From unknown Sun Sep 21 00:06:10 2025
Content-Disposition: inline
Content-Transfer-Encoding: quoted-printable
MIME-Version: 1.0
X-Mailer: MIME-tools 5.509 (Entity 5.509)
Content-Type: text/plain; charset=utf-8
From: bug#62980 <62980@debbugs.gnu.org>
To: bug#62980 <62980@debbugs.gnu.org>
Subject: Status: gnu: bpp-popgen and bppsuite: Update to 2.4.1.
Reply-To: bug#62980 <62980@debbugs.gnu.org>
Date: Sun, 21 Sep 2025 07:06:10 +0000

retitle 62980 gnu: bpp-popgen and bppsuite: Update to 2.4.1.
reassign 62980 guix-patches
submitter 62980 "MadalinIonel.Patrascu@mdc-berlin.de" <MadalinIonel.Patrasc=
u@mdc-berlin.de>
severity 62980 normal

thanks


From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 20:00:58 2023
Received: (at submit) by debbugs.gnu.org; 21 Apr 2023 00:00:59 +0000
Received: from localhost ([127.0.0.1]:38896 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces@debbugs.gnu.org>)
	id 1ppeCw-0000xl-LD
	for submit@debbugs.gnu.org; Thu, 20 Apr 2023 20:00:58 -0400
Received: from lists.gnu.org ([209.51.188.17]:60582)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <MadalinIonel.Patrascu@mdc-berlin.de>)
 id 1ppeCu-0000xd-GO
 for submit@debbugs.gnu.org; Thu, 20 Apr 2023 20:00:57 -0400
Received: from eggs.gnu.org ([2001:470:142:3::10])
 by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256)
 (Exim 4.90_1) (envelope-from <MadalinIonel.Patrascu@mdc-berlin.de>)
 id 1ppeCl-0005Mr-6a
 for guix-patches@gnu.org; Thu, 20 Apr 2023 20:00:52 -0400
Received: from c2062.mx.srv.dfn.de ([194.95.238.172])
 by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256)
 (Exim 4.90_1) (envelope-from <MadalinIonel.Patrascu@mdc-berlin.de>)
 id 1ppeCj-0000t8-0w
 for guix-patches@gnu.org; Thu, 20 Apr 2023 20:00:46 -0400
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h=
 mime-version:content-type:content-type:content-language
 :accept-language:message-id:date:date:subject:subject:from:from
 :received:received; s=mdc; t=1682035239; x=1683849640; bh=t44XEF
 tKmldMb+LZjirH5m0e84lxtFw1afT2YkkTA5Q=; b=ko96X4sC9QGeig1I/yWBxz
 jSGZicadPZdxChWFSd5E/liN0LGeaQmE6fEADRxi9sCgCLfRkLzQcRzhMrNeCmfM
 a4gzpQjpEvaLTlp2p0vh+oo06em3vK4ekQSUDJ+PQv5SdNxN3+Ds7Nz0p22awgQf
 zSKy6cm7iwq13bf0e5zWw=
Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.60;
 helo=sw-it-p-ex2.mdc-berlin.net;
 envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver=<UNKNOWN> 
Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60])
 by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id EF9E3300169
 for <guix-patches@gnu.org>; Fri, 21 Apr 2023 02:00:38 +0200 (CEST)
Received: from SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) by
 SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server
 (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id
 15.1.2507.23; Fri, 21 Apr 2023 02:00:38 +0200
Received: from SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a]) by
 SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a%2]) with mapi id
 15.01.2507.023; Fri, 21 Apr 2023 02:00:38 +0200
From: "MadalinIonel.Patrascu@mdc-berlin.de"
 <MadalinIonel.Patrascu@mdc-berlin.de>
To: "guix-patches@gnu.org" <guix-patches@gnu.org>
Subject: gnu: bpp-popgen and bppsuite: Update to 2.4.1.
Thread-Topic: bpp-popgen and bppsuite: Update to 2.4.1.
Thread-Index: AQHZc+Q9W5mFfqbN30SbqhRAnQS/Ng==
Date: Fri, 21 Apr 2023 00:00:37 +0000
Message-ID: <5f1d7d011e24483ba7785b38c3fadef3@mdc-berlin.de>
Accept-Language: en-US, de-DE
Content-Language: en-US
X-MS-Has-Attach: 
X-MS-TNEF-Correlator: 
x-originating-ip: [141.80.113.51]
x-tm-as-product-ver: SMEX-14.0.0.3092-9.0.1002-27578.003
x-tm-as-result: No-10--14.632400-5.000000
x-tmase-matchedrid: 9D5R5CjVwBYaED+N1J68lsG0UNgaZpYqGsvgUMYAn4UWzPTbxO7R+tIS
 YzBUt2RaXVsEWVqYqaivJcrLMYkA70UuXkWTSi/R30kDaWZBE1RU4sxFq6igEUqa6TyhyXvPtAg
 K4TtXrP1GUsVNd0mL6QC2F/gPANDtCdtCev19Y1LZ6cd1XW8QucogYxpm9PTbAs7f5tvs5+iEIc
 UVoa0/oH0tCKdnhB58dcD5PxhxmQOrtiDzTp2cZbVQu1GNZ+sicxYeVrfi/UIwFcMc/z9LyiNP3
 GgHWnHTxW42GFSRkgAy4x/CSM274X7cGd19dSFd
x-tm-as-user-approved-sender: Yes
x-tm-as-user-blocked-sender: No
x-tmase-result: 10--14.632400-5.000000
x-tmase-version: SMEX-14.0.0.3092-9.0.1002-27578.003
x-tm-snts-smtp: E3C8B73F949519C48E596C786A0630D6709429758C8CA404D05A2F63D504A5FE2002:F
Content-Type: multipart/alternative;
 boundary="_000_5f1d7d011e24483ba7785b38c3fadef3mdcberlinde_"
MIME-Version: 1.0
Received-SPF: pass client-ip=194.95.238.172;
 envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.mx.srv.dfn.de
X-Spam_score_int: -5
X-Spam_score: -0.6
X-Spam_bar: /
X-Spam_report: (-0.6 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1,
 DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, EMPTY_MESSAGE=2.32,
 HTML_MESSAGE=0.001, MIME_HTML_MOSTLY=0.1, PYZOR_CHECK=1.392,
 RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001,
 SPF_PASS=-0.001 autolearn=no autolearn_force=no
X-Spam_action: no action
X-Spam-Score: -1.3 (-)
X-Debbugs-Envelope-To: submit
X-BeenThere: debbugs-submit@debbugs.gnu.org
X-Mailman-Version: 2.1.18
Precedence: list
List-Id: <debbugs-submit.debbugs.gnu.org>
List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, 
 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe>
List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/>
List-Post: <mailto:debbugs-submit@debbugs.gnu.org>
List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help>
List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, 
 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe>
Errors-To: debbugs-submit-bounces@debbugs.gnu.org
Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
X-Spam-Score: -2.3 (--)

