From debbugs-submit-bounces@debbugs.gnu.org Fri Aug 05 05:15:19 2022 Received: (at submit) by debbugs.gnu.org; 5 Aug 2022 09:15:19 +0000 Received: from localhost ([127.0.0.1]:56170 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJtQN-0007Eb-FA for submit@debbugs.gnu.org; Fri, 05 Aug 2022 05:15:19 -0400 Received: from lists.gnu.org ([209.51.188.17]:55214) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJtQJ-0007ES-TU for submit@debbugs.gnu.org; Fri, 05 Aug 2022 05:15:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:44198) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oJtQJ-0000LY-LI for guix-patches@gnu.org; Fri, 05 Aug 2022 05:15:15 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:60987) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oJtQG-0005aX-Vs for guix-patches@gnu.org; Fri, 05 Aug 2022 05:15:14 -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=1659690898; x=1661505299; bh=9OSE0g Ze+JCFUMggsY6p8KMYpZcVPo42bUtF2B3WRXQ=; b=A+avnka0HmOSjCzeafCYjM T/ZoYTFeXmxUvDIh5pTVILbzhtAlm4RzA2Ru8xnMM1JgbuG6qSKvr5ngM5za8TSp /IjFqUarMU4cnU4zE3//SIY6OTFjA/rEzhrDb/u+16SkOBSlsDCvadoBj2St1IMz PVe33Lm4gtScDhsHnFOjI= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id B483816038C for ; Fri, 5 Aug 2022 11:14:57 +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 15.1.2507.9; Fri, 5 Aug 2022 11:14:57 +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%3]) with mapi id 15.01.2507.009; Fri, 5 Aug 2022 11:14:57 +0200 From: "MadalinIonel.Patrascu@mdc-berlin.de" To: "guix-patches@gnu.org" Subject: Add phyml package tools. Thread-Topic: Add phyml package tools. Thread-Index: AQHYqKu+eIMZNAr0K0ODglqYmqtgRg== Date: Fri, 5 Aug 2022 09:14:56 +0000 Message-ID: <398fc66441a34468a7c66370abb8f923@mdc-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [141.80.113.52] x-tm-as-product-ver: SMEX-14.0.0.3092-9.0.1002-27058.006 x-tm-as-result: No-10--13.884400-5.000000 x-tmase-matchedrid: a3KJLn6RIiKfkHSWeTTytMG0UNgaZpYqGsvgUMYAn4UWzPTbxO7R+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--13.884400-5.000000 x-tmase-version: SMEX-14.0.0.3092-9.0.1002-27058.006 x-tm-snts-smtp: 52F808F603AA8474F559285EC3761B8A8664086397A3AB0A652499680BA667BB2002:F Content-Type: multipart/alternative; boundary="_000_398fc66441a34468a7c66370abb8f923mdcberlinde_" MIME-Version: 1.0 Received-SPF: pass client-ip=194.95.234.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -28 X-Spam_score: -2.9 X-Spam_bar: -- X-Spam_report: (-2.9 / 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, 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=ham 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: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) --_000_398fc66441a34468a7c66370abb8f923mdcberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable --_000_398fc66441a34468a7c66370abb8f923mdcberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable


--_000_398fc66441a34468a7c66370abb8f923mdcberlinde_-- From debbugs-submit-bounces@debbugs.gnu.org Fri Aug 05 05:30:04 2022 Received: (at 56999) by debbugs.gnu.org; 5 Aug 2022 09:30:04 +0000 Received: from localhost ([127.0.0.1]:56196 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJted-0007cK-Mz for submit@debbugs.gnu.org; Fri, 05 Aug 2022 05:30:04 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:42305) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJtea-0007bK-TC for 56999@debbugs.gnu.org; Fri, 05 Aug 2022 05:30:02 -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:in-reply-to:references:message-id:date:date :subject:subject:from:from:received:received; s=mdc; t= 1659691793; x=1661506194; bh=GEShnmaA6HEI+cmxGzu6yZX3LwYI9JQD1tX mhDDGLd8=; b=TM7kW0RYyQaJX8BUvNiPj1CESsdeWswx/A5cemvFO4YyjzEj+/p 3qp3GWEty5Yv9ZjFmKUx5K/rAUckIdi8jAoTye0pWBSOW5vpyfQSVxz5buHeQwg+ W7mvVjd2a7azjt8GFIWTEBfBf3/UWvzYjT+ieEv49WqUQ9t+Lpsndxnw= 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 6476C16038C for <56999@debbugs.gnu.org>; Fri, 5 Aug 2022 11:29:53 +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 15.1.2507.9; Fri, 5 Aug 2022 11:29:49 +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%3]) with mapi id 15.01.2507.009; Fri, 5 Aug 2022 11:29:49 +0200 From: "MadalinIonel.Patrascu@mdc-berlin.de" To: "56999@debbugs.gnu.org" <56999@debbugs.gnu.org> Subject: Re: [ext] bug#56999: Acknowledgement (Add phyml package tools.) Thread-Topic: [ext] bug#56999: Acknowledgement (Add phyml package tools.) Thread-Index: AQHYqKwCzZK89uyGrE+wWxpYEOZ+Xa2gCBep Date: Fri, 5 Aug 2022 09:29:49 +0000 Message-ID: References: <398fc66441a34468a7c66370abb8f923@mdc-berlin.de>, In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [141.80.113.52] x-tm-as-product-ver: SMEX-14.0.0.3092-9.0.1002-27058.006 x-tm-as-result: No-10--15.348200-5.000000 x-tmase-matchedrid: HN1YkeHeIb5DZFBd1jLr/pTQgFTHgkhZfMhjt3b5PP1K0WT/zXAgkgPz oKxdv+wmp3Z/y3zTL99+R+CMyT2S929HrF8i9tDQIj0zFI5DoJLCXeHJwJcT9p7fzNec2D1DcmM mAcpqutN+jyPo/lRgIYF/JSUgWI0yVd0YPTyDIuqSi82OWa7YY28/sYT3XnwWb3Wpj9NSXKxR+3 1Q7sLWeiavtNrR+/mjP3ZLJxrhphW5rzEqaXlmzZ1U1lojafr/mzsJ8CsZYU6ISI683skDCtxX+ /sb6BPBn+ljherCHktaOK3wW8BDkfKFri4StE39qhcdnP91eXG//vF0tCNdItx0j1W5+aCQsB5x KruH4a5L5bwao9fzHtwoW4czCXsPCGrFz5XLS3T1A8E3bi1JHPNkoMDX+kiuNWO9z3c712SMUr8 1xLsbiSebkrhmS4/w1UfLpehmgutyJitGiXItuwvBTB90+he+vykBikB9a0DtMU8isOMR1bSm/F 1nDDav4PkIhwvBc3oQCSdrZ2TFPACwWaqH3RqntT4jIeGRd/WH50aQJE8VKJcFdomgH0lnvuX5u VexXMaAx/bc87r9b4DqTooA928nJ8j02ZegcZkuZIp941J0D/sZ8M2DpSG9EfVWNmxtMcTLy6ip Wog5Mg== x-tm-as-user-approved-sender: Yes x-tm-as-user-blocked-sender: No x-tmase-result: 10--15.348200-5.000000 x-tmase-version: SMEX-14.0.0.3092-9.0.1002-27058.006 x-tm-snts-smtp: 3B276BCE0302477B77D718D5778EECB0FEB696D95EB8856D929CDB55ACE04C1F2002:F Content-Type: multipart/alternative; boundary="_000_d03f5f3979974bffa133260aa135df40mdcberlinde_" MIME-Version: 1.0 X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 56999 Cc: "Ricardo.Wurmus@mdc-berlin.de" X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --_000_d03f5f3979974bffa133260aa135df40mdcberlinde_ Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable Dear reviewer, This package requires to do the .configure --argument and make for building= of each tool. I already tried to specific make targets, but didn't help. Also the PhyTime has issues with the building, more you can check here: https://github.com/stephaneguindon/phyml/issues/166 All the best, M=E3d=E3lin! ________________________________ From: GNU bug Tracking System Sent: Friday, August 5, 2022 11:16 To: Patrascu, Madalin Ionel Subject: [ext] bug#56999: Acknowledgement (Add phyml package tools.) Thank you for filing a new bug report with debbugs.gnu.org. This is an automatically generated reply to let you know your message has been received. Your message is being forwarded to the package maintainers and other interested parties for their attention; they will reply in due course. Your message has been sent to the package maintainer(s): guix-patches@gnu.org If you wish to submit further information on this problem, please send it to 56999@debbugs.gnu.org. Please do not send mail to help-debbugs@gnu.org unless you wish to report a problem with the Bug-tracking system. -- 56999: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D56999 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems --_000_d03f5f3979974bffa133260aa135df40mdcberlinde_ Content-Type: text/html; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable

Dear reviewer,

This package requires to do the .configure --argument and make for building of each tool.

I already tried to specific make tar= gets, but didn't help.

Also the PhyTime has issues wi= th the building, more you can check here:
https://github.com/st= ephaneguindon/phyml/issues/166


All the best,

     M=E3d=E3lin!

From: GNU bug Tracking Sy= stem <help-debbugs@gnu.org>
Sent: Friday, August 5, 2022 11:16
To: Patrascu, Madalin Ionel
Subject: [ext] bug#56999: Acknowledgement (Add phyml package tools.)=
 
Thank you for filing a new bug report with debbugs= .gnu.org.

This is an automatically generated reply to let you know your message
has been received.

Your message is being forwarded to the package maintainers and other
interested parties for their attention; they will reply in due course.

Your message has been sent to the package maintainer(s):
 guix-patches@gnu.org

If you wish to submit further information on this problem, please
send it to 56999@debbugs.gnu.org.

Please do not send mail to help-debbugs@gnu.org unless you wish
to report a problem with the Bug-tracking system.

--
56999: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D56999
GNU Bug Tracking System
Contact help-debbugs@gnu.org with problems
--_000_d03f5f3979974bffa133260aa135df40mdcberlinde_-- From debbugs-submit-bounces@debbugs.gnu.org Fri Aug 05 05:33:26 2022 Received: (at 56999) by debbugs.gnu.org; 5 Aug 2022 09:33:26 +0000 Received: from localhost ([127.0.0.1]:56229 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJthu-0007jn-2k for submit@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:26 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:55105) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJths-0007jR-BH for 56999@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:24 -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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1659691998; x=1661506399; bh=MYPDRqRBMPBzjhy J5rlGJgea7o/YW10nPogDJbR5Xx0=; b=PgSptdEBMst4W34omHdXem+o/2e091l l2ywwA33VQXAf7QoSbv97Vop8i8uvi9PWFi6AU4mHmRBVKhb9OHVVpPNuwd1MKUH zWkXhU1D928m4/1kwenUWDjl0mFSMR8ATcBhGYD3qVSXT3GcCCgJWRKLitafj5YH Xw56VmeCbxkc= 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 49F52160390 for <56999@debbugs.gnu.org>; Fri, 5 Aug 2022 11:33:18 +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 15.1.2507.9; Fri, 5 Aug 2022 11:33:17 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <56999@debbugs.gnu.org> Subject: [PATCH 1/4] gnu: Add phyml. Date: Fri, 5 Aug 2022 11:33:03 +0200 Message-ID: <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.1 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-14.0.0.3092-9.0.1002-27058.006 X-TM-AS-Result: No-10--6.417000-5.000000 X-TMASE-MatchedRID: huMMtcahIlB6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIpb wG9fIuITWtKJ53YwGGLuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/KIqAq0jIHisIubEPSkNnJli+ BaqMwTNo+LWiWMkbaVlai9f4ppdhS74MThWsvfJhi71i5on34Kj7xZyBSNBTCfw+FWPV9n7q+oA mvH3qvXYOaK7R6v2MMDKhMD70B3lMxzpurb8CqYHsZMBX90xmm1+Cp0Qg3BZ4OUs4CTUgKy1N+F 8fdIPkCYn6cI9w5Vog9hU++cg3wZdaVXJCx4JNCq5uw61JZjZCAMuqetGVetnyef22ep6XYymsk /wUE4hrE/GgTDPZQO62t1xaPjrRuM+zy/fYYl0W43+2so7gAwd4BhmE4Jsgh X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.417000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27058.006 X-TM-SNTS-SMTP: 3D47BE18CC7E45723E37BB8372FAF3D1F9EE361D4C7D82E3B046D21648BE24E12002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 56999 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/bioinformatics.scm (phyml): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 00238531db..fa91f48569 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9068,6 +9068,43 @@ (define-public phylip programs for inferring phylogenies (evolutionary trees).") (license license:bsd-2))) +(define-public phyml + (package + (name "phyml") + (version "3.3.20220408") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/stephaneguindon/phyml") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03hdqmnsgnzkcrp9r9ajdfkj33jgq4b86kra8ssjlrph65y344sa")))) + (build-system gnu-build-system) + (native-inputs + (list automake + autoconf)) + (home-page "https://github.com/stephaneguindon/phyml") + (synopsis "Programs for working on SAM/BAM files") + (description + "@code{PhyML} is a software package that uses modern statistical approaches +to analyse alignments of nucleotide or amino acid sequences in a phylogenetic +framework. The main tool in this package builds phylogenies under the maximum +likelihood criterion. It implements a large number of substitution models coupled +with efficient options to search the space of phylogenetic tree topologies. @code{ +PhyTime} is another tool in the @code{PhyML} package that focuses on divergence +date estimation in a Bayesian setting. The main strengths of @code{PhyTime} lie +in its ability to accommodate for uncertrainty in the placement of fossil +calibration and the use of realistic models of rate variation along the tree. +Finally, code{PhyREX} fits the spatial-Lambda-Fleming-Viot model to geo-referenced +genetic data. This model is similar to the structured coalescent but assumes that +individuals are distributed along a spatial continuum rather than discrete demes. +@code{PhyREX} can be used to estimate population densities and rates of dispersal. +Its output can be processed by treeannotator (from the @code{BEAST} package) as +well as @code{SPREAD}.") + (license license:gpl3))) + (define-public imp (package (name "imp") base-commit: 47a38d09696b309f6174b585465e621352444ddb -- 2.37.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Aug 05 05:33:28 2022 Received: (at 56999) by debbugs.gnu.org; 5 Aug 2022 09:33:29 +0000 Received: from localhost ([127.0.0.1]:56232 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJthw-0007k6-K4 for submit@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:28 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:41859) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJtht-0007jS-0c for 56999@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:25 -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=1659691999; x=1661506400; bh=jdFkWR08uzTCKUQpeTPwbe9guWdn6Say5qgpCfx8/bk=; b=Dhdaoh/+AIjA qsXovmEMQ4h7B0f18XAJvJP5fdng+pje4ps6SHnEBGi5icLFRP5PXGNlzxSETNHT bZBBDo/6VXXFcdl4NMLUYPMKarCcN0z2UjIuOaUuAbOMa9w/oExzcNshtcGz4y/4 2Yy/dRk3VpH1JNp469ykYZIvEvaYN3g= 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 03B56160394 for <56999@debbugs.gnu.org>; Fri, 5 Aug 2022 11:33:19 +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 15.1.2507.9; Fri, 5 Aug 2022 11:33:18 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <56999@debbugs.gnu.org> Subject: [PATCH 2/4] gnu: Add phyml-mpi. Date: Fri, 5 Aug 2022 11:33:04 +0200 Message-ID: <20220805093306.21767-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.1 In-Reply-To: <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> References: <20220805093306.21767-1-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-14.0.0.3092-9.0.1002-27058.006 X-TM-AS-Result: No-10-0.190300-5.000000 X-TMASE-MatchedRID: BrKfIHwbYjV6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VDI3 NdfFmGpMfS0Ip2eEHnwj/1Rbkzl1E95/HgWYxplM5MIx11wv+CPKayT/BQTiGk8XOMKR+RhSrDX lnqrP39YoWwp6YEIz4HLwQmh72397ISTtzMCCKYWgiZqDH7QQVDg8YCmQy4oAqVjwx1umPUCoo7 lRIplgTMWDv2TYRvIltOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.190300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27058.006 X-TM-SNTS-SMTP: A535829A769EC6E2C7DBD4DB107D8D3B764048CB37FEC02EA526826DCF988DB72002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 56999 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/bioinformatics.scm (phyml-mpi): New variable. --- gnu/packages/bioinformatics.