GNU bug report logs - #43345
[PATCH 00/12] Move some CRAN packages to (gnu packages cran).

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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 00/12] Move some CRAN packages to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:05:27 +0200

Dear,

Some clean up leading the recent discussion [1].  Now, the only remaining
'cran-uri' are from (gnu packages statistics).  Modulo maybe some packages
using "bad" uri, e.g., from r-qtl:

--8<---------------cut here---------------start------------->8---
    (uri (string-append "mirror://cran/src/contrib/qtl_"
                        version ".tar.gz"))
--8<---------------cut here---------------end--------------->8---

To ease the Copyright transfer between files, I used:

  git log --grep=<package-name>
  git log --date=format:"%Y" --format="%ad %an" \
      -- gnu/packages/<file>.scm | sort | uniq -c

After each move, I run:

  make
  ./pre-env-inst guix build <package-name>
  ./pre-env-inst guix build <package-name> --no-grafts --check

to check that everything is fine.  And at the end of all the move, I run:

  make as-derivation

to verify that "guix pull" is not broken by something.  (Well, I failed to use
the regular ./pre-env-inst guix pull --branch=my-stuff --url=$PWD -p /tmp/new
because of the "new" authentication, another story.)

Last, I have not carefully checked the imported modules, so it could be
possible to perhaps remove 1 or 2 #:use-module (gnu packages <useless>) from
gnu/packages/bioinformatics.scm.

[1] https://lists.gnu.org/archive/html/guix-commits/2020-09/msg00416.html

All the best,
simon

zimoun (12):
  gnu: r-codedepends: Comment why is in bioconductor.scm.
  gnu: r-adaptivesparsity: Move to (gnu packages cran).
  gnu: r-diffusionmap: Move to (gnu packages cran).
  gnu: r-igraph: Move to (gnu packages cran).
  gnu: r-qtl: Move to (gnu packages cran).
  gnu: r-qtl2: Move to (gnu packages cran).
  gnu: r-seqminer: Move to (gnu packages cran).
  gnu: r-maldiquant: Move to (gnu packages cran).
  gnu: r-seurat: Move to (gnu packages cran).
  gnu: r-phangorn: Move to (gnu packages cran).
  gnu: r-diversitree: Move to (gnu packages cran).
  gnu: r-absfiltergsea: Move to (gnu packages cran).

 gnu/packages/bioconductor.scm     |   1 +
 gnu/packages/bioinformatics.scm   | 250 ---------------------
 gnu/packages/cran.scm             | 346 ++++++++++++++++++++++++++++++
 gnu/packages/graph.scm            |  57 -----
 gnu/packages/machine-learning.scm |  35 ---
 5 files changed, 347 insertions(+), 342 deletions(-)


base-commit: 24e37fbbc4d7a5a4792c57f97f1f280d3ed36e01
-- 
2.28.0

Message #8 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 01/12] gnu: r-codedepends: Comment why is in bioconductor.scm.
Date: Fri, 11 Sep 2020 20:08:38 +0200

* gnu/packages/bioconductor.scm (r-codedepends): Add comment.
---
 gnu/packages/bioconductor.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 73d5fe37eb..e3e7fb88bc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1762,6 +1762,7 @@ expressed genes in DNA microarray experiments.")
 fitting of some classes of graphical Markov models.")
     (license license:gpl2+)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package.
 (define-public r-codedepends
   (package
     (name "r-codedepends")
-- 
2.28.0

Message #11 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 02/12] gnu: r-adaptivesparsity: Move to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:08:39 +0200

* gnu/packages/machine-learning.scm (r-adaptivesparsity): Move from here...
* gnu/packages/cran.scm (r-adaptivesparsity): ...to here.
---
 gnu/packages/cran.scm             | 36 +++++++++++++++++++++++++++++++
 gnu/packages/machine-learning.scm | 35 ------------------------------
 2 files changed, 36 insertions(+), 35 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index de4273892d..f701b7fde0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -23607,3 +23607,39 @@ environments (e.g.  development, test, production).  It reads values using a
 function that determines the current environment and returns the appropriate
 value.")
     (license license:gpl3)))
+
+(define-public r-adaptivesparsity
+  (package
+    (name "r-adaptivesparsity")
+    (version "1.6")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "AdaptiveSparsity" version))
+              (sha256
+               (base32
+                "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
+    (properties
+     `((upstream-name . "AdaptiveSparsity")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'link-against-armadillo
+           (lambda _
+             (substitute* "src/Makevars"
+               (("PKG_LIBS=" prefix)
+                (string-append prefix "-larmadillo"))))))))
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (inputs
+     `(("armadillo" ,armadillo)))
+    (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
+    (synopsis "Adaptive sparsity models")
+    (description
+     "This package implements the Figueiredo machine learning algorithm for
+adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
+geometric models.")
+    (license license:lgpl3+)))
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 05646dd770..0301b4964a 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -660,41 +660,6 @@ synchronization, thread-safety, concurrent data structures, and non-blocking
 I/O.")
     (license license:asl2.0)))
 
-(define-public r-adaptivesparsity
-  (package
-    (name "r-adaptivesparsity")
-    (version "1.6")
-    (source (origin
-              (method url-fetch)
-              (uri (cran-uri "AdaptiveSparsity" version))
-              (sha256
-               (base32
-                "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
-    (properties
-     `((upstream-name . "AdaptiveSparsity")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'link-against-armadillo
-           (lambda _
-             (substitute* "src/Makevars"
-               (("PKG_LIBS=" prefix)
-                (string-append prefix "-larmadillo"))))))))
-    (propagated-inputs
-     `(("r-mass" ,r-mass)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)))
-    (inputs
-     `(("armadillo" ,armadillo)))
-    (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
-    (synopsis "Adaptive sparsity models")
-    (description
-     "This package implements the Figueiredo machine learning algorithm for
-adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
-geometric models.")
-    (license license:lgpl3+)))
 
 (define-public gemmlowp-for-tensorflow
   ;; The commit hash is taken from "tensorflow/workspace.bzl".
-- 
2.28.0

Message #14 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 03/12] gnu: r-diffusionmap: Move to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:08:40 +0200

* gnu/packages/graph.scm (r-diffusionmap): Move from here ...
* gnu/packages/cran.scm (r-diffusionmap): ... to here.
---
 gnu/packages/cran.scm  | 25 +++++++++++++++++++++++++
 gnu/packages/graph.scm | 25 -------------------------
 2 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f701b7fde0..d539dc34a3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -23643,3 +23643,28 @@ value.")
 adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
 geometric models.")
     (license license:lgpl3+)))
+
+(define-public r-diffusionmap
+  (package
+    (name "r-diffusionmap")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "diffusionMap" version))
+       (sha256
+        (base32
+         "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
+    (properties `((upstream-name . "diffusionMap")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-igraph" ,r-igraph)
+       ("r-matrix" ,r-matrix)
+       ("r-scatterplot3d" ,r-scatterplot3d)))
+    (home-page "https://www.r-project.org")
+    (synopsis "Diffusion map")
+    (description "This package implements the diffusion map method of data
+parametrization, including creation and visualization of diffusion maps,
+clustering with diffusion K-means and regression using the adaptive regression
+model.")
+    (license license:gpl2)))
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 800b567e39..54ced01f6c 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -153,31 +153,6 @@ random and regular graphs, graph visualization, centrality methods and much
 more.")
     (license license:gpl2+)))
 
-(define-public r-diffusionmap
-  (package
-    (name "r-diffusionmap")
-    (version "1.2.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "diffusionMap" version))
-       (sha256
-        (base32
-         "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
-    (properties `((upstream-name . "diffusionMap")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-igraph" ,r-igraph)
-       ("r-matrix" ,r-matrix)
-       ("r-scatterplot3d" ,r-scatterplot3d)))
-    (home-page "https://www.r-project.org")
-    (synopsis "Diffusion map")
-    (description "This package implements the diffusion map method of data
-parametrization, including creation and visualization of diffusion maps,
-clustering with diffusion K-means and regression using the adaptive regression
-model.")
-    (license license:gpl2)))
-
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-- 
2.28.0

Message #17 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 04/12] gnu: r-igraph: Move to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:08:41 +0200

* gnu/packages/graph.scm (r-igraph): Move from here...
* gnu/packages/cran.scm (r-igraph): ...to here.
---
 gnu/packages/cran.scm  | 33 +++++++++++++++++++++++++++++++++
 gnu/packages/graph.scm | 32 --------------------------------
 2 files changed, 33 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d539dc34a3..717bd36d4d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -91,6 +91,7 @@
   #:use-module (gnu packages tcl)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
+  #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg))
 
