.git/commit/?id=d63f1a5f76e1fdbba9e8a3a572575492e239954e

commit d63f1a5f76e1fdbba9e8a3a572575492e239954e
Author:     Benda Xu <heroxbd@gentoo.org>
AuthorDate: 2020-05-11 06:49:17 +0000
Commit:     Benda Xu <heroxbd@gentoo.org>
CommitDate: 2020-05-11 06:58:47 +0000

    bootstrap-prefix.sh: do not use stacked-prefix in stage3.
    
    stage2 is not a complete Prefix. Furthermore, in standalone bootstrap,
    Stage 2 and 3 use different glibc and cannot be stacked.
    
    Closes: https://bugs.gentoo.org/717786
    Bug: https://bugs.gentoo.org/676096
    Signed-off-by: Benda Xu <heroxbd@gentoo.org>

 scripts/bootstrap-prefix.sh | 40 ++++++++++++++++++++--------------------
 1 file changed, 20 insertions(+), 20 deletions(-)

https://gitweb.gentoo.org/repo/proj/prefix.git/commit/?id=b8998ebd8595fcae2a13ea8050bdb758726e1275

commit b8998ebd8595fcae2a13ea8050bdb758726e1275
Author:     Benda Xu <heroxbd@gentoo.org>
AuthorDate: 2020-05-09 07:53:37 +0000
Commit:     Benda Xu <heroxbd@gentoo.org>
CommitDate: 2020-05-11 06:58:19 +0000

    bootstrap-prefix.sh: gawk depends on texinfo.
    
    gawk has to be merged with --nodeps.
    
    Closes: https://bugs.gentoo.org/717786
    Signed-off-by: Benda Xu <heroxbd@gentoo.org>

 scripts/bootstrap-prefix.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)
Comment 6 Sammy Pfeiffer 2020-05-11 13:52:45 UTC
I can confirm that the CI works now again :) Thanks for the great work Benda!
Comment 7 Benda Xu gentoo-dev 2020-05-12 10:17:29 UTC
(In reply to Sammy Pfeiffer from comment #6)
> I can confirm that the CI works now again :) Thanks for the great work Benda!

That's great!