Bug 96819 – Stabilising EMBOSS 2.10 on all arches

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Olivier Fisette (RETIRED) 2005-06-22 18:50:14 UTC]

EMBOSS 2.10 and its related EMBASSY packages have been in the tree for some time now and are not much different from version 2.9 except for some bug fixes. There are very few new features. Recent EMBOSS releases have always been very stable. I would like to get version 2.9 out of Portage. (And 2.10 might well be the last stable release ever given the actual pace of development...)

I would appreciate if the ppc and ppc-macos teams could stabilise EMBOSS and its EMBASSY packages as soon as possible. This means:

- sci-biology/emboss-2.10.0
- sci-biology/embassy-construct-1.0.0
- sci-biology/embassy-domainatrix-1.0.0-r1
- sci-biology/embassy-emnu-1.05-r1
- sci-biology/embassy-esim4-1.0.0-r1
- sci-biology/embassy-hmmer-2.1.1-r1
- sci-biology/embassy-meme-2.3.1-r1
- sci-biology/embassy-mse-1.0.0-r1
- sci-biology/embassy-phylip-3.57c-r1
- sci-biology/embassy-topo-1.0.0-r1

"r1" releases are identical to the initial releases, but built against 2.10 sources rather than 2.9. The only problem I can see is the new EMBASSY package CONSTRUCT, which is not keyworded ppc-macos.

Thanks,

[Comment 1 Joe Jezak (RETIRED) 2005-06-24 07:39:56 UTC]

Marked ppc stable.

[Comment 2 Lina Pezzella (RETIRED) 2005-06-24 20:26:01 UTC]

I'm having a bit of a problem with cutg, a dep of EMBOSS.

I get the following along with an empty /usr/share/cutg directory:

>>> Install cutg-147 into /var/tmp/portage/cutg-147/image/ category sci-biology
mv: rename *.codon to /var/tmp/portage/cutg-147/image//usr/share/cutg/*.codon: No such file or 
directory
mv: rename *.spsum to /var/tmp/portage/cutg-147/image//usr/share/cutg/*.spsum: No such file or 
directory
mv: rename * to /var/tmp/portage/cutg-147/image//usr/share/EMBOSS/data/CODONS/*: No such file 
or directory

[Comment 3 Olivier Fisette (RETIRED) 2005-06-25 07:16:07 UTC]

j4ag0n:  
  
Strange error. Version 145 is stable on ppc-macos. Is that broken too? 

[Comment 4 Lina Pezzella (RETIRED) 2005-06-25 13:34:40 UTC]

That is odd, I get the same error with cutg-145, although I don't remember getting those errors when I 
tested the package to go stable. Perhaps that is my bad memory though. ;-)

In any case, the files are not being installed to /usr/share/cutg.

[Comment 5 Olivier Fisette (RETIRED) 2005-06-25 14:39:25 UTC]

j4rg0n:  
  
"147-r1" is now in CVS. I'm not sure it will fix things, but at least the  
emerge will die rather than install an empty package. Could you test it? 

[Comment 6 Lina Pezzella (RETIRED) 2005-06-25 19:47:58 UTC]

Okay, after a bit of detective work, I find the following:

The .codon and .spsum files ARE being installed to the image. However, they're somehow being 
removed.

>>> Install cutg-147-r1 into /var/tmp/portage/cutg-147-r1/image/ category sci-biology
man:
prepallstrip:
strip: strip --strip-unneeded

This is what comes right before the error message I pasted before. At this point, ls shows me 
the .codon and .spsum files nicely installed to the image directory where they should be. I don't know 
what craziness happens afterwards.

Hope that helps.

[Comment 7 Olivier Fisette (RETIRED) 2005-06-25 20:44:01 UTC]

How strange :( It's not a disk space issue, is it? (This is more than a Gb of 
data...) 

[Comment 8 Lina Pezzella (RETIRED) 2005-06-25 21:10:18 UTC]

Definitely not a disk space issue. I have loads of disk space.

[Comment 9 Lina Pezzella (RETIRED) 2005-06-25 23:53:41 UTC]

I got ahold of a vanilla install on another machine to test. cutg installs fine there. I don't know what's 
wrong with my box, but if it works elsewhere that's fine by me - I don't run EMBOSS on my laptop 
anyways. ;-)

Sorry for the trouble. Will get to the embassy packages tomorrow.

[Comment 10 Olivier Fisette (RETIRED) 2005-06-26 06:10:50 UTC]

That's cool. It really looks like a machine-specific problem to me too, 
especially since it did work a few weeks ago. Thanks for your work. ;) 

[Comment 11 Lina Pezzella (RETIRED) 2005-06-26 14:12:15 UTC]

Since embassy-construct didn't have the ppc-macos keyword at all, it's going to have to go into testing
for a month before I can stable it. That means the "embassy" package is also going to be testing for one
month. The rest have been stabled. Sorry for the delay.

[Comment 12 Olivier Fisette (RETIRED) 2005-07-27 19:09:39 UTC]

EMBOSS and EMBASSY 2.10 is now stable on all supported arches. Thanks to 
everyone involved. I'll be removing older versions soon.