[bug#47156] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

[bug#47156] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

[zimoun]

Hi,

Janitor [1] patch set.  It moves Bioconductor packages from (gnu packages
bioinformatics) to (gnu packages bioconductor).  Far to be complete; still 5
pacth set like this one are coming...

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


To transfer the Copyright, I use:

   git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r-<name>

Then, after the move, I run:

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

and at the end of the series, I run:

    make as-derivation

to check that "guix pull" is not broken; just in case.

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

All the best,
simon

zimoun (10):
  gnu: r-grohmm: Move to (gnu packages bioconductor).
  gnu: r-biocviews: Move to (gnu packages bioconductor).
  gnu: r-biocstyle: Move to (gnu packages bioconductor).
  gnu: r-bioccheck: Move to (gnu packages bioconductor).
  gnu: r-s4vectors: Move to (gnu packages bioconductor).
  gnu: r-iranges: Move to (gnu packages bioconductor).
  gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor).
  gnu: r-genomeinfodb: Move to (gnu packages bioconductor).
  gnu: r-edger: Move to (gnu packages bioconductor).
  gnu: r-variantannotation: Move to (gnu packages bioconductor).

 gnu/packages/bioconductor.scm   | 303 +++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 307 --------------------------------
 2 files changed, 303 insertions(+), 307 deletions(-)


base-commit: 1ed435bf394eee1a6cd9c354efb405920c212f0e
-- 
2.30.1

[bug#47156] [PATCH 01/10] gnu: r-grohmm: Move to (gnu packages bioconductor).

[zimoun]

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4f8e0562b1..55f718d5ab 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8511,6 +8511,33 @@ and manages a local cache of files retrieved enabling quick and reproducible
 access.")
     (license license:artistic2.0)))
 
+(define-public r-grohmm
+  (package
+    (name "r-grohmm")
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "groHMM" version))
+       (sha256
+        (base32
+         "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
+    (properties `((upstream-name . "groHMM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-mass" ,r-mass)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://github.com/Kraus-Lab/groHMM")
+    (synopsis "GRO-seq analysis pipeline")
+    (description
+     "This package provides a pipeline for the analysis of GRO-seq data.")
+    (license license:gpl3+)))
+
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b0736d32e4..20a9385604 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7387,33 +7387,6 @@ includes software to
 ")
       (license license:cc0))))
 
-(define-public r-grohmm
-  (package
-    (name "r-grohmm")
-    (version "1.24.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "groHMM" version))
-       (sha256
-        (base32
-         "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
-    (properties `((upstream-name . "groHMM")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-mass" ,r-mass)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://github.com/Kraus-Lab/groHMM")
-    (synopsis "GRO-seq analysis pipeline")
-    (description
-     "This package provides a pipeline for the analysis of GRO-seq data.")
-    (license license:gpl3+)))
-
 (define-public vsearch
   (package
     (name "vsearch")

base-commit: 1ed435bf394eee1a6cd9c354efb405920c212f0e
-- 
2.30.1

[bug#47156] [PATCH 02/10] gnu: r-biocviews: Move to (gnu packages bioconductor).

[zimoun]

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 55f718d5ab..4761474b04 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8477,6 +8477,34 @@ monograph.")
 different graph related packages produced by Bioconductor.")
     (license license:artistic2.0)))
 
