Bugzilla Bug 230693

Hi all!

This is my first ebuild ;-D I'm a Gentoo noob, but i try...

I'm trying to emerge sci-chemistry/coot on my phenom cpu, but some sources
won't compile. Here is the first one I tried to improve: sci-chemistry/reduce.

The developers homepage contains a new version, so I took the new source and
wrote the new ebuild based on the old one and hope it's O.K.

The compiled program works on amd64, i tell you soon if it works on x86.

Thanx 4 Gentoo
Philipp

Portage 2.2_rc1 (default/linux/amd64/2008.0/desktop, gcc-4.3.1,
glibc-2.8_p20080602-r0, 2.6.25-gentoo-r6 x86_64)
=================================================================
System uname:
Linux-2.6.25-gentoo-r6-x86_64-AMD_Phenom-tm-_9750_Quad-Core_Processor-with-glibc2.2.5
Timestamp of tree: Thu, 03 Jul 2008 12:45:01 +0000
app-shells/bash:     3.2_p39
dev-java/java-config: 1.3.7, 2.1.6-r1
dev-lang/python:     2.4.4-r13, 2.5.2-r5
sys-apps/baselayout: 2.0.0
sys-apps/openrc:     0.2.5
sys-apps/sandbox:    1.2.18.1-r3
sys-devel/autoconf:  2.13, 2.62-r1
sys-devel/automake:  1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1-r1
sys-devel/binutils:  2.18-r2
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   2.2.4
virtual/os-headers:  2.6.25-r4
ACCEPT_KEYWORDS="amd64 ~amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=amdfam10 -O2 -pipe"
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/config /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/
/etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release
/etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/
/etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo
/etc/udev/rules.d"
CXXFLAGS="-march=amdfam10 -O2 -pipe"
DISTDIR="/data/gentoo/distfiles"
FEATURES="distlocks parallel-fetch preserve-libs sandbox sfperms strict
unmerge-orphans userfetch"
GENTOO_MIRRORS="ftp://linux.rz.ruhr-uni-bochum.de/gentoo-mirror/
ftp://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ http://distfiles.gentoo.org
http://www.ibiblio.org/pub/Linux/distributions/gentoo"
LANG="de_DE.UTF-8"
LDFLAGS=""
LINGUAS="de"
MAKEOPTS="-j5"
PKGDIR="/data/gentoo/pkg/k10-v1"
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/layman/zen-overlay
/usr/local/portage/local-overlay"
SYNC="rsync://192.168.26.242/gentoo-portage"
USE="# #prozzi 3dnow 3dnowext X Xaw3d a52 aac acl acpi alsa amd64 apache2 avahi
avc bash-completion berkdb bluetooth branding bzip2 cairo cdda cddb cdio cdr
cli compiz cracklib crypt css cups dbus dc1394 divx dlloader dri dts dv dvb dvd
dvdr dvdread eds emboss encode esd evo exif fam ffmpeg fftw fglrx firefox flac
font-server fontconfig fortran framebuffer gd gdbm gif gimp gnome gpm gstreamer
gtk hal httpd iconv id3tag ieee1394 imagemagic imap ipv6 isdnlog java joystick
jpeg kde kerberos latex ldap libgcrypt libnotify mad matroska md5sum
mdnsresponder-compat mesa midi mikmod mmx mmx2 mmxext mono mp2 mp3 mp4 mpeg
mplayer mudflap multilib musepack musicbrainz mysql ncurses netpbm
new-interface nls nptl nptlonly odbc ogg opengl openmp pam pcre pda pdf perl
php pic png ppds pppd pvr python qt3 qt3support qt4 quicktime rar raw readline
reflection samba sdl sdl-image session slang spell spl sse sse2 sse3 sse4a ssl
startup-notification svg swat symlink tcpd tiff tk truetype unicode unzip v4l
v4l2 vcd vcdx vorbis wifi wmf wxwindows x11 x264 xinerama xlib xml xorg
xulrunner xv xvid zip 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 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"
APACHE2_MPMS="prefork" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev"
KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001
mtxorb ncurses text" LINGUAS="de" USERLAND="GNU" VIDEO_CARDS="fglrx"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL,
PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

Created an attachment (id=159475) [edit]
ebuild

I set the environment variable REDUCE_HET_DICT to the old HET directory 'cause
the manual don't tell anything about the new.

The important part here is to keep coot working. Does coot actually work with
version 3 pdb's, with the reduce/probe integration?

Coot should work with the old version which is the default in this ebuild. If
anybody wants to test the new HET directory then the /etc/env.d/20reduce should
be changed:

old
REDUCE_HET_DICT="/usr/share/reduce/reduce_het_dict.txt"

new
REDUCE_HET_DICT="/usr/share/reduce/reduce_wwPDB_het_dict.txt"

I can't test it because my coot installation stops at sci-libs/cifparse-obj
compilation. I can't compile this library even from scratch. More in another
bug...

I just bumped this. Thanks for looking into exactly what needed to change! I
didn't base the bump off your ebuild, though -- I tried to minimize changes
from the existing one instead.