From unknown Tue Jun 24 22:35:30 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#28109 <28109@debbugs.gnu.org> To: bug#28109 <28109@debbugs.gnu.org> Subject: Status: [PATCH 00/11] Some more R things Reply-To: bug#28109 <28109@debbugs.gnu.org> Date: Wed, 25 Jun 2025 05:35:30 +0000 retitle 28109 [PATCH 00/11] Some more R things reassign 28109 guix-patches submitter 28109 Ricardo Wurmus severity 28109 normal tag 28109 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 08:56:43 2017 Received: (at submit) by debbugs.gnu.org; 16 Aug 2017 12:56:43 +0000 Received: from localhost ([127.0.0.1]:40337 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhxsJ-0004VK-5K for submit@debbugs.gnu.org; Wed, 16 Aug 2017 08:56:43 -0400 Received: from eggs.gnu.org ([208.118.235.92]:52155) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhxsH-0004V8-2M for submit@debbugs.gnu.org; Wed, 16 Aug 2017 08:56:41 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dhxsB-0004xQ-5G for submit@debbugs.gnu.org; Wed, 16 Aug 2017 08:56:35 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:45103) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1dhxsB-0004xL-25 for submit@debbugs.gnu.org; Wed, 16 Aug 2017 08:56:35 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:43113) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dhxs9-0006or-Pa for guix-patches@gnu.org; Wed, 16 Aug 2017 08:56:34 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dhxs4-0004vp-V2 for guix-patches@gnu.org; Wed, 16 Aug 2017 08:56:33 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21074) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1dhxs4-0004vX-Ng for guix-patches@gnu.org; Wed, 16 Aug 2017 08:56:28 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502888183858526.7419482492794; Wed, 16 Aug 2017 05:56:23 -0700 (PDT) From: Ricardo Wurmus To: guix-patches@gnu.org Subject: [PATCH 00/11] Some more R things Date: Wed, 16 Aug 2017 14:56:20 +0200 Message-Id: <20170816125620.10140-1-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-Debbugs-Envelope-To: submit Cc: Ricardo Wurmus 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: -4.0 (----) Hi Guix, here are some more R packages. Ricardo Wurmus (11): gnu: r-trimcluster: Update license. gnu: Add r-emdbook. gnu: Add r-fastseg. gnu: Add r-qvalue. gnu: Add r-methylkit. gnu: Add r-lpsolve. gnu: Add r-limsolve. gnu: Add r-fitdistrplus. gnu: Add r-energy. gnu: Add r-suppdists. gnu: Add r-ksamples. From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 09:09:10 2017 Received: (at 28109) by debbugs.gnu.org; 16 Aug 2017 13:09:10 +0000 Received: from localhost ([127.0.0.1]:40348 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4M-0004pk-Gj for submit@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:10 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21004) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4K-0004pZ-6U for 28109@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:08 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502888943687353.9166643452892; Wed, 16 Aug 2017 06:09:03 -0700 (PDT) From: Ricardo Wurmus To: 28109@debbugs.gnu.org Subject: [PATCH 01/10] gnu: r-trimcluster: Update license. Date: Wed, 16 Aug 2017 15:08:50 +0200 Message-Id: <20170816130859.15069-1-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/statistics.scm (r-trimcluster)[license]: Also specify GPLv3+. --- gnu/packages/statistics.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8e7b815d6..80465ea10 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4724,7 +4724,8 @@ multivariate analysis.") "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and Matran (1997). This optimizes the k-means criterion under trimming a portion of the points.") - (license license:gpl2+))) + ;; Any GPL version + (license (list license:gpl2+ license:gpl3+)))) (define-public r-fpc (package -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 09:09:13 2017 Received: (at 28109) by debbugs.gnu.org; 16 Aug 2017 13:09:13 +0000 Received: from localhost ([127.0.0.1]:40351 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4O-0004pz-Pw for submit@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:12 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21100) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4N-0004ps-Lu for 28109@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:12 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502888947212590.0671697555499; Wed, 16 Aug 2017 06:09:07 -0700 (PDT) From: Ricardo Wurmus To: 28109@debbugs.gnu.org Subject: [PATCH 02/10] gnu: Add r-emdbook. Date: Wed, 16 Aug 2017 15:08:51 +0200 Message-Id: <20170816130859.15069-2-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170816130859.15069-1-rekado@elephly.net> References: <20170816130859.15069-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-emdbook): 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 e604799c4..ae4d807dc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -734,3 +734,31 @@ package modifies and extends the @code{mle} classes in the @code{stats4} package.") ;; Any version of the GPL (license (list license:gpl2 license:gpl3)))) + +(define-public r-emdbook + (package + (name "r-emdbook") + (version "1.3.