+(define-public r-biocviews
+  (package
+    (name "r-biocviews")
+    (version "1.58.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "biocViews" version))
+              (sha256
+               (base32
+                "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
+    (properties
+     `((upstream-name . "biocViews")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-graph" ,r-graph)
+       ("r-rbgl" ,r-rbgl)
+       ("r-rcurl" ,r-rcurl)
+       ("r-xml" ,r-xml)
+       ("r-runit" ,r-runit)))
+    (home-page "https://bioconductor.org/packages/biocViews")
+    (synopsis "Bioconductor package categorization helper")
+    (description "The purpose of biocViews is to create HTML pages that
+categorize packages in a Bioconductor package repository according to keywords,
+also known as views, in a controlled vocabulary.")
+    (license license:artistic2.0)))
+
 (define-public r-experimenthub
   (package
     (name "r-experimenthub")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 20a9385604..cc6e40283b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,34 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-biocviews
-  (package
-    (name "r-biocviews")
-    (version "1.58.1")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "biocViews" version))
-              (sha256
-               (base32
-                "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
-    (properties
-     `((upstream-name . "biocViews")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-graph" ,r-graph)
-       ("r-rbgl" ,r-rbgl)
-       ("r-rcurl" ,r-rcurl)
-       ("r-xml" ,r-xml)
-       ("r-runit" ,r-runit)))
-    (home-page "https://bioconductor.org/packages/biocViews")
-    (synopsis "Bioconductor package categorization helper")
-    (description "The purpose of biocViews is to create HTML pages that
-categorize packages in a Bioconductor package repository according to keywords,
-also known as views, in a controlled vocabulary.")
-    (license license:artistic2.0)))
-
 (define-public r-biocstyle
   (package
     (name "r-biocstyle")
-- 
2.30.1

[bug#47156] [PATCH 03/10] gnu: r-biocstyle: Move to (gnu packages bioconductor).

[zimoun]

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4761474b04..91d02639a3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8477,6 +8477,34 @@ monograph.")
 different graph related packages produced by Bioconductor.")
     (license license:artistic2.0)))
 
+(define-public r-biocstyle
+  (package
+    (name "r-biocstyle")
+    (version "2.18.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BiocStyle" version))
+              (sha256
+               (base32
+                "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
+    (properties
+     `((upstream-name . "BiocStyle")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocmanager" ,r-biocmanager)
+       ("r-bookdown" ,r-bookdown)
+       ("r-knitr" ,r-knitr)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-yaml" ,r-yaml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/BiocStyle")
+    (synopsis "Bioconductor formatting styles")
+    (description "This package provides standard formatting styles for
+Bioconductor PDF and HTML documents.  Package vignettes illustrate use and
+functionality.")
+    (license license:artistic2.0)))
+
 (define-public r-biocviews
   (package
     (name "r-biocviews")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cc6e40283b..ad3ae204e1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,34 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-biocstyle
-  (package
-    (name "r-biocstyle")
-    (version "2.18.1")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "BiocStyle" version))
-              (sha256
-               (base32
-                "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
-    (properties
-     `((upstream-name . "BiocStyle")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocmanager" ,r-biocmanager)
-       ("r-bookdown" ,r-bookdown)
-       ("r-knitr" ,r-knitr)
-       ("r-rmarkdown" ,r-rmarkdown)
-       ("r-yaml" ,r-yaml)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/BiocStyle")
-    (synopsis "Bioconductor formatting styles")
-    (description "This package provides standard formatting styles for
-Bioconductor PDF and HTML documents.  Package vignettes illustrate use and
-functionality.")
-    (license license:artistic2.0)))
-
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-- 
2.30.1

[bug#47156] [PATCH 04/10] gnu: r-bioccheck: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here...
* gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
---
 gnu/packages/bioconductor.scm   | 49 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 49 ---------------------------------
 2 files changed, 49 insertions(+), 49 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 91d02639a3..7c97e52312 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8452,6 +8452,55 @@ microarray data.")
 monograph.")
     (license license:artistic2.0)))
 
+(define-public r-bioccheck
+  (package
+    (name "r-bioccheck")
+    (version "1.26.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BiocCheck" version))
+              (sha256
+               (base32
+                "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
+    (properties
+     `((upstream-name . "BiocCheck")))
+    (build-system r-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         ;; This package can be used by calling BiocCheck(<package>) from
+         ;; within R, or by running R CMD BiocCheck <package>.  This phase
+         ;; makes sure the latter works.  For this to work, the BiocCheck
+         ;; script must be somewhere on the PATH (not the R bin directory).
+         (add-after 'install 'install-bioccheck-subcommand
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (dest-dir (string-append out "/bin"))
+                    (script-dir
+                     (string-append out "/site-library/BiocCheck/script/")))
+               (mkdir-p dest-dir)
+               (symlink (string-append script-dir "/checkBadDeps.R")
+                        (string-append dest-dir "/checkBadDeps.R"))
+               (symlink (string-append script-dir "/BiocCheck")
+                        (string-append dest-dir "/BiocCheck")))
+             #t)))))
+    (propagated-inputs
+     `(("r-codetools" ,r-codetools)
+       ("r-graph" ,r-graph)
+       ("r-httr" ,r-httr)
+       ("r-knitr" ,r-knitr)
+       ("r-optparse" ,r-optparse)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-biocviews" ,r-biocviews)
+       ("r-stringdist" ,r-stringdist)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/BiocCheck")
+    (synopsis "Executes Bioconductor-specific package checks")
+    (description "This package contains tools to perform additional quality
+checks on R packages that are to be submitted to the Bioconductor repository.")
+    (license license:artistic2.0)))
+
 (define-public r-biocgraph
   (package
     (name "r-biocgraph")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ad3ae204e1..d8d64818d2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,55 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-bioccheck
-  (package
-    (name "r-bioccheck")
-    (version "1.26.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "BiocCheck" version))
-              (sha256
-               (base32
-                "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
-    (properties
-     `((upstream-name . "BiocCheck")))
-    (build-system r-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         ;; This package can be used by calling BiocCheck(<package>) from
-         ;; within R, or by running R CMD BiocCheck <package>.  This phase
-         ;; makes sure the latter works.  For this to work, the BiocCheck
-         ;; script must be somewhere on the PATH (not the R bin directory).
-         (add-after 'install 'install-bioccheck-subcommand
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (dest-dir (string-append out "/bin"))
-                    (script-dir
-                     (string-append out "/site-library/BiocCheck/script/")))
-               (mkdir-p dest-dir)
-               (symlink (string-append script-dir "/checkBadDeps.R")
-                        (string-append dest-dir "/checkBadDeps.R"))
-               (symlink (string-append script-dir "/BiocCheck")
-                        (string-append dest-dir "/BiocCheck")))
-             #t)))))
-    (propagated-inputs
-     `(("r-codetools" ,r-codetools)
-       ("r-graph" ,r-graph)
-       ("r-httr" ,r-httr)
-       ("r-knitr" ,r-knitr)
-       ("r-optparse" ,r-optparse)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biocviews" ,r-biocviews)
-       ("r-stringdist" ,r-stringdist)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/BiocCheck")
-    (synopsis "Executes Bioconductor-specific package checks")
-    (description "This package contains tools to perform additional quality
-checks on R packages that are to be submitted to the Bioconductor repository.")
-    (license license:artistic2.0)))
-
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-- 
2.30.1

[bug#47156] [PATCH 05/10] gnu: r-s4vectors: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-s4vectors): Move from here...
* gnu/packages/bioconductor.scm (r-s4vectors): ...to here.
---
 gnu/packages/bioconductor.scm   | 28 ++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 27 ---------------------------
 2 files changed, 28 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7c97e52312..ed34a9308a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
@@ -9154,6 +9155,33 @@ generated.")
 routines.")
     (license license:lgpl2.0+)))
 
