[bug#40779] Submission of CRAN Package Descriptions r-dcv r-stam r-grouped r-sgloptim r-awsmethods r-aws r-tea r-rcdd r-rxnat

[bug#40779] Submission of CRAN Package Descriptions r-dcv r-stam r-grouped r-sgloptim r-awsmethods r-aws r-tea r-rcdd r-rxnat

[Naga Malleswari]

I am writing a cover letter to generate bug ID to submit multiple patches

r-dcv

r-stam

r-grouped

r-sgloptim

r-awsmethods

r-aws

r-tea

r-rcdd

r-rxnat


-- 
Regards
NagaMalli

[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)

[Naga Malleswari]

[-- Attachment #1: Type: text/plain, Size: 899 bytes --]

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


[-- Attachment #2: 0009-gnu-Add-r-rxnat.patch --]
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From 4812d174a235f5f545f5d7109df427fee341813a Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #3: 0008-gnu-Add-r-rcdd.patch --]
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From 3fae8711be15ff332d5378a33de34b5fd70bb2af Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #4: 0007-gnu-Add-r-dcv.patch --]
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From b1bb80e24748cf63f075dcf1e749f2b7ae559478 Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #5: 0005-gnu-Add-r-grouped.patch --]
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From 9906a033dfae2e4a7e5c482d4719166f8e3d3730 Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #6: 0006-gnu-Add-r-stam.patch --]
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From 574f7921578ef96a2d1fbe82a73c1164f6fb746f Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


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From e45c000e1ac6c4c73358f2a32aa7f8ca3c92178d Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #8: 0003-gnu-Add-r-aws.patch --]
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From 4fa46cd6fd5fd00b0c81a302d61d72bfd293cccc Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


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[-- Type: text/x-patch, Size: 1465 bytes --]

From 0de70a861633665a4e971901f2ae4ea38c104b3e Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


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From de01c0bceaee3062d32fdca209bc35280695d1cd Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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

[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)

[Ricardo Wurmus]

Hi NagaMalli,

thank you for your patches!

Please run “./pre-inst-env guix lint” on each of the packages.  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.

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.

Could you please send updated patches as a reply to this email thread?

Thank you!

--
Ricardo

[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)

[Naga Malleswari]

[-- Attachment #1: Type: text/plain, Size: 1218 bytes --]

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


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From bf3b617dd6c8b82d815cbab9c5454a10cb4a4c4f Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #3: 0008-gnu-Add-r-rcdd.patch --]
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From 7d8e09d4639408bb5c17264b2f4e42170828a80f Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #4: 0007-gnu-Add-r-dcv.patch --]
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From a787d8cd05692aa735a8ec44107576d425544dfd Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #5: 0006-gnu-Add-r-stam.patch --]
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From f6ea5603e055016110f6e5878e16f3fa9dc757f1 Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #6: 0005-gnu-Add-r-grouped.patch --]
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From 0f5232af043d4e4f40a969b7082dc9f03db29c6e Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #7: 0004-gnu-Add-r-sgloptim.patch --]
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From 3ca8422b32f99e2a0ddd80e57366aef82fd16942 Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #8: 0003-gnu-Add-r-aws.patch --]
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From d3f583206b2e83b3e6737db507fd76093caea39d Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #9: 0002-gnu-Add-r-awsmethods.patch --]
[-- Type: text/x-patch, Size: 1464 bytes --]

From d2668306231f0be731a32aaf87118b00f8aecf7f Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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


[-- Attachment #10: 0001-gnu-Add-r-tea.patch --]
[-- Type: text/x-patch, Size: 1862 bytes --]

From 717f18057715559f4c847b3a7171a7e5095b7418 Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
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

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)

[Ricardo Wurmus]

Hi,

thank you for the updated patches.

I applied all of them with a number of changes:

* the indentation of a number of patches was incorrect and had to be
  adjusted
* there were a few typos and spacing issues (e.g. missing space after
  comma) in descriptions
* I changed the home page of one package from the author’s home page to
  the package page on CRAN
* a synopsis missed an important word
* I used HTTPS were possible

Thanks again!

--
Ricardo