Bug 514562 – sci-libs/libmems-1.6_p1 fails to build

• Product: Gentoo Linux
• Status: RESOLVED NEEDINFO

[Description Patrick Lauer 2014-06-23 03:38:40 UTC]

/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.0/include/g++-v4/bits/predefined_ops.h:110:12: note:   no known conversion for argument 1 from '__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>' to '__gnu_cxx::__ops::_Iter_comp_iter<mems::LabeledMemComparator>&'
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.0/include/g++-v4/bits/predefined_ops.h: In instantiation of '__gnu_cxx::__ops::_Iter_comp_iter<_Compare> __gnu_cxx::__ops::__iter_comp_iter(_Compare) [with _Compare = mems::MatchLeftEndComparator]':
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.0/include/g++-v4/bits/stl_algo.h:4707:77:   required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >**, std::vector<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*, std::allocator<mems::UngappedLocalAlignment<mems::HybridAbstractMatch<> >*> > >; _Compare = mems::MatchLeftEndComparator]'
/var/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Aligner.cpp:979:40:   required from here
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.0/include/g++-v4/bits/predefined_ops.h:127:46: error: no matching function for call to '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>)'
     { return _Iter_comp_iter<_Compare>(__comp); }
                                              ^
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.0/include/g++-v4/bits/predefined_ops.h:127:46: note: candidates are:
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.0/include/g++-v4/bits/predefined_ops.h:114:7: note: __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::_Iter_comp_iter(_Compare) [with _Compare = mems::MatchLeftEndComparator]
       _Iter_comp_iter(_Compare __comp)
       ^
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.0/include/g++-v4/bits/predefined_ops.h:114:7: note:   no known conversion for argument 1 from '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>' to 'mems::MatchLeftEndComparator'
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.0/include/g++-v4/bits/predefined_ops.h:110:12: note: __gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>::_Iter_comp_iter(__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>&)
     struct _Iter_comp_iter
            ^
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.0/include/g++-v4/bits/predefined_ops.h:110:12: note:   no known conversion for argument 1 from '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>' to '__gnu_cxx::__ops::_Iter_comp_iter<mems::MatchLeftEndComparator>&'
Makefile:748: recipe for target 'Aligner.lo' failed
make[2]: *** [Aligner.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.0/include/g++-v4/ext/hash_map:60:0,
                 from /var/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/dptables.h:43,
                 from /var/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/HomologyHMM/homology.h:27,
                 from /var/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Islands.h:25,
                 from /var/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Islands.cpp:13:
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.0/include/g++-v4/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^
libtool: compile:  x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems -I.. -I/var/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1 -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -I/usr/include -O2 -pipe -c /var/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1/libMems/Islands.cpp -o Islands.o >/dev/null 2>&1
make[2]: Leaving directory '/var/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1_build/libMems'
Makefile:529: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-libs/libmems-1.6_p1/work/libmems-1.6_p1_build'
Makefile:436: recipe for target 'all' failed
make: *** [all] Error 2
 * ERROR: sci-libs/libmems-1.6_p1::gentoo failed (compile phase):
 *   emake failed


Portage 2.2.10 (default/linux/amd64/13.0, gcc-4.9.0, glibc-2.19-r1, 3.7.10-gentoo x86_64)
=================================================================
System uname: Linux-3.7.10-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E31275_@_3.40GHz-with-gentoo-2.2
KiB Mem:    32800928 total,   1340764 free
KiB Swap:          0 total,         0 free
Timestamp of tree: Mon, 23 Jun 2014 00:00:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
app-shells/bash:          4.2_p47
dev-lang/python:          2.7.6-r1, 3.2.5-r4, 3.3.5, 3.4.0
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.69
sys-devel/automake:       1.14.1
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.9.0
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.15 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
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"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--jobs 4"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync parallel-fetch preserve-libs protect-owned sandbox sfperms split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
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"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
USE="acl amd64 berkdb bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mmx modules multilib ncurses nls nptl openmp pam pcre readline session sse sse2 ssl tcpd unicode 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" 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" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2 python3_3 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, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON

[Comment 1 Justin Lecher (RETIRED) 2014-06-23 06:40:46 UTC]

missing build.log