GNU bug report logs - #28089
[PATCH 00/29] More R packages.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: guix-patches <at> gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 00/29] More R packages.
Date: Mon, 14 Aug 2017 22:54:58 +0200

Hi Guix,

here is a series of R package definitions.

Ricardo Wurmus (29):
  gnu: Add r-interactivedisplaybase.
  gnu: Add r-annotationhub.
  gnu: Add r-auc.
  gnu: Add r-calibrate.
  gnu: Add r-shape.
  gnu: Add r-globaloptions.
  gnu: Add r-circlize.
  gnu: Add r-powerlaw.
  gnu: Add r-png.
  gnu: Add r-compare.
  gnu: Add r-dendextend.
  gnu: Add r-getoptlong.
  gnu: Add r-fastmatch.
  gnu: Add r-ff.
  gnu: Add r-ffbase.
  gnu: Add r-prettyunits.
  gnu: Add r-reshape.
  gnu: Add r-progress.
  gnu: Add r-ggally.
  gnu: Add r-proxy.
  gnu: Add r-sp.
  gnu: Add r-rook.
  gnu: Add r-rmtstat.
  gnu: Add r-lmoments.
  gnu: Add r-distillery.
  gnu: Add r-extremes.
  gnu: Add r-lmtest.
  gnu: Add r-inline.
  gnu: Add r-bbmle.

 gnu/packages/bioinformatics.scm |  58 ++++
 gnu/packages/cran.scm           | 588 +++++++++++++++++++++++++++++++++++++++-
 gnu/packages/image.scm          |  24 ++
 gnu/packages/web.scm            |  24 ++
 4 files changed, 693 insertions(+), 1 deletion(-)

-- 
2.13.3

Message #8 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 01/29] gnu: Add r-interactivedisplaybase.
Date: Mon, 14 Aug 2017 22:56:43 +0200

* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable.
---
 gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9d64294e4..717b5acec 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9229,6 +9229,30 @@ distributional differences between lanes (e.g., sequencing depth):
 global-scaling and full-quantile normalization.")
     (license license:artistic2.0)))
 
+(define-public r-interactivedisplaybase
+  (package
+    (name "r-interactivedisplaybase")
+    (version "1.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "interactiveDisplayBase" version))
+       (sha256
+        (base32
+         "12f6ap4bl3h2iwwhg8i3r9a7yyd28d8i5lb3fj1vnfvjs762r7r7"))))
+    (properties
+     `((upstream-name . "interactiveDisplayBase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-shiny" ,r-shiny)))
+    (home-page "http://bioconductor.org/packages/interactiveDisplayBase")
+    (synopsis "Base package for web displays of Bioconductor objects")
+    (description
+     "This package contains the basic methods needed to generate interactive
+Shiny-based display methods for Bioconductor objects.")
+    (license license:artistic2.0)))
+
 (define htslib-for-sambamba
   (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
     (package
-- 
2.13.3

Message #11 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 02/29] gnu: Add r-annotationhub.
Date: Mon, 14 Aug 2017 22:56:44 +0200

* gnu/packages/bioinformatics.scm (r-annotationhub): New variable.
---
 gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 717b5acec..3571cb96c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9253,6 +9253,40 @@ global-scaling and full-quantile normalization.")
 Shiny-based display methods for Bioconductor objects.")
     (license license:artistic2.0)))
 
+(define-public r-annotationhub
+  (package
+    (name "r-annotationhub")
+    (version "2.8.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "AnnotationHub" version))
+       (sha256
+        (base32
+         "1nh5si3j1nv37jcg4260582ayjg18851np47cskrm54prnvhwd9r"))))
+    (properties `((upstream-name . "AnnotationHub")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocinstaller" ,r-biocinstaller)
+       ("r-httr" ,r-httr)
+       ("r-interactivedisplaybase" ,r-interactivedisplaybase)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-yaml" ,r-yaml)))
+    (home-page "http://bioconductor.org/packages/AnnotationHub")
+    (synopsis "Client to access AnnotationHub resources")
+    (description
+     "This package provides a client for the Bioconductor AnnotationHub web
+resource.  The AnnotationHub web resource provides a central location where
+genomic files (e.g. VCF, bed, wig) and other resources from standard
+locations (e.g. UCSC, Ensembl) can be discovered.  The resource includes
+metadata about each resource, e.g., a textual description, tags, and date of
+modification.  The client creates and manages a local cache of files retrieved
+by the user, helping with quick and reproducible access.")
+    (license license:artistic2.0)))
+
 (define htslib-for-sambamba
   (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
     (package
-- 
2.13.3

