Package: guix-patches;
Reported by: zimoun <zimon.toutoune <at> gmail.com>
Date: Mon, 14 Sep 2020 16:05:02 UTC
Severity: normal
Tags: patch
Done: Ricardo Wurmus <rekado <at> elephly.net>
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guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:05:02 GMT) Full text and rfc822 format available.zimoun <zimon.toutoune <at> gmail.com>
:guix-patches <at> gnu.org
.
(Mon, 14 Sep 2020 16:05:02 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: guix-patches <at> gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 00/12] Move some BioConductor to (gnu packages bioconductor) Date: Mon, 14 Sep 2020 18:04:14 +0200
Dear, More janitoral stuff. The process is the same as described in the cover letter of #43345 <http://issues.guix.gnu.org/issue/43345>. 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:02 GMT) Full text and rfc822 format available.Message #8 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 02/12] gnu: r-preprocesscore: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:37 +0200
* 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:02 GMT) Full text and rfc822 format available.Message #11 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 01/12] gnu: r-fourcseq: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:36 +0200
* 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 <at> tobias.gr> ;;; Copyright © 2019 Simon Tournier <zimon.toutoune <at> gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau <at> gmail.com> +;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:03 GMT) Full text and rfc822 format available.Message #14 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 03/12] gnu: r-rgraphviz: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:38 +0200
* 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:03 GMT) Full text and rfc822 format available.Message #17 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 04/12] gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:39 +0200
* 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:03 GMT) Full text and rfc822 format available.Message #20 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 05/12] gnu: r-scran: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:40 +0200
* 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:04 GMT) Full text and rfc822 format available.Message #23 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 06/12] gnu: r-scater: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:41 +0200
* 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:04 GMT) Full text and rfc822 format available.Message #26 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 07/12] gnu: r-singlecellexperiment: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:42 +0200
* 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:05 GMT) Full text and rfc822 format available.Message #29 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 08/12] gnu: r-beachmat: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:43 +0200
* 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:05 GMT) Full text and rfc822 format available.Message #32 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 11/12] gnu: r-hitc: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:45 +0200
* 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:05 GMT) Full text and rfc822 format available.Message #35 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 12/12] gnu: r-fithic: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:46 +0200
* 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:06 GMT) Full text and rfc822 format available.Message #38 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 10/12] gnu: r-hdf5array: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:47 +0200
* 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
guix-patches <at> gnu.org
:bug#43400
; Package guix-patches
.
(Mon, 14 Sep 2020 16:09:06 GMT) Full text and rfc822 format available.Message #41 received at 43400 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 43400 <at> debbugs.gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 09/12] gnu: r-rhdf5lib: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:44 +0200
* 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 <at> gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau <at> gmail.com> ;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> +;;; Copyright © 2020 Jakub Kądziołka <kuba <at> 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
Ricardo Wurmus <rekado <at> elephly.net>
:zimoun <zimon.toutoune <at> gmail.com>
:Message #46 received at 43400-done <at> debbugs.gnu.org (full text, mbox):
From: Ricardo Wurmus <rekado <at> elephly.net> To: zimoun <zimon.toutoune <at> gmail.com> Cc: 43400-done <at> debbugs.gnu.org Subject: Re: [bug#43400] [PATCH 00/12] Move some BioConductor to (gnu packages bioconductor) Date: Mon, 14 Sep 2020 21:42:14 +0200
zimoun <zimon.toutoune <at> gmail.com> writes: > 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
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