Bugzilla Bug 153766

I would like all supporting arches to please stabilise EMBOSS 4.0.0 and related
packages. These were already stabilised on x86.

On amd64, ppc64:

sci-biology/prosite-19.36
sci-biology/rebase-610
sci-biology/aaindex-9.1
sci-biology/cutg-151
sci-biology/emboss-4.0.0

On ppc, ppc-macos:

sci-biology/prosite-19.36
sci-biology/rebase-610
sci-biology/aaindex-9.1
sci-biology/cutg-151
sci-biology/emboss-4.0.0
sci-biology/embassy-domainatrix-0.1.0-r1
sci-biology/embassy-domalign-0.1.0-r1
sci-biology/embassy-domsearch-0.1.0-r1
sci-biology/embassy-emnu-1.05-r3
sci-biology/embassy-esim4-1.0.0-r3
sci-biology/embassy-hmmer-2.3.2
sci-biology/embassy-memenew-0.1.0
sci-biology/embassy-mse-1.0.0-r3
sci-biology/embassy-phylipnew-3.6b
sci-biology/embassy-signature-0.1.0-r1
sci-biology/embassy-structure-0.1.0-r1
sci-biology/embassy-topo-1.0.0-r3
sci-biology/embassy-4.0.0

On sparc:

None of these packages were ever stable on sparc, but I know they work
perfectly at least on the (limited) sparc hardware I have access to. If you are
interested in supporting EMBOSS in the stable branch, the following packages
should be stabilised. Otherwise, feel free to remove your team from CC. In all
cases, you really need to remove emboss from use.mask in the sparc profiles,
but I will open another report for that.

sci-biology/primer3-1.0.0
sci-biology/aaindex-9.1
sci-biology/cutg-151
sci-biology/prints-38.0
sci-biology/prosite-19.36
sci-biology/rebase-610
sci-biology/transfac-3.2
sci-biology/emboss-4.0.0

Do you have some test cases for these packages please?

Created an attachment (id=101091) [details]
Small test suite for EMBOSS on Gentoo

Sure. Here is a small test suite. If you think something more involved is
necessary, just tell me, but I am pretty confident that if this runs correctly
and produces correct results, your EMBOSS installation is fine.

ppc-macos fully moved into prefix

Ok, the test script runs ok. Output seems ok as far as I can figure it out.
ppc done

Created an attachment (id=101225) [details]
Output of emboss test-script

Olivier: I presume the attached output is not what it should look like, is it?
This is on amd64, please advise.

Created an attachment (id=101248) [details]
output from test script

Here's my output on amd64...I'm not sure what's wrong with yours. What
character encoding are you using?

ppc64 stable

Created an attachment (id=102270) [details]
Another emboss test suite output

Let's add a third test on amd64, looks ok, so the problem seems to be on your
end, Kugelfang...

Emerges fine for me and seems to work ok.

Portage 2.1.1-r1 (default-linux/amd64/2006.1/desktop, gcc-4.1.1, glibc-2.4-r4,
2.6.18-suspend2-Dudebox-Edition x86_64)
=================================================================
System uname: 2.6.18-suspend2-Dudebox-Edition x86_64 AMD Athlon(tm) 64
Processor 3200+
Gentoo Base System version 1.12.6
Last Sync: Sat, 18 Nov 2006 05:00:01 +0000
distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632)
[enabled]
ccache version 2.3 [enabled]
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: 1.3.7, 2.0.30
dev-lang/python:     2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.3
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.60
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-r3
sys-devel/gcc-config: 1.3.13-r4
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.11-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=k8 -msse3 -Os -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/X11/xkb /usr/share/config /var/qmail/alias
/var/qmail/control /var/vpopmail/domains /var/vpopmail/etc"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf
/etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c"
CXXFLAGS="-march=k8 -msse3 -Os -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache collision-protect distcc distlocks
metadata-transfer multilib-strict parallel-fetch sandbox sfperms strict test"
GENTOO_MIRRORS="ftp://linux.rz.ruhr-uni-bochum.de/gentoo-mirror/
ftp:///ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/"
LDFLAGS="-Wl,-O1"
MAKEOPTS="-j4"
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_overlay"
SYNC="rsync://server/gentoo-portage"
USE="amd64 X alsa apache2 berkdb bitmap-fonts cairo cdr cli cracklib crypt cups
dbus dlloader dri dvd dvdr eds elibc_glibc emboss encode esd fam firefox
fortran gcj gdbm gif gpm gstreamer gtk gtk2 hal iconv imap
input_devices_keyboard input_devices_mouse isdnlog jpeg kde kdeenablefinal
kdehiddenvisibility kernel_linux libg++ mad mikmod mp3 mpeg mysql ncurses nls
nptl nptlonly objc objc++ ogg oss pam pcre perl png ppds pppd python qt3
quicktime readline reflection sdl session spell spl sqlite ssl tcpd test
truetype truetype-fonts type1-fonts udev unicode userland_GNU
video_cards_radeon vorbis xml xorg xv zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS,
PORTAGE_RSYNC_EXTRA_OPTS

amd64 done

All arches done. Thanks to everyone.