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "emdbook" version)) + (sha256 + (base32 + "09xbdyw8a4pvrsg3ryr8drby0njy4avc5wsjj4ffibdaicpchy69")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bbmle" ,r-bbmle) + ("r-coda" ,r-coda) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp))) + (home-page "http://www.math.mcmaster.ca/bolker/emdbook") + (synopsis "Support functions and data for \"Ecological Models and Data\"") + (description + "This package provides auxiliary functions and data sets for \"Ecological +Models and Data\", a book presenting maximum likelihood estimation and related +topics for ecologists (ISBN 978-0-691-12522-0).") + ;; Any GPL version + (license (list license:gpl2 license:gpl3)))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 09:09:19 2017 Received: (at 28109) by debbugs.gnu.org; 16 Aug 2017 13:09:19 +0000 Received: from localhost ([127.0.0.1]:40355 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4T-0004qM-0y for submit@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:18 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21104) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4R-0004q8-9Z for 28109@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:15 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502888950122874.9280513111004; Wed, 16 Aug 2017 06:09:10 -0700 (PDT) From: Ricardo Wurmus To: 28109@debbugs.gnu.org Subject: [PATCH 03/10] gnu: Add r-fastseg. Date: Wed, 16 Aug 2017 15:08:52 +0200 Message-Id: <20170816130859.15069-3-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170816130859.15069-1-rekado@elephly.net> References: <20170816130859.15069-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/bioinformatics.scm (r-fastseg): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3571cb96c..4207b2a9d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9287,6 +9287,36 @@ modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.") (license license:artistic2.0))) +(define-public r-fastseg + (package + (name "r-fastseg") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fastseg" version)) + (sha256 + (base32 + "083wiz03q9mynwchs9frlpp6c84dncri5ncibx6h82p228cpja6h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "http://www.bioinf.jku.at/software/fastseg/index.html") + (synopsis "Fast segmentation algorithm for genetic sequencing data") + (description + "Fastseg implements a very fast and efficient segmentation algorithm. +It can segment data from DNA microarrays and data from next generation +sequencing for example to detect copy number segments. Further it can segment +data from RNA microarrays like tiling arrays to identify transcripts. Most +generally, it can segment data given as a matrix or as a vector. Various data +formats can be used as input to fastseg like expression set objects for +microarrays or GRanges for sequencing data.") + (license license:lgpl2.0+))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 09:09:19 2017 Received: (at 28109) by debbugs.gnu.org; 16 Aug 2017 13:09:19 +0000 Received: from localhost ([127.0.0.1]:40357 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4V-0004qQ-24 for submit@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:19 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21116) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4R-0004q9-KL for 28109@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:16 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502888952668830.8157972744654; Wed, 16 Aug 2017 06:09:12 -0700 (PDT) From: Ricardo Wurmus To: 28109@debbugs.gnu.org Subject: [PATCH 04/10] gnu: Add r-qvalue. Date: Wed, 16 Aug 2017 15:08:53 +0200 Message-Id: <20170816130859.15069-4-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170816130859.15069-1-rekado@elephly.net> References: <20170816130859.15069-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/bioinformatics.scm (r-qvalue): New variable. --- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4207b2a9d..7cc48b3df 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9317,6 +9317,35 @@ formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.") (license license:lgpl2.0+))) +(define-public r-qvalue + (package + (name "r-qvalue") + (version "2.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "qvalue" version)) + (sha256 + (base32 + "1dxdwa767a9r8n61r272ypi09qblcdfpzzwkmri74y5mbp1r3y4i")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-reshape2" ,r-reshape2))) + (home-page "http://github.com/jdstorey/qvalue") + (synopsis "Q-value estimation for false discovery rate control") + (description + "This package takes a list of p-values resulting from the simultaneous +testing of many hypotheses and estimates their q-values and local @dfn{false +discovery rate} (FDR) values. The q-value of a test measures the proportion +of false positives incurred when that particular test is called significant. +The local FDR measures the posterior probability the null hypothesis is true +given the test's p-value. Various plots are automatically generated, allowing +one to make sensible significance cut-offs. The software can be applied to +problems in genomics, brain imaging, astrophysics, and data mining.") + ;; Any version of the LGPL. + (license license:lgpl3+))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 09:09:24 2017 Received: (at 28109) by debbugs.gnu.org; 16 Aug 2017 13:09:24 +0000 Received: from localhost ([127.0.0.1]:40360 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4Y-0004qm-Bl for submit@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:23 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21130) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4V-0004qX-HG for 28109@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:20 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502888955332515.5404565430881; Wed, 16 Aug 2017 06:09:15 -0700 (PDT) From: Ricardo Wurmus To: 28109@debbugs.gnu.org Subject: [PATCH 05/10] gnu: Add r-lpsolve. Date: Wed, 16 Aug 2017 15:08:54 +0200 Message-Id: <20170816130859.15069-5-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170816130859.15069-1-rekado@elephly.net> References: <20170816130859.15069-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-lpsolve): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ae4d807dc..a912394da 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -762,3 +762,25 @@ Models and Data\", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).") ;; Any GPL version (license (list license:gpl2 license:gpl3)))) + +(define-public r-lpsolve + (package + (name "r-lpsolve") + (version "5.6.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "lpSolve" version)) + (sha256 + (base32 + "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m")))) + (properties `((upstream-name . "lpSolve"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/lpSolve") + (synopsis "R interface to Lp_solve to solve linear/integer programs") + (description + "Lp_solve is software for solving linear, integer and mixed integer +programs. This implementation supplies a \"wrapper\" function in C and some R +functions that solve general linear/integer problems, assignment problems, and +transportation problems.") + (license license:lgpl2.0))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 09:09:25 2017 Received: (at 28109) by debbugs.gnu.org; 16 Aug 2017 13:09:25 +0000 Received: from localhost ([127.0.0.1]:40364 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4b-0004rA-1I for submit@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:25 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21024) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4Y-0004ql-59 for 28109@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:23 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502888957837564.1193262023402; Wed, 16 Aug 2017 06:09:17 -0700 (PDT) From: Ricardo Wurmus To: 28109@debbugs.gnu.org Subject: [PATCH 06/10] gnu: Add r-limsolve. Date: Wed, 16 Aug 2017 15:08:55 +0200 Message-Id: <20170816130859.15069-6-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170816130859.15069-1-rekado@elephly.net> References: <20170816130859.15069-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-limsolve): 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 a912394da..746c778b2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23,6 +23,7 @@ #:use-module (guix utils) #:use-module (guix build-system r) #:use-module (gnu packages gcc) + #:use-module (gnu packages maths) #:use-module (gnu packages perl) #:use-module (gnu packages statistics) #:use-module (gnu packages web)) @@ -784,3 +785,37 @@ programs. This implementation supplies a \"wrapper\" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems.") (license license:lgpl2.0))) + +(define-public r-limsolve + (package + (name "r-limsolve") + (version "1.5.5.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "limSolve" version)) + (sha256 + (base32 + "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg")))) + (properties `((upstream-name . "limSolve"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lpsolve" ,r-lpsolve) + ("r-mass" ,r-mass) + ("r-quadprog" ,r-quadprog))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/limSolve") + (synopsis "Solving linear inverse models") + (description + "This package provides functions that: + +@enumerate +@item find the minimum/maximum of a linear or quadratic function, +@item sample an underdetermined or overdetermined system, +@item solve a linear system Ax=B for the unknown x. +@end enumerate + +It includes banded and tridiagonal linear systems. The package calls Fortran +functions from LINPACK.") + ;; Any GPL version. + (license (list license:gpl2+ license:gpl3+)))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 09:09:25 2017 Received: (at 28109) by debbugs.gnu.org; 16 Aug 2017 13:09:25 +0000 Received: from localhost ([127.0.0.1]:40366 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4b-0004rC-Cy for submit@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:25 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21133) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4Y-0004qo-Tm for 28109@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:23 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502888960491299.991397564335; Wed, 16 Aug 2017 06:09:20 -0700 (PDT) From: Ricardo Wurmus To: 28109@debbugs.gnu.org Subject: [PATCH 07/10] gnu: Add r-fitdistrplus. Date: Wed, 16 Aug 2017 15:08:56 +0200 Message-Id: <20170816130859.15069-7-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170816130859.15069-1-rekado@elephly.net> References: <20170816130859.15069-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-fitdistrplus): 