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Bug 115468 - sci-biology/phylip-3.65-r1 should be stabilised
Summary: sci-biology/phylip-3.65-r1 should be stabilised
Status: RESOLVED CANTFIX
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Olivier Fisette (RETIRED)
URL:
Whiteboard:
Keywords:
Depends on: 115482
Blocks:
  Show dependency tree
 
Reported: 2005-12-13 14:45 UTC by Olivier Fisette (RETIRED)
Modified: 2006-01-21 08:40 UTC (History)
1 user (show)

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


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Description Olivier Fisette (RETIRED) gentoo-dev 2005-12-13 14:45:02 UTC
I would like all supporting arches to please stabilise    
sci-biology/phylip-3.65. Here is how to test the package:    
     
Prepare the testing environment:      
  $ mkdir phylip-test      
  $ cd phylip-test      
  $ wget pelican.rsvs.ulaval.ca/distfiles/seq/glxrs.phylip     
  $ wget pelican.rsvs.ulaval.ca/distfiles/seq/consense-ref.tree     
  $ cp /usr/share/phylip/fonts/font1 .     
     
Bootstrap the alignment (create 100 small sequence variations that will be     
used to assess the robustness of the tree):     
  $ cp glxrs.phylip infile      
  $ seqboot      
  (Accept default parameters, use seed 13.)      
  $ cp outfile seqboot.out      
  $ rm infile outfile     
     
Construct phylogenetic trees (one for each of the 100 variants) using the     
parsimony algorithm:     
  $ cp seqboot.out infile      
  $ protpars     
  (Accept default parameters.)     
  $ cp outfile protpars.out     
  $ cp outtree protpars.tree     
  $ rm infile outfile outtree     
     
Calculate the consensus for all 100 trees:     
  $ cp protpars.tree intree     
  $ consense     
  (Accept default parameters.)     
  $ cp outfile consense.out     
  $ cp outtree consense.tree     
  $ rm intree outfile outtree     
     
Compare the tree with the reference one:     
  $ diff -u consense-ref.tree consense.tree     
  (There should not be any difference between the two files.)     
     
Draw the tree on screen:     
  $ cp consense.tree intree     
  $ drawgram     
  (Use font1 as the fontfile, accept default parameters.)     
  (The tree should be drawn in a new X window.)     
  File > Quit   
   
If the computed tree is identical to the reference one, and the tree can be   
drawn on screen, PHYLIP is working.  
 
Thanks in advance,
Comment 1 Lares Moreau 2005-12-13 16:45:46 UTC
This is actually a blocker.  THis bug cannot go to stable before this collision
is fixed.
Comment 2 Lares Moreau 2005-12-13 16:58:03 UTC
Everything works according to test procedure.  Recommend stable after collision fix.
Comment 3 Olivier Fisette (RETIRED) gentoo-dev 2005-12-14 08:31:33 UTC
Collision fixed. Ebuild to stabilise is 3.65-r1. 
Comment 4 Petteri Räty (RETIRED) gentoo-dev 2005-12-14 08:45:20 UTC
DEPEND="virtual/libc
        virtual/x11"

phylip is not part of the system and as such the virtual/libc dependency should
not be there.
Comment 5 Olivier Fisette (RETIRED) gentoo-dev 2005-12-14 10:58:18 UTC
I am unclear about the dependency on virtual/libc. It has been in the ebuild   
ever since it was commited to Portage and there are lots of other packages   
that depend on libc that have nothing to do with system. On the other hand,  
most packages in the tree depend on libc but do not declare it. Could you  
explain what virtual/libc is for in more details? Should dependencies on  
virtual/libc be removed from all non-system packages? (I could not find a 
tracker bug for that.) 
Comment 6 Petteri Räty (RETIRED) gentoo-dev 2005-12-14 11:52:33 UTC
(In reply to comment #5)
> I am unclear about the dependency on virtual/libc. It has been in the ebuild   
> ever since it was commited to Portage and there are lots of other packages   
> that depend on libc that have nothing to do with system. On the other hand,  
> most packages in the tree depend on libc but do not declare it. Could you  
> explain what virtual/libc is for in more details? Should dependencies on  
> virtual/libc be removed from all non-system packages? (I could not find a 
> tracker bug for that.) 

http://dev.gentoo.org/~plasmaroo/devmanual//general-concepts/dependencies/

Yes, not everything in the tree is up to standards so that is why I like to do
checkups when people are asking stuff to be marked stable.

virtual/libc exists because we provide different alternatives for a c library
like uclibc.
Comment 7 Olivier Fisette (RETIRED) gentoo-dev 2005-12-14 12:07:03 UTC
Thanks for the explanation, Petteri. I removed the dependency (and will do so 
for other packages the sci herd maintains). 
Comment 8 Hasan Khalil (RETIRED) gentoo-dev 2005-12-14 13:10:34 UTC
(In reply to comment #0)
>   $ drawgram     
>   (Use font1 as the fontfile, accept default parameters.)     
>   (The tree should be drawn in a new X window.)     
>   File > Quit   
>    
> If the computed tree is identical to the reference one, and the tree can be   
> drawn on screen, PHYLIP is working.

This is the only part that fails on ppc-macos on my end. Otherwise, things work great. I'm not sure that 
phylip's X stuff is even supposed to work on Apple's X11 (there are native packages for the phylip GUI 
stuff IIRC). Apart from that, I'm happy with it. Let me know what you think.
Comment 9 Olivier Fisette (RETIRED) gentoo-dev 2005-12-14 13:27:17 UTC
Hasan:  
  
Your call. However, since there is already a stable version, I think you  
should either stabilise this one or put 3.64 back to ~ppc-macos too. If you  
decide to stabilise, maybe you should add a note regarding X11 support for  
MacOS users in the README.Gentoo.  
Comment 10 Fabian Groffen gentoo-dev 2005-12-14 13:42:32 UTC
also read the ppc-macos keywording policy thing, please.
Comment 11 Joshua Jackson (RETIRED) gentoo-dev 2005-12-14 19:14:36 UTC
stable on x86, thanks for the test cases :)
Comment 12 nixnut (RETIRED) gentoo-dev 2005-12-17 22:29:56 UTC
tested on ppc
works for me
Comment 13 Tobias Scherbaum (RETIRED) gentoo-dev 2005-12-23 11:37:51 UTC
ppc stable, thanks for testing nixnut :)
Comment 14 Hasan Khalil (RETIRED) gentoo-dev 2006-01-21 08:01:40 UTC
Sorry about the delays --  have been travelling.

I've dropped the stable keyword from phylip-3.64, in accordance with my interpretation of the intentions of the ppc-macos interim keywording policy.
Comment 15 Olivier Fisette (RETIRED) gentoo-dev 2006-01-21 08:40:38 UTC
Cannot be stabilised on ppc-macos.