From unknown Wed Jun 18 00:20:01 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#38489 <38489@debbugs.gnu.org> To: bug#38489 <38489@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-qtl2. Reply-To: bug#38489 <38489@debbugs.gnu.org> Date: Wed, 18 Jun 2025 07:20:01 +0000 retitle 38489 [PATCH] gnu: Add r-qtl2. reassign 38489 guix-patches submitter 38489 Efraim Flashner severity 38489 normal tag 38489 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Wed Dec 04 03:58:57 2019 Received: (at submit) by debbugs.gnu.org; 4 Dec 2019 08:58:57 +0000 Received: from localhost ([127.0.0.1]:41425 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1icQUr-0000AB-Bs for submit@debbugs.gnu.org; Wed, 04 Dec 2019 03:58:57 -0500 Received: from lists.gnu.org ([209.51.188.17]:58180) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1icQUo-00009p-3G for submit@debbugs.gnu.org; Wed, 04 Dec 2019 03:58:54 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:45640) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1icQUi-0003Ff-Ob for guix-patches@gnu.org; Wed, 04 Dec 2019 03:58:50 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1icQUb-0006Fq-HJ for guix-patches@gnu.org; Wed, 04 Dec 2019 03:58:44 -0500 Received: from flashner.co.il ([178.62.234.194]:51030) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1icQUb-0004dO-AW for guix-patches@gnu.org; Wed, 04 Dec 2019 03:58:41 -0500 Received: from localhost (unknown [141.226.13.108]) by flashner.co.il (Postfix) with ESMTPSA id 18AD44020F; Wed, 4 Dec 2019 08:58:07 +0000 (UTC) From: Efraim Flashner To: guix-patches@gnu.org Subject: [PATCH] gnu: Add r-qtl2. Date: Wed, 4 Dec 2019 10:57:35 +0200 Message-Id: <20191204085735.23318-1-efraim@flashner.co.il> X-Mailer: git-send-email 2.24.0 MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 178.62.234.194 X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: Efraim Flashner 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 (--) * gnu/packages/bioinformatics.scm (r-qtl2): New variable. --- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm index b0d070b4e7..522cde959e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8239,6 +8239,35 @@ identify genotyping errors, and to perform single-= QTL and two-QTL, two-dimensional genome scans.") (license license:gpl3))) =20 +(define-public r-qtl2 + (package + (name "r-qtl2") + (version "0.20") + (source (origin + (method git-fetch) + ;; Not yet available in cran. + (uri (git-reference + (url "https://github.com/rqtl/qtl2.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0l1asr28q25jzbwrbg5490962sg3y4sjrd0qf09p78ws1aq8vfs0")))= ) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-jsonlite" ,r-jsonlite) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rsqlite" ,r-rsqlite) + ("r-yaml" ,r-yaml))) + (home-page "https://kbroman.org/qtl2/") + (synopsis + "QTL analysis software for high-dimensional data and complex cross = designs") + (description + "R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis softwa= re +R/qtl, to better handle high-dimensional data and complex cross designs.