From 4bed3b101253e5f82c6423f0eb55b307ec839f53 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 5 Jun 2019 19:37:00 +0200 Subject: [PATCH 001/224] gnu: mesa: Disable failing test on i686. * gnu/packages/gl.scm (mesa)[arguments]: Add phase when building for i686. --- gnu/packages/gl.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm index cfa392191a..3680a8979d 100644 --- a/gnu/packages/gl.scm +++ b/gnu/packages/gl.scm @@ -328,6 +328,15 @@ also known as DXTn or DXTC) for Mesa.") (substitute* "src/intel/genxml/gen_pack_header.py" (("/usr/bin/env python2") (which "python"))) #t)) + ,@(if (string-prefix? "i686" (%current-system)) + ;; Disable new test from Mesa 19 that fails on i686. Upstream + ;; report: . + `((add-after 'unpack 'disable-failing-test + (lambda _ + (substitute* "src/gallium/tests/unit/meson.build" + (("'u_format_test',") "")) + #t))) + '()) (add-before 'configure 'fix-dlopen-libnames (lambda* (#:key inputs outputs #:allow-other-keys) From 2916deb91bd7ea3e76ff9693a283c244e3ffd0be Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Wed, 12 Jun 2019 17:49:23 +0100 Subject: [PATCH 002/224] gnu: perl-io-socket-ssl: Update to 2.066. The previous version failed to build, but this updated version does build successfully. * gnu/packages/web.scm (perl-io-socket-ssl): Update to 2.066. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 27fe0f6942..d022c6be46 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3083,14 +3083,14 @@ and IPv6 sockets, intended as a replacement for IO::Socket::INET.") (define-public perl-io-socket-ssl (package (name "perl-io-socket-ssl") - (version "2.038") + (version "2.066") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/S/SU/SULLR/" "IO-Socket-SSL-" version ".tar.gz")) (sha256 (base32 - "11fiifxyvn7njc9p52wgygyw24jz7rh7gnz2ikjphr4l4x9f03rx")) + "1kgbws7dwp2hh16qid7169dfkhmcwg7dz9ffbm6k0id5h53hciqd")) (patches (search-patches "perl-io-socket-ssl-openssl-1.0.2f-fix.patch")))) (build-system perl-build-system) From 3745909dc9f810844d169e5e2089707df8174462 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 2 Jun 2019 01:03:08 +0200 Subject: [PATCH 003/224] gnu: Add ri-li. * gnu/packages/games.scm (ri-li): New variable. * gnu/packages/patches/ri-li-modernize_cpp.patch: New file. * gnu/local.mk (dist_patch_DATA): Reference patch. --- gnu/local.mk | 1 + gnu/packages/games.scm | 70 ++++ .../patches/ri-li-modernize_cpp.patch | 391 ++++++++++++++++++ 3 files changed, 462 insertions(+) create mode 100644 gnu/packages/patches/ri-li-modernize_cpp.patch diff --git a/gnu/local.mk b/gnu/local.mk index 7f3fcae07e..81de156cf2 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1239,6 +1239,7 @@ dist_patch_DATA = \ %D%/packages/patches/readline-6.2-CVE-2014-2524.patch \ %D%/packages/patches/red-eclipse-remove-gamma-name-hack.patch \ %D%/packages/patches/reposurgeon-add-missing-docbook-files.patch \ + %D%/packages/patches/ri-li-modernize_cpp.patch \ %D%/packages/patches/ripperx-missing-file.patch \ %D%/packages/patches/rpcbind-CVE-2017-8779.patch \ %D%/packages/patches/rtags-separate-rct.patch \ diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 7a433a0bfd..86bdf99a32 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -7385,3 +7385,73 @@ full of enemies that can hurt it, obstacles and food to be eaten. The goal of the game is to stay alive and collect prizes. The robot program conveniently may be written in a plain text file in the Scheme programming language.") (license license:gpl3+))) + +(define-public ri-li + (package + (name "ri-li") + (version "2.0.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/ri-li/" + "Ri-li%20Linux_Unix/Ri-li%20V" version "/" + "Ri-li-" version ".tar.bz2")) + (sha256 + (base32 + "1gcdsgnnbbn1mb1hkpwniv3fhkaj1nn8gq33v5c16q3wqchcq77p")) + ;; Taken from + ;; . + ;; It doesn't build otherwise. + (patches (search-patches "ri-li-modernize_cpp.patch")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; Remove "gentoo" subdirectory from Makefile, as it is + ;; missing a make file and generates a build failure. + (add-after 'configure 'fix-build + (lambda _ + (substitute* "Makefile" + ((" gentoo") "")) + #t)) + (add-after 'install 'install-desktop-file + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (apps (string-append out "/share/applications")) + (pixmaps (string-append out "/share/pixmaps"))) + (for-each (lambda (f) (install-file f pixmaps)) + (find-files "data" "\\.(png|ico)$")) + (mkdir-p apps) + (with-output-to-file (string-append apps "/ri-li.desktop") + (lambda _ + (format #t + "[Desktop Entry]~@ + Name=Ri-li~@ + Exec=~a/bin/Ri_li~@ + Icon=~a/Ri-li-icon-32x32.png~@ + Categories=Game;ArcadeGame;~@ + Keywords=toy;train;wooden;snake-like;engine;~@ + Comment=a toy simulator game~@ + Comment[de]=Ein Spiel mit einem kleinen Zug~@ + Comment[fr]=un jeu de petit train~@ + Comment[ro_RO]=un joc cu un tren de jucărie~@ + Terminal=false~@ + Type=Application~%" + out pixmaps)))) + #t)) + (add-after 'install-desktop-file 'remove-spurious-files + ;; Delete redundant files already installed somewhere else. + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each delete-file + (find-files (string-append out "/share/Ri-li") + "\\.(png|ico)|COPYING")) + #t)))))) + (inputs + `(("sdl" ,(sdl-union (list sdl sdl-mixer))))) + (home-page "http://www.ri-li.org") + (synopsis "Toy train simulation game") + (description "Ri-li is a game in which you drive a wooden toy +steam locomotive across many levels and collect all the coaches to +win.") + ;; The project is dual-licensed GPL2+ and GPL3+. + (license (list license:gpl2+ license:gpl3+)))) diff --git a/gnu/packages/patches/ri-li-modernize_cpp.patch b/gnu/packages/patches/ri-li-modernize_cpp.patch new file mode 100644 index 0000000000..3d076afb39 --- /dev/null +++ b/gnu/packages/patches/ri-li-modernize_cpp.patch @@ -0,0 +1,391 @@ +diff -r -u Ri-li-2.0.1.orig/src/audio.cc Ri-li-2.0.1/src/audio.cc +--- Ri-li-2.0.1.orig/src/audio.cc 2012-01-22 00:40:56.928609371 -0800 ++++ Ri-li-2.0.1/src/audio.cc 2012-01-22 00:28:33.360636539 -0800 +@@ -22,8 +22,8 @@ + // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + + #include +-#include +-#include ++#include ++#include + + #include "audio.h" + #include "utils.h" +@@ -57,7 +57,7 @@ + char PathFile[512]; + + if(Mix_OpenAudio(22050,AUDIO_S16,1,1024)) { +- cerr <<"Enable to init Sound card ! "< ++#include + #include + #include + #include +diff -r -u Ri-li-2.0.1.orig/src/editeur.cc Ri-li-2.0.1/src/editeur.cc +--- Ri-li-2.0.1.orig/src/editeur.cc 2007-11-02 04:48:17.000000000 -0700 ++++ Ri-li-2.0.1/src/editeur.cc 2012-01-22 00:28:59.632635579 -0800 +@@ -25,10 +25,10 @@ + #include + #endif + +-#include ++#include + #include + #include +-#include ++#include + #include + #include + +@@ -374,7 +374,7 @@ + + // Sauve le niveau + if(Niveau.Save()==false) { +- cerr <<"ERREUR Saving levels!"< + #endif + +-#include ++#include + #include + #include +-#include ++#include + #include + #include + +diff -r -u Ri-li-2.0.1.orig/src/loco.cc Ri-li-2.0.1/src/loco.cc +--- Ri-li-2.0.1.orig/src/loco.cc 2007-11-02 04:48:18.000000000 -0700 ++++ Ri-li-2.0.1/src/loco.cc 2012-01-22 00:14:17.878797797 -0800 +@@ -21,10 +21,10 @@ + // with this program; if not, write to the Free Software Foundation, Inc., + // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +-#include ++#include + #include + #include +-#include ++#include + #include + #include "preference.h" + #include "loco.h" +diff -r -u Ri-li-2.0.1.orig/src/main.cc Ri-li-2.0.1/src/main.cc +--- Ri-li-2.0.1.orig/src/main.cc 2007-11-02 04:48:19.000000000 -0700 ++++ Ri-li-2.0.1/src/main.cc 2012-01-22 00:29:40.080634136 -0800 +@@ -23,8 +23,8 @@ + + #include + #include +-#include +-#include ++#include ++#include + #include + #include + +@@ -115,7 +115,7 @@ + + // Initilise SDL + if( SDL_Init(SDL_INIT_VIDEO|SDL_INIT_TIMER|SDL_INIT_AUDIO|SDL_INIT_NOPARACHUTE) < 0 ) { +- cerr <<"Impossible d'initialiser SDL:"<vfmt->BitsPerPixel==8) { +- cerr <<"Impossible d'utiliser 8bits pour la vidéo !"<vfmt->BitsPerPixel,vOption); + + if(sdlVideo==NULL) { +- cerr <<"Impossible de passer dans le mode vidéo 800x600 !"< ++#include + #include + #include +-#include ++#include + #include "preference.h" + #include "menu.h" + #include "sprite.h" +@@ -92,7 +92,7 @@ + // Teste la resolution video + sdlVideoInfo=(SDL_VideoInfo*)SDL_GetVideoInfo(); + if(sdlVideoInfo->vfmt->BitsPerPixel==8) { +- cerr <<"Impossible d'utiliser 8bits pour la vidéo !"<vfmt->BitsPerPixel,vOption); + if(sdlVideo==NULL) { +- cerr <<"Impossible de passer dans le mode vidéo 800x600 !"< ++#include + #include + #include "mouse.h" + #include "preference.h" +diff -r -u Ri-li-2.0.1.orig/src/sprite.cc Ri-li-2.0.1/src/sprite.cc +--- Ri-li-2.0.1.orig/src/sprite.cc 2007-11-02 04:48:20.000000000 -0700 ++++ Ri-li-2.0.1/src/sprite.cc 2012-01-22 00:30:43.640631779 -0800 +@@ -21,10 +21,10 @@ + // with this program; if not, write to the Free Software Foundation, Inc., + // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +-#include ++#include + #include + #include +-#include ++#include + #include + #include "sprite.h" + #include "preference.h" +@@ -84,7 +84,7 @@ + strcpy(PathFile,Langue[Pref.Langue]); + GetPath(PathFile); + if(FileExiste(PathFile)==false) { +- cerr <<"Impossible de trouver "< ++#include + #include + #include + #include "preference.h" +diff -r -u Ri-li-2.0.1.orig/src/utils.cc Ri-li-2.0.1/src/utils.cc +--- Ri-li-2.0.1.orig/src/utils.cc 2007-11-02 04:48:22.000000000 -0700 ++++ Ri-li-2.0.1/src/utils.cc 2012-01-22 00:31:30.944630051 -0800 +@@ -21,10 +21,10 @@ + // with this program; if not, write to the Free Software Foundation, Inc., + // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +-#include ++#include + #include + #include +-#include ++#include + + #ifdef WINDOWS + #include +@@ -77,7 +77,7 @@ + + file=fopen(Path,"r"); + if(!file) { +- cerr <<"ERREUR: Impossible d'ouvrir '"<1024) { + AfficheChargeur(); + if( fread(Po,1,1024,file) != 1024 ) { +- cerr <<"ERREUR de lecture du fichier '"<512) { + if( fwrite(Buf,1,512,file) != 512 ) { +- cerr <<"ERREUR d'ecriture du fichier '"<0) { + if( fwrite(Buf,1,(size_t)L,file) != (size_t)L ) { +- cerr <<"ERREUR d'ecriture du fichier '"< Date: Thu, 13 Jun 2019 14:08:32 +0200 Subject: [PATCH 004/224] gnu: gstreamer: Skip failing test on 32-bit systems. * gnu/packages/gstreamer.scm (gstreamer)[arguments]: When building for a 32-bit system, add #:phases. --- gnu/packages/gstreamer.scm | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index d5d14152fb..2a818e078c 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2016, 2018 Leo Famulari ;;; Copyright © 2017 Ricardo Wurmus ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2019 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -118,7 +119,19 @@ arrays of data.") `(#:configure-flags (list (string-append "--with-html-dir=" (assoc-ref %outputs "doc") - "/share/gtk-doc/html")))) + "/share/gtk-doc/html")) + + ,@(if (not (target-64bit?)) + ;; Skip test that fails on 32-bit systems: + ;; . + `(#:phases (modify-phases %standard-phases + (add-before 'check 'disable-gstbufferpool-test + (lambda _ + (substitute* "tests/check/Makefile" + (("^[[:blank:]]+gst/gstbufferpool.*$") + "")) + #t)))) + '()))) (propagated-inputs `(("glib" ,glib))) ; required by gstreamer-1.0.pc. (native-inputs `(("bison" ,bison) From 5f9f2c82e6829823cf5bb1cc27f8b1333a1e2096 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 27 May 2019 21:56:17 +0200 Subject: [PATCH 005/224] build-system/haskell: Fix Haddock phase docstring. * guix/build/haskell-build-system.scm (haddock): Fix docstring. Signed-off-by: Timothy Sample --- guix/build/haskell-build-system.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/build/haskell-build-system.scm b/guix/build/haskell-build-system.scm index 23d97e6602..513c08096d 100644 --- a/guix/build/haskell-build-system.scm +++ b/guix/build/haskell-build-system.scm @@ -260,7 +260,7 @@ given Haskell package." #t) (define* (haddock #:key outputs haddock? haddock-flags #:allow-other-keys) - "Run the test suite of a given Haskell package." + "Generate the Haddock documentation of a given Haskell package." (when haddock? (run-setuphs "haddock" haddock-flags)) #t) From ed8d3f33a5236a1b9fde80bf4ad04e0ecc22a47a Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 27 May 2019 21:56:18 +0200 Subject: [PATCH 006/224] build-system/haskell: Generate Setup.hs if needed. The default Setup.hs is boilerplate that is frequently left out of source packages. Several packages already add a phase to generate it, so moving this phase to the build system is just factoring out an existing pattern. See . * guix/build/haskell-build-system.scm (generate-setuphs): New procedure. (%standard-phases): Add it after 'unpack'. * gnu/packages/haskell.scm (ghc-foundation, ghc-inline-c, ghc-inline-c-cpp, ghc-rio): Remove 'arguments'. Signed-off-by: Timothy Sample --- gnu/packages/haskell.scm | 42 ----------------------------- guix/build/haskell-build-system.scm | 12 +++++++++ 2 files changed, 12 insertions(+), 42 deletions(-) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 97b4fd9a55..cfbd3bfb76 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -9703,16 +9703,6 @@ packages.") (base32 "1q43y8wfj0wf9gdq2kzphwjwq6m5pvryy1lqgk954aq5z3ks1lsf")))) (build-system haskell-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'add-setup-script - (lambda _ - ;; The usual "Setup.hs" script is missing from the source. - (with-output-to-file "Setup.hs" - (lambda () - (format #t "import Distribution.Simple~%") - (format #t "main = defaultMain~%")))))))) (inputs `(("ghc-basement" ,ghc-basement))) (home-page "https://github.com/haskell-foundation/foundation") (synopsis "Alternative prelude with batteries and no dependencies") @@ -10590,16 +10580,6 @@ widths to the Char type.") (base32 "064h8a4hp53a479d3ak0vmqbx8hi0cpg7zn4wp23rjy26dka8p7g")))) (build-system haskell-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'add-setup-script - (lambda _ - ;; The usual "Setup.hs" script is missing from the source. - (with-output-to-file "Setup.hs" - (lambda () - (format #t "import Distribution.Simple~%") - (format #t "main = defaultMain~%")))))))) (inputs `(("ghc-exceptions" ,ghc-exceptions) ("ghc-hashable" ,ghc-hashable) @@ -11122,17 +11102,6 @@ DOS/Windows paths and markup languages (such as XML).") (base32 "0vbfrsqsi7mdziqsnj68bsqlwbqxxhvrmy9rv6w8z18d1m8w3n6h")))) (build-system haskell-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'create-Setup.hs - (lambda _ - (with-output-to-file "Setup.hs" - (lambda _ - (display "\ -import Distribution.Simple -main = defaultMain"))) - #t))))) (inputs `(("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint) ("ghc-cryptohash" ,ghc-cryptohash) @@ -11266,17 +11235,6 @@ handling wrong.") (base32 "1rk7fmpkmxw9hhwr8df29kadnf0ybnwj64ggdbnsdrpfyhnkisci")))) (build-system haskell-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'create-Setup.hs - (lambda _ - (with-output-to-file "Setup.hs" - (lambda _ - (display "\ -import Distribution.Simple -main = defaultMain"))) - #t))))) (inputs `(("ghc-inline-c" ,ghc-inline-c) ("ghc-safe-exceptions" ,ghc-safe-exceptions))) diff --git a/guix/build/haskell-build-system.scm b/guix/build/haskell-build-system.scm index 513c08096d..91f62138d0 100644 --- a/guix/build/haskell-build-system.scm +++ b/guix/build/haskell-build-system.scm @@ -275,9 +275,21 @@ given Haskell package." (_ (error "Could not find a Cabal file to patch.")))) #t) +(define* (generate-setuphs #:rest empty) + "Generate a default Setup.hs if needed." + (when (not (or (file-exists? "Setup.hs") + (file-exists? "Setup.lhs"))) + (format #t "generating missing Setup.hs~%") + (with-output-to-file "Setup.hs" + (lambda () + (format #t "import Distribution.Simple~%") + (format #t "main = defaultMain~%")))) + #t) + (define %standard-phases (modify-phases gnu:%standard-phases (add-after 'unpack 'patch-cabal-file patch-cabal-file) + (add-after 'unpack 'generate-setuphs generate-setuphs) (delete 'bootstrap) (add-before 'configure 'setup-compiler setup-compiler) (add-before 'install 'haddock haddock) From 9062fde4c66859aa3110e1bf08838323174c106c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 13 Jun 2019 20:42:30 +0300 Subject: [PATCH 007/224] gnu: parcimonie: Update source and home-page. * gnu/packages/gnupg.scm (parcimonie)[source]: Update to new url. [home-page]: Same. --- gnu/packages/gnupg.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index ba8d31eb25..abd1d6f419 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -940,8 +940,8 @@ files, to verify signatures, and to manage the private and public keys.") (version "0.10.3") (source (origin (method url-fetch) - (uri (string-append "https://gaffer.ptitcanardnoir.org/" - "intrigeri/files/parcimonie/App-Parcimonie-" + (uri (string-append "https://gaffer.boum.org/intrigeri/files/" + "parcimonie/App-Parcimonie-" version ".tar.gz")) (sha256 (base32 @@ -1011,7 +1011,7 @@ files, to verify signatures, and to manage the private and public keys.") `("PERL5LIB" ":" prefix (,(string-append perllib ":" (getenv "PERL5LIB"))))) #t)))))) - (home-page "https://gaffer.ptitcanardnoir.org/intrigeri/code/parcimonie/") + (home-page "https://gaffer.boum.org/intrigeri/code/parcimonie/") (synopsis "Incrementally refreshes a GnuPG keyring") (description "Parcimonie incrementaly refreshes a GnuPG keyring in a way that makes it hard to correlate the keyring content to an individual, and From c56a65aae7533de8d3e6fe32bb11e167cad63e22 Mon Sep 17 00:00:00 2001 From: Oleg Pykhalov Date: Thu, 13 Jun 2019 18:02:38 +0300 Subject: [PATCH 008/224] gnu: Add emacs-xtest. * gnu/packages/emacs-xyz.scm (emacs-xtest): New variable. --- gnu/packages/emacs-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 81f668409a..1fb8ce1da9 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7984,6 +7984,27 @@ running tests easier.") (define-public ert-runner (deprecated-package "ert-runner" emacs-ert-runner)) +(define-public emacs-xtest + (package + (name "emacs-xtest") + (version "1.1.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/promethial/xtest.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1wqx6hlqcmqiljydih5fx89dw06g8w728pyn4iqsap8jwgjngb09")))) + (arguments + `(#:exclude '())) + (build-system emacs-build-system) + (home-page "https://github.com/promethial/xtest/") + (synopsis "Simple testing with Emacs") + (description "This package provides a simple testing library for Emacs.") + (license license:gpl3+))) + (define-public emacs-disable-mouse (package (name "emacs-disable-mouse") From 9989e06fda9f60dc08272435629ab9f065bb0da5 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Sun, 9 Jun 2019 09:00:05 -0500 Subject: [PATCH 009/224] gnu: Add emacs-elfeed-org. * gnu/packages/emacs-xyz.scm (emacs-elfeed-org): New variable. Signed-off-by: Oleg Pykhalov --- gnu/packages/emacs-xyz.scm | 44 +++++++++++++++++++++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1fb8ce1da9..ef29177c8b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13,7 +13,7 @@ ;;; Copyright © 2016 Matthew Jordan ;;; Copyright © 2016, 2017 Roel Janssen ;;; Copyright © 2016, 2017 ng0 -;;; Copyright © 2016 Alex Griffin +;;; Copyright © 2016, 2019 Alex Griffin ;;; Copyright © 2016, 2017, 2018, 2019 Nicolas Goaziou ;;; Copyright © 2016, 2017, 2018 Alex Vong ;;; Copyright © 2016, 2017, 2018, 2019 Arun Isaac @@ -5233,6 +5233,48 @@ If you want to mark a folder manually as a project just create an empty and RSS, with a user interface inspired by notmuch.") (license license:gpl3+))) +(define-public emacs-elfeed-org + (let ((commit "77b6bbf222487809813de260447d31c4c59902c9")) + (package + (name "emacs-elfeed-org") + (version (git-version "0.1" "1" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/remyhonig/elfeed-org.