+(define-public r-s4vectors
+  (package
+    (name "r-s4vectors")
+    (version "0.28.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "S4Vectors" version))
+              (sha256
+               (base32
+                "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh"))))
+    (properties
+     `((upstream-name . "S4Vectors")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)))
+    (home-page "https://bioconductor.org/packages/S4Vectors")
+    (synopsis "S4 implementation of vectors and lists")
+    (description
+     "The S4Vectors package defines the @code{Vector} and @code{List} virtual
+classes and a set of generic functions that extend the semantic of ordinary
+vectors and lists in R.  Package developers can easily implement vector-like
+or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
+In addition, a few low-level concrete subclasses of general interest (e.g.
+@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
+S4Vectors package itself.")
+    (license license:artistic2.0)))
+
 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
 ;; Bioconductor package.
 (define-public r-wgcna
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d8d64818d2..1fcb436f0d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,33 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-s4vectors
-  (package
-    (name "r-s4vectors")
-    (version "0.28.1")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "S4Vectors" version))
-              (sha256
-               (base32
-                "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh"))))
-    (properties
-     `((upstream-name . "S4Vectors")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)))
-    (home-page "https://bioconductor.org/packages/S4Vectors")
-    (synopsis "S4 implementation of vectors and lists")
-    (description
-     "The S4Vectors package defines the @code{Vector} and @code{List} virtual
-classes and a set of generic functions that extend the semantic of ordinary
-vectors and lists in R.  Package developers can easily implement vector-like
-or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
-In addition, a few low-level concrete subclasses of general interest (e.g.
-@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
-S4Vectors package itself.")
-    (license license:artistic2.0)))
-
 (define-public r-iranges
   (package
     (name "r-iranges")
-- 
2.30.1

[bug#47156] [PATCH 06/10] gnu: r-iranges: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-iranges): Move from here...
* gnu/packages/bioconductor.scm (r-iranges): ...to here.
---
 gnu/packages/bioconductor.scm   | 30 ++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 29 -----------------------------
 2 files changed, 30 insertions(+), 29 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ed34a9308a..68c5ed7768 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
+;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
@@ -1244,6 +1245,35 @@ and evaluate clustering results.")
 arbitrary genomic intervals along chromosomal ideogram.")
     (license license:gpl2)))
 
+(define-public r-iranges
+  (package
+    (name "r-iranges")
+    (version "2.24.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "IRanges" version))
+              (sha256
+               (base32
+                "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52"))))
+    (properties
+     `((upstream-name . "IRanges")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/IRanges")
+    (synopsis "Infrastructure for manipulating intervals on sequences")
+    (description
+     "This package provides efficient low-level and highly reusable S4 classes
+for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
+generally, data that can be organized sequentially (formally defined as
+@code{Vector} objects), as well as views on these @code{Vector} objects.
+Efficient list-like classes are also provided for storing big collections of
+instances of the basic classes.  All classes in the package use consistent
+naming and share the same rich and consistent \"Vector API\" as much as
+possible.")
+    (license license:artistic2.0)))
+
 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
 ;; from Bioconductor.
 (define-public r-deconstructsigs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1fcb436f0d..36ecf47467 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,35 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-iranges
-  (package
-    (name "r-iranges")
-    (version "2.24.1")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "IRanges" version))
-              (sha256
-               (base32
-                "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52"))))
-    (properties
-     `((upstream-name . "IRanges")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://bioconductor.org/packages/IRanges")
-    (synopsis "Infrastructure for manipulating intervals on sequences")
-    (description
-     "This package provides efficient low-level and highly reusable S4 classes
-for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
-generally, data that can be organized sequentially (formally defined as
-@code{Vector} objects), as well as views on these @code{Vector} objects.
-Efficient list-like classes are also provided for storing big collections of
-instances of the basic classes.  All classes in the package use consistent
-naming and share the same rich and consistent \"Vector API\" as much as
-possible.")
-    (license license:artistic2.0)))
-
 (define-public r-genomeinfodbdata
   (package
     (name "r-genomeinfodbdata")
-- 
2.30.1