 (define-public r-rticles
@@ -23668,3 +23669,35 @@ parametrization, including creation and visualization of diffusion maps,
 clustering with diffusion K-means and regression using the adaptive regression
 model.")
     (license license:gpl2)))
+
+(define-public r-igraph
+  (package
+    (name "r-igraph")
+    (version "1.2.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "igraph" version))
+       (sha256
+        (base32
+         "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (inputs
+     `(("gmp" ,gmp)
+       ("glpk" ,glpk)
+       ("libxml2" ,libxml2)
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-magrittr" ,r-magrittr)
+       ("r-matrix" ,r-matrix)
+       ("r-pkgconfig" ,r-pkgconfig)))
+    (home-page "https://igraph.org")
+    (synopsis "Network analysis and visualization")
+    (description
+     "This package provides routines for simple graphs and network analysis.
+It can handle large graphs very well and provides functions for generating
+random and regular graphs, graph visualization, centrality methods and much
+more.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 54ced01f6c..a307fee808 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -121,38 +121,6 @@ more.")
     (home-page "https://pypi.org/project/python-igraph/")
     (synopsis "Python bindings for the igraph network analysis library")))
 
-(define-public r-igraph
-  (package
-    (name "r-igraph")
-    (version "1.2.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "igraph" version))
-       (sha256
-        (base32
-         "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
-    (build-system r-build-system)
-    (native-inputs
-     `(("gfortran" ,gfortran)))
-    (inputs
-     `(("gmp" ,gmp)
-       ("glpk" ,glpk)
-       ("libxml2" ,libxml2)
-       ("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-magrittr" ,r-magrittr)
-       ("r-matrix" ,r-matrix)
-       ("r-pkgconfig" ,r-pkgconfig)))
-    (home-page "https://igraph.org")
-    (synopsis "Network analysis and visualization")
-    (description
-     "This package provides routines for simple graphs and network analysis.
-It can handle large graphs very well and provides functions for generating
-random and regular graphs, graph visualization, centrality methods and much
-more.")
-    (license license:gpl2+)))
-
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-- 
2.28.0

Message #20 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 05/12] gnu: r-qtl: Move to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:08:42 +0200

* gnu/packages/bioinformatics.scm (r-qtl): Move from here ...
* gnu/packages/cran.scm (r-qtl): ... to here.
---
 gnu/packages/bioinformatics.scm | 25 -------------------------
 gnu/packages/cran.scm           | 26 ++++++++++++++++++++++++++
 2 files changed, 26 insertions(+), 25 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cab3df222c..ae728f09dc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8510,31 +8510,6 @@ Stephens (1990).")
 throughput genetic sequencing data sets using regression methods.")
     (license license:artistic2.0)))
 
-(define-public r-qtl
- (package
-  (name "r-qtl")
-  (version "1.46-2")
-  (source
-   (origin
-    (method url-fetch)
-    (uri (string-append "mirror://cran/src/contrib/qtl_"
-                        version ".tar.gz"))
-    (sha256
-     (base32
-      "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
-  (build-system r-build-system)
-  (home-page "https://rqtl.org/")
-  (synopsis "R package for analyzing QTL experiments in genetics")
-  (description "R/qtl is an extension library for the R statistics
-system.  It is used to analyze experimental crosses for identifying
-genes contributing to variation in quantitative traits (so-called
-quantitative trait loci, QTLs).
-
-Using a hidden Markov model, R/qtl estimates genetic maps, to
-identify genotyping errors, and to perform single-QTL and two-QTL,
-two-dimensional genome scans.")
-  (license license:gpl3)))
-
 (define-public r-qtl2
   (package
     (name "r-qtl2")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 717bd36d4d..868f660e41 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado <at> elephly.net>
 ;;; Copyright © 2015 Andreas Enge <andreas <at> enge.fr>
+;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix <at> thebird.nl>
 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben <at> gmail.com>
 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel <at> gnu.org>
 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me <at> tobias.gr>
@@ -23701,3 +23702,28 @@ It can handle large graphs very well and provides functions for generating
 random and regular graphs, graph visualization, centrality methods and much
 more.")
     (license license:gpl2+)))
+
+(define-public r-qtl
+ (package
+  (name "r-qtl")
+  (version "1.46-2")
+  (source
+   (origin
+    (method url-fetch)
+    (uri (string-append "mirror://cran/src/contrib/qtl_"
+                        version ".tar.gz"))
+    (sha256
+     (base32
+      "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
+  (build-system r-build-system)
+  (home-page "https://rqtl.org/")
+  (synopsis "R package for analyzing QTL experiments in genetics")
+  (description "R/qtl is an extension library for the R statistics
+system.  It is used to analyze experimental crosses for identifying
+genes contributing to variation in quantitative traits (so-called
+quantitative trait loci, QTLs).
+
+Using a hidden Markov model, R/qtl estimates genetic maps, to
+identify genotyping errors, and to perform single-QTL and two-QTL,
+two-dimensional genome scans.")
+  (license license:gpl3)))
-- 
2.28.0

