GNU bug report logs - #28109
[PATCH 00/11] Some more R things

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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 00/11] Some more R things
Date: Wed, 16 Aug 2017 14:56:20 +0200

Hi Guix,

here are some more R packages.


Ricardo Wurmus (11):
  gnu: r-trimcluster: Update license.
  gnu: Add r-emdbook.
  gnu: Add r-fastseg.
  gnu: Add r-qvalue.
  gnu: Add r-methylkit.
  gnu: Add r-lpsolve.
  gnu: Add r-limsolve.
  gnu: Add r-fitdistrplus.
  gnu: Add r-energy.
  gnu: Add r-suppdists.
  gnu: Add r-ksamples.

Message #8 received at 28109 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 01/10] gnu: r-trimcluster: Update license.
Date: Wed, 16 Aug 2017 15:08:50 +0200

* gnu/packages/statistics.scm (r-trimcluster)[license]: Also specify GPLv3+.
---
 gnu/packages/statistics.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 8e7b815d6..80465ea10 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4724,7 +4724,8 @@ multivariate analysis.")
      "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
 Matran (1997).  This optimizes the k-means criterion under trimming a portion
 of the points.")
-    (license license:gpl2+)))
+    ;; Any GPL version
+    (license (list license:gpl2+ license:gpl3+))))
 
 (define-public r-fpc
   (package
-- 
2.13.3

Message #11 received at 28109 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 02/10] gnu: Add r-emdbook.
Date: Wed, 16 Aug 2017 15:08:51 +0200

* gnu/packages/cran.scm (r-emdbook): 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 e604799c4..ae4d807dc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -734,3 +734,31 @@ package modifies and extends the @code{mle} classes in the @code{stats4}
 package.")
     ;; Any version of the GPL
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-emdbook
+  (package
+    (name "r-emdbook")
+    (version "1.3.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "emdbook" version))
+       (sha256
+        (base32
+         "09xbdyw8a4pvrsg3ryr8drby0njy4avc5wsjj4ffibdaicpchy69"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bbmle" ,r-bbmle)
+       ("r-coda" ,r-coda)
+       ("r-lattice" ,r-lattice)
+       ("r-mass" ,r-mass)
+       ("r-plyr" ,r-plyr)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
+    (synopsis "Support functions and data for \"Ecological Models and Data\"")
+    (description
+     "This package provides auxiliary functions and data sets for \"Ecological
+Models and Data\", a book presenting maximum likelihood estimation and related
+topics for ecologists (ISBN 978-0-691-12522-0).")
+    ;; Any GPL version
+    (license (list license:gpl2 license:gpl3))))
-- 
2.13.3

Message #14 received at 28109 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 03/10] gnu: Add r-fastseg.
Date: Wed, 16 Aug 2017 15:08:52 +0200

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3571cb96c..4207b2a9d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9287,6 +9287,36 @@ 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-public r-fastseg
+  (package
+    (name "r-fastseg")
+    (version "1.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "fastseg" version))
+       (sha256
+        (base32
+         "083wiz03q9mynwchs9frlpp6c84dncri5ncibx6h82p228cpja6h"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "http://www.bioinf.jku.at/software/fastseg/index.html")
+    (synopsis "Fast segmentation algorithm for genetic sequencing data")
+    (description
+     "Fastseg implements a very fast and efficient segmentation algorithm.
+It can segment data from DNA microarrays and data from next generation
+sequencing for example to detect copy number segments.  Further it can segment
+data from RNA microarrays like tiling arrays to identify transcripts.  Most
+generally, it can segment data given as a matrix or as a vector.  Various data
+formats can be used as input to fastseg like expression set objects for
+microarrays or GRanges for sequencing data.")
+    (license license:lgpl2.0+)))
+
 (define htslib-for-sambamba
   (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
     (package
-- 
2.13.3

Message #17 received at 28109 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 04/10] gnu: Add r-qvalue.
Date: Wed, 16 Aug 2017 15:08:53 +0200

* gnu/packages/bioinformatics.scm (r-qvalue): New variable.
---
 gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4207b2a9d..7cc48b3df 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9317,6 +9317,35 @@ formats can be used as input to fastseg like expression set objects for
 microarrays or GRanges for sequencing data.")
     (license license:lgpl2.0+)))
 
