From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:470:142:3::10]:60666) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jRijV-00007Y-EW for guix-patches@gnu.org; Thu, 23 Apr 2020 16:46:10 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.90_1) (envelope-from ) id 1jRijT-0006M6-RB for guix-patches@gnu.org; Thu, 23 Apr 2020 16:46:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:44377) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1jRijT-0006Lw-8a for guix-patches@gnu.org; Thu, 23 Apr 2020 16:46:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jRijS-0008SR-4D for guix-patches@gnu.org; Thu, 23 Apr 2020 16:46:02 -0400 Subject: [bug#40779] [Version 2] : bug#40779: Acknowledgement (Submission of CRAN Package Descriptions r-dcv r-stam r-grouped r-sgloptim r-awsmethods r-aws r-tea r-rcdd r-rxnat) Resent-Message-ID: References: <16bc2796-7e78-a7a5-7962-1c220752904a@riseup.net> <87368ukzjo.fsf@elephly.net> From: Naga Malleswari Message-ID: Date: Fri, 24 Apr 2020 02:15:10 +0530 MIME-Version: 1.0 In-Reply-To: <87368ukzjo.fsf@elephly.net> Content-Type: multipart/mixed; boundary="------------FA544175A58990B4D04A8764" Content-Language: en-US List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: Ricardo Wurmus Cc: Danny Milosavljevic , =?UTF-8?Q?G=C3=A1bor?= Boskovits , 40779@debbugs.gnu.org This is a multi-part message in MIME format. --------------FA544175A58990B4D04A8764 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Hi On 23/04/20 8:41 pm, Ricardo Wurmus wrote: > Hi NagaMalli, > > thank you for your patches! > > Please run “./pre-inst-env guix lint” on each of the packages. Yes i actually done lint adding all packages which i realized i have to do it individually. This took me so long to finish the edits. > Please > pay special attention to the description and synopsis fields. The > descriptions often contain sentence fragments – we prefer to have > complete sentences. Make sure that there are two spaces after end of > sentence periods — not zero spaces and not just one space either. I made the changes as per the suggestions. > For the synopses please only capitalize proper names (like “Bayes”) and > the first word. CRAN packages use capitalization for all words, so we > need to change that. > > Please also run etc/indent-code.el to fix the indentation. The importer > doesn’t do the right thing because it doesn’t know about our > conventions. I have done and it worked for individual packages > Could you please send updated patches as a reply to this email thread? > > Thank you! And lastly i built everything and sending the patches. Please review. > -- > Ricardo -- Regards NagaMalli --------------FA544175A58990B4D04A8764 Content-Type: text/x-patch; charset=UTF-8; name="0009-gnu-Add-r-rxnat.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0009-gnu-Add-r-rxnat.patch" >From bf3b617dd6c8b82d815cbab9c5454a10cb4a4c4f Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Fri, 24 Apr 2020 02:08:12 +0530 Subject: [PATCH 9/9] gnu: Add r-rxnat. * gnu/packages/cran.scm (r-rxnat): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b9a62aa932..ba635854c5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21377,3 +21377,30 @@ and as convex hull of set of points and rays. Also does linear programming and redundant generator elimination. All functions can use exact infinite-precision rational arithmetic.") (license license:gpl2))) + +(define-public r-rxnat + (package + (name "r-rxnat") + (version "1.0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rxnat" version)) + (sha256 + (base32 + "12xcs2l6vn50bwzfmv60j1qahjw2npfm1a3yjhffcxzh6p8chwbg")))) + (properties + `((upstream-name . "Rxnat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-httr" ,r-httr) + ("r-rcurl" ,r-rcurl))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/Rxnat") + (synopsis "Queries and extracts images from extensible neuroimaging archive toolkit") + (description + "This package allows communication with extensible neuroimaging archive +toolkit. Rxnat uses the XNAT REST API to perform data queries and download +images.") + (license license:gpl2))) -- 2.25.1 --------------FA544175A58990B4D04A8764 Content-Type: text/x-patch; charset=UTF-8; name="0008-gnu-Add-r-rcdd.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0008-gnu-Add-r-rcdd.patch" >From 7d8e09d4639408bb5c17264b2f4e42170828a80f Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Fri, 24 Apr 2020 02:03:20 +0530 Subject: [PATCH 8/9] gnu: Add r-rcdd. * gnu/packages/cran.scm (r-rcdd): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 44c47839bd..b9a62aa932 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21351,3 +21351,29 @@ methods for climate-growth model in the climate reconstruction from tree rings, including Sign Test statistic, Reduction of Error statistic, Product Mean Test, Durbin-Watson statistic etc.") (license license:gpl2))) + +(define-public r-rcdd + (package + (name "r-rcdd") + (version "1.2-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rcdd" version)) + (sha256 + (base32 + "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric")))) + (properties + `((upstream-name . "rcdd"))) + (build-system r-build-system) + (inputs + `(("gmp" ,gmp))) + (home-page "http://www.stat.umn.edu/geyer/rcdd/") + (synopsis "Computational Geometry") + (description + "This package converts back and forth between two representations of a +convex polytope: as solution of a set of linear equalities and inequalities +and as convex hull of set of points and rays. Also does linear programming +and redundant generator elimination. All functions can use exact +infinite-precision rational arithmetic.") + (license license:gpl2))) -- 2.25.1 --------------FA544175A58990B4D04A8764 Content-Type: text/x-patch; charset=UTF-8; name="0007-gnu-Add-r-dcv.