Message #14 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 03/29] gnu: Add r-auc.
Date: Mon, 14 Aug 2017 22:56:45 +0200

* gnu/packages/cran.scm (r-auc): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index feae80111..c874ff880 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -148,3 +148,27 @@ where the bound function accepts additional arguments.")
      "This package provides an easy way to fill an environment with active
 bindings that call a C++ function.")
     (license license:expat)))
+
+(define-public r-auc
+  (package
+    (name "r-auc")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AUC" version))
+       (sha256
+        (base32
+         "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
+    (properties `((upstream-name . "AUC")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/AUC")
+    (synopsis "Compute the area under the curve of selected measures")
+    (description
+     "This package includes functions to compute the area under the curve of
+selected measures: the area under the sensitivity curve (AUSEC), the area
+under the specificity curve (AUSPC), the area under the accuracy
+curve (AUACC), and the area under the receiver operating characteristic
+curve (AUROC).  The curves can also be visualized.  Support for partial areas
+is provided.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #17 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 04/29] gnu: Add r-calibrate.
Date: Mon, 14 Aug 2017 22:56:46 +0200

* gnu/packages/cran.scm (r-calibrate): New variable.
---
 gnu/packages/cran.scm | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c874ff880..5ec8d4921 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21,7 +21,8 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix utils)
-  #:use-module (guix build-system r))
+  #:use-module (guix build-system r)
+  #:use-module (gnu packages statistics))
 
 (define-public r-colorspace
   (package
@@ -172,3 +173,24 @@ curve (AUACC), and the area under the receiver operating characteristic
 curve (AUROC).  The curves can also be visualized.  Support for partial areas
 is provided.")
     (license license:gpl2+)))
+
+(define-public r-calibrate
+  (package
+    (name "r-calibrate")
+    (version "1.7.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "calibrate" version))
+       (sha256
+        (base32
+         "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)))
+    (home-page "http://cran.r-project.org/web/packages/calibrate")
+    (synopsis "Calibration of scatterplot and biplot axes")
+    (description
+     "This is a package for drawing calibrated scales with tick marks
+on (non-orthogonal) variable vectors in scatterplots and biplots.")
+    (license license:gpl2)))
-- 
2.13.3

Message #20 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 05/29] gnu: Add r-shape.
Date: Mon, 14 Aug 2017 22:56:47 +0200

* gnu/packages/cran.scm (r-shape): New variable.
---
 gnu/packages/cran.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5ec8d4921..de7c56f6d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -194,3 +194,22 @@ is provided.")
      "This is a package for drawing calibrated scales with tick marks
 on (non-orthogonal) variable vectors in scatterplots and biplots.")
     (license license:gpl2)))
+
+(define-public r-shape
+  (package
+    (name "r-shape")
+    (version "1.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shape" version))
+       (sha256
+        (base32
+         "0yk3cmsa57svcvbnm21pyr0s0qbhnllka8nmsg4yb41frjlqph66"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/shape")
+    (synopsis "Functions for plotting graphical shapes")
+    (description
+     "This package provides functions for plotting graphical shapes such as
+ellipses, circles, cylinders, arrows, ...")
+    (license license:gpl3+)))
-- 
2.13.3

Message #23 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 06/29] gnu: Add r-globaloptions.
Date: Mon, 14 Aug 2017 22:56:48 +0200

* gnu/packages/cran.scm (r-globaloptions): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index de7c56f6d..7179ceb5c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -213,3 +213,23 @@ on (non-orthogonal) variable vectors in scatterplots and biplots.")
      "This package provides functions for plotting graphical shapes such as
 ellipses, circles, cylinders, arrows, ...")
     (license license:gpl3+)))
+
+(define-public r-globaloptions
+  (package
+    (name "r-globaloptions")
+    (version "0.0.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "GlobalOptions" version))
+       (sha256
+        (base32
+         "1abpc03cfvazbwj2sx6qgngs5pgpzysvxkana20hyvb4n7ws77f0"))))
+    (properties `((upstream-name . "GlobalOptions")))
+    (build-system r-build-system)
+    (home-page "https://github.com/jokergoo/GlobalOptions")
+    (synopsis "Generate functions to get or set global options")
+    (description
+     "This package provides more controls on the option values such as
+validation and filtering on the values, making options invisible or private.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #26 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 07/29] gnu: Add r-circlize.
Date: Mon, 14 Aug 2017 22:56:49 +0200

