checking for uname... yes checking to see that gcc is at least version 4.3.2... Yes, gcc version 4.4.3 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.broad.mit.edu/crd/wiki/index.php/Build_FAQ configure: We also offer email support at crdhelp@broad.mit.edu configure: error: in `/var/tmp/portage/sci-biology/vaal-1.2-r1/work/VAAL': configure: error: configure failed. See `config.log' for more details. !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-biology/vaal-1.2-r1/work/VAAL/config.log * ERROR: sci-biology/vaal-1.2-r1 failed: * econf failed * * Call stack: * ebuild.sh, line 54: Called src_configure * environment, line 2436: Called base_src_configure * environment, line 239: Called econf * ebuild.sh, line 544: Called die * The specific snippet of code: * die "econf failed" *
Created attachment 223265 [details] build.log
# emerge --info Portage 2.1.8.1 (default/linux/amd64/10.0, gcc-4.4.3, glibc-2.11-r1, 2.6.32-default x86_64) ================================================================= System uname: Linux-2.6.32-default-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9300_@_2.50GHz-with-gentoo-2.0.1 Timestamp of tree: Thu, 11 Mar 2010 00:00:11 +0000 app-shells/bash: 4.1_p2 dev-java/java-config: 2.1.10 dev-lang/python: 2.5.4-r4, 2.6.4-r1, 3.1.1-r1 dev-util/cmake: 2.8.0-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.6.0-r1 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.65 sys-devel/automake: 1.5, 1.9.6-r2, 1.10.3, 1.11.1 sys-devel/binutils: 2.20-r1 sys-devel/gcc: 4.3.4, 4.4.3 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.32 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 /usr/share/X11/xkb /usr/share/config /var/qmail/alias /var/qmail/control /var/spool/torque" 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 distlocks fixpackages news nostrip parallel-fetch protect-owned sandbox sfperms splitdebug strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1" LINGUAS="en cs cz" MAKEOPTS="-j5" 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" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X amd64 berkdb bzip2 cracklib crypt cxx dbus dri 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 openssl pam pcre perl png python qt3support qt4 readline server session sse sse2 ssl suexec svg sysfs syslog tcpd threads 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 authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en cs cz" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS # emerge -s boost Searching... [ Results for search key : boost ] [ Applications found : 4 ] * app-admin/eselect-boost Latest version available: 0.3 Latest version installed: 0.3 Size of files: 0 kB Homepage: http://www.gentoo.org/proj/en/eselect/ Description: boost module for eselect License: GPL-2 * dev-libs/boost Latest version available: 1.42.0 Latest version installed: 1.42.0 Size of files: 32,643 kB Homepage: http://www.boost.org/ Description: Boost Libraries for C++ License: Boost-1.0 * dev-python/boostpythongenerator Latest version available: 0.3.3 Latest version installed: [ Not Installed ] Size of files: 31 kB Homepage: http://www.pyside.org/ Description: A tool for creating Python bindings for C++ libraries License: LGPL-2.1 * dev-util/boost-build Latest version available: 1.42.0 Latest version installed: 1.42.0 Size of files: 32,643 kB Homepage: http://www.boost.org/doc/tools/build/index.html Description: A system for large project software construction, which is simple to use and powerful. License: Boost-1.0 #
Created attachment 223267 [details] config.log
I wonder if the upstream could be asked to package this program correctly, that is to include configure.ac and any custom m4 macros they've used.
Since boost-1.42 static libraries aren't build by default (needs USE="static-libs"). The configure script checks for the static libs instead of the shared, but it compiles fine without the static libs (after hacking the configure script).
Please check the vaal-1.6 commit, should be fixed.
Created attachment 248187 [details] build.log from 1.6 1.6 fails somewhere else.
Martin, that's a distcc configuration error. Please turn distcc off before reporting. -ak
Actually, I see now that the problem is the autocasting issue previously seen on x86. Unfortunately I don't have time to support x86, so I've dropped the keyword for it. Feel free to supply the patch - it will have to fix all casting issues that you see of the type that shows up in your build log.
I tried to contact upstream at crdhelp@broadinstitute.org but no answer for a month. :(
(In reply to comment #10) > I tried to contact upstream at crdhelp@broadinstitute.org but no answer for a > month. :( > Upstream said: I'm sorry to report that VAAL does not support 32-bit Linux, only 64-bit Linux. This requirement exists because we usually allocate more then 4GBs of RAM. We apologize for the inconvenience. However, they did not answer to the other issues in this bug report. :( Anyway, unless somebody provides a patch drop x86 ARCH from the ebuild.
+ 25 Jun 2012; Justin Lecher <jlec@gentoo.org> -vaal-1.2-r1.ebuild, + vaal-1.6.ebuild, files/vaal-1.6-respect-flags.patch: + Drop old, #309127; Handle openmp, don't install license +