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0007-gnu-Add-r-dcv.patch" >From a787d8cd05692aa735a8ec44107576d425544dfd Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Fri, 24 Apr 2020 01:58:15 +0530 Subject: [PATCH 7/9] gnu: Add r-dcv. * gnu/packages/cran.scm (r-dcv): 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 156f1faba0..44c47839bd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21326,3 +21326,28 @@ under the coarsened at random assumption.") Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and Inferred Spatio-Temporal Modelling.") (license license:gpl2+))) + +(define-public r-dcv + (package + (name "r-dcv") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "dcv" version)) + (sha256 + (base32 + "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj")))) + (properties + `((upstream-name . "dcv"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lmtest" ,r-lmtest))) + (home-page "https://cran.r-project.org/web/packages/dcv") + (synopsis "Conventional cross-validation statistics for climate-growth model") + (description + "This package performs several conventional cross-validation statistical +methods for climate-growth model in the climate reconstruction from +tree rings, including Sign Test statistic, Reduction of Error statistic, +Product Mean Test, Durbin-Watson statistic etc.") + (license license:gpl2))) -- 2.25.1 --------------FA544175A58990B4D04A8764 Content-Type: text/x-patch; charset=UTF-8; name="0006-gnu-Add-r-stam.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0006-gnu-Add-r-stam.patch" >From f6ea5603e055016110f6e5878e16f3fa9dc757f1 Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Fri, 24 Apr 2020 01:51:33 +0530 Subject: [PATCH 6/9] gnu: Add r-stam. * gnu/packages/cran.scm (r-stam): 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 e913bac48a..156f1faba0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21301,3 +21301,28 @@ doParallel packages.") "This package provides regression models for grouped and coarse data, under the coarsened at random assumption.") (license license:gpl2+))) + +(define-public r-stam + (package + (name "r-stam") + (version "0.0-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "stam" version)) + (sha256 + (base32 + "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv")))) + (properties + `((upstream-name . "stam"))) + (build-system r-build-system) + (propagated-inputs + `(("r-np" ,r-np) + ("r-sp" ,r-sp))) + (home-page "https://cran.r-project.org/web/packages/stam") + (synopsis "Spatio-Temporal analysis and modelling") + (description + "This package provide various methods to conduct Spatio-Temporal +Analysis and Modelling, including Exploratory Spatio-Temporal Analysis +and Inferred Spatio-Temporal Modelling.") + (license license:gpl2+))) -- 2.25.1 --------------FA544175A58990B4D04A8764 Content-Type: text/x-patch; charset=UTF-8; name="0005-gnu-Add-r-grouped.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0005-gnu-Add-r-grouped.patch" >From 0f5232af043d4e4f40a969b7082dc9f03db29c6e Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Fri, 24 Apr 2020 01:43:29 +0530 Subject: [PATCH 5/9] gnu: Add r-grouped. * gnu/packages/cran.scm (r-grouped): 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 28dc2b86a8..e913bac48a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21278,3 +21278,26 @@ applicable to a broad class of loss functions. Use of parallel computing for cross validation and subsampling is supported through the foreach and doParallel packages.") (license license:gpl2+))) + +(define-public r-grouped + (package + (name "r-grouped") + (version "0.6-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "grouped" version)) + (sha256 + (base32 + "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976")))) + (properties + `((upstream-name . "grouped"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/grouped") + (synopsis "Regression analysis of grouped and coarse data") + (description + "This package provides regression models for grouped and coarse data, +under the coarsened at random assumption.") + (license license:gpl2+))) -- 2.25.1 --------------FA544175A58990B4D04A8764 Content-Type: text/x-patch; charset=UTF-8; name="0004-gnu-Add-r-sgloptim.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0004-gnu-Add-r-sgloptim.patch" >From 3ca8422b32f99e2a0ddd80e57366aef82fd16942 Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Fri, 24 Apr 2020 01:37:05 +0530 Subject: [PATCH 4/9] gnu: Add r-sgloptim. * gnu/packages/cran.scm (r-sgloptim): New variable. --- gnu/packages/cran.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 627201796f..28dc2b86a8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21242,3 +21242,39 @@ Propagation-Separation Approach to adaptive smoothing, the Intersecting Confidence Intervals (@dfn{ICI}), variational approaches and a non-local means filter.") (license license:gpl2+))) + +(define-public r-sgloptim + (package + (name "r-sgloptim") + (version "1.3.