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.)
