From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 01 02:21:23 2023 Received: (at submit) by debbugs.gnu.org; 1 Mar 2023 07:21:23 +0000 Received: from localhost ([127.0.0.1]:52465 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGmB-00076l-8b for submit@debbugs.gnu.org; Wed, 01 Mar 2023 02:21:23 -0500 Received: from lists.gnu.org ([209.51.188.17]:53462) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGm9-00076b-3I for submit@debbugs.gnu.org; Wed, 01 Mar 2023 02:21:22 -0500 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 1pXGm0-0001uI-MH for guix-patches@gnu.org; Wed, 01 Mar 2023 02:21:17 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pXGlv-00084M-GU for guix-patches@gnu.org; Wed, 01 Mar 2023 02:21:12 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:subject :subject:from:from:content-language:user-agent:mime-version:date :date:message-id:received; s=mdc; t=1677655245; x=1679469646; bh=dx3PaYT5vHgBEqwGbS2uKZfa65tHOBnVIHOpuBYWfAk=; b=iQ2DQ5TLpwtB ZEwGl+6NTsu3EnkFzUqyChcFoLA8M1Ils1LchsdQWiMEJ7v6eJHxBYWaH6epPVvF 2bmUZ/iXmBvF0gcyym/g4L6UBM5mve847sH/EvmO5zxjsq0lfcvbaZu/FQe5Faha 3klXMAwmkSJV4LE1wgunfYFRfrYQ5rw= 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 C752116010D for ; Wed, 1 Mar 2023 08:20:45 +0100 (CET) Received: from [192.168.1.220] (77.23.232.54) 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 15.1.2507.21; Wed, 1 Mar 2023 08:20:45 +0100 Message-ID: Date: Wed, 1 Mar 2023 08:20:44 +0100 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:102.0) Gecko/20100101 Thunderbird/102.7.1 Content-Language: en-US To: From: =?UTF-8?B?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= Subject: [PATCH] gnu: Add r-biglm, r-cplm, r-som, r-chemometrics, r-metagenomeseq, r-maaslin2, r-mmuphin. 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From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 01 02:24:09 2023 Received: (at 61891) by debbugs.gnu.org; 1 Mar 2023 07:24:09 +0000 Received: from localhost ([127.0.0.1]:52476 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGop-0007C5-5w for submit@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:09 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:47363) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGom-0007BF-2D for 61891@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:05 -0500 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=1677655435; x=1679469836; bh=qfZQC3hDfVtYLubaEVLw+a6bUC1A8oiUvr5hUSGjkSI=; b=iKDhozEERU0x QWfzBiKIB1QzfCbdkaYas9Q8ki/xcANUwqVJwYH+tLVyR62QLwX2A4nEDjQ+Uu5s 7KO9aR87zAq7D+1pmhc64YGNpeQqi15jGQHPvivLuH3e98C+CwGDOGpxADu2tK1w i9sXLwztrzHpIXzs3ZE2gFUX9eRPEyg= 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 C7BCAA0116 for <61891@debbugs.gnu.org>; Wed, 1 Mar 2023 08:23:55 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.21; Wed, 1 Mar 2023 08:23:55 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61891@debbugs.gnu.org> Subject: [PATCH 2/7] gnu: Add r-cplm. Date: Wed, 1 Mar 2023 08:23:38 +0100 Message-ID: <20230301072343.708693-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> References: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27476.006 X-TM-AS-Result: No-10-3.997400-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkrhPNSdY0/OGdR1HJpsacenVTWWiNp+v8XjfR3d0weRq2J8/jkO8ZJjFK /NcS7G4kywNy6JN5lrYCokZpBcVCcmHOFLpmlzgFYKMMlFh4BnYCRtjr/tqtg9kCABefJILzmi1 6k8x6URM8Nwo6L2y1CYd00a6+9/yijxYyRBa/qJcFwgTvxipFa9xS3mVzWUuAojN1lLei7Ra6wz UiKI9xgHnoCJ0kUuNHUIriEpf0d3GnhdXtfQAxinlbwibElT4K81WHA6LOVDvI5wxmglIBO6xfO bU/XaRQUIZtxV5ql91koJqWxWZxCNZA9irUk5qtj27eUrb9iufzsdE1PQouS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-3.997400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27476.006 X-TM-SNTS-SMTP: D1F34A87BEC68B08BB186BC6B02E891966457409D5B8228693A59DE0B62565612002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61891 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-cplm): New variable. --- gnu/packages/cran.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fc8fe1a449..ddff93aa0d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -325,6 +325,41 @@ (define-public r-collections queues, stacks, deques, dicts and ordered dicts.") (license license:expat))) +(define-public r-cplm + (package + (name "r-cplm") + (version "0.7-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "cplm" version)) + (sha256 + (base32 "0mqjk10265hq9bc5ihmgbx1l8fzay1gpdlvx3pirqmvr3w1kwlxk")))) + (properties `((upstream-name . "cplm"))) + (build-system r-build-system) + (propagated-inputs + (list r-biglm + r-coda + r-ggplot2 + r-matrix + r-minqa + r-nlme + r-reshape2 + r-statmod + r-tweedie)) + (home-page "https://github.com/actuaryzhang/cplm") + (synopsis "Compound Poisson linear models") + (description "The Tweedie compound Poisson distribution is a mixture of a +degenerate distribution at the origin and a continuous distribution on the positive +real line. It has been applied in a wide range of fields in which continuous data +with exact zeros regularly arise. The cplm package provides likelihood based and +Bayesian procedures for fitting common Tweedie compound Poisson linear models. +In particular, models with hierarchical structures or extra zero inflation can be +handled. Further, the package implements the Gini index based on an ordered version +of the Lorenz curve as a robust model comparison tool involving zero-inflated and +highly skewed distributions.") + (license license:gpl2+))) + (define-public r-curry (package (name "r-curry") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 01 02:24:10 2023 Received: (at 61891) by debbugs.gnu.org; 1 Mar 2023 07:24:10 +0000 Received: from localhost ([127.0.0.1]:52479 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGor-0007CC-Py for submit@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:10 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:53247) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGom-0007BM-MY for 61891@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:05 -0500 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=1677655438; x=1679469839; bh=yTg5+iUI7UvmDbr JK24+DDkkALmF+IEDFuarnCbfSgo=; b=aoi3aNQGsMFd1BHzDGINGVjdy4BjTjc Is2m3MDrQLWFRRavMkwaJmgBLSQkB8Ftqzl/jDFlhc0UxtQhMcUsvIsCxjP+VX13 WZ11DYtyuZD31JHi781cO2hzZKvo7zvQ/KzfaPRaXXXbfDXjGSwsMS/54J8iIIXv M0EAAfPrmcFA= 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 9D3A9A017D for <61891@debbugs.gnu.org>; Wed, 1 Mar 2023 08:23:58 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.21; Wed, 1 Mar 2023 08:23:55 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61891@debbugs.gnu.org> Subject: [PATCH 1/7] gnu: Add r-biglm. Date: Wed, 1 Mar 2023 08:23:37 +0100 Message-ID: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27476.006 X-TM-AS-Result: No-10--1.465900-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeM3ZbGC9oP/O4+3 KSYQd9C0RRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v/kwFzTzcgzhO7WrSUXpNoUeVs 0skyEaS2GsZX0q3FpiOhAZQXEXXZuCxH+nTDZ1NOrm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu3aDLLDbFMGFdriiurVMbw8SlI2UE6AOpBi5VAgJIVoXgMtbJIqO/tXS4sicluRYMZE2Y 1P76ix8YKW3urm/3/Jp5Uv6hlE5RqWlF9USgFybx6Xh3Vy4y2+O91s7FwLn8xC2a7GIAOqG8ody TXpQo3UZHwBcdw5+Mg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.465900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27476.006 X-TM-SNTS-SMTP: 46BCD5B937F68DFBB25D8C0942E6861ADB8DE5EFD8FADD5AB3A9B71A7096672F2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61891 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-biglm): 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 c7a81b96eb..fc8fe1a449 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1145,6 +1145,25 @@ (define-public r-bezier degree elevation and curve fitting.") (license license:gpl2+))) +(define-public r-biglm + (package + (name "r-biglm") + (version "0.9-2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "biglm" version)) + (sha256 + (base32 "0iy9xr2bq42wlizgwlz7w5kh9206yqkw9h2cr6mcsmizgjg3rkvd")))) + (properties `((upstream-name . "biglm"))) + (build-system r-build-system) + (propagated-inputs (list r-dbi)) + (native-inputs (list gfortran)) + (home-page "https://cran.r-project.org/package=biglm") + (synopsis "Bounded memory linear and generalized linear models") + (description "Regression for data too large to fit in memory.") + (license (list license:gpl2+ license:gpl3+)))) ;;expanded from GPL + (define-public r-bwstest (package (name "r-bwstest") base-commit: efa091f9f4e77068353dff24f0ccd2d0613c3f48 -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 01 02:24:11 2023 Received: (at 61891) by debbugs.gnu.org; 1 Mar 2023 07:24:11 +0000 Received: from localhost ([127.0.0.1]:52481 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGos-0007CR-IS for submit@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:11 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:36265) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGom-0007BJ-37 for 61891@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:05 -0500 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=1677655437; x=1679469838; bh=2EaKsxHUNxQ/s5MYsPCCjwNApbCNZz9A3WpgnuHuD+o=; b=MwQri1DqJZhv Mgoh9xdqewzRDOQwHsleV9RMWLAX7z267pTW4/m77Rh5yuW3W1qOMqWPv+wfX0xa mXMOLRT5t2N5ioTxJoaluwKYdIkl2xJM6R+jP9Szhe3rbYT5fzd+X0AeIfdEsHg8 KFe6++hz/TW8zvicorpq4O7RksGF/os= 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 08C25A016C for <61891@debbugs.gnu.org>; Wed, 1 Mar 2023 08:23:57 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.21; Wed, 1 Mar 2023 08:23:55 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61891@debbugs.gnu.org> Subject: Date: Wed, 1 Mar 2023 08:23:39 +0100 Message-ID: <20230301072343.708693-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> References: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27476.006 X-TM-AS-Result: No-10--5.977600-5.000000 X-TMASE-MatchedRID: p6hhkqyLiWQPK2Dvdm/TZqoXHZz/dXlx+pWKzc1+6WtYC5LPd7Bvbb8F Hrw7frluf146W0iUu2vNs+hSjQLHECq+GZ9ZHxIhuW77/y896siFzNNPDc6umBHfiujuTbedvmK TdxbGqLLklvPIaBvBZarP+04pA0BmH8AvQUBdeeMVai/PlsEu5hDkv2q7d+VDlwV2iaAfSWf4cK Zpr+0wdmmRqNBHmBveVDC1CbuJXmMqtq5d3cxkNZd/mwLf2BVUhxCxzlmhVeL0cS/bzwMtrPcMr UIPvjNMzgYAr4ZPa3qUTGVAhB5EbQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.977600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27476.006 X-TM-SNTS-SMTP: 74B92C78FB22EC422D73A345F911F293EA80280010026D36007B426792FA2C532002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 61891 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: -1.3 (-) Date: Thu, 23 Feb 2023 00:56:33 +0100 Subject: [PATCH 3/7] gnu: Add r-som. * gnu/packages/cran.scm (r-som): 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 ddff93aa0d..b3aff2ee2c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16017,6 +16017,34 @@ (define-public r-softimpute components).") (license license:gpl2))) +(define-public r-som + (package + (name "r-som") + (version "0.3-5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "som" version)) + (sha256 + (base32 "1fbza1jxvwrkf5x3inkj36vshhkn7mz0ajqlxalbfmk6ngjw1x56")))) + (properties `((upstream-name . "som"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=som") + (synopsis "Self-organizing map") + (description + "This package implements a self-organizing map which has application in gene +clustering. It provides functions like: +@itemize +@item filtering data by certain floor, ceiling, max/min ratio, and max - min +difference; +@item normalization of the data; +@item get the average distortion measure; +@item train a self-organizing map; +@item summarize a som object; +@item yeast cell cycle. +@end itemize") + (license license:gpl3+))) + (define-public r-fftwtools (package (name "r-fftwtools") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 01 02:24:12 2023 Received: (at 61891) by debbugs.gnu.org; 1 Mar 2023 07:24:12 +0000 Received: from localhost ([127.0.0.1]:52485 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGou-0007Cu-Cw for submit@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:12 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:52563) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGon-0007BO-MM for 61891@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:10 -0500 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=1677655439; x=1679469840; bh=cVKPtrhzjcxKI40dmOxIDVR8vgsZ68ux46oM8cXyizw=; b=Ie1qro4cDkGL bwokUR8SOd9XdjfjvqjA8QtIK9UtALtVYUUkTgpnfQZHSurSyh8j28z4wrWv59HS Rl/jme81UWyTt0DCMQGQuZ/uhfTdyi6KC7LUr5gIM1VCyEIvFgADlMYGkNHqT8Y6 x14yZFD+7FjzOriQwLKK0NXBbQC5PBM= 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 55FFEA0184 for <61891@debbugs.gnu.org>; Wed, 1 Mar 2023 08:23:59 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.21; Wed, 1 Mar 2023 08:23:55 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61891@debbugs.gnu.org> Subject: Date: Wed, 1 Mar 2023 08:23:41 +0100 Message-ID: <20230301072343.708693-5-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> References: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27476.006 X-TM-AS-Result: No-10--2.268600-5.000000 X-TMASE-MatchedRID: OF2WlFkPn4APK2Dvdm/TZqoXHZz/dXlxKQNhMboqZlrAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtINkIN4ouKvbzqA3 Rnhce1qiRhTaskKypHTcIFFpSt9CPcjSyEYBzsV7dCok3ibXlQeuLFZZYlisfWiL2z3SO94YURS Scn+QSXt0H8LFZNFG7doMssNsUwYXqFU+1SnqAhinppZub+aY3Cs2ZZtS9Aejs5L4AzyF2kSfA8 ZbNA/A1RCkP6g0nIH8HDwaaDaBNAwktnXrSC8jSkHzCmp7EnFPHpeHdXLjLb473WzsXAufzELZr sYgA6obyh3JNelCjdRkfAFx3Dn4y X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.268600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27476.006 X-TM-SNTS-SMTP: 4DA425FC0FF2B1B0061C6A890CBE4F0C81BB862DF56510E5314FA1003FD139292002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 61891 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: -1.3 (-) Date: Thu, 23 Feb 2023 01:35:43 +0100 Subject: [PATCH 5/7] gnu: Add r-metagenomeseq. * gnu/packages/bioconductor.scm (r-metagenomeseq): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4b5ec7db28..7de5750e09 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6644,6 +6644,39 @@ (define-public r-maser and visualizaton of alternative splicing events generated by rMATS.") (license license:expat))) +(define-public r-metagenomeseq + (package + (name "r-metagenomeseq") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "metagenomeSeq" version)) + (sha256 + (base32 "01wjw4kcm8ysa5sn3cqg4a9i5pyksnwmbdqp5fr6n2l9hllkc9jy")))) + (properties `((upstream-name . "metagenomeSeq"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-foreach + r-glmnet + r-gplots + r-limma + r-matrix + r-matrixstats + r-rcolorbrewer + r-wrench)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/HCBravoLab/metagenomeSeq") + (synopsis "Statistical analysis for sparse high-throughput sequencing") + (description + "MetagenomeSeq is designed to determine features (be it @acronym{OTU, Operational +Taxanomic Unit}, species, etc.) that are differentially abundant between two or +more groups of multiple samples. This package is designed to address the effects +of both normalization and under-sampling of microbial communities on disease +association detection and the testing of feature correlations.") + (license license:artistic2.0))) + (define-public r-metaneighbor (package (name "r-metaneighbor") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 01 02:24:13 2023 Received: (at 61891) by debbugs.gnu.org; 1 Mar 2023 07:24:13 +0000 Received: from localhost ([127.0.0.1]:52487 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGou-0007Cx-N8 for submit@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:13 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:39659) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGop-0007BT-8Q for 61891@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:10 -0500 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=1677655440; x=1679469841; bh=jcvGS7tnryK7nN2jd5pdkaTEAite7FH8UHUXeyBRywo=; b=GwuJ1nvqmMCP TnHL+Kig4nNdqGpAT+VCOOj1jH+zV6FGwmr0T8YUGnk+dnPGD0jo32m3gwO1pXrD JMe9mc2EXBAG5OPY+4jUR91lzUFfakdosHY9Py85kzCInyqWZi9sP3xXXy9fYILK Op9mwkbWIcd1BWYlexUw0+16ss6+9aM= 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 5492DA0188 for <61891@debbugs.gnu.org>; Wed, 1 Mar 2023 08:24:00 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.21; Wed, 1 Mar 2023 08:23:55 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61891@debbugs.gnu.org> Subject: Date: Wed, 1 Mar 2023 08:23:40 +0100 Message-ID: <20230301072343.708693-4-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> References: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27476.006 X-TM-AS-Result: No-10--6.380400-5.000000 X-TMASE-MatchedRID: mGX4zkTg7WUPK2Dvdm/TZqoXHZz/dXlxKQNhMboqZlrAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvs0T0PE+KHuX6lYrNzX7pa0JZ5MDd4/kUssb EkSX6c0mnzxLRYWF2LRW+e9CryH+Xz5ey3IkHnU68v8ObWdQ92TUOwhhXXSQ1Ipz++XQI8PGeAi CmPx4NwOn4v73d4AhohYfw868k05b3PDiXO/tFSfcUt5lc1lLgoGRyAacnhaZSn1zI/TIOaKbJh Wqn+PtHM6s/q3Kh7whtY3hnvLiedn7cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.380400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27476.006 X-TM-SNTS-SMTP: 361C71DD1007C2C4571F91E19A0999E3C2B2A47C3931D38D01D1704704FFC28F2002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 61891 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: -1.3 (-) Date: Thu, 23 Feb 2023 01:20:10 +0100 Subject: [PATCH 4/7] gnu: Add r-chemometrics. * gnu/packages/cran.scm (r-chemometrics): New variable. --- gnu/packages/cran.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b3aff2ee2c..fc24f3eafc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17025,6 +17025,44 @@ (define-public r-chemometricswithr Life Sciences\" by Ron Wehrens, Springer (2011).") (license license:gpl2+))) +(define-public r-chemometrics + (package + (name "r-chemometrics") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "chemometrics" version)) + (sha256 + (base32 "0shqns0n964pfwnd0q5sadglrlpgs4g5fbv45fsj9p37l4pq61dp")))) + (properties `((upstream-name . "chemometrics"))) + (build-system r-build-system) + (propagated-inputs + (list r-class + r-e1071 + r-lars + r-mass + r-mclust + r-nnet + r-pcapp + r-pls + r-robustbase + r-rpart + r-som)) + (home-page "http://www.statistik.tuwien.ac.at/public/filz/") + (synopsis "Multivariate statistical analysis in Chemometrics") + (description + "Multivariate data analysis is the simultaneous observation of more than one +characteristic. In contrast to the analysis of univariate data, in this approach +not only a single variable or the relation between two variables can be investigated, +but the relations between many attributes can be considered. For the statistical +analysis of chemical data one has to take into account the special structure of +this type of data. This package contains about 30 functions, mostly for regression, +classification and model evaluation and includes some data sets used in the R help +examples. It was designed as a R companion to the book \"Introduction to Multivariate +Statistical Analysis in Chemometrics\" written by K. Varmuza and P. Filzmoser (2009).") + (license license:gpl3+))) + (define-public r-als (package (name "r-als") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 01 02:24:13 2023 Received: (at 61891) by debbugs.gnu.org; 1 Mar 2023 07:24:13 +0000 Received: from localhost ([127.0.0.1]:52489 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGov-0007D4-4a for submit@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:13 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:54015) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGos-0007Br-FJ for 61891@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:11 -0500 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=1677655441; x=1679469842; bh=rZId94e1ohBuMYWTMS0oZAPGHaIWsCRjj6K/hsc9k34=; b=aHgU2NW5J3V+ cXh/Gc8aEwg2ACBUNbWyZNzXrRZBN/UWyfdQT8SfYUC3Fv2qzJvRpUk0RUYDqLcF o5X0s5pdw+Jtf69yoDWMBRx7N/SpOmEZFPCyxNfLCCwcp34fExHfmtm8vDvOcefn VEFFgyLryUE5b45irMDZZSXuCRsDPT4= 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 DED17A018B for <61891@debbugs.gnu.org>; Wed, 1 Mar 2023 08:24:01 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.21; Wed, 1 Mar 2023 08:23:56 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61891@debbugs.gnu.org> Subject: Date: Wed, 1 Mar 2023 08:23:43 +0100 Message-ID: <20230301072343.708693-7-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> References: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27476.006 X-TM-AS-Result: No-10-1.431000-5.000000 X-TMASE-MatchedRID: 8hYOgsqT2ysPK2Dvdm/TZqoXHZz/dXlxKQNhMboqZlrAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvPKN38CLPK0H6UU2arQpzTXsM22rGusNzD82 kkqrfQUf9Ktxj1mXhOuPRJuyjz/feI2+ozn+aJKxMkYTBFuMYZbx0P+dKYkf3pjlkbDvDJ4exA1 85qFVOTJC6QfsZ5OsWElOOOz3JPpijxYyRBa/qJcfVu8Ug18kdwgn7iDBesS3CttcwYNipX/oJl cuVXWZJGDxml9Dj6K2J2BUypdqiXJA8PaUv4rIn2gbO52qqWF3Rf2RCZYhiOrMn9dyFDGQQvwdk cZSQHZ1VE2XDUuHdcU3+N2+8NJqlKEIODKywTy6jfJglXzHQ6sxRVzSzXt2xf+rhMPa/srU= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.431000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27476.006 X-TM-SNTS-SMTP: 833931C92CA60AC5233B589302693E86788F6CA2E0720BF3DFAD362C18F9FE0D2002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 61891 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: -1.3 (-) Date: Wed, 1 Mar 2023 08:16:27 +0100 Subject: [PATCH 7/7] gnu: Add r-mmuphin. * gnu/packages/bioconductor.scm (r-mmuphin): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c7f623343e..afe969e5de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6811,6 +6811,46 @@ (define-public r-methylkit TAB-Seq.") (license license:artistic2.0))) +(define-public r-mmuphin + (package + (name "r-mmuphin") + (version "1.12.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MMUPHin" version)) + (sha256 + (base32 "0vpap3avmrjy187s3dva6f008al6d935kpdf816xzl5gxl7zvf62")))) + (properties `((upstream-name . "MMUPHin"))) + (build-system r-build-system) + (arguments + (list #:tests? #f)) ;; non deterministic, also it requieres http access + (inputs (list glpk)) + (propagated-inputs + (list r-cowplot + r-biocstyle + r-dplyr + r-fpc + r-ggplot2 + r-igraph + r-maaslin2 + r-metafor + r-stringr + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/MMUPHin") + (synopsis "Meta-analysis with uniform pipeline for heterogeneity in microbiome") + (description + "MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It +has function interfaces for: +@itemize +@item covariate-controlled batch- and cohort effect adjustment; +@item meta-analysis differential abundance testing; +@item meta-analysis unsupervised discrete structure (clustering) discovery; +@item meta-analysis unsupervised continuous structure discovery. +@end itemize") + (license license:expat))) + (define-public r-motifrg (package (name "r-motifrg") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 01 02:24:13 2023 Received: (at 61891) by debbugs.gnu.org; 1 Mar 2023 07:24:13 +0000 Received: from localhost ([127.0.0.1]:52491 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGov-0007DB-Ha for submit@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:13 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:53623) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXGos-0007Bs-Fk