Bug 330507 – dev-libs/nss-3.12.6-r2 file collision with sci-biology/emboss-6.1.0-r1 on /usr/bin/digest

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Martin Mokrejš 2010-07-30 13:57:58 UTC]

>>> Installing (32 of 88) dev-libs/nss-3.12.6-r2
 * This package will overwrite one or more files that may belong to other
 * packages (see list below). You can use a command such as `portageq
 * owners / <filename>` to identify the installed package that owns a
 * file. If portageq reports that only one package owns a file then do
 * NOT file a bug report. A bug report is only useful if it identifies at
 * least two or more packages that are known to install the same file(s).
 * If a collision occurs and you can not explain where the file came from
 * then you should simply ignore the collision since there is not enough
 * information to determine if a real problem exists. Please do NOT file
 * a bug report at http://bugs.gentoo.org unless you report exactly which
 * two packages install the same file(s). Once again, please do NOT file
 * a bug report unless you have completely understood the above message.
 * 
 * Detected file collision(s):
 * 
 *      /usr/bin/digest
 * 
 * Searching all installed packages for file collisions...
 * 
 * Press Ctrl-C to Stop
 * 
 * sci-biology/emboss-6.1.0-r1
 *      /usr/bin/digest
 * 
 * Package 'dev-libs/nss-3.12.6-r2' NOT merged due to file collisions. If
 * necessary, refer to your elog messages for the whole content of the
 * above message.

[Comment 1 Jory A. Pratt 2010-07-31 13:24:06 UTC]

This should be fixed in emboss. 

[Comment 2 Diego Elio Pettenò (RETIRED) 2010-08-07 15:05:37 UTC]

I don't think either should really install a binary with such a generic name..

[Comment 3 Martin Mokrejš 2010-08-12 20:30:53 UTC]

Created attachment 242671 [details, diff]
emboss/Makefile.am.patch

[Comment 4 Martin Mokrejš 2010-08-12 20:31:09 UTC]

Created attachment 242673 [details, diff]
emboss/Makefile.in.patch

[Comment 5 Martin Mokrejš 2010-08-12 20:36:32 UTC]

Created attachment 242675 [details, diff]
emboss-6.1.0-r1.ebuild.patch

I made up patches to rename the binary into tryptic_digest and tested. I have also emailed upstream at their bugs@ list but haven't received any bug tracking number, so not really sure whether it went through. Nevertheless I propose you go straight ahead and commit this and keep the bug open until we hear from upstream. I have no idea if some 3rd party tools or other emboss programs call the "digest" binary. I just believe it is used mostly manually from the command-line directly, by the user.

[Comment 6 Martin Mokrejš 2010-08-18 20:00:31 UTC]

emboss will change the name in next minor release, probably digesttryptic (no underscores, for some reason they are "bad for EMBOSS", whatever that means).
Once I know the final name I'll post it here ([e-mail]
archives are closed to non-members at least).

[Comment 7 Lars Wendler (Polynomial-C) (RETIRED) 2010-09-09 09:17:10 UTC]

*** Bug 336573 has been marked as a duplicate of this bug. ***

[Comment 8 Christian Faulhammer (RETIRED) 2010-09-09 09:22:24 UTC]

Sticking to the nomenclature makes findings of bugs a lot easier.

[Comment 9 Nirbheek Chauhan (RETIRED) 2010-09-16 14:12:55 UTC]

fwiw, nss-3.12.7 doesn't install /usr/bin/digest

[Comment 10 Joost Ruis 2010-10-29 13:55:19 UTC]

 * Detected file collision(s):
 * 
 *      /usr/bin/digest
 * 
 * Searching all installed packages for file collisions...
 * 
 * Press Ctrl-C to Stop
 * 
 * dev-libs/nss-3.12.8
 *      /usr/bin/digest

[Comment 11 Martin Mokrejš 2010-11-25 23:35:24 UTC]

(In reply to comment #6)
> emboss will change the name in next minor release, probably digesttryptic (no
> underscores, for some reason they are "bad for EMBOSS", whatever that means).
> Once I know the final name I'll post it here ([e-mail]
> archives are closed to non-members at least).
> 

Upstream replied now: The name will be "pepdigest", it'll be renamed in the January release or over the next week or so if you get the CVS version. The file in sci-biology/emboss ebuild can now renamed to the future name.

[Comment 12 Justin Lecher (RETIRED) 2011-03-09 11:54:06 UTC]

Current emboss release-6.3.1 doesn't hast the change, but we will do it now. Hope upstream will stick to their decision.

[Comment 13 Justin Lecher (RETIRED) 2011-03-09 12:00:44 UTC]

+*emboss-6.3.1 (09 Mar 2011)
+
+  09 Mar 2011; Justin Lecher <[e-mail]>
+  +files/6.3.1-unbundle-libs.patch, +files/emboss-README.Gentoo-2,
+  emboss-4.0.0.ebuild, emboss-6.0.1.ebuild, emboss-6.1.0-r1.ebuild,
+  +emboss-6.3.1.ebuild, metadata.xml:
+  Version Bump #335603, Unbundled libs, removed old, fix clash with
+  /usr/bin/digest, #330507
+

[Comment 14 Martin Mokrejš 2011-03-12 09:26:10 UTC]

(In reply to comment #12)
> Current emboss release-6.3.1 doesn't hast the change, but we will do it now.
> Hope upstream will stick to their decision.

usptream says:
<quote>
We decided not to release in January ... far too many new features in EMBOSS we are still working on.

digest is renamed to pepdigest in the current developers CVS code.

The next EMBOSS release will be 6.4.0 on 15th July.

regards,

Peter Rice
EMBOSS Team 
</quote>

[Comment 15 Justin Lecher (RETIRED) 2011-03-12 12:00:43 UTC]

(In reply to comment #14)
Thanks for taking care on this.