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "sglOptim" version)) + (sha256 + (base32 + "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr")))) + (properties + `((upstream-name . "sglOptim"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rcppprogress" ,r-rcppprogress))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/nielsrhansen/sglOptim") + (synopsis "Generic sparse group Lasso solver") + (description + "Fast generic solver for sparse group lasso optimization problems. +The loss (objective) function must be defined in a C++ module. The +optimization problem is solved using a coordinate gradient descent +algorithm. Convergence of the algorithm is established and the algorithm is +applicable to a broad class of loss functions. Use of parallel computing for +cross validation and subsampling is supported through the foreach and +doParallel packages.") + (license license:gpl2+))) -- 2.25.1 --------------FA544175A58990B4D04A8764 Content-Type: text/x-patch; charset=UTF-8; name="0003-gnu-Add-r-aws.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0003-gnu-Add-r-aws.patch" >From d3f583206b2e83b3e6737db507fd76093caea39d Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Fri, 24 Apr 2020 01:32:33 +0530 Subject: [PATCH 3/9] gnu: Add r-aws. * gnu/packages/cran.scm (r-aws): 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 912a42190c..627201796f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21213,3 +21213,32 @@ is also implemented here.") support as needed in several packages like @code{aws},@code{adimpro}, @code{fmri},@code{dwi}.") (license license:gpl2+))) + +(define-public r-aws + (package + (name "r-aws") + (version "2.4-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "aws" version)) + (sha256 + (base32 + "1czlsy64nx6j7h1smgb561yyv3f98pwqwglk77yla4mx3fp14bvq")))) + (properties + `((upstream-name . "aws"))) + (build-system r-build-system) + (propagated-inputs + `(("r-awsmethods" ,r-awsmethods) + ("r-gsl" ,r-gsl))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://www.wias-berlin.de/people/polzehl/") + (synopsis "Adaptive weights smoothing") + (description + "This package provide a collection of R-functions implementing +adaptive smoothing procedures in 1D, 2D and 3D. This includes the +Propagation-Separation Approach to adaptive smoothing, the Intersecting +Confidence Intervals (@dfn{ICI}), variational approaches and a non-local +means filter.") + (license license:gpl2+))) -- 2.25.1 --------------FA544175A58990B4D04A8764 Content-Type: text/x-patch; charset=UTF-8; name="0002-gnu-Add-r-awsmethods.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0002-gnu-Add-r-awsmethods.patch" >From d2668306231f0be731a32aaf87118b00f8aecf7f Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Fri, 24 Apr 2020 01:27:55 +0530 Subject: [PATCH 2/9] gnu: Add r-awsmethods. * gnu/packages/cran.scm (r-awsmethods): 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 2dba2b0a93..912a42190c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21191,3 +21191,25 @@ is the number of data in the tail. The third class is motivated by graphical inspection. In addition, a sequential testing procedure for GPD-GoF-tests is also implemented here.") (license license:gpl3))) + +(define-public r-awsmethods + (package + (name "r-awsmethods") + (version "1.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "awsMethods" version)) + (sha256 + (base32 + "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh")))) + (properties + `((upstream-name . "awsMethods"))) + (build-system r-build-system) + (home-page "http://www.wias-berlin.de/software/imaging/") + (synopsis "Class and methods definitions") + (description + "This package defines the method extract and provides @code{openMP} +support as needed in several packages like @code{aws},@code{adimpro}, +@code{fmri},@code{dwi}.") + (license license:gpl2+))) -- 2.25.1 --------------FA544175A58990B4D04A8764 Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-Add-r-tea.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-r-tea.patch" >From 717f18057715559f4c847b3a7171a7e5095b7418 Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Fri, 24 Apr 2020 01:23:25 +0530 Subject: [PATCH 1/9] gnu: Add r-tea. * gnu/packages/cran.scm (r-tea): 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 70cb7cc700..2dba2b0a93 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21162,3 +21162,32 @@ evaluated interactively.") Bayes factors, posterior model probabilities, and normalizing constants in general, via different versions of bridge sampling.") (license license:gpl2+))) + +(define-public r-tea + (package + (name "r-tea") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tea" version)) + (sha256 + (base32 + "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn")))) + (properties + `((upstream-name . "tea"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix))) + (home-page "https://cran.r-project.org/web/packages/tea") + (synopsis "Threshold estimation approaches") + (description + "This package provide different approaches for selecting the threshold +in generalized Pareto distributions. Most of them are based on minimizing the +AMSE-criterion or atleast by reducing the bias of the assumed GPD-model. +Others are heuristically motivated by searching for stable sample paths, i.e. +a nearly constant region of the tail index estimator with respect to k, which +is the number of data in the tail. The third class is motivated by graphical +inspection. In addition, a sequential testing procedure for GPD-GoF-tests +is also implemented here.") + (license license:gpl3))) -- 2.25.1 --------------FA544175A58990B4D04A8764--