diff options
Diffstat (limited to 'gnu')
61 files changed, 2057 insertions, 916 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 3e355ac9b3..c4299fcbe4 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -816,7 +816,6 @@ dist_patch_DATA = \ %D%/packages/patches/hplip-remove-imageprocessor.patch \ %D%/packages/patches/hydra-disable-darcs-test.patch \ %D%/packages/patches/icecat-avoid-bundled-libraries.patch \ - %D%/packages/patches/icecat-CVE-2018-12383.patch \ %D%/packages/patches/icecat-use-system-graphite2+harfbuzz.patch \ %D%/packages/patches/icecat-use-system-media-libs.patch \ %D%/packages/patches/icedtea-6-hotspot-gcc-segfault-workaround.patch \ @@ -1048,6 +1047,7 @@ dist_patch_DATA = \ %D%/packages/patches/plink-1.07-unclobber-i.patch \ %D%/packages/patches/plink-endian-detection.patch \ %D%/packages/patches/plotutils-libpng-jmpbuf.patch \ + %D%/packages/patches/poppler-CVE-2018-19149.patch \ %D%/packages/patches/portaudio-audacity-compat.patch \ %D%/packages/patches/portmidi-modular-build.patch \ %D%/packages/patches/potrace-tests.patch \ diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 3c65ce102c..0da35ea62e 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -981,7 +981,7 @@ system administrator.") (define-public sudo (package (name "sudo") - (version "1.8.25p1") + (version "1.8.26") (source (origin (method url-fetch) (uri @@ -991,7 +991,7 @@ system administrator.") version ".tar.gz"))) (sha256 (base32 - "0nqri46d4dpycj96zin2f2wszmhm7q9mr68hhj9sp81pgmx9rjcx")) + "1qpyyfga8rs02p3186sns8qvh2bzwa48ka845nrcqh83dyd23nj0")) (modules '((guix build utils))) (snippet '(begin diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 28447552f2..6dc0d82668 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -572,13 +572,14 @@ based on human speech recordings.") (name "infamous-plugins") (version "0.2.04") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ssj71/infamousPlugins/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ssj71/infamousPlugins.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1n6rhqsmvad7692w2h01niw5gqg5yk7a09wxl5ivs77zyp93vf7z")))) + "0hmqk80w4qxq09iag7b7srf2g0wigkyhzq0ywxvhz2iz0hq9k0dh")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; there are no tests @@ -610,13 +611,14 @@ envelope follower, distortion effects, tape effects and more.") (name "swh-plugins-lv2") (version "1.0.16") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/swh/" - "lv2/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/swh/lv2.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0j1mih0lp4fds07knp5i32in515sh0df1qi6694pmyz2wqnm295w")))) + "0y7nnww864mm4k6ayy2lhcws3wlbhb2gkyjbrwk921fvc18qk9mz")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no check target @@ -654,14 +656,14 @@ emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.") (name "csound") (version "6.11.0") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/csound/csound/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/csound/csound.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "072pk5h9w0vhw0ncc9dn90haw1yv18v04iwwjn8nsp6930w7dvxd")))) + "1hlkrnv3gghx4v382nl6v6k2k1dzm5ddk35m5g3q6pzc959726s7")))) (build-system cmake-build-system) (inputs `(("alsa-lib" ,alsa-lib) @@ -1174,19 +1176,15 @@ PS, and DAB+.") (define-public faust-2 (package (inherit faust) - (version "2.1.0") + (version "2.5.23") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/grame-cncm/faust.git") - (commit (string-append "v" - (string-map (lambda (c) - (if (char=? c #\.) #\- c)) - version))))) - (file-name (string-append "faust-" version "-checkout")) + (method url-fetch) + (uri (string-append "https://github.com/grame-cncm/faust/" + "releases/download/" version + "/faust-" version ".tar.gz")) (sha256 (base32 - "06km0ygwxxwgw1lqldccqidxhmjfz8ck0wnbd95qk5sg8sbpc068")))) + "1yz5jnr76hh7rmxkpdi7gyrw1wp4gyqfpq8zyl97qdi5ga5gjznq")))) (build-system gnu-build-system) (arguments (substitute-keyword-arguments (package-arguments faust) @@ -1194,7 +1192,7 @@ PS, and DAB+.") `(list (string-append "prefix=" (assoc-ref %outputs "out")) "world")))) (native-inputs - `(("llvm" ,llvm-with-rtti) + `(("llvm" ,llvm-3.8-with-rtti) ("which" ,which) ("xxd" ,xxd) ("ctags" ,emacs-minimal) ; for ctags @@ -1881,14 +1879,14 @@ software.") (name "lvtk") (version "1.2.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/lvtk/lvtk/archive/" - version - ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/lvtk/lvtk.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "03nbj2cqcklqwh50zj2gwm07crh5iwqbpxbpzwbg5hvgl4k4rnjd")))) + "1b01zvzl70ana6l1kn8fgyr7msnn3c7x61cgw7fdpp50322352p8")))) (build-system waf-build-system) (arguments `(#:tests? #f ; no check target @@ -2274,36 +2272,32 @@ tempo and pitch of an audio recording independently of one another.") (name "rtmidi") (version "2.1.0") (source (origin - (method url-fetch) - (uri - (string-append "https://github.com/powertab/rtmidi/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/powertab/rtmidi.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0d49lapnmdgmjxh4vw57h6xk74nn5r0zwysv7jbd7m8kqhpq5rjj")))) + "106v177y3nrjv2l1yskch4phpqd8h97b67zj0jiq9pc3c69jr1ay")))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target - #:phases (modify-phases %standard-phases - (add-after - 'unpack 'autoconf - (lambda _ (invoke "autoreconf" "-vfi"))) - (add-before - 'build 'fix-makefile - (lambda _ - (substitute* "Makefile" - (("/bin/ln") "ln") - (("RtMidi.h RtError.h") "RtMidi.h")) - #t)) - (add-before - 'install 'make-target-dirs - (lambda _ - (let ((out (assoc-ref %outputs "out"))) - (mkdir-p (string-append out "/bin")) - (mkdir (string-append out "/lib")) - (mkdir (string-append out "/include"))) - #t))))) + #:phases + (modify-phases %standard-phases + (add-before 'build 'fix-makefile + (lambda _ + (substitute* "Makefile" + (("/bin/ln") "ln") + (("RtMidi.h RtError.h") "RtMidi.h")) + #t)) + (add-before 'install 'make-target-dirs + (lambda _ + (let ((out (assoc-ref %outputs "out"))) + (mkdir-p (string-append out "/bin")) + (mkdir (string-append out "/lib")) + (mkdir (string-append out "/include"))) + #t))))) (inputs `(("jack" ,jack-1) ("alsa-lib" ,alsa-lib))) @@ -2754,20 +2748,14 @@ portions of LAME.") ;; TODO: Add ASIHPI. `(("alsa-lib" ,alsa-lib) ("jack" ,jack-1))) + ;; Autoreconf is necessary because the audacity-compat patch modifies .in + ;; files. (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("libtool" ,libtool) ("pkg-config" ,pkg-config))) - (arguments - '(#:phases - ;; Autoreconf is necessary because the audacity-compat patch modifies - ;; .in files. - (modify-phases %standard-phases - (add-after 'unpack 'autoreconf - (lambda _ - (invoke "autoreconf" "-vif")))) - #:tests? #f)) ;no 'check' target + (arguments '(#:tests? #f)) ;no 'check' target (home-page "http://www.portaudio.com/") (synopsis "Audio I/O library") (description @@ -2813,12 +2801,13 @@ synthesizer written in C++.") (version "1.1") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/Themaister/RSound/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/Themaister/RSound.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "1wzs40c0k5zpkmm5ffl6c17xmr399sxli7ys0fbb9ib0fd334knx")))) + (base32 "0gspmr3klwnq98h17p5hc6ifygya4p80g4g8r7a1qavm3mv19waf")))) (build-system gnu-build-system) (inputs `(("alsa-lib" ,alsa-lib) @@ -2851,14 +2840,14 @@ with a much different focus than most other audio daemons.") (name "xjackfreak") (version "1.0") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/johnhldavis/xjackfreak/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/johnhldavis/xjackfreak.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0xj6gpxfnw9jbdgwgm0x23xgfvj2kwmwb1nk0drw8lxgcchkq7d9")))) + "18c546qidbrj0f5wfiq5llii2192xpln0ab3r4vpr7i3wybxqjfz")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -3026,15 +3015,16 @@ point audio data.") (name "cuetools") (version "1.4.1") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/svend/cuetools/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/svend/cuetools.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "01xi3rvdmil9nawsha04iagjylqr1l9v9vlzk99scs8c207l58i4")))) + "02ksv1ahf1v4cr2xbclsfv5x17m9ivzbssb5r8xjm97yh8a7spa3")))) (build-system gnu-build-system) - ;; The source tarball is not bootstrapped. + ;; The source checkout is not bootstrapped. (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -3075,13 +3065,14 @@ use them split WAVE data into multiple files.") (name "dcadec") (version "0.2.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/foo86/dcadec/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/foo86/dcadec.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0i0dpypgqkhhi4v1fmsp2way6w9kbcix3c7q79pmg39yvrzj17gd")))) + "07nd0ajizrp1w02bsyfcv18431r8m8rq8gjfmz9wmckpg7cxj2hs")))) (build-system gnu-build-system) (arguments ;; Test files are missing: https://github.com/foo86/dcadec/issues/53 @@ -3386,13 +3377,14 @@ the following features: (version "1.6") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/dpayne/cli-visualizer/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dpayne/cli-visualizer.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "07zkm87f2fr8kc6531zrkya7q81sdanm6813y2f54mg13g41y6hi")))) + "0mirp8bk398di5xyq95iprmdyvplfghxqmrfj7jdnpy554vx7ppc")))) (build-system gnu-build-system) (native-inputs `(("which" ,which))) @@ -3440,14 +3432,14 @@ representations.") (name "cava") (version "0.6.1") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/karlstav/cava/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/karlstav/cava.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "13d72swnjs894llf0paandmhf1lf90dz6ygkcdw4bv84wzkq1f4q")))) + "1kvhqgijs29909w3sq9m0bslx2zxxn4b3i07kdz4hb0dqkppxpjy")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 52afcbc676..c927a14673 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com> ;;; Copyright © 2018 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com> +;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,6 +31,7 @@ (define-module (gnu packages backup) #:use-module (guix packages) #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix git-download) #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system gnu) @@ -132,22 +134,18 @@ spying and/or modification by the server.") (name "par2cmdline") (version "0.8.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/Parchive/par2cmdline/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/Parchive/par2cmdline.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1jpshmmcr81mxly0md2rr231qz9c8c680bbvcmhh100dg9i4a6s6")))) + "0f1jsd5sw2wynjzi7yjqjaf13yhyjfdid91p8yh0jn32y03kjyrz")))) (native-inputs `(("automake" ,automake) ("autoconf" ,autoconf))) (build-system gnu-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoreconf - (lambda _ (invoke "autoreconf" "-vfi")))))) (synopsis "File verification and repair tools") (description "Par2cmdline uses Reed-Solomon error-correcting codes to generate and verify PAR2 recovery files. These files can be distributed @@ -889,6 +887,7 @@ is like a time machine for your data. ") ,version) ;; Disable 'restic self-update'. It makes little sense in Guix. (substitute* "build.go" (("selfupdate") "")) + (setenv "HOME" (getcwd)) ; for $HOME/.cache/go-build (invoke "go" "run" "build.go")))) (replace 'check diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bab6b2b64d..95c722ac40 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -969,3 +969,64 @@ using pre-clustering with the k-means algorithm. Functions are also provided to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.") (license license:gpl3))) + +(define-public r-destiny + (package + (name "r-destiny") + (version "2.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "destiny" version)) + (sha256 + (base32 + "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-fnn" ,r-fnn) + ("r-ggthemes" ,r-ggthemes) + ("r-hmisc" ,r-hmisc) + ("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-proxy" ,r-proxy) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-scales" ,r-scales) + ("r-scatterplot3d" ,r-scatterplot3d) + ("r-smoother" ,r-smoother) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-vim" ,r-vim))) + (home-page "https://bioconductor.org/packages/destiny/") + (synopsis "Create and plot diffusion maps") + (description "This package provides tools to create and plot diffusion +maps.") + ;; Any version of the GPL + (license license:gpl3+))) + +(define-public r-savr + (package + (name "r-savr") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "savR" version)) + (sha256 + (base32 + "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7")))) + (properties `((upstream-name . "savR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) + ("r-xml" ,r-xml))) + (home-page "https://github.com/bcalder/savR") + (synopsis "Parse and analyze Illumina SAV files") + (description + "This package provides tools to parse Illumina Sequence Analysis +Viewer (SAV) files, access data, and generate QC plots.") + (license license:agpl3+))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8820ba0d8e..58cee5cbbe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7099,13 +7099,13 @@ Bioconductor, CRAN, and Github.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.50.1") + (version "1.50.5") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0hjm3r58i0r9qhyar9pk250cx7sfijg0lnvi12a9s6brmmbip1a3")))) + "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7268,13 +7268,13 @@ abnormal copy number.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.20.0") + (version "0.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0qgiykjhnsvvpcp3zwmrnpx3bv3msvj0szchyvb1yb0fxw716xc5")))) + "18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -7349,7 +7349,7 @@ possible.") (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -7359,7 +7359,7 @@ possible.") version ".tar.gz")) (sha256 (base32 - "0k1hsjx6n2i1sf14hyrgdhxqxm5mxk0bgnivhiax944whcicmzbf")))) + "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c")))) (properties `((upstream-name . "GenomeInfoDbData"))) (build-system r-build-system) @@ -7657,13 +7657,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.50.0") + (version "2.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0zw0dj67fnpbz4iqnam5fxs92c1c8w8d7mzl0rkq4ksx0xl8vgg7")))) + "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -7910,7 +7910,7 @@ extracting the desired features in a convenient format.") (define-public r-go-db (package (name "r-go-db") - (version "3.6.0") + (version "3.7.0") (source (origin (method url-fetch) (uri (string-append "https://www.bioconductor.org/packages/" @@ -7918,7 +7918,7 @@ extracting the desired features in a convenient format.") version ".tar.gz")) (sha256 (base32 - "0fi2qywr9apg5lwfqfq9qq6bgrnv4rdhxx25656qn4bsy62i838j")))) + "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5")))) (properties `((upstream-name . "GO.db"))) (build-system r-build-system) @@ -8121,7 +8121,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.10.0") + (version "1.14.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8131,7 +8131,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") "genomationData_" version ".tar.gz")) (sha256 (base32 - "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla")))) + "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7")))) (build-system r-build-system) ;; As this package provides little more than large data files, it doesn't ;; make sense to build substitutes. @@ -8149,7 +8149,7 @@ downloaded from Encode.") (define-public r-org-hs-eg-db (package (name "r-org-hs-eg-db") - (version "3.5.0") + (version "3.7.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8159,7 +8159,7 @@ downloaded from Encode.") "org.Hs.eg.db_" version ".tar.gz")) (sha256 (base32 - "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927")))) + "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) (properties `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) @@ -8175,7 +8175,7 @@ on mapping using Entrez Gene identifiers.") (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") - (version "3.5.0") + (version "3.7.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8185,7 +8185,7 @@ on mapping using Entrez Gene identifiers.") "org.Ce.eg.db_" version ".tar.gz")) (sha256 (base32 - "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9")))) + "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) (properties `((upstream-name . "org.Ce.eg.db"))) (build-system r-build-system) @@ -8201,7 +8201,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.") (define-public r-org-dm-eg-db (package (name "r-org-dm-eg-db") - (version "3.5.0") + (version "3.7.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8211,7 +8211,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.") "org.Dm.eg.db_" version ".tar.gz")) (sha256 (base32 - "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d")))) + "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) (properties `((upstream-name . "org.Dm.eg.db"))) (build-system r-build-system) @@ -8227,7 +8227,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.") (define-public r-org-mm-eg-db (package (name "r-org-mm-eg-db") - (version "3.5.0") + (version "3.7.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8237,7 +8237,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.") "org.Mm.eg.db_" version ".tar.gz")) (sha256 (base32 - "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g")))) + "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) (properties `((upstream-name . "org.Mm.eg.db"))) (build-system r-build-system) @@ -8368,7 +8368,7 @@ in Biostrings objects.") (define-public r-txdb-mmusculus-ucsc-mm10-knowngene (package (name "r-txdb-mmusculus-ucsc-mm10-knowngene") - (version "3.4.0") + (version "3.4.4") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -8379,7 +8379,7 @@ in Biostrings objects.") version ".tar.gz")) (sha256 (base32 - "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb")))) + "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39")))) (properties `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) @@ -10215,14 +10215,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.6.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "12jqz9h6w4mxyfr43w5qbwmacn512aw0mnl0zvhsg5i7p4qj45ks")))) + "1js05dcv1dj4g2vj7lzlg0rgjcjlk2irdr9rxqpwxmivm8nbvf36")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -14118,6 +14118,85 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering. absolute GSEA.") (license license:gpl2))) +(define-public jamm + (package + (name "jamm") + (version "1.0.7.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mahmoudibrahim/JAMM.git") + (commit (string-append "JAMMv" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "JAMM.sh" + (("^sPath=.