* gnu/packages/cran.scm (r-circlize): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7179ceb5c..0fc158768 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -233,3 +233,33 @@ ellipses, circles, cylinders, arrows, ...")
      "This package provides more controls on the option values such as
 validation and filtering on the values, making options invisible or private.")
     (license license:gpl2+)))
+
+(define-public r-circlize
+  (package
+    (name "r-circlize")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "circlize" version))
+       (sha256
+        (base32
+         "0p1zx1aawkblz48kzzfn5w1k3lbwv9wrk1k5gcfjrr2b4sz1pp5b"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-colorspace" ,r-colorspace)
+       ("r-globaloptions" ,r-globaloptions)
+       ("r-shape" ,r-shape)))
+    (home-page "https://github.com/jokergoo/circlize")
+    (synopsis "Circular visualization")
+    (description
+     "Circular layout is an efficient way for the visualization of huge
+amounts of information.  This package provides an implementation of circular
+layout generation in R as well as an enhancement of available software.  The
+flexibility of the package is based on the usage of low-level graphics
+functions such that self-defined high-level graphics can be easily implemented
+by users for specific purposes.  Together with the seamless connection between
+the powerful computational and visual environment in R, it gives users more
+convenience and freedom to design figures for better understanding complex
+patterns behind multiple dimensional data.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #29 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 08/29] gnu: Add r-powerlaw.
Date: Mon, 14 Aug 2017 22:56:50 +0200

* gnu/packages/cran.scm (r-powerlaw): 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 0fc158768..83f246d4d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -263,3 +263,28 @@ the powerful computational and visual environment in R, it gives users more
 convenience and freedom to design figures for better understanding complex
 patterns behind multiple dimensional data.")
     (license license:gpl2+)))
+
+(define-public r-powerlaw
+  (package
+    (name "r-powerlaw")
+    (version "0.70.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "poweRlaw" version))
+       (sha256
+        (base32
+         "1p2la3hslxq2xa8jkwvci6zcpn47cvyr9xqd5agp1riwwp2xw5gh"))))
+    (properties `((upstream-name . "poweRlaw")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-vgam" ,r-vgam)))
+    (home-page "https://github.com/csgillespie/poweRlaw")
+    (synopsis "Tools for the analysis of heavy tailed distributions")
+    (description
+     "This package provides an implementation of maximum likelihood estimators
+for a variety of heavy tailed distributions, including both the discrete and
+continuous power law distributions.  Additionally, a goodness-of-fit based
+approach is used to estimate the lower cut-off for the scaling region.")
+    ;; Any of these GPL versions.
+    (license (list license:gpl2 license:gpl3))))
-- 
2.13.3

Message #32 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 09/29] gnu: Add r-png.
Date: Mon, 14 Aug 2017 22:56:51 +0200

* gnu/packages/image.scm (r-png): New variable.
---
 gnu/packages/image.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 95a4c91b1..ad9ff4ee0 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -61,6 +61,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system r)
   #:use-module (srfi srfi-1))
 
 (define-public libpng
@@ -176,6 +177,29 @@ APNG patch provides APNG support to libpng.")
        (sha256
         (base32 "1n2lrzjkm5jhfg2bs10q398lkwbbx742fi27zgdgx0x23zhj0ihg"))))))
 
+(define-public r-png
+  (package
+    (name "r-png")
+    (version "0.1-7")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "png" version))
+              (sha256
+               (base32
+                "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
+    (build-system r-build-system)
+    (inputs
+     `(("libpng" ,libpng)
+       ("zlib" ,zlib)))
+    (home-page "http://www.rforge.net/png/")
+    (synopsis "Read and write PNG images")
+    (description
+     "This package provides an easy and simple way to read, write and display
+bitmap images stored in the PNG format.  It can read and write both files and
+in-memory raw vectors.")
+    ;; Any of these GPL versions.
+    (license (list license:gpl2 license:gpl3))))
+
 (define-public pngcrunch
   (package
    (name "pngcrunch")
-- 
2.13.3

Message #35 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 10/29] gnu: Add r-compare.
Date: Mon, 14 Aug 2017 22:56:52 +0200

