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

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Package: guix-patches;

Reported by: Nicolas Vallet <nls.vallet <at> gmail.com>

Date: Tue, 26 Oct 2021 21:38:01 UTC

Severity: normal

Tags: patch

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

Bug is archived. No further changes may be made.

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Report forwarded to guix-patches <at> gnu.org:
bug#51422; Package guix-patches. (Tue, 26 Oct 2021 21:38:02 GMT) Full text and rfc822 format available.

Acknowledgement sent to Nicolas Vallet <nls.vallet <at> gmail.com>:
New bug report received and forwarded. Copy sent to guix-patches <at> gnu.org. (Tue, 26 Oct 2021 21:38:02 GMT) Full text and rfc822 format available.

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

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





Reply sent to Ricardo Wurmus <rekado <at> elephly.net>:
You have taken responsibility. (Wed, 01 Dec 2021 08:36:01 GMT) Full text and rfc822 format available.

Notification sent to Nicolas Vallet <nls.vallet <at> gmail.com>:
bug acknowledged by developer. (Wed, 01 Dec 2021 08:36:01 GMT) Full text and rfc822 format available.

Message #10 received at 51422-done <at> debbugs.gnu.org (full text, mbox):

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




bug archived. Request was from Debbugs Internal Request <help-debbugs <at> gnu.org> to internal_control <at> debbugs.gnu.org. (Wed, 29 Dec 2021 12:24:05 GMT) Full text and rfc822 format available.

This bug report was last modified 2 years and 80 days ago.

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