Bug 118832 – sci-biology/rebase-512 should be stabilised

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Olivier Fisette (RETIRED) 2006-01-12 18:53:12 UTC]

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,

[Comment 1 Olivier Fisette (RETIRED) 2006-01-12 18:57:46 UTC]

Fixed summary. Sorry for the spam.

[Comment 2 Patrick McLean 2006-01-12 20:15:59 UTC]

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

[Comment 3 Tobias Scherbaum (RETIRED) 2006-01-14 00:54:32 UTC]

Created attachment 77054 [details]
test-case output on ppc

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

[Comment 4 Fabian Groffen 2006-01-14 01:37:04 UTC]

Created attachment 77059 [details, diff]
test case output ppc-macos

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

[Comment 5 Olivier Fisette (RETIRED) 2006-01-14 07:37:37 UTC]

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.)

[Comment 6 Tobias Scherbaum (RETIRED) 2006-01-14 07:45:28 UTC]

(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 :)

[Comment 7 Fabian Groffen 2006-01-14 07:51:43 UTC]

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

[Comment 8 Marcus D. Hanwell (RETIRED) 2006-01-14 18:49:04 UTC]

Stable on amd64 too.

[Comment 9 Markus Rothe (RETIRED) 2006-01-18 13:29:08 UTC]

late, but done: stable on ppc64.