diff options
Diffstat (limited to 'gnu')
47 files changed, 5976 insertions, 1055 deletions
diff --git a/gnu/bootloader/u-boot.scm b/gnu/bootloader/u-boot.scm index e21526eb7e..3e892c5475 100644 --- a/gnu/bootloader/u-boot.scm +++ b/gnu/bootloader/u-boot.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 David Craven <david@craven.ch> -;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com> +;;; Copyright © 2017, 2019 Mathieu Othacehe <m.othacehe@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -33,6 +33,7 @@ u-boot-nintendo-nes-classic-edition-bootloader u-boot-novena-bootloader u-boot-pine64-plus-bootloader + u-boot-pine64-lts-bootloader u-boot-pinebook-bootloader u-boot-puma-rk3399-bootloader u-boot-rock64-rk3328-bootloader @@ -206,6 +207,11 @@ (inherit u-boot-allwinner64-bootloader) (package u-boot-pine64-plus))) +(define u-boot-pine64-lts-bootloader + (bootloader + (inherit u-boot-allwinner-bootloader) + (package u-boot-pine64-lts))) + (define u-boot-pinebook-bootloader (bootloader (inherit u-boot-allwinner64-bootloader) diff --git a/gnu/build/vm.scm b/gnu/build/vm.scm index 89d685b352..9a9e5bd001 100644 --- a/gnu/build/vm.scm +++ b/gnu/build/vm.scm @@ -131,14 +131,7 @@ the #:references-graphs parameter of 'derivation'." ;; The serial port name differs between emulated ;; architectures/machines. " console=" - (if target-arm? "ttyAMA0" "ttyS0")) - - ;; NIC is not supported on ARM "virt" machine, so use a user mode - ;; network stack instead. - ,@(if target-arm? - '("-device" "virtio-net-pci,netdev=mynet" - "-netdev" "user,id=mynet") - '("-net" "nic,model=virtio")))) + (if target-arm? "ttyAMA0" "ttyS0")))) (when make-disk-image? (format #t "creating ~a image of ~,2f MiB...~%" @@ -163,6 +156,7 @@ the #:references-graphs parameter of 'derivation'." ;; CPU with the maximum possible feature set otherwise. "-cpu" "max" "-m" (number->string memory-size) + "-nic" "user,model=virtio-net-pci" "-object" "rng-random,filename=/dev/urandom,id=guixsd-vm-rng" "-device" "virtio-rng-pci,rng=guixsd-vm-rng" "-virtfs" diff --git a/gnu/local.mk b/gnu/local.mk index f4a9829239..7b88e00706 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -969,7 +969,6 @@ dist_patch_DATA = \ %D%/packages/patches/hdf4-shared-fortran.patch \ %D%/packages/patches/hdf4-tirpc.patch \ %D%/packages/patches/hdf5-config-date.patch \ - %D%/packages/patches/hdf5-mpi-deprecations.patch \ %D%/packages/patches/hdf5-1.8-mpi-deprecations.patch \ %D%/packages/patches/hdf-eos2-build-shared.patch \ %D%/packages/patches/hdf-eos2-remove-gctp.patch \ diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 24c294b8e2..e6e89c0064 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -3331,7 +3331,7 @@ mixers.") (define-public bluez-alsa (package (name "bluez-alsa") - (version "1.2.0") + (version "2.0.0") (source (origin ;; The tarballs are mere snapshots and don't contain a ;; bootstrapped build system. @@ -3339,11 +3339,19 @@ mixers.") (uri (git-reference (url "https://github.com/Arkq/bluez-alsa.git") (commit (string-append "v" version)))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "1qinf41wl2ihx54zmmhanycihwjkn7dn1cicq6pp4rqbiv79b95x")))) + "08mppgnjf1j2733bk9yf0cny6rfxxwiys0s62lz2zd2lpdl6d9lz")))) (build-system gnu-build-system) + (arguments + `(#:configure-flags + (list (string-append "--with-alsaplugindir=" + (assoc-ref %outputs "out") + "/lib/alsa-lib") + (string-append "--with-dbusconfdir=" + (assoc-ref %outputs "out") + "/etc/dbus-1")))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -3352,6 +3360,7 @@ mixers.") (inputs `(("alsa-lib" ,alsa-lib) ("bluez" ,bluez) + ("dbus" ,dbus) ("glib" ,glib) ("libbsd" ,libbsd) ("ncurses" ,ncurses) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e584a7bced..6d91dcf2e4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -32,6 +32,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages maths) @@ -40,11 +41,34 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web) + #:use-module (gnu packages xml) #:use-module (srfi srfi-1)) ;;; Annotations +(define-public r-reactome-db + (package + (name "r-reactome-db") + (version "1.70.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "reactome.db" version 'annotation)) + (sha256 + (base32 + "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg")))) + (properties `((upstream-name . "reactome.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/reactome.db/") + (synopsis "Annotation maps for reactome") + (description + "This package provides a set of annotation maps for the REACTOME +database, assembled using data from REACTOME.") + (license license:cc-by4.0))) + (define-public r-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") @@ -876,19 +900,72 @@ examples' of Affymetrix data, unlike the artificial examples included in the package @code{affy}.") (license license:gpl2+))) +(define-public r-curatedtcgadata + (package + (name "r-curatedtcgadata") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) + (sha256 + (base32 + "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) + (properties + `((upstream-name . "curatedTCGAData"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-experimenthub" ,r-experimenthub) + ("r-hdf5array" ,r-hdf5array) + ("r-multiassayexperiment" ,r-multiassayexperiment) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/curatedTCGAData/") + (synopsis "Curated data from The Cancer Genome Atlas") + (description + "This package provides publicly available data from The Cancer Genome +Atlas (TCGA) as @code{MultiAssayExperiment} objects. +@code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy +number, mutation, microRNA, protein, and others) with clinical / pathological +data. It also links assay barcodes with patient identifiers, enabling +harmonized subsetting of rows (features) and columns (patients / samples) +across the entire multi-'omics experiment.") + (license license:artistic2.0))) + ;;; Packages +(define-public r-biocversion + (package + (name "r-biocversion") + (version "3.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocVersion" version)) + (sha256 + (base32 + "0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f")))) + (properties `((upstream-name . "BiocVersion"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/BiocVersion/") + (synopsis "Set the appropriate version of Bioconductor packages") + (description + "This package provides repository information for the appropriate version +of Bioconductor.") + (license license:artistic2.0))) + (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.30.0") + (version "0.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f")))) + "1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -902,14 +979,14 @@ packages.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n")))) + "0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) @@ -923,14 +1000,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs")))) + "10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) @@ -951,14 +1028,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp")))) + "0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -976,14 +1053,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.56.0") + (version "1.58.2") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s")))) + "0cgy9phwdk4x9lr11xh6zs7v8r5xq959fmsmzwrpnd50dr7hzkvd")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -1015,14 +1092,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33")))) + "03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -1043,14 +1120,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs")))) + "0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -1070,14 +1147,14 @@ microarrays.") (define-public r-hpar (package (name "r-hpar") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5")))) + "1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") @@ -1088,14 +1165,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.16.5") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h")))) + "0m073hrqp62zpd2blnqm5ka539hcilir05m8av14vdhzhjzp13ya")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -1117,14 +1194,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc")))) + "0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -1165,14 +1242,14 @@ browser.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb")))) + "1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -1190,14 +1267,14 @@ browser.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72")))) + "02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -1225,14 +1302,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df")))) + "01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -1259,14 +1336,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5")))) + "0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -1288,14 +1365,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-diffbind (package (name "r-diffbind") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich")))) + "1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs @@ -1333,14 +1410,14 @@ occupancy (overlap) analysis and plotting functions.") (define-public r-ripseeker (package (name "r-ripseeker") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 - "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43")))) + "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs @@ -1366,14 +1443,14 @@ processing to visualization and annotation.") (define-public r-multtest (package (name "r-multtest") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv")))) + "0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) @@ -1404,13 +1481,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w")))) + "1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) @@ -1451,14 +1528,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.18.2") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779")))) + "0hp3s3shnrb55cxvx9wrdl67wqw9f55gdgx7262s4mahpxjswfsa")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -1507,12 +1584,12 @@ enrichedGO (addGeneIDs).") (define-public r-marray (package (name "r-marray") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz")))) + (base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) @@ -1526,12 +1603,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm")))) + (base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -1546,12 +1623,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93")))) + (base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -1569,20 +1646,21 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz")))) + (base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) - ("r-biocparallel" ,r-biocparallel) ("r-cghbase" ,r-cghbase) ("r-cghcall" ,r-cghcall) ("r-dnacopy" ,r-dnacopy) + ("r-future" ,r-future) + ("r-future-apply" ,r-future-apply) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats) @@ -1601,14 +1679,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w")))) + "040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -1627,14 +1705,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y")))) + "0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -1661,14 +1739,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9")))) + "0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -1700,14 +1778,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga")))) + "1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -1728,14 +1806,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6")))) + "0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -1760,14 +1838,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p")))) + "10kwb70c9aq0bfqpq48h186lsbwgrg18m14r9z8x6n8l7cds5azc")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -1799,14 +1877,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am")))) + "0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") @@ -1819,14 +1897,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw")))) + "11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -1845,14 +1923,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x")))) + "1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs @@ -1872,14 +1950,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77")))) + "08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -1896,14 +1974,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp")))) + "0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -1921,14 +1999,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r")))) + "043066zygf2y2jp6dvfwl56hkzcdvkmymhjx3gh4mhi48l71zqv9")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -1937,12 +2015,13 @@ genes or proteins in these datasets.") ("r-biocparallel" ,r-biocparallel) ("r-deseq2" ,r-deseq2) ("r-desolve" ,r-desolve) + ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) ("r-plgem" ,r-plgem) - ("r-preprocesscore" ,r-preprocesscore) ("r-proc" ,r-proc) ("r-rootsolve" ,r-rootsolve) ("r-rsamtools" ,r-rsamtools) @@ -1963,14 +2042,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0")))) + "0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -1990,14 +2069,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33")))) + "1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -2016,19 +2095,19 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.2.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg")))) + "05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) + `(("r-biocparallel" ,r-biocparallel) + ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcppannoy" ,r-rcppannoy) ("r-rcpphnsw" ,r-rcpphnsw) @@ -2047,14 +2126,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5")))) + "0qd7r2k56ym7ivjgapxbk7fyj2d7396f1ad1hkgnicgyw1an5q1r")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -2079,29 +2158,37 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "2.14.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3")))) + "0vj9nk8g6i4vzm6cnzvbsqcvyk6fhmx0a0nxxrciarffyhqk81yz")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) + ("r-ggplot-multistats" ,r-ggplot-multistats) ("r-ggplot2" ,r-ggplot2) ("r-ggthemes" ,r-ggthemes) - ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-knn-covertree" ,r-knn-covertree) ("r-matrix" ,r-matrix) + ("r-pcamethods" ,r-pcamethods) ("r-proxy" ,r-proxy) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) + ("r-rcpphnsw" ,r-rcpphnsw) + ("r-rspectra" ,r-rspectra) ("r-scales" ,r-scales) ("r-scatterplot3d" ,r-scatterplot3d) + ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-smoother" ,r-smoother) ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect) ("r-vim" ,r-vim))) (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") @@ -2113,14 +2200,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h")))) + "1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs @@ -2139,14 +2226,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj")))) + "044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -2177,13 +2264,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp")))) + "0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -2200,14 +2287,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa")))) + "119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -2251,14 +2338,14 @@ clusters).") (define-public r-deds (package (name "r-deds") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEDS" version)) (sha256 (base32 - "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs")))) + "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8")))) (properties `((upstream-name . "DEDS"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/DEDS/") @@ -2300,14 +2387,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83")))) + "0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -2324,14 +2411,14 @@ gene and isoform level using RNA-seq data") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv")))) + "0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran) @@ -2354,14 +2441,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz")))) + "0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -2384,14 +2471,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q")))) + "1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -2418,19 +2505,18 @@ interactive exploration of results.") (define-public r-mast (package (name "r-mast") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx")))) + "1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) - ("r-blme" ,r-blme) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) @@ -2452,14 +2538,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z")))) + "18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2569,14 +2655,14 @@ qPCR data, but could be used with other types as well.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j")))) + "1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -2596,14 +2682,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf")))) + "0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -2632,14 +2718,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck")))) + "1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) @@ -2672,14 +2758,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.52.0") + (version "2.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr")))) + "0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs @@ -2703,14 +2789,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.26.0") + (version "0.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8")))) + "1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) @@ -2724,14 +2810,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib")))) + "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2750,14 +2836,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx")))) + "1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -2784,14 +2870,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd")))) + "177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) @@ -2833,14 +2919,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f")))) + "0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -2877,14 +2963,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba")))) + "0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -2916,14 +3002,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5")))) + "15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -2975,14 +3061,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y")))) + "1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -3104,14 +3190,14 @@ published results; and a routine for graphical display.") (define-public r-triform (package (name "r-triform") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "triform" version)) (sha256 (base32 - "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya")))) + "12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -3128,14 +3214,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql")))) + "0aafcprsqbn1xl8jqnxfl8r2d0lmzhssqpr26lam2cprh3yk0xiv")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -3168,14 +3254,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6")))) + "0hx5gqgh4xrkx37ccprq7azj9jziff137bdk0gvrixcx52ws6h89")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -3193,14 +3279,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg")))) + "0pqnlgdvh5szjhwc1mw1snjgpj9lrsnk44bn164cl3zwvdayccya")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -3220,14 +3306,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c")))) + "1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) @@ -3251,14 +3337,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7")))) + "057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -3273,14 +3359,14 @@ phenotype of interest.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6")))) + "0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -3303,14 +3389,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.10.2") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj")))) + "0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -3337,14 +3423,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h")))) + "1jblx00b869xhx1c4n9m2g1hqr00rm9ywr1hrlx42bdd8k5ax1xh")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -3360,8 +3446,7 @@ data.") ("r-igraph" ,r-igraph) ("r-purrr" ,r-purrr) ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-upsetr" ,r-upsetr))) + ("r-reshape2" ,r-reshape2))) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description @@ -3373,14 +3458,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.12.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq")))) + "0mm9iafrsjb8sj27k9mg40ab13vq4rmrzhaajm6g1wdkb2jqikjk")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -3406,14 +3491,14 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1c1hciwy37zpr5bzdjj2xxx2r4jdfmr5w0zmg010lm2985z41gqh")))) + "1vnzqd3y3jk1wgxybckzrcgwk0ly7zgcz5ki1ib0bk1jwv6xk5x8")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -3447,14 +3532,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9")))) + "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16")))) (build-system r-build-system) (arguments `(#:phases @@ -3483,14 +3568,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7")))) + "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -3506,14 +3591,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0")))) + "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -3534,14 +3619,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr")))) + "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -3556,14 +3641,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj")))) + "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -3579,14 +3664,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1")))) + "0dgqyq4dnlcik5qqygnhxlhfr98sh6kmdcj2qllhrwyk0lmsfk01")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -3611,14 +3696,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy")))) + "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4")))) (build-system r-build-system) (propagated-inputs `(("r-a4base" ,r-a4base) @@ -3636,14 +3721,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r")))) + "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -3682,14 +3767,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q")))) + "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) @@ -3707,14 +3792,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18")))) + "14ylbrzb9haqwfdd9g813mzhll6gwvqf2r7cmbaxz5lkl0j0nglx")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -3732,14 +3817,14 @@ genomic sequence data.") (define-public r-motiv (package (name "r-motiv") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotIV" version)) (sha256 (base32 - "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf")))) + "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k")))) (properties `((upstream-name . "MotIV"))) (build-system r-build-system) (inputs @@ -3747,6 +3832,7 @@ genomic sequence data.") (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-rgadem" ,r-rgadem) @@ -3763,19 +3849,20 @@ distributions, modules and filter motifs.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f")))) + "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) ("r-biostrings" ,r-biostrings) + ("r-ggplot2" ,r-ggplot2) ("r-grimport2" ,r-grimport2) ("r-htmlwidgets" ,r-htmlwidgets) ("r-motiv" ,r-motiv) @@ -3794,14 +3881,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy")))) + "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -3825,14 +3912,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.8.5") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp")))) + "12ix0bvwk50d48z85f3453k7szm1j27gk4qgw56az4fxra472rlh")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -3870,14 +3957,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm")))) + "0hmi13pz923fm95asys615rih63b1i2nvynfczr1zcsc9fzn4h35")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -3917,14 +4004,14 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48")))) + "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs @@ -3947,14 +4034,14 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.") (define-public r-annotationfuncs (package (name "r-annotationfuncs") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFuncs" version)) (sha256 (base32 - "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3")))) + "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq")))) (properties `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) @@ -3972,14 +4059,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1")))) + "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -3997,14 +4084,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng")))) + "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -4038,21 +4125,23 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b")))) + "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) + `(("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) ("r-gseabase" ,r-gseabase) ("r-mixtools" ,r-mixtools) ("r-r-utils" ,r-r-utils) + ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/AUCell/") @@ -4073,14 +4162,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.26.0") + (version "4.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq")))) + "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -4112,14 +4201,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23")))) + "1n49a2vg1667wycrjww29xfafngllvpb5nq5wy6pgn0akva91nky")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -4144,14 +4233,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix")))) + "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) @@ -4171,14 +4260,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx")))) + "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -4208,14 +4297,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q")))) + "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -4248,14 +4337,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4")))) + "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -4284,14 +4373,14 @@ gene-specific bidning is expected.") (define-public r-simpleaffy (package (name "r-simpleaffy") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simpleaffy" version)) (sha256 (base32 - "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a")))) + "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -4312,14 +4401,14 @@ generating high resolution journal figures.") (define-public r-yaqcaffy (package (name "r-yaqcaffy") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yaqcaffy" version)) (sha256 (base32 - "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670")))) + "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz")))) (build-system r-build-system) (propagated-inputs `(("r-simpleaffy" ,r-simpleaffy))) @@ -4334,14 +4423,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab")))) + "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4365,14 +4454,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6")))) + "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4400,14 +4489,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7")))) + "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -4429,14 +4518,14 @@ sites and alignments obtained from standard RNA-seq experiments.") (define-public r-xbseq (package (name "r-xbseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XBSeq" version)) (sha256 (base32 - "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy")))) + "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp")))) (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs @@ -4466,14 +4555,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72")))) + "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -4490,19 +4579,20 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.6.2") + (version "3.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "0icww3f1kahyk96mc07yhsbyiranzm2614n509as09jf8bdhq23v")))) + "18iglvlvlxrdwn2apdvihj9jxmx0kwm5z37rml67xcj9sfdi3bjb")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) + ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-massspecwavelet" ,r-massspecwavelet) ("r-msnbase" ,r-msnbase) @@ -4526,14 +4616,14 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wrench (package (name "r-wrench") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i")))) + "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs @@ -4550,14 +4640,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.8.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0")))) + "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -4582,14 +4672,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a")))) + "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -4603,14 +4693,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz")))) + "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) @@ -4636,14 +4726,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz")))) + "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -4663,14 +4753,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4")))) + "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs @@ -4686,14 +4776,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw")))) + "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) (home-page "https://github.com/saezlab/progeny") @@ -4708,14 +4798,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1")))) + "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -4731,14 +4821,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "1.8.0") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb")))) + "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -4761,14 +4851,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq")))) + "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -4791,14 +4881,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f")))) + "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (inputs @@ -4814,14 +4904,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s")))) + "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -4855,18 +4945,28 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.0.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5")))) + "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) - (native-inputs - `(("which" ,which))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-reproducible + (lambda _ + (substitute* "src/Makefile" + (("`hostname`") "guix") + (("`date`") "0") + ;; Avoid shelling out to "which". + (("^CC =.*") (which "gcc")) + (("^CPP =.*") (which "g++"))) + #t))))) (propagated-inputs `(("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) @@ -4883,14 +4983,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx")))) + "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (inputs @@ -4928,14 +5028,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g")))) + "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -4969,14 +5069,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.16.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518")))) + "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs @@ -4998,14 +5098,14 @@ routines to analyse the resulting networks and their natural projections.") (define-public r-birta (package (name "r-birta") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "birta" version)) (sha256 (base32 - "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2")))) + "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5024,19 +5124,56 @@ conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.") (license license:gpl2+))) +(define-public r-multidataset + (package + (name "r-multidataset") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MultiDataSet" version)) + (sha256 + (base32 + "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj")))) + (properties `((upstream-name . "MultiDataSet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-qqman" ,r-qqman) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/MultiDataSet/") + (synopsis "Implementation of MultiDataSet and ResultSet") + (description + "This package provides an implementation of the BRGE's (Bioinformatic +Research Group in Epidemiology from Center for Research in Environmental +Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for +integrating multi omics data sets and ResultSet is a container for omics +results. This package contains base classes for MEAL and rexposome +packages.") + (license license:expat))) + (define-public r-ropls (package (name "r-ropls") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2")))) + "05w1zrq92w3jfwq5sdyj27m5qjg4zv7acywia8vd6y5fbgcnyzlp")))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-multidataset" ,r-multidataset))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") @@ -5063,18 +5200,19 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b")))) + "1kdfhw629qczrfms0jmphqz0ksjzi8js00xj92h1lnv092npfk0j")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-e1071" ,r-e1071) + ("r-multidataset" ,r-multidataset) ("r-randomforest" ,r-randomforest) ("r-ropls" ,r-ropls))) (native-inputs @@ -5098,14 +5236,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f")))) + "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -5137,14 +5275,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "1.34.7") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y")))) + "0l8q9y2a4m1di0w5nlxhq9jgliinhgr2fwjpm5ixnqx5j3iprlwd")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -5161,14 +5299,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm")))) + "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs @@ -5187,14 +5325,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8")))) + "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -5209,29 +5347,46 @@ and to both short and long sequence reads.") cluster count and membership by stability evidence in unsupervised analysis.") (license license:gpl2))) +(define-public r-cytolib + (package + (name "r-cytolib") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "cytolib" version)) + (sha256 + (base32 + "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9")))) + (properties `((upstream-name . "cytolib"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/cytolib/") + (synopsis "C++ infrastructure for working with gated cytometry") + (description + "This package provides the core data structure and API to represent and +interact with gated cytometry data.") + (license license:artistic2.0))) + (define-public r-flowcore (package (name "r-flowcore") - (version "1.50.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan")))) + "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-corpcor" ,r-corpcor) - ("r-graph" ,r-graph) - ("r-mass" ,r-mass) + ("r-cytolib" ,r-cytolib) ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rrcov" ,r-rrcov))) + ("r-rcpp" ,r-rcpp))) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description @@ -5242,14 +5397,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2")))) + "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -5265,25 +5420,361 @@ Cytometry data using non-parametric clustering and segmented-regression-based change point detection.") (license license:artistic2.0))) +(define-public r-ncdfflow + (package + (name "r-ncdfflow") + (version "2.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ncdfFlow" version)) + (sha256 + (base32 + "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i")))) + (properties `((upstream-name . "ncdfFlow"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-flowcore" ,r-flowcore) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/ncdfFlow/") + (synopsis "HDF5 based storage for flow cytometry data") + (description + "This package provides HDF5 storage based methods and functions for +manipulation of flow cytometry data.") + (license license:artistic2.0))) + +(define-public r-ggcyto + (package + (name "r-ggcyto") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ggcyto" version)) + (sha256 + (base32 + "165qszvy5z176h1l3dnjb5dcm279b6bjl5n5gzz8wfn4xpn8anc8")))) + (properties `((upstream-name . "ggcyto"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-flowcore" ,r-flowcore) + ("r-flowworkspace" ,r-flowworkspace) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-ncdfflow" ,r-ncdfflow) + ("r-plyr" ,r-plyr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales))) + (home-page "https://github.com/RGLab/ggcyto/issues") + (synopsis "Visualize Cytometry data with ggplot") + (description + "With the dedicated fortify method implemented for @code{flowSet}, +@code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow +cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper +and some custom layers also make it easy to add gates and population +statistics to the plot.") + (license license:artistic2.0))) + +(define-public r-flowviz + (package + (name "r-flowviz") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowViz" version)) + (sha256 + (base32 + "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7")))) + (properties `((upstream-name . "flowViz"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-flowcore" ,r-flowcore) + ("r-hexbin" ,r-hexbin) + ("r-idpmisc" ,r-idpmisc) + ("r-kernsmooth" ,r-kernsmooth) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-mass" ,r-mass) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://bioconductor.org/packages/flowViz/") + (synopsis "Visualization for flow cytometry") + (description + "This package provides visualization tools for flow cytometry data.") + (license license:artistic2.0))) + +(define-public r-flowclust + (package + (name "r-flowclust") + (version "3.