GNU bug report logs - #46524
[PATCH 0/2] Add r-samr and r-gsa.

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

From: Tim Howes <timhowes <at> lavabit.com>
To: guix-patches <at> gnu.org
Subject: [PATCH 0/2] Add r-samr and r-gsa.
Date: Sun, 14 Feb 2021 21:40:29 -0800

Hello,

This adds the packages samr and GSA for gene expression analysis in R.

Tim Howes (2):
  gnu: Add r-gsa.
  gnu: Add r-samr.

 gnu/packages/cran.scm | 52 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)

-- 
2.30.1

Message #8 received at 46524 <at> debbugs.gnu.org (full text, mbox):

From: Tim Howes <timhowes <at> lavabit.com>
To: 46524 <at> debbugs.gnu.org
Subject: [PATCH 1/2] gnu: Add r-gsa.
Date: Sun, 14 Feb 2021 21:44:36 -0800

* gnu/packages/cran.scm (r-gsa): 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 1fe90619cd..86b2df0a9f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -33,6 +33,7 @@
 ;;; Copyright © 2020 Magali Lemes <magalilemes00 <at> gmail.com>
 ;;; Copyright © 2020 Simon Tournier <zimon.toutoune <at> gmail.com>
 ;;; Copyright © 2020 Aniket Patil <aniket112.patil <at> gmail.com>
+;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26851,3 +26852,23 @@ from a source package.  @code{pkgdown} converts your documentation, vignettes,
 README file, and more to HTML making it easy to share information about your
 package online.")
     (license license:expat)))
+
+(define-public r-gsa
+  (package
+    (name "r-gsa")
+    (version "1.03.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "GSA" version))
+        (sha256
+          (base32
+            "05x9wspah1cdznjpncqam1iawsxdiigyl8v2anyhss2k7wwd94p1"))))
+    (properties `((upstream-name . "GSA")))
+    (build-system r-build-system)
+    (home-page
+      "https://statweb.stanford.edu/~tibs/GSA/")
+    (synopsis "Gene Set Analysis")
+    (description "Inference on gene sets in microarray studies.")
+    ;; Any version of the LGPL
+    (license license:lgpl3+)))
-- 
2.30.1

Message #11 received at 46524 <at> debbugs.gnu.org (full text, mbox):

From: Tim Howes <timhowes <at> lavabit.com>
To: 46524 <at> debbugs.gnu.org
Subject: [PATCH 2/2] gnu: Add r-samr.
Date: Sun, 14 Feb 2021 21:44:37 -0800

* gnu/packages/cran.scm (r-samr): 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 86b2df0a9f..d151f1cb50 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -26872,3 +26872,34 @@ package online.")
     (description "Inference on gene sets in microarray studies.")
     ;; Any version of the LGPL
     (license license:lgpl3+)))
+
+(define-public r-samr
+  (package
+    (name "r-samr")
+    (version "3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "samr" version))
+        (sha256
+          (base32
+            "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
+    (properties `((upstream-name . "samr")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-gsa" ,r-gsa)
+        ("r-impute" ,r-impute)
+        ("r-matrixstats" ,r-matrixstats)
+        ("r-openxlsx" ,r-openxlsx)
+        ("r-shiny" ,r-shiny)
+        ("r-shinyfiles" ,r-shinyfiles)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page
+      "https://statweb.stanford.edu/~tibs/SAM/")
+    (synopsis
+      "Significance Analysis of Microarrays")
+    (description
+      "Significance Analysis of Microarrays for differential expression
+analysis, RNAseq data and related problems.")
+    ;; Any version of the LGPL
+    (license license:lgpl3+)))
-- 
2.30.1

Message #16 received at 46524-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Tim Howes <timhowes <at> lavabit.com>
Cc: 46524-done <at> debbugs.gnu.org
Subject: Re: [bug#46524] [PATCH 0/2] Add r-samr and r-gsa.
Date: Fri, 26 Mar 2021 10:14:47 +0100

Hi Tim,

I’m sorry for the delay!

> This adds the packages samr and GSA for gene expression analysis in R.
>
> Tim Howes (2):
>   gnu: Add r-gsa.
>   gnu: Add r-samr.
>
>  gnu/packages/cran.scm | 52 +++++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 52 insertions(+)

I applied these with minor changes with commit e9741ad623.

Thank you!

-- 
Ricardo

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