From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:470:142:3::10]:34638) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jRLcP-0004wY-53 for guix-patches@gnu.org; Wed, 22 Apr 2020 16:05:29 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.90_1) (envelope-from ) id 1jRLcH-0002mb-LU for guix-patches@gnu.org; Wed, 22 Apr 2020 16:05:12 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:41840) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1jRLcE-0002i3-Oo for guix-patches@gnu.org; Wed, 22 Apr 2020 16:05:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jRLcE-0006xP-HZ for guix-patches@gnu.org; Wed, 22 Apr 2020 16:05:02 -0400 Subject: [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> From: Naga Malleswari Message-ID: Date: Thu, 23 Apr 2020 01:34:11 +0530 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/mixed; boundary="------------2A44BD8E34A7629FB4C00A2E" 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: 40779@debbugs.gnu.org, Danny Milosavljevic , Ricardo Wurmus Cc: =?UTF-8?Q?G=C3=A1bor?= Boskovits This is a multi-part message in MIME format. --------------2A44BD8E34A7629FB4C00A2E Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit Submitting Patches for CRAN PACKAGES r-dcv r-stam r-grouped r-sgloptim r-awsmethods r-aws r-tea r-rcdd r-rxnat I have done these patches earlier while practice. Submitting them to the guix system. On 23/04/20 1:11 am, GNU bug Tracking System wrote: > Thank you for filing a new bug report with debbugs.gnu.org. > > This is an automatically generated reply to let you know your message > has been received. > > Your message is being forwarded to the package maintainers and other > interested parties for their attention; they will reply in due course. > > Your message has been sent to the package maintainer(s): > guix-patches@gnu.org > > If you wish to submit further information on this problem, please > send it to 40779@debbugs.gnu.org. > > Please do not send mail to help-debbugs@gnu.org unless you wish > to report a problem with the Bug-tracking system. > -- Regards NagaMalli --------------2A44BD8E34A7629FB4C00A2E 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 4812d174a235f5f545f5d7109df427fee341813a Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Thu, 23 Apr 2020 01:29:26 +0530 Subject: [PATCH 9/9] gnu: Add r-rxnat. * gnu/packages/cran.scm (r-rxnat): 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 b6a9a88067..09a561e219 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21375,3 +21375,29 @@ 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 + "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 --------------2A44BD8E34A7629FB4C00A2E 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 3fae8711be15ff332d5378a33de34b5fd70bb2af Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Thu, 23 Apr 2020 01:28:31 +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 e4efa402d5..b6a9a88067 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21349,3 +21349,29 @@ 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 + "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 --------------2A44BD8E34A7629FB4C00A2E 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 b1bb80e24748cf63f075dcf1e749f2b7ae559478 Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Thu, 23 Apr 2020 01:24:04 +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 a2949d9d6e..e4efa402d5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21324,3 +21324,28 @@ at Random assumption.") to conduct Spatio-Temporal 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 --------------2A44BD8E34A7629FB4C00A2E 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 9906a033dfae2e4a7e5c482d4719166f8e3d3730 Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Thu, 23 Apr 2020 01:22:22 +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 2f4d53c970..93e691a26b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21276,3 +21276,26 @@ 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 + "Regression models for grouped and coarse data, under the Coarsened +at Random assumption.") + (license license:gpl2+))) -- 2.25.1 --------------2A44BD8E34A7629FB4C00A2E 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 574f7921578ef96a2d1fbe82a73c1164f6fb746f Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Thu, 23 Apr 2020 01:23:07 +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 93e691a26b..a2949d9d6e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21299,3 +21299,28 @@ doParallel packages.") "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 + "Stam is an evolving package that target on the 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 --------------2A44BD8E34A7629FB4C00A2E 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 e45c000e1ac6c4c73358f2a32aa7f8ca3c92178d Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Thu, 23 Apr 2020 01:21:19 +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 5f55fd62d4..2f4d53c970 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21240,3 +21240,39 @@ 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+))) + +(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 --------------2A44BD8E34A7629FB4C00A2E 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 4fa46cd6fd5fd00b0c81a302d61d72bfd293cccc Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Thu, 23 Apr 2020 01:20:01 +0530 Subject: [PATCH 3/9] gnu: Add r-aws. * gnu/packages/cran.scm (r-aws): 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 c856d133b7..5f55fd62d4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21212,3 +21212,31 @@ GPD-GoF-tests is also implemented here.") "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+))) + +(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 + "We 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 --------------2A44BD8E34A7629FB4C00A2E 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 0de70a861633665a4e971901f2ae4ea38c104b3e Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Thu, 23 Apr 2020 01:15:40 +0530 Subject: [PATCH 2/9] gnu: Add r-awsmethods. * gnu/packages/cran.scm (r-awsmethods): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ac55916964..c856d133b7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21191,3 +21191,24 @@ 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))) + +(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 + "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 --------------2A44BD8E34A7629FB4C00A2E 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 de01c0bceaee3062d32fdca209bc35280695d1cd Mon Sep 17 00:00:00 2001 From: Naga Malleswari Date: Thu, 23 Apr 2020 01:13:12 +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..ac55916964 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 + "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 --------------2A44BD8E34A7629FB4C00A2E--