* gnu/packages/cran.scm (r-compare): 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 83f246d4d..25f52a143 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -288,3 +288,24 @@ continuous power law distributions.  Additionally, a goodness-of-fit based
 approach is used to estimate the lower cut-off for the scaling region.")
     ;; Any of these GPL versions.
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-compare
+  (package
+    (name "r-compare")
+    (version "0.2-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "compare" version))
+       (sha256
+        (base32
+         "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/compare")
+    (synopsis "Comparing objects for differences")
+    (description
+     "This package provides functions to compare a model object to a
+comparison object.  If the objects are not identical, the functions can be
+instructed to explore various modifications of the objects (e.g., sorting
+rows, dropping names) to see if the modified versions are identical.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #38 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 11/29] gnu: Add r-dendextend.
Date: Mon, 14 Aug 2017 22:56:53 +0200

* gnu/packages/cran.scm (r-dendextend): 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 25f52a143..b2502e182 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -309,3 +309,32 @@ comparison object.  If the objects are not identical, the functions can be
 instructed to explore various modifications of the objects (e.g., sorting
 rows, dropping names) to see if the modified versions are identical.")
     (license license:gpl2+)))
+
+(define-public r-dendextend
+  (package
+    (name "r-dendextend")
+    (version "1.5.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "dendextend" version))
+       (sha256
+        (base32
+         "04jz58apibfrkjcrdmw2hmsav6qpb5cs6qdai81k1v1iznfcya42"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-fpc" ,r-fpc)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-magrittr" ,r-magrittr)
+       ("r-viridis" ,r-viridis)
+       ("r-whisker" ,r-whisker)))
+    (home-page "https://cran.r-project.org/web/packages/dendextend")
+    (synopsis "Extending 'dendrogram' functionality in R")
+    (description
+     "This package offers a set of functions for extending @code{dendrogram}
+objects in R, letting you visualize and compare trees of hierarchical
+clusterings.  You can adjust a tree's graphical parameters (the color, size,
+type, etc of its branches, nodes and labels) and visually and statistically
+compare different dendrograms to one another.")
+    ;; Any of these versions
+    (license (list license:gpl2 license:gpl3))))
-- 
2.13.3

Message #41 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 12/29] gnu: Add r-getoptlong.
Date: Mon, 14 Aug 2017 22:56:54 +0200

* gnu/packages/cran.scm (r-getoptlong): New variable.
---
 gnu/packages/cran.scm | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b2502e182..abdff54db 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22,7 +22,9 @@
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system r)
-  #:use-module (gnu packages statistics))
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages web))
 
 (define-public r-colorspace
   (package
@@ -338,3 +340,29 @@ type, etc of its branches, nodes and labels) and visually and statistically
 compare different dendrograms to one another.")
     ;; Any of these versions
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-getoptlong
+  (package
+    (name "r-getoptlong")
+    (version "0.1.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "GetoptLong" version))
+       (sha256
+        (base32
+         "1d98gcvlvp9nz5lbnzr0kkpc2hbkx74hlhrnybqhg1gdwc3g09pm"))))
+    (properties `((upstream-name . "GetoptLong")))
+    (build-system r-build-system)
+    (inputs
+     `(("perl" ,perl)))
+    (propagated-inputs
+     `(("r-globaloptions" ,r-globaloptions)
+       ("r-rjson" ,r-rjson)))
+    (home-page "https://github.com/jokergoo/GetoptLong")
+    (synopsis "Parsing command-line arguments and variable interpolation")
+    (description
+     "This is yet another command-line argument parser which wraps the
+powerful Perl module @code{Getopt::Long} and with some adaptation for easier
+use in R.  It also provides a simple way for variable interpolation in R.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #44 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 13/29] gnu: Add r-fastmatch.
Date: Mon, 14 Aug 2017 22:56:55 +0200

* gnu/packages/cran.scm (r-fastmatch): 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 abdff54db..c959beee0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -366,3 +366,24 @@ compare different dendrograms to one another.")
 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
 use in R.  It also provides a simple way for variable interpolation in R.")
     (license license:gpl2+)))
+
+(define-public r-fastmatch
+  (package
+    (name "r-fastmatch")
+    (version "1.1-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fastmatch" version))
+       (sha256
+        (base32
+         "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
+    (build-system r-build-system)
+    (home-page "http://www.rforge.net/fastmatch")
+    (synopsis "Fast match function")
+    (description
+     "This package provides a fast @code{match} replacement for cases that
+require repeated look-ups.  It is slightly faster that R's built-in
+@code{match} function on first match against a table, but extremely fast on
+any subsequent lookup as it keeps the hash table in memory.")
+    (license license:gpl2)))
-- 
2.13.3