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa91f48569..f448341031 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9105,6 +9105,17 @@ (define-public phyml well as @code{SPREAD}.") (license license:gpl3))) +(define-public phyml-mpi + (package (inherit phyml) + (name "phyml-mpi") + (arguments + `(#:configure-flags + (list "--enable-phyml-mpi"))) + (native-inputs + (list autoconf + automake + openmpi)))) + (define-public imp (package (name "imp") -- 2.37.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Aug 05 05:33:29 2022 Received: (at 56999) by debbugs.gnu.org; 5 Aug 2022 09:33:29 +0000 Received: from localhost ([127.0.0.1]:56234 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJthw-0007k8-Su for submit@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:29 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:47203) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJtht-0007jU-Tm for 56999@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:26 -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=1659691999; x=1661506400; bh=QC7InJfAdZjam8o6E5aHvbZh9gc5sEi6Mt4ghO8c9to=; b=VqXo39FEiZ4+ Kn6hiIT8VC6D5OrEWpwdyy/KxUboeW7P5SLYzRMXQqh4bgJhWJ29ytD+p2G1a0As FC6dkgKdB1dzexYwEYzM84xo8cINSPYwZfogIsL+78Edzfzgs8Y0ssKjh5u5Czz1 15b9bYTGnr0Xpfdkz/+UlkzQoMRINBE= 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 A65BE160398 for <56999@debbugs.gnu.org>; Fri, 5 Aug 2022 11:33:19 +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 15.1.2507.9; Fri, 5 Aug 2022 11:33:18 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <56999@debbugs.gnu.org> Subject: [PATCH 3/4] gnu: Add phyml-phyrex. Date: Fri, 5 Aug 2022 11:33:05 +0200 Message-ID: <20220805093306.21767-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.1 In-Reply-To: <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> References: <20220805093306.21767-1-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-14.0.0.3092-9.0.1002-27058.006 X-TM-AS-Result: No-10-0.190300-5.000000 X-TMASE-MatchedRID: BrKfIHwbYjV6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VDI3 NdfFmGpMfS0Ip2eEHnwj/1Rbkzl1E95/HgWYxplM5MIx11wv+CPKayT/BQTiGl6l++H8AVY9cGL tymQ2jAfd9ZDjW7EKJGbAMZMnf5wgDE9+4LiYESkQ3yaNtjB3vVDm1jZL+hG5zEtoW2aeDiKM9A CWHdUHZgAQiNUjB8O8tOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.190300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27058.006 X-TM-SNTS-SMTP: AFECD8AA2B064EFCA07F4526B68332D45288276267A081925C7D0D64B6538C262002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 56999 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/bioinformatics.scm (phyml-phyrex): New variable. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f448341031..1cb2b49eea 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9116,6 +9116,13 @@ (define-public phyml-mpi automake openmpi)))) +(define-public phyml-phyrex + (package (inherit phyml) + (name "phyml-phyrex") + (arguments + `(#:configure-flags + (list "--enable-phyrex"))))) + (define-public imp (package (name "imp") -- 2.37.