[gentoo-science] g-cran master and portage master incompatible

[gentoo-science] g-cran master and portage master incompatible

[James Cloos]

I find that g-cran and portage master branches are incompatible.

Any attempt to merge or update a dev-R ebuild fails:

An example of an update attempt, where the distfile is already
downloaded (copied over from a cran mirror):

:; emerge -v dev-R/sp

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild     U  ] dev-R/sp-0.9.80 [0.9.78] USE="doc" 0 kB [1]

Total: 1 package (1 upgrade), Size of downloads: 0 kB
Portage tree and overlays:
 [0] /usr/portage
 [1] /usr/local/portage/Overlays/g-cran


>>> Emerging (1 of 1) dev-R/sp-0.9.80 from g-cran
!!! Fetched file: sp_0.9-80.tar.gz VERIFY FAILED!
!!! Reason: Insufficient data for checksum verification
!!! Got:      
!!! Expected: MD5 RMD160 SHA1 SHA256
 * Fetch failed for 'dev-R/sp-0.9.80', Log file:
 *  '/var/log/portage/build/dev-R/sp-0.9.80:20110416-221838.log'

>>> Failed to emerge dev-R/sp-0.9.80, Log file:

>>>  '/var/log/portage/build/dev-R/sp-0.9.80:20110416-221838.log'

 * Messages for package dev-R/sp-0.9.80:

 * Fetch failed for 'dev-R/sp-0.9.80', Log file:
 *  '/var/log/portage/build/dev-R/sp-0.9.80:20110416-221838.log'


And here is one where the distfile still needs downloading:

:; emerge -v dev-R/AIM

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  N     ] dev-R/AIM-1.01  USE="doc" 0 kB [1]

Total: 1 package (1 new), Size of downloads: 0 kB
Portage tree and overlays:
 [0] /usr/portage
 [1] /usr/local/portage/Overlays/g-cran


>>> Emerging (1 of 1) dev-R/AIM-1.01 from g-cran
!!! Fetched file: AIM_1.01.tar.gz VERIFY FAILED!
!!! Reason: Insufficient data for checksum verification
!!! Got:      
!!! Expected: MD5 RMD160 SHA1 SHA256
 * Fetch failed for 'dev-R/AIM-1.01', Log file:
 *  '/var/log/portage/build/dev-R/AIM-1.01:20110416-221950.log'

>>> Failed to emerge dev-R/AIM-1.01, Log file:

>>>  '/var/log/portage/build/dev-R/AIM-1.01:20110416-221950.log'

 * Messages for package dev-R/AIM-1.01:

 * Fetch failed for 'dev-R/AIM-1.01', Log file:
 *  '/var/log/portage/build/dev-R/AIM-1.01:20110416-221950.log'


Which is essentially the same error.

Re-merging g-cran does not help.

If it matters:

:; eselect python list
Available Python interpreters:
  [1]   python2.5
  [2]   python2.6
  [3]   python2.7 *
  [4]   python3.1

Of course, the fact that the Manifest files were never real was always a
bug.  I wanted to write a replacement before reporting this, but the tuits
have been too pointy....

-JimC
-- 
James Cloos <cloos@jhcloos.com>         OpenPGP: 1024D/ED7DAEA6

Re: [gentoo-science] g-cran master and portage master incompatible

[Donnie Berkholz]

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On 17:14 Mon 18 Apr     , James Cloos wrote:
> I find that g-cran and portage master branches are incompatible.

Jim,

Ever do anything with this? Just tried g-cran myself and I'm hitting it 
too, on portage 2.2.

-- 
Thanks,
Donnie

Donnie Berkholz
Science developer
Gentoo Linux
Blog: http://dberkholz.com

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Re: [gentoo-science] g-cran master and portage master incompatible

[James Cloos]

>>>>> "DB" == Donnie Berkholz <dberkholz@gentoo.org> writes:

JC> I find that g-cran and portage master branches are incompatible.

DB> Ever do anything with this? Just tried g-cran myself and I'm hitting
DB> it too, on portage 2.2.

No, I just spent some time thinking about the problem.

I hat to sound to critical, given that it was written as a gsoc project,
but the lack of real Manifest files made g-cran highly unreliable, even
when it worked at all.  A common problem I had was failed downloads, due
to network issues.  Unlike with other packages, after such a file one
has to manually remove the g-cran downloads before portage can download
a working copy.  And you can't use ebuild(1) to debug build issues with
c-cran ebuilds; only emerge(1) ever worked.

There were also some dependency bugs.  Both unnecessary and
unfulfillable deps, and also some missing deps.  I doubt that the
latter can be reliably fixed, but the former can be filtered out.

Given that osuosl is a cran mirror, I think a better solution would be
an overlay published on git.overlays.gentoo.org, updated daily after
the mirror updates.  With local access to the src files, the script
can generate proper Manifest files.

The SRC_URIs should point at the (IIRC) archive locations rather than
at the src/crontib locations, to ensure that out-of-date overlays still
work.  And it should have ebuilds for two or three versions, just in
case there are any issues.

Such an overlay would alleviate most of the issues, and if done at a
site (such as osuosl) which is already a cran mirror, would not require
excessive network bandwidth.

I'd be happy to spend some time a script to build such an overlay, and
can do some limited testing of it, but do not have the net bw to run
such a script in production, or to fully test it.

-JimC
-- 
James Cloos <cloos@jhcloos.com>         OpenPGP: 1024D/ED7DAEA6