From unknown Wed Jun 18 23:17:33 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#32259 <32259@debbugs.gnu.org> To: bug#32259 <32259@debbugs.gnu.org> Subject: Status: Add R packages from CRAN Reply-To: bug#32259 <32259@debbugs.gnu.org> Date: Thu, 19 Jun 2025 06:17:33 +0000 retitle 32259 Add R packages from CRAN reassign 32259 guix-patches submitter 32259 Ricardo Wurmus severity 32259 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Jul 24 08:20:23 2018 Received: (at submit) by debbugs.gnu.org; 24 Jul 2018 12:20:23 +0000 Received: from localhost ([127.0.0.1]:54656 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fhwIg-0008US-P8 for submit@debbugs.gnu.org; Tue, 24 Jul 2018 08:20:22 -0400 Received: from eggs.gnu.org ([208.118.235.92]:45982) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fhwIe-0008U9-LY for submit@debbugs.gnu.org; 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Tue, 24 Jul 2018 14:19:58 +0200 (CEST) Received: from localhost (141.80.113.51) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server id 14.3.399.0; Tue, 24 Jul 2018 14:19:58 +0200 User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: Subject: Add R packages from CRAN 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 Date: Tue, 24 Jul 2018 14:19:48 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.51] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-23988.006 X-TM-AS-Result: No-0.057800-8.000000-10 X-TMASE-MatchedRID: r78SC5iivxwURSScn+QSXudOY0QPe0XVkUgIuOSoR8mSU/0rQ3GY0N0H 8LFZNFG71sULACB0qRIlkAKwwQ/Hha1R2T3Nhv9aggD7zwtLzFtYq9qzaYJQvsrXdwU6Yl5RmFl lhUsvADwoMgk22krxYAoQrmSQoP9udoJ1mUfJPv5+3BndfXUhXQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.057800-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-23988.006 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) 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: -6.0 (------) This patch series adds a few more R packages from CRAN. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Tue Jul 24 08:22:29 2018 Received: (at 32259) by debbugs.gnu.org; 24 Jul 2018 12:22:29 +0000 Received: from localhost ([127.0.0.1]:54661 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fhwKj-00007l-61 for submit@debbugs.gnu.org; Tue, 24 Jul 2018 08:22:29 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:59698) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fhwKh-00007a-4V for 32259@debbugs.gnu.org; Tue, 24 Jul 2018 08:22:27 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 2CFBE99D5C4 for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:22:26 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:x-mailer:message-id:date :date:subject:subject:from:from:received:received:received; s= mdc; t=1532434940; x=1534249341; bh=7YHEf4KdyNXvNgE0ULxBjjRc89Gf cUbWrsk3EzbFLiY=; b=e2FmZyV8PZZWV3onralMJjXH5Y+2DKz3jTDSDIXq2npR L4i4uyOkMS/C3YtpsvvFMgpNMpM+4b7e5p2rArtMAaWf6w4Bw8Bm1HGtnzIkpluI lt49gUAz3CpGGihwSN8HyfOkd3Rky5DiNNmJH2qpLGgva7NbzvcV4VKPCMqf60A= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id BMeyYnyUkXCo for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:22:20 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:22:20 +0200 (CEST) Received: from localhost (141.80.113.51) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server id 14.3.399.0; Tue, 24 Jul 2018 14:22:20 +0200 From: Ricardo Wurmus To: <32259@debbugs.gnu.org> Subject: [PATCH 1/4] gnu: Add r-doby. Date: Tue, 24 Jul 2018 14:22:05 +0200 Message-ID: <20180724122208.24086-1-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.51] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-23988.006 X-TM-AS-Result: No-1.633400-8.000000-10 X-TMASE-MatchedRID: pO1GJeE+rkt7qToVEfwBPAPZZctd3P4BuKSyOjKDwbhu4FknyqyshKLn eXF/QRDTkk0LFuQcd2XoTOKxGVevbkhrEQpQtQpn/jkwiY2tJnI/KKWJiVzXMmmj1qXcLu1ijlm DZvUCWMAPCe0YNAOA0kc59M+MxRoO/6PuZfWUoL4zw5Ejs3g1lkXDBOJVUNJLmyiLZetSf8lBgw 5G4NYCZN9pjzubZ2rHwrbXMGDYqV99R4Ss0oUmJ+TC8m2jZ8fKjikAqQ00cMOtPz/9CzxbSQvKC /V1t6dVbwnheZTcLrZ/qc52y93BT08ZktX5daVQ89dgARKRrJuShia9BV5+OHMlKjd7kJW0P2nr hpzTnX4SFeEaqul3aIOFrOPMaJ4V X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.633400-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-23988.006 