GNU bug report logs - #58828
[PATCH] gnu: Add r-dmwr2 and r-debcam.

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

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-dmwr2 and r-debcam.
Date: Fri, 28 Oct 2022 04:56:29 +0000

[Message part 1 (text/plain, inline)]

* gnu/packages/cran.scm (r-dmwr2): New variable.

* gnu/packages/bioconductor.scm (r-debcam): New variable.


All the best!

Mădălin Ionel Patrașcu

[Message part 2 (text/html, inline)]

Message #8 received at 58828 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <58828 <at> debbugs.gnu.org>
Subject: [PATCH 1/2] gnu: Add r-dmwr2.
Date: Fri, 28 Oct 2022 07:02:34 +0200

* gnu/packages/cran.scm (r-dmwr2): 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 f969da5b3c..eb4532a62a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -402,6 +402,36 @@ (define-public r-dixontest
 Gaussian quadrature for a numerical solution.")
     (license license:gpl3)))
 
+(define-public r-dmwr2
+  (package
+    (name "r-dmwr2")
+    (version "0.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "DMwR2" version))
+              (sha256
+               (base32
+                "1vzfbz2k05j8r2hpig3d2grb99rnnh2s1sviii3prcyqicxfh0i9"))))
+    (properties `((upstream-name . "DMwR2")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-class
+           r-dbi
+           r-dplyr
+           r-quantmod
+           r-readr
+           r-rpart
+           r-xts
+           r-zoo))
+    (home-page "https://github.com/ltorgo/DMwR2")
+    (synopsis
+     "Functions and data for the second edition of \"Data Mining with R\"")
+    (description
+     "This package provides functions and data accompanying the second edition
+of the book \"Data Mining with R, learning with case studies\" by Luis Torgo,
+published by CRC Press.")
+    (license license:gpl2+)))
+
 (define-public r-emdist
   (package
     (name "r-emdist")

base-commit: ac51b9c86d58cfdb13ee643a2fdc8e979939a260
-- 
2.38.0

Message #11 received at 58828 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <58828 <at> debbugs.gnu.org>
Subject: [PATCH 2/2] gnu: Add r-debcam.
Date: Fri, 28 Oct 2022 07:02:35 +0200

* gnu/packages/bioconductor.scm (r-debcam): New variable.
---
 gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b8535250f9..994b3b0137 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -48,6 +48,7 @@ (define-module (gnu packages bioconductor)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages java)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages netpbm)
   #:use-module (gnu packages python)
@@ -3051,6 +3052,45 @@ (define-public r-dearseq
 set analyses, and can deal with repeated or longitudinal data.")
     (license license:gpl2)))
 
+(define-public r-debcam
+  (package
+    (name "r-debcam")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "debCAM" version))
+              (sha256
+               (base32
+                "1ynz57kkxl8nx80zhh1vhhydqb5n6r9d7p69f0k9nj8rp4hdgng7"))))
+    (properties `((upstream-name . "debCAM")))
+    (build-system r-build-system)
+    (inputs (list openjdk))
+    (propagated-inputs
+     (list r-apcluster
+           r-biobase
+           r-biocparallel
+           r-corpcor
+           r-dmwr2
+           r-geometry
+           r-nmf
+           r-nnls
+           r-pcapp
+           r-rjava
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/debCAM")
+    (synopsis "Deconvolution by convex analysis of mixtures")
+    (description
+     "This package is an R implementation for fully unsupervised deconvolution
+of complex tissues.  @code{DebCAM} provides basic functions to perform unsupervised
+deconvolution on mixture expression profiles by @acronym{CAM, Convex Analysis
+of Mixtures} and some auxiliary functions to help understand the subpopulation-
+specific results.  It also implements functions to perform supervised deconvolution
+based on prior knowledge of molecular markers, S matrix or A matrix.  Combining
+molecular markers from CAM and from prior knowledge can achieve semi-supervised
+deconvolution of mixtures.")
+    (license license:gpl2)))
+
 (define-public r-decipher
   (package
     (name "r-decipher")
-- 
2.38.0

Message #16 received at 58828-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 58828-done <at> debbugs.gnu.org
Subject: Re: [bug#58828] [PATCH 1/2] gnu: Add r-dmwr2.
Date: Fri, 28 Oct 2022 15:14:27 +0200

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> * gnu/packages/cran.scm (r-dmwr2): New variable.

Applied, thanks!

-- 
Ricardo

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