From unknown Sat Aug 16 21:01:40 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#64250 <64250@debbugs.gnu.org> To: bug#64250 <64250@debbugs.gnu.org> Subject: Status: [PATCH 00/15] *** R package (scriabin) *** Reply-To: bug#64250 <64250@debbugs.gnu.org> Date: Sun, 17 Aug 2025 04:01:40 +0000 retitle 64250 [PATCH 00/15] *** R package (scriabin) *** reassign 64250 guix-patches submitter 64250 Navid Afkhami severity 64250 normal tag 64250 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:46:52 2023 Received: (at submit) by debbugs.gnu.org; 23 Jun 2023 13:46:52 +0000 Received: from localhost ([127.0.0.1]:37898 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qCh7k-00073a-7C for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:46:52 -0400 Received: from lists.gnu.org ([209.51.188.17]:48988) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qCh7h-00073R-Ny for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:46:50 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qCh7h-0008F5-Hy for guix-patches@gnu.org; Fri, 23 Jun 2023 09:46:49 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qCh7f-0005jg-K8 for guix-patches@gnu.org; Fri, 23 Jun 2023 09:46:49 -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=1687528003; x=1689342404; bh=ln71/jyan3ZWKpo O7o5CiSblJc2/HIYgzbGluap2DGU=; b=E7pZ5BpC/e4xPPczkljfZaZF6Jilhml ufKVFDi4LgZ+GEZI80wkaZcMy/SQgpV4lBczHMoBUHHOWV3jsNOrcXnCeGX2/zS5 8vpDdcQ/TymQ5LaDlt3l57IWmVEZP6cdSLMiP290wl+PnbXGSDKk8GpwVIa3E+kR 77O8auAVJ09k= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 767B1A01EE for ; Fri, 23 Jun 2023 15:46:43 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:46:42 +0200 From: Navid Afkhami To: Subject: [PATCH 00/15] *** R package (scriabin) *** Date: Fri, 23 Jun 2023 13:46:40 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--7.194000-5.000000 X-TMASE-MatchedRID: lbdkQWb+CNbvsNWMI3fHiEWtyNepX5gA82SgwNf6SK4wc9ThMH3qV14G GHdq7rdYuUYMES0LuKezE1I26BnC6IdhJvvq7rh/CCpgeMk1Yd4Jlr1xKkE5ueuLH9BII+4qrKs axUiN/ymhG6+lR+E7mZsoi2XrUn/J8m+hzBStansUGm4zriL0oQtuKBGekqUpOlxBO2IcOBaceW 96P1wFUdUKkGkqkgqU/gxTXmhmvjK3t1kdt5dXH9CQypxyxLFt X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.194000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: 76CE86C61C15DC96277A125994B63A878A42F6BAC517005B113886CCBA4C70B12002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: Navid Afkhami 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 (--) Hi, An R package + all the dependencies. Your review is highly appreciated. Thank you Navid Afkhami (15): gnu: Add r-paramhelpers. gnu: Add r-smoof. gnu: Add r-parallelmap. gnu: Add r-mlr. gnu: Add r-mlrmbo. gnu: Add r-emoa. gnu: Add r-diagrammer. gnu: Add r-tidyft. gnu: Add r-ggfittext. gnu: Add r-dunn-test. gnu: Add r-cellid. gnu: Add r-dicekriging. gnu: Add r-nichenetr. gnu: Add r-fsa. gnu: Add r-scriabin. gnu/packages/bioconductor.scm | 44 +++++ gnu/packages/bioinformatics.scm | 111 +++++++++++ gnu/packages/cran.scm | 318 ++++++++++++++++++++++++++++++++ 3 files changed, 473 insertions(+) base-commit: f25529b08e356f89ca7cecc44295085531a8faba -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:20 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:20 +0000 Received: from localhost ([127.0.0.1]:37910 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChA7-0007Cu-UX for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:20 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:40313) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChA4-0007CP-Mp for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:18 -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=1687528150; x=1689342551; bh=3ZS3VLgBN0rEGwRjyUgdcng4486xkCmz5FQrcDgevCI=; b=eBlPRw0HQkxV rZyTITavjCUOwB1AwaO7FJATNcNG5dFa2Y6PAv501DuZgLwn1LjGc1fK0fQXseI6 6FPmVZyDiMnkAYrTCOI8WoQTHu/IIl5jEYUnfLZPLTNSL8grVUtLJiEsAIULgWBG 4fvVfcAGr+419TNIFt5LD0Tsj/2xVCw= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 6D38FA01EE for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:10 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:09 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 01/15] gnu: Add r-paramhelpers. Date: Fri, 23 Jun 2023 13:48:45 +0000 Message-ID: <9d8c0cec7064590b00d025f4b014c4f92916c8fb.1687527674.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--7.218400-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkECQ3 3TtXQitx8Fi8X0eaqJHuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIDFLXllDxJZTAeL RQLNS4qhbCUrKZ7Nzgspf42zmkyPkbo3W7m3jXyNtN2GsBybzwj1HD6GgxDF0YDnmdMm9y0fizy 75l6H5qX0tCKdnhB58I/9UW5M5dRNp7qEhmmPgy/cUt5lc1lLgxwGX+abRI5wzjuSYNNcL7JWPs v0BmOUIavIPbWUMSQayAzSdrBmwDBhugevjSl+R X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.218400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: 2922EFDC6069C04452F14663677181028A8432EB48F732D2E640B3F7A0A87E6B2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-paramhelpers): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ba81580258..d9a1914eb0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2408,6 +2408,29 @@ (define-public r-paralleldist naming conventions as distance methods of existing R packages.") (license license:gpl2+))) +(define-public r-paramhelpers + (package + (name "r-paramhelpers") + (version "1.14.1") + (source (origin + (method url-fetch) + (uri (cran-uri "ParamHelpers" version)) + (sha256 + (base32 + "088sl3az4ysq8cyw82brdn9xm5yy7rqskxih462d1m5hi62gyl04")))) + (properties `((upstream-name . "ParamHelpers"))) + (build-system r-build-system) + (propagated-inputs (list r-backports r-bbmisc r-checkmate r-fastmatch)) + (home-page "https://paramhelpers.mlr-org.com") + (synopsis + "Helpers for parameters in black-box ptimization, tuning and machine learning") + (description + "Package for parameter description and operations in optimization, tuning and machine learning. +Parameters can be described (type, constraints, defaults, etc.), combined +to parameter sets and can in general be programmed on. A useful OptPath +object (archive) to log function evaluations is also provided.") + (license license:bsd-2))) + (define-public r-pheatmap (package (name "r-pheatmap") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:23 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:23 +0000 Received: from localhost ([127.0.0.1]:37914 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAB-0007DN-99 