From unknown Sun Jun 22 11:35:41 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#56819 <56819@debbugs.gnu.org> To: bug#56819 <56819@debbugs.gnu.org> Subject: Status: gnu: Add r-phyclust and r-infercnv. (New variables) Reply-To: bug#56819 <56819@debbugs.gnu.org> Date: Sun, 22 Jun 2025 18:35:41 +0000 retitle 56819 gnu: Add r-phyclust and r-infercnv. (New variables) reassign 56819 guix-patches submitter 56819 "MadalinIonel.Patrascu@mdc-berlin.de" severity 56819 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Thu Jul 28 17:35:50 2022 Received: (at submit) by debbugs.gnu.org; 28 Jul 2022 21:35:50 +0000 Received: from localhost ([127.0.0.1]:59504 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oHBAc-0002oR-Ih for submit@debbugs.gnu.org; Thu, 28 Jul 2022 17:35:50 -0400 Received: from lists.gnu.org ([209.51.188.17]:48496) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oHBAZ-0002oI-FS for submit@debbugs.gnu.org; Thu, 28 Jul 2022 17:35:49 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41426) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oHBAX-0002ge-OT for guix-patches@gnu.org; Thu, 28 Jul 2022 17:35:47 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:56213) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oHBAU-0006uA-Db for guix-patches@gnu.org; Thu, 28 Jul 2022 17:35:45 -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=1659044137; x=1660858538; bh=tmljuw /nBlvla1RXi2dcP3tzsu/zI7zXp2tD/auhE0A=; b=Uxl0mF4srCDDEBd65gNige WO7LfMZoAxK+BwetDD5pd1sCe4px6WA63le6C3VQHeS797hOxwUHHV6WEvd1r7g8 l5iXLPL6wtK4mEKYBVnHv34szWNsJPZ0DPYKWv3d9aNgrBf32mo3DyOw/UURaYxm meYTRjjgtH2tjUi9O/xks= Received: from SW-IT-P-EX1.mdc-berlin.net (mgw1.mdc-berlin.de [141.80.113.54]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 222A8A037C for ; Thu, 28 Jul 2022 23:35:36 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) by SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.9; Thu, 28 Jul 2022 23:35:36 +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; Thu, 28 Jul 2022 23:35:36 +0200 From: "MadalinIonel.Patrascu@mdc-berlin.de" To: "guix-patches@gnu.org" Subject: gnu: Add r-phyclust and r-infercnv. (New variables) Thread-Topic: Add r-phyclust and r-infercnv. (New variables) Thread-Index: AQHYosnmf5E1jaM2ZU+n42yEpv1SbA== Date: Thu, 28 Jul 2022 21:35:36 +0000 Message-ID: <3f5cff2631864372b7a0b1233e11ce86@mdc-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [141.80.113.51] x-tm-as-product-ver: SMEX-14.0.0.3092-9.0.1002-27044.002 x-tm-as-result: No-10--5.229900-5.000000 x-tmase-matchedrid: 54gb2yeIOXSfkHSWeTTytMG0UNgaZpYqGsvgUMYAn4UWzPTbxO7R+tIS YzBUt2RaXVsEWVqYqaivJcrLMYkA70UuXkWTSi/R30kDaWZBE1RU4sxFq6igEUqa6TyhyXvPW4Z nuvI7TMrlFuDg0vwE6RJTjjs9yT6Yo8WMkQWv6iUijR+AXJl/FWIb+/Y4wLs7H2TDzR13hu4l3N BFqEMZIfcnh42ZQ233eg4sgIdWqwfaRcEqGxsiQQj6hK3BlG+TBNkzPOBLk8tBYKYxlX9v2wVGE OlQY0mqcj8NMQ6TNk0mzjbWvNYF+Q== x-tm-as-user-approved-sender: Yes x-tm-as-user-blocked-sender: No x-tmase-result: 10--5.229900-5.000000 x-tmase-version: SMEX-14.0.0.3092-9.0.1002-27044.002 x-tm-snts-smtp: 047F08A139B7B69E495A887D40CE7D58D9E0B429BB8AB15C253AFB396BD61F842002:F Content-Type: multipart/alternative; boundary="_000_3f5cff2631864372b7a0b1233e11ce86mdcberlinde_" MIME-Version: 1.0 Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.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_3f5cff2631864372b7a0b1233e11ce86mdcberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable --_000_3f5cff2631864372b7a0b1233e11ce86mdcberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable


--_000_3f5cff2631864372b7a0b1233e11ce86mdcberlinde_-- From debbugs-submit-bounces@debbugs.gnu.org Thu Jul 28 17:39:23 2022 Received: (at 56819) by debbugs.gnu.org; 28 Jul 2022 21:39:23 +0000 Received: from localhost ([127.0.0.1]:59510 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oHBE3-0002uR-3M for submit@debbugs.gnu.org; Thu, 28 Jul 2022 17:39:23 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:47021) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oHBE0-0002u8-UU for 56819@debbugs.gnu.org; Thu, 28 Jul 2022 17:39:22 -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=1659044354; x=1660858755; bh=egkAkUi9IUru4H216Fl/W4CYeBYCPeLsNqUxt7XKvGI=; b=YVDxlLcms0jO 5FCFwUcwBtGugD6iiegDwXEpdbEzvfZ6rEYPU8W0xiCqCvAFgNwgAt2yzmifONlO AhIyBiogtnFh8LjipmeQJ06AlweLPDO31qndWzRW4NTkK9GCnaSQHMNBZHQMfbgK 1tbPuGmo1t8iuESH4IxjgATnzp9kJAQ= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id B8C6030031C for <56819@debbugs.gnu.org>; Thu, 28 Jul 2022 23:39:14 +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; Thu, 28 Jul 2022 23:39:13 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <56819@debbugs.gnu.org> Subject: [PATCH 2/2] gnu: Add r-infercnv. Date: Thu, 28 Jul 2022 23:38:59 +0200 Message-ID: <20220728213859.21641-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.1 In-Reply-To: <20220728213859.21641-1-madalinionel.patrascu@mdc-berlin.de> References: <20220728213859.21641-1-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-14.0.0.3092-9.0.1002-27044.002 X-TM-AS-Result: No-10--0.353900-5.000000 X-TMASE-MatchedRID: HRm6Pbbemxf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEObH aDxe+U4pMecv2pRSXP/uNT8xdcEnQwE+dA3RWUSvnMRCqQzD5eeTIp+F7SfdPaWq3wF1koS+3Zz X3J+8J0KOXcmvTm49paCaZ3gvLsy8L/fdNahJQfqRgPzABkqxIKn/3nyhTdZwm1Z19KV0SXAX3r 77y8r98b++B3z986tGSsWvYVVnFvdvCIuDq0C/xd0KiTeJteVB64sVlliWKx8fE8yM4pjsDwtuK BGekqUpOlxBO2IcOBaAGZzlhUDRC081g186HgamKXw1QgjixPsUJKrs0WIMt7IvxdQvOys8oXMO sLGOr0eqpKwlSEtl+j+p2vr9Vw2VLh4l4HGge97fImrURI36QxPJ2/Q8HUOAto20mm9aYNFI8Ra cJ+d0jn4Y+QmZJksi X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.353900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27044.002 X-TM-SNTS-SMTP: 958CF1388B2CE12B70C9D201770B1EEEC3788C592D50A34E5219A5F5320D32E42002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 56819 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/bioconductor.scm (r-infercnv): New variable. --- gnu/packages/bioconductor.scm | 60 +++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31484799b2..e9bfbed9b5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -49,6 +49,7 @@ (define-module (gnu packages bioconductor) #:use-module (gnu packages image) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) + #:use-module (gnu packages python) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) @@ -2647,6 +2648,65 @@ (define-public r-ideoviz arbitrary genomic intervals along chromosomal ideogram.") (license license:gpl2))) +(define-public r-infercnv + (package + (name "r-infercnv") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "infercnv" version)) + (sha256 + (base32 + "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl")))) + (properties `((upstream-name . "infercnv"))) + (build-system r-build-system) + (inputs (list python)) + (propagated-inputs + (list r-ape + r-argparse + r-biocgenerics + r-catools + r-coda + r-coin + r-digest + r-doparallel + r-dplyr + r-edger + r-fastcluster + r-fitdistrplus + r-foreach + r-futile-logger + r-future + r-ggplot2 + r-gplots + r-gridextra + r-hiddenmarkov + r-leiden + r-matrix + r-paralleldist + r-phyclust + r-rann + r-rcolorbrewer + r-reshape + r-rjags + r-singlecellexperiment + r-summarizedexperiment + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/broadinstitute/inferCNV/wiki") + (synopsis "Infer copy number variation from single-cell RNA-Seq data") + (description + "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify +evidence for somatic large-scale chromosomal copy number alterations, such as gains +or deletions of entire chromosomes or large segments of chromosomes. This is done +by exploring expression intensity of genes across positions of a tumor genome in +comparison to a set of reference \"normal\" cells. A heatmap is generated +illustrating the relative expression intensities across each chromosome, and it +often becomes readily apparent as to which regions of the tumor genome are +over-abundant or less-abundant as compared to that of normal cells.") + (license license:bsd-3))) + (define-public r-iranges (package (name "r-iranges") -- 2.37.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Jul 28 17:39:43 2022 Received: (at 56819) by debbugs.gnu.org; 28 Jul 2022 21:39:43 +0000 Received: from localhost ([127.0.0.1]:59512 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oHBE8-0002uf-H0 for submit@debbugs.gnu.org; Thu, 28 Jul 2022 17:39:43 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:34007) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oHBE0-0002u7-UV for 56819@debbugs.gnu.org; Thu, 28 Jul 2022 17:39:22 -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=1659044353; x=1660858754; bh=UZeoarDbp/stkp/ s/bw5lJi4xmFvf5zS63vp9tkFLho=; b=F0Ge0RMbaEarUsqAgn+r1hhXJTKvMGs AwZNwNhVgEiEyWUprT++qqaBRZDDN3qv/Nr12qDYjKAHKh8BgrkeOgnkwAZYF0DW bRXVF+luhFQTo/uWBSIdGLkb2LduSt8yfqndav2bAD8hVuoEtLOoAAUlTUfC9m5l Roz9FkrBd7zY= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id E0531300317 for <56819@debbugs.gnu.org>; Thu, 28 Jul 2022 23:39:13 +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; Thu, 28 Jul 2022 23:39:13 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <56819@debbugs.gnu.org> Subject: [PATCH 1/2] gnu: Add r-phyclust. Date: Thu, 28 Jul 2022 23:38:58 +0200 Message-ID: <20220728213859.21641-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.1 MIME-Version: 1.0 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-14.0.0.3092-9.0.1002-27044.002 X-TM-AS-Result: No-10--5.870000-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6MKPrF7dK57MXjfR3d0weRpYkvtv1NL4WXDP v05mLM2E+bgIM/tOpHc3AAUMpO5epWi8Qip68Ngc7lKkz03w06+uLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKcCe26BkR9xPoGRyAacnhabEnkALH5vYFtEOVr2nHEpcCjBud3XrBhH4UzdvTFUewX7cG d19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.870000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27044.002 X-TM-SNTS-SMTP: 7A1D9660CBCE2E8CA1D5EA747232C574215C2E5E13122A5DB17276FF9E1DE87D2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 56819 