--_000_5f1d7d011e24483ba7785b38c3fadef3mdcberlinde_
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable



--_000_5f1d7d011e24483ba7785b38c3fadef3mdcberlinde_
Content-Type: text/html; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<html>
<head>
<meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3Diso-8859-=
1">
<style type=3D"text/css" style=3D"display:none;"><!-- P {margin-top:0;margi=
n-bottom:0;} --></style>
</head>
<body dir=3D"ltr">
<div id=3D"divtagdefaultwrapper" style=3D"font-size:12pt;color:#000000;font=
-family:Calibri,Helvetica,sans-serif;" dir=3D"ltr">
<p><br>
</p>
<div id=3D"Signature">
<div id=3D"divtagdefaultwrapper" dir=3D"ltr" style=3D"font-size: 12pt; colo=
r: rgb(0, 0, 0); font-family: Calibri, Helvetica, sans-serif, EmojiFont, &q=
uot;Apple Color Emoji&quot;, &quot;Segoe UI Emoji&quot;, NotoColorEmoji, &q=
uot;Segoe UI Symbol&quot;, &quot;Android Emoji&quot;, EmojiSymbols;">
<div class=3D"BodyFragment"><font size=3D"2"><span style=3D"font-size:10pt"=
>
<div class=3D"PlainText"></div>
</span></font></div>
</div>
</div>
</div>
</body>
</html>