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32259 Cc: Ricardo Wurmus 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: -6.0 (------) * gnu/packages/cran.scm (r-doby): New variable. --- gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fc4baa5b5..da9b67bff 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4646,3 +4646,35 @@ matches version and feature constraints.") write shebang scripts that gracefully accept positional and optional arguments and automatically generate usage notices.") (license license:gpl2+))) + +(define-public r-doby + (package + (name "r-doby") + (version "4.6-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "doBy" version)) + (sha256 + (base32 + "1y02awzid23bxz8hx6j8pxd6i7jaq8pdw3k60rag8y6m69incrw5")))) + (properties `((upstream-name . "doBy"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-magrittr" ,r-magrittr) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-plyr" ,r-plyr))) + (home-page "http://people.math.aau.dk/~sorenh/software/doBy/") + (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") + (description + "This package contains: + +@itemize +@item facilities for working with grouped data: @code{do} + something to data stratified @code{by} some variables. +@item implementations of least-squares means, general linear contrasts, and +@item miscellaneous other utilities. +@end itemize") + (license license:gpl2+))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Jul 24 08:22:40 2018 Received: (at 32259) by debbugs.gnu.org; 24 Jul 2018 12:22:40 +0000 Received: from localhost ([127.0.0.1]:54664 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fhwKu-00008J-Et for submit@debbugs.gnu.org; Tue, 24 Jul 2018 08:22:40 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:35418) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fhwKs-000087-1Q for 32259@debbugs.gnu.org; Tue, 24 Jul 2018 08:22:39 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 2969B380F27 for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:22:37 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1532434956; x=1534249357; bh=Bbex9bodNNYWC6EjymbZxs3q6SUkfB1VBCCYlij0Njo=; b=JX6eHSQV/D0A GuJ71jTtAikvbVKogR7DOYXkdpe1/scmba8zTjx6BI3dfi+2SLbPIS4zBZ+xGim4 H6dvXWR7zziUQyXv9GQ7ohVXwN67xofKseAm4azRt121dXH7+L9fG/nr7s1tdQpV txsCstaisfl6vgAFcOijBk7f5THR0vw= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id sIxgX0WpQvis for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:22:36 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:22:36 +0200 (CEST) Received: from localhost (141.80.113.51) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server id 14.3.399.0; Tue, 24 Jul 2018 14:22:36 +0200 From: Ricardo Wurmus To: <32259@debbugs.gnu.org> Subject: [PATCH 2/4] gnu: Add r-refgenome. Date: Tue, 24 Jul 2018 14:22:06 +0200 Message-ID: <20180724122208.24086-2-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 In-Reply-To: <20180724122208.24086-1-ricardo.wurmus@mdc-berlin.de> References: <20180724122208.24086-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.51] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-23988.006 X-TM-AS-Result: No-2.516600-8.000000-10 X-TMASE-MatchedRID: GeocjSabTAh7qToVEfwBPAPZZctd3P4BGK57kZ/2makNmPMcsvd5FpAP 6Djd73MAbqZQduIGtox3Q9v+2uuRnFNI1uaZzQXGbBu6+EIezdzXRXVqJuifskQnEdji/6xZo8W MkQWv6iXBcIE78YqRWvcUt5lc1lLgKIzdZS3ou0XVFTXikVsAJBKrK6RXlwhNWymtFSWlCbMCmY 3J4qLlb8J+48aQZALWq3MydOCiL40ncIpsaxvz2Zb2En7SVuEBXIAx8N2VBMQV4remnWxifeiPY vP0WKzlGj81Ipo8t/JeZSAxBsC8ng== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.516600-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-23988.006 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32259 Cc: Ricardo Wurmus 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: -6.0 (------) * gnu/packages/cran.scm (r-refgenome): New variable. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index da9b67bff..693a891a0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4678,3 +4678,31 @@ and automatically generate usage notices.") @item miscellaneous other utilities. @end itemize") (license license:gpl2+))) + +(define-public r-refgenome + (package + (name "r-refgenome") + (version "1.7.