From f4d920b9f7ac404b245693fe21b39b7c41a49a61 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:36 +0200 Subject: gnu: r-fourcseq: Move to (gnu packages bioconductor). * gnu/packages/cran.scm (r-fourcseq): Move from here... * gnu/packages/bioconductor.scm (r-fourcseq): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a9f8ff21c5..5505747f67 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019 Simon Tournier ;;; Copyright © 2020 Peter Lo +;;; Copyright © 2020 Mădălin Ionel Patrașcu ;;; ;;; This file is part of GNU Guix. ;;; @@ -8242,3 +8243,47 @@ 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+))) -- cgit v1.2.3 From 6e0ab26f31cd2bb7e5d88719d3d458df68c1963e Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:37 +0200 Subject: gnu: r-preprocesscore: Move to (gnu packages bioconductor). * gnu/packages/statistics.scm (r-preprocesscore): Move from here... * gnu/packages/bioconductor.scm (r-preprocesscore): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ gnu/packages/statistics.scm | 21 --------------------- 2 files changed, 21 insertions(+), 21 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5505747f67..1f4ae8170f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8287,3 +8287,24 @@ 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 82f97c679e..03a63e6ba1 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") -- cgit v1.2.3 From b3a998374c37964820a51182fa7be7a546fc4d46 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:38 +0200 Subject: gnu: r-rgraphviz: Move to (gnu packages bioconductor). * gnu/packages/graph.scm (r-rgraphviz): Move from here... * gnu/packages/bioconductor.scm (r-rgraphviz): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 38 ++++++++++++++++++++++++++++++++++++++ gnu/packages/graph.scm | 38 -------------------------------------- 2 files changed, 38 insertions(+), 38 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1f4ae8170f..db853bfae3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8308,3 +8308,41 @@ 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) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-reproducible + (lambda _ + ;; The replacement value is taken from src/graphviz/builddate.h + (substitute* "src/graphviz/configure" + (("VERSION_DATE=.*") + "VERSION_DATE=20200427.2341\n")) + #t))))) + ;; 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 ccffccb050..db390fed5e 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -121,44 +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) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'make-reproducible - (lambda _ - ;; The replacement value is taken from src/graphviz/builddate.h - (substitute* "src/graphviz/configure" - (("VERSION_DATE=.*") - "VERSION_DATE=20200427.2341\n")) - #t))))) - ;; 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")) -- cgit v1.2.3 From 8c7c6db408ab11e1bed9607d044727af7593151b Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:39 +0200 Subject: gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Move from here... * gnu/packages/bioconductor.scm (r-delayedmatrixstats): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 36 ------------------------------------ 2 files changed, 36 insertions(+), 36 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db853bfae3..8d7daaeec0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8346,3 +8346,39 @@ 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")) -- cgit v1.2.3 From 1193b77e60a20c2b2751b2abb500d36ab505080e Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:40 +0200 Subject: gnu: r-scran: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-scran): Move from here... * gnu/packages/bioconductor.scm (r-scran): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 ----------------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8d7daaeec0..56ceed36c3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8347,6 +8347,49 @@ 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")) -- cgit v1.2.3 From 6b1946b334b9d3808d78dcd7963c0dab2ce7a908 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:41 +0200 Subject: gnu: r-scater: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-scater): Move from here... * gnu/packages/bioconductor.scm (r-scater): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 37 ------------------------------------- 2 files changed, 37 insertions(+), 37 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 56ceed36c3..3fec500abb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8347,6 +8347,43 @@ 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")) -- cgit v1.2.3 From 916a3e59ab1df1d530f7558b8d653d01a846ee1b Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:42 +0200 Subject: gnu: r-singlecellexperiment: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-singlecellexperiment): Move from here... * gnu/packages/bioconductor.scm (r-singlecellexperiment): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3fec500abb..fbdb7eedb2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8347,6 +8347,35 @@ 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")) -- cgit v1.2.3 From 8863c14cd856d917552017646dbf4a36654e9515 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:43 +0200 Subject: gnu: r-beachmat: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-beachmat): Move from here... * gnu/packages/bioconductor.scm (r-beachmat): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 25 ------------------------- 2 files changed, 25 insertions(+), 25 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbdb7eedb2..2796f4f90e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8347,6 +8347,31 @@ 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")) -- cgit v1.2.3 From c61268c1b74557bf6b8a26a9c95a47b1bea39d20 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:44 +0200 Subject: gnu: r-rhdf5lib: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 83 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 82 ---------------------------------------- 2 files changed, 83 insertions(+), 82 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2796f4f90e..e7db82741d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2019 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020 Mădălin Ionel Patrașcu +;;; Copyright © 2020 Jakub Kądziołka ;;; ;;; This file is part of GNU Guix. ;;; @@ -8347,6 +8348,88 @@ 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")) -- cgit v1.2.3 From 63b75c01c2374edc38437215278f50b617a12c08 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:47 +0200 Subject: gnu: r-hdf5array: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-hdf5array): Move from here... * gnu/packages/bioconductor.scm (r-hdf5array): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7db82741d..b2247e8cb6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8348,6 +8348,36 @@ 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")) -- cgit v1.2.3 From 7df42d3774778dfbb92e935df720f6eb52965e66 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:45 +0200 Subject: gnu: r-hitc: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-hitc): Move from here... * gnu/packages/bioconductor.scm (r-hitc): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b2247e8cb6..aeb89ae237 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8348,6 +8348,35 @@ 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")) -- cgit v1.2.3 From 3292f6eda0a89f65a0e3d5c0dc9fee71895dfa25 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:46 +0200 Subject: gnu: r-fithic: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-fithic): Move from here... * gnu/packages/bioconductor.scm (r-fithic): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aeb89ae237..f52025da91 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8348,6 +8348,32 @@ 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")) -- cgit v1.2.3 From 3159fcf14519f02c79ad84b441985982cb1efeb9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 14 Sep 2020 21:37:22 +0200 Subject: gnu: r-wgcna: Move to (gnu packages bioconductor). This is a follow-up to commit 6e0ab26f31cd2bb7e5d88719d3d458df68c1963e. * gnu/packages/cran.scm (r-wgcna): Move from here... * gnu/packages/bioconductor.scm (r-wgcna): ...to here. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 38 -------------------------------------- 2 files changed, 40 insertions(+), 38 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f52025da91..9d5c69e45e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8310,6 +8310,46 @@ generated.") routines.") (license license:lgpl2.0+))) +;; This is a CRAN package, but it depends on preprocessorcore, which is a +;; Bioconductor package. +(define-public r-wgcna + (package + (name "r-wgcna") + (version "1.69") + (source + (origin + (method url-fetch) + (uri (cran-uri "WGCNA" version)) + (sha256 + (base32 + "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f")))) + (properties `((upstream-name . "WGCNA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-doparallel" ,r-doparallel) + ("r-dynamictreecut" ,r-dynamictreecut) + ("r-fastcluster" ,r-fastcluster) + ("r-foreach" ,r-foreach) + ("r-go-db" ,r-go-db) + ("r-hmisc" ,r-hmisc) + ("r-impute" ,r-impute) + ("r-rcpp" ,r-rcpp) + ("r-survival" ,r-survival) + ("r-matrixstats" ,r-matrixstats) + ("r-preprocesscore" ,r-preprocesscore))) + (home-page + "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") + (synopsis "Weighted correlation network analysis") + (description + "This package provides functions necessary to perform Weighted +Correlation Network Analysis on high-dimensional data. It includes functions +for rudimentary data cleaning, construction and summarization of correlation +networks, module identification and functions for relating both variables and +modules to sample traits. It also includes a number of utility functions for +data manipulation and visualization.") + (license license:gpl2+))) + (define-public r-rgraphviz (package (name "r-rgraphviz") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5169800fef..684244456b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14477,44 +14477,6 @@ authoring books and technical documents with R Markdown.") that accept short and long options.") (license license:gpl2+))) -(define-public r-wgcna - (package - (name "r-wgcna") - (version "1.69") - (source - (origin - (method url-fetch) - (uri (cran-uri "WGCNA" version)) - (sha256 - (base32 - "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f")))) - (properties `((upstream-name . "WGCNA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-doparallel" ,r-doparallel) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-fastcluster" ,r-fastcluster) - ("r-foreach" ,r-foreach) - ("r-go-db" ,r-go-db) - ("r-hmisc" ,r-hmisc) - ("r-impute" ,r-impute) - ("r-rcpp" ,r-rcpp) - ("r-survival" ,r-survival) - ("r-matrixstats" ,r-matrixstats) - ("r-preprocesscore" ,r-preprocesscore))) - (home-page - "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") - (synopsis "Weighted correlation network analysis") - (description - "This package provides functions necessary to perform Weighted -Correlation Network Analysis on high-dimensional data. It includes functions -for rudimentary data cleaning, construction and summarization of correlation -networks, module identification and functions for relating both variables and -modules to sample traits. It also includes a number of utility functions for -data manipulation and visualization.") - (license license:gpl2+))) - (define-public r-kernlab (package (name "r-kernlab") -- cgit v1.2.3 From 7230f6d5dda8d1351d16c786c0f86eca55aca09a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 22 Sep 2020 21:31:52 +0200 Subject: gnu: Fix typoes in package descriptions. * gnu/packages/audio.scm (caps-plugins-lv2)[synopsis]: Fix typo. * gnu/packages/bioconductor.scm (r-karyoploter, r-anota, r-gcrma) (r-bigmemoryextras)[description]: Likewise. * gnu/packages/cran.scm (r-geometry)[synopsis]: Likewise. (r-stringdist, r-patchwork, r-depth, r-tea)[description]: Likewise. * gnu/packages/crates-io.scm (rust-assert-fs-0.11, rust-notify-4) (rust-tokio-fs-0.1)[synopsis, description]: Likewise. (rust-blas-sys-0.7)[description]: Likewise. (rust-fs-extra-1.1, rust-xattr-0.2)[synopsis]: Likewise. * gnu/packages/databases.scm (perl-mysql-config)[description]: Likewise. * gnu/packages/disk.scm (hddtemp)[description]: Likewise. * gnu/packages/django.scm (python-djangorestframework)[description]: Likewise. * gnu/packages/documentation.scm (doc++)[description]: Likewise. * gnu/packages/emacs-xyz.scm (emacs-kakoune, emacs-pyim-basedict, eless) (emacs-scpaste)[description]: Likewise. * gnu/packages/file-systems.scm (dbxfs)[description]: Likewise. * gnu/packages/finance.scm (python-stdnum)[description]: Likewise. * gnu/packages/fontutils.scm (woff2)[description]: Likewise. * gnu/packages/games.scm (openttd-opengfx)[description]: Likewise. * gnu/packages/gnome-xyz.scm (gnome-shell-extension-topicons-redux) [description]: Likewise. * gnu/packages/gnome.scm (libgrss)[description]: Likewise. * gnu/packages/golang.scm (go-github-com-mitchellh-reflectwalk) [description]: Likewise. (go-github-com-go-git-go-billy)[synopsis, description]: Likewise. * gnu/packages/haskell-check.scm (ghc-inspection-testing)[description]: Likewise. * gnu/packages/haskell-web.scm (ghc-yesod-form)[description]: Likewise. * gnu/packages/haskell-xyz.scm (ghc-hex)[description]: Likewise. * gnu/packages/hyperledger.scm (hyperledger-iroha-ed25519)[description]: Likewise. * gnu/packages/java.scm (java-mail)[synopsis]: Likewise. (java-native-access-platform)[description]: Likewise. * gnu/packages/kde-frameworks.scm (kactivities-stats)[description]: Likewise. * gnu/packages/kde-utils.scm (krusader)[description]: Likewise. * gnu/packages/language.scm (praat)[description]: Likewise. * gnu/packages/linux.scm (light)[description]: Likewise. * gnu/packages/lisp-xyz.scm (sbcl-hu.dwim.defclass-star)[description]: Likewise. * gnu/packages/mail.scm (dovecot-trees, sieve-connect)[description]: Likewise. * gnu/packages/ocaml.scm (ocaml-opam-file-format, ocaml-cppo) (ocaml4.07-ppx-variants-conv)[description]: Likewise. * gnu/packages/perl.scm (perl-convert-binhex)[description]: Likewise. * gnu/packages/python-crypto.scm (python-ecdsa)[description]: Likewise. * gnu/packages/python-web.scm (python-html5lib)[synopsis, description]: Likewise. (python-venusian)[synopsis]: Likewise. * gnu/packages/python-xyz.scm (python-readlike, python-gssapi) (python-flufl-i18n)[description]: Likewise. (python-pox, python-watchdog, python-xattr)[synopsis, description]: Likewise. * gnu/packages/ruby.scm (ruby-sorcerer)[description]: Likewise. * gnu/packages/rust-apps.scm (watchexec)[description]: Likewise. * gnu/packages/rust.scm (mrustc)[synopsis]: Likewise. * gnu/packages/shells.scm (s-shell)[description]: Likewise. * gnu/packages/ssh.scm (sshpass)[description]: Likewise. * gnu/packages/terminals.scm (beep)[description]: Likewise. * gnu/packages/web.scm (perl-lwp-useragent-cached)[description]: Likewise. * gnu/packages/wv.scm (wv)[description]: Likewise. --- gnu/packages/audio.scm | 2 +- gnu/packages/bioconductor.scm | 8 ++++---- gnu/packages/cran.scm | 10 +++++----- gnu/packages/crates-io.scm | 18 +++++++++--------- gnu/packages/databases.scm | 2 +- gnu/packages/disk.scm | 2 +- gnu/packages/django.scm | 2 +- gnu/packages/documentation.scm | 2 +- gnu/packages/emacs-xyz.scm | 8 ++++---- gnu/packages/file-systems.scm | 2 +- gnu/packages/finance.scm | 2 +- gnu/packages/fontutils.scm | 2 +- gnu/packages/games.scm | 2 +- gnu/packages/gnome-xyz.scm | 2 +- gnu/packages/gnome.scm | 4 ++-- gnu/packages/golang.scm | 12 ++++++------ gnu/packages/haskell-check.scm | 2 +- gnu/packages/haskell-web.scm | 2 +- gnu/packages/haskell-xyz.scm | 4 ++-- gnu/packages/hyperledger.scm | 2 +- gnu/packages/java.scm | 4 ++-- gnu/packages/kde-frameworks.scm | 2 +- gnu/packages/kde-utils.scm | 2 +- gnu/packages/language.scm | 4 ++-- gnu/packages/linux.scm | 6 ++---- gnu/packages/lisp-xyz.scm | 2 +- gnu/packages/mail.scm | 4 ++-- gnu/packages/ocaml.scm | 8 ++++---- gnu/packages/perl.scm | 2 +- gnu/packages/python-crypto.scm | 2 +- gnu/packages/python-web.scm | 6 +++--- gnu/packages/python-xyz.scm | 24 ++++++++++++------------ gnu/packages/ruby.scm | 4 ++-- gnu/packages/rust-apps.scm | 2 +- gnu/packages/rust.scm | 2 +- gnu/packages/shells.scm | 5 +++-- gnu/packages/ssh.scm | 2 +- gnu/packages/terminals.scm | 2 +- gnu/packages/web.scm | 2 +- gnu/packages/wv.scm | 2 +- 40 files changed, 88 insertions(+), 89 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index c6734a35f3..f26b3eceae 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1046,7 +1046,7 @@ tools (analyzer, mono/stereo tools, crossovers).") `(("lv2" ,lv2))) ;; home-page of the original LADSPA version: http://quitte.de/dsp/caps.html (home-page "https://github.com/moddevices/caps-lv2") - (synopsis "LV2 port of the CAPS audio plugin colection") + (synopsis "LV2 port of the CAPS audio plugin collection") (description "LV2 port of CAPS, a collection of audio plugins comprising basic virtual guitar amplification and a small range of classic effects, signal processors and diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9d5c69e45e..d655253cf1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2736,7 +2736,7 @@ gene and isoform level using RNA-seq data") (home-page "https://bioconductor.org/packages/karyoploteR/") (synopsis "Plot customizable linear genomes displaying arbitrary data") (description "This package creates karyotype plots of arbitrary genomes and -offers a complete set of functions to plot arbitrary data on them. It mimicks +offers a complete set of functions to plot arbitrary data on them. It mimics many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates.") @@ -3674,7 +3674,7 @@ sets of GO terms, gene products and gene clusters.") (description "Genome wide studies of translational control is emerging as a tool to study various biological conditions. The output from such analysis is both -the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively +the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e. differences in @@ -4843,7 +4843,7 @@ a more complex way than the simple GC content. Instead, the base types (A, T, G or C) at each position along the probe determine the affinity of each probe. The parameters of the position-specific base contributions to the probe affinity is estimated in an NSB experiment in which only NSB but no -gene-specific bidning is expected.") +gene-specific binding is expected.") ;; Any version of the LGPL (license license:lgpl2.1+))) @@ -7478,7 +7478,7 @@ networks and estimated fluxes can be visualized with hypergraphs.") safety and convenience features to the @code{filebacked.big.matrix} class from the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by monitoring and gracefully restoring the connection to on-disk data and it also -protects against accidental data modification with a filesystem-based +protects against accidental data modification with a file-system-based permissions system. Utilities are provided for using @code{BigMatrix}-derived classes as @code{assayData} matrices within the @code{Biobase} package's @code{eSet} family of classes. @code{BigMatrix} provides some optimizations diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 684244456b..50ce111123 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3401,7 +3401,7 @@ Optimization problems by using the simplex algorithm.") ("r-rcpp" ,r-rcpp) ("r-rcppprogress" ,r-rcppprogress))) (home-page "http://geometry.r-forge.r-project.org/") - (synopsis "Mesh generation and surface tesselation") + (synopsis "Mesh generator and surface tessellator") (description "This package makes the qhull library available in R, in a similar manner as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace @@ -3743,7 +3743,7 @@ color labels, layout, etc.") (description "This package implements an approximate string matching version of R's native @code{match} function. It can calculate various string distances based -on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), +on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding @@ -16497,7 +16497,7 @@ guaranteeing well-connected communities.\" .") "The @code{ggplot2} package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. Patchwork is a package that expands the API to allow for arbitrarily -complex composition of plots by providing mathmatical operators for combining +complex composition of plots by providing mathematical operators for combining multiple plots.") (license license:expat))) @@ -19616,7 +19616,7 @@ on distances rather than on unit x variables.") "This package provides tools for depth functions methodology applied to multivariate analysis. Besides allowing calculation of depth values and depth-based location estimators, the package includes functions or drawing -contour plots and perspective plots of depth functions. Euclidian and +contour plots and perspective plots of depth functions. Euclidean and spherical depths are supported.") (license license:gpl2))) @@ -22103,7 +22103,7 @@ general, via different versions of bridge sampling.") (description "This package provides different approaches for selecting the threshold in generalized Pareto distributions. Most of them are based on minimizing the -AMSE-criterion or atleast by reducing the bias of the assumed GPD-model. +AMSE-criterion or at least by reducing the bias of the assumed GPD-model. Others are heuristically motivated by searching for stable sample paths, i.e. a nearly constant region of the tail index estimator with respect to k, which is the number of data in the tail. The third class is motivated by graphical diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ba02406848..96b47394a6 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -984,9 +984,9 @@ Mac, and Unix.") #:cargo-development-inputs (("rust-docmatic" ,rust-docmatic-0.1)))) (home-page "https://github.com/assert-rs/assert_fs") - (synopsis "Filesystem fixtures and assertions for testing") + (synopsis "File system fixtures and assertions for testing") (description - "Filesystem fixtures and assertions for testing.") + "File system fixtures and assertions for testing.") (license (list license:expat license:asl2.0)))) (define-public rust-assert-matches-1.3 @@ -1977,7 +1977,7 @@ BLAKE2bp hash functions.") (home-page "https://github.com/blas-lapack-rs/blas-sys") (synopsis "Bindings to BLAS (Fortran)") (description - "Ths package provides bindings to BLAS (Fortran).") + "This package provides bindings to BLAS (Fortran).") (license (list license:asl2.0 license:expat)))) @@ -7945,7 +7945,7 @@ duplication.") (build-system cargo-build-system) (arguments '(#:skip-build? #t)) (home-page "https://github.com/webdesus/fs_extra") - (synopsis "Extra filesystem methods") + (synopsis "Extra file system methods") (description "Expanding opportunities standard library @code{std::fs} and @code{std::io}. Recursively copy folders with recept information about process and much more.") @@ -15245,9 +15245,9 @@ with all line endings.") #:cargo-development-inputs (("rust-tempfile" ,rust-tempfile-3)))) (home-page "https://github.com/passcod/notify") - (synopsis "Cross-platform filesystem notification library") + (synopsis "Cross-platform file system notification library") (description - "Cross-platform filesystem notification library.") + "Cross-platform file system notification library.") (license license:cc0))) (define-public rust-num-0.2 @@ -27178,8 +27178,8 @@ the current thread.") ("rust-tokio-codec" ,rust-tokio-codec-0.1) ("rust-tokio-io" ,rust-tokio-io-0.1)))) (home-page "https://tokio.rs") - (synopsis "Filesystem API for Tokio") - (description "Filesystem API for Tokio.") + (synopsis "File system API for Tokio") + (description "File system API for Tokio.") (license license:expat))) ;; Cyclic dependencies with tokio and tokio-current-thread @@ -30508,7 +30508,7 @@ color in a Windows console.") #:cargo-development-inputs (("rust-tempfile" ,rust-tempfile-3)))) (home-page "https://github.com/Stebalien/xattr") - (synopsis "Unix extended filesystem attributes") + (synopsis "Unix extended file system attributes") (description "This package provide a small library for setting, getting, and listing extended attributes.") diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index a9798cbc33..c86297b293 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1780,7 +1780,7 @@ module, and nothing else.") (synopsis "Parse and utilize MySQL's /etc/my.cnf and ~/.my.cnf files") (description "@code{MySQL::Config} emulates the @code{load_defaults} function from -libmysqlclient. It will fill an aray with long options, ready to be parsed by +libmysqlclient. It will fill an array with long options, ready to be parsed by @code{Getopt::Long}.") (license license:perl-license))) diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index 79e187e283..1e538ef60e 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -1038,6 +1038,6 @@ of choice for all light thinking Unix addicts!") (home-page "https://savannah.nongnu.org/projects/hddtemp/") (synopsis "Report the temperature of hard drives from S.M.A.R.T. information") (description "@command{hddtemp} is a small utility that gives you the -temperature of your hard drive by reading S.M.A.R.T. informations (for drives +temperature of your hard drive by reading S.M.A.R.T. information (for drives that support this feature).") (license license:gpl2+))) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 3fee18a102..43339720f2 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -1029,7 +1029,7 @@ Django projects, which allows association of a number of tags with any (synopsis "Toolkit for building Web APIs with Django") (description "The Django REST framework is for building Web APIs with Django. It -provides features like a web browseable API and authentication policies.") +provides features like a Web-browsable API and authentication policies.") (license license:bsd-2))) (define-public python-django-sekizai diff --git a/gnu/packages/documentation.scm b/gnu/packages/documentation.scm index 9c30fc832a..6532bb4704 100644 --- a/gnu/packages/documentation.scm +++ b/gnu/packages/documentation.scm @@ -273,7 +273,7 @@ and to some extent D.") (description "DOC++ is a documentation system for C, C++, IDL, and Java. It can generate both TeX output for high-quality hardcopies or HTML output for online -brwosing. The documentation is extracted directly from the C/C++/IDL source +browsing. The documentation is extracted directly from the C/C++/IDL source or Java class files.") (license gpl2+))) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 43add530af..2957641c14 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2800,7 +2800,7 @@ running Extempore process, and more.") (description "This package provides many, but not all of the editing primitives in the Kakoune editor. Unlike Evil mode for Vim, this is a very shallow emulation, which seeks to do as little work as possible, leveraging -Emacs native editing commmands and the work of other packages wherever +Emacs native editing commands and the work of other packages wherever possible.") (license license:expat)))) @@ -11105,7 +11105,7 @@ function to be used by other frontend programs.") (home-page "https://github.com/tumashu/pyim-basedict") (synopsis "Input method dictionary of pyim") (description "Pyim-basedict is the default pinyin input method dictionary, -containing words from the rime project.") +containing words from the Rime project.") (license license:gpl2+))) (define-public emacs-pyim @@ -12974,7 +12974,7 @@ buffer.") (description "@code{eless} provides a combination of Bash script and a minimal Emacs view-mode. -Feautures: +Features: @itemize @item Independent of a user’s Emacs config. @@ -24633,7 +24633,7 @@ displayed for sharing.") buffer on an active webserver to which the user has SSH access. It is similar in purpose to services such as Gist or Pastebin, but is much simpler since it assumes the user has access to a -publically-accessible HTTP server.") +publicly-accessible HTTP server.") (license license:gpl3+)))) (define-public emacs-company-reftex diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index b8612ac3b2..046deb67ab 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -917,5 +917,5 @@ Dropbox API v2.") (synopsis "User-space file system for Dropbox") (description "@code{dbxfs} allows you to mount your Dropbox folder as if it were a -local filesystem using FUSE.") +local file system using FUSE.") (license license:gpl3+))) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index de3b687410..863914bd35 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -1061,7 +1061,7 @@ amongst which a great number of VAT and other tax numbers, personal identity and company identification codes, international standard numbers (ISBN, IBAN, EAN, etc.) and various other formats. -The module also inclused implementations of the Verhoeff, +The module also includes implementations of the Verhoeff, Luhn and family of ISO/IEC 7064 check digit algorithms. ") (license license:lgpl2.1+))) diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm index 96557b963c..94473991f7 100644 --- a/gnu/packages/fontutils.scm +++ b/gnu/packages/fontutils.scm @@ -303,7 +303,7 @@ work with most software requiring Type 1 fonts.") (inputs `(("brotli" ,google-brotli))) (synopsis "Libraries and tools for WOFF2 font format") - (description "WOFF2 provides libraires and tools to handle the Web Open + (description "WOFF2 provides libraries and tools to handle the Web Open Font Format (WOFF).") (home-page "https://w3c.github.io/woff/woff2/") (license license:expat))) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index d54a3bd1a9..b819cd104f 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -3903,7 +3903,7 @@ engine. When you start it you will be prompted to download a graphics set.") (home-page "http://dev.openttdcoop.org/projects/opengfx") (synopsis "Base graphics set for OpenTTD") (description - "The OpenGFX projects is an implementation of the OpenTTD base grahics + "The OpenGFX project is an implementation of the OpenTTD base graphics set that aims to ensure the best possible out-of-the-box experience. OpenGFX provides you with... diff --git a/gnu/packages/gnome-xyz.scm b/gnu/packages/gnome-xyz.scm index 75ba0f5636..7f3ae41d17 100644 --- a/gnu/packages/gnome-xyz.scm +++ b/gnu/packages/gnome-xyz.scm @@ -234,7 +234,7 @@ some media players, are meant to run long-term in the background even after you close their window. These applications remain accessible by adding an icon to the GNOME Shell Legacy Tray. However, the Legacy Tray was removed in GNOME 3.26. TopIcons Redux brings those icons back into the top panel so that it's -easier to keep track of apps running in the backround.") +easier to keep track of applications running in the background.") (license license:gpl2+))) (define-public gnome-shell-extension-dash-to-dock diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index d727f18ed8..762e48f572 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -357,8 +357,8 @@ services.") ("libsoup" ,libsoup) ("libxml2" ,libxml2))) (synopsis "Glib library for feeds") - (description "LibGRSS is a Glib abstaction to handle feeds in RSS, Atom and -other formats.") + (description "LibGRSS is a Glib abstraction to handle feeds in RSS, Atom, +and other formats.") (home-page "https://wiki.gnome.org/Projects/Libgrss") (license license:lgpl3+))) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 8723592b51..001c864505 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -2822,7 +2822,7 @@ cross-compilation.") (synopsis "Walk a value in Go using reflection") (description "reflectwalk is a Go library for \"walking\" a value in Go using reflection, in the same way a directory tree can be \"walked\" on the -filesystem. Walking a complex structure can allow you to do manipulations on +file system. Walking a complex structure can allow you to do manipulations on unknown structures such as those decoded from JSON.") (license license:expat))) @@ -5237,11 +5237,11 @@ errors (warnings).") (native-inputs `(("go-gopkg-in-check-v1" ,go-gopkg-in-check-v1))) (home-page "https://github.com/go-git/go-billy/") - (synopsis "Filesystem abstraction for Go") - (description "Billy implements an interface based on the os standard -library, allowing to develop applications without dependency on the underlying -storage. Makes it virtually free to implement mocks and testing over -filesystem operations.") + (synopsis "File system abstraction for Go") + (description "Billy implements an interface based on the OS's standard +library to develop applications without depending on the underlying storage. +This makes it virtually free to implement mocks and testing over +file system operations.") (license license:asl2.0))) (define-public go-github-com-jbenet-go-context diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm index 7f7bc22da5..b5546f97f8 100644 --- a/gnu/packages/haskell-check.scm +++ b/gnu/packages/haskell-check.scm @@ -1033,7 +1033,7 @@ library's promised without anyone noticing. This package provides a disciplined way of specifying such properties, and have them checked by the compiler. This way, this checking can be part of the -ususal development cycle and regressions caught early. +regular development cycle and regressions caught early. See the documentation in \"Test.Inspection\" or the project webpage for more examples and more information.") diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm index 98d163566c..a4269599f6 100644 --- a/gnu/packages/haskell-web.scm +++ b/gnu/packages/haskell-web.scm @@ -1349,7 +1349,7 @@ from Yesod.") ("ghc-hspec" ,ghc-hspec))) (home-page "https://www.yesodweb.com") (synopsis "Form handling support for Yesod Web Framework") - (description "This Haskell package provies a set of basic form inputs such + (description "This Haskell package provides a set of basic form inputs such as text, number, time, checkbox, select, textarea, etc through the @code{Yesod.Form.Fields} module. Also, there is @code{Yesod.Form.Nic} module providing richtext field using Nic editor. ") diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index f4af00283c..5b9da15630 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -5524,8 +5524,8 @@ Vim.") (build-system haskell-build-system) (home-page "https://hackage.haskell.org/package/hex") (synopsis "Convert strings into hexadecimal and back") - (description "This package provides conversion functions between -bytestrings and their hexademical representation.") + (description "This package converts between bytestrings and their +hexadecimal string representation.") (license license:bsd-3))) (define-public ghc-highlighting-kate diff --git a/gnu/packages/hyperledger.scm b/gnu/packages/hyperledger.scm index c1b8215584..82680cd5e4 100644 --- a/gnu/packages/hyperledger.scm +++ b/gnu/packages/hyperledger.scm @@ -141,7 +141,7 @@ Originally Ed25519 consists of three modules: @itemize @item digital signature algorithm itself @item SHA512 hash function -@item random number generator, to generate keypairs +@item random number generator, to generate key pairs @end itemize This project offers at least two different C implementations for every diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 8c594f5fe2..40b0a8c1dd 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -10949,7 +10949,7 @@ application components to create, send, receive, and read messages.") `(("junit" ,java-junit) ("hamcrest" ,java-hamcrest-core))) (home-page "https://javaee.github.io/javamail/") - (synopsis "Mail-related functionnalities in Java") + (synopsis "Mail-related functionality in Java") (description "The JavaMail API provides a platform-independent and protocol-independent framework to build mail and messaging applications.") ;; General Public License Version 2 only ("GPL") or the Common Development @@ -12226,7 +12226,7 @@ Java method invocation.") (inputs `(("java-native-access" ,java-native-access))) (synopsis "Cross-platform mappings for jna") - (description "java-native-access-platfrom has cross-platform mappings + (description "java-native-access-platform has cross-platform mappings and mappings for a number of commonly used platform functions, including a large number of Win32 mappings as well as a set of utility classes that simplify native access."))) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index d264ca5bbe..c4479de995 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -2215,7 +2215,7 @@ maintaining an index of the contents of your files.") (home-page "https://community.kde.org/Frameworks") (synopsis "Access usage statistics collected by the activity manager") (description "The KActivitiesStats library provides a querying mechanism for -the data that the activitiy manager collects - which documents have been opened +the data that the activity manager collects---which documents have been opened by which applications, and what documents have been linked to which activity.") ;; triple licensed (license (list license:lgpl2.0+ license:lgpl2.1+ license:lgpl3+)))) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 5e6a872314..4d9f3736c8 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -289,7 +289,7 @@ twin-panel (commander-style) file manager, similar to Midnight Commander or Total Commander It provides all the file management features you could possibly want. Plus: -extensive archive handling, mounted filesystem support, FTP, advanced search +extensive archive handling, mounted file system support, FTP, advanced search module, an internal viewer/editor, directory synchronisation, file content comparisons, powerful batch renaming and much much more. It supports a wide variety of archive formats and can handle other KIO slaves such as smb or diff --git a/gnu/packages/language.scm b/gnu/packages/language.scm index 0c59cd1bf7..89e5e307eb 100644 --- a/gnu/packages/language.scm +++ b/gnu/packages/language.scm @@ -1100,7 +1100,7 @@ noun phrases, verb phrases, etc.).") `(("pkg-config" ,pkg-config))) (home-page "http://www.fon.hum.uva.nl/praat/") (synopsis "Doing phonetics by computer") - (description "Praat is a tool to perform phonetics tasks. It can do speach -analysis (pitch, formant, intensity, ...), speach synthesis, labeling, segmenting + (description "Praat is a tool to perform phonetics tasks. It can do speech +analysis (pitch, formant, intensity, ...), speech synthesis, labelling, segmenting and manipulation.") (license gpl2+))) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 2c80bda7ce..f443299dfc 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -6008,10 +6008,8 @@ under GNU/Linux. Features include: @item Light can automatically figure out the best controller to use, making full use of underlying hardware. @item It is possible to set a minimum brightness value, as some controllers -set the screen to be pitch black at a vaĺue of 0 (or higher). -@end itemize - -Light is the successor of lightscript.") +set the screen to be pitch black at a value of 0 (or higher). +@end itemize\n") (license license:gpl3+))) (define-public brightnessctl diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index ef08960497..69ebdb3eb8 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -13656,7 +13656,7 @@ simplify class and condition declarations. Features include: @itemize @item Automatically export all or select slots at compile time. -@item Define the @code{:initarg} and @code{:accesor} automatically. +@item Define the @code{:initarg} and @code{:accessor} automatically. @item Specify a name transformer for both the @code{:initarg} and @code{:accessor}, etc. @item Specify the @code{:initform} as second slot value. diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index fcdefbb577..70e2fcd76b 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1712,7 +1712,7 @@ scripts to prevent embarrassing errors later on.") "Technology for Resting Email Encrypted Storage (TREES) is a NaCL-based Dovecot encryption plugin. This plugin adds individually encrypted mail storage to the Dovecot IMAP server. It is inspired by Posteo's scrambler -which uses OpenSSL and RSA keypairs. TREES works in a similar way, but uses +which uses OpenSSL and RSA key pairs. TREES works in a similar way, but uses the Sodium crypto library (based on NaCL). How it works: @@ -2590,7 +2590,7 @@ transfer protocols.") (description "Sieve-connect lets you view, upload, edit, delete, and otherwise manage Sieve scripts on any mail server that speaks the @dfn{ManageSieve} protocol, -as specifed in RFC 5804. +as specified in RFC 5804. @dfn{Sieve} (RFC 5228) is a specialised language for e-mail filtering. Sieve scripts are stored on the server and run whenever mail arrives. They can diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 33c3fa0494..f92d62691f 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -429,7 +429,7 @@ repository-wide uninstallability checks.") (home-page "https://opam.ocaml.org") (synopsis "Parser and printer for the opam file syntax") (description "This package contains a parser and a pretty-printer for -the opam file fomat.") +the opam file format.") ;; With static-linking exception (license license:lgpl2.1+))) @@ -2577,9 +2577,9 @@ from the oasis build log (home-page "https://github.com/mjambon/cppo") (synopsis "Equivalent of the C preprocessor for OCaml programs") (description "Cppo is an equivalent of the C preprocessor for OCaml -programs. It allows the definition of simple macros and file inclusion. Cpp ois: +programs. It allows the definition of simple macros and file inclusion. Cppo is: @enumerate -@item more OCaml-friendly than cpp +@item more OCaml-friendly than @command{cpp} @item easy to learn without consulting a manual @item reasonably fast @item simple to install and to maintain. @@ -4369,7 +4369,7 @@ definitions.") "https://github.com/janestreet/ppx_variants_conv") (synopsis "Generation of accessor and iteration functions for OCaml variant types") (description - "This package generates accessors and interation functions for OCaml + "This package generates accessors and iteration functions for OCaml variant types.") (license license:asl2.0))) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index bd6e746b67..1c3d999d79 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -1961,7 +1961,7 @@ the caller.") (synopsis "Extract data from Macintosh BinHex files") (description "BinHex is a format for transporting files safely through electronic -mail, as short-lined, 7-bit, semi-compressed data streams. Ths module +mail, as short-lined, 7-bit, semi-compressed data streams. This module provides a means of converting those data streams back into into binary data.") (license license:perl-license))) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 22b1a1ebe3..f39695a850 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -286,7 +286,7 @@ Python interface around SSH networking concepts.") (description "This is an easy-to-use implementation of ECDSA cryptography (Elliptic Curve Digital Signature Algorithm), implemented purely in Python. With this -library, you can quickly create keypairs (signing key and verifying key), sign +library, you can quickly create key pairs (signing key and verifying key), sign messages, and verify the signatures. The keys and signatures are very short, making them easy to handle and incorporate into other protocols.") (license license:expat))) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index c0d0d5662b..aa7d825f2a 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -730,9 +730,9 @@ both of which are installed automatically if you install this library.") (home-page "https://github.com/html5lib/html5lib-python") (synopsis - "Python HTML parser based on the WHATWG HTML specifcation") + "Python HTML parser based on the WHATWG HTML specification") (description - "Html5lib is an HTML parser based on the WHATWG HTML specifcation + "Html5lib is an HTML parser based on the WHATWG HTML specification and written in Python.") (license license:expat))) @@ -4723,7 +4723,7 @@ major web browsers.") ("python-pytest-cov" ,python-pytest-cov))) (arguments '(#:test-target "pytest")) (home-page "https://docs.pylonsproject.org/projects/venusian") - (synopsis "Library for defering decorator actions") + (synopsis "Library for deferring decorator actions") (description "Venusian is a library which allows framework authors to defer decorator actions. Instead of taking actions when a function (or class) decorator is diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index af557fd009..1cd0305fe1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18940,7 +18940,7 @@ with a non-list @code{cdr}.") (description "This Python module provides line editing functions similar to the default Emacs-style ones of GNU Readline. Unlike the Python standard library's -@code{readline} package, this one allows access to those capabilties in settings +@code{readline} package, this one allows access to those capabilities in settings outside of a standard command-line interface. It is especially well-suited to interfacing with Urwid, due to a shared syntax for describing key inputs. @@ -20087,11 +20087,11 @@ load balancing.") `(("python-pytest" ,python-pytest) ("which" ,which))) (home-page "https://pypi.org/project/pox/") - (synopsis "Python utilities for filesystem exploration and automated builds") + (synopsis "Python utilities for file system exploration and automated builds") (description "Pox provides a collection of utilities for navigating and manipulating -filesystems. This module is designed to facilitate some of the low level -operating system interactions that are useful when exploring a filesystem on a +file systems. This module is designed to facilitate some of the low-level +operating system interactions that are useful when exploring a file system on a remote host. Pox provides Python equivalents of several shell commands such as @command{which} and @command{find}. These commands allow automated discovery of what has been installed on an operating system, and where the @@ -20440,7 +20440,7 @@ tests.") (description "Python-GSSAPI provides both low-level and high level wrappers around the GSSAPI C libraries. While it focuses on the Kerberos mechanism, it should -also be useable with other GSSAPI mechanisms.") +also be usable with other GSSAPI mechanisms.") (license license:isc))) (define-public python-check-manifest @@ -20516,8 +20516,8 @@ files. These files are used to translate strings in android apps.") `(("python-pytest-cov" ,python-pytest-cov) ("python-pytest-timeout" ,python-pytest-timeout))) (home-page "https://github.com/gorakhargosh/watchdog") - (synopsis "Filesystem events monitoring") - (description "This package provides a way to monitor filesystem events + (synopsis "File system events monitoring") + (description "This package provides a way to monitor file system events such as a file modification and trigger an action. This is similar to inotify, but portable.") (license license:asl2.0))) @@ -20817,9 +20817,9 @@ content models.") `(("python-cffi" ,python-cffi))) (home-page "https://github.com/xattr/xattr") (synopsis - "Python wrapper for extended filesystem attributes") + "Python wrapper for extended file system attributes") (description "This package provides a Python wrapper for using extended -filesystem attributes. Extended attributes extend the basic attributes of files +file system attributes. Extended attributes extend the basic attributes of files and directories in the file system. They are stored as name:data pairs associated with file system objects (files, directories, symlinks, etc).") (license license:expat))) @@ -21832,10 +21832,10 @@ RFC 3464.") (home-page "https://flufli18n.readthedocs.io") (synopsis "API for Python internationalization") (description - "This package provides a high level, convenient API for managing -internationalization translation contexts in Python application. There is a + "This package provides a high-level, convenient API for managing +internationalization/translation contexts in Python applications. There is a simple API for single-context applications, such as command line scripts which -only need to translate into one language during the entire course of thei +only need to translate into one language during the entire course of their execution. There is a more flexible, but still convenient API for multi-context applications, such as servers, which may need to switch language contexts for different tasks.") diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index c562ade153..3266db3fe8 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -648,8 +648,8 @@ outcomes of a code example.") (synopsis "Ripper-style abstract syntax tree to Ruby source generator") (description "Sorcerer generates Ruby code from a Ripper-like abstract syntax tree (i.e. S-Expressions). Sorcerer is targeted mainly at small -snippets of Ruby code, expressable in a single line. Longer examples may be -re-sourced, but they will be rendered in a single line format.") +snippets of Ruby code, expressible in a single line. Longer examples may be +re-sourced, but they will be rendered in a single-line format.") (home-page "https://github.com/rspec-given/sorcerer") (license license:expat))) diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index 0700167521..dba1b26e50 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -465,7 +465,7 @@ Example use cases: Features: @itemize @bullet -@item Coalesces multiple filesystem events into one, for editors that +@item Coalesces multiple file system events into one, for editors that use swap/backup files during saving @item By default, uses @code{.gitignore} and @code{.ignore} to determine which files to ignore notifications for diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm index d5914f012b..e44e78de75 100644 --- a/gnu/packages/rust.scm +++ b/gnu/packages/rust.scm @@ -449,7 +449,7 @@ test = { path = \"../libtest\" } (variable "LIBRARY_PATH") (files '("lib" "lib64"))))) - (synopsis "Compiler for the Rust progamming language") + (synopsis "Compiler for the Rust programming language") (description "Rust is a systems programming language that provides memory safety and thread safety guarantees.") (home-page "https://www.rust-lang.org") diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 5225e12064..6783af24ee 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -701,8 +701,9 @@ Its features include: (home-page "https://github.com/rain-1/s") (synopsis "Extremely minimal shell with the simplest syntax possible") (description - "S is a new shell that aims to be extremely simple. -S does not implemnt the POSIX shell standard. + "S is a new shell that aims to be extremely simple. It does not +implement the POSIX shell standard. + There are no globs or \"splatting\" where a variable $FOO turns into multiple command line arguments. One token stays one token forever. This is a \"no surprises\" straightforward approach. diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm index 79f8256a3f..4cac75d5fa 100644 --- a/gnu/packages/ssh.scm +++ b/gnu/packages/ssh.scm @@ -694,7 +694,7 @@ manipulating key files.") (base32 "0q7fblaczb7kwbsz0gdy9267z0sllzgmf0c7z5c9mf88wv74ycn6")))) (build-system gnu-build-system) - (description "sshpass is a tool for non-interactivly performing password + (description "sshpass is a tool for non-interactively performing password authentication with SSH's so-called @dfn{interactive keyboard password authentication}.") (license license:gpl2+))) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index 57c84d7718..5d81619646 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -426,7 +426,7 @@ to all types of devices that provide serial consoles.") allowing different sounds to indicate different events. While it can be run quite happily on the command line, its intended place of residence is within scripts, notifying the user when something interesting occurs. Of course, it -has no notion of what's interesing, but it's very good at that notifying part.") +has no notion of what's interesting, but it's very good at that notifying part.") (home-page "https://github.com/spkr-beep/beep") (license license:gpl2+))) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 7ce087866e..21c227d8eb 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3713,7 +3713,7 @@ https schemed URLs with LWP.") (home-page "https://metacpan.org/release/LWP-UserAgent-Cached") (synopsis "Simple caching for LWP::UserAgent") (description "LWP::UserAgent::Cached is an LWP::UserAgent subclass with -cache support. It returns responses from the local filesystem if available +cache support. It returns responses from the local file system, if available, instead of making an HTTP request.") (license license:perl-license))) diff --git a/gnu/packages/wv.scm b/gnu/packages/wv.scm index d5888674a7..a8c0d3cbaf 100644 --- a/gnu/packages/wv.scm +++ b/gnu/packages/wv.scm @@ -57,7 +57,7 @@ Word 9, 8, 7, and 6) to HTML or LaTeX. Word 2 documents can still be converted to plain text but will lack formatting. -Othe programs can use wv as a library to convert Word documents to other +Other programs can use wv as a library to convert Word documents to other formats. AbiWord uses it as its Word importer, and KWord uses concepts and code from wv in theirs.") (home-page "http://wvware.sourceforge.net/") -- cgit v1.2.3 From 871539f3ad1d30967950f9bf3a1b7ad271ba3360 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Mon, 28 Sep 2020 17:06:56 +0200 Subject: gnu: r-chippeakanno: Update to 3.22.4. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.22.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d655253cf1..7eef0485be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1797,14 +1797,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.22.3") + (version "3.22.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y")))) + "0wxgjdikinkqj7jvs2725ak0291q6zhikyf1c93w8cngwvd9i1gq")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1628d57bb5c6ab30a04202c229de642b94faac85 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 30 Sep 2020 08:57:27 +0300 Subject: gnu: Fix package references. * gnu/packages/algebra.scm (iml)[inputs]: Correctly refer to package inputs. * gnu/packages/astronomy.scm (xplanet), * gnu/packages/audio.scm (redkite, libaudec, lv2lint, lv2toweb), * gnu/packages/bioconductor.scm (r-cummerbund), * gnu/packages/chicken.scm (chicken), * gnu/packages/conky.scm (conky), * gnu/packages/cran.scm (r-latex2exp), * gnu/packages/crates-io.scm (rust-rgb), * gnu/packages/databases.scm (mariadb), * gnu/packages/diffoscope.scm (reprotest), * gnu/packages/file-systems.scm (glusterfs), * gnu/packages/finance.scm (electron-cash), * gnu/packages/games.scm (rinutils, ksudoku, kdiamond, kigo), * gnu/packages/geo.scm (grass), * gnu/packages/gnome.scm (libmediaart, gnome-contacts, geoclue), * gnu/packages/gnucash.scm (aqbanking), * gnu/packages/image.scm (mtpaint), * gnu/packages/kde-internet.scm (kopete, ktorrent), * gnu/packages/kde-utils.scm (kmousetool, kmouth, kronometer), * gnu/packages/linphone.scm (liblinphone), * gnu/packages/maths.scm (ppl), * gnu/packages/mercury.scm (mercury-minimal), * gnu/packages/music.scm (bjumblr, bschaffl, lsp-plugins, spectacle-analyzer, helm, tap-lv2, wolf-shaper, shiru-lv2), * gnu/packages/networking.scm (restinio), * gnu/packages/prolog.scm (swi-prolog), * gnu/packages/python-web.scm (gunicorn), * gnu/packages/python-xyz.scm (python-docusign-esign), * gnu/packages/ruby.scm (ruby-cucumber, ruby_version, ruby-addressable), * gnu/packages/sagemath.scm (python-cypari2), * gnu/packages/skarnet.scm (s6-linux-init), * gnu/packages/vpn.scm (sshuttle), * gnu/packages/web.scm (libcyaml), * gnu/packages/xdisorg.scm (kbdd), * gnu/packages/xorg.scm (xpra): Same. --- gnu/packages/algebra.scm | 2 +- gnu/packages/astronomy.scm | 2 +- gnu/packages/audio.scm | 20 ++++++------- gnu/packages/bioconductor.scm | 2 +- gnu/packages/chicken.scm | 2 +- gnu/packages/conky.scm | 2 +- gnu/packages/cran.scm | 2 +- gnu/packages/crates-io.scm | 2 +- gnu/packages/databases.scm | 2 +- gnu/packages/diffoscope.scm | 2 +- gnu/packages/file-systems.scm | 10 +++---- gnu/packages/finance.scm | 4 +-- gnu/packages/games.scm | 8 ++--- gnu/packages/geo.scm | 2 +- gnu/packages/gnome.scm | 6 ++-- gnu/packages/gnucash.scm | 2 +- gnu/packages/image.scm | 6 ++-- gnu/packages/kde-internet.scm | 4 +-- gnu/packages/kde-utils.scm | 8 ++--- gnu/packages/linphone.scm | 2 +- gnu/packages/maths.scm | 4 +-- gnu/packages/mercury.scm | 2 +- gnu/packages/music.scm | 68 +++++++++++++++++++++---------------------- gnu/packages/networking.scm | 4 +-- gnu/packages/prolog.scm | 2 +- gnu/packages/python-web.scm | 2 +- gnu/packages/python-xyz.scm | 14 ++++----- gnu/packages/ruby.scm | 6 ++-- gnu/packages/sagemath.scm | 2 +- gnu/packages/skarnet.scm | 2 +- gnu/packages/vpn.scm | 2 +- gnu/packages/web.scm | 2 +- gnu/packages/xdisorg.scm | 2 +- gnu/packages/xorg.scm | 2 +- 34 files changed, 102 insertions(+), 102 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 262a7939df..912ec2fe64 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1553,7 +1553,7 @@ structure constants of Schubert polynomials.") "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x")))) (build-system gnu-build-system) (inputs - `(("gmp", gmp) + `(("gmp" ,gmp) ("cblas" ,openblas))) ; or any other BLAS library; the documentation ; mentions ATLAS in particular (arguments diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 785d281887..353ba96a32 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -328,7 +328,7 @@ Mechanics, Astrometry and Astrodynamics library.") ("freetype" ,freetype) ("pango" ,pango) ("giflib" ,giflib) - ("libjpeg", libjpeg-turbo) + ("libjpeg" ,libjpeg-turbo) ("libpng" ,libpng) ("libtiff" ,libtiff) ("netpbm" ,netpbm) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index a50266965b..0e93a7263e 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -4519,7 +4519,7 @@ workstations as well as consumer software such as music players.") (inputs `(("cairo" ,cairo))) (native-inputs - `(("pkg-config", pkg-config))) + `(("pkg-config" ,pkg-config))) (synopsis "Small GUI toolkit") (description "Redkite is a small GUI toolkit developed in C++17 and inspired from other well known GUI toolkits such as Qt and GTK. It is @@ -4665,7 +4665,7 @@ in the package.") `(("libsamplerate" ,libsamplerate) ("libsndfile" ,libsndfile))) (native-inputs - `(("pkg-config", pkg-config))) + `(("pkg-config" ,pkg-config))) (synopsis "Library for reading and resampling audio files") (description "libaudec is a wrapper library over ffmpeg, sndfile and libsamplerate for reading and resampling audio files, based on Robin Gareus' @@ -4693,11 +4693,11 @@ libsamplerate for reading and resampling audio files, based on Robin Gareus' `("-Delf-tests=true" ; for checking symbol visibility "-Donline-tests=true"))) ; for checking URI existence (inputs - `(("curl", curl) - ("libelf", libelf) - ("lilv", lilv))) + `(("curl" ,curl) + ("libelf" ,libelf) + ("lilv" ,lilv))) (native-inputs - `(("pkg-config", pkg-config))) + `(("pkg-config" ,pkg-config))) (synopsis "LV2 plugin lint tool") (description "lv2lint is an LV2 lint-like tool that checks whether a given plugin and its UI(s) match up with the provided metadata and adhere @@ -4728,11 +4728,11 @@ to well-known best practices.") (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("jalv", jalv) - ("lilv", lilv))) + `(("jalv" ,jalv) + ("lilv" ,lilv))) (native-inputs - `(("help2man", help2man) - ("pkg-config", pkg-config))) + `(("help2man" ,help2man) + ("pkg-config" ,pkg-config))) (synopsis "Documentation generator for LV2 plugins") (description "lv2toweb allows the user to create an xhtml page with information diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7eef0485be..4ca0906fbf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1115,7 +1115,7 @@ how the coverage distributed across the genome.") (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-fastcluster", r-fastcluster) + ("r-fastcluster" ,r-fastcluster) ("r-ggplot2" ,r-ggplot2) ("r-gviz" ,r-gviz) ("r-plyr" ,r-plyr) diff --git a/gnu/packages/chicken.scm b/gnu/packages/chicken.scm index 7b86a58012..729cf25a6c 100644 --- a/gnu/packages/chicken.scm +++ b/gnu/packages/chicken.scm @@ -59,7 +59,7 @@ ;; Parallel builds are not supported, as noted in README. #:parallel-build? #f)) - (propagated-inputs `(("gcc-toolchain", gcc-toolchain))) + (propagated-inputs `(("gcc-toolchain" ,gcc-toolchain))) (home-page "https://www.call-cc.org/") (synopsis "R5RS Scheme implementation that compiles native code via C") (description diff --git a/gnu/packages/conky.scm b/gnu/packages/conky.scm index 6bae336b1c..0df6d1f760 100644 --- a/gnu/packages/conky.scm +++ b/gnu/packages/conky.scm @@ -79,7 +79,7 @@ ("libxext" ,libxext) ("libxft" ,libxft) ("libxinerama" ,libxinerama) - ("pulseaudio", pulseaudio) + ("pulseaudio" ,pulseaudio) ("lua" ,lua) ("ncurses" ,ncurses) ("curl" ,curl))) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 50ce111123..0939c4d5a6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21899,7 +21899,7 @@ appropriate dog and cat images for many status codes.") (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr) - ("r-magrittr", r-magrittr))) + ("r-magrittr" ,r-magrittr))) (home-page "https://github.com/stefano-meschiari/latex2exp/") (synopsis "Use LaTeX expressions in plots") (description "@code{latex2exp} parses and converts LaTeX math formulas to diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 5c31a66208..37e4e69d3f 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -21255,7 +21255,7 @@ uses finite automata and guarantees linear time matching on all inputs.") (arguments `(#:cargo-inputs (("rust-bytemuck" ,rust-bytemuck-1) - ("rust-serde", rust-serde-1)) + ("rust-serde" ,rust-serde-1)) #:cargo-development-inputs (("rust-serde-json" ,rust-serde-json-1)))) (home-page "https://lib.rs/crates/rgb") diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index c86297b293..a3eef034a6 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -944,7 +944,7 @@ Language.") `(("bison" ,bison) ;; XXX: On armhf, use GCC 5 to work around . ,@(if (string-prefix? "armhf" (%current-system)) - `(("gcc@5", gcc-5)) + `(("gcc@5" ,gcc-5)) '()) ("perl" ,perl))) (inputs diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index 9480f1f226..3e7ab7d7ba 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -254,7 +254,7 @@ install.") (inputs `(("python-debian" ,python-debian) ("python-distro" ,python-distro) - ("python-libarchive-c", python-libarchive-c) + ("python-libarchive-c" ,python-libarchive-c) ("python-rstr" ,python-rstr))) (native-inputs `(("diffoscope" ,diffoscope) diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index 046deb67ab..0d897a6307 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -504,8 +504,8 @@ non-determinism in the build process.") (lambda _ (invoke "./autogen.sh")))))) (native-inputs `(("pkg-config" ,pkg-config) - ("libtirpc", libtirpc) - ("rpcsvc-proto", rpcsvc-proto) + ("libtirpc" ,libtirpc) + ("rpcsvc-proto" ,rpcsvc-proto) ("python-2" ,python-2) ; must be version 2 ("flex" ,flex) ("bison" ,bison) @@ -515,15 +515,15 @@ non-determinism in the build process.") ("cmocka" ,cmocka))) (inputs `(("acl" ,acl) - ("fuse", fuse) + ("fuse" ,fuse) ("openssl" ,openssl) ("liburcu" ,liburcu) ("libuuid" ,util-linux "lib") ("libxml2" ,libxml2) ("readline" ,readline) ("zlib" ,zlib) - ("libaio", libaio) - ("rdma-core", rdma-core))) + ("libaio" ,libaio) + ("rdma-core" ,rdma-core))) (home-page "https://www.gluster.org") (synopsis "Distributed file system") (description "GlusterFS is a distributed scalable network file system diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 863914bd35..05cb0ad88b 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -493,10 +493,10 @@ other machines/servers. Electrum does not download the Bitcoin blockchain.") (build-system python-build-system) (inputs `(("libevent" ,libevent) - ("libsecp256k1", libsecp256k1-bitcoin-cash) + ("libsecp256k1" ,libsecp256k1-bitcoin-cash) ("openssl" ,openssl) ("python-cython" ,python-cython) - ("python-dateutil", python-dateutil) + ("python-dateutil" ,python-dateutil) ("python-dnspython" ,python-dnspython) ("python-ecdsa" ,python-ecdsa) ("python-hidapi" ,python-hidapi) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index a90e708ab3..4423d51336 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -7180,7 +7180,7 @@ original.") ("pkg-config" ,pkg-config))) (inputs `(("cmocka" ,cmocka) - ("perl-env-path", perl-env-path) + ("perl-env-path" ,perl-env-path) ("perl-inline" ,perl-inline) ("perl-inline-c" ,perl-inline-c) ("perl-string-shellquote" ,perl-string-shellquote) @@ -10176,7 +10176,7 @@ This package is part of the KDE games module.") `(("extra-cmake-modules" ,extra-cmake-modules) ("kdoctools" ,kdoctools))) (inputs - `(("karchive", karchive) + `(("karchive" ,karchive) ("kconfig" ,kconfig) ("kconfigwidgets" ,kconfigwidgets) ("kcoreaddons" ,kcoreaddons) @@ -10322,7 +10322,7 @@ This package is part of the KDE games module.") `(("extra-cmake-modules" ,extra-cmake-modules) ("kdoctools" ,kdoctools))) (inputs - `(("kcompletion", kcompletion) + `(("kcompletion" ,kcompletion) ("kconfig" ,kconfig) ("kconfigwidgets" ,kconfigwidgets) ("kcoreaddons" ,kcoreaddons) @@ -10714,7 +10714,7 @@ This package is part of the KDE games module.") ("kdbusaddons" ,kdbusaddons) ("ki18n" ,ki18n) ("kio" ,kio) - ("knewstuff", knewstuff) + ("knewstuff" ,knewstuff) ("ktextwidgets" ,ktextwidgets) ("kxmlgui" ,kxmlgui) ("libkdegames" ,libkdegames) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 291b928338..0605d84c0e 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1776,7 +1776,7 @@ track your position right from your laptop.") (base32 "1fwsm99kz0bxvjk7442qq1h45ikrmhba8bqclafb61gqg1q6ymrk")))) (build-system gnu-build-system) (inputs - `(("bzip2", bzip2) + `(("bzip2" ,bzip2) ("cairo" ,cairo) ("fftw" ,fftw) ("freetype" ,freetype) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 77ed6678cd..da4b2771e8 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1299,7 +1299,7 @@ and implementation of UPnP A/V profiles.") `(("gdk-pixbuf" ,gdk-pixbuf) ("gettext" ,gettext-minimal) ("gobject-introspection" ,gobject-introspection) - ("gtk+:doc", gtk+ "doc") + ("gtk+:doc" ,gtk+ "doc") ("vala" ,vala))) (synopsis "Media art library for the GNOME desktop") (description @@ -1961,7 +1961,7 @@ commonly used macros.") ("telepathy-glib" ,telepathy-glib) ("vala" ,vala))) (propagated-inputs - `(("folks", folks) + `(("folks" ,folks) ("telepathy-mission-control" ,telepathy-mission-control))) (synopsis "GNOME's integrated address book") (description @@ -5025,7 +5025,7 @@ output devices.") ("gobject-introspection" ,gobject-introspection) ("modem-manager" ,modem-manager) ("libnotify" ,libnotify) - ("gtk-doc", gtk-doc) + ("gtk-doc" ,gtk-doc) ("intltool" ,intltool))) (inputs `(("avahi" ,avahi) diff --git a/gnu/packages/gnucash.scm b/gnu/packages/gnucash.scm index 43aad3ed02..8f58ce332a 100644 --- a/gnu/packages/gnucash.scm +++ b/gnu/packages/gnucash.scm @@ -293,7 +293,7 @@ applications and libraries. It is used by AqBanking.") ("gnutls" ,gnutls))) (native-inputs `(("pkg-config" ,pkg-config) - ("gettext-minimal", gettext-minimal) + ("gettext-minimal" ,gettext-minimal) ("libltdl" ,libltdl))) (home-page "https://www.aquamaniac.de/sites/aqbanking/index.php") (synopsis "Interface for online banking tasks") diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index bec03886a6..8fbdd0b4ae 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -2180,12 +2180,12 @@ by AOM, including with alpha.") `(("imlib2" ,imlib2) ("libtiff" ,libtiff) ("libpng" ,libpng) - ("libungif", libungif) - ("libjpeg", libjpeg-turbo) + ("libungif" ,libungif) + ("libjpeg" ,libjpeg-turbo) ("libwebp" ,libwebp) ("openjpeg" ,openjpeg) ("lcms" ,lcms) - ("zlib", zlib) + ("zlib" ,zlib) ("glib" ,glib) ;; Support for gtk3 is in the testing stage. ("gtk+" ,gtk+-2))) diff --git a/gnu/packages/kde-internet.scm b/gnu/packages/kde-internet.scm index f9cd29e9b8..800554a36e 100644 --- a/gnu/packages/kde-internet.scm +++ b/gnu/packages/kde-internet.scm @@ -297,7 +297,7 @@ Features are: ("libxml2" ,libxml2) ("libxstl" ,libxslt) ;; TODO: Mediastreamer - ("openssl", openssl) + ("openssl" ,openssl) ("ortp" ,ortp) ("phonon" ,phonon) ("qca" ,qca) @@ -403,7 +403,7 @@ This package is part of the KDE networking module.") ("knotifyconfig" ,knotifyconfig) ("kparts" ,kparts) ("kplotting" ,kplotting) - ("kross", kross) + ("kross" ,kross) ("kwidgetsaddons" ,kwidgetsaddons) ("kwindowsystem" ,kwindowsystem) ("kxmlgui" ,kxmlgui) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 4d9f3736c8..00ef15b9d9 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -149,7 +149,7 @@ artists to web-designers to people with low vision.") (inputs `(("kauth" ,kauth) ("kcoreaddons" ,kcoreaddons) - ("kconfigwidgets", kconfigwidgets) + ("kconfigwidgets" ,kconfigwidgets) ("kdbusaddons" ,kdbusaddons) ("ki18n" ,ki18n) ("kiconthemes" ,kiconthemes) @@ -187,8 +187,8 @@ whom pressing buttons hurts.") ("kdoctools" ,kdoctools))) (inputs `(("kcompletion" ,kcompletion) - ("kconfig", kconfig) - ("kconfigwidgets", kconfigwidgets) + ("kconfig" ,kconfig) + ("kconfigwidgets" ,kconfigwidgets) ("kcoreaddons" ,kcoreaddons) ("kcrash" ,kcrash) ("ki18n" ,ki18n) @@ -228,7 +228,7 @@ sentences to be re-spoken.") (inputs `(("kauth" ,kauth) ("kconfig" ,kconfig) - ("kconfigwidgets", kconfigwidgets) + ("kconfigwidgets" ,kconfigwidgets) ("kcoreaddons" ,kcoreaddons) ("kcrash" ,kcrash) ("ki18n" ,ki18n) diff --git a/gnu/packages/linphone.scm b/gnu/packages/linphone.scm index a6492893c8..777485b9ea 100644 --- a/gnu/packages/linphone.scm +++ b/gnu/packages/linphone.scm @@ -483,7 +483,7 @@ including media capture, encoding and decoding, and rendering.") `(("bctoolbox" ,bctoolbox) ("belcard" ,belcard) ("bellesip" ,belle-sip) - ("bzrtp", bzrtp) + ("bzrtp" ,bzrtp) ("iconv" ,libiconv) ("glib" ,glib) ("gtk2" ,gtk+-2) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ce393cba80..93ee2db60a 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5764,10 +5764,10 @@ compiled against the nauty library.") "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb")))) (build-system gnu-build-system) (native-inputs - `(("m4", m4))) + `(("m4" ,m4))) (inputs `(("glpk" ,glpk) - ("gmp", gmp))) + ("gmp" ,gmp))) (home-page "https://www.bugseng.com/parma-polyhedra-library") (synopsis "Parma Polyhedra Library for computations with polyhedra") diff --git a/gnu/packages/mercury.scm b/gnu/packages/mercury.scm index a6ae451e63..bab8909862 100644 --- a/gnu/packages/mercury.scm +++ b/gnu/packages/mercury.scm @@ -138,7 +138,7 @@ (native-inputs `(("texinfo" ,texinfo) ("flex" ,flex) - ("tcsh", tcsh) + ("tcsh" ,tcsh) ("bison" ,bison) ("readline" ,readline) ("libatomic-ops" ,(package-source diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 54c8e14669..1727bac7b8 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -1391,9 +1391,9 @@ B.Choppr is the successor of B.Slizr.") (base32 "0kl6hrxmqrdf0195bfnzsa2h1073fgiqrfhg2276fm1954sm994v")))) (inputs - `(("cairo", cairo) - ("libsndfile", libsndfile) - ("lv2", lv2))) + `(("cairo" ,cairo) + ("libsndfile" ,libsndfile) + ("lv2" ,lv2))) (synopsis "Pattern-controlled audio stream/sample re-sequencer LV2 plugin") (description "B.Jumblr is a pattern-controlled audio stream / sample re-sequencer LV2 plugin.") @@ -1416,11 +1416,11 @@ re-sequencer LV2 plugin.") (base32 "1c09acqrbd387ba41f8ch1qykdap5h6cg9if5pgd16i4dmjnpghj")))) (inputs - `(("cairo", cairo) + `(("cairo" ,cairo) ("fontconfig" ,fontconfig) - ("libsndfile", libsndfile) + ("libsndfile" ,libsndfile) ("libx11" ,libx11) - ("lv2", lv2))) + ("lv2" ,lv2))) (home-page "https://github.com/sjaehn/BSchaffl") (synopsis "Pattern-controlled MIDI amp & time stretch LV2 plugin") (description "This package provides an LV2 plugin that allows for @@ -5098,15 +5098,15 @@ and reverb.") (delete 'configure)) ; no configure #:test-target "test")) (inputs - `(("cairo", cairo) - ("hicolor-icon-theme", hicolor-icon-theme) - ("jack", jack-1) - ("ladspa", ladspa) - ("libsndfile", libsndfile) - ("lv2", lv2) - ("mesa", mesa))) + `(("cairo" ,cairo) + ("hicolor-icon-theme" ,hicolor-icon-theme) + ("jack" ,jack-1) + ("ladspa" ,ladspa) + ("libsndfile" ,libsndfile) + ("lv2" ,lv2) + ("mesa" ,mesa))) (native-inputs - `(("pkg-config", pkg-config))) + `(("pkg-config" ,pkg-config))) (synopsis "Audio plugin collection") (description "LSP (Linux Studio Plugins) is a collection of audio plugins available as LADSPA/LV2 plugins and as standalone JACK @@ -5216,12 +5216,12 @@ as a whole to realisticly reproduce the features and flaws of the real deal.") `(("pkg-config" ,pkg-config) ("xxd" ,xxd))) (inputs - `(("cairo", cairo) - ("fftw", fftw) - ("fftwf", fftwf) - ("jack", jack-1) - ("lv2", lv2) - ("mesa", mesa))) + `(("cairo" ,cairo) + ("fftw" ,fftw) + ("fftwf" ,fftwf) + ("jack" ,jack-1) + ("lv2" ,lv2) + ("mesa" ,mesa))) (synopsis "Realtime graphical spectrum analyzer") (description "Spectacle is a real-time spectral analyzer using the short-time Fourier transform, available as LV2 audio plugin and JACK client.") @@ -5515,12 +5515,12 @@ MIDI drums and comes as two separate drumkits: Black Pearl and Red Zeppelin.") ("freetype2" ,freetype) ("hicolor-icon-theme" ,hicolor-icon-theme) ("libxcursor" ,libxcursor) - ("libxinerama", libxinerama) - ("jack", jack-1) + ("libxinerama" ,libxinerama) + ("jack" ,jack-1) ("mesa" ,mesa))) (native-inputs `(("pkg-config" ,pkg-config) - ("lv2", lv2))) + ("lv2" ,lv2))) (home-page "https://tytel.org/helm/") (synopsis "Polyphonic synth with lots of modulation") (description "Helm is a cross-platform polyphonic synthesizer available standalone @@ -5845,9 +5845,9 @@ plugin and a standalone JACK application.") "/lib/lv2") "install")))))) (inputs - `(("lv2", lv2))) + `(("lv2" ,lv2))) (native-inputs - `(("pkg-config", pkg-config))) + `(("pkg-config" ,pkg-config))) (synopsis "Audio plugin collection") (description "TAP (Tom's Audio Processing) plugins is a collection of audio effect plugins originally released as LADSPA plugins. This package @@ -5903,9 +5903,9 @@ plugin and a standalone JACK application.") (native-inputs `(("pkg-config" ,pkg-config))) (inputs - `(("jack", jack-1) - ("lv2", lv2) - ("mesa", mesa))) + `(("jack" ,jack-1) + ("lv2" ,lv2) + ("mesa" ,mesa))) (synopsis "Waveshaper plugin") (description "Wolf Shaper is a waveshaper plugin with a graph editor. It is provided as an LV2 plugin and as a standalone Jack application.") @@ -5985,12 +5985,12 @@ It is provided as an LV2 plugin and as a standalone Jack application.") (native-inputs `(("pkg-config" ,pkg-config))) (inputs - `(("cairo", cairo) - ("glu", glu) - ("jack", jack-1) - ("lv2", lv2) - ("mesa", mesa) - ("pango", pango))) + `(("cairo" ,cairo) + ("glu" ,glu) + ("jack" ,jack-1) + ("lv2" ,lv2) + ("mesa" ,mesa) + ("pango" ,pango))) (synopsis "Audio plugin collection") (description "Shiru plugins is a collection of audio plugins created by Shiru, ported to LV2 by the Linux MAO project using the DISTRHO plugin diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 8b46bd7d24..7679d62059 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -3275,9 +3275,9 @@ communication over HTTP.") ("pcre2" ,pcre2) ("sobjectizer" ,sobjectizer))) (propagated-inputs - `(("asio", asio) + `(("asio" ,asio) ("fmt" ,fmt) - ("http-parser", http-parser))) + ("http-parser" ,http-parser))) (arguments `(#:configure-flags '("-DRESTINIO_INSTALL=on") #:tests? #f ; TODO: The tests are called from the root CMakelist, need RESTINIO_TEST=on. diff --git a/gnu/packages/prolog.scm b/gnu/packages/prolog.scm index 86b4bd2107..0e5f4b9b01 100644 --- a/gnu/packages/prolog.scm +++ b/gnu/packages/prolog.scm @@ -125,7 +125,7 @@ manner. It also features an interactive interpreter.") ("texinfo" ,texinfo) ("libarchive" ,libarchive) ("libunwind" ,libunwind) - ("libjpeg", libjpeg-turbo) + ("libjpeg" ,libjpeg-turbo) ("libxft" ,libxft) ("fontconfig" ,fontconfig) ("perl" ,perl) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index bb2fc850c9..dde0e447e3 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -4118,7 +4118,7 @@ event loop. It is implemented in Cython and uses libuv under the hood.") #t))))) (native-inputs `(("binutils" ,binutils) ;; for ctypes.util.find_library() - ("python-aiohttp", python-aiohttp) + ("python-aiohttp" ,python-aiohttp) ("python-pytest" ,python-pytest) ("python-pytest-cov" ,python-pytest-cov) ("python-sphinx" ,python-sphinx) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6c3e991de8..22a356d11b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20788,13 +20788,13 @@ content models.") ;; Testing requires undocumented setup changes, and so testing is disabled here. (arguments `(#:tests? #f)) (propagated-inputs - `(("python-certifi", python-certifi) - ("python-six", python-six) - ("python-dateutil", python-dateutil) - ("python-urllib3", python-urllib3) - ("python-pyjwt", python-pyjwt) - ("python-cryptography", python-cryptography) - ("python-nose", python-nose))) + `(("python-certifi" ,python-certifi) + ("python-six" ,python-six) + ("python-dateutil" ,python-dateutil) + ("python-urllib3" ,python-urllib3) + ("python-pyjwt" ,python-pyjwt) + ("python-cryptography" ,python-cryptography) + ("python-nose" ,python-nose))) (synopsis "DocuSign Python Client") (description "The Official DocuSign Python Client Library used to interact with the eSign REST API. Send, sign, and approve documents using this client.") diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 3266db3fe8..7348f29eb1 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -7792,7 +7792,7 @@ master/html-formatter/ruby") (native-inputs `(;; Use a untested version of aruba, to avoid a circular dependency, as ;; ruby-aruba depends on ruby-cucumber. - ("ruby-aruba", ruby-aruba-without-tests) + ("ruby-aruba" ,ruby-aruba-without-tests) ("ruby-rspec" ,ruby-rspec) ("ruby-pry" ,ruby-pry) ("ruby-nokogiri" ,ruby-nokogiri) @@ -8851,7 +8851,7 @@ display width of strings in Ruby.") (native-inputs `(("ruby-rdoc" ,ruby-rdoc) ("ruby-rspec" ,ruby-rspec) - ("ruby-rubygems-tasks", ruby-rubygems-tasks))) + ("ruby-rubygems-tasks" ,ruby-rubygems-tasks))) (synopsis "Ruby library to help check the Ruby version") (description "@code{ruby_version} provides a @code{RubyVersion} module to simplify checking for the right Ruby version in software.") @@ -9963,7 +9963,7 @@ all known public suffixes.") ("bundler" ,bundler) ("ruby-idn-ruby" ,ruby-idn-ruby) ("ruby-sporkmonger-rack-mount" ,ruby-sporkmonger-rack-mount) - ("ruby-rspec-its", ruby-rspec-its-minimal) + ("ruby-rspec-its" ,ruby-rspec-its-minimal) ("ruby-yard" ,ruby-yard) ("ruby-simplecov" ,ruby-simplecov))) (propagated-inputs diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 8c837fdaeb..943e9ba5b9 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -59,7 +59,7 @@ `(("python-cysignals" ,python-cysignals))) (inputs `(("gmp" ,gmp) - ("pari-gp", pari-gp))) + ("pari-gp" ,pari-gp))) (home-page "https://cypari2.readthedocs.io/") (synopsis "Python interface to the number theory library libpari") diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 8032a5e505..f171967957 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -307,7 +307,7 @@ systems and other constrained environments, but they work everywhere."))) (build-system gnu-build-system) (inputs `(("execline" ,execline) - ("s6", s6) + ("s6" ,s6) ("skalibs" ,skalibs))) (arguments '(#:configure-flags diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index c704106221..d22f9ccd5d 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -405,7 +405,7 @@ private network between hosts on the internet.") (native-inputs `(("python-setuptools-scm" ,python-setuptools-scm) ;; For tests only. - ("python-flake8", python-flake8) + ("python-flake8" ,python-flake8) ("python-mock" ,python-mock) ("python-pytest-cov" ,python-pytest-cov) ("python-pytest-runner" ,python-pytest-runner))) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 21c227d8eb..ab8daf31cf 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -5050,7 +5050,7 @@ written in C. It is developed as part of the NetSurf project.") (inputs `(("libyaml" ,libyaml))) (native-inputs - `(("pkg-config", pkg-config))) + `(("pkg-config" ,pkg-config))) (synopsis "C library for reading and writing YAML") (description "LibCYAML is a C library written in ISO C11 for reading and writing diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index bbbbd0d7f5..5398761c65 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -2437,7 +2437,7 @@ After selection, the clip is put onto the PRIMARY and CLIPBOARD X selections.") ("glib" ,glib "bin") ("pkg-config" ,pkg-config))) (inputs - `(("dbus-glib", dbus-glib) + `(("dbus-glib" ,dbus-glib) ("glib" ,glib) ("libx11" ,libx11))) (home-page "https://github.com/qnikst/kbdd") diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 8df6407e26..8ff62a1a84 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -6339,7 +6339,7 @@ basic eye-candy effects.") ("python-pillow" ,python-pillow) ;; Optional dependencies. ("python-rencode" ,python-rencode) ; For speed. - ("python-numpy", python-numpy) + ("python-numpy" ,python-numpy) ("python-pyopengl" ,python-pyopengl) ; Drawing acceleration. ("python-pyopengl-accelerate" ,python-pyopengl-accelerate) ; Same. ("python-paramiko" ,python-paramiko) ; Tunneling over SSH. -- cgit v1.2.3 From 5412da848ec9a2caf94bf71355e4ffe90bcfad03 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 5 Oct 2020 22:12:09 +0200 Subject: gnu: r-activedriverwgs: Update to 1.1.1. * gnu/packages/bioconductor.scm (r-activedriverwgs): Update to 1.1.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4ca0906fbf..8e5ec27ea8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7161,14 +7161,14 @@ data.") (define-public r-activedriverwgs (package (name "r-activedriverwgs") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "ActiveDriverWGS" version)) (sha256 (base32 - "0l6h0f54zjvcx19ngq3kp01dypsjqf28vssjm8yzccmpyacfypag")))) + "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say")))) (properties `((upstream-name . "ActiveDriverWGS"))) (build-system r-build-system) -- cgit v1.2.3 From 65e361f98f442ad3c8e84d467d8f731a49836fc9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 5 Oct 2020 22:12:13 +0200 Subject: gnu: r-interval: Update to 1.1-0.7. * gnu/packages/bioconductor.scm (r-interval): Update to 1.1-0.7. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e5ec27ea8..ba55099bef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8187,14 +8187,14 @@ truncated data.") (define-public r-interval (package (name "r-interval") - (version "1.1-0.1") + (version "1.1-0.7") (source (origin (method url-fetch) (uri (cran-uri "interval" version)) (sha256 (base32 - "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8")))) + "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9")))) (properties `((upstream-name . "interval"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d7cfdc122939f87363f3f535f7f7c5f0d403b171 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 5 Oct 2020 22:12:16 +0200 Subject: gnu: r-fhtest: Update to 1.5. * gnu/packages/bioconductor.scm (r-fhtest): Update to 1.5. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ba55099bef..b8cdcbc885 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8214,14 +8214,14 @@ plot them, and perform logrank or Wilcoxon type tests.") (define-public r-fhtest (package (name "r-fhtest") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "FHtest" version)) (sha256 (base32 - "1wsn0j9ydpp9nfswiqg21p09kgkvaq8fh0y0h8syqgizah7i8vs2")))) + "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q")))) (properties `((upstream-name . "FHtest"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From dce2d06fccac0891bb2efd6f63c00967f1c14b23 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Oct 2020 13:11:40 +0200 Subject: gnu: r-diffbind: Update to 2.16.2. * gnu/packages/bioconductor.scm (r-diffbind): Update to 2.16.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b8cdcbc885..ce64448b9e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1609,14 +1609,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-diffbind (package (name "r-diffbind") - (version "2.16.0") + (version "2.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5")))) + "11y9kigdikqcd0cnksh306nsaadak0kgivk7773mv3yszrxxwzj1")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From d7314e4747389b4671c17ddc5fafd479a9487d7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Oct 2020 13:11:50 +0200 Subject: gnu: r-karyoploter: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.14.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ce64448b9e..781dcd8608 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2707,13 +2707,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs")))) + "1wlnzkq58baqj9854nzf5rbglchb2xy4wsp3s0q8xfq8v0p3baxf")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From f000fab88ffdaf67f6564eed8b43204697907f50 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Oct 2020 13:11:53 +0200 Subject: gnu: r-gosemsim: Update to 2.14.2. * gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.14.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 781dcd8608..3c5cafb2e7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3628,14 +3628,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.14.1") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln")))) + "02r7m1x6g8bb7q8l0hpvakdzdv5v1nplhx5lbiy798a7c3xg895b")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 56bca8965acb56c581841935c268dc323db7a173 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Oct 2020 13:11:56 +0200 Subject: gnu: r-atacseqqc: Update to 1.12.5. * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.12.5. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3c5cafb2e7..3aea798240 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4364,14 +4364,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.12.4") + (version "1.12.5") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh")))) + "1103daz82k97vzmxjmf7jwm2nd3w8i0jwplrsi9996bkih11qwbf")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 40b86e20eb87cbdf095d102ff9537b6419a13735 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Oct 2020 13:11:59 +0200 Subject: gnu: r-xcms: Update to 3.10.2. * gnu/packages/bioconductor.scm (r-xcms): Update to 3.10.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3aea798240..414ded3fa1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5062,14 +5062,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.10.1") + (version "3.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "1aa11gy1v7kkamv3hsnvdx715q8f1saw9p664j6wifyjj0hx13kn")))) + "0sk53jcl7sjrpw2ncdpl8sw1b1j9mizlrj517rinr1qrbm6lsn8f")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 7337615d1c31017800bb3eaf02b1b25ebac5becc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Oct 2020 13:12:02 +0200 Subject: gnu: r-bgx: Update to 1.54.1. * gnu/packages/bioconductor.scm (r-bgx): Update to 1.54.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 414ded3fa1..f30f2fd117 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7247,14 +7247,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.54.0") + (version "1.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx")))) + "0a10fg9n5p024jrmbis102gqpbz23sc6vdn1sal2697hlxikzb46")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3