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0a2ibka82xq1dhy2z7rd2y9zhcj8rna8357881yz49wf55ccgm53")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-elfeed" ,emacs-elfeed) + ("emacs-org" ,emacs-org) + ("emacs-dash" ,emacs-dash) + ("emacs-s" ,emacs-s))) + (native-inputs + `(("ert-runner" ,emacs-ert-runner) + ("emacs-xtest" ,emacs-xtest))) + (arguments + `(#:tests? #t + #:test-command '("ert-runner" "-L" "org-mode/lisp") + #:phases + (modify-phases %standard-phases + (add-before 'check 'chmod + (lambda _ + (chmod "test/fixture-mark-feed-ignore.org" #o644) + #t))))) + (home-page "https://github.com/remyhonig/elfeed-org") + (synopsis "Configure Elfeed with an Org-mode file") + (description + "@code{elfeed-org} lets you manage your Elfeed subscriptions +in Org-mode. Maintaining tags for all RSS feeds is cumbersome using +the regular flat list, where there is no hierarchy and tag names are +duplicated a lot. Org-mode makes the book keeping of tags and feeds +much easier.") + (license license:gpl3+)))) + (define-public emacs-el-x (package (name "emacs-el-x") From fdcd50b93bf29efcd757f3100391f5da45c143b6 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Sun, 9 Jun 2019 09:00:48 -0500 Subject: [PATCH 010/224] gnu: Add emacs-restart-emacs. * gnu/packages/emacs-xyz.scm (emacs-restart-emacs): New variable. Signed-off-by: Oleg Pykhalov --- gnu/packages/emacs-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ef29177c8b..fe0613cd33 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10689,6 +10689,28 @@ macro takes a first argument (whose value must be an alist) and a body.") your Emacs.") (license license:gpl2+)))) +(define-public emacs-restart-emacs + (let ((commit "9aa90d3df9e08bc420e1c9845ee3ff568e911bd9") + (revision "1")) + (package + (name "emacs-restart-emacs") + (version (git-version "0.1.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/iqbalansari/restart-emacs.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "02x1a85k7r95z8091zgjiaj9nf0zvx1jy4xvl3hr12qbnrx1wfav")))) + (build-system emacs-build-system) + (home-page "https://github.com/iqbalansari/restart-emacs") + (synopsis "Restart Emacs from within Emacs") + (description "This package provides a simple command to restart Emacs from +within Emacs.") + (license license:gpl3+)))) + (define-public emacs-sourcemap (package (name "emacs-sourcemap") From 4df1d31b5472795c980a812ae762dbf339c2d868 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Sun, 9 Jun 2019 09:01:34 -0500 Subject: [PATCH 011/224] gnu: Add emacs-mixed-pitch. * gnu/packages/emacs-xyz.scm (emacs-mixed-pitch): New variable. Signed-off-by: Oleg Pykhalov --- gnu/packages/emacs-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index fe0613cd33..543061d3f7 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11668,6 +11668,29 @@ interactive behavior should be different.") decreasing the default font size in all GUI Emacs frames.") (license license:gpl3+)))) +(define-public emacs-mixed-pitch + (package + (name "emacs-mixed-pitch") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/jabranham/mixed-pitch.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1458sy5b6bis1i0k23jdqk6hfqg0ghk637r3ajql2g19ym48rf58")))) + (build-system emacs-build-system) + (home-page "https://gitlab.com/jabranham/mixed-pitch") + (synopsis "Mix variable- and fixed-pitch fonts in the same Emacs buffer") + (description + "@code{mixed-pitch-mode} is a minor mode that enables mixing +variable-pitch and fixed-pitch fonts in the same buffer. The list +@code{mixed-pitch-fixed-pitch-faces} defines the faces that are kept +fixed-pitch,everything else becomes variable-pitch.") + (license license:gpl3+))) + (define-public emacs-visual-regexp (package (name "emacs-visual-regexp") From 6bb5a7e08c524d53cb7412636c14a8c42834800e Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Sun, 9 Jun 2019 09:02:04 -0500 Subject: [PATCH 012/224] gnu: Add emacs-solaire-mode. * gnu/packages/emacs-xyz.scm (emacs-solaire-mode): New variable. Signed-off-by: Oleg Pykhalov --- gnu/packages/emacs-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 543061d3f7..77b89f8182 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4123,6 +4123,29 @@ of sixteen colors suitable for a wide range of applications. Base16 is not a single theme but a set of guidelines with numerous implementations.") (license license:expat))) +(define-public emacs-solaire-mode + (package + (name "emacs-solaire-mode") + (version "1.0.9") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hlissner/emacs-solaire-mode.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "011m4r7s6i9lgjymh7jgq5jwwrpz4vmpvp3c8d4ix96v5hi04kzg")))) + (build-system emacs-build-system) + (home-page "https://github.com/hlissner/emacs-solaire-mode") + (synopsis "Change background of file-visiting buffers in Emacs") + (description + "@code{solaire-mode} is inspired by editors which visually distinguish +code-editing windows from sidebars, popups, terminals, ecetera. It changes the +background of file-visiting buffers (and certain aspects of the UI) to make +them easier to distinguish from other, less important buffers.") + (license license:expat))) + (define-public emacs-prescient (package (name "emacs-prescient") From a3abc3fdfca159906c6a730d13810f054e1e803f Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Mon, 10 Jun 2019 21:41:28 -0500 Subject: [PATCH 013/224] gnu: perl-db-file: Update to 1.852. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/databases.scm (perl-db-file): Update to 1.852. Signed-off-by: Ludovic Courtès --- gnu/packages/databases.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 55f7a46dc5..acffc56a27 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -34,6 +34,7 @@ ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Maxim Cournoyer ;;; Copyright © 2019 Jack Hill +;;; Copyright © 2019 Alex Griffin ;;; ;;; This file is part of GNU Guix. ;;; @@ -1879,7 +1880,7 @@ database.") (define-public perl-db-file (package (name "perl-db-file") - (version "1.843") + (version "1.852") (source (origin (method url-fetch) @@ -1889,7 +1890,7 @@ database.") ".tar.gz")) (sha256 (base32 - "0sildz1i3fmh949w1scpjsyjx0cbmfw0yna3y70mc6vbwp8y696y")))) + "14c30xyqx9c1hxw40bqbzls41al8gmklxv5jbk2kknmn4dsrbdrs")))) (build-system perl-build-system) (inputs `(("bdb" ,bdb))) (native-inputs `(("perl-test-pod" ,perl-test-pod))) From 15f836efc17e9e6229c38f3bf6b377a61a5d9caa Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Mon, 10 Jun 2019 21:47:20 -0500 Subject: [PATCH 014/224] gnu: perl-canary-stability: Update to 2013. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/perl.scm (perl-canary-stability): Update to 2013. Signed-off-by: Ludovic Courtès --- gnu/packages/perl.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 8e9410e37a..a0096deaf3 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2018, 2019 Oleg Pykhalov ;;; Copyright © 2018, 2019 Pierre Neidhardt ;;; Copyright © 2018 Kei Kebreau +;;; Copyright © 2019 Alex Griffin ;;; ;;; This file is part of GNU Guix. ;;; @@ -711,14 +712,14 @@ is captured while being passed through to the original file handles.") (define-public perl-canary-stability (package (name "perl-canary-stability") - (version "2012") + (version "2013") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/M/ML/MLEHMANN/" "Canary-Stability-" version ".tar.gz")) (sha256 (base32 - "01vih43hvpqy67m6a6fwmlswli91mqpv8n8ccglvlkc33l8hn97x")))) + "1smnsx371x9zrqmylgq145991xh8561mraqfyrlbiz4mrxi1rjd5")))) (build-system perl-build-system) (home-page "https://metacpan.org/release/Canary-Stability") (synopsis "Check compatibility with the installed perl version") From 1682368932e6fd5968900ca554136e0c33d53b4c Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Mon, 10 Jun 2019 21:49:50 -0500 Subject: [PATCH 015/224] gnu: perl-yaml-libyaml: Update to 0.78. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/perl.scm (perl-yaml-libyaml): Update to 0.78. Signed-off-by: Ludovic Courtès --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index a0096deaf3..3875c71911 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -9430,7 +9430,7 @@ on the YAML 1.0 specification.") (define-public perl-yaml-libyaml (package (name "perl-yaml-libyaml") - (version "0.76") + (version "0.78") (source (origin (method url-fetch) @@ -9439,7 +9439,7 @@ on the YAML 1.0 specification.") version ".tar.gz")) (sha256 - (base32 "1m94g36sl9rasjlvlsf65xcal5hvkc3gbzd7l68h17az75269kyy")))) + (base32 "03plv3wfqqqf7g8mxr8f6wlki2af8w3rg9xcfii1z5l1f1iarxx1")))) (build-system perl-build-system) (home-page "https://metacpan.org/release/YAML-LibYAML") From 1aa2c25560328215936a9f2c52b8de8d7cc04382 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Mon, 10 Jun 2019 21:05:28 -0500 Subject: [PATCH 016/224] gnu: ikiwiki: Update to 3.20190228. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/web.scm (ikiwiki): Update to 3.20190228. Signed-off-by: Ludovic Courtès --- gnu/packages/web.scm | 19 ++++++------------- 1 file changed, 6 insertions(+), 13 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index d022c6be46..1ed113cd20 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -32,6 +32,7 @@ ;;; Copyright © 2018 Alex Vong ;;; Copyright © 2019 Nicolas Goaziou ;;; Copyright © 2019 Brendan Tildesley +;;; Copyright © 2019 Alex Griffin ;;; ;;; This file is part of GNU Guix. ;;; @@ -4234,27 +4235,19 @@ NetSurf project.") (define-public ikiwiki (package (name "ikiwiki") - (version "3.20170111") + (version "3.20190228") (source (origin (method url-fetch) (uri (string-append "http://snapshot.debian.org/archive/debian/" - "20170111T215449Z/pool/main/i/ikiwiki/ikiwiki_" - version ".tar.xz")) + "20190301T035241Z/pool/main/i/ikiwiki/ikiwiki_" + version ".orig.tar.xz")) (sha256 (base32 - "00d7yzv426fvqbhvzyafddv7fa6b4j2647b0wi371wd5yjj9j3sz")))) + "17pyblaqhkb61lxl63bzndiffism8k859p54k3k4sghclq6lsynh")))) (build-system perl-build-system) (arguments - `(;; Image tests fail - ;; - ;; Test Summary Report - ;; ------------------- - ;; t/img.t (Wstat: 2304 Tests: 62 Failed: 9) - ;; Failed tests: 21, 27-28, 30-35 - ;; Non-zero exit status: 9 - #:tests? #f - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'include-PERL5LIB-in-wrapper (lambda _ From 576cb396eac4e8cea2b54d96382f8e77f3584e89 Mon Sep 17 00:00:00 2001 From: Dimakakos Dimos Date: Wed, 12 Jun 2019 16:26:04 +0300 Subject: [PATCH 017/224] gnu: Add emacs-org-noter MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-org-noter): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 77b89f8182..a8eb141452 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -15988,3 +15988,31 @@ corresponding Evil keys.") (description "@code{xterm-color.el} is an ANSI control sequence to text-property translator.") (license license:bsd-2)))) + +(define-public emacs-org-noter + (package + (name "emacs-org-noter") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://stable.melpa.org/packages/org-noter-" + version + ".el")) + (sha256 + (base32 + "1hczwva73gsyanl1ldhdvql01gy0hy2g861yzkaklyb763sx58x4")))) + (build-system emacs-build-system) + (propagated-inputs `(("emacs-org" ,emacs-org))) + (home-page + "https://github.com/weirdNox/org-noter") + (synopsis + "Synchronized, Org-mode, document annotator") + (description + "The idea is to let you create notes that are kept in sync when you +scroll through the document, but that are external to it - the notes +themselves live in an Org-mode file. As such, this leverages the power of +Org-mode (the notes may have outlines, latex fragments, babel, etc...) while +acting like notes that are made /in/ the document.") + (license license:gpl3+))) From 30825c46298c70028f70da1470eadbadf1e0d858 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 13 Jun 2019 23:27:34 +0200 Subject: [PATCH 018/224] gnu: emacs-org-noter: Tweak. * gnu/packages/emacs-xyz.scm (emacs-org-noter): Adjust indentation and description. --- gnu/packages/emacs-xyz.scm | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a8eb141452..d341501cc0 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16005,14 +16005,12 @@ text-property translator.") "1hczwva73gsyanl1ldhdvql01gy0hy2g861yzkaklyb763sx58x4")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-org" ,emacs-org))) - (home-page - "https://github.com/weirdNox/org-noter") - (synopsis - "Synchronized, Org-mode, document annotator") + (home-page "https://github.com/weirdNox/org-noter") + (synopsis "Synchronized, Org-mode, document annotator") (description - "The idea is to let you create notes that are kept in sync when you -scroll through the document, but that are external to it - the notes + "This package lets you create notes that are kept in sync when you +scroll through the document, but that are external to it---the notes themselves live in an Org-mode file. As such, this leverages the power of Org-mode (the notes may have outlines, latex fragments, babel, etc...) while -acting like notes that are made /in/ the document.") +acting like notes that are made @emph{in} the document.") (license license:gpl3+))) From ca45da9fc9b1eee399ce4344b18cbb129daeca4c Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Thu, 13 Jun 2019 21:39:14 +0200 Subject: [PATCH 019/224] import: hackage: Handle Hackage revisions. Hackage packages can have metadata revisions (Cabal file only) that are not reflected in the source archive. The Haskell build system has support for this, but until now the Hackage importer would create a package based on the revised Cabal file which would then build using the old Cabal file. Fixes . * guix/import/cabal.scm (): Add 'revision' field. (eval-cabal): Parse 'x-revision:' property. * guix/import/hackage.scm (read-cabal-and-hash): New procedure. (hackage-fetch-and-hash): New procedure. (hackage-fetch): Rewrite using 'hackage-fetch-and-hash'. (hackage-module->sexp): Add 'cabal-hash' argument and use it to populate the '#:cabal-revision' argument. (hackage->guix-package): Use the new '-and-hash' functions to get the hash of the Cabal file and pass it to 'hackage-module->sexp'. * guix/tests/hackage.scm: Test import of Cabal file revision. Signed-off-by: Timothy Sample --- guix/import/cabal.scm | 7 +++-- guix/import/hackage.scm | 62 +++++++++++++++++++++++++++++------------ tests/hackage.scm | 45 ++++++++++++++++++++++++++++++ 3 files changed, 94 insertions(+), 20 deletions(-) diff --git a/guix/import/cabal.scm b/guix/import/cabal.scm index 1a87be0b00..7dfe771e41 100644 --- a/guix/import/cabal.scm +++ b/guix/import/cabal.scm @@ -40,6 +40,7 @@ cabal-package? cabal-package-name cabal-package-version + cabal-package-revision cabal-package-license cabal-package-home-page cabal-package-source-repository @@ -638,13 +639,14 @@ If #f use the function 'port-filename' to obtain it." ;; information of the Cabal file, but only the ones we currently are ;; interested in. (define-record-type - (make-cabal-package name version license home-page source-repository + (make-cabal-package name version revision license home-page source-repository synopsis description executables lib test-suites flags eval-environment custom-setup) cabal-package? (name cabal-package-name) (version cabal-package-version) + (revision cabal-package-revision) (license cabal-package-license) (home-page cabal-package-home-page) (source-repository cabal-package-source-repository) @@ -838,6 +840,7 @@ See the manual for limitations."))))))) (define (cabal-evaluated-sexp->package evaluated-sexp) (let* ((name (lookup-join evaluated-sexp "name")) (version (lookup-join evaluated-sexp "version")) + (revision (lookup-join evaluated-sexp "x-revision")) (license (lookup-join evaluated-sexp "license")) (home-page (lookup-join evaluated-sexp "homepage")) (home-page-or-hackage @@ -856,7 +859,7 @@ See the manual for limitations."))))))) (custom-setup (match (make-cabal-section evaluated-sexp 'custom-setup) ((x) x) (_ #f)))) - (make-cabal-package name version license home-page-or-hackage + (make-cabal-package name version revision license home-page-or-hackage source-repository synopsis description executables lib test-suites flags eval-environment custom-setup))) diff --git a/guix/import/hackage.scm b/guix/import/hackage.scm index 366256b40d..6f426af900 100644 --- a/guix/import/hackage.scm +++ b/guix/import/hackage.scm @@ -117,19 +117,34 @@ version is returned." (#f name) (m (match:substring m 1))))))) +(define (read-cabal-and-hash port) + "Read a Cabal file from PORT and return it and its hash in nix-base32 +format as two values." + (let-values (((port get-hash) (open-sha256-input-port port))) + (values (read-cabal (canonical-newline-port port)) + (bytevector->nix-base32-string (get-hash))))) + +(define (hackage-fetch-and-hash name-version) + "Fetch the latest Cabal revision for the package NAME-VERSION, and return +two values: the parsed Cabal file and its hash in nix-base32 format. If the +version part is omitted from the package name, then fetch the latest +version. On failure, both return values will be #f." + (guard (c ((and (http-get-error? c) + (= 404 (http-get-error-code c))) + (values #f #f))) ;"expected" if package is unknown + (let*-values (((name version) (package-name->name+version name-version)) + ((url) (hackage-cabal-url name version)) + ((port _) (http-fetch url)) + ((cabal hash) (read-cabal-and-hash port))) + (close-port port) + (values cabal hash)))) + (define (hackage-fetch name-version) "Return the Cabal file for the package NAME-VERSION, or #f on failure. If the version part is omitted from the package name, then return the latest version." - (guard (c ((and (http-get-error? c) - (= 404 (http-get-error-code c))) - #f)) ;"expected" if package is unknown - (let-values (((name version) (package-name->name+version name-version))) - (let* ((url (hackage-cabal-url name version)) - (port (http-fetch url)) - (result (read-cabal (canonical-newline-port port)))) - (close-port port) - result)))) + (let-values (((cabal hash) (hackage-fetch-and-hash name-version))) + cabal)) (define string->license ;; List of valid values from @@ -198,15 +213,20 @@ package being processed and is used to filter references to itself." (cons own-name ghc-standard-libraries)))) dependencies)) -(define* (hackage-module->sexp cabal #:key (include-test-dependencies? #t)) +(define* (hackage-module->sexp cabal cabal-hash + #:key (include-test-dependencies? #t)) "Return the `package' S-expression for a Cabal package. CABAL is the -representation of a Cabal file as produced by 'read-cabal'." +representation of a Cabal file as produced by 'read-cabal'. CABAL-HASH is +the hash of the Cabal file." (define name (cabal-package-name cabal)) (define version (cabal-package-version cabal)) + + (define revision + (cabal-package-revision cabal)) (define source-url (hackage-source-url name version)) @@ -252,9 +272,14 @@ representation of a Cabal file as produced by 'read-cabal'." (list 'quasiquote inputs)))))) (define (maybe-arguments) - (if (not include-test-dependencies?) - '((arguments `(#:tests? #f))) - '())) + (match (append (if (not include-test-dependencies?) + '(#:tests? #f) + '()) + (if (not (string-null? revision)) + `(#:cabal-revision (,revision ,cabal-hash)) + '())) + (() '()) + (args `((arguments (,'quasiquote ,args)))))) (let ((tarball (with-store store (download-to-store store source-url)))) @@ -294,10 +319,11 @@ symbol 'true' or 'false'. The value associated with other keys has to conform to the Cabal file format definition. The default value associated with the keys \"os\", \"arch\" and \"impl\" is \"linux\", \"x86_64\" and \"ghc\" respectively." - (let ((cabal-meta (if port - (read-cabal (canonical-newline-port port)) - (hackage-fetch package-name)))) - (and=> cabal-meta (compose (cut hackage-module->sexp <> + (let-values (((cabal-meta cabal-hash) + (if port + (read-cabal-and-hash port) + (hackage-fetch-and-hash package-name)))) + (and=> cabal-meta (compose (cut hackage-module->sexp <> cabal-hash #:include-test-dependencies? include-test-dependencies?) (cut eval-cabal <> cabal-environment))))) diff --git a/tests/hackage.scm b/tests/hackage.scm index 38a5825af7..14176b2cf9 100644 --- a/tests/hackage.scm +++ b/tests/hackage.scm @@ -274,6 +274,51 @@ executable cabal (test-assert "hackage->guix-package test multiline desc (braced)" (eval-test-with-cabal test-cabal-multiline-braced match-ghc-foo)) +;; Check Hackage Cabal revisions. +(define test-cabal-revision + "name: foo +version: 1.0.0 +x-revision: 2 +homepage: http://test.org +synopsis: synopsis +description: description +license: BSD3 +executable cabal + build-depends: + HTTP >= 4000.2.5 && < 4000.3, + mtl >= 2.0 && < 3 +") + +(define-package-matcher match-ghc-foo-revision + ('package + ('name "ghc-foo") + ('version "1.0.0") + ('source + ('origin + ('method 'url-fetch) + ('uri ('string-append + "https://hackage.haskell.org/package/foo/foo-" + 'version + ".tar.gz")) + ('sha256 + ('base32 + (? string? hash))))) + ('build-system 'haskell-build-system) + ('inputs + ('quasiquote + (("ghc-http" ('unquote 'ghc-http))))) + ('arguments + ('quasiquote + ('#:cabal-revision + ("2" "0xxd88fb659f0krljidbvvmkh9ppjnx83j0nqzx8whcg4n5qbyng")))) + ('home-page "http://test.org") + ('synopsis (? string?)) + ('description (? string?)) + ('license 'bsd-3))) + +(test-assert "hackage->guix-package test cabal revision" + (eval-test-with-cabal test-cabal-revision match-ghc-foo-revision)) + (test-assert "read-cabal test 1" (match (call-with-input-string test-read-cabal-1 read-cabal) ((("name" ("test-me")) From 830a0fe64e28995991c3a4147ce83fd222ee3a2c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 14 Jun 2019 11:47:02 +0200 Subject: [PATCH 020/224] gnu: cups-filters: Update to 1.25.0. * gnu/packages/cups.scm (cups-filters): Update to 1.25.0. --- gnu/packages/cups.