--_000_5f1d7d011e24483ba7785b38c3fadef3mdcberlinde_--




From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 20:04:27 2023
Received: (at 62980) by debbugs.gnu.org; 21 Apr 2023 00:04:27 +0000
Received: from localhost ([127.0.0.1]:38902 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces@debbugs.gnu.org>)
	id 1ppeGJ-00013j-7v
	for submit@debbugs.gnu.org; Thu, 20 Apr 2023 20:04:27 -0400
Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:47033)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <MadalinIonel.Patrascu@mdc-berlin.de>)
 id 1ppeGF-00013S-SJ
 for 62980@debbugs.gnu.org; Thu, 20 Apr 2023 20:04:24 -0400
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h=
 content-transfer-encoding:content-type:content-type:mime-version
 :x-mailer:message-id:date:date:subject:subject:from:from
 :received; s=mdc; t=1682035457; x=1683849858; bh=rGtaXtO3/AHM8SP
 J4rdmqcwwoxgjf3VfGhDy3f71HV0=; b=U4dpoenqz+QtglMf9CbY8Jwlpp4PcZf
 lgYjZ1YgumAyTbAwQyOhJqc1P4vsZuUHI5jfL0B2b+2cBEcDoGrUFrYj/fBhGvQf
 LqZNG6Fl24/IXpqJ7cWqb0k8fADbpCpC4Khq77iaM4wzWpv2vN5VxehGpFZCWZ0P
 j0Bnir+rHPfQ=
Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62;
 helo=sw-it-p-ex4.mdc-berlin.net;
 envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver=<UNKNOWN> 
Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62])
 by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 8007C160123
 for <62980@debbugs.gnu.org>; Fri, 21 Apr 2023 02:04:17 +0200 (CEST)
Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net
 (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2,
 cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.23; Fri, 21 Apr
 2023 02:04:15 +0200
From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?=
 <madalinionel.patrascu@mdc-berlin.de>
To: <62980@debbugs.gnu.org>
Subject: [PATCH 1/2] gnu: bpp-popgen: Update to 2.4.1.
Date: Fri, 21 Apr 2023 02:03:57 +0200
Message-ID: <20230421000358.11316-1-madalinionel.patrascu@mdc-berlin.de>
X-Mailer: git-send-email 2.39.2
X-Debbugs-Cc: rekado@elephly.net
MIME-Version: 1.0
Content-Type: text/plain; charset="UTF-8"
Content-Transfer-Encoding: 8bit
X-Originating-IP: [141.80.113.106]
X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To
 SW-IT-P-EX4.mdc-berlin.net (141.80.113.62)
X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.003
X-TM-AS-Result: No-10--3.511100-5.000000
X-TMASE-MatchedRID: 8iOsdbjc4EnBP9kF6SLh5hIRh9wkXSlFyiKgKtIyB4qAI7Mvq/sL54PN
 dYXFrfiyIVOe0TAdekipgf1jMun5ewV2NKF6aideEXjPIvKd74BMkOX0Uoduuc3wMjzgVvguChb
 10lmaN/ZYzJcD0gVKSpzSLZJ1HkA9+YQ9ocFzl0vece0aRiX9Wn607foZgOWypjlkbDvDJ4dU82
 kILwgVLQ1RxwBNHJ3Uh6Tqy0vOnV4qACWCM+Film9OepgphdNGEOS/art35UOXBXaJoB9JZ4MbH
 85DUZXy3wtt/1c/bBwXvQkGi3tjz/cUt5lc1lLgKIzdZS3ou0XYe+4pAcUAuiLBJq0qUXetrOJy
 I5Skqs9/srIR4pXmuZiuxBoOVGvdYBkKFGzNFj71irJpp6s6FgR/Ol8WNETk2qgVOBb5vuxZKCa
 lsVmcQjWQPYq1JOarY9u3lK2/Yrn87HRNT0KLkg==
X-TM-AS-User-Approved-Sender: Yes
X-TM-AS-User-Blocked-Sender: No
X-TMASE-Result: 10--3.511100-5.000000
X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.003
X-TM-SNTS-SMTP: 3FE7DB78EF4B509B71EADEA0BCA50F9F0669CE3648AEBC9BE910D0754D0200542002:F
X-Spam-Score: -2.3 (--)
X-Debbugs-Envelope-To: 62980
X-BeenThere: debbugs-submit@debbugs.gnu.org
X-Mailman-Version: 2.1.18
Precedence: list
List-Id: <debbugs-submit.debbugs.gnu.org>
List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, 
 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe>
List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/>
List-Post: <mailto:debbugs-submit@debbugs.gnu.org>
List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help>
List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, 
 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe>
Errors-To: debbugs-submit-bounces@debbugs.gnu.org
Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
X-Spam-Score: -3.3 (---)

