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Bug 604764 - sci-libs/mpir-2.6.0-r2 : preinv_divrem_1.c:(.text+<snip>): multiple definition of `__gmpn_preinv_divrem_1'
Summary: sci-libs/mpir-2.6.0-r2 : preinv_divrem_1.c:(.text+<snip>): multiple definitio...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2017-01-05 16:01 UTC by Toralf Förster
Modified: 2017-01-15 22:53 UTC (History)
3 users (show)

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


Attachments
config.log (config.log,185.96 KB, text/plain)
2017-01-05 16:01 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,307.60 KB, text/plain)
2017-01-05 16:01 UTC, Toralf Förster
Details
environment (environment,107.41 KB, text/plain)
2017-01-05 16:01 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,22.01 KB, application/x-bzip)
2017-01-05 16:01 UTC, Toralf Förster
Details
sci-libs:mpir-2.6.0-r2:20170105-155024.log (sci-libs:mpir-2.6.0-r2:20170105-155024.log,436.83 KB, text/plain)
2017-01-05 16:01 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2017-01-05 16:01:24 UTC
mpn/.libs/preinv_divrem_1.o: In function `__gmpn_preinv_divrem_1':
preinv_divrem_1.c:(.text+0x0): multiple definition of `__gmpn_preinv_divrem_1'
mpn/.libs/divrem_euclidean_qr_1.o:divrem_euclidean_qr_1.as:(.text+0x0): first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:845: libmpir.la] Error 1

  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named desktop-libressl-unstable_20161230-194738) at a hardened host acting as a tinderbox.

  -----------------------------------------------------------------
  from make.conf:
USE="  -openssl -gnutls libressl pax_kernel xtpax -cdinstall -oci8 -bindist ssp avformat -bugzilla dvb -dvd eglfs -evdev ffmpeg fitz fluidsynth gles libinput logrotate -lvm melt mp3 mysql mysqli plasma -pypy secure-delete traceroute uxa vim x265 xvfb xvmc"

gcc-config -l:
 [1] x86_64-pc-linux-gnu-5.4.0 *
llvm-config --version:
3.9.1
Available Java Virtual Machines:
  [1]   icedtea-bin-7 
  [2]   icedtea-bin-8  system-vm
Available Python interpreters, in order of preference:
  [1]   python3.4
  [2]   python3.5 (fallback)
  [3]   python2.7 (fallback)
  [4]   jython2.7 (fallback)

java-config:
The following VMs are available for generation-2:
1)	IcedTea JDK 7.2.6.8 [icedtea-bin-7]
*)	IcedTea JDK 3.2.0 [icedtea-bin-8]
  -----------------------------------------------------------------



$ cat emerge-info.txt
Portage 2.3.3 (python 3.4.5-final-0, default/linux/amd64/13.0/desktop, gcc-5.4.0, glibc-2.24, 4.8.15-hardened x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.8.15-hardened-x86_64-Intel-R-_Core-TM-_i7-3930K_CPU_@_3.20GHz-with-gentoo-2.3
KiB Mem:    65285560 total,   3413480 free
KiB Swap:   67108860 total,  67086144 free
Timestamp of repository gentoo: Thu, 05 Jan 2017 14:22:52 +0000
sh bash 4.4_p5-r1
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
distcc 3.2rc1 x86_64-pc-linux-gnu [disabled]
app-shells/bash:          4.4_p5-r1::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.1_rc4::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo, 3.5.2::gentoo
dev-util/cmake:           3.7.1::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.23::gentoo
sys-apps/sandbox:         2.10-r3::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.10.3-r2::gentoo, 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo, 2.27::gentoo
sys-devel/gcc:            5.4.0-r2::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.9::gentoo (virtual/os-headers)
sys-libs/glibc:           2.24::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: 1