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowClust" version)) + (sha256 + (base32 + "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s")))) + (properties `((upstream-name . "flowClust"))) + (build-system r-build-system) + (arguments + `(#:configure-flags + (list "--configure-args=--enable-bundled-gsl=no"))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-clue" ,r-clue) + ("r-corpcor" ,r-corpcor) + ("r-ellipse" ,r-ellipse) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-graph" ,r-graph) + ("r-mnormt" ,r-mnormt))) + (inputs + `(("gsl" ,gsl))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://bioconductor.org/packages/flowClust") + (synopsis "Clustering for flow cytometry") + (description + "This package provides robust model-based clustering using a t-mixture +model with Box-Cox transformation.") + (license license:artistic2.0))) + +;; TODO: this package bundles an old version of protobuf. It's not easy to +;; make it use our protobuf package instead. +(define-public r-rprotobuflib + (package + (name "r-rprotobuflib") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RProtoBufLib" version)) + (sha256 + (base32 + "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm")))) + (properties `((upstream-name . "RProtoBufLib"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-bundled-sources + (lambda _ + (with-directory-excursion "src" + (invoke "tar" "xf" "protobuf-2.6.0.tgz")) + #t))))) + (home-page "https://bioconductor.org/packages/RProtoBufLib/") + (synopsis "C++ headers and static libraries of Protocol buffers") + (description + "This package provides the headers and static library of Protocol buffers +for other R packages to compile and link against.") + (license license:bsd-3))) + +(define-public r-flowworkspace + (package + (name "r-flowworkspace") + (version "3.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowWorkspace" version)) + (sha256 + (base32 + "0hvbkxyylsygra31l1lxyvbsr5hc50lqy1y7gwrfgrfil4a2m762")))) + (properties `((upstream-name . "flowWorkspace"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cytolib" ,r-cytolib) + ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) + ("r-dplyr" ,r-dplyr) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-graph" ,r-graph) + ("r-gridextra" ,r-gridextra) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-matrixstats" ,r-matrixstats) + ("r-ncdfflow" ,r-ncdfflow) + ("r-rbgl" ,r-rbgl) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rprotobuflib" ,r-rprotobuflib) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr))) + (home-page "https://bioconductor.org/packages/flowWorkspace/") + (synopsis "Infrastructure for working with cytometry data") + (description + "This package is designed to facilitate comparison of automated gating +methods against manual gating done in flowJo. This package allows you to +import basic flowJo workspaces into BioConductor and replicate the gating from +flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of +samples, compensation, and transformation are performed so that the output +matches the flowJo analysis.") + (license license:artistic2.0))) + +(define-public r-flowstats + (package + (name "r-flowstats") + (version "3.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowStats" version)) + (sha256 + (base32 + "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w")))) + (properties `((upstream-name . "flowStats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cluster" ,r-cluster) + ("r-fda" ,r-fda) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-flowworkspace" ,r-flowworkspace) + ("r-kernsmooth" ,r-kernsmooth) + ("r-ks" ,r-ks) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-ncdfflow" ,r-ncdfflow) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rrcov" ,r-rrcov))) + (home-page "http://www.github.com/RGLab/flowStats") + (synopsis "Statistical methods for the analysis of flow cytometry data") + (description + "This package provides methods and functionality to analyze flow data +that is beyond the basic infrastructure provided by the @code{flowCore} +package.") + (license license:artistic2.0))) + +(define-public r-opencyto + (package + (name "r-opencyto") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "openCyto" version)) + (sha256 + (base32 + "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb")))) + (properties `((upstream-name . "openCyto"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-clue" ,r-clue) + ("r-data-table" ,r-data-table) + ("r-flowclust" ,r-flowclust) + ("r-flowcore" ,r-flowcore) + ("r-flowstats" ,r-flowstats) + ("r-flowviz" ,r-flowviz) + ("r-flowworkspace" ,r-flowworkspace) + ("r-graph" ,r-graph) + ("r-gtools" ,r-gtools) + ("r-ks" ,r-ks) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-ncdfflow" ,r-ncdfflow) + ("r-plyr" ,r-plyr) + ("r-r-utils" ,r-r-utils) + ("r-rbgl" ,r-rbgl) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rrcov" ,r-rrcov))) + (home-page "https://bioconductor.org/packages/openCyto") + (synopsis "Hierarchical gating pipeline for flow cytometry data") + (description + "This package is designed to facilitate the automated gating methods in a +sequential way to mimic the manual gating strategy.") + (license license:artistic2.0))) + +(define-public r-cytoml + (package + (name "r-cytoml") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CytoML" version)) + (sha256 + (base32 + "0m8x18wkvis85cawv7j07pk59w76wnzy93ia99gd24j82z4h97p1")))) + (properties `((upstream-name . "CytoML"))) + (build-system r-build-system) + (inputs + `(("libxml2" ,libxml2))) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-corpcor" ,r-corpcor) + ("r-cytolib" ,r-cytolib) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-flowcore" ,r-flowcore) + ("r-flowworkspace" ,r-flowworkspace) + ("r-ggcyto" ,r-ggcyto) + ("r-graph" ,r-graph) + ("r-jsonlite" ,r-jsonlite) + ("r-lattice" ,r-lattice) + ("r-ncdfflow" ,r-ncdfflow) + ("r-opencyto" ,r-opencyto) + ("r-plyr" ,r-plyr) + ("r-rbgl" ,r-rbgl) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rprotobuflib" ,r-rprotobuflib) + ("r-runit" ,r-runit) + ("r-xml" ,r-xml) + ("r-yaml" ,r-yaml))) + (home-page "https://github.com/RGLab/CytoML") + (synopsis "GatingML interface for cross platform cytometry data sharing") + (description + "This package provides an interface to implementations of the GatingML2.0 +standard to exchange gated cytometry data with other software platforms.") + (license license:artistic2.0))) + (define-public r-flowsom (package (name "r-flowsom") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l")))) + "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-consensusclusterplus" ,r-consensusclusterplus) + ("r-cytoml" ,r-cytoml) ("r-flowcore" ,r-flowcore) - ("r-flowutils" ,r-flowutils) + ("r-flowworkspace" ,r-flowworkspace) ("r-igraph" ,r-igraph) + ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-tsne" ,r-tsne) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/FlowSOM/") @@ -5296,14 +5787,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.8.5") + (version "6.10.6") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7")))) + "18jwrdyc4pnx917y1kskxz3fqvlrkyy4ny0xqrfcidz0j7p0b7wr")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -5338,29 +5829,21 @@ delete entire rows with missing data.") (define-public r-depecher (package (name "r-depecher") - (version "1.0.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h")))) + "1f6zbc0fq7xjflh3mkjx1n83mpppw663dj22rlpxzwp1kpmf6wm5")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-syntax-error - (lambda _ - (substitute* "src/Makevars" - ((" & ") " && ")) - #t))))) (propagated-inputs `(("r-beanplot" ,r-beanplot) - ("r-biocparallel" ,r-biocparallel) ("r-dosnow" ,r-dosnow) ("r-dplyr" ,r-dplyr) + ("r-fnn" ,r-fnn) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-gplots" ,r-gplots) @@ -5371,6 +5854,7 @@ delete entire rows with missing data.") ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-reshape2" ,r-reshape2) + ("r-robustbase" ,r-robustbase) ("r-viridis" ,r-viridis))) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") @@ -5388,14 +5872,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd")))) + "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -5423,14 +5907,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr")))) + "0mmm7vvzq50b5fayid0bw82b5lar3xm9fwl2ya30q0p4db2y6wnz")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -5530,14 +6014,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx")))) + "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs `(("r-reshape2" ,r-reshape2))) @@ -5551,16 +6035,18 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c")))) + "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) + (propagated-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") (description @@ -5597,14 +6083,14 @@ data.") (define-public r-watermelon (package (name "r-watermelon") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z")))) + "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -5634,14 +6120,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy")) + "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -5691,14 +6177,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9")))) + "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -5719,14 +6205,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw")))) + "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs @@ -5747,14 +6233,14 @@ genome sequence.") (define-public r-reqon (package (name "r-reqon") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a")))) + "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs @@ -5772,14 +6258,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2")))) + "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -5818,14 +6304,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y")))) + "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) @@ -5857,14 +6343,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17")))) + "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -5904,14 +6390,14 @@ populations, splice site strength, conservation, etc.") (define-public r-genomegraphs (package (name "r-genomegraphs") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeGraphs" version)) (sha256 (base32 - "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd")))) + "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags")))) (properties `((upstream-name . "GenomeGraphs"))) (build-system r-build-system) (propagated-inputs @@ -5932,14 +6418,14 @@ same genome coordinate system.") (define-public r-wavetiling (package (name "r-wavetiling") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "waveTiling" version)) (sha256 (base32 - "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir")))) + "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) (properties `((upstream-name . "waveTiling"))) (build-system r-build-system) (propagated-inputs @@ -5963,14 +6449,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd")))) + "1ygx7f2sp4b7ilgspm6vqcbjxs7br9s6g3gwcdb978kx03ymp4i8")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -6005,14 +6491,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7")))) + "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs @@ -6038,14 +6524,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a")))) + "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) @@ -6059,3 +6545,863 @@ features (e.g. genes, microRNAs).") data. This modified test allows for testing differential expression in qPCR data.") (license license:gpl2+))) + +;; This is a CRAN package, but it depends on Bioconductor packages, so we put +;; it here. +(define-public r-activedriverwgs + (package + (name "r-activedriverwgs") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActiveDriverWGS" version)) + (sha256 + (base32 + "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1")))) + (properties + `((upstream-name . "ActiveDriverWGS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-plyr" ,r-plyr) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") + (synopsis "Driver discovery tool for cancer whole genomes") + (description + "This package provides a method for finding an enrichment of cancer +simple somatic mutations (SNVs and Indels) in functional elements across the +human genome. ActiveDriverWGS detects coding and noncoding driver elements +using whole genome sequencing data.") + (license license:gpl3))) + +;; This is a CRAN package, but it depends on Bioconductor packages, so we put +;; it here. +(define-public r-activepathways + (package + (name "r-activepathways") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActivePathways" version)) + (sha256 + (base32 + "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20")))) + (properties + `((upstream-name . "ActivePathways"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-ggplot2" ,r-ggplot2) + ("r-metap" ,r-metap))) + (home-page "https://cran.r-project.org/web/packages/ActivePathways/") + (synopsis "Multivariate pathway enrichment analysis") + (description + "This package represents an integrative method of analyzing multi omics +data that conducts enrichment analysis of annotated gene sets. ActivePathways +uses a statistical data fusion approach, rationalizes contributing evidence +and highlights associated genes, improving systems-level understanding of +cellular organization in health and disease.") + (license license:gpl3))) + +(define-public r-bgmix + (package + (name "r-bgmix") + (version "1.46.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BGmix" version)) + (sha256 + (base32 + "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683")))) + (properties `((upstream-name . "BGmix"))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernsmooth" ,r-kernsmooth))) + (home-page "https://bioconductor.org/packages/BGmix/") + (synopsis "Bayesian models for differential gene expression") + (description + "This package provides fully Bayesian mixture models for differential +gene expression.") + (license license:gpl2))) + +(define-public r-bgx + (package + (name "r-bgx") + (version "1.52.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bgx" version)) + (sha256 + (base32 + "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm")))) + (properties `((upstream-name . "bgx"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-gcrma" ,r-gcrma) + ("r-rcpp" ,r-rcpp))) + (home-page "https://bioconductor.org/packages/bgx/") + (synopsis "Bayesian gene expression") + (description + "This package provides tools for Bayesian integrated analysis of +Affymetrix GeneChips.") + (license license:gpl2))) + +(define-public r-bhc + (package + (name "r-bhc") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BHC" version)) + (sha256 + (base32 + "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh")))) + (properties `((upstream-name . "BHC"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/BHC/") + (synopsis "Bayesian hierarchical clustering") + (description + "The method implemented in this package performs bottom-up hierarchical +clustering, using a Dirichlet Process (infinite mixture) to model uncertainty +in the data and Bayesian model selection to decide at each step which clusters +to merge. This avoids several limitations of traditional methods, for example +how many clusters there should be and how to choose a principled distance +metric. This implementation accepts multinomial (i.e. discrete, with 2+ +categories) or time-series data. This version also includes a randomised +algorithm which is more efficient for larger data sets.") + (license license:gpl3))) + +(define-public r-bicare + (package + (name "r-bicare") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BicARE" version)) + (sha256 + (base32 + "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs")))) + (properties `((upstream-name . "BicARE"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-gseabase" ,r-gseabase) + ("r-multtest" ,r-multtest))) + (home-page "http://bioinfo.curie.fr") + (synopsis "Biclustering analysis and results exploration") + (description + "This is a package for biclustering analysis and exploration of +results.") + (license license:gpl2))) + +(define-public r-bifet + (package + (name "r-bifet") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiFET" version)) + (sha256 + (base32 + "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k")))) + (properties `((upstream-name . "BiFET"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicranges" ,r-genomicranges) + ("r-poibin" ,r-poibin))) + (home-page "https://bioconductor.org/packages/BiFET") + (synopsis "Bias-free footprint enrichment test") + (description + "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are +over-represented in target regions compared to background regions after +correcting for the bias arising from the imbalance in read counts and GC +contents between the target and background regions. For a given TF k, BiFET +tests the null hypothesis that the target regions have the same probability of +having footprints for the TF k as the background regions while correcting for +the read count and GC content bias.") + (license license:gpl3))) + +(define-public r-rsbml + (package + (name "r-rsbml") + (version "2.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rsbml" version)) + (sha256 + (base32 + "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa")))) + (properties `((upstream-name . "rsbml"))) + (build-system r-build-system) + (inputs + `(("libsbml" ,libsbml) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-graph" ,r-graph))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://www.sbml.org") + (synopsis "R support for SBML") + (description + "This package provides an R interface to libsbml for SBML parsing, +validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") + (license license:artistic2.0))) + +(define-public r-hypergraph + (package + (name "r-hypergraph") + (version "1.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hypergraph" version)) + (sha256 + (base32 + "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m")))) + (properties `((upstream-name . "hypergraph"))) + (build-system r-build-system) + (propagated-inputs + `(("r-graph" ,r-graph))) + (home-page "https://bioconductor.org/packages/hypergraph") + (synopsis "Hypergraph data structures") + (description + "This package implements some simple capabilities for representing and +manipulating hypergraphs.") + (license license:artistic2.0))) + +(define-public r-hyperdraw + (package + (name "r-hyperdraw") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hyperdraw" version)) + (sha256 + (base32 + "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj")))) + (properties `((upstream-name . "hyperdraw"))) + (build-system r-build-system) + (inputs `(("graphviz" ,graphviz))) + (propagated-inputs + `(("r-graph" ,r-graph) + ("r-hypergraph" ,r-hypergraph) + ("r-rgraphviz" ,r-rgraphviz))) + (home-page "https://bioconductor.org/packages/hyperdraw") + (synopsis "Visualizing hypergraphs") + (description + "This package provides functions for visualizing hypergraphs.") + (license license:gpl2+))) + +(define-public r-biggr + (package + (name "r-biggr") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiGGR" version)) + (sha256 + (base32 + "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif")))) + (properties `((upstream-name . "BiGGR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-hyperdraw" ,r-hyperdraw) + ("r-hypergraph" ,r-hypergraph) + ("r-lim" ,r-lim) + ("r-limsolve" ,r-limsolve) + ("r-rsbml" ,r-rsbml) + ("r-stringr" ,r-stringr))) + (home-page "https://bioconductor.org/packages/BiGGR/") + (synopsis "Constraint based modeling using metabolic reconstruction databases") + (description + "This package provides an interface to simulate metabolic reconstruction +from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic +reconstruction databases. The package facilitates @dfn{flux balance +analysis} (FBA) and the sampling of feasible flux distributions. Metabolic +networks and estimated fluxes can be visualized with hypergraphs.") + (license license:gpl3+))) + +(define-public r-bigmemoryextras + (package + (name "r-bigmemoryextras") + (version "1.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bigmemoryExtras" version)) + (sha256 + (base32 + "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq")))) + (properties + `((upstream-name . "bigmemoryExtras"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bigmemory" ,r-bigmemory))) + (home-page "https://github.com/phaverty/bigmemoryExtras") + (synopsis "Extension of the bigmemory package") + (description + "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds +safety and convenience features to the @code{filebacked.big.matrix} class from +the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by +monitoring and gracefully restoring the connection to on-disk data and it also +protects against accidental data modification with a filesystem-based +permissions system. Utilities are provided for using @code{BigMatrix}-derived +classes as @code{assayData} matrices within the @code{Biobase} package's +@code{eSet} family of classes. @code{BigMatrix} provides some optimizations +related to attaching to, and indexing into, file-backed matrices with +dimnames. Additionally, the package provides a @code{BigMatrixFactor} class, +a file-backed matrix with factor properties.") + (license license:artistic2.0))) + +(define-public r-bigpint + (package + (name "r-bigpint") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bigPint" version)) + (sha256 + (base32 + "10vs0lzfyxp6sm4r9pxfwipjvzmmaqnvwn1hc5q37s5qz44fg0hk")))) + (properties `((upstream-name . "bigPint"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggally" ,r-ggally) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-hexbin" ,r-hexbin) + ("r-hmisc" ,r-hmisc) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-plotly" ,r-plotly) + ("r-plyr" ,r-plyr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape" ,r-reshape) + ("r-shiny" ,r-shiny) + ("r-shinycssloaders" ,r-shinycssloaders) + ("r-shinydashboard" ,r-shinydashboard) + ("r-stringr" ,r-stringr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/lindsayrutter/bigPint") + (synopsis "Big multivariate data plotted interactively") + (description + "This package provides methods for visualizing large multivariate +datasets using static and interactive scatterplot matrices, parallel +coordinate plots, volcano plots, and litre plots. It includes examples for +visualizing RNA-sequencing datasets and differentially expressed genes.") + (license license:gpl3))) + +(define-public r-chemminer + (package + (name "r-chemminer") + (version "3.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChemmineR" version)) + (sha256 + (base32 + "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga")))) + (properties `((upstream-name . "ChemmineR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-bh" ,r-bh) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dbi" ,r-dbi) + ("r-digest" ,r-digest) + ("r-dt" ,r-dt) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-png" ,r-png) + ("r-rcpp" ,r-rcpp) + ("r-rcurl" ,r-rcurl) + ("r-rjson" ,r-rjson) + ("r-rsvg" ,r-rsvg))) + (home-page "https://github.com/girke-lab/ChemmineR") + (synopsis "Cheminformatics toolkit for R") + (description + "ChemmineR is a cheminformatics package for analyzing drug-like small +molecule data in R. It contains functions for efficient processing of large +numbers of molecules, physicochemical/structural property predictions, +structural similarity searching, classification and clustering of compound +libraries with a wide spectrum of algorithms. In addition, it offers +visualization functions for compound clustering results and chemical +structures.") + (license license:artistic2.0))) + +(define-public r-bioassayr + (package + (name "r-bioassayr") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bioassayR" version)) + (sha256 + (base32 + "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw")))) + (properties `((upstream-name . "bioassayR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-chemminer" ,r-chemminer) + ("r-dbi" ,r-dbi) + ("r-matrix" ,r-matrix) + ("r-rjson" ,r-rjson) + ("r-rsqlite" ,r-rsqlite) + ("r-xml" ,r-xml))) + (home-page "https://github.com/TylerBackman/bioassayR") + (synopsis "Cross-target analysis of small molecule bioactivity") + (description + "bioassayR is a computational tool that enables simultaneous analysis of +thousands of bioassay experiments performed over a diverse set of compounds +and biological targets. Unique features include support for large-scale +cross-target analyses of both public and custom bioassays, generation of +@dfn{high throughput screening fingerprints} (HTSFPs), and an optional +preloaded database that provides access to a substantial portion of publicly +available bioactivity data.") + (license license:artistic2.0))) + +(define-public r-biobroom + (package + (name "r-biobroom") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biobroom" version)) + (sha256 + (base32 + "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb")))) + (properties `((upstream-name . "biobroom"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/StoreyLab/biobroom") + (synopsis "Turn Bioconductor objects into tidy data frames") + (description + "This package contains methods for converting standard objects +constructed by bioinformatics packages, especially those in Bioconductor, and +converting them to @code{tidy} data. It thus serves as a complement to the +@code{broom} package, and follows the same tidy, augment, glance division of +tidying methods. Tidying data makes it easy to recombine, reshape and +visualize bioinformatics analyses.") + ;; Any version of the LGPL. + (license license:lgpl3+))) + +(define-public r-graphite + (package + (name "r-graphite") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "graphite" version)) + (sha256 + (base32 + "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd")))) + (properties `((upstream-name . "graphite"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-checkmate" ,r-checkmate) + ("r-graph" ,r-graph) + ("r-httr" ,r-httr) + ("r-rappdirs" ,r-rappdirs))) + (home-page "https://bioconductor.org/packages/graphite/") + (synopsis "Networks from pathway databases") + (description + "Graphite provides networks derived from eight public pathway databases, +and automates the conversion of node identifiers (e.g. from Entrez IDs to gene +symbols).") + (license license:agpl3+))) + +(define-public r-reactomepa + (package + (name "r-reactomepa") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ReactomePA" version)) + (sha256 + (base32 + "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1")))) + (properties `((upstream-name . "ReactomePA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dose" ,r-dose) + ("r-enrichplot" ,r-enrichplot) + ("r-ggplot2" ,r-ggplot2) + ("r-ggraph" ,r-ggraph) + ("r-graphite" ,r-graphite) + ("r-igraph" ,r-igraph) + ("r-reactome-db" ,r-reactome-db))) + (home-page "https://guangchuangyu.github.io/software/ReactomePA") + (synopsis "Reactome pathway analysis") + (description + "This package provides functions for pathway analysis based on the +REACTOME pathway database. It implements enrichment analysis, gene set +enrichment analysis and several functions for visualization.") + (license license:gpl2))) + +(define-public r-ebarrays + (package + (name "r-ebarrays") + (version "2.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EBarrays" version)) + (sha256 + (base32 + "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13")))) + (properties `((upstream-name . "EBarrays"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-cluster" ,r-cluster) + ("r-lattice" ,r-lattice))) + (home-page "https://bioconductor.org/packages/EBarrays/") + (synopsis "Gene clustering and differential expression identification") + (description + "EBarrays provides tools for the analysis of replicated/unreplicated +microarray data.") + (license license:gpl2+))) + +(define-public r-bioccasestudies + (package + (name "r-bioccasestudies") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocCaseStudies" version)) + (sha256 + (base32 + "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd")))) + (properties + `((upstream-name . "BiocCaseStudies"))) + (build-system r-build-system) + (propagated-inputs `(("r-biobase" ,r-biobase))) + (home-page "https://bioconductor.org/packages/BiocCaseStudies") + (synopsis "Support for the case studies monograph") + (description + "This package provides software and data to support the case studies +monograph.") + (license license:artistic2.0))) + +(define-public r-biocgraph + (package + (name "r-biocgraph") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biocGraph" version)) + (sha256 + (base32 + "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw")))) + (properties `((upstream-name . "biocGraph"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-geneplotter" ,r-geneplotter) + ("r-graph" ,r-graph) + ("r-rgraphviz" ,r-rgraphviz))) + (home-page "https://bioconductor.org/packages/biocGraph/") + (synopsis "Graph examples and use cases in Bioinformatics") + (description + "This package provides examples and code that make use of the +different graph related packages produced by Bioconductor.") + (license license:artistic2.0))) + +(define-public r-experimenthub + (package + (name "r-experimenthub") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ExperimentHub" version)) + (sha256 + (base32 + "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24")))) + (properties `((upstream-name . "ExperimentHub"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-biocfilecache" ,r-biocfilecache) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-curl" ,r-curl) + ("r-rappdirs" ,r-rappdirs) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/ExperimentHub/") + (synopsis "Client to access ExperimentHub resources") + (description + "This package provides a client for the Bioconductor ExperimentHub web +resource. ExperimentHub provides a central location where curated data from +experiments, publications or training courses can be accessed. Each resource +has associated metadata, tags and date of modification. The client creates +and manages a local cache of files retrieved enabling quick and reproducible +access.") + (license license:artistic2.0))) + +(define-public r-multiassayexperiment + (package + (name "r-multiassayexperiment") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MultiAssayExperiment" version)) + (sha256 + (base32 + "0hqg0b0hd5msnb4jcn1nbfyy1n1llfkipy2ivwncivkmbdn8psp4")))) + (properties + `((upstream-name . "MultiAssayExperiment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tidyr" ,r-tidyr))) + (home-page "http://waldronlab.io/MultiAssayExperiment/") + (synopsis "Integration of multi-omics experiments in Bioconductor") + (description + "MultiAssayExperiment harmonizes data management of multiple assays +performed on an overlapping set of specimens. It provides a familiar +Bioconductor user experience by extending concepts from +@code{SummarizedExperiment}, supporting an open-ended mix of standard data +classes for individual assays, and allowing subsetting by genomic ranges or +rownames.") + (license license:artistic2.0))) + +(define-public r-bioconcotk + (package + (name "r-bioconcotk") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocOncoTK" version)) + (sha256 + (base32 + "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj")))) + (properties `((upstream-name . "BiocOncoTK"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bigrquery" ,r-bigrquery) + ("r-car" ,r-car) + ("r-complexheatmap" ,r-complexheatmap) + ("r-curatedtcgadata" ,r-curatedtcgadata) + ("r-dbi" ,r-dbi) + ("r-dplyr" ,r-dplyr) + ("r-dt" ,r-dt) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-ggpubr" ,r-ggpubr) + ("r-graph" ,r-graph) + ("r-httr" ,r-httr) + ("r-iranges" ,r-iranges) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rjson" ,r-rjson) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/BiocOncoTK") + (synopsis "Bioconductor components for general cancer genomics") + (description + "The purpose of this package is to provide a central interface to various +tools for genome-scale analysis of cancer studies.") + (license license:artistic2.0))) + +(define-public r-biocor + (package + (name "r-biocor") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioCor" version)) + (sha256 + (base32 + "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl")))) + (properties `((upstream-name . "BioCor"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-gseabase" ,r-gseabase) + ("r-matrix" ,r-matrix))) + (home-page "https://llrs.github.io/BioCor/") + (synopsis "Functional similarities") + (description + "This package provides tools to calculate functional similarities based +on the pathways described on KEGG and REACTOME or in gene sets. These +similarities can be calculated for pathways or gene sets, genes, or clusters +and combined with other similarities. They can be used to improve networks, +gene selection, testing relationships, and so on.") + (license license:expat))) + +(define-public r-biocpkgtools + (package + (name "r-biocpkgtools") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocPkgTools" version)) + (sha256 + (base32 + "0gyhb3071pxmvaxla7cxy9k97s3z3ynl62jnqz9jnkd53c7jnd53")))) + (properties `((upstream-name . "BiocPkgTools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocmanager" ,r-biocmanager) + ("r-biocviews" ,r-biocviews) + ("r-dplyr" ,r-dplyr) + ("r-dt" ,r-dt) + ("r-gh" ,r-gh) + ("r-graph" ,r-graph) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-httr" ,r-httr) + ("r-igraph" ,r-igraph) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-rbgl" ,r-rbgl) + ("r-readr" ,r-readr) + ("r-rex" ,r-rex) + ("r-rvest" ,r-rvest) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-xml2" ,r-xml2))) + (home-page "https://github.com/seandavi/BiocPkgTools") + (synopsis "Collection of tools for learning about Bioconductor packages") + (description + "Bioconductor has a rich ecosystem of metadata around packages, usage, +and build status. This package is a simple collection of functions to access +that metadata from R. The goal is to expose metadata for data mining and +value-added functionality such as package searching, text mining, and +analytics on packages.") + (license license:expat))) + +(define-public r-biocset + (package + (name "r-biocset") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocSet" version)) + (sha256 + (base32 + "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9")))) + (properties `((upstream-name . "BiocSet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dplyr" ,r-dplyr) + ("r-keggrest" ,r-keggrest) + ("r-plyr" ,r-plyr) + ("r-rlang" ,r-rlang) + ("r-rtracklayer" ,r-rtracklayer) + ("r-tibble" ,r-tibble))) + (home-page + "https://bioconductor.org/packages/BiocSet") + (synopsis + "Representing Different Biological Sets") + (description + "BiocSet displays different biological sets in a triple tibble format. +These three tibbles are @code{element}, @code{set}, and @code{elementset}. +The user has the abilty to activate one of these three tibbles to perform +common functions from the @code{dplyr} package. Mapping functionality and +accessing web references for elements/sets are also available in BiocSet.") + (license license:artistic2.0))) + +(define-public r-biocworkflowtools + (package + (name "r-biocworkflowtools") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocWorkflowTools" version)) + (sha256 + (base32 + "1v4bhnpdkmllm7aghms9b7369hkrgz7mn69wbrqg1x42pgkf30ad")))) + (properties + `((upstream-name . "BiocWorkflowTools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocstyle" ,r-biocstyle) + ("r-bookdown" ,r-bookdown) + ("r-git2r" ,r-git2r) + ("r-httr" ,r-httr) + ("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-rstudioapi" ,r-rstudioapi) + ("r-stringr" ,r-stringr) + ("r-usethis" ,r-usethis))) + (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") + (synopsis "Tools to aid the development of Bioconductor Workflow packages") + (description + "This package provides functions to ease the transition between +Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") + (license license:expat))) + +(define-public r-biodist + (package + (name "r-biodist") + (version "1.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bioDist" version)) + (sha256 + (base32 + "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q")))) + (properties `((upstream-name . "bioDist"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-kernsmooth" ,r-kernsmooth))) + (home-page "https://bioconductor.org/packages/bioDist/") + (synopsis "Different distance measures") + (description + "This package provides a collection of software tools for calculating +distance measures.") + (license license:artistic2.0))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bdb3ff761b..528b603476 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6669,14 +6669,14 @@ information as possible.