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "refGenome" version)) + (sha256 + (base32 + "15p0ra2p1pwhy5ixbhsz1g79c5sc2aap4i4c8kil0m2syg9y45sn")))) + (properties `((upstream-name . "refGenome"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dbi" ,r-dbi) + ("r-doby" ,r-doby) + ("r-rsqlite" ,r-rsqlite))) + (home-page "https://cran.r-project.org/web/packages/refGenome/") + (synopsis + "Gene and splice site annotation using annotation data from Ensembl and UCSC") + (description + "This package contains functionality for importing and managing of +downloaded genome annotation data from the Ensembl genome browser (European +Bioinformatics Institute) and from the UCSC genome browser (University of +California, Santa Cruz) and annotation routines for genomic positions and +splice site positions.") + (license license:gpl2))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Jul 24 08:22:55 2018 Received: (at 32259) by debbugs.gnu.org; 24 Jul 2018 12:22:55 +0000 Received: from localhost ([127.0.0.1]:54667 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fhwL8-00008w-Np for submit@debbugs.gnu.org; Tue, 24 Jul 2018 08:22:55 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:59706) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fhwL7-00008m-Bo for 32259@debbugs.gnu.org; Tue, 24 Jul 2018 08:22:53 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id CCA5299D5C9 for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:22:52 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1532434967; x=1534249368; bh=GKTtvGQDyBU3wOKyQa5YQxVgNrHUdbosPGsspBLQwwU=; b=GVvHM79aeBoF 8EnwofC7An9TOWjfNyTbzT8I17ZUa/Xn94Pl6R1IUnROaiSThhpksHudZRPb+3WX D/iAiu5NH+PLZHMoEoVZhvOPFcnpQY/yJzcr8EpBiXC4BV/hxIhQ+UY0XkY3Me3C nEWal1SGbqL8l1uqsBdE5go9VS6mf1o= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id pXLw04eA9Fjj for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:22:47 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:22:47 +0200 (CEST) Received: from localhost (141.80.113.51) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server id 14.3.399.0; Tue, 24 Jul 2018 14:22:47 +0200 From: Ricardo Wurmus To: <32259@debbugs.gnu.org> Subject: [PATCH 3/4] gnu: Add r-basix. Date: Tue, 24 Jul 2018 14:22:07 +0200 Message-ID: <20180724122208.24086-3-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 In-Reply-To: <20180724122208.24086-1-ricardo.wurmus@mdc-berlin.de> References: <20180724122208.24086-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.51] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-23988.006 X-TM-AS-Result: No-2.650200-8.000000-10 X-TMASE-MatchedRID: zoFxOq+IDXN7qToVEfwBPAPZZctd3P4BYqLHQV0bLx9gOcGYycfRsGB5 N6RCXcCHppR2x0hY+75p0oDM6nL2ljPfG+JZNtQpdXu122+iJtpbAoaK+wS4jdvpj5+dNlQvmRd H/a1EAe3i8zVgXoAltsIJ+4gwXrEtwrbXMGDYqV8X9rpBZuBDbSTXk4SIymjwKCk+WTEPiwrusZ O6BSL3VxrP5wl9QP62TFKAHSXb+YBh/fKkHnd+COvj1eBDNy7h/VwPuA37bKScSV7cFygsn3MlK jd7kJW0P2nrhpzTnX4SFeEaqul3aIOFrOPMaJ4V X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.650200-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-23988.006 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32259 Cc: Ricardo Wurmus 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: -6.0 (------) * gnu/packages/cran.scm (r-basix): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 693a891a0..f1511c097 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4706,3 +4706,23 @@ Bioinformatics Institute) and from the UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.") (license license:gpl2))) + +(define-public r-basix + (package + (name "r-basix") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "BASIX" version)) + (sha256 + (base32 + "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id")))) + (properties `((upstream-name . "BASIX"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/BASIX/") + (synopsis "Efficient C/C++ toolset for R") + (description + "BASIX provides some efficient C/C++ implementations to speed up +calculations in R.") + (license license:gpl2))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Jul 24 08:23:06 2018 Received: (at 32259) by