* gnu/packages/bioinformatics.scm (bpp-popgen): Update to 2.4.1.
[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
---
 gnu/packages/bioinformatics.scm | 49 +++++++++++++++------------------
 1 file changed, 22 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c4cea24632..3969e205b3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2296,35 +2296,30 @@ (define-public bpp-phyl-omics
     (license license:cecill)))
 
 (define-public bpp-popgen
-  ;; The last release was in 2014 and the recommended way to install from source
-  ;; is to clone the git repository, so we do this.
-  ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
-  (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
-    (package
-      (name "bpp-popgen")
-      (version (string-append "2.2.0-1." (string-take commit 7)))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "http://biopp.univ-montp2.fr/git/bpp-popgen")
-                      (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
-                (sha256
-                 (base32
-                  "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
-      (build-system cmake-build-system)
-      (arguments
-       `(#:parallel-build? #f
-         #:tests? #f)) ; There are no tests.
-      (inputs
-       (list bpp-core bpp-seq))
-      (home-page "http://biopp.univ-montp2.fr")
-      (synopsis "Bio++ population genetics library")
-      (description
-       "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+  (package
+    (name "bpp-popgen")
+    (version "2.4.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/BioPP/bpp-popgen")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0bz0fhrq3dri6a0hvfc3zlvrns8mrzzlnicw5pyfa812gc1qwfvh"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list #:tests? #f)) ; There are no tests.
+    (inputs
+     (list bpp-core bpp-seq))
+    (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-popgen/html/")
+    (synopsis "Bio++ population genetics library")
+    (description
+     "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
 analysis, phylogenetics, molecular evolution and population genetics.  This
 library provides population genetics-related modules.")
-      (license license:cecill-c))))
+    (license license:cecill-c)))
 
 (define-public bpp-seq
   (package

base-commit: 2d06dfc050114dba44e791d8decc8eaa705fee01
prerequisite-patch-id: 5853dbe5778b2160c2bf5dca3f01be75fcbb678c
prerequisite-patch-id: 4af2ed7c595ec571d717d161aff1ef51a8dfc365
prerequisite-patch-id: e460dac992e961a5f13af1ed99bfad48d2f0ceb5
prerequisite-patch-id: 4241e6e34dc593a321a69e135db83293eaf011f7
prerequisite-patch-id: 78c7d0a29aee256ae2df1759863ef7e6dc34102f
prerequisite-patch-id: 4dc46155f0d7730f6996403f20442c2892e08a7c
-- 
2.39.2





