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Bug 722784

Summary: Gentoo Prefix boostrap stuck on Stage 3 Unpacking coreutils-8.32.tar.xz on x86
Product: Gentoo/Alt Reporter: Sammy Pfeiffer <sammypfeiffer>
Component: Prefix SupportAssignee: Gentoo Prefix <prefix>
Status: RESOLVED OBSOLETE    
Severity: normal    
Priority: Normal    
Version: unspecified   
Hardware: x86   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---

Description Sammy Pfeiffer 2020-05-13 02:31:10 UTC 
Stage 3 log available here (too big for the bug tracker): https://dev.azure.com/12719821/e566c963-8f77-4f01-b7bc-ae2d91b1334f/_apis/build/builds/1898/logs/41


There is no error though, it's just stuck forever here:

2020-05-12T10:34:27.8248599Z USE=-acl -berkdb -fortran -gdbm -git -libcxx -nls -pcre -ssl -python -qmanifest -qtegrity bootstrap clang internal-glib PKG=sys-apps/coreutils
2020-05-12T10:34:28.4359284Z WARNING: One or more repositories have been ignored due to duplicate
2020-05-12T10:34:28.4360340Z   profiles/repo_name entries:
2020-05-12T10:34:28.4360697Z 
2020-05-12T10:34:28.4361129Z   /tmp/gentoo/, gentoo, /tmp/gentoo/var/db/repos/gentoo overrides
2020-05-12T10:34:28.4361631Z     /tmp/gentoo/tmp/var/db/repos/gentoo
2020-05-12T10:34:28.4361961Z 
2020-05-12T10:34:28.4362395Z   All profiles/repo_name entries must be unique in order to avoid having
2020-05-12T10:34:28.4362943Z   duplicates ignored. Set PORTAGE_REPO_DUPLICATE_WARN="0" in
2020-05-12T10:34:28.4363495Z   /etc/portage/make.conf if you would like to disable this warning.
2020-05-12T10:34:28.4364117Z 
2020-05-12T10:34:28.4364382Z 
2020-05-12T10:34:28.4589746Z 
2020-05-12T10:34:28.4590451Z These are the packages that would be merged, in order:
2020-05-12T10:34:28.4590733Z 
2020-05-12T10:34:28.6387345Z Calculating dependencies  ... done!
2020-05-12T10:34:28.6457059Z [ebuild  N     ] app-arch/xz-utils-5.2.5::gentoo  USE="extra-filters (split-usr) threads -nls -static-libs" 0 KiB
2020-05-12T10:34:28.6458237Z [ebuild  N     ] sys-apps/coreutils-8.32-r1::gentoo  USE="(split-usr) -acl -caps -gmp -hostname -kill -multicall -nls (-selinux) -static -test -vanilla -xattr" 5424 KiB
2020-05-12T10:34:28.6462980Z 
2020-05-12T10:34:28.6463501Z Total: 2 packages (2 new), Size of downloads: 5424 KiB
2020-05-12T10:34:28.6701818Z 
2020-05-12T10:34:28.6702585Z >>> Verifying ebuild manifests
2020-05-12T10:34:28.6707231Z 
2020-05-12T10:34:28.6917191Z 
2020-05-12T10:34:28.6918692Z >>> Emerging (1 of 2) app-arch/xz-utils-5.2.5::gentoo


-------------------------------------------------------
... (app-arch/xz-utils-5.2.5::gentoo emerges correctly)
-------------------------------------------------------


2020-05-12T10:34:47.8294811Z >>> Emerging (2 of 2) sys-apps/coreutils-8.32-r1::gentoo
2020-05-12T10:34:47.8401184Z  * Fetching files in the background.
2020-05-12T10:34:47.8401761Z  * To view fetch progress, run in another terminal:
2020-05-12T10:34:47.8402550Z  * tail -f /tmp/gentoo/var/log/emerge-fetch.log
2020-05-12T10:34:51.3774439Z  * coreutils-8.32.tar.xz BLAKE2B SHA512 size ;-) ...                     [ ok ]
2020-05-12T10:34:51.3776027Z  * coreutils-8.30-patches-01.tar.xz BLAKE2B SHA512 size ;-) ...          [ ok ]
2020-05-12T10:34:51.9540830Z >>> Unpacking source...
2020-05-12T10:34:51.9555989Z >>> Unpacking coreutils-8.32.tar.xz to /tmp/gentoo/var/tmp/portage/sys-apps/coreutils-8.32-r1/work


I observe the same behavior in the 32bit (on centos6,7,8, ubuntu16, opensuse15...) builds from haubi. amd64 works fine.