for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:23 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:37263) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChA7-0007CS-4v for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:20 -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=1687528152; x=1689342553; bh=ctO3CtVA6WjxR9nKvHuRzft0wAAV8NzU+hEnwgxwAc0=; b=PnLHsi5pXc1t 3GcSbhfFB/FOyyvvJ+0hDWcc92ouMV1OywAExXQ3J352oBn+lIzvmgEv25ZiilQg 6OS4dUykM90nvWpZDhwd4a++aYy+6VRVN4DKAnJGwwetux2OOoYn81diTUwUbeb8 CYs4txX5eIU7LNzpCHKL3rGY/jQLyyw= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 7FFA8160231 for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:12 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:11 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 02/15] gnu: Add r-smoof. Date: Fri, 23 Jun 2023 13:48:46 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--2.387400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6MKPrF7dK57Nr2qJoNIuCjaY5ZGw7wyeHAaX 1NfHWjBdWB1RwyLtLNRj8sm2zlCu+dSOTAPyejIX+xRIVoKNMvBDkv2q7d+VDlwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7IhKJwzCNgn8X9rpBZuBDbb6gjn33bIUBwQK5TP5mBgaZkHhCx8ndAl+24 q8Rr1cnGyH/UIio7iYgAaDhzCwlnQ9FhHzKGjDeDB9RuwibyLdMRgtZb7w9aMbG0bMSRYDWFhno KW4f7Mf1c8RJIeS1QFmKmfpzNHMN X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.387400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: 99EC5B807D94C459DA3FDBE1A817B6CA7EE3DB1C20E4BD40E54F8DDCAEDDF8C62002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-smoof): 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 d9a1914eb0..3eec62f9c2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8159,6 +8159,34 @@ (define-public r-sm and density estimation") (license license:gpl2+))) +(define-public r-smoof + (package + (name "r-smoof") + (version "1.6.0.3") + (source (origin + (method url-fetch) + (uri (cran-uri "smoof" version)) + (sha256 + (base32 + "1cazhnd0m5jjzixaqgqh2h3rsa2sw3k8slj5cmgm8v47aaqn91mg")))) + (properties `((upstream-name . "smoof"))) + (build-system r-build-system) + (propagated-inputs (list r-bbmisc + r-checkmate + r-ggplot2 + r-paramhelpers + r-rcpp + r-rcpparmadillo)) + (home-page "https://jakobbossek.github.io/smoof/") + (synopsis "Single and multi-objective optimization test functions") + (description + "This tool generates high number of both single- and multi-objective test functions. +These functions are frequently used for the benchmarking of +(numerical) optimization algorithms. Moreover, it offers a +set of convenient functions to generate, plot and work with +objective functions.") + (license license:bsd-2))) + (define-public r-smurf (package (name "r-smurf") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:24 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:24 +0000 Received: from localhost ([127.0.0.1]:37917 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAB-0007DS-MK for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:24 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:35365) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChA9-0007Ch-C7 for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:21 -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=1687528155; x=1689342556; bh=+Q3CzFyC8LlF4dkJR8xlNsX33gl2bUuNhpfOOGHipEw=; b=IEyKRs3WCEvl zgK/ll1DcGN9C4iUt7/ne2q0NIZkR1OdgzrwQQnxNNEo1xeYr7Zlati1/RIG4lvO YHqrntBgzF0hJmaJpq7IL2m4zfIoAwex8hpHlrZMHlJ1+SSC6KaEsybcq2OVfvTN 88poUv6S2ZDvyefmRG3kXWGq/4EjWv8= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 4647C3001A3 for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:15 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:14 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 03/15] gnu: Add r-parallelmap. Date: Fri, 23 Jun 2023 13:48:47 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--7.262400-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEDt4 oEU19f2KoekUdArZ14G9JXaxspVSa+2s4cFTx/b4fOaYwP8dcX5IvK4LrXs1aQjxoTu0kNRwte+ ocL7MBZeKbindmE5bmKSHnUpJSz+Fql/dd8Z/6DLNgrlT5Ajc7qEetkTb5Lzr9xnqtROPY4aYDT IhMw3OOX0tCKdnhB589yM15V5aWpj6C0ePs7A07f40HKwxUZujIJfrCzKSF2LK9I9xPnsB3EJ2X 0fYcuGopxgNqRJmAJfF+ggN8VIK1Q== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.262400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: 9EC81627EBDA25679E07C31233D262A583F8F8AE79DA63502527A3144F94C7582002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-parallelmap): 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 3eec62f9c2..7deebbe72f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2431,6 +2431,30 @@ (define-public r-paramhelpers object (archive) to log function evaluations is also provided.") (license license:bsd-2))) +(define-public r-parallelmap + (package + (name "r-parallelmap") + (version "1.5.1") + (source (origin + (method url-fetch) + (uri (cran-uri "parallelMap" version)) + (sha256 + (base32 + "1qg7zpz5sd9jp8wzjqahkhipwj1jn192llwg06q4gv9mlcsac261")))) + (properties `((upstream-name . "parallelMap"))) + (build-system r-build-system) + (propagated-inputs (list r-bbmisc r-checkmate)) + (home-page "https://parallelmap.mlr-org.com") + (synopsis "Unified interface to parallelization back-ends") + (description + "Unified parallelization framework for multiple back-end. +This package is designed for internal package and interactive usage. +The main operation is parallel mapping over lists. Supports local', +multicore', mpi and BatchJobs mode. Allows tagging of the parallel +operation with a level name that can be later selected by the user to +switch on parallel execution for exactly this operation.") + (license license:bsd-2))) + (define-public r-pheatmap (package (name "r-pheatmap") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:30 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:31 +0000 Received: from localhost ([127.0.0.1]:37925 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAI-0007EJ-6v for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:30 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:43025) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAA-0007Ck-QL for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:23 -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=1687528156; x=1689342557; bh=2MBD9p0grxMLVYZ8Y0mjRVjZFfT0Lah6gzGG/5eiZVU=; b=jZX3ycE2hBhM /ZWP4NET375Fv2O1dIwQs0bC47sl3J8ht78Eum+uSmR/Qs9h33k4n4VIjrlYRm0Q D+1xTHWR9xtuQ7acjErv9u8xIyIbZgIV+BfBgg2nv15AGog7LrF2JkUUZH1hjFr/ 