From: Naga Malleswari <nagamalli@riseup.net>
To: Ricardo Wurmus <rekado@elephly.net>
Cc: "Danny Milosavljevic" <dannym@scratchpost.org>,
"Gábor Boskovits" <boskovits@gmail.com>,
40779@debbugs.gnu.org
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)
Date: Fri, 24 Apr 2020 02:15:10 +0530 [thread overview]
Message-ID: <a6ae6747-28d6-5e44-9f1c-b38066c978ba@riseup.net> (raw)
In-Reply-To: <87368ukzjo.fsf@elephly.net>
[-- 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
[-- Attachment #2: 0009-gnu-Add-r-rxnat.patch --]
[-- Type: text/x-patch, Size: 1625 bytes --]
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 --]
[-- Type: text/x-patch, Size: 1641 bytes --]
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 --]
[-- Type: text/x-patch, Size: 1605 bytes --]
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 --]
[-- Type: text/x-patch, Size: 1501 bytes --]
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 --]
[-- Type: text/x-patch, Size: 1461 bytes --]
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 --]
[-- Type: text/x-patch, Size: 2056 bytes --]
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 --]
[-- Type: text/x-patch, Size: 1652 bytes --]
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
next prev parent reply other threads:[~2020-04-23 20:46 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-04-22 19:40 [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
[not found] ` <handler.40779.B.158758445324052.ack@debbugs.gnu.org>
2020-04-22 20:04 ` [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
2020-04-23 15:11 ` Ricardo Wurmus
2020-04-23 20:45 ` Naga Malleswari [this message]
2020-04-24 14:00 ` bug#40779: [Version 2] : bug#40779: " Ricardo Wurmus
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