*") + (string-append ""))) + #t)) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (libexec (string-append out "/libexec/jamm")) + (bin (string-append out "/bin"))) + (substitute* '("JAMM.sh" + "SignalGenerator.sh") + (("^sPath=.*") + (string-append "sPath=\"" libexec "\"\n"))) + (for-each (lambda (file) + (install-file file libexec)) + (list "bincalculator.r" + "peakfinder.r" + "peakhelper.r" + "signalmaker.r" + "xcorr.r" + "xcorrhelper.r" + ;; Perl scripts + "peakfilter.pl" + "readshifter.pl")) + + (for-each + (lambda (script) + (chmod script #o555) + (install-file script bin) + (wrap-program (string-append bin "/" script) + `("PATH" ":" prefix + (,(string-append (assoc-ref inputs "coreutils") "/bin") + ,(string-append (assoc-ref inputs "gawk") "/bin") + ,(string-append (assoc-ref inputs "perl") "/bin") + ,(string-append (assoc-ref inputs "r-minimal") "/bin"))) + `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB"))) + `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))) + (list "JAMM.sh" "SignalGenerator.sh"))) + #t))))) + (inputs + `(("bash" ,bash) + ("coreutils" ,coreutils) + ("gawk" ,gawk) + ("perl" ,perl) + ("r-minimal" ,r-minimal) + ;;("r-parallel" ,r-parallel) + ("r-signal" ,r-signal) + ("r-mclust" ,r-mclust))) + (home-page "https://github.com/mahmoudibrahim/JAMM") + (synopsis "Peak finder for NGS datasets") + (description + "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq, +ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak +boundaries accurately. JAMM is applicable to both broad and narrow +datasets.") + (license license:gpl3+))) + (define-public ngless (package (name "ngless") diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 7f6857d260..6c3d88e7cb 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -133,10 +133,7 @@ in compression.") `(#:phases (modify-phases %standard-phases (add-after 'unpack 'enter-source - (lambda _ (chdir "contrib/minizip") #t)) - (add-after 'enter-source 'autoreconf - (lambda _ - (invoke "autoreconf" "-vif")))))) + (lambda _ (chdir "contrib/minizip") #t))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -188,12 +185,7 @@ utility. Instead of being written in Java, FastJar is written in C.") "02cihzl77ia0dcz7z2cga2412vyhhs5pa2355q4wpwbyga2lrwjh")) (patches (search-patches "libtar-CVE-2013-4420.patch")))) (build-system gnu-build-system) - (arguments - `(#:tests? #f ;no "check" target - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoconf - (lambda _ (invoke "sh" "autoreconf" "-vfi")))))) + (arguments `(#:tests? #f)) ; no "check" target (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -1122,13 +1114,14 @@ smaller than those produced by @code{Xdelta}.") (version "3.1.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/jmacd/xdelta/archive/v" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/jmacd/xdelta.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "17g2pbbqy6h20qgdjq7ykib7kg5ajh8fwbsfgyjqg8pwg19wy5bm")) - (file-name (string-append name "-" version ".tar.gz")) + "09mmsalc7dwlvgrda56s2k927rpl3a5dzfa88aslkqcjnr790wjy")) (snippet ;; This file isn't freely distributable and has no effect on building. '(begin @@ -1142,9 +1135,7 @@ smaller than those produced by @code{Xdelta}.") `(#:phases (modify-phases %standard-phases (add-after 'unpack 'enter-build-directory - (lambda _ (chdir "xdelta3") #t)) - (add-after 'enter-build-directory 'autoconf - (lambda _ (invoke "autoreconf" "-vfi")))))) + (lambda _ (chdir "xdelta3") #t))))) (home-page "http://xdelta.org") (synopsis "Delta encoder for binary files") (description "xdelta encodes only the differences between two binary files diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ec950ce0ac..6ce9bdd16f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32,11 +32,15 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system r) + #:use-module (gnu packages base) #:use-module (gnu packages compression) + #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) + #:use-module (gnu packages gl) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell) + #:use-module (gnu packages image) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -45,7 +49,8 @@ #:use-module (gnu packages python) #:use-module (gnu packages statistics) #:use-module (gnu packages tls) - #:use-module (gnu packages web)) + #:use-module (gnu packages web) + #:use-module (gnu packages xorg)) (define-public r-clipr (package @@ -566,14 +571,16 @@ you to rapidly iterate while developing a package.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.19") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "10mmiaawv9iwglc6z4y51mdpsfb1sivqmwr6xnfqkllcnpabdbk3")))) + (base32 "1hlbw4k79q9ich4w27b01gsvwrsnrflii8zjlcmgfzm1vpq8ndxp")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") (description @@ -2042,17 +2049,18 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.") (define-public r-jomo (package (name "r-jomo") - (version "2.6-4") + (version "2.6-5") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 - "05g2rj9g7rgyb22b0gybw042nydyqsqsb31v05hifzavri8ij01x")))) + "109q5m69clrvvialxdxznd0wdb54ajhx84nj8slx8bf909a427mj")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) ("r-ordinal" ,r-ordinal) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/jomo/") @@ -3071,6 +3079,26 @@ Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, Cambridge University Press, 1993.") (license license:gpl2))) +(define-public r-aggregation + (package + (name "r-aggregation") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "aggregation" version)) + (sha256 + (base32 + "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/aggregation/") + (synopsis "Methods for p-value aggregation") + (description + "This package contains functionality for performing the following methods +of p-value aggregation: Fisher's method, the Lancaster method (weighted +Fisher's method), and Sidak correction.") + (license license:gpl3))) + (define-public r-quantmod (package (name "r-quantmod") @@ -3452,6 +3480,36 @@ dendrograms.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) +(define-public r-h5 + (package + (name "r-h5") + (version "0.9.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "h5" version)) + (sha256 + (base32 + "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib) + ("hdf5" ,hdf5))) + (native-inputs + `(("which" ,which))) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/mannau/h5") + (synopsis "Interface to the HDF5 Library") + (description + "This package provides an S4 interface to the HDF5 library supporting +fast storage and retrieval of R-objects like vectors, matrices and arrays to +binary files in a language independent format. The HDF5 format can therefore +be used as an alternative to R's save/load mechanism. Since h5 is able to +access only subsets of stored data it can also handle data sets which do not +fit into memory.") + (license license:bsd-2))) + (define-public r-cgdsr (package (name "r-cgdsr") @@ -4392,14 +4450,14 @@ and adds the annotation to the plot.") (define-public r-ggpubr (package (name "r-ggpubr") - (version "0.1.8") + (version "0.1.9") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 - "0psl2zndm4wk6nnj1nv305islpxfvfgd87gjh2ph8yqn4mxpnfi1")))) + "0rvfgii2gxarra7d33n6c63ky0mivxxyx35acsrn94xkbd8mbcsj")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) @@ -4670,6 +4728,32 @@ Extract argument descriptions and other parts of the help pages of functions.") (license license:gpl2+))) +(define-public r-rjags + (package + (name "r-rjags") + (version "4-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "rjags" version)) + (sha256 + (base32 + "17xmjksj69f9wk4x71jxk4cgiqhaf2fj6bjm0mgzp4qln5x84a8m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-coda" ,r-coda))) + (inputs + `(("jags" ,jags))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://mcmc-jags.sourceforge.net") + (synopsis "Bayesian graphical models using MCMC") + (description + "This package provides an R interface to the JAGS MCMC library. JAGS is +Just Another Gibbs Sampler. It is a program for analysis of Bayesian +hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") + (license license:gpl2))) + (define-public r-rdpack (package (name "r-rdpack") @@ -4732,6 +4816,112 @@ be added or removed. When working with Word documents, a cursor can be used to help insert or delete content at a specific location in the document.") (license license:gpl3))) +(define-public r-abn + (package + (name "r-abn") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "abn" version)) + (sha256 + (base32 + "00k0razgdb5y5f62622fm7rxkcxrxg470nyyb02dvpfp60254kvs")))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-cairo" ,r-cairo) + ("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-nnet" ,r-nnet) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rjags" ,r-rjags))) + (home-page "http://www.r-bayesian-networks.org") + (synopsis "Modelling multivariate data with additive bayesian networks") + (description + "Bayesian network analysis is a form of probabilistic graphical models +which derives from empirical data a directed acyclic graph, DAG, describing +the dependency structure between random variables. An additive Bayesian +network model consists of a form of a DAG where each node comprises a +@dfn{generalized linear model} (GLM). Additive Bayesian network models are +equivalent to Bayesian multivariate regression using graphical modelling, they +generalises the usual multivariable regression, GLM, to multiple dependent +variables. This package provides routines to help determine optimal Bayesian +network models for a given data set, where these models are used to identify +statistical dependencies in messy, complex data.") + (license license:gpl2+))) + +(define-public r-acd + (package + (name "r-acd") + (version "1.5.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACD" version)) + (sha256 + (base32 + "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6")))) + (properties `((upstream-name . "ACD"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ACD/") + (synopsis "Categorical data analysis with complete or missing responses") + (description + "This package provides tools for categorical data analysis with complete +or missing responses.") + (license license:gpl2+))) + +(define-public r-acdm + (package + (name "r-acdm") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACDm" version)) + (sha256 + (base32 + "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil")))) + (properties `((upstream-name . "ACDm"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-plyr" ,r-plyr) + ("r-rsolnp" ,r-rsolnp) + ("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/ACDm/") + (synopsis "Tools for Autoregressive Conditional Duration Models") + (description + "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle +and Russell, 1998) models. It creates trade, price or volume durations from +transactions (tic) data, performs diurnal adjustments, fits various ACD models +and tests them.") + (license license:gpl2+))) + +(define-public r-overlap + (package + (name "r-overlap") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "overlap" version)) + (sha256 + (base32 + "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/overlap/") + (synopsis "Estimates of coefficient of overlapping for animal activity patterns") + (description + "This package provides functions to fit kernel density functions to data +on temporal activity patterns of animals; estimate coefficients of overlapping +of densities for two species; and calculate bootstrap estimates of confidence +intervals.") + (license license:gpl3+))) + (define-public r-snakecase (package (name "r-snakecase") @@ -6507,14 +6697,14 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.7.14") + (version "1.7.15") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "0bpc504nz8xfwr8ack52dj4hpjcykn6zyf8n228z32dw9d5n96dl")))) + "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs @@ -6885,14 +7075,14 @@ directories or URLs with their associated programs.") (define-public r-rcmdcheck (package (name "r-rcmdcheck") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "rcmdcheck" version)) (sha256 (base32 - "1ga19jqix0zs7xyz2j155zyagwbv22r6dgv55g6wdjigc67qfsix")))) + "0ys1nd7690mhwzslyzg8fq1wxr28nz8g6av5iykkrshb8lkxg7ly")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -7325,3 +7515,242 @@ netCDF files.") "This package provides a convenient tool to install and update Bioconductor packages.") (license license:artistic2.0))) + +(define-public r-rgl + (package + (name "r-rgl") + (version "0.99.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "rgl" version)) + (sha256 + (base32 + "0q8sg8fr0140ilssqhscaxkjc29w1rpp6f4k50amw3zzs9g58ak9")))) + (build-system r-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("freetype" ,freetype) + ("libpng" ,libpng) + ("glu" ,glu) + ("libx11" ,libx11) + ("ghc-pandoc" ,ghc-pandoc) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-crosstalk" ,r-crosstalk) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jsonlite" ,r-jsonlite) + ("r-knitr" ,r-knitr) + ("r-magrittr" ,r-magrittr) + ("r-manipulatewidget" ,r-manipulatewidget) + ("r-shiny" ,r-shiny))) + (home-page "https://r-forge.r-project.org/projects/rgl/") + (synopsis "3D visualization using OpenGL") + (description + "This package provides medium to high level functions for 3D interactive graphics, +including functions modelled on base graphics (@code{plot3d()}, etc.) as well +as functions for constructing representations of geometric +objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to +various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D +image formats, including PNG, Postscript, SVG, PGF.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-multicool + (package + (name "r-multicool") + (version "0.1-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "multicool" version)) + (sha256 + (base32 + "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v")))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/multicool/") + (synopsis "Permutations of multisets in cool-lex order") + (description + "This package provides a set of tools to permute multisets without loops +or hash tables and to generate integer partitions. Cool-lex order is similar +to colexicographical order.") + (license license:gpl2))) + +(define-public r-misc3d + (package + (name "r-misc3d") + (version "0.8-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "misc3d" version)) + (sha256 + (base32 + "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/misc3d/") + (synopsis "Miscellaneous 3D Plots") + (description + "This package provides a collection of miscellaneous 3d plots, including +isosurfaces.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-ks + (package + (name "r-ks") + (version "1.11.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ks" version)) + (sha256 + (base32 + "0z749c3xzpf6n0g7xcfplrhap1di8k7kcfr7vigh95ywnigyhs8d")))) + (build-system r-build-system) + (propagated-inputs + `(("r-fnn" ,r-fnn) + ("r-kernlab" ,r-kernlab) + ("r-kernsmooth" ,r-kernsmooth) + ("r-matrix" ,r-matrix) + ("r-mclust" ,r-mclust) + ("r-mgcv" ,r-mgcv) + ("r-misc3d" ,r-misc3d) + ("r-multicool" ,r-multicool) + ("r-mvtnorm" ,r-mvtnorm))) + (home-page "http://www.mvstat.net/tduong/") + (synopsis "Kernel smoothing") + (description + "This package provides kernel smoothers for univariate and multivariate +data, including density functions, density derivatives, cumulative +distributions, modal clustering, discriminant analysis, and two-sample +hypothesis testing.") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-feature + (package + (name "r-feature") + (version "1.2.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "feature" version)) + (sha256 + (base32 + "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ks" ,r-ks) + ("r-misc3d" ,r-misc3d) + ("r-rgl" ,r-rgl))) + (home-page "http://www.mvstat.net/tduong/") + (synopsis "Inferential feature significance for kernel density estimation") + (description + "The feature package contains functions to display and compute kernel +density estimates, significant gradient and significant curvature regions. +Significant gradient and/or curvature regions often correspond to significant +features (e.g. local modes).") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-arm + (package + (name "r-arm") + (version "1.10-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "arm" version)) + (sha256 + (base32 + "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-coda" ,r-coda) + ("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-nlme" ,r-nlme))) + (home-page "https://cran.r-project.org/web/packages/arm/") + (synopsis "Data analysis using regression and multilevel/hierarchical models") + (description + "This package provides functions to accompany A. Gelman and J. Hill, +Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge +University Press, 2007.") + (license license:gpl3+))) + +(define-public r-circular + (package + (name "r-circular") + (version "0.4-93") + (source + (origin + (method url-fetch) + (uri (cran-uri "circular" version)) + (sha256 + (base32 + "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn")))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot) + ("r-mvtnorm" ,r-mvtnorm))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/circular/") + (synopsis "Circular statistics") + (description + "This package provides tools for circular statistics, from \"Topics in +circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World +Scientific.") + (license license:gpl2+))) + +(define-public r-activity + (package + (name "r-activity") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "activity" version)) + (sha256 + (base32 + "1lqajgxfps2h6amz1791vp3f52rs9ghmanq1nqfxqd2jmk3idkrx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-circular" ,r-circular) + ("r-overlap" ,r-overlap) + ("r-pbapply" ,r-pbapply))) + (home-page "https://cran.r-project.org/web/packages/activity/") + (synopsis "Animal activity statistics") + (description + "This package provides functions to fit kernel density functions to +animal activity time data; plot activity distributions; quantify overall +levels of activity; statistically compare activity metrics through +bootstrapping; and evaluate variation in linear variables with time (or other +circular variables).") + (license license:gpl3))) + +(define-public r-ouch + (package + (name "r-ouch") + (version "2.11-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ouch" version)) + (sha256 + (base32 + "0xkwwi62vdahlcg3k32zb1nfwsx87zdssk79mvcxgfsw9bw4gahx")))) + (build-system r-build-system) + (propagated-inputs `(("r-subplex" ,r-subplex))) + (home-page "http://kingaa.github.io/ouch/") + (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") + (description + "This package provides tools to fit and compare Ornstein-Uhlenbeck models +for evolution along a phylogenetic tree.") + (license license:gpl2+))) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 29d9a3d6ab..e8062f0e1f 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 David Thompson <davet@gnu.org> -;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018 Leo Famulari <leo@famulari.name> ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox> ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> @@ -164,34 +164,31 @@ OpenBSD tool of the same name.") "See base64.c in the distribution for the license from IBM."))))) - (define-public opendht (package (name "opendht") (version "0.6.1") - (source - (origin - (method url-fetch) - (uri - (string-append - "https://github.com/savoirfairelinux/" name - "/archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file-recursively "src/argon2") - (substitute* "src/Makefile.am" - (("./argon2/libargon2.la") "") - (("SUBDIRS = argon2") "")) - (substitute* "src/crypto.cpp" - (("argon2/argon2.h") "argon2.h")) - (substitute* "configure.ac" - (("src/argon2/Makefile") "")) - #t)) - (sha256 - (base32 - "09yvkmbqbym3b5md4n96qc1s9sf2n8ji404hagih45rmsj49599x")))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/savoirfairelinux/opendht.git") + (commit version))) + (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/argon2") + (substitute* "src/Makefile.am" + (("./argon2/libargon2.la") "") + (("SUBDIRS = argon2") "")) + (substitute* "src/crypto.cpp" + (("argon2/argon2.h") "argon2.h")) + (substitute* "configure.ac" + (("src/argon2/Makefile") "")) + #t)) + (sha256 + (base32 + "1akk613f18rc8kqs0cxdm34iq7wwc9kffhgp5rng09arwlw8gw3w")))) (build-system gnu-build-system) (inputs `(("gnutls" ,gnutls) @@ -206,11 +203,7 @@ OpenBSD tool of the same name.") ("automake" ,automake) ("libtool" ,libtool))) (arguments - `(#:configure-flags '("--disable-tools" "--disable-python") - #:phases (modify-phases %standard-phases - (add-after 'unpack 'autoconf - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) + `(#:configure-flags '("--disable-tools" "--disable-python"))) (home-page "https://github.com/savoirfairelinux/opendht/") (synopsis "Distributed Hash Table (DHT) library") (description "OpenDHT is a Distributed Hash Table (DHT) library. It may diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 1617c28b1e..05bebed6a6 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -803,14 +803,14 @@ as a drop-in replacement of MySQL.") (define-public postgresql (package (name "postgresql") - (version "10.5") + (version "10.6") (source (origin (method url-fetch) (uri (string-append "https://ftp.postgresql.org/pub/source/v" version "/postgresql-" version ".tar.bz2")) (sha256 (base32 - "04a07jkvc5s6zgh6jr78149kcjmsxclizsqabjw44ld4j5n633kc")))) + "0jv26y3f10svrjxzsgqxg956c86b664azyk2wppzpa5x11pjga38")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-uuid=e2fs") @@ -2087,13 +2087,14 @@ for ODBC.") (version "0.7.1") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/brianb/mdbtools/archive/" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/brianb/mdbtools.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "05hbmxcq173kzb899gdi3bz2qcc1vi3n1qbbkwpsvrq7ggf11wyw")) - (file-name (string-append name "-" version ".tar.gz")))) + "0gwcpp9y09xhs21g7my2fs8ncb8i6ahlyixcx8jd3q97jbzj441l")))) (build-system gnu-build-system) (inputs `(("glib" ,glib))) @@ -2104,12 +2105,6 @@ for ODBC.") ("pkg-config" ,pkg-config) ("txt2man" ,txt2man) ("which" ,which))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoreconf - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) (home-page "http://mdbtools.sourceforge.net/") (synopsis "Read Microsoft Access databases") (description "MDB Tools is a set of tools and applications to read the diff --git a/gnu/packages/datastructures.scm b/gnu/packages/datastructures.scm index 8517654def..4e5e59a2e3 100644 --- a/gnu/packages/datastructures.scm +++ b/gnu/packages/datastructures.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -48,6 +49,29 @@ binary trees, binary search trees, red-black trees, 2D arrays, permutations and heaps.") (license license:gpl2+))) +(define-public marisa + (package + (name "marisa") + (version "0.2.5") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/s-yata/marisa-trie" + "/releases/download/v" version "/" name "-" + version ".tar.gz")) + (sha256 + (base32 "19ifrcmnbr9whaaf4ly3s9ndyiq9sjqhnfkrxbz9zsb44w2n36hf")))) + (build-system gnu-build-system) + (home-page "https://github.com/s-yata/marisa-trie") + (synopsis "Trie data structure C++ library") + (description "Matching Algorithm with Recursively Implemented +StorAge (MARISA) is a static and space-efficient trie data structure C++ +library.") + + ;; Dual-licensed, according to docs/readme.en.html (source files lack + ;; copyright/license headers.) + (license (list license:bsd-2 license:lgpl2.1+)))) + (define-public sparsehash (package (name "sparsehash") diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index c6008e6a94..3e32998a9f 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -40,6 +40,7 @@ ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr> ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com> ;;; Copyright © 2018 Thorsten Wilms <t_w_@freenet.de> +;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -3848,6 +3849,31 @@ use it, call @code{M-x ivy-yasnippet} (but make sure you have enabled @code{yas-minor-mode} first).") (license license:gpl3+)))) +(define-public emacs-ivy-rich + (package + (name "emacs-ivy-rich") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/Yevgnen/ivy-rich/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "14r3mx5rkd4wz0ls5pv5w6c7la3z9iy93d3jfind3xyg4kywy95c")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-ivy" ,emacs-ivy))) + (home-page "https://github.com/Yevgnen/ivy-rich") + (synopsis "More friendly interface for @code{ivy}") + (description + "This package extends @code{ivy} by showing more information in the +minibuffer for each candidate. It adds columns showing buffer modes, file +sizes, docstrings, etc. If @code{emacs-all-the-icons} is installed, it can +show icons as well.") + (license license:gpl3+))) + (define-public emacs-avy (package (name "emacs-avy") @@ -7688,17 +7714,17 @@ value of the access token.") (define-public emacs-circe (package (name "emacs-circe") - (version "2.6") + (version "2.10") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/jorgenschaefer/circe.git") (commit (string-append "v" version)))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "19h3983zy3f15cgs86irvbdzz55qyjm48qd7gjlzcxplr7vnnh0j")))) + "10gi14kwxd81blddpvqh95lgmpbfgp0m955naxix3bs3r6a75n4s")))) (build-system emacs-build-system) ;; In order to securely connect to an IRC server using TLS, Circe requires ;; the GnuTLS binary. diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm index 38c76cd737..f20d1e17c7 100644 --- a/gnu/packages/embedded.scm +++ b/gnu/packages/embedded.scm @@ -321,12 +321,6 @@ languages are C and C++.") ("pkg-config" ,pkg-config))) (inputs `(("libusb" ,libusb))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoreconf - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) (home-page "http://repo.or.cz/w/libjaylink.git") (synopsis "Library to interface Segger J-Link devices") (description "libjaylink is a shared library written in C to access @@ -404,9 +398,9 @@ language.") "presto" "openjtag"))) #:phases (modify-phases %standard-phases + ;; Required because of patched sources. (add-before 'configure 'autoreconf - (lambda _ - (zero? (system* "autoreconf" "-vfi")))) + (lambda _ (invoke "autoreconf" "-vfi") #t)) (add-after 'autoreconf 'change-udev-group (lambda _ (substitute* "contrib/60-openocd.rules" @@ -417,7 +411,8 @@ language.") (install-file "contrib/60-openocd.rules" (string-append (assoc-ref outputs "out") - "/lib/udev/rules.d/"))))))) + "/lib/udev/rules.d/")) + #t))))) (home-page "http://openocd.org") (synopsis "On-Chip Debugger") (description "OpenOCD provides on-chip programming and debugging support diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index da1675820b..1f73025db7 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -399,13 +399,14 @@ support.") (name "tiled") (version "1.2.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/bjorn/tiled/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/bjorn/tiled.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "13dlf5kzvhhjkhy19118x3diakmraz4m9kxrsdam8dms6xivb6lp")))) + "1rra48hlkcgqxwxi802fb182p1q0723c9hhfvkd5inz9467idd4c")))) (build-system gnu-build-system) (inputs `(("qtbase" ,qtbase) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 4481e21ddf..fa2b259d7c 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -549,14 +549,14 @@ coordinates.") (define-public r-rgooglemaps (package (name "r-rgooglemaps") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "RgoogleMaps" version)) (sha256 (base32 - "112mdm53qx92n2m4ms02sbppckp44l1z19vy99j6gw3jrdprjydl")))) + "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4")))) (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs `(("r-png" ,r-png))) diff --git a/gnu/packages/gnustep.scm b/gnu/packages/gnustep.scm index bd28ceaa00..dd7c67d553 100644 --- a/gnu/packages/gnustep.scm +++ b/gnu/packages/gnustep.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2016, 2017 Kei Kebreau <kkebreau@posteo.net> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -167,14 +168,7 @@ interface. It is fast, feature rich, easy to configure, and easy to use.") (base32 "084a3irxbmgms4bqaga80mlx9wgvlkx6d2w0ns939yrpfzg87laj")))) (build-system gnu-build-system) - (arguments - `(#:tests? #f ; no "check" target - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoconf - (lambda _ - (invoke "autoreconf" "-vfi") - #t))))) + (arguments '(#:tests? #f)) ; no "check" target (inputs `(("glib" ,glib) ("libx11" ,libx11) @@ -262,18 +256,11 @@ on.") (base32 "1lx276ba8r2yydhmwj1g586jdqg695ad89ng36fr3mb067gvb2rz")))) (build-system gnu-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoconf - (lambda _ - (invoke "autoreconf" "-vfi") - #t))))) - ;; wmclock requires autoreconf to generate its configure script. (inputs `(("libx11" ,libx11) ("libxext" ,libxext) ("libxpm" ,libxpm))) + ;; wmclock requires autoreconf to generate its configure script. (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 1dd0e930d3..e1abe8c2cd 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -482,83 +482,33 @@ security standards.") (define-public icecat (package (name "icecat") - (version "60.2.0-gnu1") + (version "60.3.0-gnu1") (source (origin (method url-fetch) - ;; Temporary URL pending official release: - (uri "https://alpha.gnu.org/gnu/gnuzilla/60.2.0/icecat-60.2.0-gnu1.tar.bz2") - #; (uri (string-append "mirror://gnu/gnuzilla/" (first (string-split version #\-)) "/" name "-" version ".tar.bz2")) (sha256 (base32 - "0lqx7g79x15941rhjr3qsfwsny6vzc7d7abdmvjy6jjbqkqlc1zl")) + "0icnl64nxcyf7dprpdpygxhabsvyhps8c3ixysj9bcdlj9q34ib1")) (patches (list (search-patch "icecat-avoid-bundled-libraries.patch") (search-patch "icecat-use-system-graphite2+harfbuzz.patch") (search-patch "icecat-use-system-media-libs.patch") - (mozilla-patch "icecat-CVE-2018-12385.patch" "80a4a7ef2813" "1vgcbimpnfjqj934v0cryq1g13xac3wfmd4jyhcb5s60x8xyssf5") - (search-patch "icecat-CVE-2018-12383.patch") - (mozilla-patch "icecat-bug-1489744.patch" "6546ee839d30" "11mhvj77r789b428bfxqq5wdx8yr7lbrdjzr8qjj6fw197pldn51") - (mozilla-patch "icecat-CVE-2018-12386.patch" "4808fcb2e6ca" "05sc881l7sh8bag8whd2ggdn198lskqcxq8f41scfpqscw6xs5d5") - (mozilla-patch "icecat-CVE-2018-12387.patch" "b8f5c37486e1" "0lvmbh126m695kgdbasy1y5xh9n1j08cwdhn071mgvj6yn8cns5z") - (mozilla-patch "icecat-bug-1464751.patch" "d5d00faf0465" "1mj7dbb06brwrk0mvap0z4lfl2hwz1cj6dwjvdrisxm046pdw98i") - (mozilla-patch "icecat-bug-1472538.patch" "11462f2b98f2" "1nxgh0plzilylx8r73r7d74pv66qwjqxmd7nqii33p0snl2jjfzs") - (mozilla-patch "icecat-bug-1478685.patch" "098585dc86fc" "1b0x4qdh6isvffmibvc8ad8z62m3iky9q6jq0z6gyvn8q252cqal") - (mozilla-patch "icecat-bug-1486080.patch" "3f8d57d936ea" "0pz2c18wcgj44v0j8my9xbm90m4bsjcvzmavj569fi8bh6s6zz8p") - (mozilla-patch "icecat-bug-1423278.patch" "878ceaee5634" "0i47s5nvrx9vqbnj6s9y9f4ffww20p8nviqa6frg676y1188xlyl") - (mozilla-patch "icecat-CVE-2018-12390-pt01.patch" "87be1b98ec9a" "15f4l18c7hz9aqn89gg3dwmdidfwgn10dywgpzydm8mps45amx7j") - (mozilla-patch "icecat-bug-1484559.patch" "99e58b5307ce" "02fdgbliwzi2r2376wg6k1rky1isfka0smac4ii2cll01jhpfrn6") - (mozilla-patch "icecat-CVE-2018-12390-pt02.patch" "f25ce451a492" "18nzg39iyxza1686180qk9cc88l5j2hf1h35d62lrqmdgd9vcj33") - (mozilla-patch "icecat-CVE-2018-12390-pt03.patch" "35c26bc231df" "0qh8d4z6y03h5xh7djci26a01l6zq667lg2k11f6zzg7z2j0h67x") - (mozilla-patch "icecat-bug-1488061.patch" "050d0cfa8e3d" "05ql798ynbyz5pvyri4b95j4ixmgnny3zl7sd2ckfrrbm9mxh627") - (mozilla-patch "icecat-bug-1434963-pt1.patch" "1e6dad87efed" "1v00a6cmgswjk54041jyv1ib129fxshpzwk6mn6lr0v5hylk3bx9") - (mozilla-patch "icecat-bug-1434963-pt2.patch" "6558c46df9ea" "0vdy9dm9w5k1flhcfxwvvff0aa415b5mgmmq5r37i83686768xfb") - (mozilla-patch "icecat-bug-1434963-pt3.patch" "686fcfa8abd6" "0ihqr11aq4b0y7mx7bwn8yzn25mv3k2gdphm951mj1g85qg35ann") - (mozilla-patch "icecat-bug-1491132.patch" "14120e0c74d6" "188c5fbhqqhmlk88p70l6d97skh7xy4jhqdby1ri3h9ix967515j") - (mozilla-patch "icecat-bug-1492065.patch" "ec4b5969c6ae" "18gfwn15kh0826vlg6lhrx3q4gv82i7v1k3y5jp72mvrjq154gy0") - (mozilla-patch "icecat-bug-1492064.patch" "528cabdd9665" "0rdwpkfma24hn8namfb9saw4rgi9yyyj4af5h2ijrvadw6r8lyyn") - (mozilla-patch "icecat-bug-1489757.patch" "46f19852aaa6" "0dga7mw847klm8x6il2fyzpjxqxxgx1q5cya658f1w66kxms1f29") - (mozilla-patch "icecat-bug-1492897.patch" "c3a48066f383" "09n6sdck4jzzmznzrq0iixg5nsgrc5ibpdfsh3i7ppwad3fsy2m3") - (mozilla-patch "icecat-bug-1492915.patch" "2d280e557331" "11x2n61pw5way9cg8lbrfl3lqvgfnbmcs1fwm78i06kmfwj0msk3") - (mozilla-patch "icecat-CVE-2018-12390-pt04.patch" "b80f94262165" "1hw43h4sgf77x323745rixyp6cci3fb6d3fnp33q82m4ssdb5623") - (mozilla-patch "icecat-bug-1492484.patch" "1b3e6759cf3a" "1yn2cd2227ncg90c88ymdi5fyfs4hk335bd16vkkgljs0924yy0m") - (mozilla-patch "icecat-bug-1493590.patch" "d9fe3b2025fc" "06783hj1aqms2f9a3mp18bk8hgijk3pz70bpccn173v4w0zlbbd4") - (mozilla-patch "icecat-CVE-2018-12390-pt05.patch" "20c59797e994" "1vxnhpirjsj040hrq9xmq2xhkpq4l5mnnzqy0nda92dfh47zvidj") - (mozilla-patch "icecat-CVE-2018-12390-pt06.patch" "1749661dfd28" "0g0sj2fgp3asj0yvxksnhrc59yxncn35bz5nzlvkpgdf7h06gscd") - (mozilla-patch "icecat-CVE-2018-12390-pt07.patch" "a511a9242406" "1hhfrvdmkccnhs4skbi06174x37rmvf4ic86xawyyzr67yga73b2") - (mozilla-patch "icecat-bug-1495404.patch" "3232bb3b622f" "1pnaxf8r9h0wldjc4qgl7z3rk34fpz9h1vd3zmhswa6mvyln5jhg") - (mozilla-patch "icecat-bug-1465388.patch" "a9577451dcc2" "0v29s0v3vv9vblkcachhh46qvwjcrmv2bkcdb7sj2asc503l0lqv") - (mozilla-patch "icecat-CVE-2018-12390-pt08.patch" "e965f6f6ed75" "0hh091854xj5j0x1r8pg46xmn00fqi5n212xhzbdpgyf96rsf513") - (mozilla-patch "icecat-bug-1445528.patch" "8a503e022a29" "1y2ll3h0yz8sfdddjmk90qjfxcr1ffhw7a9ww3yw26gyhnbpg404") - (mozilla-patch "icecat-bug-1409570.patch" "8d326641d1c0" "0w29s6dixi7b7q3nicshrp29n9sj5awssdln00yx664m8a8a8ihs") - (mozilla-patch "icecat-bug-1496094.patch" "6cdd6d88eca9" "1ssqa4fy2xpbr63ph3av3hkpl92g4yszx402fq9d2xn9482q43dp") - (mozilla-patch "icecat-CVE-2018-12391.patch" "0fa07c704ca4" "055xdyb3g2l4rj188235i579qnr50v19q36jjpliws9nik129iqy") - (mozilla-patch "icecat-bug-1462162.patch" "739e898cb7c8" "17m9y0pskmqx15dkgkw4k93njph14mpsf37wb1azwkq3xx7s0fhx") - (mozilla-patch "icecat-bug-1492764.patch" "16310ab35452" "1kq5r3w9i4n6q9msmw2qsqa0jd4qw1mjlyyz8aq14fwlbkhvv199") - (mozilla-patch "icecat-CVE-2018-12390-pt09.patch" "9b669d047d55" "063ig49gx9468nvc9w8259j819qfdjvq0sbbz8n4kj5r6hcxjc5l") - (mozilla-patch "icecat-CVE-2018-12390-pt10.patch" "9d51e65c797a" "0m23cq9zl22w80dvx5rlgpbam1l3d6v56h7g9wzamzl21bwxq9fv") - (mozilla-patch "icecat-CVE-2018-12390-pt11.patch" "efc0596dd381" "1alvbb6wvawxxh6isisk9c40vhdiv59fy0af0n10yn1dgy8ffv5i") - (mozilla-patch "icecat-CVE-2018-12393.patch" "c4fb48bb5d28" "09izww9dsg9n8cish8f3y7phxibsnd12bfkcxd7rzcdhg10nr4pl") - (mozilla-patch "icecat-CVE-2018-12390-pt12.patch" "b3359becd7b1" "188byxmbgrvrid2fcz34w5xdvaw571frxx1c6nqaa9k03iljdzjr") - (mozilla-patch "icecat-CVE-2018-12390-pt13.patch" "791c8ecf252d" "02h37594aba0pklxm3g7w1wv8vz9xmcf30fd0az8pfaccsklmx74") - (mozilla-patch "icecat-bug-1494328.patch" "333276fac37c" "0qyq42jl0al63m6pwj9gva7nj82l76szzbj7sklsygx0a9mqs13z") - (mozilla-patch "icecat-CVE-2018-12397.patch" "cb73374a0e4e" "0x2s1nwgwdag9df5hkwzvjj0qznp5c3d6w6y63rn2y287jn9m3vl") - (mozilla-patch "icecat-CVE-2018-12392.patch" "f6bb138ad0ab" "0f0z9dsyw2a11p4p31mdyic571153jpfgy2q04i4v6dmmcz76pm3") - (mozilla-patch "icecat-CVE-2018-12396.patch" "f27145bd5502" "0vznmlm1fbl3ynax2zpi6xxzr9qp9b83afr3mv90jgrhlgpzdbcz") - (mozilla-patch "icecat-CVE-2018-12395-pt1.patch" "133a99a8f3ca" "0im7m4jmc273mg9kih0i70hxsgzy04j6ydm9zmaz2933hkhdf4iw") - (mozilla-patch "icecat-CVE-2018-12395-pt2.patch" "82176a4a9b14" "0g3yqx4854d4mx5a0ghb7p7saj6y5d5bm2lfhabvkwybcd477zmc") - (mozilla-patch "icecat-bug-1474265.patch" "e8abd9a8ce6e" "1q2sv5h081rvnhsx6g1y8a43hwv6hsg0cr6zdcij58mkgzf6hyvd") - (mozilla-patch "icecat-bug-1492737-pt1.patch" "eeb9060379dc" "1d2mf0x4rni7anvi0sgra4dg87fmc6g7zhizzl9jv2x8va27ycbp") - (mozilla-patch "icecat-bug-1492737-pt2.patch" "99eae0d15092" "0f9j6cvhrbrrxa95p4pkcn285r9wmi9yj13nwj5x0gkglwx6idbk") - (mozilla-patch "icecat-CVE-2018-12389-pt1.patch" "23b23e12c548" "0nsdycggki5rhh59yvmh41nf1ahjmgii89fx38jryprhspy3wg62") - (mozilla-patch "icecat-CVE-2018-12390-pt14.patch" "023133ff02ec" "1g22qxnmgiy8bgrn2nv6har6vpz4p2h5pdas8ib1yyz7p2ic8652") - (mozilla-patch "icecat-CVE-2018-12390-pt15.patch" "9461988ff462" "0yq2cr5grqskr0kz4nxcwmnywy9g0xyv6k6q44i490jcj8x2y1vw") - (mozilla-patch "icecat-CVE-2018-12390-pt16.patch" "09939be135d8" "1546xlk368v4hnjd3hf4w868i6m8r4wfd34qxz4wg1cdpr4m5mik") - (mozilla-patch "icecat-CVE-2018-12389-pt2.patch" "ea9412b18ca8" "0fmdncrylbmjh0bcb6dmw1rq7zww8a0v9v9p1pxqfz0vbc6v9l5d"))) + (mozilla-patch "icecat-bug-1464061.patch" "d28761dbff18" "1f58rzwx4s1af66fdwn9lgkcd1ksmq8kn8imvf78p90jqi24h7b4") + (mozilla-patch "icecat-bug-1479853.patch" "4faeb696dd06" "12891xx9c15s6kby6d3zk64v5nqgaq7sw597zv1fkd3a6x69hlva") + (mozilla-patch "icecat-bug-1488295.patch" "12ba39f69876" "1piyq44f0xa0a9z2748aqwpaziaxwp61d86gyhalbyag8lcxfb3p") + (mozilla-patch "icecat-bug-1500011.patch" "a0adabeedf26" "0f5wazha3zxzhy2j8f93hx62l9p02b1p40vi07qah3ar67h4ccj9") + (mozilla-patch "icecat-bug-1503082.patch" "19604eb26230" "1wqxgph4z14ijhk2j2m4av5p6gx72d02lzz83q6yy0k065kw8psb") + (mozilla-patch "icecat-bug-1499861.patch" "98737ab09270" "0fyl6wv0jxcxpkfpsff46y93k49n8lrw0k7c1p45g8da015dx27a") + (mozilla-patch "icecat-bug-1504452.patch" "1cf7d80355d5" "19jp4x32vyxam54d1r9fm7jwf6krhhf3xazfqmxb9aw4iwdil7dl") + (mozilla-patch "icecat-bug-1494752.patch" "c264774b8913" "1hxyi131x8jwawrq90cgkph833iv9ixrdrgzl1r978gbzwq10xz2") + (mozilla-patch "icecat-bug-1477773.patch" "ec13fda7c9b0" "0zj7aylgw55g0y7plaafn5gq8jwcsdr1bpdxacs0hq914nm8zy9z") + (mozilla-patch "icecat-bug-1500759.patch" "5e1a9644aeef" "1qimrpgyrd8zkiri7w57j0aymk20y9b34am5w7rvr6qj1lhrbfla") + (mozilla-patch "icecat-bug-1485655.patch" "9055726e2d89" "1pppxr94zqh6zmi2mn1ih21qap09vk5ivbhnwxqr8iszvygjg44g") + (mozilla-patch "icecat-bug-1410214.patch" "9e641345e2ef" "0542xss2jdb8drh4g50cfy32l300x69dyywgx3dqs03vgr3qplxy"))) (modules '((guix build utils))) (snippet '(begin diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 49fe34f13d..60890bf724 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -537,7 +537,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") (setenv "GOGC" "400") #t))))))))) -(define-public go go-1.9) +(define-public go go-1.11) (define-public go-github-com-alsm-ioprogress (let ((commit "063c3725f436e7fba0c8f588547bee21ffec7ac5") @@ -2161,26 +2161,28 @@ generate ANSI colored strings.") (base32 "1d9hr29i36cza98afj3g6rs3l7xbkprwzz0blcxsr9dd7nak20di")))) (build-system go-build-system) - (native-inputs + ;; From go-1.10 onward, "pkg" compiled libraries are not re-used, so + ;; when this package required as input for another one, it will have to + ;; be built again. Thus its CGO requirements must be made available in + ;; the environment, that is, they must be propagated. + (propagated-inputs `(("lua" ,lua))) (arguments `(#:unpack-path "github.com/aarzilli/golua" #:import-path "github.com/aarzilli/golua/lua" #:phases (modify-phases %standard-phases - (replace 'build - (lambda* (#:key import-path #:allow-other-keys) - (invoke "go" "install" - "-v" ; print the name of packages as they are compiled - "-x" ; print each command as it is invoked - "-ldflags=-s -w" ; strip the symbol table and debug - "-tags" "llua" ; Latest Lua on Guix does not have a version number. - import-path))) - (replace 'check - (lambda* (#:key import-path #:allow-other-keys) - (invoke "go" "test" - "-tags" "llua" ; Latest Lua on Guix does not have a version number. - import-path)))))) + ;; While it's possible to fix the CGO_LDFLAGS with the "-tags" + ;; command line argument, go-1.10+ does not re-use the produced pkg + ;; for dependencies, which means we would need to propagate the + ;; same "-tags" argument to all golua referrers. A substitution is + ;; more convenient here. We also need to propagate the lua + ;; dependency to make it available to referrers. + (add-after 'unpack 'fix-lua-ldflags + (lambda _ + (substitute* "src/github.com/aarzilli/golua/lua/lua.go" + (("#cgo linux,!llua,!luaa LDFLAGS: -llua5.3") + "#cgo linux,!llua,!luaa LDFLAGS: -llua"))))))) (home-page "https://github.com/aarzilli/golua") (synopsis "Go Bindings for the Lua C API") (description "This package provides @code{lua}, a Go module that can @@ -2428,11 +2430,24 @@ and lookup requests. Browse requests are not supported yet.") (base32 "1cpjqnrviwflz150g78iir5ndrp3hh7a93zbp4dwbg6sb2q141p2")))) (build-system go-build-system) - (native-inputs + ;; From go-1.10 onward, "pkg" compiled libraries are not re-used, so + ;; when this package required as input for another one, it will have to + ;; be built again. Thus its CGO requirements must be made available in + ;; the environment, that is, they must be propagated. + (propagated-inputs `(("pkg-config" ,pkg-config) ("taglib" ,taglib))) (arguments - `(#:import-path "github.com/wtolson/go-taglib")) + `(#:import-path "github.com/wtolson/go-taglib" + ;; Tests don't pass "vet" on go-1.11. See + ;; https://github.com/wtolson/go-taglib/issues/12. + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key import-path #:allow-other-keys) + (invoke "go" "test" + "-vet=off" + import-path)))))) (home-page "https://github.com/wtolson/go-taglib") (synopsis "Go wrapper for taglib") (description "Go wrapper for taglib") diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 66456ab1e2..08f92df96c 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com> ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1413,7 +1414,12 @@ information.") (string-append (assoc-ref inputs "docbook-xsl") "/xml/xsl/docbook-xsl-" ,(package-version docbook-xsl) - "/html/chunk.xsl"))) + "/html/chunk.xsl")) + (("http://docbook.sourceforge.net/release/xsl/current/common/en.xml") + (string-append (assoc-ref inputs "docbook-xsl") + "/xml/xsl/docbook-xsl-" + ,(package-version docbook-xsl) + "/common/en.xml"))) #t)) (add-after 'patch-gtk-doc-scan 'patch-test-out (lambda _ diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index a77cacffe1..f3eb2dcd36 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2015, 2017 Christopher Allan Webber <cwebber@dustycloud.org> ;;; Copyright © 2016 Alex Sassmannshausen <alex@pompo.co> -;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016 Erik Edrosa <erik.edrosa@gmail.com> ;;; Copyright © 2016 Eraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2017 Alex Kost <alezost@gmail.com> @@ -486,10 +486,7 @@ AM_SCM_LOG_FLAGS = --no-auto-compile -s") ;; FIXME: one of the database tests fails for unknown ;; reasons. It does not fail when run outside of Guix. (("tests/database.scm") "")) - #t)) - (add-after 'fix-bug-22 'autogen - (lambda _ - (zero? (system* "sh" "autogen.sh"))))))) + #t))))) (inputs `(("guile" ,guile-2.0))) (native-inputs @@ -829,14 +826,6 @@ provides tight coupling to Guix.") (base32 "0qjjvadr7gibdq9jvwkmlkb4afsw9n2shfj9phpiadinxk3p4m2g")))) (build-system gnu-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack 'autoreconf - (lambda _ - ;; Repository comes with a broken symlink - (delete-file "README") - (symlink "README.org" "README") - (zero? (system* "autoreconf" "-fi"))))))) (native-inputs `(("autoconf" ,autoconf-wrapper) ("automake" ,automake) @@ -1550,10 +1539,7 @@ $(datadir)/guile/site/$(GUILE_EFFECTIVE_VERSION)\n")) (("^guilesitedir =.*$") "guilesitedir = \ $(datadir)/guile/site/$(GUILE_EFFECTIVE_VERSION)\n")) - #t)) - (add-after 'unpack 'autoreconf - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) + #t))))) (home-page "https://github.com/artyom-poptsov/guile-dsv") (synopsis "DSV module for Guile") (description @@ -2244,6 +2230,60 @@ using S-expressions.") tracker's SOAP service, such as @url{https://bugs.gnu.org}.") (license license:gpl3+))) +(define-public guile-email + (let ((commit "fa52eac55e5946db89621a6c583d2aa357864dee") + (revision "1")) + (package + (name "guile-email") + (version (git-version "0.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.systemreboot.net/guile-email") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1037mbz7qd9bzaqp8ysyhnl9ipd97fmj3b9jr8qfzx9179vvsj63")))) + (build-system gnu-build-system) + (native-inputs + `(("pkg-config" ,pkg-config) + ("autoconf" ,autoconf) + ("automake" ,automake))) + (inputs + `(("guile" ,guile-2.2))) + (home-page "https://git.systemreboot.net/guile-email") + (synopsis "Guile email parser") + (description "This package provides an email parser written in pure +Guile.") + (license license:agpl3+)))) + +(define-public guile-debbugs-next + (let ((commit "75a331d561c8b6f8efcf16216dab961c17759efe") + (revision "1")) + (package (inherit guile-debbugs) + (name "guile-debbugs") + (version (git-version "0.0.3" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.savannah.gnu.org/git/guile-debbugs.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0br3mgbw41bpc9x57jlghl0i8dz9nl63r4wzs5l47aqszf84870y")))) + (build-system gnu-build-system) + (native-inputs + `(("pkg-config" ,pkg-config) + ("autoconf" ,autoconf) + ("automake" ,automake) + ("texinfo" ,texinfo))) + (inputs + `(("guile" ,guile-2.2) + ("guile-email" ,guile-email)))))) + ;; There has not been any release yet. (define-public guile-newt (let ((commit "4eaa3cf84b9b426cc0ff7bec48b76cca6ca3ec83") diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm index 08fce5f6fb..a2687ac8c3 100644 --- a/gnu/packages/ibus.scm +++ b/gnu/packages/ibus.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2016 Chris Marusich <cmmarusich@gmail.com> ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -24,185 +25,193 @@ #:use-module (guix licenses) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) + #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system glib-or-gtk) #:use-module (gnu packages) #:use-module (gnu packages anthy) #:use-module (gnu packages autotools) #:use-module (gnu packages base) + #:use-module (gnu packages boost) + #:use-module (gnu packages cmake) #:use-module (gnu packages databases) + #:use-module (gnu packages datastructures) #:use-module (gnu packages freedesktop) #:use-module (gnu packages gettext) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) #:use-module (gnu packages iso-codes) + #:use-module (gnu packages logging) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages serialization) + #:use-module (gnu packages textutils) #:use-module (gnu packages xorg)) (define-public ibus (package - (name "ibus") - (version "1.5.19") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ibus/ibus/" - "releases/download/" - version "/ibus-" version ".tar.gz")) - (sha256 - (base32 - "0a94bnpm24581317hdnihwr4cniriml10p4ffgxg14xhvaccfrjb")))) - (build-system glib-or-gtk-build-system) - (arguments - `(#:tests? #f ; tests fail because there's no connection to dbus - #:configure-flags `("--disable-emoji-dict" ; cannot find emoji.json path - "--disable-python2" - "--enable-python-library" - ,(string-append "--with-ucd-dir=" - (getcwd) "/ucd") - "--enable-wayland") - #:make-flags - (list "CC=gcc" - (string-append "pyoverridesdir=" - (assoc-ref %outputs "out") - "/lib/python3.6/site-packages/gi/overrides/")) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'prepare-ucd-dir - (lambda* (#:key inputs #:allow-other-keys) - (mkdir-p "../ucd") - (symlink (assoc-ref inputs "unicode-blocks") "../ucd/Blocks.txt") - (symlink (assoc-ref inputs "unicode-nameslist") "../ucd/NamesList.txt") - #t)) - (add-before 'configure 'disable-dconf-update - (lambda _ - (substitute* "data/dconf/Makefile.in" - (("dconf update") "echo dconf update")) - #t)) - (add-after 'unpack 'delete-generated-files - (lambda _ - (for-each (lambda (file) - (let ((c (string-append (string-drop-right file 4) "c"))) - (when (file-exists? c) - (format #t "deleting ~a\n" c) - (delete-file c)))) - (find-files "." "\\.vala")) - #t)) - (add-after 'unpack 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "src/ibusenginesimple.c" - (("/usr/share/X11/locale") - (string-append (assoc-ref inputs "libx11") - "/share/X11/locale"))) - (substitute* "ui/gtk3/xkblayout.vala" - (("\"(setxkbmap|xmodmap)\"" _ prog) - (string-append "\"" (assoc-ref inputs prog) "\""))) - #t)) - (add-after 'wrap-program 'wrap-with-additional-paths - (lambda* (#:key outputs #:allow-other-keys) - ;; Make sure 'ibus-setup' runs with the correct PYTHONPATH and - ;; GI_TYPELIB_PATH. - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/bin/ibus-setup") - `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH"))) - `("GI_TYPELIB_PATH" ":" prefix - (,(getenv "GI_TYPELIB_PATH") - ,(string-append out "/lib/girepository-1.0"))))) - #t))))) - (inputs - `(("dbus" ,dbus) - ("dconf" ,dconf) - ("gconf" ,gconf) - ("gtk2" ,gtk+-2) - ("gtk+" ,gtk+) - ("intltool" ,intltool) - ("json-glib" ,json-glib) - ("libnotify" ,libnotify) - ("libx11" ,libx11) - ("setxkbmap" ,setxkbmap) - ("wayland" ,wayland) - ("xmodmap" ,xmodmap) - ("iso-codes" ,iso-codes) - ("pygobject2" ,python-pygobject) - ("python" ,python))) - (native-inputs - `(("glib" ,glib "bin") ; for glib-genmarshal - ("gobject-introspection" ,gobject-introspection) ; for g-ir-compiler - ("unicode-nameslist" - ,(origin - (method url-fetch) - (uri "https://www.unicode.org/Public/UNIDATA/NamesList.txt") - (sha256 - (base32 "0yr2h0nfqhirfi3bxl33z6cc94qqshlpgi06c25xh9754irqsgv8")))) - ("unicode-blocks" - ,(origin - (method url-fetch) - (uri "https://www.unicode.org/Public/UNIDATA/Blocks.txt") - (sha256 - (base32 "0lnh9iazikpr548bd7nkaq9r3vfljfvz0rg2462prac8qxk7ni8b")))) - ("vala" ,vala) - ("pkg-config" ,pkg-config))) - (native-search-paths - (list (search-path-specification - (variable "IBUS_COMPONENT_PATH") - (files '("share/ibus/component"))))) - (synopsis "Input method framework") - (description - "IBus is an input framework providing a full-featured and user-friendly + (name "ibus") + (version "1.5.19") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ibus/ibus/" + "releases/download/" + version "/ibus-" version ".tar.gz")) + (sha256 + (base32 + "0a94bnpm24581317hdnihwr4cniriml10p4ffgxg14xhvaccfrjb")))) + (build-system glib-or-gtk-build-system) + (arguments + `(#:tests? #f ; tests fail because there's no connection to dbus + #:configure-flags `("--disable-emoji-dict" ; cannot find emoji.json path + "--disable-python2" + "--enable-python-library" + ,(string-append "--with-ucd-dir=" + (getcwd) "/ucd") + "--enable-wayland") + #:make-flags + (list "CC=gcc" + (string-append "pyoverridesdir=" + (assoc-ref %outputs "out") + "/lib/python3.6/site-packages/gi/overrides/")) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'prepare-ucd-dir + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "../ucd") + (symlink (assoc-ref inputs "unicode-blocks") "../ucd/Blocks.txt") + (symlink (assoc-ref inputs "unicode-nameslist") "../ucd/NamesList.txt") + #t)) + (add-before 'configure 'disable-dconf-update + (lambda _ + (substitute* "data/dconf/Makefile.in" + (("dconf update") "echo dconf update")) + #t)) + (add-after 'unpack 'delete-generated-files + (lambda _ + (for-each (lambda (file) + (let ((c (string-append (string-drop-right file 4) "c"))) + (when (file-exists? c) + (format #t "deleting ~a\n" c) + (delete-file c)))) + (find-files "." "\\.vala")) + #t)) + (add-after 'unpack 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/ibusenginesimple.c" + (("/usr/share/X11/locale") + (string-append (assoc-ref inputs "libx11") + "/share/X11/locale"))) + (substitute* "ui/gtk3/xkblayout.vala" + (("\"(setxkbmap|xmodmap)\"" _ prog) + (string-append "\"" (assoc-ref inputs prog) "\""))) + #t)) + (add-after 'wrap-program 'wrap-with-additional-paths + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure 'ibus-setup' runs with the correct PYTHONPATH and + ;; GI_TYPELIB_PATH. + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/ibus-setup") + `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH"))) + `("GI_TYPELIB_PATH" ":" prefix + (,(getenv "GI_TYPELIB_PATH") + ,(string-append out "/lib/girepository-1.0"))))) + #t))))) + (inputs + `(("dbus" ,dbus) + ("dconf" ,dconf) + ("gconf" ,gconf) + ("gtk2" ,gtk+-2) + ("gtk+" ,gtk+) + ("intltool" ,intltool) + ("json-glib" ,json-glib) + ("libnotify" ,libnotify) + ("libx11" ,libx11) + ("setxkbmap" ,setxkbmap) + ("wayland" ,wayland) + ("xmodmap" ,xmodmap) + ("iso-codes" ,iso-codes) + ("pygobject2" ,python-pygobject) + ("python" ,python))) + (native-inputs + `(("glib" ,glib "bin") ; for glib-genmarshal + ("gobject-introspection" ,gobject-introspection) ; for g-ir-compiler + ("unicode-nameslist" + ,(origin + (method url-fetch) + (uri "https://www.unicode.org/Public/UNIDATA/NamesList.txt") + (sha256 + (base32 "0yr2h0nfqhirfi3bxl33z6cc94qqshlpgi06c25xh9754irqsgv8")))) + ("unicode-blocks" + ,(origin + (method url-fetch) + (uri "https://www.unicode.org/Public/UNIDATA/Blocks.txt") + (sha256 + (base32 "0lnh9iazikpr548bd7nkaq9r3vfljfvz0rg2462prac8qxk7ni8b")))) + ("vala" ,vala) + ("pkg-config" ,pkg-config))) + (native-search-paths + (list (search-path-specification + (variable "IBUS_COMPONENT_PATH") + (files '("share/ibus/component"))))) + (synopsis "Input method framework") + (description + "IBus is an input framework providing a full-featured and user-friendly input method user interface. It comes with multilingual input support. It may also simplify input method development.") - (home-page "https://github.com/ibus/ibus/wiki") - (license lgpl2.1+))) + (home-page "https://github.com/ibus/ibus/wiki") + (license lgpl2.1+))) (define-public ibus-libpinyin (package - (name "ibus-libpinyin") - (version "1.10.0") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/libpinyin/ibus-libpinyin/" - "releases/download/" version - "/ibus-libpinyin-" version ".tar.gz")) - (sha256 - (base32 - "0yq8aw4lddiviag8cnik6fp52vvk8lxv6bym13a3xya84c6zii3c")))) - (build-system glib-or-gtk-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'wrap-program 'wrap-with-additional-paths - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Make sure 'ibus-setup-libpinyin' runs with the correct - ;; PYTHONPATH and GI_TYPELIB_PATH. - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/libexec/ibus-setup-libpinyin") - `("PYTHONPATH" ":" prefix - (,(getenv "PYTHONPATH") - ,(string-append (assoc-ref inputs "ibus") - "/lib/girepository-1.0"))) - `("GI_TYPELIB_PATH" ":" prefix - (,(string-append (assoc-ref inputs "ibus") - "/lib/girepository-1.0")))) - #t)))))) - (inputs - `(("ibus" ,ibus) - ("libpinyin" ,libpinyin) - ("bdb" ,bdb) - ("sqlite" ,sqlite) - ("python" ,python) - ("pyxdg" ,python-pyxdg) - ("gtk+" ,gtk+))) - (native-inputs - `(("pkg-config" ,pkg-config) - ("intltool" ,intltool) - ("glib" ,glib "bin"))) - (synopsis "Chinese pinyin and ZhuYin input methods for IBus") - (description - "This package includes a Chinese pinyin input method and a Chinese + (name "ibus-libpinyin") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/libpinyin/ibus-libpinyin/" + "releases/download/" version + "/ibus-libpinyin-" version ".tar.gz")) + (sha256 + (base32 + "0yq8aw4lddiviag8cnik6fp52vvk8lxv6bym13a3xya84c6zii3c")))) + (build-system glib-or-gtk-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'wrap-program 'wrap-with-additional-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Make sure 'ibus-setup-libpinyin' runs with the correct + ;; PYTHONPATH and GI_TYPELIB_PATH. + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/libexec/ibus-setup-libpinyin") + `("PYTHONPATH" ":" prefix + (,(getenv "PYTHONPATH") + ,(string-append (assoc-ref inputs "ibus") + "/lib/girepository-1.0"))) + `("GI_TYPELIB_PATH" ":" prefix + (,(string-append (assoc-ref inputs "ibus") + "/lib/girepository-1.0")))) + #t)))))) + (inputs + `(("ibus" ,ibus) + ("libpinyin" ,libpinyin) + ("bdb" ,bdb) + ("sqlite" ,sqlite) + ("python" ,python) + ("pyxdg" ,python-pyxdg) + ("gtk+" ,gtk+))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("intltool" ,intltool) + ("glib" ,glib "bin"))) + (synopsis "Chinese pinyin and ZhuYin input methods for IBus") + (description + "This package includes a Chinese pinyin input method and a Chinese ZhuYin (Bopomofo) input method based on libpinyin for IBus.") - (home-page "https://github.com/libpinyin/ibus-libpinyin") - (license gpl2+))) + (home-page "https://github.com/libpinyin/ibus-libpinyin") + (license gpl2+))) (define-public libpinyin (package @@ -279,3 +288,369 @@ applications allow text input via IBus, installing this package will enable Japanese language input in most graphical applications.") (home-page "https://github.com/fujiwarat/ibus-anthy") (license gpl2+))) + +(define-public librime + (package + (name "librime") + (version "1.3.