Message #23 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 06/12] gnu: r-qtl2: Move to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:08:43 +0200

* gnu/packages/bioinformatics.scm (r-qtl2): Move from here ...
* gnu/packages/cran.scm (r-qtl2): ... to here.
---
 gnu/packages/bioinformatics.scm | 26 --------------------------
 gnu/packages/cran.scm           | 27 +++++++++++++++++++++++++++
 2 files changed, 27 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ae728f09dc..4de52f3aaa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8510,32 +8510,6 @@ Stephens (1990).")
 throughput genetic sequencing data sets using regression methods.")
     (license license:artistic2.0)))
 
-(define-public r-qtl2
-  (package
-    (name "r-qtl2")
-    (version "0.22-11")
-    (source (origin
-              (method url-fetch)
-              (uri (cran-uri "qtl2" version))
-              (sha256
-               (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-data-table" ,r-data-table)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcppeigen" ,r-rcppeigen)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-yaml" ,r-yaml)))
-    (home-page "https://kbroman.org/qtl2/")
-    (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
-    (description
-     "This package provides a set of tools to perform @dfn{Quantitative Trait
-Locus} (QTL) analysis in experimental crosses.  It is a reimplementation of the
-@code{R/qtl} package to better handle high-dimensional data and complex cross
-designs.  Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
-    (license license:gpl3)))
-
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 868f660e41..bd36e1bacb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19,6 +19,7 @@
 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms <at> gmail.com>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny <at> vurv.cz>
 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab <at> web.de>
+;;; Copyright © 2019, 2020 Efraim Flashner <efraim <at> flashner.co.il>
 ;;; Copyright © 2020 Todor Kondić <tk.code <at> protonmail.com>
 ;;; Copyright © 2020 Danjela Lura <danielaluraa <at> gmail.com>
 ;;; Copyright © 2020 Naga Malleswari <nagamalli <at> riseup.net>
@@ -23727,3 +23728,29 @@ Using a hidden Markov model, R/qtl estimates genetic maps, to
 identify genotyping errors, and to perform single-QTL and two-QTL,
 two-dimensional genome scans.")
   (license license:gpl3)))
+
+(define-public r-qtl2
+  (package
+    (name "r-qtl2")
+    (version "0.22-11")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "qtl2" version))
+              (sha256
+               (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-yaml" ,r-yaml)))
+    (home-page "https://kbroman.org/qtl2/")
+    (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
+    (description
+     "This package provides a set of tools to perform @dfn{Quantitative Trait
+Locus} (QTL) analysis in experimental crosses.  It is a reimplementation of the
+@code{R/qtl} package to better handle high-dimensional data and complex cross
+designs.  Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
+    (license license:gpl3)))
-- 
2.28.0

Message #26 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 07/12] gnu: r-seqminer: Move to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:08:44 +0200

* gnu/packages/bioinformatics.scm (r-seqminer): Move from here ...
* gnu/packages/cran.scm (r-seqminer): ... to here.
---
 gnu/packages/bioinformatics.scm | 22 ----------------------
 gnu/packages/cran.scm           | 22 ++++++++++++++++++++++
 2 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4de52f3aaa..40c6363859 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9393,28 +9393,6 @@ imaging data that can be used in subsequent analyses to adjust for unknown,
 unmodeled, or latent sources of noise.")
     (license license:artistic2.0)))
 
-(define-public r-seqminer
-  (package
-    (name "r-seqminer")
-    (version "8.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "seqminer" version))
-       (sha256
-        (base32
-         "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
-    (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
-    (home-page "http://seqminer.genomic.codes")
-    (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
-    (description
-     "This package provides tools to integrate nucleotide sequencing
-data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
-    ;; Any version of the GPL is acceptable
-    (license (list license:gpl2+ license:gpl3+))))
-
 (define-public r-raremetals2
   (package
     (name "r-raremetals2")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index bd36e1bacb..5d1e248cc4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -23754,3 +23754,25 @@ Locus} (QTL) analysis in experimental crosses.  It is a reimplementation of the
 @code{R/qtl} package to better handle high-dimensional data and complex cross
 designs.  Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
     (license license:gpl3)))
+
+(define-public r-seqminer
+  (package
+    (name "r-seqminer")
+    (version "8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "seqminer" version))
+       (sha256
+        (base32
+         "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "http://seqminer.genomic.codes")
+    (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
+    (description
+     "This package provides tools to integrate nucleotide sequencing
+data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
+    ;; Any version of the GPL is acceptable
+    (license (list license:gpl2+ license:gpl3+))))
-- 
2.28.0

Message #29 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 08/12] gnu: r-maldiquant: Move to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:08:45 +0200

* gnu/packages/bioinformatics.scm (r-maldiquant): Move from here ...
* gnu/packages/cran.scm (r-maldiquant): ... to here.
---
 gnu/packages/bioinformatics.scm | 26 --------------------------
 gnu/packages/cran.scm           | 26 ++++++++++++++++++++++++++
 2 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 40c6363859..fecb3c072d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9425,32 +9425,6 @@ for analyzing gene-level association tests in meta-analyses for binary
 trait.")
     (license license:gpl3)))
 
-(define-public r-maldiquant
-  (package
-    (name "r-maldiquant")
-    (version "1.19.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "MALDIquant" version))
-       (sha256
-        (base32
-         "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
-    (properties `((upstream-name . "MALDIquant")))
-    (build-system r-build-system)
-    (home-page "https://cran.r-project.org/web/packages/MALDIquant")
-    (synopsis "Quantitative analysis of mass spectrometry data")
-    (description
-     "This package provides a complete analysis pipeline for matrix-assisted
-laser desorption/ionization-time-of-flight (MALDI-TOF) and other
-two-dimensional mass spectrometry data.  In addition to commonly used plotting
-and processing methods it includes distinctive features, namely baseline
-subtraction methods such as morphological filters (TopHat) or the
-statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
-alignment using warping functions, handling of replicated measurements as well
-as allowing spectra with different resolutions.")
-    (license license:gpl3+)))
-
 (define-public r-protgenerics
   (package
     (name "r-protgenerics")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5d1e248cc4..a6c2518978 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -23776,3 +23776,29 @@ designs.  Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
     ;; Any version of the GPL is acceptable
     (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-maldiquant
+  (package
+    (name "r-maldiquant")
+    (version "1.19.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "MALDIquant" version))
+       (sha256
+        (base32
+         "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
+    (properties `((upstream-name . "MALDIquant")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/MALDIquant")
+    (synopsis "Quantitative analysis of mass spectrometry data")
+    (description
+     "This package provides a complete analysis pipeline for matrix-assisted
+laser desorption/ionization-time-of-flight (MALDI-TOF) and other
+two-dimensional mass spectrometry data.  In addition to commonly used plotting
+and processing methods it includes distinctive features, namely baseline
+subtraction methods such as morphological filters (TopHat) or the
+statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
+alignment using warping functions, handling of replicated measurements as well
+as allowing spectra with different resolutions.")
+    (license license:gpl3+)))
-- 
2.28.0

Message #32 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 09/12] gnu: r-seurat: Move to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:08:46 +0200

* gnu/packages/bioinformatics.scm (r-seurat): Move from here ...
* gnu/packages/cran.scm (r-seurat): ... to here.
---
 gnu/packages/bioinformatics.scm | 65 ---------------------------------
 gnu/packages/cran.scm           | 65 +++++++++++++++++++++++++++++++++
 2 files changed, 65 insertions(+), 65 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fecb3c072d..a6505099fc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9735,71 +9735,6 @@ contains a number of utilities to explore the MS/MS results and assess missed
 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
     (license license:artistic2.0)))
 