for 61891@debbugs.gnu.org; Wed, 01 Mar 2023 02:24:11 -0500 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=1677655442; x=1679469843; bh=yc2ZExmidKlPKavYFbaEMkT4P8N7CtoITJr4ISOovYI=; b=Q+o0FFnwigHU tlDA4TjXPY9j15K49VMXL2n76je7dA24gHkZI9lF0DkClgBPl7IBsNf0QL06vQyR Vp4l5Fb5WW+KXUbyp4Q0I/hs4ksOmA2gq4Cuy0XVfHAz2WtDrIx83JuZw9Ij7ITV H69d/GcY62LARuYIoUcLqfUO7yVcB9A= 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 D65E5A0196 for <61891@debbugs.gnu.org>; Wed, 1 Mar 2023 08:24:02 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.21; Wed, 1 Mar 2023 08:23:56 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61891@debbugs.gnu.org> Subject: Date: Wed, 1 Mar 2023 08:23:42 +0100 Message-ID: <20230301072343.708693-6-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> References: <20230301072343.708693-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27476.006 X-TM-AS-Result: No-10--2.901400-5.000000 X-TMASE-MatchedRID: DosEHPCMGzUPK2Dvdm/TZqoXHZz/dXlxKQNhMboqZlrAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvPKN38CLPK0Fr2qJoNIuCjYEBeX0uQ+npMRO 6upoJau7ZxJnpOW5LmePRJuyjz/fep1C54qLS4Jv8dMpK2wMYwheN9Hd3TB5G5NmGF/U2QANcRZ dhNa0YwhdqVqQkxv86GWDZgS8Jg+Ibcm3b1gDB8KubsOtSWY2QgDLqnrRlXrYfE8yM4pjsDxZ4y lU2GwzAxEHRux+uk8jfhP1xgyx3DFDhSOZAN0f8pr9uATmULpzDJv3FbJTpVlZnRojrGxzc/fl/ B8gbecXcK+E/3qDOXJwlHW7T9dx1igc8Mxo55hR6WDdqYdSnRtxSR7be7fnTFTs4ljtt094P2K/ +wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.901400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27476.006 X-TM-SNTS-SMTP: 5C15CC18E65519C44E6D35B045058255EC367D1AFBF6183621D657759CFC2B102002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 61891 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: -1.3 (-) Date: Wed, 1 Mar 2023 04:17:48 +0100 Subject: [PATCH 6/7] gnu: Add r-maaslin2. * gnu/packages/bioconductor.scm (r-maaslin2): New variable. --- gnu/packages/bioconductor.scm | 51 +++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7de5750e09..c7f623343e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6533,6 +6533,57 @@ (define-public r-limma different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-maaslin2 + (package + (name "r-maaslin2") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Maaslin2" version)) + (sha256 + (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89")))) + (properties `((upstream-name . "Maaslin2"))) + (build-system r-build-system) + (arguments (list #:tests? #f)) ;test suite is non-deterministic :( + (propagated-inputs + (list r-biglm + r-car + r-chemometrics + r-cplm + r-data-table + r-dplyr + r-edger + r-ggplot2 + r-glmmtmb + r-hash + r-lme4 + r-lmertest + r-logging + r-lpsymphony + r-mass + r-mumin + r-metagenomeseq + r-optparse + r-pbapply + r-pcapp + r-pheatmap + r-pscl + r-rmarkdown + r-robustbase + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "http://huttenhower.sph.harvard.edu/maaslin2") + (synopsis + "Multivariable association discovery in population-scale meta-omics studies") + (description + "MaAsLin2 is comprehensive R package for efficiently determining multivariable +association between clinical metadata and microbial meta'omic features. This +package relies on general linear models to accommodate most modern epidemiological +study designs, including cross-sectional and longitudinal, and offers a variety +of data exploration, normalization, and transformation methods.") + (license license:expat))) + (define-public r-made4 (package (name "r-made4") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 01 05:54:02 2023 Received: (at 61891) by debbugs.gnu.org; 1 Mar 2023 10:54:02 +0000 Received: from localhost ([127.0.0.1]:52837 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXK5y-0003L4-2t for submit@debbugs.gnu.org; Wed, 01 Mar 2023 05:54:02 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:40865) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXK5w-0003Ka-Gz for 61891@debbugs.gnu.org; Wed, 01 Mar 2023 05:54:01 -0500 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=1677668033; x=1679482434; bh=CwkRCUeDs0vZ6yG LC2pI2z/XwEYddjfeBJNAO9RmUNU=; b=c7D3TXi3rBV7Ok8PvXmQAc9eFgJOyZs aOxz6AQQHRt2uPefDD6y35XGh6VCPRYje5r0BD4+B3CJrqVu/7YtI4QGALo4ywTs 5RvJ3pA2Ai1a17yjALKxtu3znow9imEl9bgsxcIRldMS9OvNhUZB7yFLD+h29I7Z tJO49GNKHhDg= 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 ED6F43001AD for <61891@debbugs.gnu.org>; Wed, 1 Mar 2023 11:53:50 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.21; Wed, 1 Mar 2023 11:53:49 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61891@debbugs.gnu.org> Subject: Date: Wed, 1 Mar 2023 11:53:39 +0100 Message-ID: <20230301105339.709043-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27476.007 