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Merge branch 'master' into staging

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Marius Bakke 2020-01-29 11:12:49 +01:00
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6
build-aux/git-authenticate.scm
View file

@ -166,8 +166,12 @@ (define %committers
"0154 E1B9 1CC9 D9EF 7764 8DE7 F3A7 27DB 44FC CA36")
("roelj"
"17CB 2812 EB63 3DFF 2C7F 0452 C3EC 1DCA 8430 72E1")
("roptat"
("roptat (old)"
"B5FA E628 5B41 3728 B2A0 FAED 4311 1F45 2008 6A0C")
("roptat"
;; From commit 2cbede5935eb6a40173bbdf30a9ad22bf7574c22 (Jan. 2020). See
;; <https://lists.gnu.org/archive/html/guix-devel/2020-01/msg00499.html>.
"1EFB 0909 1F17 D28C CBF9 B13A 53D4 57B2 D636 EE82")
("samplet"
;; primary: "D6B0 C593 DA8C 5EDC A44C 7A58 C336 91F7 1188 B004"
"A02C 2D82 0EF4 B25B A6B5 1D90 2AC6 A5EC 1C35 7C59")

37
gnu/packages/audio.scm
View file

@ -23,7 +23,7 @@
;;; Copyright © 2019 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2019 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2019 Alexandros Theodotou <alex@zrythm.org>
;;; Copyright © 2019, 2020 Alexandros Theodotou <alex@zrythm.org>
;;; Copyright © 2019 Christopher Lemmer Webber <cwebber@dustycloud.org>
;;; Copyright © 2019 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
;;; Copyright © 2019 Hartmt Goebel <h.goebel@crazy-compilers.com>
@ -54,6 +54,7 @@ (define-module (gnu packages audio)
#:use-module (guix build-system waf)
#:use-module (guix build-system trivial)
#:use-module (guix build-system cmake)
#:use-module (guix build-system meson)
#:use-module (guix build-system python)
#:use-module (guix build-system glib-or-gtk)
#:use-module (gnu packages)
@ -2043,7 +2044,7 @@ (define-public lvtk
(define-public openal
(package
(name "openal")
(version "1.20.0")
(version "1.20.1")
(source (origin
(method url-fetch)
(uri (string-append
@ -2051,7 +2052,7 @@ (define-public openal
version ".tar.bz2"))
(sha256
(base32
"03p6s5gap0lvig2fs0a8nib5rxsc24dbqjsydpwvlm5l49wlk2f0"))))
"0vax0b1lgd4212bpxa1rciz52d4mv3dkfvcbbhzw4cjp698v1kmn"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; no check target
@ -4009,3 +4010,33 @@ (define-public ecasound
;; (see the file 'COPYING.LGPL'). This allows writing ECI applications
;; that are not licensed under GPL.
(license (list license:gpl2 license:lgpl2.1))))
(define-public libaudec
(package
(name "libaudec")
(version "0.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.zrythm.org/git/libaudec")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0lfydvs92b0hr72z71ci3yi356rjzi162pgms8dphgg18bz8dazv"))))
(build-system meson-build-system)
(arguments
`(#:configure-flags `("-Denable_tests=true -Denable_ffmpeg=true")))
(inputs
`(("libsamplerate" ,libsamplerate)
("libsndfile" ,libsndfile)
("ffmpeg" ,ffmpeg)))
(native-inputs
`(("pkg-config", pkg-config)))
(synopsis "Library for reading and resampling audio files")
(description "libaudec is a wrapper library over ffmpeg, sndfile and
libsamplerate for reading and resampling audio files, based on Robin Gareus'
@code{audio_decoder} code.")
(home-page "https://git.zrythm.org/cgit/libaudec")
(license license:agpl3+)))

44
gnu/packages/bioconductor.scm
View file

@ -694,6 +694,34 @@ (define-public r-illuminahumanmethylationepicmanifest
"This is a manifest package for Illumina's EPIC methylation arrays.")
(license license:artistic2.0)))
;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
;; from Bioconductor.
(define-public r-deconstructsigs
(package
(name "r-deconstructsigs")
(version "1.8.0")
(source (origin
(method url-fetch)
(uri (cran-uri "deconstructSigs" version))
(sha256
(base32
"014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
(properties
`((upstream-name . "deconstructSigs")))
(build-system r-build-system)
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)
("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
("r-genomeinfodb" ,r-genomeinfodb)
("r-reshape2" ,r-reshape2)))
(home-page "https://github.com/raerose01/deconstructSigs")
(synopsis "Identifies signatures present in a tumor sample")
(description "This package takes sample information in the form of the
fraction of mutations in each of 96 trinucleotide contexts and identifies
the weighted combination of published signatures that, when summed, most
closely reconstructs the mutational profile.")
(license license:gpl2+)))
(define-public r-do-db
(package
(name "r-do-db")
@ -2160,14 +2188,14 @@ (define-public r-biocsingular
(define-public r-destiny
(package
(name "r-destiny")
(version "3.0.0")
(version "3.0.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "destiny" version))
(sha256
(base32
"0vj9nk8g6i4vzm6cnzvbsqcvyk6fhmx0a0nxxrciarffyhqk81yz"))))
"1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@ -3165,14 +3193,14 @@ (define-public r-mutoss
(define-public r-metap
(package
(name "r-metap")
(version "1.2")
(version "1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "metap" version))
(sha256
(base32
"0pfbcixjrzx81l9wqhlp55khg9k63zf8pvg2n39c19akr4ppzhvf"))))
"1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)
@ -5164,14 +5192,14 @@ (define-public r-multidataset
(define-public r-ropls
(package
(name "r-ropls")
(version "1.18.6")
(version "1.18.8")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ropls" version))
(sha256
(base32
"1sm2fmygrra9gdcs90lmk5y1ag6arga6159kggx4ij8bkhyc66vb"))))
"033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@ -7177,14 +7205,14 @@ (define-public r-experimenthub
(define-public r-multiassayexperiment
(package
(name "r-multiassayexperiment")
(version "1.12.1")
(version "1.12.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MultiAssayExperiment" version))
(sha256
(base32
"0xpi5qpffg9pn8szkvicpc43a0r534wngyqwvsip8w66zi8c9kpc"))))
"0722f3jl1xq8k8w7vrv986jd16bgysqp3n07pgmdn0hh1zh2mcqc"))))
(properties
`((upstream-name . "MultiAssayExperiment")))
(build-system r-build-system)

38
gnu/packages/bioinformatics.scm
View file

@ -7349,13 +7349,13 @@ (define-public r-bioccheck
(define-public r-s4vectors
(package
(name "r-s4vectors")
(version "0.24.2")
(version "0.24.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
"1s1h00k2ki7sd0hz4l8n41xr6ixszag7lm0ryrbb08idgcy16ipn"))))
"01f7dms4kw9ajwqlvh5s47riv748xrrs41na03byhjvn4fbdc44y"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
@ -7930,13 +7930,13 @@ (define-public r-rtracklayer
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
(version "1.38.0")
(version "1.38.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
"0xd9rlsicycbanbcfhc97cj8b8vk94g7lkbmhk37w1511bq35wz5"))))
"1c1x29f447dv0i1wi88paji645lfsgmg4ckn19hyhlra72smhzqc"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@ -10317,14 +10317,14 @@ (define-public r-gqtlstats
(define-public r-gviz
(package
(name "r-gviz")
(version "1.30.0")
(version "1.30.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
"1p7n4yc77272rd8ybsim3rcg6kf6wmc95pwwav40b754imxn263z"))))
"03jj193fzmhvkjw8f5zk6wgflkvm3phny0q38scawcplfsyb8z64"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
@ -12937,14 +12937,14 @@ (define-public mantis
(define-public r-diversitree
(package
(name "r-diversitree")
(version "0.9-11")
(version "0.9-13")
(source
(origin
(method url-fetch)
(uri (cran-uri "diversitree" version))
(sha256
(base32
"1jqfjmmaigq581l4zxysmkhld0xv6izlbr1hihf9zplkix36majc"))))
"00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@ -14626,21 +14626,23 @@ (define-public pplacer
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(copy-recursively "bin" bin))
#t)))))
#t)))
#:ocaml ,ocaml-4.07
#:findlib ,ocaml4.07-findlib))
(inputs
`(("zlib" ,zlib "static")
("gsl" ,gsl)
("ocaml-ounit" ,ocaml-ounit)
("ocaml-batteries" ,ocaml-batteries)
("ocaml-camlzip" ,camlzip)
("ocaml-csv" ,ocaml-csv)
("ocaml-sqlite3" ,ocaml-sqlite3)
("ocaml-xmlm" ,ocaml-xmlm)
("ocaml-mcl" ,ocaml-mcl)
("ocaml-gsl" ,ocaml-gsl-1)))
("ocaml-ounit" ,(package-with-ocaml4.07 ocaml-ounit))
("ocaml-batteries" ,(package-with-ocaml4.07 ocaml-batteries))
("ocaml-camlzip" ,(package-with-ocaml4.07 camlzip))
("ocaml-csv" ,(package-with-ocaml4.07 ocaml-csv))
("ocaml-sqlite3" ,ocaml4.07-sqlite3)
("ocaml-xmlm" ,(package-with-ocaml4.07 ocaml-xmlm))
("ocaml-mcl" ,(package-with-ocaml4.07 ocaml-mcl))
("ocaml-gsl" ,ocaml4.07-gsl-1)))
(native-inputs
`(("cddlib-src" ,(package-source cddlib))
("ocamlbuild" ,ocamlbuild)
("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild))
("pkg-config" ,pkg-config)))
(propagated-inputs
`(("pplacer-scripts" ,pplacer-scripts)))

4
gnu/packages/check.scm
View file

@ -26,7 +26,7 @@
;;; Copyright © 2017 ng0 <ng0@n0.is>
;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2017, 2018, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2019 Chris Marusich <cmmarusich@gmail.com>
@ -1441,8 +1441,6 @@ (define-public python-testpath
#:modules ((guix build python-build-system)
(guix build utils)
(srfi srfi-1))
#:imported-modules (,@%python-build-system-modules
(srfi srfi-1))
#:phases
(modify-phases %standard-phases
(delete 'install)

