konnector.cc:698:15: required from ‘void connectPairs(const Graph&, const Bloom&, FastaStream&, const ConnectPairsParams&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&) [with Graph = DBGBloom<BloomFilter>; FastaStream = FastaConcat; Bloom = BloomFilter; std::ofstream = std::basic_ofstream<char>]’ konnector.cc:979:29: required from here /usr/include/boost/graph/graph_concepts.hpp:131:19: error: ‘degree’ was not declared in this scope n = degree(v, g); ~~~~~~^~~~~~ make[2]: *** [Makefile:422: konnector-konnector.o] Error 1 $ cat emerge-info.txt ----------------------------------------------------------------- This is an unstable amd64 chroot image (named amd64-13.0-systemd-libressl-unstable_20160928-212025) at a hardened host acting as a tinderbox. ----------------------------------------------------------------- USE flags ... ... in make.conf: USE=" -openssl -gnutls libressl pax_kernel xtpax -cdinstall -oci8 -bindist ssp apache cairo cdda cddb cgroups clang consolekit curl custom-cflags egl eglfs evdev ext4 ffmpeg fitz fluidsynth fortran -gpg graphtft hdf5 hpn ibus infinality jadetex javascript javaxml kerberos lapack libinput mpeg3 mpg123 mssql -mysqli ncurses networking odbc ogg opencv -opengl openmpi -osc png -policykit postproc -postscript -scrypt smpeg sockets source sourceview spice sqlite3 ssh-askpass sslv3 ssp system-cairo system-ffmpeg system-icu system-jpeg system-llvm szip theora -tools udisks vim vorbis -wma -xslt zenmap" ... in /etc/portage/package.use/*: mail-mta/ssmtp ssl mta net-misc/wget ssl app-crypt/pinentry -qt4 app-editors/emacs -dbus -svg -ssl -gtk -gtk3 app-text/xmlto -latex dev-libs/boehm-gc threads dev-libs/libpcre pcre16 dev-lang/python threads dev-qt/qtgui egl eglfs net-nds/openldap -sasl dev-util/cmake -qt4 -qt5 dev-vcs/git -perl media-libs/mesa -vaapi sys-apps/kmod tools mail-mta/ssmtp libressl -gnutls entries in /etc/portage/package.unmask/*: ~dev-libs/boost-1.62.0 ~dev-util/boost-build-1.62.0 ~sys-apps/sandbox-2.11 media-video/ffmpeg sys-devel/gcc:6.2.0 ----------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-4.9.3 [2] x86_64-pc-linux-gnu-6.2.0 * llvm-config --version: 3.8.1 Available Python interpreters, in order of preference: [1] python3.4 [2] python2.7 (fallback) [3] pypy3 (fallback) ----------------------------------------------------------------- Portage 2.3.1 (python 3.4.5-final-0, default/linux/amd64/13.0/systemd, gcc-6.2.0, glibc-2.23-r2, 4.7.6-hardened x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.7.6-hardened-x86_64-Intel-R-_Core-TM-_i7-3930K_CPU_@_3.20GHz-with-gentoo-2.3 KiB Mem: 65285480 total, 1546776 free KiB Swap: 67108860 total, 67107300 free Timestamp of repository gentoo: Mon, 03 Oct 2016 00:32:21 +0000 sh bash 4.4 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 distcc 3.2rc1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.4::gentoo dev-lang/perl: 5.24.0-r1::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.5::gentoo dev-util/cmake: 3.6.2::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/openrc: 0.22.1::gentoo sys-apps/sandbox: 2.11-r2::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r2::gentoo sys-devel/automake: 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.25.1-r1::gentoo, 2.26.1::gentoo sys-devel/gcc: 4.9.3::gentoo, 6.2.0-r1::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r2::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: 1 local location: /usr/local/portage masters: gentoo priority: 2 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/omega.conf /usr/share/config /usr/share/gnupg/qualified.txt /var/rancid/.cloginrc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/apache2-php7.0/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/php/cli-php7.0/ext-active/ /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" DISTDIR="/var/tmp/distfiles" EMERGE_DEFAULT_OPTS="--verbose --verbose-conflicts --color=n --nospinner --tree --quiet-build" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox parallel-fetch preserve-libs protect-owned sandbox sfperms strict test-fail-continue 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 --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="acl amd64 apache berkdb bzip2 cairo cdda cddb cgroups clang cli cracklib crypt curl custom-cflags cxx dri egl eglfs evdev ext4 ffmpeg fitz fluidsynth fortran gdbm graphtft hdf5 hpn ibus iconv infinality ipv6 jadetex javascript javaxml kerberos lapack libinput libressl mmx mmxext modules mpeg3 mpg123 mssql multilib ncurses networking nls nptl odbc ogg opencv openmp openmpi pam pax_kernel pcre png postproc readline seccomp session smpeg sockets source sourceview spice sqlite3 sse sse2 ssh-askpass ssl sslv3 ssp system-cairo system-ffmpeg system-icu system-jpeg system-llvm systemd szip tcpd theora udev udisks unicode vim vorbis xattr xtpax zenmap 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" CURL_SSL="libressl" 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" L10N="om ru zh-CN" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 448950 [details] config.log
Created attachment 448952 [details] emerge-history.txt
Created attachment 448954 [details] environment
Created attachment 448956 [details] sci-biology:abyss-1.9.0-r1:20161003-052044.log
I think it's boost-1.62 this time, gcc-6 was supposedly fixed in bug #594254 . Did not look at the error closely yet.
(In reply to Toralf Förster from comment #0) > konnector.cc:698:15: required from ‘void connectPairs(const Graph&, const > Bloom&, FastaStream&, const ConnectPairsParams&, std::ofstream&, > std::ofstream&, std::ofstream&, std::ofstream&) [with Graph = > DBGBloom<BloomFilter>; FastaStream = FastaConcat; Bloom = BloomFilter; > std::ofstream = std::basic_ofstream<char>]’ > konnector.cc:979:29: required from here > /usr/include/boost/graph/graph_concepts.hpp:131:19: error: ‘degree’ was not > declared in this scope > n = degree(v, g); > ~~~~~~^~~~~~ > make[2]: *** [Makefile:422: konnector-konnector.o] Error 1 (In reply to Sergei Trofimovich from comment #5) > I think it's boost-1.62 this time, gcc-6 was supposedly fixed in bug #594254 > . Did not look at the error closely yet. Agreed. These lines preceding the last error message are a little more telling: > /usr/include/boost/graph/graph_concepts.hpp: In instantiation of 'boost::concepts::BidirectionalGraph<G>::~BidirectionalGraph() [with G = DBGBloom<BloomFilter>]': > /usr/include/boost/graph/graph_concepts.hpp:114:87: required from 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::BidirectionalGraphConcept<DBGBloom<BloomFilter> >]' > /usr/include/boost/concept_check.hpp:50:55: required from 'void boost::function_requires(Model*) [with Model = boost::concepts::BidirectionalGraphConcept<DBGBloom<BloomFilter> >]'
boost commit adding degree concept check: https://github.com/boostorg/graph/commit/50bfd8dad0ded59e3335d7f577549c968b371a80
I've filed https://github.com/bcgsc/abyss/issues/130 upstream with a hint on how to fix it properly.
Bumped up to 2.0.2 where upstream fixed boost-1.62 compat issue: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4c8a5799cd9b07143e1c1b9ba865c3e9bbbf5f3e Thanks!
