From unknown Wed Jun 18 00:24:23 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#38259 <38259@debbugs.gnu.org> To: bug#38259 <38259@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-harmony. Reply-To: bug#38259 <38259@debbugs.gnu.org> Date: Wed, 18 Jun 2025 07:24:23 +0000 retitle 38259 [PATCH] gnu: Add r-harmony. reassign 38259 guix-patches submitter 38259 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 38259 normal tag 38259 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 18 12:23:08 2019 Received: (at submit) by debbugs.gnu.org; 18 Nov 2019 17:23:08 +0000 Received: from localhost ([127.0.0.1]:46168 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iWkk0-00063W-6x for submit@debbugs.gnu.org; Mon, 18 Nov 2019 12:23:08 -0500 Received: from lists.gnu.org ([209.51.188.17]:51513) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iWkjy-00063O-6Q for submit@debbugs.gnu.org; Mon, 18 Nov 2019 12:23:06 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:56481) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iWkjw-0003HT-GK for guix-patches@gnu.org; Mon, 18 Nov 2019 12:23:06 -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,RCVD_IN_DNSWL_NONE, 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 1iWkju-0004WP-Sk for guix-patches@gnu.org; Mon, 18 Nov 2019 12:23:04 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:52453) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1iWkju-0004H6-9C for guix-patches@gnu.org; Mon, 18 Nov 2019 12:23:02 -0500 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 979B7160075 for ; Mon, 18 Nov 2019 18:22:45 +0100 (CET) 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:received:received; s=mdc; t=1574097765; x=1575912166; bh=NxJwWhh3I9pxCmu3aTy1ttMSA9aD0A6PbuycO9XynAE=; b=DUv3dPtmRLaw 9CedLujruqp3oSqK+JZYlrrujgCbHeKR+s9VrKGyTlev6lJfFntQZ8ULcGqda/X5 R6Zm1tuPijMHrM1ZWmuqx1CEQAWBfIqFY46sSnq8NNI9icPI3zgtf7Tsd5tLDeYV cjfHEvwALGEwf0gwrcBWYZSJvUiFFdE= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id I4wG3tH219tp for ; Mon, 18 Nov 2019 18:22:45 +0100 (CET) Received: from SW-IT-P-CAS3.mdc-berlin.net (mgw10-3.mdc-berlin.de [141.80.113.58]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Mon, 18 Nov 2019 18:22:44 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-CAS3.mdc-berlin.net (141.80.113.58) with Microsoft SMTP Server (TLS) id 14.3.468.0; Mon, 18 Nov 2019 18:22:44 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-harmony. Date: Mon, 18 Nov 2019 18:22:16 +0100 Message-ID: <20191118172216.21813-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25052.000 X-TM-AS-Result: No-3.580700-8.000000-10 X-TMASE-MatchedRID: aQJ0g3G0xD+4WGh1vUSL/3ycvC6I0dJIS1zwNuiBtITfUZT83lbkEA2o 6ebnCAbg09C7KD0jIx5De7JiJBQl19FbcK5rmPO1OVoNrnTEUFrIEQTlh1/QMatkcxxU6EVIeyY Rtv+ZW85LVtcjSeah83NERYbQXfHtY4zV0YEQAfZNP1m95I8DFeJNcHLvRNpEEEQaSVu4yLi+1l 2jbBu0KP75956eQfQ/pA12q7wOhpdKGzvueD4sBnYZxYoZm58FXVlxHIm91HKXBXaJoB9JZ4MbH 85DUZXygMf23PO6/W/6C0ePs7A07ba607moR85RA0p4Wyuc8kpEfJnIWW63f3QwVf/VFjzeugq5 r7LDVAX63KRI3ft6Q39RgtVRvXoUtD0YUK6Ijn0feOyS4eTgy5/QhV1TbGIhh/iXdbS1V7u7j2r WxYQLt0cGnllPWffhN10+4fC3tMDFhXMjdQIJpg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.580700-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25052.000 X-TM-SNTS-SMTP: 5C9E1D0B27BF51704709E8C9DBF13A62A551668E1A3B8B56FA60652AB5894F1B2000:9 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-Received-From: 194.95.234.172 X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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: -2.4 (--) * gnu/packages/bioinformatics.scm (r-harmony): New variable. --- gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++- 1 file changed, 37 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm index 07c70fb82c..5da95d66a6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +11,7 @@ ;;; Copyright =C2=A9 2017 Arun Isaac ;;; Copyright =C2=A9 2018 Joshua Sierles, Nextjournal ;;; Copyright =C2=A9 2018 G=C3=A1bor Boskovits -;;; Copyright =C2=A9 2018 M=C4=83d=C4=83lin Ionel Patra=C8=99cu +;;; Copyright =C2=A9 2018, 2019 M=C4=83d=C4=83lin Ionel Patra=C8=99cu ;;; Copyright =C2=A9 2019 Maxim Cournoyer ;;; Copyright =C2=A9 2019 Brian Leung ;;; @@ -15349,3 +15349,39 @@ methylation metrics from them. MethylDackel req= uires an indexed fasta file containing the reference genome as well.") ;; See https://github.com/dpryan79/MethylDackel/issues/85 (license license:expat))) + +(define-public r-harmony + (let ((commit "1a6d77aae524a08a2ca91737a152ab2047ccee78") + (revision "1")) + (package + (name "r-harmony") + (version (git-version "1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/immunogenomics/harmony.