From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 20:04:28 2023
Received: (at 62980) by debbugs.gnu.org; 21 Apr 2023 00:04:28 +0000
Received: from localhost ([127.0.0.1]:38904 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces@debbugs.gnu.org>)
	id 1ppeGJ-00013o-Ol
	for submit@debbugs.gnu.org; Thu, 20 Apr 2023 20:04:28 -0400
Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:49559)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <MadalinIonel.Patrascu@mdc-berlin.de>)
 id 1ppeGF-00013Q-LP
 for 62980@debbugs.gnu.org; Thu, 20 Apr 2023 20:04:24 -0400
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h=
 content-type:content-type:content-transfer-encoding:mime-version
 :references:in-reply-to:x-mailer:message-id:date:date:subject
 :subject:from:from:received; s=mdc; t=1682035456; x=1683849857;
 bh=QN5f0NKfIKYtqufqM56hdEqcMKP95oQAJO4GI/kF+ag=; b=HSmmKLTZN2XX
 dXqn2IcJsD7xB1hniSMJvObP/HwlUUn5zqKq6A4qUnUpud3jGEnkikDL+0a+dqI7
 Y7ZzJPw4347JXHcqQ09TLfyL8oBoP9woNcizrkC9POgtfZ+8k8C7h7i9WQtJXYfY
 KwKWXAlNr9O6YNAiCkucjnNWxz3Y7B8=
Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62;
 helo=sw-it-p-ex4.mdc-berlin.net;
 envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver=<UNKNOWN> 
Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62])
 by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 65AE716011B
 for <62980@debbugs.gnu.org>; Fri, 21 Apr 2023 02:04:16 +0200 (CEST)
Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net
 (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2,
 cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.23; Fri, 21 Apr
 2023 02:04:15 +0200
From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?=
 <madalinionel.patrascu@mdc-berlin.de>
To: <62980@debbugs.gnu.org>
Subject: [PATCH 2/2] gnu: bppsuite: Update to 2.4.1.
Date: Fri, 21 Apr 2023 02:03:58 +0200
Message-ID: <20230421000358.11316-2-madalinionel.patrascu@mdc-berlin.de>
X-Mailer: git-send-email 2.39.2
In-Reply-To: <20230421000358.11316-1-madalinionel.patrascu@mdc-berlin.de>
References: <20230421000358.11316-1-madalinionel.patrascu@mdc-berlin.de>
MIME-Version: 1.0
X-Debbugs-Cc: rekado@elephly.net
Content-Transfer-Encoding: 8bit
Content-Type: text/plain
X-Originating-IP: [141.80.113.106]
X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To
 SW-IT-P-EX4.mdc-berlin.net (141.80.113.62)
X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.003
X-TM-AS-Result: No-10--4.391300-5.000000
X-TMASE-MatchedRID: LfY4/T2Qrh/BP9kF6SLh5hIRh9wkXSlFyiKgKtIyB4qAI7Mvq/sL54PN
 dYXFrfiyIVOe0TAdeki1I4luQL/dnS/7QU2czuUNA9lly13c/gEfNd74n18052mj1qXcLu1ii0x
 TsP0eePKgltKRXQwrjATM3L6p7JLEmcUNCy5hvn91e7Xbb6Im2s78PItWKHEPLYKyZ0Y2szznAw
 8yp081LJE8Rz8q1MV03OMkc4Rb08PQ3sOMB3Fk1OLzNWBegCW2VqaJ/kmaJoBt1O49r1VEa8RB0
 bsfrpPI34T9cYMsdwyv4ARpxPtBduHMg8A0KzWMDVWoOsadqUF9bTqtmCWvI9iH9lGifyH3l0iN
 tYo+5vD1d0SgpkmhioW0MfgeOW7qPMA9H2Ll48LcUke23u350xU7OJY7bdPeD9iv/sJMsVc7Oyi
 /ulxQeKUgZdIaXg4f
X-TM-AS-User-Approved-Sender: Yes
X-TM-AS-User-Blocked-Sender: No
X-TMASE-Result: 10--4.391300-5.000000
X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.003
X-TM-SNTS-SMTP: 437AFF10CAA265D6640DA6D62E981B50D8EC5F95F78B1DE4093EE9636B3B19F32002:F
X-Spam-Score: -2.3 (--)
X-Debbugs-Envelope-To: 62980
X-BeenThere: debbugs-submit@debbugs.gnu.org
X-Mailman-Version: 2.1.18
Precedence: list
List-Id: <debbugs-submit.debbugs.gnu.org>
List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, 
 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe>
List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/>
List-Post: <mailto:debbugs-submit@debbugs.gnu.org>
List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help>
List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, 
 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe>
Errors-To: debbugs-submit-bounces@debbugs.gnu.org
Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
X-Spam-Score: -3.3 (---)

* gnu/packages/bioinformatics.scm (bppsuite): Update to 2.4.1.
[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build.
[inputs]: Use list.
[home-page]: Changed to github page.
---
 gnu/packages/bioinformatics.scm | 56 ++++++++++++++-------------------
 1 file changed, 24 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3969e205b3..625dd5a409 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2367,40 +2367,32 @@ (define-public bpp-seq-omics
     (license license:cecill)))
 