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/librime.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1y0h3nnz97smx9z8h5fzk4c27mvrwv8kajxffqc43bhyvxvb2jd6")))) + (build-system cmake-build-system) + (inputs + `(("boost" ,boost) + ("glog" ,glog) + ("leveldb" ,leveldb) + ("marisa" ,marisa) + ("opencc" ,opencc) + ("yaml-cpp" ,yaml-cpp))) + (home-page "https://rime.im/") + (synopsis "The core library of Rime Input Method Engine") + (description "@dfn{librime} is the core library of Rime Input Method +Engine, which is a lightweight, extensible input method engine supporting +various input schemas including glyph-based input methods, romanization-based +input methods as well as those for Chinese dialects. It has the ability to +compose phrases and sentences intelligently and provide very accurate +traditional Chinese output.") + (license bsd-3))) + +(define-public rime-data + (package + (name "rime-data") + (version "0.38.20181029") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/plum.git") + (commit "fb4f829da2007f2dbb37d60a79bc67c25ea16568"))) + (file-name "plum-checkout") + (sha256 + (base32 "1m1wiv9j5bay4saga58c7dj4h8gqivsbyp16y245ifvxvp9czj67")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) + "no_update=1") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda _ + ;; Set .DEFAULT_GOAL to `all'. + ;; Don't build binary schemas. The output is not deterministic. + (substitute* "Makefile" + (("^\\.DEFAULT_GOAL := preset") + ".DEFAULT_GOAL := all")) + #t)) + ;; Add schema packages into "package/rime" directory. + (add-after 'unpack 'add-packages + (lambda* (#:key inputs #:allow-other-keys) + (let* ((dest-dir "package/rime")) + (mkdir-p dest-dir) + (for-each (lambda (pkg) + (symlink (assoc-ref inputs pkg) + (string-append dest-dir "/" pkg))) + '("array" + "bopomofo" + "cangjie" + "combo-pinyin" + "double-pinyin" + "emoji" + "essay" + "ipa" + "jyutping" + "luna-pinyin" + "middle-chinese" + "pinyin-simp" + "prelude" + "quick" + "scj" + "soutzoe" + "stenotype" + "stroke" + "terra-pinyin" + "wubi" + "wugniu"))) + #t)) + (delete 'configure)))) + (native-inputs + `(("array" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-array.git") + (commit "906e923902147584b0b0247028a782abbfbfd8a0"))) + (file-name "rime-array-checkout") + (sha256 + (base32 + "1alk6ghn4ji4kvp7lfm57bwm2gjh99i79r0w9naz6wkdim8idvb1")))) + ("bopomofo" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-bopomofo.git") + (commit "8dc44ca1b6ef4e45b452e070b9da737f5da165e3"))) + (file-name "rime-bopomofo-checkout") + (sha256 + (base32 + "16k6wfhcrw3a77rmbrp21ca0gmsmb3f68s193c1cfwr8i68k46nf")))) + ("cangjie" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-cangjie.git") + (commit "ab085e90856b3399b374dc3c8b4cb40d11f307a8"))) + (file-name "rime-cangjie-checkout") + (sha256 + (base32 + "11fgj0rbv9nyzfijwm2l8pm8fznhif4h27ndrrcaaylkp7p5zsx2")))) + ("combo-pinyin" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-combo-pinyin.git") + (commit "f1bae63f20504f2b8113c5cbdf2700e858aa91eb"))) + (file-name "rime-combo-pinyin-checkout") + (sha256 + (base32 + "1l1079akwm1hw4kkn0q6x9fpylnl2ka6z2fn7lmdpfpsr0xgn0n7")))) + ("double-pinyin" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-double-pinyin.git") + (commit "2101a5cd40e511ec38835769aa66d2dddf059c2e"))) + (file-name "rime-double-pinyin-checkout") + (sha256 + (base32 + "19hh2qm0njbfk2js678hfm2hw9b796s43vs11yy3m1v9m0gk2vi7")))) + ("emoji" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-emoji.git") + (commit "6e6611b315f03ee4c33f958f9dbe960b13a0ed19"))) + (file-name "rime-emoji-checkout") + (sha256 + (base32 + "1brfs3214w36j3345di9ygp468hbvbqdqpkjxxs1dbp437rayhyy")))) + ("essay" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-essay.git") + (commit "5e5c7a0ef41c9b030abdad81a9df07b56b1661e9"))) + (file-name "rime-essay-checkout") + (sha256 + (base32 + "0ana9is0zhh79m4gjshvmaxbrg3jiqysydx5bpm151i7i6vw5y1i")))) + ("ipa" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-ipa.git") + (commit "02a9e2c181921a2e95e1a81f88188c41132755c3"))) + (file-name "rime-ipa-checkout") + (sha256 + (base32 + "1szrxgvqlgmxapj2aflw2cvbv0p6pl0sw0gyxa13dvdhhf7s9rvr")))) + ("jyutping" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-jyutping.git") + (commit "1402ec3d6cc0973f952fe3f9ef531294e4ffe9e0"))) + (file-name "rime-jyutping-checkout") + (sha256 + (base32 + "17g03dy4gw6vyc9da1wjn3iy9hx64dfnwiwsfc7bkzan22x2m4dv")))) + ("luna-pinyin" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-luna-pinyin.git") + (commit "3b05132576f5c347ff8a70857d2dae080936ac3b"))) + (file-name "rime-luna-pinyin-checkout") + (sha256 + (base32 + "0kgnpxjn10dm2d9718r12rdjlwqd2s2h84jvkhxhh5v0dkv1anl2")))) + ("middle-chinese" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-middle-chinese.git") + (commit "9ba8d70330654b9a730f882d35cfad7dbeddfd75"))) + (file-name "rime-middle-chinese-checkout") + (sha256 + (base32 + "0hwg5zby5kphh0bcfay8mfxwr5bwqhamiw3cmmmf7kp9fbns5s23")))) + ("pinyin-simp" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-pinyin-simp.git") + (commit "74357ffd62c05fb60edf6eab5b86bc8c8c1907d0"))) + (file-name "rime-pinyin-simp-checkout") + (sha256 + (base32 + "1paw3c7pv5bl54abnp9pidfxrkchdacyxy5m9zb311p5sgm7fhxh")))) + ("prelude" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-prelude.git") + (commit "33040568c3ddb2ee6340c9b669494317db21b77c"))) + (file-name "rime-prelude-checkout") + (sha256 + (base32 + "1gwcasyyg6f0ib6s4qsrrjcqr1lcs7j3xqxl65rznsw44nhnbwwq")))) + ("quick" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-quick.git") + (commit "910a97d403ad8e72f322488da146da79c19d623f"))) + (file-name "rime-quick-checkout") + (sha256 + (base32 + "0yrq3gbfmm29xlr52rmxc41mqfrb0295q7sdhbc3ax71677mpr0y")))) + ("scj" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-scj.git") + (commit "e0eae889f4376d2a434ac3b38523e0da7400db68"))) + (file-name "rime-scj-checkout") + (sha256 + (base32 + "1whnv9zs349kvy0zi7dnmpqwil8i6gqwrzvhy3qdrjzy58y6gwxn")))) + ("soutzoe" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-soutzoe.git") + (commit "e47841a8ad6341731c41cdb814b7a25c837603c4"))) + (file-name "rime-soutzoe-checkout") + (sha256 + (base32 + "1rgpmkxa72jy6gyy44fn8azpk3amk9s9lrdf7za03nv95d0fvm0p")))) + ("stenotype" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-stenotype.git") + (commit "d4ff379314fd95283853d1734854979cf3cbd287"))) + (file-name "rime-stenotype-checkout") + (sha256 + (base32 + "1kckpi4l4884hvydr3d6vid3v7rsc1app29kmk7v8jf8vn16afhl")))) + ("stroke" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-stroke.git") + (commit "cfd29c675c46cf70b7a7f0a3836a913059316a0a"))) + (file-name "rime-stroke-checkout") + (sha256 + (base32 + "135is9c1p4lm98fd9l1gxyflkm69cv5an129ka7sk614bq84m08d")))) + ("terra-pinyin" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-terra-pinyin.git") + (commit "15b5c73a796571cd6f9ef6c89f96656cb9df86f9"))) + (file-name "rime-terra-pinyin-checkout") + (sha256 + (base32 + "1xsd84h1zw417h5hr4dbgyk5009zi7q2p9774w3ccr5sxgc3i3cm")))) + ("wubi" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-wubi.git") + (commit "d44403728a0b1cd8b47cb1f81b83f58e5f790b74"))) + (file-name "rime-wubi-checkout") + (sha256 + (base32 + "0ld31bdn94lncxd1ka44w4sbl03skh08mc927dhdmwq5bpvrgn36")))) + ("wugniu" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/rime-wugniu.git") + (commit "65bcc354ada3839591d7546a64c71dbdd0592b02"))) + (file-name "rime-wugniu-checkout") + (sha256 + (base32 + "0g31awp40s778sp5c290x40s8np86n8aw011s17sslxrqhhb0bkx")))))) + (home-page "https://rime.im/") + (synopsis "Schema data of Rime Input Method Engine") + (description "@dfn{rime-data} provides the schema data of Rime Input +Method Engine.") + (license lgpl3+))) + +(define-public ibus-rime + (package + (name "ibus-rime") + (version "1.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rime/ibus-rime.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1nqi7ymv34a9kx24say3xj98lkrs9nkpv1n2ijb91wdz3cr012ly")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Define RIME_DATA_DIR. It's required but not used by the code. + (substitute* "Makefile" + (("cmake") + (string-append "cmake -DRIME_DATA_DIR=" + (assoc-ref inputs "rime-data") + "/share/rime-data"))) + ;; rime_config.h defines the actual data directory. + (substitute* "rime_config.h" + (("^#define IBUS_RIME_INSTALL_PREFIX .*$") + (string-append "#define IBUS_RIME_INSTALL_PREFIX \"" + (assoc-ref outputs "out") + "\"\n")) + (("^#define IBUS_RIME_SHARED_DATA_DIR .*$") + (string-append "#define IBUS_RIME_SHARED_DATA_DIR \"" + (assoc-ref inputs "rime-data") + "/share/rime-data\"\n"))) + #t)) + (delete 'configure)))) + (inputs + `(("gdk-pixbuf" ,gdk-pixbuf) + ("glib" ,glib) + ("ibus" ,ibus) + ("libnotify" ,libnotify) + ("librime" ,librime) + ("rime-data" ,rime-data))) + (native-inputs + `(("cmake" ,cmake) + ("pkg-config" ,pkg-config))) + (home-page "https://rime.im/") + (synopsis "Rime Input Method Engine for IBus") + (description "@dfn{ibus-rime} provides the Rime input method engine for +IBus. Rime is a lightweight, extensible input method engine supporting +various input schemas including glyph-based input methods, romanization-based +input methods as well as those for Chinese dialects. It has the ability to +compose phrases and sentences intelligently and provide very accurate +traditional Chinese output.") + (license gpl3+))) diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm index 518417707f..029d5b5443 100644 --- a/gnu/packages/image-viewers.scm +++ b/gnu/packages/image-viewers.scm @@ -60,7 +60,7 @@ (define-public feh (package (name "feh") - (version "2.28.1") + (version "3.0") (home-page "https://feh.finalrewind.org/") (source (origin (method url-fetch) @@ -68,7 +68,7 @@ name "-" version ".tar.bz2")) (sha256 (base32 - "0wian0gnx0yfxf8x9b8wr57fjd6rnmi3y3xj83ni6x0xqrjnf1lp")))) + "00fwf8yz7k8vzd30ly5ndlj6ax9w85dkjzjnlk95vd0zdrf4wyxn")))) (build-system gnu-build-system) (arguments '(#:phases (modify-phases %standard-phases (delete 'configure)) diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm index e29ec6255b..fe0923f479 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -47,14 +48,14 @@ ;; The 7 release series has an incompatible API, while the 6 series is still ;; maintained. Don't update to 7 until we've made sure that the ImageMagick ;; users are ready for the 7-series API. - (version "6.9.10-12") + (version "6.9.10-14") (source (origin (method url-fetch) (uri (string-append "mirror://imagemagick/ImageMagick-" version ".tar.xz")) (sha256 (base32 - "0ri96yqihdk921k5qx23y2sbhraxbp2avdccxiy6m3srjkirym2l")))) + "0vcfjvdk9in92x808djvy94l5gylpgds4a7mlr8jrxsv9snx88yi")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch") diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 02d30bacf4..955ad436b7 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -423,8 +423,8 @@ It has been modified to remove all non-free binary blobs.") #:patches %linux-libre-4.19-patches #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.79") -(define %linux-libre-4.14-hash "000rd4h2yk6k68wjg37v53hqnqw1mgwhdxbcvy8iywy8za9r12c8") +(define %linux-libre-4.14-version "4.14.80") +(define %linux-libre-4.14-hash "0h4hi5lqizdx5nk0f3immbcv2n7p5jh26m80v4x6bw4wi5b44fra") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version @@ -433,14 +433,14 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.135" - "07v5s6hl08ls2z9xdkbqq1s210mqayfchqbckhp8hlaw089ap71f" + (make-linux-libre "4.9.136" + "1kk6px1jcwbgkpfmf9pdklk6kz90h5l8fvdqwmvnk4bz6b2xrrfp" %intel-compatible-systems #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.162" - "1anb2k9i03369lvbwlw24vimxvk8zpcql4ryz0ydvf3pxv8lirm2" + (make-linux-libre "4.4.163" + "05j0dm0cxilanp5z40n8kgjz9vn1p4rg63kksicd2v48w8ka82z6" %intel-compatible-systems #:configuration-file kernel-config)) @@ -1968,20 +1968,15 @@ for systems using the Linux kernel. This includes commands such as (name "inotify-tools") (version "3.20.1") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/rvoicilas/inotify-tools/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/rvoicilas/inotify-tools.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1b22c8x4pjnz3abx4dikpbj43zprjw79pdkd4xw111dsxlfwqcx4")))) + "14dci1i4mhsd5sa33k8h3ayphk19kizynh5ql9ryibdpmcanfiyq")))) (build-system gnu-build-system) - (arguments - `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'bootstrap - (lambda _ - (invoke "autoreconf" "-vif")))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -2916,7 +2911,7 @@ MPEG-2 and audio over Linux IEEE 1394.") (define-public mdadm (package (name "mdadm") - (version "4.0") + (version "4.1") (source (origin (method url-fetch) (uri (string-append @@ -2924,7 +2919,7 @@ MPEG-2 and audio over Linux IEEE 1394.") version ".tar.xz")) (sha256 (base32 - "1ad3mma641946wn5lsllwf0lifw9lps34fv1nnkhyfpd9krffshx")))) + "0jjgjgqijpdp7ijh8slzzjjw690kydb1jjadf0x5ilq85628hxmb")))) (build-system gnu-build-system) (inputs `(("udev" ,eudev))) @@ -3949,7 +3944,7 @@ are exceeded.") (define-public mtd-utils (package (name "mtd-utils") - (version "1.5.2") + (version "2.0.2") (source (origin (method url-fetch) (uri (string-append @@ -3957,18 +3952,18 @@ are exceeded.") "mtd-utils-" version ".tar.bz2")) (sha256 (base32 - "007lhsd8yb34l899r4m37whhzdw815cz4fnjbpnblfha524p7dax")))) + "1f30jszknc5v6ykmil8ajxgksmcg54q3rsp84jsancp9x0dycggv")))) + (arguments + '(#:configure-flags '("--enable-unit-tests"))) + (native-inputs + `(("cmocka" ,cmocka) + ("pkg-config" ,pkg-config))) (inputs - `(("acl" ,acl) + `(("acl" ,acl) ; for XATTR ("libuuid" ,util-linux) ("lzo" ,lzo) ("zlib" ,zlib))) (build-system gnu-build-system) - (arguments - `(#:test-target "tests" - #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))) - #:phases (modify-phases %standard-phases - (delete 'configure)))) (synopsis "MTD Flash Storage Utilities") (description "This package provides utilities for testing, partitioning, etc of flash storage.") diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index 54a17be8f4..f57e263449 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -91,17 +91,6 @@ languages is in development. The compiler infrastructure includes mirror sets of programming tools as well as libraries with equivalent functionality.") (license license:ncsa))) -(define-public llvm-with-rtti - (package (inherit llvm) - (name "llvm-with-rtti") - (arguments - (substitute-keyword-arguments (package-arguments llvm) - ((#:configure-flags flags) - `(append '("-DCMAKE_SKIP_BUILD_RPATH=FALSE" - "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE" - "-DLLVM_REQUIRES_RTTI=1") - ,flags)))))) - (define* (clang-runtime-from-llvm llvm hash #:optional (patches '())) (package @@ -292,6 +281,18 @@ code analysis tools.") (base32 "1ybmnid4pw2hxn12ax5qa5kl1ldfns0njg8533y3mzslvd5cx0kf")))))) +;; This is for Faust 2 +(define-public llvm-3.8-with-rtti + (package (inherit llvm-3.8) + (name "llvm-with-rtti") + (arguments + (substitute-keyword-arguments (package-arguments llvm) + ((#:configure-flags flags) + `(append '("-DCMAKE_SKIP_BUILD_RPATH=FALSE" + "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE" + "-DLLVM_REQUIRES_RTTI=1") + ,flags)))))) + (define-public clang-runtime-3.8 (clang-runtime-from-llvm llvm-3.8 diff --git a/gnu/packages/lxde.scm b/gnu/packages/lxde.scm index c45beb8bbb..1f32ec3bb1 100644 --- a/gnu/packages/lxde.scm +++ b/gnu/packages/lxde.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Ison111 <ison111@protonmail.com> ;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -419,10 +420,10 @@ in LXDE.") (modify-phases %standard-phases (add-after 'unpack 'rm-stamp (lambda _ - (for-each delete-file (find-files "." "\\.stamp$")))) - (add-after 'rm-stamp 'autoreconf - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) + (for-each delete-file (find-files "." "\\.stamp$")) + ;; Force regeneration of configure script. + (delete-file "configure") + #t))))) (inputs `(("gtk+-2" ,gtk+-2) ("polkit" ,polkit))) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 35b7d27df3..74b1d489a3 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -110,7 +110,9 @@ #:use-module (gnu packages xorg) #:use-module (gnu packages docbook) #:use-module ((guix licenses) - #:select (fdl1.1+ gpl2 gpl2+ gpl3 gpl3+ lgpl2.1 lgpl2.1+ lgpl3+ + #:select (fdl1.1+ + agpl3+ + gpl2 gpl2+ gpl3 gpl3+ lgpl2.1 lgpl2.1+ lgpl3+ non-copyleft (expat . license:expat) bsd-3 public-domain bsd-4 isc (openssl . license:openssl) bsd-2 x11-style agpl3 asl2.0 perl-license)) @@ -119,6 +121,7 @@ #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system gnu) + #:use-module (guix build-system guile) #:use-module (guix build-system perl) #:use-module (guix build-system python) #:use-module (guix build-system trivial)) @@ -2640,3 +2643,50 @@ replacement for the @code{urlview} program.") "TNEF is a tar-like program that unpacks MIME attachments of type @code{application/ms-tnef}.") (license gpl2+))) + +(define-public mumi + (let ((commit "bfd96ce76b4600ae232e6548b26c9365095fd174") + (revision "2")) + (package + (name "mumi") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.elephly.net/software/mumi.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "05miwfi1bh0v9x2gvn15bwkb3gn4xy53z506ysjzns2y497zkc5h")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-executable + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (scm (string-append out "/share/guile/site/2.2")) + (go (string-append out "/lib/guile/2.2/site-ccache"))) + (wrap-program (string-append bin "/mumi") + `("GUILE_LOAD_PATH" ":" prefix + (,scm ,(getenv "GUILE_LOAD_PATH"))) + `("GUILE_LOAD_COMPILED_PATH" ":" prefix + (,go ,(getenv "GUILE_LOAD_COMPILED_PATH")))) + #t)))))) + (inputs + `(("guile-debbugs" ,guile-debbugs-next) + ("guile-email" ,guile-email) + ("guile-fibers" ,guile-fibers) + ("guile-json" ,guile-json) + ("guile-syntax-highlight" ,guile-syntax-highlight) + ("guile" ,guile-2.2))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("pkg-config" ,pkg-config))) + (home-page "https://git.elephly.net/software/mumi.git") + (synopsis "Debbugs web interface") + (description "Mumi is a Debbugs web interface.") + (license agpl3+)))) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index de33d737e2..c22cacfd36 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -549,14 +549,14 @@ simultaneously and therefore appear under the same nickname on IRC.") (define-public python-nbxmpp (package (name "python-nbxmpp") - (version "0.6.7") + (version "0.6.8") (source (origin (method url-fetch) (uri (pypi-uri "nbxmpp" version)) (sha256 (base32 - "0fas4iawjfdmkz8vr042wpq6b2qispi6fy35g4a62jw50jb1saav")))) + "1iip8ijxp86fx4bl1h67p2lp02p2zm1ga2p3q43nv30smj54nawc")))) (build-system python-build-system) (arguments `(#:tests? #f)) ; no tests @@ -574,7 +574,7 @@ was initially a fork of xmpppy, but uses non-blocking sockets.") (define-public gajim (package (name "gajim") - (version "1.0.3") + (version "1.1.0") (source (origin (method url-fetch) (uri (string-append "https://gajim.org/downloads/" @@ -582,10 +582,11 @@ was initially a fork of xmpppy, but uses non-blocking sockets.") "/gajim-" version ".tar.bz2")) (sha256 (base32 - "0ds4rqwfrpj89a489w6yih8gx5zi7qa4ffgld950fk7s0qxvcfnb")))) + "1qis8vs7y7g1zn5i5dshwrszidc22qpflycwb4nixvp9lbmkq0va")))) (build-system python-build-system) (arguments - `(#:phases + `(#:test-target "test_nogui" + #:phases (modify-phases %standard-phases (add-after 'install 'wrap-program (lambda* (#:key outputs #:allow-other-keys) @@ -598,20 +599,6 @@ was initially a fork of xmpppy, but uses non-blocking sockets.") `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path))))) '("gajim" "gajim-remote" "gajim-history-manager"))) #t)) - (add-before 'check 'remove-test-resolver - ;; This test requires network access. - (lambda _ - (substitute* "test/runtests.py" - (("'integration.test_resolver',") "")) - #t)) - (add-before 'check 'start-xserver - ;; Tests require a running X server. - (lambda* (#:key inputs #:allow-other-keys) - (let ((xorg-server (assoc-ref inputs "xorg-server")) - (display ":1")) - (setenv "DISPLAY" display) - (zero? (system (string-append xorg-server "/bin/Xvfb " - display " &")))))) (add-after 'install 'install-icons (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -636,9 +623,11 @@ was initially a fork of xmpppy, but uses non-blocking sockets.") ;; For GtkFileChooserDialog. `("GSETTINGS_SCHEMA_DIR" = (,(string-append (assoc-ref inputs "gtk+") - "/share/glib-2.0/schemas"))))))))) + "/share/glib-2.0/schemas")))) + #t))))) (native-inputs `(("intltool" ,intltool) + ("python-docutils" ,python-docutils) ("xorg-server" ,xorg-server))) (inputs `(("adwaita-icon-theme" ,adwaita-icon-theme) @@ -648,12 +637,13 @@ was initially a fork of xmpppy, but uses non-blocking sockets.") ("hicolor-icon-theme" ,hicolor-icon-theme) ("libsecret" ,libsecret) ("python-axolotl" ,python-axolotl) + ("python-cssutils" ,python-cssutils) ("python-dbus" ,python-dbus) - ("python-docutils" ,python-docutils) ("python-gnupg" ,python-gnupg) + ("python-keyring" ,python-keyring) ("python-nbxmpp" ,python-nbxmpp) ("python-pillow" ,python-pillow) - ("python-pyasn1" ,python-pyasn1) + ("python-precis-i18n" ,python-precis-i18n) ("python-pycairo" ,python-pycairo) ("python-pygobject" ,python-pygobject) ("python-pyopenssl" ,python-pyopenssl) @@ -828,8 +818,8 @@ protocols.") (license license:x11))) (define-public libtoxcore - (let ((revision "1") - (commit "755f084e8720b349026c85afbad58954cb7ff1d4")) + (let ((revision "2") + (commit "bf69b54f64003d160d759068f4816b2d9b2e1e21")) (package (name "libtoxcore") (version (string-append "0.0.0" "-" @@ -842,26 +832,19 @@ protocols.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0ap1gvlyihnfivv235dbrgsxsiiz70bhlmlr5gn1027w3h5kqz8w")))) + "11lqra4yd7v293cp286ynff5lqz1pprzg8vn3wq6vryj08g88zqb")))) (build-system gnu-build-system) + (arguments `(#:tests? #f)) ; FIXME: tests hang, some fail. (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("libtool" ,libtool) - ;; TODO: Add when test suite is capable of passing. - ;; ("check" ,check) + ("check" ,check) ("pkg-config" ,pkg-config))) (inputs `(("libsodium" ,libsodium) ("opus" ,opus) ("libvpx" ,libvpx))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoconf - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))) - #:tests? #f)) ; FIXME: Testsuite fails, reasons unspecific. (synopsis "Library for the Tox encrypted messenger protocol") (description "C library implementation of the Tox encrypted messenger protocol.") @@ -877,13 +860,14 @@ protocols.") (version "0.2.8") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/TokTok/c-toxcore/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/TokTok/c-toxcore.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0qlkimlvbd24nlj7w9b5rpz1r807magqxmfylc1mlxsqhmfi5zj7")))) + "0xgnraysz25fbws5zwjk92mwnl8k1yih701qam8kgm3rxh50kyhm")))) (arguments `(#:tests? #f)) ; FIXME: Testsuite seems to stay stuck on test 3. Disable ; for now. diff --git a/gnu/packages/mtools.scm b/gnu/packages/mtools.scm index e4750f579f..5e3c3dd378 100644 --- a/gnu/packages/mtools.scm +++ b/gnu/packages/mtools.scm @@ -28,15 +28,15 @@ (define-public mtools (package (name "mtools") - (version "4.0.19") + (version "4.0.20") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/mtools/mtools-" - version ".tar.gz")) + version ".tar.bz2")) (sha256 (base32 - "003qnj4rs22v2sih3is55scvav8xq9p1dp5b7gnyl67a60ky516r")))) + "1vcahr9s6zv1hnrx2bgjnzcas2y951q90r1jvvv4q9v5kwfd6qb0")))) (build-system gnu-build-system) (home-page "https://www.gnu.org/software/mtools/") (synopsis "Access MS-DOS disks without mounting") diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 89ef58e80c..fca26edcbb 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -887,9 +887,10 @@ Sega Master System/Mark III, Sega Genesis/Mega Drive, BBC Micro #t)) (add-after 'install 'install-info (lambda _ - (zero? (system* "make" - "-j" (number->string (parallel-job-count)) - "conf=www" "install-info"))))))) + (invoke "make" + "-j" (number->string (parallel-job-count)) + "conf=www" "install-info") + #t))))) (inputs `(("guile" ,guile-1.8) ("font-dejavu" ,font-dejavu) @@ -1255,12 +1256,14 @@ Editor. It is compatible with Power Tab Editor 1.7 and Guitar Pro.") (name "jalv-select") (version "0.8") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/brummer10/jalv_select/" - "archive/V" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/brummer10/jalv_select.git") + (commit (string-append "V" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0zraagwr681b5s3qifxf399c7q93jz23c8sr42gmff9zqnvxc75q")))) + "0gqh768sbvn9ffyx1vqg9i57py9x9v4l65bk6wjsvgga4d7m83k1")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -1275,6 +1278,13 @@ Editor. It is compatible with Power Tab Editor 1.7 and Guitar Pro.") (string-append "ls -1 " (assoc-ref inputs "jalv") "/bin"))) (substitute* "jalv.select.h" (("gtkmm.h") "gtkmm-2.4/gtkmm.h")) + #t)) + (add-before 'reset-gzip-timestamps 'make-manpages-writable + (lambda* (#:key outputs #:allow-other-keys) + (for-each make-file-writable + (find-files (string-append (assoc-ref outputs "out") + "/share/man") + ".*\\.gz$")) #t))))) (inputs `(("lilv" ,lilv) @@ -1857,13 +1867,14 @@ using a system-independent interface.") (name "portmidi-for-extempore") (version "217") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/extemporelang/portmidi/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/extemporelang/portmidi.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0gjikwciyr8kk4y3qiv1pcq58xpgw38ql1m2gs6g0qc1s8sx4235")))) + "1inriyrjf7xx2b7r54x0vmf9ngyqgr7g5060c22bwkbsgg53apzv")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; no tests (native-inputs '()) @@ -2279,13 +2290,14 @@ follows a traditional multi-track tape recorder control paradigm.") (version "1.2.1") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/blablack/ams-lv2/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/blablack/ams-lv2.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1xacxyzqcj83g9c1gwfn36gg1c6yi15v7km4vidfidrjzb4x27fq")))) + "1n1dnqnj24xhiy9323lj52nswr5120cj56fpckg802miss05sr6x")))) (build-system waf-build-system) (arguments `(#:phases @@ -2320,13 +2332,14 @@ and hold, etc.") (name "gxtuner") (version "2.4") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/brummer10/gxtuner/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/brummer10/gxtuner.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1hn5qjac7qd00v0sp7ijhhc3sb26ks9bni06nngivva21h61xrjr")))) + "1fxd2akan2njlr7fpkh84830783qhh1gg7yakswqk5dd466dcn96")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -2432,13 +2445,14 @@ tune-in sender list from @url{http://opml.radiotime.com}.") (name "pianobar") (version "2016.06.02") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/PromyLOPh/" - name "/archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/PromyLOPh/pianobar.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1hi5rr6jcr0kwf4xfz007ndwkjkp287lhwlsgfz6iryqa5n6jzcp")))) + "058fbdxp7n35hxwy3b8slfy4pb4n63cb173vfmywqa06wh1dv6f6")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests @@ -2719,14 +2733,14 @@ of tools for manipulating and accessing your music.") (name "milkytracker") (version "1.02.00") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/milkytracker/" - "MilkyTracker/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/milkytracker/MilkyTracker.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "08v0l4ipvvwkwv4ywkc6c8a6xnpkyb02anj36w8q6gikxrs6xjvb")) + "05a6d7l98k9i82dwrgi855dnccm3f2lkb144gi244vhk1156n0ca")) (modules '((guix build utils))) ;; Remove non-FSDG compliant sample songs. (snippet @@ -2761,14 +2775,14 @@ for improved Amiga ProTracker 2/3 compatibility.") (name "schismtracker") (version "20180513") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/" name "/" name "/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/schismtracker/schismtracker.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1yjfd02arb51n0vyv11qgpn6imh7hcqnc3953cbvgwb4cnrswk9f")) + "0fayix1zbl96zhkfszgj71qr25dnddgy9hr6149nslww4gl7jk36")) (modules '((guix build utils))) (snippet ;; Remove use of __DATE__ and __TIME__ for reproducibility. @@ -2781,8 +2795,6 @@ for improved Amiga ProTracker 2/3 compatibility.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'autoconf - (lambda _ (invoke "autoreconf" "-vfi"))) (add-before 'configure 'link-libm (lambda _ (setenv "LIBS" "-lm") #t))))) (native-inputs @@ -3520,13 +3532,14 @@ are a C compiler and glib. Full API documentation and examples are included.") (version "1.1.3") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/LMMS/lmms/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/LMMS/lmms.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1g76z7ha3hd53vbqaq9n1qg6s3lw8zzaw51iny6y2bz0j1xqwcsr")))) + "03hhymc6d73fa3wbcqb7rm1l03zkw605k5i9kvkvjmv488bqh3pd")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; no tests @@ -4143,17 +4156,15 @@ at @code{musicbrainz.org}.") (version "0.10") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/trizen/clyrics/archive/" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/trizen/clyrics.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1l0cg26afnjv8cgk0jbiavbyvq55q1djyigzmi526rpcjjwq9jwn")) - (file-name (string-append name "-" version ".tar.gz")))) + "1qvj4dyipkkdccx5hci4z0q23i54ldk6hh7x5m35a7f70rrj6fbk")))) (build-system trivial-build-system) - (native-inputs `(("tar" ,tar) - ("gzip" ,gzip))) (inputs `(("bash" ,bash) ;for the wrapped program ("perl" ,perl) @@ -4170,17 +4181,12 @@ at @code{musicbrainz.org}.") (ice-9 match) (srfi srfi-26)) (let* ((source (assoc-ref %build-inputs "source")) - (tar (assoc-ref %build-inputs "tar")) - (gzip (assoc-ref %build-inputs "gzip")) (output (assoc-ref %outputs "out"))) (setenv "PATH" (string-append - (assoc-ref %build-inputs "gzip") "/bin" ":" (assoc-ref %build-inputs "bash") "/bin" ":" (assoc-ref %build-inputs "perl") "/bin" ":")) - (invoke (string-append tar "/bin/tar") "xvf" - source) - (chdir ,(string-append "clyrics-" version)) + (copy-recursively source (getcwd)) (patch-shebang "clyrics") (substitute* "clyrics" (("/usr/share") output)) diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm index 8f96b605a6..057e8c3bd9 100644 --- a/gnu/packages/nano.scm +++ b/gnu/packages/nano.scm @@ -30,7 +30,7 @@ (define-public nano (package (name "nano") - (version "3.1") + (version "3.2") (source (origin (method url-fetch) @@ -38,7 +38,7 @@ version ".tar.xz")) (sha256 (base32 - "17kinzyv6vwgyx2d0ym1kp65qbf7kxzwpyg21ic1rijv1aj2rh0l")))) + "0jb3zq0v84xb0chyynkcp2jhs9660wmpkic294p4p6c96npp69yi")))) (build-system gnu-build-system) (inputs `(("gettext" ,gettext-minimal) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 717e7021cf..fe784ffaa1 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -102,8 +102,8 @@ ;; Note: the 'update-guix-package.scm' script expects this definition to ;; start precisely like this. (let ((version "0.15.0") - (commit "f9a8fce10f2d99efec7cb1dd0f6c5f0df9d1b2df") - (revision 6)) + (commit "f5a2724ae453f4a4b55ff848f4ad7e30efb6eef8") + (revision 7)) (package (name "guix") @@ -119,7 +119,7 @@ (commit commit))) (sha256 (base32 - "1733d5id0h44rrkyj9xw4fcqr1wawcfi8igpgk5wsn1iq4qqwv5f")) + "12glmvifbwvl6lmxh1mc8nbcp0f5qgw40rmf8n1icxvj0mnjrwp4")) (file-name (string-append "guix-" version "-checkout")))) (build-system gnu-build-system) (arguments diff --git a/gnu/packages/patches/icecat-CVE-2018-12383.patch b/gnu/packages/patches/icecat-CVE-2018-12383.patch deleted file mode 100644 index 17ca0f3773..0000000000 --- a/gnu/packages/patches/icecat-CVE-2018-12383.patch +++ /dev/null @@ -1,103 +0,0 @@ -Based on upstream changeset: - https://hg.mozilla.org/releases/mozilla-esr60/rev/300efdbc9fe1 -but with the git binary patch and related test changes omitted, -and adapted to apply cleanly to GNU IceCat. - -# HG changeset patch -# User David Keeler <dkeeler@mozilla.com> -# Date 1531860660 25200 -# Node ID 300efdbc9fe1f9165428c7934861033935b5abfa -# Parent 80a4a7ef281374dbb2afda8edac54665b14b9ef8 -Bug 1475775 - Clean up old NSS DB file after upgrade if necessary. r=franziskus, r=mattn, a=RyanVM - -Reviewers: franziskus, mattn - -Bug #: 1475775 - -Differential Revision: https://phabricator.services.mozilla.com/D2202 - -diff --git a/security/manager/ssl/nsNSSComponent.cpp b/security/manager/ssl/nsNSSComponent.cpp ---- a/security/manager/ssl/nsNSSComponent.cpp -+++ b/security/manager/ssl/nsNSSComponent.cpp -@@ -1935,16 +1935,61 @@ AttemptToRenameBothPKCS11ModuleDBVersion - NS_NAMED_LITERAL_CSTRING(sqlModuleDBFilename, "pkcs11.txt"); - nsresult rv = AttemptToRenamePKCS11ModuleDB(profilePath, - legacyModuleDBFilename); - if (NS_FAILED(rv)) { - return rv; - } - return AttemptToRenamePKCS11ModuleDB(profilePath, sqlModuleDBFilename); - } -+ -+// When we changed from the old dbm database format to the newer sqlite -+// implementation, the upgrade process left behind the existing files. Suppose a -+// user had not set a password for the old key3.db (which is about 99% of -+// users). After upgrading, both the old database and the new database are -+// unprotected. If the user then sets a password for the new database, the old -+// one will not be protected. In this scenario, we should probably just remove -+// the old database (it would only be relevant if the user downgraded to a -+// version of IceCat before 58, but we have to trade this off against the -+// user's old private keys being unexpectedly unprotected after setting a -+// password). -+// This was never an issue on Android because we always used the new -+// implementation. -+static void -+MaybeCleanUpOldNSSFiles(const nsACString& profilePath) -+{ -+ UniquePK11SlotInfo slot(PK11_GetInternalKeySlot()); -+ if (!slot) { -+ return; -+ } -+ // Unfortunately we can't now tell the difference between "there already was a -+ // password when the upgrade happened" and "there was not a password but then -+ // the user added one after upgrading". -+ bool hasPassword = PK11_NeedLogin(slot.get()) && -+ !PK11_NeedUserInit(slot.get()); -+ if (!hasPassword) { -+ return; -+ } -+ nsCOMPtr<nsIFile> dbFile = do_CreateInstance("@mozilla.org/file/local;1"); -+ if (!dbFile) { -+ return; -+ } -+ nsresult rv = dbFile->InitWithNativePath(profilePath); -+ if (NS_FAILED(rv)) { -+ return; -+ } -+ NS_NAMED_LITERAL_CSTRING(keyDBFilename, "key3.db"); -+ rv = dbFile->AppendNative(keyDBFilename); -+ if (NS_FAILED(rv)) { -+ return; -+ } -+ // Since this isn't a directory, the `recursive` argument to `Remove` is -+ // irrelevant. -+ Unused << dbFile->Remove(false); -+} - #endif // ifndef ANDROID - - // Given a profile directory, attempt to initialize NSS. If nocertdb is true, - // (or if we don't have a profile directory) simply initialize NSS in no DB mode - // and return. Otherwise, first attempt to initialize in read/write mode, and - // then read-only mode if that fails. If both attempts fail, we may be failing - // to initialize an NSS DB collection that has FIPS mode enabled. Attempt to - // ascertain if this is the case, and if so, rename the offending PKCS#11 module -@@ -1966,16 +2011,19 @@ InitializeNSSWithFallbacks(const nsACStr - - // Try read/write mode. If we're in safeMode, we won't load PKCS#11 modules. - #ifndef ANDROID - PRErrorCode savedPRErrorCode1; - #endif // ifndef ANDROID - SECStatus srv = ::mozilla::psm::InitializeNSS(profilePath, false, !safeMode); - if (srv == SECSuccess) { - MOZ_LOG(gPIPNSSLog, LogLevel::Debug, ("initialized NSS in r/w mode")); -+#ifndef ANDROID -+ MaybeCleanUpOldNSSFiles(profilePath); -+#endif // ifndef ANDROID - return NS_OK; - } - #ifndef ANDROID - savedPRErrorCode1 = PR_GetError(); - PRErrorCode savedPRErrorCode2; - #endif // ifndef ANDROID - // That failed. Try read-only mode. - srv = ::mozilla::psm::InitializeNSS(profilePath, true, !safeMode); diff --git a/gnu/packages/patches/poppler-CVE-2018-19149.patch b/gnu/packages/patches/poppler-CVE-2018-19149.patch new file mode 100644 index 0000000000..3641f5f078 --- /dev/null +++ b/gnu/packages/patches/poppler-CVE-2018-19149.patch @@ -0,0 +1,80 @@ +Fix CVE-2018-19149: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-19149 +https://gitlab.freedesktop.org/poppler/poppler/issues/664 + +Patch copied from upstream source repository: + +https://gitlab.freedesktop.org/poppler/poppler/commit/f162ecdea0dda5dbbdb45503c1d55d9afaa41d44 + +From f162ecdea0dda5dbbdb45503c1d55d9afaa41d44 Mon Sep 17 00:00:00 2001 +From: Marek Kasik <mkasik@redhat.com> +Date: Fri, 20 Apr 2018 