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm index b48da35e8e..b87203cab6 100644 --- a/gnu/packages/cups.scm +++ b/gnu/packages/cups.scm @@ -57,7 +57,7 @@ (define-public cups-filters (package (name "cups-filters") - (version "1.23.0") + (version "1.25.0") (source(origin (method url-fetch) (uri @@ -65,7 +65,7 @@ "cups-filters-" version ".tar.xz")) (sha256 (base32 - "1lyzxf03kdfvkbb6p7hxlarbb35lq5bh094g49v3bz9z4z9065p2")) + "1laiscq8yvynw862calkgbz9irrdkmd5l821q6a6wik1ifd186c1")) (modules '((guix build utils))) (snippet ;; install backends, banners and filters to cups-filters output From 14b53192a4dce71f947d4e44b1676a3eec911bc5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 14 Jun 2019 11:47:21 +0200 Subject: [PATCH 021/224] gnu: libsigc++: Update to 2.10.2. * gnu/packages/glib.scm (libsigc++): Update to 2.10.2. --- gnu/packages/glib.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index 7af7c86853..b5ddc19ef9 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -482,7 +482,7 @@ by GDBus included in Glib.") (define libsigc++ (package (name "libsigc++") - (version "2.10.1") + (version "2.10.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/libsigc++/" @@ -490,7 +490,7 @@ by GDBus included in Glib.") name "-" version ".tar.xz")) (sha256 (base32 - "00v08km4wwzbh6vjxb21388wb9dm6g2xh14rgwabnv4c2wk5z8n9")))) + "163s14d1rqp82gc1vsm3q0wzsbdicb9q6307kz0zk5lm6x9h5jmi")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) ("m4" ,m4))) From 16c38e2b9cf2a004cb1d3425593b8872e5c1f7b4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 14 Jun 2019 11:47:41 +0200 Subject: [PATCH 022/224] gnu: imagemagick: Update to 6.9.10-49. * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-49. --- gnu/packages/imagemagick.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm index 16f9a6e4bd..dba193d8e5 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -48,14 +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 "6.9.10-46") + (version "6.9.10-49") (source (origin (method url-fetch) (uri (string-append "mirror://imagemagick/ImageMagick-" version ".tar.xz")) (sha256 (base32 - "1qx3x48q1dy39g1bb8mnyaq9jwy1smf0x6zfly4r0mj3m01i2dyb")))) + "1w4vsppyn1h58x3z4hgly5qxp16q66l18y9rwavrravw0kiq64fs")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch") From 753eb4118c974e4e9c685f81c8ffb45fc1be7274 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 14 Jun 2019 11:48:10 +0200 Subject: [PATCH 023/224] gnu: python-markupsafe: Update to 1.1.1. * gnu/packages/python-xyz.scm (python-markupsafe): Update to 1.1.1. [arguments]: New field. Override check phase. [native-inputs]: Add PYTHON-PYTEST. --- gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a7c88e9187..ac23e23bc2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2298,15 +2298,33 @@ e.g. filters, callbacks and errbacks can all be promises.") (define-public python-markupsafe (package (name "python-markupsafe") - (version "1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (pypi-uri "MarkupSafe" version)) (sha256 (base32 - "0rdn1s8x9ni7ss8rfiacj7x1085lx8mh2zdwqslnw8xc3l4nkgm6")))) + "0sqipg4fk7xbixqd8kq6rlkxj664d157bdwbh93farcphf92x1r9")))) (build-system python-build-system) + (arguments + `(#:modules ((ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26) + (guix build utils) + (guix build python-build-system)) + #:phases (modify-phases %standard-phases + (replace 'check + (lambda _ + (let ((cwd (getcwd)) + (libdir (find (cut string-prefix? "lib." <>) + (scandir "build")))) + (setenv "PYTHONPATH" + (string-append cwd "/build/" libdir ":" + (getenv "PYTHONPATH"))) + (invoke "pytest" "-vv"))))))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/mitsuhiko/markupsafe") (synopsis "XML/HTML/XHTML markup safe string implementation for Python") (description From 950c3a2d5ef7b722b24e6529c3819fb3c6fa504f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 14 Jun 2019 11:48:52 +0200 Subject: [PATCH 024/224] gnu: python-mako: Update to 1.0.12. * gnu/packages/python-xyz.scm (python-mako): Update to 1.0.12. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ac23e23bc2..e1d0b7f50a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8363,14 +8363,14 @@ python-xdo for newer bindings.)") (define-public python-mako (package (name "python-mako") - (version "1.0.10") + (version "1.0.12") (source (origin (method url-fetch) (uri (pypi-uri "Mako" version)) (sha256 (base32 - "0r9rysn19fmrxnzfcn7sg20kjhcrx9qri0my9n5vdzp1g2g92rbi")))) + "0qj16ai937wrbpv1a9g395gybb9s06rmdj3arbp8fpl37bg6byhc")))) (build-system python-build-system) (propagated-inputs `(("python-markupsafe" ,python-markupsafe))) From bbeeeb148efdb3e604f44d4e643731c49f46f684 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 14 Jun 2019 11:49:12 +0200 Subject: [PATCH 025/224] gnu: Sphinx: Update to 2.1.1. * gnu/packages/sphinx.scm (python-sphinx): Update to 2.1.1. --- gnu/packages/sphinx.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 1bc7149c24..0b86398a68 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -45,14 +45,14 @@ (define-public python-sphinx (package (name "python-sphinx") - (version "2.0.1") + (version "2.1.1") (source (origin (method url-fetch) (uri (pypi-uri "Sphinx" version)) (sha256 (base32 - "0js0rnbzm0nsb4gm2v4z79wlbmr05awqzic57kfl8ydkdxj80cj2")))) + "1ym150xpzc2nsv8zy77q3q4gxgwfnfvd7459dykzmiw6wxk3250m")))) (build-system python-build-system) (arguments `(#:phases From 4e8284f031323678f078a15d8af1742332b326e5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 14 Jun 2019 11:49:31 +0200 Subject: [PATCH 026/224] gnu: speexdsp: Update to 1.2.0. * gnu/packages/xiph.scm (speexdsp): Update to 1.2.0. --- gnu/packages/xiph.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xiph.scm b/gnu/packages/xiph.scm index 8f900cf90d..804cfd39a7 100644 --- a/gnu/packages/xiph.scm +++ b/gnu/packages/xiph.scm @@ -160,14 +160,14 @@ stereo encoding, and voice activity detection.") (define speexdsp (package (name "speexdsp") - (version "1.2rc3") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://downloads.xiph.org/releases/speex/" "speexdsp-" version ".tar.gz")) (sha256 (base32 - "1wcjyrnwlkayb20zdhp48y260rfyzg925qpjpljd5x9r01h8irja")))) + "0wa7sqpk3x61zz99m7lwkgr6yv62ml6lfgs5xja65vlvdzy44838")))) (build-system gnu-build-system) (arguments `(#:configure-flags '(,@(if (string=? "aarch64-linux" From 54200da4b3248639b12ba28d3bfa5e85daf3e1cc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 14 Jun 2019 11:42:02 +0200 Subject: [PATCH 027/224] gnu: ungoogled-chromium: Update to 75.0.3770.90-0.5d8abc3 [fixes CVE-2019-5842]. * gnu/packages/chromium.scm (%chromium-version): Update to 75.0.3770.90. (%debian-revision): Update to 'debian/75.0.3770.90-1'. (%chromium-origin): Update hashes. --- gnu/packages/chromium.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index dce992a0c5..2127e402d7 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -226,9 +226,9 @@ from forcing GEXP-PROMISE." #:system system #:guile-for-build guile))) -(define %chromium-version "75.0.3770.80") +(define %chromium-version "75.0.3770.90") (define %ungoogled-revision "5d8abc38b43a62f379615a0dc972b29d9aebb4b4") -(define %debian-revision "debian/75.0.3770.80-1") +(define %debian-revision "debian/75.0.3770.90-1") (define package-revision "0") (define %package-version (string-append %chromium-version "-" package-revision "." @@ -242,7 +242,7 @@ from forcing GEXP-PROMISE." %chromium-version ".tar.xz")) (sha256 (base32 - "1mk6gb3iif8i6zq41wjn3lhqqlqp1syzpav1nj0170l7v348p0ns")))) + "0f9qjhxvk8sajj7qa061crfmln65q7sniylrgp0qijwyw6xrmddi")))) (define %ungoogled-origin (origin @@ -267,7 +267,7 @@ from forcing GEXP-PROMISE." (string-take %debian-revision 7)))) (sha256 (base32 - "16z4bncc2q1d5bymywq8291bzkcvba447ql3vsq20rwcdjckyimx")))) + "0sh6z2lx44zb31qrpa29vm0sw09dxi7i9h6fsq3ivfxjs7v98bbx")))) ;; This is a "computed" origin that does the following: ;; *) Runs the Ungoogled scripts on a pristine Chromium tarball. From 71bfbe9ba8806aeeec7963e1019e583565ee32d7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 14 Jun 2019 11:43:07 +0200 Subject: [PATCH 028/224] gnu: whois: Update to 5.4.3. * gnu/packages/networking.scm (whois): Update to 5.4.3. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 2ea65f270c..6ade8ed85d 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -549,7 +549,7 @@ and up to 1 Mbit/s downstream.") (define-public whois (package (name "whois") - (version "5.4.2") + (version "5.4.3") (source (origin (method url-fetch) @@ -557,7 +557,7 @@ and up to 1 Mbit/s downstream.") name "_" version ".tar.xz")) (sha256 (base32 - "0mqzs0g2qxd29ihammisg9qf4503sr7d4zas26zjz4an78xkmqzf")))) + "1hqg14k0q4979a1amgms4sa1d2iiid51rra3jyqmv63hkw189ypy")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no test suite From e23b6a68008321179508d55780f9725cf649c610 Mon Sep 17 00:00:00 2001 From: Meiyo Peng Date: Sun, 9 Jun 2019 16:15:50 +0800 Subject: [PATCH 029/224] gnu: sway: Hardcode path to swaybg. * gnu/packages/wm.scm (sway)[arguments]: Hardcode path to swaybg. [inputs]: Add swaybg. Signed-off-by: Marius Bakke --- gnu/packages/wm.scm | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index f0589e98f1..eac17e0837 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -17,7 +17,7 @@ ;;; Copyright © 2017 Oleg Pykhalov ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018 Pierre-Antoine Rouby -;;; Copyright © 2018 Meiyo Peng +;;; Copyright © 2018, 2019 Meiyo Peng ;;; Copyright © 2019 Rutger Helling ;;; Copyright © 2019 Timothy Sample ;;; @@ -1201,6 +1201,12 @@ modules for building a Wayland compositor.") (modify-phases %standard-phases (add-before 'configure 'hardcode-paths (lambda* (#:key inputs #:allow-other-keys) + ;; Hardcode path to swaybg. + (substitute* "sway/config.c" + (("strdup..swaybg..") + (string-append "strdup(\"" (assoc-ref inputs "swaybg") + "/bin/swaybg\")"))) + ;; Hardcode path to scdoc. (substitute* "meson.build" (("scdoc.get_pkgconfig_variable..scdoc..") (string-append "'" (assoc-ref inputs "scdoc") @@ -1214,6 +1220,7 @@ modules for building a Wayland compositor.") ("libinput" ,libinput) ("libxkbcommon" ,libxkbcommon) ("pango" ,pango) + ("swaybg" ,swaybg) ("wayland" ,wayland) ("wlroots" ,wlroots))) (native-inputs `(("git" ,git) From f063f0efebe484a0f4cb1aed6e49053860fdd822 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Fri, 14 Jun 2019 17:00:50 +0200 Subject: [PATCH 030/224] doc: Fix typo. * doc/guix.texi: Switch URI and description in @uref for hpcguix-web. --- doc/guix.texi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index 9dc1d2a9ca..052be47bdb 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -19833,7 +19833,7 @@ A simple setup for cat-avatar-generator can look like this: @subsubheading Hpcguix-web @cindex hpcguix-web -The @uref{hpcguix-web, https://github.com/UMCUGenetics/hpcguix-web/} +The @uref{https://github.com/UMCUGenetics/hpcguix-web/, hpcguix-web} program is a customizable web interface to browse Guix packages, initially designed for users of high-performance computing (HPC) clusters. From bc70516bbae8a6388f3ed19008d3e10efd1577a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 14 Jun 2019 17:26:27 +0200 Subject: [PATCH 031/224] gnu: Remove r-loomr. The loomR package is actually non-free software according to its author. See https://github.com/mojaveazure/loomR/pull/24. * gnu/packages/bioinformatics.scm (r-loomr): Remove variable. --- gnu/packages/bioinformatics.scm | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8dbcd5dd33..b950b8cf53 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13086,35 +13086,6 @@ known and yet unknown splice junctions. Circular-to-linear ratios of circRNAs can be calculated, and a number of descriptive plots easily generated.") (license license:artistic2.0))) -(define-public r-loomr - (let ((commit "df0144bd2bbceca6fadef9edc1bbc5ca672d4739") - (revision "1")) - (package - (name "r-loomr") - (version (git-version "0.2.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/mojaveazure/loomR.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1b1g4dlmfdyhn56bz1mkh9ymirri43wiz7rjhs7py3y7bdw1s3yr")))) - (build-system r-build-system) - (propagated-inputs - `(("r-r6" ,r-r6) - ("r-hdf5r" ,r-hdf5r) - ("r-iterators" ,r-iterators) - ("r-itertools" ,r-itertools) - ("r-matrix" ,r-matrix))) - (home-page "https://github.com/mojaveazure/loomR") - (synopsis "R interface for loom files") - (description "This package provides an R interface to access, create, -and modify loom files. loomR aims to be completely compatible with loompy.") - (license license:gpl3)))) - (define-public gffread ;; We cannot use the tagged release because it is not in sync with gclib. ;; See https://github.com/gpertea/gffread/issues/26 From 4c7e8c234d7d1729adf7290a8bb761e3a0cc4b6b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= Date: Fri, 14 Jun 2019 23:07:56 +0200 Subject: [PATCH 032/224] gnu: Add benchmark. * gnu/packages/benchmark.scm(benchmark): New variable. * gnu/packages/patches/benchmark-unbundle-googletest.patch: New file. * gnu/local.mk(dist_patch_DATA): Add it. --- gnu/local.mk | 3 +- gnu/packages/benchmark.scm | 28 ++++++++ .../benchmark-unbundle-googletest.patch | 69 +++++++++++++++++++ 3 files changed, 99 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/benchmark-unbundle-googletest.patch diff --git a/gnu/local.mk b/gnu/local.mk index 75fb24a0c5..9ff668ef8b 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -15,7 +15,7 @@ # Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice # Copyright © 2017, 2018 Clément Lassieur # Copyright © 2017 Mathieu Othacehe -# Copyright © 2017, 2018 Gábor Boskovits +# Copyright © 2017, 2018, 2019 Gábor Boskovits # Copyright © 2018 Amirouche Boubekki # Copyright © 2018, 2019 Oleg Pykhalov # Copyright © 2018 Stefan Stefanović @@ -691,6 +691,7 @@ dist_patch_DATA = \ %D%/packages/patches/bazaar-CVE-2017-14176.patch \ %D%/packages/patches/beets-python-3.7-fix.patch \ %D%/packages/patches/beignet-correct-file-names.patch \ + %D%/packages/patches/benchmark-unbundle-googletest.patch \ %D%/packages/patches/biber-fix-encoding-write.patch \ %D%/packages/patches/binutils-loongson-workaround.patch \ %D%/packages/patches/blender-2.79-newer-ffmpeg.patch \ diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index 970df735aa..c513370e74 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018, 2019 Ricardo Wurmus ;;; Copyright © 2019 Eric Bavier +;;; Copyright © 2019 Gábor Boskovits ;;; ;;; This file is part of GNU Guix. ;;; @@ -25,7 +26,10 @@ #: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 (gnu packages) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages linux) #:use-module (gnu packages maths) @@ -193,3 +197,27 @@ extension to @code{time} which runs a command multiple times and prints the timing means, standard deviations, mins, medians, and maxes having done so. This can give a much better understanding of the command's performance.") (license license:expat))) + +(define-public benchmark + (package + (name "benchmark") + (version "1.5.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/google/benchmark.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0r9dbg4cbk47gwmayys31a83m3y67k0kh1f6pl8i869rbd609ndh")) + (patches (search-patches "benchmark-unbundle-googletest.patch")))) + (build-system cmake-build-system) + (native-inputs + `(("googletest" ,googletest))) + (home-page "https://github.com/google/benchmark") + (synopsis "Microbenchmark support library") + (description + "Benchmark is a library to benchmark code snippets, +similar to unit tests.") + (license license:asl2.0))) diff --git a/gnu/packages/patches/benchmark-unbundle-googletest.patch b/gnu/packages/patches/benchmark-unbundle-googletest.patch new file mode 100644 index 0000000000..4dce8f59f1 --- /dev/null +++ b/gnu/packages/patches/benchmark-unbundle-googletest.patch @@ -0,0 +1,69 @@ +From 5eb306618196ea78b8c9390e22ea2edce20760fe Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= +Date: Fri, 14 Jun 2019 22:15:49 +0200 +Subject: [PATCH] Remove googletest lookup from build system. + +--- + cmake/GoogleTest.cmake | 18 +++++++++--------- + cmake/GoogleTest.cmake.in | 12 ++++++------ + 2 files changed, 15 insertions(+), 15 deletions(-) + +diff --git a/cmake/GoogleTest.cmake b/cmake/GoogleTest.cmake +index fb7c6be..a6c473b 100644 +--- a/cmake/GoogleTest.cmake ++++ b/cmake/GoogleTest.cmake +@@ -27,15 +27,15 @@ endif() + # settings on Windows + set(gtest_force_shared_crt ON CACHE BOOL "" FORCE) + +-include(${GOOGLETEST_PREFIX}/googletest-paths.cmake) ++#include(${GOOGLETEST_PREFIX}/googletest-paths.cmake) + + # Add googletest directly to our build. This defines + # the gtest and gtest_main targets. +-add_subdirectory(${GOOGLETEST_SOURCE_DIR} +- ${GOOGLETEST_BINARY_DIR} +- EXCLUDE_FROM_ALL) +- +-set_target_properties(gtest PROPERTIES INTERFACE_SYSTEM_INCLUDE_DIRECTORIES $) +-set_target_properties(gtest_main PROPERTIES INTERFACE_SYSTEM_INCLUDE_DIRECTORIES $) +-set_target_properties(gmock PROPERTIES INTERFACE_SYSTEM_INCLUDE_DIRECTORIES $) +-set_target_properties(gmock_main PROPERTIES INTERFACE_SYSTEM_INCLUDE_DIRECTORIES $) ++#add_subdirectory(${GOOGLETEST_SOURCE_DIR} ++# ${GOOGLETEST_BINARY_DIR} ++# EXCLUDE_FROM_ALL) ++ ++#set_target_properties(gtest PROPERTIES INTERFACE_SYSTEM_INCLUDE_DIRECTORIES $) ++#set_target_properties(gtest_main PROPERTIES INTERFACE_SYSTEM_INCLUDE_DIRECTORIES $) ++#set_target_properties(gmock PROPERTIES INTERFACE_SYSTEM_INCLUDE_DIRECTORIES $) ++#set_target_properties(gmock_main PROPERTIES INTERFACE_SYSTEM_INCLUDE_DIRECTORIES $) +diff --git a/cmake/GoogleTest.cmake.in b/cmake/GoogleTest.cmake.in +index 28818ee..13b0888 100644 +--- a/cmake/GoogleTest.cmake.in ++++ b/cmake/GoogleTest.cmake.in +@@ -31,7 +31,7 @@ if(EXISTS "${GOOGLETEST_PATH}" AND IS_DIRECTORY "${GOOGLETEST_PATH}" + ) + else() + if(NOT ALLOW_DOWNLOADING_GOOGLETEST) +- message(SEND_ERROR "Did not find Google Test sources! Either pass correct path in GOOGLETEST_PATH, or enable ALLOW_DOWNLOADING_GOOGLETEST, or disable BENCHMARK_ENABLE_GTEST_TESTS / BENCHMARK_ENABLE_TESTING.") ++ message(WARNING "Did not find Google Test sources! Either pass correct path in GOOGLETEST_PATH, or enable ALLOW_DOWNLOADING_GOOGLETEST, or disable BENCHMARK_ENABLE_GTEST_TESTS / BENCHMARK_ENABLE_TESTING.") + else() + message(WARNING "Did not find Google Test sources! Fetching from web...") + ExternalProject_Add( +@@ -51,8 +51,8 @@ else() + endif() + endif() + +-ExternalProject_Get_Property(googletest SOURCE_DIR BINARY_DIR) +-file(WRITE googletest-paths.cmake +-"set(GOOGLETEST_SOURCE_DIR \"${SOURCE_DIR}\") +-set(GOOGLETEST_BINARY_DIR \"${BINARY_DIR}\") +-") ++#ExternalProject_Get_Property(googletest SOURCE_DIR BINARY_DIR) ++#file(WRITE googletest-paths.cmake ++#"set(GOOGLETEST_SOURCE_DIR \"${SOURCE_DIR}\") ++#set(GOOGLETEST_BINARY_DIR \"${BINARY_DIR}\") ++#") +-- +2.22.0 + From d95503ab8273adb3d51cd7de550ea44539803f27 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 15 Jun 2019 09:13:48 +0200 Subject: [PATCH 033/224] gnu: libtirpc: Update to 1.1.4. * gnu/packages/onc-rpc.scm (libtirpc): Update to 1.1.4. --- gnu/packages/onc-rpc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/onc-rpc.scm b/gnu/packages/onc-rpc.scm index 64887212d3..3f67d91031 100644 --- a/gnu/packages/onc-rpc.scm +++ b/gnu/packages/onc-rpc.scm @@ -33,7 +33,7 @@ (define-public libtirpc (package (name "libtirpc") - (version "1.0.