[PATCH 00/12] Move some BioConductor to (gnu packages bioconductor)

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2 participants
  • Ricardo Wurmus
  • zimoun
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unassigned
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zimoun
Severity
normal
Z
Z
zimoun wrote on 14 Sep 2020 18:04
(address . guix-patches@gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160414.7572-1-zimon.toutoune@gmail.com
Dear,

More janitoral stuff. The process is the same as described in the cover


All the best,
simon

zimoun (12):
gnu: r-fourcseq: Move to (gnu packages bioconductor).
gnu: r-preprocesscore: Move to (gnu packages bioconductor).
gnu: r-rgraphviz: Move to (gnu packages bioconductor).
gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor).
gnu: r-scran: Move to (gnu packages bioconductor).
gnu: r-scater: Move to (gnu packages bioconductor).
gnu: r-singlecellexperiment: Move to (gnu packages bioconductor).
gnu: r-beachmat: Move to (gnu packages bioconductor).
gnu: r-rhdf5lib: Move to (gnu packages bioconductor).
gnu: r-hdf5array: Move to (gnu packages bioconductor).
gnu: r-hitc: Move to (gnu packages bioconductor).
gnu: r-fithic: Move to (gnu packages bioconductor).

gnu/packages/bioconductor.scm | 432 ++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 337 -------------------------
gnu/packages/cran.scm | 44 ----
gnu/packages/graph.scm | 28 ---
gnu/packages/statistics.scm | 21 --
5 files changed, 432 insertions(+), 430 deletions(-)


base-commit: c22c6de453a4685bc65bf38f92f823c733d62290
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 02/12] gnu: r-preprocesscore: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-2-zimon.toutoune@gmail.com
* gnu/packages/statistics.scm (r-preprocesscore): Move from here...
* gnu/packages/bioconductor.scm (r-preprocesscore): ...to here.
---
gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++
gnu/packages/statistics.scm | 21 ---------------------
2 files changed, 21 insertions(+), 21 deletions(-)

Toggle diff (63 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 01c4748500..57755e1116 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8286,3 +8286,24 @@ a Python script to demultiplex libraries and trim off primer sequences. With
a standard alignment software the required bam files can be then be
generated.")
(license license:gpl3+)))
+
+(define-public r-preprocesscore
+ (package
+ (name "r-preprocesscore")
+ (version "1.50.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "preprocessCore" version))
+ (sha256
+ (base32
+ "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
+ (properties
+ `((upstream-name . "preprocessCore")))
+ (build-system r-build-system)
+ (home-page "https://github.com/bmbolstad/preprocessCore")
+ (synopsis "Collection of pre-processing functions")
+ (description
+ "This package provides a library of core pre-processing and normalization
+routines.")
+ (license license:lgpl2.0+)))
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 70a85e8b60..f6de1a329c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4079,27 +4079,6 @@ framework, with additional code inspection and report generation tools.")
hierarchical clustering dendrograms.")
(license license:gpl2+)))
-(define-public r-preprocesscore
- (package
- (name "r-preprocesscore")
- (version "1.50.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "preprocessCore" version))
- (sha256
- (base32
- "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
- (properties
- `((upstream-name . "preprocessCore")))
- (build-system r-build-system)
- (home-page "https://github.com/bmbolstad/preprocessCore")
- (synopsis "Collection of pre-processing functions")
- (description
- "This package provides a library of core pre-processing and normalization
-routines.")
- (license license:lgpl2.0+)))
-
(define-public r-fastcluster
(package
(name "r-fastcluster")
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 01/12] gnu: r-fourcseq: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-1-zimon.toutoune@gmail.com
* gnu/packages/cran.scm (r-fourcseq): Move from here...
* gnu/packages/bioconductor.scm (r-fourcseq): ...to here.
---
gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++
gnu/packages/cran.scm | 44 ----------------------------------
2 files changed, 45 insertions(+), 44 deletions(-)

Toggle diff (117 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index db1fdcad17..01c4748500 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,6 +4,7 @@
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
+;;; Copyright © 2020 M?d?lin Ionel Patra?cu <madalinionel.patrascu@mdc-berlin.de>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -8241,3 +8242,47 @@ with:
@end itemize
")
(license license:gpl2+)))
+
+(define-public r-fourcseq
+ (package
+ (name "r-fourcseq")
+ (version "1.22.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "FourCSeq" version))
+ (sha256
+ (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
+ (properties `((upstream-name . "FourCSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biostrings" ,r-biostrings)
+ ("r-deseq2" ,r-deseq2)
+ ("r-fda" ,r-fda)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggbio" ,r-ggbio)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gtools" ,r-gtools)
+ ("r-lsd" ,r-lsd)
+ ("r-matrix" ,r-matrix)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
+ (synopsis "Analysis of multiplexed 4C sequencing data")
+ (description
+ "This package is an R package dedicated to the analysis of (multiplexed)
+4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
+interactions between DNA elements and identify differential interactions
+between conditions. The statistical analysis in R starts with individual bam
+files for each sample as inputs. To obtain these files, the package contains
+a Python script to demultiplex libraries and trim off primer sequences. With
+a standard alignment software the required bam files can be then be
+generated.")
+ (license license:gpl3+)))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index be66533b0b..1ba763ff66 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22572,50 +22572,6 @@ Try a demo of the LSD by running @code{demotour()}.")
;; Either version
(license (list license:gpl2 license:gpl3))))
-(define-public r-fourcseq
- (package
- (name "r-fourcseq")
- (version "1.22.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "FourCSeq" version))
- (sha256
- (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
- (properties `((upstream-name . "FourCSeq")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biostrings" ,r-biostrings)
- ("r-deseq2" ,r-deseq2)
- ("r-fda" ,r-fda)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggbio" ,r-ggbio)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gtools" ,r-gtools)
- ("r-lsd" ,r-lsd)
- ("r-matrix" ,r-matrix)
- ("r-reshape2" ,r-reshape2)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page
- "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
- (synopsis "Analysis of multiplexed 4C sequencing data")
- (description
- "This package is an R package dedicated to the analysis of (multiplexed)
-4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
-interactions between DNA elements and identify differential interactions
-between conditions. The statistical analysis in R starts with individual bam
-files for each sample as inputs. To obtain these files, the package contains
-a Python script to demultiplex libraries and trim off primer sequences. With
-a standard alignment software the required bam files can be then be
-generated.")
- (license license:gpl3+)))
-
(define-public r-phylogram
(package
(name "r-phylogram")
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 03/12] gnu: r-rgraphviz: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-3-zimon.toutoune@gmail.com
* gnu/packages/graph.scm (r-rgraphviz): Move from here...
* gnu/packages/bioconductor.scm (r-rgraphviz): ...to here.
---
gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++
gnu/packages/graph.scm | 28 ----------------------------
2 files changed, 28 insertions(+), 28 deletions(-)

Toggle diff (77 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 57755e1116..dea0862b64 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8307,3 +8307,31 @@ generated.")
"This package provides a library of core pre-processing and normalization
routines.")
(license license:lgpl2.0+)))
+
+(define-public r-rgraphviz
+ (package
+ (name "r-rgraphviz")
+ (version "2.32.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rgraphviz" version))
+ (sha256
+ (base32
+ "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
+ (properties `((upstream-name . "Rgraphviz")))
+ (build-system r-build-system)
+ ;; FIXME: Rgraphviz bundles the sources of an older variant of
+ ;; graphviz. It does not build with the latest version of graphviz, so
+ ;; we do not add graphviz to the inputs.
+ (inputs `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-graph" ,r-graph)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (home-page "https://bioconductor.org/packages/Rgraphviz")
+ (synopsis "Plotting capabilities for R graph objects")
+ (description
+ "This package interfaces R with the graphviz library for plotting R graph
+objects from the @code{graph} package.")
+ (license license:epl1.0)))
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index a307fee808..db390fed5e 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -121,34 +121,6 @@ more.")
(home-page "https://pypi.org/project/python-igraph/")
(synopsis "Python bindings for the igraph network analysis library")))
-(define-public r-rgraphviz
- (package
- (name "r-rgraphviz")
- (version "2.32.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "Rgraphviz" version))
- (sha256
- (base32
- "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
- (properties `((upstream-name . "Rgraphviz")))
- (build-system r-build-system)
- ;; FIXME: Rgraphviz bundles the sources of an older variant of
- ;; graphviz. It does not build with the latest version of graphviz, so
- ;; we do not add graphviz to the inputs.
- (inputs `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-graph" ,r-graph)))
- (native-inputs
- `(("pkg-config" ,pkg-config)))
- (home-page "https://bioconductor.org/packages/Rgraphviz")
- (synopsis "Plotting capabilities for R graph objects")
- (description
- "This package interfaces R with the graphviz library for plotting R graph
-objects from the @code{graph} package.")
- (license license:epl1.0)))
-
(define-public r-rbiofabric
(let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
(revision "1"))
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 04/12] gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-4-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Move from here...
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): ...to here.
---
gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 36 ---------------------------------
2 files changed, 36 insertions(+), 36 deletions(-)

Toggle diff (93 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dea0862b64..e81e9cd726 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8335,3 +8335,39 @@ routines.")
"This package interfaces R with the graphviz library for plotting R graph
objects from the @code{graph} package.")
(license license:epl1.0)))
+
+(define-public r-delayedmatrixstats
+ (package
+ (name "r-delayedmatrixstats")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DelayedMatrixStats" version))
+ (sha256
+ (base32
+ "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
+ (properties
+ `((upstream-name . "DelayedMatrixStats")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-hdf5array" ,r-hdf5array)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
+ (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
+ (description
+ "This package provides a port of the @code{matrixStats} API for use with
+@code{DelayedMatrix} objects from the @code{DelayedArray} package. It
+contains high-performing functions operating on rows and columns of
+@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
+@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
+are optimized per data type and for subsetted calculations such that both
+memory usage and processing time is minimized.")
+ (license license:expat)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ffa2618458..ccdc693e08 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10900,42 +10900,6 @@ cell-specific biases, assignment of cell cycle phase, and detection of highly
variable and significantly correlated genes.")
(license license:gpl3)))
-(define-public r-delayedmatrixstats
- (package
- (name "r-delayedmatrixstats")
- (version "1.10.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "DelayedMatrixStats" version))
- (sha256
- (base32
- "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
- (properties
- `((upstream-name . "DelayedMatrixStats")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-delayedarray" ,r-delayedarray)
- ("r-hdf5array" ,r-hdf5array)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-matrixstats" ,r-matrixstats)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
- (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
- (description
- "This package provides a port of the @code{matrixStats} API for use with
-@code{DelayedMatrix} objects from the @code{DelayedArray} package. It
-contains high-performing functions operating on rows and columns of
-@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
-@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
-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-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 05/12] gnu: r-scran: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-5-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-scran): Move from here...
* gnu/packages/bioconductor.scm (r-scran): ...to here.
---
gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 43 ---------------------------------
2 files changed, 43 insertions(+), 43 deletions(-)

Toggle diff (110 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e81e9cd726..77de0e2275 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8336,6 +8336,49 @@ routines.")
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-scran
+ (package
+ (name "r-scran")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scran" version))
+ (sha256
+ (base32
+ "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beachmat" ,r-beachmat)
+ ("r-bh" ,r-bh)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocneighbors" ,r-biocneighbors)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biocsingular" ,r-biocsingular)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+ ("r-dqrng" ,r-dqrng)
+ ("r-edger" ,r-edger)
+ ("r-igraph" ,r-igraph)
+ ("r-iranges" ,r-iranges)
+ ("r-limma" ,r-limma)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scater" ,r-scater)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-statmod" ,r-statmod)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/scran")
+ (synopsis "Methods for single-cell RNA-Seq data analysis")
+ (description "This package implements a variety of low-level analyses of
+single-cell RNA-seq data. Methods are provided for normalization of
+cell-specific biases, assignment of cell cycle phase, and detection of highly
+variable and significantly correlated genes.")
+ (license license:gpl3)))
+
(define-public r-delayedmatrixstats
(package
(name "r-delayedmatrixstats")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ccdc693e08..dcafbb2d21 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10857,49 +10857,6 @@ various analyses of single-cell RNA-seq gene expression data, with a focus on
quality control.")
(license license:gpl2+)))
-(define-public r-scran
- (package
- (name "r-scran")
- (version "1.16.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "scran" version))
- (sha256
- (base32
- "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-bh" ,r-bh)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocneighbors" ,r-biocneighbors)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocsingular" ,r-biocsingular)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-dqrng" ,r-dqrng)
- ("r-edger" ,r-edger)
- ("r-igraph" ,r-igraph)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scater" ,r-scater)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-statmod" ,r-statmod)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/scran")
- (synopsis "Methods for single-cell RNA-Seq data analysis")
- (description "This package implements a variety of low-level analyses of
-single-cell RNA-seq data. Methods are provided for normalization of
-cell-specific biases, assignment of cell cycle phase, and detection of highly
-variable and significantly correlated genes.")
- (license license:gpl3)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 06/12] gnu: r-scater: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-6-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-scater): Move from here...
* gnu/packages/bioconductor.scm (r-scater): ...to here.
---
gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 37 ---------------------------------
2 files changed, 37 insertions(+), 37 deletions(-)

Toggle diff (98 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 77de0e2275..52685a4df1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8336,6 +8336,43 @@ routines.")
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-scater
+ (package
+ (name "r-scater")
+ (version "1.16.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scater" version))
+ (sha256
+ (base32
+ "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beachmat" ,r-beachmat)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocneighbors" ,r-biocneighbors)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biocsingular" ,r-biocsingular)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+ ("r-ggbeeswarm" ,r-ggbeeswarm)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rlang" ,r-rlang)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-viridis" ,r-viridis)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/davismcc/scater")
+ (synopsis "Single-cell analysis toolkit for gene expression data in R")
+ (description "This package provides a collection of tools for doing
+various analyses of single-cell RNA-seq gene expression data, with a focus on
+quality control.")
+ (license license:gpl2+)))
+
(define-public r-scran
(package
(name "r-scran")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dcafbb2d21..8dea6df8a1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10820,43 +10820,6 @@ factors for each cell, along with the usual metadata for genes and
libraries.")
(license license:gpl3)))
-(define-public r-scater
- (package
- (name "r-scater")
- (version "1.16.2")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "scater" version))
- (sha256
- (base32
- "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocneighbors" ,r-biocneighbors)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocsingular" ,r-biocsingular)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-ggbeeswarm" ,r-ggbeeswarm)
- ("r-ggplot2" ,r-ggplot2)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-rlang" ,r-rlang)
- ("r-s4vectors" ,r-s4vectors)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-viridis" ,r-viridis)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/davismcc/scater")
- (synopsis "Single-cell analysis toolkit for gene expression data in R")
- (description "This package provides a collection of tools for doing
-various analyses of single-cell RNA-seq gene expression data, with a focus on
-quality control.")
- (license license:gpl2+)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 07/12] gnu: r-singlecellexperiment: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-7-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Move from here...
* gnu/packages/bioconductor.scm (r-singlecellexperiment): ...to here.
---
gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 29 -----------------------------
2 files changed, 29 insertions(+), 29 deletions(-)

Toggle diff (82 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 52685a4df1..d9f7a9fb67 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8336,6 +8336,35 @@ routines.")
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-singlecellexperiment
+ (package
+ (name "r-singlecellexperiment")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "SingleCellExperiment" version))
+ (sha256
+ (base32
+ "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
+ (properties
+ `((upstream-name . "SingleCellExperiment")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/SingleCellExperiment")
+ (synopsis "S4 classes for single cell data")
+ (description "This package defines an S4 class for storing data from
+single-cell experiments. This includes specialized methods to store and
+retrieve spike-in information, dimensionality reduction coordinates and size
+factors for each cell, along with the usual metadata for genes and
+libraries.")
+ (license license:gpl3)))
+
(define-public r-scater
(package
(name "r-scater")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8dea6df8a1..ef6d6fc2d8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10791,35 +10791,6 @@ variety of commonly used matrix types, including sparse and HDF5-backed
matrices.")
(license license:gpl3)))
-(define-public r-singlecellexperiment
- (package
- (name "r-singlecellexperiment")
- (version "1.10.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "SingleCellExperiment" version))
- (sha256
- (base32
- "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
- (properties
- `((upstream-name . "SingleCellExperiment")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/SingleCellExperiment")
- (synopsis "S4 classes for single cell data")
- (description "This package defines an S4 class for storing data from
-single-cell experiments. This includes specialized methods to store and
-retrieve spike-in information, dimensionality reduction coordinates and size
-factors for each cell, along with the usual metadata for genes and
-libraries.")
- (license license:gpl3)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 08/12] gnu: r-beachmat: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-8-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-beachmat): Move from here...
* gnu/packages/bioconductor.scm (r-beachmat): ...to here.
---
gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 25 -------------------------
2 files changed, 25 insertions(+), 25 deletions(-)

Toggle diff (74 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d9f7a9fb67..0ecb460bc4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8336,6 +8336,31 @@ routines.")
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-beachmat
+ (package
+ (name "r-beachmat")
+ (version "2.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "beachmat" version))
+ (sha256
+ (base32
+ "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-matrix" ,r-matrix)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/beachmat")
+ (synopsis "Compiling Bioconductor to handle each matrix type")
+ (description "This package provides a consistent C++ class interface for a
+variety of commonly used matrix types, including sparse and HDF5-backed
+matrices.")
+ (license license:gpl3)))
+
(define-public r-singlecellexperiment
(package
(name "r-singlecellexperiment")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ef6d6fc2d8..a84d19727c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10766,31 +10766,6 @@ block processing.")
packages.")
(license license:artistic2.0)))
-(define-public r-beachmat
- (package
- (name "r-beachmat")
- (version "2.4.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "beachmat" version))
- (sha256
- (base32
- "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-delayedarray" ,r-delayedarray)
- ("r-matrix" ,r-matrix)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/beachmat")
- (synopsis "Compiling Bioconductor to handle each matrix type")
- (description "This package provides a consistent C++ class interface for a
-variety of commonly used matrix types, including sparse and HDF5-backed
-matrices.")
- (license license:gpl3)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 11/12] gnu: r-hitc: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-10-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-hitc): Move from here...
* gnu/packages/bioconductor.scm (r-hitc): ...to here.
---
gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 29 -----------------------------
2 files changed, 29 insertions(+), 29 deletions(-)

Toggle diff (82 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b6a09c4ce4..5878c43a3d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8337,6 +8337,35 @@ routines.")
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-hitc
+ (package
+ (name "r-hitc")
+ (version "1.32.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "HiTC" version))
+ (sha256
+ (base32
+ "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
+ (properties `((upstream-name . "HiTC")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rtracklayer" ,r-rtracklayer)))
+ (home-page "https://bioconductor.org/packages/HiTC")
+ (synopsis "High throughput chromosome conformation capture analysis")
+ (description
+ "The HiTC package was developed to explore high-throughput \"C\" data
+such as 5C or Hi-C. Dedicated R classes as well as standard methods for
+quality controls, normalization, visualization, and further analysis are also
+provided.")
+ (license license:artistic2.0)))
+
(define-public r-hdf5array
(package
(name "r-hdf5array")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d874fe9a13..6bbcc3fe00 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10625,35 +10625,6 @@ intra-chromosomal contact maps produced by genome-wide genome architecture
assays such as Hi-C.")
(license license:gpl2+)))
-(define-public r-hitc
- (package
- (name "r-hitc")
- (version "1.32.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "HiTC" version))
- (sha256
- (base32
- "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
- (properties `((upstream-name . "HiTC")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rtracklayer" ,r-rtracklayer)))
- (home-page "https://bioconductor.org/packages/HiTC")
- (synopsis "High throughput chromosome conformation capture analysis")
- (description
- "The HiTC package was developed to explore high-throughput \"C\" data
-such as 5C or Hi-C. Dedicated R classes as well as standard methods for
-quality controls, normalization, visualization, and further analysis are also
-provided.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 12/12] gnu: r-fithic: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-11-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-fithic): Move from here...
* gnu/packages/bioconductor.scm (r-fithic): ...to here.
---
gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 26 --------------------------
2 files changed, 26 insertions(+), 26 deletions(-)

Toggle diff (76 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5878c43a3d..9473f3a286 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8337,6 +8337,32 @@ routines.")
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-fithic
+ (package
+ (name "r-fithic")
+ (version "1.14.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "FitHiC" version))
+ (sha256
+ (base32
+ "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
+ (properties `((upstream-name . "FitHiC")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-fdrtool" ,r-fdrtool)
+ ("r-rcpp" ,r-rcpp)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/FitHiC")
+ (synopsis "Confidence estimation for intra-chromosomal contact maps")
+ (description
+ "Fit-Hi-C is a tool for assigning statistical confidence estimates to
+intra-chromosomal contact maps produced by genome-wide genome architecture
+assays such as Hi-C.")
+ (license license:gpl2+)))
+
(define-public r-hitc
(package
(name "r-hitc")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6bbcc3fe00..71369affaf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10599,32 +10599,6 @@ EMBL-EBI GWAS catalog.")
visualizations for publication-quality multi-panel figures.")
(license license:gpl2+)))
-(define-public r-fithic
- (package
- (name "r-fithic")
- (version "1.14.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "FitHiC" version))
- (sha256
- (base32
- "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
- (properties `((upstream-name . "FitHiC")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-fdrtool" ,r-fdrtool)
- ("r-rcpp" ,r-rcpp)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/FitHiC")
- (synopsis "Confidence estimation for intra-chromosomal contact maps")
- (description
- "Fit-Hi-C is a tool for assigning statistical confidence estimates to
-intra-chromosomal contact maps produced by genome-wide genome architecture
-assays such as Hi-C.")
- (license license:gpl2+)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 10/12] gnu: r-hdf5array: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-12-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-hdf5array): Move from here...
* gnu/packages/bioconductor.scm (r-hdf5array): ...to here.
---
gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 30 ------------------------------
2 files changed, 30 insertions(+), 30 deletions(-)

Toggle diff (84 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0e63c486ee..b6a09c4ce4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8337,6 +8337,36 @@ routines.")
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-hdf5array
+ (package
+ (name "r-hdf5array")
+ (version "1.16.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "HDF5Array" version))
+ (sha256
+ (base32
+ "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
+ (properties `((upstream-name . "HDF5Array")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-rhdf5" ,r-rhdf5)
+ ("r-rhdf5lib" ,r-rhdf5lib)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/HDF5Array")
+ (synopsis "HDF5 back end for DelayedArray objects")
+ (description "This package provides an array-like container for convenient
+access and manipulation of HDF5 datasets. It supports delayed operations and
+block processing.")
+ (license license:artistic2.0)))
+
(define-public r-rhdf5lib
(package
(name "r-rhdf5lib")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8bd42c9429..d874fe9a13 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10654,36 +10654,6 @@ quality controls, normalization, visualization, and further analysis are also
provided.")
(license license:artistic2.0)))
-(define-public r-hdf5array
- (package
- (name "r-hdf5array")
- (version "1.16.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "HDF5Array" version))
- (sha256
- (base32
- "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
- (properties `((upstream-name . "HDF5Array")))
- (build-system r-build-system)
- (inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-delayedarray" ,r-delayedarray)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-rhdf5" ,r-rhdf5)
- ("r-rhdf5lib" ,r-rhdf5lib)
- ("r-s4vectors" ,r-s4vectors)))
- (home-page "https://bioconductor.org/packages/HDF5Array")
- (synopsis "HDF5 back end for DelayedArray objects")
- (description "This package provides an array-like container for convenient
-access and manipulation of HDF5 datasets. It supports delayed operations and
-block processing.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.28.0
Z
Z
zimoun wrote on 14 Sep 2020 18:07
[PATCH 09/12] gnu: r-rhdf5lib: Move to (gnu packages bioconductor).
(address . 43400@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200914160747.8983-9-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here.
---
gnu/packages/bioconductor.scm | 83 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 82 --------------------------------
2 files changed, 83 insertions(+), 82 deletions(-)

