Bug 619130 – sci-chemistry/openbabel-2.4.1 fails to build - make: *** [Makefile:139: all] Error 2

• Product: Gentoo Linux
• Status: RESOLVED INVALID

[Description Thomas Albers 2017-05-21 00:11:04 UTC]

Created attachment 473564 [details]
build.log

sybil ta # emerge openbabel
...
make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/openbabel-2.4.1/work/openbabel-2.4.1_build'
[100%] Built target test_runner
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/openbabel-2.4.1/work/openbabel-2.4.1_build'
make: *** [Makefile:139: all] Error 2

ta@sybil ~ $ emerge --info '=sci-chemistry/openbabel-2.4.1::gentoo'
Portage 2.3.5 (python 2.7.12-final-0, default/linux/amd64/13.0/desktop, gcc-5.4.0, glibc-2.23-r3, 4.9.16-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.9.16-gentoo-x86_64-Intel-R-_Core-TM-_i5-3570_CPU_@_3.40GHz-with-gentoo-2.3
KiB Mem:    16392096 total,  14747584 free
KiB Swap:    8388604 total,   8388604 free
Timestamp of repository gentoo: Sat, 20 May 2017 00:45:01 +0000
sh bash 4.3_p48-r1
ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1
app-shells/bash:          4.3_p48-r1::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.1-r1::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo
dev-util/cmake:           3.7.2::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.26.2::gentoo
sys-apps/sandbox:         2.10-r3::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69::gentoo
sys-devel/automake:       1.15-r2::gentoo
sys-devel/binutils:       2.26.1::gentoo
sys-devel/gcc:            4.8.5::gentoo, 5.4.0-r3::gentoo
sys-devel/gcc-config:     1.7.3::gentoo
sys-devel/libtool:        2.4.6-r3::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.4::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r3::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/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"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync 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://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j5"
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 bindist bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif glamor gpm gtk iconv jpeg lcms ldap libnotify lock mad mng modules mp3 mp4 mpeg multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds qt3support readline sdl seccomp session spell ssl startup-notification svg thunar tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xattr xcb xinerama xml xv xvid zlib" ABI_X86="64 32" 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" GRUB_PLATFORMS="pc" INPUT_DEVICES="evdev" KERNEL="linux" L10N="en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python3_4" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby21 ruby22" USERLAND="GNU" VIDEO_CARDS="nvidia" 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"
USE_PYTHON="2.7"
Unset:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

ta@sybil ~ $ emerge -pqv '=sci-chemistry/openbabel-2.4.1::gentoo'
[ebuild     U ] sci-chemistry/openbabel-2.4.1 [2.3.2-r1] USE="openmp wxwidgets -doc {-test}"

[Comment 1 Thomas Albers 2017-05-22 15:07:59 UTC]

This error occurred at the linking phase and was due to the switch to gcc 5 and the new c++ ABI. A dependency was still compiled with gcc 4, this caused linking to fail.