debbugs.gnu.org; 24 Jul 2018 12:23:06 +0000 Received: from localhost ([127.0.0.1]:54673 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fhwLK-0000AK-5H for submit@debbugs.gnu.org; Tue, 24 Jul 2018 08:23:06 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:35430) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fhwLI-0000A9-4H for 32259@debbugs.gnu.org; Tue, 24 Jul 2018 08:23:04 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 94A9B380BA3 for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:23:03 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1532434983; x=1534249384; bh=hoNvXAVVZbbLWn+FV4HuSjhr/3RmIkekHFfrDG4kFho=; b=CVDs+4tZvEkE /tWkSN2WUBD1Zi8e43S12jFA/Tj8L1UM163IvbFFMdrrOs2oVLU1XjPghSI3+zzY KHg3aOPSTjbjxvxu9FMV31iJoZtwLWHeN9UiCGJT3jPJZ40si6Biew3Mdlqkf+Kv Qw7tRyE3NsbMm+9gt7GgXIL2a3L5LlE= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id wR8W-bnuD_M4 for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:23:03 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32259@debbugs.gnu.org>; Tue, 24 Jul 2018 14:23:03 +0200 (CEST) Received: from localhost (141.80.113.51) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server id 14.3.399.0; Tue, 24 Jul 2018 14:23:02 +0200 From: Ricardo Wurmus To: <32259@debbugs.gnu.org> Subject: [PATCH 4/4] gnu: Add r-blockfest. Date: Tue, 24 Jul 2018 14:22:08 +0200 Message-ID: <20180724122208.24086-4-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 In-Reply-To: <20180724122208.24086-1-ricardo.wurmus@mdc-berlin.de> References: <20180724122208.24086-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.51] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-23988.006 X-TM-AS-Result: No-1.746700-8.000000-10 X-TMASE-MatchedRID: WY68sLfT9697qToVEfwBPAPZZctd3P4BmsxcVyENyJz1Cq+9xx01OJ/p 6742jA2BrcUJLrFUTpm7/LlTYfsWi+o3TaQdFshVnVTWWiNp+v/0/gDTuyWA5FGVsgO8+3kgFmD /LBWj5jyagJoQSDIhqrBuXDodorqahkzPKp8AvSTBVprK8rvWX30tCKdnhB589yM15V5aWpj6C0 ePs7A07ba607moR85RSBJA3BjaJ96hhTspUnjk+/GC6qsgujvEbCSA459rY/ehoDWsgfT5sSsBS yZOYNtVNiWcIvxOGZBEe54UPY0PiYFmqLUUh3g4h/iXdbS1V7u7j2rWxYQLt0cGnllPWffhN10+ 4fC3tMDFhXMjdQIJpg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.746700-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-23988.006 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32259 Cc: Ricardo Wurmus 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: -6.0 (------) * gnu/packages/cran.scm (r-blockfest): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f1511c097..c04598141 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4726,3 +4726,27 @@ splice site positions.") "BASIX provides some efficient C/C++ implementations to speed up calculations in R.") (license license:gpl2))) + +(define-public r-blockfest + (package + (name "r-blockfest") + (version "1.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "BlockFeST" version)) + (sha256 + (base32 + "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5")))) + (properties `((upstream-name . "BlockFeST"))) + (build-system r-build-system) + (propagated-inputs `(("r-basix" ,r-basix))) + (home-page "https://cran.r-project.org/web/packages/BlockFeST/") + (synopsis "Bayesian calculation of region-specific fixation index") + (description + "This package provides an R implementation of an extension of the +BayeScan software for codominant markers, adding the option to group +individual SNPs into pre-defined blocks. A typical application of this new +approach is the identification of genomic regions, genes, or gene sets +containing one or more SNPs that evolved under directional selection.") + (license license:gpl2))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Sun Jul 29 09:33:55 2018 Received: (at 32259) by debbugs.gnu.org; 29 Jul 2018 13:33:55 +0000 Received: from localhost ([127.0.0.1]:33286 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fjlpa-00050J-Pg for submit@debbugs.gnu.org; Sun, 29 Jul 2018 09:33:54 -0400 Received: from eggs.gnu.org ([208.118.235.92]:38661) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fjlpY-000505-8m for 32259@debbugs.gnu.org; Sun, 29 Jul 2018 09:33:52 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fjlpR-0006uS-QI