Bug 557822 – sci-chemistry/autodock_vina-1.1.2 : ld: cannot find -lboost_thread

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2015-08-15 08:29:17 UTC]

x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o ssd.o -c ../../../src/lib/ssd.cpp 
x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o terms.o -c ../../../src/lib/terms.cpp 
x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o weighted_terms.o -c ../../../src/lib/weighted_terms.cpp 
x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -Wl,-O1 -Wl,--as-needed -L. -o vina main.o cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manifold.o model.o monte_carlo.o mutate.o my_pid.o naive_non_cache.o non_cache.o parallel_mc.o parse_pdbqt.o pdb.o quasi_newton.o quaternion.o random.o ssd.o terms.o weighted_terms.o -lboost_system -lboost_thread -lboost_serialization -lboost_filesystem -lboost_program_options -lpthread
/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_thread
collect2: error: ld returned 1 exit status
../../makefile_common:34: recipe for target 'vina' failed
make: *** [vina] Error 1
 * ERROR: sci-chemistry/autodock_vina-1.1.2::gentoo failed (compile phase):
 *   emake failed
 * 


$ cat info
  -----------------------------------------------------------------

  This is an stable amd64 chroot image (named amd64-hardened-stable_20150813-194347) at a hardened host acting as a tinderbox.

  Portage 2.2.20.1 (python 3.4.1-final-0, hardened/linux/amd64, gcc-4.8.4, glibc-2.20-r2, 4.1.4-hardened x86_64)
=================================================================
System uname: Linux-4.1.4-hardened-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16164628 total,   3036636 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Sat, 15 Aug 2015 01:45:02 +0000
sh bash 4.3_p39_pre0
ld GNU ld (Gentoo 2.24 p1.4) 2.24
app-shells/bash:          4.3_p39_pre0::gentoo
dev-java/java-config:     2.2.0::gentoo
dev-lang/perl:            5.20.2::gentoo
dev-lang/python:          2.7.9-r1::gentoo, 3.4.1::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.17::gentoo
sys-apps/sandbox:         2.6-r1::gentoo
sys-devel/autoconf:       2.69::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.11.6-r1::gentoo, 1.13.4::gentoo, 1.15::gentoo
sys-devel/binutils:       2.24-r3::gentoo
sys-devel/gcc:            4.8.4::gentoo
sys-devel/gcc-config:     1.7.3::gentoo
sys-devel/libtool:        2.4.6::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 3.18::gentoo (virtual/os-headers)
sys-libs/glibc:           2.20-r2::gentoo
Repositories:

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

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: 9999

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
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/env.d /etc/fonts/fonts.conf /etc/games/angband/edit/ /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--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="acl aes-ni alsa amd64 avx2 berkdb btrfs bzip2 cli consolekit cracklib crypt cups curl custom-cflags custom-optimization cxx dnssec dri drmkms dvd ecc elp fontconfig gdbm git gpg gtk gui hardened help hpn iconv imap ipv6 jadetex jpeg justify ldap logrotate mbox mmx mmxext modules multilib multitarget mysql mysqli ncurses nls nptl obj odbc opencv openmp openmpi pam pax_kernel pcre pdo pie png policykit postgres pwquality python qemu qt3support qt4 readline scrpyt session smartcard spice sqlite3 sse sse2 sse4 sse4_2 ssh-askpass ssl ssp system-libvpx system-sqlite tcpd theora truetype unicode urandom usbredir v4l2 video vpx webkit wxwidgets x264 xa xattr xml xslt xtpax xvfb 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="ruby19 ruby20" 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:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

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

[Comment 1 Toralf Förster 2015-08-15 08:29:20 UTC]

Created attachment 409050 [details]
emerge-history.txt

[Comment 2 Toralf Förster 2015-08-15 08:29:22 UTC]

Created attachment 409052 [details]
sci-chemistry:autodock_vina-1.1.2:20150815-060622.log

[Comment 3 Justin Lecher (RETIRED) 2015-08-16 11:34:42 UTC]

* commit 5652c5a6a40ad158042bcd84f55c13e20f07c490
* Author: Justin Lecher <[e-mail]>
* Date:   Sun Aug 16 13:33:39 2015 +0200
*
*     sci-chemistry/autodock_vina: Require thread support in boost, bug #557822
*
*     Package-Manager: portage-2.2.20.1
*     Signed-off-by: Justin Lecher <[e-mail]>
*