= ") + (license license:gpl3))) + (define-public r-zlibbioc (package (name "r-zlibbioc") --=20 2.24.0 From debbugs-submit-bounces@debbugs.gnu.org Fri Dec 06 13:14:39 2019 Received: (at 38489) by debbugs.gnu.org; 6 Dec 2019 18:14:39 +0000 Received: from localhost ([127.0.0.1]:47017 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1idI7j-0004VS-JM for submit@debbugs.gnu.org; Fri, 06 Dec 2019 13:14:39 -0500 Received: from mail-qk1-f194.google.com ([209.85.222.194]:38737) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1idI7g-0004Um-Rr for 38489@debbugs.gnu.org; Fri, 06 Dec 2019 13:14:37 -0500 Received: by mail-qk1-f194.google.com with SMTP id k6so7260855qki.5 for <38489@debbugs.gnu.org>; Fri, 06 Dec 2019 10:14:36 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=haNSBSjZoleqWAWJv1Fy/8pxAJ4ASwDdRuQwT4OJFFg=; b=t8jK1GAqGr8SVHWpDNJzLVOc+sUS3nmkOWFaEr+YfsnqUZ4uupe/7Ug6J6/0M6alTy 5KHhrbZZR03PsGGd1VmjTY7He+VeU9PzOtEK1dJMmyb9/j8Viih/g1ns+BNZZnUtSCl7 HgBdbk37saBuPNg2Ytn0+J/7VLTFlXjpyuXhx057UOfYwuquGlcBcEwRv1A0DCFIpVuU aG2wwPdxiLCYiqGrClEkfMEXVZfBpRR3oGnfzViZeu04t+CJrmE3RNDxiMpFrs53xw0L Z84JPD0L2Le+0wqgdoGwLI05M31ll2yVYMZlLVIa/EtUR7mwscS1lEUBQ+DgZTMNlben ooOw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=haNSBSjZoleqWAWJv1Fy/8pxAJ4ASwDdRuQwT4OJFFg=; b=q80iSuu7iw+nv6Je/L4ZKB5433tW+ntUNqgfkKHl6Xx5Qfs7Udajs9IrsMoO4MCw28 u1jKE55ERII2vf3eV8KvMDBhYG+mfqVN+QoiENXufPx8eWdPO+FwNz2gzePDT6iXxjSm k8BaC5LNqvTgERLmR8RWSxuFIp/XMbXlue/Gd/Zmo6oo2zDXuFfG/r6qiDKAma+Gsk/l I3HBZ/M4ao2gnOc3JVQuHEB2nokklEc3OcaYKF1F1H4uVIIsTh0ePJUMGRfV0akUkCuf PGwPgutC6qezJNCGnT4LADxnUo1mvV35mHgymibVrsrMMmJ+oXm60q1ieUOKpJATgi7l RLPw== X-Gm-Message-State: APjAAAXFcu+N/0Fjkj6JmfCER92Prjzg74xNB4oX5QpRwRzv3Ua0BGpE m4r3VTt02+2I7f+na6cZEfk7u1JpUviIvDhZ1FPhVg== X-Google-Smtp-Source: APXvYqx6t1003G3fB34/jZ+8jrYxelEU75LzbHQTRIluAhmNLu5VZE0YVOe5+r91GncCE+bRHFbZqJr/hnHujCHXUl0= X-Received: by 2002:a05:620a:1453:: with SMTP id i19mr13902586qkl.304.1575656071353; Fri, 06 Dec 2019 10:14:31 -0800 (PST) MIME-Version: 1.0 References: <20191204085735.23318-1-efraim@flashner.co.il> In-Reply-To: <20191204085735.23318-1-efraim@flashner.co.il> From: zimoun Date: Fri, 6 Dec 2019 19:14:20 +0100 Message-ID: Subject: Re: [bug#38489] [PATCH] gnu: Add r-qtl2. To: Efraim Flashner Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 38489 Cc: 38489@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 (-) Hi Efraim, On Wed, 4 Dec 2019 at 10:03, Efraim Flashner wrote: > > * gnu/packages/bioinformatics.scm (r-qtl2): New variable. > --- > gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ > 1 file changed, 29 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index b0d070b4e7..522cde959e 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -8239,6 +8239,35 @@ identify genotyping errors, and to perform single-QTL and two-QTL, > two-dimensional genome scans.") > (license license:gpl3))) > > +(define-public r-qtl2 > + (package > + (name "r-qtl2") > + (version "0.20") > + (source (origin > + (method git-fetch) > + ;; Not yet available in cran. > + (uri (git-reference > + (url "https://github.com/rqtl/qtl2.git") > + (commit version))) > + (file-name (git-file-name name version)) > + (sha256 > + (base32 "0l1asr28q25jzbwrbg5490962sg3y4sjrd0qf09p78ws1aq8vfs0")))) > + (build-system r-build-system) > + (propagated-inputs > + `(("r-data-table" ,r-data-table) > + ("r-jsonlite" ,r-jsonlite) > + ("r-rcpp" ,r-rcpp) > + ("r-rcppeigen" ,r-rcppeigen) > + ("r-rsqlite" ,r-rsqlite) > + ("r-yaml" ,r-yaml))) > + (home-page "https://kbroman.org/qtl2/") > + (synopsis > + "QTL analysis software for high-dimensional data and complex cross designs") > + (description > + "R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software > +R/qtl, to better handle high-dimensional data and complex cross designs.") > + (license license:gpl3))) > + LGTM. All the best, simon From debbugs-submit-bounces@debbugs.gnu.org Tue Dec 10 06:13:38 2019 Received: (at 38489-done) by debbugs.gnu.org; 10 Dec 2019 11:13:38 +0000 Received: from localhost ([127.0.0.1]:55005 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iedST-0003N8-VI for submit@debbugs.gnu.org; Tue, 10 Dec 2019 06:13:38 -0500 Received: from flashner.co.il ([178.62.234.194]:52504) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iedSS-0003Mu-4w for 38489-done@debbugs.gnu.org; Tue, 10 Dec 2019 06:13:36 -0500 Received: from localhost (unknown [141.226.13.108]) by flashner.co.il (Postfix) with ESMTPSA id F1778401C6; Tue, 10 Dec 2019 11:13:29 +0000 (UTC) Date: Tue, 10 Dec 2019 13:12:59 +0200 From: Efraim Flashner To: zimoun Subject: Re: [bug#38489] [PATCH] gnu: Add r-qtl2. Message-ID: <20191210111259.GA8302@E5400> References: <20191204085735.23318-1-efraim@flashner.co.il> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="zhXaljGHf11kAtnf" Content-Disposition: inline In-Reply-To: X-PGP-Key-ID: 0x41AAE7DCCA3D8351 X-PGP-Key: https://flashner.co.il/~efraim/efraim_flashner.asc X-PGP-Fingerprint: A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 User-Agent: Mutt/1.12.2 (2019-09-21) X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 38489-done Cc: 38489-done@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 (-) --zhXaljGHf11kAtnf Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Thanks. Patch pushed. --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --zhXaljGHf11kAtnf Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIyBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAl3vfboACgkQQarn3Mo9 g1FA8A/4xHNDQRS3BvMqf7IDqOf5e840oq6MwwkQ3ygu5QKN6CYGc0g9EVGs6gu7 ulSqDqQ6KhlWItLzKhQzosh7H29ULitX/Y2DpQxLhpvK+s/QMNvULixZXQIy0cFu dz0lXKzVmdFdmNTxN971Zr5ZnOMOdhZbCtVGWFL872msukbJeh42jfMFz1aKgOC1 EwVijgg0TU2GBndwd9OK/eo8rnqtUEyrNhSNpJ9otf4QIKBjlTqjo+hUlAo1Mvwt S3WEISaqH/WhZqslMvvY5jVY5F4/NzLMgVub49+S3lVTo9cEC6mru4mwh0kYueMc nePSSYB6jwZBHcMbGT/pRW/3Ei4/e7eTETPBverzuifK73jPuKLC4rDdh4H/N36c jGgLno6XIchqsrZIUl8zDlZoekK3dBewo7VkyaOvWxaKlsVyR7EnrUOxSGHccC5A nlQQwLfe7s2Itwp18uVnt2Ha+D2i07HsfoJpCr8Ok5q2hEOtMDDTkP3pEEcxswvq 0sXMpVyfa2wTAsAZ2pC/NZBdnHqp3zpjmMynFRoyG5w5num79k5i6BBkZ3fFkeKo 7hEZMBxU8UueXQrjPipmR6Aa+FX1BhduBibfOVrA4vM7a9aYOllBTuiM3GRIFYpw YwvOtYvQ6hmS/h9Oj6hb4jaiYT/kNd11+hGt2PyDU+l+gf53FQ== =hXje -----END PGP SIGNATURE----- --zhXaljGHf11kAtnf-- From unknown Wed Jun 18 00:20:01 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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