182
gnu/packages/cran.scm
View file

@ -423,14 +423,14 @@ (define-public r-reprex
(define-public r-callr
(package
(name "r-callr")
(version "3.4.0")
(version "3.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "callr" version))
(sha256
(base32
"1hvxw2glizq8g0qnxakcxh8jc5scn0hp1x8i70fdpqwwbgx49slr"))))
"0nyba0knzd44zz2xmr7zd9qh3rny0q8msysxf49843d9rlyv6y70"))))
(build-system r-build-system)
(propagated-inputs
`(("r-r6" ,r-r6)
@ -1293,14 +1293,14 @@ (define-public r-mapproj
(define-public r-rgooglemaps
(package
(name "r-rgooglemaps")
(version "1.4.5.1")
(version "1.4.5.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "RgoogleMaps" version))
(sha256
(base32
"1lrbl0nax7rzk460mh6rq9hydahdi3ckxk4kxx3xij29jl3lmijh"))))
"1y2dinxmzx6mg6ynpk2q7f4k4rxjm66my185gafdcvpc4rl7svs7"))))
(properties `((upstream-name . "RgoogleMaps")))
(build-system r-build-system)
(propagated-inputs `(("r-png" ,r-png)))
@ -2034,14 +2034,14 @@ (define-public r-ffbase
(define-public r-prettyunits
(package
(name "r-prettyunits")
(version "1.1.0")
(version "1.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "prettyunits" version))
(sha256
(base32
"0453vvslpkj1ysyv0cy9hw98q5wlnj7bvvz7vzl5ld8ij82lwy5c"))))
"1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
(build-system r-build-system)
(home-page "https://github.com/gaborcsardi/prettyunits")
(synopsis "Pretty, human readable formatting of quantities")
@ -2438,14 +2438,14 @@ (define-public r-emdbook
(define-public r-lpsolve
(package
(name "r-lpsolve")
(version "5.6.13.3")
(version "5.6.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "lpSolve" version))
(sha256
(base32
"1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
"1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
(properties `((upstream-name . "lpSolve")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/lpSolve")
@ -3065,14 +3065,14 @@ (define-public r-generics
(define-public r-broom
(package
(name "r-broom")
(version "0.5.3")
(version "0.5.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "broom" version))
(sha256
(base32
"177m249dxbf9pf249610qrl58v025ws41ipfihy66751pwsv2n8d"))))
"1w35v1qrg8d0bm7a4gsdqkmrl9nmymsvmamy48vc046a1axzgzq1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
@ -3563,14 +3563,14 @@ (define-public r-rsofia
(define-public r-xts
(package
(name "r-xts")
(version "0.11-2")
(version "0.12-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "xts" version))
(sha256
(base32
"1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
"0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
(build-system r-build-system)
(propagated-inputs `(("r-zoo" ,r-zoo)))
(home-page "https://github.com/joshuaulrich/xts")
@ -3887,14 +3887,14 @@ (define-public r-processx
(define-public r-tsp
(package
(name "r-tsp")
(version "1.1-7")
(version "1.1-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "TSP" version))
(sha256
(base32
"0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
"0g44f2a4m7rfx6y51cdbr6vcmmpbwgyzpvfjksq3lb7gcpbr7xrx"))))
(properties `((upstream-name . "TSP")))
(build-system r-build-system)
(propagated-inputs `(("r-foreach" ,r-foreach)))
@ -4067,22 +4067,20 @@ (define-public r-zeallot
(define-public r-vctrs
(package
(name "r-vctrs")
(version "0.2.1")
(version "0.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "vctrs" version))
(sha256
(base32
"0rlwjfvvhv3s5mj4lqhwlqwddpizyp46i1qbcvw0mzb5q8b0nkz0"))))
"008xjmlj5a5vm303wxac7bliamqwaj7mcj0jv6n9ibc8p8h93aqd"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
("r-digest" ,r-digest)
`(("r-digest" ,r-digest)
("r-ellipsis" ,r-ellipsis)
("r-glue" ,r-glue)
("r-rlang" ,r-rlang)
("r-zeallot" ,r-zeallot)))
("r-rlang" ,r-rlang)))
(home-page "https://github.com/r-lib/vctrs")
(synopsis "Vector helpers")
(description
@ -4322,14 +4320,14 @@ (define-public r-ttr
(define-public r-leaps
(package
(name "r-leaps")
(version "3.0")
(version "3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "leaps" version))
(sha256
(base32
"11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
"1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/leaps/")
@ -5940,14 +5938,14 @@ (define-public r-flashclust
(define-public r-factominer
(package
(name "r-factominer")
(version "2.0")
(version "2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "FactoMineR" version))
(sha256
(base32
"0qiw60ypf3bf5xsqz2b9l82i4jvprjm8lzpp12lhl8d9j5s8m0j8"))))
"1b2jsv8vlaynknd7nlra6fdmr56n7678q5s28rqmagbadiqwvj4h"))))
(properties `((upstream-name . "FactoMineR")))
(build-system r-build-system)
(propagated-inputs
@ -6409,22 +6407,18 @@ (define-public r-insight
(define-public r-sjlabelled
(package
(name "r-sjlabelled")
(version "1.1.1")
(version "1.1.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjlabelled" version))
(sha256
(base32
"0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
"1vnx067mxnvz4jzhmpiarda8ln6habzj02qikvkix5piiy85sqcw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-haven" ,r-haven)
("r-insight" ,r-insight)
("r-magrittr" ,r-magrittr)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
("r-tidyselect" ,r-tidyselect)))
("r-insight" ,r-insight)))
(home-page "https://github.com/strengejacke/sjlabelled")
(synopsis "Labelled data utility functions")
(description
@ -7808,14 +7802,14 @@ (define-public r-mitools
(define-public r-magick
(package
(name "r-magick")
(version "2.2")
(version "2.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "magick" version))
(sha256
(base32
"1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
"182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8"))))
(build-system r-build-system)
(inputs
`(("imagemagick" ,imagemagick)
@ -7841,14 +7835,14 @@ (define-public r-magick
(define-public r-survey
(package
(name "r-survey")
(version "3.36")
(version "3.37")
(source
(origin
(method url-fetch)
(uri (cran-uri "survey" version))
(sha256
(base32
"0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
"1f31dvh48gzzan13pdrwh84ls35x9116095i7mdrcbrhz809r8dy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)
@ -8407,18 +8401,19 @@ (define-public r-tmb
(define-public r-sjstats
(package
(name "r-sjstats")
(version "0.17.7")
(version "0.17.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjstats" version))
(sha256
(base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6"))))
(base32 "0gagqbcmimlvxhpjkmd3s17mbrz5n937qksca1hvm6kj4rk37hzb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
("r-broom" ,r-broom)
("r-dplyr" ,r-dplyr)
("r-effectsize" ,r-effectsize)
("r-emmeans" ,r-emmeans)
("r-insight" ,r-insight)
("r-lme4" ,r-lme4)
@ -8481,14 +8476,14 @@ (define-public r-glmmtmb
(define-public r-bayestestr
(package
(name "r-bayestestr")
(version "0.4.0")
(version "0.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayestestR" version))
(sha256
(base32
"1d3f50rzjzgzclwd6j887dssyhv7hdq7pik9nnlr3w775v3f69zc"))))
"01kqvky1ndd1q64rzmqh5yfzz36ci8yhy4w16gjnw4c257ikhvd8"))))
(properties `((upstream-name . "bayestestR")))
(build-system r-build-system)
(propagated-inputs
@ -8506,14 +8501,14 @@ (define-public r-bayestestr
(define-public r-performance
(package
(name "r-performance")
(version "0.4.2")
(version "0.4.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "performance" version))
(sha256
(base32
"1pcjmqqm178dvdcpzkv5p4sj7glsppcny7znljb2nqkxh539a59p"))))
"1164585ywbnrcy7an57kifh2gdb6g08z9pxw75ywqdcfyd51i3dz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
@ -8564,14 +8559,14 @@ (define-public r-ggeffects
(define-public r-effectsize
(package
(name "r-effectsize")
(version "0.0.1")
(version "0.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "effectsize" version))
(sha256
(base32
"07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb"))))
"0dd7nbkg8kmash9zh2gg08m7hbpsqwpkvkdhinfqkbg5d0jinhq8"))))
(properties `((upstream-name . "effectsize")))
(build-system r-build-system)
(propagated-inputs
@ -8589,13 +8584,13 @@ (define-public r-effectsize
(define-public r-sjplot
(package
(name "r-sjplot")
(version "2.8.1")
(version "2.8.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjPlot" version))
(sha256
(base32 "0rmfc2pq80w0kxh6icljhqm31q580s0czvllsfxk6crmpyfgxkp7"))))
(base32 "16721a5006q0gv45zjcwnkykxhjkzpq5n35vhik0g0ixgm3a2vci"))))
(properties `((upstream-name . "sjPlot")))
(build-system r-build-system)
(propagated-inputs
@ -8605,17 +8600,11 @@ (define-public r-sjplot
("r-forcats" ,r-forcats)
("r-ggeffects" ,r-ggeffects)
("r-ggplot2" ,r-ggplot2)
("r-ggrepel" ,r-ggrepel)
("r-glmmtmb" ,r-glmmtmb)
("r-insight" ,r-insight)
("r-knitr" ,r-knitr)
("r-lme4" ,r-lme4)
("r-magrittr" ,r-magrittr)
("r-mass" ,r-mass)
("r-modelr" ,r-modelr)
("r-parameters" ,r-parameters)
("r-performance" ,r-performance)
("r-psych" ,r-psych)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
("r-scales" ,r-scales)
@ -8660,17 +8649,18 @@ (define-public r-ini
(define-public r-gh
(package
(name "r-gh")
(version "1.0.1")
(version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "gh" version))
(sha256
(base32
"1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
"1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-httr" ,r-httr)
`(("r-cli" ,r-cli)
("r-httr" ,r-httr)
("r-ini" ,r-ini)
("r-jsonlite" ,r-jsonlite)))
(home-page "https://github.com/r-lib/gh#readme")
@ -9087,14 +9077,14 @@ (define-public r-mvabund
(define-public r-afex
(package
(name "r-afex")
(version "0.25-1")
(version "0.26-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "afex" version))
(sha256
(base32
"12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
"0h3p1svgk1ap3lj08fi8nzdb3710h99bv150krf1x8wci1a0r1if"))))
(build-system r-build-system)
(propagated-inputs
`(("r-car" ,r-car)
@ -10663,14 +10653,14 @@ (define-public r-bigrquery
(define-public r-gmp
(package
(name "r-gmp")
(version "0.5-13.5")
(version "0.5-13.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "gmp" version))
(sha256
(base32
"042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
"0j2sz2nw41y9306rl1b8hbn0spz7453z5iawcq0bvslyrhc1d9ir"))))
(build-system r-build-system)
(arguments
'(#:phases
@ -10690,20 +10680,23 @@ (define-public r-gmp
(define-public r-rmpfr
(package
(name "r-rmpfr")
(version "0.7-2")
(version "0.8-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rmpfr" version))
(sha256
(base32
"1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
"09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
(properties `((upstream-name . "Rmpfr")))
(build-system r-build-system)
(inputs
`(("mpfr" ,mpfr)))
`(("mpfr" ,mpfr)
("gmp" ,gmp)))
(propagated-inputs
`(("r-gmp" ,r-gmp)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://rmpfr.r-forge.r-project.org/")
(synopsis "R bindings to the MPFR library")
(description
@ -11656,14 +11649,14 @@ (define-public r-globals
(define-public r-future
(package
(name "r-future")
(version "1.15.1")
(version "1.16.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "future" version))
(sha256
(base32
"101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd"))))
"1xaqh0b2knf5bp23mc0kriq0iqhqna31q3b7d960piqjhzrb03dm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
@ -11795,20 +11788,19 @@ (define-public r-capushe
(define-public r-dorng
(package
(name "r-dorng")
(version "1.7.1")
(version "1.8.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "doRNG" version))
(sha256
(base32
"1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
"1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
(properties `((upstream-name . "doRNG")))
(build-system r-build-system)
(propagated-inputs
`(("r-foreach" ,r-foreach)
("r-iterators" ,r-iterators)
("r-pkgmaker" ,r-pkgmaker)
("r-rngtools" ,r-rngtools)))
(home-page "https://renozao.github.io/doRNG/")
(synopsis "Generic reproducible parallel backend for foreach loops")
@ -12029,14 +12021,14 @@ (define-public r-compositions
(define-public r-cobs
(package
(name "r-cobs")
(version "1.3-3")
(version "1.3-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "cobs" version))
(sha256
(base32
"1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
"0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-quantreg" ,r-quantreg)
@ -13215,14 +13207,14 @@ (define-public r-spdep
(define-public r-adegenet
(package
(name "r-adegenet")
(version "2.1.1")
(version "2.1.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "adegenet" version))
(sha256
(base32
"0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
"01fgrgbiddz2q4l3mx637hhwbs7r0c43yw7vpwl8p8pwbm3nykz0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ade4" ,r-ade4)
@ -14063,14 +14055,14 @@ (define-public r-gridgraphics
(define-public r-farver
(package
(name "r-farver")
(version "2.0.1")
(version "2.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "farver" version))
(sha256
(base32
"0aq1hk561pz3s3lpay1adwsihha6mxp7zbj4n1m6307g34awlhhn"))))
"1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
(build-system r-build-system)
(home-page "https://github.com/thomasp85/farver")
(synopsis "Vectorized color conversion and comparison")
@ -14444,14 +14436,14 @@ (define-public r-gbm
(define-public r-threejs
(package
(name "r-threejs")
(version "0.3.1")
(version "0.3.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "threejs" version))
(sha256
(base32
"1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
"1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
(build-system r-build-system)
(arguments
`(#:modules ((guix build utils)
@ -14468,8 +14460,8 @@ (define-public r-threejs
(unzip2
`((,(assoc-ref inputs "js-jquery")
"htmlwidgets/lib/jquery/jquery.min.js")
(,(assoc-ref inputs "js-threejs-85")
"htmlwidgets/lib/threejs-85/three.min.js"))))
(,(assoc-ref inputs "js-threejs-111")
"htmlwidgets/lib/threejs-111/three.min.js"))))
(lambda (sources targets)
(for-each (lambda (source target)
(format #t "Processing ~a --> ~a~%"
@ -14491,17 +14483,17 @@ (define-public r-threejs
("js-jquery"
,(origin
(method url-fetch)
(uri "https://code.jquery.com/jquery-3.3.1.js")
(uri "https://code.jquery.com/jquery-1.12.4.js")
(sha256
(base32
"1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
("js-threejs-85"
"0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
("js-threejs-111"
,(origin
(method url-fetch)
(uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
(uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
(sha256
(base32
"17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
"1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
(home-page "https://bwlewis.github.io/rthreejs")
(synopsis "Interactive 3D scatter plots, networks and globes")
(description
@ -15462,14 +15454,14 @@ (define-public r-glasso
(define-public r-rhpcblasctl
(package
(name "r-rhpcblasctl")
(version "0.18-205")
(version "0.20-17")
(source
(origin
(method url-fetch)
(uri (cran-uri "RhpcBLASctl" version))
(sha256
(base32
"1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
"0iwc06blr5sx7rylwczi2jrha8sk8qs0jklflwpidl0zj1jxdggp"))))
(properties `((upstream-name . "RhpcBLASctl")))
(build-system r-build-system)
(home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
@ -15530,14 +15522,14 @@ (define-public r-rann-l1
(define-public r-leiden
(package
(name "r-leiden")
(version "0.3.1")
(version "0.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "leiden" version))
(sha256
(base32
"19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
"0kf6fxqf5l5vilm9g7vspc18daw84cwhpafs5szb1skwd6vrfdzw"))))
(properties `((upstream-name . "leiden")))
(build-system r-build-system)
(propagated-inputs
@ -15877,14 +15869,14 @@ (define-public r-assertr
(define-public r-parameters
(package
(name "r-parameters")
(version "0.4.0")
(version "0.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "parameters" version))
(sha256
(base32
"0z1hdxgippchij28h8xbbz6l29kkyakwxxj5vxnpic40cpkqqdd6"))))
"0xkdn1079sr6kgyhc1zmn9imca4bghnxs3f91h0z7vkzjj73qdbi"))))
(properties `((upstream-name . "parameters")))
(build-system r-build-system)
(propagated-inputs
@ -16124,14 +16116,14 @@ (define-public r-txtplot
(define-public r-bio3d
(package
(name "r-bio3d")
(version "2.4-0")
(version "2.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "bio3d" version))
(sha256
(base32
"0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s"))))
"07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
(properties `((upstream-name . "bio3d")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@ -16967,14 +16959,14 @@ (define-public r-ace2fastq
(define-public r-rngwell
(package
(name "r-rngwell")
(version "0.10-5")
(version "0.10-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "rngWELL" version))
(sha256
(base32
"0b4ys525gksgqwqx9id4bdgyi9mwj6n3r87xdzf4fc9hp3cc16jb"))))
"0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
(properties `((upstream-name . "rngWELL")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/rngWELL/")
@ -18766,14 +18758,14 @@ (define-public r-adamethods
(define-public r-idpmisc
(package
(name "r-idpmisc")
(version "1.1.19")
(version "1.1.20")
(source
(origin
(method url-fetch)
(uri (cran-uri "IDPmisc" version))
(sha256
(base32
"13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd"))))
"0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
(properties `((upstream-name . "IDPmisc")))
(build-system r-build-system)
(propagated-inputs
@ -18944,14 +18936,14 @@ (define-public r-lim
(define-public r-shinycssloaders
(package
(name "r-shinycssloaders")
(version "0.2.0")
(version "0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinycssloaders" version))
(sha256
(base32
"1bpzsm7m7c366sjl1qndp4m5dg2vlm68rjgdy9n1ija9xbp0r2g4"))))
"1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
(properties
`((upstream-name . "shinycssloaders")))
(build-system r-build-system)

