diff options
| -rw-r--r-- | gnu/packages/audio.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/bioconductor.scm | 428 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 405 | ||||
| -rw-r--r-- | gnu/packages/cran.scm | 26 | ||||
| -rw-r--r-- | gnu/packages/education.scm | 6 | ||||
| -rw-r--r-- | gnu/packages/emacs-xyz.scm | 8 | ||||
| -rw-r--r-- | gnu/packages/games.scm | 248 | ||||
| -rw-r--r-- | gnu/packages/geo.scm | 2 | ||||
| -rw-r--r-- | gnu/packages/gnome.scm | 12 | ||||
| -rw-r--r-- | gnu/packages/gstreamer.scm | 31 | ||||
| -rw-r--r-- | gnu/packages/linux.scm | 18 | ||||
| -rw-r--r-- | gnu/packages/music.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/qt.scm | 9 | ||||
| -rw-r--r-- | gnu/packages/ruby.scm | 14 | ||||
| -rw-r--r-- | gnu/packages/video.scm | 131 | ||||
| -rw-r--r-- | gnu/packages/vnc.scm | 86 | ||||
| -rw-r--r-- | gnu/packages/web.scm | 12 |
17 files changed, 790 insertions, 654 deletions
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 4ac70d7b24..87c7e6f4de 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -3047,7 +3047,7 @@ for loudness normalisation.") (define-public timidity++ (package (name "timidity++") - (version "2.14.0") + (version "2.15.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/timidity/TiMidity++" @@ -3055,7 +3055,7 @@ for loudness normalisation.") "/TiMidity++-" version ".tar.bz2")) (sha256 (base32 - "0xk41w4qbk23z1fvqdyfblbz10mmxsllw0svxzjw5sa9y11vczzr")))) + "1xf8n6dqzvi6nr2asags12ijbj1lwk1hgl3s27vm2szib8ww07qn")))) (build-system gnu-build-system) (arguments '(#:configure-flags diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 33f66ce8be..f1af34844f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -389,6 +389,33 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-homo-sapiens + (package + (name "r-homo-sapiens") + (version "1.3.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Homo.sapiens" version 'annotation)) + (sha256 + (base32 + "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) + (properties + `((upstream-name . "Homo.sapiens"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicfeatures" ,r-genomicfeatures) + ("r-go-db" ,r-go-db) + ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) + ("r-organismdbi" ,r-organismdbi) + ("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/Homo.sapiens/") + (synopsis "Annotation package for the Homo.sapiens object") + (description + "This package contains the Homo.sapiens object to access data from +several related annotation packages.") + (license license:artistic2.0))) + (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") @@ -9241,6 +9268,296 @@ preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.") (license license:gpl2+))) +(define-public r-erma + (package + (name "r-erma") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "erma" version)) + (sha256 + (base32 + "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-homo-sapiens" ,r-homo-sapiens) + ("r-iranges" ,r-iranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/erma") + (synopsis "Epigenomic road map adventures") + (description + "The epigenomics road map describes locations of epigenetic marks in DNA +from a variety of cell types. Of interest are locations of histone +modifications, sites of DNA methylation, and regions of accessible chromatin. +This package presents a selection of elements of the road map including +metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines +by Ernst and Kellis.") + (license license:artistic2.0))) + +(define-public r-ggbio + (package + (name "r-ggbio") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ggbio" version)) + (sha256 + (base32 + "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; See https://github.com/tengfei/ggbio/issues/117 + ;; This fix will be included in the next release. + (add-after 'unpack 'fix-typo + (lambda _ + (substitute* "R/GGbio-class.R" + (("fechable") "fetchable")) + #t))))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-biovizbase" ,r-biovizbase) + ("r-bsgenome" ,r-bsgenome) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggally" ,r-ggally) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-organismdbi" ,r-organismdbi) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://www.tengfei.name/ggbio/") + (synopsis "Visualization tools for genomic data") + (description + "The ggbio package extends and specializes the grammar of graphics for +biological data. The graphics are designed to answer common scientific +questions, in particular those often asked of high throughput genomics data. +All core Bioconductor data structures are supported, where appropriate. The +package supports detailed views of particular genomic regions, as well as +genome-wide overviews. Supported overviews include ideograms and grand linear +views. High-level plots include sequence fragment length, edge-linked +interval to data view, mismatch pileup, and several splicing summaries.") + (license license:artistic2.0))) + +(define-public r-gqtlbase + (package + (name "r-gqtlbase") + (version "1.21.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gQTLBase" version)) + (sha256 + (base32 + "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh")))) + (properties `((upstream-name . "gQTLBase"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; This is an upstream bug. + (add-after 'unpack 'fix-imports + (lambda _ + (substitute* "NAMESPACE" + ((".*maxffmode.*") "") + (("importFrom\\(ff,.*") "import(ff)\n")) + #t))))) + (propagated-inputs + `(("r-batchjobs" ,r-batchjobs) + ("r-bbmisc" ,r-bbmisc) + ("r-biocgenerics" ,r-biocgenerics) + ("r-bit" ,r-bit) + ("r-doparallel" ,r-doparallel) + ("r-ff" ,r-ff) + ("r-ffbase" ,r-ffbase) + ("r-foreach" ,r-foreach) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/gQTLBase") + (synopsis "Infrastructure for eQTL, mQTL and similar studies") + (description + "The purpose of this package is to simplify the storage and interrogation +of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, +and more.") + (license license:artistic2.0))) + +(define-public r-gqtlstats + (package + (name "r-gqtlstats") + (version "1.21.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gQTLstats" version)) + (sha256 + (base32 + "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl")))) + (properties `((upstream-name . "gQTLstats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-batchjobs" ,r-batchjobs) + ("r-bbmisc" ,r-bbmisc) + ("r-beeswarm" ,r-beeswarm) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) + ("r-erma" ,r-erma) + ("r-ffbase" ,r-ffbase) + ("r-foreach" ,r-foreach) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbeeswarm" ,r-ggbeeswarm) + ("r-ggplot2" ,r-ggplot2) + ("r-gqtlbase" ,r-gqtlbase) + ("r-hardyweinberg" ,r-hardyweinberg) + ("r-homo-sapiens" ,r-homo-sapiens) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-mgcv" ,r-mgcv) + ("r-plotly" ,r-plotly) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-snpstats" ,r-snpstats) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/gQTLstats") + (synopsis "Computationally efficient analysis for eQTL and allied studies") + (description + "This package provides tools for the computationally efficient analysis +of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc. +The software in this package aims to support refinements and functional +interpretation of members of a collection of association statistics on a +family of feature/genome hypotheses.") + (license license:artistic2.0))) + +(define-public r-gviz + (package + (name "r-gviz") + (version "1.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Gviz" version)) + (sha256 + (base32 + "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2")))) + (properties `((upstream-name . "Gviz"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-biovizbase" ,r-biovizbase) + ("r-bsgenome" ,r-bsgenome) + ("r-digest" ,r-digest) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-matrixstats" ,r-matrixstats) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/Gviz") + (synopsis "Plotting data and annotation information along genomic coordinates") + (description + "Genomic data analyses requires integrated visualization of known genomic +information and new experimental data. Gviz uses the biomaRt and the +rtracklayer packages to perform live annotation queries to Ensembl and UCSC +and translates this to e.g. gene/transcript structures in viewports of the +grid graphics package. This results in genomic information plotted together +with your data.") + (license license:artistic2.0))) + +(define-public r-gwascat + (package + (name "r-gwascat") + (version "2.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gwascat" version)) + (sha256 + (base32 + "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-readr" ,r-readr) + ("r-s4vectors" ,r-s4vectors) + ("r-snpstats" ,r-snpstats) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/gwascat") + (synopsis "Tools for data in the EMBL-EBI GWAS catalog") + (description + "This package provides tools for representing and modeling data in the +EMBL-EBI GWAS catalog.") + (license license:artistic2.0))) + (define-public r-kegggraph (package (name "r-kegggraph") @@ -9267,6 +9584,68 @@ maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.") (license license:gpl2+))) +(define-public r-ldblock + (package + (name "r-ldblock") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ldblock" version)) + (sha256 + (base32 + "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfiles" ,r-genomicfiles) + ("r-httr" ,r-httr) + ("r-matrix" ,r-matrix) + ("r-rsamtools" ,r-rsamtools) + ("r-snpstats" ,r-snpstats) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/ldblock") + (synopsis "Data structures for linkage disequilibrium measures in populations") + (description + "This package defines data structures for @dfn{linkage +disequilibrium} (LD) measures in populations. Its purpose is to simplify +handling of existing population-level data for the purpose of flexibly +defining LD blocks.") + (license license:artistic2.0))) + +;; This is a CRAN package, but it depends on r-snpstats, which is a +;; Bioconductor package. +(define-public r-ldheatmap + (package + (name "r-ldheatmap") + (version "1.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "LDheatmap" version)) + (sha256 + (base32 + "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7")))) + (properties `((upstream-name . "LDheatmap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genetics" ,r-genetics) + ("r-rcpp" ,r-rcpp) + ("r-snpstats" ,r-snpstats))) + (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html") + (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") + (description + "This package provides tools to produce a graphical display, as a heat +map, of measures of pairwise linkage disequilibria between SNPs. Users may +optionally include the physical locations or genetic map distances of each SNP +on the plot.") + (license license:gpl3))) + (define-public r-pathview (package (name "r-pathview") @@ -9300,3 +9679,52 @@ graph with the mapped data. In addition, @code{r-pathview} also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.") (license license:gpl3+))) + +(define-public r-snpstats + (package + (name "r-snpstats") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "snpStats" version)) + (sha256 + (base32 + "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24")))) + (properties `((upstream-name . "snpStats"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-matrix" ,r-matrix) + ("r-survival" ,r-survival) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/snpStats") + (synopsis "Methods for SNP association studies") + (description + "This package provides classes and statistical methods for large +@dfn{single-nucleotide polymorphism} (SNP) association studies. This extends +the earlier snpMatrix package, allowing for uncertainty in genotypes.") + (license license:gpl3))) + +(define-public r-sushi + (package + (name "r-sushi") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Sushi" version)) + (sha256 + (base32 + "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p")))) + (properties `((upstream-name . "Sushi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biomart" ,r-biomart) + ("r-zoo" ,r-zoo))) + (home-page "https://bioconductor.org/packages/Sushi") + (synopsis "Tools for visualizing genomics data") + (description + "This package provides flexible, quantitative, and integrative genomic +visualizations for publication-quality multi-panel figures.") + (license license:gpl2+))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 96fa22f1a3..512abcd8fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10484,411 +10484,6 @@ high-level packages for biological data visualization. This saves development effort and encourages consistency.") (license license:artistic2.0))) -(define-public r-ggbio - (package - (name "r-ggbio") - (version "1.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ggbio" version)) - (sha256 - (base32 - "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; See https://github.com/tengfei/ggbio/issues/117 - ;; This fix will be included in the next release. - (add-after 'unpack 'fix-typo - (lambda _ - (substitute* "R/GGbio-class.R" - (("fechable") "fetchable")) - #t))))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-organismdbi" ,r-organismdbi) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "http://www.tengfei.name/ggbio/") - (synopsis "Visualization tools for genomic data") - (description - "The ggbio package extends and specializes the grammar of graphics for -biological data. The graphics are designed to answer common scientific -questions, in particular those often asked of high throughput genomics data. -All core Bioconductor data structures are supported, where appropriate. The -package supports detailed views of particular genomic regions, as well as -genome-wide overviews. Supported overviews include ideograms and grand linear -views. High-level plots include sequence fragment length, edge-linked -interval to data view, mismatch pileup, and several splicing summaries.") - (license license:artistic2.0))) - -(define-public r-gqtlbase - (package - (name "r-gqtlbase") - (version "1.21.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gQTLBase" version)) - (sha256 - (base32 - "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh")))) - (properties `((upstream-name . "gQTLBase"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; This is an upstream bug. - (add-after 'unpack 'fix-imports - (lambda _ - (substitute* "NAMESPACE" - ((".*maxffmode.*") "") - (("importFrom\\(ff,.*") "import(ff)\n")) - #t))))) - (propagated-inputs - `(("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-biocgenerics" ,r-biocgenerics) - ("r-bit" ,r-bit) - ("r-doparallel" ,r-doparallel) - ("r-ff" ,r-ff) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/gQTLBase") - (synopsis "Infrastructure for eQTL, mQTL and similar studies") - (description - "The purpose of this package is to simplify the storage and interrogation -of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, -and more.") - (license license:artistic2.0))) - -(define-public r-snpstats - (package - (name "r-snpstats") - (version "1.40.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "snpStats" version)) - (sha256 - (base32 - "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24")))) - (properties `((upstream-name . "snpStats"))) - (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-matrix" ,r-matrix) - ("r-survival" ,r-survival) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/snpStats") - (synopsis "Methods for SNP association studies") - (description - "This package provides classes and statistical methods for large -@dfn{single-nucleotide polymorphism} (SNP) association studies. This extends -the earlier snpMatrix package, allowing for uncertainty in genotypes.") - (license license:gpl3))) - -(define-public r-homo-sapiens - (package - (name "r-homo-sapiens") - (version "1.3.1") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "Homo.sapiens_" - version ".tar.gz")) - (sha256 - (base32 - "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) - (properties - `((upstream-name . "Homo.sapiens"))) - (build-system r-build-system) - (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) - ("r-organismdbi" ,r-organismdbi) - ("r-annotationdbi" ,r-annotationdbi))) - (home-page "https://bioconductor.org/packages/Homo.sapiens/") - (synopsis "Annotation package for the Homo.sapiens object") - (description - "This package contains the Homo.sapiens object to access data from -several related annotation packages.") - (license license:artistic2.0))) - -(define-public r-erma - (package - (name "r-erma") - (version "1.6.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "erma" version)) - (sha256 - (base32 - "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/erma") - (synopsis "Epigenomic road map adventures") - (description - "The epigenomics road map describes locations of epigenetic marks in DNA -from a variety of cell types. Of interest are locations of histone -modifications, sites of DNA methylation, and regions of accessible chromatin. -This package presents a selection of elements of the road map including -metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines -by Ernst and Kellis.") - (license license:artistic2.0))) - -(define-public r-ldblock - (package - (name "r-ldblock") - (version "1.20.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ldblock" version)) - (sha256 - (base32 - "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-httr" ,r-httr) - ("r-matrix" ,r-matrix) - ("r-rsamtools" ,r-rsamtools) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/ldblock") - (synopsis "Data structures for linkage disequilibrium measures in populations") - (description - "This package defines data structures for @dfn{linkage -disequilibrium} (LD) measures in populations. Its purpose is to simplify -handling of existing population-level data for the purpose of flexibly -defining LD blocks.") - (license license:artistic2.0))) - -(define-public r-gqtlstats - (package - (name "r-gqtlstats") - (version "1.21.3") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gQTLstats" version)) - (sha256 - (base32 - "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl")))) - (properties `((upstream-name . "gQTLstats"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-beeswarm" ,r-beeswarm) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-erma" ,r-erma) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gqtlbase" ,r-gqtlbase) - ("r-hardyweinberg" ,r-hardyweinberg) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-mgcv" ,r-mgcv) - ("r-plotly" ,r-plotly) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-snpstats" ,r-snpstats) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/gQTLstats") - (synopsis "Computationally efficient analysis for eQTL and allied studies") - (description - "This package provides tools for the computationally efficient analysis -of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc. -The software in this package aims to support refinements and functional -interpretation of members of a collection of association statistics on a -family of feature/genome hypotheses.") - (license license:artistic2.0))) - -(define-public r-gviz - (package - (name "r-gviz") - (version "1.34.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Gviz" version)) - (sha256 - (base32 - "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2")))) - (properties `((upstream-name . "Gviz"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-digest" ,r-digest) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-matrixstats" ,r-matrixstats) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/Gviz") - (synopsis "Plotting data and annotation information along genomic coordinates") - (description - "Genomic data analyses requires integrated visualization of known genomic -information and new experimental data. Gviz uses the biomaRt and the -rtracklayer packages to perform live annotation queries to Ensembl and UCSC -and translates this to e.g. gene/transcript structures in viewports of the -grid graphics package. This results in genomic information plotted together -with your data.") - (license license:artistic2.0))) - -(define-public r-gwascat - (package - (name "r-gwascat") - (version "2.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gwascat" version)) - (sha256 - (base32 - "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-readr" ,r-readr) - ("r-s4vectors" ,r-s4vectors) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/gwascat") - (synopsis "Tools for data in the EMBL-EBI GWAS catalog") - (description - "This package provides tools for representing and modeling data in the -EMBL-EBI GWAS catalog.") - (license license:artistic2.0))) - -(define-public r-sushi - (package - (name "r-sushi") - (version "1.28.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Sushi" version)) - (sha256 - (base32 - "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p")))) - (properties `((upstream-name . "Sushi"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biomart" ,r-biomart) - ("r-zoo" ,r-zoo))) - (home-page "https://bioconductor.org/packages/Sushi") - (synopsis "Tools for visualizing genomics data") - (description - "This package provides flexible, quantitative, and integrative genomic -visualizations for publication-quality multi-panel figures.") - (license license:gpl2+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 10212e2a68..0483af3d6b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14718,32 +14718,6 @@ effects. It is applicable to backcrosses, doubled haploids, recombinant inbred lines, F2 intercrosses, and association mapping populations.") (license license:gpl2))) -(define-public r-ldheatmap - (package - (name "r-ldheatmap") - (version "1.0-4") - (source - (origin - (method url-fetch) - (uri (cran-uri "LDheatmap" version)) - (sha256 - (base32 - "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7")))) - (properties `((upstream-name . "LDheatmap"))) - (build-system r-build-system) - (propagated-inputs - `(("r-genetics" ,r-genetics) - ("r-rcpp" ,r-rcpp) - ("r-snpstats" ,r-snpstats))) - (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html") - (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") - (description - "This package provides tools to produce a graphical display, as a heat -map, of measures of pairwise linkage disequilibria between SNPs. Users may -optionally include the physical locations or genetic map distances of each SNP -on the plot.") - (license license:gpl3))) - (define-public r-hwde (package (name "r-hwde") diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 9f07922535..07862291a7 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -677,15 +677,15 @@ language and very flexible regarding to new or unknown keyboard layouts.") (define-public ktouch (package (name "ktouch") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" + (uri (string-append "mirror://kde/stable/release-service/" version "/src/ktouch-" version ".tar.xz")) (sha256 (base32 - "0dqxb3xsjc2rwc9779l5fnr4crhq51bc8ln4azbgnnkzldvq6a4a")))) + "1s8pcwakx94aygfyjmyps5b43j4kv6dmfw7n12japcka2yfp9bi2")))) (build-system qt-build-system) (arguments `(#:phases diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index cb83dd71e4..99df0a72e0 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2068,14 +2068,14 @@ as a library for other Emacs packages.") (define-public emacs-auctex (package (name "emacs-auctex") - (version "13.0.0") + (version "13.0.1") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "auctex-" version ".tar")) (sha256 - (base32 "10bk4h5d14ainx9jrqahdnbng399wpic6xzv1fkr43yr1l3g4y1v")))) + (base32 "1y5q3phd0xr7342i757hr4hic8nad4kkdf1zk56mlj5snwr0g0w7")))) (build-system emacs-build-system) ;; We use 'emacs' because AUCTeX requires dbus at compile time ;; ('emacs-minimal' does not provide dbus). @@ -22592,14 +22592,14 @@ well as an option for visually flashing evaluated s-expressions.") (define-public emacs-tramp (package (name "emacs-tramp") - (version "2.4.4.4") + (version "2.5.0") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "tramp-" version ".tar")) (sha256 - (base32 "1f2d02xz3kpy50186wcy688lx76dv0gmrbkj2qdvifcwhyc26sz8")))) + (base32 "1jpnqyk108nksaym2b9v243y5zkpr4px9d070wsb9cwm3xrcd8rh")))) (build-system emacs-build-system) (arguments `(#:emacs ,emacs ;need D-Bus diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 735e653900..d1a076e091 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -9864,17 +9864,18 @@ can be downloaded from @url{https://zero.sjeng.org/best-network}.") (define-public ktuberling (package (name "ktuberling") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/ktuberling-" version ".tar.xz")) (sha256 - (base32 "1qdf4q6wjh1lnlqw5c8z4rpj9w5vbyjfri1dah6yjm3mwppbc12j")))) + (base32 "0mlv9qllg70p26dbrcsr820c70d3ib88hapc1z6wgjhdpmc12ni1")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) + ("kdoctools" ,kdoctools) ("perl" ,perl))) (inputs `(("kcompletion" ,kcompletion) @@ -9882,11 +9883,12 @@ can be downloaded from @url{https://zero.sjeng.org/best-network}.") ("kcoreaddons" ,kcoreaddons) ("kcrash" ,kcrash) ("kdbusaddons" ,kdbusaddons) - ("kdelibs4support" ,kdelibs4support) ("ki18n" ,ki18n) + ("kio" ,kio) ("kwidgetsaddons" ,kwidgetsaddons) ("kxmlgui" ,kxmlgui) ("libkdegames" ,libkdegames) + ("python" ,python-wrapper) ("qtbase" ,qtbase) ("qtmultimedia" ,qtmultimedia) ("qtdeclarative" ,qtdeclarative) @@ -9913,14 +9915,14 @@ This package is part of the KDE games module.") (define-public picmi (package (name "picmi") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/picmi-" version ".tar.xz")) (sha256 - (base32 "0z9mpmv49w914gqdx274brdzl6d1bz9j9nkvbwgmr3iq1ba49m3f")))) + (base32 "1dfq9m4njh0czz8zws46rkz6xq2n6xra5w223m3s2f5civiw5msz")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -9950,14 +9952,14 @@ This package is part of the KDE games module.") (define-public kolf (package (name "kolf") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kolf-" version ".tar.xz")) (sha256 - (base32 "06sfd0llr5cc3zf1vrpcxgw9bm009ky7y8822kynic9ipcd4z1hw")))) + (base32 "1lpp6pzr5dgd4si4a8c7hcvgxgqy0bgyhkx9m6jqb0zhll6dxj10")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -9998,14 +10000,14 @@ This package is part of the KDE games module.") (define-public libkmahjongg (package (name "libkmahjongg") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" + (uri (string-append "mirror://kde/stable/release-service/" version "/src/libkmahjongg-" version ".tar.xz")) (sha256 - (base32 "0rdimk11hrc8qrmiv26z0ddjzi1k6806c0rfskx4cwmildmh6zgx")))) + (base32 "10ljzbf7qki5flydankrbksaihhkqpfyljb8c71fbwqwmkr7rgfq")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules))) @@ -10029,14 +10031,14 @@ other Mah Jongg like games.") (define-public kmahjongg (package (name "kmahjongg") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kmahjongg-" version ".tar.xz")) (sha256 - (base32 "08na845h0nhmfrszdmvfq5y1dy7kgbrlzjp0f5snvbbf7w44ci6p")))) + (base32 "1fcj4jb2zzbaxp7cp04w36y0c7lh77yzin66fmvrcxkl11xi2wwd")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10069,14 +10071,14 @@ This package is part of the KDE games module.") (define-public kshisen (package (name "kshisen") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kshisen-" version ".tar.xz")) (sha256 - (base32 "1bq5m48af4h5apfp3bfsp76nlpv6h5sc0gd544zv7cgpfznz1sds")))) + (base32 "1hrwr0f1kidivsp8lnwdbqz3xxagjvjwh72r3gma8smfilybygfb")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10108,15 +10110,24 @@ This package is part of the KDE games module.") (define-public kajongg (package (name "kajongg") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kajongg-" version ".tar.xz")) (sha256 - (base32 "0ql6p5zifdpdf65r7ki9ml123azpwwk9x3x8r9ij6xhjnf7p7x6w")))) + (base32 "03fdbnx7zx7vgcxvwd1h1098ks9gq162bwz35fhpyzpynr667m5r")))) (build-system qt-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'wrap + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/kajongg") + `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))) + #t)))))) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) ;("perl" ,perl) @@ -10128,12 +10139,10 @@ This package is part of the KDE games module.") ("ki18n" ,ki18n) ("libkmahjongg" ,libkmahjongg) ("python" ,python) + ("python-twisted" ,python-twisted) + ("python-pyqt" ,python-pyqt) ("qtbase" ,qtbase) ("qtsvg" ,qtsvg))) - (propagated-inputs - `(("python-twisted" ,python-twisted) - ("python-pyqt" ,python-pyqt))) - ;; FIXME: Need to wrap PYTHONPATH (home-page "https://games.kde.org/") (synopsis "Classical Mah Jongg game for 4 players") (description "Kajongg is the ancient Chinese board game for 4 players. @@ -10152,14 +10161,14 @@ This package is part of the KDE games module.") (define-public kbreakout (package (name "kbreakout") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kbreakout-" version ".tar.xz")) (sha256 - (base32 "0gwzx1z9mxrjlcjzglg8cxkyd6900whcar3b5j9laxxarc6xhj8w")))) + (base32 "0kqj2cx0ny3qq65c6w5fpnzmrwl9irg8slzvpd3anck5cnvma3j4")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10190,14 +10199,14 @@ This package is part of the KDE games module.") (define-public kmines (package (name "kmines") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kmines-" version ".tar.xz")) (sha256 - (base32 "0ac3za36lh8hpx6mqfic9amwmzhzhzplm9hg3pw12gxl5a9mvfsf")))) + (base32 "0hqjwh3jq2npqwkvh67fyn2xnq8swiasdw5jz8f0ikl0k28id775")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10228,14 +10237,14 @@ This package is part of the KDE games module.") (define-public konquest (package (name "konquest") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" + (uri (string-append "mirror://kde/stable/release-service/" version "/src/konquest-" version ".tar.xz")) (sha256 - (base32 "02gjxskhi10a1sqh3skcild8zria7wncz1a4sbz7ax1p851q76k1")))) + (base32 "0lnwj06vv4qx05hr8pzysnvrxh8y04asajrph0rsj37v8hs9g5lh")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10268,14 +10277,14 @@ This package is part of the KDE games module.") (define-public kbounce (package (name "kbounce") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kbounce-" version ".tar.xz")) (sha256 - (base32 "02rfv0qzz5cmyfx8f56a45hbm9gsp6m3dcy8ajwx88rw5wpbrr11")))) + (base32 "0ymy0z1qlw3n653xs3dsa1xm78q4xaj09dnnci4km77rzis26vb6")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10307,14 +10316,14 @@ This package is part of the KDE games module.") (define-public kblocks (package (name "kblocks") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kblocks-" version ".tar.xz")) (sha256 - (base32 "0qrm0dihzhkxsq9l49ndzms802x6jn92vvabb2zf2q9z593m69cx")))) + (base32 "09yfm9mzbamp294cvc5finq6ilxvxr68i0dnb0m72pa4sfzmij32")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10348,14 +10357,14 @@ This package is part of the KDE games module.") (define-public ksudoku (package (name "ksudoku") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" + (uri (string-append "mirror://kde/stable/release-service/" version "/src/ksudoku-" version ".tar.xz")) (sha256 - (base32 "0rcscz91hilm7l3am5w02n0n8l7xhi4l0n4sskznh68kblw0ggw2")))) + (base32 "0pj6ry7ak1rnpb93mqypaxrcbmrhwg9ir6zhb3ybzfkfcrh67g12")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10409,14 +10418,14 @@ This package is part of the KDE games module.") (define-public klines (package (name "klines") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/klines-" version ".tar.xz")) (sha256 - (base32 "1g1f46jp0rb8gpqkgcf915ydpsscn1sxk3gjvm8bcqgx9ddq59xa")))) + (base32 "0y8lnwawrkl4ixn7v4dg48k2zpr083krv7dv4d94b2dpkh7xfvih")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10453,14 +10462,14 @@ This package is part of the KDE games module.") (define-public kgoldrunner (package (name "kgoldrunner") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version "/src/kgoldrunner-" - version ".tar.xz")) + (uri (string-append "mirror://kde/stable/release-service/" version + "/src/kgoldrunner-" version ".tar.xz")) (sha256 - (base32 "16rcvq796r3asz4v4ap75xvwnxd3dd2nsq5r9vxvzl6rrf1w9bj4")))) + (base32 "17ra5d3r9ajy2inj17gwd5xphzhvbzx5kpvdwyj6msx4dd9wxgfi")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10494,14 +10503,14 @@ This package is part of the KDE games module.") (define-public kdiamond (package (name "kdiamond") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kdiamond-" version ".tar.xz")) (sha256 - (base32 "1v5yb9hb26lk277zhw8d37ks829yfqr5anzx1qhms44gca5kqhva")))) + (base32 "1iyxrx3422asa58kh0siwvi1svds5kccrym6gdfpdhlmhmciqlzi")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10533,14 +10542,14 @@ This package is part of the KDE games module.") (define-public kfourinline (package (name "kfourinline") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kfourinline-" version ".tar.xz")) (sha256 - (base32 "1vprs6dc1ccn3g6k594i9s94xy4b91vzlqjysyc6fqcq2fs54ny3")))) + (base32 "0plx3lv35fc8q9svbyl71mms3ji6zn58j306bvm1f8kkgg0x395b")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10551,7 +10560,6 @@ This package is part of the KDE games module.") ("kconfigwidgets" ,kconfigwidgets) ("kcoreaddons" ,kcoreaddons) ("kcrash" ,kcrash) - ("kdelibs4support" ,kdelibs4support) ("kdnssd" ,kdnssd) ("ki18n" ,ki18n) ("kxmlgui" ,kxmlgui) @@ -10573,14 +10581,14 @@ This package is part of the KDE games module.") (define-public kblackbox (package (name "kblackbox") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kblackbox-" version ".tar.xz")) (sha256 - (base32 "1x42sfpf75c6mavwkc7g7dm11y9s5dpj8igphly5kvm0pajqby0n")))) + (base32 "0la5w44b0gl72g3wfp0pw8gwnm287lh7nd9k5ikpszw5nn49db0h")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10614,14 +10622,14 @@ This package is part of the KDE games module.") (define-public knetwalk (package (name "knetwalk") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/knetwalk-" version ".tar.xz")) (sha256 - (base32 "1i340salzgqdw8y33wrrydmpgx3pvwf5wrbljlh67cjf6s4csx7d")))) + (base32 "060kj06vpigdy570izsjfgnmqqrpmb8bkr9arqc109hg3avl5wjz")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10656,14 +10664,14 @@ This package is part of the KDE games module.") (define-public bomber (package (name "bomber") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/bomber-" version ".tar.xz")) (sha256 - (base32 "1lvzd0mzgq25akvwvkm57l3plm65k731v2i1ahakn985bb5gc3is")))) + (base32 "1fjcwm591jgx3bgqpi0j5fnb2l2r2h3r6lav3vhaxz4rkf56pg2a")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10698,14 +10706,14 @@ This package is part of the KDE games module.") (define-public granatier (package (name "granatier") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/granatier-" version ".tar.xz")) (sha256 - (base32 "141qmdinz7ikbbrs8dq6cap3nl22sl7pw62r80pf3xxwn2q4phpa")))) + (base32 "1fyh7zyacb3pnlfd29jw2jmyl8a7sjw354pi234nd5x5999xw5z6")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10736,14 +10744,14 @@ This package is part of the KDE games module.") (define-public ksirk (package (name "ksirk") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/ksirk-" version ".tar.xz")) (sha256 - (base32 "1b1wixs2hp5qnvdygfwa3kvy0kn94ysa4ifmx90q6r3yfr2lpfca")))) + (base32 "10y7nm0x6zcc0gh3am69bbxyyb8azbbfyrdqsa023ggr7n04cn21")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10792,14 +10800,14 @@ This package is part of the KDE games module.") (define-public palapeli (package (name "palapeli") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/palapeli-" version ".tar.xz")) (sha256 - (base32 "1g91ydbc0x2y2gn3lcb5w03mn7k78l5bq4cb1s59kx6yjbflv3pw")))) + (base32 "0xxz9g4zxljlg20g88a5lkbwzzm9yg4vxnrfigk8m018cz0nqd5b")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10840,14 +10848,14 @@ This package is part of the KDE games module.") (define-public kiriki (package (name "kiriki") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kiriki-" version ".tar.xz")) (sha256 - (base32 "1xg25dj95g81dc5l7k47am4j52abrwwfx4h73lvsbn4lc8lfmshw")))) + (base32 "0milc8fl1rj4yrwdvm60ampd47dyiys1xvqi5f0g7y6mgymgyk4x")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10879,14 +10887,14 @@ This package is part of the KDE games module.") (define-public kigo (package (name "kigo") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kigo-" version ".tar.xz")) (sha256 - (base32 "00l5gcbi8xyj9c1lngkrddka3a4m4cd78prfplrpq32ma9xq681f")))) + (base32 "088752yzmfsnppd27p8hld4x5s7sw5fagm08024l5ra1mlicdfz9")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10926,14 +10934,14 @@ This package is part of the KDE games module.") (define-public kubrick (package (name "kubrick") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kubrick-" version ".tar.xz")) (sha256 - (base32 "0ma8wja4rqlsmsr8cyicfpkwlgqva4450ls4c0ql53p0kabf04gx")))) + (base32 "0h3mypwd67sss08j5vvrih5f5ss85m9kax6412y40xmsm51lz2pq")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -10968,14 +10976,14 @@ This package is part of the KDE games module.") (define-public lskat (package (name "lskat") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/lskat-" version ".tar.xz")) (sha256 - (base32 "1qk5hd27zb42pbcxq5wyzz62nj5f0qdmgy54r9rnk92pzzzk94s9")))) + (base32 "1wg9zxp64kwjxqs4qw0h7j8yhgffbmvh8j9d4dgmz45dscngnjli")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -11007,14 +11015,14 @@ This package is part of the KDE games module.") (define-public kapman (package (name "kapman") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kapman-" version ".tar.xz")) (sha256 - (base32 "03pq38caam30q4bw14c045kayw2d87xq1yaa3s2jkrylylfq3p0f")))) + (base32 "14x3v6li4r3gzzwfd6ar9saq2rhc7yxs0sp9ygalzq8vq4d7i1kh")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -11047,14 +11055,14 @@ This package is part of the KDE games module.") (define-public kspaceduel (package (name "kspaceduel") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kspaceduel-" version ".tar.xz")) (sha256 - (base32 "1hppni0ihs7psc0dly5rxyy2a38nzhlig9yfyhi3lkh36z05pql8")))) + (base32 "1aixh6ygif2cm1a5g32sl5y6b5x68139pzihaxq4334c6avamdai")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -11083,14 +11091,14 @@ This package is part of the KDE games module.") (define-public bovo (package (name "bovo") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/bovo-" version ".tar.xz")) (sha256 - (base32 "0dbpng0w52nahmx7brsll66zw23ql1g6pcvn2k4g2lnvxch0i59g")))) + (base32 "18qbac366m0xma3ary11q9zxz0wgnysppcl7kpypl6ic3nf61wqz")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -11120,14 +11128,14 @@ This package is part of the KDE games module.") (define-public killbots (package (name "killbots") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/killbots-" version ".tar.xz")) (sha256 - (base32 "1qi86q7diw7glkp9v33yim9nhz2da4balbxa1hjrdgjdv8zdbxbm")))) + (base32 "1296gww42nwnai7y6m2qpjqpyc30p7z9chfv5rv0n48jvdhva88y")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -11162,14 +11170,14 @@ This package is part of the KDE games module.") (define-public ksnakeduel (package (name "ksnakeduel") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/ksnakeduel-" version ".tar.xz")) (sha256 - (base32 "0mprrnpax8pv7ab36zwhvdfj8id52w8g6x76nnj8qvkdlkjiqdnn")))) + (base32 "0mp6g258n3xzvgf23jnhkw10xgwqwqdzqfdc6r9jq6a6m8v77swz")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -11201,14 +11209,14 @@ This package is part of the KDE games module.") (define-public kollision (package (name "kollision") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kollision-" version ".tar.xz")) (sha256 - (base32 "1p7qrn3d0ybpvc9k6k5wzj54dsrp1rqh39844maz0ay2fhvmch12")))) + (base32 "180ybafizpwjsg80npy0l9142cjsnlyxwv9dz3bq6r8v4smn2g6b")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -11239,14 +11247,14 @@ This package is part of the KDE games module.") (define-public knavalbattle (package (name "knavalbattle") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version -"/src/knavalbattle-" version ".tar.xz")) + (uri (string-append "mirror://kde/stable/release-service/" version + "/src/knavalbattle-" version ".tar.xz")) (sha256 - (base32 "0sdfjplqkb30x2mvh66pkzay6vn5px87779sh2s8lpl6fcw0v9g4")))) + (base32 "03rqf4avn61b0v340ymmzgp7s0axygjgxq1nlp5aaqbx70zcb4lq")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -11280,14 +11288,14 @@ This package is part of the KDE games module.") (define-public kreversi (package (name "kreversi") - (version "19.08.3") + (version "20.08.3") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version -"/src/kreversi-" version ".tar.xz")) + (uri (string-append "mirror://kde/stable/release-service/" version + "/src/kreversi-" version ".tar.xz")) (sha256 - (base32 "0b6q8df2bawgnrswhq59z37axad0q3zpvvzxdds7sz1lw505xw9h")))) + (base32 "0d3y072q61xcik9lf0pz0c9njvarwlvf6hqv5fp5jyqaf2902pmi")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -11323,14 +11331,14 @@ This package is part of the KDE games module.") (define-public ksquares (package (name "ksquares") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/ksquares-" version ".tar.xz")) (sha256 - (base32 "0hv8hls5s627lys08nnw72rfzsafj3dmp49mh2afzmh6lgk9h5vy")))) + (base32 "0chd30byl2kww1k699vkygrxq2wdyvi84m2bimk23q96fl8h831y")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) @@ -11360,14 +11368,14 @@ This package is part of the KDE games module.") (define-public kjumpingcube (package (name "kjumpingcube") - (version "19.08.3") + (version "20.12.0") (source (origin (method url-fetch) - (uri (string-append "mirror://kde/stable/applications/" version + (uri (string-append "mirror://kde/stable/release-service/" version "/src/kjumpingcube-" version ".tar.xz")) (sha256 - (base32 "0d67zqkf2xffjkj671gl2n6nj6jajyn6rgqqj5i6gm500mqi9rm1")))) + (base32 "1mk73il4jh15z5pm3fp65hsyvmrga11c3h7w96yamy2n2bbniapq")))) (build-system qt-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index f7f18cf79f..c0c1ef96c6 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1680,7 +1680,7 @@ QLandkarte GT application.") (uri (string-append "https://www.gaia-gis.it/gaia-sins/" "readosm-" version ".tar.gz")) (sha256 - (base32 "0zv6p352pqjcv70nvcaf2x3011z35jqa24dcdm27a4ns1wha3cjc")))) + (base32 "0igif2bxf4dr82glxz9gyx5mmni0r2dsnx9p9k6pxv3c4lfhaz6v")))) (build-system gnu-build-system) (inputs `(("expat" ,expat) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 39de01d080..af94175a14 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -2999,7 +2999,7 @@ some form of information without getting in the user's way.") (define-public libpeas (package (name "libpeas") - (version "1.24.1") + (version "1.28.0") (source (origin (method url-fetch) @@ -3008,7 +3008,7 @@ some form of information without getting in the user's way.") name "-" version ".tar.xz")) (sha256 (base32 - "1162dr7smmfb02czmhshr0f93hqj7w0nw29bys5lzfvwarxcyflw")))) + "05cb7drn6arc4gi02wgsvzibigi2riz5gnfnmlb0zmbfnj9ikna2")))) (build-system meson-build-system) (arguments '(#:phases @@ -4678,7 +4678,7 @@ libxml to ease remote use of the RESTful API.") (define-public libsoup (package (name "libsoup") - (version "2.70.0") + (version "2.72.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/libsoup/" @@ -4686,7 +4686,7 @@ libxml to ease remote use of the RESTful API.") "libsoup-" version ".tar.xz")) (sha256 (base32 - "0hjk9lgppc5435my0lyywbpmj7ib5vvcylwfin8ki97g9bvj1c2l")))) + "11skbyw2pw32178q3h8pi7xqa41b2x4k6q4k9f75zxmh8s23y30p")))) (build-system meson-build-system) (outputs '("out" "doc")) (arguments @@ -6942,7 +6942,7 @@ share them with others via social networking and more.") (define-public file-roller (package (name "file-roller") - (version "3.32.3") + (version "3.38.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/file-roller/" @@ -6950,7 +6950,7 @@ share them with others via social networking and more.") "file-roller-" version ".tar.xz")) (sha256 (base32 - "0ap2hxvjljh4p6wsd9ikh2my3vsxp9r2nvjxxj3v87nwfyw1y4dy")))) + "06ikvjjcgb8nxabkn2rywy76a1c7s6w8dszaxvaxldbxarp1qgbj")))) (build-system meson-build-system) (native-inputs `(("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index 9da348548d..10d9011401 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -890,6 +890,8 @@ decoders, muxers, and demuxers provided by FFmpeg.") ("libxml2" ,libxml2))) (native-inputs `(("flex" ,flex) + ("gobject-introspection" ,gobject-introspection) + ("glib:bin" ,glib "bin") ("gst-plugins-bad" ,gst-plugins-bad) ("gst-plugins-good" ,gst-plugins-good) ("perl" ,perl) @@ -902,6 +904,35 @@ decoders, muxers, and demuxers provided by FFmpeg.") non-linear editors.") (license license:gpl2+))) +(define-public gst-plugins/selection + (lambda* (pkg #:key plugins configure-flags) + "Build PKG with only PLUGINS enabled. Optionally, if CONFIGURE-FLAGS are +given, also pass them to the build system instead of the ones used by PKG." + (package/inherit pkg + (arguments + (substitute-keyword-arguments (package-arguments pkg) + ((#:configure-flags flags `(,@(or configure-flags '()))) + `(append + (list + ,@(map (lambda (plugin) + (string-append "-D" plugin "=enabled")) + plugins)) + (list ,@(or configure-flags flags)))) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'disable-auto-plugins + (lambda _ + (substitute* "meson_options.txt" + (("'auto'") "'disabled'")) + #t))))))))) + +(define-public gst-transcoder + (deprecated-package + "gst-transcoder" + (gst-plugins/selection gst-plugins-bad + #:plugins '("transcoder") + #:configure-flags '("-Dintrospection=enabled")))) + (define-public python-gst (package (name "python-gst") diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a7cf6fcb4b..80b526d0b3 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -394,7 +394,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.19))) -(define-public linux-libre-4.14-version "4.14.212") +(define-public linux-libre-4.14-version "4.14.213") (define deblob-scripts-4.14 (linux-libre-deblob-scripts linux-libre-4.14-version @@ -402,12 +402,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1qij18inijj6c3ma8hv98yjagnzxdxyn134da9fd23ky8q6hbvky"))) (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "0y8ck8pfxm8862wi4cz8qp9x9b18yl448i8m7bpbphs290nc66qf"))) + (hash (base32 "079axkl14jp8lz30h21q4gmhmjw6zf5ycmxji65kgcgyg7dwwyzx"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) -(define-public linux-libre-4.9-version "4.9.248") +(define-public linux-libre-4.9-version "4.9.249") (define deblob-scripts-4.9 (linux-libre-deblob-scripts linux-libre-4.9-version @@ -415,12 +415,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0fxajshb75siq39lj5h8xvhdj8lcmddkslwlyj65rhlwk6g2r4b2"))) (define-public linux-libre-4.9-pristine-source (let ((version linux-libre-4.9-version) - (hash (base32 "1kzczy0lz3lnjkhvx90dgjmzn3d3y55qxlihiclkr4y9c602d1s6"))) + (hash (base32 "0kjcw0vgga9msgqnipgg028v3rcc5am2d094v3hqkkjvzyb8dwxi"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.9))) -(define-public linux-libre-4.4-version "4.4.248") +(define-public linux-libre-4.4-version "4.4.249") (define deblob-scripts-4.4 (linux-libre-deblob-scripts linux-libre-4.4-version @@ -428,7 +428,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0hhin1jpfkd6nwrb6xqxjzl3hdxy4pn8a15hy2d3d83yw6pflbsf"))) (define-public linux-libre-4.4-pristine-source (let ((version linux-libre-4.4-version) - (hash (base32 "1z1xbkm0z0v6k3scszii5hi24pn391332g0li93p3n1rnv74jap5"))) + (hash (base32 "04pb4vgia6zaindf6804gq9jn3mhmy01yijqmpi79sh9rlqzzh1i"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.4))) @@ -1146,8 +1146,8 @@ RTL8812AU, RTL8821AU, and RTL8814AU chips.") (license license:gpl2+)))) (define-public rtl8821ce-linux-module - (let ((commit "fe97b5003f2f3dd070f76ec38c00b83798c1cdea") - (revision "1")) + (let ((commit "14b536f0c9ad2d0abbdab8afc7ade684900ca9cf") + (revision "2")) (package (name "rtl8821ce-linux-module") (version (git-version "0.0.0" revision commit)) @@ -1160,7 +1160,7 @@ RTL8812AU, RTL8821AU, and RTL8814AU chips.") (file-name (git-file-name name version)) (sha256 (base32 - "10mrp63npbqb39c442vx8mra278hw7sczb3b6bjrpr3gan6ljshn")))) + "0z7r7spsgn22gwv9pcmkdjn9ingi8jj7xkxasph8118h46fw8ip2")))) (build-system linux-module-build-system) (arguments `(#:make-flags diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 1e6da43cba..ab881845ed 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3485,7 +3485,7 @@ websites such as Libre.fm.") (define-public milkytracker (package (name "milkytracker") - (version "1.02.00") + (version "1.03.00") (source (origin (method git-fetch) (uri (git-reference @@ -3494,7 +3494,7 @@ websites such as Libre.fm.") (file-name (git-file-name name version)) (sha256 (base32 - "05a6d7l98k9i82dwrgi855dnccm3f2lkb144gi244vhk1156n0ca")) + "025fj34gq2kmkpwcswcyx7wdxb89vm944dh685zi4bxx0hz16vvk")) (modules '((guix build utils))) ;; Remove non-FSDG compliant sample songs. (snippet diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 864e5afe9a..612c94e218 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -2220,7 +2220,7 @@ itself.") (define-public python2-pyqt-4 (package (inherit python-pyqt) (name "python2-pyqt") - (version "4.12") + (version "4.12.3") (source (origin (method url-fetch) @@ -2230,11 +2230,12 @@ itself.") version ".tar.gz")) (sha256 (base32 - "1nw8r88a5g2d550yvklawlvns8gd5slw53yy688kxnsa65aln79w")))) + "0wnlasg62rm5d39nq1yw4namcx2ivxgzl93r5f2vb9s0yaz5l3x0")))) (native-inputs - `(("python-sip" ,python2-sip) - ("qt" ,qt-4))) + `(("qt" ,qt-4))) (inputs `(("python" ,python-2))) + (propagated-inputs + `(("python-sip" ,python2-sip))) (arguments `(#:tests? #f ; no check target #:modules ((srfi srfi-1) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 5a89288166..c5b1af79d3 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -188,6 +188,20 @@ a focus on simplicity and productivity.") (native-inputs `(("autoconf" ,autoconf))))) +(define-public ruby-3.0 + (package + (inherit ruby-2.7) + (version "3.0.0") + (source + (origin + (method url-fetch) + (uri (string-append "http://cache.ruby-lang.org/pub/ruby/" + (version-major+minor version) + "/ruby-" version ".tar.xz")) + (sha256 + (base32 + "1cbcixwnr0y8q0lg67wjgplp06kjd6p6hjjh680csv3v0bpsxgv8")))))) + (define-public ruby-2.5 (package (inherit ruby) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index f347afbf62..9edb6aff68 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -4000,33 +4000,72 @@ tools for styling them, including a built-in real-time video preview.") ; by upstream). See https://github.com/Aegisub/Aegisub/blob/master/LICENCE ; src/MatroskaParser.(c|h) is under bsd-3 with permission from the author -(define-public gst-transcoder - (package - (name "gst-transcoder") - (version "1.12.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/pitivi/gst-transcoder") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0nw1zykqc6c8xs3ri55pm00pwyz93z4y4nd880apfiwj7yv5p3az")))) - (build-system meson-build-system) - (inputs - `(("gobject-introspection" ,gobject-introspection) - ("glib" ,glib) - ("gstreamer" ,gstreamer) - ("gst-plugins-base" ,gst-plugins-base))) +(define-public pitivi + ;; Pitivi switched to a non-semantic versioning scheme close before 1.0 + (let ((latest-semver "0.999.0") + (%version "2020.09.2")) + (package + (name "pitivi") + (version (string-append latest-semver "-" %version)) + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnome/sources/" name "/" + (version-major+minor %version) "/" + name "-" %version ".tar.xz")) + (sha256 + (base32 + "0hzvv4wia4rk0kvq16y27imq2qd4q5lg3vx99hdcjdb1x3zqqfg0")))) + (build-system meson-build-system) + (inputs + `(("glib" ,glib) + ("gst-editing-services" ,gst-editing-services) + ("gstreamer" ,gstreamer) + ("gst-plugins-base" ,gst-plugins-base) + ("gst-plugins-good" ,gst-plugins-good) + ("gst-plugins-bad" + ,(gst-plugins/selection gst-plugins-bad + #:plugins '("debugutils" "transcoder") + #:configure-flags '("-Dintrospection=enabled"))) + ("gst-libav" ,gst-libav) + ("gsound" ,gsound) + ("gtk+" ,gtk+) + ("gdk-pixbuf+svg" ,gdk-pixbuf+svg) + ("libpeas" ,libpeas) + ("libnotify" ,libnotify) + ("pango" ,pango) + ("python-gst" ,python-gst) + ("python-numpy" ,python-numpy) + ("python-matplotlib" ,python-matplotlib) + ("python-pycairo" ,python-pycairo) + ("python-pygobject" ,python-pygobject))) (native-inputs - `(("python" ,python) + `(("gettext" ,gettext-minimal) + ("glib:bin" ,glib "bin") + ("itstool" ,itstool) ("pkg-config" ,pkg-config))) - (home-page "https://github.com/pitivi/gst-transcoder/") - (synopsis "GStreamer Transcoding API") - (description "GStreamer Transcoding API") - (license license:lgpl2.1))) + (arguments + `(#:glib-or-gtk? #t + #:phases + (modify-phases %standard-phases + (add-after 'glib-or-gtk-wrap 'wrap-other-dependencies + (lambda* (#:key outputs #:allow-other-keys) + (let ((prog (string-append (assoc-ref outputs "out") + "/bin/pitivi"))) + (wrap-program prog + `("PYTHONPATH" = (,(getenv "PYTHONPATH"))) + `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH"))) + ;; We've only added inputs for what Pitivi deems either + ;; necessary or optional. Let the user's packages take + ;; precedence in case they have e.g. the full gst-plugins-bad. + `("GST_PLUGIN_SYSTEM_PATH" suffix + (,(getenv "GST_PLUGIN_SYSTEM_PATH"))))) + #t))))) + (home-page "http://www.pitivi.org") + (synopsis "Video editor based on GStreamer Editing Services") + (description "Pitivi is a video editor built upon the GStreamer Editing +Services. It aims to be an intuitive and flexible application that can appeal +to newbies and professionals alike.") + (license license:lgpl2.1+)))) (define-public gavl (package @@ -4604,14 +4643,14 @@ transcode or reformat the videos in any way, producing perfect backups.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/OpenVisualCloud/SVT-AV1") + (url "https://github.com/AOMediaCodec/SVT-AV1") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1wzamg89azi1f93wxvdy7silsgklckc754ca066k33drvyacicyw")))) (build-system cmake-build-system) - ;; SVT-AV1 only supports Intel-compatible CPUs. - (supported-systems '("x86_64-linux" "i686-linux")) + ;; SVT-AV1 only supports 64-bit Intel-compatible CPUs. + (supported-systems '("x86_64-linux")) (arguments ;; The test suite tries to download test data and git clone a 3rd-party ;; fork of libaom. Skip it. @@ -4630,7 +4669,41 @@ transcode or reformat the videos in any way, producing perfect backups.") (description "SVT-AV1 is an AV1 codec implementation. The encoder is a work-in-progress, aiming to support video-on-demand and live streaming applications. It only supports Intel-compatible CPUs (x86).") - (home-page "https://github.com/OpenVisualCloud/SVT-AV1") + (home-page "https://github.com/AOMediaCodec/SVT-AV1") + (license license:bsd-2))) + +(define-public svt-vp9 + (package + (name "svt-vp9") + (version "0.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/OpenVisualCloud/SVT-VP9") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ypdiw4cq22llvm8jyszxdq6r1aydkj80dsxjarjn5b7c1f2q3ar")))) + ;; SVT-AV1 only supports 64-bit Intel-compatible CPUs. + (supported-systems '("x86_64-linux")) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ; No test suite + #:phases + (modify-phases %standard-phases + (add-after 'install 'install-documentation + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref %outputs "out")) + (doc (string-append out "/share/doc/" ,name "-" ,version))) + (copy-recursively "../source/Docs" doc) + #t)))))) + (native-inputs + `(("yasm" ,yasm))) + (home-page "https://github.com/OpenVisualCloud/SVT-VP9") + (synopsis "VP9 video encoder") + (description "SVT-VP9 is a VP9 video encoder implementation. It is focused +on supporting video-on-demand and live encoding on Intel Xeon processors.") (license license:bsd-2))) (define-public w-scan diff --git a/gnu/packages/vnc.scm b/gnu/packages/vnc.scm index ab89bad7aa..b8979b2921 100644 --- a/gnu/packages/vnc.scm +++ b/gnu/packages/vnc.scm @@ -1,8 +1,9 @@ -;;; GNU Guix --- Functional package management for GNU +;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019 Todor Kondić <tk.code@protonmail.com> ;;; Copyright © 2020 Oleg Pykhalov <go.wigust@gmail.com> ;;; Copyright © 2020 Hartmut Goebel <h.goebel@crazy-compilers.com> ;;; Copyright © 2020 Marius Bakke <marius@gnu.org> +;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -41,55 +42,56 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages sdl) #:use-module (gnu packages tls) + #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg)) (define-public tigervnc-client - (let ((commit "920d9c4d6562ecabf79497bc901d50522d4bc661")) - (package - (name "tigervnc-client") - (version (git-version "1.10.1" "1" commit)) - (source (origin - (method git-fetch) - (uri - (git-reference - (url "https://github.com/TigerVNC/tigervnc") - (commit commit))) - (sha256 - (base32 - "1lp6mxl5dqlkrzx0q145jzgpbwvhsni3fj6x9ngf8v5s63x82q1p")) - (file-name (git-file-name name version)))) - (build-system cmake-build-system) - (arguments - '(#:tests? #f ; Tests that do exists are not automated. - #:phases (modify-phases %standard-phases - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (with-directory-excursion "vncviewer" - (invoke "make" "install"))))))) - (native-inputs - `(("autoconf" ,autoconf) - ("gettext-minimal" ,gettext-minimal) - ("automake" ,automake))) - (inputs - `(("zlib" ,zlib) - ("gnutls" ,gnutls) - ("libjpeg-turbo" ,libjpeg-turbo) - ("fltk" ,fltk) - ("linux-pam" ,linux-pam) - ("libx11" ,libx11) - ("libxext" ,libxext) - ("libxtst" ,libxtst) - ("libxrandr" ,libxrandr) - ("libxdamage" ,libxdamage))) - (home-page "https://tigervnc.org/") - (synopsis "High-performance, platform-neutral + (package + (name "tigervnc-client") + (version "1.11.0") + (source (origin + (method git-fetch) + (uri + (git-reference + (url "https://github.com/TigerVNC/tigervnc") + (commit (string-append "v" version)))) + (sha256 + (base32 + "1bg79ahr4mzy48ak0caxy3ckdsxmhpchypggaz6lxjjk92hgsz91")) + (file-name (git-file-name name version)))) + (build-system cmake-build-system) + (arguments + '(#:tests? #f ; Tests that do exists are not automated. + #:phases (modify-phases %standard-phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (with-directory-excursion "vncviewer" + (invoke "make" "install"))))))) + (native-inputs + `(("autoconf" ,autoconf) + ("gettext-minimal" ,gettext-minimal) + ("automake" ,automake))) + (inputs + `(("zlib" ,zlib) + ("gnutls" ,gnutls) + ("libjpeg-turbo" ,libjpeg-turbo) + ("fltk" ,fltk) + ("linux-pam" ,linux-pam) + ("libx11" ,libx11) + ("libxext" ,libxext) + ("libxtst" ,libxtst) + ("libxrandr" ,libxrandr) + ("libxdamage" ,libxdamage) + ("pixman" ,pixman))) + (home-page "https://tigervnc.org/") + (synopsis "High-performance, platform-neutral implementation of VNC (client)") - (description "TigerVNC is a client/server implementation of VNC (Virtual + (description "TigerVNC is a client/server implementation of VNC (Virtual Network Computing). It provides enough performance to run even 3D and video applications. It also provides extensions for advanced authentication methods and TLS encryption. This package installs only the VNC client, the application which is needed to connect to VNC servers.") - (license license:gpl2)))) + (license license:gpl2))) ;; A VNC server is, in fact, an X server so it seems like a good idea ;; to build on the work already done for xorg-server package. This is diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 5dc0b4dea4..50a837f51b 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -7957,7 +7957,17 @@ It contains the code shared by all Kiwix ports.") (lambda* (#:key inputs #:allow-other-keys) (substitute* "kiwix-desktop.pro" (("webenginewidgets" all) (string-append all " printsupport"))) - #t))))) + #t)) + (add-after 'install 'wrap-qt-process-path + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin/kiwix-desktop")) + (qt-process-path (string-append + (assoc-ref inputs "qtwebengine") + "/lib/qt5/libexec/QtWebEngineProcess"))) + (wrap-program bin + `("QTWEBENGINEPROCESS_PATH" = (,qt-process-path))) + #t)))))) (inputs `(("curl" ,curl) ("icu4c" ,icu4c) |