The vienna-rna ebuild -- which is not marked neither amd64 nor ~amd64 -- does not compile on AMD64, unless one adds -fPIC to CFLAGS. After having done that, though, the ebuild installs fine and seems to work (after trying out just RNAduplex). emerge --info: Portage 2.0.54 (default-linux/amd64/2005.1, gcc-3.4.4, glibc-2.3.5-r2, 2.6.15-gentoo-r1 x86_64) ================================================================= System uname: 2.6.15-gentoo-r1 x86_64 AMD Opteron(tm) Processor 246 Gentoo Base System version 1.6.14 ccache version 2.3 [enabled] dev-lang/python: 2.3.5-r2, 2.4.2 sys-apps/sandbox: 1.2.12 sys-devel/autoconf: 2.13, 2.59-r6 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.16.1 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.11-r2 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="" ARCH="amd64" AUTOCLEAN="yes" BASH_ENV="/etc/spork/is/not/valid/profile.env" CBUILD="x86_64-pc-linux-gnu" CCACHE_DIR="/var/tmp/ccache" CCACHE_SIZE="2G" CDEFINE_amd64="__x86_64__" CDEFINE_x86="__i386__" CFLAGS="-march=opteron -mtune=opteron -O2 -pipe" CFLAGS_x86="-m32 -L/emul/linux/x86/lib -L/emul/linux/x86/usr/lib" CHOST="x86_64-pc-linux-gnu" CHOST_amd64="x86_64-pc-linux-gnu" CHOST_x86="i686-pc-linux-gnu" CLEAN_DELAY="5" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" CXXFLAGS="-march=opteron -mtune=opteron -O2 -pipe" DEFAULT_ABI="amd64" DISTDIR="/usr/portage/distfiles" ELIBC="glibc" EMERGE_WARNING_DELAY="10" FEATURES="autoconfig buildpkg ccache distlocks fixpackages sandbox sfperms strict" FETCHCOMMAND="/usr/bin/wget -t 5 --passive-ftp -P ${DISTDIR} ${URI}" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" HOME="/home/dl" KERNEL="linux" LDFLAGS_x86="-m elf_i386 -L/emul/linux/x86/lib -L/emul/linux/x86/usr/lib" LIBDIR_amd64="lib64" LIBDIR_x86="lib32" LOGNAME="root" MAKEOPTS="-j3" MULTILIB_ABIS="x86 amd64" MULTILIB_STRICT_DENY="64-bit.*shared object" MULTILIB_STRICT_DIRS="/lib /usr/lib /usr/kde/*/lib /usr/qt/*/lib /usr/X11R6/lib" MULTILIB_STRICT_EXEMPT="(perl5|gcc|gcc-lib|eclipse-3|debug|portage)" PATH="/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/3.4.4:/opt/stuffit/bin:/opt/blackdown-jdk-1.4.2.02/bin:/opt/blackdown-jdk-1.4.2.02/jre/bin:/usr/qt/3/bin:/usr/kde/3.4/sbin:/usr/kde/3.4/bin:/usr/kde/3.3/sbin:/usr/kde/3.3/bin" PKGDIR="/usr/portage/packages" PORTAGE_ARCHLIST="alpha amd64 arm hppa ia64 m68k mips ppc ppc64 ppc-macos s390 sh sparc x86" PORTAGE_BINHOST_CHUNKSIZE="3000" PORTAGE_CALLER="emerge" PORTAGE_GID="250" PORTAGE_MASTER_PID="15749" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PRELINK_PATH="" PRELINK_PATH_MASK="" RESUMECOMMAND="/usr/bin/wget -c -t 5 --passive-ftp -P ${DISTDIR} ${URI}" RPMDIR="/usr/portage/rpm" RSYNC_RETRIES="3" RSYNC_TIMEOUT="180" SHELL="/bin/bash" SUDO_COMMAND="/usr/bin/emerge -av --info" SUDO_GID="100" SUDO_UID="1000" SUDO_USER="dl" SYMLINK_LIB="yes" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" TERM="screen" USE="amd64 X a52 alsa apache2 audiofile avi bash-completion berkdb bitmap-fonts bzip2 cairo cdparanoia crypt cups curl divx4linux dv dvdread eds emboss encode exif expat fam fame flac foomaticdb fortran freetype gd gdbm gif glitz glut glx gmp gpm gstreamer gtk gtk2 idn imagemagick imap imlib ipv6 java jpeg junit kde lcms libwww livecd lzw lzw-tiff mng modperl motif mozdevelop mozilla mozsvg mp3 mpeg mpi mpm-prefork ncurses nls nptl nsplugin ogg opengl oss pam pcre pdflib perl png ppds python qt quicktime readline ruby sdl smp spell ssl syslog tcltk tcpd tetex threads tiff tlctk truetype truetype-fonts type1-fonts udev unicode usb userlocales vorbis wxgtk1 xml2 xpm xprint xv zlib userland_GNU kernel_linux elibc_glibc" USER="root" USERLAND="GNU" USE_EXPAND="FRITZCAPI_CARDS FCDSL_CARDS VIDEO_CARDS DVB_CARDS INPUT_DEVICES LINGUAS USERLAND KERNEL ELIBC" XARGS="xargs -r"
applying -fPIC to the whole package is not acceptable, please provide a patch for the build-system to only compile shared libraries with -fPIC