118
gnu/packages/crates-io.scm
View file

@ -4408,10 +4408,12 @@ (define-public rust-grep-pcre2-0.1
"1wjc3gsan20gapga8nji6jcrmwn9n85q5zf2yfq6g50c7abkc2ql"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
`(#:cargo-inputs
(("rust-grep-matcher" ,rust-grep-matcher-0.1)
("rust-pcre2" ,rust-pcre2-0.2))))
(native-inputs
`(("pcre2" ,pcre2)
("pkg-config" ,pkg-config)))
(home-page
"https://github.com/BurntSushi/ripgrep")
(synopsis "Use PCRE2 with the grep crate")
@ -5328,10 +5330,13 @@ (define-public rust-jemalloc-sys-0.3
(origin
(method url-fetch)
(uri (crate-uri "jemalloc-sys" version))
(file-name (string-append name "-" version ".crate"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0ify9vlql01qhfxlj7d4p9jvcp90mj2h69nkbq7slccvbhzryfqd"))))
"0ify9vlql01qhfxlj7d4p9jvcp90mj2h69nkbq7slccvbhzryfqd"))
(modules '((guix build utils)))
(snippet
'(begin (delete-file-recursively "jemalloc") #t))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@ -5344,11 +5349,6 @@ (define-public rust-jemalloc-sys-0.3
(add-after 'configure 'override-jemalloc
(lambda* (#:key inputs #:allow-other-keys)
(let ((jemalloc (assoc-ref inputs "jemalloc")))
(delete-file-recursively "jemalloc")
(delete-file-recursively
(string-append "guix-vendor/rust-jemalloc-sys-"
,(package-version rust-jemalloc-sys-0.3)
".crate/jemalloc"))
(setenv "JEMALLOC_OVERRIDE"
(string-append jemalloc "/lib/libjemalloc_pic.a")))
#t)))))
@ -5603,10 +5603,13 @@ (define-public rust-libgit2-sys-0.10
(origin
(method url-fetch)
(uri (crate-uri "libgit2-sys" version))
(file-name (string-append name "-" version ".crate"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0l9fvki7qxsl97vgzqwlv75nl213a5vxw7b1jaik97ala356pv6r"))))
"0l9fvki7qxsl97vgzqwlv75nl213a5vxw7b1jaik97ala356pv6r"))
(modules '((guix build utils)))
(snippet
'(begin (delete-file-recursively "libgit2") #t))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@ -5623,21 +5626,6 @@ (define-public rust-libgit2-sys-0.10
(lambda* (#:key inputs #:allow-other-keys)
(let ((openssl (assoc-ref inputs "openssl")))
(setenv "OPENSSL_DIR" openssl))
(delete-file-recursively "libgit2")
(delete-file-recursively
(string-append "guix-vendor/rust-libgit2-sys-"
,(package-version rust-libgit2-sys-0.10)
".crate/libgit2"))
(delete-file-recursively
(string-append "guix-vendor/rust-libz-sys-"
,(package-version rust-libz-sys-1.0)
".crate/src/zlib"))
(delete-file-recursively
(string-append "guix-vendor/rust-libssh2-sys-"
,(package-version rust-libssh2-sys-0.2)
".crate/libssh2"))
(setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1")
(setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
#t)))))
(native-inputs
`(("libgit2" ,libgit2)
@ -5720,10 +5708,13 @@ (define-public rust-libssh2-sys-0.2
(origin
(method url-fetch)
(uri (crate-uri "libssh2-sys" version))
(file-name (string-append name "-" version ".crate"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"042gsgbvxgm5by4mk906j3zm4qdvzcfhjxrb55is1lrr6f0nxain"))))
"042gsgbvxgm5by4mk906j3zm4qdvzcfhjxrb55is1lrr6f0nxain"))
(modules '((guix build utils)))
(snippet
'(begin (delete-file-recursively "libssh2") #t))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t ; it wants rust-openssl-src
@ -5741,16 +5732,6 @@ (define-public rust-libssh2-sys-0.2
(lambda* (#:key inputs #:allow-other-keys)
(let ((openssl (assoc-ref inputs "openssl")))
(setenv "OPENSSL_DIR" openssl))
(delete-file-recursively "libssh2")
(delete-file-recursively
(string-append "guix-vendor/rust-libssh2-sys-"
,(package-version rust-libssh2-sys-0.2)
".crate/libssh2"))
(delete-file-recursively
(string-append "guix-vendor/rust-libz-sys-"
,(package-version rust-libz-sys-1.0)
".crate/src/zlib"))
(setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
#t)))))
(native-inputs
`(("libssh2" ,libssh2)
@ -5903,26 +5884,19 @@ (define-public rust-lzma-sys-0.1
(origin
(method url-fetch)
(uri (crate-uri "lzma-sys" version))
(file-name (string-append name "-" version ".crate"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"14gyj256yh0wm77jbvmlc39v7lfn0navpfrja4alczarzlc8ir2k"))))
"14gyj256yh0wm77jbvmlc39v7lfn0navpfrja4alczarzlc8ir2k"))
(modules '((guix build utils)))
(snippet
'(begin (delete-file-recursively "xz-5.2") #t))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-libc" ,rust-libc-0.2)
("rust-cc" ,rust-cc-1.0)
("rust-pkg-config" ,rust-pkg-config-0.3))
#:phases
(modify-phases %standard-phases
(add-after 'configure 'unbundle-xz
(lambda _
(delete-file-recursively "xz-5.2")
(delete-file-recursively
(string-append "guix-vendor/rust-lzma-sys-"
,(package-version rust-lzma-sys-0.1)
".crate/xz-5.2"))
#t)))))
("rust-pkg-config" ,rust-pkg-config-0.3))))
(native-inputs
`(("pkg-config" ,pkg-config)
("xz" ,xz)))
@ -6591,10 +6565,13 @@ (define-public rust-libz-sys-1.0
(origin
(method url-fetch)
(uri (crate-uri "libz-sys" version))
(file-name (string-append name "-" version ".crate"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1gjycyl2283525abks98bhxa4r259m617xfm5z52p3p3c8ry9d9f"))))
"1gjycyl2283525abks98bhxa4r259m617xfm5z52p3p3c8ry9d9f"))
(modules '((guix build utils)))
(snippet
'(begin (delete-file-recursively "src/zlib") #t))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@ -6602,17 +6579,7 @@ (define-public rust-libz-sys-1.0
;; Build dependencies:
("rust-cc" ,rust-cc-1.0)
("rust-pkg-config" ,rust-pkg-config-0.3)
("rust-vcpkg" ,rust-vcpkg-0.2))
#:phases
(modify-phases %standard-phases
(add-after 'configure 'delete-vendored-zlib
(lambda _
(delete-file-recursively "src/zlib")
(delete-file-recursively
(string-append "guix-vendor/rust-libz-sys-"
,(package-version rust-libz-sys-1.0)
".crate/src/zlib"))
#t)))))
("rust-vcpkg" ,rust-vcpkg-0.2))))
(native-inputs
`(("pkg-config" ,pkg-config)
("zlib" ,zlib)))
@ -7522,12 +7489,14 @@ (define-public rust-pcre2-0.2
"103i66a998g1fjrqf9sdyvi8qi83hwglz3pjdcq9n2r207hsagb0"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
`(#:cargo-inputs
(("rust-libc" ,rust-libc-0.2)
("rust-log" ,rust-log-0.4)
("rust-pcre2-sys" ,rust-pcre2-sys-0.2)
("rust-thread-local" ,rust-thread-local-0.3))))
(native-inputs
`(("pcre2" ,pcre2)
("pkg-config" ,pkg-config)))
(home-page "https://github.com/BurntSushi/rust-pcre2")
(synopsis "High level wrapper library for PCRE2")
(description
@ -7546,23 +7515,16 @@ (define-public rust-pcre2-sys-0.2
(string-append name "-" version ".tar.gz"))
(sha256
(base32
"0nwdvc43dkb89qmm5q8gw1zyll0wsfqw7kczpn23mljra3874v47"))))
"0nwdvc43dkb89qmm5q8gw1zyll0wsfqw7kczpn23mljra3874v47"))
(modules '((guix build utils)))
(snippet
'(begin (delete-file-recursively "pcre2") #t))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-libc" ,rust-libc-0.2)
("rust-pkg-config" ,rust-pkg-config-0.3)
("rust-cc" ,rust-cc-1.0))
#:phases
(modify-phases %standard-phases
(add-after 'configure 'unbundle-sources
(lambda _
(delete-file-recursively "pcre2")
(delete-file-recursively
(string-append "guix-vendor/rust-pcre2-sys-"
,(package-version rust-pcre2-sys-0.2)
".tar.gz/pcre2"))
#t)))))
("rust-cc" ,rust-cc-1.0))))
(native-inputs
`(("pcre2" ,pcre2)
("pkg-config" ,pkg-config)))