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/libtirpc/libtirpc/" @@ -41,7 +41,7 @@ version ".tar.bz2")) (sha256 (base32 - "0ppxl3k3nsz0qdakq844i2kj4fvh9h937lhx26bgmpmxq67sghw6")))) + "07anqypf7c719x9y683qz65cxllmzlgmlab2hlahrqcj4bq2k99c")))) (build-system gnu-build-system) (arguments `(#:phases From fd641a23f5438bb289041d9b738388ad26c5d343 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 15 Jun 2019 09:18:51 +0200 Subject: [PATCH 034/224] gnu: libnsl: Do not use unstable tarball. * gnu/packages/onc-rpc.scm (libnsl)[source]: Switch to GIT-FETCH. --- gnu/packages/onc-rpc.scm | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/gnu/packages/onc-rpc.scm b/gnu/packages/onc-rpc.scm index 3f67d91031..8f66b07527 100644 --- a/gnu/packages/onc-rpc.scm +++ b/gnu/packages/onc-rpc.scm @@ -23,6 +23,7 @@ #:use-module (guix licenses) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (gnu packages) #:use-module (gnu packages autotools) #:use-module (gnu packages gettext) @@ -105,13 +106,14 @@ universal addresses.") (name "libnsl") (version "1.2.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/thkukuk/libnsl/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/thkukuk/libnsl.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1y6kmxmv1difzvdhx7grqzw0j2v2b74mg4kjb803m8jcgkqqx8m5")))) + "1chzqhcgh0yia9js8mh92cmhyka7rh32ql6b3mgdk26n94dqzs8b")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) From af847bd88f729456b09f26831bd7164e6baae371 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 15 Jun 2019 09:22:40 +0200 Subject: [PATCH 035/224] gnu: xorg-server-for-tests: Update to 1.20.5. * gnu/packages/xorg.scm (xorg-server-for-tests)[source, version]: Remove. --- gnu/packages/xorg.scm | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 27966f038a..0f2231ca8d 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5198,16 +5198,7 @@ draggable titlebars and borders.") (define-public xorg-server-for-tests (hidden-package (package - (inherit xorg-server) - (version "1.20.4") - (source (origin - (inherit (package-source xorg-server)) - (uri (string-append - "mirror://xorg/individual/xserver/" - "xorg-server-" version ".tar.bz2")) - (sha256 - (base32 - "1vk6j7hmigfill9x8m7a6vvgb3s50ji2yf6yprbgqfz9xf9x83zy"))))))) + (inherit xorg-server)))) (define-public xorg-server-xwayland (package From c7fbf6186565ed24ebeee870b27a019a77525b5d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 15 Jun 2019 09:42:12 +0200 Subject: [PATCH 036/224] gnu: Remove leftover patch. This is a follow-up to commit d680a8afd1190aac46742d3abf2a0de1a45ea10f. * gnu/packages/patches/inkscape-poppler-compat3.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - .../patches/inkscape-poppler-compat3.patch | 499 ------------------ 2 files changed, 500 deletions(-) delete mode 100644 gnu/packages/patches/inkscape-poppler-compat3.patch diff --git a/gnu/local.mk b/gnu/local.mk index 9ff668ef8b..5b6dd31b11 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -932,7 +932,6 @@ dist_patch_DATA = \ %D%/packages/patches/id3lib-CVE-2007-4460.patch \ %D%/packages/patches/idris-test-no-node.patch \ %D%/packages/patches/ilmbase-fix-tests.patch \ - %D%/packages/patches/inkscape-poppler-compat3.patch \ %D%/packages/patches/intltool-perl-compatibility.patch \ %D%/packages/patches/irrlicht-use-system-libs.patch \ %D%/packages/patches/isl-0.11.1-aarch64-support.patch \ diff --git a/gnu/packages/patches/inkscape-poppler-compat3.patch b/gnu/packages/patches/inkscape-poppler-compat3.patch deleted file mode 100644 index eaaf7d93f1..0000000000 --- a/gnu/packages/patches/inkscape-poppler-compat3.patch +++ /dev/null @@ -1,499 +0,0 @@ -Fix compatibility with Poppler >= 0.69. - -This is a combination of these upstream commits: -https://gitlab.com/inkscape/inkscape/commit/722e121361d0f784083d10e897155b7d4e44e515 -https://gitlab.com/inkscape/inkscape/commit/402c0274420fe39fd2f3393bc7d8d8879d436358 - -...with slight adjustments for the 0.92.3 release tarball. - -diff --git a/CMakeScripts/DefineDependsandFlags.cmake b/CMakeScripts/DefineDependsandFlags.cmake ---- a/CMakeScripts/DefineDependsandFlags.cmake -+++ b/CMakeScripts/DefineDependsandFlags.cmake -@@ -116,18 +116,6 @@ if(ENABLE_POPPLER) - set(HAVE_POPPLER_GLIB ON) - endif() - endif() -- if(POPPLER_VERSION VERSION_GREATER "0.26.0" OR -- POPPLER_VERSION VERSION_EQUAL "0.26.0") -- set(POPPLER_EVEN_NEWER_COLOR_SPACE_API ON) -- endif() -- if(POPPLER_VERSION VERSION_GREATER "0.29.0" OR -- POPPLER_VERSION VERSION_EQUAL "0.29.0") -- set(POPPLER_EVEN_NEWER_NEW_COLOR_SPACE_API ON) -- endif() -- if(POPPLER_VERSION VERSION_GREATER "0.58.0" OR -- POPPLER_VERSION VERSION_EQUAL "0.58.0") -- set(POPPLER_NEW_OBJECT_API ON) -- endif() - else() - set(ENABLE_POPPLER_CAIRO OFF) - endif() -diff --git a/src/extension/internal/pdfinput/pdf-input.cpp b/src/extension/internal/pdfinput/pdf-input.cpp ---- a/src/extension/internal/pdfinput/pdf-input.cpp -+++ b/src/extension/internal/pdfinput/pdf-input.cpp -@@ -793,7 +793,7 @@ PdfInput::open(::Inkscape::Extension::Input * /*mod*/, const gchar * uri) { - dlg->getImportSettings(prefs); - - // Apply crop settings -- PDFRectangle *clipToBox = NULL; -+ _POPPLER_CONST PDFRectangle *clipToBox = NULL; - double crop_setting; - sp_repr_get_double(prefs, "cropTo", &crop_setting); - -diff --git a/src/extension/internal/pdfinput/pdf-input.h b/src/extension/internal/pdfinput/pdf-input.h ---- a/src/extension/internal/pdfinput/pdf-input.h -+++ b/src/extension/internal/pdfinput/pdf-input.h -@@ -15,6 +15,7 @@ - #endif - - #ifdef HAVE_POPPLER -+#include "poppler-transition-api.h" - - #include - -diff --git a/src/extension/internal/pdfinput/pdf-parser.cpp b/src/extension/internal/pdfinput/pdf-parser.cpp ---- a/src/extension/internal/pdfinput/pdf-parser.cpp -+++ b/src/extension/internal/pdfinput/pdf-parser.cpp -@@ -36,6 +36,7 @@ extern "C" { - #include "pdf-parser.h" - #include "util/units.h" - -+#include "glib/poppler-features.h" - #include "goo/gmem.h" - #include "goo/GooString.h" - #include "GlobalParams.h" -@@ -294,8 +295,8 @@ PdfParser::PdfParser(XRef *xrefA, - int /*pageNum*/, - int rotate, - Dict *resDict, -- PDFRectangle *box, -- PDFRectangle *cropBox) : -+ _POPPLER_CONST PDFRectangle *box, -+ _POPPLER_CONST PDFRectangle *cropBox) : - xref(xrefA), - builder(builderA), - subPage(gFalse), -@@ -317,7 +318,7 @@ PdfParser::PdfParser(XRef *xrefA, - builder->setDocumentSize(Inkscape::Util::Quantity::convert(state->getPageWidth(), "pt", "px"), - Inkscape::Util::Quantity::convert(state->getPageHeight(), "pt", "px")); - -- double *ctm = state->getCTM(); -+ const double *ctm = state->getCTM(); - double scaledCTM[6]; - for (int i = 0; i < 6; ++i) { - baseMatrix[i] = ctm[i]; -@@ -352,7 +353,7 @@ PdfParser::PdfParser(XRef *xrefA, - PdfParser::PdfParser(XRef *xrefA, - Inkscape::Extension::Internal::SvgBuilder *builderA, - Dict *resDict, -- PDFRectangle *box) : -+ _POPPLER_CONST PDFRectangle *box) : - xref(xrefA), - builder(builderA), - subPage(gTrue), -@@ -571,7 +572,7 @@ const char *PdfParser::getPreviousOperator(unsigned int look_back) { - - void PdfParser::execOp(Object *cmd, Object args[], int numArgs) { - PdfOperator *op; -- char *name; -+ const char *name; - Object *argPtr; - int i; - -@@ -619,7 +620,7 @@ void PdfParser::execOp(Object *cmd, Object args[], int numArgs) { - (this->*op->func)(argPtr, numArgs); - } - --PdfOperator* PdfParser::findOp(char *name) { -+PdfOperator* PdfParser::findOp(const char *name) { - int a = -1; - int b = numOps; - int cmp = -1; -@@ -1751,7 +1752,7 @@ void PdfParser::doShadingPatternFillFallback(GfxShadingPattern *sPat, - GBool stroke, GBool eoFill) { - GfxShading *shading; - GfxPath *savedPath; -- double *ctm, *btm, *ptm; -+ const double *ctm, *btm, *ptm; - double m[6], ictm[6], m1[6]; - double xMin, yMin, xMax, yMax; - double det; -@@ -1993,7 +1994,7 @@ void PdfParser::doFunctionShFill1(GfxFunctionShading *shading, - GfxColor color0M, color1M, colorM0, colorM1, colorMM; - GfxColor colors2[4]; - double functionColorDelta = colorDeltas[pdfFunctionShading-1]; -- double *matrix; -+ const double *matrix; - double xM, yM; - int nComps, i, j; - -@@ -2173,7 +2174,7 @@ void PdfParser::doPatchMeshShFill(GfxPatchMeshShading *shading) { - } - } - --void PdfParser::fillPatch(GfxPatch *patch, int nComps, int depth) { -+void PdfParser::fillPatch(_POPPLER_CONST GfxPatch *patch, int nComps, int depth) { - GfxPatch patch00 = blankPatch(); - GfxPatch patch01 = blankPatch(); - GfxPatch patch10 = blankPatch(); -@@ -2581,7 +2582,11 @@ void PdfParser::opShowSpaceText(Object args[], int /*numArgs*/) - } - } - -+#if POPPLER_CHECK_VERSION(0,64,0) - void PdfParser::doShowText(const GooString *s) { -+#else -+void PdfParser::doShowText(GooString *s) { -+#endif - GfxFont *font; - int wMode; - double riseX, riseY; -@@ -2590,11 +2595,15 @@ void PdfParser::doShowText(const GooString *s) { - double x, y, dx, dy, tdx, tdy; - double originX, originY, tOriginX, tOriginY; - double oldCTM[6], newCTM[6]; -- double *mat; -+ const double *mat; - Object charProc; - Dict *resDict; - Parser *oldParser; -+#if POPPLER_CHECK_VERSION(0,64,0) -+ const char *p; -+#else - char *p; -+#endif - int len, n, uLen; - - font = state->getFont(); -@@ -2630,7 +2639,7 @@ void PdfParser::doShowText(const GooString *s) { - double lineX = state->getLineX(); - double lineY = state->getLineY(); - oldParser = parser; -- p = g_strdup(s->getCString()); -+ p = s->getCString(); - len = s->getLength(); - while (len > 0) { - n = font->getNextChar(p, len, &code, -@@ -2685,7 +2694,7 @@ void PdfParser::doShowText(const GooString *s) { - - } else { - state->textTransformDelta(0, state->getRise(), &riseX, &riseY); -- p = g_strdup(s->getCString()); -+ p = s->getCString(); - len = s->getLength(); - while (len > 0) { - n = font->getNextChar(p, len, &code, -@@ -2731,7 +2740,11 @@ void PdfParser::opXObject(Object args[], int /*numArgs*/) - { - Object obj1, obj2, obj3, refObj; - -- char *name = g_strdup(args[0].getName()); -+#if POPPLER_CHECK_VERSION(0,64,0) -+ const char *name = args[0].getName(); -+#else -+ char *name = args[0].getName(); -+#endif - #if defined(POPPLER_NEW_OBJECT_API) - if ((obj1 = res->lookupXObject(name)).isNull()) { - #else -@@ -3656,7 +3669,6 @@ void PdfParser::opBeginImage(Object /*args*/[], int /*numArgs*/) - Stream *PdfParser::buildImageStream() { - Object dict; - Object obj; -- char *key; - Stream *str; - - // build dictionary -@@ -3674,26 +3686,17 @@ Stream *PdfParser::buildImageStream() { - obj.free(); - #endif - } else { -- key = copyString(obj.getName()); --#if defined(POPPLER_NEW_OBJECT_API) -- obj = parser->getObj(); --#else -- obj.free(); -- parser->getObj(&obj); --#endif -- if (obj.isEOF() || obj.isError()) { -- gfree(key); -+ Object obj2; -+ _POPPLER_CALL(obj2, parser->getObj); -+ if (obj2.isEOF() || obj2.isError()) { -+ _POPPLER_FREE(obj); - break; - } --#if defined(POPPLER_NEW_OBJECT_API) -- dict.dictAdd(key, std::move(obj)); -- } -- obj = parser->getObj(); --#else -- dict.dictAdd(key, &obj); -+ _POPPLER_DICTADD(dict, obj.getName(), obj2); -+ _POPPLER_FREE(obj); -+ _POPPLER_FREE(obj2); - } -- parser->getObj(&obj); --#endif -+ _POPPLER_CALL(obj, parser->getObj); - } - if (obj.isEOF()) { - error(errSyntaxError, getPos(), "End of file in inline image"); -diff --git a/src/extension/internal/pdfinput/pdf-parser.h b/src/extension/internal/pdfinput/pdf-parser.h ---- a/src/extension/internal/pdfinput/pdf-parser.h -+++ b/src/extension/internal/pdfinput/pdf-parser.h -@@ -9,6 +9,7 @@ - #define PDF_PARSER_H - - #ifdef HAVE_POPPLER -+#include "poppler-transition-api.h" - - #ifdef USE_GCC_PRAGMAS - #pragma interface -@@ -25,6 +26,7 @@ namespace Inkscape { - // TODO clean up and remove using: - using Inkscape::Extension::Internal::SvgBuilder; - -+#include "glib/poppler-features.h" - #include "goo/gtypes.h" - #include "Object.h" - -@@ -127,11 +129,14 @@ public: - - // Constructor for regular output. - PdfParser(XRef *xrefA, SvgBuilder *builderA, int pageNum, int rotate, -- Dict *resDict, PDFRectangle *box, PDFRectangle *cropBox); -+ Dict *resDict, -+ _POPPLER_CONST PDFRectangle *box, -+ _POPPLER_CONST PDFRectangle *cropBox); - - // Constructor for a sub-page object. - PdfParser(XRef *xrefA, Inkscape::Extension::Internal::SvgBuilder *builderA, -- Dict *resDict, PDFRectangle *box); -+ Dict *resDict, -+ _POPPLER_CONST PDFRectangle *box); - - virtual ~PdfParser(); - -@@ -185,7 +190,7 @@ private: - - void go(GBool topLevel); - void execOp(Object *cmd, Object args[], int numArgs); -- PdfOperator *findOp(char *name); -+ PdfOperator *findOp(const char *name); - GBool checkArg(Object *arg, TchkType type); - int getPos(); - -@@ -256,7 +261,7 @@ private: - double x2, double y2, GfxColor *color2, - int nComps, int depth); - void doPatchMeshShFill(GfxPatchMeshShading *shading); -- void fillPatch(GfxPatch *patch, int nComps, int depth); -+ void fillPatch(_POPPLER_CONST GfxPatch *patch, int nComps, int depth); - void doEndPath(); - - // path clipping operators -@@ -287,7 +292,12 @@ private: - void opMoveShowText(Object args[], int numArgs); - void opMoveSetShowText(Object args[], int numArgs); - void opShowSpaceText(Object args[], int numArgs); -+#if POPPLER_CHECK_VERSION(0,64,0) - void doShowText(const GooString *s); -+#else -+ void doShowText(GooString *s); -+#endif -+ - - // XObject operators - void opXObject(Object args[], int numArgs); -diff --git a/src/extension/internal/pdfinput/poppler-transition-api.h b/src/extension/internal/pdfinput/poppler-transition-api.h -new file mode 100644 ---- /dev/null -+++ b/src/extension/internal/pdfinput/poppler-transition-api.h -@@ -0,0 +1,39 @@ -+#ifndef SEEN_POPPLER_TRANSITION_API_H -+#define SEEN_POPPLER_TRANSITION_API_H -+ -+#include -+ -+#if POPPLER_CHECK_VERSION(0,70,0) -+#define _POPPLER_CONST const -+#else -+#define _POPPLER_CONST -+#endif -+ -+#if POPPLER_CHECK_VERSION(0,69,0) -+#define _POPPLER_DICTADD(dict, key, obj) (dict).dictAdd(key, std::move(obj)) -+#elif POPPLER_CHECK_VERSION(0,58,0) -+#define _POPPLER_DICTADD(dict, key, obj) (dict).dictAdd(copyString(key), std::move(obj)) -+#else -+#define _POPPLER_DICTADD(dict, key, obj) (dict).dictAdd(copyString(key), &obj) -+#endif -+ -+#if POPPLER_CHECK_VERSION(0,58,0) -+#define POPPLER_NEW_OBJECT_API -+#define _POPPLER_FREE(obj) -+#define _POPPLER_CALL(ret, func) (ret = func()) -+#define _POPPLER_CALL_ARGS(ret, func, ...) (ret = func(__VA_ARGS__)) -+#else -+#define _POPPLER_FREE(obj) (obj).free() -+#define _POPPLER_CALL(ret, func) (*func(&ret)) -+#define _POPPLER_CALL_ARGS(ret, func, ...) (*func(__VA_ARGS__, &ret)) -+#endif -+ -+#if POPPLER_CHECK_VERSION(0, 29, 0) -+#define POPPLER_EVEN_NEWER_NEW_COLOR_SPACE_API -+#endif -+ -+#if POPPLER_CHECK_VERSION(0, 25, 0) -+#define POPPLER_EVEN_NEWER_COLOR_SPACE_API -+#endif -+ -+#endif -diff --git a/src/extension/internal/pdfinput/svg-builder.cpp b/src/extension/internal/pdfinput/svg-builder.cpp ---- a/src/extension/internal/pdfinput/svg-builder.cpp -+++ b/src/extension/internal/pdfinput/svg-builder.cpp -@@ -625,7 +625,7 @@ gchar *SvgBuilder::_createPattern(GfxPattern *pattern, GfxState *state, bool is_ - if ( pattern != NULL ) { - if ( pattern->getType() == 2 ) { // Shading pattern - GfxShadingPattern *shading_pattern = static_cast(pattern); -- double *ptm; -+ const double *ptm; - double m[6] = {1, 0, 0, 1, 0, 0}; - double det; - -@@ -672,7 +672,7 @@ gchar *SvgBuilder::_createTilingPattern(GfxTilingPattern *tiling_pattern, - - Inkscape::XML::Node *pattern_node = _xml_doc->createElement("svg:pattern"); - // Set pattern transform matrix -- double *p2u = tiling_pattern->getMatrix(); -+ const double *p2u = tiling_pattern->getMatrix(); - double m[6] = {1, 0, 0, 1, 0, 0}; - double det; - det = _ttm[0] * _ttm[3] - _ttm[1] * _ttm[2]; // see LP Bug 1168908 -@@ -698,7 +698,7 @@ gchar *SvgBuilder::_createTilingPattern(GfxTilingPattern *tiling_pattern, - pattern_node->setAttribute("patternUnits", "userSpaceOnUse"); - // Set pattern tiling - // FIXME: don't ignore XStep and YStep -- double *bbox = tiling_pattern->getBBox(); -+ const double *bbox = tiling_pattern->getBBox(); - sp_repr_set_svg_double(pattern_node, "x", 0.0); - sp_repr_set_svg_double(pattern_node, "y", 0.0); - sp_repr_set_svg_double(pattern_node, "width", bbox[2] - bbox[0]); -@@ -751,7 +751,7 @@ gchar *SvgBuilder::_createTilingPattern(GfxTilingPattern *tiling_pattern, - */ - gchar *SvgBuilder::_createGradient(GfxShading *shading, double *matrix, bool for_shading) { - Inkscape::XML::Node *gradient; -- Function *func; -+ _POPPLER_CONST Function *func; - int num_funcs; - bool extend0, extend1; - -@@ -865,7 +865,7 @@ static bool svgGetShadingColorRGB(GfxShading *shading, double offset, GfxRGB *re - - #define INT_EPSILON 8 - bool SvgBuilder::_addGradientStops(Inkscape::XML::Node *gradient, GfxShading *shading, -- Function *func) { -+ _POPPLER_CONST Function *func) { - int type = func->getType(); - if ( type == 0 || type == 2 ) { // Sampled or exponential function - GfxRGB stop1, stop2; -@@ -877,9 +877,9 @@ bool SvgBuilder::_addGradientStops(Inkscape::XML::Node *gradient, GfxShading *sh - _addStopToGradient(gradient, 1.0, &stop2, 1.0); - } - } else if ( type == 3 ) { // Stitching -- StitchingFunction *stitchingFunc = static_cast(func); -- double *bounds = stitchingFunc->getBounds(); -- double *encode = stitchingFunc->getEncode(); -+ auto stitchingFunc = static_cast<_POPPLER_CONST StitchingFunction*>(func); -+ const double *bounds = stitchingFunc->getBounds(); -+ const double *encode = stitchingFunc->getEncode(); - int num_funcs = stitchingFunc->getNumFuncs(); - - // Add stops from all the stitched functions -@@ -890,7 +890,7 @@ bool SvgBuilder::_addGradientStops(Inkscape::XML::Node *gradient, GfxShading *sh - svgGetShadingColorRGB(shading, bounds[i + 1], &color); - // Add stops - if (stitchingFunc->getFunc(i)->getType() == 2) { // process exponential fxn -- double expE = (static_cast(stitchingFunc->getFunc(i)))->getE(); -+ double expE = (static_cast<_POPPLER_CONST ExponentialFunction*>(stitchingFunc->getFunc(i)))->getE(); - if (expE > 1.0) { - expE = (bounds[i + 1] - bounds[i])/expE; // approximate exponential as a single straight line at x=1 - if (encode[2*i] == 0) { // normal sequence -@@ -1020,9 +1020,9 @@ void SvgBuilder::updateFont(GfxState *state) { - GfxFont *font = state->getFont(); - // Store original name - if (font->getName()) { -- _font_specification = g_strdup(font->getName()->getCString()); -+ _font_specification = font->getName()->getCString(); - } else { -- _font_specification = (char*) "Arial"; -+ _font_specification = "Arial"; - } - - // Prune the font name to get the correct font family name -@@ -1030,7 +1030,7 @@ void SvgBuilder::updateFont(GfxState *state) { - char *font_family = NULL; - char *font_style = NULL; - char *font_style_lowercase = NULL; -- char *plus_sign = strstr(_font_specification, "+"); -+ const char *plus_sign = strstr(_font_specification, "+"); - if (plus_sign) { - font_family = g_strdup(plus_sign + 1); - _font_specification = plus_sign + 1; -@@ -1148,7 +1148,7 @@ void SvgBuilder::updateFont(GfxState *state) { - Inkscape::CSSOStringStream os_font_size; - double css_font_size = _font_scaling * state->getFontSize(); - if ( font->getType() == fontType3 ) { -- double *font_matrix = font->getFontMatrix(); -+ const double *font_matrix = font->getFontMatrix(); - if ( font_matrix[0] != 0.0 ) { - css_font_size *= font_matrix[3] / font_matrix[0]; - } -@@ -1193,7 +1193,7 @@ void SvgBuilder::updateTextPosition(double tx, double ty) { - void SvgBuilder::updateTextMatrix(GfxState *state) { - _flushText(); - // Update text matrix -- double *text_matrix = state->getTextMat(); -+ const double *text_matrix = state->getTextMat(); - double w_scale = sqrt( text_matrix[0] * text_matrix[0] + text_matrix[2] * text_matrix[2] ); - double h_scale = sqrt( text_matrix[1] * text_matrix[1] + text_matrix[3] * text_matrix[3] ); - double max_scale; -diff --git a/src/extension/internal/pdfinput/svg-builder.h b/src/extension/internal/pdfinput/svg-builder.h ---- a/src/extension/internal/pdfinput/svg-builder.h -+++ b/src/extension/internal/pdfinput/svg-builder.h -@@ -15,6 +15,7 @@ - #endif - - #ifdef HAVE_POPPLER -+#include "poppler-transition-api.h" - - class SPDocument; - namespace Inkscape { -@@ -80,7 +81,7 @@ struct SvgGlyph { - bool style_changed; // Set to true if style has to be reset - SPCSSAttr *style; - int render_mode; // Text render mode -- char *font_specification; // Pointer to current font specification -+ const char *font_specification; // Pointer to current font specification - }; - - /** -@@ -174,7 +175,7 @@ private: - void _addStopToGradient(Inkscape::XML::Node *gradient, double offset, - GfxRGB *color, double opacity); - bool _addGradientStops(Inkscape::XML::Node *gradient, GfxShading *shading, -- Function *func); -+ _POPPLER_CONST Function *func); - gchar *_createTilingPattern(GfxTilingPattern *tiling_pattern, GfxState *state, - bool is_stroke=false); - // Image/mask creation -@@ -202,7 +203,7 @@ private: - - SPCSSAttr *_font_style; // Current font style - GfxFont *_current_font; -- char *_font_specification; -+ const char *_font_specification; - double _font_scaling; - bool _need_font_update; - Geom::Affine _text_matrix; From 24087364f5267409078aec3a749e3cabe485d91b Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 15 Jun 2019 13:44:57 +0200 Subject: [PATCH 037/224] gnu: emacs-desktop-environment: Update to 0.2.2. * gnu/packages/emacs-xyz.scm (emacs-desktop-environment): Update to 0.2.