11:38:13 +0200 +Subject: [PATCH] Fix crash on missing embedded file + +Check whether an embedded file is actually present in the PDF +and show warning in that case. + +https://bugs.freedesktop.org/show_bug.cgi?id=106137 +https://gitlab.freedesktop.org/poppler/poppler/issues/236 +--- + glib/poppler-attachment.cc | 26 +++++++++++++++++--------- + glib/poppler-document.cc | 3 ++- + 2 files changed, 19 insertions(+), 10 deletions(-) + +diff --git a/glib/poppler-attachment.cc b/glib/poppler-attachment.cc +index c6502e9d..11ba5bb5 100644 +--- a/glib/poppler-attachment.cc ++++ b/glib/poppler-attachment.cc +@@ -111,17 +111,25 @@ _poppler_attachment_new (FileSpec *emb_file) + attachment->description = _poppler_goo_string_to_utf8 (emb_file->getDescription ()); + + embFile = emb_file->getEmbeddedFile(); +- attachment->size = embFile->size (); ++ if (embFile != NULL && embFile->streamObject()->isStream()) ++ { ++ attachment->size = embFile->size (); + +- if (embFile->createDate ()) +- _poppler_convert_pdf_date_to_gtime (embFile->createDate (), (time_t *)&attachment->ctime); +- if (embFile->modDate ()) +- _poppler_convert_pdf_date_to_gtime (embFile->modDate (), (time_t *)&attachment->mtime); ++ if (embFile->createDate ()) ++ _poppler_convert_pdf_date_to_gtime (embFile->createDate (), (time_t *)&attachment->ctime); ++ if (embFile->modDate ()) ++ _poppler_convert_pdf_date_to_gtime (embFile->modDate (), (time_t *)&attachment->mtime); + +- if (embFile->checksum () && embFile->checksum ()->getLength () > 0) +- attachment->checksum = g_string_new_len (embFile->checksum ()->getCString (), +- embFile->checksum ()->getLength ()); +- priv->obj_stream = embFile->streamObject()->copy(); ++ if (embFile->checksum () && embFile->checksum ()->getLength () > 0) ++ attachment->checksum = g_string_new_len (embFile->checksum ()->getCString (), ++ embFile->checksum ()->getLength ()); ++ priv->obj_stream = embFile->streamObject()->copy(); ++ } ++ else ++ { ++ g_warning ("Missing stream object for embedded file"); ++ g_clear_object (&attachment); ++ } + + return attachment; + } +diff --git a/glib/poppler-document.cc b/glib/poppler-document.cc +index 83f6aea6..ea319344 100644 +--- a/glib/poppler-document.cc ++++ b/glib/poppler-document.cc +@@ -670,7 +670,8 @@ poppler_document_get_attachments (PopplerDocument *document) + attachment = _poppler_attachment_new (emb_file); + delete emb_file; + +- retval = g_list_prepend (retval, attachment); ++ if (attachment != NULL) ++ retval = g_list_prepend (retval, attachment); + } + return g_list_reverse (retval); + } +-- +2.19.1 + diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 062ef02efe..28737c36e4 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -82,6 +82,7 @@ (define-public poppler (package (name "poppler") + (replacement poppler/fixed) (version "0.68.0") (source (origin (method url-fetch) @@ -131,6 +132,14 @@ (license license:gpl2+) (home-page "https://poppler.freedesktop.org/"))) +(define poppler/fixed + (package + (inherit poppler) + (source (origin + (inherit (package-source poppler)) + (patches (append (origin-patches (package-source poppler)) + (search-patches "poppler-CVE-2018-19149.patch"))))))) + (define-public poppler-data (package (name "poppler-data") @@ -162,14 +171,14 @@ When present, Poppler is able to correctly render CJK and Cyrillic text.") license:gpl2)))) (define-public poppler-qt4 - (package (inherit poppler) + (package/inherit poppler (name "poppler-qt4") (inputs `(("qt-4" ,qt-4) ,@(package-inputs poppler))) (synopsis "Qt4 frontend for the Poppler PDF rendering library"))) (define-public poppler-qt5 - (package (inherit poppler) + (package/inherit poppler (name "poppler-qt5") (inputs `(("qtbase" ,qtbase) ,@(package-inputs poppler))) @@ -227,26 +236,23 @@ Poppler PDF rendering library.") (name "libharu") (version "2.3.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/libharu/libharu/archive/" - "RELEASE_" - (string-join (string-split version #\.) "_") - ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/libharu/libharu.git") + (commit (string-append + "RELEASE_" + (string-join (string-split version #\.) "_"))))) + (file-name (git-file-name name version)) (sha256 (base32 - "1lm4v539y9cb1lvbq387j57sy7yxda3yv8b1pk8m6zazbp66i7lg")))) + "15s9hswnl3qqi7yh29jyrg0hma2n99haxznvcywmsp8kjqlyg75q")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list (string-append "--with-zlib=" (assoc-ref %build-inputs "zlib")) (string-append "--with-png=" - (assoc-ref %build-inputs "libpng"))) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'autogen - (lambda _ (invoke "autoreconf" "-vif")))))) + (assoc-ref %build-inputs "libpng"))))) (inputs `(("zlib" ,zlib) ("libpng" ,libpng))) diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm index 466b26c238..a28cb31e5c 100644 --- a/gnu/packages/php.scm +++ b/gnu/packages/php.scm @@ -53,7 +53,7 @@ (define-public php (package (name "php") - (version "7.2.10") + (version "7.2.12") (home-page "https://secure.php.net/") (source (origin (method url-fetch) @@ -61,7 +61,7 @@ name "-" version ".tar.xz")) (sha256 (base32 - "1w0432i5wjga9z8x3rhc72h2ij1jd2aimg5xmhc0hg4f7951bhh1")) + "1qbz2j9kzqxxp0mmx02zavvz20ji7izqdnri25g1mrwyhz60974q")) (modules '((guix build utils))) (snippet '(with-directory-excursion "ext" @@ -176,6 +176,11 @@ (substitute* "ext/standard/tests/streams/bug60602.phpt" (("'ls'") (string-append "'" (which "ls") "'"))) + ;; The expected output is slightly different from what is given, + ;; in a section that's not related to the actual test + (substitute* "sapi/cli/tests/upload_2G.phpt" + (("Test\\\\n") "Test\n\n")) + ;; Drop tests that are known to fail. (for-each delete-file '("ext/posix/tests/posix_getgrgid.phpt" ; Requires /etc/group. diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 41c2a1f7ee..c2f73e3f5c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -14626,3 +14626,22 @@ on regular expressions.") (propagated-inputs `(("python2-enum34" ,python2-enum34) ,@(package-propagated-inputs reparser)))))) + +(define-public python-precis-i18n + (package + (name "python-precis-i18n") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "precis_i18n" version)) + (sha256 + (base32 + "0gjhvwd8aifx94rl1ag08vlmndyx2q3fkyqb0c4i46x3p2bc2yi2")))) + (build-system python-build-system) + (home-page "https://github.com/byllyfish/precis_i18n") + (synopsis "Implementation of the PRECIS framework") + (description + "This module implements the PRECIS Framework as described in RFC 8264, +RFC 8265 and RFC 8266.") + (license license:expat))) diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm index 48dc3cddb9..22ea21dd94 100644 --- a/gnu/packages/rdf.scm +++ b/gnu/packages/rdf.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr> -;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. @@ -22,6 +22,7 @@ #:use-module ((guix licenses) #:select (non-copyleft isc gpl2 lgpl2.1 lgpl2.1+)) #:use-module (guix packages) + #:use-module (guix git-download) #:use-module (guix download) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) @@ -122,13 +123,14 @@ Java Lucene text search engine API to C++.") (name "lrdf") (version "0.6.1") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/swh/LRDF/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/swh/LRDF.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1vxii4mlcpyi16dizcmnqfl2j9gffgr986yd8ic67hvs8xy42yfm")))) + "00wzkfb8y0aqd519ypz067cq099dpc89w69zw8ln39vl6f9x2pd4")))) (build-system gnu-build-system) (arguments '(#:phases @@ -140,9 +142,9 @@ Java Lucene text search engine API to C++.") (("instances_test remove_test") "instances_test") (("\\$\\(TESTS\\) remove_test") "$(TESTS)")) #t)) - (add-after 'remove-out-of-tree-references 'autoreconf - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) + ;; The default bootstrap phase executes autogen.sh, which fails. + (replace 'bootstrap + (lambda _ (invoke "autoreconf" "-vif") #t))))) (inputs `(("raptor" ,raptor2) ("cyrus-sasl" ,cyrus-sasl) diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm index 470643ec4f..b927bbbf9b 100644 --- a/gnu/packages/samba.scm +++ b/gnu/packages/samba.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be> ;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -73,10 +74,6 @@ (arguments `(#:phases (modify-phases %standard-phases - ;; The 6.7 tarball is missing ‘install.sh’. Create it. - (add-after 'unpack 'autoreconf - (lambda _ - (invoke "autoreconf" "-i"))) (add-before 'configure 'set-root-sbin (lambda _ ; Don't try to install in "/sbin". (setenv "ROOTSBINDIR" diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 40b3d1bae0..2df0ce1364 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -99,7 +99,6 @@ arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON.") (license license:bsd-3))) - (define-public msgpack (package (name "msgpack") @@ -132,13 +131,6 @@ such as compact binary encodings, XML, or JSON.") ;; zbuffer.hpp) which #include <zlib.h>. However, 'guix gc --references' ;; does not detect a store reference to zlib since these headers are not ;; compiled. - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoconf - (lambda _ - (invoke "autoreconf" "-vfi") - #t))))) (home-page "https://www.msgpack.org") (synopsis "Binary serialization library") (description "Msgpack is a library for C/C++ that implements binary diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 3e9d797e2c..38eeaa7831 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2015 Jeff Mickey <j@codemac.net> ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2016 Stefan Reichör <stefan@xsteve.at> -;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2017, 2018 Nils Gillmann <ng0@n0.is> ;;; Copyright © 2017, 2018 Leo Famulari <leo@famulari.name> ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> @@ -414,10 +414,7 @@ use of experts and novices alike.") "/rx"))) (delete-file-recursively "rx") (symlink rxpath "rx")) - #t)) - (add-after 'unpack 'autoreconf - (lambda _ - (invoke "autoreconf")))))) + #t))))) (inputs `(("scheme48" ,scheme48) ("scheme48-rx" ,scheme48-rx))) diff --git a/gnu/packages/shellutils.scm b/gnu/packages/shellutils.scm index 3020fdd210..0978300c9b 100644 --- a/gnu/packages/shellutils.scm +++ b/gnu/packages/shellutils.scm @@ -116,9 +116,10 @@ are already there.") '(#:test-target "test" #:make-flags (list (string-append "DESTDIR=" (assoc-ref %outputs "out"))) #:phases (modify-phases %standard-phases (delete 'configure)))) + (inputs + `(("go" ,go-1.9))) (native-inputs - `(("go" ,go) - ("which" ,which))) + `(("which" ,which))) (home-page "https://direnv.net/") (synopsis "Environment switcher for the shell") (description diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm index e708d726bb..fb121a0581 100644 --- a/gnu/packages/spice.scm +++ b/gnu/packages/spice.scm @@ -250,7 +250,7 @@ Internet and from a wide variety of machine architectures.") (add-after 'unpack 'patch-spice-vdagent.desktop (lambda* (#:key outputs #:allow-other-keys) (substitute* "data/spice-vdagent.desktop" - (("Exec=/usr/bin/spice-vdagent\n") + (("Exec=/usr/bin/spice-vdagent") (string-append "Exec=" (assoc-ref outputs "out") "/bin/spice-vdagent"))) #t))))) diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm index f12c6ed1b0..5c954eae35 100644 --- a/gnu/packages/ssh.scm +++ b/gnu/packages/ssh.scm @@ -71,13 +71,7 @@ (source (origin (method git-fetch) (uri (git-reference - ;; git.libssh.org does not support the fast "smart" HTTP - ;; Git protocol. The "dumb" HTTP Git protocol is extremely - ;; slow, and does not support shallow clones, so we use the - ;; plain Git protocol despite its flaws. This offers an - ;; incredible speedup and reduces the size of the the - ;; source by more than half. - (url "git://git.libssh.org/projects/libssh.git") + (url "https://git.libssh.org/projects/libssh.git") (commit (string-append "libssh-" version)))) (patches (search-patches "libssh-hostname-parser-bug.patch")) (sha256 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9bfa4c5683..57fb99ef28 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -115,6 +115,36 @@ can be imported from spreadsheets, text files and database sources and it can be output in text, PostScript, PDF or HTML.") (license license:gpl3+))) +(define-public jags + (package + (name "jags") + (version "4.3.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/" + (version-major version) ".x/Source/" + "JAGS-" version ".tar.gz")) + (sha256 + (base32 + "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica")))) + (build-system gnu-build-system) + (home-page "http://mcmc-jags.sourceforge.net/") + (native-inputs + `(("gfortran" ,gfortran) + ("lapack" ,lapack))) + (synopsis "Gibbs sampler") + (description "JAGS is Just Another Gibbs Sampler. It is a program for +analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) +simulation not wholly unlike BUGS. JAGS was written with three aims in mind: + +@enumerate +@item To have a cross-platform engine for the BUGS language; +@item To be extensible, allowing users to write their own functions, + distributions and samplers; +@item To be a platform for experimentation with ideas in Bayesian modelling. +@end enumerate\n") + (license license:gpl2))) + ;; Update this package together with the set of recommended packages: r-boot, ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice, ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival. @@ -1620,13 +1650,13 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "0.7.7") + (version "0.7.8") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "196lwck3i3m25jnn1f1nrda9svnjqqi89s0is79gbrphamddnlq5")))) + "06p59nhli8c1sarghzxq0y4pk6lyyz3xwkarp55b252dfg2rly9p")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -2528,13 +2558,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.9.100.5.0") + (version "0.9.200.4.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1iyjqhfjip1nxrkllzh7r1m01jjnx7cahqkf3s557w34p987f2l1")))) + "1ayvpyi4hgaqrhx1kqi640iillc2byj4kam7vydlgqmdrzpgrfvz")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (native-inputs @@ -3268,14 +3298,14 @@ the way current RNG settings can be changed.") (define-public r-rtsne (package (name "r-rtsne") - (version "0.13") + (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "Rtsne" version)) (sha256 (base32 - "17crbdi80q4g2pwp9v7j3bdaznk96qlrqx01zvj3wwqippizyfqw")))) + "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn")))) (properties `((upstream-name . "Rtsne"))) (build-system r-build-system) (propagated-inputs @@ -5123,14 +5153,14 @@ algorithms.") (define-public r-lme4 (package (name "r-lme4") - (version "1.1-18-1") + (version "1.1-19") (source (origin (method url-fetch) (uri (cran-uri "lme4" version)) (sha256 (base32 - "01ar4fak8zj7c1vmh9m576wchxj5qzpfqn637s7fh3fl6cpz0alq")))) + "0j8xhkkcdv45ilab960s9jrcjk6jbzvd7w7myswv5fmalrpq52pf")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp) @@ -5325,14 +5355,14 @@ first and second order derivatives.") (define-public r-sn (package (name "r-sn") - (version "1.5-2") + (version "1.5-3") (source (origin (method url-fetch) (uri (cran-uri "sn" version)) (sha256 (base32 - "16gwr68zzj5v83bqfmzxnzwig3dnjrkxdhs6clri1caqkvrq6aig")))) + "10via4lg0vx9pzq350vwhz5wv1dhzxr2l3r6jq99nk37vmyvj8fc")))) (build-system r-build-system) (propagated-inputs `(("r-mnormt" ,r-mnormt) diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index 5d681b816e..c29c88a588 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -900,7 +900,16 @@ the current goroutine's ID.") "0bg26pfg25vr16jmczig2m493mja2nxjxyswz3hha7avxw20rpi5")))) (build-system go-build-system) (arguments - '(#:import-path "github.com/AudriusButkevicius/cli")) + '(#:import-path "github.com/AudriusButkevicius/cli" + ;; Tests don't pass "vet" on go-1.11. See + ;; https://github.com/AudriusButkevicius/cli/pull/1. + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key import-path #:allow-other-keys) + (invoke "go" "test" + "-vet=off" + import-path)))))) (synopsis "Library for building command-line interfaces in Go") (description "This package provides a library for building command-line interfaces in Go.") @@ -1097,7 +1106,14 @@ message streaming.") (string-append (assoc-ref outputs "out") "/src/github.com/prometheus/common/expfmt/testdata/") ".*\\.gz$")) - #t))))) + #t)) + (replace 'check + ;; Tests don't pass "vet" on go-1.11. See + ;; https://github.com/syncthing/syncthing/issues/5311. + (lambda* (#:key import-path #:allow-other-keys) + (invoke "go" "test" + "-vet=off" + import-path)))))) (propagated-inputs `(("go-github-com-golang-protobuf-proto" ,go-github-com-golang-protobuf-proto) @@ -1251,7 +1267,16 @@ Prometheus HTTP API.") "1y8bvzbxpw0lfnn7pbcdwzqj4l90qj6xf88dvv9pxd9yl5g6cskx")))) (build-system go-build-system) (arguments - '(#:import-path "gopkg.in/asn1-ber.v1")) + '(#:import-path "gopkg.in/asn1-ber.v1" + ;; Tests don't pass "vet" on go-1.11. See + ;; https://github.com/go-asn1-ber/asn1-ber/issues/20. + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key import-path #:allow-other-keys) + (invoke "go" "test" + "-vet=off" + import-path)))))) (synopsis "ASN.1 BER encoding and decoding in Go") (description "This package provides ASN.1 BER encoding and decoding in the Go language.") diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm index 05916cde5c..63709935c3 100644 --- a/gnu/packages/telephony.scm +++ b/gnu/packages/telephony.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org> ;;; Copyright © 2016 Francesco Frassinelli <fraph24@gmail.com> ;;; Copyright © 2016, 2017 Nils Gillmann <ng0@n0.is> -;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Jovany Leandro G.C <bit4bit@riseup.net> ;;; @@ -295,26 +295,19 @@ protocol (RFC 3550).") (version (string-append "0.0.0-1." (string-take commit 7))) (source (origin - (method url-fetch) - (uri - (string-append - "https://gitlab.savoirfairelinux.com/sflphone/libiax2/" - "repository/archive.tar.gz?ref=" - commit)) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://gitlab.savoirfairelinux.com/sflphone/libiax2.git") + (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 - "0cj5293bixp3k5x3hjwyd0iq7z8w5p7yavxvvkqk5817hjq386y2")))) + "0d269474kk1933c55hx4azw3sak5ycfrxkw6ida0sb2cm00kfich")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("libtool" ,libtool))) - (arguments - `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'autoconf - (lambda _ - (invoke "autoreconf" "-vfi")))))) (home-page "https://gitlab.savoirfairelinux.com/sflphone/libiax2") (synopsis "Inter-Asterisk-Protocol library") (description "LibIAX2 implements the Inter-Asterisk-Protocol for relaying diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index 084017dbde..e9a4ab3d68 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> -;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Jelle Licht <jlicht@fsfe.org> @@ -15,6 +15,7 @@ ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz> +;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -197,11 +198,6 @@ encoding, supporting Unicode version 9.0.0.") (sha256 (base32 "0jiybkb2z58wa2msvllnphr4js2hvjvh988pavb3mzkgr6ihwbkr")))) (build-system gnu-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoreconf - (lambda _ (zero? (system* "autoreconf" "-vif"))))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -572,22 +568,16 @@ categories.") (name "dotconf") (version "1.3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/williamh/dotconf/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/williamh/dotconf.