-(define-public r-seurat
-  (package
-    (name "r-seurat")
-    (version "3.2.0")
-    (source (origin
-              (method url-fetch)
-              (uri (cran-uri "Seurat" version))
-              (sha256
-               (base32
-                "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
-    (properties `((upstream-name . "Seurat")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-ape" ,r-ape)
-       ("r-cluster" ,r-cluster)
-       ("r-cowplot" ,r-cowplot)
-       ("r-fitdistrplus" ,r-fitdistrplus)
-       ("r-future" ,r-future)
-       ("r-future-apply" ,r-future-apply)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggrepel" ,r-ggrepel)
-       ("r-ggridges" ,r-ggridges)
-       ("r-httr" ,r-httr)
-       ("r-ica" ,r-ica)
-       ("r-igraph" ,r-igraph)
-       ("r-irlba" ,r-irlba)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-leiden" ,r-leiden)
-       ("r-lmtest" ,r-lmtest)
-       ("r-mass" ,r-mass)
-       ("r-matrix" ,r-matrix)
-       ("r-miniui" ,r-miniui)
-       ("r-patchwork" ,r-patchwork)
-       ("r-pbapply" ,r-pbapply)
-       ("r-plotly" ,r-plotly)
-       ("r-png" ,r-png)
-       ("r-rann" ,r-rann)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcppannoy" ,r-rcppannoy)
-       ("r-rcppeigen" ,r-rcppeigen)
-       ("r-rcppprogress" ,r-rcppprogress)
-       ("r-reticulate" ,r-reticulate)
-       ("r-rlang" ,r-rlang)
-       ("r-rocr" ,r-rocr)
-       ("r-rsvd" ,r-rsvd)
-       ("r-rtsne" ,r-rtsne)
-       ("r-scales" ,r-scales)
-       ("r-sctransform" ,r-sctransform)
-       ("r-shiny" ,r-shiny)
-       ("r-spatstat" ,r-spatstat)
-       ("r-tibble" ,r-tibble)
-       ("r-uwot" ,r-uwot)))
-    (home-page "http://www.satijalab.org/seurat")
-    (synopsis "Seurat is an R toolkit for single cell genomics")
-    (description
-     "This package is an R package designed for QC, analysis, and
-exploration of single cell RNA-seq data.  It easily enables widely-used
-analytical techniques, including the identification of highly variable genes,
-dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
-algorithms; density clustering, hierarchical clustering, k-means, and the
-discovery of differentially expressed genes and markers.")
-    (license license:gpl3)))
-
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a6c2518978..8b2a5fc1dc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -23802,3 +23802,68 @@ statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
 alignment using warping functions, handling of replicated measurements as well
 as allowing spectra with different resolutions.")
     (license license:gpl3+)))
+
+(define-public r-seurat
+  (package
+    (name "r-seurat")
+    (version "3.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "Seurat" version))
+              (sha256
+               (base32
+                "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
+    (properties `((upstream-name . "Seurat")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-cluster" ,r-cluster)
+       ("r-cowplot" ,r-cowplot)
+       ("r-fitdistrplus" ,r-fitdistrplus)
+       ("r-future" ,r-future)
+       ("r-future-apply" ,r-future-apply)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggrepel" ,r-ggrepel)
+       ("r-ggridges" ,r-ggridges)
+       ("r-httr" ,r-httr)
+       ("r-ica" ,r-ica)
+       ("r-igraph" ,r-igraph)
+       ("r-irlba" ,r-irlba)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-kernsmooth" ,r-kernsmooth)
+       ("r-leiden" ,r-leiden)
+       ("r-lmtest" ,r-lmtest)
+       ("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-miniui" ,r-miniui)
+       ("r-patchwork" ,r-patchwork)
+       ("r-pbapply" ,r-pbapply)
+       ("r-plotly" ,r-plotly)
+       ("r-png" ,r-png)
+       ("r-rann" ,r-rann)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppannoy" ,r-rcppannoy)
+       ("r-rcppeigen" ,r-rcppeigen)
+       ("r-rcppprogress" ,r-rcppprogress)
+       ("r-reticulate" ,r-reticulate)
+       ("r-rlang" ,r-rlang)
+       ("r-rocr" ,r-rocr)
+       ("r-rsvd" ,r-rsvd)
+       ("r-rtsne" ,r-rtsne)
+       ("r-scales" ,r-scales)
+       ("r-sctransform" ,r-sctransform)
+       ("r-shiny" ,r-shiny)
+       ("r-spatstat" ,r-spatstat)
+       ("r-tibble" ,r-tibble)
+       ("r-uwot" ,r-uwot)))
+    (home-page "http://www.satijalab.org/seurat")
+    (synopsis "Seurat is an R toolkit for single cell genomics")
+    (description
+     "This package is an R package designed for QC, analysis, and
+exploration of single cell RNA-seq data.  It easily enables widely-used
+analytical techniques, including the identification of highly variable genes,
+dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
+algorithms; density clustering, hierarchical clustering, k-means, and the
+discovery of differentially expressed genes and markers.")
+    (license license:gpl3)))
-- 
2.28.0

Message #35 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 11/12] gnu: r-diversitree: Move to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:08:47 +0200