 (define-public bppsuite
-  ;; The last release was in 2014 and the recommended way to install from source
-  ;; is to clone the git repository, so we do this.
-  ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
-  (let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
-    (package
-      (name "bppsuite")
-      (version (string-append "2.2.0-1." (string-take commit 7)))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "http://biopp.univ-montp2.fr/git/bppsuite")
-                      (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
-                (sha256
-                 (base32
-                  "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
-      (build-system cmake-build-system)
-      (arguments
-       `(#:parallel-build? #f
-         #:tests? #f)) ; There are no tests.
-      (native-inputs
-       (list groff man-db texinfo))
-      (inputs
-       `(("bpp-core" ,bpp-core)
-         ("bpp-seq" ,bpp-seq)
-         ("bpp-phyl" ,bpp-phyl)
-         ("bpp-phyl" ,bpp-popgen)))
-      (home-page "http://biopp.univ-montp2.fr")
-      (synopsis "Bioinformatics tools written with the Bio++ libraries")
-      (description
-       "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+  (package
+    (name "bppsuite")
+    (version "2.4.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/BioPP/bppsuite")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1wdwcgczqbc3m116vakvi0129wm3acln3cfc7ivqnalwvi6lrpds"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list #:tests? #f)) ; There are no tests.
+    (native-inputs
+     (list groff man-db texinfo))
+    (inputs
+     (list bpp-core bpp-seq bpp-phyl bpp-popgen))
+    (home-page "https://github.com/BioPP")
+    (synopsis "Bioinformatics tools written with the Bio++ libraries")
+    (description
+     "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
 analysis, phylogenetics, molecular evolution and population genetics.  This
 package provides command line tools using the Bio++ library.")
-      (license license:cecill-c))))
+    (license license:cecill-c)))
 
 (define-public blast+
   (package
-- 
2.39.2





From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 20:06:06 2023
Received: (at control) by debbugs.gnu.org; 21 Apr 2023 00:06:06 +0000
Received: from localhost ([127.0.0.1]:38911 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces@debbugs.gnu.org>)
	id 1ppeHu-000171-CH
	for submit@debbugs.gnu.org; Thu, 20 Apr 2023 20:06:06 -0400
Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:54595)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <MadalinIonel.Patrascu@mdc-berlin.de>)
 id 1ppeHs-00016W-De
 for control@debbugs.gnu.org; Thu, 20 Apr 2023 20:06:04 -0400
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h=
 mime-version:content-type:content-type:content-language
 :accept-language:message-id:date:date:subject:subject:from:from
 :received:received; s=mdc; t=1682035556; x=1683849957; bh=31Odxb
 v/NV8u++wp/KSF8jLtEWOMCwJrMvJd2B5YZq0=; b=nFUtXYU6vOP0deVuAGxwCL
 aB1Ur1TU7qHRmDSjELJnj5Ioy7JylUa5NSUfrW7+OG5WEAqCeW4r+nvdNi877VSs
 ehoAthTn7+k2C31ufD/lhxvX0TidD4huC1Rb3dJvxde3d1h/yespRQgxq4NlNo2B
 oTu/2Ca1Q+feUX9aeLHTo=
Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62;
 helo=sw-it-p-ex4.mdc-berlin.net;
 envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver=<UNKNOWN> 
Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62])
 by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id D57F5300195
 for <control@debbugs.gnu.org>; Fri, 21 Apr 2023 02:05:56 +0200 (CEST)
Received: from SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) by
 SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server
 (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id
 15.1.2507.23; Fri, 21 Apr 2023 02:05:56 +0200
Received: from SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a]) by
 SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a%2]) with mapi id
 15.01.2507.023; Fri, 21 Apr 2023 02:05:56 +0200
From: "MadalinIonel.Patrascu@mdc-berlin.de"
 <MadalinIonel.Patrascu@mdc-berlin.de>
To: "control@debbugs.gnu.org" <control@debbugs.gnu.org>
Subject: control message for bug #62980 and #62978
Thread-Topic: control message for bug #62980 and #62978
Thread-Index: AQHZc+T5krzxNHW2nkSU6C8qGfZN6A==
Date: Fri, 21 Apr 2023 00:05:56 +0000
Message-ID: <641438e8ad6e43ce85e505f242959209@mdc-berlin.de>
Accept-Language: en-US, de-DE
Content-Language: en-US
X-MS-Has-Attach: 
X-MS-TNEF-Correlator: 
x-originating-ip: [141.80.113.51]
x-tm-as-product-ver: SMEX-14.0.0.3092-9.0.1002-27578.003
x-tm-as-result: No-10--10.664600-5.000000
x-tmase-matchedrid: MnV6/QBRMnAaED+N1J68lsG0UNgaZpYqGsvgUMYAn4UWzPTbxO7R+tIS
 YzBUt2RaXVsEWVqYqaivJcrLMYkA70UuXkWTSi/R30kDaWZBE1RU4sxFq6igEUqa6TyhyXvPtAg
 K4TtXrP1GUsVNd0mL6QC2F/gPANDtCdtCev19Y1LZ6cd1XW8QucogYxpm9PTbAs7f5tvs5+iEIc
 UVoa0/oH0tCKdnhB58dcD5PxhxmQM+8FJNGdxYq80z+VHYZXoPZHgDHw9doex1gVIsurBVFv3y1
 lL2MimFqKSa7+1FelwwPvERclccVw==
x-tm-as-user-approved-sender: Yes
x-tm-as-user-blocked-sender: No
x-tmase-result: 10--10.664600-5.000000
x-tmase-version: SMEX-14.0.0.3092-9.0.1002-27578.003
x-tm-snts-smtp: 07AEA2113FA8D6F3927FA6FDB2DC3C509D7490B3AC348383D546BA6F18F129092002:F
Content-Type: multipart/alternative;
 boundary="_000_641438e8ad6e43ce85e505f242959209mdcberlinde_"
MIME-Version: 1.0
X-Spam-Score: -2.3 (--)
X-Debbugs-Envelope-To: control
X-BeenThere: debbugs-submit@debbugs.gnu.org
X-Mailman-Version: 2.1.18
Precedence: list
List-Id: <debbugs-submit.debbugs.gnu.org>
List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, 
 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe>
List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/>
List-Post: <mailto:debbugs-submit@debbugs.gnu.org>
List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help>
List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, 
 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe>
Errors-To: debbugs-submit-bounces@debbugs.gnu.org
Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
X-Spam-Score: -3.3 (---)