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1jq7lam4dnbvz55lx93kcl9afl8xfjd6xs374d35m21bkay418kj")))) + "1xjr02qhldspjwd6y374wgik18fgywb6408wsz471i8b4ik98ckc")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -6684,7 +6684,7 @@ information as possible.") `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) - ("r-s4vectors" ,r-s4vectors) + ("r-biocgenerics" ,r-biocgenerics) ("r-survival" ,r-survival))) (home-page "https://bioconductor.org/packages/genefilter") (synopsis "Filter genes from high-throughput experiments") @@ -6696,14 +6696,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0fkk326addm2cw688gnmdzsmri5qx8j6ldnr4xin6kjnwicqhlqd")))) + "1lmbhznfs8dz9ipd53z4ccwvwxqwzx1ayw56jlrvlsambaj8fash")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -6733,14 +6733,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1b2s0vwm97g0wgm4ms0f4pqkqiqmxscnhg700aybl5vx0m2fa8xm")))) + "0sqqb65ckliif2nmvlvc7w49id59z0nvqcdz5gry8l2mn6azrf6a")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6776,14 +6776,14 @@ exploration of the results.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0m4w8n2711wr28znv646cfc7m5jqlr8friz334zdyjmhg7m2xkb7")))) + "0h2r60v339ajk5r6xq4iwwcpihdvf12fi8255byr2dhglzrd8xl7")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -6806,14 +6806,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.60.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "06brn9hl6lybx6hdfp1sycwj6wn1bjfi8xyhpy0v122v1z8d5mbz")))) + "0ixbkdirf08i400db587r262j52sdwdgk3884nxk5xkbhx2m6vg0")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -6829,14 +6829,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0vh53xk2prjbdkbr3hwfiflx1gh7ilrqs3j1p3lyd6syy3rn9n83")))) + "0kcb90sxlf19d5dxhdbqk9x62svky4262cccl0wxarbq6gf3bd57")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -6856,14 +6856,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.50.0") + (version "2.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "1n36xfnwn2np5f0lix9abvv9w6jb25jqz3xzvqzklz9s1af4k6x4")))) + "0ga0ij9hyzsxa5pavwmv35i8xggia2wygrk4m4z8an0qcvgy3v5g")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -6887,14 +6887,14 @@ analysis.") (define-public r-gostats (package (name "r-gostats") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "1a95i6awm2a8xv42fg2z3n29fg9z29i45kd80hxf6mvqqgzj80xp")))) + "19f4gxm3sbprqrnwzvskvywv6j4ibm8xkrbgg4h0fvh2b5331nwc")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -6918,14 +6918,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "1irqzdgsavjqsq0vva4966qh8qgn7xn9382dmhahm1hxb94qmi59")))) + "18v2khq53za1m8i9va1z4wynah55gccbb42nq769vdcw7bl80wpa")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -6960,14 +6960,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "18s5vpmw766pm64w7bwwfgpsv9yzhwclf0ya1rpqz8qslw7bbdjf")))) + "17r25v9wcglyma2v1c8fka80dm7fx86saxlsb2aprmwi4h3dhb0j")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -7007,14 +7007,14 @@ annotation infrastructure.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1p368qf8ab1vy8gl2j7rx0l7bvva4m7w06i364rqzs0sdyzlbm3y")))) + "0ywr8f6bfhg2ia3n4rmsxr4v1xqmlyhkwh0rvkgh3yqgnbvihndg")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -7240,13 +7240,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.52.2") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0qwrsd9fcpkv7hhzy1scnj7ahdxi6cjary28kqk6b36gkzmnrw4r")))) + "0yn8jys1900d31haayz0ppqk5y79mwjajwp4alz6pln3dbs70f3g")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7268,13 +7268,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.12.0") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "029x8r9rcx6zy0xixdpwxai4jv4ynb161821fzac6z4r8k418398")))) + "0nc1cbzp5zdwc0rss4r6v7cpgynmmnj3sczwmajr58nabkndwsvf")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -7294,13 +7294,13 @@ functionality.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1gkw9s6dhdryga9ap5yhvcqg9jsy4cn417ayqk1qiv6fy91fd124")))) + "1qnvl5yajgh67ijkq6gdsafri1k5hyw5gzn2ccqk9ymx6i2xd80g")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -7341,13 +7341,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.22.1") + (version "0.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0cpxqb18wd3pjd7bi8lry13sm5ffqahcvvxpk5pwm5xcj30cdlm9")))) + "1rr7ml3gn83g8fbvhgvryyzlh4p3qgpwcrsz6ii4y7gh1hqxggpx")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -7368,13 +7368,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.18.3") + (version "2.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "05rw2b2bwns443n7d6lf97zdv1jbqdii2nprhs6x852w73m2a2g3")))) + "0qssp04wfrc1r92hd3szy03n8sdz8vrqjdxa2mcrsc0k0n9bchz5")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7420,13 +7420,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0zkhms81b3jz30q7ag81a1mq1rgqg4izyfdvcni68gvn8gm7kdyk")))) + "07zljs2mfi8rf31g903f43v2f7767xbnflfrx9qjnmgf7bm039x0")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7448,13 +7448,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.26.8") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1wwimzviy2vklp80faz7sbbp74qcw2csbmlfgvzj7b785vwarpwg")))) + "1m7l6fbyik1b79v0h9qkmpa39svij1yiw24gxahbdqjg7fzsavh3")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7476,13 +7476,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "144x3d3b9a3q5jy4aqrk1nf2yavwjhwlf71s7qyr4x3ms3wmvf8i")))) + "009s7rzp78s2w6iybizina42qx2w8qv3xwjbkpqphmm451maykgs")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7515,13 +7515,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.40.6") + (version "3.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8")))) + "0cfynv6qbnar5rl7vjh5lvddd381g9wqx1zd6a7l130hf59mwswn")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7534,13 +7534,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.24.0") + (version "0.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "12y09pwy86h1za6cmaxs960r7fs0vjzhl0li8jn59vqq9liza1ap")))) + "0s2gg84yzl5ffkzp6n7kh0jjk1vd90z189f5hkfn18rn67cy2nv7")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -7570,13 +7570,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "1yid84gn0052v52h84685lvk854grl1wl65psmlmxx9yyykgc0jn")))) + "0xdds6ws7jjdfy4x3mb0qhy43kpxdmifmpw0jdk4wgw999zabb50")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -7599,13 +7599,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "15yl92niqamx3lmwd11zlk0xniibqnh1gi280iadxicmchi83npc")))) + "1gx41083dqlm59vwqdxvc4ny31x91j48mda9n3scg0f2zwasvqgl")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -7621,13 +7621,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.46.1") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "13nanz4nzy0mcda8ljz2g8d81hpqfz6jky7ydz5hpk0g2264b9ga")))) + "09piz1f0xpbb4amskx4ilby6lfrn27hhwk75il2c4lq6m3hr4w8s")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -7648,21 +7648,23 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.40.5") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1kjvxnkpsx3j2hji3cg3ka2gv8a9mg117lzzxyqjb7qa4zw7dipx")))) + "0difh4dsccjzhpfkvajy2adh98ym9164gd6clnsnic6qr6sk86ss")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) ("r-httr" ,r-httr) + ("r-openssl" ,r-openssl) ("r-progress" ,r-progress) - ("r-rcurl" ,r-rcurl) + ("r-rappdirs" ,r-rappdirs) ("r-stringr" ,r-stringr) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/biomaRt") @@ -7681,13 +7683,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1j6wbls4qgvi5gj99c51r00jhxrzxk3x3258wg7dcjzbfqypvyw3")))) + "1wgnad4089xn8yxl9md7xprgh3vswcbyxg7di0931ik6x54m9zws")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -7706,13 +7708,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0inrl97hli3qz6cfxcikc4picmbrqc8phdgqi18ynlvxy5ql64h4")))) + "0pq7g2hflx2cjlpwdj6mscw9hnxvlf5y50dxf48lbrf9r3q9kmyp")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -7732,13 +7734,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.0.3") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "03qfpaqbffirpnby88mv6h45njfapli28crdvg35h2zi2jkkmhvp")))) + "0hpdc88prpq1gcja89n5s1ndcg81523qrkbkm9gbhm7rm8wmi8cl")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -7777,13 +7779,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.10.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0l907ggxndn3f29zvsd5pppmp4c31rb22r6zkhvgph7xdxahyy6z")))) + "0329n1gbg2bq2vjhxfqqgakg75cdzcrcrgcwafjbg5zhkq86lc0q")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -7809,13 +7811,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f")))) + "04ljfw49ydgshrjv71qv9xr6y23a9vb8kp5fdjvpa8f6gzlb2a8m")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -7840,13 +7842,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.20.1") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0s3q97q4pgj5jwn4g95al44rahrwsncsf45v01v4071msx3xmjxq")))) + "065xvy4pkda0ajvl1b75iski95k1pnbhxwdq7vkfl8v55915vqh6")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7873,13 +7875,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.44.4") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0dnifr58j2si2qbnvap2wslz3xgjv3h4l7a6v7nmmc57hq6kdbym")))) + "0lp9xsm8kqrgpwgwj7qaqcv1z6qynbz084grlpwp94zsp2ppf0n6")))) (build-system r-build-system) (arguments `(#:phases @@ -7920,13 +7922,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.36.4") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k")))) + "0xd9rlsicycbanbcfhc97cj8b8vk94g7lkbmhk37w1511bq35wz5")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7985,13 +7987,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.36.0") + (version "2.37.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "09z42jwz5vh289ijz3x68zv5vmgkgcbhlp73vvmna1gld5lh5kz1")))) + "1cplr92aq3pa266ilvmg9xfmc95gag89b5jka04a5mh88j24y2ca")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -8018,13 +8020,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "0zwx42s73hc1vhn0v82i67mcixdwwc6n6q5h5vpnhpxlm4qwgqzp")))) + "0nn1b3h4hmnx5whf2cmzmyxdrcf4myj8c38rwr0sw4rc07xfzndy")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -8048,13 +8050,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "144jb889979cv3il2zxqk724v3sj1wnzjm3lkspxcvk29dbb9q8j")))) + "0igz1phjd1j9bg9z4kyy7j8v9bxi9sdwz4df26r51i2vavlbrf4q")))) (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) @@ -8068,13 +8070,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "1ljqscbmrmi5d4lzzvg2d86sqzch26yxw57d33qyid300wm60db2")))) + "1gxrq6s2hiyac69idh5r1nbr1s69n0hg4ap2skm4g6857av9pwqf")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -8095,13 +8097,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "06i711pwq9znd7plh0p25skxnnh5dyl61c33k9gma243wvlzmlkj")))) + "1sba928h23b67gr3i4yj1bg655g24l3bcgsf5gvymzrv5idrss1l")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -8169,14 +8171,14 @@ downloaded from Encode.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1z63imr1a24nqijpvxaxlakykcsadfqyxl2b3vlllncxnjjvb52b")))) + "0s94aahp8ma1crmp83dz65ifjwrx6wqi3q6005lmbp8yk2x1rkj4")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/seqLogo") @@ -8190,14 +8192,14 @@ Stephens (1990).") (define-public r-motifrg (package (name "r-motifrg") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "02c7fbjwdq7pk96bd2rn07l9r2hqy00s3hfpli5ybmwgvc9h9z4z")))) + "0s6wdr036lra9x93r9k8wvicbkgzypjh3jp46h92yacw8d829k0d")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs @@ -8271,13 +8273,13 @@ R/qtl, to better handle high-dimensional data and complex cross designs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1h0a2ps2rfk9azzps7p23sxj5z1giv8gcx0ypzgyz7fkr4xi9z7k")))) + "1xh7qan0w62mzsmanbx9vcj6ygdfhzw1abaxijkq7f4nh5w87idj")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -8313,21 +8315,22 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.16.3") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "1lmrfr32nrz36abn440kvzzck53y2320xjxqzs2jw7m2a9h3ryak")))) + "04inkq44lxwymqv51mxgaphasqjcdc9rl5p58imnrdm0kszs8prm")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, ;; which makes R abort the build. (arguments '(#:configure-flags '("--no-staged-install"))) (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) + `(("curl" ,curl) + ("r-zlibbioc" ,r-zlibbioc))) (inputs `(("zlib" ,zlib))) (native-inputs @@ -8343,14 +8346,14 @@ of other R packages who wish to make use of HTSlib.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "15q1q51dwl9qxfkf10yppw4m194ba03nq9plsrbj8fqj00v4729i")))) + "0699b0pqbs0dvs91yjibcjc90lxj9mg8rcml4a6wchfr9md7n74w")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8373,13 +8376,13 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz")))) + "1s3gvvxi1029d1vfwnjh21nnw3mlx08kcwz63891hml9y850cvsn")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -8474,14 +8477,14 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "1k3r06xj1nim1s8as1i7fykfa6fbb4x456kslbzdvbf83ppx34z3")))) + "08715l6swrlccviw7932v5hyrd2x4c6049vy9qnxk0lw3sp1zvsf")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8579,13 +8582,13 @@ factors bound at the specific regions.") (define-public r-tximport (package (name "r-tximport") - (version "1.12.3") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "070nx0blvvfhsnkbb5j899wy7dgalrh4xfcciir9l2xl67lna1zf")))) + "09r23n2812q89by0r0cz2fx1gfnmn3jb3hwbg61m52bika82pakj")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") @@ -8601,13 +8604,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.28.1") + (version "2.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "027cv1kh3xl66lrrahv2jgfmvgcwfpcj9dpgdj5fd9ybf5nyjcwb")))) + "18pv74jj4wr1981r92ss10qkgf5g1b09dsbz3im3j70a4l5l0df0")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) @@ -8628,13 +8631,13 @@ the available RAM.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "15qh4jwxxqsnb308nxzj99gckfk18rhp8g26q1xwgkr57zc5kcrx")))) + "1l9sxhlvnwn6327vgg02h11ppmqr2zr07ff8wmcng0i1jbqwa8q5")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -8933,14 +8936,14 @@ common bioinformatics tools.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1835nhrxcaqpqf1kxrsk1js8bf7x33z1n3bqjvm8404091acqyma")))) + "1ln6bn08xig3j6ryak1xfkjhvpnlm2vf1czz9hlj6f02299nbs6l")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8985,14 +8988,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0kv3k58wyyicq1hhq7bddh0v3b2ksz6fa47skvnp8f193csza9g6")))) + "0llg1zpxg7qnvja5f5w1z1xic0jdg6zc4mfn97h2sm44skxxcyl1")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -9025,13 +9028,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "1z687vpi5kwcqpnd6r74c5y72hcsbqlwg0bk95kksgpi81q710qj")))) + "0klwc0sbmrxj1lxbz16pl39rxjm0pi57gjw547hlgnac1p9fspzy")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9072,14 +9075,14 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.32.1") + (version "3.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0jj6klfha5v5qmx2sjblf1an6s2zqd7mmgsp7sfmh4k2jpqi3jm9")))) + "1bzms6idx30s4nxl610zwa8rjxsyxb5pf3vxsdfmxg8j4pab9gh1")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) @@ -9182,14 +9185,14 @@ as allowing spectra with different resolutions.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "12jjwmg58b4xbivxlw4pffq0qfi2c1c5hyrci0sfyphrc99fvx0i")))) + "1k1ggjgx2la8b21841a4ngkp6xfxwz0czv7x960r7i1jqif8y48z")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -9202,14 +9205,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1pr1pcrg3r3pccm5ag6l8ic6rpqbk9jnlb9mm7g4ak5jwrajbzjq")) + "1cwd7phlc5jbx6r6cznyfbdpvcin5fvsaasbbi65zn0s92a80r13")) (modules '((guix build utils))) (snippet '(begin @@ -9231,7 +9234,7 @@ proteomics packages.") #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.18.1. + ;; mzR version 2.20.0. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs @@ -9256,14 +9259,14 @@ previously been used in XCMS.") (define-public r-affyio (package (name "r-affyio") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "1s78hm51fgac3i2j4bbdy0z6g14370154s6km8lldc9zpahx8b6p")))) + "0sbkadxdlx7qzxc8z8iv90y6j9b2f62mk3i54dijjh56x3hjy3hb")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) @@ -9280,14 +9283,14 @@ CDF file formats.") (define-public r-affy (package (name "r-affy") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "05vz0vf3472s1ivfhc0gc8yz98y4rvvp7cf6kfbxhy1b23im1bgk")))) + "131za66wbaz9y86gvjqcc2yd1f2ngl2b796xw726g75djhdgxgap")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) @@ -9308,14 +9311,14 @@ analysis.") (define-public r-vsn (package (name "r-vsn") - (version "3.52.0") + (version "3.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1vqmyxg06kgq9m3w6n0jykqm4jgsjw879r4s216wlcq4xc94dh1r")))) + "1naqzb2m0km8fzr6chf9z71sisrwviy1fdi9b3hn4i8p18b4kqzh")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -9342,14 +9345,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0vnyg7jlmy7ain7gmjwhqyqr664znrvrdlh7zd63563vhb87qarn")))) + "1glcv096bn6pxlw89dlij1nzpwnjvrbxysvw2gm6qgm7rhxlaxrw")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9372,14 +9375,14 @@ specific parser.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "0svf4n7l0afy4wwgs6x8x4dm330r3311l5vmsxw2f0r4axkh3bzk")))) + "1wir67kfjm0m9gf0ki8qmvh45n4gx2k0wfl9pd1hp4g62fbrj1pj")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -9402,14 +9405,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.10.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0z63yqazkycq0zbbarq9ida6al35hv3g7g9g7s7bss4gh0hk7lhd")))) + "1z889xkfphqqmv31i8hh5xqyclv660ic26rfck5bjpgk3s2zzwi6")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9445,14 +9448,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb")))) + "0m71f2y12hmwvng45kzz4r4qrgc2jbd7j9gprmw8y5laawpdaifg")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs @@ -9484,13 +9487,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "3.1.1") + (version "3.1.2") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "084lr2fjdksshsmv1ww82bgn3a9mml7kswsidjrs89snabgvn360")))) + "0m1qi39snbmkkv1p07bzg1r7snc9x6a1y0dghvpk1nzgcfpmnsj4")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -9546,14 +9549,14 @@ discovery of differentially expressed genes and markers.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.14.0") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "0a1prl4jhbqpa85i2vyia1ks9iippzl8np50fvm9wx8kbjxna5l6")))) + "0cgdg650j4dl0b45pwaw49ib97dwjazrv9sqzkygrjmcnnfxry8x")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -9573,14 +9576,14 @@ classes.") (define-public r-deseq (package (name "r-deseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "0jppqrikg9qfqcfw5qd3m5c7bag9g23bc0kcpk5zfkk1wv09mnlm")))) + "14pys93gsl50xmq5pc7pp1g20v3ywlg0yzkkhwb3kiy8573xn9nc")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs @@ -9604,14 +9607,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "0mmc9bij17w4mfwcc566zbj5fvqgl8gfqs0qvj6ri4mbcql9jxb3")))) + "19mgzbv8yxgvw86wpq401l27q55ygawlngl775yavwccz1zbhjnj")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -9643,14 +9646,14 @@ global-scaling and full-quantile normalization.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "1kkyv7hkygacmksvld9gs3ycf6wlblqcwi11nny0hq3l0ha265v5")))) + "0zwf3ma6wf4zypl6bgjp0n72k2hmp0g16gzl4v3y4157rxcbpl0n")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -9667,14 +9670,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.16.1") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "0c773cmhng907839f0bq161jky7362lxxny36ac55qxiz1giqi8j")))) + "19vj3bk8jz68q84g3j8xs1s9bqz90lbwbciig1h45zvn2zc6087m")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -9682,6 +9685,7 @@ Shiny-based display methods for Bioconductor objects.") ("r-biocfilecache" ,r-biocfilecache) ("r-biocgenerics" ,r-biocgenerics) ("r-biocmanager" ,r-biocmanager) + ("r-biocversion" ,r-biocversion) ("r-curl" ,r-curl) ("r-dplyr" ,r-dplyr) ("r-httr" ,r-httr) @@ -9705,14 +9709,14 @@ by the user, helping with quick and reproducible access.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "03gggz29nf8kyy9clkifqr0xm8v0yb0kl0gjfb5c0vrjmwkfqvdf")))) + "1cys6frmbizc8bf933mwvvnr31sfya9ahcc0wm66pbd1x3mygkmk")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -9735,14 +9739,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.24.1") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0yxp3iajdy61q6mjgp1nxdgmf2yb58cvqmdgab7lqxr0ky1wkfkr")))) + "1cgjvv9n88y3ah21356mh8z2l08vjn42hjy8hcljsibknzc4v247")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -9759,14 +9763,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "08d5yg7n4rx4xsginc8bx0sycpj06pi1k7i44ff757444p20srwq")))) + "1qxfmg0id19iy3ia8h5nrvk3d1azqb28kl7m08i23654wb6b45c6")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -9788,14 +9792,14 @@ analysis using other methods.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "122g0yhpsm6fyvv38agp57clagl13h324rk06mlgb2xz104a1j4i")))) + "1x6q827ms2l5lwzha1vsgfrshh35n9f19jq57xagrqlafxgpz86s")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -9821,14 +9825,14 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1imnb72r10csl2h12sckic7hcsb8v2z0y3dyw1ax2fpykmsmq776")))) + "1pj6a6rmqckk033pkklk6hr4066rzavamy6w194rfdhind90rk0p")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -9853,14 +9857,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "0qirvhnbv4wd50ln4pqbk4dj6h2935ipf9p4sw1x62qqhwxidqk4")))) + "0knmncmkkf2ypyqfcl5s8nmyyf9nrzkqprzn9w3w8182c0v49r0s")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -9882,14 +9886,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.8.1") + (version "2.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "103z902104ljdp6s9y2dmgrl5wkdz8vvlbbqgk8r4drkg7m3d4lj")))) + "02lnpyp85zchmz404hr5381zmihvq4x9zgxdrbn2afi352vg0vab")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -9925,14 +9929,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "14azk69pmwlhza0mhsxigsg127w3mgsx9hhrbdcdqmy3vzfbfaqq")))) + "1bvfyh733mhka9zd00hrzpalgjs255c2blnxyf60ipzk5jg7yllb")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -9957,14 +9961,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.32.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "1lba1801ak0a4vz6f8jffp9d525q27p0dhi2bp4f68mvdwwl2994")))) + "04vvj907bgs67w8rb7n1haf80p6cd0qj5fdxw0dwryb455y35vir")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -9999,14 +10003,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "10s6hnffnrrsx3896adqdc5g55fzd5y6qhnp1mq0c641nw833rwd")))) + "13wzwh40anh8l53yp19bg4w5cpxykcaf228dc8cxvjndyib711qb")))) (build-system r-build-system) (arguments `(#:phases @@ -10086,14 +10090,14 @@ organisms via the @code{g:Profiler} toolkit.") (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "1n2cizb88g2ankngvhxv377gizg80y3fhlx67sgm0z4ilm6a30ql")))) + "1qr8dqjbmj1mdjbzbnxwzfrm8f02wqfsgic8ws5kv7pmsby63y4x")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (propagated-inputs @@ -10121,14 +10125,14 @@ and more.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "0drfd24a5pkrhzmpidlh717bgh2dm68mpn6vj1vlpkilfbkifl34")))) + "1xq1rjljg70h5mshdza56dis0iv1a20sivs6dav3w5jbdd1l5qkh")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -10180,14 +10184,14 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "0j7ggp63m5y88cxgi49vcql1s1avzifwvvd2hydj4lj3yrmzib48")))) + "085qsr73p8nyp435f15l4l1jkfd64bfd9gl4z496nfxdnqn95srz")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10218,14 +10222,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.14.3") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "154yvrvs8ik7ifcny1681cmqra0i163j00k4vbvkvl701p5gsp5q")))) + "0xpigfidmylfawy6vzshqnsw1lzjs4qms8q7zffij6bkvkv7920x")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -10233,8 +10237,6 @@ by Ernst and Kellis.") ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfiles" ,r-genomicfiles) - ("r-go-db" ,r-go-db) - ("r-homo-sapiens" ,r-homo-sapiens) ("r-httr" ,r-httr) ("r-matrix" ,r-matrix) ("r-rsamtools" ,r-rsamtools) @@ -10252,14 +10254,14 @@ defining LD blocks.") (define-public r-gqtlstats (package (name "r-gqtlstats") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 - "17xadfn8qh1pwzlpcbds5wrjr9bzhsnmv90wffxmp02hq20qkrh5")))) + "1dly4p9r4231hf31xg1nzqiyvjbcfjljfmhb88ic1jxwnvniyv2f")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs @@ -10306,14 +10308,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.28.3") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0347r1ly0vzpilflzbyzsjdf4cday294lw3fxzx61clblrmws1ki")))) + "1p7n4yc77272rd8ybsim3rcg6kf6wmc95pwwav40b754imxn263z")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -10352,14 +10354,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.16.1") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0d4krqx8zjniwp6k2vzwqgfws39w03x51kqiwd5dks1fp05sw4xh")))) + "038vhfsk2vs7inn5di093cmjbb81k7j0af385sg7l01jj70bdqq1")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10383,13 +10385,13 @@ EMBL-EBI GWAS catalog.") (define-public r-sushi (package (name "r-sushi") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "1hgh3jfcx0bh3fyvp85v7435hvsk3ah1hxx5117ss93v03iwjf1g")))) + "15xng21hd09fb234ravrry3b872zg82w8x9lijxab9n96xihcpz5")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs @@ -10405,13 +10407,13 @@ visualizations for publication-quality multi-panel figures.") (define-public r-fithic (package (name "r-fithic") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1qrxy4v8vmykrk8y6g3bs5wh5xhbs6pxyydbxy3vnj2mjirnxr6d")))) + "1irwkwi4afdj395134k31mvx7c2vpdd0rv8zrblnldascdsb04kc")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -10429,13 +10431,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "059a1xxv2kb0bb32flymg2s8ylhavnv3j8l4125rfidagcgxgzjq")))) + "0byahi0fz0dzjyklz8v9whax9ygg7gwb4pl1j3zbl6z8a9qx8pps")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -10458,14 +10460,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.12.3") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1037j6f0yyw4cf6p051810qamxi1sji5w4d0fgq5lyzyl5d36fm6")))) + "04hd02zd5jix5p2zg10asmwjg1fynqgmclbhbmk7fb6arx5hm11f")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -10474,6 +10476,7 @@ provided.") `(("r-biocgenerics" ,r-biocgenerics) ("r-delayedarray" ,r-delayedarray) ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) ("r-rhdf5" ,r-rhdf5) ("r-rhdf5lib" ,r-rhdf5lib) ("r-s4vectors" ,r-s4vectors))) @@ -10487,14 +10490,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0q68n5jm7w99paibj8vkxbdksbyrxilzwc9dkp3zf8zrdc5qfxzy")) + "17lhwnm9rqsvbqkvwp0m07vjrk63a4389p2y39zffv8fgznxqzd7")) (modules '((guix build utils))) (snippet '(begin @@ -10511,10 +10514,14 @@ block processing.") (for-each delete-file '("configure" "configure.ac")) ;; Do not make other packages link with the proprietary libsz. (substitute* "R/zzz.R" - (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'") - "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'") - (("'%s/libhdf5.a %s/libsz.a -lz'") - "'%s/libhdf5.a %s/libhdf5.a -lz'")) + (("'\"%s/libhdf5.a\" \"%s/libsz.a\" -lz'") + "'\"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'") + (("'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libsz.a\" -lz'") + "'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'") + (("'%s/libhdf5_hl.a %s/libhdf5.a %s/libsz.a -lz'") + "'%s/libhdf5_hl.a %s/libhdf5.a %s/libhdf5.a -lz'") + (("'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'") + "'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) @@ -10539,6 +10546,14 @@ block processing.") (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") + (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") + (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") + (("HDF5_HL_LIB=.*") + (string-append "HDF5_HL_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) + (("HDF5_HL_CXX_LIB=.*") + (string-append "HDF5_HL_CXX_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) ;; szip is non-free software (("cp \"\\$\\{SZIP_LIB\\}.*") "") (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) @@ -10558,18 +10573,19 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.0.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "14cz19fw97s8mhm9r2n5li44vckx069k8nqsyy64c3lkfm4vy4zx")))) + "1bpnlw2kdy9yc2vq948k980r0j25ipb80llhvn0j3kxjiwyfgs3i")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray))) + ("r-delayedarray" ,r-delayedarray) + ("r-matrix" ,r-matrix))) (home-page "https://bioconductor.org/packages/beachmat") (synopsis "Compiling Bioconductor to handle each matrix type") (description "This package provides a consistent C++ class interface for a @@ -10580,14 +10596,14 @@ matrices.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "0m3yjnv1njb4gyzcjfk7a0lz2vgggp2wjz382gqrb0qhhwcgfkj5")))) + "11pqb3cigi9xbhxq2k3n7z23v1ibd03ws1lcrh5c5ffgb33nlyw5")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -10607,13 +10623,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.12.2") + (version "1.14.5") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "16a17161xlhh6qpna9qxph3anlc7ydgyrczmy4alfiw8si7pzmxa")))) + "1c2p1dqz4lckk657v5g0labxrf0i21l0wa3rvszslmrszn60mkif")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10623,7 +10639,6 @@ libraries.") ("r-biocsingular" ,r-biocsingular) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dplyr" ,r-dplyr) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) ("r-matrix" ,r-matrix) @@ -10642,14 +10657,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.12.1") + (version "1.14.5") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "17mknpkvs7mgnlbf2hv9k7rwbx2vlg60yrwfyb8nn3nxsb6vm7yn")))) + "0ydy6gvpgpvrs4ryk1qvmmxp6cpaizs294jwg42jawxndkds1l3y")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10661,7 +10676,6 @@ quality control.") ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dqrng" ,r-dqrng) - ("r-dynamictreecut" ,r-dynamictreecut) ("r-edger" ,r-edger) ("r-igraph" ,r-igraph) ("r-limma" ,r-limma) @@ -10683,14 +10697,14 @@ variable and significantly correlated genes.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1riyzfsq4bd513hidkw3cfkx3jywk3x87j89q70v459xsdfdc95b")))) + "0mv2rl6a6l404piabcazxz1s6ars016pxhjf5v40hhr6y1r0wbqy")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -13419,14 +13433,14 @@ bgzipped text file that contains a pair of genomic coordinates per line.") (define-public python-pyfaidx (package (name "python-pyfaidx") - (version "0.5.4.2") + (version "0.5.7") (source (origin (method url-fetch) (uri (pypi-uri "pyfaidx" version)) (sha256 (base32 - "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8")))) + "02jvdx3ksy6w5gd29i1d0g0zsabbz7c14qg482ff7pza6sdl0b2i")))) (build-system python-build-system) (propagated-inputs `(("python-six" ,python-six))) @@ -15370,3 +15384,92 @@ methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.") ;; See https://github.com/dpryan79/MethylDackel/issues/85 (license license:expat))) + +(define-public python-gffutils + ;; The latest release is older more than a year than the latest commit + (let ((commit "4034c54600813b1402945e12faa91b3a53162cf1") + (revision "1")) + (package + (name "python-gffutils") + (version (git-version "0.9" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/daler/gffutils.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rwafjdnbir5wnk0ap06ww4lra3p5frhy7mfs03rlldgfnwxymsn")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + ;; Tests need to access the HOME directory + (setenv "HOME" "/tmp") + (invoke "nosetests" "-a" "!slow"))) + (add-after 'unpack 'make-gz-files-writable + (lambda _ + (for-each make-file-writable + (find-files "." "\\.gz")) + #t))))) + (propagated-inputs + `(("python-argcomplete" ,python-argcomplete) + ("python-argh" ,python-argh) + ("python-biopython" ,python-biopython) + ("python-pybedtools" ,python-pybedtools) + ("python-pyfaidx" ,python-pyfaidx) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six))) + (native-inputs + `(("python-nose" , python-nose))) + (home-page "https://github.com/daler/gffutils") + (synopsis "Tool for manipulation of GFF and GTF files") + (description + "python-gffutils is a Python package for working with and manipulating +the GFF and GTF format files typically used for genomic annotations. The +files are loaded into a SQLite database, allowing much more complex +manipulation of hierarchical features (e.g., genes, transcripts, and exons) +than is possible with plain-text methods alone.") + (license license:expat)))) + +(define-public libsbml + (package + (name "libsbml") + (version "5.18.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/sbml/libsbml/" + version "/stable/libSBML-" + version "-core-src.tar.gz")) + (sha256 + (base32 + "0slkagrk3nfi2qsksv6b1brj6zhx4bj4bkib2sdycvrcd10ql2lh")))) + (build-system cmake-build-system) + (arguments + `(#:test-target "test" + #:configure-flags + (list "-DWITH_CHECK=ON" + (string-append "-DLIBXML_LIBRARY=" + (assoc-ref %build-inputs "libxml2") + "/lib/libxml2.so") + (string-append "-DLIBXML_INCLUDE_DIR=" + (assoc-ref %build-inputs "libxml2") + "/include/libxml2")))) + (propagated-inputs + `(("libxml2" ,libxml2))) + (native-inputs + `(("check" ,check) + ("swig" ,swig))) + (home-page "http://sbml.org/Software/libSBML") + (synopsis "Process SBML files and data streams") + (description "LibSBML is a library to help you read, write, manipulate, +translate, and validate SBML files and data streams. The @dfn{Systems Biology +Markup Language} (SBML) is an interchange format for computer models of +biological processes. SBML is useful for models of metabolism, cell +signaling, and more. It continues to be evolved and expanded by an +international community.") + (license license:lgpl2.1+))) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 156e4c4cdd..21b32a1ab1 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019 nee <nee@cock.li> +;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -28,7 +29,7 @@ (define-module (gnu packages bootloaders) #:use-module (gnu packages) #:use-module (gnu packages admin) - #:use-module ((gnu packages algebra) #:select (bc)) + #:use-module (gnu packages algebra) #:use-module (gnu packages assembly) #:use-module (gnu packages base) #:use-module (gnu packages disk) @@ -661,9 +662,11 @@ it fits within common partitioning schemes.") ((#:phases phases) `(modify-phases ,phases (add-after 'unpack 'set-environment - (lambda* (#:key inputs #:allow-other-keys) - (let ((bl31 (string-append (assoc-ref inputs "firmware") - "/bl31.bin"))) + (lambda* (#:key native-inputs inputs #:allow-other-keys) + (let ((bl31 + (string-append + (assoc-ref (or native-inputs inputs) "firmware") + "/bl31.bin"))) (setenv "BL31" bl31) ;; This is necessary when we're using the bundled dtc. ;(setenv "PATH" (string-append (getenv "PATH") ":" @@ -677,6 +680,9 @@ it fits within common partitioning schemes.") (define-public u-boot-pine64-plus (make-u-boot-sunxi64-package "pine64_plus" "aarch64-linux-gnu")) +(define-public u-boot-pine64-lts + (make-u-boot-sunxi64-package "pine64-lts" "aarch64-linux-gnu")) + (define-public u-boot-pinebook (make-u-boot-sunxi64-package "pinebook" "aarch64-linux-gnu")) diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm index 68030376fc..14ecf246d4 100644 --- a/gnu/packages/commencement.scm +++ b/gnu/packages/commencement.scm @@ -2601,4 +2601,17 @@ an d binaries, plus debugging symbols in the @code{debug} output), and Binutils (define-public gcc-toolchain-9 (make-gcc-toolchain gcc-9)) +;; Provide the Fortran toolchain package only for the version of gfortran that +;; is used by Guix internally to build Fortran libraries, because combining +;; code compiled with different versions can cause problems. + +(define-public gfortran-toolchain + (package (inherit (make-gcc-toolchain gfortran)) + (synopsis "Complete GCC tool chain for Fortran development") + (description "This package provides a complete GCC tool chain for +Fortran development to be installed in user profiles. This includes +gfortran, as well as libc (headers and binaries, plus debugging symbols +in the @code{debug} output), and binutils."))) + + ;;; commencement.scm ends here diff --git a/gnu/packages/connman.scm b/gnu/packages/connman.scm index 1185561bc4..0098cb8dc7 100644 --- a/gnu/packages/connman.scm +++ b/gnu/packages/connman.scm @@ -137,7 +137,7 @@ sharing) to clients via USB, ethernet, WiFi, cellular and Bluetooth.") (define-public cmst (package (name "cmst") - (version "2017.09.19") + (version "2019.01.13") (source (origin (method url-fetch) @@ -145,7 +145,7 @@ sharing) to clients via USB, ethernet, WiFi, cellular and Bluetooth.") "https://github.com/andrew-bibb/cmst/releases/download/cmst-" version "/cmst-" version ".tar.xz")) (sha256 - (base32 "0dh4639n3l8a19svaagib41hdq5q7x70bnc28dmnwy4jflf38yrm")))) + (base32 "1cn6xz2rpkf5kx5d6p2x2lh85zppjacp59l6gj3n6x12p90al1vl")))) (inputs `(("qtbase" ,qtbase))) (native-inputs diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ad8c6ebe67..040c2ead4a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -73,6 +73,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages statistics) + #:use-module (gnu packages tcl) #:use-module (gnu packages tls) #:use-module (gnu packages web) #:use-module (gnu packages xorg)) @@ -729,10 +730,34 @@ objects in HTML format.") and vice-versa.") (license license:gpl2+))) +(define-public r-fastmap + (package + (name "r-fastmap") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "fastmap" version)) + (sha256 + (base32 + "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27")))) + (properties `((upstream-name . "fastmap"))) + (build-system r-build-system) + (home-page "https://r-lib.github.io/fastmap/") + (synopsis "Fast implementation of a key-value store") + (description + "This package provides a fast implementation of a key-value store. +Environments are commonly used as key-value stores, but every time a new key +is used, it is added to R's global symbol table, causing a small amount of +memory leakage. This can be problematic in cases where many different keys +are used. Fastmap avoids this memory leak issue by implementing the map using +data structures in C++.") + (license license:expat))) + (define-public r-shiny (package (name "r-shiny") - (version "1.2.0") + (version "1.4.0") (source (origin (method git-fetch) @@ -742,7 +767,7 @@ and vice-versa.") (file-name (git-file-name name version)) (sha256 (base32 - "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4")))) + "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7")))) (build-system r-build-system) (arguments `(#:modules ((guix build r-build-system) @@ -771,7 +796,7 @@ and vice-versa.") "/share/javascript/html5shiv.min.js")) (replace-file "json2-min.js" (string-append (assoc-ref inputs "js-json2") - "/share/javascript/json2.min.js")) + "/share/javascript/json2-min.js")) (replace-file "strftime/strftime-min.js" (string-append (assoc-ref inputs "js-strftime") "/share/javascript/strftime.min.js")) @@ -802,10 +827,15 @@ and vice-versa.") ("shiny.js" . "shiny.min.js") ("jquery.js" . - "jquery.min.js"))))) + "jquery.min.js") + ("legacy/jquery.js" . + "legacy/jquery.min.js") + ("showdown/src/showdown.js" . + "showdown/compressed/showdown.js"))))) #t))))) (propagated-inputs `(("r-crayon" ,r-crayon) + ("r-fastmap" ,r-fastmap) ("r-httpuv" ,r-httpuv) ("r-mime" ,r-mime) ("r-jsonlite" ,r-jsonlite) @@ -1262,14 +1292,14 @@ coordinates.") (define-public r-rgooglemaps (package (name "r-rgooglemaps") - (version "1.4.4") + (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "RgoogleMaps" version)) (sha256 (base32 - "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x")))) + "1acf0qc9597apcidjzrpvwhg9ihypr38jigc10jvqn33qbn1i9s7")))) (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs `(("r-png" ,r-png))) @@ -1394,13 +1424,13 @@ embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") (define-public r-amap (package (name "r-amap") - (version "0.8-17") + (version "0.8-18") (source (origin (method url-fetch) (uri (cran-uri "amap" version)) (sha256 (base32 - "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b")))) + "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -2747,14 +2777,14 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.17") + (version "0.10.18") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm")))) + "0r4626sk78fhlgivr0c7mwg9mj29ayr0iz5x90rdl4d5nc2r6kq4")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs @@ -3015,14 +3045,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.5.2") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn")))) + "177m249dxbf9pf249610qrl58v025ws41ipfihy66751pwsv2n8d")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -3206,14 +3236,14 @@ with the package @code{optim}.") (define-public r-ordinal (package (name "r-ordinal") - (version "2019.4-25") + (version "2019.12-10") (source (origin (method url-fetch) (uri (cran-uri "ordinal" version)) (sha256 (base32 - "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8")))) + "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -3306,14 +3336,14 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.6.0") + (version "3.7.