36sG7FZuZf8sze1I0RdPko9koWwyQY4= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 55AB0A01F4 for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:16 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:15 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 04/15] gnu: Add r-mlr. Date: Fri, 23 Jun 2023 13:48:48 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--0.128400-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEC3Y EkYbeXgrVutEw2gfYZDuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIMyyYdKBPktRkYd nzk6dz7YzxdCZZZikVhn4NDrLArHyjHFMyUt7B90mZusHWPhfCnkjN8pVE4GznlfxNjiSAuvizy 75l6H5qX0tCKdnhB589yM15V5aWpj6C0ePs7A07f40HKwxUZuj0XP2ISnkaT7A5J52F795qLcmV YdQo5rW+yvTKjUDjM8VjF2iR0EPl2Ej2Hi2mLTKLeNJHEoiTSeLAwJaLpO9TKN5nn7gVVTLt0oQ Iuj+SVeFEVfQxs3N6ZDgmt8QekvB5maCeNv/LIzVGQdqwsDiEg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.128400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: 9D2842E00E174EB6B46291AC0C345798F0737539CB7CEF5CCAD515C26FC7693B2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-mlr): New variable. --- gnu/packages/cran.scm | 47 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7deebbe72f..0fa8680e9c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35206,6 +35206,53 @@ (define-public r-mhg \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.") (license license:gpl2))) +(define-public r-mlr + (package + (name "r-mlr") + (version "2.19.1") + (source (origin + (method url-fetch) + (uri (cran-uri "mlr" version)) + (sha256 + (base32 + "00jjhvaqifj6glqsyzixlp56bvlch5smck8kk3klcmwx9pasyllx")))) + (properties `((upstream-name . "mlr"))) + (build-system r-build-system) + (inputs (list gdal + geos + glu + gmp + gsl + jags + mpfr + openmpi + proj + udunits)) + (propagated-inputs (list r-backports + r-bbmisc + r-checkmate + r-data-table + r-ggplot2 + r-parallelmap + r-paramhelpers + r-stringi + r-survival + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://mlr.mlr-org.com") + (synopsis "Machine learning in R") + (description + "Interface to a large number of classification and regression techniques. +These technics include machine-readable parameter descriptions. There is also +an experimental extension for survival analysis, clustering and general, +example-specific cost-sensitive learning. Generic resampling, including +cross-validation, bootstrapping and subsampling. Hyperparameter tuning with +modern optimization techniques, for single- and multi-objective problems. +Filter and wrapper methods for feature selection. Extension of basic learners +with additional operations common in machine learning, also allowing for easy +nested resampling. Most operations can be parallelized.") + (license license:bsd-2))) + (define-public r-mlr3measures (package (name "r-mlr3measures") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:31 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:31 +0000 Received: from localhost ([127.0.0.1]:37927 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAI-0007ER-V8 for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:31 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:54641) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAB-0007Cl-Be for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:23 -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=1687528157; x=1689342558; bh=aDE6878tlmjlunmgImxRqDjlQfYJoYvEcMU31ShR6C4=; b=eyqrl/PXu+oR 5t78LwYDRALwlz1s2zzJa4ajiy6EtY76pxJIU05OiNxjDPv0qXBdV5BFHtio0iqA C69toXzCeNS2bRsfCl/+4RAsagY2nAavsjCBPw3SUGUFYwSiEYfxCJjWkurajuOL 3/abmrBYkQ3pwEFu650km/phS/d2WtI= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 7CC82160239 for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:17 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:17 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 05/15] gnu: Add r-mlrmbo. Date: Fri, 23 Jun 2023 13:48:49 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--5.725400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6eF+RZWvOjHUXjfR3d0weRjvzvGpLgmDXOQA nedj/xIkEXNC0UxRHOd1q/1P5Wa+jOEt+E9fCvHu1ely0q8aUoT3mFVAoNi0cU72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8hfNjF5BHUO+5olEm7N8iq4S1b976MuSCLI+iyfLsWksLFxB KvbvnVH0furAPT46FE= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.725400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: C1B727BCB447BAFE83D4AD94755CC87DB0C625ECF619CCD377D7A88C562244D72002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-mlrmbo): New variable. --- gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0fa8680e9c..4e9ea8b67e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35253,6 +35253,40 @@ (define-public r-mlr nested resampling. Most operations can be parallelized.") (license license:bsd-2))) +(define-public r-mlrmbo + (package + (name "r-mlrmbo") + (version "1.1.5.1") + (source (origin + (method url-fetch) + (uri (cran-uri "mlrMBO" version)) + (sha256 + (base32 + "16fwj7m28g4km7yalqppxmh3lw2jln0z072l6awia38qkdg6xwhc")))) + (properties `((upstream-name . "mlrMBO"))) + (build-system r-build-system) + (propagated-inputs (list r-backports + r-bbmisc + r-checkmate + r-data-table + r-lhs + r-mlr + r-parallelmap + r-paramhelpers + r-smoof)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mlr-org/mlrMBO") + (synopsis "Model-based optimization with mlr") + (description + "Flexible and comprehensive R toolbox for model-based optimization. +It implements Efficient Global Optimization Algorithm for single- and +multi-objective optimization. Supports mixed parameters. The machine +learning toolbox mlr offers regression learners. Provides various +infill criteria. Features batch proposal, parallel execution, +visualization, logging. Modular implementation allows easy customization +by the user.") + (license license:bsd-2))) + (define-public r-mlr3measures (package (name "r-mlr3measures") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:31 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:32 +0000 Received: from localhost ([127.0.0.1]:37930 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAJ-0007EY-C8 for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:31 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:51701) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAD-0007D5-J6 for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:25 -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=1687528159; x=1689342560; bh=d9e4FZUR7+mtuMY4DAnY8hCpIPsfM/r94Ul9lRdfZS0=; b=HeJjuHY3qmqb