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 (-) * gnu/packages/cran.scm (r-phyclust): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 731facb4e5..e63cb28e19 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11699,6 +11699,31 @@ (define-public r-nleqslv singular or ill-conditioned Jacobian.") (license license:gpl2+))) +(define-public r-phyclust + (package + (name "r-phyclust") + (version "0.1-30") + (source (origin + (method url-fetch) + (uri (cran-uri "phyclust" version)) + (sha256 + (base32 + "0fy9q95vmlm9idpax7alhpfwn30gflnc9md72g91jypyxkx5nr7p")))) + (properties `((upstream-name . "phyclust"))) + (build-system r-build-system) + (propagated-inputs (list r-ape)) + (home-page "https://snoweye.github.io/phyclust/") + (synopsis "Studying phyloclustering and exploring DNA sequence data") + (description + "@dfn{Phylogenetic clustering} (phyloclustering) is an evolutionary continuous +time Markov Chain model-based approach to identify population structure from +molecular data without assuming linkage equilibrium. The package @code{phyclust} +provides a convenient implementation of phyloclustering for DNA and SNP data, +capable of clustering individuals into subpopulations and identifying molecular +sequences representative of those subpopulations. It is designed in @code{C} for +performance and interfaced with @code{R} for visualization.") + (license license:gpl2+))) + (define-public r-physicalactivity (package (name "r-physicalactivity") base-commit: bdb2e262fcbea76de807cd829c2d2270661546a5 -- 2.37.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 01 10:21:04 2022 Received: (at 56819) by debbugs.gnu.org; 1 Aug 2022 14:21:04 +0000 Received: from localhost ([127.0.0.1]:41359 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oIWI3-0007ZY-Qu for submit@debbugs.gnu.org; Mon, 01 Aug 2022 10:21:04 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21033) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oIWHy-0007Yy-FN for 56819@debbugs.gnu.org; Mon, 01 Aug 2022 10:21:02 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1659363654; cv=none; d=zohomail.com; s=zohoarc; b=EsTKUqnqhiNvbv+EemkqruC69vZd3cWDp7GcmX/R14+KB8E7Cwlp2S6V647BA75UekL0LogpijHG0QamzCxWJmLwnLMTpypukGnMIgpKuUq9l+j1PLBiPwguXZMxKzxkGxADzXT7BEp/H252eerTDRvZejrSZpIZBbt3JkNAFww= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1659363654; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=s97DxkrCx3MzV3PMI7lE5sVBjG1R0tAXegk8e6zA6GA=; b=RZ+sW033Cdoi02wN7szoYUCrKFINpMJSqDQemVKrdrARe0fYJUP9C0jQ7fpZEcZAU4A0RwwM2u3o99bISkyqQU34EO9IsKYDqb0E8bqEk2TIJp4rNX1UuYLIWz0+YragrVnfjkeClZcndTnZgG/GanQtJ1+CHVw1MPRP5NUGKe0= 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=1659363654; 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=s97DxkrCx3MzV3PMI7lE5sVBjG1R0tAXegk8e6zA6GA=; b=VUEdCaYo8WGILM8OcHTlPPpyc/XhOvokjEB7vt+FMdMAb9Sig0A23/87ysv7/SBk /40I+0vwnhrKedXf9Ueor/5IMqMPCYgTTPX4SE6cpS7msdnFHYfGJgTY3ufHDoIArZ9 3uoRFBVq+b+tocMxDsza9yJQPMcN7sV8pyNae1+M= Received: from localhost (i5E862C69.versanet.de [94.134.44.105]) by mx.zohomail.com with SMTPS id 1659363653516983.0852694874804; Mon, 1 Aug 2022 07:20:53 -0700 (PDT) References: <20220728213859.21641-1-madalinionel.patrascu@mdc-berlin.de> <20220728213859.21641-2-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.6.11; emacs 28.