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Aug 05 05:33:29 2022 Received: (at 56999) by debbugs.gnu.org; 5 Aug 2022 09:33:29 +0000 Received: from localhost ([127.0.0.1]:56236 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJthx-0007kG-7M for submit@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:29 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:51595) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJthu-0007jW-Of for 56999@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:27 -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=1659692000; x=1661506401; bh=8y0I+UGTO0FhNX/OZbTJ6l0QrMk2jivE2M98kt9PnMY=; b=JYDaGL2ALRDB dtkqXTyirKbNlTkleLWZwcG3n9HruMGb6PAQ1vRwVycSAEv7JI4C73AB/vxBLBm1 IzczyYH0Ci6BkVW4Pu9knnsopX3siHMAjPEOqxO+WC5ksE4ppIK/4CNv/zKegVdj kwv7msD8n+rJvPhRQz6LLf1Pcg4UyWg= 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 89A6A16039C for <56999@debbugs.gnu.org>; Fri, 5 Aug 2022 11:33:20 +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 15.1.2507.9; Fri, 5 Aug 2022 11:33:18 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <56999@debbugs.gnu.org> Subject: [PATCH 4/4] nu: Add phyml-rf. Date: Fri, 5 Aug 2022 11:33:06 +0200 Message-ID: <20220805093306.21767-4-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.1 In-Reply-To: <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> References: <20220805093306.21767-1-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-14.0.0.3092-9.0.1002-27058.006 X-TM-AS-Result: No-10-0.190300-5.000000 X-TMASE-MatchedRID: BrKfIHwbYjV6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VDI3 NdfFmGpMfS0Ip2eEHnwj/1Rbkzl1E95/HgWYxplM5MIx11wv+CPKayT/BQTiGkIDt2uBz9KIOyI 7AFZtmW1yIfI5dpyhAqBc3vfzzcupjWU4sJab/dxCIuSpCpztlUKYoZ94Dz0MD9MxYchzixskPa 3VsTm8eQAQiNUjB8O8tOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.190300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27058.006 X-TM-SNTS-SMTP: A4C86503F8D5B2A5A4AB35716BCE9C190E5CBFEC088B24E4E19E86D28FB4FBF02002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 56999 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/bioinformatics.scm (phyml-rf): New variable. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1cb2b49eea..5421a987b7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9123,6 +9123,13 @@ (define-public phyml-phyrex `(#:configure-flags (list "--enable-phyrex"))))) +(define-public phyml-rf + (package (inherit phyml) + (name "phyml-rf") + (arguments + `(#:configure-flags + (list "--enable-rf"))))) + (define-public imp (package (name "imp") -- 2.37.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 08 04:10:52 2022 Received: (at 56999) by debbugs.gnu.org; 8 Aug 2022 08:10:52 +0000 Received: from localhost ([127.0.0.1]:39115 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oKxqd-0005y3-KF for submit@debbugs.gnu.org; Mon, 08 Aug 2022 04:10:51 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21056) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oKxqY-0005xq-NS for 56999@debbugs.gnu.org; Mon, 08 Aug 2022 04:10:50 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1659946242; cv=none; d=zohomail.com; s=zohoarc; b=V3E0ZCAsahI+cuwrlRRJUp1WzWjY6+KfhpHKlsTb63PD8zaGUybZg5SlKgfk1ofLV6nNB2VEmrmsABNcovPDEy7tfpYAjf3ZUfoHms7nC++MIHHqIHxw3bRSM0udSGZeYGMdMjMVePCZ/FTHGjbdarK8oIpBV1+Tuq3Uy8DOMDI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1659946242; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=Q1bXqGbErxjTQ9U1s3x+T26oN4095RXLUed6BDcVYUE=; b=h7dlx/2UeKPRi6O1otLr/sarXhlJceTl0d9CIw+w5JULtkqRQ9xKHBpggqJXxQ6z/r32fnCciQC7XtZel5nSzWWDzYhBiVZ6xowEHHD3SNAujvku5beqORLMk603suIm3SXkpc+m1UNS4FLTOnXcodD/Eu8Lto3fASFx2DBrlr4= 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= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1659946242; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=Q1bXqGbErxjTQ9U1s3x+T26oN4095RXLUed6BDcVYUE=; b=GjcM9SnlW7VuBfsjCdBFxyQngHZ1GadKRvab3/J9ABRV9wMgcXaMdWLheU3xqPs7 hgTR94eav/PnDz3gB+aXmdW1ysBO1asvw/9ALL0Tv9QbNCJplHjsv9+5d1inJidFJpD yLpaApg6TsZeZ8lLkdjTU8gIMGDaEiVosaTmlgX8= Received: from localhost (i5E862C12.versanet.de [94.134.44.18]) by mx.zohomail.com with SMTPS id 1659946239922474.4420415548036; Mon, 8 Aug 2022 01:10:39 -0700 (PDT) References: <398fc66441a34468a7c66370abb8f923@mdc-berlin.de> <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.7; emacs 28.