GNU bug report logs - #51422
[PATCH] gnu: Add r-phyloseq

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#51422: closed ([PATCH] gnu: Add r-phyloseq)
Date: Wed, 01 Dec 2021 08:36:01 +0000

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Your message dated Wed, 01 Dec 2021 09:34:05 +0100
with message-id <87wnkosoy4.fsf <at> elephly.net>
and subject line [PATCH] gnu: Add r-phyloseq
has caused the debbugs.gnu.org bug report #51422,
regarding [PATCH] gnu: Add r-phyloseq
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


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51422: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=51422
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From: Nicolas Vallet <nls.vallet <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: Nicolas Vallet <nicolas.vallet <at> inserm.fr>
Subject: [PATCH] gnu: Add r-phyloseq
Date: Tue, 26 Oct 2021 23:27:52 +0200

From: Nicolas Vallet <nicolas.vallet <at> inserm.fr>

* gnu/packages/cran.scm (r-phyloseq): 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 90a0e1f288..8dc875de69 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
+;;; Copyright © 2021 Nicolas Vallet <nls.vallet <at> gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -14813,3 +14814,42 @@ and other associated metadata.  De novo transcriptomes can be linked to the
 appropriate sources with linkedTxomes and shared for computational
 reproducibility.")
     (license license:gpl2)))
+
+
+(define-public r-phyloseq
+  (package
+   (name "r-phyloseq")
+   (version "1.36.0")
+   (source
+    (origin
+     (method url-fetch)
+     (uri (bioconductor-uri "phyloseq" version))
+     (sha256
+      (base32 "192gv00xfnv9ljkgb0iw8sqzsay4f3vllyyc1slzsn15713fc4pi"))))
+   (properties `((upstream-name . "phyloseq")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-ade4" ,r-ade4)
+      ("r-ape" ,r-ape)
+      ("r-biobase" ,r-biobase)
+      ("r-biocgenerics" ,r-biocgenerics)
+      ("r-biomformat" ,r-biomformat)
+      ("r-biostrings" ,r-biostrings)
+      ("r-cluster" ,r-cluster)
+      ("r-data-table" ,r-data-table)
+      ("r-foreach" ,r-foreach)
+      ("r-ggplot2" ,r-ggplot2)
+      ("r-igraph" ,r-igraph)
+      ("r-multtest" ,r-multtest)
+      ("r-plyr" ,r-plyr)
+      ("r-reshape2" ,r-reshape2)
+      ("r-scales" ,r-scales)
+      ("r-vegan" ,r-vegan)))
+   (native-inputs `(("r-knitr" ,r-knitr)))
+   (home-page "https://github.com/joey711/phyloseq")
+   (synopsis "Handling and analysis of high-throughput microbiome census data")
+   (description
+    "Phyloseq provides a set of classes and
+tools to facilitate the import, storage, analysis,
+and graphical display of microbiome census data.")
+   (license license:agpl3+)))

base-commit: c6adc0947396daa6d85ab08837f9cbc86f4d8722
-- 
2.25.1

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 51422-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-phyloseq
Date: Wed, 01 Dec 2021 09:34:05 +0100

Hi,

thank you for the patch!  I applied it to the “master” branch with 
trivial changes.  I also upgraded it to 1.38.0.

My apologies for the delay!

-- 
Ricardo

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