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#56819] [PATCH 2/2] gnu: Add r-infercnv. Date: Mon, 01 Aug 2022 16:20:12 +0200 In-reply-to: <20220728213859.21641-2-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: <87k07sniyl.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: 56819 Cc: 56819@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/bioconductor.scm (r-infercnv): New variable. [=E2=80=A6] > + r-phyclust This variable is not defined anywhere, or maybe I just can=E2=80=99t find i= t. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Tue Aug 02 04:24:24 2022 Received: (at 56819-done) by debbugs.gnu.org; 2 Aug 2022 08:24:25 +0000 Received: from localhost ([127.0.0.1]:42247 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oInCS-0003aF-IQ for submit@debbugs.gnu.org; Tue, 02 Aug 2022 04:24:24 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21091) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oInCP-0003a5-DH for 56819-done@debbugs.gnu.org; Tue, 02 Aug 2022 04:24:22 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1659428659; cv=none; d=zohomail.com; s=zohoarc; b=l6UAuTuQkrSgw4oliO3udeliKdctOvJIqCQ0XaPhncxjRfWXf+uMfbAMuhqHz4FHAkpqA4ZZ4+2a0ZFouGGZqzjR5Nq0c9EoDt12hxn0A0Zd9XUI8jvu+MgMqCQ2Mf6Ljd0e3TXm7PGAcYl2fCoSmUF5d3MbvJVZvmYN2VIorHU= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1659428659; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=2KWJQSUCDe3uIB/YpJEPPoUrCO+RKXSt6sguDZ4TjJY=; b=YvKQv+KDybaypr12r/OZU51xp1Vi79x6CwtZgAkl/mESJXjw3pCpoFUF1kMbick2nfq/9jqCJJmKHmMEGRfTuqCtSPL3M3R0VNyLPCoxMuM0Bxd7V40siChS9T8cPSnJfSbYQ704g5zGG/22Vs619m7lz0fqoKohz1S1h7+AMPs= 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=1659428659; 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=2KWJQSUCDe3uIB/YpJEPPoUrCO+RKXSt6sguDZ4TjJY=; b=VPyC1e4p/Reel8Nf3YpmaexqZs+Hda6bz+u8A5bXlJxjkIocCCLYtxZTWTV9txlq kRVOD8clOlpBIsEklDcVO9tZbU6UunQ/2JysVDUy7opzvgmPoKmEFDKFJtNYOZFm9xX RqUaG+S6Aj/6YQPynAfF/TbKmZptElJiSKpZUeVs= Received: from localhost (i5E862CF7.versanet.de [94.134.44.247]) by mx.zohomail.com with SMTPS id 1659428656490673.1264685879023; Tue, 2 Aug 2022 01:24:16 -0700 (PDT) References: <20220728213859.21641-1-madalinionel.patrascu@mdc-berlin.de> <20220728213859.21641-2-madalinionel.patrascu@mdc-berlin.de> <87k07sniyl.fsf@elephly.net> User-agent: mu4e 1.6.11; emacs 28.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#56819] [PATCH 2/2] gnu: Add r-infercnv. Date: Tue, 02 Aug 2022 10:23:02 +0200 In-reply-to: <87k07sniyl.fsf@elephly.net> 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: <87pmhjm4sy.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: 56819-done Cc: 56819-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 (-) Ricardo Wurmus writes: > M=C4=83d=C4=83lin Ionel Patra=C8=99cu writes: > >> * gnu/packages/bioconductor.scm (r-infercnv): New variable. > [=E2=80=A6] >> + r-phyclust > > This variable is not defined anywhere, or maybe I just can=E2=80=99t find= it. The problem was that I only received the second email; the first one wasn=E2=80=99t cc=E2=80=99d to me. I then saw that the first patch is righ= t there on issues.guix.gnu.org, so I applied them both. Sorry for the confusion! --=20 Ricardo From unknown Sun Jun 22 11:35:41 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 30 Aug 2022 11:24:05 +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