+(define-public r-qvalue
+  (package
+    (name "r-qvalue")
+    (version "2.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "qvalue" version))
+       (sha256
+        (base32
+         "1dxdwa767a9r8n61r272ypi09qblcdfpzzwkmri74y5mbp1r3y4i"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-reshape2" ,r-reshape2)))
+    (home-page "http://github.com/jdstorey/qvalue")
+    (synopsis "Q-value estimation for false discovery rate control")
+    (description
+     "This package takes a list of p-values resulting from the simultaneous
+testing of many hypotheses and estimates their q-values and local @dfn{false
+discovery rate} (FDR) values.  The q-value of a test measures the proportion
+of false positives incurred when that particular test is called significant.
+The local FDR measures the posterior probability the null hypothesis is true
+given the test's p-value.  Various plots are automatically generated, allowing
+one to make sensible significance cut-offs.  The software can be applied to
+problems in genomics, brain imaging, astrophysics, and data mining.")
+    ;; Any version of the LGPL.
+    (license license:lgpl3+)))
+
 (define htslib-for-sambamba
   (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
     (package
-- 
2.13.3

Message #20 received at 28109 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 05/10] gnu: Add r-lpsolve.
Date: Wed, 16 Aug 2017 15:08:54 +0200

* gnu/packages/cran.scm (r-lpsolve): 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 ae4d807dc..a912394da 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -762,3 +762,25 @@ Models and Data\", a book presenting maximum likelihood estimation and related
 topics for ecologists (ISBN 978-0-691-12522-0).")
     ;; Any GPL version
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-lpsolve
+  (package
+    (name "r-lpsolve")
+    (version "5.6.13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lpSolve" version))
+       (sha256
+        (base32
+         "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m"))))
+    (properties `((upstream-name . "lpSolve")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/lpSolve")
+    (synopsis "R interface to Lp_solve to solve linear/integer programs")
+    (description
+     "Lp_solve is software for solving linear, integer and mixed integer
+programs.  This implementation supplies a \"wrapper\" function in C and some R
+functions that solve general linear/integer problems, assignment problems, and
+transportation problems.")
+    (license license:lgpl2.0)))
-- 
2.13.3

Message #23 received at 28109 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 06/10] gnu: Add r-limsolve.
Date: Wed, 16 Aug 2017 15:08:55 +0200

* gnu/packages/cran.scm (r-limsolve): New variable.
---
 gnu/packages/cran.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a912394da..746c778b2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -23,6 +23,7 @@
   #:use-module (guix utils)
   #:use-module (guix build-system r)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages maths)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web))
@@ -784,3 +785,37 @@ programs.  This implementation supplies a \"wrapper\" function in C and some R
 functions that solve general linear/integer problems, assignment problems, and
 transportation problems.")
     (license license:lgpl2.0)))
+
+(define-public r-limsolve
+  (package
+    (name "r-limsolve")
+    (version "1.5.5.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "limSolve" version))
+       (sha256
+        (base32
+         "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg"))))
+    (properties `((upstream-name . "limSolve")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lpsolve" ,r-lpsolve)
+       ("r-mass" ,r-mass)
+       ("r-quadprog" ,r-quadprog)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://cran.r-project.org/web/packages/limSolve")
+    (synopsis "Solving linear inverse models")
+    (description
+     "This package provides functions that:
+
+@enumerate
+@item find the minimum/maximum of a linear or quadratic function,
+@item sample an underdetermined or overdetermined system,
+@item solve a linear system Ax=B for the unknown x.
+@end enumerate
+
+It includes banded and tridiagonal linear systems.  The package calls Fortran
+functions from LINPACK.")
+    ;; Any GPL version.
+    (license (list license:gpl2+ license:gpl3+))))
-- 
2.13.3

Message #26 received at 28109 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 07/10] gnu: Add r-fitdistrplus.
Date: Wed, 16 Aug 2017 15:08:56 +0200

* gnu/packages/cran.scm (r-fitdistrplus): 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 746c778b2..134139017 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -819,3 +819,31 @@ It includes banded and tridiagonal linear systems.  The package calls Fortran
 functions from LINPACK.")
     ;; Any GPL version.
     (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-fitdistrplus
+  (package
+    (name "r-fitdistrplus")
+    (version "1.0-9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fitdistrplus" version))
+       (sha256
+        (base32
+         "18x9454g598d54763k3hvi33iszifk7sxvhd1zg5r8z1vpixx3z6"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-survival" ,r-survival)))
+    (home-page "http://riskassessment.r-forge.r-project.org")
+    (synopsis "Fitting a parametric distribution from data")
+    (description
+     "This package extends the @code{fitdistr} function of the MASS package
+with several functions to help the fit of a parametric distribution to
+non-censored or censored data.  Censored data may contain left-censored,
+right-censored and interval-censored values, with several lower and upper
+bounds.  In addition to @dfn{maximum likelihood estimation} (MLE), the package
+provides moment matching (MME), quantile matching (QME) and maximum
+goodness-of-fit estimation (MGE) methods (available only for non-censored
+data).  Weighted versions of MLE, MME and QME are available.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #29 received at 28109 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 08/10] gnu: Add r-energy.
Date: Wed, 16 Aug 2017 15:08:57 +0200

