great. the updated patch is attached. for ORG-NEWS:

,----
| *** Links
| **** Links stored by org-gnus-store-link in nnir groups
| 
| Since gnus nnir groups are temporary, org-gnus-store-link
| now refers to the article's original group.
`----

best 


Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Thomas Alexander Gerds <t...@biostat.ku.dk> writes:
>
>> sometimes after searching for mail with notmuch, I want to save a
>> link to one of the articles shown in the nnir summary. since nnir
>> groups are temporary I would like org-gnus-store-link to treat nnir
>> groups differently and to use the articles orginal group when
>> creating the link. the following 3 lines change of
>> org-gnus-store-link does this for me. if this is interesting for
>> others maybe it could be integrated ... if not, I could either
>> advice org-gnus-store-link or add a modified version to
>> org-store-link-functions. comments?
>
> Sounds good. Thank you.
>
>>        (when (eq (car (gnus-find-method-for-group
>> gnus-newsgroup-name)) 'nnvirtual) (setq group (car
>> (nnvirtual-map-article (gnus-summary-article-number))))) + (when (eq
>> (car (gnus-find-method-for-group gnus-newsgroup-name)) + 'nnir) +
>> (setq group (nnir-article-group (gnus-summary-article-number))))
>
> I think the above could be wrapped within a cl-case, if only to
> compute (car (gnus-find-method-for-group gnus-newsgroup-name)) only
> once. Also, it may require an entry in ORG-NEWS, and a proper commit
> message.
>
> Would you mind sending an updated patch?
>
> Regards,
Thomas A. Gerds -- Assoc. Prof. Department of Biostatistics
University of Copenhagen, Oester Farimagsgade 5, 1014 Copenhagen, Denmark
Office: CSS-15.2.07 (Gamle Kommunehospital)
tel: 35327914 (sec: 35327901) 

commit f56d29a57ed965029c1b5f3929f3085423e46f18
Author: Thomas Alexander Gerds <t...@biostat.ku.dk>
Date:   Thu Dec 17 06:57:11 2015 +0100

    org-gnus: avoid links to nnir groups

diff --git a/lisp/org-gnus.el b/lisp/org-gnus.el
index c7b46af..06ba4df 100644
--- a/lisp/org-gnus.el
+++ b/lisp/org-gnus.el
@@ -172,10 +172,12 @@ If `org-store-link' was called with a prefix arg the 
meaning of
           (subject (copy-sequence (mail-header-subject header)))
           (to (cdr (assq 'To (mail-header-extra header))))
           newsgroups x-no-archive desc link)
-      (when (eq (car (gnus-find-method-for-group gnus-newsgroup-name))
-                 'nnvirtual)
-       (setq group (car (nnvirtual-map-article
-                         (gnus-summary-article-number)))))
+      (cl-case  (car (gnus-find-method-for-group gnus-newsgroup-name))
+       (nnvirtual 
+        (setq group (car (nnvirtual-map-article
+                          (gnus-summary-article-number)))))
+       (nnir
+        (setq group (nnir-article-group (gnus-summary-article-number)))))
       ;; Remove text properties of subject string to avoid Emacs bug
       ;; #3506
       (set-text-properties 0 (length subject) nil subject)

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