tinderbox
    location: /tmp/tb/data/portage
    masters: gentoo
    priority: 2

local
    location: /usr/local/portage
    masters: gentoo
    priority: 99

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=native -Wall"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/omega.conf /opt/openfire/resources/security/ /usr/lib64/fax /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf /var/lib/hsqldb /var/rancid/.cloginrc /var/spool/fax/etc"
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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-O2 -pipe -march=native"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--verbose --verbose-conflicts --color=n --nospinner --tree --quiet-build"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox parallel-fetch preserve-libs protect-owned sandbox sfperms strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/packages"
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"
USE="X a52 aac acl acpi alsa amd64 avformat berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvb dvdr eglfs emboss encode exif fam ffmpeg firefox fitz flac fluidsynth fortran gdbm gif glamor gles gpm gtk iconv ipv6 jpeg lcms ldap libinput libnotify libressl logrotate mad melt mmx mmxext mng modules mp3 mp4 mpeg multilib mysql mysqli ncurses nls nptl ogg opengl openmp pam pango pax_kernel pcre pdf plasma png policykit ppds qt3support qt4 readline sdl seccomp secure-delete session spell sse sse2 ssl ssp startup-notification svg tcpd tiff traceroute truetype udev udisks unicode upower usb uxa vim vorbis wxwidgets x264 x265 xattr xcb xml xtpax xv xvfb xvid xvmc zlib" ABI_X86="64" ALSA_CARDS="hda-intel" 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="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" CURL_SSL="libressl" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev synaptics" KERNEL="linux" L10N="brx de-1901 pt-PT zh-TW" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby21" USERLAND="GNU" VIDEO_CARDS="intel i965" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 1 Toralf Förster gentoo-dev 2017-01-05 16:01:27 UTC
Created attachment 458840 [details]
config.log
Comment 2 Toralf Förster gentoo-dev 2017-01-05 16:01:30 UTC
Created attachment 458842 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2017-01-05 16:01:33 UTC
Created attachment 458844 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2017-01-05 16:01:36 UTC
Created attachment 458846 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2017-01-05 16:01:39 UTC
Created attachment 458848 [details]
sci-libs:mpir-2.6.0-r2:20170105-155024.log
Comment 6 François Bissey 2017-01-05 19:45:13 UTC
I couldn't reproduce it with my mostly stable setup. Your log spouts a lot of warnings from `sed` during configure. And quite a few things rely on `sed` during setup of the source files. So I am wondering if this comes from using sed-4.3 (unstable) instead of 4.2.2 (stable). 

Also mpir-2.6.0 is old, we should get 2.7.2 (latest) in the tree. Since this is still more than a year old there is a chance that it will fail too. In which case I should have word upstream.
Comment 7 Justin Lecher (RETIRED) gentoo-dev 2017-01-15 19:29:13 UTC
I can reproduce it on ~arch. Bumped to 2.7.2 which has the same error.
Comment 8 David Seifert gentoo-dev 2017-01-15 19:39:44 UTC
Have you tried randomly jamming -std=gnu89 into CFLAGS? This sounds like a Gnu89 <-> C99 inline/extern interaction.
Comment 9 François Bissey 2017-01-15 20:00:50 UTC
I got it confirmed with 2.7.2 by people on debian sid. Downgrading `sed` solved the problem for them. I have been away, I will get in touch with upstream to see if they are aware of the problem.
Comment 10 François Bissey 2017-01-15 20:05:10 UTC
The guy from debian I talked to actually reported it upstream and there is a fix merged upstream:
https://github.com/wbhart/mpir/pull/184
Comment 11 Justin Lecher (RETIRED) gentoo-dev 2017-01-15 22:53:20 UTC
commit 5f34df490cc12bdb24e89fac3424d4e2ebb5596c
Author: Justin Lecher <jlec@gentoo.org>
Date:   Sun Jan 15 22:52:41 2017 +0000

    sci-libs/mpir: Backport patch for newer sed

    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=604764

    Package-Manager: Portage-2.3.3, Repoman-2.3.1
    Signed-off-by: Justin Lecher <jlec@gentoo.org>

    https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5f34df490cc12bdb24e89fac3424d4e2ebb5596c