Given we run the CI in the same platform, it may have something to do with the Azure Pipelines provided machines. I'm currently trying to run a bootstrap in local machine to discard that (but I'm having some issues with the gentoo distfiles being updated as I write this).
Comment 1 Sammy Pfeiffer 2020-05-15 03:33:23 UTC 
The bootstrap in my local machine reports the same behaviour.

Specifically I see the process being stuck doing something forever (using 12% CPU) with the command:

xz -d -c -- /tmp/gentoo/var/cache/distfiles/coreutils-8.32.tar.xz


xz in the bootstrapped environment is version:
app-arch/xz-utils-5.2.5

I tried to use the same command with the same file, obtained with:

wget http://distfiles.gentoo.org/distfiles/coreutils-8.32.tar.xz


And in my Ubuntu 16.04 system reporting the same xz version:
xz (XZ Utils) 5.1.0alpha
liblzma 5.1.0alpha

And in this environment the command finishes.
Comment 2 Fabian Groffen gentoo-dev 2020-06-21 10:26:59 UTC 
ok, so xz is b0rkend or something on 32-bits
Comment 3 Fabian Groffen gentoo-dev 2020-06-21 10:29:22 UTC 
does xz-utils-5.2.4-r3 work?
Comment 4 Benda Xu gentoo-dev 2020-06-28 12:18:19 UTC 
Is this probably an xz bug?
Comment 5 Fabian Groffen gentoo-dev 2020-06-30 06:25:53 UTC 
I think we should mask this version of xz on x86-linux profile
Comment 6 Sammy Pfeiffer 2020-07-13 14:15:51 UTC 
This is getting weird...

I just tried to use:

app-arch/xz-utils-5.2.4-r3
app-arch/xz-utils-5.2.4-r2

And both get stuck just as app-arch/xz-utils-5.2.5

I did so by adding a $EPREFIX/etc/portage/package.mask with those versions before running Stage 3.

But then I thought of... just adding a
$EPREFIX/etc/portage/profile/package.provided
with contents:
app-arch/xz-utils

before emerging sys-apps/coreutils

I also executed xz --version... which gave me version 5.2.5, fun.

My modifications were, on bootstrap-prefix.sh I added:

        emerge -C app-arch/xz-utils
        echo "Trying to extract with xz"
        xz --version
        xz -d -c --  /tmp/gentoo/var/cache/distfiles/coreutils-8.32.tar.xz > /home/user/test.txt
        echo "done"

Just before the lines (in bootstrap_stage3):
# Build portage and dependencies.
        pkgs=(
                sys-apps/coreutils
                sys-apps/findutils

And two surprising things happened:
On one hand, 'xz -d -c --  /tmp/gentoo/var/cache/distfiles/coreutils-8.32.tar.xz > /home/user/test.txt' succeeded.
And on the other hand, that actually emerged coreutils! Or almost? I got the following weird output that may be a hint for someone more expert than me:

