Aside from the fact the ebuild should be fixed to require boost >=1.37 (bug #348977) I cannot make configure happy anyway for some reason. It dies with: checking to see that gcc is at least version 4.3.2... Yes, gcc version 4.5.2 is fine checking for boostlib >= 1.37.0... yes found boost version checking for boost library name... Failed... configure: Configure failed with the error message: Failed to resolve boost library name configure: configure: Common error conditions in the build process are documented on our wiki page, configure: http://www.broadinstitute.org/crd/wiki/index.php/Build_FAQ configure: We also offer email support at crdhelp@broadinstitute.org configure: error: in `/var/tmp/portage/sci-biology/allpaths-3.1/work/AllPaths': configure: error: configure failed. See `config.log' for more details. !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-biology/allpaths-3.1/work/AllPaths/config.log * ERROR: sci-biology/allpaths-3.1 failed: * econf failed * * Call stack: * ebuild.sh, line 56: Called src_configure * environment, line 2442: Called base_src_configure * environment, line 238: Called econf * ebuild.sh, line 557: Called die * The specific snippet of code: * die "econf failed" * * If you need support, post the output of 'emerge --info =sci-biology/allpaths-3.1', * the complete build log and the output of 'emerge -pqv =sci-biology/allpaths-3.1'. * The complete build log is located at '/var/tmp/portage/sci-biology/allpaths-3.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/allpaths-3.1/temp/environment'. * S: '/var/tmp/portage/sci-biology/allpaths-3.1/work/AllPaths' # emerge --info Portage 2.1.9.33 (default/linux/amd64/10.0, gcc-4.5.2, glibc-2.12.2-r0, 2.6.36-gentoo-r5 x86_64) ================================================================= System uname: Linux-2.6.36-gentoo-r5-x86_64-Intel-R-_Xeon-R-_CPU_X5680_@_3.33GHz-with-gentoo-2.0.1 Timestamp of tree: Tue, 18 Jan 2011 20:00:01 +0000 app-shells/bash: 4.1_p9 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.6.6-r1, 2.7.1, 3.1.3 dev-util/cmake: 2.8.3-r1 sys-apps/baselayout: 2.0.1-r1 sys-apps/openrc: 0.7.0 sys-apps/sandbox: 2.4 sys-devel/autoconf: 2.68 sys-devel/automake: 1.11.1 sys-devel/binutils: 2.21 sys-devel/gcc: 4.4.5, 4.5.2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82 virtual/os-headers: 2.6.36.1 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=nocona" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /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 -pipe -march=nocona" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news nostrip parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en cs cz" MAKEOPTS="-j23" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X amd64 berkdb bzip2 cracklib crypt cxx dbus dri fontconfig fortran gdbm gnutls hal iconv innodb java jce jpeg jpg kde laptop mmx modules mpi mpich2 multilib mysql ncurses nfs nls nptl nptlonly nsplugin opengl openmp openssl pam pcre perl png python qt3support qt4 readline server session sse sse2 ssl suexec svg sysfs syslog tcpd threads tiff truetype unicode usb xorg zlib" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dbd deflate dir disk_cache env expires ext_filter file_cache filter headers icu ident imagemap include info log_config mem_cache mime mime_magic rewrite setenvif speling status unique_id userdir usertrack vhost_alias negotiation" 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 ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en cs cz" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vesa matrox" 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, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Created attachment 260580 [details] build.log
Created attachment 260581 [details] config.log
Created attachment 260582 [details] configure
AFAICT, it fails while looking for a *static* boost_filesystem. Arguably, a flaw of build system perhaps it should be changed. Is your dev-libs/boost built with static-libs useflag ?
# emerge -pv boost These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] dev-libs/boost-1.42.0-r2 USE="eselect mpi python -debug -doc -icu -static-libs -test -tools" 0 kB
(In reply to comment #4) > AFAICT, it fails while looking for a *static* boost_filesystem. > Arguably, a flaw of build system perhaps it should be changed. That's what should happen (unless it links against the static libs). As a workaround enable the static-libs use flag for boost.
Unfortunately, it seems it's one of those upstreams, that simply fail to ship autotools source of their build system. On unrelated note: it seems upstream tarball for 3.1 is gone.
sci-biology/allpaths moved to sci-biology/allpathslg, all old ebuilds will be dropped. Please check if the problem persists with the latest sci-biology/allpathslg and reopen the bug if appropriate.
(In reply to comment #8) > sci-biology/allpaths moved to sci-biology/allpathslg, all old ebuilds will be > dropped. Please check if the problem persists with the latest > sci-biology/allpathslg and reopen the bug if appropriate. > So I tested the svn version 35725 of allpathslg on a different ~amd64: g++ version is >= 4.3.3... yes checking for Boost headers version >= 103800... yes checking for Boost's header version... 1_42 checking for the toolset name used by Boost for x86_64-pc-linux-gnu-g++... configure: WARNING: could not figure out which toolset name to use for x86_64-pc-linux-gnu-g++ checking boost/system/error_code.hpp usability... yes checking boost/system/error_code.hpp presence... yes checking for boost/system/error_code.hpp... yes checking for the Boost system library... yes checking boost/filesystem/path.hpp usability... yes checking boost/filesystem/path.hpp presence... yes checking for boost/filesystem/path.hpp... yes checking for the Boost filesystem library... yes but because the compile process used x86_64-pc-linux-gnu-g++ in the end I believe it did fallback to a correct compiler and the package installed fine. # emerge -pv boost These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] dev-libs/boost-1.42.0-r2 USE="eselect mpi python -debug -doc -icu -static-libs -test -tools" 0 kB