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#56999] [PATCH 1/4] gnu: Add phyml. Date: Mon, 08 Aug 2022 10:09:05 +0200 In-reply-to: <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <875yj32m0z.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 56999 Cc: 56999@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/bioinformatics.scm (phyml): New variable. Thanks for the patch. > + "@code{PhyML} is a software package that uses modern statistical ap= proaches > +to analyse alignments of nucleotide or amino acid sequences in a phyloge= netic > +framework. The main tool in this package builds phylogenies under the m= aximum > +likelihood criterion. It implements a large number of substitution mode= ls coupled > +with efficient options to search the space of phylogenetic tree topologi= es. @code{ > +PhyTime} is another tool in the @code{PhyML} package that focuses on div= ergence > +date estimation in a Bayesian setting. The main strengths of @code{PhyT= ime} lie > +in its ability to accommodate for uncertrainty in the placement of fossil > +calibration and the use of realistic models of rate variation along the = tree. > +Finally, code{PhyREX} fits the spatial-Lambda-Fleming-Viot model to geo-= referenced > +genetic data. This model is similar to the structured coalescent but as= sumes that > +individuals are distributed along a spatial continuum rather than discre= te demes. > +@code{PhyREX} can be used to estimate population densities and rates of = dispersal. > +Its output can be processed by treeannotator (from the @code{BEAST} pack= age) as > +well as @code{SPREAD}.") The description mentions PhyTime and PhyREX, neither of which are included in this package. I=E2=80=99ll try to integrate this package with the definitions of phyml-mpi, phyml-phyrex, and phyml-rf that you=E2=80=99ve sent here. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 08 06:40:30 2022 Received: (at 56999) by debbugs.gnu.org; 8 Aug 2022 10:40:30 +0000 Received: from localhost ([127.0.0.1]:39322 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oL0BO-0001db-IC for submit@debbugs.gnu.org; Mon, 08 Aug 2022 06:40:30 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:33469) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oL0BL-0001dC-Q2 for 56999@debbugs.gnu.org; Mon, 08 Aug 2022 06:40:25 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:in-reply-to :date:date:subject:subject:from:from:user-agent:references :received; s=mdc; t=1659955215; x=1661769616; bh=RN7v9Wsa2EBh2Qj MOiu6PlH31UUoeXPhVT6NVrs++yU=; b=jPdYujEuA3FShmtLanBwEWaw193UmpW fDNkfswghBAhCsde+HPbSxwHu7Ej6+2IxOx7uxQroJe/dwD3qGeCAs4K62Y6CORi 28+kmEH6nVEvBzZb59PcdTEM9VkquEeB4Uz9jIyPWfKXs1RfV2bI/CCDr85nNgyQ pKfB2BpGsqNY= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 3B53B16037B for <56999@debbugs.gnu.org>; Mon, 8 Aug 2022 12:40:14 +0200 (CEST) Received: from localhost (94.134.44.18) 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 15.1.2507.9; Mon, 8 Aug 2022 12:40:13 +0200 References: <398fc66441a34468a7c66370abb8f923@mdc-berlin.de> User-agent: mu4e 1.8.7; emacs 28.1 From: Ricardo Wurmus To: "Patrascu, Madalin Ionel" Subject: Re: [ext] bug#56999: Acknowledgement (Add phyml package tools.) Date: Mon, 8 Aug 2022 12:35:28 +0200 In-Reply-To: X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <871qtr2f3n.fsf@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [94.134.44.18] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27064.007 