Hi, time to time it happens to me that I cannot compile an application, which seems is the gcc-5.x ABI incompatibility issue but cannot get rid of it even after switching back to gcc-4.9.4 and recompiling "everything" (emerge -e @system; emerge -e @world; emerge =sys-devel/gcc-4.9.4; emerge =sys-devel/gcc-5.4.0-r3; emerge glibc; emerge -uN wgs-assembler) The last package still hits the issue: x86_64-pc-linux-gnu-g++ -Wl,-O1 -Wl,--as-needed -o /apps/gentoo/var/tmp/portage/sci-biology/wgs-assembler-7.0-r1/work/wgs-7.0/Linux-amd64/bin/markUniqueUnique /apps/gentoo/var/tmp/portage/sci-biology/wgs-assembler-7.0-r1/work/wgs-7.0/Linux-amd64/obj/markUniqueUnique.o /apps/gentoo/var/tmp/portage/sci-biology/wgs-assembler-7.0-r1/work/wgs-7.0/Linux-amd64/lib/libCA.a -L/apps/gentoo/var/tmp/portage/sci-biology/wgs-assembler-7.0-r1/work/wgs-7.0/Linux-amd64/lib -L/apps/gentoo/var/tmp/portage/sci-biology/wgs-assembler-7.0-r1/work/wgs-7.0/Linux-amd64/lib -L/usr/lib64 -L/usr/X11R6/lib64 -pthread -lm /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc++.so: undefined reference to `memcpy@GLIBC_2.14' /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc++.so: undefined reference to `__cxa_thread_atexit_impl@GLIBC_2.18' /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17' collect2: error: ld returned 1 exit status make[1]: *** [/apps/gentoo/var/tmp/portage/sci-biology/wgs-assembler-7.0-r1/work/wgs-7.0/src/c_make.gen:403: fragmentDepth] Error 1 $ ls -latr /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc* -rw-r--r-- 1 mmokrejs mmokrejs 6997650 Feb 18 12:04 /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc++fs.a lrwxrwxrwx 1 mmokrejs mmokrejs 19 Feb 18 12:04 /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc++.so.6 -> libstdc++.so.6.0.21 lrwxrwxrwx 1 mmokrejs mmokrejs 19 Feb 18 12:04 /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc++.so -> libstdc++.so.6.0.21 -rw-r--r-- 1 mmokrejs mmokrejs 23352620 Feb 18 12:04 /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc++.a -rwxr-xr-x 1 mmokrejs mmokrejs 12202424 Feb 18 12:05 /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc++.so.6.0.21 $ All the libs were rebuild just recently, using my current glibc (on Gentoo::RAP). The host system is RedHat with glibc-2.12 and I have glibc-2.24 in Gentoo::RAP. Where glibc-2.18 come from I have no idea. Umm, well maybe both come from the RedHat: $ ls -latr /usr/lib64/libstdc+* -rwxr-xr-x 1 root root 825480 Jun 28 2010 /usr/lib64/libstdc++.so.5.0.7 lrwxrwxrwx 1 root root 18 Feb 9 2015 /usr/lib64/libstdc++.so.5 -> libstdc++.so.5.0.7 -rwxr-xr-x 1 root root 987096 Jun 1 2015 /usr/lib64/libstdc++.so.6.0.13 lrwxrwxrwx 1 root root 19 Jun 9 2016 /usr/lib64/libstdc++.so.6 -> libstdc++.so.6.0.13 $ Maybe if bootstrap-rap.sh gave me gcc-4.9.4 instead of 5.3.0 I would have less troubles. ;) $ emerge --info Portage 2.3.3 (python 3.4.5-final-0, prefix/linux-standalone/amd64, gcc-5.4.0, glibc-2.24-r1, 2.6.32-573.26.1.100hz.el6.noc0w.x86_64 x86_64) ================================================================= System uname: Linux-2.6.32-573.26.1.100hz.el6.noc0w.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5-4627_v2_@_3.30GHz-with-redhat-6.7-Santiago KiB Mem: 3331383420 total,3307646032 free KiB Swap: 7812028 total, 7762892 free Timestamp of repository gentoo: Fri, 17 Feb 2017 17:00:01 +0000 sh bash 4.4_p12 ld GNU ld (Gentoo 2.27 p1.0) 2.27 app-shells/bash: 4.4_p12::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 dev-util/cmake: 3.7.2::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/sandbox: 2.10-r3::gentoo sys-devel/autoconf: 2.69-r2::gentoo sys-devel/automake: 1.15-r2::gentoom sys-devel/binutils: 2.27::gentoo sys-devel/gcc: 4.9.4::gentoo, 5.4.0-r3::gentoo sys-devel/gcc-config: 1.8_p20160608::rap 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-r1::gentoo Repositories: gentoo location: /apps/gentoo/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 eclass-overrides: rap rap location: /apps/gentoo/usr/portage-stage sync-type: git sync-uri: https://anongit.gentoo.org/git/proj/android.git masters: gentoo eclass-overrides: rap ACCEPT_KEYWORDS="amd64 ~amd64 ~amd64-linux" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright AdobeFlash-11.x Intel-SDP OPERA-2014" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe -O2 -pipe -march=native" DISTDIR="/apps/gentoo/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync news nostrip parallel-fetch preserve-libs protect-owned sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j16" PKGDIR="/apps/gentoo/usr/portage/packages" PORTAGE_CONFIGROOT="/apps/gentoo/" 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="/apps/gentoo/var/tmp" USE="X alsa amd64 apache apache2 avx avx2 berkdb boost bzip2 cairo cgi cli coin cracklib crypt cryptlib cxx dbus device-mapper dhcp dri emboss encode fax fbcon ffmpeg fontconfig fortran gbm gd gdbm gimp glpk gnutls gtk hal hwdb iconv imaging innodb ithreads java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack lcms libnotify lm_sensors mad mmx modules mpi mpich2 mysql ncurses nfs nls nptl nptlonly nscd objc openmp openssl pcre pdf perl php png policykit polkit ppds pppd prefix python qt3support readline resolvconf seccomp server session slideshow sndfile sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 suexec svg syslog tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xcb xml xorg xrandr xv xvid xvmc 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" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en_US en_GB en cs" 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="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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Could you please attach the full build log?