W2ryUN6gdg/+Eud9LCycGJXH3PybzSen5FAjEHLPGvyUaAS6wnkiymVKw2XTvEQD Yc/g1OzKwh63QLMqa38R4WXrKJJoKkRUcbmkQTyUtT0xpRiQkzWviVF2pa9i2Iia 2/j53uRf+Sq+BhhNlWO4C5fSORWgMqE= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 AA5063001B5 for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:19 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:19 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 07/15] gnu: Add r-diagrammer. Date: Fri, 23 Jun 2023 13:48:51 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--5.356800-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6Yy6AtAy7YZcXjfR3d0weRjtHHuh6tnefKhl cUl+ZaDtJEOblfSh2IAzOs/jCyBCKLxEFvMLiU9/dCok3ibXlQeuLFZZYlisfHxPMjOKY7A9qHX ONfTwSQsRB0bsfrpPIXzYxeQR1Dvu+W+dlYQDk5KGkrx7TgR5R4QpGk8K438QhZhqt5uhkh2pfl pVrrSQ+ X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.356800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: C6DBD8E822C8C247F99E43D9D0B6C43CCE80DEBFC30D8755D89161E3C3BEA00A2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-diagrammer): New variable. --- gnu/packages/cran.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 34d4749b14..247f9a6f96 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28898,6 +28898,46 @@ (define-public r-diagram Francesca Mazzia (2012).") (license license:gpl2+))) +(define-public r-diagrammer + (package + (name "r-diagrammer") + (version "1.0.10") + (source (origin + (method url-fetch) + (uri (cran-uri "DiagrammeR" version)) + (sha256 + (base32 + "147q7zgwhd7vc0l134sqkkf6n6s6bznxvcmsrdx2f5df12bsixkj")))) + (properties `((upstream-name . "DiagrammeR"))) + (build-system r-build-system) + (propagated-inputs (list r-downloader + r-dplyr + r-glue + r-htmltools + r-htmlwidgets + r-igraph + r-magrittr + r-purrr + r-rcolorbrewer + r-readr + r-rlang + r-rstudioapi + r-scales + r-stringr + r-tibble + r-tidyr + r-viridis + r-visnetwork)) + (native-inputs (list esbuild)) + (home-page "https://github.com/rich-iannone/DiagrammeR") + (synopsis "Graph/network visualization") + (description + "DiagrammeR creates, modifies, analyzes, and visualizes network graph diagrams. +The output can be incorporated into R Markdown documents, integrated +with Shiny web apps, converted to other graph formats, or exported as +image files.") + (license license:expat))) + (define-public r-lim (package (name "r-lim") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:32 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:32 +0000 Received: from localhost ([127.0.0.1]:37932 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAJ-0007El-Qf for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:32 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:56379) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAD-0007Ct-1D for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:26 -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=1687528159; x=1689342560; bh=T75uL7pyiUuW+jQV5kD4TcuAmim4n/ZEqq5gdiJkxTQ=; b=hsXrh3eVOv8g kusZEh3XI2HLhMGqIYD0vHagdVH+5mIckeF/iyA8Jzw8mOWJjfGA4R2mrAEB2lj0 TuwMgImtQ9JlbKm6QRwab/P7z//2f0Du72Ry+kNhNln0Cklw7l+r483Uy5k9eLkL L1gtk18tOd/P8NomljbJ3875pnFuVkM= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 061963001AD for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:19 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:18 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 06/15] gnu: Add r-emoa. Date: Fri, 23 Jun 2023 13:48:50 +0000 Message-ID: <67f4837d05f089fd106f71583df0a12ec7f0f12b.1687527674.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10-3.959600-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEDhb uaUQKXpsRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v/kwFzTzcgzhJGUtqer5GwUd93 A76AVNsDmkARWCzWILBJTjjs9yT6Yo8WMkQWv6iV3LAytsQR4e42j49Ftap9Eymsk/wUE4hrfft Qqxx/itJpwd4z4FIwOX/tzWTHaCN+TugMvhpfYxyHWKMNqmDsKZpY0SWt5Cx1K8IBHjbcMvWZ6R uqlMWoiaESld9CUMU8DvOHg0Q4e7Hhb+tXQ0Z2H9HOalI4Kiyr2JUHlN8ax9F7RiZtjf98i X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-3.959600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: D82F5434BA59FB11DCE1483C0ECA3263EB8A71D0AFA5EEB06A38565A830632252002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-emoa): New variable. --- gnu/packages/cran.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4e9ea8b67e..34d4749b14 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26111,6 +26111,24 @@ (define-public r-showtext such as Ghostscript is needed to use this package.") (license license:asl2.0))) +(define-public r-emoa + (package + (name "r-emoa") + (version "0.5-0.2") + (source (origin + (method url-fetch) + (uri (cran-uri "emoa" version)) + (sha256 + (base32 + "0fr4ia3hkv8c7wkl64a51s6ynldppc812ynwldvbwy25dhlbvs6r")))) + (properties `((upstream-name . "emoa"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/emoa/") + (synopsis "Evolutionary multiobjective optimization algorithms") + (description + "Building blocks for the design and analysis of multiobjective optimization algorithms.") + (license license:gpl2))) + (define-public r-emojifont (package (name "r-emojifont") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:32 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:32 +0000 Received: from localhost ([127.0.0.1]:37935 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAK-0007Eu-An for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:32 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:45465) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAE-0007D9-BQ for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:26 -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=1687528160; x=1689342561; bh=9nYbguEI6W5g4ZstWCXm4yJOwkZ+QdAoJCqejOpfQls=; b=IH4K9ysmlccD k6RdbaK7f+UKV05OKsEDdl72k5uaGdSm8O3GvXAN9v9ZMa70FDD/0aEab1UDzGb5 v+3VcOBFbHpxpVjAHiZnebAbsGInOfUiV6ypl4j5Xu01Raj/1aMgwKhB22iF6z4v P9vFmYxHB7U3LHHcJ+iv/WZZdwIU0Kg= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 9C930A01EE for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:20 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:20 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 08/15] gnu: Add r-tidyft. Date: Fri, 23 Jun 2023 13:48:52 +0000 Message-ID: <60983004638ee8e33e4429614b5288fdca7256d7.1687527675.