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d341501cc0..37bf9a06b9 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -12494,7 +12494,7 @@ autosuggestions with: (define-public emacs-desktop-environment (package (name "emacs-desktop-environment") - (version "0.2.1") + (version "0.2.2") (source (origin (method git-fetch) @@ -12504,7 +12504,7 @@ autosuggestions with: (file-name (git-file-name name version)) (sha256 (base32 - "0n5sa94dwhnkfp3x42pggsbr5db38m85hl8ddb3qs7yfdi9bjm52")))) + "14ija2rrz3zjhjbzxg84j5fq6xph4ah7w9bkqnq37by040cydvhw")))) (build-system emacs-build-system) (home-page "https://gitlab.petton.fr/DamienCassou/desktop-environment") (synopsis "Control your GNU/Linux desktop environment from Emacs") From ddd401d28fb09f1f8ce96f2fc24226887a812412 Mon Sep 17 00:00:00 2001 From: Meiyo Peng Date: Sun, 9 Jun 2019 18:10:20 +0800 Subject: [PATCH 038/224] gnu: swayidle: Add elogind support. * gnu/packages/wm.scm (swayidle)[arguments]: Add #:configure-flags. [inputs]: Add elogind. Signed-off-by: Marius Bakke --- gnu/packages/wm.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index eac17e0837..d5344dc31d 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -1249,7 +1249,10 @@ modules for building a Wayland compositor.") (sha256 (base32 "04agcbhc473jkk7npb40i94ny8naykxzpjcw2lvl05kxv65y5d9v")))) (build-system meson-build-system) - (inputs `(("wayland" ,wayland))) + (arguments + `(#:configure-flags '("-Dlogind-provider=elogind"))) + (inputs `(("elogind" ,elogind) + ("wayland" ,wayland))) (native-inputs `(("pkg-config" ,pkg-config) ("scdoc" ,scdoc) ("wayland-protocols" ,wayland-protocols))) From f3d797005374e5333c7596fe86b4a524ab1b9b11 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 15 Jun 2019 17:38:16 +0200 Subject: [PATCH 039/224] services: Remove unneeded imports that led to cycles. Fixes . Reported by Jack Hill . * gnu/services/admin.scm: Remove unneeded import of (gnu services base). * gnu/services/mcron.scm: Likewise. --- gnu/services/admin.scm | 3 +-- gnu/services/mcron.scm | 1 - 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/gnu/services/admin.scm b/gnu/services/admin.scm index a3e43dd1c1..df3cb01646 100644 --- a/gnu/services/admin.scm +++ b/gnu/services/admin.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 Jan Nieuwenhuizen -;;; Copyright © 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -19,7 +19,6 @@ (define-module (gnu services admin) #:use-module (gnu packages admin) - #:use-module (gnu packages base) #:use-module (gnu services) #:use-module (gnu services mcron) #:use-module (gnu services shepherd) diff --git a/gnu/services/mcron.scm b/gnu/services/mcron.scm index fd84589c19..7238665404 100644 --- a/gnu/services/mcron.scm +++ b/gnu/services/mcron.scm @@ -18,7 +18,6 @@ (define-module (gnu services mcron) #:use-module (gnu services) - #:use-module (gnu services base) #:use-module (gnu services shepherd) #:autoload (gnu packages guile-xyz) (mcron) #:use-module (guix deprecation) From b3f02caeecbb393fedb0a5e3cb7189b5b0d4be54 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 15 Jun 2019 18:23:38 +0200 Subject: [PATCH 040/224] gnu: libmicrohttpd: Update to 0.9.64. * gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.64. --- gnu/packages/gnunet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm index 09fad6a268..f2f8647730 100644 --- a/gnu/packages/gnunet.scm +++ b/gnu/packages/gnunet.scm @@ -146,14 +146,14 @@ tool to extract metadata from a file and print the results.") (define-public libmicrohttpd (package (name "libmicrohttpd") - (version "0.9.63") + (version "0.9.64") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/libmicrohttpd/libmicrohttpd-" version ".tar.gz")) (sha256 (base32 - "173lj66crwvhzwp1r812sc5h1hda7g6lb9l1y5zf7w3pw4dnzhrp")))) + "03imzkd1hl2mkkpi84vg5xq9x6b58gwsv86ym85km0lhb7nxi4p7")))) (build-system gnu-build-system) (inputs `(("curl" ,curl) From d2de780272a000d72c0a2d3898f968c57fd2cf2e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 15 Jun 2019 18:24:52 +0200 Subject: [PATCH 041/224] gnu: dico: Update to 2.9. * gnu/packages/dico.scm (dico): Update to 2.9. --- gnu/packages/dico.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dico.scm b/gnu/packages/dico.scm index d96dbb86d9..f6ab56887c 100644 --- a/gnu/packages/dico.scm +++ b/gnu/packages/dico.scm @@ -38,14 +38,14 @@ (define-public dico (package (name "dico") - (version "2.7") + (version "2.9") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/dico/dico-" version ".tar.xz")) (sha256 (base32 - "0dg4aacnmlf3ljssd7dwh8z5644xzq8k1501mbsx8nz8p8a9mbsq")))) + "0i9xqhy3h5nlizcmav4mv5ay8ivdgn4l4k0k7fxix3fsc87nijyr")))) (build-system gnu-build-system) (arguments '(#:configure-flags (list (string-append "--with-guile-site-dir=" %output From 02dad49d423146c2f86df00df2466d6616c0f6a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 15 Jun 2019 18:28:13 +0200 Subject: [PATCH 042/224] gnu: gengetopt: Update to 2.23. * gnu/packages/popt.scm (gengetopt): Update to 2.23. [native-inputs]: New field. --- gnu/packages/popt.scm | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/gnu/packages/popt.scm b/gnu/packages/popt.scm index e3f5fa1895..7f6a2e8e6a 100644 --- a/gnu/packages/popt.scm +++ b/gnu/packages/popt.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2016 Ludovic Courtès +;;; Copyright © 2013, 2014, 2016, 2019 Ludovic Courtès ;;; Copyright © 2015, 2016 Ricardo Wurmus ;;; Copyright © 2017, 2019 Tobias Geerinckx-Rice ;;; @@ -24,7 +24,8 @@ #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) - #:use-module (guix licenses)) + #:use-module (guix licenses) + #:use-module (gnu packages texinfo)) (define-public argtable (package @@ -126,19 +127,21 @@ appropriately.") (define-public gengetopt (package (name "gengetopt") - (version "2.22.6") + (version "2.23") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/gengetopt/gengetopt-" - version ".tar.gz")) + version ".tar.xz")) (sha256 (base32 - "1xq1kcfs6hri101ss4dhym0jn96z4v6jdvx288mfywadc245mc1h")))) + "1b44fn0apsgawyqa4alx2qj5hls334mhbszxsy6rfr0q074swhdr")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported #:parallel-tests? #f)) ; likewise + (native-inputs + `(("texinfo" ,texinfo))) (synopsis "Create parsers for command line options") (description "GNU Gengetopt is a program to generate a C/C++ function for parsing From 25cb591ce4a76e774a7bca565b27330eed07148d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 15 Jun 2019 18:29:31 +0200 Subject: [PATCH 043/224] gnu: wget: Update to 1.20.3. * gnu/packages/wget.scm (wget): Update to 1.20.3. --- gnu/packages/wget.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index 2c1562fb49..7261137cab 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -46,7 +46,7 @@ (define-public wget (package (name "wget") - (version "1.20.1") + (version "1.20.3") (source (origin (method url-fetch) @@ -54,7 +54,7 @@ version ".tar.lz")) (sha256 (base32 - "0a29qsqxkk8145vkyy35q5a1wc7qzwx3qj3gmfrkmi9xs96yhqqg")))) + "1frajd86ds8vz2hprq30wq8ya89z9dcxnwm8nwk12bbc47l7qq39")))) (build-system gnu-build-system) (inputs `(("gnutls" ,gnutls) From a59902ff11a80ca55a8fc644aebe429c426386c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 15 Jun 2019 18:29:45 +0200 Subject: [PATCH 044/224] gnu: rush: Update to 1.9. * gnu/packages/rush.scm (rush): Update to 1.9. --- gnu/packages/rush.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/rush.scm b/gnu/packages/rush.scm index 1b4ea6bb5d..b1ba7daaaa 100644 --- a/gnu/packages/rush.scm +++ b/gnu/packages/rush.scm @@ -26,14 +26,14 @@ (define-public rush (package (name "rush") - (version "1.8") + (version "1.9") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/rush/rush-" version ".tar.gz")) (sha256 (base32 - "1vxdb81ify4xcyygh86250pi50krb16dkj42i5ii4ns3araiwckz")))) + "12x7dyi9vl3lwlv618156nzpi5s0li93wcx2c26h4z7la20yq2yk")))) (build-system gnu-build-system) (home-page "https://www.gnu.org/software/rush/") (synopsis "Restricted user (login) shell") From 494a8cd03af6607bde7c7c369cbdcc1e1aa2ccc2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 15 Jun 2019 18:29:58 +0200 Subject: [PATCH 045/224] gnu: units: Update to 2.19. * gnu/packages/maths.scm (units): Update to 2.19. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index a0a077cf99..6d8fb9cec5 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -290,13 +290,13 @@ programming language.") (define-public units (package (name "units") - (version "2.18") + (version "2.19") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/units/units-" version ".tar.gz")) (sha256 (base32 - "0y26kj349i048y4z3xrk90bvciw2j6ds3rka7r7yn3183hirr5b4")))) + "0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2")))) (build-system gnu-build-system) (inputs `(("readline" ,readline) From f5be51040c5535f9aefefb6c6a582279b5c44e16 Mon Sep 17 00:00:00 2001 From: Florian Pelz Date: Thu, 13 Jun 2019 19:17:05 +0200 Subject: [PATCH 046/224] services: Add usb-modeswitch-service-type. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/networking.scm (usb-modeswitch-service-type): New variable. (usb-modeswitch-configuration): New variable. (usb-modeswitch-sh): New procedure. (usb-modeswitch-configuration->udev-rules): New procedure. * doc/guix.texi (Networking Services): Document it. Signed-off-by: Ludovic Courtès --- doc/guix.texi | 35 ++++++++++++ gnu/services/networking.scm | 104 ++++++++++++++++++++++++++++++++++++ 2 files changed, 139 insertions(+) diff --git a/doc/guix.texi b/doc/guix.texi index 052be47bdb..bd535f82db 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -12668,6 +12668,41 @@ The ModemManager package to use. @end table @end deftp +@cindex USB_ModeSwitch +@cindex Modeswitching + +@defvr {Scheme Variable} usb-modeswitch-service-type +This is the service type for the +@uref{http://www.draisberghof.de/usb_modeswitch/, USB_ModeSwitch} service. The +value for this service type is a @code{usb-modeswitch-configuration} record. + +When plugged in, some USB modems (and other USB devices) initially present +themselves as a read-only storage medium and not as a modem. They need to be +@dfn{modeswitched} before they are usable. The USB_ModeSwitch service type +installs udev rules to automatically modeswitch these devices when they are +plugged in. +@end defvr + +@deftp {Data Type} usb-modeswitch-configuration +Data type representing the configuration of USB_ModeSwitch. + +@table @asis +@item @code{usb-modeswitch} (default: @code{usb-modeswitch}) +The USB_ModeSwitch package providing the binaries for modeswitching. + +@item @code{usb-modeswitch-data} (default: @code{usb-modeswitch-data}) +The package providing the device data and udev rules file used by +USB_ModeSwitch. + +@item @code{config-file} (default: @code{#~(string-append #$usb-modeswitch:dispatcher "/etc/usb_modeswitch.conf")}) +Which config file to use for the USB_ModeSwitch dispatcher. By default the +config file shipped with USB_ModeSwitch is used which disables logging to +@file{/var/log} among other default settings. If set to @code{#f}, no config +file is used. + +@end table +@end deftp + @cindex NetworkManager @defvr {Scheme Variable} network-manager-service-type diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index 082a85f63d..73acb3b17f 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Chris Marusich ;;; Copyright © 2018 Arun Isaac +;;; Copyright © 2019 Florian Pelz ;;; ;;; This file is part of GNU Guix. ;;; @@ -33,10 +34,13 @@ #:use-module (gnu system shadow) #:use-module (gnu system pam) #:use-module (gnu packages admin) + #:use-module (gnu packages base) + #:use-module (gnu packages bash) #:use-module (gnu packages connman) #:use-module (gnu packages freedesktop) #:use-module (gnu packages linux) #:use-module (gnu packages tor) + #:use-module (gnu packages usb-modeswitch) #:use-module (gnu packages messaging) #:use-module (gnu packages networking) #:use-module (gnu packages ntp) @@ -104,6 +108,12 @@ modem-manager-configuration? modem-manager-service-type + usb-modeswitch-configuration + usb-modeswitch-configuration? + usb-modeswitch-configuration-usb-modeswitch + usb-modeswitch-configuration-usb-modeswitch-data + usb-modeswitch-service-type + wpa-supplicant-configuration wpa-supplicant-configuration? @@ -1041,6 +1051,100 @@ a network connection manager.")))) ModemManager}, a modem management daemon that aims to simplify dialup networking.")))) + +;;; +;;; USB_ModeSwitch +;;; + +(define-record-type* + usb-modeswitch-configuration make-usb-modeswitch-configuration + usb-modeswitch-configuration? + (usb-modeswitch usb-modeswitch-configuration-usb-modeswitch + (default usb-modeswitch)) + (usb-modeswitch-data usb-modeswitch-configuration-usb-modeswitch-data + (default usb-modeswitch-data)) + (config-file usb-modeswitch-configuration-config-file + (default #~(string-append #$usb-modeswitch:dispatcher + "/etc/usb_modeswitch.conf")))) + +(define (usb-modeswitch-sh usb-modeswitch config-file) + "Build a copy of usb_modeswitch.sh located in package USB-MODESWITCH, +modified to pass the CONFIG-FILE in its calls to usb_modeswitch_dispatcher, +and wrap it to actually find the dispatcher in USB-MODESWITCH. The script +will be run by USB_ModeSwitch’s udev rules file when a modeswitchable USB +device is detected." + (computed-file + "usb_modeswitch-sh" + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + (let ((cfg-param + #$(if config-file + #~(string-append " --config-file=" #$config-file) + ""))) + (mkdir #$output) + (install-file (string-append #$usb-modeswitch:dispatcher + "/lib/udev/usb_modeswitch") + #$output) + + ;; insert CFG-PARAM into usb_modeswitch_dispatcher command-lines + (substitute* (string-append #$output "/usb_modeswitch") + (("(exec usb_modeswitch_dispatcher .*)( 2>>)" _ left right) + (string-append left cfg-param right)) + (("(exec usb_modeswitch_dispatcher .*)( &)" _ left right) + (string-append left cfg-param right))) + + ;; wrap-program needs bash in PATH: + (putenv (string-append "PATH=" #$bash "/bin")) + (wrap-program (string-append #$output "/usb_modeswitch") + `("PATH" ":" = (,(string-append #$coreutils "/bin") + ,(string-append + #$usb-modeswitch:dispatcher + "/bin"))))))))) + +(define (usb-modeswitch-configuration->udev-rules config) + "Build a rules file for extending udev-service-type from the rules in the +usb-modeswitch package specified in CONFIG. The rules file will invoke +usb_modeswitch.sh from the usb-modeswitch package, modified to pass the right +config file." + (match config + (($ usb-modeswitch data config-file) + (computed-file + "usb_modeswitch.rules" + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + (let ((in (string-append #$data "/udev/40-usb_modeswitch.rules")) + (out (string-append #$output "/lib/udev/rules.d")) + (script #$(usb-modeswitch-sh usb-modeswitch config-file))) + (mkdir-p out) + (chdir out) + (install-file in out) + (substitute* "40-usb_modeswitch.rules" + (("PROGRAM=\"usb_modeswitch") + (string-append "PROGRAM=\"" script "/usb_modeswitch")) + (("RUN\\+=\"usb_modeswitch") + (string-append "RUN+=\"" script "/usb_modeswitch")))))))))) + +(define usb-modeswitch-service-type + (service-type + (name 'usb-modeswitch) + (extensions + (list + (service-extension + udev-service-type + (lambda (config) + (let ((rules (usb-modeswitch-configuration->udev-rules config))) + (list rules)))))) + (default-value (usb-modeswitch-configuration)) + (description "Run @uref{http://www.draisberghof.de/usb_modeswitch/, +USB_ModeSwitch}, a mode switching tool for controlling USB devices with +multiple @dfn{modes}. When plugged in for the first time many USB +devices (primarily high-speed WAN modems) act like a flash storage containing +installers for Windows drivers. USB_ModeSwitch replays the sequence the +Windows drivers would send to switch their mode from storage to modem (or +whatever the thing is supposed to do)."))) + ;;; ;;; WPA supplicant From 7dbeb5a791fe6b8cb66ceb4e9261aa77f04e2fbc Mon Sep 17 00:00:00 2001 From: Florian Pelz Date: Wed, 12 Jun 2019 11:16:57 +0200 Subject: [PATCH 047/224] services: Include USB_ModeSwitch in %desktop-services. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . * gnu/services/desktop.scm (%desktop-services): Add usb-modeswitch-service-type. * doc/guix.texi (Networking Services): Document it. Signed-off-by: Ludovic Courtès --- doc/guix.texi | 3 +++ gnu/services/desktop.scm | 1 + 2 files changed, 4 insertions(+) diff --git a/doc/guix.texi b/doc/guix.texi index bd535f82db..033ad9ea8e 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -12681,6 +12681,9 @@ themselves as a read-only storage medium and not as a modem. They need to be @dfn{modeswitched} before they are usable. The USB_ModeSwitch service type installs udev rules to automatically modeswitch these devices when they are plugged in. + +This service is part of @code{%desktop-services} (@pxref{Desktop +Services}). @end defvr @deftp {Data Type} usb-modeswitch-configuration diff --git a/gnu/services/desktop.scm b/gnu/services/desktop.scm index 652f7b1b02..343d507c14 100644 --- a/gnu/services/desktop.scm +++ b/gnu/services/desktop.scm @@ -1067,6 +1067,7 @@ dispatches events from it."))) profile-service-type (list network-manager-applet)) (service modem-manager-service-type) + (service usb-modeswitch-service-type) ;; The D-Bus clique. (service avahi-service-type) From 121d9d1a7a2406a9b1cbe22c34343775f5955b34 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= Date: Wed, 12 Jun 2019 22:46:38 +0200 Subject: [PATCH 048/224] gnu: Add spdlog. * gnu/packages/logging.scm(spdlod): New variable. --- gnu/packages/logging.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/logging.scm b/gnu/packages/logging.scm index f1f3a4e8d3..e936733136 100644 --- a/gnu/packages/logging.scm +++ b/gnu/packages/logging.