104
gnu/packages/education.scm
View file

@ -4,7 +4,7 @@
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018, 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2018, 2019, 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -485,6 +485,108 @@ (define-public childsplay
(home-page "http://www.schoolsplay.org")
(license license:gpl3+)))
(define-public omnitux
(package
(name "omnitux")
(version "1.2.1")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/omnitux/omnitux/"
"v" version "/omnitux-" version ".tar.bz2"))
(sha256
(base32 "1wmmmbzmxd0blhn00d4g91xwavnab143a31ca3i8hrqgzh6qz9w6"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove pre-compiled .pyc files from source.
(for-each delete-file (find-files "bin" "\\.pyc$"))
#t))))
(build-system python-build-system)
(inputs
`(("python2-pygame" ,python2-pygame)
("python2-pygtk" ,python2-pygtk)))
(arguments
`(#:tests? #f ;no test
#:python ,python-2
#:phases
(modify-phases %standard-phases
(delete 'build) ;no setup.py
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(share (string-append out "/share"))
(data (string-append share "/omnitux")))
;; Install documentation.
(let ((doc (string-append share "/doc/" ,name "-" ,version)))
(for-each (lambda (f) (install-file f doc))
'("LICENSE.txt" "README.txt")))
;; Install data.
(install-file "omnitux.sh" data)
(for-each (lambda (d)
(copy-recursively d (string-append data "/" d)))
'("bin" "data"))
;; Install the launcher.
(let* ((bin (string-append out "/bin"))
(script (string-append bin "/omnitux"))
(bash (string-append (assoc-ref %build-inputs "bash")
"/bin/bash"))
(python (string-append (assoc-ref %build-inputs "python")
"/bin/python2")))
(mkdir-p bin)
(with-output-to-file script
(lambda ()
(format #t "#!~a~%" bash)
(format #t
"cd ~a; ~a menu.py~%"
(string-append data "/bin")
python)))
(chmod script #o755))
;; Install icon and desktop file.
(let ((pixmaps (string-append share "/pixmaps")))
(install-file "data/default/icons/Omnitux_logo.svg" pixmaps))
(let ((apps (string-append out "/share/applications")))
(mkdir-p apps)
(with-output-to-file (string-append apps "/omnitux.desktop")
(lambda _
(format #t
"[Desktop Entry]~@
Name=Omnitux~@
GenericName=Omnitux
Comment=An educational game based on multimedia elements.~@
Comment[fr]=Un jeu ludo-éducatif basé sur des éléments multimédias.~@
Exec=~a/bin/omnitux~@
Type=Application~@
Categories=Game;Education;~@
Terminal=false~@
Icon=Omnitux_logo.svg~@"
out))))
#t))))))
(home-page "http://omnitux.sourceforge.net/")
(synopsis "Educational activities based on multimedia elements")
(description "The project aims to provide various educational
activities around multimedia elements (images, sounds, texts). Types
of activities include:
@itemize
@item associations,
@item items to place on a map or a schema,
@item counting activities,
@item puzzles,
@item card faces to remember,
@item find differences between two pictures,
@item ...
@end itemize
Activities are available in English, French, German, Polish,
Portuguese, Spanish and Italian.")
;; Project's license is GPL3+, but multimedia elements are
;; released under various licenses.
(license (list license:gpl3+
license:gpl2+
license:cc-by-sa2.0
license:cc-by-sa3.0
license:public-domain))))
(define-public fet
(package
(name "fet")

248
gnu/packages/emacs-xyz.scm
View file

@ -51,7 +51,7 @@
;;; Copyright © 2019 Baptiste Strazzulla <bstrazzull@hotmail.fr>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
;;; Copyright © 2019 Amin Bandali <mab@gnu.org>
;;; Copyright © 2019, 2020 Amin Bandali <mab@gnu.org>
;;; Copyright © 2019 Jelle Licht <jlicht@fsfe.org>
;;; Copyright © 2019 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2019 Stephen Webber <montokapro@gmail.com>
@ -8053,14 +8053,13 @@ (define-public emacs-org
(name "emacs-org")
;; emacs-org-contrib inherits from this package. Please update it as
;; well.
(version "9.3.1")
(source (origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/org-"
version ".tar"))
(sha256
(base32
"1n79h6ihhsaxxbnl9hw511aav0215m3pa51sa5fh3ddknjfplian"))))
(version "9.3.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/org-" version ".tar"))
(sha256
(base32 "1275s3hzyka2wwxl6nc2sndnwyl7kbc1nnl0hrznxb3wpy2abfd6"))))
(build-system emacs-build-system)
(home-page "https://orgmode.org/")
(synopsis "Outline-based notes management and organizer")
@ -8074,14 +8073,14 @@ (define-public emacs-org-contrib
(package
(inherit emacs-org)
(name "emacs-org-contrib")
(version "20191226")
(source (origin
(method url-fetch)
(uri (string-append "https://orgmode.org/elpa/"
"org-plus-contrib-" version ".tar"))
(sha256
(base32
"08h6qiplvm7rvrb1pv2arwdlv6p31p0a6h0fk64kb79g6br8rk8i"))))
(version "20200126")
(source
(origin
(method url-fetch)
(uri (string-append "https://orgmode.org/elpa/"
"org-plus-contrib-" version ".tar"))
(sha256
(base32 "08yik0i8ya2x5j4vsnwxdcdlcxbiq58lvy30vcbdbf0hqrd40kjv"))))
(arguments
`(#:modules ((guix build emacs-build-system)
(guix build utils)
@ -12357,7 +12356,7 @@ (define-public emacs-org-super-agenda
(define-public emacs-org-make-toc
(package
(name "emacs-org-make-toc")
(version "0.3")
(version "0.4")
(source (origin
(method git-fetch)
(uri (git-reference
@ -12366,7 +12365,7 @@ (define-public emacs-org-make-toc
(file-name (git-file-name name version))
(sha256
(base32
"0syhj8q4pv33xgl5qa6x27yhwqvfhffw5xqp819hj4qs1ddlc7j5"))))
"0348iq3bc3rxs5bqdvskyly4agqxiapamqkfm0323620kxl70agw"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-org" ,emacs-org)
@ -15378,56 +15377,54 @@ (define-public emacs-fish-completion
(license license:gpl3+)))
(define-public emacs-gif-screencast
(let ((commit "248d1e158405e6cba2c65ecaed40e2c59b089cd8")
(revision "2"))
(package
(name "emacs-gif-screencast")
(version (git-version "1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/Ambrevar/emacs-gif-screencast.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"19xqi5mgalnnhb4hw0fh7py2s2dllldx1xxbhwhknkdpifai8hl8"))))
(build-system emacs-build-system)
(inputs
`(("scrot" ,scrot)
("imagemagick" ,imagemagick)
("gifsicle" ,gifsicle)))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((scrot (assoc-ref inputs "scrot"))
(imagemagick (assoc-ref inputs "imagemagick"))
(gifsicle (assoc-ref inputs "gifsicle")))
(make-file-writable "gif-screencast.el")
;; Specify the absolute file names of the various
;; programs so that everything works out-of-the-box.
(emacs-substitute-variables
"gif-screencast.el"
("gif-screencast-program"
(string-append scrot "/bin/scrot"))
("gif-screencast-convert-program"
(string-append imagemagick "/bin/convert"))
("gif-screencast-cropping-program"
(string-append imagemagick "/bin/mogrify"))
("gif-screencast-optimize-program"
(string-append gifsicle "/bin/gifsicle")))))))))
(home-page
"https://gitlab.com/Ambrevar/emacs-gif-screencast")
(synopsis "One-frame-per-action GIF recording")
(description
"Call @code{gif-screencast} to start a recording.
(package
(name "emacs-gif-screencast")
(version "1.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/Ambrevar/emacs-gif-screencast.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1g1by8lvf8c9vzm4wwsi5kp285kaj0ahsl54048ympin4pi0njw9"))))
(build-system emacs-build-system)
(inputs
`(("scrot" ,scrot)
("imagemagick" ,imagemagick)
("gifsicle" ,gifsicle)))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((scrot (assoc-ref inputs "scrot"))
(imagemagick (assoc-ref inputs "imagemagick"))
(gifsicle (assoc-ref inputs "gifsicle")))
(make-file-writable "gif-screencast.el")
;; Specify the absolute file names of the various
;; programs so that everything works out-of-the-box.
(emacs-substitute-variables
"gif-screencast.el"
("gif-screencast-program"
(string-append scrot "/bin/scrot"))
("gif-screencast-convert-program"
(string-append imagemagick "/bin/convert"))
("gif-screencast-cropping-program"
(string-append imagemagick "/bin/mogrify"))
("gif-screencast-optimize-program"
(string-append gifsicle "/bin/gifsicle")))))))))
(home-page
"https://gitlab.com/Ambrevar/emacs-gif-screencast")
(synopsis "One-frame-per-action GIF recording")
(description
"Call @code{gif-screencast} to start a recording.
A screenshot is taken for every user action. Call
@code{gif-screencast-stop} (<f9> by default) to finish recording and create
the GIF result.")
(license license:gpl3+))))
(license license:gpl3+)))
(define-public emacs-google-translate
(package
@ -20209,7 +20206,7 @@ (define-public emacs-doom-themes
(define-public emacs-modus-themes
(package
(name "emacs-modus-themes")
(version "0.3.0")
(version "0.4.0")
(source
(origin
(method git-fetch)
@ -20218,8 +20215,7 @@ (define-public emacs-modus-themes
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1xrrjhpdxi9bgx877gvq8xrc2ph5qp9y5j3ssdphy333x9km1px1"))))
(base32 "0c4y3y9mjf6x2b9087fk6nkxvgvm9f5l1p2vdwqny80vp4krsb8r"))))
(build-system emacs-build-system)
(home-page "https://gitlab.com/protesilaos/modus-themes")
(synopsis "Emacs themes designed for colour-contrast accessibility")
@ -21127,3 +21123,117 @@ (define-public emacs-metal-mercury-mode
mercury-mode provided by Emacs as a wrapper around prolog-mode.")
(home-page "https://github.com/ahungry/metal-mercury-mode")
(license license:gpl3+))))
(define-public emacs-boxquote
;; The following commit is 2.1 release with a switch to GPL3+ license.
(let ((commit "7e47e0e2853bc1215739b2e28f260e9eed93b2c5")
(revision "0"))
(package
(name "emacs-boxquote")
(version (git-version "2.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/davep/boxquote.el.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1aqhg24gajvllbqxb0zxrnx6sddas37k2ldfinqyszd856sjhsg3"))))
(build-system emacs-build-system)
(home-page "https://github.com/davep/boxquote.el")
(synopsis "Quote text with different kinds of boxes")
(description "@code{boxquote} provides a set of functions for using
a text quoting style that partially boxes in the left hand side of an area of
text, such a marking style might be used to show externally included text or
example code.")
(license license:gpl3+))))
(define-public emacs-company-ebdb
(package
(name "emacs-company-ebdb")
(version "1.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/"
"company-ebdb-" version ".el"))
(sha256
(base32 "146qpiigz12zp1823ggxfrx090g0mxs7gz1ba7sa0iq6ibgzwwm9"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-company" ,emacs-company)))
(home-page "https://elpa.gnu.org/packages/company-ebdb.html")
(synopsis "Company completion backend for EBDB in Message mode")
(description "@code{company-ebdb} provides Company mode integration for
EBDB. It is copied more or less intact from @code{company-bbdb}, originally
by Jan Tatarik.")
(license license:gpl3+)))
(define-public emacs-mwim
;; Use the latest commit not in a release version as of yet, since it
;; contains a bug fix for the cases where `comment-start-skip' is nil.
(let ((commit "b4f3edb4c0fb8f8b71cecbf8095c2c25a8ffbf85")
(revision "0"))
(package
(name "emacs-mwim")
(version (git-version "0.4" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/alezost/mwim.el.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0l3k611gp9g2x2vfmh92wnhnda81dslpwwpb8mxmzk308man77ya"))))
(build-system emacs-build-system)
(home-page "https://github.com/alezost/mwim.el")
(synopsis "Move to the beginning/end of line, code or comment")
(description "@code{mwim} provides several commands to switch between
various line positions, like moving to the beginning/end of code, line, or
comment.")
(license license:gpl3+))))
(define-public emacs-delight
(package
(name "emacs-delight")
(version "1.5")
(source
(origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/"
"delight-" version ".el"))
(sha256
(base32 "0kzlvzwmn6zj0874086q2xw0pclyi7wlkq48zh2lkd2796xm8vw7"))))
(build-system emacs-build-system)
(home-page "https://elpa.gnu.org/packages/delight.html")
(synopsis "Dimmer switch for your mode-line lighter text")
(description "@code{delight} enables customizing or hiding the
mode-line text (lighter) of major and minor modes.")
(license license:gpl3+)))
(define-public emacs-unkillable-scratch
;; Use the latest (unreleased) commit as of now, since it contains a handy
;; `unkillable-scratch-do-not-reset-scratch-buffer' customization to not
;; repopulate the scratch buffer with `initial-scratch-message'.
(let ((commit "b24c2a760529833f230c14cb02ff6e7ec92288ab")
(revision "0"))
(package
(name "emacs-unkillable-scratch")
(version (git-version "1.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/EricCrosson/unkillable-scratch.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "13wjbcxr3km4s96yhpavgs5acs5pvqv3ih1p84diqb3x3i6wd4pa"))))
(build-system emacs-build-system)
(home-page "https://github.com/EricCrosson/unkillable-scratch")
(synopsis "Prevents the *scratch* buffer from being killed")
(description "@code{unkillable-scratch} helps prevent killing buffers
matching a given regexp.")
(license license:gpl2+))))

14
gnu/packages/emulators.scm
View file

@ -1478,12 +1478,22 @@ (define-public pcsxr
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'cd-subdir
(lambda _ (chdir "pcsxr")))
(lambda _ (chdir "pcsxr") #t))
(add-before 'configure 'fix-cdio-lookup
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "cmake/FindCdio.cmake"
(("/usr/include/cdio")
(string-append (assoc-ref inputs "libcdio") "/include/cdio"))))))))
(string-append (assoc-ref inputs "libcdio") "/include/cdio")))
#t))
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(wrap-program (string-append (assoc-ref outputs "out")
"/bin/pcsxr")
;; For GtkFileChooserDialog.
`("GSETTINGS_SCHEMA_DIR" =
(,(string-append (assoc-ref inputs "gtk+")
"/share/glib-2.0/schemas"))))
#t)))))
(native-inputs
`(("pkg-config" ,pkg-config)
("intltool" ,intltool)

61
gnu/packages/file-systems.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017, 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
@ -37,6 +37,7 @@ (define-module (gnu packages file-systems)
#:use-module (gnu packages bison)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages crypto)
#:use-module (gnu packages curl)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages documentation)
@ -52,8 +53,66 @@ (define-module (gnu packages file-systems)
#:use-module (gnu packages readline)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages tls)
#:use-module (gnu packages valgrind)
#:use-module (gnu packages xml))
(define-public bcachefs-tools
(let ((commit "ab2f1ec24f5307b0cf1e3c4ad19bf350d9f54d9f")
(revision "0"))
(package
(name "bcachefs-tools")
(version (git-version "0.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://evilpiepirate.org/git/bcachefs-tools.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "10pafvaxg1lvwnqjv3a4rsi96bghbpcsgh3vhqilndi334k3b0hd"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(list (string-append "PREFIX=" (assoc-ref %outputs "out"))
"INITRAMFS_DIR=$(PREFIX)/share/initramfs-tools"
"CC=gcc"
"PYTEST=pytest")
#:phases
(modify-phases %standard-phases
(delete 'configure)) ; no configure script
#:tests? #f)) ; XXX 6 valgrind tests fail
(native-inputs
`(("pkg-config" ,pkg-config)
;; For tests.
("python-pytest" ,python-pytest)
("valgrind" ,valgrind)))
(inputs
`(("keyutils" ,keyutils)
("libaio" ,libaio)
("libscrypt" ,libscrypt)
("libsodium" ,libsodium)
("liburcu" ,liburcu)
("util-linux" ,util-linux) ; lib{blkid,uuid}
("lz4" ,lz4)
("zlib" ,zlib)
("zstd:lib" ,zstd "lib")))
(home-page "https://bcachefs.org/")
(synopsis "Tools to create and manage bcachefs file systems")
(description
"The bcachefs-tools are command-line utilites for creating, checking,
and otherwise managing bcachefs file systems.
Bcachefs is a @acronym{CoW, copy-on-write} file system supporting native
encryption, compression, snapshots, and (meta)data checksums. It can use
multiple block devices for replication and/or performance, similar to RAID.
In addition, bcachefs provides all the functionality of bcache, a block-layer
caching system, and lets you assign different roles to each device based on its
performance and other characteristics.")
(license license:gpl2+))))
(define-public httpfs2
(package
(name "httpfs2")

78
gnu/packages/game-development.scm
View file

@ -18,6 +18,7 @@
;;; Copyright © 2019, 2020 Leo Prikler <leo.prikler@student.tugraz.at>
;;; Copyright © 2019 Jethro Cao <jethrocao@gmail.com>
;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2020 Timotej Lazar <timotej.lazar@araneo.si>
;;;
;;; This file is part of GNU Guix.
;;;
@ -77,6 +78,7 @@ (define-module (gnu packages game-development)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages music)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages pcre)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages pulseaudio)
#:use-module (gnu packages python)
@ -723,7 +725,7 @@ (define-public allegro-4
multimedia programming. It handles common, low-level tasks such as creating
windows, accepting user input, loading data, drawing images, playing sounds,
etc.")
(home-page "http://liballeg.org")
(home-page "https://liballeg.org")
(license license:giftware)))
(define-public allegro
@ -764,7 +766,7 @@ (define-public allegro
multimedia programming. It handles common, low-level tasks such as creating
windows, accepting user input, loading data, drawing images, playing sounds,
etc.")
(home-page "http://liballeg.org")
(home-page "https://liballeg.org")
(license license:bsd-3)))
(define-public allegro-5.0
@ -1503,7 +1505,7 @@ (define-public openmw
(define-public godot
(package
(name "godot")
(version "3.0.6")
(version "3.1.2")
(source (origin
(method git-fetch)
(uri (git-reference
@ -1512,25 +1514,43 @@ (define-public godot
(file-name (git-file-name name version))
(sha256
(base32
"0g64h0x8dlv6aa9ggfcidk2mknkfl5li7z1phcav8aqp9srj8avf"))
(modules '((guix build utils)))
"12305wj2i4067jc50l8r0wmb7zjcna24fli8vb8kiaild0jrlip6"))
(modules '((guix build utils)
(ice-9 ftw)
(srfi srfi-1)))
(snippet
'(begin
;; Drop libraries that we take from Guix. Note that some
;; of these may be modified; see "thirdparty/README.md".
;; Keep only those bundled files we have not (yet) replaced
;; with Guix versions. Note that some of these may be
;; modified; see "thirdparty/README.md".
(with-directory-excursion "thirdparty"
(for-each delete-file-recursively
'("freetype"
"libogg"
"libpng"
"libtheora"
"libvorbis"
"libvpx"
"libwebp"
"openssl"
"opus"
"zlib"))
#t)))))
(let* ((preserved-files
'("README.md"
"b2d_convexdecomp"
"certs"
"cvtt"
"enet"
"etc2comp"
"fonts"
"glad"
"jpeg-compressor"
"libsimplewebm"
"libwebsockets"
"miniupnpc"
"minizip"
"misc"
"nanosvg"
"pvrtccompressor"
"recastnavigation"
"squish"
"thekla_atlas"
"tinyexr"
"xatlas")))
(for-each delete-file-recursively
(lset-difference string=?
(scandir ".")
(cons* "." ".." preserved-files)))))
#t))))
(build-system scons-build-system)
(arguments
`(#:scons ,scons-python2
@ -1541,6 +1561,7 @@ (define-public godot
'())
;; Avoid using many of the bundled libs.
;; Note: These options can be found in the SConstruct file.
"builtin_bullet=no"
"builtin_freetype=no"
"builtin_glew=no"
"builtin_libmpdec=no"
@ -1550,9 +1571,11 @@ (define-public godot
"builtin_libvorbis=no"
"builtin_libvpx=no"
"builtin_libwebp=no"
"builtin_openssl=no"
"builtin_mbedtls=no"
"builtin_opus=no"
"builtin_zlib=no")
"builtin_pcre2=no"
"builtin_zlib=no"
"builtin_zstd=no")
#:tests? #f ; There are no tests
#:phases
(modify-phases %standard-phases
@ -1599,6 +1622,7 @@ (define-public godot
#t))))))
(native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("alsa-lib" ,alsa-lib)
("bullet" ,bullet)
("freetype" ,freetype)
("glew" ,glew)
("glu" ,glu)
@ -1611,10 +1635,12 @@ (define-public godot
("libxi" ,libxi)
("libxinerama" ,libxinerama)
("libxrandr" ,libxrandr)
("mbedtls" ,mbedtls-apache)
("mesa" ,mesa)
("openssl" ,openssl)
("opusfile" ,opusfile)
("pulseaudio" ,pulseaudio)))
("pcre2" ,pcre2)
("pulseaudio" ,pulseaudio)
("zstd" ,zstd "lib")))
(home-page "https://godotengine.org/")
(synopsis "Advanced 2D and 3D game engine")
(description
@ -1999,9 +2025,9 @@ (define-public ode
(build-system cmake-build-system)
(arguments
;; Tests fail on all systems but x86_64.
`(#:tests? ,(string=? "x86_64-linux"
(or (%current-target-system)
(%current-system)))
`(#:tests? ,(string-prefix? "x86_64-"
(or (%current-target-system)
(%current-system)))
#:configure-flags '("-DODE_WITH_LIBCCD_SYSTEM=ON")
#:phases
(modify-phases %standard-phases