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv")))) + "1wx1s1gc07iz63w4m8z0i1n5mc273f89grp5d3hfla7ypicjkasf")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -3769,14 +3799,14 @@ rules, boxes, trees, and Unicode symbols with ASCII alternatives.") (define-public r-argparser (package (name "r-argparser") - (version "0.4") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "argparser" version)) (sha256 (base32 - "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9")))) + "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x")))) (build-system r-build-system) (home-page "https://bitbucket.org/djhshih/argparser") (synopsis "Command-line argument parser") @@ -4102,14 +4132,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.17") + (version "0.18") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "0mgxrbj4gam2gvxfk26nq820vsfjggj81m2l7j9m8vp361k15r0w")))) + "04mpbhadixbxmnazj0q6cj973cajchscvyh1k6a5b3qk26dp5krr")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -4195,14 +4225,14 @@ detect possible inconsistencies.") (define-public r-sna (package (name "r-sna") - (version "2.4") + (version "2.5") (source (origin (method url-fetch) (uri (cran-uri "sna" version)) (sha256 (base32 - "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2")))) + "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k")))) (build-system r-build-system) (propagated-inputs `(("r-network" ,r-network) @@ -4248,14 +4278,14 @@ of these tests are also included.") (define-public r-ttr (package (name "r-ttr") - (version "0.23-5") + (version "0.23-6") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 - "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6")))) + "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs @@ -5598,14 +5628,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-renv (package (name "r-renv") - (version "0.9.1") + (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "0mwqpcay6v1hnvhggsrn1chvdlhi9hwvsswas8ysygfy5wxxz1sm")))) + "1jwnabryn77s29ybwdfzlnd7c8m05xmi69kp5qbvdxy2gjwjzcdr")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (home-page "https://rstudio.github.io/renv") @@ -6118,14 +6148,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rdpack (package (name "r-rdpack") - (version "0.11-0") + (version "0.11-1") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g")))) + "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs @@ -6686,14 +6716,14 @@ Group (Non-)Overlap considerations.") (define-public r-deriv (package (name "r-deriv") - (version "3.9.0") + (version "4.0") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 - "0hlqm216bg3l79gq6m0am0xz6vd3l2hgjnjm6lym3mkmgkka4kxw")))) + "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n")))) (properties `((upstream-name . "Deriv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/Deriv") @@ -7821,16 +7851,68 @@ analysis.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) +(define-public r-gee + (package + (name "r-gee") + (version "4.13-20") + (source + (origin + (method url-fetch) + (uri (cran-uri "gee" version)) + (sha256 + (base32 + "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak")))) + (properties `((upstream-name . "gee"))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/gee/") + (synopsis "Generalized estimation equation solver") + (description + "This package provides a solver for generalized estimation equations.") + (license license:gpl2))) + +(define-public r-tab + (package + (name "r-tab") + (version "4.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tab" version)) + (sha256 + (base32 + "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm")))) + (properties `((upstream-name . "tab"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-gee" ,r-gee) + ("r-knitr" ,r-knitr) + ("r-mass" ,r-mass) + ("r-survey" ,r-survey) + ("r-survival" ,r-survival) + ("r-xtable" ,r-xtable))) + (home-page "https://cran.r-project.org/web/packages/tab/") + (synopsis "Create summary tables for statistical reports") + (description + "This package contains functions for creating various types of summary +tables, e.g. comparing characteristics across levels of a categorical variable +and summarizing fitted generalized linear models, generalized estimating +equations, and Cox proportional hazards models. Functions are available to +handle data from simple random samples as well as complex surveys.") + (license license:gpl3+))) + (define-public r-dvmisc (package (name "r-dvmisc") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "dvmisc" version)) (sha256 - (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv")))) + (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi")))) (build-system r-build-system) (propagated-inputs `(("r-cubature" ,r-cubature) @@ -7840,10 +7922,10 @@ analysis.") ("r-mass" ,r-mass) ("r-mvtnorm" ,r-mvtnorm) ("r-pracma" ,r-pracma) - ("r-purrr" ,r-purrr) ("r-rbenchmark" ,r-rbenchmark) ("r-rcpp" ,r-rcpp) - ("r-survey" ,r-survey))) + ("r-survey" ,r-survey) + ("r-tab" ,r-tab))) (home-page "https://cran.r-project.org/web/packages/dvmisc/") (synopsis "Faster computation of common statistics and miscellaneous functions") (description @@ -8118,14 +8200,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-10") + (version "1.4-11") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19")))) + "0jw9661hs4396wz9vflk3rak0ryzj1cg2pnndsn1gb4fjyf2vlhb")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) @@ -8403,14 +8485,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.4.0") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "0lxpmp9smn5r3xvfik36nr608wcpmmximjh0v2sckyvjf7hnb4s0")))) + "1pcjmqqm178dvdcpzkv5p4sj7glsppcny7znljb2nqkxh539a59p")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) @@ -8430,22 +8512,20 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.13.0") + (version "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "0ryfbaav0k874kbwmhbiv7fan93dmkpaimm1iw5kryjhhs3917lb")))) + "1djz82xww86h8f33m2vm40lliicppgyhm6hyn3h6rzrqjrlrsmdw")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-insight" ,r-insight) + `(("r-insight" ,r-insight) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) ("r-sjlabelled" ,r-sjlabelled) ("r-sjmisc" ,r-sjmisc))) (home-page "https://github.com/strengejacke/ggeffects") @@ -9011,14 +9091,14 @@ experiments using ANOVA or mixed models.") (define-public r-lmertest (package (name "r-lmertest") - (version "3.1-0") + (version "3.1-1") (source (origin (method url-fetch) (uri (cran-uri "lmerTest" version)) (sha256 (base32 - "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b")))) + "0r2vvs3nl6p8xla3gd943khb4ixp0alvspqpnz2y6n3wk8zgh3jj")))) (properties `((upstream-name . "lmerTest"))) (build-system r-build-system) (propagated-inputs @@ -9456,14 +9536,14 @@ for evolution along a phylogenetic tree.") (define-public r-fmsb (package (name "r-fmsb") - (version "0.6.3") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 - "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5")))) + "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45")))) (build-system r-build-system) (home-page "http://minato.sip21c.org/msb/") (synopsis "Functions for medical statistics book with demographic data") @@ -9637,14 +9717,14 @@ Processing.") (define-public r-tm (package (name "r-tm") - (version "0.7-6") + (version "0.7-7") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 - "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r")))) + "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs @@ -9733,13 +9813,13 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy")))) + (base32 "1bnzs62z2l8ck2h9gabmxvayizv4nfn8dmyzry83fv0cspjbyiv7")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) @@ -11053,13 +11133,13 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.") (define-public r-spam (package (name "r-spam") - (version "2.5-0") + (version "2.5-1") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 - (base32 "1wfv45jq8zy8kyjr308zicc1461y1777qll1cy6lw4071f9rvba2")))) + (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi")))) (build-system r-build-system) (propagated-inputs `(("r-dotcall64" ,r-dotcall64))) @@ -12402,14 +12482,14 @@ compatible with @code{rzmq} are also provided.") (define-public r-repr (package (name "r-repr") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 - "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc")))) + "0wn9fdddqjgn0bdfl75x89rcxahbgqs324bhg0pfq6va5q2mlbbw")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -15940,27 +16020,28 @@ programming problems.") `(("gfortran" ,gfortran))) (home-page "https://desolve.r-forge.r-project.org/") (synopsis "Solvers for initial value problems of differential equations") - (description "This package provides functions that solve initial -value problems of a system of first-order ordinary differential equations (ODE), -of partial differential equations (PDE), of differential algebraic equations -(DAE), and of delay differential equations. The functions provide an interface -to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, -to the FORTRAN functions dvode and daspk and a C-implementation of solvers of -the Runge-Kutta family with fixed or variable time steps. The package contains -routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial -differential equations (PDE) that have been converted to ODEs by numerical -differencing.") + (description "This package provides functions that solve initial value +problems of a system of first-order @dfn{ordinary differential +equations} (ODE), of @dfn{partial differential equations} (PDE), of +@dfn{differential algebraic equations} (DAE), and of delay differential +equations. The functions provide an interface to the FORTRAN functions +@code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK +collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a +C-implementation of solvers of the Runge-Kutta family with fixed or variable +time steps. The package contains routines designed for solving ODEs resulting +from 1-D, 2-D and 3-D partial differential equations that have been converted +to ODEs by numerical differencing.") (license license:gpl2+))) (define-public r-pracma (package (name "r-pracma") - (version "2.2.5") + (version "2.2.9") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g")))) + (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") @@ -16012,3 +16093,2876 @@ graphics directly in the terminal window. This package provides a basic plotting function (and equivalents of curve, density, acf and barplot) as well as a boxplot function.") (license license:lgpl3+))) + +(define-public r-bio3d + (package + (name "r-bio3d") + (version "2.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "bio3d" version)) + (sha256 + (base32 + "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s")))) + (properties `((upstream-name . "bio3d"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "http://thegrantlab.org/bio3d/") + (synopsis "Biological structure analysis") + (description + "This package provides utilities to process, organize and explore protein +structure, sequence and dynamics data. Features include the ability to read +and write structure, sequence and dynamic trajectory data, perform sequence +and structure database searches, data summaries, atom selection, alignment, +superposition, rigid core identification, clustering, torsion analysis, +distance matrix analysis, structure and sequence conservation analysis, normal +mode analysis, principal component analysis of heterogeneous structure data, +and correlation network analysis from normal mode and molecular dynamics data. +In addition, various utility functions are provided to enable the statistical +and graphical power of the R environment to work with biological sequence and +structural data.") + (license license:gpl2+))) + +(define-public r-bios2cor + (package + (name "r-bios2cor") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "Bios2cor" version)) + (sha256 + (base32 + "1rrz0vs6wbkwys3l5jv1rdnlhyb4r1q9pv7jlnmsx6c1b4f4vz5n")))) + (properties `((upstream-name . "Bios2cor"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bigmemory" ,r-bigmemory) + ("r-bio3d" ,r-bio3d) + ("r-circular" ,r-circular) + ("r-igraph" ,r-igraph))) + (home-page "https://cran.r-project.org/web/packages/Bios2cor/") + (synopsis "From biological sequences and simulations to correlation analysis") + (description + "This package provides utilities for computation and analysis of +correlation/covariation in multiple sequence alignments and in side chain +motions during molecular dynamics simulations. Features include the +computation of correlation/covariation scores using a variety of scoring +functions between either sequence positions in alignments or side chain +dihedral angles in molecular dynamics simulations and utilities to analyze the +correlation/covariation matrix through a variety of tools including network +representation and principal components analysis. In addition, several +utility functions are based on the R graphical environment to provide friendly +tools for help in data interpretation.") + (license license:gpl2+))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-networkd3 + (package + (name "r-networkd3") + (version "0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "networkD3" version)) + (sha256 + (base32 + "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k")) + (snippet + '(begin + (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js") + #t)))) + (properties `((upstream-name . "networkD3"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "d3.v4.js") + "d3-4.5.0/d3.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (call-with-output-file target + (lambda (port) + (dump-port minified port))))) + sources targets)))) + #t))))) + (native-inputs + `(("uglify-js" ,uglify-js) + ;; NOTE: Make sure that this version of d3 is still valid when + ;; upgrading the package. + ("d3.v4.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v4.js") + (sha256 + (base32 + "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) + (propagated-inputs + `(("r-htmlwidgets" ,r-htmlwidgets) + ("r-igraph" ,r-igraph) + ("r-magrittr" ,r-magrittr))) + (home-page "https://cran.r-project.org/package=networkD3") + (synopsis "D3 JavaScript network graphs from R") + (description + "This package creates D3 JavaScript network, tree, dendrogram, and Sankey +graphs from R.") + (license license:gpl3+))) + +(define-public r-aasea + (package + (name "r-aasea") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "aaSEA" version)) + (sha256 + (base32 + "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h")))) + (properties `((upstream-name . "aaSEA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bios2cor" ,r-bios2cor) + ("r-dt" ,r-dt) + ("r-hmisc" ,r-hmisc) + ("r-magrittr" ,r-magrittr) + ("r-networkd3" ,r-networkd3) + ("r-plotly" ,r-plotly) + ("r-seqinr" ,r-seqinr) + ("r-shiny" ,r-shiny) + ("r-shinydashboard" ,r-shinydashboard))) + (home-page "https://cran.r-project.org/web/packages/aaSEA/") + (synopsis "Amino acid substitution effect analyzer") + (description + "Given a protein multiple sequence alignment, it is a daunting task to +assess the effects of substitutions along sequence length. The aaSEA package +is intended to help researchers to rapidly analyze property changes caused by +single, multiple and correlated amino acid substitutions in proteins.") + (license license:gpl3))) + +(define-public r-abacus + (package + (name "r-abacus") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABACUS" version)) + (sha256 + (base32 + "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i")))) + (properties `((upstream-name . "ABACUS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-shiny" ,r-shiny))) + (home-page "https://shiny.abdn.ac.uk/Stats/apps/") + (synopsis "Apps-based activities for communicating and understanding statistics") + (description + "This package provides a set of Shiny apps for effective communication +and understanding in statistics. The current version includes properties of +normal distribution, properties of sampling distribution, one-sample z and t +tests, two samples independent (unpaired) t test and analysis of variance.") + (license license:gpl3))) + +(define-public r-abc-rap + (package + (name "r-abc-rap") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABC.RAP" version)) + (sha256 + (base32 + "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk")))) + (properties `((upstream-name . "ABC.RAP"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ABC.RAP/") + (synopsis "Array-based CpG region analysis pipeline") + (description + "This package aims to identify candidate genes that are differentially +methylated between cases and controls. It applies Student's t-test and delta +beta analysis to identify candidate genes containing multiple CpG sites.") + (license license:gpl3))) + +(define-public r-abcadm + (package + (name "r-abcadm") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abcADM" version)) + (sha256 + (base32 + "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10")))) + (properties `((upstream-name . "abcADM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/abcADM/") + (synopsis "Fit accumulated damage models and estimate reliability using ABC") + (description + "This package provides tools to estimate parameters of accumulated +damage (load duration) models based on failure time data under a Bayesian +framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess +long-term reliability under stochastic load profiles.") + (license license:gpl3))) + +(define-public r-rglpk + (package + (name "r-rglpk") + (version "0.6-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rglpk" version)) + (sha256 + (base32 + "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2")))) + (properties `((upstream-name . "Rglpk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-slam" ,r-slam))) + (inputs + `(("glpk" ,glpk))) + (home-page "http://R-Forge.R-project.org/projects/rglp/") + (synopsis "R interface to the GNU Linear Programming Kit") + (description + "This package provides an R interface to the GNU Linear Programming Kit, +software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed +integer linear programming} (MILP) and other related problems.") + ;; Either license + (license (list license:gpl2 license:gpl3)))) + +(define-public r-abcdefba + (package + (name "r-abcdefba") + (version "0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "abcdeFBA" version)) + (sha256 + (base32 + "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4")))) + (properties `((upstream-name . "abcdeFBA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-corrplot" ,r-corrplot) + ("r-lattice" ,r-lattice) + ("r-rgl" ,r-rgl) + ("r-rglpk" ,r-rglpk))) + (home-page "https://cran.r-project.org/web/packages/abcdeFBA/") + (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package") + (description + "This package provides functions for Constraint Based Simulation using +Flux Balance Analysis and informative analysis of the data generated during +simulation.") + (license license:gpl2))) + +(define-public r-abcrlda + (package + (name "r-abcrlda") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abcrlda" version)) + (sha256 + (base32 + "0j29ifsvmxfx2g6v4bpbb4s6miwfpf4vlkpbgj6f2q078s4clc85")))) + (properties `((upstream-name . "abcrlda"))) + (build-system r-build-system) + (home-page "https://ieeexplore.ieee.org/document/8720003/") + (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis") + (description + "This package offers methods to perform @dfn{asymptotically +bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for +cost-sensitive binary classification. The bias-correction is an estimate of +the bias term added to regularized discriminant analysis that minimizes the +overall risk.") + (license license:gpl3))) + +(define-public r-abemus + (package + (name "r-abemus") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abemus" version)) + (sha256 + (base32 + "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb")))) + (properties `((upstream-name . "abemus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table))) + (home-page "https://cran.r-project.org/web/packages/abemus/") + (synopsis "Adaptive base error model in ultra-deep sequencing data") + (description + "This package provides an implementation of @dfn{Adaptive Base Error +Model in Ultra-deep Sequencing data} (ABEMUS), which combines +platform-specific genetic knowledge and empirical signal to readily detect and +quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating +cell free DNA} (cfDNA).") + (license license:gpl3))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-rintrojs + (package + (name "r-rintrojs") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rintrojs" version)) + (sha256 + (base32 + "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427")))) + (properties `((upstream-name . "rintrojs"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/javascript/introjs/" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "intro.js") + "intro.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (call-with-output-file target + (lambda (port) + (dump-port minified port))))) + sources targets)))) + #t))))) + (native-inputs + `(("uglify-js" ,uglify-js) + ("intro.js" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js") + (sha256 + (base32 + "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8")))))) + (propagated-inputs + `(("r-jsonlite" ,r-jsonlite) + ("r-shiny" ,r-shiny))) + (home-page "https://github.com/carlganz/rintrojs") + (synopsis "Wrapper for the Intro.js library") + (description + "This package provides a wrapper for the @url{http://www.introjs.com, +Intro.js} library. This package makes it easy to include step-by-step +introductions, and clickable hints in a Shiny application. It supports both +static introductions in the UI, and programmatic introductions from the +server-side.") + (license license:agpl3+))) + +(define-public r-sysfonts + (package + (name "r-sysfonts") + (version "0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "sysfonts" version)) + (sha256 + (base32 + "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43")))) + (properties `((upstream-name . "sysfonts"))) + (build-system r-build-system) + (inputs + `(("freetype" ,freetype) + ("libpng" ,libpng) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/yixuan/sysfonts") + (synopsis "Loading fonts into R") + (description + "This is a package to simplify loading of system fonts and Google Fonts +into R, in order to support other packages.") + (license license:gpl2))) + +(define-public r-showtextdb + (package + (name "r-showtextdb") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "showtextdb" version)) + (sha256 + (base32 + "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh")))) + (properties `((upstream-name . "showtextdb"))) + (build-system r-build-system) + (propagated-inputs + `(("r-sysfonts" ,r-sysfonts))) + (home-page "https://cran.r-project.org/web/packages/showtextdb/") + (synopsis "Font files for the 'showtext' package") + (description + "This package provides font files that can be used by the @code{showtext} +package.") + (license license:asl2.0))) + +(define-public r-showtext + (package + (name "r-showtext") + (version "0.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "showtext" version)) + (sha256 + (base32 + "1ihgqzfia36b0n9aa41p1w98wxxvs1lxh1zz0570hbfqmph1sk73")))) + (properties `((upstream-name . "showtext"))) + (build-system r-build-system) + (inputs + `(("freetype" ,freetype) + ("libpng" ,libpng) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-showtextdb" ,r-showtextdb) + ("r-sysfonts" ,r-sysfonts))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/yixuan/showtext") + (synopsis "Using fonts more easily in R graphs") + (description + "This package aims to make it easy to use various types of +fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports +most output formats of R graphics including PNG, PDF and SVG. Text glyphs +will be converted into polygons or raster images, hence after the plot has +been created, it no longer relies on the font files. No external software +such as Ghostscript is needed to use this package.") + (license license:asl2.0))) + +(define-public r-emojifont + (package + (name "r-emojifont") + (version "0.5.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "emojifont" version)) + (sha256 + (base32 + "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k")))) + (properties `((upstream-name . "emojifont"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-proto" ,r-proto) + ("r-showtext" ,r-showtext) + ("r-sysfonts" ,r-sysfonts))) + (home-page "https://guangchuangyu.github.io/emojifont") + (synopsis "Emoji and Font Awesome in R graphics") + (description + "This package enables the use of emoji and the Font Awesome glyphs in +both base and ggplot2 graphics.") + (license license:artistic2.0))) + +(define-public r-abstractr + (package + (name "r-abstractr") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abstractr" version)) + (sha256 + (base32 + "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig")))) + (properties `((upstream-name . "abstractr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-colourpicker" ,r-colourpicker) + ("r-emojifont" ,r-emojifont) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-rintrojs" ,r-rintrojs) + ("r-shiny" ,r-shiny) + ("r-shinythemes" ,r-shinythemes))) + (home-page "https://matt-kumar.shinyapps.io/portfolio") + (synopsis "R-Shiny application for creating visual abstracts") + (description + "This package provides an R Shiny application to create visual abstracts +for original research. A variety of user defined options and formatting are +included.") + (license license:gpl3))) + +(define-public r-abtest + (package + (name "r-abtest") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abtest" version)) + (sha256 + (base32 + "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws")))) + (properties `((upstream-name . "abtest"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-mvtnorm" ,r-mvtnorm) + ("r-plotrix" ,r-plotrix) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-sn" ,r-sn) + ("r-truncnorm" ,r-truncnorm) + ("r-vgam" ,r-vgam))) + (home-page "https://cran.r-project.org/web/packages/abtest/") + (synopsis "Bayesian A/B testing") + (description + "This package provides functions for Bayesian A/B testing including prior +elicitation options based on Kass and Vaidyanathan (1992) +@url{doi:10.1111/j.2517-6161.1992.tb01868.x}.") + (license license:gpl2+))) + +(define-public r-accept + (package + (name "r-accept") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "accept" version)) + (sha256 + (base32 + "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx")))) + (properties `((upstream-name . "accept"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-extrafont" ,r-extrafont) + ("r-mass" ,r-mass) + ("r-plotly" ,r-plotly) + ("r-stringr" ,r-stringr) + ("r-viridis" ,r-viridis))) + (home-page "https://cran.r-project.org/web/packages/accept/") + (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)") + (description + "This package allows clinicians to predict the rate and severity of +future acute exacerbation in @dfn{Chronic Obstructive Pulmonary +Disease} (COPD) patients, based on the clinical prediction model published in +Adibi et al. (2019) @url{doi:10.1101/651901}.") + (license license:gpl3))) + +(define-public r-smpracticals + (package + (name "r-smpracticals") + (version "1.4-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "SMPracticals" version)) + (sha256 + (base32 + "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf")))) + (properties `((upstream-name . "SMPracticals"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ellipse" ,r-ellipse) + ("r-mass" ,r-mass) + ("r-nlme" ,r-nlme) + ("r-survival" ,r-survival))) + (home-page "http://statwww.epfl.ch/davison/SM/") + (synopsis "Practicals for use with Davison (2003) Statistical Models") + (description + "This package contains the datasets and a few functions for use with the +practicals outlined in Appendix A of the book Statistical Models (Davison, +2003, Cambridge University Press). The practicals themselves can be found at +@url{http://statwww.epfl.ch/davison/SM/}.") + (license license:gpl2+))) + +(define-public r-fgui + (package + (name "r-fgui") + (version "1.0-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "fgui" version)) + (sha256 + (base32 + "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv")))) + (properties `((upstream-name . "fgui"))) + (build-system r-build-system) + (home-page + "https://sites.google.com/site/thomashoffmannproject/software/fgui") + (synopsis "Create GUI for R functions") + (description + "Rapidly create a GUI for a function you created by automatically +creating widgets for arguments of the function. This package automatically +parses help routines for context-sensitive help to these arguments. The +interface is essentially a wrapper to some Tcl/Tk routines to both simplify +and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be +incorporated into the interface for greater customization for the more +experienced.