Compiling graph tool 2.2.35 leads to the following error: graph_subgraph_isomorphism.cc:108:114: error: 'vf2_subgraph_mono' was not declared in this scope >>> Emerge info: Portage 2.2.8-r2 (default/linux/x86/13.0, gcc-4.8.3, glibc-2.19-r1, 3.14.16-gentoo i686) ================================================================= System Settings ================================================================= System uname: Linux-3.14.16-gentoo-i686-Intel-R-_Core-TM-_i7-2670QM_CPU_@_2.20GHz-with-gentoo-2.2 KiB Mem: 8067800 total, 3943532 free KiB Swap: 5121020 total, 5097528 free Timestamp of tree: Sun, 05 Oct 2014 14:15:01 +0000 ld GNU ld (GNU Binutils) 2.23.2 ccache version 3.1.9 [enabled] app-shells/bash: 4.2_p52 dev-java/java-config: 2.2.0 dev-lang/perl: 5.18.2-r1 dev-lang/python: 2.7.7, 3.3.5-r1 dev-util/ccache: 3.1.9-r3 dev-util/cmake: 2.8.12.2-r1 dev-util/pkgconfig: 0.28-r1 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.4 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.11.6, 1.12.6, 1.13.4 sys-devel/binutils: 2.23.2 sys-devel/gcc: 4.8.3 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4.2-r1 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.13 (virtual/os-headers) sys-libs/glibc: 2.19-r1 Repositories: gentoo tud_overlay ACCEPT_KEYWORDS="x86" ACCEPT_LICENSE="* -@EULA" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=i686 -pipe" CHOST="i686-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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -march=i686 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -march=i686 -pipe" FEATURES="assume-digests binpkg-logs ccache 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" FFLAGS="-O2 -march=i686 -pipe" GENTOO_MIRRORS="http://de-mirror.org/gentoo/" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j8" 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="/usr/local/portage" SYNC="rsync://rsync3.de.gentoo.org/gentoo-portage" USE="3dnow X acl acpi alsa bash-completion berkdb bzip2 cli cracklib crypt cxx dri dri2 dvi fortran gdbm iconv ipv6 jpeg jpeg2k jpg keymap mmx modules ncurses networkmanager nptl opengl openmp pam pcre png qt3support readline sdl session sse sse2 sse3 sse4a ssl ssse3 tcpd threads unicode v4l vaapi x86 xinerama zlib" ABI_X86="32" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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="evdev synaptics" 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_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="intel 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" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 386086 [details] build.log.tar.bz2
Boost version used: dev-libs/boost-1.53.0-r1
Comment on attachment 386086 [details] build.log.tar.bz2 That's bzip, not gzip, and it's a single file in a tar archive for no apparent reason.
(In reply to Jeroen Roovers from comment #3) > Comment on attachment 386086 [details] > build.log.tar.bz2 > > That's bzip, not gzip, and it's a single file in a tar archive for no > apparent reason. The reason was a size of 8.3MB which is too much for uploading (error message).
I bumped this and it took hours to build, but it built. Is this something you observed after it built effectively? Alternately, did it abort and fail to complete? A log of a size of 8.3MB suggests it got a very long way. Frankly a build log of that dimension is a logistical nightmare. When it comes down to it the opening couple of dozen lines and the lines where it fell sideways are all that ever help. The rest of effective compiling is, well,...
(In reply to Ian Delaney from comment #5) > I bumped this and it took hours to build, but it built. > > Is this something you observed after it built effectively? > Alternately, did it abort and fail to complete? A log of a size of 8.3MB > suggests it got a very long way. Frankly a build log of that dimension is a > logistical nightmare. When it comes down to it the opening couple of dozen > lines and the lines where it fell sideways are all that ever help. The rest > of effective compiling is, well,... 2.2.31 worked for me and I wanted to upgrade to 2.2.35. Perhaps the error derives from ccache. I'll clear the cache, try to recompile it and post the result in the next days.
Created attachment 386318 [details] 2nd compilation with cleared ccache
The 2nd compilation didn't succeed either. Which use-flags did you use? I suppose my bleeding edge gcc compiler is also a certain bug-factor.
Now it works: the reason was boost. graph-tool needs boost>=1.53 BUT 1.53.0-r1 doesn't seem to be enough. I switched to 1.55.0-r2 and everything works fine.
(In reply to mike from comment #9) > Now it works: the reason was boost. graph-tool needs boost>=1.53 BUT > 1.53.0-r1 doesn't seem to be enough. I switched to 1.55.0-r2 and everything > works fine. I found a version recommend in work/graph-tool-2.2.35/configure which I had apparently missed, not being well practiced in packages with C builds and sourcing their deps. boost_lib_version_req=1.53.0. At minimum the ebuild requires adjusting to this however dev-libs/boost has a version 1.54.0-r1 & 1.55.0-r1. However; 1. This ideally requires confirmation with cross testing. 2. For me; $ time USE="cairo openmp" ebuild graph-tool-2.2.35.ebuild clean tall took real 823m44.690s user 338m43.625s sys 8m12.945s 3. You have to be keen. The evidence here suggests >=dev-libs/boost-1.53.0 is inadequate and therefore requires filing upstream to prompt to upgrade the version requirement for this bumped version. Ideally it needs greater certainty before filing. The build time for this is extraordinary. 4. he build in my system was done with dev-libs/boost-1.55.0-r1.
[U] dev-libs/boost Installed versions: 1.54.0-r1(13:53:00 12/10/14)(nls python threads -debug -doc -icu -mpi -static-libs -tools PYTHON_TARGETS="python2_7 python3_3 -python3_2") [U] dev-util/boost-build Installed versions: 1.54.0(12:38:29 12/10/14)(-examples -python -test) archtester graph-tool # time ebuild graph-tool-2.2.35.ebuild clean merge -------------------------------------------------------------------------- >>> Regenerating /etc/ld.so.cache... real 341m37.563s user 335m29.546s sys 8m14.614s Still need someone to confirm failure under what configure sets as required; boost_lib_version_req=1.53.0.
Here's the break down of my testing this against various versions of boost: dev-libs/boost-1.55.0-r2: pass dev-libs/boost-1.55.0-r1: pass I'll do more when I get the chance but I also saw a stabilization request for this version come across: 525286 Perhaps the issue will shortly be moot?
[U] dev-libs/boost Installed versions: 1.53.0-r1(08:36:08 14/10/14)(nls python threads PYTHON_TARGETS="python2_7 python3_3 -python3_2") [U] dev-util/boost-build Installed versions: 1.53.0(08:31:32 14/10/14) ~/cvsPortage/gentoo-x86/dev-python/graph-tool $ time ebuild graph-tool-2.2.35.ebuild install Could the maintainer care to file upstream. 14 Oct 2014; Ian Delaney <idella4@gentoo.org> graph-tool-2.2.35.ebuild, graph-tool-9999.ebuild: reset border version of dev-libs/boost, fixes Bug #524524