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--0.109400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6qug9vIA2WOBYL/tox9XQkSXp36F4VOPX2Lg EVfggSli1QaUgxvkwgq6mxI5SoosYoY9/dvpCF96rm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu3aDLLDbFMGFUk29kgvdVPySIRj3FXbo33CtXUlDxX1yc/me8z9qhiYK2EbrXJw2SfzHg WkL8lnHlG80HFBchbZ3K8/uYwcnMAdKUn2O6Fj/1+xhfuuIbsi45jSrrr4GpqGCNXqyLhLFvoNk WY9hSsutAp7vUZi6bw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.109400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: ACC9A86DBBF630C8C28BE6B69C03DD6F8620BFE1657B075CA5C0075B24CE17CC2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-tidyft): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 247f9a6f96..9938d07dd9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3005,6 +3005,29 @@ (define-public r-vegan data types as well.") (license license:gpl2+))) +(define-public r-tidyft + (package + (name "r-tidyft") + (version "0.5.7") + (source (origin + (method url-fetch) + (uri (cran-uri "tidyft" version)) + (sha256 + (base32 + "00qcsr2sx8fwyil384vgppx0q72qjrkj7h5nv4mdxdi8f9h6ph2r")))) + (properties `((upstream-name . "tidyft"))) + (build-system r-build-system) + (propagated-inputs (list r-data-table r-fst r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hope-data-science/tidyft") + (synopsis "Fast and memory efficient data operations in tidy syntax") + (description "Tidyft is an extension of data.table. +It uses modifiification by reference whenever possible. +This toolkit is designed for big data analysis in +high-performance desktop or laptop computers. The syntax +of the package is similar or identical to tidyverse.") + (license license:expat))) + (define-public r-tidyverse (package (name "r-tidyverse") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:33 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:33 +0000 Received: from localhost ([127.0.0.1]:37937 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAK-0007F3-OG for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:33 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:51991) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAF-0007DG-VP for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:28 -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=1687528162; x=1689342563; bh=JMnOPOQpbkNGkxLPnr8PYs1sWzNNJ/go1bBak5yANBQ=; b=QbHgFNFyMVH1 XXrGqvECM5xyupsLv4VUUvJj3rTp0iGPhhgjwjkb49fw9BUDf1lJRVYx0h02Z/sj F1oL2LbBXUIhqbK4lSUoPc3RnFQ+I6+NK+Qm8asNf/G2+2OAMVWZMspMz3B71ZVw ZQAXzxm/plE1jv1yZQl0O/lcD4g+CkI= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 E4001160231 for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:21 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:21 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 09/15] gnu: Add r-ggfittext. Date: Fri, 23 Jun 2023 13:48:53 +0000 Message-ID: <2d18fe91a165af42582d19bc109122c14513f48e.1687527675.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--0.614400-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEFxc aPG5Iqk8RRa406V/YwyBUGewL2YXt0eKEkxzpnyvwLYk+NSxc5r4qCLIu0mtIPPlAor2K6GjmA0 yITMNzjl9LQinZ4QefCP/VFuTOXUTae6hIZpj4Mv3FLeZXNZS4Edmmr9ZdqiyRqNxDJ27Upj255 a7xrEwbulj3sC0KqJL4BSkkpjx6geSN3/Bw0tQ0+5AuN92ypAoyfUmHCA4JtX7e4ppkycmBOryA 2APdf0Oa4sJOPPPqqLapBrPywRGWvBBWAh1UbgUTloPhkiH7TGOEw7cMCn7Sw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.614400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: C0F8127D97968863369A3B700894F9B293D1C197745D6E94F52B7B641FC65D832002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-ggfittext): 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 9938d07dd9..bb09a8d774 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -722,6 +722,26 @@ (define-public r-ggalt text annotations.") (license license:agpl3))) +(define-public r-ggfittext + (package + (name "r-ggfittext") + (version "0.10.0") + (source (origin + (method url-fetch) + (uri (cran-uri "ggfittext" version)) + (sha256 + (base32 + "06xfv552nhw13wc8dixyqhhmw5zh8hphrabw090nzb33cpfwzin8")))) + (properties `((upstream-name . "ggfittext"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 r-gridtext r-shades r-stringi)) + (native-inputs (list r-knitr)) + (home-page "https://wilkox.org/ggfittext/") + (synopsis "Ggfittext is a ggplot2 extension for fitting text into boxes") + (description + "Ggfittext is a ggplot2 extension for fitting text into boxes.") + (license license:gpl2))) + (define-public r-glmpca (package (name "r-glmpca") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:33 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:33 +0000 Received: from localhost ([127.0.0.1]:37940 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAL-0007FE-4G for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:33 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:54249) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAG-0007DO-Nk for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:29 -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=1687528162; x=1689342563; bh=g2wNlSdqoLabFDmYY1yfpkW885ZkPkMPRRL4dEmT8W4=; b=mmkejzGp08fv TTf1MV41g3x4JYV/J5OfMwDHxLG1oWV427IDF7l1fQkKUKTfsTeBLv5/6+FoJRWs MdDNWsw8Wa94olrGGHU8mnoZum6rFLPYQRqola147BWtQx7HJIUCTxGJMy7TRZ2X HeTZrs7gzjvMuv3gUoRew5Uoma01UYk= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 9D3FE16023D for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:22 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:22 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 10/15] gnu: Add r-dunn-test. Date: Fri, 23 Jun 2023 13:48:54 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--2.012400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfM5rof3b4z0VArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v/kwFzTzcgzhIVp4/bVf2/Ad93 A76AVNsC1f2BdK69qIkX8+yFgdi/b/ZFa3ewZqA8M6z3iDvziB2Te2a932n/yIpz++XQI8PGeAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DND+O5VnjJW23sFUHHTJ3UpiCW+lwuWuWAR4+ T9scFyMOhQycU87OeMv3WF7PYiWd1KL6bkTyxS2j0v4Oi8KK34E835+Tyqzf2uLCTjzz6qi2qQa z8sERlrwQVgIdVG4FE5aD4ZIh+0xjhMO3DAp+0s= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.012400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: D3FC09BF2C84F962AB686DC58C4EFFEC7F6DA210DB88F523FB349701EB34B9B32002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-dunn-test): 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 bb09a8d774..2873c3ce10 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27314,6 +27314,31 @@ (define-public r-dummies classes into dummy/indicator variables.") (license license:gpl2+))) +(define-public r-dunn-test + (package + (name "r-dunn-test") + (version "1.3.5") + (source (origin + (method url-fetch) + (uri (cran-uri "dunn.test" version)) + (sha256 + (base32 + "0lqwvyl3pyygfc73nf81gzw3zl3w43r7ki0yw2dgrzhkpb2iji4a")))) + (properties `((upstream-name . "dunn.test"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=dunn.test") + (synopsis "Dunn's test of multiple comparisons using rank sums") + (description + "Dunn's test computes stochastic dominance & reports pairwise comparisons. +This is done following a Kruskal-Wallis test (Kruskal and Wallis, 1952). +It employs Dunn's z-test-statistic approximations for rank statistics, +conducting k(k-1)/2 comparisons. The null hypothesis assumes that the +probability of a randomly selected value from the first group being +larger than one from the second group is one half, similar to the +Wilcoxon-Mann-Whitney test. Dunn's test serves as a test for median +difference and takes into account tied ranks.") + (license license:gpl2))) + (define-public r-acrm (package (name "r-acrm") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:48 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:48 +0000 Received: from localhost ([127.0.0.1]:37943 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAZ-0007Fp-QD for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:48 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:34055) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAH-0007Dj-Ve for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:30 -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=1687528163; x=1689342564; bh=TdWMgzNHqn9HxVueSavSEd/0GtopxhbcnDMeWnYwAu8=; b=n5ElqFrH+exz EdYJQSKPo+avNfQmHlMqC9rGN5PzfCsDJ/e33I/domowGCIEKpLL5P2ORh1Im3ny V2/0ZPoAg9xI3VZGk2l/pXzEIEz6+OL8pJpRuO0KCPkVhP0mm12dKBTJAnVkJecD SGRepEkLZn/rwmPzhYcbYUlsx+Ml/X4= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 D55863001A3 for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:23 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:23 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 11/15] gnu: Add r-cellid. Date: Fri, 23 Jun 2023 13:48:55 +0000 Message-ID: <136afa3705c111fa1e341c41b9ef84edf22a1fcf.1687527675.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--3.105100-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6vybt3bgNxoI06Sf95fXiV1wa5O54mQ0iv7G DbroLG9qqpvQgIDqq9l9lT2CKLCMpKWxJDoeFc5erm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGtf/SIq+QYRp5Q4jLKq41cFYOj+cr+VeWr9rHtxF/vblftV+Cd++ggTsxjjZLfWmyI+EB 04+3Wjji5vnl1W74/FdYcen6jnu2uM2GbTpTbWTeFv61dDRnYf0c5qUjgqLKvYlQeU3xrH0XtGJ m2N/3yI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.105100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: 039FFDC877E570DBC6FCC547011269FA0D1108FC841D4F9A1A6423E38FA15FC32002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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-cellid): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 00701c4463..78cab7171b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1436,6 +1436,50 @@ (define-public r-celldex single-cell data or deconvolution of bulk RNA-seq.") (license license:gpl3))) +(define-public r-cellid + (package + (name "r-cellid") + (version "1.8.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "CelliD" version)) + (sha256 + (base32 + "0vigvqjrlqbi5kviaj8qvyq3v8afgbc5pjrz7zmx2ckf4hdp0g03")))) + (properties `((upstream-name . "CelliD"))) + (build-system r-build-system) + (propagated-inputs (list r-data-table + r-biocparallel + r-fastmatch + r-fgsea + r-ggplot2 + r-glue + r-irlba + r-matrix + r-matrixstats + r-pbapply + r-rcpp + r-rcpparmadillo + r-reticulate + r-rtsne + r-seurat + r-stringr + r-tictoc + r-singlecellexperiment + r-summarizedexperiment + r-umap)) + (native-inputs (list r-knitr r-scater)) + (home-page "https://bioconductor.org/packages/CelliD") + (synopsis + "Single cell gene signature extraction using multiple correspondence analysis") + (description + "CelliD is a clustering-free method for extracting per-cell gene signatures from scRNA-seq. +CelliD allows unbiased cell identity recognition across different donors, +tissues-of-origin, model organisms and single-cell omics protocols. The +package can also be used to explore functional pathways enrichment in +single cell data.") + (license license:gpl3))) + (define-public r-champdata (package (name "r-champdata") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:49 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:49 +0000 Received: from localhost ([127.0.0.1]:37945 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAa-0007Ft-NB for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:49 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:34293) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAI-0007Dl-Ur for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:31 -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=1687528164; x=1689342565; bh=yETrsHOZqkV2qhhKtVh2NfmkpTEwv8jvKehe6sDyS4A=; b=ABSMTrmmQFOC x/laxHvxOMYejanMbrVEzTP7dBHkrW6Ln0RSM1Nrf1cSt7pUoEO8x9ctYkcLcj7x Ap2Se+7fBgR1JBvOF0hi8ZLsNW+sX1JHa4Ytqfl1us6Q8dm/+73a5CzVtuJC1yZb ThYN6tCiyn6IqDamhAjiPR858CAhO/I= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id DD0DAA01F4 for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:24 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:24 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 12/15] gnu: Add r-dicekriging. Date: Fri, 23 Jun 2023 13:48:56 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--2.128000-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEO87 m+OkgjhuYH6xxdG5ek4njvpTqmXN2iq+GZ9ZHxIhuW77/y896siFzNNPDc6umMicqvB+icULi0x TsP0eePKnzxLRYWF2LT3mnWKOM3JFLJutez2dKWfi8zVgXoAltr8hWd4lAsFlC24oEZ6SpSnAnt ugZEfcTyiM3WUt6LtFvE+ozmVP2r3BaNXbPYgImPWl+IvAvrOdvqUAOYxFEZiLmu0w1W+iNFaaj gOdKN4GwWoQs4nCfHIE4UlGxY6xqwbIY/jiJo/WNUhZ7098bYP2V6KaaFydpd7iGSOCYkyWEDyO B8C3mhA= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.128000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: 2981D3332EC700DBA594D5E3A61D72DC294BD095B181EF7295B934658FA3F2F62002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-dicekriging): New variable. --- gnu/packages/cran.scm | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2873c3ce10..2f53c2f70d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33926,6 +33926,23 @@ (define-public r-dicedesign Design} (SFD) and to test their quality.") (license license:gpl3))) +(define-public r-dicekriging + (package + (name "r-dicekriging") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (cran-uri "DiceKriging" version)) + (sha256 + (base32 + "0jfb2li6b93fkwgjkr4jwxnvv7zb0aqk9lkf2mnv2awzh0r16pdb")))) + (properties `((upstream-name . "DiceKriging"))) + (build-system r-build-system) + (home-page "https://dicekrigingclub.github.io/www/") + (synopsis "Kriging Methods for Computer Experiments") + (description "Estimation, validation and prediction of kriging models.") + (license license:gpl2+))) + (define-public r-dials (package (name "r-dials") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:49 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:49 +0000 Received: from localhost ([127.0.0.1]:37947 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAb-0007Fz-3Y for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:49 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:38085) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAJ-0007Dx-Qh for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:32 -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=1687528166; x=1689342567; bh=ph27Qh8fZWanuCHXpXMtmx9rR5VMzw2t3xy6Lima8ZA=; b=DFBz3FUyaG2C Dk/v7vULmKbVsb66SzZWLuVm8hq82XNhIwD+Uq1qGlQ5McqikEBFy3mDdeJF0nQu UBQUJUGBs9t3PBS01dkRYO9p0bcGb6FO5Cg8t/YPSBOAhmx3xv/zXcUnmiWXtlBm 6ZKkBo7/46hcF1WCa+uTztkVCLaQpyo= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 0433B160239 for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:26 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:25 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 13/15] gnu: Add r-nichenetr. Date: Fri, 23 Jun 2023 13:48:57 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--1.769400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIECxZTVRS20SJEb gebEoSmUSdh6xz9sQYzYU67xNGCLSGLfMLzDH98yBQTHl0mqX8ULixrsCJ1jTIpz++XQI8PGeAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DGrZ5qG+v8TKpGmd7F6KLEiS4iQwN8o8DIutT yzubotouiqUDhDVnirc6W0J1PcPWd/+maJ+xpzkzhejr/nUAeKci6fSEqtWU2uLCTjzz6qi2qQa z8sERlrwQVgIdVG4FE5aD4ZIh+0xjhMO3DAp+0s= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.769400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: D8B74BA8F79B7C19F4D380FC09111963B7852D9338D72AD85718E7D60CB334E32002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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 (r-nichenetr): New variable. --- gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 87e7c33b90..9de0470f7e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14800,6 +14800,63 @@ (define-public r-liana interaction inference from scRNA-seq data.") (license license:gpl3)))) +(define-public r-nichenetr + (let ((commit "cc3bcedfd6271df2e8ca85c8b771f7faa914cd3d") + (revision "1")) + (package + (name "r-nichenetr") + (version (git-version "1.1.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saeyslab/nichenetr") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0jxkrk7cpwx0lbbgjrd885jxahdgk9ysfqp2drq22g486k6p2s9y")))) + (properties `((upstream-name . "nichenetr"))) + (build-system r-build-system) + (propagated-inputs (list r-caret + r-catools + r-circlize + r-complexheatmap + r-cowplot + r-data-table + r-diagrammer + r-dicekriging + r-dplyr + r-e1071 + r-emoa + r-fdrtool + r-ggplot2 + r-ggpubr + r-hmisc + r-igraph + r-limma + r-magrittr + r-matrix + r-mlrmbo + r-parallelmap + r-purrr + r-randomforest + r-readr + r-rocr + r-seurat + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/saeyslab/nichenetr") + (synopsis "The R implementation of the NicheNet method") + (description + "The goal of NicheNet is to study intercellular communication from a computational perspective. +NicheNet uses human or mouse gene expression data of interacting cells +as input and combines this with a prior model that integrates existing +knowledge on ligand-to-target signaling paths. This allows to predict +ligand-receptor interactions that might drive gene expression changes +in cells of interest.") + (license license:gpl3)))) + (define-public r-circus (package (name "r-circus") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:49 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:49 +0000 Received: from localhost ([127.0.0.1]:37949 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAb-0007G6-Ft for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:49 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:51647) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAK-0007E4-Va for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:33 -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=1687528167; x=1689342568; bh=UGSqWAdoCpS4b6SkTh0futR3lNxKguPi81sc288RbMI=; b=Qn06OU/rDt2l C2dEHr2KEUAwA5gQf1L5CFFyI5NRjjEf47diAdENPZwPs1Y8Iz8E4akQewzj7Ljr o8fdI7xCA52pILb0Kkbd9dF1cBHKbXLXqkH7GTSTZ8KJrXa19+QfJT4wDXUe9ZPb E1qUolTVeiUtMvEkG5+pNkBs7FiawEU= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 2996C3001AD for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:27 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:26 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 14/15] gnu: Add r-fsa. Date: Fri, 23 Jun 2023 13:48:58 +0000 Message-ID: <92d0d93079865f7bf08fdf91dead62588355c193.1687527675.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--8.229700-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEJHZ G0RmPiikRRa406V/YwyBUGewL2YXt5r9F4bPByvNwLYk+NSxc5r4qCLIu0mtIOo8Y3/9edRyRmk sNu/RZSoevfN9eU+/vhf6uqcdjTP5D6W8CogwpHarm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRuyISicMwjYJ/ifGCYEa4FxdOLEfTyOr4+eraCbHtsHbU7GM05jn+4y06QWGkA/dM+g== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--8.229700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: D37458D584BF39130EECDA55E2D64FA926DFE1FDC75832C9D7264B76C90F0D512002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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/cran.scm (r-fsa): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2f53c2f70d..054c7c6f96 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11319,6 +11319,25 @@ (define-public r-dosnow using the @code{snow} package.") (license license:gpl2))) +(define-public r-fsa + (package + (name "r-fsa") + (version "0.9.4") + (source (origin + (method url-fetch) + (uri (cran-uri "FSA" version)) + (sha256 + (base32 + "0m63pik6bcqsbzizq8zjzilr2pxjl8b64ivdqzdnz09gmck73r5h")))) + (properties `((upstream-name . "FSA"))) + (build-system r-build-system) + (propagated-inputs (list r-car r-dunn-test r-lmtest r-plotrix r-withr)) + (home-page "https://fishr-core-team.github.io/FSA/") + (synopsis "Simple fisheries stock assessment methods") + (description + "This package provides a variety of simple fish stock assessment methods.") + (license license:gpl2+))) + (define-public r-fstcore (package (name "r-fstcore") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 23 09:49:50 2023 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:50 +0000 Received: from localhost ([127.0.0.1]:37951 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAb-0007GE-Ri for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:50 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:35577) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAL-0007E6-Tm for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:34 -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=1687528168; x=1689342569; bh=tmhgofMu4w7yryO5FK0ZJxyhm00TqJ/L/VlVXJXeKSs=; b=EASkCY/ffg8V H08RI6stzA/nVZx9/DoacUW4iCFBMClUcjFDCSr0HurMcKFqFGtQuneZAHVoZJhW 5eYHz0SZXFO3izJWbUz8zj2c4FsY8+hDLlGtjP7SqNrIJJ+RvFzY2ywJtIbdxRnw 8kS0FpCvTKv2ptT2hgtAKmHepUdlijo= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 0C853A01EE for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:28 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:27 +0200 From: Navid Afkhami To: <64250@debbugs.gnu.org> Subject: [PATCH 15/15] gnu: Add r-scriabin. Date: Fri, 23 Jun 2023 13:48:59 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--6.759400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIMIubEPSkNnJj46 v2aqkNBmp4L5MAnrh2PV58hdT3FI3bALuZMRear0EClJgjzpjqJ1Eh/SbOOeGU72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8hfNjF5BHUO+/VqC+U9hSeSgPHwcgcWutVvHX1XAKL+cK/lm jDcIZIN6eOhReWN/oI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.759400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: 486E43B6087BD55872D60C934680A0B18A5D08071C830ABB6C381392F4A516962002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64250 Cc: Navid Afkhami 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 (r-scriabin): New variable. --- gnu/packages/bioinformatics.scm | 54 +++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9de0470f7e..ca24263c79 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9866,6 +9866,60 @@ (define-public r-sccustomize visualization and analysis of single-cell data using R.") (license license:gpl3+)))) +(define-public r-scriabin + (let ((commit "313d15e9150413e6bcad0947215da3a09c0257f5") + (revision "1")) + (package + (name "r-scriabin") + (version (git-version "0.0.0.9000" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BlishLab/scriabin") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0k8khwcr3a281pa33h6l3wdk5igyqc4xknydiazk7qyf5w25g9zg")))) + (properties `((upstream-name . "scriabin"))) + (build-system r-build-system) + (propagated-inputs (list r-ade4 + r-cellid + r-circlize + r-clipr + r-complexheatmap + r-complexheatmap + r-cowplot + r-dplyr + r-factoextra + r-fsa + r-genefilter + r-ggalluvial + r-ggfittext + r-ggplot2 + r-ggsci + r-limma + r-magrittr + r-matrix + r-matrixstats + r-networkd3 + r-nichenetr + r-pbapply + r-qlcmatrix + r-scales + r-scater + r-seurat + r-tibble + r-tidyft + r-wgcna)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/BlishLab/scriabin") + (synopsis "Single-cell resolved interaction analysis through binning") + (description + "Scriabin aims to provide a comprehensive view of cell-cell communication (CCC). +It achieves this without requiring subsampling or aggregation.") + (license license:expat)))) + (define-public r-markdownhelpers (let ((commit "793372d28ebed607cc1d35f909a1caedb2b41ffe") (revision "1")) -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Jul 03 04:08:34 2023 Received: (at 64250-done) by debbugs.gnu.org; 3 Jul 2023 08:08:34 +0000 Received: from localhost ([127.0.0.1]:33079 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGEbq-0001k3-EC for submit@debbugs.gnu.org; Mon, 03 Jul 2023 04:08:34 -0400 Received: from sender3-of-o58.zoho.com ([136.143.184.58]:21815) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGEbn-0001jt-7L for 64250-done@debbugs.gnu.org; Mon, 03 Jul 2023 04:08:33 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1688371708; cv=none; d=zohomail.com; s=zohoarc; b=YVNfr6I0LzcxmMxRa/7pTrFDkQYVqBlU1/8P1cr5DmOWUhcnrA7NDTYBaRfU7K0LzXKWnLyooO93EzrWXujloREppa+18DYJ2VLkpktlfUBOnl/w6wnz3VkydLooRYmvEYzwvtiB4l1CShkPLFc9BMIkTWxE54C9xbxY3ch2xQY= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1688371708; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=Hiegx29U7ss9yW2yb6wnY8MFimXXnRGTnwZP4jg4glE=; b=im7fGlRtisyvJWaGCHMqBMdCBxBkrrj5E7Q0XlT4btGKqR2R9TlSb951+mIVB0dTwZTg5mdKJykz4460nJiqplJsYkCqs1S8G8xo21HuX6Q68mJCs5Y7qefVD5eNihCl7yOjq/KBOvkhy6QB5OFjx6Jmhw+ZwhHRq8oOkHVi3ns= 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=1688371708; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=Hiegx29U7ss9yW2yb6wnY8MFimXXnRGTnwZP4jg4glE=; b=QTEjM6pzYjj8+OYGhwg8RR37lc6ad60sIJ+fU+gdzjyPvu7ZcLi1ZhudZkGD+vtY SFErUJrr3KeQ+Nodom1ZtdxeJ+r712tNBV9S/oPgLUE3ak1nxXBBsdSoK84u91vzZnD 2QEoOfjGIorMl+8isDHdYQhNcCuvC+kLWxH4SAto= Received: from localhost (45-110-142-46.pool.kielnet.net [46.142.110.45]) by mx.zohomail.com with SMTPS id 16883717059691012.8566154183129; Mon, 3 Jul 2023 01:08:25 -0700 (PDT) User-agent: mu4e 1.10.3; emacs 28.2 From: Ricardo Wurmus To: 64250-done@debbugs.gnu.org Subject: [PATCH 00/15] *** R package (scriabin) *** Date: Mon, 03 Jul 2023 10:02:57 +0200 Message-ID: <87r0ppto21.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 64250-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: -1.0 (-) My apologies for the delay. Since r-diagrammer contains a lot of minified JavaScript without a way for us to build it fully from source it has been moved to guix-science (where we already had version 1.0.9). As a consequence r-nichenetr and r-scriabin were also moved to guix-science. Everything else has been pushed to the Guix master branch with minor changes to formatting and descriptions. Thank you! -- Ricardo From unknown Sat Aug 16 21:01:40 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Mon, 31 Jul 2023 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