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* [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move to (gnu packages bioconductor).
  2020-09-14 16:04 [bug#43400] [PATCH 00/12] Move some BioConductor to (gnu packages bioconductor) zimoun
@ 2020-09-14 16:07 ` zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 02/12] gnu: r-preprocesscore: " zimoun
                     ` (10 more replies)
  0 siblings, 11 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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 Mădălin Ionel Patrașcu <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





^ permalink raw reply	[flat|nested] 12+ messages in thread

* [bug#43400] [PATCH 02/12] gnu: r-preprocesscore: Move to (gnu packages bioconductor).
  2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
@ 2020-09-14 16:07   ` zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 03/12] gnu: r-rgraphviz: " zimoun
                     ` (9 subsequent siblings)
  10 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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





^ permalink raw reply	[flat|nested] 12+ messages in thread

* [bug#43400] [PATCH 03/12] gnu: r-rgraphviz: Move to (gnu packages bioconductor).
  2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 02/12] gnu: r-preprocesscore: " zimoun
@ 2020-09-14 16:07   ` zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 04/12] gnu: r-delayedmatrixstats: " zimoun
                     ` (8 subsequent siblings)
  10 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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





^ permalink raw reply	[flat|nested] 12+ messages in thread

* [bug#43400] [PATCH 04/12] gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor).
  2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 02/12] gnu: r-preprocesscore: " zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 03/12] gnu: r-rgraphviz: " zimoun
@ 2020-09-14 16:07   ` zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 05/12] gnu: r-scran: " zimoun
                     ` (7 subsequent siblings)
  10 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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





^ permalink raw reply	[flat|nested] 12+ messages in thread

* [bug#43400] [PATCH 05/12] gnu: r-scran: Move to (gnu packages bioconductor).
  2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
                     ` (2 preceding siblings ...)
  2020-09-14 16:07   ` [bug#43400] [PATCH 04/12] gnu: r-delayedmatrixstats: " zimoun
@ 2020-09-14 16:07   ` zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 06/12] gnu: r-scater: " zimoun
                     ` (6 subsequent siblings)
  10 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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





^ permalink raw reply	[flat|nested] 12+ messages in thread

* [bug#43400] [PATCH 06/12] gnu: r-scater: Move to (gnu packages bioconductor).
  2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
                     ` (3 preceding siblings ...)
  2020-09-14 16:07   ` [bug#43400] [PATCH 05/12] gnu: r-scran: " zimoun
@ 2020-09-14 16:07   ` zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 07/12] gnu: r-singlecellexperiment: " zimoun
                     ` (5 subsequent siblings)
  10 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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





^ permalink raw reply	[flat|nested] 12+ messages in thread

* [bug#43400] [PATCH 07/12] gnu: r-singlecellexperiment: Move to (gnu packages bioconductor).
  2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
                     ` (4 preceding siblings ...)
  2020-09-14 16:07   ` [bug#43400] [PATCH 06/12] gnu: r-scater: " zimoun
@ 2020-09-14 16:07   ` zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 08/12] gnu: r-beachmat: " zimoun
                     ` (4 subsequent siblings)
  10 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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





^ permalink raw reply	[flat|nested] 12+ messages in thread

* [bug#43400] [PATCH 08/12] gnu: r-beachmat: Move to (gnu packages bioconductor).
  2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
                     ` (5 preceding siblings ...)
  2020-09-14 16:07   ` [bug#43400] [PATCH 07/12] gnu: r-singlecellexperiment: " zimoun
@ 2020-09-14 16:07   ` zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 09/12] gnu: r-rhdf5lib: " zimoun
                     ` (3 subsequent siblings)
  10 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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





^ permalink raw reply	[flat|nested] 12+ messages in thread

* [bug#43400] [PATCH 09/12] gnu: r-rhdf5lib: Move to (gnu packages bioconductor).
  2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
                     ` (6 preceding siblings ...)
  2020-09-14 16:07   ` [bug#43400] [PATCH 08/12] gnu: r-beachmat: " zimoun
@ 2020-09-14 16:07   ` zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 11/12] gnu: r-hitc: " zimoun
                     ` (2 subsequent siblings)
  10 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020 Jakub Kądziołka <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





^ permalink raw reply	[flat|nested] 12+ messages in thread

* [bug#43400] [PATCH 11/12] gnu: r-hitc: Move to (gnu packages bioconductor).
  2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
                     ` (7 preceding siblings ...)
  2020-09-14 16:07   ` [bug#43400] [PATCH 09/12] gnu: r-rhdf5lib: " zimoun
@ 2020-09-14 16:07   ` zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 12/12] gnu: r-fithic: " zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 10/12] gnu: r-hdf5array: " zimoun
  10 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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





^ permalink raw reply	[flat|nested] 12+ messages in thread

* [bug#43400] [PATCH 12/12] gnu: r-fithic: Move to (gnu packages bioconductor).
  2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
                     ` (8 preceding siblings ...)
  2020-09-14 16:07   ` [bug#43400] [PATCH 11/12] gnu: r-hitc: " zimoun
@ 2020-09-14 16:07   ` zimoun
  2020-09-14 16:07   ` [bug#43400] [PATCH 10/12] gnu: r-hdf5array: " zimoun
  10 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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





^ permalink raw reply	[flat|nested] 12+ messages in thread

* [bug#43400] [PATCH 10/12] gnu: r-hdf5array: Move to (gnu packages bioconductor).
  2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
                     ` (9 preceding siblings ...)
  2020-09-14 16:07   ` [bug#43400] [PATCH 12/12] gnu: r-fithic: " zimoun
@ 2020-09-14 16:07   ` zimoun
  10 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2020-09-14 16:07 UTC (permalink / raw)
  To: 43400; +Cc: zimoun

* 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(-)

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





^ permalink raw reply	[flat|nested] 12+ messages in thread

end of thread, other threads:[~2020-09-14 18:01 UTC | newest]

Thread overview: 12+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2020-09-14 16:04 [bug#43400] [PATCH 00/12] Move some BioConductor to (gnu packages bioconductor) zimoun
2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
2020-09-14 16:07   ` [bug#43400] [PATCH 02/12] gnu: r-preprocesscore: " zimoun
2020-09-14 16:07   ` [bug#43400] [PATCH 03/12] gnu: r-rgraphviz: " zimoun
2020-09-14 16:07   ` [bug#43400] [PATCH 04/12] gnu: r-delayedmatrixstats: " zimoun
2020-09-14 16:07   ` [bug#43400] [PATCH 05/12] gnu: r-scran: " zimoun
2020-09-14 16:07   ` [bug#43400] [PATCH 06/12] gnu: r-scater: " zimoun
2020-09-14 16:07   ` [bug#43400] [PATCH 07/12] gnu: r-singlecellexperiment: " zimoun
2020-09-14 16:07   ` [bug#43400] [PATCH 08/12] gnu: r-beachmat: " zimoun
2020-09-14 16:07   ` [bug#43400] [PATCH 09/12] gnu: r-rhdf5lib: " zimoun
2020-09-14 16:07   ` [bug#43400] [PATCH 11/12] gnu: r-hitc: " zimoun
2020-09-14 16:07   ` [bug#43400] [PATCH 12/12] gnu: r-fithic: " zimoun
2020-09-14 16:07   ` [bug#43400] [PATCH 10/12] gnu: r-hdf5array: " zimoun

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