[bug#47156] [PATCH 07/10] gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.
---
 gnu/packages/bioconductor.scm   | 20 ++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 23 -----------------------
 2 files changed, 20 insertions(+), 23 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 68c5ed7768..53f025ec61 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
@@ -391,6 +392,25 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
 in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-genomeinfodbdata
+  (package
+    (name "r-genomeinfodbdata")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
+              (sha256
+               (base32
+                "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
+    (properties
+     `((upstream-name . "GenomeInfoDbData")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
+    (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
+    (description "This package contains data for mapping between NCBI taxonomy
+ID and species.  It is used by functions in the GenomeInfoDb package.")
+    (license license:artistic2.0)))
+
 (define-public r-homo-sapiens
   (package
     (name "r-homo-sapiens")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 36ecf47467..25ade2b9db 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,29 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-genomeinfodbdata
-  (package
-    (name "r-genomeinfodbdata")
-    (version "1.2.0")
-    (source (origin
-              (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://bioconductor.org/packages/release/"
-                                  "data/annotation/src/contrib/GenomeInfoDbData_"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
-    (properties
-     `((upstream-name . "GenomeInfoDbData")))
-    (build-system r-build-system)
-    (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
-    (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
-    (description "This package contains data for mapping between NCBI taxonomy
-ID and species.  It is used by functions in the GenomeInfoDb package.")
-    (license license:artistic2.0)))
-
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-- 
2.30.1

[bug#47156] [PATCH 08/10] gnu: r-genomeinfodb: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.
---
 gnu/packages/bioconductor.scm   | 30 ++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 30 ------------------------------
 2 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 53f025ec61..b4456d13c8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1712,6 +1712,36 @@ exploration of the results.")
 high-throughput sequencing experiments.")
     (license license:artistic2.0)))
 
+(define-public r-genomeinfodb
+  (package
+    (name "r-genomeinfodb")
+    (version "1.26.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GenomeInfoDb" version))
+              (sha256
+               (base32
+                "092izc49maxjhf6m4b0qx21ad16dz7bmxy5pysp3vkyhdrfa2f7v"))))
+    (properties
+     `((upstream-name . "GenomeInfoDb")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomeinfodbdata" ,r-genomeinfodbdata)
+       ("r-iranges" ,r-iranges)
+       ("r-rcurl" ,r-rcurl)
+       ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/GenomeInfoDb")
+    (synopsis "Utilities for manipulating chromosome identifiers")
+    (description
+     "This package contains data and functions that define and allow
+translation between different chromosome sequence naming conventions (e.g.,
+\"chr1\" versus \"1\"), including a function that attempts to place sequence
+names in their natural, rather than lexicographic, order.")
+    (license license:artistic2.0)))
+
 (define-public r-gostats
   (package
     (name "r-gostats")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 25ade2b9db..ff6996011e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,36 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-genomeinfodb
-  (package
-    (name "r-genomeinfodb")
-    (version "1.26.2")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "GenomeInfoDb" version))
-              (sha256
-               (base32
-                "092izc49maxjhf6m4b0qx21ad16dz7bmxy5pysp3vkyhdrfa2f7v"))))
-    (properties
-     `((upstream-name . "GenomeInfoDb")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomeinfodbdata" ,r-genomeinfodbdata)
-       ("r-iranges" ,r-iranges)
-       ("r-rcurl" ,r-rcurl)
-       ("r-s4vectors" ,r-s4vectors)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/GenomeInfoDb")
-    (synopsis "Utilities for manipulating chromosome identifiers")
-    (description
-     "This package contains data and functions that define and allow
-translation between different chromosome sequence naming conventions (e.g.,
-\"chr1\" versus \"1\"), including a function that attempts to place sequence
-names in their natural, rather than lexicographic, order.")
-    (license license:artistic2.0)))
-
 (define-public r-edger
   (package
     (name "r-edger")
-- 
2.30.1

[bug#47156] [PATCH 09/10] gnu: r-edger: Move to (gnu packages bioconductor).