42
gnu/packages/hexedit.scm
View file

@ -2,6 +2,7 @@
;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2017 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -24,6 +25,7 @@ (define-module (gnu packages hexedit)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages compression)
#:use-module (gnu packages man)
#:use-module (gnu packages ncurses)
#:use-module (guix download)
#:use-module (guix git-download)
@ -43,12 +45,26 @@ (define-public hexedit
(base32
"1xsxa5mip892jkvz9jshj73y6c7j3mgp8y393ciihqlyf2nmfs67"))))
(build-system gnu-build-system)
(arguments '(#:tests? #f)) ; no check target
(arguments
`(#:tests? #f ; no check target
#:phases
(modify-phases %standard-phases
;; Make F1 open the man page even if man-db is not in the profile.
(add-after 'unpack 'patch-man-path
(lambda* (#:key inputs outputs #:allow-other-keys)
(substitute* "interact.c"
(("\"man\"")
(string-append "\"" (assoc-ref inputs "man-db") "/bin/man\""))
(("\"hexedit\"")
(string-append "\"" (assoc-ref outputs "out")
"/share/man/man1/hexedit.1.gz\"")))
#t)))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)))
(inputs
`(("ncurses" ,ncurses)))
`(("man-db" ,man-db)
("ncurses" ,ncurses)))
(synopsis "View and edit files or devices in hexadecimal or ASCII")
(description "hexedit shows a file both in ASCII and in hexadecimal. The
file can be a device as the file is read a piece at a time. You can modify
@ -80,3 +96,25 @@ (define-public ht
Development Environment} (IDE).")
(home-page "http://hte.sourceforge.net/")
(license license:gpl2)))
(define-public bvi
(package
(name "bvi")
(version "1.4.1")
(source (origin
(method url-fetch)
(uri (string-append
"mirror://sourceforge/bvi/bvi/" version
"/bvi-" version ".src.tar.gz"))
(sha256
(base32
"0a0yl0dcyff31k3dr4dpgqmlwygp8iaslnr5gmb6814ylxf2ad9h"))))
(build-system gnu-build-system)
(arguments '(#:tests? #f)) ; no check target
(inputs
`(("ncurses" ,ncurses)))
(synopsis "Binary file editor")
(description "@command{bvi} is a display-oriented editor for binary files,
based on the @command{vi} text editor.")
(home-page "http://bvi.sourceforge.net/")
(license license:gpl3+)))

27
gnu/packages/linux.scm
View file

@ -365,18 +365,18 @@ (define-public linux-libre-5.4-pristine-source
(%upstream-linux-source version hash)
deblob-scripts-5.4)))
(define-public linux-libre-4.19-version "4.19.98")
(define-public linux-libre-4.19-version "4.19.99")
(define-public linux-libre-4.19-pristine-source
(let ((version linux-libre-4.19-version)
(hash (base32 "0dr9vnaaycq77r49mj001zvkxhdyxkgh27dbjsaxcq1dq8xv3zli")))
(hash (base32 "1axmspnqir2zz7lail95y5yaamxl86k39sd4im3c77dgjkwj3g4d")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.19)))
(define-public linux-libre-4.14-version "4.14.167")
(define-public linux-libre-4.14-version "4.14.168")
(define-public linux-libre-4.14-pristine-source
(let ((version linux-libre-4.14-version)
(hash (base32 "0hzyb5k6adhg4vkhix21kg7z6gdzyk1dnzylvbsz9yh2m73qzdrb")))
(hash (base32 "1ziixdg4jsr17kgfa9dpckczk0r2mc5jayqb2f6br19al79pfmyv")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.14)))
@ -1788,7 +1788,7 @@ (define-public ebtables
(define-public iproute
(package
(name "iproute2")
(version "5.3.0")
(version "5.5.0")
(source (origin
(method url-fetch)
(uri (string-append
@ -1796,7 +1796,7 @@ (define-public iproute
version ".tar.xz"))
(sha256
(base32
"0gvv269wjn4279hxr5zzwsk2c5qgswr47za3hm1x4frsk52iw76b"))))
"0ywg70f98wgfai35jl47xzpjp45a6n7crja4vc8ql85cbi1l7ids"))))
(build-system gnu-build-system)
(arguments
`( ;; There is a test suite, but it wants network namespaces and sudo.
@ -5042,6 +5042,21 @@ (define-public light
(base32 "0zrjipd392bzjvxx0rjrb0cgi0ix1d83fwgw1mcy8kc4d16cgyjg"))
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-udev-rules-absolute-path-bins
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "90-backlight.rules"
(("/bin/chgrp") (which "chgrp"))
(("/bin/chmod") (which "chmod")))
#t))
(add-after 'install 'install-udev-rules
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file
"90-backlight.rules" (string-append out "/lib/udev/rules.d"))
#t))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)))

2
gnu/packages/lxqt.scm
View file

@ -1386,5 +1386,5 @@ (define-public lxqt
("qterminal" ,qterminal)))
(synopsis "The Lightweight Qt Desktop Environment")
(description "LXQt is a lightweight Qt desktop environment.")
(home-page "https://lxde.org")
(home-page "https://lxqt.org/")
(license license:gpl2+)))

9
gnu/packages/mail.scm
View file

@ -2367,14 +2367,14 @@ (define-public opensmtpd
(define-public opensmtpd-next
(package
(name "opensmtpd-next")
(version "6.6.1p1")
(version "6.6.2p1")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.opensmtpd.org/archives/"
"opensmtpd-" version ".tar.gz"))
(sha256
(base32 "1ngil8j13m2rq07g94j4yjr6zmaimzy8wbfr17shi7rxnazys6zb"))))
(base32 "16nz2n4s3djlasd6m6dqfwggf6igyfxzq5igny5i0qb8lnn13f33"))))
(build-system gnu-build-system)
(inputs
`(("bdb" ,bdb)
@ -3169,6 +3169,10 @@ (define-public public-inbox
(substitute* "t/ds-leak.t"
(("/bin/sh") (which "sh")))
(invoke "./certs/create-certs.perl")
;; XXX: This test fails due to zombie process is not reaped by
;; the builder.
(substitute* "t/httpd-unix.t"
(("^SKIP: \\{") "SKIP: { skip('Guix');"))
#t))
(add-after 'install 'wrap-programs
(lambda* (#:key inputs outputs #:allow-other-keys)
@ -3199,6 +3203,7 @@ (define-public public-inbox
("perl-email-mime-contenttype" ,perl-email-mime-contenttype)
("perl-email-mime" ,perl-email-mime)
("perl-email-simple" ,perl-email-simple)
("perl-net-server" ,perl-net-server)
("perl-filesys-notify-simple" ,perl-filesys-notify-simple)
("perl-plack-middleware-deflater" ,perl-plack-middleware-deflater)
("perl-plack-middleware-reverseproxy" ,perl-plack-middleware-reverseproxy)

40
gnu/packages/monitoring.scm
View file

@ -401,28 +401,26 @@ (define-public python2-prometheus-client
(package-with-python2 python-prometheus-client))
(define-public go-github-com-prometheus-node-exporter
(let ((commit "55c32fcf02492fe4946f7ab563547cc5df7fc61e")
(revision "0"))
(package
(name "go-github-com-prometheus-node-exporter")
(version (git-version "0.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/prometheus/node_exporter.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"041b87a0sid23c29swqmi5hw6cxbxvkfj3415jg73cm2pi8wh5s6"))))
(build-system go-build-system)
(arguments
'(#:import-path "github.com/prometheus/node_exporter"))
(synopsis "Prometheus exporter for hardware and OS metrics")
(description "Prometheus exporter for metrics exposed by *NIX kernels,
(package
(name "go-github-com-prometheus-node-exporter")
(version "0.18.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/prometheus/node_exporter.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0s3sp1gj86p7npxl38hkgs6ymd3wjjmc5hydyg1b5wh0x3yvpx07"))))
(build-system go-build-system)
(arguments
'(#:import-path "github.com/prometheus/node_exporter"))
(synopsis "Prometheus exporter for hardware and OS metrics")
(description "Prometheus exporter for metrics exposed by *NIX kernels,
written in Go with pluggable metric collectors.")
(home-page "https://github.com/prometheus/node_exporter")
(license license:asl2.0))))
(home-page "https://github.com/prometheus/node_exporter")
(license license:asl2.0)))
(define-public fswatch
(package

49
gnu/packages/music.scm
View file

@ -24,7 +24,7 @@
;;; Copyright © 2019 Jakob L. Kreuze <zerodaysfordays@sdf.lonestar.org>
;;; Copyright © 2019 raingloom <raingloom@protonmail.com>
;;; Copyright © 2019 David Wilson <david@daviwil.com>
;;; Copyright © 2019 Alexandros Theodotou <alex@zrythm.org>
;;; Copyright © 2019, 2020 Alexandros Theodotou <alex@zrythm.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -5138,3 +5138,50 @@ (define-public helm
(description "Helm is a cross-platform polyphonic synthesizer available standalone
and as an LV2 plugin.")
(license license:gpl3+)))
(define-public zrythm
(package
(name "zrythm")
(version "0.7.345")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.zrythm.org/releases/zrythm-"
version ".tar.xz"))
(sha256
(base32
"1csiwq38a1ckx23lairfpl7qjkz71wsa7a9vsxl3k58f9ybibiil"))))
(build-system meson-build-system)
(arguments
`(#:glib-or-gtk? #t
#:configure-flags
`("-Denable_tests=true" "-Dmanpage=true"
"-Dinstall_dseg_font=false" "-Denable_ffmpeg=true")))
(inputs
`(("alsa-lib" ,alsa-lib)
("jack" ,jack-1)
("font-dseg", font-dseg)
("ffmpeg", ffmpeg)
("fftw", fftw)
("fftwf", fftwf)
("gettext", gettext-minimal)
("glibc", glibc)
("gtk+", gtk+)
("libsamplerate" ,libsamplerate)
("libsndfile" ,libsndfile)
("libyaml" ,libyaml)
("lilv", lilv)
("xdg-utils", xdg-utils)
("rubberband", rubberband)))
(native-inputs
`(("pkg-config", pkg-config)
("help2man", help2man)
("libaudec" ,libaudec)
("lv2", lv2)
("glib" ,glib "bin"))) ;for 'glib-compile-resources'
(synopsis "Digital audio workstation focusing on usability")
(description "Zrythm is a digital audio workstation designed to be
featureful and easy to use. It offers unlimited automation options, LV2
plugin support, JACK support and chord assistance.")
(home-page "https://www.zrythm.org")
(license license:agpl3+)))

4
gnu/packages/networking.scm
View file

@ -559,14 +559,14 @@ (define-public iodine
(define-public whois
(package
(name "whois")
(version "5.5.4")
(version "5.5.5")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://debian/pool/main/w/whois/"
"whois_" version ".tar.xz"))
(sha256
(base32 "0k97aiz7ngkjz3vhzvk27kqhnmqmkskdfx310c94qnh8fd7hiqfi"))))
(base32 "03akwma24gzfnsmwpjxmkzmcaxzg6fc68hmyaz0xmsl28i28l3n3"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no test suite

18
gnu/packages/nutrition.scm
View file

@ -2,6 +2,7 @@
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -21,7 +22,7 @@
(define-module (gnu packages nutrition)
#:use-module (guix packages)
#:use-module (guix licenses)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages databases)
@ -38,13 +39,14 @@ (define-public gourmet
(version "0.17.4")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/thinkle/gourmet/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/thinkle/gourmet")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1qvz175arzqm10lpfx8ffadrgirs3240zzqcp0h7sl53qfwx7v8k"))))
"09a2zk140l4babwdj8pwcgl9v7rvwff9cn7h3ppfhm3yvsgkrx07"))))
(build-system python-build-system)
(native-inputs
`(("distutils-extra" ,python2-distutils-extra)
@ -64,9 +66,9 @@ (define-public gourmet
#:phases
(modify-phases %standard-phases
(replace 'install
(lambda* (#:key make-flags #:allow-other-keys)
(lambda* (#:key outputs #:allow-other-keys)
(invoke "python" "setup.py" "install" "--prefix"
(assoc-ref %outputs "out")))))))
(assoc-ref outputs "out")))))))
(home-page "https://thinkle.github.io/gourmet/")
(synopsis "Recipe organizer")
(description

1132
gnu/packages/ocaml.scm
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File diff suppressed because it is too large Load diff

33
gnu/packages/password-utils.scm
View file

@ -24,6 +24,7 @@
;;; Copyright © 2018, 2019 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
;;; Copyright © 2019 Tanguy Le Carrour <tanguy@bioneland.org>
;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -56,6 +57,7 @@ (define-module (gnu packages password-utils)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages crypto)
#:use-module (gnu packages cryptsetup)
#:use-module (gnu packages curl)
#:use-module (gnu packages file)
#:use-module (gnu packages freedesktop)
@ -114,7 +116,7 @@ (define-public pwgen
(define-public keepassxc
(package
(name "keepassxc")
(version "2.5.2")
(version "2.5.3")
(source
(origin
(method url-fetch)
@ -122,7 +124,7 @@ (define-public keepassxc
"/releases/download/" version "/keepassxc-"
version "-src.tar.xz"))
(sha256
(base32 "0lvwc3nxyz7d7vymb6cmgwxylb9g6gsjnq247vbh4lk1ifjir58j"))))
(base32 "1sx647mp1xikig50p9bb6vxv18ymdfj3wkxj6qfdr1zfcv7gn005"))))
(build-system cmake-build-system)
(arguments
'(#:configure-flags '("-DWITH_XC_ALL=YES"
@ -1066,3 +1068,30 @@ (define-public hashcat-utils
function. Since they all work with @code{STDIN} and @code{STDOUT} you can
group them into chains.")
(license license:expat)))
(define-public bruteforce-luks
(package
(name "bruteforce-luks")
(version "1.4.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/glv2/bruteforce-luks/releases/download/"
version
"/bruteforce-luks-"
version
".tar.lz"))
(sha256
(base32 "0yawrlbbklhmvwr99wm7li3r0d5kxvpkwf33a12rji7z0ya5p340"))))
(build-system gnu-build-system)
(native-inputs
`(("lzip" ,lzip)))
(inputs
`(("cryptsetup" ,cryptsetup)))
(synopsis "LUKS encrypted volume cracker")
(description
"This is a cracker for LUKS encrypted volumes. It can be used either in
exhaustive mode to try every password given a charset or in dictionary mode to
try every password contained in a file.")
(home-page "https://github.com/glv2/bruteforce-luks")
(license license:gpl3+)))

14
gnu/packages/plotutils.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2016, 2017, 2019, 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@ -99,6 +99,11 @@ (define-public guile-charting
(modules '((guix build utils)))
(snippet
'(begin
;; Allow builds with Guile 3.0.
(substitute* "configure"
(("2\\.2 2\\.0")
"3.0 2.2 2.0"))
;; By default, .go files would be installed to
;; $libdir/…/ccache instead of $libdir/…/site-ccache. Fix
;; that.
@ -116,6 +121,13 @@ (define-public guile-charting
using the Cairo drawing library.")
(license license:lgpl2.1+)))
(define-public guile3.0-charting
(package
(inherit guile-charting)
(name "guile3.0-charting")
(inputs `(("guile" ,guile-3.0)))
(propagated-inputs `(("guile-cairo" ,guile3.0-cairo)))))
(define-public ploticus
(package
(name "ploticus")

30
gnu/packages/python-xyz.scm
View file

@ -68,6 +68,7 @@
;;; 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>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -17436,3 +17437,32 @@ (define-public offlate
dedicated platform. The tool proposes a unified interface for any format and
an upload option to send your work back to the platform.")
(license license:gpl3+)))
(define-public python-pypng
(package
(name "python-pypng")
(version "0.0.20")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pypng" version))
(sha256
(base32 "02qpa22ls41vwsrzw9r9qhj1nhq05p03hb5473pay6y980s86chh"))))
(build-system python-build-system)
(home-page "https://github.com/drj11/pypng")
(synopsis "Pure Python PNG image encoder/decoder")
(description
"The PyPNG module implements support for PNG images. It reads and writes
PNG files with all allowable bit depths (1/2/4/8/16/24/32/48/64 bits per
pixel) and colour combinations: greyscale (1/2/4/8/16 bit); RGB, RGBA,
LA (greyscale with alpha) with 8/16 bits per channel; colour mapped
images (1/2/4/8 bit). Adam7 interlacing is supported for reading and writing.
A number of optional chunks can be specified (when writing) and
understood (when reading): tRNS, bKGD, gAMA.
PyPNG is not a high level toolkit for image processing (like PIL) and does not
aim at being a replacement or competitor. Its strength lies in fine-grained
extensive support of PNG features. It can also read and write Netpbm PAM
files, with a focus on its use as an intermediate format for implementing
custom PNG processing.")
(license license:expat)))

16
gnu/packages/rust-apps.scm
View file

@ -143,21 +143,7 @@ (define-public tokei
(add-after 'configure 'unvendor-libraries-from-crates
(lambda* (#:key inputs #:allow-other-keys)
(let ((openssl (assoc-ref inputs "openssl")))
(setenv "OPENSSL_DIR" openssl)
(setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1")
(setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
(delete-file-recursively
(string-append "guix-vendor/rust-libgit2-sys-"
,(package-version rust-libgit2-sys-0.10)
".crate/libgit2"))
(delete-file-recursively
(string-append "guix-vendor/rust-libssh2-sys-"
,(package-version rust-libssh2-sys-0.2)
".crate/libssh2"))
(delete-file-recursively
(string-append "guix-vendor/rust-libz-sys-"
,(package-version rust-libz-sys-1.0)
".crate/src/zlib")))
(setenv "OPENSSL_DIR" openssl))
#t)))))
(native-inputs
`(("libgit2" ,libgit2)

7
gnu/packages/scheme.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015, 2016, 2018, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015, 2016 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
@ -637,13 +637,10 @@ (define-public sicp
("source" ,source)
("texinfo" ,texinfo)))
(arguments
`(#:modules ((guix build utils)
(srfi srfi-1)
(srfi srfi-26))
`(#:modules ((guix build utils))
#:builder
(begin
(use-modules (guix build utils)
(srfi srfi-1)
(srfi srfi-26))
(let ((gzip (assoc-ref %build-inputs "gzip"))
(source (assoc-ref %build-inputs "source"))

12
gnu/packages/skarnet.scm
View file

@ -116,7 +116,7 @@ (define-public s6
(inputs `(("skalibs" ,skalibs)
("execline" ,execline)))
(arguments
'(#:configure-flags (list
`(#:configure-flags (list
(string-append "--with-lib="
(assoc-ref %build-inputs "skalibs")
"/lib/skalibs")
@ -126,7 +126,15 @@ (define-public s6
(string-append "--with-sysdeps="
(assoc-ref %build-inputs "skalibs")
"/lib/skalibs/sysdeps"))
#:tests? #f)) ; no tests exist
#:tests? #f ; no tests exist
#:phases
(modify-phases %standard-phases
(add-after 'install 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(doc (string-append out "/share/doc/s6-" ,version)))
(copy-recursively "doc" doc)
#t))))))
(home-page "https://skarnet.org/software/s6")
(license isc)
(synopsis "Small suite of programs for process supervision")

65
gnu/packages/statistics.scm
View file

@ -504,14 +504,14 @@ (define-public r-codetools
(define-public r-foreign
(package
(name "r-foreign")
(version "0.8-74")
(version "0.8-75")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreign" version))
(sha256
(base32
"047w772msiki85rxxhqkxya37gmw4331l32651rr09dl2vq02pgj"))))
"0g4mi101srjbl17ydb2hl3854m3xj0llj6861lfr30sp08nkqavl"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/foreign")
(synopsis "Read data stored by other statistics software")
@ -1400,13 +1400,13 @@ (define-public r-yaml
(define-public r-knitr
(package
(name "r-knitr")
(version "1.26")
(version "1.27")
(source (origin
(method url-fetch)
(uri (cran-uri "knitr" version))
(sha256
(base32
"08f3bdd5cnnbigybr9vmkhq12n64pbmn4layl3w5rwk8xi5kbnrq"))))
"02nysgnx6xv0kd351s1d59yx4g0drsd9lmcgxs0rsw5f1jiycgdg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-evaluate" ,r-evaluate)
@ -1607,13 +1607,13 @@ (define-public r-r6
(define-public r-rlang
(package
(name "r-rlang")
(version "0.4.2")
(version "0.4.3")
(source (origin
(method url-fetch)
(uri (cran-uri "rlang" version))
(sha256
(base32
"0fczcp17kaz3s4p0nd4126bppwl20vpxfybhsndpcky9h75wklgv"))))
"0qsqfikbsj55x5brghnkzzp7pz0japr4xnzm993f668mlls3f6i4"))))
(build-system r-build-system)
(home-page "http://rlang.tidyverse.org")
(synopsis "Functions for base types, core R and Tidyverse features")
@ -2565,13 +2565,13 @@ (define-public r-latticeextra
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
(version "0.9.800.3.0")
(version "0.9.800.4.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
"0kpcspg3mafi5kncjfhnbcwimvlf19jvrxilvhbpd20sap473mh3"))))
"1csh54v4d0ccwmk4bqj4rca1d5rqpafvb4459x3q6k9sys0charx"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
;; All needed for vignettes
@ -2617,13 +2617,13 @@ (define-public r-bitops
(define-public r-catools
(package
(name "r-catools")
(version "1.17.1.4")
(version "1.18.0")
(source (origin
(method url-fetch)
(uri (cran-uri "caTools" version))
(sha256
(base32
"151vsfakg32jn9msfdjcizhizm8k8yxlfpnsbagns9ihr59s3w49"))))
"0y1kgyiy322yhb0phzwvf2zgjz9awp13lhzhk9v1ddg88656jhq3"))))
(properties `((upstream-name . "caTools")))
(build-system r-build-system)
(propagated-inputs
@ -2663,13 +2663,13 @@ (define-public r-rprojroot
(define-public r-rmarkdown
(package
(name "r-rmarkdown")
(version "2.0")
(version "2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmarkdown" version))
(sha256
(base32 "1bm3n17wa0pf1cq7qmwhbnn02x2pld7zzmmzjcvwy6apanch9fl7"))))
(base32 "0pa5xs0vzwn9vsgysjqbks9v5lbqphxh5agciskllibc40hhwigg"))))
(properties `((upstream-name . "rmarkdown")))
(build-system r-build-system)
(propagated-inputs
@ -2755,17 +2755,16 @@ (define-public r-pkgconfig
(define-public r-blob
(package
(name "r-blob")
(version "1.2.0")
(version "1.2.1")
(source (origin
(method url-fetch)
(uri (cran-uri "blob" version))
(sha256
(base32
"08z071jzac4gasgfgab0y5g3ilfmlw08ln813wphxg07hsiczw8s"))))
"1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-prettyunits" ,r-prettyunits)
("r-rlang" ,r-rlang)
`(("r-rlang" ,r-rlang)
("r-vctrs" ,r-vctrs)))
(home-page "https://github.com/hadley/blob")
(synopsis "Simple S3 Class for representing vectors of binary data")
@ -2850,13 +2849,13 @@ (define-public r-rcurl
(define-public r-xml
(package
(name "r-xml")
(version "3.98-1.20")
(version "3.99-0.3")
(source (origin
(method url-fetch)
(uri (cran-uri "XML" version))
(sha256
(base32
"0n28m8iz1wfgixr7fjswl238c5w9kggsrw0c8hdzp859dqvqdbs6"))))
"0lzpqwajs5xaqdna50vl24qkp9xvh00zypjjzy6kgdzk11isgdw1"))))
(properties
`((upstream-name . "XML")))
(build-system r-build-system)
@ -3235,17 +3234,18 @@ (define-public r-glmnet
(define-public r-pkgmaker
(package
(name "r-pkgmaker")
(version "0.27")
(version "0.31")
(source
(origin
(method url-fetch)
(uri (cran-uri "pkgmaker" version))
(sha256
(base32
"0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
"0cc6v6kpwxwwh7k7zyw13wqdp0f9qzzr1a7vv02lskgii54aa4nb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bibtex" ,r-bibtex)
`(("r-assertthat" ,r-assertthat)
("r-bibtex" ,r-bibtex)
("r-codetools" ,r-codetools)
("r-digest" ,r-digest)
("r-magrittr" ,r-magrittr)
@ -3284,19 +3284,17 @@ (define-public r-registry
(define-public r-rngtools
(package
(name "r-rngtools")
(version "1.4")
(version "1.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "rngtools" version))
(sha256
(base32
"1kivj594bn774lbn29ws2rmzy2km99sza0j3jqvhal6hwmk27a9s"))))
"0xgmg3qb6insc157as47mcm9sdjdpy9jirh7w06bxb7pfcxqfx42"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
("r-pkgmaker" ,r-pkgmaker)
("r-stringr" ,r-stringr)))
`(("r-digest" ,r-digest)))
(home-page "https://renozao.github.io/rngtools")
(synopsis "Utility functions for working with random number generators")
(description
@ -3714,14 +3712,14 @@ (define-public r-tidyselect
(define-public r-tidyr
(package
(name "r-tidyr")
(version "1.0.0")
(version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyr" version))
(sha256
(base32
"1403j0xd93l0r7qj738ryd5zc79hbcghrzybib3c3hrnaq5s78cj"))))
"0safj8bcf8libwr0jx4059bmarngvhfddrcv8k5iw39m9lpxs0r4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@ -4835,18 +4833,17 @@ (define-public r-pcapp
(define-public r-rrcov
(package
(name "r-rrcov")
(version "1.4-9")
(version "1.5-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "rrcov" version))
(sha256
(base32
"11zvxidlb1pr2j5dzvmbjqdgsmmicsq8ppjf5wcfykfyf2fkcmz7"))))
"0m62k58nabw7hjz1qyyf9a0d6lvcz5vcvpksjnq93zcfra9inr57"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cluster" ,r-cluster)
("r-lattice" ,r-lattice)
`(("r-lattice" ,r-lattice)
("r-mvtnorm" ,r-mvtnorm)
("r-pcapp" ,r-pcapp)
("r-robustbase" ,r-robustbase)))
@ -4939,14 +4936,14 @@ (define-public r-trimcluster
(define-public r-fpc
(package
(name "r-fpc")
(version "2.2-3")
(version "2.2-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "fpc" version))
(sha256
(base32
"1dy3pla4jjgs46izqg2kxajlxr80sbr9896jbzb1qszrdx7af041"))))
"1gsnl5sbdg86b2wdrsy6wq83xj6mrziiq7rxa8cqksgljc7gp6yf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-class" ,r-class)

7
gnu/packages/terminals.scm
View file

@ -17,6 +17,7 @@
;;; Copyright © 2019 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -138,6 +139,11 @@ (define-public termite
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-xdg-open
(lambda _
(substitute* "termite.cc"
(("xdg-open") (which "xdg-open")))
#t))
(delete 'configure))
#:tests? #f
;; This sets the destination when installing the necessary terminal
@ -150,6 +156,7 @@ (define-public termite
(inputs
`(("vte" ,vte-ng)
("gtk+" ,gtk+)
("xdg-utils" ,xdg-utils)
("ncurses" ,ncurses)))
(native-inputs
`(("pkg-config" ,pkg-config)))

4
gnu/packages/text-editors.scm
View file

@ -468,7 +468,7 @@ (define-public ghostwriter
(define-public manuskript
(package
(name "manuskript")
(version "0.10.0")
(version "0.11.0")
(source
(origin
(method git-fetch)
@ -477,7 +477,7 @@ (define-public manuskript
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0q413vym7hzjpyg3krj5y63hwpncdifjkyswqmr76zg5yqnklnh3"))))
(base32 "1l6l9k6k69yv8xqpll0zv9cwdqqg4zvxy90l6sx5nv2yywh5crla"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ;no test

13
gnu/packages/tls.scm
View file

@ -122,15 +122,15 @@ (define-public asn1c
(define-public p11-kit
(package
(name "p11-kit")
(version "0.23.18.1")
(version "0.23.19")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/p11-glue/p11-kit/releases/"
"download/" version "/p11-kit-" version ".tar.gz"))
"download/" version "/p11-kit-" version ".tar.xz"))
(sha256
(base32
"0vrwab1082f7l5sbzpb28nrs3q4d2q7wzbi8c977rpah026bvhrl"))))
"1w7i4f5lc8darjkfjsm1ldvhkv0x29mvwg89klmh5kb2xqf6x4wi"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
@ -858,7 +858,7 @@ (define-public acme-client
(define-public mbedtls-apache
(package
(name "mbedtls-apache")
(version "2.16.3")
(version "2.16.4")
(source
(origin
(method url-fetch)
@ -868,11 +868,12 @@ (define-public mbedtls-apache
version "-apache.tgz"))
(sha256
(base32
"0qd65lnr63vmx2gxla6lcmm5gawlnaj4wy4h4vmdc3h9h9nyw6zc"))))
"1yxj5wahaj87xhdi89zbk78ig77b166h464yrj5gb3lwv8mz6h9l"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
(list "-DUSE_SHARED_MBEDTLS_LIBRARY=ON")))
(list "-DUSE_SHARED_MBEDTLS_LIBRARY=ON"
"-DUSE_STATIC_MBEDTLS_LIBRARY=OFF")))
(native-inputs
`(("perl" ,perl)
("python" ,python)))

34
gnu/packages/vim.scm
View file

@ -938,3 +938,37 @@ (define-public python-pynvim
(define-public python2-pynvim
(package-with-python2 python-pynvim))
(define-public vim-guix-vim
(package
(name "vim-guix-vim")
(version "0.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/Efraim/guix.vim")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1f8h8m96fqh3f9hy87spgh9kdqzyxl11n9s3rywvyq5xhn489bnk"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(vimfiles (string-append out "/share/vim/vimfiles")))
(for-each
(lambda (dir)
(copy-recursively dir (string-append vimfiles "/" dir)))
'("compiler" "doc" "indent" "ftdetect" "ftplugin" "syntax"))
#t))))))
(home-page "https://gitlab.com/Efraim/guix.vim")
(synopsis "Guix integration in Vim")
(description "This package provides support for GNU Guix in Vim.")
(license license:vim)))

7
gnu/services/xorg.scm
View file

@ -862,7 +862,12 @@ (define (gdm-configuration-file config)
"#TimedLoginEnable=false\n"
"#TimedLogin=\n"
"#TimedLoginDelay=0\n"
"#InitialSetupEnable=true\n"
;; Disable initial system setup inside GDM.
;; Whatever settings are set there should already be
;; taken care of through `guix system'.
;; See also
;; <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=39281>.
"InitialSetupEnable=false\n"
;; Enable me once X is working.
"WaylandEnable=false\n"
"\n"

20
guix/build-system/ocaml.scm
View file

@ -92,7 +92,11 @@ (define (default-ocaml4.07-findlib)
(let ((module (resolve-interface '(gnu packages ocaml))))
(module-ref module 'ocaml4.07-findlib)))
(define* (package-with-explicit-ocaml ocaml findlib old-prefix new-prefix
(define (default-ocaml4.07-dune)
(let ((module (resolve-interface '(gnu packages ocaml))))
(module-ref module 'ocaml4.07-dune)))
(define* (package-with-explicit-ocaml ocaml findlib dune old-prefix new-prefix
#:key variant-property)
"Return a procedure of one argument, P. The procedure creates a package
with the same fields as P, which is assumed to use OCAML-BUILD-SYSTEM, such
@ -100,6 +104,10 @@ (define* (package-with-explicit-ocaml ocaml findlib old-prefix new-prefix
recursively accordingly. If the name of P starts with OLD-PREFIX, this is
replaced by NEW-PREFIX; otherwise, NEW-PREFIX is prepended to the name.
When the package uses the DUNE-BUILD-SYSTEM, the procedure creates a package
with the same fields as P, such that it is compiled with OCAML, FINDLIB and DUNE
instead.
When VARIANT-PROPERTY is present, it is used as a key to search for
pre-defined variants of this transformation recorded in the 'properties' field
of packages. The property value must be the promise of a package. This is a
@ -132,10 +140,15 @@ (define (transform p)
name))))
(arguments
(let ((ocaml (if (promise? ocaml) (force ocaml) ocaml))
(findlib (if (promise? findlib) (force findlib) findlib)))
(findlib (if (promise? findlib) (force findlib) findlib))
(dune (if (promise? dune) (force dune) dune)))
(ensure-keyword-arguments (package-arguments p)
`(#:ocaml ,ocaml
#:findlib ,findlib))))))
#:findlib ,findlib
,@(if (eq? (package-build-system p)
(default-dune-build-system))
`(#:dune ,dune)
'())))))))
(else p)))
(define (cut? p)
@ -148,6 +161,7 @@ (define (cut? p)
(define package-with-ocaml4.07
(package-with-explicit-ocaml (delay (default-ocaml4.07))
(delay (default-ocaml4.07-findlib))
(delay (default-ocaml4.07-dune))
"ocaml-" "ocaml4.07-"
#:variant-property 'ocaml4.07-variant))

6
guix/build/cargo-build-system.scm
View file

@ -2,7 +2,7 @@
;;; Copyright © 2016 David Craven <david@craven.ch>
;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2019 Ivan Petkov <ivanppetkov@gmail.com>
;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -58,7 +58,7 @@ (define (has-executable-target?)
(define (crate-src? path)
"Check if PATH refers to a crate source, namely a gzipped tarball with a
Cargo.toml file present at its root."
(and (gzip-file? path)
(and (not (directory-exists? path)) ; not a tarball
;; First we print out all file names within the tarball to see if it
;; looks like the source of a crate. However, the tarball will include
;; an extra path component which we would like to ignore (since we're
@ -119,6 +119,8 @@ (define* (configure #:key inputs
;; upgrading the compiler for example.
(setenv "RUSTFLAGS" "--cap-lints allow")
(setenv "CC" (string-append (assoc-ref inputs "gcc") "/bin/gcc"))
(setenv "LIBGIT2_SYS_USE_PKG_CONFIG" "1")
(setenv "LIBSSH2_SYS_USE_PKG_CONFIG" "1")
;; We don't use the Cargo.lock file to determine the package versions we use
;; during building, and in any case if one is not present it is created

2
guix/licenses.scm
View file

@ -286,7 +286,7 @@ (define freetype
(define giftware
(license "Giftware"
"http://liballeg.org/license.html"
"https://liballeg.org/license.html"
"The Allegro 4 license"))
(define gpl1