Created attachment 466878 [details] build.log.bz2
Here is the info info from the host I used to obtain build.log: $ emerge --info '=sci-biology/wgs-assembler-8.3_rc2::science' Portage 2.3.3 (python 2.7.12-final-0, prefix/linux-standalone/amd64, gcc-4.9.4, glibc-2.24-r1, 2.6.32-642.6.2.el6.Bull.104.x86_64 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.32-642.6.2.el6.Bull.104.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5-2670_0_@_2.60GHz-with-redhat-6.4-Santiago KiB Mem: 131942608 total, 58169412 free KiB Swap: 65536128 total, 65174440 free Timestamp of repository gentoo: Thu, 02 Mar 2017 18:30:01 +0000 sh bash 4.4_p12 ld GNU ld (Gentoo 2.27 p1.0) 2.27 app-shells/bash: 4.4_p12::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.1::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.5::gentoo, 3.5.2::gentoo dev-util/cmake: 3.7.2::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/sandbox: 2.10-r3::gentoo sys-devel/autoconf: 2.69-r2::gentoo sys-devel/automake: 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.27::gentoo sys-devel/gcc: 3.4.6-r2::gentoo, 4.1.2::gentoo, 4.2.4-r1::gentoo, 4.4.7::gentoo, 4.5.4::gentoo, 4.7.4::gentoo, 4.8.5::gentoo, 4.9.3::gentoo, 4.9.4::gentoo sys-devel/gcc-config: 1.8_p20160608::rap 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-r1::gentoo Repositories: gentoo location: /apps/gentoo/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 eclass-overrides: rap rap location: /apps/gentoo/usr/portage-stage sync-type: git sync-uri: https://anongit.gentoo.org/git/proj/android.git masters: gentoo eclass-overrides: rap x-portage location: /apps/gentoo/usr/local/portage masters: gentoo priority: 0 eclass-overrides: rap haskell location: /apps/gentoo/var/lib/layman/haskell masters: gentoo priority: 50 eclass-overrides: rap science location: /apps/gentoo/var/lib/layman/science masters: gentoo priority: 50 eclass-overrides: rap ACCEPT_KEYWORDS="amd64 ~amd64 ~amd64-linux" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright AdobeFlash-11.x Intel-SDP OPERA-2014" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf" 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 -O2 -pipe -march=native" DISTDIR="/apps/gentoo/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync news nostrip parallel-fetch preserve-libs protect-owned sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j8" PKGDIR="/apps/gentoo/usr/portage/packages" PORTAGE_CONFIGROOT="/apps/gentoo/" 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="/apps/gentoo/var/tmp" USE="X alsa amd64 apache apache2 avx berkdb boost bzip2 cairo cgi cli coin cracklib crypt cryptlib cxx dbus device-mapper dhcp dri emboss encode fax fbcon ffmpeg fontconfig fortran gbm gd gdbm gimp glpk gnutls gtk hal hwdb iconv imaging innodb ithreads java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack lcms libnotify lm_sensors mad mmx modules mpi mpich2 mysql ncurses nfs nls nptl nptlonly nscd objc openmp openssl pcre pdf perl php png policykit polkit ppds pppd prefix python qt3support readline resolvconf seccomp server session sftp slideshow sndfile spell sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 suexec svg syslog tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xcb xml xorg xrandr xv xvid xvmc 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" 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 isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en_US en_GB en cs" 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="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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
looks like a prefix problem to me. you're trying to compile/run/link things that are using a newer glibc under /apps/gentoo but with a runtime of an older glibc in /. you can't mix them. the symbols libstdc++ is complaining about are from glibc itself.
@vapier: Thanks for your analysis, I had the impression it somehow uses glibc outside the prefix. There must be something wrong with the Makefile of the package itself which then uses glibc or some application outside prefix.
this version is no longer in the tree