for 32259@debbugs.gnu.org; Sun, 29 Jul 2018 09:33:46 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:40100) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fjlpR-0006uN-M4; Sun, 29 Jul 2018 09:33:45 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=47574 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1fjlpQ-0003tO-Ea; Sun, 29 Jul 2018 09:33:44 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Ricardo Wurmus Subject: Re: [bug#32259] [PATCH 3/4] gnu: Add r-basix. References: <20180724122208.24086-1-ricardo.wurmus@mdc-berlin.de> <20180724122208.24086-3-ricardo.wurmus@mdc-berlin.de> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 11 Thermidor an 226 de la =?utf-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Sun, 29 Jul 2018 15:33:42 +0200 In-Reply-To: <20180724122208.24086-3-ricardo.wurmus@mdc-berlin.de> (Ricardo Wurmus's message of "Tue, 24 Jul 2018 14:22:07 +0200") Message-ID: <874lgii2tl.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32259 Cc: 32259@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: -6.0 (------) Hi! Ricardo Wurmus skribis: > + (home-page "https://cran.r-project.org/web/packages/BASIX/") > + (synopsis "Efficient C/C++ toolset for R") > + (description > + "BASIX provides some efficient C/C++ implementations to speed up > +calculations in R.") Perhaps write =E2=80=9Cimplementations of X and Y=E2=80=9D to clarify. Oth= erwise these 4 patches LGTM, thanks! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 16 11:06:30 2018 Received: (at 32259-done) by debbugs.gnu.org; 16 Aug 2018 15:06:30 +0000 Received: from localhost ([127.0.0.1]:52688 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fqJr4-00078D-0I for submit@debbugs.gnu.org; Thu, 16 Aug 2018 11:06:30 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:39080) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fqJr3-000785-0a for 32259-done@debbugs.gnu.org; Thu, 16 Aug 2018 11:06:29 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id F0371380BA3 for <32259-done@debbugs.gnu.org>; Thu, 16 Aug 2018 17:06:27 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :in-reply-to:subject:subject:from:from:user-agent:references :received:received:received; s=mdc; t=1534431987; x=1536246388; bh=cz0Y5KJCk1d79vQhY+sRUe0RxyBN32lVxCrzDc7GCvw=; b=UcATHJ8uy7nk +VV5+O5jyoP4ViFtOWYi/CW4g2fjrfmiuIuIe/o/PXqKSYkS+aQRAFhI/FVERjDL NtffB56wMJUHcSKUxbO3hmeVYS/chdnEVo3j+lJ9muBjUkUgnTNOzNXH7tINO5Tv YpRq7vcuEPQe5fePeUrgFk6zVoT3kj4= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 2otpRjYWQvCo for <32259-done@debbugs.gnu.org>; Thu, 16 Aug 2018 17:06:27 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32259-done@debbugs.gnu.org>; Thu, 16 Aug 2018 17:06:27 +0200 (CEST) Received: from localhost (141.80.246.28) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server (TLS) id 14.3.408.0; Thu, 16 Aug 2018 17:06:27 +0200 References: <20180724122208.24086-1-ricardo.wurmus@mdc-berlin.de> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: <32259-done@debbugs.gnu.org> Subject: Re: [PATCH 1/4] gnu: Add r-doby. In-Reply-To: <20180724122208.24086-1-ricardo.wurmus@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 Date: Thu, 16 Aug 2018 17:06:22 +0200 Message-ID: <874lfuuz9t.fsf@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.246.28] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24036.001 X-TM-AS-Result: No-2.836700-8.000000-10 X-TMASE-MatchedRID: 4kTn4W3NajPUaFx23KkikWwbuvhCHs3cnophrTcsI7abKItl61J/yfJv ocwUrWp7gZK4jdUf7rU+Aoot6UqUmMRB0bsfrpPIHm9ggFVoCcCXzSghUrrdAMQvKgl9wDNJ0hK TRdsPdrd0ouIL+aMzXcwLew+f0T2f7AIQ6NwbxaelTiV4y2c+kRQAVhDuYR+VLKhCgqe9WmI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.836700-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24036.001 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32259-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: -6.0 (------) I pushed these with minor changes to the description of r-basix. Thanks to Ludo for the review! -- Ricardo From unknown Wed Jun 18 23:17:33 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 14 Sep 2018 11:24:06 +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