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-tcltk2 + (package + (name "r-tcltk2") + (version "1.2-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "tcltk2" version)) + (sha256 + (base32 + "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d")))) + (properties `((upstream-name . "tcltk2"))) + (build-system r-build-system) + (inputs + `(("tcl" ,tcl) + ("tk" ,tk))) + (home-page "http://www.sciviews.org/SciViews-R") + (synopsis "Tcl/Tk additions") + (description + "This package provides a series of additional Tcl commands and Tk widgets +with style and various functions to supplement the tcltk package") + (license license:lgpl3))) + +(define-public r-accrual + (package + (name "r-accrual") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "accrual" version)) + (sha256 + (base32 + "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z")))) + (properties `((upstream-name . "accrual"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fgui" ,r-fgui) + ("r-smpracticals" ,r-smpracticals) + ("r-tcltk2" ,r-tcltk2))) + (home-page "https://cran.r-project.org/web/packages/accrual/") + (synopsis "Bayesian accrual prediction") + (description + "Subject recruitment for medical research is challenging. Slow patient +accrual leads to delay in research. Accrual monitoring during the process of +recruitment is critical. Researchers need reliable tools to manage the +accrual rate. This package provides an implementation of a Bayesian method +that integrates researcher's experience on previous trials and data from the +current study, providing reliable prediction on accrual rate for clinical +studies. It provides functions for Bayesian accrual prediction which can be +easily used by statisticians and clinical researchers.") + (license license:gpl2))) + +(define-public r-accrued + (package + (name "r-accrued") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "accrued" version)) + (sha256 + (base32 + "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5")))) + (properties `((upstream-name . "accrued"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/accrued/") + (synopsis "Data quality visualization tools for partially accruing data") + (description + "This is a package for visualizing data quality of partially accruing +data.") + (license license:gpl3))) + +(define-public r-mda + (package + (name "r-mda") + (version "0.4-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "mda" version)) + (sha256 + (base32 + "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh")))) + (properties `((upstream-name . "mda"))) + (build-system r-build-system) + (propagated-inputs `(("r-class" ,r-class))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/mda/") + (synopsis "Mixture and flexible discriminant analysis") + (description + "This is a package for mixture and flexible discriminant analysis, +@dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.") + (license license:gpl2))) + +(define-public r-elasticnet + (package + (name "r-elasticnet") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "elasticnet" version)) + (sha256 + (base32 + "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb")))) + (properties `((upstream-name . "elasticnet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lars" ,r-lars))) + (home-page "http://www.stat.umn.edu/~hzou") + (synopsis "Elastic-Net for sparse estimation and sparse PCA") + (description + "This package provides functions for fitting the entire solution path of +the Elastic-Net and also provides functions for estimating sparse Principal +Components. The Lasso solution paths can be computed by the same function.") + (license license:gpl2+))) + +(define-public r-sparselda + (package + (name "r-sparselda") + (version "0.1-9") + (source + (origin + (method url-fetch) + (uri (cran-uri "sparseLDA" version)) + (sha256 + (base32 + "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb")))) + (properties `((upstream-name . "sparseLDA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-elasticnet" ,r-elasticnet) + ("r-mass" ,r-mass) + ("r-mda" ,r-mda))) + (home-page "http://www.imm.dtu.dk/~lhc") + (synopsis "Sparse discriminant analysis") + (description + "This package performs sparse linear discriminant analysis for Gaussians +and mixture of Gaussian models.") + (license license:gpl2+))) + +(define-public r-accsda + (package + (name "r-accsda") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "accSDA" version)) + (sha256 + (base32 + "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61")))) + (properties `((upstream-name . "accSDA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-ggthemes" ,r-ggthemes) + ("r-gridextra" ,r-gridextra) + ("r-mass" ,r-mass) + ("r-rarpack" ,r-rarpack) + ("r-sparselda" ,r-sparselda))) + (home-page "https://github.com/gumeo/accSDA/wiki") + (synopsis "Accelerated sparse discriminant analysis") + (description + "This package provides an implementation of sparse linear discriminant +analysis, which is a supervised classification method for multiple classes. +Various novel optimization approaches to this problem are implemented +including @dfn{alternating direction method of multipliers} (ADMM), +@dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG). +Functions for performing cross validation are also supplied along with basic +prediction and plotting functions. @dfn{Sparse zero variance +discriminant} (SZVD) analysis is also included in the package.") + (license license:gpl2+))) + +(define-public r-ace2fastq + (package + (name "r-ace2fastq") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ace2fastq" version)) + (sha256 + (base32 + "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic")))) + (properties `((upstream-name . "ace2fastq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-stringr" ,r-stringr))) + (home-page "https://github.com/c5sire/ace2fastq") + (synopsis "ACE file to FASTQ converter") + (description + "The ACE file format is used in genomics to store contigs from sequencing +machines. This tools converts it into FASTQ format. Both formats contain the +sequence characters and their corresponding quality information. Unlike the +FASTQ file, the ACE file stores the quality values numerically. The +conversion algorithm uses the standard Sanger formula. The package +facilitates insertion into pipelines, and content inspection.") + (license license:gpl3))) + +(define-public r-rngwell + (package + (name "r-rngwell") + (version "0.10-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "rngWELL" version)) + (sha256 + (base32 + "0b4ys525gksgqwqx9id4bdgyi9mwj6n3r87xdzf4fc9hp3cc16jb")))) + (properties `((upstream-name . "rngWELL"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rngWELL/") + (synopsis "Toolbox for WELL random number generators") + (description + "This is a dedicated package to WELL pseudo random generators, which were +introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based +on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") + (license license:bsd-3))) + +(define-public r-randtoolbox + (package + (name "r-randtoolbox") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "randtoolbox" version)) + (sha256 + (base32 + "141p13ajgzmb2s89rlac7zrra92mi1izvpfrngb4kqzlf3igdsqd")))) + (properties `((upstream-name . "randtoolbox"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rngwell" ,r-rngwell))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/randtoolbox/") + (synopsis "Toolbox for pseudo and quasi random number generation") + (description + "This package provides + +@enumerate +@item pseudo random generators, such as general linear +congruential generators, multiple recursive generators and generalized +feedback shift register (SF-Mersenne Twister algorithm and WELL +generators) + +@item quasi random generators, such as the Torus algorithm, the Sobol +sequence, the Halton sequence (including the Van der Corput sequence), and + +@item some generator tests: the gap test, the serial test, the poker test. +@end enumerate + +See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") + (license license:bsd-3))) + +(define-public r-lhs + (package + (name "r-lhs") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lhs" version)) + (sha256 + (base32 + "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4")))) + (properties `((upstream-name . "lhs"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/bertcarnell/lhs") + (synopsis "Latin Hypercube Samples") + (description + "This package provides a number of methods for creating and augmenting +Latin Hypercube Samples.") + (license license:gpl3))) + +(define-public r-acebayes + (package + (name "r-acebayes") + (version "1.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "acebayes" version)) + (sha256 + (base32 + "1xm6bw0qm2vlcrk274x0bawzb2lnacb1wsmzba5mg3i75a55pqln")))) + (properties `((upstream-name . "acebayes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-compare" ,r-compare) + ("r-lhs" ,r-lhs) + ("r-randtoolbox" ,r-randtoolbox) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://cran.r-project.org/web/packages/acebayes/") + (synopsis "Optimal Bayesian experimental design using the ACE algorithm") + (description + "Finding an optimal Bayesian experimental design involves maximizing an +objective function given by the expectation of some appropriately chosen +utility function with respect to the joint distribution of unknown +quantities (including responses). This objective function is usually not +available in closed form and the design space can be continuous and of high +dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE) +to maximise an approximation to the expectation of the utility function.") + (license license:gpl2))) + +(define-public r-acet + (package + (name "r-acet") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACEt" version)) + (sha256 + (base32 + "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq")))) + (properties `((upstream-name . "ACEt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://cran.r-project.org/web/packages/ACEt/") + (synopsis "Estimating dynamic heritability and twin model comparison") + (description + "This package supports twin models that are able to estimate the dynamic +behaviour of the variance components in the classical twin models with respect +to age using B-splines and P-splines.") + (license license:gpl2+))) + +(define-public r-acfmperiod + (package + (name "r-acfmperiod") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acfMPeriod" version)) + (sha256 + (base32 + "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5")))) + (properties `((upstream-name . "acfMPeriod"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/acfMPeriod/") + (synopsis "Estimation of the ACF from the M-periodogram") + (description + "This package support non-robust and robust computations of the sample +autocovariance (ACOVF) and sample autocorrelation functions (ACF) of +univariate and multivariate processes. The methodology consists in reversing +the diagonalization procedure involving the periodogram or the +cross-periodogram and the Fourier transform vectors, and, thus, obtaining the +ACOVF or the ACF as discussed in Fuller (1995) +@url{doi:10.1002/9780470316917}. The robust version is obtained by fitting +robust M-regressors to obtain the M-periodogram or M-cross-periodogram as +discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") + (license license:gpl2+))) + +(define-public r-gamlss-data + (package + (name "r-gamlss-data") + (version "5.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "gamlss.data" version)) + (sha256 + (base32 + "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd")))) + (properties `((upstream-name . "gamlss.data"))) + (build-system r-build-system) + (home-page "http://www.gamlss.org/") + (synopsis "GAMLSS data") + (description + "This package provides data used as examples to demonstrate GAMLSS +models.") + ;; Either version of the license + (license (list license:gpl2 license:gpl3)))) + +(define-public r-gamlss + (package + (name "r-gamlss") + (version "5.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "gamlss" version)) + (sha256 + (base32 + "0gcngfck0dk2rhjg0z1fnc61dqs0s049jy2rkywaf57531s2k8bc")))) + (properties `((upstream-name . "gamlss"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gamlss-data" ,r-gamlss-data) + ("r-gamlss-dist" ,r-gamlss-dist) + ("r-mass" ,r-mass) + ("r-nlme" ,r-nlme) + ("r-survival" ,r-survival))) + (home-page "http://www.gamlss.org/") + (synopsis "Generalized additive models for location scale and shape") + (description + "This package provides functions for fitting the generalized additive +models for location scale and shape introduced by Rigby and +Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models +use a distributional regression approach where all the parameters of the +conditional distribution of the response variable are modelled using +explanatory variables.") + ;; Either version of the license + (license (list license:gpl2 license:gpl3)))) + +(define-public r-acid + (package + (name "r-acid") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "acid" version)) + (sha256 + (base32 + "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd")))) + (properties `((upstream-name . "acid"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gamlss" ,r-gamlss) + ("r-gamlss-dist" ,r-gamlss-dist) + ("r-hmisc" ,r-hmisc))) + (home-page "https://cran.r-project.org/web/packages/acid/") + (synopsis "Analysing conditional income distributions") + (description + "This package provides functions for the analysis of income distributions +for subgroups of the population as defined by a set of variables like age, +gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture +distribution as well as functions for moments, inequality measures, entropy +measures and polarisation measures of income distributions. This package thus +aides the analysis of income inequality by offering tools for the exploratory +analysis of income distributions at the disaggregated level.") + (license license:gpl3))) + +(define-public r-acm4r + (package + (name "r-acm4r") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acm4r" version)) + (sha256 + (base32 + "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa")))) + (properties `((upstream-name . "acm4r"))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/acm4r/") + (synopsis "Align-and-count method comparisons of RFLP data") + (description + "This is a package to compare sequence fragment lengths or molecular +weights from pairs of lanes. The number of matching bands in the +@dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using +the align-and-count method.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-filematrix + (package + (name "r-filematrix") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "filematrix" version)) + (sha256 + (base32 + "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b")))) + (properties `((upstream-name . "filematrix"))) + (build-system r-build-system) + ;; These inputs are needed for vignettes + (native-inputs + `(("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("pandoc-citeproc" ,ghc-pandoc-citeproc))) + (home-page "https://github.com/andreyshabalin/filematrix") + (synopsis "File-backed matrix class with convenient read and write access") + (description + "This package provides an interface for working with large matrices +stored in files, not in computer memory. It supports multiple non-character +data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4 +byte real values). Access to parts of the matrix is done by indexing, exactly +as with usual R matrices. It supports very large matrices; the package has +been tested on multi-terabyte matrices. It allows for more than 2^32 rows or +columns, ad allows for quick addition of extra columns to a filematrix.") + (license license:lgpl3))) + +(define-public r-acmeeqtl + (package + (name "r-acmeeqtl") + (version "1.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACMEeqtl" version)) + (sha256 + (base32 + "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz")))) + (properties `((upstream-name . "ACMEeqtl"))) + (build-system r-build-system) + (propagated-inputs + `(("r-filematrix" ,r-filematrix))) + (home-page "https://github.com/andreyshabalin/ACMEeqtl") + (synopsis "Estimation of interpretable eQTL effect sizes") + (description + "This package provides a non-linear model, termed ACME, that reflects a +parsimonious biological model for allelic contributions of cis-acting eQTLs. +With non-linear least-squares algorithm the maximum likelihood parameters can +be estimated. The ACME model provides interpretable effect size estimates and +p-values with well controlled Type-I error.") + (license license:lgpl3))) + +(define-public r-acmer + (package + (name "r-acmer") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acmeR" version)) + (sha256 + (base32 + "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7")))) + (properties `((upstream-name . "acmeR"))) + (build-system r-build-system) + (propagated-inputs `(("r-foreign" ,r-foreign))) + (home-page "https://cran.r-project.org/web/packages/acmeR/") + (synopsis "ACME estimator of bird and bat mortality by wind turbines") + (description + "This package provides an implementation of the ACME estimator, described +in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran +Mortality at Wind Turbines. Unlike most other models, this estimator supports +decreasing-hazard Weibull model for persistence; decreasing search proficiency +as carcasses age; variable bleed-through at successive searches; and interval +mortality estimates. The package provides, based on search data, functions +for estimating the mortality inflation factor in Frequentist and Bayesian +settings.") + (license license:expat))) + +(define-public r-r-huge + (package + (name "r-r-huge") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "R.huge" version)) + (sha256 + (base32 + "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi")))) + (properties `((upstream-name . "R.huge"))) + (build-system r-build-system) + (propagated-inputs + `(("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.huge") + (synopsis "Methods for accessing huge amounts of data") + (description + "This is a deprecated package for accessing huge amounts of data. + Cross-platform alternatives are the following packages: bigmemory (CRAN), +ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside +the @code{aroma.affymetrix} package.") + (license license:lgpl2.1+))) + +(define-public r-r-filesets + (package + (name "r-r-filesets") + (version "2.13.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "R.filesets" version)) + (sha256 + (base32 + "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg")))) + (properties `((upstream-name . "R.filesets"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-r-cache" ,r-r-cache) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.filesets") + (synopsis "Easy handling of and access to files") + (description + "This package provides classes and methods to locate, setup, subset, +navigate and iterate file sets, i.e. sets of files located in one or more +directories on the file system. The API is designed such that these classes +can be extended via inheritance to provide a richer API for special file +formats. Moreover, a specific name format is defined such that filenames and +directories can be considered to have full names which consists of a name +followed by comma-separated tags. This adds additional flexibility to +identify file sets and individual files.") + (license license:lgpl2.1+))) + +(define-public r-r-devices + (package + (name "r-r-devices") + (version "2.16.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "R.devices" version)) + (sha256 + (base32 + "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd")))) + (properties `((upstream-name . "R.devices"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.devices") + (synopsis "Unified handling of graphics devices") + (description + "This package provides functions for creating plots and image files in a +unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). +Default device options as well as scales and aspect ratios are controlled in a +uniform way across all device types. Switching output format requires minimal +changes in code. This package is ideal for large-scale batch processing, +because it will never leave open graphics devices or incomplete image files +behind, even on errors or user interrupts.") + (license license:lgpl2.1+))) + +(define-public r-acnr + (package + (name "r-acnr") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acnr" version)) + (sha256 + (base32 + "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym")))) + (properties `((upstream-name . "acnr"))) + (build-system r-build-system) + (home-page "https://github.com/mpierrejean/acnr") + (synopsis "Annotated copy-number regions") + (description + "This package provides SNP array data from different types of copy-number +regions. These regions were identified manually by the authors of the package +and may be used to generate realistic data sets with known truth.") + (license license:lgpl2.1+))) + +(define-public r-acopula + (package + (name "r-acopula") + (version "0.9.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "acopula" version)) + (sha256 + (base32 + "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln")))) + (properties `((upstream-name . "acopula"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/acopula/") + (synopsis "Modelling dependence with multivariate Archimax copulas") + (description + "Archimax copulas are a mixture of Archimedean and EV copulas. This +package provides definitions of several parametric families of generator and +dependence function, computes CDF and PDF, estimates parameters, tests for +goodness of fit, generates random sample and checks copula properties for +custom constructs. In the 2-dimensional case explicit formulas for density +are used, contrary to higher dimensions when all derivatives are linearly +approximated. Several non-archimax families (normal, FGM, Plackett) are +provided as well.") + (license license:gpl2))) + +(define-public r-tuner + (package + (name "r-tuner") + (version "1.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "tuneR" version)) + (sha256 + (base32 + "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx")))) + (properties `((upstream-name . "tuneR"))) + (build-system r-build-system) + (propagated-inputs `(("r-signal" ,r-signal))) + (home-page "https://cran.r-project.org/web/packages/tuneR/") + (synopsis "Analysis of music and speech") + (description + "This is a package for the analysis of music and speech. Analyze music +and speech, extract features like MFCCs, handle wave files and their +representation in various ways, read MP3, read MIDI, perform steps of a +transcription, ...") + ;; Either of these versions. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-seewave + (package + (name "r-seewave") + (version "2.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "seewave" version)) + (sha256 + (base32 + "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi")))) + (properties `((upstream-name . "seewave"))) + (build-system r-build-system) + (propagated-inputs + `(("r-tuner" ,r-tuner))) + (home-page "http://rug.mnhn.fr/seewave") + (synopsis "Sound analysis and synthesis") + (description + "This package provides functions for analysing, manipulating, displaying, +editing and synthesizing time waves (particularly sound). This package +processes time analysis (oscillograms and envelopes), spectral content, +resonance quality factor, entropy, cross correlation and autocorrelation, +zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D +and 3D spectrograms and many other analyses.") + (license license:gpl2+))) + +(define-public r-acousticndlcoder + (package + (name "r-acousticndlcoder") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "AcousticNDLCodeR" version)) + (sha256 + (base32 + "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb")))) + (properties + `((upstream-name . "AcousticNDLCodeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-seewave" ,r-seewave) + ("r-tuner" ,r-tuner) + ("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/") + (synopsis "Coding sound files for use with NDL") + (description + "Make acoustic cues to use with the R package @code{ndl}. +The package implements functions used in the PLoS ONE paper \"Words from +spontaneous conversational speech can be recognized with human-like accuracy +by an error-driven learning algorithm that discriminates between meanings +straight from smart acoustic features, bypassing the phoneme as recognition +unit.\" @url{doi:10.1371/journal.pone.0174623}") + (license license:gpl2+))) + +(define-public r-acp + (package + (name "r-acp") + (version "2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "acp" version)) + (sha256 + (base32 + "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn")))) + (properties `((upstream-name . "acp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-quantmod" ,r-quantmod) + ("r-tseries" ,r-tseries))) + (home-page "https://cran.r-project.org/web/packages/acp/") + (synopsis "Autoregressive conditional Poisson") + (description + "This package supports the analysis of count data exhibiting +autoregressive properties, using the @dfn{Autoregressive Conditional Poisson} +model (ACP(p,q)) proposed by Heinen (2003).") + (license license:gpl2))) + +(define-public r-ada + (package + (name "r-ada") + (version "2.0-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "ada" version)) + (sha256 + (base32 + "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r")))) + (properties `((upstream-name . "ada"))) + (build-system r-build-system) + (propagated-inputs `(("r-rpart" ,r-rpart))) + (home-page "https://cran.r-project.org/web/packages/ada/") + (synopsis "Stochastic boosting") + (description + "This package provides a straightforward, well-documented, and broad +boosting routine for classification, ideally suited for small to +moderate-sized data sets. It performs discrete, real, and gentle boost under +both exponential and logistic loss on a given data set.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-genalg + (package + (name "r-genalg") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "genalg" version)) + (sha256 + (base32 + "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s")))) + (properties `((upstream-name . "genalg"))) + (build-system r-build-system) + (home-page "https://github.com/egonw/genalg") + (synopsis "R based genetic algorithm") + (description + "This package provides an R based genetic algorithm for binary and +floating point chromosomes.") + (license license:gpl2))) + +(define-public r-kernelfactory + (package + (name "r-kernelfactory") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "kernelFactory" version)) + (sha256 + (base32 + "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j")))) + (properties `((upstream-name . "kernelFactory"))) + (build-system r-build-system) + (propagated-inputs + `(("r-auc" ,r-auc) + ("r-genalg" ,r-genalg) + ("r-kernlab" ,r-kernlab) + ("r-randomforest" ,r-randomforest))) + (home-page "https://cran.r-project.org/web/packages/kernelFactory/") + (synopsis "Ensemble of kernel machines") + (description + "Kernel factory is an ensemble method where each base classifier (random +forest) is fit on the kernel matrix of a subset of the training data.") + (license license:gpl2+))) + +(define-public r-dummies + (package + (name "r-dummies") + (version "1.5.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "dummies" version)) + (sha256 + (base32 + "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm")))) + (properties `((upstream-name . "dummies"))) + (build-system r-build-system) + (home-page "http://www.decisionpatterns.com") + (synopsis "Create dummy/indicator variables flexibly and efficiently") + (description + "This package lets you expand factors, characters and other eligible +classes into dummy/indicator variables.") + (license license:gpl2+))) + +(define-public r-acrm + (package + (name "r-acrm") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "aCRM" version)) + (sha256 + (base32 + "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v")))) + (properties `((upstream-name . "aCRM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ada" ,r-ada) + ("r-dummies" ,r-dummies) + ("r-kernelfactory" ,r-kernelfactory) + ("r-randomforest" ,r-randomforest))) + (home-page "https://cran.r-project.org/web/packages/aCRM/") + (synopsis "Convenience functions for analytical customer relationship management") + (description + "This package provides convenience functions for data preparation and +modeling often used in @dfn{analytical customer relationship +management} (aCRM).") + (license license:gpl2+))) + +(define-public r-treeclust + (package + (name "r-treeclust") + (version "1.1-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "treeClust" version)) + (sha256 + (base32 + "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z")))) + (properties `((upstream-name . "treeClust"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-rpart" ,r-rpart))) + (home-page "https://cran.r-project.org/web/packages/treeClust/") + (synopsis "Cluster distances through trees") + (description + "This package provides tools to create a measure of inter-point +dissimilarity useful for clustering mixed data, and, optionally, perform the +clustering.") + (license license:gpl2+))) + +(define-public r-acrosstic + (package + (name "r-acrosstic") + (version "1.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "AcrossTic" version)) + (sha256 + (base32 + "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0")))) + (properties `((upstream-name . "AcrossTic"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lpsolve" ,r-lpsolve) + ("r-treeclust" ,r-treeclust))) + (home-page "https://cran.r-project.org/web/packages/AcrossTic/") + (synopsis "Cost-minimal regular spanning subgraph with TreeClust") + (description + "This is a package for constructing minimum-cost regular spanning +subgraph as part of a non-parametric two-sample test for equality of +distribution.") + (license license:gpl2+))) + +(define-public r-acrt + (package + (name "r-acrt") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "acrt" version)) + (sha256 + (base32 + "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s")))) + (properties `((upstream-name . "acrt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-sandwich" ,r-sandwich))) + (home-page "https://cran.r-project.org/web/packages/acrt/") + (synopsis "Autocorrelation robust testing") + (description + "This package provides functions for testing affine hypotheses on the +regression coefficient vector in regression models with autocorrelated +errors.") + (license license:gpl2))) + +(define-public r-acs + (package + (name "r-acs") + (version "2.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "acs" version)) + (sha256 + (base32 + "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5")))) + (properties `((upstream-name . "acs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-httr" ,r-httr) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-stringr" ,r-stringr) + ("r-xml" ,r-xml))) + (home-page "http://dusp.mit.edu/faculty/ezra-glenn") + (synopsis "Work with data from the US Census") + (description + "This package provides a general toolkit for downloading, managing, +analyzing, and presenting data from the +@url{https://www.census.gov/data/developers/data-sets.html, U.S. Census}, +including SF1 (Decennial short-form), SF3 (Decennial long-form), and the +American Community Survey (ACS). Confidence intervals provided with ACS data +are converted to standard errors to be bundled with estimates in complex +@code{acs} objects. The package provides new methods to conduct standard +operations on @code{acs} objects and present/plot data in statistically +appropriate ways.") + (license license:gpl3))) + +(define-public r-acss-data + (package + (name "r-acss-data") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acss.data" version)) + (sha256 + (base32 + "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv")))) + (properties `((upstream-name . "acss.data"))) + (build-system r-build-system) + (home-page "http://complexitycalculator.com/methodology.html") + (synopsis "Data for algorithmic complexity of short strings") + (description + "This is a data only package providing the algorithmic complexity of +short strings, computed using the coding theorem method. For a given set of +symbols in a string, all possible or a large number of random samples of +Turing machines with a given number of states (e.g., 5) and number of symbols +corresponding to the number of symbols in the strings were simulated until +they reached a halting state or failed to end. This package contains data on +4.5 million strings from length 1 to 12 simulated on Turing machines with 2, +4, 5, 6, and 9 symbols. The complexity of the string corresponds to the +distribution of the halting states.") + (license license:gpl2+))) + +(define-public r-acss + (package + (name "r-acss") + (version "0.2-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "acss" version)) + (sha256 + (base32 + "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk")))) + (properties `((upstream-name . "acss"))) + (build-system r-build-system) + (propagated-inputs + `(("r-acss-data" ,r-acss-data) + ("r-zoo" ,r-zoo))) + (home-page "http://complexitycalculator.com/methodology.html") + (synopsis "Algorithmic complexity for short strings") + (description + "The main purpose of this package is to provide the algorithmic +complexity for short strings, an approximation of the Kolmogorov Complexity of +a short string using the coding theorem method. While the database containing +the complexity is provided in the data only package @code{acss.data}, this +package provides functions accessing the data such as @code{prob_random} +returning the posterior probability that a given string was produced by a +random process. In addition, two traditional (but problematic) measures of +complexity are also provided: entropy and change complexity.") + (license license:gpl2+))) + +(define-public r-acswr + (package + (name "r-acswr") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACSWR" version)) + (sha256 + (base32 + "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n")))) + (properties `((upstream-name . "ACSWR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ACSWR/") + (synopsis "Companion package for the book \"A Course in Statistics with R\"") + (description + "This is a companion package for the book \"A Course in Statistics with +R\" (ISBN 978-1-119-15272-9.)") + (license license:gpl2))) + +(define-public r-alabama + (package + (name "r-alabama") + (version "2015.3-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "alabama" version)) + (sha256 + (base32 + "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036")))) + (properties `((upstream-name . "alabama"))) + (build-system r-build-system) + (propagated-inputs `(("r-numderiv" ,r-numderiv))) + (home-page "https://cran.r-project.org/web/packages/alabama/") + (synopsis "Constrained nonlinear optimization") + (description + "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization +Algorithm; it is used for optimizing smooth nonlinear objective functions with +constraints. Linear or nonlinear equality and inequality constraints are +allowed.") + (license license:gpl2+))) + +(define-public r-gdina + (package + (name "r-gdina") + (version "2.7.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "GDINA" version)) + (sha256 + (base32 + "0875xfbm36gqzr0116xzlbm8rlff85rybr4s4hjzfflfvjdhgvfx")))) + (properties `((upstream-name . "GDINA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-alabama" ,r-alabama) + ("r-ggplot2" ,r-ggplot2) + ("r-mass" ,r-mass) + ("r-nloptr" ,r-nloptr) + ("r-numderiv" ,r-numderiv) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rsolnp" ,r-rsolnp) + ("r-shiny" ,r-shiny) + ("r-shinydashboard" ,r-shinydashboard))) + (home-page "https://github.com/Wenchao-Ma/GDINA") + (synopsis "Generalized DINA model framework") + (description + "This package provides a set of psychometric tools for cognitive +diagnosis modeling based on the generalized deterministic inputs, noisy and +gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7} +and its extensions, including the sequential G-DINA model by Ma and de la +Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the +polytomous G-DINA model by Chen and de la Torre +@url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute +distribution can be independent, saturated, higher-order, loglinear smoothed +or structured. Q-matrix validation, item and model fit statistics, model +comparison at test and item level and differential item functioning can also +be conducted. A graphical user interface is also provided.") + (license license:gpl3))) + +(define-public r-actcd + (package + (name "r-actcd") + (version "1.2-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACTCD" version)) + (sha256 + (base32 + "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p")))) + (properties `((upstream-name . "ACTCD"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gdina" ,r-gdina) + ("r-r-methodss3" ,r-r-methodss3))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/ACTCD/") + (synopsis "Asymptotic classification theory for cognitive diagnosis") + (description + "This is a package supporting cluster analysis for cognitive diagnosis +based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; +@url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of +sum-scores, cluster analysis techniques can be used to classify examinees into +latent classes based on their attribute patterns. In addition to the +algorithms used to classify data, three labeling approaches are proposed to +label clusters so that examinees' attribute profiles can be obtained.") + (license license:gpl2+))) + +(define-public r-ineq + (package + (name "r-ineq") + (version "0.2-13") + (source + (origin + (method url-fetch) + (uri (cran-uri "ineq" version)) + (sha256 + (base32 + "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0")))) + (properties `((upstream-name . "ineq"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ineq/") + (synopsis "Measuring inequality, concentration, and poverty") + (description + "This package provides tools for measuring inequality, concentration, and +poverty measures. It provides both empirical and theoretical Lorenz curves.") + ;; Either of these two versions. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-actfrag + (package + (name "r-actfrag") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActFrag" version)) + (sha256 + (base32 + "06l5a679j6289008ls57v420mnzpq9a4ln7svi5bh0vpvws7sr9d")))) + (properties `((upstream-name . "ActFrag"))) + (build-system r-build-system) + (propagated-inputs + `(("r-accelerometry" ,r-accelerometry) + ("r-dplyr" ,r-dplyr) + ("r-ineq" ,r-ineq) + ("r-survival" ,r-survival) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/junruidi/ActFrag") + (synopsis "Activity fragmentation metrics extraction") + (description + "This package provides functions to extract commonly used fragmentation +metrics to quantify time accumulation strategies based on minute level +actigraphy-measured activity counts data.") + (license license:gpl3))) + +(define-public r-fda + (package + (name "r-fda") + (version "2.4.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "fda" version)) + (sha256 + (base32 + "0n39rzbhg1hipzn51rzmbchn2358qgapg08iv7lmiqj5y7i9qns2")))) + (properties `((upstream-name . "fda"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix))) + (home-page "http://www.functionaldata.org") + (synopsis "Functional data analysis") + (description + "These functions were developed to support functional data analysis as +described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data +Analysis. The package includes data sets and script files working many +examples.") + (license license:gpl2+))) + +(define-public r-actigraphy + (package + (name "r-actigraphy") + (version "1.