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)

From: Naga Malleswari <[email-masked]>
Date: Fri, 24 Apr 2020 02:15:10 +0530

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

>From bf3b617dd6c8b82d815cbab9c5454a10cb4a4c4f Mon Sep 17 00:00:00 2001
From: Naga Malleswari <[email-masked]>
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

>From 7d8e09d4639408bb5c17264b2f4e42170828a80f Mon Sep 17 00:00:00 2001
From: Naga Malleswari <[email-masked]>
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

>From a787d8cd05692aa735a8ec44107576d425544dfd Mon Sep 17 00:00:00 2001
From: Naga Malleswari <[email-masked]>
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

>From f6ea5603e055016110f6e5878e16f3fa9dc757f1 Mon Sep 17 00:00:00 2001
From: Naga Malleswari <[email-masked]>
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

>From 0f5232af043d4e4f40a969b7082dc9f03db29c6e Mon Sep 17 00:00:00 2001
From: Naga Malleswari <[email-masked]>
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

>From 3ca8422b32f99e2a0ddd80e57366aef82fd16942 Mon Sep 17 00:00:00 2001
From: Naga Malleswari <[email-masked]>
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

>From d3f583206b2e83b3e6737db507fd76093caea39d Mon Sep 17 00:00:00 2001
From: Naga Malleswari <[email-masked]>
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

>From d2668306231f0be731a32aaf87118b00f8aecf7f Mon Sep 17 00:00:00 2001
From: Naga Malleswari <[email-masked]>
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

>From 717f18057715559f4c847b3a7171a7e5095b7418 Mon Sep 17 00:00:00 2001
From: Naga Malleswari <[email-masked]>
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