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1905qsbl5iv3kxki73gmyzshyb8zc6asdaymywndscn7mjkwm7aw"= )))) + (build-system r-build-system) + (propagated-inputs + `(("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-irlba" ,r-irlba) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rcppprogress" ,r-rcppprogress) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/immunogenomics/harmony.git") + (synopsis "Fast, sensitive, and accurate integration of single cel= l data") + (description + "Harmony software is the R implementation of the algorithm with t= he same +name for single cell integration, described in Korsunsky et al 2018. Pa= ckage +includes a standalone Harmony function and interfaces to external framew= orks.") + (license license:gpl3)))) --=20 2.17.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Nov 21 05:21:58 2019 Received: (at 38259-done) by debbugs.gnu.org; 21 Nov 2019 10:21:58 +0000 Received: from localhost ([127.0.0.1]:51304 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iXjb3-0000Eu-N4 for submit@debbugs.gnu.org; Thu, 21 Nov 2019 05:21:57 -0500 Received: from eggs.gnu.org ([209.51.188.92]:33838) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iXjb1-0000Ei-W5 for 38259-done@debbugs.gnu.org; Thu, 21 Nov 2019 05:21:56 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:56022) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1iXjav-00024K-Hn; Thu, 21 Nov 2019 05:21:49 -0500 Received: from wifi-eduroam-20-234.siege.inria.fr ([128.93.20.234]:53990 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1iXjas-0001Dx-It; Thu, 21 Nov 2019 05:21:46 -0500 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#38259] [PATCH] gnu: Add r-harmony. References: <20191118172216.21813-1-madalinionel.patrascu@mdc-berlin.de> Date: Thu, 21 Nov 2019 11:21:44 +0100 In-Reply-To: <20191118172216.21813-1-madalinionel.patrascu@mdc-berlin.de> (=?utf-8?B?Ik3Eg2TEg2xpbg==?= Ionel =?utf-8?Q?Patra=C8=99cu=22's?= message of "Mon, 18 Nov 2019 18:22:16 +0100") Message-ID: <87ftihil6v.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 38259-done Cc: 38259-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: -3.3 (---) --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hello M=C4=83d=C4=83lin, M=C4=83d=C4=83lin Ionel Patra=C8=99cu = skribis: > * gnu/packages/bioinformatics.scm (r-harmony): New variable. Applied with the changes below. Thank you! Ludo=E2=80=99. --=-=-= Content-Type: text/x-patch Content-Disposition: inline diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5da95d66a6..d1d17dc3d5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15382,6 +15382,6 @@ containing the reference genome as well.") (synopsis "Fast, sensitive, and accurate integration of single cell data") (description "Harmony software is the R implementation of the algorithm with the same -name for single cell integration, described in Korsunsky et al 2018. Package +name for single cell integration, described in Korsunsky et al 2018. The package includes a standalone Harmony function and interfaces to external frameworks.") - (license license:gpl3)))) + (license license:gpl3+)))) --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Thu Nov 21 05:47:36 2019 Received: (at 38259) by debbugs.gnu.org; 21 Nov 2019 10:47:36 +0000 Received: from localhost ([127.0.0.1]:51352 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iXjzr-0002oc-Vx for submit@debbugs.gnu.org; Thu, 21 Nov 2019 05:47:36 -0500 Received: from eggs.gnu.org ([209.51.188.92]:37749) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iXjzn-0002oN-7o for 38259@debbugs.gnu.org; Thu, 21 Nov 2019 05:47:34 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:56217) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1iXjzf-00015N-RW; Thu, 21 Nov 2019 05:47:24 -0500 Received: from wifi-eduroam-20-234.siege.inria.fr ([128.93.20.234]:53994 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1iXjzd-0006ZY-EQ; Thu, 21 Nov 2019 05:47:22 -0500 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#38259] [PATCH] gnu: Add r-harmony. References: <20191118172216.21813-1-madalinionel.patrascu@mdc-berlin.de> Date: Thu, 21 Nov 2019 11:47:19 +0100 In-Reply-To: <20191118172216.21813-1-madalinionel.patrascu@mdc-berlin.de> (=?utf-8?B?Ik3Eg2TEg2xpbg==?