Message #47 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 14/29] gnu: Add r-ff.
Date: Mon, 14 Aug 2017 22:56:56 +0200

* gnu/packages/cran.scm (r-ff): 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 c959beee0..b1cb0c409 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -387,3 +387,24 @@ require repeated look-ups.  It is slightly faster that R's built-in
 @code{match} function on first match against a table, but extremely fast on
 any subsequent lookup as it keeps the hash table in memory.")
     (license license:gpl2)))
+
+(define-public r-ff
+  (package
+    (name "r-ff")
+    (version "2.2-13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ff" version))
+       (sha256
+        (base32
+         "1nvd6kx46xzyc99a44mgynd94pvd2h495m5a7b1g67k5w2phiywb"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-bit" ,r-bit)))
+    (home-page "http://ff.r-forge.r-project.org/")
+    (synopsis "Memory-efficient storage of large data on disk and access functions")
+    (description
+     "This package provides data structures that are stored on disk but
+behave (almost) as if they were in RAM by transparently mapping only a section
+in main memory.")
+    (license license:gpl2)))
-- 
2.13.3

Message #50 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 15/29] gnu: Add r-ffbase.
Date: Mon, 14 Aug 2017 22:56:57 +0200

* gnu/packages/cran.scm (r-ffbase): 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 b1cb0c409..80ed0bc26 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -408,3 +408,26 @@ any subsequent lookup as it keeps the hash table in memory.")
 behave (almost) as if they were in RAM by transparently mapping only a section
 in main memory.")
     (license license:gpl2)))
+
+(define-public r-ffbase
+  (package
+    (name "r-ffbase")
+    (version "0.12.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ffbase" version))
+       (sha256
+        (base32
+         "1nz97bndxxkzp8rq6va8ff5ky9vkaib1jybm6j852awwb3n9had5"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bit" ,r-bit)
+       ("r-fastmatch" ,r-fastmatch)
+       ("r-ff" ,r-ff)))
+    (home-page "http://github.com/edwindj/ffbase")
+    (synopsis "Basic statistical functions for package 'ff'")
+    (description
+     "This package extends the out of memory vectors of @code{ff} with
+statistical functions and other utilities to ease their usage.")
+    (license license:gpl3)))
-- 
2.13.3

Message #53 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 16/29] gnu: Add r-prettyunits.
Date: Mon, 14 Aug 2017 22:56:58 +0200

* gnu/packages/cran.scm (r-prettyunits): 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 80ed0bc26..637ddfe4f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -431,3 +431,25 @@ in main memory.")
      "This package extends the out of memory vectors of @code{ff} with
 statistical functions and other utilities to ease their usage.")
     (license license:gpl3)))
+
+(define-public r-prettyunits
+  (package
+    (name "r-prettyunits")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "prettyunits" version))
+       (sha256
+        (base32
+         "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-assertthat" ,r-assertthat)
+       ("r-magrittr" ,r-magrittr)))
+    (home-page "https://github.com/gaborcsardi/prettyunits")
+    (synopsis "Pretty, human readable formatting of quantities")
+    (description
+     "This package provides tools for pretty, human readable formatting of
+quantities.")
+    (license license:expat)))
-- 
2.13.3

Message #56 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 17/29] gnu: Add r-reshape.
Date: Mon, 14 Aug 2017 22:56:59 +0200

* gnu/packages/cran.scm (r-reshape): 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 637ddfe4f..fa75317e9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -453,3 +453,25 @@ statistical functions and other utilities to ease their usage.")
      "This package provides tools for pretty, human readable formatting of
 quantities.")
     (license license:expat)))
+
+(define-public r-reshape
+  (package
+    (name "r-reshape")
+    (version "0.8.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "reshape" version))
+       (sha256
+        (base32
+         "1f1ngalc22knhdm9djv1m6abnjqpv1frdzxfkpakhph2l67bk7fq"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-plyr" ,r-plyr)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "http://had.co.nz/reshape")
+    (synopsis "Flexibly reshape data")
+    (description
+     "Flexibly restructure and aggregate data using just two functions:
+@code{melt} and @code{cast}.  This package provides them.")
+    (license license:expat)))
-- 
2.13.3

Message #59 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 18/29] gnu: Add r-progress.
Date: Mon, 14 Aug 2017 22:57:00 +0200

* gnu/packages/cran.scm (r-progress): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index fa75317e9..d88202ca5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -475,3 +475,27 @@ quantities.")
      "Flexibly restructure and aggregate data using just two functions:
 @code{melt} and @code{cast}.  This package provides them.")
     (license license:expat)))
+
+(define-public r-progress
+  (package
+    (name "r-progress")
+    (version "1.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "progress" version))
+       (sha256
+        (base32
+         "1fxakchfjr5vj59s9sxynd7crpz97xj42438rmkhkf3rjpyspx59"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-prettyunits" ,r-prettyunits)
+       ("r-r6" ,r-r6)))
+    (home-page "https://github.com/gaborcsardi/progress")
+    (synopsis "Terminal progress bars")
+    (description
+     "This package provides configurable progress bars.  They may include
+percentage, elapsed time, and/or the estimated completion time.  They work in
+terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app.  The
+package also provides a C++ API, that works with or without Rcpp.")
+    (license license:expat)))
-- 
2.13.3

Message #62 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 20/29] gnu: Add r-proxy.
Date: Mon, 14 Aug 2017 22:57:02 +0200

* gnu/packages/cran.scm (r-proxy): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 35d096514..752649337 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -530,3 +530,23 @@ these functions include a pairwise plot matrix, a two group pairwise plot
 matrix, a parallel coordinates plot, a survival plot, and several functions to
 plot networks.")
     (license license:gpl2+)))
+
+(define-public r-proxy
+  (package
+    (name "r-proxy")
+    (version "0.4-17")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "proxy" version))
+       (sha256
+        (base32
+         "0bg1fn96qrj8whmnl7c3gv244ksm2ykxxsd0zrmw4lb6465pizl2"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/proxy")
+    (synopsis "Distance and similarity measures")
+    (description
+     "This package provides an extensible framework for the efficient
+calculation of auto- and cross-proximities, along with implementations of the
+most popular ones.")
+    (license license:gpl2)))
-- 
2.13.3

Message #65 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 19/29] gnu: Add r-ggally.
Date: Mon, 14 Aug 2017 22:57:01 +0200

* gnu/packages/cran.scm (r-ggally): New variable.
---
 gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d88202ca5..35d096514 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -499,3 +499,34 @@ percentage, elapsed time, and/or the estimated completion time.  They work in
 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app.  The
 package also provides a C++ API, that works with or without Rcpp.")
     (license license:expat)))
+
+(define-public r-ggally
+  (package
+    (name "r-ggally")
+    (version "1.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "GGally" version))
+       (sha256
+        (base32
+         "12ddab0nd0f9c7bb6cx3c22mliyvc8xsxv26aqz3cvfbla8crp3b"))))
+    (properties `((upstream-name . "GGally")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-gtable" ,r-gtable)
+       ("r-plyr" ,r-plyr)
+       ("r-progress" ,r-progress)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-reshape" ,r-reshape)))
+    (home-page "https://ggobi.github.io/ggally")
+    (synopsis "Extension to ggplot2")
+    (description
+     "The R package ggplot2 is a plotting system based on the grammar of
+graphics.  GGally extends ggplot2 by adding several functions to reduce the
+complexity of combining geometric objects with transformed data.  Some of
+these functions include a pairwise plot matrix, a two group pairwise plot
+matrix, a parallel coordinates plot, a survival plot, and several functions to
+plot networks.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #68 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 21/29] gnu: Add r-sp.
Date: Mon, 14 Aug 2017 22:57:03 +0200

* gnu/packages/cran.scm (r-sp): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 752649337..811dd9ba7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -550,3 +550,27 @@ plot networks.")
 calculation of auto- and cross-proximities, along with implementations of the
 most popular ones.")
     (license license:gpl2)))
+
+(define-public r-sp
+  (package
+    (name "r-sp")
+    (version "1.2-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sp" version))
+       (sha256
+        (base32
+         "0crba3j00mb2xv2yk60rpa57gn97xq4ql3a6p9cjzqjxzv2cknk2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lattice" ,r-lattice)))
+    (home-page "http://cran.r-project.org/web/packages/sp")
+    (synopsis "Classes and methods for spatial data")
+    (description
+     "This package provides classes and methods for spatial data; the classes
+document where the spatial location information resides, for 2D or 3D data.
+Utility functions are provided, e.g. for plotting data as maps, spatial
+selection, as well as methods for retrieving coordinates, for subsetting,
+print, summary, etc.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #71 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 22/29] gnu: Add r-rook.
Date: Mon, 14 Aug 2017 22:57:04 +0200

* gnu/packages/web.scm (r-rook): New variable.
---
 gnu/packages/web.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 5459a3051..2649d68a2 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4879,3 +4879,27 @@ responsive, and powerful applications with minimal effort.")
 communicate with each other, with Shiny or without (i.e.  static @code{.html}
 files).  It currently supports linked brushing and filtering.")
     (license l:expat)))
+
+(define-public r-rook
+  (package
+    (name "r-rook")
+    (version "1.1-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Rook" version))
+       (sha256
+        (base32
+         "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
+    (properties `((upstream-name . "Rook")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-brew" ,r-brew)))
+    (home-page "http://cran.r-project.org/web/packages/Rook")
+    (synopsis "Web server interface for R")
+    (description
+     "This package contains the Rook specification and convenience software
+for building and running Rook applications.  A Rook application is an R
+reference class object that implements a @code{call} method or an R closure
+that takes exactly one argument, an environment, and returns a list with three
+named elements: the @code{status}, the @code{headers}, and the @code{body}.")
+    (license l:gpl2)))
-- 
2.13.3

Message #74 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 23/29] gnu: Add r-rmtstat.
Date: Mon, 14 Aug 2017 22:57:05 +0200

* gnu/packages/cran.scm (r-rmtstat): 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 811dd9ba7..88e275c73 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -574,3 +574,24 @@ Utility functions are provided, e.g. for plotting data as maps, spatial
 selection, as well as methods for retrieving coordinates, for subsetting,
 print, summary, etc.")
     (license license:gpl2+)))
+
+(define-public r-rmtstat
+  (package
+    (name "r-rmtstat")
+    (version "0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RMTstat" version))
+       (sha256
+        (base32
+         "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
+    (properties `((upstream-name . "RMTstat")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/RMTstat")
+    (synopsis "Distributions, statistics and tests derived from random matrix theory")
+    (description
+     "This package provides functions for working with the Tracy-Widom laws
+and other distributions related to the eigenvalues of large Wishart
+matrices.")
+    (license license:bsd-3)))
-- 
2.13.3

Message #77 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 25/29] gnu: Add r-distillery.
Date: Mon, 14 Aug 2017 22:57:07 +0200

* gnu/packages/cran.scm (r-distillery): 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 7bf8e1e13..024796313 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -617,3 +617,24 @@ L-moments from the data.  It also contains functions to estimate the
 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
 quantile mixture from L-moments and trimmed L-moments.")
     (license license:gpl2)))
+
+(define-public r-distillery
+  (package
+    (name "r-distillery")
+    (version "1.0-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "distillery" version))
+       (sha256
+        (base32
+         "12m4cacvc18fd3aayc8iih5q6bwsmvf29b55fwp7vs8wp1h8nd8c"))))
+    (build-system r-build-system)
+    (home-page "http://www.ral.ucar.edu/staff/ericg")
+    (synopsis "Functions for confidence intervals and object information")
+    (description
+     "This package provides some very simple method functions for confidence
+interval calculation and to distill pertinent information from a potentially
+complex object; primarily used in common with the packages extRemes and
+SpatialVx.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #80 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 24/29] gnu: Add r-lmoments.
Date: Mon, 14 Aug 2017 22:57:06 +0200

* gnu/packages/cran.scm (r-lmoments): 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 88e275c73..7bf8e1e13 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -595,3 +595,25 @@ print, summary, etc.")
 and other distributions related to the eigenvalues of large Wishart
 matrices.")
     (license license:bsd-3)))
+
+(define-public r-lmoments
+  (package
+    (name "r-lmoments")
+    (version "1.2-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Lmoments" version))
+       (sha256
+        (base32
+         "13p0r4w16jvjnyjmkhkp3dwdfr1gap2l0k4k5jy41m8nc5fvcx79"))))
+    (properties `((upstream-name . "Lmoments")))
+    (build-system r-build-system)
+    (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
+    (synopsis "L-moments and quantile mixtures")
+    (description
+     "This package contains functions to estimate L-moments and trimmed
+L-moments from the data.  It also contains functions to estimate the
+parameters of the normal polynomial quantile mixture and the Cauchy polynomial
+quantile mixture from L-moments and trimmed L-moments.")
+    (license license:gpl2)))
-- 
2.13.3

Message #83 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 26/29] gnu: Add r-extremes.
Date: Mon, 14 Aug 2017 22:57:08 +0200