Toggle diff (196 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0ecb460bc4..0e63c486ee 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5,6 +5,7 @@
;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
;;; Copyright © 2020 M?d?lin Ionel Patra?cu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020 Jakub K?dzio?ka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -8336,6 +8337,88 @@ routines.")
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-rhdf5lib
+ (package
+ (name "r-rhdf5lib")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rhdf5lib" version))
+ (sha256
+ (base32
+ "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete bundled binaries
+ (delete-file-recursively "src/wininclude/")
+ (delete-file-recursively "src/winlib-4.9.3/")
+ (delete-file-recursively "src/winlib-8.3.0/")
+ (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
+ #t))))
+ (properties `((upstream-name . "Rhdf5lib")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'do-not-use-bundled-hdf5
+ (lambda* (#:key inputs #:allow-other-keys)
+ (for-each delete-file '("configure" "configure.ac"))
+ ;; Do not make other packages link with the proprietary libsz.
+ (substitute* "R/zzz.R"
+ ((" \"%s/libsz.a\"") ""))
+ (with-directory-excursion "src"
+ (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
+ (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
+ "hdf5")
+ ;; Remove timestamp and host system information to make
+ ;; the build reproducible.
+ (substitute* "hdf5/src/libhdf5.settings.in"
+ (("Configured on: @CONFIG_DATE@")
+ "Configured on: Guix")
+ (("Uname information:.*")
+ "Uname information: Linux\n")
+ ;; Remove unnecessary store reference.
+ (("C Compiler:.*")
+ "C Compiler: GCC\n"))
+ (rename-file "Makevars.in" "Makevars")
+ (substitute* "Makevars"
+ (("@ZLIB_LIB@") "-lz")
+ (("@ZLIB_INCLUDE@") "")
+ (("HDF5_CXX_LIB=.*")
+ (string-append "HDF5_CXX_LIB="
+ (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
+ (("HDF5_LIB=.*")
+ (string-append "HDF5_LIB="
+ (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
+ (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
+ (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
+ (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
+ (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
+ (("HDF5_HL_LIB=.*")
+ (string-append "HDF5_HL_LIB="
+ (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
+ (("HDF5_HL_CXX_LIB=.*")
+ (string-append "HDF5_HL_CXX_LIB="
+ (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
+ ;; szip is non-free software
+ (("cp \"\\$\\{SZIP_LIB\\}.*") "")
+ (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
+ #t)))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("hdf5" ,hdf5-1.10)))
+ (native-inputs
+ `(("hdf5-source" ,(package-source hdf5-1.10))
+ ("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/Rhdf5lib")
+ (synopsis "HDF5 library as an R package")
+ (description "This package provides C and C++ HDF5 libraries for use in R
+packages.")
+ (license license:artistic2.0)))
+
(define-public r-beachmat
(package
(name "r-beachmat")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a84d19727c..8bd42c9429 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10684,88 +10684,6 @@ access and manipulation of HDF5 datasets. It supports delayed operations and
block processing.")
(license license:artistic2.0)))
-(define-public r-rhdf5lib
- (package
- (name "r-rhdf5lib")
- (version "1.10.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "Rhdf5lib" version))
- (sha256
- (base32
- "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- ;; Delete bundled binaries
- (delete-file-recursively "src/wininclude/")
- (delete-file-recursively "src/winlib-4.9.3/")
- (delete-file-recursively "src/winlib-8.3.0/")
- (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
- #t))))
- (properties `((upstream-name . "Rhdf5lib")))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'do-not-use-bundled-hdf5
- (lambda* (#:key inputs #:allow-other-keys)
- (for-each delete-file '("configure" "configure.ac"))
- ;; Do not make other packages link with the proprietary libsz.
- (substitute* "R/zzz.R"
- ((" \"%s/libsz.a\"") ""))
- (with-directory-excursion "src"
- (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
- (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
- "hdf5")
- ;; Remove timestamp and host system information to make
- ;; the build reproducible.
- (substitute* "hdf5/src/libhdf5.settings.in"
- (("Configured on: @CONFIG_DATE@")
- "Configured on: Guix")
- (("Uname information:.*")
- "Uname information: Linux\n")
- ;; Remove unnecessary store reference.
- (("C Compiler:.*")
- "C Compiler: GCC\n"))
- (rename-file "Makevars.in" "Makevars")
- (substitute* "Makevars"
- (("@ZLIB_LIB@") "-lz")
- (("@ZLIB_INCLUDE@") "")
- (("HDF5_CXX_LIB=.*")
- (string-append "HDF5_CXX_LIB="
- (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
- (("HDF5_LIB=.*")
- (string-append "HDF5_LIB="
- (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
- (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
- (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
- (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
- (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
- (("HDF5_HL_LIB=.*")
- (string-append "HDF5_HL_LIB="
- (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
- (("HDF5_HL_CXX_LIB=.*")
- (string-append "HDF5_HL_CXX_LIB="
- (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
- ;; szip is non-free software
- (("cp \"\\$\\{SZIP_LIB\\}.*") "")
- (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
- #t)))))
- (inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("hdf5" ,hdf5-1.10)))
- (native-inputs
- `(("hdf5-source" ,(package-source hdf5-1.10))
- ("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/Rhdf5lib")
- (synopsis "HDF5 library as an R package")
- (description "This package provides C and C++ HDF5 libraries for use in R
-packages.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.28.0
R
R
Ricardo Wurmus wrote on 14 Sep 2020 21:42
Re: [bug#43400] [PATCH 00/12] Move some BioConductor to (gnu packages bioconductor)
(name . zimoun)(address . zimon.toutoune@gmail.com)(address . 43400-done@debbugs.gnu.org)
87d02oxi09.fsf@elephly.net
zimoun <zimon.toutoune@gmail.com> writes:

Toggle quote (3 lines)
> More janitoral stuff. The process is the same as described in the cover
> letter of #43345 <http://issues.guix.gnu.org/issue/43345>.

Thank you. I applied them all and added a commit to move a CRAN package
to (gnu packages bioconductor) because r-preprocesscore had been moved.

Pushed to “master” branch with commit 3159fcf145.

--
Ricardo
Closed
?