GNU bug report logs - #37666
[PATCH 0/2] Add r-htqpcr and r-unifiedwmwqpcr.

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

From: zimoun <zimon.toutoune <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 0/2] Add r-htqpcr and r-unifiedwmwqpcr.
Date: Tue,  8 Oct 2019 18:53:07 +0200

Dear,

These patches add two BioConductor packages.

The licenses are compliant with the ones find in the file 'DESCRIPTION' but
`guix build' reports:

  installing 0 license files from '.'


All the best,
simon


zimoun (2):
  gnu: Add r-htqpcr.
  gnu: Add r-unifiedwmwqpcr.

 gnu/packages/bioconductor.scm | 59 +++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

-- 
2.21.0

Message #8 received at 37666 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 37666 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 1/2] gnu: Add r-htqpcr.
Date: Tue,  8 Oct 2019 19:35:16 +0200

* gnu/packages/bioconductor.scm (r-htqpcr): New variable.
---
 gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7b0405427c..4fc4ffbce2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado <at> elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel <at> gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me <at> tobias.gr>
+;;; Copyright © 2019 Simon Tournier <zimon.toutoune <at> gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -6048,3 +6049,36 @@ attributable to individual, tissue, time point, or technical variables.  The
 package includes dream differential expression analysis for repeated
 measures.")
     (license license:gpl2+)))
+
+(define-public r-htqpcr
+  (package
+    (name "r-htqpcr")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "HTqPCR" version))
+       (sha256
+        (base32
+         "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7"))))
+    (properties `((upstream-name . "HTqPCR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affy" ,r-affy)
+       ("r-biobase" ,r-biobase)
+       ("r-gplots" ,r-gplots)
+       ("r-limma" ,r-limma)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+    (home-page "http://www.ebi.ac.uk/bertone/software")
+    (synopsis "Automated analysis of high-throughput qPCR data")
+    (description
+     "Analysis of Ct values from high throughput quantitative real-time
+PCR (qPCR) assays across multiple conditions or replicates.  The input data
+can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
+OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
+Laboratories; conventional 96- or 384-well plates; or microfluidic devices
+such as the Dynamic Arrays from Fluidigm Corporation.  HTqPCR handles data
+loading, quality assessment, normalization, visualization and parametric or
+non-parametric testing for statistical significance in Ct values between
+features (e.g.  genes, microRNAs).")
+    (license license:artistic2.0)))
-- 
2.21.0

Message #11 received at 37666 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 37666 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 1/1] gnu: Add r-unifiedwmwqpcr.
Date: Tue,  8 Oct 2019 19:35:17 +0200

* gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): New variable.
---
 gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4fc4ffbce2..9cd36fc69c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6082,3 +6082,28 @@ loading, quality assessment, normalization, visualization and parametric or
 non-parametric testing for statistical significance in Ct values between
 features (e.g.  genes, microRNAs).")
     (license license:artistic2.0)))
+
+(define-public r-unifiedwmwqpcr
+  (package
+    (name "r-unifiedwmwqpcr")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "unifiedWMWqPCR" version))
+       (sha256
+        (base32
+         "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a"))))
+    (properties
+     `((upstream-name . "unifiedWMWqPCR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-htqpcr" ,r-htqpcr)))
+    (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
+    (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
+    (description
+     "This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR
+data.  This modified test allows for testing differential expression in qPCR
+data.")
+    (license license:gpl2+)))
-- 
2.21.0

Message #14 received at 37666 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 37666 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 2/2] gnu: Add r-unifiedwmwqpcr.
Date: Tue,  8 Oct 2019 19:35:18 +0200

* gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): New variable.
---
 gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4fc4ffbce2..9cd36fc69c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6082,3 +6082,28 @@ loading, quality assessment, normalization, visualization and parametric or
 non-parametric testing for statistical significance in Ct values between
 features (e.g.  genes, microRNAs).")
     (license license:artistic2.0)))
+
+(define-public r-unifiedwmwqpcr
+  (package
+    (name "r-unifiedwmwqpcr")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "unifiedWMWqPCR" version))
+       (sha256
+        (base32
+         "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a"))))
+    (properties
+     `((upstream-name . "unifiedWMWqPCR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-htqpcr" ,r-htqpcr)))
+    (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
+    (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
+    (description
+     "This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR
+data.  This modified test allows for testing differential expression in qPCR
+data.")
+    (license license:gpl2+)))
-- 
2.21.0

Message #19 received at 37666-done <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 37666-done <at> debbugs.gnu.org
Subject: Re: [bug#37666] [PATCH 1/2] gnu: Add r-htqpcr.
Date: Tue, 15 Oct 2019 14:13:40 +0200

Hello!

zimoun <zimon.toutoune <at> gmail.com> skribis:

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

[...]

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

Applied, thanks!  :-)

Ludo’.

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