Bugzilla Bug 108340

"sci-biology/t-coffee-2.66" should be stabilised on supporting arches.

Could you provide some sort of test to preform?  I must admit I've got no clue
what this package 
does, and the description just loses me more :)  Can you give a testcase for
functionality checks? 

Links to a random sample of .fasta and .aln files would be nice.  Preferably
ones that are know to be of correct Syntax and format, and play nice with the
available online servers.
We can Read the manual to get the execution sequence.

Also, after completion, how do we know it is correct. (For all us "ribosome is a
thing in a Cell Right" kinda people)

Created an attachment (id=70497) [details]
sample_seq1.aln - Sample sequence alignment for testing

Sure :)

After compiling t-coffee, copy the "sample_seq1.fasta" file from
"/usr/share/t-coffee/example" to your home directory. This file contains the
amino acid sequences for four homologs of a protein in different species.

Run "t_coffee sample_seq1.fasta" to have t-coffee align the sequences,
calculate the alignment scores, construct a dendrogram, etc. Output files are
created in the working directory.

At the end, file "t_coffee.log" should contain only the names of the aligned
proteins, no error or warning message. You can check the validity of the
calculations by comparing the file "sample_seq1.aln" with the file I am
attaching. (This output file is also available in the example directory, but it
was created with an old version of the program, and the formatting is a bit
different so you would have to compare the files manually. With the provided
file, a diff should suffice.) The only difference between the files should be
the CPU time used for the calculations. (And even this may not differ since
small calculations like those require almost 0 CPU time.)

Thanks,

Thanks :) Working fine for me here... no difference at all between the two, and
no errors/warnings 
when running any of the tests here  


Portage 2.0.53_rc5 (default-linux/x86/2005.1, gcc-3.3.6, glibc-2.3.5-r1,
2.6.12-9-386 i686) 
================================================================= 
System uname: 2.6.12-9-386 i686 AMD Athlon(tm) XP 2500+ 
Gentoo Base System version 1.6.13 
dev-lang/python:     2.3.5-r2, 2.4.1-r1 
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:  2.15.92.0.2-r10 
sys-devel/libtool:   1.5.18-r1 
virtual/os-headers:  2.6.11-r2 
ACCEPT_KEYWORDS="x86" 
AUTOCLEAN="yes" 
CBUILD="i686-pc-linux-gnu" 
CFLAGS="-O2 -march=athlon-xp -pipe" 
CHOST="i686-pc-linux-gnu" 
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config
/usr/share/config /var/qmail/control" 
CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" 
CXXFLAGS="-O2 -march=athlon-xp -pipe" 
DISTDIR="/usr/portage/distfiles" 
FEATURES="autoconfig distlocks maketest sandbox sfperms strict test" 
GENTOO_MIRRORS="http://gentoo.mirrors.pair.com http://gentoo.mirrors.tds.net" 
LANG="en_US.UTF-8" 
PKGDIR="/usr/portage/packages" 
PORTAGE_TMPDIR="/var/tmp" 
PORTDIR="/usr/portage" 
SYNC="rsync://rsync.gentoo.org/gentoo-portage" 
USE="x86 X alsa apache2 apm arts avi berkdb bitmap-fonts crypt curl eds emboss
encode fam flac 
foomaticdb fortran gd gdbm gif gnome gpm gstreamer gtk gtk2 imlib ipv6 jpeg kde
libg++ libwww 
mad mikmod motif mp3 mpeg mysql ncurses nls ogg oggvorbis opengl oss pam pdflib
perl png 
python qt quicktime readline sdl spell ssl tcpd truetype truetype-fonts
type1-fonts vorbis xine xml2 
xmms xv zlib userland_GNU kernel_linux elibc_glibc" 
Unset:  ASFLAGS, CTARGET, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS, PORTDIR_OVERLAY 

For the sake of completeness, Oliver could you provide a more taxing sequence
to
'stress test' t_coffee, Perhaps one that would take 15min of cpu time.

Completed simple test as per Oliver.
No Errors, compiled without issue.

Portage 2.0.51.22-r3 (default-linux/x86/2005.0, gcc-3.3.6, glibc-2.3.5-r2,
2.6.11-hardened-r15 i686)
=================================================================
System uname: 2.6.11-hardened-r15 i686 AMD Athlon(tm) XP 2200+
Gentoo Base System version 1.6.13
distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632)
[disabled]
ccache version 2.3 [disabled]
dev-lang/python:     2.3.5-r2, 2.4.1-r1
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:  2.15.92.0.2-r10
sys-devel/libtool:   1.5.18-r1
virtual/os-headers:  2.6.11-r2
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -mcpu=athlon-xp -march=athlon-xp -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config
/usr/share/config /var/bind /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-O2 -mcpu=athlon-xp -march=athlon-xp -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks sandbox sfperms strict"
GENTOO_MIRRORS="http://distfiles.gentoo.org
http://distro.ibiblio.org/pub/Linux/distributions/gentoo"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 alsa apache2 apm arts avi berkdb bitmap-fonts crypt cups curl doc eds
emboss encode foomatic foomaticdb fortran gd gdbm gif gpm gstreamer imagemagick
imlib innodb ipv6 jpeg libg++ libwww mad mikmod motif mp3 mpeg mysql ncurses
nls
ogg oggvorbis opengl oss pam pdflib perl png postgres ppds python pyton
quicktime readline samba sdl spell ssl tcpd tiff truetype truetype-fonts
type1-fonts vorbis xml2 xmms xv zlib userland_GNU kernel_linux elibc_glibc"
Unset:  ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS,
PORTDIR_OVERLAY

Created an attachment (id=70521) [details]
glxrs.fasta - Sample sequences for testing

Created an attachment (id=70522) [details]
glxrs.aln - Sample sequence alignment for testing

Why not? Let us align 32 sequences, and iterate the process by extracting each
sequence in turn and realigning it with the multiple sequence alignment (after
the initial MSA is computed). Download the "glxrs.fasta" file and execute:
"t_coffee -iterate -1 -seq glxrs.fasta". You can then compare the resulting
alignment with the one I am attaching.

New Test completed.
No Errors/warnings.

Same emerge info as above. No need to restate.

Recommend Stable.

x86 done

Thanks for the tests, Lares.  
  
(BTW, stabilise is the correct ortograph in British/European/Australian 
English. Stabilize is the American ortograph. ;-)  

Seems to work alright on ppc too, thanks for giving us something to test with.
:)

All arches are done.