Bugzilla Bug 118832

I would like all supporting arches to please stabilise   
sci-biology/rebase-512. Here is a (small) test case using EMBOSS:  

$ wget pelican.rsvs.ulaval.ca/distfiles/seq/phikz-orf144.fasta  
$ wget pelican.rsvs.ulaval.ca/distfiles/seq/phikz-orf144-ref.restrict  
$ restrict -enzymes all -sitelen 4 phikz-orf144.fasta phikz-orf144.restrict  
$ diff -u phikz-orf144-ref.restrict phikz-orf144.restrict 

The only difference should be the timestamp of the report.    

Thanks in advance,

Fixed summary. Sorry for the spam.

Works fine on amd64.

Portage 2.1_pre3-r1 (default-linux/amd64/2005.1, gcc-3.4.5, glibc-2.3.6-r2,
2.6.15-gentoo x86_64)
=================================================================
System uname: 2.6.15-gentoo x86_64 AMD Athlon(tm) 64 Processor 3400+
Gentoo Base System version 1.12.0_pre13
dev-lang/python:     2.4.2
sys-apps/sandbox:    1.2.17
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-r1
sys-devel/binutils:  2.16.1-r1
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.11-r3
ACCEPT_KEYWORDS="amd64 ~amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=athlon64 -O3 -fomit-frame-pointer -ffast-math -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config
/usr/lib64/mozilla/defaults/pref /usr/share/X11/xkb /usr/share/config
/var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/texmf/web2c /etc/env.d"
CXXFLAGS="-march=athlon64 -O3 -fomit-frame-pointer -ffast-math -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks multilib-strict sandbox sfperms strict"
GENTOO_MIRRORS="ftp://cs.ubishops.ca/pub/gentoo ftp://gentoo.risq.qc.ca
http://gentoo.oregonstate.edu http://distfiles.gentoo.org"
LDFLAGS="-Wl,-O1"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage /usr/local/mod-x"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="amd64 X a52 aac aalib alsa audiofile avi bash-completion berkdb
bitmap-fonts bmp bzip2 c++ cairo caps cdparanoia cdr crypt cscope css cups curl
dbus doc dri dts dv dvd dvdr dvdread dvi edl eds emboss encode esd ethereal evo
exif expat fam fat ffmpeg fftw flac foomaticdb fortran gb gcj gd gdbm gif gimp
gimpprint glitz glut gmail gmp gnome gnutls gphoto2 gpm gstreamer gtk gtk2
guile gzip hal hfs howl idea idn ieee1394 imagemagick imap imlib imlib2
iproute2 jabber java jfs jpeg junit lcms libcaca libgda libwww linuxkeys live
lzo lzw lzw-tiff mad matroska mikmod mmap mng mod mono mozdevelop mozilla
mozsvg mp3 mpeg mplayer msn mythtv native nautilus ncurses network nfs nls
no-old-linux no_wxgtk1 noantlr nob nobcel nobeanutils nobsh nocommonslogging
nocommonsnet nojsch nolog4j nomotif noplugin norhino noxalan noxerces nptl
nptlonly offensive ogg oggvorbis openal opengl pam pcre pda pdflib perl plugin
png python quicktime radeon readline real reiserfs rtc ruby samba sdl slang
sndfile speex spell sqlite ssl stream subversion svg tcltk tcpd tetex tga
theora tiff transcode truetype truetype-fonts type1-fonts udev unicode usb
userlocales v4l v4l2 vcd vorbis wmf wxwindows xanim xine xml2 xpm xprint
xscreensaver xv xvid xvmc zlib elibc_glibc kernel_linux userland_GNU"
Unset:  ASFLAGS, CTARGET, LANG, LC_ALL, LINGUAS

Created an attachment (id=77054) [edit]
test-case output on ppc

Tested on ppc, the test-case differs on more than the timestamp. Please have a
look.

Created an attachment (id=77059) [edit]
test case output ppc-macos

I also get diffs.  Different ones than ppc.  See attach.

Fabian/mac-os:

If you sort your diff, you will see that the only differences are the order of
appearance of the enzymes in the list. (This is not obvious at first glance
because there are so many hits.) Given this output, I think you can go ahead
and stabilise the package. (I will provide a better test case next time.)

Tobias/ppc:

This is an interesting case where lots of enzymes match the same restriction
pattern (isoschizomers) and only one of them is printed. The embossre.equ file
determines the enzyme to print (prototype enzyme). However, for some less known
isoschizomers, no prototype is available, so the chosen enzyme may vary. This
is not a problem. Given this output, I think you can go ahead and stabilise the
package. (I will issue EMBOSS and Rebase revisions that will force prototypes
that are consistent across arches in the future.)

(In reply to comment #5)
> Tobias/ppc:
> 
> This is an interesting case where lots of enzymes match the same restriction
> pattern (isoschizomers) and only one of them is printed. The embossre.equ file
> determines the enzyme to print (prototype enzyme). However, for some less known
> isoschizomers, no prototype is available, so the chosen enzyme may vary. This
> is not a problem. Given this output, I think you can go ahead and stabilise the
> package. (I will issue EMBOSS and Rebase revisions that will force prototypes
> that are consistent across arches in the future.)
> 

ppc stable, thanks Olivier :)

ppc-macos stable.  Thanks Olivier for all your help.

Stable on amd64 too.

late, but done: stable on ppc64.