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "Actigraphy" version)) + (sha256 + (base32 + "0y0ccmxhdfhdmi4k6pbfvnqknkqbgvfsf2qf7z7rc4xpfgym6574")))) + (properties `((upstream-name . "Actigraphy"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fda" ,r-fda) + ("r-sdmtools" ,r-sdmtools))) + (home-page "https://cran.r-project.org/web/packages/Actigraphy/") + (synopsis "Actigraphy data analysis") + (description + "This package provides tools for functional linear modeling and analysis +of actigraphy data.") + (license license:asl2.0))) + +(define-public r-activedriver + (package + (name "r-activedriver") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActiveDriver" version)) + (sha256 + (base32 + "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa")))) + (properties `((upstream-name . "ActiveDriver"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ActiveDriver/") + (synopsis "Tools for finding cancer driver proteins") + (description + "This package provides a mutation analysis tool that discovers cancer +driver genes with frequent mutations in protein signalling sites such as +post-translational modifications (phosphorylation, ubiquitination, etc). The +Poisson generalized linear regression model identifies genes where cancer +mutations in signalling sites are more frequent than expected from the +sequence of the entire gene. Integration of mutations with signalling +information helps find new driver genes and propose candidate mechanisms to +known drivers.") + (license license:gpl2+))) + +(define-public r-activitycounts + (package + (name "r-activitycounts") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "activityCounts" version)) + (sha256 + (base32 + "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz")))) + (properties + `((upstream-name . "activityCounts"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-seewave" ,r-seewave) + ("r-signal" ,r-signal) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/walkabillylab/activityCounts") + (synopsis "Generate ActiLife counts") + (description + "ActiLife generates activity counts from data collected by Actigraph +accelerometers. Actigraph is one of the most common research-grade +accelerometers. There is considerable research validating and developing +algorithms for human activity using ActiLife counts. Unfortunately, ActiLife +counts are proprietary and difficult to implement if researchers use different +accelerometer brands. The code creates ActiLife counts from raw acceleration +data for different accelerometer brands.") + (license license:gpl3))) + +(define-public r-activityindex + (package + (name "r-activityindex") + (version "0.3.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActivityIndex" version)) + (sha256 + (base32 + "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk")))) + (properties `((upstream-name . "ActivityIndex"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-matrixstats" ,r-matrixstats) + ("r-r-utils" ,r-r-utils))) + (home-page "https://cran.r-project.org/web/packages/ActivityIndex/") + (synopsis "Activity Index calculation using raw accelerometry data") + (description + "This is a package to read raw accelerometry from GT3X+ accelerometry +data and plain table data to calculate the Activity Index from Bai et +al. (2016) @url{doi:10.1371/journal.pone.0160644}.") + (license license:gpl3))) + +(define-public r-activpal + (package + (name "r-activpal") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "activPAL" version)) + (sha256 + (base32 + "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na")))) + (properties `((upstream-name . "activPAL"))) + (build-system r-build-system) + (propagated-inputs + `(("r-devtools" ,r-devtools) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://cran.r-project.org/web/packages/activPAL") + (synopsis "Processing and chart generation from activPAL events files") + (description + "This package contains functions to generate pre-defined summary +statistics from activPAL events files. The package also contains functions to +produce informative graphics that visualize physical activity behaviour and +trends. This includes generating graphs that align physical activity +behaviour with additional time based observations described by other data +sets, such as sleep diaries and continuous glucose monitoring data.") + (license license:gpl3))) + +(define-public r-activpalprocessing + (package + (name "r-activpalprocessing") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "activpalProcessing" version)) + (sha256 + (base32 + "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1")))) + (properties + `((upstream-name . "activpalProcessing"))) + (build-system r-build-system) + (propagated-inputs + `(("r-chron" ,r-chron))) + (home-page "https://cran.r-project.org/web/packages/activpalProcessing/") + (synopsis "Process activPAL events files") + (description + "This package performs estimation of physical activity and sedentary +behavior variables from activPAL events files.") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-actogrammr + (package + (name "r-actogrammr") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "actogrammr" version)) + (sha256 + (base32 + "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa")))) + (properties `((upstream-name . "actogrammr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-lubridate" ,r-lubridate) + ("r-readr" ,r-readr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://cran.r-project.org/web/packages/actogrammr/") + (synopsis "Read in activity data and plot actograms") + (description + "Read in activity measurements from standard file formats used by +circadian rhythm researchers, currently only ClockLab format, and process and +plot the data. The central type of plot is the actogram, as first described +in \"Activity and distribution of certain wild mice in relation to biotic +communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.") + (license license:gpl3))) + +(define-public r-expint + (package + (name "r-expint") + (version "0.1-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "expint" version)) + (sha256 + (base32 + "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7")))) + (properties `((upstream-name . "expint"))) + (build-system r-build-system) + (home-page "https://gitlab.com/vigou3/expint") + (synopsis "Exponential integral and incomplete Gamma function") + (description + "This package provides the exponential integrals @code{E_1(x)}, +@code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma +function @code{G(a, x)} defined for negative values of its first argument. +The package also gives easy access to the underlying C routines through an +API; see the package vignette for details.") + (license license:gpl2+))) + +(define-public r-actuar + (package + (name "r-actuar") + (version "2.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "actuar" version)) + (sha256 + (base32 + "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih")))) + (properties `((upstream-name . "actuar"))) + (build-system r-build-system) + (propagated-inputs `(("r-expint" ,r-expint))) + (home-page "https://gitlab.com/vigou3/actuar") + (synopsis "Actuarial functions and heavy tailed distributions") + (description + "This package provides functions and data sets for actuarial science: +modeling of loss distributions; risk theory and ruin theory; simulation of +compound models, discrete mixtures and compound hierarchical models; +credibility theory. It boasts support for many additional probability +distributions to model insurance loss amounts and loss frequency: 19 +continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete +distribution; zero-truncated and zero-modified extensions of the standard +discrete distributions. It also supports phase-type distributions commonly +used to compute ruin probabilities.") + (license license:gpl2+))) + +(define-public r-bmp + (package + (name "r-bmp") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "bmp" version)) + (sha256 + (base32 + "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx")))) + (properties `((upstream-name . "bmp"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/bmp/") + (synopsis "Read Bitmap (BMP) images") + (description + "This package provides pure R tools to read BMP format images. It is +currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") + (license license:gpl2+))) + +(define-public r-readbitmap + (package + (name "r-readbitmap") + (version "0.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "readbitmap" version)) + (sha256 + (base32 + "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk")))) + (properties `((upstream-name . "readbitmap"))) + (build-system r-build-system) + (inputs + `(("libjpeg" ,libjpeg) + ("libpng" ,libpng))) + (propagated-inputs + `(("r-bmp" ,r-bmp) + ("r-jpeg" ,r-jpeg) + ("r-png" ,r-png) + ("r-tiff" ,r-tiff))) + (home-page "https://github.com/jefferis/readbitmap") + (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)") + (description + "This package provides tools to identify and read BMP, JPEG, PNG, and +TIFF format bitmap images. Identification defaults to the use of the magic +number embedded in the file rather than the file extension.") + (license license:gpl2+))) + +(define-public r-imager + (package + (name "r-imager") + (version "0.41.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "imager" version)) + (sha256 + (base32 + "19fqgjhg04garbipx20g72h9dd6k0jj4ac48nby6km4h665vrs4v")))) + (properties `((upstream-name . "imager"))) + (build-system r-build-system) + (inputs + `(("fftw" ,fftw) + ("libtiff" ,libtiff) + ("libx11" ,libx11) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-cairo" ,r-cairo) + ("r-downloader" ,r-downloader) + ("r-igraph" ,r-igraph) + ("r-jpeg" ,r-jpeg) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-png" ,r-png) + ("r-purrr" ,r-purrr) + ("r-rcpp" ,r-rcpp) + ("r-readbitmap" ,r-readbitmap) + ("r-stringr" ,r-stringr))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "http://dahtah.github.io/imager") + (synopsis "Image processing library") + (description + "This is a package for fast image processing for images in up to 4 +dimensions (two spatial dimensions, one time/depth dimension, one color +dimension). It provides most traditional image processing tools (filtering, +morphology, transformations, etc.) as well as various functions for easily +analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a +simple, modern C++ library for image processing.") + (license license:lgpl3))) + +(define-public r-acuityview + (package + (name "r-acuityview") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "AcuityView" version)) + (sha256 + (base32 + "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l")))) + (properties `((upstream-name . "AcuityView"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fftwtools" ,r-fftwtools) + ("r-imager" ,r-imager) + ("r-plotrix" ,r-plotrix))) + (home-page "https://cran.r-project.org/web/packages/AcuityView/") + (synopsis "Display scenes as seen by an animal with less acute vision") + (description + "This package provides a simple method for representing a visual scene as +it may be seen by an animal with less acute vision.") + (license license:gpl2+))) + +(define-public r-adabag + (package + (name "r-adabag") + (version "4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "adabag" version)) + (sha256 + (base32 + "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7")))) + (properties `((upstream-name . "adabag"))) + (build-system r-build-system) + (propagated-inputs + `(("r-caret" ,r-caret) + ("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-rpart" ,r-rpart))) + (home-page "https://cran.r-project.org/web/packages/adabag/") + (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging") + (description + "This package implements Freund and Schapire's Adaboost.M1 algorithm and +Breiman's Bagging algorithm using classification trees as individual +classifiers. Once these classifiers have been trained, they can be used to +predict on new data. Also, cross validation estimation of the error can be +done.") + (license license:gpl2+))) + +(define-public r-adagio + (package + (name "r-adagio") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "adagio" version)) + (sha256 + (base32 + "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k")))) + (properties `((upstream-name . "adagio"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/adagio/") + (synopsis "Discrete and global optimization routines") + (description + "This package provides methods and algorithms for discrete optimization, +e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and +Hooke-Jeeves minimization, and some (evolutionary) global optimization +functions.") + (license license:gpl3+))) + +(define-public r-univoutl + (package + (name "r-univoutl") + (version "0.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "univOutl" version)) + (sha256 + (base32 + "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi")))) + (properties `((upstream-name . "univOutl"))) + (build-system r-build-system) + (propagated-inputs + `(("r-hmisc" ,r-hmisc) + ("r-robustbase" ,r-robustbase))) + (home-page "https://github.com/marcellodo/univOutl") + (synopsis "Detection of univariate outliers") + (description + "This package provides well-known outlier detection techniques in the +univariate case. Methods to deal with skewed distribution are included too. +The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of +historical data is implemented as well. When available, survey weights can be +used in outliers detection.") + (license license:gpl2+))) + +(define-public r-tolerance + (package + (name "r-tolerance") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tolerance" version)) + (sha256 + (base32 + "17qh4ad1f3fbcpwlxxqh8qr9bnwjcl4yxk0l3fkbr6b2l4rc5p86")))) + (properties `((upstream-name . "tolerance"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rgl" ,r-rgl))) + (home-page "https://cran.r-project.org/web/packages/tolerance/") + (synopsis "Statistical tolerance intervals and regions") + (description + "This package provides functions for estimating tolerance +limits (intervals) for various univariate distributions (binomial, Cauchy, +discrete Pareto, exponential, two-parameter exponential, extreme value, +hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric, +normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot), +Bayesian normal tolerance limits, multivariate normal tolerance regions, +nonparametric tolerance intervals, tolerance bands for regression +settings (linear regression, nonlinear regression, nonparametric regression, +and multivariate regression), and analysis of variance tolerance intervals. +Visualizations are also available for most of these settings.") + (license license:gpl2+))) + +(define-public r-additivitytests + (package + (name "r-additivitytests") + (version "1.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "additivityTests" version)) + (sha256 + (base32 + "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw")))) + (properties + `((upstream-name . "additivityTests"))) + (build-system r-build-system) + (home-page "https://github.com/simecek/additivityTests") + (synopsis "Additivity tests in the two way Anova with single sub-class numbers") + (description + "This package provides an implementation of the Tukey, Mandel, +Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.") + (license license:gpl3))) + +(define-public r-flexclust + (package + (name "r-flexclust") + (version "1.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "flexclust" version)) + (sha256 + (base32 + "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2")))) + (properties `((upstream-name . "flexclust"))) + (build-system r-build-system) + (propagated-inputs + `(("r-class" ,r-class) + ("r-lattice" ,r-lattice) + ("r-modeltools" ,r-modeltools))) + (home-page "https://cran.r-project.org/web/packages/flexclust/") + (synopsis "Flexible cluster algorithms") + (description + "The main function @code{kcca} implements a general framework for +k-centroids cluster analysis supporting arbitrary distance measures and +centroid computation. Further cluster methods include hard competitive +learning, neural gas, and QT clustering. There are numerous visualization +methods for cluster results (neighborhood graphs, convex cluster hulls, +barcharts of centroids, ...), and bootstrap methods for the analysis of +cluster stability.") + (license license:gpl2))) + +(define-public r-biclust + (package + (name "r-biclust") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "biclust" version)) + (sha256 + (base32 + "1y5n6wfa1lx88ck3x09rcg0dh3pw89225h85hmq2la1s1fpa48i0")))) + (properties `((upstream-name . "biclust"))) + (build-system r-build-system) + (propagated-inputs + `(("r-additivitytests" ,r-additivitytests) + ("r-colorspace" ,r-colorspace) + ("r-flexclust" ,r-flexclust) + ("r-ggplot2" ,r-ggplot2) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-tidyr" ,r-tidyr))) + (home-page "https://cran.r-project.org/web/packages/biclust/") + (synopsis "BiCluster algorithms") + (description + "The main function @code{biclust()} provides several algorithms to find +biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax. +In addition, the package provides methods for data +preprocessing (normalization and discretization), visualization, and +validation of bicluster solutions.") + (license license:gpl3))) + +(define-public r-icge + (package + (name "r-icge") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ICGE" version)) + (sha256 + (base32 + "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa")))) + (properties `((upstream-name . "ICGE"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ICGE/") + (synopsis "Cluster estimation and identification of atypical units") + (description + "ICGE is a package that helps to estimate the number of real clusters in +data as well as to identify atypical units. The underlying methods are based +on distances rather than on unit x variables.") + (license license:gpl2+))) + +(define-public r-depth + (package + (name "r-depth") + (version "2.1-1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "depth" version)) + (sha256 + (base32 + "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m")))) + (properties `((upstream-name . "depth"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-circular" ,r-circular) + ("r-rgl" ,r-rgl))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/depth/") + (synopsis "Nonparametric depth functions for multivariate analysis") + (description + "This package provides tools for depth functions methodology applied to +multivariate analysis. Besides allowing calculation of depth values and +depth-based location estimators, the package includes functions or drawing +contour plots and perspective plots of depth functions. Euclidian and +spherical depths are supported.") + (license license:gpl2))) + +(define-public r-archetypes + (package + (name "r-archetypes") + (version "2.2-0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "archetypes" version)) + (sha256 + (base32 + "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0")))) + (properties `((upstream-name . "archetypes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-modeltools" ,r-modeltools) + ("r-nnls" ,r-nnls))) + (home-page "https://cran.r-project.org/web/packages/archetypes") + (synopsis "Archetypal analysis") + (description + "The main function @code{archetypes} implements a framework for +archetypal analysis supporting arbitrary problem solving mechanisms for the +different conceptual parts of the algorithm.") + (license license:gpl2+))) + +(define-public r-shapes + (package + (name "r-shapes") + (version "1.2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "shapes" version)) + (sha256 + (base32 + "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s")))) + (properties `((upstream-name . "shapes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-minpack-lm" ,r-minpack-lm) + ("r-rgl" ,r-rgl) + ("r-scatterplot3d" ,r-scatterplot3d))) + (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes") + (synopsis "Statistical shape analysis") + (description + "This package provides routines for the statistical analysis of landmark +shapes, including Procrustes analysis, graphical displays, principal +components analysis, permutation and bootstrap tests, thin-plate spline +transformation grids and comparing covariance matrices. See Dryden, I.L. and +Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd +Edition), John Wiley and Sons.") + (license license:gpl2))) + +(define-public r-anthropometry + (package + (name "r-anthropometry") + (version "1.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "Anthropometry" version)) + (sha256 + (base32 + "1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8")))) + (properties `((upstream-name . "Anthropometry"))) + (build-system r-build-system) + (propagated-inputs + `(("r-archetypes" ,r-archetypes) + ("r-biclust" ,r-biclust) + ("r-cluster" ,r-cluster) + ("r-depth" ,r-depth) + ("r-fnn" ,r-fnn) + ("r-icge" ,r-icge) + ("r-nnls" ,r-nnls) + ("r-rgl" ,r-rgl) + ("r-shapes" ,r-shapes))) + (home-page "https://cran.r-project.org/web/packages/Anthropometry/") + (synopsis "Statistical methods for anthropometric data") + (description + "This package provides statistical methods especially developed to +analyze anthropometric data. These methods are aimed at providing effective +solutions to some commons problems related to Ergonomics and Anthropometry. +They are based on clustering, the statistical concept of data depth, +statistical shape analysis and archetypal analysis.") + (license license:gpl2+))) + +(define-public r-adamethods + (package + (name "r-adamethods") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "adamethods" version)) + (sha256 + (base32 + "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh")))) + (properties `((upstream-name . "adamethods"))) + (build-system r-build-system) + (propagated-inputs + `(("r-anthropometry" ,r-anthropometry) + ("r-archetypes" ,r-archetypes) + ("r-fnn" ,r-fnn) + ("r-foreach" ,r-foreach) + ("r-nnls" ,r-nnls) + ("r-tolerance" ,r-tolerance) + ("r-univoutl" ,r-univoutl))) + (home-page "https://cran.r-project.org/web/packages/adamethods/") + (synopsis "Archetypoid algorithms and anomaly detection") + (description + "This package is a collection of several algorithms to obtain +archetypoids with small and large databases and with both classical +multivariate data and functional data (univariate and multivariate). Some of +these algorithms also allow to detect anomalies (outliers).") + (license license:gpl2+))) + +(define-public r-idpmisc + (package + (name "r-idpmisc") + (version "1.1.19") + (source + (origin + (method url-fetch) + (uri (cran-uri "IDPmisc" version)) + (sha256 + (base32 + "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd")))) + (properties `((upstream-name . "IDPmisc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "https://cran.r-project.org/web/packages/IDPmisc/") + (synopsis "Functions for data analyses and visualization") + (description + "This package provides different high-level graphics functions for +displaying large datasets, displaying circular data in a very flexible way, +finding local maxima, brewing color ramps, drawing nice arrows, zooming +2D-plots, creating figures with differently colored margin and plot region. +In addition, the package contains auxiliary functions for data manipulation +like omitting observations with irregular values or selecting data by logical +vectors, which include NAs. Other functions are especially useful in +spectroscopy and analyses of environmental data: robust baseline fitting, +finding peaks in spectra, converting humidity measures.") + (license license:gpl3+))) + +(define-public r-qqman + (package + (name "r-qqman") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "qqman" version)) + (sha256 + (base32 + "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s")))) + (properties `((upstream-name . "qqman"))) + (build-system r-build-system) + (propagated-inputs + `(("r-calibrate" ,r-calibrate))) + (home-page "https://cran.r-project.org/web/packages/qqman/") + (synopsis "Q-Q and Manhattan plots for GWAS data") + (description + "This package allows you to create Q-Q and Manhattan plots for GWAS data +from PLINK results.") + (license license:gpl3))) + +(define-public r-ggplot-multistats + (package + (name "r-ggplot-multistats") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggplot.multistats" version)) + (sha256 + (base32 + "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il")))) + (properties + `((upstream-name . "ggplot.multistats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-hexbin" ,r-hexbin) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales))) + (home-page "https://github.com/flying-sheep/ggplot.multistats") + (synopsis "Multiple summary statistics for binned stats/geometries") + (description + "This package provides the ggplot binning layer @code{stat_summaries_hex()}, +which functions similar to its singular form, but allows the use of multiple +statistics per bin. Those statistics can be mapped to multiple bin +aesthetics.") + (license license:gpl3))) + +(define-public r-knn-covertree + (package + (name "r-knn-covertree") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "knn.covertree" version)) + (sha256 + (base32 + "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz")))) + (properties `((upstream-name . "knn.covertree"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (home-page "https://github.com/flying-sheep/knn.covertree") + (synopsis "Accurate kNN Implementation with multiple distance measures") + (description + "Similarly to the FNN package, this package allows calculation of the k +nearest neighbors (kNN) of a data matrix. The implementation is based on +cover trees introduced by Alina Beygelzimer, Sham Kakade, and John +Langford (2006) @url{doi:10.1145/1143844.1143857}.") + (license license:agpl3+))) + +(define-public r-poibin + (package + (name "r-poibin") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "poibin" version)) + (sha256 + (base32 + "1rllgmk7yanb5amysl33kmi11lx86q5kqblyb8qqb3ckj2w4jhm2")))) + (properties `((upstream-name . "poibin"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/poibin/") + (synopsis "Poisson binomial distribution") + (description + "This package provides an implementation of both the exact and +approximation methods for computing the @dfn{cumulative distribution +function} (CDF) of the Poisson binomial distribution. It also provides the +@dfn{probability mass function} (PMF), quantile function, and random number +generation for the Poisson binomial distribution.") + (license license:gpl2))) + +(define-public r-diagram + (package + (name "r-diagram") + (version "1.6.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "diagram" version)) + (sha256 + (base32 + "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw")))) + (properties `((upstream-name . "diagram"))) + (build-system r-build-system) + (propagated-inputs + `(("r-shape" ,r-shape))) + (home-page "https://cran.r-project.org/web/packages/diagram/") + (synopsis "Visualize simple graphs (networks) and plot flow diagrams") + (description + "This package provides tools to visualize simple graphs (networks) based +on a transition matrix, utilities to plot flow diagrams, visualizing webs, +electrical networks, etc. It also includes supporting material for the book +\"A practical guide to ecological modelling - using R as a simulation +platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book +\"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and +Francesca Mazzia (2012).") + (license license:gpl2+))) + +(define-public r-lim + (package + (name "r-lim") + (version "1.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "LIM" version)) + (sha256 + (base32 + "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8")))) + (properties `((upstream-name . "LIM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-diagram" ,r-diagram) + ("r-limsolve" ,r-limsolve))) + (home-page "https://cran.r-project.org/web/packages/LIM/") + (synopsis "Linear inverse model examples and solution methods") + (description + "This package provides functions that read and solve linear inverse +problems (food web problems, linear programming problems).") + (license license:gpl2+))) + +(define-public r-shinycssloaders + (package + (name "r-shinycssloaders") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinycssloaders" version)) + (sha256 + (base32 + "1bpzsm7m7c366sjl1qndp4m5dg2vlm68rjgdy9n1ija9xbp0r2g4")))) + (properties + `((upstream-name . "shinycssloaders"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-glue" ,r-glue) + ("r-shiny" ,r-shiny))) + (home-page "https://github.com/andrewsali/shinycssloaders") + (synopsis "Add CSS loading animations to Shiny outputs") + (description + "This package provides tools to create a lightweight Shiny wrapper for +the css-loaders created by Luke Hass +@url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will +automatically show a loader when the output is (re)calculating.") + (license license:gpl3))) + +(define-public r-rsvg + (package + (name "r-rsvg") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "rsvg" version)) + (sha256 + (base32 + "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g")))) + (properties `((upstream-name . "rsvg"))) + (build-system r-build-system) + (inputs + `(("librsvg" ,librsvg) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/jeroen/rsvg#readme") + (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays") + (description + "This package allows you to render vector-based SVG images into +high-quality custom-size bitmap arrays using the librsvg2 library. The +resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In +addition, the package can convert images directly to various formats such as +PDF or PostScript.") + (license license:expat))) + +(define-public r-influencer + (package + (name "r-influencer") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "influenceR" version)) + (sha256 + (base32 + "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag")))) + (properties `((upstream-name . "influenceR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix))) + (home-page "https://github.com/rcc-uchicago/influenceR") + (synopsis "Tools to quantify structural importance of nodes in a network") + (description + "This package provides functionality to compute various node centrality +measures on networks. Included are functions to compute betweenness +centrality (by utilizing Madduri and Bader's SNAP library), implementations of +Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's +algorithm to identify key players, and Valente's bridging metric. The +betweenness, Key Players, and bridging implementations are parallelized with +OpenMP.") + (license license:gpl2))) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index e63823de2c..db39166d45 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -884,10 +884,10 @@ trivial to build for local use. Portability is emphasized over performance.") (license license:unlicense))) (define-public libsecp256k1 - (let ((commit "e34ceb333b1c0e6f4115ecbb80c632ac1042fa49")) + (let ((commit "d644dda5c9dbdecee52d1aa259235510fdc2d4ee")) (package (name "libsecp256k1") - (version (git-version "20181126" "1" commit)) + (version (git-version "20191213" "1" commit)) (source (origin (method git-fetch) (uri (git-reference @@ -895,7 +895,7 @@ trivial to build for local use. Portability is emphasized over performance.") (commit commit))) (sha256 (base32 - "0as78s179hcr3ysk3fw98k5wzabgnwri7vkkc17wg31lyz6ids6c")) + "0zmx32746khsm2cx0p3pdy3j2vkwmafvf7axiixijhgcg0xjv93i")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 0f04647a73..2482977c66 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -17,7 +17,7 @@ ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org> ;;; Copyright © 2016 Andy Patterson <ajpatter@uwaterloo.ca> ;;; Copyright © 2016 Danny Milosavljevic <dannym+a@scratchpost.org> -;;; Copyright © 2016, 2017, 2018 Marius Bakke <mbakke@fastmail.com> +;;; Copyright © 2016, 2017, 2018, 2019 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2017, 2018 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be> ;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org> @@ -125,6 +125,7 @@ #:use-module (guix build-system ruby) #:use-module (guix build-system cmake) #:use-module (guix build-system scons) + #:use-module (guix build-system trivial) #:use-module ((guix build utils) #:hide (which)) #:use-module (guix utils) #:use-module (srfi srfi-1) @@ -913,6 +914,33 @@ Language.") as a drop-in replacement of MySQL.") (license license:gpl2))) +;; TODO: mysql_install_db is broken in MariaDB. This package is here as +;; a workaround for packages that need it. Merge with 'mariadb' in the next +;; rebuild cycle. +(define-public mariadb/fixed-install-db + (hidden-package + (package/inherit + mariadb + (name "mariadb-fixed") + (native-inputs '()) + (inputs + `(("mariadb" ,mariadb) + ("mariadb:lib" ,mariadb "lib"))) + (outputs '("out")) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules ((guix build utils))) + (let ((out (assoc-ref %outputs "out"))) + (copy-recursively (assoc-ref %build-inputs "mariadb") out) + (substitute* (string-append out "/bin/mysql_install_db") + (("\\$basedir/share/mysql") + (string-append (assoc-ref %build-inputs "mariadb:lib") + "/share/mysql"))) + #t))))))) + ;; Don't forget to update the other postgresql packages when upgrading this one. (define-public postgresql (package @@ -3247,25 +3275,29 @@ simultaneous database connections by using this framework.") "0m680h8cc4428xin4p733azysamzgzcmv4psjvraykrsaz6ymlj3")))) (build-system gnu-build-system) (native-inputs - `(("inetutils" ,inetutils) - ("glibc-locales" ,glibc-locales))) + `(;; For tests. + ("inetutils" ,inetutils) + ("glibc-locales" ,glibc-locales) + ("mariadb" ,mariadb/fixed-install-db))) (inputs `(("libdbi" ,libdbi) - ("mysql" ,mariadb) + ("mariadb:dev" ,mariadb "dev") + ("mariadb:lib" ,mariadb "lib") ("postgresql" ,postgresql) ("sqlite" ,sqlite))) (arguments `(#:configure-flags (let ((libdbi (assoc-ref %build-inputs "libdbi")) - (mysql (assoc-ref %build-inputs "mysql")) + (mysql:inc (assoc-ref %build-inputs "mariadb:dev")) + (mysql:lib (assoc-ref %build-inputs "mariadb:lib")) (postgresql (assoc-ref %build-inputs "postgresql")) (sqlite (assoc-ref %build-inputs "sqlite"))) (list "--disable-docs" (string-append "--with-dbi-incdir=" libdbi "/include") (string-append "--with-dbi-libdir=" libdbi "/lib") "--with-mysql" - (string-append "--with-mysql-incdir=" mysql "/include/mysql") - (string-append "--with-mysql-libdir=" mysql "/lib") + (string-append "--with-mysql-incdir=" mysql:inc "/include/mysql") + (string-append "--with-mysql-libdir=" mysql:lib "/lib") "--with-pgsql" (string-append "--with-pgsql-incdir=" postgresql "/include") (string-append "--with-pgsql-libdir=" postgresql "/lib") @@ -3279,7 +3311,7 @@ simultaneous database connections by using this framework.") (substitute* "tests/test_mysql.sh" (("^MYMYSQLD=.*") (string-append "MYMYSQLD=" - (assoc-ref inputs "mysql") + (assoc-ref inputs "mariadb") "/bin/mysqld"))) #t)) (add-after 'install 'remove-empty-directories diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index 7fe7766a15..93630f3bb6 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -67,7 +67,7 @@ #:use-module (ice-9 match)) (define-public diffoscope - (let ((version "131")) + (let ((version "133")) (package (name "diffoscope") (version version) @@ -79,7 +79,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0jai3kycjlrc64f4vg8yklri6ds1451qy6r6sw2646bhjr0gs233")))) + "0mvg5iyd3zjxsm66vax3qb89214j3wxcklvbhfrr8jlbzaw9pznh")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -90,6 +90,12 @@ (lambda _ (substitute* "setup.py" (("'python-magic',") "")))) + ;; Patch in support for known tools + (add-after 'unpack 'add-known-tools + (lambda _ + (substitute* "diffoscope/external_tools.py" + (("'debian': 'zstd'") + "'debian': 'zstd', 'guix': 'zstd'")))) ;; This test is broken because our `file` package has a ;; bug in berkeley-db file type detection. (add-after 'unpack 'remove-berkeley-test @@ -209,7 +215,8 @@ ("wabt" ,wabt) ("xxd" ,xxd) ("xz" ,xz) - ("zip" ,zip))) + ("zip" ,zip) + ("zstd" ,zstd))) (home-page "https://diffoscope.org/") (synopsis "Compare files, archives, and directories in depth") (description diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ae7e7a64cc..1fd75a8240 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1241,6 +1241,30 @@ or unexpected behavior inside an elisp configuration file (typically "Emacs-wget is an emacs interface for the wget file downloader.") (license license:gpl2+))) +(define-public emacs-eww-lnum + (package + (name "emacs-eww-lnum") + (version "1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/m00natic/eww-lnum.