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Bug 579320 - [science overlay] sci-libs/trilinos-12.2.1 missing dependency sys-libs/binutils-libs
Summary: [science overlay] sci-libs/trilinos-12.2.1 missing dependency sys-libs/binuti...
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
Depends on:
Reported: 2016-04-08 09:40 UTC by Marco
Modified: 2016-07-09 12:39 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


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Description Marco 2016-04-08 09:40:23 UTC
Emerging  sci-libs/trilinos-12.2.1  from the science overlay the build
fails during configuration with

Processing enabled TPL: BinUtils (enabled explicitly, disable with
-- Must find at least one lib in each of the lib sets "bfd;iberty"
-- Searching for libs in BinUtils_LIBRARY_DIRS=''
-- Searching for a lib in the set "bfd":
--   Searching for lib 'bfd' ...
-- ERROR: Did not find a lib in the lib set "bfd" for the TPL 'BinUtils'!
-- Searching for a lib in the set "iberty":
--   Searching for lib 'iberty' ...
-- ERROR: Did not find a lib in the lib set "iberty" for the TPL
-- ERROR: Could not find the libraries for the TPL 'BinUtils'!
-- TIP: If the TPL 'BinUtils' is on your system then you can set:
   to point to the directories where these libraries may be found.
   Or, just set:
   to point to the full paths for the libraries which will
   bypass any search for libraries and these libraries will be used without
   question in the build.  (But this will result in a build-time error
   if not all of the necessary symbols are found.)
-- ERROR: Failed finding all of the parts of TPL 'BinUtils' (see
above), Aborting!

The problem is fixed emerging sys-libs/binutils-libs, which owns the
fle  /usr/include/bfd.h .

This seems to fit in the description given here:

so, probably a dependency on sys-libs/binutils-libs is missing in the
trilinos ebuild.
Comment 1 Adam Feldman gentoo-dev 2016-04-13 17:35:43 UTC
@Marco: emerge --info sci-libs/trilinos please this package's maintainer does not have a bugzilla account.   Please update the metadata.xml accordingly or get the maintainer to register on BGO please.
Comment 2 Marco 2016-04-14 08:00:39 UTC
(In reply to NP-Hardass from comment #1)
> @Marco: emerge --info sci-libs/trilinos please

# emerge --info sci-libs/trilinos
Portage 2.2.26 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop, gcc-4.9.3, glibc-2.22-r4, 3.12.13-gentoo x86_64)
                         System Settings
System uname: Linux-3.12.13-gentoo-x86_64-Intel-R-_Core-TM-_i3-2120_CPU_@_3.30GHz-with-gentoo-2.2
KiB Mem:     3926120 total,    101472 free
KiB Swap:   15999996 total,  13513104 free
Timestamp of repository gentoo: Wed, 13 Apr 2016 08:30:01 +0000
sh bash 4.3_p42-r1
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p42-r1::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.20.2::gentoo
dev-lang/python:          2.7.10-r1::gentoo, 3.4.3-r1::gentoo
dev-util/cmake:           3.3.1-r1::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.19.1::gentoo
sys-apps/sandbox:         2.10-r1::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69::gentoo
sys-devel/automake:       1.11.6-r1::gentoo, 1.12.6::gentoo, 1.14.1::gentoo, 1.15::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::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: 4.3::gentoo (virtual/os-headers)
sys-libs/glibc:           2.22-r4::gentoo

    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://
    priority: -1000

    location: /var/lib/layman/science
    masters: gentoo
    priority: 0

    location: /var/lib/layman/sage-on-gentoo
    masters: gentoo science
    priority: 1

    location: /var/lib/myebuild
    masters: gentoo
    priority: 2

CFLAGS="-march=native -O2 -pipe"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt"
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"
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 splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
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"
USE="X a52 aac acl acpi afs alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus djvu dri dts dvd dvdr dvi emboss encode exif fam firefox flac fortran fortran2003 gdbm gif glamor gpm gtk iconv icu ipv6 jpeg kerberos latex lcms ldap libnotify lua luatex mad mate mmx mmxext mng modules mp3 mp4 mpeg multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds qt3support qt4 readline sdl seccomp session spell sse sse2 ssl startup-notification svg tcpd tetex tiff truetype udev udisks unicode upower usb vim vim-syntax vorbis wxwidgets x264 xattr xcb xml xv xvid zlib" ABI_X86="32 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="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" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_US ar de eo es es_ES it af br da cy fy he is nds nl oc yi el hr sr" 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" 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"

                        Package Settings

sci-libs/trilinos-12.2.1::science was built with the following:
USE="qt4 zlib -adolc -arprec -boost -clp -cppunit -cuda -eigen -glpk -gtest -hdf5 -hwloc -hypre -matio -metis -mkl -mumps -netcdf -petsc -qd -scalapack -scotch -sparse -superlu -taucs -tbb -test -threads -tvmet -yaml" ABI_X86="64"
Comment 3 Matthias Maier gentoo-dev 2016-07-09 12:39:03 UTC
commit 92ab1d46cfbb4b93e40fcb0fce5a8e28bab84f07
Author: Matthias Maier <>
Date:   Sat Jul 9 07:38:39 2016 -0500

    sci-libs/trilinos: Add missing dependency, bug #579320
    Package-Manager: portage-2.2.28