>>> /tmp/gentoo/usr/share/doc/coreutils-8.32-r1/
>>> /tmp/gentoo/usr/share/doc/coreutils-8.32-r1/AUTHORS.bz2
>>> /tmp/gentoo/usr/share/doc/coreutils-8.32-r1/THANKS.bz2
>>> /tmp/gentoo/usr/share/doc/coreutils-8.32-r1/TODO.bz2
>>> /tmp/gentoo/usr/share/doc/coreutils-8.32-r1/README.bz2
>>> /tmp/gentoo/usr/share/doc/coreutils-8.32-r1/ChangeLog.bz2
>>> /tmp/gentoo/usr/share/doc/coreutils-8.32-r1/NEWS.bz2
--- /tmp/gentoo/usr/share/info/
>>> /tmp/gentoo/usr/share/info/coreutils.info.bz2
--- /tmp/gentoo/etc/
>>> /tmp/gentoo/etc/DIR_COLORS
 * Make sure you run 'hash -r' in your active shells.
 * You should also re-source your shell settings for LS_COLORS
 *   changes, such as: source /etc/profile
>>> sys-apps/coreutils-8.32-r1 merged.
>>> Regenerating /etc/ld.so.cache...
Warning: File compression unsupported zstd. Missing package: app-arch/zstd
rm: cannot remove '/tmp/gentoo/var/tmp/portage/sys-apps/coreutils-8.32-r1/work/coreutils-8.32/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/confdir3/c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File name too long


And the following package to emerge fails:

>>> Unpacking source...
>>> Unpacking findutils-4.7.0.tar.xz to /tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/work
>>> Source unpacked in /tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/work
>>> Preparing source in /tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/work/findutils-4.7.0 ...
>>> Source prepared.
>>> Configuring source in /tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/work/findutils-4.7.0 ...
cp: preserving times for './configure._portage_tmp_.2546': Operation not permitted
 * ERROR: sys-apps/findutils-4.7.0::gentoo failed (configure phase):
 *   (no error message)
 * 
 * Call stack:
 *          ebuild.sh, line  125:  Called src_configure
 *        environment, line 2445:  Called econf '--with-packager=Gentoo' '--with-packager-version=4.7.0' '--with-packager-bug-reports=https://bugs.gentoo.org/' '--program-prefix=' '--disable-nls' '--without-selinux' '--libexecdir=$(libdir)/find'
 *   phase-helpers.sh, line  583:  Called die
 * The specific snippet of code:
 *   			cp -p "${ECONF_SOURCE}/configure" "${ECONF_SOURCE}/configure._portage_tmp_.${pid}" || die
 * 
 * If you need support, post the output of `emerge --info '=sys-apps/findutils-4.7.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sys-apps/findutils-4.7.0::gentoo'`.
 * The complete build log is located at '/tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/temp/build.log'.
 * The ebuild environment file is located at '/tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/temp/environment'.
 * Working directory: '/tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/work/findutils-4.7.0'
 * S: '/tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/work/findutils-4.7.0'

>>> Failed to emerge sys-apps/findutils-4.7.0, Log file:

>>>  '/tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/temp/build.log'
 * Messages for package sys-apps/findutils-4.7.0:
 * ERROR: sys-apps/findutils-4.7.0::gentoo failed (configure phase):
 *   (no error message)
 * 
 * Call stack:
 *          ebuild.sh, line  125:  Called src_configure
 *        environment, line 2445:  Called econf '--with-packager=Gentoo' '--with-packager-version=4.7.0' '--with-packager-bug-reports=https://bugs.gentoo.org/' '--program-prefix=' '--disable-nls' '--without-selinux' '--libexecdir=$(libdir)/find'
 *   phase-helpers.sh, line  583:  Called die
 * The specific snippet of code:
 *   			cp -p "${ECONF_SOURCE}/configure" "${ECONF_SOURCE}/configure._portage_tmp_.${pid}" || die
 * 
 * If you need support, post the output of `emerge --info '=sys-apps/findutils-4.7.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sys-apps/findutils-4.7.0::gentoo'`.
 * The complete build log is located at '/tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/temp/build.log'.
 * The ebuild environment file is located at '/tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/temp/environment'.
 * Working directory: '/tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/work/findutils-4.7.0'
 * S: '/tmp/gentoo/var/tmp/portage/sys-apps/findutils-4.7.0/work/findutils-4.7.0'


I'm lost. I have no idea what is going on.
Comment 7 Sammy Pfeiffer 2020-07-19 06:35:03 UTC 
For some reason the builds (Gentoo Prefix over x86) are going through again.

No update on app-arch/xz-utils (still 5.2.5) and no update on sys-apps/coreutils (still 8.32-r1)... but it builds.

I'm confused, but I'm closing as Obsolete. Thanks to everyone that looked into it.