* gnu/packages/cran.scm (r-energy): 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 134139017..ce2c2b531 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -847,3 +847,32 @@ provides moment matching (MME), quantile matching (QME) and maximum
 goodness-of-fit estimation (MGE) methods (available only for non-censored
 data).  Weighted versions of MLE, MME and QME are available.")
     (license license:gpl2+)))
+
+(define-public r-energy
+  (package
+    (name "r-energy")
+    (version "1.7-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "energy" version))
+       (sha256
+        (base32
+         "1g4hqi6mgsnd1w4q7dd2m40ljh2jdmvad91ksbq9fscnrqpvji1x"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-boot" ,r-boot)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "http://cran.r-project.org/web/packages/energy")
+    (synopsis "Multivariate inference via the energy of data")
+    (description
+     "This package provides e-statistics (energy) tests and statistics for
+multivariate and univariate inference, including distance correlation,
+one-sample, two-sample, and multi-sample tests for comparing multivariate
+distributions, are implemented.  Measuring and testing multivariate
+independence based on distance correlation, partial distance correlation,
+multivariate goodness-of-fit tests, clustering based on energy distance,
+testing for multivariate normality, distance components (disco) for
+non-parametric analysis of structured data, and other energy
+statistics/methods are implemented.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #32 received at 28109 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 09/10] gnu: Add r-suppdists.
Date: Wed, 16 Aug 2017 15:08:58 +0200

* gnu/packages/cran.scm (r-suppdists): 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 ce2c2b531..d1f684e37 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -876,3 +876,27 @@ testing for multivariate normality, distance components (disco) for
 non-parametric analysis of structured data, and other energy
 statistics/methods are implemented.")
     (license license:gpl2+)))
+
+(define-public r-suppdists
+  (package
+    (name "r-suppdists")
+    (version "1.1-9.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "SuppDists" version))
+       (sha256
+        (base32
+         "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
+    (properties `((upstream-name . "SuppDists")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/SuppDists")
+    (synopsis "Supplementary distributions")
+    (description
+     "This package provides ten distributions supplementing those built into
+R.  Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
+Spearman's rho, maximum F ratio, the Pearson product moment correlation
+coefficient, Johnson distributions, normal scores and generalized
+hypergeometric distributions.  In addition two random number generators of
+George Marsaglia are included.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #35 received at 28109 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH 10/10] gnu: Add r-ksamples.
Date: Wed, 16 Aug 2017 15:08:59 +0200

* gnu/packages/cran.scm (r-ksamples): 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 d1f684e37..bb7576352 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -900,3 +900,31 @@ coefficient, Johnson distributions, normal scores and generalized
 hypergeometric distributions.  In addition two random number generators of
 George Marsaglia are included.")
     (license license:gpl2+)))
+
+(define-public r-ksamples
+  (package
+    (name "r-ksamples")
+    (version "1.2-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "kSamples" version))
+       (sha256
+        (base32
+         "1pbam0zqq44slpxdgl2s2fsfdgl7i0pgm8bzlvnm0fy0na24bgdj"))))
+    (properties `((upstream-name . "kSamples")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-suppdists" ,r-suppdists)))
+    (home-page "http://cran.r-project.org/web/packages/kSamples")
+    (synopsis "K-Sample rank tests and their combinations")
+    (description
+     "This package provides tools to compares k samples using the
+Anderson-Darling test, Kruskal-Wallis type tests with different rank score
+criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
+test.  It computes asymptotic, simulated or (limited) exact P-values, all
+valid under randomization, with or without ties, or conditionally under random
+sampling from populations, given the observed tie pattern.  Except for Steel's
+test and the JT test it also combines these tests across several blocks of
+samples.")
+    (license license:gpl2+)))
-- 
2.13.3

Message #38 received at 28109 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109 <at> debbugs.gnu.org
Subject: Re: [PATCH 00/11] Some more R things
Date: Wed, 16 Aug 2017 15:11:51 +0200

Ricardo Wurmus <rekado <at> elephly.net> writes:

>   gnu: r-trimcluster: Update license.
>   gnu: Add r-emdbook.
>   gnu: Add r-fastseg.
>   gnu: Add r-qvalue.
>   gnu: Add r-methylkit.

My git repo got corrupted again(!) so I had to remove this commit.  Will
add it later.


--
Ricardo

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

Message #43 received at 28109-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 28109-done <at> debbugs.gnu.org
Subject: Re: [PATCH 01/10] gnu: r-trimcluster: Update license.
Date: Thu, 17 Aug 2017 18:03:06 +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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