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gs6bi3s2sszc6v2b26929azmn5513kvyin99n4d0ark1jdbjmv2")))) + (build-system emacs-build-system) + (home-page "https://github.com/m00natic/eww-lnum") + (synopsis "Conkeror-like functionality for Eww") + (description "This is extension to the Emacs browser Eww that adds +Conkeror-like functionality. In short, currently visible links, forms, +buttons are temporarily assigned numbers with which the former can be +immediately activated. Also filtering can be applied so selection can be +incrementally confined in Isearch manner.") + (license license:gpl3+))) + + ;;; ;;; Multimedia. @@ -1586,7 +1610,7 @@ rather than the contents of files.") (package (name "emacs-async") (home-page "https://github.com/jwiegley/emacs-async") - (version "1.9.3") + (version "1.9.4") (source (origin (method git-fetch) (uri (git-reference @@ -1595,7 +1619,7 @@ rather than the contents of files.") (file-name (git-file-name name version)) (sha256 (base32 - "1zsnb6dy8p6y68xgidv3dfxaga4biramfw8fq7wac0sc50vc98vq")))) + "0hhpyxb3d531jb2f3wvzx25183f0anm8nxv6mh0p825q2gkm6ly7")))) (build-system emacs-build-system) (synopsis "Asynchronous processing in Emacs") (description @@ -1720,7 +1744,7 @@ Emacs buffer.") (define-public emacs-direnv (package (name "emacs-direnv") - (version "1.5.0") + (version "2.0.0") (source (origin (method git-fetch) @@ -1730,7 +1754,7 @@ Emacs buffer.") (file-name (git-file-name name version)) (sha256 (base32 - "02blhinkkfh3iai6j1k5swplf5mkwijy3p7wy38rnd1gnyj2z4la")))) + "005ibyzsx1fdyrl5iyhqpb1bg83mphzahq7zvw58x00syyqi2z49")))) (build-system emacs-build-system) (propagated-inputs `(("dash" ,emacs-dash) @@ -2682,16 +2706,16 @@ keep pressing the key until it selects what you want. There's also (define-public emacs-fill-column-indicator (package (name "emacs-fill-column-indicator") - (version "1.89") + (version "1.90") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/alpaker/Fill-Column-Indicator.git") - (commit (string-append "v" version)))) + (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "010kf8jsly74y7m6mmkn1h6y205kz23zphs50zgy2nag2p88rz9y")))) + (base32 "0snjznxdwwfdgccdcvrnk467416r244r2r5qcm2sga8l0ha9gw9z")))) (build-system emacs-build-system) (home-page "https://www.emacswiki.org/emacs/FillColumnIndicator") (synopsis "Graphically indicate the fill column") @@ -2786,16 +2810,16 @@ Emacs shell script.") (define-public emacs-undercover (package (name "emacs-undercover") - (version "0.6.0") + (version "0.6.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/sviridov/undercover.el.git") - (commit (string-append "v" version)))) + (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "06qcvbp5rd0kh3ibrxj5p6r578lwsrgd7yj5c6slwmkdmna2fj33")))) + (base32 "080bmfwyfi8663y8x594770hqz7mff7zvj2v03qdfwbhdr9w9y29")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) @@ -2810,7 +2834,7 @@ Lisp.") (define-public emacs-paren-face (package (name "emacs-paren-face") - (version "1.0.0") + (version "1.0.4") (source (origin (method git-fetch) @@ -2819,7 +2843,8 @@ Lisp.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0f128gqn170s6hl62n44i9asais75ns1mpvb4l8vzy1sc0v16c0k")))) + (base32 + "1cr0vnm57lxs48z17ddcv7qlfvks7wdsp01zsw0c7i3h5ajl8myp")))) (build-system emacs-build-system) (home-page "https://github.com/tarsius/paren-face") (synopsis "Face for parentheses in lisp modes") @@ -3053,7 +3078,7 @@ their original location with another.") (define-public emacs-rich-minority (package (name "emacs-rich-minority") - (version "1.0.1") + (version "1.0.3") (source (origin (method git-fetch) @@ -3062,7 +3087,8 @@ their original location with another.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "11hwf9y5ax207w6rwrsmi3pmn7pn7ap6iys0z8hni2f5zzxjrmx3")))) + (base32 + "1kn7c9qr9ykj68iqffzzmjsr6aazwac8cxb7j960sjb282rq0yyj")))) (build-system emacs-build-system) (home-page "https://github.com/Malabarba/rich-minority") (synopsis "Clean-up and beautify the list of minor modes") @@ -3468,16 +3494,16 @@ minibuffer to enable editing the minibuffer input in another buffer with (define-public emacs-ob-ipython (package (name "emacs-ob-ipython") - (version "20150704.8807064693") + (version "20180224") (source (origin (method git-fetch) (uri (git-reference - (commit "880706469338ab59b5bb7dbe8460016f89755364") + (commit "7147455230841744fb5b95dcbe03320313a77124") (url "https://github.com/gregsexton/ob-ipython.git"))) (file-name (git-file-name name version)) (sha256 (base32 - "1scf25snbds9ymagpny30ijbsg479r3nm0ih01dy4m9d0g7qryb7")))) + "1a10fc2jk37ni5sjjvf87s5nyaz2a6h2mlj5dxh4dhv5sd3bb85p")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-f" ,emacs-f))) @@ -4363,7 +4389,7 @@ and popup menus.") (define-public emacs-jedi (package (name "emacs-jedi") - (version "0.2.7") + (version "0.2.8") (source (origin (method git-fetch) (uri (git-reference @@ -4372,7 +4398,7 @@ and popup menus.") (file-name (git-file-name name version)) (sha256 (base32 - "0xbp9fcxgbf298w05hvf52z41kk7r52975ailgdn8sg60xc98fa7")))) + "1bckxppfzd5gwn0aw4h86igb7igal9axqncq7j8zmflg7zppncf1")))) (build-system emacs-build-system) (native-inputs `(("emacs-mocker" ,emacs-mocker))) @@ -4669,7 +4695,7 @@ overview of tasks in a subtree.") (define-public emacs-org-trello (package (name "emacs-org-trello") - (version "0.8.0") + (version "0.8.1") (source (origin (method git-fetch) @@ -4678,7 +4704,8 @@ overview of tasks in a subtree.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0m5hyhb6211hdmyp1bq6f3fklfgw3957knd96bfdafj727vdnlzm")))) + (base32 + "02gx3kv4mkij69ln8x8wf9n28x17pbb4kv85v78d3lxph7ykqimc")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) @@ -6352,7 +6379,7 @@ and tooling.") (define-public emacs-elfeed (package (name "emacs-elfeed") - (version "3.2.0") + (version "3.3.0") (source (origin (method git-fetch) @@ -6361,7 +6388,7 @@ and tooling.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0m0a35210pb4yf6m8mzaq6nkl9x6fphjjqyl3dzygnmmzxkc8aw2")))) + (base32 "0j8a94val4ml7g1vcjgzk1w89h55sxfdrwnncmz6qbh1y2xsz8c5")))) (build-system emacs-build-system) (arguments `(#:tests? #t @@ -6479,7 +6506,7 @@ maximizes flexibility (at the expense of conciseness).") (define-public emacs-find-file-in-project (package (name "emacs-find-file-in-project") - (version "5.4.7") + (version "5.7.7") (source (origin (method git-fetch) (uri (git-reference @@ -6488,19 +6515,13 @@ maximizes flexibility (at the expense of conciseness).") (file-name (git-file-name name version)) (sha256 (base32 - "1sdnyqv69mipbgs9yax88m9b6crsa59rjhwrih197pifl4089awr")))) + "1skjbh7m0cck2rwmgzrrds51gipqf1jqghyfx15drc1n6kwivx3h")))) (build-system emacs-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'set-shell - ;; Otherwise Emacs shell-file-name is set to "/bin/sh", which doesn't - ;; work. - (lambda _ - (setenv "SHELL" (which "sh")) - #t))) - #:tests? #t - #:test-command '("./tests/test.sh"))) + `(#:tests? #t + #:test-command '("ert-runner" "tests"))) + (native-inputs + `(("ert-runner" ,emacs-ert-runner))) (home-page "https://github.com/technomancy/find-file-in-project") (synopsis "File/directory finder for Emacs") (description "@code{find-file-in-project} allows to find files or @@ -6646,7 +6667,7 @@ completion, interactive development and more.") (define-public emacs-rainbow-delimiters (package (name "emacs-rainbow-delimiters") - (version "2.1.3") + (version "2.1.4") (source (origin (method git-fetch) (uri (git-reference @@ -6655,7 +6676,7 @@ completion, interactive development and more.") (file-name (git-file-name name version)) (sha256 (base32 - "0vs9pf8lqq5p5qz1770pxgw47ym4xj8axxmwamn66br59mykdhv0")))) + "1zr2669savnmkc68hiqsq9wccm6bs1j6jbmlac1xqh6nq7xgq36g")))) (build-system emacs-build-system) (home-page "https://github.com/Fanael/rainbow-delimiters") (arguments @@ -6740,7 +6761,7 @@ window edge.") (define-public emacs-writeroom (package (name "emacs-writeroom") - (version "3.7") + (version "3.9") (source (origin (method git-fetch) @@ -6749,7 +6770,8 @@ window edge.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "13nbls5qxz5z8firjxaip8m9vzfbbpxmwrmr01njbk4axpwrpj0z")))) + (base32 + "1nrppnfqsaki6myp58w8jhmzb94rzskh5n98glcn4ghr8sqnafi8")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-visual-fill-column" ,emacs-visual-fill-column))) @@ -6909,7 +6931,7 @@ ack, ag, helm and pt.") (define-public emacs-helm (package (name "emacs-helm") - (version "3.5.0") + (version "3.6.0") (source (origin (method git-fetch) @@ -6918,7 +6940,7 @@ ack, ag, helm and pt.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "07bijcnfkv60l3swasxv53x32l6glds05mxnbb3xbnmkgm1pm9if")))) + (base32 "0miq2q52pbicijp7pmj0widk252qixswywc03d120s4hya2b7vd7")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-async" ,emacs-async) @@ -6936,8 +6958,8 @@ not tied in the trap of backward compatibility.") (license license:gpl3+))) (define-public emacs-helm-org - (let ((commit "542dda7bc9a3b9dfb439e4f8a1e5f60cfb6cc256") - (revision "1")) + (let ((commit "b9a1167b0716a22a69670f4c35e0ac59d2e0b220") + (revision "2")) (package (name "emacs-helm-org") (version (git-version "1.0" revision commit)) @@ -6949,7 +6971,7 @@ not tied in the trap of backward compatibility.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1xa32w80icrykpyfb89fhb0s4l7ysi0sc7f7lfwqz5najwbgqipl")))) + (base32 "1gc27i4azqpgijva1f4ckfdp4s52mc9pnfcmzhkwhknr6pd6jlcr")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-helm" ,emacs-helm))) @@ -7146,7 +7168,7 @@ target will call @code{compile} on it.") (define-public emacs-cider (package (name "emacs-cider") - (version "0.21.0") + (version "0.23.0") (source (origin (method git-fetch) @@ -7156,7 +7178,7 @@ target will call @code{compile} on it.") (file-name (git-file-name name version)) (sha256 (base32 - "0lbrwj67fnvynkdkzvnzp3p8vqlz0ldrcs317vg60bqfhx7hvqkj")))) + "05yjkqc6d4grq9z5pxmv3anqh4zlhfg4v46jlccp6ynh030g7axs")))) (build-system emacs-build-system) (arguments '(#:exclude ; Don't exclude 'cider-test.el'. @@ -7164,10 +7186,12 @@ target will call @code{compile} on it.") (propagated-inputs `(("emacs-clojure-mode" ,emacs-clojure-mode) ("emacs-sesman" ,emacs-sesman) + ("emacs-seq" ,emacs-seq) ("emacs-spinner" ,emacs-spinner) + ("emacs-parseedn" ,emacs-parseedn) ("emacs-pkg-info" ,emacs-pkg-info) ("emacs-queue" ,emacs-queue))) - (home-page "https://cider.readthedocs.io/") + (home-page "https://cider.mx/") (synopsis "Clojure development environment for Emacs") (description "CIDER (Clojure Interactive Development Environment that Rocks) aims to @@ -9134,7 +9158,7 @@ to the home page or read the comments in the source file, (define-public emacs-htmlize (package (name "emacs-htmlize") - (version "1.53") + (version "1.55") (source (origin (method git-fetch) @@ -9143,7 +9167,7 @@ to the home page or read the comments in the source file, (commit (string-append "release/" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0dr235c0z8is3pi5xdgqyqljg6px0b2aya6qb79zkyi477bmz4ip")))) + (base32 "0gi3xshscpa53qrj8yplfsqahcilc2ybcc2p7gnh5nbnf2n1n97x")))) (build-system emacs-build-system) (home-page "https://github.com/hniksic/emacs-htmlize") (synopsis "Convert buffer text and decorations to HTML") @@ -19783,38 +19807,47 @@ contrast and few colors.") (license license:gpl3+)))) (define-public emacs-doom-themes - (package - (name "emacs-doom-themes") - (version "2.1.6") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/hlissner/emacs-doom-themes.git") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "042pzcdhxi2z07jcscgjbaki9nrrm0cbgbbrnymd1r4q8ckkn8l9")))) - (build-system emacs-build-system) - (native-inputs - `(("emacs-ert-runner" ,emacs-ert-runner))) - (arguments - `(#:tests? #t - #:test-command '("ert-runner") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'move-themes - (lambda _ - ;; Move the source files to the top level, which is in the - ;; EMACSLOADPATH. - (for-each (lambda (f) - (rename-file f (basename f))) - (find-files "./themes" ".*\\.el$")) - #t))))) - (synopsis "Wide collection of color themes for Emacs") - (description "Emacs-doom-themes contains numerous popular color themes for + (let ((commit "088bfad9a6983c42016da33cd11b9ee855451dcb") + (revision "2") + (version "2.1.6")) + (package + (name "emacs-doom-themes") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hlissner/emacs-doom-themes.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1dmq0vja1k907id56y4012cm3f49vf106v3gglk9sf4kbi9cash2")))) + (build-system emacs-build-system) + (native-inputs + `(("emacs-ert-runner" ,emacs-ert-runner))) + (arguments + `(#:tests? #t + #:test-command '("ert-runner") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'move-themes + (lambda _ + ;; Move the source files to the top level, which is in the + ;; EMACSLOADPATH. + (for-each (lambda (f) + (rename-file f (basename f))) + (find-files "./themes" ".*\\.el$")) + #t)) + ;; XXX: There is a byte-code overflow issue in the latest + ;; checkout which affects byte-compilation for several theme + ;; files. The easiest way to work around this is to disable + ;; byte-compilation until the issue is resolved. + ;; <https://github.com/hlissner/emacs-doom-themes/issues/314> + (delete 'build)))) + (synopsis "Wide collection of color themes for Emacs") + (description "Emacs-doom-themes contains numerous popular color themes for Emacs that integrate with major modes like Org-mode.") - (home-page "https://github.com/hlissner/emacs-doom-themes") - (license license:expat))) + (home-page "https://github.com/hlissner/emacs-doom-themes") + (license license:expat)))) (define-public emacs-modus-themes (package @@ -20048,34 +20081,35 @@ Google guidelines.") (license license:gpl3+)))) (define-public emacs-helm-fish-completion - (let ((commit "ef764dd123040fe67ef8b62a1c13842e940b0963") - (revision "1")) - (package - (name "emacs-helm-fish-completion") - (version (git-version "0.1" revision commit)) - (home-page "https://github.com/emacs-helm/helm-fish-completion") - (source - (origin - (method git-fetch) - (uri (git-reference - (url home-page) - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0k80kpapwfq2rv1lb0r994d0w6czl92xrmnkmrg0a05f4b3q0lb4")))) - (build-system emacs-build-system) - (propagated-inputs - `(("helm" ,emacs-helm) - ("fish-completion" ,emacs-fish-completion))) - (synopsis "Helm interface for Emacs fish-completion") - (description "Helm Fish Completion is a Helm interface for Emacs + (package + (name "emacs-helm-fish-completion") + (version "0.2") + (home-page "https://github.com/emacs-helm/helm-fish-completion") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "089gp2k22xwn33z8brpyb7r18vpyralq2cwxj1xsc8b2sj9s4896")))) + (build-system emacs-build-system) + (propagated-inputs + `(("helm" ,emacs-helm) + ("fish-completion" ,emacs-fish-completion))) + (synopsis "Helm interface for Emacs fish-completion") + (description "Helm Fish Completion is a Helm interface for Emacs fish-completion. It can be used in both Eshell and M-x shell.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-telega + ;; This package has versions newer than indicated on MELPA. + ;; Get the current version from `telega-version` in telega.el. + ;; or by running M-x telega-version. (let ((commit "6184e76990db395bea02f7b5d3169e746111e1ad") - (revision "2") - (version "0.5.2")) + (revision "1") + (version "0.5.3")) (package (name "emacs-telega") (version (git-version version revision commit)) @@ -20113,10 +20147,24 @@ fish-completion. It can be used in both Eshell and M-x shell.") (("python3 run_tests.py") "")) #t)) - ;; Modify telega-util to reflect unique dir name in - ;; `telega-install-data' phase. - (add-after 'unpack 'telega-data-patch - (lambda _ + (add-after 'unpack 'telega-paths-patch + (lambda* (#:key inputs #:allow-other-keys) + ;; Hard-code paths to `ffplay` and `ffmpeg`. + (let ((ffplay-bin (string-append (assoc-ref inputs "ffmpeg") + "/bin/ffplay")) + (ffmpeg-bin (string-append (assoc-ref inputs "ffmpeg") + "/bin/ffmpeg"))) + (substitute* "telega-ffplay.el" + (("\\(executable-find \"ffplay\"\\)") + (string-append + "(and (file-executable-p \"" ffplay-bin "\")" + "\"" ffplay-bin "\")")) + (("\\(executable-find \"ffmpeg\"\\)") + (string-append + "(and (file-executable-p \"" ffmpeg-bin "\")" + "\"" ffmpeg-bin "\")")))) + ;; Modify telega-util to reflect unique dir name in + ;; `telega-install-data' phase. (substitute* "telega-util.el" (("\\(concat \"etc/\" filename\\) telega--lib-directory") "(concat \"telega-data/\" filename) @@ -20149,7 +20197,6 @@ fish-completion. It can be used in both Eshell and M-x shell.") (invoke "python3" "server/run_tests.py") #t)) (delete 'configure) - ;; Build emacs-side using `emacs-build-system' (add-after 'compress-documentation 'emacs-add-source-to-load-path (assoc-ref emacs:%standard-phases 'add-source-to-load-path)) @@ -20168,9 +20215,10 @@ fish-completion. It can be used in both Eshell and M-x shell.") (assoc-ref emacs:%standard-phases 'build)) (add-after 'emacs-build 'emacs-make-autoloads (assoc-ref emacs:%standard-phases 'make-autoloads))))) + (inputs + `(("ffmpeg" ,ffmpeg))) ; mp4/gif support. (propagated-inputs `(("emacs-visual-fill-column" ,emacs-visual-fill-column) - ("ffmpeg" ,ffmpeg) ; mp4/gif support. ("libwebp" ,libwebp))) ; sticker support. (native-inputs `(("tdlib" ,tdlib) @@ -20186,7 +20234,7 @@ Telegram messaging platform.") (define-public emacs-doom-modeline (package (name "emacs-doom-modeline") - (version "2.8.0") + (version "2.8.2") (source (origin (method git-fetch) (uri (git-reference @@ -20194,7 +20242,7 @@ Telegram messaging platform.") (commit (string-append "v" version)))) (sha256 (base32 - "12zksk0rwpgpdc00km3z0hmc8wm1j1r8lbwn4kivniw56mgy0n22")) + "11srz1mr821axggs2jcmdhihxx09a2dniqv3n039wbdfaimfaidz")) (file-name (git-file-name name version)))) (build-system emacs-build-system) (arguments @@ -20499,3 +20547,73 @@ on removable volumes in Linux.") data, including buffers, window configuration, variables, and more.") (home-page "https://github.com/thierryvolpiatto/psession") (license license:gpl3+)))) + +(define-public emacs-parseedn + (package + (name "emacs-parseedn") + (version "0.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/clojure-emacs/parseedn.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "11wi3hwcgmy54p6ivpijqm7v0hj6j75a19qk5z779bqfrp79b4pc")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-a" ,emacs-a) + ("emacs-parseclj" ,emacs-parseclj))) + (home-page "https://cider.mx") + (synopsis "EDN parser for Emacs Lisp") + (description + "An Emacs Lisp library for parsing EDN (Clojure) data. +It uses parseclj's shift-reduce parser internally.") + (license license:gpl3+))) + +(define-public emacs-parseclj + (package + (name "emacs-parseclj") + (version "0.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/clojure-emacs/parseclj.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03bm5dm4hmkqimv4wqxjjh5814pxysmm7z54bv2rf7zwv1x7dggr")))) + (build-system emacs-build-system) + (propagated-inputs `(("emacs-a" ,emacs-a))) + (home-page "https://cider.mx") + (synopsis "Clojure parser for Emacs Lisp") + (description + "An Emacs Lisp library for parsing Clojure code and EDN data. +It supports several input and output formats, all powered by the +same shift-reduce parser function.") + (license license:gpl3+))) + +(define-public emacs-hide-mode-line + (package + (name "emacs-hide-mode-line") + (version "1.0.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hlissner/emacs-hide-mode-line.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0dfzjgxfkcw4wisbyldsm1km18pfp9j8xgadn6qnsz11l55bpgyp")))) + (build-system emacs-build-system) + (synopsis "Emacs plugin that hides the mode-line") + (description "A minor mode that hides the mode-line in your current +buffer. It can be used to toggle an alternative mode-line, toggle its visibility, +or simply disable the mode-line in buffers where it is not very useful.") + (home-page "https://github.com/hlissner/emacs-hide-mode-line") + (license license:expat))) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 5588fe00ea..ce3033c054 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -445,28 +445,31 @@ other machines/servers. Electrum does not download the Bitcoin blockchain.") (package (inherit electrum) (name "electron-cash") - (version "4.0.10") + (version "4.0.12") (source (origin - (method url-fetch) - (uri (string-append "https://electroncash.org/downloads/" - version - "/win-linux/Electron-Cash-" - version - ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/Electron-Cash/Electron-Cash.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1rcywlma6hk52ymisx536jvkdwa73rhn1jxhsbs4wbvajl90w9s8")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Delete the bundled dependencies. - (delete-file-recursively "packages") - #t)))) + "0gidrx8499v7rig7ljhd70wssshs1qm0gp1553g70i323hcbf62x")))) (inputs `(,@(package-inputs electrum) + ("libsecp256k1", libsecp256k1) ("python-dateutil", python-dateutil) ("python-dnspython", python-dnspython))) + (arguments + (substitute-keyword-arguments (package-arguments electrum) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'use-libsecp256k1-input + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "lib/secp256k1.py" + (("library_paths = .* 'libsecp256k1.so.0'.") + (string-append "library_paths = ('" (assoc-ref inputs "libsecp256k1") "/lib/libsecp256k1.so.0'"))))))))) (home-page "https://electroncash.org/") (synopsis "Bitcoin Cash wallet") (description diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 833f00b77c..febe15fa57 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz> ;;; Copyright © 2019 Leo Prikler <leo.prikler@student.tugraz.at> +;;; Copyright © 2019 Jethro Cao <jethrocao@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -653,6 +654,37 @@ programming language.") (home-page "https://love2d.org/") (license license:zlib))) +(define-public love-nuklear + (let ((version "v2.6") + (commit "fef4e00a602efb16c57ae962850b6e7a01f7a29a")) + (package + (name "love-nuklear") + (version (git-version version "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/keharriso/love-nuklear/") + (commit commit) + (recursive? #t))) + ;; NOTE: the HEAD of the Nuklear git-submodule is at commit + ;; "adc52d710fe3c87194b99f540c53e82eb75c2521" of Oct 1 2019 + (file-name (git-file-name name version)) + (sha256 + (base32 + "15qmy8mfwkxy2x9rmxs6f9cyvjvwwj6yf78bs863xmc56dmjzzbn")))) + (build-system cmake-build-system) + (arguments + `(#:build-type "Release" + #:tests? #f)) + (inputs + `(("luajit" ,luajit))) + (synopsis "Lightweight immediate mode GUI for LÖVE games") + (description "LÖVE is a Lua framework for making 2D games. Nuklear +is a minimal state immediate mode graphical user interface toolkit. This +package is the Nuklear bindings for LÖVE created by Kevin Harrison.") + (home-page "https://github.com/keharriso/love-nuklear/") + (license license:expat)))) + (define-public allegro-4 (package (name "allegro") diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index ded27c1f63..c8d671bbdc 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -502,6 +502,45 @@ cows can think too: all you have to do is run @command{cowthink}. If you're tired of cows, a variety of other ASCII-art messengers are available.") (license license:gpl3+))) +(define-public lolcat + (let ((commit "35dca3d0a381496d7195cd78f5b24aa7b62f2154") + (revision "0")) + (package + (name "lolcat") + (version (git-version "1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jaseg/lolcat.git") + (commit commit))) + (sha256 + (base32 + "0jjbkqcc2ikjxd1xgdyv4rb0vsw218181h89f2ywg29ffs3ypd8g")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;; no check target + #:make-flags (list "CC=gcc") + #:phases + (modify-phases %standard-phases + (delete 'bootstrap) + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (dest (string-append out "/bin"))) + (mkdir-p dest) + (install-file "lolcat" dest) + (install-file "censor" dest) + #t)))))) + (home-page "https://github.com/jaseg/lolcat") + (synopsis "Rainbow coloring effect for text console display") + (description "@command{lolcat} concatenates files and streams like +regular @command{cat}, but it also adds terminal escape codes between +characters and lines resulting in a rainbow effect.") + (license license:wtfpl2)))) + (define-public freedoom (package (name "freedoom") diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index bda6a2b48a..29b9d34569 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -649,32 +649,39 @@ as the 'native-search-paths' field." (files '("lib" "lib64"))))) (define-public gfortran-4.8 - (custom-gcc gcc-4.8 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-4.8 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-4.9 - (custom-gcc gcc-4.9 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-4.9 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-5 - (custom-gcc gcc-5 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-5 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-6 - (custom-gcc gcc-6 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-6 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-7 - (custom-gcc gcc-7 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-7 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-8 - (custom-gcc gcc-8 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-8 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran-9 - (custom-gcc gcc-9 "gfortran" '("fortran") - %generic-search-paths)) + (hidden-package + (custom-gcc gcc-9 "gfortran" '("fortran") + %generic-search-paths))) (define-public gfortran ;; Note: Update this when GCC changes! We cannot use diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 41801ed0e6..278ece094c 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1081,7 +1081,7 @@ an independent project by the JOSM team.") (define-public josm (package (name "josm") - (version "15492") + (version "15553") (source (origin (method svn-fetch) (uri (svn-reference @@ -1090,7 +1090,7 @@ an independent project by the JOSM team.") (recursive? #f))) (sha256 (base32 - "12xkwcv77as30a61w1c8a0i2b0kiiks71d487gbdfv7azlj4vqia")) + "091pbcn4fnmk42fmxplhis3nw5dbljf6ws8acyhx5dflyn49xzmx")) (file-name (string-append name "-" version "-checkout")) (modules '((guix build utils))) (snippet diff --git a/gnu/packages/gnome-xyz.scm b/gnu/packages/gnome-xyz.scm index d05bdf0ac0..00ad701ad8 100644 --- a/gnu/packages/gnome-xyz.scm +++ b/gnu/packages/gnome-xyz.scm @@ -213,3 +213,37 @@ It uses ES6 syntax and claims to be more actively maintained than others.") dark elements. It supports GNOME, Unity, Xfce, and Openbox.") (home-page "https://numixproject.github.io") (license license:gpl3+))) + +(define-public papirus-icon-theme + (let ((version "0.0.0") ;; The package does not use semver + (revision "0") + (tag "20191201")) + (package + (name "papirus-icon-theme") + (version (git-version version revision tag)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PapirusDevelopmentTeam/papirus-icon-theme.git") + (commit tag))) + (sha256 + (base32 + "0lnz1kmz28xh1f4slbsx7ycji5hgszyiyprbf5w5fbjhvi5gzw1h")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f + #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'bootstrap) + (delete 'configure) + (delete 'build)))) + (native-inputs + `(("gtk+:bin" ,gtk+ "bin"))) + (home-page "https://git.io/papirus-icon-theme") + (synopsis "Fork of Paper icon theme with a lot of new icons and a few extras") + (description "Papirus is a fork of the icon theme Paper with a lot of new icons +and a few extra features.") + (license license:gpl3)))) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 1d4d7563a5..0a9087eaff 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -193,9 +193,9 @@ (version "3.12.2") (source (origin (method url-fetch) - (uri (string-append "mirror://gnome/sources/" name "/" + (uri (string-append "mirror://gnome/sources/brasero/" (version-major+minor version) "/" - name "-" version ".tar.xz")) + "brasero-" version ".tar.xz")) (sha256 (base32 "0h90y674j26rvjahb8cc0w79zx477rb6zaqcj26wzvq8kmpic8k8")))) @@ -219,6 +219,7 @@ `(("hicolor-icon-theme" ,hicolor-icon-theme))) (native-inputs `(("intltool" ,intltool) + ("itstool" ,itstool) ("glib" ,glib "bin") ; glib-compile-schemas, etc. ("gobject-introspection" ,gobject-introspection) ("pkg-config" ,pkg-config))) @@ -229,14 +230,13 @@ ("gstreamer" ,gstreamer) ("gst-plugins-base" ,gst-plugins-base) ("gtk+" ,gtk+) - ("itstool" ,itstool) ("libcanberra" ,libcanberra) ("libice" ,libice) ("libnotify" ,libnotify) ("libsm" ,libsm) ("libxml2" ,libxml2) ("totem-pl-parser" ,totem-pl-parser))) - (home-page "https://projects.gnome.org/brasero/") + (home-page "https://wiki.gnome.org/Apps/Brasero") (synopsis "CD/DVD burning tool for Gnome") (description "Brasero is an application to burn CD/DVD for the Gnome Desktop. It is designed to be as simple as possible and has some unique @@ -328,39 +328,40 @@ either on a local, or remote machine via a number of methods.") (let ((commit "fbc306168edab63db80b904956117cbbdc514ee4")) (package (name "dia") - (version (string-append "0.97.2-" (string-take commit 7))) + (version (git-version "0.97.3" "1" commit)) (source (origin (method git-fetch) (uri (git-reference - (url "https://git.gnome.org/browse/dia") + (url "https://gitlab.gnome.org/GNOME/dia.git/") (commit commit))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 "1b4bba0k8ph4cwgw8xjglss0p6n111bpd5app67lrq79mp0ad06l")))) (build-system gnu-build-system) (inputs - `(("glib" ,glib "bin") - ("pango" ,pango) + `(("freetype" ,freetype) ("gdk-pixbuf" ,gdk-pixbuf) ("gtk+" ,gtk+-2) + ("libart-lgpl" ,libart-lgpl) ("libxml2" ,libxml2) - ("freetype" ,freetype) - ("libart-lgpl" ,libart-lgpl))) + ("pango" ,pango))) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config) + `(("autoconf" ,autoconf) ("automake" ,automake) - ("autoconf" ,autoconf) + ("intltool" ,intltool) + ("glib" ,glib "bin") ("libtool" ,libtool) ("perl" ,perl) + ("pkg-config" ,pkg-config) ("python-wrapper" ,python-wrapper))) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'run-autogen + (add-before 'bootstrap 'dont-configure-during-bootstrap (lambda _ - (system* "sh" "autogen.sh")))))) + (setenv "NOCONFIGURE" "true") + #t))))) (home-page "https://wiki.gnome.org/Apps/Dia") (synopsis "Diagram creation for GNOME") (description "Dia can be used to draw different types of diagrams, and @@ -1779,10 +1780,9 @@ library.") (version "0.8.14") (source (origin (method url-fetch) - (uri (let ((upstream-name "libIDL")) - (string-append "mirror://gnome/sources/" upstream-name "/" - (version-major+minor version) "/" - upstream-name "-" version ".tar.bz2"))) + (uri (string-append "mirror://gnome/sources/libIDL/" + (version-major+minor version) "/" + "libIDL-" version ".tar.bz2")) (sha256 (base32 "08129my8s9fbrk0vqvnmx6ph4nid744g5vbwphzkaik51664vln5")))) @@ -1799,6 +1799,7 @@ Definition Language (idl) files, which is a specification for defining portable interfaces. libidl was initially written for orbit (the orb from the GNOME project, and the primary means of libidl distribution). However, the functionality was designed to be as reusable and portable as possible.") + (properties `((upstream-name . "libIDL"))) (license license:lgpl2.0+))) @@ -5092,32 +5093,38 @@ metadata in photo and video files of various formats.") "1m9i8r4gyd2hzlxjjwfyck4kz7gdg2vz2k6l6d0ga9hdfq2l4p9l")))) (build-system meson-build-system) (arguments - '(#:glib-or-gtk? #t)) + '(#:glib-or-gtk? #t + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'skip-gtk-update-icon-cache + (lambda _ + (substitute* "build-aux/meson/postinstall.py" + (("gtk-update-icon-cache") (which "true")) + (("update-desktop-database") (which "true"))) + #t))))) (propagated-inputs `(("dconf" ,dconf))) (native-inputs - `(("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database - ("gettext" ,gettext-minimal) - ("gtk+" ,gtk+ "bin") ; gtk-update-icon-cache + `(("gettext" ,gettext-minimal) + ("glib:bin" ,glib "bin") ("itstool" ,itstool) ("pkg-config" ,pkg-config) ("vala" ,vala))) (inputs - `(("glib:bin" ,glib "bin") - ("gstreamer" ,gstreamer) + `(("gcr" ,gcr) + ("gexiv2" ,gexiv2) ("gst-plugins-base" ,gst-plugins-base) + ("gstreamer" ,gstreamer) + ("json-glib" ,json-glib) ("libgdata" ,libgdata) ("libgee" ,libgee) - ("gexiv2" ,gexiv2) + ("libgphoto2" ,libgphoto2) + ("libgudev" ,libgudev) ("libraw" ,libraw) - ("json-glib" ,json-glib) - ("webkitgtk" ,webkitgtk) - ("sqlite" ,sqlite) ("libsoup" ,libsoup) ("libxml2" ,libxml2) - ("libgudev" ,libgudev) - ("libgphoto2" ,libgphoto2) - ("gcr" ,gcr))) + ("sqlite" ,sqlite) + ("webkitgtk" ,webkitgtk))) (home-page "https://wiki.gnome.org/Apps/Shotwell") (synopsis "Photo manager for GNOME 3") (description diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm index 9d53ca5b80..8a9597a68c 100644 --- a/gnu/packages/gnunet.scm +++ b/gnu/packages/gnunet.scm @@ -149,14 +149,14 @@ tool to extract metadata from a file and print the results.") (define-public libmicrohttpd (package (name "libmicrohttpd") - (version "0.9.68") + (version "0.9.69") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/libmicrohttpd/libmicrohttpd-" version ".tar.gz")) (sha256 (base32 - "0q8bc4hrxn6llml7w2vam6n833x8injs39wgdkhwkawr50m6wwf5")))) + "0zp34zgcahym5kp2r83gfb5wnr8yf643a26k6zk96x3qica6p6zv")))) (build-system gnu-build-system) (inputs `(("curl" ,curl) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 9576f79333..b31280e39b 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -456,7 +456,7 @@ gpgpme starting with version 1.7.") (define-public guile-gcrypt (package (name "guile-gcrypt") - (version "0.2.0") + (version "0.2.1") (home-page "https://notabug.org/cwebber/guile-gcrypt") (source (origin (method git-fetch) @@ -465,7 +465,7 @@ gpgpme starting with version 1.7.") (commit (string-append "v" version)))) (sha256 (base32 - "1mhc5m4xygkfj7x18f8apiqpfdn9mrql0am5sk13cf5xn8x1r63z")) + "0n232iyayc46f7hywmjw0jr7pbmmz5h4b04jskhkzz9gxz0ci99c")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (native-inputs diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 52db619fb3..4095926af3 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -165,14 +165,14 @@ model.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "0nivz8fshaqig6ynjqbya2gmxsy4hm7jnd8fhb853z5g0ydp7g0c")))) + "00lrkbgbb4payybckcmazsv8skysgdlglyqbl7yjb37vv3gnfc6c")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) ;; FIXME: Rgraphviz bundles the sources of an older variant of diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 674b24e594..f0a022be2d 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2002,59 +2002,67 @@ The picture values can directly be displayed in Geiser.") (license license:lgpl3+)))) (define-public guile-studio - (let ((commit "98fbbbd08de396cd8a0e45f2a4badf1c733a5772") - (revision "3")) - (package - (name "guile-studio") - (version (git-version "0.0.1" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://git.elephly.net/software/guile-studio.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0rxl5gv2mavycwkl33lcwyb3z71j2f4zyzk60k7vl3hzszpr08iq")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; there are none - #:make-flags - (list (string-append "ICONS_DIR=" - (assoc-ref %build-inputs "adwaita-icon-theme") - "/share/icons/Adwaita/") - (string-append "PICT_DIR=" - (assoc-ref %build-inputs "guile-picture-language")) - (string-append "EMACS_DIR=" - (assoc-ref %build-inputs "emacs")) - (string-append "GUILE_DIR=" - (assoc-ref %build-inputs "guile")) - (string-join (cons "INPUTS=" (map cdr %build-inputs))) - (string-append "PREFIX=" (assoc-ref %outputs "out"))) - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'install)))) - (inputs - `(("guile" ,guile-2.2) - ("guile-picture-language" ,guile-picture-language) - ("emacs" ,emacs) - ("emacs-geiser" ,emacs-geiser) - ("emacs-company" ,emacs-company) - ("emacs-flycheck" ,emacs-flycheck) - ("emacs-smart-mode-line" ,emacs-smart-mode-line) - ("emacs-paren-face" ,emacs-paren-face) - ("adwaita-icon-theme" ,adwaita-icon-theme))) - (native-inputs - `(("texinfo" ,texinfo))) - (home-page "https://gnu.org/software/guile") - (synopsis "IDE for Guile") - (description - "This is Emacs with a few settings that make working with Guile easier + (package + (name "guile-studio") + (version "0.0.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.elephly.net/software/guile-studio.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10ls4ra148hd9ra7sin4kh9vv0am5pwk48p7dsjhrlg2l1hsh4hi")))) + (build-system gnu-build-system) + (arguments + `(#:modules + ((ice-9 match) + (srfi srfi-1) + ,@%gnu-build-system-modules) + #:tests? #f ; there are none + #:make-flags + (list (string-append "ICONS_DIR=" + (assoc-ref %build-inputs "adwaita-icon-theme") + "/share/icons/Adwaita/") + (string-append "PICT_DIR=" + (assoc-ref %build-inputs "guile-picture-language")) + (string-append "EMACS_DIR=" + (assoc-ref %build-inputs "emacs")) + (string-append "GUILE_DIR=" + (assoc-ref %build-inputs "guile")) + (string-join (cons "INPUTS=" + (filter-map + (lambda (input) + (match input + ((label . pkg) + (and (string-prefix? "emacs" label) pkg)))) + %build-inputs))) + (string-append "PREFIX=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'install)))) + (inputs + `(("guile" ,guile-2.2) + ("guile-picture-language" ,guile-picture-language) + ("emacs" ,emacs) + ("emacs-geiser" ,emacs-geiser) + ("emacs-company" ,emacs-company) + ("emacs-flycheck" ,emacs-flycheck) + ("emacs-smart-mode-line" ,emacs-smart-mode-line) + ("emacs-paren-face" ,emacs-paren-face) + ("adwaita-icon-theme" ,adwaita-icon-theme))) + (native-inputs + `(("texinfo" ,texinfo))) + (home-page "https://gnu.org/software/guile") + (synopsis "IDE for Guile") + (description + "This is Emacs with a few settings that make working with Guile easier for people new to Emacs. Features include: CUA mode, Geiser, tool bar icons to evaluate Guile buffers, support for Guile's very own picture language, code completion, a simple mode line, etc.