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 746c778b2..134139017 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -819,3 +819,31 @@ It includes banded and tridiagonal linear systems. The package calls Fortran functions from LINPACK.") ;; Any GPL version. (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-fitdistrplus + (package + (name "r-fitdistrplus") + (version "1.0-9") + (source + (origin + (method url-fetch) + (uri (cran-uri "fitdistrplus" version)) + (sha256 + (base32 + "18x9454g598d54763k3hvi33iszifk7sxvhd1zg5r8z1vpixx3z6")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-survival" ,r-survival))) + (home-page "http://riskassessment.r-forge.r-project.org") + (synopsis "Fitting a parametric distribution from data") + (description + "This package extends the @code{fitdistr} function of the MASS package +with several functions to help the fit of a parametric distribution to +non-censored or censored data. Censored data may contain left-censored, +right-censored and interval-censored values, with several lower and upper +bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package +provides moment matching (MME), quantile matching (QME) and maximum +goodness-of-fit estimation (MGE) methods (available only for non-censored +data). Weighted versions of MLE, MME and QME are available.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 09:09:29 2017 Received: (at 28109) by debbugs.gnu.org; 16 Aug 2017 13:09:29 +0000 Received: from localhost ([127.0.0.1]:40370 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4e-0004rd-QQ for submit@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:28 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21121) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4d-0004rQ-HA for 28109@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:27 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502888963197811.2734560132358; Wed, 16 Aug 2017 06:09:23 -0700 (PDT) From: Ricardo Wurmus To: 28109@debbugs.gnu.org Subject: [PATCH 08/10] gnu: Add r-energy. Date: Wed, 16 Aug 2017 15:08:57 +0200 Message-Id: <20170816130859.15069-8-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170816130859.15069-1-rekado@elephly.net> References: <20170816130859.15069-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-energy): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 134139017..ce2c2b531 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -847,3 +847,32 @@ provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.") (license license:gpl2+))) + +(define-public r-energy + (package + (name "r-energy") + (version "1.7-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "energy" version)) + (sha256 + (base32 + "1g4hqi6mgsnd1w4q7dd2m40ljh2jdmvad91ksbq9fscnrqpvji1x")))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot) + ("r-rcpp" ,r-rcpp))) + (home-page "http://cran.r-project.org/web/packages/energy") + (synopsis "Multivariate inference via the energy of data") + (description + "This package provides e-statistics (energy) tests and statistics for +multivariate and univariate inference, including distance correlation, +one-sample, two-sample, and multi-sample tests for comparing multivariate +distributions, are implemented. Measuring and testing multivariate +independence based on distance correlation, partial distance correlation, +multivariate goodness-of-fit tests, clustering based on energy distance, +testing for multivariate normality, distance components (disco) for +non-parametric analysis of structured data, and other energy +statistics/methods are implemented.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 09:09:31 2017 Received: (at 28109) by debbugs.gnu.org; 16 Aug 2017 13:09:31 +0000 Received: from localhost ([127.0.0.1]:40373 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4h-0004rt-1N for submit@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:31 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21031) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4e-0004rX-Bh for 28109@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:28 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502888965933838.2985560345372; Wed, 16 Aug 2017 06:09:25 -0700 (PDT) From: Ricardo Wurmus To: 28109@debbugs.gnu.org Subject: [PATCH 09/10] gnu: Add r-suppdists. Date: Wed, 16 Aug 2017 15:08:58 +0200 Message-Id: <20170816130859.15069-9-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170816130859.15069-1-rekado@elephly.net> References: <20170816130859.15069-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-suppdists): 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 ce2c2b531..d1f684e37 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -876,3 +876,27 @@ testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.") (license license:gpl2+))) + +(define-public r-suppdists + (package + (name "r-suppdists") + (version "1.1-9.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "SuppDists" version)) + (sha256 + (base32 + "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw")))) + (properties `((upstream-name . "SuppDists"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/SuppDists") + (synopsis "Supplementary distributions") + (description + "This package provides ten distributions supplementing those built into +R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, +Spearman's rho, maximum F ratio, the Pearson product moment correlation +coefficient, Johnson distributions, normal scores and generalized +hypergeometric distributions. In addition two random number generators of +George Marsaglia are included.