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Merge remote-tracking branch 'origin/master' into staging

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Efraim Flashner 2020-12-30 10:53:39 +02:00
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4
gnu/packages/audio.scm
View file

@ -3047,7 +3047,7 @@ (define-public libebur128
(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 @@ (define-public timidity++
"/TiMidity++-" version ".tar.bz2"))
(sha256
(base32
"0xk41w4qbk23z1fvqdyfblbz10mmxsllw0svxzjw5sa9y11vczzr"))))
"1xf8n6dqzvi6nr2asags12ijbj1lwk1hgl3s27vm2szib8ww07qn"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags

428
gnu/packages/bioconductor.scm
View file

@ -389,6 +389,33 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10
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 @@ (define-public r-catalyst
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 @@ (define-public r-kegggraph
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 @@ (define-public r-pathview
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+)))

405
gnu/packages/bioinformatics.scm
View file

@ -10484,411 +10484,6 @@ (define-public r-biovizbase
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"))

26
gnu/packages/cran.scm
View file

@ -14718,32 +14718,6 @@ (define-public r-dlmap
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")

6
gnu/packages/education.scm
View file

@ -677,15 +677,15 @@ (define-public klavaro
(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

8
gnu/packages/emacs-xyz.scm
View file

@ -2068,14 +2068,14 @@ (define-public emacs-async
(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 @@ (define-public emacs-counsel-tramp
(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

248
gnu/packages/games.scm
View file

@ -9864,17 +9864,18 @@ (define-public q5go
(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 @@ (define-public ktuberling
("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 @@ (define-public ktuberling
(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 @@ (define-public picmi
(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 @@ (define-public kolf
(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 @@ (define-public libkmahjongg
(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 @@ (define-public kmahjongg
(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 @@ (define-public kshisen
(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 @@ (define-public kajongg
("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 @@ (define-public kajongg
(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 @@ (define-public kbreakout
(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 @@ (define-public kmines
(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 @@ (define-public konquest
(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 @@ (define-public kbounce
(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 @@ (define-public kblocks
(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 @@ (define-public ksudoku
(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 @@ (define-public klines
(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 @@ (define-public kgoldrunner
(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 @@ (define-public kdiamond
(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 @@ (define-public kfourinline
("kconfigwidgets" ,kconfigwidgets)
("kcoreaddons" ,kcoreaddons)
("kcrash" ,kcrash)
("kdelibs4support" ,kdelibs4support)
("kdnssd" ,kdnssd)
("ki18n" ,ki18n)
("kxmlgui" ,kxmlgui)
@ -10573,14 +10581,14 @@ (define-public kfourinline
(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 @@ (define-public kblackbox
(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 @@ (define-public knetwalk
(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 @@ (define-public bomber
(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 @@ (define-public granatier
(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 @@ (define-public ksirk
(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 @@ (define-public palapeli
(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 @@ (define-public kiriki
(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 @@ (define-public kigo
(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 @@ (define-public kubrick
(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 @@ (define-public lskat
(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 @@ (define-public kapman
(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 @@ (define-public kspaceduel
(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 @@ (define-public bovo
(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 @@ (define-public killbots
(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 @@ (define-public ksnakeduel
(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 @@ (define-public kollision
(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 @@ (define-public knavalbattle
(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 @@ (define-public kreversi
(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 @@ (define-public ksquares
(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)

2
gnu/packages/geo.scm
View file

@ -1680,7 +1680,7 @@ (define-public readosm
(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)

12
gnu/packages/gnome.scm
View file

@ -2999,7 +2999,7 @@ (define-public libnotify
(define-public libpeas
(package
(name "libpeas")
(version "1.24.1")
(version "1.28.0")
(source
(origin
(method url-fetch)
@ -3008,7 +3008,7 @@ (define-public libpeas
name "-" version ".tar.xz"))
(sha256
(base32
"1162dr7smmfb02czmhshr0f93hqj7w0nw29bys5lzfvwarxcyflw"))))
"05cb7drn6arc4gi02wgsvzibigi2riz5gnfnmlb0zmbfnj9ikna2"))))
(build-system meson-build-system)
(arguments
'(#:phases
@ -4678,7 +4678,7 @@ (define-public rest
(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 @@ (define-public libsoup
"libsoup-" version ".tar.xz"))
(sha256
(base32
"0hjk9lgppc5435my0lyywbpmj7ib5vvcylwfin8ki97g9bvj1c2l"))))
"11skbyw2pw32178q3h8pi7xqa41b2x4k6q4k9f75zxmh8s23y30p"))))
(build-system meson-build-system)
(outputs '("out" "doc"))
(arguments
@ -6942,7 +6942,7 @@ (define-public shotwell
(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 @@ (define-public file-roller
"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

31
gnu/packages/gstreamer.scm
View file

@ -890,6 +890,8 @@ (define-public gst-editing-services
("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 @@ (define-public gst-editing-services
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")

18
gnu/packages/linux.scm
View file

@ -394,7 +394,7 @@ (define-public linux-libre-4.19-pristine-source
(%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 @@ (define deblob-scripts-4.14
(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 @@ (define deblob-scripts-4.9
(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 @@ (define deblob-scripts-4.4
(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 @@ (define-public rtl8812au-aircrack-ng-linux-module
(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 @@ (define-public rtl8821ce-linux-module
(file-name (git-file-name name version))
(sha256
(base32
"10mrp63npbqb39c442vx8mra278hw7sczb3b6bjrpr3gan6ljshn"))))
"0z7r7spsgn22gwv9pcmkdjn9ingi8jj7xkxasph8118h46fw8ip2"))))
(build-system linux-module-build-system)
(arguments
`(#:make-flags

4
gnu/packages/music.scm
View file

@ -3485,7 +3485,7 @@ (define-public beets-bandcamp
(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 @@ (define-public milkytracker
(file-name (git-file-name name version))
(sha256
(base32
"05a6d7l98k9i82dwrgi855dnccm3f2lkb144gi244vhk1156n0ca"))
"025fj34gq2kmkpwcswcyx7wdxb89vm944dh685zi4bxx0hz16vvk"))
(modules '((guix build utils)))
;; Remove non-FSDG compliant sample songs.
(snippet

9
gnu/packages/qt.scm
View file

@ -2220,7 +2220,7 @@ (define-public python2-pyqtwebengine
(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 @@ (define-public python2-pyqt-4
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)

14
gnu/packages/ruby.scm
View file

@ -188,6 +188,20 @@ (define-public ruby-2.7
(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)

131
gnu/packages/video.scm
View file

@ -4000,33 +4000,72 @@ (define-public aegisub
; 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 @@ (define-public svt-av1
(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 @@ (define-public svt-av1
(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

86
gnu/packages/vnc.scm
View file

@ -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 @@ (define-module (gnu packages vnc)
#: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

12
gnu/packages/web.scm
View file

@ -7957,7 +7957,17 @@ (define-public kiwix-desktop
(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)