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2017 Stefan Reichör ;;; Copyright © 2017 Eric Bavier ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2019 Gábor Boskovits ;;; ;;; This file is part of GNU Guix. ;;; @@ -26,6 +27,7 @@ #:use-module (guix utils) #: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 python) #:use-module (gnu packages) @@ -181,3 +183,27 @@ commands, displaying the results via a web interface.") "MultiTail allows you to monitor logfiles and command output in multiple windows in a terminal, colorize, filter and merge.") (license license:gpl2+))) + +(define-public spdlog + (package + (name "spdlog") + (version "1.3.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gabime/spdlog.git") + (commit (string-append "v" version)))) + (sha256 + (base32 + "1rd4zmrlkcdjx0m0wpmjm1g9srj7jak6ai08qkhbn2lsn0niifzd")))) + (build-system cmake-build-system) + ;; TODO run benchmark. Currently not possible, as adding + ;; (gnu packages benchmark) forms a dependency cycle + (arguments + '(#:configure-flags + (list "-DSPDLOG_BUILD_BENCH=OFF"))) + (home-page "https://github.com/gabime/spdlog") + (synopsis "Fast C++ logging library") + (description "Spdlog is a very fast header-only/compiled C++ logging library.") + (license license:expat))) ; MIT license From 7a1d6a770878fe5a45af8763559a86da0258b0f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= Date: Wed, 12 Jun 2019 14:20:56 +0200 Subject: [PATCH 049/224] gnu: Add waybar. * gnu/packages/wm.scm(waybar): New variable. --- gnu/packages/wm.scm | 46 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index d5344dc31d..5737fea8d9 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -20,6 +20,7 @@ ;;; Copyright © 2018, 2019 Meiyo Peng ;;; Copyright © 2019 Rutger Helling ;;; Copyright © 2019 Timothy Sample +;;; Copyright © 2019 Gábor Boskovits ;;; ;;; This file is part of GNU Guix. ;;; @@ -85,6 +86,10 @@ #:use-module (gnu packages version-control) #:use-module (gnu packages man) #:use-module (gnu packages textutils) + #:use-module (gnu packages pretty-print) + #:use-module (gnu packages logging) + #:use-module (gnu packages serialization) + #:use-module (gnu packages commencement) ; TODO remove when default gcc version >=7 #:use-module (guix download) #:use-module (guix git-download)) @@ -1315,3 +1320,44 @@ modules for building a Wayland compositor.") (synopsis "Screen wallpaper utility for Wayland compositors") (description "Swaybg is a wallpaper utility for Wayland compositors.") (license license:expat))) ; MIT license + +(define-public waybar + (package + (name "waybar") + (version "0.6.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Alexays/Waybar.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0wyp1p9r1k8jnjq8clp2fx8xa3f4lfrgbp67fxrjh9718p4br0ab")))) + (build-system meson-build-system) + (arguments + `(#:configure-flags + (list (string-append "-Dout=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + ;; TODO remove when issue #30756 is resolved + (add-before 'configure 'fix-gcc + (lambda _ + (unsetenv "C_INCLUDE_PATH") + (unsetenv "CPLUS_INCLUDE_PATH") + #t))))) + (inputs `(("fmt" ,fmt) + ("gtkmm" ,gtkmm) + ("jsoncpp" ,jsoncpp) + ("libinput" ,libinput) + ("spdlog" ,spdlog) + ("wayland" ,wayland))) + (native-inputs `(("gcc-toolchain" ,gcc-toolchain-7) ; TODO remove when default gcc version >=7 + ("glib:bin" ,glib "bin") + ("pkg-config" ,pkg-config) + ("wayland-protocols" ,wayland-protocols))) + (home-page "https://github.com/Alexays/Waybar") + (synopsis "Wayland bar for Sway and Wlroots based compositors.") + (description "Waybar is a highly customisable Wayland bar for Sway and +Wlroots based compositors.") + (license license:expat))) ; MIT license From 466595eeb246a47d93cd4f320f5d2f2703532692 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 16 Jun 2019 04:08:06 -0400 Subject: [PATCH 050/224] gnu: linux-libre@4.14: Update to 4.14.126. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.126. (%linux-libre-4.14-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index ec0ac2add2..57b53cbe9c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -466,8 +466,8 @@ It has been modified to remove all non-free binary blobs.") (make-linux-libre-headers %linux-libre-4.19-version %linux-libre-4.19-hash)) -(define %linux-libre-4.14-version "4.14.125") -(define %linux-libre-4.14-hash "1ms7ai7c6xspq8r2amgjfsdyl87x10dc4b1c3iacrhrxaqqmab01") +(define %linux-libre-4.14-version "4.14.126") +(define %linux-libre-4.14-hash "111whcprb72mdr4ivy49va1xx9qmnbqwgli4ql52g49ssfxkvc2c") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version From fc6290fb1fd6dead7e2a669d6fcdf829fd4e9873 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 16 Jun 2019 04:09:12 -0400 Subject: [PATCH 051/224] gnu: linux-libre@4.19: Update to 4.19.51. * gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.51. (%linux-libre-4.19-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 57b53cbe9c..a3c52080de 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -448,8 +448,8 @@ It has been modified to remove all non-free binary blobs.") (make-linux-libre-headers %linux-libre-version %linux-libre-hash)) -(define %linux-libre-4.19-version "4.19.50") -(define %linux-libre-4.19-hash "0j1p459al3y77cv2xwjx7ppghc8ixs3wm3w9a10sc3ckbq1hw8ly") +(define %linux-libre-4.19-version "4.19.51") +(define %linux-libre-4.19-hash "0xzgwv70inddbml8nvfknp2zaz5dvs00nzqa1r9iqmsxlmssipz7") (define %linux-libre-4.19-patches (list %boot-logo-patch From 86c05c4465dee12f140baff107dab1816214305b Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 16 Jun 2019 04:11:07 -0400 Subject: [PATCH 052/224] gnu: linux-libre: Update to 5.1.10. * gnu/packages/linux.scm (%linux-libre-version): Update to 5.1.10. (%linux-libre-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a3c52080de..caa121c49a 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -430,8 +430,8 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." It has been modified to remove all non-free binary blobs.") (license license:gpl2))) -(define %linux-libre-version "5.1.9") -(define %linux-libre-hash "1l1nhq3giqyv7zir1sl8m32xbbpmqhsw8dgf90kf4qcnh6bvjin1") +(define %linux-libre-version "5.1.10") +(define %linux-libre-hash "0gpvp3p927wg31gmh4bakxcvzanx68s7d6dj6v89md7z146954k9") (define %linux-libre-5.1-patches (list %boot-logo-patch From 8bae6c744c9074727ca446ac4c1bfd0a31eca222 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 16 Jun 2019 14:26:38 +0300 Subject: [PATCH 053/224] gnu: keepassxc: Update to 2.4.3. * gnu/packages/password-utils.scm (keepassxc): Update to 2.4.3. --- gnu/packages/password-utils.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index ed890f73c3..10d04b1dbc 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Steve Sprang -;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner +;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner ;;; Copyright © 2015 Aljosha Papsch ;;; Copyright © 2016 Christopher Allan Webber ;;; Copyright © 2016 Jessica Tallon @@ -108,7 +108,7 @@ human.") (define-public keepassxc (package (name "keepassxc") - (version "2.4.2") + (version "2.4.3") (source (origin (method url-fetch) @@ -117,7 +117,7 @@ human.") version "-src.tar.xz")) (sha256 (base32 - "0f31lmpbkw0wrhq0qa4yw5b51bjv7vqp3ikr355qcm905456vyhm")))) + "0d17izx6qvcsxsxlsmaa17rgn38fvxsp5yzqqf4pc11i44cm5jfp")))) (build-system cmake-build-system) (arguments '(#:configure-flags '("-DWITH_XC_NETWORKING=YES" From 4fce1ff1299e78770828f4e2fb35e61063b0b9dc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 16 Jun 2019 02:00:33 +0200 Subject: [PATCH 054/224] gnu: Add font-anonymous-pro-minus. * gnu/packages/fonts.scm (font-anonymous-pro-minus): New public variable. --- gnu/packages/fonts.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 0ac0b7b207..c24e58de0d 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -613,6 +613,28 @@ character set, with support for most Western and Central European Latin-based languages, plus Greek and Cyrillic.") (license license:silofl1.1))) +(define-public font-anonymous-pro-minus + (package + (inherit font-anonymous-pro) + (name "font-anonymous-pro-minus") + ;; The -Minus variant doesn't necessarily track the regular version above. + (version "1.003") + (source + (origin + (method url-fetch) + (uri (string-append "https://www.marksimonson.com/assets/content/fonts/" + "AnonymousProMinus-" version ".zip")) + (sha256 + (base32 "1p2n91jja37d2cshp5pjwld9lq0v7gnpk7ywwn2blq7k46q6vq38")))) + (synopsis "Fixed-width fonts designed with coding in mind, without bitmaps") + (description "Anonymous Pro is a family of four fixed-width fonts designed +with coding in mind. Anonymous Pro features an international, Unicode-based +character set, with support for most Western and Central European Latin-based +languages, plus Greek and Cyrillic. + +Anonymous Pro Minus is identical to Anonymous Pro, minus its embedded bitmaps +for use at smaller text sizes"))) + (define-public font-gnu-unifont (package (name "font-gnu-unifont") From fa67073f13a889589b4b0207e83891fe9226f2dc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 16 Jun 2019 02:58:43 +0200 Subject: [PATCH 055/224] gnu: dstat: Fix Python 3 deprecation warning. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/admin.scm (dstat)[arguments]: Add ‘fix-python3-DeprecationWarning’ phase. --- gnu/packages/admin.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 9392c59521..a897afdc0e 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2142,6 +2142,11 @@ results (ndiff), and a packet generation and response analysis tool (nping).") "prefix=/")) #:phases (modify-phases %standard-phases + (add-after 'unpack 'fix-python3-DeprecationWarning + (lambda _ + (substitute* "dstat" + (("collections") "collections.abc")) + #t)) (delete 'configure) ; no configure script (add-after 'install 'wrap (lambda* (#:key outputs #:allow-other-keys) @@ -2150,8 +2155,6 @@ results (ndiff), and a packet generation and response analysis tool (nping).") `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))) #t)))))) (inputs - ;; Python 3 is supposedly supported but prints a DeprecationWarning. - ;; Upstream is dead. See . `(("python" ,python-wrapper) ("python-six" ,python-six))) (synopsis "Versatile resource statistics tool") From 10a32973893f5229c963241b6339ecab05b6098e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 16 Jun 2019 03:00:29 +0200 Subject: [PATCH 056/224] gnu: dstat: Add two patches, fix two bugs. * gnu/packages/admin.scm (dstat)[source]: Add patches. * gnu/packages/patches/dstat-fix-crash-when-specifying-delay.patch, gnu/packages/patches/dstat-skip-devices-without-io.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. --- gnu/local.mk | 2 + gnu/packages/admin.scm | 4 +- ...stat-fix-crash-when-specifying-delay.patch | 48 +++++++++++++++++++ .../dstat-skip-devices-without-io.patch | 32 +++++++++++++ 4 files changed, 85 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/dstat-fix-crash-when-specifying-delay.patch create mode 100644 gnu/packages/patches/dstat-skip-devices-without-io.patch diff --git a/gnu/local.mk b/gnu/local.mk index 5b6dd31b11..da3245ea18 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -753,6 +753,8 @@ dist_patch_DATA = \ %D%/packages/patches/docker-use-fewer-modprobes.patch \ %D%/packages/patches/dovecot-trees-support-dovecot-2.3.patch \ %D%/packages/patches/doxygen-test.patch \ + %D%/packages/patches/dstat-fix-crash-when-specifying-delay.patch \ + %D%/packages/patches/dstat-skip-devices-without-io.patch \ %D%/packages/patches/dvd+rw-tools-add-include.patch \ %D%/packages/patches/elfutils-tests-ptrace.patch \ %D%/packages/patches/elixir-path-length.patch \ diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index a897afdc0e..4ae0733fbb 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2133,7 +2133,9 @@ results (ndiff), and a packet generation and response analysis tool (nping).") (commit (string-append "v" version)))) (file-name (git-file-name "dstat" version)) (sha256 - (base32 "1qnmkhqmjd1m3if05jj29dvr5hn6kayq9bkkkh881w472c0zhp8v")))) + (base32 "1qnmkhqmjd1m3if05jj29dvr5hn6kayq9bkkkh881w472c0zhp8v")) + (patches (search-patches "dstat-fix-crash-when-specifying-delay.patch" + "dstat-skip-devices-without-io.patch")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no make check diff --git a/gnu/packages/patches/dstat-fix-crash-when-specifying-delay.patch b/gnu/packages/patches/dstat-fix-crash-when-specifying-delay.patch new file mode 100644 index 0000000000..0b59387dc9 --- /dev/null +++ b/gnu/packages/patches/dstat-fix-crash-when-specifying-delay.patch @@ -0,0 +1,48 @@ +From: Tobias Geerinckx-Rice +Date: Sun, 16 Jun 2019 02:34:10 +0200 +Subject: [PATCH] gnu: dstat: Fix crash when specifying a delay. + +Taken verbatim from a pull request[0] that will never be merged. + +[0]: https://github.com/dagwieers/dstat/pull/167 + +From 220a785321b13b6df92a536080aca6ef1cb644ad Mon Sep 17 00:00:00 2001 +From: Falko Goettsch +Date: Mon, 11 Mar 2019 20:12:49 -0700 +Subject: [PATCH] Fixed bug when specifying a delay + +The division in the 'loop' calculation in perform() was returning floating point values +after the migration to Python 3, rather than rounding down. Changed to floor division. + +I think the floating point values kept 'loop == 0' from ever being +true and the variables inside that conditional were never initialized, +causing the following error when a delay other than 1 was specified: + +You did not select any stats, using -cdngy by default. +Traceback (most recent call last): + File "/home/falko/repos/dstat/dstat", line 2825, in + main() + File "/home/falko/repos/dstat/dstat", line 2684, in main + scheduler.run() + File "/home/falko/.conda/envs/python3/lib/python3.7/sched.py", line 151, in run + action(*argument, **kwargs) + File "/home/falko/repos/dstat/dstat", line 2729, in perform + oldcols = cols +NameError: name 'cols' is not defined +--- + dstat | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/dstat b/dstat +index 9359965..3b4980f 100755 +--- a/dstat ++++ b/dstat +@@ -2697,7 +2697,7 @@ def perform(update): + + starttime = time.time() + +- loop = (update - 1 + op.delay) / op.delay ++ loop = (update - 1 + op.delay) // op.delay + step = ((update - 1) % op.delay) + 1 + + ### Get current time (may be different from schedule) for debugging diff --git a/gnu/packages/patches/dstat-skip-devices-without-io.patch b/gnu/packages/patches/dstat-skip-devices-without-io.patch new file mode 100644 index 0000000000..eb0910f501 --- /dev/null +++ b/gnu/packages/patches/dstat-skip-devices-without-io.patch @@ -0,0 +1,32 @@ +From: Tobias Geerinckx-Rice +Date: Sun, 16 Jun 2019 02:36:23 +0200 +Subject: [PATCH] gnu: dstat: Skip devices without I/O. + +Taken verbatim from a pull request[0] that will never be merged. + +[0]: https://github.com/dagwieers/dstat/pull/164 + +From 0988589ea4ee092b285bd4049d56add5f61e3f69 Mon Sep 17 00:00:00 2001 +From: Tobias Gruetzmacher +Date: Fri, 15 Feb 2019 18:46:57 +0100 +Subject: [PATCH] Skip devices without I/O + +Linux 4.18+ has added more fields to the diskstats proc file, so the +original skip condition for devices without I/O didn't apply anymore. +--- + dstat | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/dstat b/dstat +index 9359965..5c2fb53 100755 +--- a/dstat ++++ b/dstat +@@ -763,7 +763,7 @@ class dstat_disk(dstat): + ret = [] + for l in self.splitlines(): + if len(l) < 13: continue +- if l[3:] == ['0',] * 11: continue ++ if l[3:] == ['0',] * (len(l) - 3): continue + name = l[2] + ret.append(name) + for item in objlist: ret.append(item) From 914bba28096c1b85e368537c02e9841258887acb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 16 Jun 2019 19:41:21 +0200 Subject: [PATCH 057/224] gnu: docker-compose: Add required Python dependencies. * gnu/packages/python-xyz.scm (python-jsonschema-2.6): New old public variable. * gnu/packages/docker.scm (docker-compose)[inputs]: Add python-docker-pycreds and use python-jsonschema-2.6. --- gnu/packages/docker.scm | 5 ++++- gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++ 2 files changed, 30 insertions(+), 1 deletion(-) diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index eb76b85676..bb981665d6 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -91,6 +91,8 @@ pseudo-terminal (PTY) allocated to a Docker container using the Python client.") (license license:asl2.0))) +;; When updating, check whether python-jsonschema-2.6 can be removed from Guix +;; entirely. (define-public docker-compose (package (name "docker-compose") @@ -107,9 +109,10 @@ client.") (arguments '(#:tests? #f)) (inputs `(("python-docker-py" ,python-docker-py) + ("python-docker-pycreds" ,python-docker-pycreds) ("python-dockerpty" ,python-dockerpty) ("python-docopt" ,python-docopt) - ("python-jsonschema" ,python-jsonschema) + ("python-jsonschema" ,python-jsonschema-2.6) ("python-pyyaml" ,python-pyyaml) ("python-requests" ,python-requests-2.7) ("python-six" ,python-six) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a7c88e9187..284ecbd441 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1966,6 +1966,32 @@ between Julian dates and Gregorian dates.") `(("python2-functools32" ,python2-functools32) ,@(package-propagated-inputs jsonschema)))))) +;; This old version is still required by docker-compose as of 1.24.0. +(define-public python-jsonschema-2.6 + (package + (name "python-jsonschema") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "jsonschema" version)) + (sha256 + (base32 + "00kf3zmpp9ya4sydffpifn0j0mzm342a2vzh82p6r0vh10cg7xbg")))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check (lambda _ (invoke "nosetests")))))) + (native-inputs + `(("python-nose" ,python-nose) + ("python-vcversioner" ,python-vcversioner))) + (home-page "https://github.com/Julian/jsonschema") + (synopsis "Implementation of JSON Schema for Python") + (description + "Jsonschema is an implementation of JSON Schema for Python.") + (license license:expat) + (properties `((python2-variant . ,(delay python2-jsonschema)))))) + (define-public python-schema (package (name "python-schema") From 562a2a40952b06cb6c64d97539984d0c10007a31 Mon Sep 17 00:00:00 2001 From: Jesse Gibbons Date: Thu, 13 Jun 2019 18:48:43 -0600 Subject: [PATCH 058/224] gnu: Add freeorion * gnu/packages/games.scm (freeorion): New variable. --- gnu/packages/games.scm | 70 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 86bdf99a32..eed409135b 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -7455,3 +7455,73 @@ steam locomotive across many levels and collect all the coaches to win.") ;; The project is dual-licensed GPL2+ and GPL3+. (license (list license:gpl2+ license:gpl3+)))) + +(define-public freeorion + (package + (name "freeorion") + (version "0.4.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/freeorion/freeorion.git") + ;; Most recent stable release uses boost_signals (v1) which was + ;; later replaced with boost-signals2 and no longer exists. This + ;; commit builds and runs. + ;; + ;; TODO: Update this when the next stable release when it is + ;; available. + (commit "470d0711537804df3c2ca25532f674ab4bec58af"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1wsw632l1cj17px6i88nqjzs0dngp5rsr67n6qkkjlfjfxi69j0f")) + (modules '((guix build utils))) + (snippet + '(begin + ;; There are some bundled fonts. + (for-each delete-file-recursively '("default/data/fonts")) + #t)))) + (build-system cmake-build-system) + (arguments + '(#:tests? #f ;no test + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unbundle-fonts + (lambda* (#:key inputs #:allow-other-keys) + (let ((roboto-dir (string-append (assoc-ref inputs "font-roboto") + "/share/fonts/truetype/"))) + (substitute* "UI/ClientUI.cpp" + (("\\(GetRootDataDir.*?