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public guile-stis-parser (let ((commit "6e85d37ffc333b722f4413a6c648263701eb75bd") diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 9df008c413..5a5d1af56a 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -288,14 +288,14 @@ without requiring the source code to be rewritten.") (package (inherit guile-2.2) (name "guile-next") - (version "2.9.6") + (version "2.9.7") (source (origin (inherit (package-source guile-2.2)) (uri (string-append "ftp://alpha.gnu.org/gnu/guile/guile-" version ".tar.xz")) (sha256 (base32 - "09rihg5bhzhdk6hfkpav6ajny69dflabgvnm8r7lran723gy5vbf")))) + "1dskpj8a2gl3h8si4virq8z4y06v9ywyadfa92gn2fiip2qmkw0d")))) (native-search-paths (list (search-path-specification (variable "GUILE_LOAD_PATH") diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index b0005bd817..a518b69b8e 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -852,7 +852,7 @@ compose, and analyze GIF images.") (define-public imlib2 (package (name "imlib2") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (string-append @@ -860,7 +860,7 @@ compose, and analyze GIF images.") "/imlib2-" version ".tar.bz2")) (sha256 (base32 - "07b9v3ycwhici35fnczvpyjpgkc7gbcdhajpl9dwhpzdzbfl1i6g")))) + "0v8n3dswx7rxqfd0q03xwc7j2w1mv8lv18rdxv487a1xw5vklfad")))) (build-system gnu-build-system) (native-inputs `(("pkgconfig" ,pkg-config))) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index cc63ccf19a..d0e3fd8d33 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1,3 +1,4 @@ + ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016 Leo Famulari <leo@famulari.name> @@ -11478,7 +11479,7 @@ network protocols, and core version control algorithms.") (define-public abcl (package (name "abcl") - (version "1.5.0") + (version "1.6.0") (source (origin (method url-fetch) @@ -11486,7 +11487,7 @@ network protocols, and core version control algorithms.") version "/abcl-src-" version ".tar.gz")) (sha256 (base32 - "1hhvcg050nfpjbdmskc1cv2j38qi6qfl77a61b5cxx576kbff3lj")) + "0hvbcsffr8n2xwdixc8wyw1bfl9fxn2gyy0c4nma7j9zbn0wwgw9")) (patches (search-patches "abcl-fix-build-xml.patch")))) @@ -11680,7 +11681,9 @@ IPTC, XMP, ICC and more formats.") "1zv3kjdkf6iqf02x6ln76254y634j2ji448y706a65lsbfjmmicf")) (modules '((guix build utils))) (snippet - `(for-each delete-file (find-files "." ".*.jar"))) + '(begin + (for-each delete-file (find-files "." ".*.jar")) + #t)) (patches (search-patches "java-svg-salamander-Fix-non-det.patch")))) (build-system ant-build-system) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 761e75072d..038031b800 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -929,7 +929,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (define-public libreoffice (package (name "libreoffice") - (version "6.3.3.2") + (version "6.3.4.2") (source (origin (method url-fetch) @@ -939,7 +939,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (version-prefix version 3) "/libreoffice-" version ".tar.xz")) (sha256 (base32 - "1kz5950vhjc33rx7pyl5sw9lxxm90hxrj7v8y86jy34skjrfa3nl")) + "1774vmf3lr5x24ikpn1z5vqcdwrhiwfkjy7sx09jqkvpm6d5awnb")) (patches (search-patches "libreoffice-icu.patch" "libreoffice-glm.patch")) (modules '((guix build utils))) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a6f3b4cea6..014ea1239b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -188,31 +188,31 @@ defconfig. Return the appropriate make target if applicable, otherwise return (define deblob-scripts-5.3 (linux-libre-deblob-scripts - "5.3.11" + "5.3.17" (base32 "15n09zq38d69y1wl28s3nasf3377qp2yil5b887zpqrm00dif7i4") (base32 "1xk3gzgnl9m29avka32zkggl36sdxyvps40hr12hjy42l1ysfshm"))) (define deblob-scripts-4.19 (linux-libre-deblob-scripts - "4.19.84" + "4.19.90" (base32 "02zs405awaxydbapka4nz8h6lmnc0dahgczqsrs5s2bmzjyyqkcy") - (base32 "1s89hmy4ihd65by2p1xxkxj476f6c9s5g9r9yvqncb50xlhilk50"))) + (base32 "0xpcl6pd1280gm81bivz45dfhy6v16j0hghxhjynmcbasgnx8vpd"))) (define deblob-scripts-4.14 (linux-libre-deblob-scripts - "4.14.154" + "4.14.159" (base32 "091jk9jkn9jf39bxpc7395bhcb7p96nkg3a8047380ki06lnfxh6") - (base32 "1pcsfzpcv3bs30iyhwpk1x64r0gyv7wi22spnq6avzj1ayva10kw"))) + (base32 "0yd0c3qxk5rm686j4kd5v4zppjj3k9ivqnv46z4p3xh1gqmhv7cz"))) (define deblob-scripts-4.9 (linux-libre-deblob-scripts - "4.9.201" + "4.9.206" (base32 "1wvldzlv7q2xdbadas87dh593nxr4a8p5n0f8zpm72lja6w18hmg") (base32 "0is8gn4qdd7h5l6lacvhqdch26lmrbgxfm8ab7fx8n85ha7y358w"))) (define deblob-scripts-4.4 (linux-libre-deblob-scripts - "4.4.201" + "4.4.206" (base32 "0x2j1i88am54ih2mk7gyl79g25l9zz4r08xhl482l3fvjj2irwbw") (base32 "12ac4g3ky8yma8sylmxvvysqvd4hnaqjiwmxrxb6wlxggfd7zkbx"))) @@ -356,26 +356,26 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." "linux-" version ".tar.xz")) (sha256 hash))) -(define-public linux-libre-5.3-version "5.3.15") +(define-public linux-libre-5.3-version "5.3.18") (define-public linux-libre-5.3-pristine-source (let ((version linux-libre-5.3-version) - (hash (base32 "15qidl06lyfylx1b43b4wz2zfkr4000bkr7ialslmb7yi7mamj6f"))) + (hash (base32 "133342nv9ddjad2rizmcbilg9rhg339sfqr9l77j4cgkqhblkw90"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.3))) -(define-public linux-libre-4.19-version "4.19.88") +(define-public linux-libre-4.19-version "4.19.90") (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "1gizkdmq46ykw7ya3hibd6lalww2kvsia346pq3xvrk6s5mkp4n1"))) + (hash (base32 "1zgpbim9019aymvgh0fr5g2r9j2xspw14amlnk09w5mgdl56rn19"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) -(define-public linux-libre-4.14-version "4.14.158") +(define-public linux-libre-4.14-version "4.14.159") (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "1cqvr8pgqx005a9qyphqykakzwc54adq8mmdc9sgrxkkw9rfqj8d"))) + (hash (base32 "1wi6m3w40z0v9krb12g9q09s9y471r51rhcv3qa81lc53cx2vm78"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) @@ -1078,6 +1078,13 @@ at login. Local and dynamic reconfiguration are its key features.") (sha256 (base32 "16i7qzjmm6g0lzha8yzpfrlcxnvkgh95hkq9gdjd4zmzb8d0wxa1")))) (build-system gnu-build-system) + (arguments + `(,@(if (%current-target-system) + '(#:configure-flags + (list + "ac_cv_func_malloc_0_nonnull=yes" + "ac_cv_func_realloc_0_nonnull=yes")) + '()))) (inputs `(("ncurses" ,ncurses))) (home-page "https://gitlab.com/psmisc/psmisc") (synopsis "Small utilities that use the proc file system") @@ -2075,8 +2082,18 @@ configuration and monitoring interfaces.") (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("libnl" ,libnl))) (arguments - `(#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) - "CC=gcc") + `(#:make-flags + (let* ((target ,(%current-target-system)) + (gcc (if target (string-append target "-gcc") "gcc")) + (pkg-config (if target + (string-append target "-pkg-config") + "pkg-config"))) + (list + (string-append "CC=" gcc) + (string-append "PKG_CONFIG=" + (assoc-ref %build-inputs "pkg-config") + "/bin/" pkg-config) + (string-append "PREFIX=" (assoc-ref %outputs "out")))) #:phases (modify-phases %standard-phases (delete 'configure)))) (home-page "https://wireless.wiki.kernel.org/") (synopsis "Tool for configuring wireless devices") diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index d51b9a3662..e2732a478d 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -741,7 +741,7 @@ enough to play the original mainframe Zork all the way through.") (define-public txr (package (name "txr") - (version "224") + (version "229") (source (origin (method git-fetch) @@ -752,7 +752,7 @@ enough to play the original mainframe Zork all the way through.") (patches (search-patches "txr-shell.patch")) (sha256 (base32 - "1036k71f6mffy9rjwzmhr5nnp1n0wzb0rqvilpzvb8jc5yxv0810")))) + "070lqckhbcq3wn5ajyaa41hh0gypaa48wnxkk6mc5mxvmv76ml46")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("cc=gcc") diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 8364d528fd..0ed61ad4a1 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -925,7 +925,7 @@ extremely large and complex data collections.") (define-public hdf5-1.10 (package (inherit hdf5) - (version "1.10.4") + (version "1.10.5") (source (origin (method url-fetch) @@ -939,9 +939,8 @@ extremely large and complex data collections.") (take (string-split version #\.) 2)) "/src/hdf5-" version ".tar.bz2"))) (sha256 - (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj")) - (patches (search-patches "hdf5-config-date.patch" - "hdf5-mpi-deprecations.patch")))))) + (base32 "0i3g6v521vigzbx8wpd32ibsiiw92r65ca3qdbn0d8fj8f4fmmk8")) + (patches (search-patches "hdf5-config-date.patch")))))) (define-public hdf-java (package diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 134fe7ed51..f80fb067e8 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2185,7 +2185,7 @@ capabilities, custom envelopes, effects, etc.") (define-public yoshimi (package (name "yoshimi") - (version "1.6.0.3") + (version "1.6.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/yoshimi/" @@ -2193,7 +2193,7 @@ capabilities, custom envelopes, effects, etc.") "/yoshimi-" version ".tar.bz2")) (sha256 (base32 - "1z2mnmm299ng6jcwa61dzr1ilwa5fjgsggxl2wa5smji6b4npmx7")))) + "1shnz429zgl0b4y5bpb61frk1747jwqfahq4hx44c972580zghzh")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; there are no tests diff --git a/gnu/packages/patches/hdf5-mpi-deprecations.patch b/gnu/packages/patches/hdf5-mpi-deprecations.patch deleted file mode 100644 index eb5d1cb681..0000000000 --- a/gnu/packages/patches/hdf5-mpi-deprecations.patch +++ /dev/null @@ -1,61 +0,0 @@ ---- a/src/H5.c -+++ b/src/H5.c -@@ -138,7 +138,7 @@ - if (mpi_initialized && !mpi_finalized) { - int key_val; - -- if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_NULL_COPY_FN, -+ if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN, - (MPI_Comm_delete_attr_function *)H5_mpi_delete_cb, - &key_val, NULL))) - HMPI_GOTO_ERROR(FAIL, "MPI_Comm_create_keyval failed", mpi_code) ---- hdf5-1.10.4/testpar/t_cache.c -+++ hdf5-1.10.4/testpar/t_cache.c -@@ -1217,20 +1217,20 @@ - struct mssg_t sample; /* used to compute displacements */ - - /* setup the displacements array */ -- if ( ( MPI_SUCCESS != MPI_Address(&sample.req, &displs[0]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.src, &displs[1]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.dest, &displs[2]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.mssg_num, &displs[3]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.base_addr, &displs[4]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.len, &displs[5]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.ver, &displs[6]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.count, &displs[7]) ) || -- ( MPI_SUCCESS != MPI_Address(&sample.magic, &displs[8]) ) ) { -+ if ( ( MPI_SUCCESS != MPI_Get_address(&sample.req, &displs[0]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.src, &displs[1]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.dest, &displs[2]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.mssg_num, &displs[3]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.base_addr, &displs[4]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.len, &displs[5]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.ver, &displs[6]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.count, &displs[7]) ) || -+ ( MPI_SUCCESS != MPI_Get_address(&sample.magic, &displs[8]) ) ) { - - nerrors++; - success = FALSE; - if ( verbose ) { -- HDfprintf(stdout, "%d:%s: MPI_Address() call failed.\n", -+ HDfprintf(stdout, "%d:%s: MPI_Get_address() call failed.\n", - world_mpi_rank, FUNC); - } - -@@ -1245,14 +1245,14 @@ - - if ( success ) { - -- result = MPI_Type_struct(9, block_len, displs, mpi_types, &mpi_mssg_t); -+ result = MPI_Type_create_struct(9, block_len, displs, mpi_types, &mpi_mssg_t); - - if ( result != MPI_SUCCESS ) { - - nerrors++; - success = FALSE; - if ( verbose ) { -- HDfprintf(stdout, "%d:%s: MPI_Type_struct() call failed.\n", -+ HDfprintf(stdout, "%d:%s: MPI_Type_create_struct() call failed.\n", - world_mpi_rank, FUNC); - } - } diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index f6d86f0857..0867433245 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -361,7 +361,7 @@ photographic equipment.") (define-public darktable (package (name "darktable") - (version "2.6.2") + (version "2.6.3") (source (origin (method url-fetch) @@ -369,27 +369,25 @@ photographic equipment.") "https://github.com/darktable-org/darktable/releases/" "download/release-" version "/darktable-" version ".tar.xz")) (sha256 - (base32 "0igvgyd042j7hm4y8fcm6dc1qqjs4d1r7y6f0pzpa0x416xyzfcw")))) + (base32 "1w3q3dhcxa0bs590zbsj61ap8z84wmn04xs5q3gjwisqhjf9j655")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; there are no tests #:configure-flags '("-DBINARY_PACKAGE_BUILD=On") - #:make-flags - (list - (string-append "CPATH=" (assoc-ref %build-inputs "ilmbase") - "/include/OpenEXR:" (or (getenv "CPATH") ""))) #:phases (modify-phases %standard-phases - (add-before 'configure 'set-ldflags - (lambda* (#:key outputs #:allow-other-keys) + (add-before 'configure 'set-LDFLAGS-and-CPATH + (lambda* (#:key inputs outputs #:allow-other-keys) (setenv "LDFLAGS" (string-append "-Wl,-rpath=" (assoc-ref outputs "out") "/lib/darktable")) + + ;; Ensure the OpenEXR headers are found. + (setenv "CPATH" + (string-append (assoc-ref inputs "ilmbase") + "/include/OpenEXR:" (or (getenv "CPATH") ""))) #t))))) - (native-inputs - `(("llvm" ,llvm-3.9.1) - ("clang" ,clang-3.9.1))) (inputs `(("libxslt" ,libxslt) ("libxml2" ,libxml2) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index af51ae04b6..63d3be17c2 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -232,16 +232,24 @@ Python interface around SSH networking concepts.") (define-public python-ecdsa (package (name "python-ecdsa") - (version "0.13.3") + (version "0.14.1") (source (origin (method url-fetch) (uri (pypi-uri "ecdsa" version)) (sha256 - (base32 "0k9xxklf865g6x43gkfarwb25ffrkmpvkzkh71rylqx7cjq80g0n")))) + (base32 "13nx5cbfxc0gnax5zwdmp9xc40qd1llk62mv85jyrvqkbw017ik4")))) (build-system python-build-system) - (inputs - `(("openssl" ,openssl))) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ (invoke "pytest")))))) + (propagated-inputs + `(("python-six" ,python-six))) + (native-inputs + `(("openssl" ,openssl) + ("python-pytest" ,python-pytest))) (home-page "https://github.com/warner/python-ecdsa") (synopsis "ECDSA cryptographic signature library (pure python)") (description diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 1632d7ade5..179e64e0a1 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2532,14 +2532,14 @@ CSS tidy. Also supports URL rewriting in CSS files.") (define-public python-elasticsearch (package (name "python-elasticsearch") - (version "6.1.1") + (version "7.1.0") (source (origin (method url-fetch) (uri (pypi-uri "elasticsearch" version)) (sha256 (base32 - "1kjxl45yvvgfb5fmamx0kfsfg9pzphiqrwbkns3s28r1w7ya74cd")))) + "0rnjvlhw4v3vg14l519qliy1s1zpmx3827q0xfviwvk42rr7hh01")))) (build-system python-build-system) (native-inputs `(("python-mock" ,python-mock) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9fac87648a..f0490f248c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -67,6 +67,7 @@ ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org> ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz> ;;; Copyright © 2019 Tanguy Le Carrour <tanguy@bioneland.org> +;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -15889,41 +15890,63 @@ append on old values. Partd excels at shuffling operations.") (define-public python2-partd (package-with-python2 python-partd)) +(define-public python-fsspec + (package + (name "python-fsspec") + (version "0.6.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fsspec" version)) + (sha256 + (base32 + "1g9ba8v04s1nrh7pvzfm2md7ivl2mrz3hcq3y9d1a44gd62h17zj")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; there are none + (home-page "https://github.com/intake/filesystem_spec") + (synopsis "File-system specification") + (description "The purpose of this package is to produce a template or +specification for a file-system interface, that specific implementations +should follow, so that applications making use of them can rely on a common +behavior and not have to worry about the specific internal implementation +decisions with any given backend.") + (license license:bsd-3))) + (define-public python-dask (package (name "python-dask") - (version "1.2.2") + (version "2.9.0") (source (origin (method url-fetch) (uri (pypi-uri "dask" version)) (sha256 - (base32 "0b29gvf96gmp20wicly3v3mhyc93zbm3mdv935fka6x0wax7cy2y")))) + (base32 "1w1hqr8vyx6ygwflj2737dcy0mmgvrc0s602gnny8pzlcbs9m76b")))) (build-system python-build-system) - ;; A single test out of 5000+ fails. This test is marked as xfail when - ;; pytest-xdist is used. (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'disable-broken-test + (add-after 'unpack 'disable-broken-tests (lambda _ + ;; This test is marked as xfail when pytest-xdist is used. (substitute* "dask/tests/test_threaded.py" (("def test_interrupt\\(\\)" m) (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" m))) - (when (which "python2") - ;; This test fails with recent Pandas: - ;; <https://github.com/dask/dask/issues/3794>. - (substitute* "dask/dataframe/tests/test_dataframe.py" - (("def test_info\\(\\)" m) - (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - m)))) + ;; This one fails with a type error: + ;; TypeError: Already tz-aware, use tz_convert to convert. + (substitute* "dask/dataframe/tests/test_shuffle.py" + (("def test_set_index_timestamp\\(\\)" m) + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + m))) #t)) (replace 'check (lambda _ (invoke "pytest" "-vv")))))) (propagated-inputs `(("python-cloudpickle" ,python-cloudpickle) + ("python-fsspec" ,python-fsspec) ("python-numpy" ,python-numpy) + ("python-packaging" ,python-packaging) ("python-pandas" ,python-pandas) ("python-partd" ,python-partd) ("python-toolz" ,python-toolz) @@ -15942,9 +15965,6 @@ larger-than-memory or distributed environments. These parallel collections run on top of the dynamic task schedulers. ") (license license:bsd-3))) -(define-public python2-dask - (package-with-python2 python-dask)) - (define-public python-ilinkedlist (package (name "python-ilinkedlist") @@ -16786,3 +16806,78 @@ services to what you expect in your tests.") (define-public python2-ujson (package-with-python2 python-ujson)) + +(define-public python-iocapture + ;; The latest release is more than a year older than this commit. + (let ((commit "fdc021c431d0840303908dfc3ca8769db383595c") + (revision "1")) + (package + (name "python-iocapture") + (version "0.1.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/oinume/iocapture.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mkbhqibxvgwg0p7slr8dfraa3g2s6bsayladhax2jccwj4kcndz")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "py.test" "-v" "tests") + #t))))) + (propagated-inputs + `(("python-flexmock" ,python-flexmock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-six" ,python-six))) + (home-page "https://github.com/oinume/iocapture") + (synopsis "Python capturing tool for stdout and stderr") + (description + "This package helps you to capture the standard out (stdout) and the +standard error channel (stderr) in your program.") + (license license:expat)))) + +(define-public python-argh + ;; There are 21 commits since the latest release containing important + ;; improvements. + (let ((commit "dcd3253f2994400a6a58a700c118c53765bc50a4") + (revision "1")) + (package + (name "python-argh") + (version (git-version "0.26.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/neithere/argh.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1p5h3dnpbsjmqrvil96s71asc6i3gpinmbrabqmwnrsxprz7r3ns")))) + (build-system python-build-system) + (propagated-inputs + `(("python-iocapture" ,python-iocapture) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-xdist" ,python-pytest-xdist) + ("python-tox" ,python-tox))) + (home-page "https://github.com/neithere/argh/") + (synopsis "Argparse wrapper with natural syntax") + (description + "python-argh is a small library that provides several layers of +abstraction on top of @code{python-argparse}. The layers can be mixed. It is +always possible to declare a command with the highest possible (and least +flexible) layer and then tune the behaviour with any of the lower layers +including the native API of @code{python-argparse}.") + (license license:lgpl3+)))) diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 40a59635b1..1d2f754e4a 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2019 Meiyo Peng <meiyo.peng@gmail.com> ;;; Copyright © 2019 Timothy Sample <samplet@ngyro.com> +;;; Copyright © 2019 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -794,30 +795,22 @@ is commonly written.") (define-public gash (package (name "gash") - (version "0.1") + (version "0.2.0") (source (origin (method url-fetch) (uri (string-append "mirror://savannah/gash/gash-" version ".tar.gz")) (sha256 (base32 - "00m3lif64zyxd41cnk208kc81nl6qz659676qgiaqgwrw0brzrid")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "Makefile.in" - (("^moddir = (.*)/guile/(.*)" _ before after) - (string-append "moddir = " before "/guile/site/" - after)) - (("^ccachedir = (.*)/ccache/(.*)" _ before after) - (string-append "ccachedir = " before - "/site-ccache/" after))) - #t)))) + "13m0yz5h9nj3x40mr6wr5xcpq1lscndfwcicw3skrz801025hhgf")) + (modules '((guix build utils))))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("guile" ,guile-2.2))) + (arguments + '(#:make-flags '("XFAIL_TESTS=tests/redirects.org"))) (home-page "https://savannah.nongnu.org/projects/gash/") (synopsis "POSIX-compatible shell written in Guile Scheme") (description "Gash is a POSIX-compatible shell written in Guile diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 8075406c99..35d8a72492 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr> +;;; Copyright © 2019 Alexandros Theodotou <alex@zrythm.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -565,3 +566,26 @@ and several other projects.") (description "This package is an extension to reStructuredText and Sphinx to be able to read and render the Doxygen xml output.") (license license:bsd-3))) + +(define-public python-sphinx-intl + (package + (name "python-sphinx-intl") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sphinx-intl" version)) + (sha256 + (base32 + "0zbf1bh23b3kza8bnjykmv2k21xmmr4gamhi3lnicnr6ypnrphr5")))) + (build-system python-build-system) + (propagated-inputs + `(("python-sphinx" ,python-sphinx) + ("python-click" ,python-click))) + (home-page "https://github.com/sphinx-doc/sphinx-intl") + (synopsis + "Sphinx utility that makes it easy to translate and to apply translation") + (description + "A utility tool that provides several features that make it easy to +translate and to apply translation to Sphinx generated document.") + (license license:bsd-2))) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c3054473a2..9222bba0f6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -590,13 +590,13 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-nlme (package (name "r-nlme") - (version "3.1-142") + (version "3.1-143") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 - (base32 "0figfb1i22hfkkhzpprmpp723s01r43x725a1ab0pc9gsxqg90nx")))) + (base32 "13iixbs2ibldc75rl7rav5n5kx33zwm33xnfw1yvlkpcqf38bd22")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -933,15 +933,15 @@ in which the whole-plots or split-plots or both can be freely exchangeable.") (define-public r-plyr (package (name "r-plyr") - (version "1.8.4") + (version "1.8.5") (source (origin (method url-fetch) (uri (cran-uri "plyr" version)) (sha256 - (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0")))) + (base32 "0x4mbb3rgv1ayxqidw0p9i10khbg51fz5r62vw4il8d7licqq07a")))) (build-system r-build-system) - (native-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "http://had.co.nz/plyr") (synopsis "Tools for Splitting, Applying and Combining Data") (description @@ -1240,13 +1240,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "1x8wy2vg2gcgd9bww04qmf0dsn3kp0rfjd8q8j1r2x9zxccg25pz")))) + "1r03j9rdcxb9bhxk40dkmy10ikz4yzsxhy3f9k9ix3x577xbfvd9")))) (build-system r-build-system) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") @@ -1260,13 +1260,13 @@ R/DBMS implementations.") (define-public r-bh (package (name "r-bh") - (version "1.69.0-1") + (version "1.72.0-1") (source (origin (method url-fetch) (uri (cran-uri "BH" version)) (sha256 (base32 - "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0")))) + "1cm3gawky0dlfj8awv356j3f5pfv732rz10wlfnix2s2xf5cdz4a")))) (build-system r-build-system) (home-page "https://github.com/eddelbuettel/bh") (synopsis "R package providing subset of Boost headers") @@ -2662,13 +2662,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.18") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "0fykzbb5kjsqc8v6gjcdma7rmq0gailp30qij6plgna4d8nhjw3w")))) + (base32 "1bm3n17wa0pf1cq7qmwhbnn02x2pld7zzmmzjcvwy6apanch9fl7")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2972,14 +2972,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "1.0-0") + (version "1.1-0") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "1igsfkffpa60zn6j45lhw1zgr5pz6rjknv2f3sylnx5l9fdwibgf")))) + "06cxdrqgnpk5fvbam5i7qa4n71wry0yvlj0jpwbxf267mvpx10fh")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/segmented") (synopsis "Regression models with breakpoints estimation") @@ -3013,16 +3013,16 @@ worker processes and collect and return the results on the master.") (define-public r-sparsem (package (name "r-sparsem") - (version "1.77") + (version "1.78") (source (origin (method url-fetch) (uri (cran-uri "SparseM" version)) (sha256 (base32 - "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9")))) + "0cmlm0lps3daalvp5jzjnjfys388hgkyc8yw0g5r2351h749xdyn")))) (properties `((upstream-name . "SparseM"))) - (inputs + (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html") @@ -3207,13 +3207,13 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "3.0-1") + (version "3.0-2") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 - (base32 "04wa926mnss53p1fhx0mjgxnmwmmqls12sc0sy7w09kbmyqa3fq7")))) + (base32 "0b3nnfzp8dxcdkvxr0yvy6d58yk3xg4kz1wqa42bxqppbakmd2gl")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -4080,14 +4080,14 @@ hierarchical clustering dendrograms.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "0iiyn42hlvmc5vabg5x15mls11124i23sh4qijwk0narh438cqm0")))) + "0zrb9hx60vppkg0priczdb301nhq5f0dj8lkc8rcc4xrqqr915qm")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -5107,13 +5107,13 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.52") + (version "5.54") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 - (base32 "0rq9as31wiz41lmi9hmdq3gknpcbpwqzfcn065ysjdxzjdb57dcy")))) + (base32 "19nh79qrkb75q348nk148l8wqjwnq5jgq29wpzqym5cfv1kjqfvh")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) diff --git a/gnu/packages/texinfo.scm b/gnu/packages/texinfo.scm index 1edeea2425..44800b3961 100644 --- a/gnu/packages/texinfo.scm +++ b/gnu/packages/texinfo.scm @@ -2,7 +2,8 @@ ;;; Copyright © 2012, 2013, 2015, 2016, 2017, 2019 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014, 2016 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org> -;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2017, 2019 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -22,12 +23,17 @@ (define-module (gnu packages texinfo) #:use-module (guix licenses) #:use-module (guix packages) + #:use-module (guix utils) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (gnu packages) + #:use-module (gnu packages autotools) #:use-module (gnu packages compression) + #:use-module (gnu packages gettext) #:use-module (gnu packages ncurses) - #:use-module (gnu packages perl)) + #:use-module (gnu packages perl) + #:use-module (gnu packages readline)) (define-public texinfo (package @@ -181,3 +187,52 @@ of the GNU Texinfo implementation) do not intend to make further releases of Texi2HTML.") ;; Files in /lib under lgpl2.1+ and x11 (license gpl2+))) + +(define-public pinfo + (package + (name "pinfo") + (version "0.6.13") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/baszoetekouw/pinfo.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "173d2p22irwiabvr4z6qvr6zpr6ysfkhmadjlyhyiwd7z62larvy")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-Werror + (lambda _ + (substitute* "configure.ac" + (("-Werror") "")) + #t)) + (add-after 'unpack 'embed-reference-to-clear + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("src/manual.c" + "src/mainfunction.c" + "src/utils.c") + (("\"clear\"") + (string-append "\"" (which "clear") "\""))) + #t))))) + (inputs + `(("ncurses" ,ncurses) + ("readline" ,readline))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("gettext" ,gnu-gettext) + ("libtool" ,libtool) + ("texinfo" ,texinfo))) + (home-page "https://github.com/baszoetekouw/pinfo") + (synopsis "Lynx-style Info file and man page reader") + (description + "Pinfo is an Info file viewer. Pinfo is similar in use to the Lynx web +browser. You just move across info nodes, and select links, follow them, etc. +It supports many colors. Pinfo also supports viewing of manual pages -- they +are colorized like in the midnight commander's viewer, and additionaly they +are hypertextualized.") + (license gpl2+))) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 3280114878..ef60767236 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -24,7 +24,7 @@ ;;; Copyright © 2017, 2018, 2019 Rutger Helling <rhelling@mykolab.com> ;;; Copyright © 2018 Roel Janssen <roel@gnu.org> ;;; Copyright © 2018, 2019 Marius Bakke <mbakke@fastmail.com> -;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz> +;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz> ;;; Copyright © 2018, 2019 Leo Famulari <leo@famulari.name> ;;; Copyright © 2018 Brendan Tildesley <mail@brendan.scot> ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net> @@ -3677,3 +3677,42 @@ user interface features a builtin video player and is designed with attention to convenience of translating and batch processing of multiple documents.") (home-page "https://otsaloma.io/gaupol/") (license license:gpl3+))) + +(define-public theorafile + (let ((commit "404b14d7602b5918d117eaa64e8aa6601ede8593")) + (package + (name "theorafile") + (version (git-version "0.0.0" "1" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/FNA-XNA/Theorafile.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "128c3pjzqbgrj020glm5jd6ss18vl19471lj615w2brjwb7c1f0z")))) + (build-system gnu-build-system) + (arguments + '(#:make-flags '("CC=gcc") + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'check + (lambda _ + (setenv "CC" "gcc") + (invoke "make" "test"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "libtheorafile.so" (string-append out "/lib")) + (install-file "theorafile.h" (string-append out "/include"))) + #t))))) + (native-inputs + ;; For tests. + `(("sdl2" ,sdl2))) + (home-page "https://github.com/FNA-XNA/Theorafile") + (synopsis "Ogg Theora Video Decoder Library") + (description "Theorafile is a library for quickly and easily decoding Ogg +Theora videos. Theorafile was written to be used for FNA's VideoPlayer.") + (license license:zlib)))) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index e83ae43da2..f5ccfcb593 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -57,6 +57,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages gtk) #:use-module (gnu packages image) + #:use-module (gnu packages libbsd) #:use-module (gnu packages libusb) #:use-module (gnu packages linux) #:use-module (gnu packages ncurses) @@ -690,14 +691,14 @@ domains, their live performance and resource utilization statistics.") (define-public criu (package (name "criu") - (version "3.11") + (version "3.13") (source (origin (method url-fetch) (uri (string-append "http://download.openvz.org/criu/criu-" version ".tar.bz2")) (sha256 (base32 - "03nimyn3wy5mlw30gq7bvlzvvprqjv8f25240yj5arzlld8mhsw8")))) + "1yn9ix9lqvqvjrs3a3g6g1wqfniyf9n7giy0mr3jvijmrcm7y0pa")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -705,7 +706,11 @@ domains, their live performance and resource utilization statistics.") #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) (string-append "LIBDIR=" (assoc-ref %outputs "out") - "/lib")) + "/lib") + (string-append "ASCIIDOC=" (assoc-ref %build-inputs "asciidoc") + "/bin/asciidoc") + (string-append "XMLTO=" (assoc-ref %build-inputs "xmlto") + "/bin/xmlto")) #:phases (modify-phases %standard-phases (replace 'configure @@ -721,21 +726,17 @@ domains, their live performance and resource utilization statistics.") ;; which define some of the same constants. (assoc-ref inputs "kernel-headers") "/include")) - ;; Prevent xmlto from failing the install phase. + #t)) + (add-after 'configure 'fix-documentation + (lambda* (#:key inputs outputs #:allow-other-keys) (substitute* "Documentation/Makefile" - (("XMLTO.*:=.*") - (string-append "XMLTO:=" - (assoc-ref inputs "xmlto") - "/bin/xmlto" - " --skip-validation " - " -x " - (assoc-ref inputs "docbook-xsl") - "/xml/xsl/docbook-xsl-" - ,(package-version docbook-xsl) - "/manpages/docbook.xsl")) - (("\\$\\(XMLTO\\);") - (string-append (assoc-ref inputs "xmlto") - "/bin/xmlto;"))) + (("-m custom.xsl") + (string-append + "-m custom.xsl --skip-validation -x " + (assoc-ref inputs "docbook-xsl") "/xml/xsl/" + ,(package-name docbook-xsl) "-" + ,(package-version docbook-xsl) + "/manpages/docbook.xsl"))) #t)) (add-after 'unpack 'hardcode-variables (lambda* (#:key inputs #:allow-other-keys) @@ -783,7 +784,8 @@ domains, their live performance and resource utilization statistics.") ("libaio" ,libaio) ("libcap" ,libcap) ("libnet" ,libnet) - ("libnl" ,libnl))) + ("libnl" ,libnl) + ("libbsd" ,libbsd))) (native-inputs `(("pkg-config" ,pkg-config) ("perl" ,perl) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 749bc06fa9..19017fb9ea 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4194,8 +4194,8 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (package-with-python2 python-feedparser)) (define-public guix-data-service - (let ((commit "156b7eea7e7d538e332d8cfcf482c5ebec0a25c0") - (revision "7")) + (let ((commit "a019a5ed821cf1b7b2c2b0e1bd2dc25a51bbcb84") + (revision "8")) (package (name "guix-data-service") (version (string-append "0.0.1-" revision "." (string-take commit 7))) @@ -4207,7 +4207,7 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (file-name (git-file-name name version)) (sha256 (base32 - "1cg7jzk7pabfp3mgnkpycasv7fs522xp3nqdvna1y76aif3pd3zh")))) + "1kckfdgh8v9mmxxrsz6n2ibs78jr821qpbqh4mz8fyavm28c7h3f")))) (build-system gnu-build-system) (arguments '(#:modules ((guix build utils) @@ -7011,3 +7011,36 @@ endpoint that will be used to trigger the task. Poussetaches makes HTTP requests with the registered payload until the right status code is returned.") (license license:isc))) + +(define-public htmlcxx + (package + (name "htmlcxx") + (version "0.87") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/htmlcxx/v" + version "/htmlcxx-" version ".tar.gz")) + (sha256 + (base32 "1j3mzjlczjrk4ahc43s6kzpvzypzjmqz4sillnca5yadrwwgjf2x")))) + (build-system gnu-build-system) + (home-page "http://htmlcxx.sourceforge.net/") + (synopsis "Simple non-validating CSS1 and HTML parser for C++") + (description "htmlcxx is a simple non-validating CSS1 and HTML parser for +C++. Although there are several other HTML parsers available, htmlcxx has some +characteristics that make it unique: +@itemize +@item STL like navigation of DOM tree, using excelent's tree.hh library from +Kasper Peeters +@item It is possible to reproduce exactly, character by character, the original +document from the parse tree +@item Bundled CSS parser +@item Optional parsing of attributes +@item C++ code that looks like C++ (not so true anymore) +@item Offsets of tags/elements in the original document are stored in the nodes +of the DOM tree +@end itemize") + (license (list license:lgpl2.0 + license:gpl2 + license:asl2.0)))) diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index 8609bd2ace..81b2e06ba2 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -927,7 +927,6 @@ with '-virtfs' options for the host file systems listed in SHARED-FS." '()) "-no-reboot" - "-net nic,model=virtio" "-object" "rng-random,filename=/dev/urandom,id=guixsd-vm-rng" "-device" "virtio-rng-pci,rng=guixsd-vm-rng" @@ -1046,8 +1045,8 @@ FORWARDINGS is a list of host-port/guest-port pairs." (($ <virtual-machine> os qemu graphic? memory-size disk-image-size forwardings) (let ((options - `("-net" ,(string-append - "user," + `("-nic" ,(string-append + "user,model=virtio-net-pci," (port-forwardings->qemu-options forwardings))))) (system-qemu-image/shared-store-script os #:qemu qemu diff --git a/gnu/tests.scm b/gnu/tests.scm index 27cb39c2b9..cc72e56858 100644 --- a/gnu/tests.scm +++ b/gnu/tests.scm @@ -98,7 +98,7 @@ (or (pred x) (one-of rest ...)))))) (one-of symbol? string? keyword? pair? null? array? - number? boolean?))) + number? boolean? char?))) (match (primitive-fork) (0 |