* gnu/packages/cran.scm (r-extremes): 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 024796313..b1eb91345 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -638,3 +638,28 @@ interval calculation and to distill pertinent information from a potentially
 complex object; primarily used in common with the packages extRemes and
 SpatialVx.")
     (license license:gpl2+)))
+
+(define-public r-extremes
+  (package
+    (name "r-extremes")
+    (version "2.0-8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "extRemes" version))
+       (sha256
+        (base32
+         "0pnpib3g2r9x8hfqhvq23j8m3jh62lp28ipnqir5yadnzv850gfm"))))
+    (properties `((upstream-name . "extRemes")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-car" ,r-car)
+       ("r-distillery" ,r-distillery)
+       ("r-lmoments" ,r-lmoments)))
+    (home-page "http://www.assessment.ucar.edu/toolkit/")
+    (synopsis "Extreme value analysis")
+    (description
+     "ExtRemes is a suite of functions for carrying out analyses on the
+extreme values of a process of interest; be they block maxima over long blocks
+or excesses over a high threshold.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #86 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 27/29] gnu: Add r-lmtest.
Date: Mon, 14 Aug 2017 22:57:09 +0200

* gnu/packages/cran.scm (r-lmtest): 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 b1eb91345..8200ccfaf 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22,6 +22,7 @@
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system r)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web))
@@ -663,3 +664,28 @@ SpatialVx.")
 extreme values of a process of interest; be they block maxima over long blocks
 or excesses over a high threshold.")
     (license license:gpl2+)))
+
+(define-public r-lmtest
+  (package
+    (name "r-lmtest")
+    (version "0.9-35")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lmtest" version))
+       (sha256
+        (base32
+         "107br1l7p52wxvazs031f4h5ryply97qywg9dzrkw4ydnvqq4j9g"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-zoo" ,r-zoo)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://cran.r-project.org/web/packages/lmtest")
+    (synopsis "Testing linear regression models")
+    (description
+     "This package provides a collection of tests, data sets, and examples for
+diagnostic checking in linear regression models.  Furthermore, some generic
+tools for inference in parametric models are provided.")
+    ;; Either version is okay
+    (license (list license:gpl2 license:gpl3))))
-- 
2.13.3

Message #89 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 28/29] gnu: Add r-inline.
Date: Mon, 14 Aug 2017 22:57:10 +0200

* gnu/packages/cran.scm (r-inline): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8200ccfaf..9e50eed3c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -689,3 +689,23 @@ diagnostic checking in linear regression models.  Furthermore, some generic
 tools for inference in parametric models are provided.")
     ;; Either version is okay
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-inline
+  (package
+    (name "r-inline")
+    (version "0.3.14")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "inline" version))
+              (sha256
+               (base32
+                "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/inline")
+    (synopsis "Functions to inline C, C++, Fortran function calls from R")
+    (description
+     "This package provides functionality to dynamically define R functions
+and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
+@code{.Call} calling conventions.")
+    ;; Any version of the LGPL.
+    (license license:lgpl3+)))
-- 
2.13.3

Message #92 received at 28089 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 29/29] gnu: Add r-bbmle.
Date: Mon, 14 Aug 2017 22:57:11 +0200

* gnu/packages/cran.scm (r-bbmle): 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 9e50eed3c..e604799c4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -709,3 +709,28 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
 @code{.Call} calling conventions.")
     ;; Any version of the LGPL.
     (license license:lgpl3+)))
+
+(define-public r-bbmle
+  (package
+    (name "r-bbmle")
+    (version "1.0.19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bbmle" version))
+       (sha256
+        (base32
+         "014h6mw16gv4acs2p78dy7lla7s428n633aybsb1mbi6250dg0p8"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lattice" ,r-lattice)
+       ("r-mass" ,r-mass)
+       ("r-numderiv" ,r-numderiv)))
+    (home-page "http://cran.r-project.org/web/packages/bbmle")
+    (synopsis "Tools for General Maximum Likelihood Estimation")
+    (description
+     "Methods and functions for fitting maximum likelihood models in R.  This
+package modifies and extends the @code{mle} classes in the @code{stats4}
+package.")
+    ;; Any version of the GPL
+    (license (list license:gpl2 license:gpl3))))
-- 
2.13.3

Message #97 received at 28089-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28089-done <at> debbugs.gnu.org
Subject: Re: [PATCH 01/29] gnu: Add r-interactivedisplaybase.
Date: Thu, 17 Aug 2017 18:03:52 +0200

I’ve pushed these patches to master.

-- 
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

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