Bug 284397 – embassy and many embassy-* sub-package emerges fail

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Robert Bradbury 2009-09-10 03:56:59 UTC]

Attempting to emerge embassy (-6.1.0) attempts to pull in many embassy-* subpackages (embassy-cbstools, embassy-domainatrix, etc.).  The up-to-date ebuilds appear to fail, seemingly because the source file archive have not been distributed to the Gentoo mirror sites.

Is there any reason for this?
Is there any reason the source archives aren't simply downloaded from emboss.open-bio,.org (esp. if the gentoo mirrors fail!)?

Reproducible: Always

Steps to Reproduce:
1. emerge embassy (after allowing development versions in package.keywords)
or
2. emerge embassy-cbstools (after adding to package.keywords)
3. etc.

Actual Results:  
FTP of package sources fails after going through multiple gentoo mirror sites.

Expected Results:  
Packages should fall back to original source site if gentoo mirrors are not available.

Why aren't the updated ebuilds released only *after* the mirrors are updated to contain the sources?

[Comment 1 Jaroslaw Kalinowski 2009-09-11 19:31:40 UTC]

[ebuild     U ] sci-biology/emboss-6.1.0 [6.0.1] USE="X png -minimal" 0 kB [0]
[ebuild     U ] sci-biology/embassy-iprscan-4.3.1-r1 [4.3.1] USE="X png" 336 kB [0]
[ebuild     U ] sci-biology/embassy-mse-1.0.0-r7 [1.0.0-r6] USE="X png" 415 kB [0]
[ebuild     U ] sci-biology/embassy-emnu-1.05-r6 [1.05-r5] USE="X png" 357 kB [0]
[ebuild     U ] sci-biology/embassy-topo-1.0.0-r6 [1.0.0-r5] USE="X png" 370 kB [0]
[ebuild     U ] sci-biology/embassy-domainatrix-0.1.0-r4 [0.1.0-r3] USE="X png" 391 kB [0]
[ebuild     U ] sci-biology/embassy-domsearch-0.1.0-r4 [0.1.0-r3] USE="X png" 434 kB [0]
[ebuild     U ] sci-biology/embassy-cbstools-1.0.0-r1 [1.0.0] USE="X png" 349 kB [0]
[ebuild     U ] sci-biology/embassy-vienna-1.7.2-r1 [1.7.2] USE="X png" 621 kB [0]
[ebuild     U ] sci-biology/embassy-structure-0.1.0-r4 [0.1.0-r3] USE="X png" 508 kB [0]
[ebuild     U ] sci-biology/embassy-esim4-1.0.0-r6 [1.0.0-r5] USE="X png" 396 kB [0]
[ebuild     U ] sci-biology/embassy-domalign-0.1.0-r4 [0.1.0-r3] USE="X png" 425 kB [0]
[ebuild     U ] sci-biology/embassy-signature-0.1.0-r4 [0.1.0-r3] USE="X png" 542 kB [0]
[ebuild     U ] sci-biology/embassy-phylipnew-3.68 [3.67] USE="X png" 1,589 kB [0]
[ebuild     U ] sci-biology/embassy-mira-2.8.2-r1 [2.8.2] USE="X png" 334 kB [0]
[ebuild     U ] sci-biology/embassy-hmmer-2.3.2-r3 [2.3.2-r2] USE="X png" 530 kB [0]
[ebuild     U ] sci-biology/embassy-memenew-4.0.0 [0.1.0-r1] USE="X png" 482 kB [0]
[ebuild     U ] sci-biology/prosite-20.36 [19.36] USE="emboss -minimal" 0 kB [0]
[ebuild     U ] sci-biology/cutg-160 [151] USE="emboss -minimal" 0 kB [0]
[ebuild     U ] sci-biology/rebase-909 [905] USE="emboss -minimal" 0 kB [0]
[ebuild     U ] sci-biology/embassy-6.1.0 [6.0.1] 0 kB [0]

[Comment 2 Jaroslaw Kalinowski 2009-09-11 19:34:52 UTC]

I noticed that for most packages only the revision number has changed and I was surprised that any download is necessary...

[Comment 3 Robert Bradbury 2009-09-14 07:26:30 UTC]

It looks to me like there is a conflict between the names expected by the ebuilds (EBOV=6.1.0) and the names which are in the mirror archives (embassy-NAME-6.0.1-vsn.tar.gz).  At least all of the embassy packages were updated in the SANDIA mirror this evening and they had the 6.0.1 names.

But there seems to be some sub-version numbering problems as well.  For example, the SANDIA mirror has "embassy-6.0.1-phylipnew-3.67.tar.gz" while the emerge fetch seems to want "embassy-6.1.0-phylipnew-3.68.tar.gz".  Though if I go back to the open-bio.org site, the listing for the source is "1626990 Jul 15 10:46 PHYLIPNEW-3.68.tar.gz" (I'm assuming there is some difference between the distributed source and the gentoo source but am unclear as to what it might be).

Could we get some comments by the person or persons responsible for this as to why the mirrors are not reflecting whatever the source should in theory be?  At some point if there is no "ease-of-use" or "value-added" to the package implementation under Gentoo, it simply becomes easier for me to download and build the packages myself (though that doesn't support the gentoo community).

[Comment 4 Andreas K. Hüttel 2010-10-02 16:07:07 UTC]

It seems like this has been fixed. Emerges fine here.