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Bug 108816 - mrbayes works perfectly but could use ~amd64 KEYWORD
Summary: mrbayes works perfectly but could use ~amd64 KEYWORD
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: AMD64 Linux
: High enhancement
Assignee: AMD64 Project
URL:
Whiteboard:
Keywords: TESTED
Depends on:
Blocks:
 
Reported: 2005-10-10 20:23 UTC by Ashton Trey Belew
Modified: 2006-09-12 13:51 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---

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Description Ashton Trey Belew 2005-10-10 20:23:06 UTC 
I only tested with an old alignment, but the tree generated looked sane.

Reproducible: Always
Steps to Reproduce:
1.
2.
3.
Comment 1 AJ Armstrong 2006-01-08 16:00:15 UTC 
Tested sci-biology/mrbayes-3.1.1 for ~amd64.

Compiles, installs and loads.  Ran through tutorial at http://mrbayes.csit.fsu.edu/wiki/index.php/Tutorial , and was able to generate the following:

Phylogram:

   /-------------------------------- Tarsius_syrichta (1)
   |                                                                               
   |----------------------- Lemur_catta (2)
   |                                                                               
   |                                                   /------- Homo_sapiens (3)
   |                                               /---+                           
   |                                               |   \--------- Pan (4)
   |                                      /--------+                               
   |                                      |        \---------- Gorilla (5)
   |                                 /----+                                        
   +                                 |    \---------------- Pongo (6)
   |                        /--------+                                             
   |                        |        \------------------- Hylobates (7)
   |                        |                                                      
   |                        |                              /--- Macaca_fuscata (8)
   |               /--------+                         /----+                       
   |               |        |                         |    \---- M_mulatta (9)
   |               |        |                   /-----+                            
   |               |        |                   |     \-------- M_fascicularis (10)
   \---------------+        \-------------------+                                  
                   |                            \----------- M_sylvanus (11)
                   |                                                               
                   \------------------------------- Saimiri_sciureus (12)

Which looks (at least to me) to be working.  I fail to see how the Flying Spaghetti Monster figures in, thought.

Tests good for ~amd64
Portage 2.0.53 (default-linux/amd64/2005.1, gcc-4.0.2, glibc-2.3.6-r1, 2.6.14-gentoo-r5 x86_64)
=================================================================
System uname: 2.6.14-gentoo-r5 x86_64 AMD Athlon(tm) 64 Processor 3500+
Gentoo Base System version 1.6.13
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:   1.5.20
virtual/os-headers:  2.6.11-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.4/env /usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/kde/3/share/config /usr/lib/X11/xkb /usr/lib64/mozilla/defaults/pref /usr/share/config /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks multilib-strict sandbox sfperms strict"
GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/etc/portage/overlay"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="amd64 alsa avi berkdb bitmap-fonts bzip2 crypt cups eds emboss encode expat foomaticdb fortran gdbm gif gmp gpm gstreamer gtk2 imlib ipv6 java jpeg ldap lzw lzw-tiff mp3 mpeg mysql ncurses nls opengl pam pdflib perl png python quicktime readline ruby sdl spell ssl tcpd tiff truetype-fonts type1-fonts udev usb userlocales xpm xv zlib userland_GNU kernel_linux elibc_glibc"
Unset:  ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS
Comment 2 Homer Parker (RETIRED) gentoo-dev 2006-01-08 16:26:39 UTC 
Fixed in cvs, thanks for reporting/testing
Comment 3 Olivier Fisette (RETIRED) gentoo-dev 2006-09-12 13:51:22 UTC 
Just for the record, I had to remove the amd64 keyword from the ebuilds, as the code is not 64-bit safe. For instance, the sumt function will always segfault on 64-bit archs. Upstream has no fix yet.