= Ionel =?utf-8?Q?Patra=C8=99cu=22's?= message of "Mon, 18 Nov 2019 18:22:16 +0100") Message-ID: <87blt5ik08.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (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-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 38259 Cc: 38259@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 (---) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = skribis: > * gnu/packages/bioinformatics.scm (r-harmony): New variable. It took me a while but I then realized the package was already in, only in a different file, cran.scm. So I=E2=80=99ve not pushed your version, but let us know if you=E2=80=99d l= ike to change the existing package! Thanks, Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Thu Nov 21 05:59:14 2019 Received: (at 38259) by debbugs.gnu.org; 21 Nov 2019 10:59:14 +0000 Received: from localhost ([127.0.0.1]:51356 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iXkB7-000352-Ok for submit@debbugs.gnu.org; Thu, 21 Nov 2019 05:59:13 -0500 Received: from mail-qk1-f194.google.com ([209.85.222.194]:46184) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iXkB6-00034n-3N for 38259@debbugs.gnu.org; Thu, 21 Nov 2019 05:59:12 -0500 Received: by mail-qk1-f194.google.com with SMTP id h15so2569765qka.13 for <38259@debbugs.gnu.org>; Thu, 21 Nov 2019 02:59:11 -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:content-transfer-encoding; bh=dDuqoagzLYA6HwCxraTEw7lbvoOIfrjORsDrWZS/pHc=; b=nVjrYnlBuoRyqfRiu3GlT7bRSxP74Bya67zP/w9PD/IxMOiWbeHYj47U3V44Qev1Z4 UCY4MHA7umq/RpEI4k4SUFywMfb+0oa83jtuEyayLEv7Wrw3c2W2iY3o3sK4tkLsO0we pKK3kQKzizj8jPJlhLJLQZ7/+I2iIoWZEdOGKgZZjmIb4p6eCZo6+MSfKlA+KsOgFB5n 1RF74Asi56lIBfAPI1QpDsx/DT/k5uP93h3objWvFMx7UalJ/wGA9TLDlTcZzYvF/Y74 T0+CaGB0QtJa9GTDllsot2PbcUmoKuFs6Y495QDtS6n6+MuIJ/7VomoJ+4I8HEc1E0IE 959g== 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:content-transfer-encoding; bh=dDuqoagzLYA6HwCxraTEw7lbvoOIfrjORsDrWZS/pHc=; b=BuJEqAgEECfwIKAjvtKUqFLTil9BL3i29nzLZL5f3ADDQOYggvjL03SMoiILL+hfhX rYK+XpCd4aXTPWHsL5VmVtinwrLfrBuMG7YsTMqBBuE3+HqCg6PecUeCSBJWIZc0nIj/ XC94QdWFtpdMM7nLa/KxbAnXrnm1U88bVKuRtPn7cKsVdHc738nkOQknKO7cF67VJG1A UXEoBfcSA1d3Sn/+PRU3N5nmQDg0nYq9HrqqAU3vxm/84qvW7QsJXfBGRx3+VgEh2bzW DGHdx/7IzOs9Rt6fmCiyYzck/5qh8LhFDoojlHS7beD2bn1KdgQWRe/h1D+u2ZiTiC3Y RNiQ== X-Gm-Message-State: APjAAAUzjMz8LiHEuUCq03ZOpk0B0taqYmL+8grcpDjQPVUl54itE3TR K3klIBfEURUwIgWmv1bn+/6cAhwkbNECm9X4QO8= X-Google-Smtp-Source: APXvYqy3Xihoxn0jPC41VEHngOaR3pAHrM51Fw6BffveL7619T7RJYT5hBpSQtV58bsHFSxmtdy0BHKb94KT7co42Os= X-Received: by 2002:a37:584:: with SMTP id 126mr6544276qkf.304.1574333946308; Thu, 21 Nov 2019 02:59:06 -0800 (PST) MIME-Version: 1.0 References: <20191118172216.21813-1-madalinionel.patrascu@mdc-berlin.de> <87blt5ik08.fsf@gnu.org> In-Reply-To: <87blt5ik08.fsf@gnu.org> From: zimoun Date: Thu, 21 Nov 2019 11:58:54 +0100 Message-ID: Subject: Re: [bug#38259] [PATCH] gnu: Add r-harmony. To: =?UTF-8?Q?Ludovic_Court=C3=A8s?= Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 38259 Cc: 38259@debbugs.gnu.org, =?UTF-8?B?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= 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, On Thu, 21 Nov 2019 at 11:48, Ludovic Court=C3=A8s wrote: > It took me a while but I then realized the package was already in, only > in a different file, cran.scm. IMHO, some packages need to be moved in the right files. For example this one. It is not a CRAN package because it does not come from the CRAN archive but a Bioinformatics one written in R language. In the same topic, I moved [1] packages fetched from the CRAN archive to the cran.scm file. [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D38184 To me, keeping a clear file organisation helps. :-) All the best, simon From unknown Wed Jun 18 00:24:23 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 19 Dec 2019 12:24:04 +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