--_000_641438e8ad6e43ce85e505f242959209mdcberlinde_
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

block 62980 by 62978


--_000_641438e8ad6e43ce85e505f242959209mdcberlinde_
Content-Type: text/html; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<html>
<head>
<meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3Diso-8859-=
1">
<style type=3D"text/css" style=3D"display:none;"><!-- P {margin-top:0;margi=
n-bottom:0;} --></style>
</head>
<body dir=3D"ltr">
<div id=3D"divtagdefaultwrapper" style=3D"font-size:12pt;color:#000000;font=
-family:Calibri,Helvetica,sans-serif;" dir=3D"ltr">
<p><span style=3D"font-size: 12pt;">block <span style=3D"color: rgb(51, 51,=
 51); font-size: 21px;">
62980</span> by <span style=3D"color: rgb(51, 51, 51); font-size: 21px;">62=
978</span></span><br>
</p>
<p><br>
</p>
<div id=3D"Signature">
<div id=3D"divtagdefaultwrapper" dir=3D"ltr" style=3D"font-size: 12pt; colo=
r: rgb(0, 0, 0); font-family: Calibri, Helvetica, sans-serif, EmojiFont, &q=
uot;Apple Color Emoji&quot;, &quot;Segoe UI Emoji&quot;, NotoColorEmoji, &q=
uot;Segoe UI Symbol&quot;, &quot;Android Emoji&quot;, EmojiSymbols;">
<div class=3D"BodyFragment"><font size=3D"2"><span style=3D"font-size:10pt"=
>
<div class=3D"PlainText"></div>
</span></font></div>
</div>
</div>
</div>
</body>
</html>