X-TM-AS-Result: No-10--1.948100-5.000000 X-TMASE-MatchedRID: tWdWe73PBg0PK2Dvdm/TZqqHmm/V4M/P+VJ6lZyB0s+BAXl9LkPp6b8F Hrw7frluf146W0iUu2u8gDYpN21y0MQTSPZE5H8ga87CDXaKRVJITEcvqjcF4IwnGKAoIKJLKWF xEPEOC9vxgwYhHpmqNUVLVHt/d4qU0lfl7pOHNvaqFx2c/3V5ccXSSNhWWhyhg1CUneBzTgvUh5 yQ6tsoTKHpFHQK2deBZMt3AWpK5qXUp7hH95oViI6MisxJraxHFei5YP5NvsKkob0Y35+HFDETu rqaCWru3cE6DYTDQbOzEeVI4VC5O/Pfj/RbxQwm194/5X9VfCzerJbrvn4Rhc42FQxklqQf1X/R sKePD9eObUP13PcwQ7Bm/FaV75+81AacdAplL3NFwYcRXRYHEPioIsi7Sa0guAzeO3IdJJCiTxq FJurDEnkkuIWcvwsp8Oc2TevSU1FaLxCKnrw2B29OepgphdNGEOS/art35UOXBXaJoB9JZ/hwpm mv7TB2m4n49vyf9XG4NlOhazXSZkkpbiYOUmwxwrbXMGDYqV8HTT+SR4FPAOeVwAFBuYVjqqH3A zSLfVTqSmNJc6eitZoVlgIKgfUmHUUNYo8E2uWb1ZnROo1XPPAR5Uh3pKLp45snJvgxqKn/r18e YskJzyhCDgyssE8uo3yYJV8x0OrMUVc0s17dsX/q4TD2v7K1 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.948100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27476.007 X-TM-SNTS-SMTP: 8C4314006F7E0D436441574FE7B4EF8AB8F1E10DD581A4B5FEBC06814D9B059F2002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 61891 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: -1.3 (-) Date: Wed, 1 Mar 2023 11:50:40 +0100 Subject: [PATCH] gnu: Test builds for r-maaslin and r-mmuphin.scm This is my try to make the build of these two package reproducible. I send this only in the case if the reviewer wants to dig more and maybe he can solve the non deterministic build. --- gnu/packages/bioconductor.scm | 138 ++++++++++++++++++++++++++++++++++ 1 file changed, 138 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7de5750e09..15fad711af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -33,6 +33,7 @@ (define-module (gnu packages bioconductor) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) @@ -6533,6 +6534,80 @@ (define-public r-limma different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-maaslin2 + (package + (name "r-maaslin2") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Maaslin2" version)) + (sha256 + (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89")))) + (properties `((upstream-name . "Maaslin2"))) + (build-system r-build-system) + (arguments (list ;;#:tests? #f)) ;test suite is non-deterministic :( + #:phases + #~(modify-phases %standard-phases + ;; During the check there is needed for writable cache directory + ;; Fontconfig error: No writable cache directories + (add-before 'check 'set-cache + (lambda _ + (setenv "XDG_CACHE_HOME" "/tmp/xdg-cache"))) + ;; The check phase generates some log and pdf files. This cause that + ;; the build to be not reproducible + (add-after 'check 'make-reproducible + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out") "/site-library/Maaslin2/"))) + (for-each delete-file-recursively + (list ;;(string-append out "Maaslin2-Ex.Rout") + ;;(string-append #$output "/Maaslin2-Ex.pdf") + ;;(string-append #$output "/Maaslin2-tests/testthat/output") + ;;(string-append #$output "/Maaslin2-tests/testthat/output2") + ;;(string-append #$output "Maaslin2-tests/testthat.Rout") + (string-append out "doc/demo_output/maaslin2.log") + (string-append out "doc/demo_output/figures") + ;;"doc/demo_output" + ))))) + ))) + (propagated-inputs + (list r-biglm + r-car + r-chemometrics + r-cplm + r-data-table + r-dplyr + r-edger + r-ggplot2 + r-glmmtmb + r-hash + r-lme4 + r-lmertest + r-logging + r-lpsymphony + r-mass + r-mumin + r-metagenomeseq + r-optparse + r-pbapply + r-pcapp + r-pheatmap + r-pscl + r-rmarkdown + r-robustbase + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "http://huttenhower.sph.harvard.edu/maaslin2") + (synopsis + "Multivariable association discovery in population-scale meta-omics studies") + (description + "MaAsLin2 is comprehensive R package for efficiently determining multivariable +association between clinical metadata and microbial meta'omic features. This +package relies on general linear models to accommodate most modern epidemiological +study designs, including cross-sectional and longitudinal, and offers a variety +of data exploration, normalization, and transformation methods.") + (license license:expat))) + (define-public r-made4 (package (name "r-made4") @@ -6760,6 +6835,69 @@ (define-public r-methylkit TAB-Seq.") (license license:artistic2.0))) +(define-public r-mmuphin + (package + (name "r-mmuphin") + (version "1.12.