As similar reports are found http://bugs.gentoo.org/show_bug.cgi?id=130851 and http://bugs.gentoo.org/show_bug.cgi?id=131883 some programs do not work nicely with make-3.81. ncbi-tools needs to have a requirement for 3.80-r4 in it right now in order to compile. On a related note, there are many updates to ncbi-tools (like 20060526) that would be nice to see, but those also suffer from this problem. # emerge --info Portage 2.1 (default-linux/amd64/2005.1, gcc-4.1.1/amd64-vanilla, glibc-2.4-r3, 2.6.16-suspend2-r5 x86_64) ================================================================= System uname: 2.6.16-suspend2-r5 x86_64 AMD Turion(tm) 64 Mobile Technology MT-40 Gentoo Base System version 1.12.1 dev-lang/python: 2.3.5-r2, 2.4.3-r1 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: [Not Present] dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.18.1 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r2 sys-devel/gcc-config: 2.0.0_rc1 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.16 ACCEPT_KEYWORDS="amd64 ~amd64" AUTOCLEAN="yes" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=k8 -pipe -O2 -mfpmath=sse -ftree-vectorize " CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/eselect/compiler /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-march=k8 -pipe -O2 -mfpmath=sse -ftree-vectorize " DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LDFLAGS="-Wl,-O1" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --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="amd64 3dnowex X acpi alsa apache2 avi berkdb bitmap-fonts cli crypt cups divx4linux dri dvdr emboss encode foomaticdb fortran gif gpm gstreamer gtk gtk2 hal ieee1394 imlib ipv6 isdnlog jpeg kde logrotate lzw lzw-tiff mp3 mpeg ncurses nls nptl nptlonly oggvorbis opengl pam pcre pdflib perl png pppd python qt quicktime readline reflection samba sdl session spell spl ssh ssl svg tcpd tiff truetype truetype-fonts type1-fonts usb vhosts xcomposite xml2 xorg xpm xscreensaver xv zlib elibc_glibc input_devices_keyboard input_devices_mouse input_devices_synaptics kernel_linux userland_GNU video_cards_fglrx video_cards_ati video_cards_vesa" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS
Hi Greg, Thanks for reporting. I just updated the NCBI tools in Portage to version 20060507, and switched to using pmake instead of GNU make for upstream Makefiles, which is the solution Debian also uses. (The proper solution would be to patch the Makefiles, so I am closing this as WONTFIX; the build system is extremely convoluted and I think no one is interested in wasting time fixing it.)