--_000_641438e8ad6e43ce85e505f242959209mdcberlinde_--




From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 21 08:05:03 2023
Received: (at 62980-done) by debbugs.gnu.org; 21 Apr 2023 12:05:03 +0000
Received: from localhost ([127.0.0.1]:39525 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces@debbugs.gnu.org>)
	id 1pppVf-0001NG-Fc
	for submit@debbugs.gnu.org; Fri, 21 Apr 2023 08:05:03 -0400
Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21053)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <rekado@elephly.net>) id 1pppVd-0001Mn-92
 for 62980-done@debbugs.gnu.org; Fri, 21 Apr 2023 08:05:02 -0400
ARC-Seal: i=1; a=rsa-sha256; t=1682078698; cv=none; 
 d=zohomail.com; s=zohoarc; 
 b=LGV5S/mKP1EN+SqsMLBvE0/3hatQwIy1Fn1LiTr47nUFJ+DUaJ2kPGvBWEWLdqDssqrr80/JKJABqFnC8rGyzTAtwt3oiVTUiuxxYZz5QfjqPOOzcFnkfao6SNQDHJIVBw8JoLvMKjWIyi+hgzEi3RY6c/qwcFG5qOMiUH0qtAI=
ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com;
 s=zohoarc; 
 t=1682078698; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; 
 bh=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=; 
 b=YznuzPY4hwB68eTSHSciKwIYEC3bfABOgSQJglQs4/BSuebq6fAb57oBbsbEFey/jKvuJbOKMDhQuVw1Ll5LfM6xg+q88y6Uy8E2UWRlZHAveOIZHgs3QCcGs9yU1gPZYEwPzaWROFQ4XJzyAAdoOdz5kwKkofmDW5SBoO+bY44=
ARC-Authentication-Results: i=1; mx.zohomail.com;
 dkim=pass  header.i=elephly.net;
 spf=pass  smtp.mailfrom=rekado@elephly.net;
 dmarc=pass header.from=<rekado@elephly.net>
DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1682078698; 
 s=zoho; d=elephly.net; i=rekado@elephly.net;
 h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc;
 bh=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=;
 b=emGngDSfKhDIPX2FZyIGQLs55Qnw3+6sinE4Rdff+NTc6pvsvD0PeKZjiG23PH1M
 mzcGOD8O/wVyKDas6PwHumzK7woaZtl33UDausqlUr92HbnIGQj61n89XndIqOZMWYV
 zpgSiCjcRgayGC3U9Y2VfwxHKmaTAwG+E2OHH+3Y=
Received: from localhost (i5E862DF4.versanet.de [94.134.45.244]) by
 mx.zohomail.com with SMTPS id 1682078697299654.5078912278753;
 Fri, 21 Apr 2023 05:04:57 -0700 (PDT)
User-agent: mu4e 1.10.2; emacs 28.2
From: Ricardo Wurmus <rekado@elephly.net>
To: 62980-done@debbugs.gnu.org
Subject: gnu: bpp-popgen and bppsuite: Update to 2.4.1.
Date: Fri, 21 Apr 2023 14:04:41 +0200
Message-ID: <878relphjt.fsf@elephly.net>
MIME-Version: 1.0
Content-Type: text/plain
X-ZohoMailClient: External
X-Spam-Score: -0.0 (/)
X-Debbugs-Envelope-To: 62980-done
X-BeenThere: debbugs-submit@debbugs.gnu.org
X-Mailman-Version: 2.1.18
Precedence: list
List-Id: <debbugs-submit.debbugs.gnu.org>
List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, 
 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=unsubscribe>
List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/>
List-Post: <mailto:debbugs-submit@debbugs.gnu.org>
List-Help: <mailto:debbugs-submit-request@debbugs.gnu.org?subject=help>
List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, 
 <mailto:debbugs-submit-request@debbugs.gnu.org?subject=subscribe>
Errors-To: debbugs-submit-bounces@debbugs.gnu.org
Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
X-Spam-Score: -1.0 (-)

Applied, thank you!

-- 
Ricardo




From unknown Sun Sep 21 00:06:10 2025
Received: (at fakecontrol) by fakecontrolmessage;
To: internal_control@debbugs.gnu.org
From: Debbugs Internal Request <help-debbugs@gnu.org>
Subject: Internal Control
Message-Id: bug archived.
Date: Sat, 20 May 2023 11:24:11 +0000
User-Agent: Fakemail v42.6.9

# This is a fake control message.
#
# The action:
# bug archived.
thanks
# This fakemail brought to you by your local debbugs
# administrator