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MMUPHin" version)) + (sha256 + (base32 "0vpap3avmrjy187s3dva6f008al6d935kpdf816xzl5gxl7zvf62")))) + (properties `((upstream-name . "MMUPHin"))) + (build-system r-build-system) + (arguments + (list ;;#:tests? #f)) ;; non deterministic, also it requieres http access + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjusts-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "inst/doc/MMUPHin.Rmd" + (("../man/figures") + (string-append #$output "/site-library/MMUPHin/help/figures"))) + ;;(substitute* "inst/doc/MMUPHin.R" + ;; (("library(ggplot2)") "library(ggplot2)\ngetwd()")) + )) + (add-after 'install 'add-files + (lambda* (#:key inputs outputs #:allow-other-keys) + (install-file "man/figures/structure_types.PNG" + (string-append #$output "/site-library/MMUPHin/help/figures")) + (install-file "vignettes/references.bib" + (string-append #$output "/site-library/MMUPHin/doc")))) + (add-before 'check 'set-cache + (lambda _ + (setenv "XDG_CACHE_HOME" "/tmp/xdg-cache"))) + ))) + (inputs (list glpk + ; ;;pandoc + ; ;;r-rmarkdown + )) + (propagated-inputs + (list r-cowplot + r-biocstyle + r-dplyr + r-fpc + r-ggplot2 + r-igraph + r-maaslin2 + r-metafor + r-stringr + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/MMUPHin") + (synopsis "Meta-analysis with uniform pipeline for heterogeneity in microbiome") + (description + "MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It +has function interfaces for: +@itemize +@item covariate-controlled batch- and cohort effect adjustment; +@item meta-analysis differential abundance testing; +@item meta-analysis unsupervised discrete structure (clustering) discovery; +@item meta-analysis unsupervised continuous structure discovery. +@end itemize") + (license license:expat))) + (define-public r-motifrg (package (name "r-motifrg") base-commit: efa091f9f4e77068353dff24f0ccd2d0613c3f48 prerequisite-patch-id: 9e08f9ff2621a13d751e3d82c0837144b09494e4 prerequisite-patch-id: 4cfeb51eeb402b18b0d23c6782255a3bc1f1ff43 prerequisite-patch-id: cf4c417ccd15ef1f795ada39f3faee9f59bb3c36 prerequisite-patch-id: d79a8e82e46ec03cf54f25ec101a5b54592fdb1b prerequisite-patch-id: 81871608ddab1ba624de7432ad473e52221efc08 -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 02 16:12:15 2023 Received: (at 61891-done) by debbugs.gnu.org; 2 Mar 2023 21:12:16 +0000 Received: from localhost ([127.0.0.1]:58487 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXqDn-0001vR-Ky for submit@debbugs.gnu.org; Thu, 02 Mar 2023 16:12:15 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21019) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXqDj-0001vD-Sq for 61891-done@debbugs.gnu.org; Thu, 02 Mar 2023 16:12:13 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1677791528; cv=none; d=zohomail.com; s=zohoarc; b=KDhV4RDghsiU2ERvX1Lr2Hfy2eDhacrUmGdaEQi6nqEbFPB0KqAZ6QkRkVvAV2vf/XT4MWnGem+8SoxytrYDPAnhH60s3V30+WLAPqEQMvvDzFwog1S18LcS5un1SRs+z+04RDzvdrJRuuvQL36YHNQYE1xVnMOlkMGkv00h6nM= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1677791528; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=aKqaUTzScgg1F/2RAN2HJqM6CEX2PvC4wn86FN+6uTs=; b=R/VYYZ8+S6cmpYUU4TK1xhbZM/pxuvWlGDnc+jFmJMuIiQQSUOfL2fiuB2K/VsruLMvUScMLs+zdevs4BAWY8CVyNXlTKXH2ntqz+CVpJl7Di+dTENBERelpxGRwGyVnegj1vn4XoENTtmBEPWm5KhvuYMeqFM81zN7XQrf6Gck= 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=1677791528; 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=aKqaUTzScgg1F/2RAN2HJqM6CEX2PvC4wn86FN+6uTs=; b=JU2ph1x3bMOx9U0zvJ6+WpXLxi1NIlgsURE5BHnNwcezwBRvnSA3SClMg1yGUSgx g15sPfWDrH7fKpLpaotyhbVaD3C9APAMjujg44/UIX+2X1YSEd+bS9YNAz2917nsjRe xmv8t/udXVU7wv9SEEcvCu2hfN4wyOXG5F1N7+Ao= Received: from localhost (i5E862DD1.versanet.de [94.134.45.209]) by mx.zohomail.com with SMTPS id 1677791527336823.4182363342079; Thu, 2 Mar 2023 13:12:07 -0800 (PST) References: <20230301105339.709043-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#61891] Date: Thu, 02 Mar 2023 22:09:30 +0100 In-reply-to: <20230301105339.709043-1-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: <87356mg8nw.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: 61891-done Cc: 61891-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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > Date: Wed, 1 Mar 2023 11:50:40 +0100 > Subject: [PATCH] gnu: Test builds for r-maaslin and r-mmuphin.scm > > This is my try to make the build of these two package reproducible. > > I send this only in the case if the reviewer wants to dig more and maybe = he can > solve the non deterministic build. I managed to get r-mmuphin to build reproducibly, but for r-maaslin the problem is that the scatterplots are non-deterministic. I=E2=80=99ve opene= d a new bug report for that and pushed the rest of the patches. --=20 Ricardo From unknown Sat Jun 21 10:40:46 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 31 Mar 2023 11:24:12 +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