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 09:09:31 2017 Received: (at 28109) by debbugs.gnu.org; 16 Aug 2017 13:09:31 +0000 Received: from localhost ([127.0.0.1]:40375 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4h-0004rv-9c for submit@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:31 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21045) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy4f-0004re-8G for 28109@debbugs.gnu.org; Wed, 16 Aug 2017 09:09:29 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502888968426453.8310864053336; Wed, 16 Aug 2017 06:09:28 -0700 (PDT) From: Ricardo Wurmus To: 28109@debbugs.gnu.org Subject: [PATCH 10/10] gnu: Add r-ksamples. Date: Wed, 16 Aug 2017 15:08:59 +0200 Message-Id: <20170816130859.15069-10-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170816130859.15069-1-rekado@elephly.net> References: <20170816130859.15069-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-ksamples): 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 d1f684e37..bb7576352 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -900,3 +900,31 @@ coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions. In addition two random number generators of George Marsaglia are included.") (license license:gpl2+))) + +(define-public r-ksamples + (package + (name "r-ksamples") + (version "1.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "kSamples" version)) + (sha256 + (base32 + "1pbam0zqq44slpxdgl2s2fsfdgl7i0pgm8bzlvnm0fy0na24bgdj")))) + (properties `((upstream-name . "kSamples"))) + (build-system r-build-system) + (propagated-inputs + `(("r-suppdists" ,r-suppdists))) + (home-page "http://cran.r-project.org/web/packages/kSamples") + (synopsis "K-Sample rank tests and their combinations") + (description + "This package provides tools to compares k samples using the +Anderson-Darling test, Kruskal-Wallis type tests with different rank score +criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) +test. It computes asymptotic, simulated or (limited) exact P-values, all +valid under randomization, with or without ties, or conditionally under random +sampling from populations, given the observed tie pattern. Except for Steel's +test and the JT test it also combines these tests across several blocks of +samples.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 16 09:12:00 2017 Received: (at 28109) by debbugs.gnu.org; 16 Aug 2017 13:12:00 +0000 Received: from localhost ([127.0.0.1]:40394 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy76-0004x5-3b for submit@debbugs.gnu.org; Wed, 16 Aug 2017 09:12:00 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21066) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhy74-0004wv-8G for 28109@debbugs.gnu.org; Wed, 16 Aug 2017 09:11:58 -0400 Received: from localhost (141.80.247.215 [141.80.247.215]) by mx.zohomail.com with SMTPS id 1502889114155442.80420116165044; Wed, 16 Aug 2017 06:11:54 -0700 (PDT) References: <20170816125620.10140-1-rekado@elephly.net> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: 28109@debbugs.gnu.org Subject: Re: [PATCH 00/11] Some more R things In-reply-to: <20170816125620.10140-1-rekado@elephly.net> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Wed, 16 Aug 2017 15:11:51 +0200 Message-ID: <87r2wbk67c.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) Ricardo Wurmus writes: > gnu: r-trimcluster: Update license. > gnu: Add r-emdbook. > gnu: Add r-fastseg. > gnu: Add r-qvalue. > gnu: Add r-methylkit. My git repo got corrupted again(!) so I had to remove this commit. Will add it later. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 17 12:03:15 2017 Received: (at 28109-done) by debbugs.gnu.org; 17 Aug 2017 16:03:15 +0000 Received: from localhost ([127.0.0.1]:42989 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1diNGN-0001ls-0A for submit@debbugs.gnu.org; Thu, 17 Aug 2017 12:03:15 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21084) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1diNGL-0001ll-PM for 28109-done@debbugs.gnu.org; Thu, 17 Aug 2017 12:03:14 -0400 Received: from localhost (141.80.245.197 [141.80.245.197]) by mx.zohomail.com with SMTPS id 1502985789657588.882141589646; Thu, 17 Aug 2017 09:03:09 -0700 (PDT) References: <20170816130859.15069-1-rekado@elephly.net> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: 28109-done@debbugs.gnu.org Subject: Re: [PATCH 01/10] gnu: r-trimcluster: Update license. In-reply-to: <20170816130859.15069-1-rekado@elephly.net> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 17 Aug 2017 18:03:06 +0200 Message-ID: <8760dmji6d.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28109-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 (+) I’ve pushed these patches to master. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From unknown Tue Jun 24 22:35:30 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, 15 Sep 2017 11:24:04 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator