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Merge branch 'master' into staging

master
Marius Bakke 2020-01-29 11:12:49 +01:00
parent 333d15790c 602059e794
commit 0895002f68
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36 changed files with 1637 additions and 890 deletions
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6
build-aux/git-authenticate.scm
View File

@ -166,8 +166,12 @@
"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
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@ -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 @@
#: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 @@ lv2-c++-tools.")
(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 @@ lv2-c++-tools.")
version ".tar.bz2"))
(sha256
(base32
"03p6s5gap0lvig2fs0a8nib5rxsc24dbqjsydpwvlm5l49wlk2f0"))))
"0vax0b1lgd4212bpxa1rciz52d4mv3dkfvcbbhzw4cjp698v1kmn"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; no check target
@ -4009,3 +4010,33 @@ in the package.")
;; (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
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@ -694,6 +694,34 @@ annotations.")
"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 @@ possible, parallelization is achieved using the BiocParallel framework.")
(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 @@ are standardized and usable by the accompanying mutossGUI package.")
(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 @@ packages.")
(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 @@ access.")
(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 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
(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 @@ as well as query and modify the browser state, such as the current viewport.")
(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 @@ family of feature/genome hypotheses.")
(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 @@ analyses in addition to large-scale sequence-level searches.")
(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 @@ let before_space s =
(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 @@ C/C++, R, and more, and uploads it to the @code{codecov.io} service.")
#: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 @@ such as copy/paste from an R session.")
(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 @@ coordinates.")
(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 @@ statistical functions and other utilities to ease their usage.")
(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 @@ topics for ecologists (ISBN 978-0-691-12522-0).")
(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 @@ by base R methods related to model fitting.")
(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 @@ training models for classification or ranking.")
(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 @@ timeout. It can also poll several processes at once.")
(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 @@ to variables on the left-hand side of the assignment.")
(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 @@ rules with R.")
(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 @@ clustering.")
(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 @@ information are missing.")
(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 @@ multiple-imputation datasets.")
(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 @@ console, resulting in an interactive editing environment.")
(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 @@ detection, parallelism through BLAS and parallel user templates.")
(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 @@ differentiation.")
(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 @@ ROPE percentage and pd).")
(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 @@ results using @code{ggplot2}.")
(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 @@ conversion of indices such as Cohen's d, r, odds, etc.")
(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 @@ conversion of indices such as Cohen's d, r, odds, etc.")
("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 @@ back to file after modifications.")
(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 @@ analysing multivariate abundance data in community ecology.")
(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 @@ preparing, executing, and processing HTTP requests.")
(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 @@ limitations\" using the GNU Multiple Precision library.")
(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 @@ them in distributed compute environments.")
(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 @@ heuristics.")
(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 @@ numbers (e.g. concentrations).")
(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 @@ spanning tree.")
(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 @@ consists of @code{grid} grobs and viewports that can then be manipulated with
(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 @@ and Learning to Rank measures (LambdaMart).")
(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 @@ and Learning to Rank measures (LambdaMart).")
(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 @@ and Learning to Rank measures (LambdaMart).")
("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 @@ path of values for the regularization parameter.")
(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 @@ computed using the L1 (Manhattan, taxicab) metric.")
(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 @@ in pipelines.")
(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 @@ as a boxplot function.")
(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 @@ facilitates insertion into pipelines, and content inspection.")
(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 @@ these algorithms also allow to detect anomalies (outliers).")
(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 @@ problems (food web problems, linear programming problems).")
(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 @@ the regex engine it uses pluggable.")
"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 @@ wasm-bindgen crate.")
(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 @@ wasm-bindgen crate.")
(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 @@ values of all the exported APIs match the platform that libc is compiled for.")
(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 @@ values of all the exported APIs match the platform that libc is compiled for.")
(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 @@ functions and static variables these libraries contain.")
(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 @@ functions and static variables these libraries contain.")
(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 @@ functions and static variables these libraries contain.")
(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 @@ types as proposed in RFC 1158.")
(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 @@ types as proposed in RFC 1158.")
;; 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 @@ deserialization, and interpreter in Rust.")
"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 @@ deserialization, and interpreter in Rust.")
(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 @@ letters of the alphabet, spelling, eye-hand coordination, etc.")
(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 @@ passive voice.")
(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 @@ programming and reproducible research.")
(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 @@ into sections while preserving the structure imposed by any timestamps.")
(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 @@ into sections while preserving the structure imposed by any timestamps.")
(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 @@ try completing. See @code{fish-completion-fallback-on-bash-p}.")
(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 @@ Emacs that integrate with major modes like Org-mode.")
(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 @@ Emacs that integrate with major modes like Org-mode.")
(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 @@ pattern guessed from thing under current cursor position.
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 @@ functions. The source code to MAME serves as this documentation.")
#: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 @@
#: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 @@
#: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 @@
#: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 @@ package is the Nuklear bindings for LÖVE created by Kevin Harrison.")
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 @@ etc.")
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 @@ games.")
(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 @@ games.")
(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 @@ games.")
'())
;; 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 @@ games.")
"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 @@ games.")
#t))))))
(native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("alsa-lib" ,alsa-lib)
("bullet" ,bullet)
("freetype" ,freetype)
("glew" ,glew)
("glu" ,glu)
@ -1611,10 +1635,12 @@ games.")
("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 @@ a.k.a. XenoCollide) as described in Game Programming Gems 7.")
(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 @@
#: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 @@
(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 @@ low-level functionality of a debugger with the usability of an @dfn{Integrated
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 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(%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 @@ that the Ethernet protocol is much simpler than the IP protocol.")
(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 @@ that the Ethernet protocol is much simpler than the IP protocol.")
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 @@ monitoring tools for Linux. These include @code{mpstat}, @code{iostat},
(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 @@ desktop.")
("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 @@ e-mails with other systems speaking the SMTP protocol.")
(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 @@ related tools to process winmail.dat files.")
(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 @@ related tools to process winmail.dat files.")
("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 @@ WSGI and the node exporter textfile collector.")
(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 @@ MIDI drums and comes as two separate drumkits: Black Pearl and Red Zeppelin.")
(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 @@ and up to 1 Mbit/s downstream.")
(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 @@
(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 @@
#: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