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0lsnh0yaw44psmx59hq94cj1932gscp5h8d3cnh05l0svr0cy7kz")))) + "1sc95hw5k2xagpafny0v35filmcn05k1ds5ghkldfpf6xw4hakp7")))) (build-system gnu-build-system) - (arguments - `(#:tests? #f ; FIXME maketest.sh does not work. - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoreconf - (lambda _ - (zero? (system* "autoreconf" "-vif"))))))) + (arguments `(#:tests? #f)) ; FIXME maketest.sh does not work. (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -756,3 +746,26 @@ indentation. @end itemize\n") (home-page "http://docx2txt.sourceforge.net") (license license:gpl3+))) + +(define-public opencc + (package + (name "opencc") + (version "1.0.5") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/BYVoid/OpenCC" + "/archive/ver." version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "01870gbkf711msirf3206k0ajaabypjhnx3fny5wikw0ladn9q8w")))) + (build-system cmake-build-system) + (native-inputs + `(("python" ,python-wrapper))) + (home-page "https://github.com/BYVoid/OpenCC") + (synopsis "Convert between Traditional Chinese and Simplified Chinese") + (description "Open Chinese Convert (OpenCC) converts between Traditional +Chinese and Simplified Chinese, supporting character-level conversion, +phrase-level conversion, variant conversion, and regional idioms among +Mainland China, Taiwan, and Hong-Kong.") + (license license:asl2.0))) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index d9fc601066..48dceaec33 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -522,13 +522,13 @@ netcat implementation that supports TLS.") (package (name "python-acme") ;; Remember to update the hash of certbot when updating python-acme. - (version "0.27.1") + (version "0.28.0") (source (origin (method url-fetch) (uri (pypi-uri "acme" version)) (sha256 (base32 - "142gynlfx7yv0sdba3gpdxlnhg9chhz7hpdxdrp630z17h1bk9ri")))) + "11dvcbdifn5d02p4k5li8r6r39bl3p5ap9p3zjwvasm24hf2yz5z")))) (build-system python-build-system) (arguments `(#:phases @@ -579,7 +579,7 @@ netcat implementation that supports TLS.") (uri (pypi-uri name version)) (sha256 (base32 - "0anh3vjy9sif1bkp25nj76ii37xx8hh0igcx60ppag12xlabsw1m")))) + "02h959qkq7z0s13ivgf7jyl3gnc55wcck6n546k0kh155bpf5qri")))) (build-system python-build-system) (arguments `(,@(substitute-keyword-arguments (package-arguments python-acme) diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 61b0c82e30..e28a6d4f48 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com> +;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -140,14 +141,6 @@ rejects UDP traffic from the application you're using.") #:configure-flags (list (string-append "--sysconfdir=" (assoc-ref %outputs "out") "/etc/privoxy")) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'autoconf - (lambda _ - ;; Unfortunately, this is not a tarball produced by - ;; "make dist". - (invoke "autoreconf" "-vfi") - #t))) #:tests? #f)) (inputs `(("w3m" ,w3m) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index a482ef2515..94c5cf3a67 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1269,7 +1269,7 @@ access to mpv's powerful playback capabilities.") (define-public youtube-dl (package (name "youtube-dl") - (version "2018.11.03") + (version "2018.11.07") (source (origin (method url-fetch) (uri (string-append "https://yt-dl.org/downloads/" @@ -1277,7 +1277,7 @@ access to mpv's powerful playback capabilities.") version ".tar.gz")) (sha256 (base32 - "11phhwhr1g050h4625d5jsgcsjnnv7jc6xcrbn7zdzd32f6gy2lj")))) + "1rvc2m2kbm2kycqsa7fkcg5gql9f0w3hn1a7jg48zzl06ayggxk9")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index c6906b12cf..c974ebc439 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -718,7 +718,7 @@ refactor Vim in order to: (define-public vifm (package (name "vifm") - (version "0.9.1") + (version "0.10") (source (origin (method url-fetch) @@ -729,7 +729,7 @@ refactor Vim in order to: "vifm-" version ".tar.bz2"))) (sha256 (base32 - "1cz7vjjmghgdxd1lvsdwv85gvx4kz8idq14qijpwkpfrf2va9f98")))) + "1f380xcyjnm4xmcdazs6dj064bwddhywvn3mgm36k7r7b2gnjnp0")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--disable-build-timestamp") diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 3732f26eba..d56b82ce48 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6761,14 +6761,14 @@ compressed JSON header blocks. (srfi srfi-26) (ice-9 popen) (ice-9 rdelim)) - #:phases (modify-phases %standard-phases - (add-before 'configure 'autoconf + (add-before 'configure 'set-variables (lambda _ + ;; This prevents a few warnings (setenv "GUILE_AUTO_COMPILE" "0") (setenv "XDG_CACHE_HOME" (getcwd)) - (invoke "autoreconf" "-vif"))) + #t)) (add-after 'install 'wrap-program (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index d1890c8b32..82f03c7f94 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016, 2017, 2018 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz> ;;; ;;; This file is part of GNU Guix. ;;; @@ -31,6 +32,7 @@ #:use-module (gnu packages base) #:use-module (gnu packages bison) #:use-module (gnu packages databases) + #:use-module (gnu packages docbook) #:use-module (gnu packages enchant) #:use-module (gnu packages flex) #:use-module (gnu packages gcc) @@ -66,11 +68,13 @@ (base32 "147r7an41920zl4x9srdva7fxvw2znjin5ldjkhay1cndv9gih0m")))) (build-system cmake-build-system) + (outputs '("out" "doc")) (arguments '(#:tests? #f ; no tests #:build-type "Release" ; turn off debugging symbols to save space #:configure-flags (list "-DPORT=GTK" + "-DENABLE_GTKDOC=ON" ; No doc by default (string-append ; uses lib64 by default "-DLIB_INSTALL_DIR=" (assoc-ref %outputs "out") "/lib") @@ -87,7 +91,26 @@ ;; XXX Disable WOFF2 ‘web fonts’. These were never ;; supported in our previous builds. Enabling them ;; requires building libwoff2 and possibly woff2dec. - "-DUSE_WOFF2=OFF"))) + "-DUSE_WOFF2=OFF") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-gtk-doc-scan + (lambda* (#:key inputs #:allow-other-keys) + (for-each (lambda (file) + (substitute* file + (("http://www.oasis-open.org/docbook/xml/4.1.2/docbookx.dtd") + (string-append (assoc-ref inputs "docbook-xml") + "/xml/dtd/docbook/docbookx.dtd")))) + (find-files "Source" "\\.sgml$")) + #t)) + (add-after 'install 'move-doc-files + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (doc (assoc-ref outputs "doc"))) + (mkdir-p (string-append doc "/share")) + (rename-file (string-append out "/share/gtk-doc") + (string-append doc "/share/gtk-doc")) + #t)))))) (native-inputs `(("bison" ,bison) ("gettext" ,gettext-minimal) @@ -97,6 +120,8 @@ ("perl" ,perl) ("pkg-config" ,pkg-config) ("python" ,python-2) ; incompatible with Python 3 (print syntax) + ("gtk-doc" ,gtk-doc) ; For documentation generation + ("docbook-xml" ,docbook-xml) ; For documentation generation ("ruby" ,ruby))) (propagated-inputs `(("gtk+" ,gtk+) @@ -155,12 +180,13 @@ HTML/CSS applications to full-fledged web browsers.") `(("gcc" ,gcc-7) ; webkitgtk-2.22 requires gcc-6 or newer ,@(package-native-inputs webkitgtk))) (arguments - `(#:phases (modify-phases %standard-phases - (add-before 'configure 'work-around-gcc-7-include-path-issue - ;; FIXME: Work around a problem with gcc-7 includes (see - ;; <https://bugs.gnu.org/30756>). - (lambda _ - (unsetenv "C_INCLUDE_PATH") - (unsetenv "CPLUS_INCLUDE_PATH") - #t))) - ,@(package-arguments webkitgtk))))) + (substitute-keyword-arguments (package-arguments webkitgtk) + ((#:phases phases) + `(modify-phases ,phases + (add-before 'configure 'work-around-gcc-7-include-path-issue + ;; FIXME: Work around a problem with gcc-7 includes (see + ;; <https://bugs.gnu.org/30756>). + (lambda _ + (unsetenv "C_INCLUDE_PATH") + (unsetenv "CPLUS_INCLUDE_PATH") + #t)))))))) diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm index 60b2a81de8..85c71b5abb 100644 --- a/gnu/packages/wine.scm +++ b/gnu/packages/wine.scm @@ -225,7 +225,7 @@ integrate Windows applications into your desktop.") (define-public wine-staging-patchset-data (package (name "wine-staging-patchset-data") - (version "3.19") + (version "3.20") (source (origin (method git-fetch) @@ -235,7 +235,7 @@ integrate Windows applications into your desktop.") (file-name (git-file-name name version)) (sha256 (base32 - "0nmlhc6jamz0zb4b1w165l8j1a1b0j5ad1sv06aasc9jy8s12b22")))) + "049cwllf4aybrhj4l2i3vd5jvagjz4d448404zkyy0lfxr08id3p")))) (build-system trivial-build-system) (native-inputs `(("bash" ,bash) @@ -281,7 +281,7 @@ integrate Windows applications into your desktop.") (file-name (string-append name "-" version ".tar.xz")) (sha256 (base32 - "0slwgbxclx2dx0glj8az3mv0bqxmx119v9s0jvg1b5zhmqkcc8gg")))) + "063garmflbna3mhph8k0dv0bkzq8x75x5xrd0j8y0mjh10i13mik")))) (inputs `(("autoconf" ,autoconf) ; for autoreconf ("gtk+" ,gtk+) ("libva" ,libva) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 79e3b47684..f2338783d2 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -10,7 +10,7 @@ ;;; Copyright © 2015 xd1le <elisp.vim@gmail.com> ;;; Copyright © 2015 Florian Paul Schmidt <mista.tapas@gmx.net> ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org> -;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2016, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Leo Famulari <leo@famulari.name> ;;; Copyright © 2016 Alex Kost <alezost@gmail.com> @@ -1338,15 +1338,11 @@ invert colors on a specific display/screen.") (build-system gnu-build-system) (arguments '(#:configure-flags `("--enable-sound" "--enable-wave" - "--enable-alsa") - #:phases (modify-phases %standard-phases - (add-before 'configure 'autoreconf - (lambda _ - (invoke "autoreconf" "-vfi")))))) - (native-inputs `(("autoconf" ,autoconf) - ("automake" ,automake) - ("pkg-config" ,pkg-config) - ("perl" ,perl))) + "--enable-alsa"))) + (native-inputs `(("autoconf" ,autoconf) + ("automake" ,automake) + ("pkg-config" ,pkg-config) + ("perl" ,perl))) (inputs `(("libx11" ,libx11) ("alsa-lib" ,alsa-lib))) (synopsis "Daemon that performs an action every time the X11 bell is rung") diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index d3e68c4c07..5adb04a86a 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -3174,14 +3174,14 @@ This driver is intended for the spice qxl virtio device.") (define-public xf86-video-r128 (package (name "xf86-video-r128") - (version "6.11.0") + (version "6.12.0") (source (origin (method url-fetch) (uri (string-append "mirror://xorg/individual/driver/" name "-" version ".tar.bz2")) (sha256 (base32 - "0snvwmrh8dqyyaq7ggicym6yrsg4brygkx9156r0m095m7fp3rav")))) + "0mz0v5mqmmbncr2drd5zvia1fb7frz2xqwflhhqbnaxx5j48c740")))) (build-system gnu-build-system) (inputs `(("mesa" ,mesa) ("xorgproto" ,xorgproto) diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 3409bd352c..228d3c5926 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -1252,18 +1252,57 @@ the tty to run, among other things." (string-concatenate (map cache->config caches))))))) +(define (nscd-action-procedure nscd config option) + ;; XXX: This is duplicated from mcron; factorize. + #~(lambda (_ . args) + ;; Run 'nscd' in a pipe so we can explicitly redirect its output to + ;; 'current-output-port', which at this stage is bound to the client + ;; connection. + (let ((pipe (apply open-pipe* OPEN_READ #$nscd + "-f" #$config #$option args))) + (let loop () + (match (read-line pipe 'concat) + ((? eof-object?) + (catch 'system-error + (lambda () + (zero? (close-pipe pipe))) + (lambda args + ;; There's a race with the SIGCHLD handler, which could + ;; call 'waitpid' before 'close-pipe' above does. If we + ;; get ECHILD, that means we lost the race, but that's + ;; fine. + (or (= ECHILD (system-error-errno args)) + (apply throw args))))) + (line + (display line) + (loop))))))) + +(define (nscd-actions nscd config) + "Return Shepherd actions for NSCD." + ;; Make this functionality available as actions because that's a simple way + ;; to run the right 'nscd' binary with the right config file. + (list (shepherd-action + (name 'statistics) + (documentation "Display statistics about nscd usage.") + (procedure (nscd-action-procedure nscd config "--statistics"))) + (shepherd-action + (name 'invalidate) + (documentation + "Invalidate the given cache--e.g., 'hosts' for host name lookups.") + (procedure (nscd-action-procedure nscd config "--invalidate"))))) + (define (nscd-shepherd-service config) "Return a shepherd service for CONFIG, an <nscd-configuration> object." - (let ((nscd.conf (nscd.conf-file config)) + (let ((nscd (file-append (nscd-configuration-glibc config) + "/sbin/nscd")) + (nscd.conf (nscd.conf-file config)) (name-services (nscd-configuration-name-services config))) (list (shepherd-service (documentation "Run libc's name service cache daemon (nscd).") (provision '(nscd)) (requirement '(user-processes)) (start #~(make-forkexec-constructor - (list #$(file-append (nscd-configuration-glibc config) - "/sbin/nscd") - "-f" #$nscd.conf "--foreground") + (list #$nscd "-f" #$nscd.conf "--foreground") ;; Wait for the PID file. However, the PID file is ;; written before nscd is actually listening on its @@ -1277,7 +1316,12 @@ the tty to run, among other things." (string-append dir "/lib")) (list #$@name-services)) ":"))))) - (stop #~(make-kill-destructor)))))) + (stop #~(make-kill-destructor)) + (modules `((ice-9 popen) ;for the actions + (ice-9 rdelim) + (ice-9 match) + ,@%default-modules)) + (actions (nscd-actions nscd nscd.conf)))))) (define nscd-activation ;; Actions to take before starting nscd. diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm index 573efa0433..fcaedd038b 100644 --- a/gnu/services/mail.scm +++ b/gnu/services/mail.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Andy Wingo <wingo@igalia.com> -;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org> +;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org> ;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au> ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> ;;; @@ -290,11 +290,21 @@ the section name.") "Listeners for the service. A listener is either an @code{unix-listener-configuration}, a @code{fifo-listener-configuration}, or an @code{inet-listener-configuration}.") + (client-limit + (non-negative-integer 0) + "Maximum number of simultaneous client connections per process. Once this +number of connections is received, the next incoming connection will prompt +Dovecot to spawn another process. If set to 0, @code{default-client-limit} is +used instead.") (service-count (non-negative-integer 1) "Number of connections to handle before starting a new process. Typically the only useful values are 0 (unlimited) or 1. 1 is more secure, but 0 is faster. <doc/wiki/LoginProcess.txt>.") + (process-limit + (non-negative-integer 0) + "Maximum number of processes that can exist for this service. If set to 0, +@code{default-process-limit} is used instead.") (process-min-avail (non-negative-integer 0) "Number of processes to always keep waiting for more connections.") @@ -475,6 +485,8 @@ complex, customize the address and port fields of the (list (service-configuration (kind "imap-login") + (client-limit 0) + (process-limit 0) (listeners (list (inet-listener-configuration (protocol "imap") (port 143) (ssl? #f)) @@ -487,24 +499,33 @@ complex, customize the address and port fields of the (inet-listener-configuration (protocol "pop3s") (port 995) (ssl? #t))))) (service-configuration (kind "lmtp") + (client-limit 1) + (process-limit 0) (listeners (list (unix-listener-configuration (path "lmtp") (mode "0666"))))) - (service-configuration (kind "imap")) - (service-configuration (kind "pop3")) - (service-configuration (kind "auth") - ;; In what could be taken to be a bug, the default value of 1 for - ;; service-count makes it so that a PAM auth worker can't fork off - ;; subprocesses for making blocking queries. The result is that nobody - ;; can log in -- very secure, but not very useful! If we simply omit - ;; the service-count, it will default to the value of - ;; auth-worker-max-count, which is 30, instead of defaulting to 1, which - ;; is the default for all other services. As a hack, bump this value to - ;; 30. - (service-count 30) + (service-configuration + (kind "imap") + (client-limit 1) + (process-limit 1024)) + (service-configuration + (kind "pop3") + (client-limit 1) + (process-limit 1024)) + (service-configuration + (kind "auth") + (service-count 0) + (client-limit 0) + (process-limit 1) (listeners (list (unix-listener-configuration (path "auth-userdb"))))) - (service-configuration (kind "auth-worker")) - (service-configuration (kind "dict") + (service-configuration + (kind "auth-worker") + (client-limit 1) + (process-limit 0)) + (service-configuration + (kind "dict") + (client-limit 1) + (process-limit 0) (listeners (list (unix-listener-configuration (path "dict"))))))) "List of services to enable. Available services include @samp{imap}, @samp{imap-login}, @samp{pop3}, @samp{pop3-login}, @samp{auth}, and diff --git a/gnu/services/mcron.scm b/gnu/services/mcron.scm index 5757bf8cf6..120b663e3e 100644 --- a/gnu/services/mcron.scm +++ b/gnu/services/mcron.scm @@ -86,7 +86,7 @@ files." (lambda () (zero? (close-pipe pipe))) (lambda args - ;; There's with race between the SIGCHLD handler, which + ;; There's a race with the SIGCHLD handler, which ;; could call 'waitpid' before 'close-pipe' above does. If ;; we get ECHILD, that means we lost the race, but that's ;; fine. diff --git a/gnu/tests/base.scm b/gnu/tests/base.scm index 896d4a8f88..02882f4b46 100644 --- a/gnu/tests/base.scm +++ b/gnu/tests/base.scm @@ -335,6 +335,20 @@ info --version") (x (pk 'failure x #f)))) + (test-equal "nscd invalidate action" + '(#t) ;one value, #t + (marionette-eval '(with-shepherd-action 'nscd ('invalidate "hosts") + result + result) + marionette)) + + (test-equal "nscd invalidate action, wrong table" + '(#f) ;one value, #f + (marionette-eval '(with-shepherd-action 'nscd ('invalidate "xyz") + result + result) + marionette)) + (test-equal "host not found" #f (marionette-eval |