[zimoun]

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b4456d13c8..fb0127b7ca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1684,6 +1684,34 @@ testing.  The package also provides functions for the visualization and
 exploration of the results.")
     (license license:gpl3+)))
 
+(define-public r-edger
+  (package
+    (name "r-edger")
+    (version "3.32.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "edgeR" version))
+              (sha256
+               (base32
+                "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp"))))
+    (properties `((upstream-name . "edgeR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-limma" ,r-limma)
+       ("r-locfit" ,r-locfit)
+       ("r-rcpp" ,r-rcpp)
+       ("r-statmod" ,r-statmod))) ;for estimateDisp
+    (home-page "http://bioinf.wehi.edu.au/edgeR")
+    (synopsis "EdgeR does empirical analysis of digital gene expression data")
+    (description "This package can do differential expression analysis of
+RNA-seq expression profiles with biological replication.  It implements a range
+of statistical methodology based on the negative binomial distributions,
+including empirical Bayes estimation, exact tests, generalized linear models
+and quasi-likelihood tests.  It be applied to differential signal analysis of
+other types of genomic data that produce counts, including ChIP-seq, SAGE and
+CAGE.")
+    (license license:gpl2+)))
+
 (define-public r-genefilter
   (package
     (name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ff6996011e..dc0d7a2906 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,34 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-edger
-  (package
-    (name "r-edger")
-    (version "3.32.1")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "edgeR" version))
-              (sha256
-               (base32
-                "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp"))))
-    (properties `((upstream-name . "edgeR")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-limma" ,r-limma)
-       ("r-locfit" ,r-locfit)
-       ("r-rcpp" ,r-rcpp)
-       ("r-statmod" ,r-statmod))) ;for estimateDisp
-    (home-page "http://bioinf.wehi.edu.au/edgeR")
-    (synopsis "EdgeR does empirical analysis of digital gene expression data")
-    (description "This package can do differential expression analysis of
-RNA-seq expression profiles with biological replication.  It implements a range
-of statistical methodology based on the negative binomial distributions,
-including empirical Bayes estimation, exact tests, generalized linear models
-and quasi-likelihood tests.  It be applied to differential signal analysis of
-other types of genomic data that produce counts, including ChIP-seq, SAGE and
-CAGE.")
-    (license license:gpl2+)))
-
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-- 
2.30.1

[bug#47156] [PATCH 10/10] gnu: r-variantannotation: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here...
* gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
---
 gnu/packages/bioconductor.scm   | 38 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 38 ---------------------------------
 2 files changed, 38 insertions(+), 38 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fb0127b7ca..c4df090a05 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2051,6 +2051,44 @@ experimental designs is facilitated by a consistently implemented sample
 annotation infrastructure.")
     (license license:artistic2.0)))
 
+(define-public r-variantannotation
+  (package
+    (name "r-variantannotation")
+    (version "1.36.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "VariantAnnotation" version))
+              (sha256
+               (base32
+                "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
+    (properties
+     `((upstream-name . "VariantAnnotation")))
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-dbi" ,r-dbi)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixgenerics" ,r-matrixgenerics)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/VariantAnnotation")
+    (synopsis "Package for annotation of genetic variants")
+    (description "This R package can annotate variants, compute amino acid
+coding changes and predict coding outcomes.")
+    (license license:artistic2.0)))
+
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dc0d7a2906..78df3091fe 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,44 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-variantannotation
-  (package
-    (name "r-variantannotation")
-    (version "1.36.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "VariantAnnotation" version))
-              (sha256
-               (base32
-                "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
-    (properties
-     `((upstream-name . "VariantAnnotation")))
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-dbi" ,r-dbi)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixgenerics" ,r-matrixgenerics)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (build-system r-build-system)
-    (home-page "https://bioconductor.org/packages/VariantAnnotation")
-    (synopsis "Package for annotation of genetic variants")
-    (description "This R package can annotate variants, compute amino acid
-coding changes and predict coding outcomes.")
-    (license license:artistic2.0)))
-
 (define-public r-limma
   (package
     (name "r-limma")
-- 
2.30.1

bug#47156: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

[Ricardo Wurmus]

zimoun <zimon.toutoune@gmail.com> writes:
>
> Janitor [1] patch set.  It moves Bioconductor packages from (gnu packages
> bioinformatics) to (gnu packages bioconductor).  Far to be complete; still 5
> pacth set like this one are coming...

Thank you, I applied it (last commit is
bf612ead766ee5afcdccd7c8ab003b791ecea9df).

-- 
Ricardo