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gnu/packages/ocaml.scm
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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 @@
#: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 @@ human.")
(define-public keepassxc
(package
(name "keepassxc")
(version "2.5.2")
(version "2.5.3")
(source
(origin
(method url-fetch)
@ -122,7 +124,7 @@ human.")
"/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 @@ binaries. All of these utils are designed to execute only one specific
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 @@ scientific data.")
(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 @@ scientific data.")
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 @@ Project, or not such a gitlab instance when your upstream doesn't use any
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 @@ gitignore rules.")
(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 @@ threads.")
("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 @@ complexity.")))
(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 @@ complexity.")))
(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 @@ code for possible problems.")
(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 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
(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 @@ defined in different packages.")
(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 @@ well as additional utilities such as panel and axis annotation functions.")
(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 @@ vectors.")
(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 @@ certain criterion, e.g., it contains a certain regular file.")
(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 @@ that package, other packages are unaffected.")
(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 @@ ldap, and also supports cookies, redirects, authentication, etc.")
(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 @@ path-wise fashion.")
(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 @@ package registries.")
(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 @@ selection.")
(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 @@ analysis} (PCA) by projection pursuit.")
(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 @@ of the points.")
(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 @@ configurable through a graphical wizard.")
(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 @@ configurable through a graphical wizard.")
(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 @@ environment with Markdown markup.")
(define-public manuskript
(package
(name "manuskript")
(version "0.10.0")
(version "0.11.0")
(source
(origin
(method git-fetch)
@ -477,7 +477,7 @@ environment with Markdown markup.")
(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 @@ in intelligent transportation networks.")
(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 @@ then ported to the GNU / Linux environment.")
(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 @@ then ported to the GNU / Linux environment.")
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 @@ through its msgpack-rpc API.")
(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 @@ the GNOME desktop environment.")
"#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 @@
(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 @@ that it is compiled with OCAML and FINDLIB instead. The inputs are changed
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 @@ pre-defined variants."
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 @@ pre-defined variants."
(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 (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 @@ directory = '" port)
;; 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 @@ at URI, which may be a file:// URI pointing the package's tree."
(define giftware
(license "Giftware"
"http://liballeg.org/license.html"
"https://liballeg.org/license.html"
"The Allegro 4 license"))
(define gpl1