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Bug 595984

Summary: sci-biology/plink-1.90_pre140514 : plink_cluster.c:(.text+<snip>): undefined reference to `dsyevr_'
Product: Gentoo Linux Reporter: Toralf Förster <toralf>
Component: Current packagesAssignee: Gentoo Science Biology related packages <sci-biology>
Status: CONFIRMED ---    
Severity: normal    
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---
Attachments: emerge-history.txt
environment
sci-biology:plink-1.90_pre140514:20161002-193917.log

Description Toralf Förster gentoo-dev 2016-10-02 21:08:06 UTC
   ^~~~~~~~~~~
/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/cc35VU39.o: In function `mds_plot(char*, char*, unsigned long*, unsigned long, unsigned int*, char*, unsigned int, unsigned int, unsigned long, unsigned int, unsigned int, unsigned int*, unsigned int*, unsigned int, unsigned int, unsigned int, double*)':
plink_cluster.c:(.text+0x65b0): undefined reference to `dsyevr_'


$ cat emerge-info.txt
  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named amd64-13.0-no-multilib-unstable_20160928-214001) at a hardened host acting as a tinderbox.

  -----------------------------------------------------------------
  USE flags ...

  ... in make.conf:
USE="  pax_kernel xtpax -cdinstall -oci8 -bindist ssp alisp alsa apache2 bzip2 cgi -corefonts -csc -drmkms ecc exif fitz fpm graphtft gtk gtk2 gtkstyle imap introspection jadetex ldap lzma mad mikmod minimal mpg123 mta multitarget nls ogg openexr pam pdo printsupport pwquality rendering scrypt semantic-desktop smime ssh ssl ssp system-harfbuzz system-jpeg system-libevent -system-llvm tcl tls v4l2 video vlc xml xslt -xvfb xvmc zenmap -zip"

  ... in /etc/portage/package.use/*:
  mail-mta/ssmtp      ssl mta
  net-misc/wget       ssl
  app-crypt/pinentry  -qt4
  app-editors/emacs   -dbus -svg -ssl -gtk -gtk3
  app-text/xmlto      -latex
  dev-libs/boehm-gc   threads
  dev-libs/libpcre    pcre16
  dev-lang/python     threads
  dev-qt/qtgui        egl eglfs
  net-nds/openldap    -sasl
  dev-util/cmake      -qt4 -qt5
  dev-vcs/git         -perl
  media-libs/mesa     -vaapi
  sys-apps/kmod       tools
  net-misc/iputils -caps -filecaps

  entries in /etc/portage/package.unmask/*:
  ~dev-libs/boost-1.62.0
  ~dev-util/boost-build-1.62.0
  ~sys-apps/sandbox-2.11
  media-video/ffmpeg
  sys-devel/gcc:6.2.0
  -----------------------------------------------------------------

gcc-config -l:
 [1] x86_64-pc-linux-gnu-4.9.3
 [2] x86_64-pc-linux-gnu-6.2.0 *
llvm-config --version:
3.8.1

Available Python interpreters, in order of preference:
  [1]   python3.4
  [2]   python2.7 (fallback)
  [3]   pypy (fallback)

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

Portage 2.3.1 (python 3.4.5-final-0, default/linux/amd64/13.0/no-multilib, gcc-6.2.0, glibc-2.23-r2, 4.7.6-hardened x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.7.6-hardened-x86_64-Intel-R-_Core-TM-_i7-3930K_CPU_@_3.20GHz-with-gentoo-2.3
KiB Mem:    65285480 total,   1156192 free
KiB Swap:   67108860 total,  67107272 free
Timestamp of repository gentoo: Sun, 02 Oct 2016 18:30:16 +0000
sh bash 4.4
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
ccache version 3.2.7 [disabled]
app-shells/bash:          4.4::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo
dev-util/ccache:          3.2.7::gentoo
dev-util/cmake:           3.6.2::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.22.1::gentoo
sys-apps/sandbox:         2.11-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       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, 2.26.1::gentoo
sys-devel/gcc:            4.9.3::gentoo, 6.2.0-r1::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: 4.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.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/omega.conf /etc/stunnel/stunnel.conf /usr/share/config"
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="-march=native -O2 -pipe"
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="acl alisp alsa amd64 apache2 berkdb bzip2 cgi cli cracklib crypt cxx dri ecc exif fitz fortran fpm gdbm graphtft gtk gtk2 gtkstyle iconv imap introspection ipv6 jadetex ldap lzma mad mikmod minimal mmx mmxext modules mpg123 mta multitarget ncurses nls nptl ogg openexr openmp pam pax_kernel pcre pdo printsupport pwquality readline rendering scrypt seccomp semantic-desktop session smime sse sse2 ssh ssl ssp system-harfbuzz system-jpeg system-libevent tcl tcpd tls unicode v4l2 video vlc xattr xml xslt xtpax xvmc zenmap 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" L10N="as en-GB es-CL et kk pt" 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="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa 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 2016-10-02 21:08:08 UTC
Created attachment 448892 [details]
emerge-history.txt
Comment 2 Toralf Förster gentoo-dev 2016-10-02 21:08:11 UTC
Created attachment 448894 [details]
environment
Comment 3 Toralf Förster gentoo-dev 2016-10-02 21:08:14 UTC
Created attachment 448896 [details]
sci-biology:plink-1.90_pre140514:20161002-193917.log