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Bug 570252 - sci-biology/dialign-tx-1.0.2-r1 : diag.c:(.text+0x1940): undefined reference to `real_calc_weight'
Summary: sci-biology/dialign-tx-1.0.2-r1 : diag.c:(.text+0x1940): undefined reference ...
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 Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2015-12-30 14:17 UTC by Toralf Förster
Modified: 2015-12-31 16:33 UTC (History)
1 user (show)

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


Attachments
emerge-history.txt (emerge-history.txt,191.24 KB, text/plain)
2015-12-30 14:17 UTC, Toralf Förster
Details
environment (environment,73.86 KB, text/plain)
2015-12-30 14:17 UTC, Toralf Förster
Details
sci-biology:dialign-tx-1.0.2-r1:20151230-134842.log (sci-biology:dialign-tx-1.0.2-r1:20151230-134842.log,6.36 KB, text/plain)
2015-12-30 14:17 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2015-12-30 14:17:14 UTC
./diag.o: In function `find_all_diags':
diag.c:(.text+0x1940): undefined reference to `real_calc_weight'


$ cat ./info.txt
  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named amd64-13.0-unstable_20151227-130400) at a hardened host acting as a tinderbox.

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

  Portage 2.2.26 (python 2.7.11-final-0, default/linux/amd64/13.0, gcc-5.3.0, glibc-2.22-r1, 4.2.7-hardened x86_64)
=================================================================
System uname: Linux-4.2.7-hardened-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16164724 total,   1618072 free
KiB Swap:   16777212 total,  16680032 free
Timestamp of repository gentoo: Wed, 30 Dec 2015 10:42:42 +0000
sh bash 4.3_p42
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p42::gentoo
dev-lang/perl:            5.22.1::gentoo
dev-lang/python:          2.7.11-r1::gentoo, 3.4.3-r7::gentoo, 3.5.1-r2::gentoo
dev-util/cmake:           3.4.1::gentoo
dev-util/pkgconfig:       0.29::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.19.1::gentoo
sys-apps/sandbox:         2.10-r1::gentoo
sys-devel/autoconf:       2.69-r1::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r1::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::gentoo, 5.3.0::gentoo
sys-devel/gcc-config:     1.8::gentoo
sys-devel/libtool:        2.4.6-r1::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers)
sys-libs/glibc:           2.22-r1::gentoo
Repositories:

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

local
    location: /usr/local/portage
    masters: gentoo
    priority: 2

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /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-php5.5/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.5/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=native -O2 -pipe"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--verbose-conflicts --deep --color=n --nospinner --tree --quiet-build --accept-properties=-interactive --accept-restrict=-fetch"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox news parallel-fetch preserve-libs protect-owned sandbox sfperms strict 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"
PORTAGE_TMPDIR="/var/tmp"
USE="X acl aes-ni amd64 apache2 berkdb bzip2 cgoups clang cli cracklib crypt cxx dri drmkms dvb dvd egl fortran gd gdbm gif git gles2 gnomecanvas gnutls gtk3 gui hdf5 help hpn iconv imap isag javafx jpeg kerberos ldap libvirtd mmx mmxext mng modules mssql multilib multimedia mysql ncurses nls nptl nss openmp openmpi pam pax_kernel pcre pcre16 postgres pulseaudio qml qt5 readline seccomp session sockets source sse sse2 sse4 sse4_2 ssh-askpass ssl svg system-cairo system-jpeg tcpd thinkpad threads tls truetype uml unicode usbredir v4l vaapi video vpx widgets wxwidgets xattr xscreensaver xvmc zip zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" 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" 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_GB" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" 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 2015-12-30 14:17:16 UTC
Created attachment 421220 [details]
emerge-history.txt
Comment 2 Toralf Förster gentoo-dev 2015-12-30 14:17:18 UTC
Created attachment 421224 [details]
environment
Comment 3 Toralf Förster gentoo-dev 2015-12-30 14:17:20 UTC
Created attachment 421226 [details]
sci-biology:dialign-tx-1.0.2-r1:20151230-134842.log
Comment 4 Justin Lecher (RETIRED) gentoo-dev 2015-12-31 16:33:07 UTC
commit 7423912f5bd2b50c626cc0e60f8a4ecc1929baf1
Author: Ted Tanberry <ted.tanberry@gmail.com>
Date:   Thu Dec 31 15:55:26 2015 +0100

    sci-biology/dialign-tx: fixes GCC-5 inline semantics and -Wformat= warnings, #570252

    Package-Manager: portage-2.2.26

    https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7423912f5bd2b50c626cc0e60f8a4ecc1929baf1