* [bug#47156] [PATCH 02/10] gnu: r-biocviews: Move to (gnu packages bioconductor).
2021-03-15 13:01 ` [bug#47156] [PATCH 01/10] gnu: r-grohmm: Move " zimoun
@ 2021-03-15 13:01 ` zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 03/10] gnu: r-biocstyle: " zimoun
` (6 subsequent siblings)
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-15 13:01 UTC (permalink / raw)
To: 47156; +Cc: 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
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47156] [PATCH 03/10] gnu: r-biocstyle: Move to (gnu packages bioconductor).
2021-03-15 13:01 ` [bug#47156] [PATCH 01/10] gnu: r-grohmm: Move " zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 02/10] gnu: r-biocviews: " zimoun
@ 2021-03-15 13:01 ` zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 04/10] gnu: r-bioccheck: " zimoun
` (5 subsequent siblings)
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-15 13:01 UTC (permalink / raw)
To: 47156; +Cc: 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
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47156] [PATCH 04/10] gnu: r-bioccheck: Move to (gnu packages bioconductor).
2021-03-15 13:01 ` [bug#47156] [PATCH 01/10] gnu: r-grohmm: Move " zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 02/10] gnu: r-biocviews: " zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 03/10] gnu: r-biocstyle: " zimoun
@ 2021-03-15 13:01 ` zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 05/10] gnu: r-s4vectors: " zimoun
` (4 subsequent siblings)
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-15 13:01 UTC (permalink / raw)
To: 47156; +Cc: 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
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47156] [PATCH 05/10] gnu: r-s4vectors: Move to (gnu packages bioconductor).
2021-03-15 13:01 ` [bug#47156] [PATCH 01/10] gnu: r-grohmm: Move " zimoun
` (2 preceding siblings ...)
2021-03-15 13:01 ` [bug#47156] [PATCH 04/10] gnu: r-bioccheck: " zimoun
@ 2021-03-15 13:01 ` zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 06/10] gnu: r-iranges: " zimoun
` (3 subsequent siblings)
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-15 13:01 UTC (permalink / raw)
To: 47156; +Cc: 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
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47156] [PATCH 06/10] gnu: r-iranges: Move to (gnu packages bioconductor).
2021-03-15 13:01 ` [bug#47156] [PATCH 01/10] gnu: r-grohmm: Move " zimoun
` (3 preceding siblings ...)
2021-03-15 13:01 ` [bug#47156] [PATCH 05/10] gnu: r-s4vectors: " zimoun
@ 2021-03-15 13:01 ` zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 07/10] gnu: r-genomeinfodbdata: " zimoun
` (2 subsequent siblings)
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-15 13:01 UTC (permalink / raw)
To: 47156; +Cc: 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
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47156] [PATCH 07/10] gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor).
2021-03-15 13:01 ` [bug#47156] [PATCH 01/10] gnu: r-grohmm: Move " zimoun
` (4 preceding siblings ...)
2021-03-15 13:01 ` [bug#47156] [PATCH 06/10] gnu: r-iranges: " zimoun
@ 2021-03-15 13:01 ` zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 08/10] gnu: r-genomeinfodb: " zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 09/10] gnu: r-edger: " zimoun
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-15 13:01 UTC (permalink / raw)
To: 47156; +Cc: 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
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47156] [PATCH 08/10] gnu: r-genomeinfodb: Move to (gnu packages bioconductor).
2021-03-15 13:01 ` [bug#47156] [PATCH 01/10] gnu: r-grohmm: Move " zimoun
` (5 preceding siblings ...)
2021-03-15 13:01 ` [bug#47156] [PATCH 07/10] gnu: r-genomeinfodbdata: " zimoun
@ 2021-03-15 13:01 ` zimoun
2021-03-15 13:01 ` [bug#47156] [PATCH 09/10] gnu: r-edger: " zimoun
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-15 13:01 UTC (permalink / raw)
To: 47156; +Cc: 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
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47156] [PATCH 09/10] gnu: r-edger: Move to (gnu packages bioconductor).
2021-03-15 13:01 ` [bug#47156] [PATCH 01/10] gnu: r-grohmm: Move " zimoun
` (6 preceding siblings ...)
2021-03-15 13:01 ` [bug#47156] [PATCH 08/10] gnu: r-genomeinfodb: " zimoun
@ 2021-03-15 13:01 ` zimoun
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-15 13:01 UTC (permalink / raw)
To: 47156; +Cc: 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
^ permalink raw reply related [flat|nested] 12+ messages in thread