* gnu/packages/bioinformatics.scm (r-diversitree): Move from here ...
* gnu/packages/cran.scm (r-diversitree): ... to here.
---
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 gnu/packages/cran.scm           | 31 +++++++++++++++++++++++++++++++
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bec6c1dc4a..6381523009 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13084,37 +13084,6 @@ analyses in addition to large-scale sequence-level searches.")
       (supported-systems '("x86_64-linux"))
       (license license:bsd-3))))
 
-(define-public r-diversitree
-  (package
-    (name "r-diversitree")
-    (version "0.9-13")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (cran-uri "diversitree" version))
-        (sha256
-         (base32
-          "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
-    (build-system r-build-system)
-    (native-inputs
-     `(("gfortran" ,gfortran)))
-    (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
-    (propagated-inputs
-     `(("r-ape" ,r-ape)
-       ("r-desolve" ,r-desolve)
-       ("r-rcpp" ,r-rcpp)
-       ("r-subplex" ,r-subplex)))
-    (home-page "https://www.zoology.ubc.ca/prog/diversitree")
-    (synopsis "Comparative 'phylogenetic' analyses of diversification")
-    (description "This package contains a number of comparative \"phylogenetic\"
-methods, mostly focusing on analysing diversification and character evolution.
-Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
-and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
-Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
-include Markov models of discrete and continuous trait evolution and constant
-rate speciation and extinction.")
-    (license license:gpl2+)))
-
 (define-public sjcount
   ;; There is no tag for version 3.2, nor is there a release archive.
   (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 140ce11aac..5b65d2a372 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -23895,3 +23895,34 @@ discovery of differentially expressed genes and markers.")
 estimation of phylogenetic trees and networks using Maximum Likelihood,
 Maximum Parsimony, distance methods and Hadamard conjugation.")
     (license license:gpl2+)))
+
+(define-public r-diversitree
+  (package
+    (name "r-diversitree")
+    (version "0.9-13")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "diversitree" version))
+        (sha256
+         (base32
+          "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-desolve" ,r-desolve)
+       ("r-rcpp" ,r-rcpp)
+       ("r-subplex" ,r-subplex)))
+    (home-page "https://www.zoology.ubc.ca/prog/diversitree")
+    (synopsis "Comparative 'phylogenetic' analyses of diversification")
+    (description "This package contains a number of comparative \"phylogenetic\"
+methods, mostly focusing on analysing diversification and character evolution.
+Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
+and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
+Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
+include Markov models of discrete and continuous trait evolution and constant
+rate speciation and extinction.")
+    (license license:gpl2+)))
-- 
2.28.0

Message #38 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 12/12] gnu: r-absfiltergsea: Move to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:08:48 +0200

* gnu/packages/bioinformatics.scm (r-absfiltergsea): Move from here ...
* gnu/packages/cran.scm (r-absfiltergsea): ... to here.
---
 gnu/packages/bioinformatics.scm | 27 ---------------------------
 gnu/packages/cran.scm           | 27 +++++++++++++++++++++++++++
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6381523009..ffa2618458 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14083,33 +14083,6 @@ downstream analysis.  Poretools operates directly on the native FAST5, a variant
 of the Hierarchical Data Format (HDF5) standard.")
       (license license:expat))))
 
-(define-public r-absfiltergsea
-  (package
-    (name "r-absfiltergsea")
-    (version "1.5.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "AbsFilterGSEA" version))
-       (sha256
-        (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
-    (properties `((upstream-name . "AbsFilterGSEA")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-deseq" ,r-deseq)
-       ("r-limma" ,r-limma)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)))
-    (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
-    (synopsis "Improved false positive control of gene-permuting with absolute filtering")
-    (description
-     "This package provides a function that performs gene-permuting of a gene-set
-enrichment analysis (GSEA) calculation with or without the absolute filtering.
-  Without filtering, users can perform (original) two-tailed or one-tailed
-absolute GSEA.")
-    (license license:gpl2)))
-
 (define-public jamm
   (package
     (name "jamm")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5b65d2a372..f9b6930f70 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -23926,3 +23926,30 @@ Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
 include Markov models of discrete and continuous trait evolution and constant
 rate speciation and extinction.")
     (license license:gpl2+)))
+
+(define-public r-absfiltergsea
+  (package
+    (name "r-absfiltergsea")
+    (version "1.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AbsFilterGSEA" version))
+       (sha256
+        (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
+    (properties `((upstream-name . "AbsFilterGSEA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-deseq" ,r-deseq)
+       ("r-limma" ,r-limma)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
+    (synopsis "Improved false positive control of gene-permuting with absolute filtering")
+    (description
+     "This package provides a function that performs gene-permuting of a gene-set
+enrichment analysis (GSEA) calculation with or without the absolute filtering.
+  Without filtering, users can perform (original) two-tailed or one-tailed
+absolute GSEA.")
+    (license license:gpl2)))
-- 
2.28.0

