Bug 585410 – sci-biology/goby-cpp-2.0.1 : ./.../libgoby.so: undefined reference to `pcrecpp::RE::Init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, pcrecpp::RE_Options const*)'

• Product: Gentoo Linux
• Status: RESOLVED INVALID

[Description Toralf Förster 2016-06-08 18:11:04 UTC]

/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++ -pthread      -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o GobyAlignmentStats GobyAlignmentStats.o libgoby.la     
libtool: link: x86_64-pc-linux-gnu-g++ -pthread -march=native -O2 -pipe -Wl,-O1 -o .libs/GobyAlignmentStats GobyAlignmentStats.o  -Wl,--as-needed ./.libs/libgoby.so /usr/lib64/libprotobuf.so -lz -lpthread -lpcrecpp -pthread
./.libs/libgoby.so: undefined reference to `pcrecpp::RE::Init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, pcrecpp::RE_Options const*)'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:600: GobyAlignmentStats] Error 1
make[3]: Leaving directory '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build/src'


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

  This is an unstable amd64 chroot image (named amd64-gnome-unstable_20160605-225437) at a hardened host acting as a tinderbox.

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

  make.conf: USE="sse2 pax_kernel xtpax -cdinstall -oci8 -bindist cgi compat csc custom-cflags drmkms -extraengine ftp gpg kerberos mikmod mpeg mpeg2 mpi -mysqli nss openexr opengl openmpi pam policykit postproc -pulseaudio qt3support rendering semantic-desktop sockets sse4 sse4_2 ssh-askpass -system-sqlite tls tools uxa vaapi vim wav webkit x265 xcb ziffy"

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

Portage 2.3.0_rc1 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/gnome, gcc-5.3.0, glibc-2.23-r2, 4.5.6-hardened x86_64)
=================================================================
System uname: Linux-4.5.6-hardened-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16157888 total,   6178656 free
KiB Swap:   16777212 total,  16720392 free
Timestamp of repository gentoo: Wed, 08 Jun 2016 16:22:09 +0000
sh bash 4.3_p42-r2
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p42-r2::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.11-r2::gentoo, 3.4.3-r7::gentoo, 3.5.1-r3::gentoo
dev-util/cmake:           3.5.2-r1::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.21::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::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-r2::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            5.3.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2-r2::gentoo
sys-kernel/linux-headers: 4.6::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/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-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 berkdb bluetooth branding bzip2 cairo cdda cdr cgi cli colord compat consolekit cracklib crypt csc cups custom-cflags cxx dbus dri drmkms dts dvd dvdr eds emboss encode evo exif fam firefox flac fortran ftp gdbm gif glamor gnome gnome-keyring gnome-online-accounts gpg gpm gstreamer gtk iconv introspection ipv6 jpeg kerberos lcms ldap libnotify libsecret mad mikmod mmx mmxext mng modules mp3 mp4 mpeg mpeg2 mpi multilib nautilus ncurses nls nptl nss ogg openexr opengl openmp openmpi pam pango pax_kernel pcre pdf png policykit postproc ppds qt3support qt4 readline rendering sdl seccomp semantic-desktop session sockets spell sse sse2 sse4 sse4_2 ssh-askpass ssl startup-notification svg tcpd tiff tls tools tracker truetype udev udisks unicode upower usb uxa vaapi vim vorbis wav webkit wxwidgets x264 x265 xattr xcb xml xtpax xv xvid ziffy 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" 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" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" 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="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 2016-06-08 18:11:07 UTC]

Created attachment 436900 [details]
emerge-history.txt

[Comment 2 Toralf Förster 2016-06-08 18:11:09 UTC]

Created attachment 436902 [details]
environment

[Comment 3 Toralf Förster 2016-06-08 18:11:12 UTC]

Created attachment 436904 [details]
sci-biology:goby-cpp-2.0.1:20160608-180617.log

[Comment 4 Toralf Förster 2016-06-08 18:24:35 UTC]

as discussed in IRC it is a gcc upgrade issue