X-TM-AS-Result: No-10-0.454300-5.000000 X-TMASE-MatchedRID: u1zqiMeMcrr/9O/B1c/QyxIRh9wkXSlFF430d3dMHkZLNZ7t9vqFgOcD DzKnTzUsefhOSZHJL1OPiGd0HfbiFaPFjJEFr+olKE0Je8DR/D4CU1PRf9o2s90H8LFZNFG7doM ssNsUwYXnYlZBT1AIBE2ypLaP2v3W/38b6a58/grwK1B9O1Dtqx+mrtErqRYLlyX5sBgC7PsQBQ ugsIIi4bE5WfZoNmdJoCQQb4a32r4kJeS/ERgZIGRaod0r0qzYq8qcP/NDW67uL6tuaI7WB9qOT TbVrp1s X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.454300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27064.007 X-TM-SNTS-SMTP: 9A19758405030D5B82F115ADEFA1EFDC074CC4B8F8E95FB8FE7A745ADB243B7E2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 56999 Cc: "56999-done@debbugs.gnu.org" <56999@debbugs.gnu.org> X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) I modified the package definition like this: - build all tools in the same package by using separate build phases - remove any mention of PhyTime from the description - add texlive-* packages to build and install the PDF manual - remove the pre-built PDF manual from the sources - remove -march=native - set only x86_64 as supported An upstream bug (https://github.com/stephaneguindon/phyml/issues/173) made it impossible to remove -march=native completely, so I hope this is sufficient. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 31 16:48:31 2022 Received: (at 56999-done) by debbugs.gnu.org; 31 Oct 2022 20:48:31 +0000 Received: from localhost ([127.0.0.1]:42020 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1opbhv-0001pa-JZ for submit@debbugs.gnu.org; Mon, 31 Oct 2022 16:48:31 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:38063) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1opbht-0001pM-RO for 56999-done@debbugs.gnu.org; Mon, 31 Oct 2022 16:48:30 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:in-reply-to :date:date:subject:subject:from:from:user-agent:references :received; s=mdc; t=1667249302; x=1669063703; bh=ZJyQQYOAqvyxzAc 3acyUSEwCtWVI2R2FYHU2MEjSs2s=; b=BsmF9+isWiJStbhvL8b7MjtK2qzBcMl jNlQUyrN6T2ROOA3JaNMdbY2/kDOwmohJa2KLEIHNqavQzkc4Fr9xeJoYvdNQ41L eRIzi+pcxtpwfUmhnOdCm9WCZJJx6aKGziomxTnZ/01sdzYglIaEW5jGUVHXZnoy BITxx1GRWC8Y= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 4D7E6A0254 for <56999-done@debbugs.gnu.org>; Mon, 31 Oct 2022 21:48:21 +0100 (CET) Received: from localhost (46.142.111.155) 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 15.1.2507.13; Mon, 31 Oct 2022 21:48:20 +0100 References: <398fc66441a34468a7c66370abb8f923@mdc-berlin.de> <871qtr2f3n.fsf@mdc-berlin.de> User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: <56999-done@debbugs.gnu.org> Subject: Add phyml package tools Date: Mon, 31 Oct 2022 21:47:38 +0100 In-Reply-To: <871qtr2f3n.fsf@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87o7trbtyj.fsf@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [46.142.111.155] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27236.002 X-TM-AS-Result: No-10--3.074600-5.000000 X-TMASE-MatchedRID: OVdoBgHyl5CoGSK7rXzPTaubsOtSWY2QgDLqnrRlXra/fOyo7SP/86jH w73GrrCAanE1Ybb9x4X3FLeZXNZS4EZLVcXaUbdiEp6E6V/kvBGjq0+8xCUgX5aAJhhGs7sVFNn ShmCWNYTh9aSdKC5cP8OmIS1dBUe/1JbKcqUtFlmgOg8jfwSobFncnFy5i8dC X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.074600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27236.002 X-TM-SNTS-SMTP: 3A45185456029BAB18A5229917C48CED4D77AFDCD2E30DE5069BFBC3FFA64EC72002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 56999-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Closing. -- Ricardo From unknown Sun Aug 17 10:26:11 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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