Message #41 received at 43345 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 43345 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 10/12] gnu: r-phangorn: Move to (gnu packages cran).
Date: Fri, 11 Sep 2020 20:08:49 +0200

* gnu/packages/bioinformatics.scm (r-phangorn): Move from here ...
* gnu/packages/cran.scm (r-phangorn): ... to here.
---
 gnu/packages/bioinformatics.scm | 28 ----------------------------
 gnu/packages/cran.scm           | 28 ++++++++++++++++++++++++++++
 2 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a6505099fc..bec6c1dc4a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10936,34 +10936,6 @@ are optimized per data type and for subsetted calculations such that both
 memory usage and processing time is minimized.")
     (license license:expat)))
 
-(define-public r-phangorn
-  (package
-    (name "r-phangorn")
-    (version "2.5.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "phangorn" version))
-       (sha256
-        (base32
-         "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-ape" ,r-ape)
-       ("r-fastmatch" ,r-fastmatch)
-       ("r-igraph" ,r-igraph)
-       ("r-magrittr" ,r-magrittr)
-       ("r-matrix" ,r-matrix)
-       ("r-quadprog" ,r-quadprog)
-       ("r-rcpp" ,r-rcpp)))
-    (home-page "https://github.com/KlausVigo/phangorn")
-    (synopsis "Phylogenetic analysis in R")
-    (description
-     "Phangorn is a package for phylogenetic analysis in R.  It supports
-estimation of phylogenetic trees and networks using Maximum Likelihood,
-Maximum Parsimony, distance methods and Hadamard conjugation.")
-    (license license:gpl2+)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8b2a5fc1dc..140ce11aac 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -23867,3 +23867,31 @@ dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
 algorithms; density clustering, hierarchical clustering, k-means, and the
 discovery of differentially expressed genes and markers.")
     (license license:gpl3)))
+
+(define-public r-phangorn
+  (package
+    (name "r-phangorn")
+    (version "2.5.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "phangorn" version))
+       (sha256
+        (base32
+         "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-fastmatch" ,r-fastmatch)
+       ("r-igraph" ,r-igraph)
+       ("r-magrittr" ,r-magrittr)
+       ("r-matrix" ,r-matrix)
+       ("r-quadprog" ,r-quadprog)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/KlausVigo/phangorn")
+    (synopsis "Phylogenetic analysis in R")
+    (description
+     "Phangorn is a package for phylogenetic analysis in R.  It supports
+estimation of phylogenetic trees and networks using Maximum Likelihood,
+Maximum Parsimony, distance methods and Hadamard conjugation.")
+    (license license:gpl2+)))
-- 
2.28.0

Message #46 received at 43345-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 43345-done <at> debbugs.gnu.org
Subject: Re: [bug#43345] [PATCH 00/12] Move some CRAN packages to (gnu
 packages cran).
Date: Fri, 11 Sep 2020 22:07:46 +0200

Hi simon,

thank you for this janitorial work!

> Some clean up leading the recent discussion [1].  Now, the only remaining
> 'cran-uri' are from (gnu packages statistics).  Modulo maybe some packages
> using "bad" uri, e.g., from r-qtl:
>
> --8<---------------cut here---------------start------------->8---
>     (uri (string-append "mirror://cran/src/contrib/qtl_"
>                         version ".tar.gz"))
> --8<---------------cut here---------------end--------------->8---

I fixed that URL (and a few more things that became obvious during the
move).

> To ease the Copyright transfer between files, I used:
>
>   git log --grep=<package-name>
>   git log --date=format:"%Y" --format="%ad %an" \
>       -- gnu/packages/<file>.scm | sort | uniq -c
>
> After each move, I run:
>
>   make
>   ./pre-env-inst guix build <package-name>
>   ./pre-env-inst guix build <package-name> --no-grafts --check

Excellent!  Thank you for being so dilligent.  For some reason you
missed the import of (gnu packages xml) after the move of r-igraph.  I
added it.  I also updated the commit messages for consistency in
punctuation (sorry for being picky).

Pushed to the “master” branch with commit 8458490bc2.

Thanks again!

-- 
Ricardo

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