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Bug 862597

Summary: sci-libs/superlu-4.3-r2: Filesize does not match recorded size
Product: Gentoo Linux Reporter: Frank Daniel <fdan52>
Component: Current packagesAssignee: Gentoo Science Related Packages <sci>
Status: RESOLVED FIXED    
Severity: major CC: jstein, sam
Priority: High    
Version: unspecified   
Hardware: AMD64   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---
Attachments: emerge --info

Description Frank Daniel 2022-07-31 21:12:19 UTC
Tried to do a sync, but got this instead:

Manifest mismatch for sci-libs/superlu/superlu-4.3-r2.ebuild
  BLAKE2B: expected: b11715c747a425f2a7e04568a994ca9973c228b2f811423d7e502659ce6bcc723899645aaf883ed9ef9b3a696645d0263c92ba7ea988efc3a32d297498ac5f37, have: c2707d14efa118aede75bf39ed360fbaa33d7a2347b24d426725785e79bf84e4b0179f76c3e0c83f513b6cdd6d5684a00c8f0e583f1a6327bdd987fac139c442
  SHA512: expected: 0d667b80c3f443786fe0e8b6fb93c20617b0ac8a2c1393204bd1a0fb1d9a3b6612fc47af48a089e2e99daf728441e3fca07b0cc4404b249d761e188f678f5d76, have: 3396554942474b869c65b474893f0c133bb8bd8044e4f64209566fb6949cc2d9606a9b9574332693a5cd0fed7ae4f52aa38cb4f5f2a7d08784b2b4b90e8971b6


Reproducible: Always

Steps to Reproduce:
1.run "emerge --sync
2.
3.
Actual Results:  
Manifest mismatch for sci-libs/superlu/superlu-4.3-r2.ebuild
  BLAKE2B: expected: b11715c747a425f2a7e04568a994ca9973c228b2f811423d7e502659ce6bcc723899645aaf883ed9ef9b3a696645d0263c92ba7ea988efc3a32d297498ac5f37, have: c2707d14efa118aede75bf39ed360fbaa33d7a2347b24d426725785e79bf84e4b0179f76c3e0c83f513b6cdd6d5684a00c8f0e583f1a6327bdd987fac139c442
  SHA512: expected: 0d667b80c3f443786fe0e8b6fb93c20617b0ac8a2c1393204bd1a0fb1d9a3b6612fc47af48a089e2e99daf728441e3fca07b0cc4404b249d761e188f678f5d76, have: 3396554942474b869c65b474893f0c133bb8bd8044e4f64209566fb6949cc2d9606a9b9574332693a5cd0fed7ae4f52aa38cb4f5f2a7d08784b2b4b90e8971b6


Expected Results:  
completion of sync.

Portage 3.0.30 (python 3.9.13-final-0, default/linux/amd64/17.1/desktop/systemd, gcc-11.3.0, glibc-2.34-r13, 5.15.41-gentoo-x86_64 x86_64)
=================================================================
System uname: Linux-5.15.41-gentoo-x86_64-x86_64-AMD_Ryzen_7_3700X_8-Core_Processor-with-glibc2.34
KiB Mem:    16362352 total,   6428588 free
KiB Swap:    8388604 total,   8388604 free
Timestamp of repository gentoo: Thu, 30 Jun 2022 21:30:01 +0000
Head commit of repository gentoo: de362e13b3af2976bce18b2031cf5b0d5c3c479d
sh bash 5.1_p16
ld GNU ld (Gentoo 2.37_p1 p2) 2.37
ccache version 4.5.1 [enabled]
app-misc/pax-utils:        1.3.3::gentoo
app-shells/bash:           5.1_p16::gentoo
dev-lang/perl:             5.34.1-r3::gentoo
dev-lang/python:           3.8.13_p2::gentoo, 3.9.13::gentoo, 3.10.5::gentoo
dev-lang/rust-bin:         1.60.0::gentoo
dev-util/ccache:           4.5.1::gentoo
dev-util/cmake:            3.22.4::gentoo
dev-util/meson:            0.61.4-r2::gentoo
sys-apps/baselayout:       2.8::gentoo
sys-apps/sandbox:          2.29::gentoo
sys-apps/systemd:          250.7::gentoo
sys-devel/autoconf:        2.13-r2::gentoo, 2.71-r1::gentoo
sys-devel/automake:        1.16.5::gentoo
sys-devel/binutils:        2.37_p1-r2::gentoo
sys-devel/binutils-config: 5.4.1::gentoo
sys-devel/clang:           14.0.4::gentoo
sys-devel/gcc:             11.3.0::gentoo
sys-devel/gcc-config:      2.5-r1::gentoo
sys-devel/libtool:         2.4.7::gentoo
sys-devel/lld:             14.0.4::gentoo
sys-devel/llvm:            14.0.4::gentoo
sys-devel/make:            4.3::gentoo
sys-kernel/linux-headers:  5.15-r3::gentoo (virtual/os-headers)
sys-libs/glibc:            2.34-r13::gentoo
Repositories:

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

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=znver2 -O2"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /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-php7.4/ext-active/ /etc/php/apache2-php8.0/ext-active/ /etc/php/apache2-php8.1/ext-active/ /etc/php/cgi-php7.4/ext-active/ /etc/php/cgi-php8.0/ext-active/ /etc/php/cgi-php8.1/ext-active/ /etc/php/cli-php7.4/ext-active/ /etc/php/cli-php8.0/ext-active/ /etc/php/cli-php8.1/ext-active/ /etc/php/fpm-php7.4/ext-active/ /etc/php/fpm-php8.0/ext-active/ /etc/php/fpm-php8.1/ext-active/ /etc/php/phpdbg-php7.4/ext-active/ /etc/php/phpdbg-php8.0/ext-active/ /etc/php/phpdbg-php8.1/ext-active/ /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=znver2 -O2"
DISTDIR="/var/cache/distfiles"
EMERGE_DEFAULT_OPTS="-j14 -l12.6"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY 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"
FCFLAGS="-march=znver2 -O2"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live ccache config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox 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=znver2 -O2"
GENTOO_MIRRORS="http://www.gtlib.gatech.edu/pub/gentoo https://gentoo.osuosl.org/ https://mirrors.rit.edu/gentoo/ http://mirrors.rit.edu/gentoo/ http://gentoo.mirrors.tds.net/gentoo http://gentoo-mirror.flux.utah.edu/"
LANG="en_US.UTF8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j8 -l8"
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"
SHELL="/bin/bash"
USE="X a52 aac accessiblity acl acpi alsa amd64 appache2 bluetooth branding browser-intergration bzip2 cairo cdda cdr cli contrib crypt cups dbus device-mapper doc dri dts dvd dvdr efiemu elogin encode exif experimental flac fonts fortran gdbm gif gpm gtk gui iconv icu ipv6 jpeg kde lcms libglvnd libnotify libtirpc libzfs mad mng mount mp3 mp4 mpeg mpegmultilib multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds qt5 readline sdl seccomp spell split-usr ssl startup-notification svg systemd sysv-utils themes tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xattr xcb xml xv xvid zlib" ABI_X86="64" ADA_TARGET="gnat_2020" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache 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 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="libinput" KERNEL="linux" L10N="en_US" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-4 php8-0" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_9" RUBY_TARGETS="ruby27" USERLAND="GNU" VIDEO_CARDS="nouveau" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat 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, LEX, 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
Comment 1 Frank Daniel 2022-07-31 21:14:10 UTC
Created attachment 796261 [details]
emerge --info
Comment 2 Jonas Stein gentoo-dev 2022-07-31 22:36:16 UTC
Confirmed for 4.3-r2, superlu-5.3.0 is fine.

GENTOO_MIRRORS="" ebuild superlu-4.3-r2.ebuild fetch
.
.
.

/var/db/distfiles/superlu_4.3.tar.gz.__downl 100%[=============================================================================================>]   2.74M  1.25MB/s    in 2.2s    

2022-08-01 00:34:19 (1.25 MB/s) - ‘/var/db/distfiles/superlu_4.3.tar.gz.__download__’ saved [2875951/2875951]

!!! Fetched file: superlu_4.3.tar.gz VERIFY FAILED!
!!! Reason: Filesize does not match recorded size
!!! Got:      2875951
!!! Expected: 2876631
Refetching... File renamed to '/var/db/distfiles/superlu_4.3.tar.gz._checksum_failure_.tb5ejrb8'

!!! Couldn't download 'superlu_4.3.tar.gz'. Aborting.
Comment 3 Frank Daniel 2022-08-25 00:11:22 UTC
It has been almost a month since I filed this issue.  Has any work been done on it?
Comment 4 Sam James archtester Gentoo Infrastructure gentoo-dev Security 2022-08-25 00:39:53 UTC
(In reply to Frank Daniel from comment #3)
> It has been almost a month since I filed this issue.  Has any work been done
> on it?

Looking at it now, thanks, but in future, if you hit such an issue, you should make sure your GENTOO_MIRRORS is set in make.conf. Having it unset means you're exposed to upstream breaking things like this.
Comment 5 Larry the Git Cow gentoo-dev 2022-08-25 00:53:52 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5611848da693494fe7a710836779c9c25b85c0fa

commit 5611848da693494fe7a710836779c9c25b85c0fa
Author:     Sam James <sam@gentoo.org>
AuthorDate: 2022-08-25 00:51:07 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2022-08-25 00:52:15 +0000

    sci-libs/superlu: fix Manifest (fix 4.3 ebuild distfile)
    
    The 4.3 tarball (which got replaced upstream) was actually, seemingly,
    partly version 4.1 instead?
    
    Mirror the "bad" (nothing malicious, just mislabelled version) copy to my
    devspace at dev.gentoo.org and keep using it in 4.3-r2, and add
    a fixed 4.3-r3 using the fixed 4.3 upstream version.
    
    Closes: https://bugs.gentoo.org/862597
    Signed-off-by: Sam James <sam@gentoo.org>

 sci-libs/superlu/Manifest              |  1 +
 sci-libs/superlu/superlu-4.3-r2.ebuild |  8 +++-
 sci-libs/superlu/superlu-4.3-r3.ebuild | 86 ++++++++++++++++++++++++++++++++++
 3 files changed, 93 insertions(+), 2 deletions(-)