\"Roboto-(Bold|Regular)\\.ttf\"\\)\\.string\\(\\)\\);" + all type) + (string-append "\"" roboto-dir "Roboto-" type "\");"))) + #t)))))) + (inputs + `(("boost" ,boost) + ("boost_signals" ,boost-signals2) + ("font-dejavu" ,font-dejavu) + ("font-roboto" ,font-google-roboto) + ("freetype2" ,freetype) + ("glew" ,glew) + ("glu" ,glu) + ("libogg" ,libogg) + ("libpng" ,libpng) + ("libvorbis" ,libvorbis) + ("openal" ,openal) + ("python2" ,python-2.7) + ("sdl2" ,sdl2) + ("zlib" ,zlib))) + (home-page "https://www.freeorion.org/index.php/Main_Page") + (synopsis "Turn-based space empire and galactic conquest computer game") + (description + "FreeOrion is a turn-based space empire and galactic conquest (4X) +computer game being designed and built by the FreeOrion project. Control an +empire with the goal of exploring the galaxy, expanding your territory, +exploiting the resources, and exterminating rival alien empires. FreeOrion is +inspired by the tradition of the Master of Orion games, but is not a clone or +remake of that series or any other game.") + ;; Source code is released under gpl2. Artwork, music and sounds, and + ;; in-game text are released under cc-by-sa3.0. Game content scripts are + ;; released under both gpl2 and cc-by-sa3.0. Bundled Gigi library is + ;; released under lgpl2.1+. + (license (list license:gpl2 license:cc-by-sa3.0 license:lgpl2.1+)))) From 8fadac95771e6dc8114f5940c5667e9da4e5e85b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 16 Jun 2019 22:02:41 +0200 Subject: [PATCH 059/224] gnu: suil: Update to 0.10.4. * gnu/packages/audio.scm (suil): Update to 0.10.4. --- gnu/packages/audio.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 9defc59b93..290f8ceb67 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2428,17 +2428,17 @@ the Turtle syntax.") (define-public suil (package (name "suil") - (version "0.10.2") + (version "0.10.4") (source (origin - (method url-fetch) - (uri (string-append "https://download.drobilla.net/suil-" - version ".tar.bz2")) - (sha256 - (base32 - "00d43m0nai63ajb7rkm9v084jcih206y17ib3160zcvzc885ji4z")))) + (method url-fetch) + (uri (string-append "https://download.drobilla.net/suil-" + version ".tar.bz2")) + (sha256 + (base32 + "0ay7hl6nr6ip1nn9k2m8ri3b52b6sx9mhixmcy4fy3kr2a88ksd1")))) (build-system waf-build-system) (arguments - `(#:tests? #f ; no check target + `(#:tests? #f ; no check target #:configure-flags '("CXXFLAGS=-std=gnu++11"))) (inputs From 3abc9cc2426181e803dd882753e724d70b512f06 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 00:40:03 +0200 Subject: [PATCH 060/224] gnu: knot: Update to 2.8.2. * gnu/packages/dns.scm (knot): Update to 2.8.2. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 291139ef1b..e92235429b 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -577,14 +577,14 @@ Extensions} (DNSSEC).") (define-public knot (package (name "knot") - (version "2.8.1") + (version "2.8.2") (source (origin (method url-fetch) (uri (string-append "https://secure.nic.cz/files/knot-dns/" "knot-" version ".tar.xz")) (sha256 - (base32 "1im2wb8hl394mzni1wavmvfqd7il8s28kcz8w3s4v05nbhzg06xj")) + (base32 "0dx1lp4w33rpa54nns41k4vfdfin6naaskwh132r4qs0l9hl7lh0")) (modules '((guix build utils))) (snippet '(begin From 935e4b3abdc27b4a8777050c3f46753aab5c1f7d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 00:50:30 +0200 Subject: [PATCH 061/224] gnu: nsd: Update to 4.2.0. * gnu/packages/dns.scm (nsd): Update to 4.2.0. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index e92235429b..3ff83bcadb 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -302,14 +302,14 @@ asynchronous fashion.") (define-public nsd (package (name "nsd") - (version "4.1.27") + (version "4.2.0") (source (origin (method url-fetch) (uri (string-append "https://www.nlnetlabs.nl/downloads/nsd/nsd-" version ".tar.gz")) (sha256 - (base32 "1sjfbwr4vq25304hr9vmd9j821g2vzv8lpy95hpsravc80q5zaqv")))) + (base32 "0k57xl3ybdnqjqw9a3dmi7l6qmhkiic6wsghkz08ir809aj1rpsi")))) (build-system gnu-build-system) (arguments `(#:configure-flags From e605820bc568939389f39420d8fee8b9b522779c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 00:55:26 +0200 Subject: [PATCH 062/224] gnu: radare2: Don't use NAME in source URI. * gnu/packages/engineering.scm (radare2)[source]: Hard-code NAME. --- gnu/packages/engineering.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 9b0f00c7be..c63e900c0b 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -1252,7 +1252,7 @@ bindings for Python, Java, OCaml and more.") (source (origin (method url-fetch) (uri (string-append "http://radare.mikelloc.com/get/" version "/" - name "-" version ".tar.gz")) + "radare2-" version ".tar.gz")) (sha256 (base32 "17h4ba5qqahfi8mi4x2dcvq87cqpir5v2dlaqbvmay6vby4zh4v7")) From a157fb2723597e82a6bcaa90bc35531fe595859e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 00:56:04 +0200 Subject: [PATCH 063/224] gnu: radare2: Download over HTTPS. * gnu/packages/engineering.scm (radare2)[source]: Use HTTPS. --- gnu/packages/engineering.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index c63e900c0b..ad70c0878f 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -1251,7 +1251,7 @@ bindings for Python, Java, OCaml and more.") (version "2.5.0") (source (origin (method url-fetch) - (uri (string-append "http://radare.mikelloc.com/get/" version "/" + (uri (string-append "https://radare.mikelloc.com/get/" version "/" "radare2-" version ".tar.gz")) (sha256 (base32 From 58637415bedb8a91d916ab6ed6f318f7b7023c00 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 03:02:34 +0200 Subject: [PATCH 064/224] gnu: youtube-viewer: Refer to youtube-dl. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/video.scm (youtube-viewer)[inputs]: Add youtube-dl. [arguments]: Add ‘refer-to-inputs’ phase. --- gnu/packages/video.scm | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index d1fdd12177..760c057ac0 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1627,7 +1627,10 @@ audio, images) from the Web. It can use either mpv or vlc for playback.") ("perl-libwww" ,perl-libwww) ("perl-lwp-protocol-https" ,perl-lwp-protocol-https) ("perl-mozilla-ca" ,perl-mozilla-ca) - ("perl-unicode-linebreak" ,perl-unicode-linebreak))) + ("perl-unicode-linebreak" ,perl-unicode-linebreak) + + ;; Some videos play without youtube-dl, but others silently fail to. + ("youtube-dl" ,youtube-dl))) (arguments `(#:modules ((guix build perl-build-system) (guix build utils) @@ -1635,6 +1638,13 @@ audio, images) from the Web. It can use either mpv or vlc for playback.") #:module-build-flags '("--gtk") #:phases (modify-phases %standard-phases + (add-after 'unpack 'refer-to-inputs + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "lib/WWW/YoutubeViewer.pm" + (("'youtube-dl'") + (format #f "'~a/bin/youtube-dl'" + (assoc-ref inputs "youtube-dl")))) + #t)) (add-after 'install 'install-desktop (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) From d1a3a8e15ea3ae1648269b88de1665f4e87e0835 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 03:02:50 +0200 Subject: [PATCH 065/224] gnu: guile-picture-language: Update to 0.0.1-1-91d10c9. * gnu/packages/guile-xyz.scm (guile-picture-language): Update to 0.0.1-1-91d10c9. [build-system]: Use gnu-build-system. [native-inputs]: Add autoconf, automake, imagemagick, pkg-config, and texinfo. --- gnu/packages/guile-xyz.scm | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 191f32c321..6e19a38863 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -60,6 +60,7 @@ #:use-module (gnu packages guile) #:use-module (gnu packages hurd) #:use-module (gnu packages image) + #:use-module (gnu packages imagemagick) #:use-module (gnu packages libffi) #:use-module (gnu packages libunistring) #:use-module (gnu packages linux) @@ -1978,11 +1979,11 @@ format is also supported.") (deprecated-package "mcron2" mcron)) (define-public guile-picture-language - (let ((commit "1ea8b78a8bceb4f7e5eaeb3e76987072267f99bb") - (revision "2")) + (let ((commit "91d10c96708d732145006dd2802acc4de08b632e") + (revision "1")) (package (name "guile-picture-language") - (version (git-version "0" revision commit)) + (version (git-version "0.0.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -1990,10 +1991,16 @@ format is also supported.") (commit commit))) (sha256 (base32 - "1rvq6q2zq21x7dx0qq1hn568wglsl4bkd8gacbarcx1fs0rrxcqw")))) - (build-system guile-build-system) + "1ydvw9dvssdvlvhh1dr8inyzy2x6m41qgp8hsivca1xysr4gc23a")))) + (build-system gnu-build-system) (inputs `(("guile" ,guile-2.2))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("imagemagick" ,imagemagick) + ("pkg-config" ,pkg-config) + ("texinfo" ,texinfo))) (home-page "https://git.elephly.net/software/guile-picture-language.git") (synopsis "Picture language for Guile") (description From bb6c8f207b43d7de8ef061edfaaa1c28e9c7bccb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:50:45 +0200 Subject: [PATCH 066/224] gnu: guile-gi: Update to 0.0.2. * gnu/packages/guile-xyz.scm (guile-gi): Update to 0.0.2. [source]: Fetch using url-fetch. [arguments]: Add make flags to remove unexpectedly passing test from XFAIL_TESTS. [native-inputs]: Remove autoconf, automake, and texinfo. --- gnu/packages/guile-xyz.scm | 67 ++++++++++++++++++-------------------- 1 file changed, 32 insertions(+), 35 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 6e19a38863..69fca334ca 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2247,43 +2247,40 @@ list of components. This module takes care of that for you.") (license license:lgpl3+))) (define-public guile-gi - (let ((commit "26e885219ae6b31a83766564a2ecfe8c4532346f") - (revision "1")) - (package - (name "guile-gi") - (version (string-append "0.0.1-" revision "." (string-take commit 7))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/spk121/guile-gi.git") - (commit commit))) - (file-name (string-append name "-" version)) - (sha256 - (base32 - "1prbzhr4sqqihb34l6yfrz6sd8nghwd3q9wvbm36jnl2n3z2nxj8")))) - (build-system gnu-build-system) - (native-inputs `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gnu-gettext) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("texinfo" ,texinfo))) - (propagated-inputs `(("glib" ,glib) - ("gobject-introspection" ,gobject-introspection) - ("gssettings-desktop-schemas" ,gsettings-desktop-schemas) - ("gtk+" ,gtk+) - ("guile-lib" ,guile-lib) - ("webkitgtk" ,webkitgtk))) - (inputs `(("guile" ,guile-2.2))) - (arguments - `(#:configure-flags '("--with-gnu-filesystem-hierarchy"))) - (home-page "https://github.com/spk121/guile-gi") - (synopsis "GObject bindings for Guile") - (description - "Guile-GI is a library for Guile that allows using GObject-based + (package + (name "guile-gi") + (version "0.0.2") + (source (origin + (method url-fetch) + (uri (string-append "http://lonelycactus.com/tarball/guile_gi-" + version ".tar.gz")) + (sha256 + (base32 + "0hs0viqzff7nzgcmyw721ima1jyymrlzrcycpgwrs6iprscxvqwn")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags '("--with-gnu-filesystem-hierarchy") + ;; The atomic_int_set test does not actually fail. + #:make-flags '("XFAIL_TESTS=strjoinv.scm"))) + (native-inputs + `(("gettext" ,gnu-gettext) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (propagated-inputs + `(("glib" ,glib) + ("gobject-introspection" ,gobject-introspection) + ("gssettings-desktop-schemas" ,gsettings-desktop-schemas) + ("gtk+" ,gtk+) + ("guile-lib" ,guile-lib) + ("webkitgtk" ,webkitgtk))) + (inputs `(("guile" ,guile-2.2))) + (home-page "https://github.com/spk121/guile-gi") + (synopsis "GObject bindings for Guile") + (description + "Guile-GI is a library for Guile that allows using GObject-based libraries, such as GTK+3. Its README comes with the disclaimer: This is pre-alpha code.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public guile-srfi-159 (let ((commit "1bd98abda2ae4ef8f36761a167903e55c6bda7bb") From e0cd8f73404400c6bebfc976b5e55d82e758ba8f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:52:57 +0200 Subject: [PATCH 067/224] gnu: r-extradistr: Update to 1.8.11. * gnu/packages/cran.scm (r-extradistr): Update to 1.8.11. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 356595ff33..f246f49e15 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4107,14 +4107,14 @@ Cryer and Kung-Sik Chan.") (define-public r-extradistr (package (name "r-extradistr") - (version "1.8.10") + (version "1.8.11") (source (origin (method url-fetch) (uri (cran-uri "extraDistr" version)) (sha256 (base32 - "00lvqp5bb3iak5myiz4rqm887bkq9sdh7aybmz84mmfni6q01m28")))) + "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3")))) (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs From 45dcc89de7a4f587c8a3bcdcd24e7adbe421f156 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:53:04 +0200 Subject: [PATCH 068/224] gnu: r-sjmisc: Update to 2.8.0. * gnu/packages/cran.scm (r-sjmisc): Update to 2.8.0. [propagated-inputs]: Remove r-haven; add r-insight. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f246f49e15..cdbd1a7b9e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5962,18 +5962,18 @@ vice versa), or to deal with multiple declared missing values.") (define-public r-sjmisc (package (name "r-sjmisc") - (version "2.7.9") + (version "2.8.0") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 - "11iiap0w5v0dszgwx4pi3j1zf9vnlw1ml1wjvq1hg9iz1plgbfnc")))) + "0pgavkygsj8fa591pmasx78b4gd32sf2pa067yqvi82xha7dj5k4")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) - ("r-haven" ,r-haven) + ("r-insight" ,r-insight) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) From 89afd03172641a3f56fdea7a9aad73d8368de52a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:53:20 +0200 Subject: [PATCH 069/224] gnu: r-abcrf: Update to 1.8. * gnu/packages/cran.scm (r-abcrf): Update to 1.8. [propagated-inputs]: Add r-doparallel and r-foreach. --- gnu/packages/cran.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cdbd1a7b9e..acc9c7d232 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6584,16 +6584,18 @@ second male (P2) based on the best fit distribution.") (define-public r-abcrf (package (name "r-abcrf") - (version "1.7.1") + (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "abcrf" version)) (sha256 - (base32 "06vy3inikrr9hv36q4djhrgzi9zizdfnhz17wpra8kadmr7qj441")))) + (base32 "0r31ki89z8zzcffm0yvd2zw3q96rk6g6fnwwkql902mgajbrha1f")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) + `(("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-mass" ,r-mass) ("r-matrixstats" ,r-matrixstats) ("r-ranger" ,r-ranger) ("r-rcpp" ,r-rcpp) From a7794b7243f5b2e48b1756b6dfc0958fd16215bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:53:37 +0200 Subject: [PATCH 070/224] gnu: r-emmeans: Update to 1.3.5. * gnu/packages/cran.scm (r-emmeans): Update to 1.3.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index acc9c7d232..3f824b384d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7694,14 +7694,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.3.4") + (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "09gxphan34c615y4lhjdqkg5cz4ih9b1r3bb4chs3mwmiav1rxqn")))) + "0zyink60132f2a0491a94bf67hq8a0bwmw5wn19l0ms8iyiml9d2")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) From 935c6532ac10867df7de8249c22149e563dddba8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:53:42 +0200 Subject: [PATCH 071/224] gnu: r-rspectra: Update to 0.15-0. * gnu/packages/cran.scm (r-rspectra): Update to 0.15-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3f824b384d..8f63391f61 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9406,14 +9406,14 @@ definiteness of a matrix.") (define-public r-rspectra (package (name "r-rspectra") - (version "0.14-0") + (version "0.15-0") (source (origin (method url-fetch) (uri (cran-uri "RSpectra" version)) (sha256 (base32 - "12w5vnz39gyciza0fl7fw4f9i9kjw763h3mvk1sxd97c5dsn26jg")))) + "1ab975scdqaxdna9sayjl6l14hz991y0pc8c8ah48w000616km8s")))) (properties `((upstream-name . "RSpectra"))) (build-system r-build-system) (propagated-inputs From 5cc896546b41660bcea5e8d5e14b2699f8a81fb3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:53:47 +0200 Subject: [PATCH 072/224] gnu: r-tractor-base: Update to 3.3.2. * gnu/packages/cran.scm (r-tractor-base): Update to 3.3.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8f63391f61..e94608646c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9641,14 +9641,14 @@ conditional reporting based on the current \"output level\".") (define-public r-tractor-base (package (name "r-tractor-base") - (version "3.3.0") + (version "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "tractor.base" version)) (sha256 (base32 - "0i62dwra0yh565ryz75byfgqv22bqwz7138zs48w46yj2h8q9hyj")))) + "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i")))) (properties `((upstream-name . "tractor.base"))) (build-system r-build-system) (propagated-inputs From 776c62d1b29909ab36e0fea2ecfd922f8749da19 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:53:51 +0200 Subject: [PATCH 073/224] gnu: r-nor1mix: Update to 1.3-0. * gnu/packages/cran.scm (r-nor1mix): Update to 1.3-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e94608646c..4226acfe9a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11748,14 +11748,14 @@ numbers from ZIP and ZINB distributions.") (define-public r-nor1mix (package (name "r-nor1mix") - (version "1.2-3") + (version "1.3-0") (source (origin (method url-fetch) (uri (cran-uri "nor1mix" version)) (sha256 (base32 - "1bvk888qml9qr7q703s7qzgm0sqfchcjdjqwqllm5vrjx0cnapj3")))) + "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/nor1mix/") (synopsis "Normal (1-d) mixture models") From 663a50e8f9745a18a1032f7f02f9d8750f92b242 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:53:55 +0200 Subject: [PATCH 074/224] gnu: r-deldir: Update to 0.1-21. * gnu/packages/cran.scm (r-deldir): Update to 0.1-21. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4226acfe9a..d9298d0ab7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12407,14 +12407,14 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.1-16") + (version "0.1-21") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "0549kj0hlkdyvm5axsm3np30wg53fm2pxybijzw0avlgsd2y2n2q")))) + "03392pl6j8rm3n32xrfkyfx866k1vm5sj87pva70yyiwh70vrnmr")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/deldir") From 9fea25cf3299a74bb952514e02a9f0dd9cb4ba54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:00 +0200 Subject: [PATCH 075/224] gnu: r-polspline: Update to 1.1.15. * gnu/packages/cran.scm (r-polspline): Update to 1.1.15. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d9298d0ab7..349097cc30 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12647,14 +12647,14 @@ either PDF/EPS files.") (define-public r-polspline (package (name "r-polspline") - (version "1.1.14") + (version "1.1.15") (source (origin (method url-fetch) (uri (cran-uri "polspline" version)) (sha256 (base32 - "0g4s5nwi13yfs6b169yw8vrs48nvjyc014k2v7ybcxarl8z81va0")))) + "19zs4kpagsrzhng1byjbz1c4jxnfk58h4rgr096ml1bjwrgamnwc")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/polspline/") From 18242e4b52e6b3790daa57df407395c36ba1dcd4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:05 +0200 Subject: [PATCH 076/224] gnu: r-servr: Update to 0.14. * gnu/packages/cran.scm (r-servr): Update to 0.14. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 349097cc30..e0f2b3bb87 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -453,13 +453,13 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.13") + (version "0.14") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "1n5haqkshrxcx557f1k7nrisvq3wak8v370s2r6yv691b8hvbscs")))) + "0zjjnfgas9d16fihksyk24kgkkqswb4sd0rz51id2ni1ymdyasjk")))) (build-system r-build-system) (propagated-inputs `(("r-httpuv" ,r-httpuv) From 4661effbd51967621a6389b91e0796a15bd7e5bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:11 +0200 Subject: [PATCH 077/224] gnu: r-ggplot2: Update to 3.2.0. * gnu/packages/statistics.scm (r-ggplot2): Update to 3.2.0. [propagated-inputs]: Remove r-plyr. --- gnu/packages/statistics.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 156a329627..4497abda99 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1137,18 +1137,17 @@ legends.") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.1.1") + (version "3.2.0") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "0y8cks9r9hvjlx0isnvbgs3p0al167hlr3q7c3syfcj77dzjkpmz")))) + (base32 "1cvk9pw59kxx19kamqwa15h26rbznp0vvqpn7y8kgjssnrzqkdii")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-gtable" ,r-gtable) - ("r-plyr" ,r-plyr) ("r-lazyeval" ,r-lazyeval) ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) From 24868ae72e1a213ae4c2570852fb4b06eff922aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:27 +0200 Subject: [PATCH 078/224] gnu: r-formatr: Update to 1.7. * gnu/packages/statistics.scm (r-formatr): Update to 1.7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 4497abda99..e1809c14ba 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1346,13 +1346,13 @@ adapted for other output formats, such as HTML or LaTeX.") (define-public r-formatr (package (name "r-formatr") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) (uri (cran-uri "formatR" version)) (sha256 (base32 - "0a9229rg3s9qga5v2fwfdqr0z3bk2yycv8kijrcm3jh66l68zjgm")))) + "1nsxbrx31k3y6yql30qkrvdfyznlia2qfvwv95mfiy7m7wdn4rm3")))) (build-system r-build-system) (home-page "http://yihui.name/formatR") (synopsis "Format R code automatically") From e89e4bb634e553e3c1b1d6535c70dd28c5176be5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:32 +0200 Subject: [PATCH 079/224] gnu: r-mime: Update to 0.7. * gnu/packages/statistics.scm (r-mime): Update to 0.7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index e1809c14ba..c7f585dcce 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1385,13 +1385,13 @@ supported via Andre Simon's highlight package.") (define-public r-mime (package (name "r-mime") - (version "0.6") + (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "mime" version)) (sha256 (base32 - "00f4gw4sg1kn03s67gficxgb7a7fb6pwhlvrxrml05q1mc2vcxa7")))) + "12vpip67ajb90b8p96w43ir7mavrw2i61bwvpfnrlmlj9kj3w20i")))) (build-system r-build-system) (home-page "https://github.com/yihui/mime") (synopsis "R package to map filenames to MIME types") From 074dd1806c795c276ad35891b6bd63a05b13cfac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:36 +0200 Subject: [PATCH 080/224] gnu: r-rcpparmadillo: Update to 0.9.500.2.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.500.2.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c7f585dcce..1f425de502 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2596,13 +2596,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.9.400.3.0") + (version "0.9.500.2.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1c0kmp54xgg67hxpqm8bibcxmmwljbdvm9p1d9wzirp83x86v4sn")))) + "1lyvpb7n54ijlqns29qiixqr39334knf67cnixvlic58945glrhv")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) ;; All needed for vignettes From 0f4182a1377efd03c8cbfedef23563e05ec7cc45 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:40 +0200 Subject: [PATCH 081/224] gnu: r-dt: Update to 0.7. * gnu/packages/statistics.scm (r-dt): Update to 0.7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1f425de502..9e533bd4bd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3162,13 +3162,13 @@ using the multicore functionality of the parallel package.") (define-public r-dt (package (name "r-dt") - (version "0.6") + (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "05kr88yshq6siarp5q7aapvsr63vx3p0aqablwgifn8m2sfqxmif")))) + "0b6ywgzk9b35y5f69zwfz3vv7qwqqj3xsmy0xymf7nfcvrqg3qqx")))) (properties `((upstream-name . "DT"))) (build-system r-build-system) From fd61e9c5d6d63d3eb5ca7724cd0fc7e93b4ad8fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:46 +0200 Subject: [PATCH 082/224] gnu: r-r-utils: Update to 2.9.0. * gnu/packages/statistics.scm (r-r-utils): Update to 2.9.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9e533bd4bd..21fe65a08d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3542,13 +3542,13 @@ maintenance for package developers.") (define-public r-r-utils (package (name "r-r-utils") - (version "2.8.0") + (version "2.9.0") (source (origin (method url-fetch) (uri (cran-uri "R.utils" version)) (sha256 (base32 - "1jaarld1jgpzh18kh9g3rlzcrk51vdgn2n1d1y28szzxlz94vifg")))) + "1w4zn2db15bggfnh64fbyi2z2sj47rcd4xn53b28dsnkamdcramj")))) (properties `((upstream-name . "R.utils"))) (build-system r-build-system) (propagated-inputs From 7bbd06ed597b0035aa0f12782e7af9b603253aaa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:51 +0200 Subject: [PATCH 083/224] gnu: r-systempiper: Update to 1.18.1. * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b950b8cf53..fa0e610433 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6946,14 +6946,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1063vdf4g2i5xyabwvzkqfxd2j8s4zs6z4zxf8lx2ccjddhkn37a")))) + "1k57zyzagd7g7wl38l3cn9csylykxcllbfvyq7dz8pvihgkn0ssi")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs From 6dc3c5872893845935f958b260f063166dd2cae4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:56 +0200 Subject: [PATCH 084/224] gnu: r-tximport: Update to 1.12.1. * gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa0e610433..6a66e60cf0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8548,13 +8548,13 @@ factors bound at the specific regions.") (define-public r-tximport (package (name "r-tximport") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0nl4imr5klwcd0xnp5y0g61d6mcgd50q60zkl86ymfmc0id368jr")))) + "1nq8v1sgkm2ssmvr2z3qw0zsk7zy0dzb95g1mfs8fkpjqh3nqq5s")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") From 42df44f6454ff7a597493def6f57718b1b338c3d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:55:03 +0200 Subject: [PATCH 085/224] gnu: r-seurat: Update to 3.0.2. * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6a66e60cf0..90f12f41ec 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9452,13 +9452,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "3.0.1") + (version "3.0.2") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0mx2fvhdswbcsgqxhfc6d0gr92bkibwpz2bavqdzbbxrzpdpnilc")))) + "016fgcmjz3sjfxdvam5hd7mdxpmpnc7f6p5zqlh97m21dgn5vpqn")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs From 932a6c422a2ed163c4a00db82bd19129c27e3d72 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:55:12 +0200 Subject: [PATCH 086/224] gnu: r-rhisat2: Update to 1.0.3. * gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.0.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e87907fac5..a1f7b2d2a8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4467,14 +4467,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "1y3zqvk1vbcb10r1myh6f5yzjvf7bhwhpiq78bs1k6spli4bzj0q")))) + "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (native-inputs From 3c33931c8043f56db048f3b6ff51380a91dd9190 Mon Sep 17 00:00:00 2001 From: Chris Marusich Date: Sun, 16 Jun 2019 19:41:30 -0700 Subject: [PATCH 087/224] gnu: Upgrade emacs-default-encrypt to 4.4. * gnu/packages/emacs-xyz.scm (emacs-default-encrypt) : Upgrade to 4.4. : Update accordingly. : Honor changes to upstream's website. --- gnu/packages/emacs-xyz.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 37bf9a06b9..626252cb9b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7307,19 +7307,20 @@ performance-oriented and tidy.") (define-public emacs-default-encrypt (package (name "emacs-default-encrypt") - (version "4.3") + (version "4.4") (source (origin (method url-fetch) (uri (string-append - "https://www.informationelle-selbstbestimmung-im-internet.de" + "https://informationelle-selbstbestimmung-im-internet.de" "/emacs/jl-encrypt" version "/jl-encrypt.el")) (file-name (string-append "jl-encrypt-" version ".el")) (sha256 (base32 - "16i3rlfp3jxlqvndn8idylhmczync3gwmy8a019v29vyr48rnnr0")))) + "0w9ggz075j1zwg7d0rv9k8238g600p7czfnnsnawswi7yps2xk78")))) (build-system emacs-build-system) - (home-page "https://www.informationelle-selbstbestimmung-im-internet.de/Emacs.html") + (home-page + "https://informationelle-selbstbestimmung-im-internet.de/Emacs.html") (synopsis "Automatically encrypt or sign Gnus messages in Emacs") (description "DefaultEncrypt is designed to be used with Gnus in Emacs. It From 0bc010dacded4d89aa39f2d37fe75414b69b680e Mon Sep 17 00:00:00 2001 From: Chris Marusich Date: Sun, 16 Jun 2019 20:50:39 -0700 Subject: [PATCH 088/224] gnu: Add emacs-extend-smime. * gnu/packages/emacs-xyz.scm (emacs-extend-smime): New variable. --- gnu/packages/emacs-xyz.scm | 37 ++++++++++++++++++++++++++++++++++++- 1 file changed, 36 insertions(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 626252cb9b..3ef69ab9e0 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Alex Kost ;;; Copyright © 2015 Federico Beffa ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus -;;; Copyright © 2016, 2017, 2018 Chris Marusich +;;; Copyright © 2016, 2017, 2018, 2019 Chris Marusich ;;; Copyright © 2015, 2016, 2018 Christopher Lemmer Webber ;;; Copyright © 2016 Adriano Peluso ;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner @@ -7332,6 +7332,41 @@ DefaultEncrypt, please refer to the home page or read the comments in the source file, @file{jl-encrypt.el}.") (license license:gpl3+))) +(define-public emacs-extend-smime + (package + (name "emacs-extend-smime") + (version "3.3") + (source + (origin + (method url-fetch) + (uri (string-append + "https://informationelle-selbstbestimmung-im-internet.de" + "/emacs/jl-smime" version "/jl-smime.el")) + (file-name (string-append "jl-smime-" version ".el")) + (sha256 + (base32 + "1iv8s2wjmv3v5qfwlcy9hvvrmxxvp3f8m1krlr789q7bbh35jynh")))) + (build-system emacs-build-system) + (home-page + "https://informationelle-selbstbestimmung-im-internet.de/Emacs.html") + (synopsis "Improved S/MIME support for Gnus in Emacs") + (propagated-inputs + `(("emacs-default-encrypt" ,emacs-default-encrypt))) + (description + ;; TRANSLATORS: ExtendSMIME, DefaultEncrypt, and emacs-default-encrypt + ;; should not be translated. The name "emacs-default-encrypt" refers to + ;; the Guix package that provides DefaultEncrypt. + "ExtendSMIME is designed to be used with Gnus in Emacs. It enhances +DefaultEncrypt (emacs-default-encrypt) to support S/MIME (Secure/Multipurpose +Internet Mail Extensions) via LDAP (Lightweight Directory Access Protocol). +Before a message (e.g., email) is sent, ExtendSMIME searches for missing +certificates via LDAP and imports them into @code{gpgsm}. When certificates +for all recipients are available, DefaultEncrypt automatically encrypts the +message. For details and instructions on how to use ExtendSMIME, please refer +to the home page or read the comments in the source file, +@file{jl-smime.el}.") + (license license:gpl3+))) + (define-public emacs-htmlize (package (name "emacs-htmlize") From c9f0331152268c90c7cf02a14c79f1ed7ef6c81a Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Mon, 17 Jun 2019 08:27:03 +0200 Subject: [PATCH 089/224] gnu: xpra: Update to 2.5.2. * gnu/packages/xorg.scm (xpra): Update to 2.5.2. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 27966f038a..9577c4d2c6 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -6003,7 +6003,7 @@ basic eye-candy effects.") (define-public xpra (package (name "xpra") - (version "2.5.1") + (version "2.5.2") (source (origin (method url-fetch) @@ -6011,7 +6011,7 @@ basic eye-candy effects.") version ".tar.xz")) (sha256 (base32 - "14l3bs7mlkd2lphjhnbw5dr95pg7x1k61s9wk35dra4li2xjy1lm")))) + "1zbh2990crrxp02c554yh30f0s9znm6iiiklkw8vpxrlmdv1z8ks")))) (build-system python-build-system) (inputs `(("ffmpeg" ,ffmpeg) ("flac" ,flac) From ee0b4733e1a186048983ac6b6ba0bae23b3f567d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 16 Jun 2019 20:34:13 +0300 Subject: [PATCH 090/224] gnu: toybox: Don't install files to usr. * gnu/packages/busybox.scm (toybox)[arguments]: Add custom phase to remove any files installed in $PREFIX/usr. --- gnu/packages/busybox.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/gnu/packages/busybox.scm b/gnu/packages/busybox.scm index cc6257ba35..182b8ac618 100644 --- a/gnu/packages/busybox.scm +++ b/gnu/packages/busybox.scm @@ -1,8 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 John Darrington -;;; Copyright © 2016, 2017, 2018 Efraim Flashner +;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice -;;; Copyright © 2018 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -133,7 +132,12 @@ any small or embedded system.") (let ((out (assoc-ref outputs "out"))) (invoke "make" (string-append "PREFIX=" out) - "install"))))) + "install")))) + (add-after 'install 'remove-usr-directory + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (delete-file-recursively (string-append out "/usr")) + #t)))) #:test-target "tests")) (native-inputs `(("bc" ,bc))) (synopsis "Many common UNIX utilities in a single executable") From 9e3e80baa3d3093c3d7a80be27770b8b46f1789e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 16 Jun 2019 20:51:45 +0300 Subject: [PATCH 091/224] gnu: cava: Don't install files to usr. * gnu/packages/audio.scm (cava)[arguments]: In configure-flags change FONT_DIR to not use 'usr'. --- gnu/packages/audio.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 290f8ceb67..b8dbc2f00a 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -3568,7 +3568,7 @@ representations.") (arguments `(#:configure-flags (list (string-append "PREFIX=" %output) - (string-append "FONT_DIR=" %output "/usr/share/consolefonts")) + (string-append "FONT_DIR=" %output "/share/consolefonts")) #:make-flags (let ((lib (string-append %output "/lib"))) (list (string-append "cava_LDFLAGS = -L" lib " -Wl,-rpath " lib))) From 55350f8316f693401506e85684b3faf0627c4a80 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 17 Jun 2019 09:28:42 +0300 Subject: [PATCH 092/224] gnu: cmst: Don't install files to usr. * gnu/packages/connman.scm (cmst)[arguments]: Move custom 'fix-Makefiles phase before 'build. Add more substitutions. --- gnu/packages/connman.scm | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/gnu/packages/connman.scm b/gnu/packages/connman.scm index 39262b87da..df5aa7bb6d 100644 --- a/gnu/packages/connman.scm +++ b/gnu/packages/connman.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017 Efraim Flashner +;;; Copyright © 2016, 2017, 2019 Efraim Flashner ;;; Copyright © 2017 Mathieu Othacehe ;;; Copyright © 2017 Clément Lassieur ;;; Copyright © 2017 Ricardo Wurmus @@ -160,13 +160,22 @@ sharing) to clients via USB, ethernet, WiFi, cellular and Bluetooth.") (invoke "qmake" (string-append "PREFIX=" (assoc-ref outputs "out"))))) - (add-before 'install 'fix-Makefiles + (add-before 'build 'fix-Makefiles (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (substitute* (find-files "." "Makefile") (("INSTALL_ROOT)") (string-append "INSTALL_ROOT)" out)) - (("/usr/bin") "/bin")))))))) + (("/usr") "")) + (substitute* '("apps/cmstapp/cmstapp.pro" + "apps/cmstapp/code/control_box/controlbox.cpp" + "apps/rootapp/rootapp.pro" + "apps/rootapp/system/org.cmst.roothelper.service" + "cmst.pri" + "cmst.pro") + (("/usr") out) + (("/etc") (string-append out "/etc"))) + #t)))))) (home-page "https://github.com/andrew-bibb/cmst") (synopsis "Qt frontend for Connman") (description From bf95a142bbe8ab4ae6ccf87ad0df21cb56bbd3d3 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Mon, 17 Jun 2019 12:12:31 +0200 Subject: [PATCH 093/224] gnu: gap: Update to 4.10.1. * gnu/packages/algebra.scm (gap): Update to 4.10.1. Install headers and library files by hand, since the make targets have disappeared. Delete the special check phase, since the "make check" target has appeared. Remove a package that is no longer recommended, and enable two recommended packages with clarified licenses. --- gnu/packages/algebra.scm | 62 ++++++++++++++++++++++++++++------------ 1 file changed, 44 insertions(+), 18 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 69163a43d9..20ecc71b81 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -928,7 +928,7 @@ xtensor provides: (define-public gap (package (name "gap") - (version "4.10.0") + (version "4.10.1") (source (origin (method url-fetch) @@ -939,7 +939,7 @@ xtensor provides: ".tar.bz2")) (sha256 (base32 - "1dmb8v4p7j1nnf7sx8sg54b49yln36bi9acwp7w1d3a1nxj17ird")) + "136s0zvhcw41fshj5zgsrjcy2kd58cdh2m3ddp5rdizi4rx54f10")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1))) (snippet '(begin @@ -967,20 +967,20 @@ xtensor provides: ;; Optional packages, searched for at start, ;; and their depedencies. "alnuth-3.1.0" - "AutoDoc-2018.09.20" "autpgrp-1.10" "crisp-1.4.4" ; bsd-2 - ; "ctbllib" ; no explicit license, drop + "ctbllib" ; gpl3+ according to doc/chap0.txt "FactInt-1.6.2" "fga" "irredsol-1.4" ; bsd-2 - "laguna-3.9.0" + "laguna-3.9.2" "polenta-1.3.8" "polycyclic-2.14" "radiroot-2.8" "resclasses-4.7.1" "sophus-1.24" - ; "tomlib-1.2.7" ; no explicit license, drop + "tomlib-1.2.7" ; gpl2+, clarified in the git repository + ; and the next release "utils-0.59")))) #t)))) (build-system gnu-build-system) @@ -988,7 +988,11 @@ xtensor provides: `(("gmp" ,gmp) ("zlib" ,zlib))) (arguments - `(#:phases + `(#:modules ((ice-9 ftw) + (srfi srfi-26) + (guix build gnu-build-system) + (guix build utils)) + #:phases (modify-phases %standard-phases (add-after 'build 'build-packages ;; Compile all packages that have not been deleted by the @@ -1004,19 +1008,16 @@ xtensor provides: (with-directory-excursion "doc" (invoke "./make_doc")) #t)) - (replace 'check - (lambda _ - ;; "make check" is expected to appear in gap-4.10.1 - (invoke "./gap" "tst/testinstall.g") - #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin")) + (lib (string-append out "/lib")) (prog (string-append bin "/gap")) (prog-real (string-append bin "/.gap-real")) (share (string-append out "/share/gap")) - (include (string-append out "/include/gap"))) + (include (string-append out "/include/gap")) + (include-hpc (string-append include "/hpc"))) ;; Install only the gap binary; the gac compiler is left ;; for maybe later. "Wrap" it in a shell script that calls ;; the binary with the correct parameter. @@ -1030,12 +1031,37 @@ xtensor provides: prog-real share))) (chmod prog #o755) - ;; Install the headers and the library, which are needed by - ;; Sage. The Makefile targets are available in gap-4.10.0, - ;; but planned to be removed in gap-4.10.1. - (invoke "make" "install-headers") - (invoke "make" "install-libgap") + ;; Install the headers, which are needed by Sage. The + ;; Makefile target "install-headers" was available in + ;; gap-4.10.0, but has been commented out in gap-4.10.1. + (mkdir-p include-hpc) (install-file "gen/config.h" include) + (let ((file-name-predicate-without-stat + (lambda (regex) + (cut (file-name-predicate regex) <> #f)))) + (with-directory-excursion "src" + (for-each + (cut install-file <> include) + (scandir "." + (file-name-predicate-without-stat ".*\\.h$")))) + (with-directory-excursion "src/hpc" + (for-each + (cut install-file <> include-hpc) + (scandir "." + (file-name-predicate-without-stat ".*\\.h$"))))) + ;; Install the library, which is needed by Sage. The + ;; Makefile target "install-libgap" was available in + ;; gap-4.10.0, but has been commented out in gap-4.10.1. + ;; Compared to the Makefile, which used libtool, the + ;; following approach of copying files and making symlinks + ;; is rather pedestrian. There is hope that some later + ;; version of gap reinstates and completes the install + ;; targets. + (invoke "make" "libgap.la") + (install-file "libgap.la" lib) + (install-file ".libs/libgap.so.0.0.0" lib) + (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so")) + (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0")) ;; Install a certain number of files and directories to ;; SHARE, where the wrapped shell script expects them. ;; Remove information on the build directory from sysinfo.gap. From 123b9c02dddd21b61858fbf01fb356c14f220f21 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 16 Jun 2019 15:22:15 +0200 Subject: [PATCH 094/224] gnu: open-zwave: Unbundle hidapi. * gnu/packages/patches/open-zwave-hidapi.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/zwave.scm (open-zwave)[source](patches): New field. (snippet): Delete 'cpp/hidapi'. [native-inputs]: Add PKG-CONFIG. [inputs]: Add HIDAPI. --- gnu/local.mk | 1 + gnu/packages/patches/open-zwave-hidapi.patch | 15 +++++++++++++++ gnu/packages/zwave.scm | 9 +++++++++ 3 files changed, 25 insertions(+) create mode 100644 gnu/packages/patches/open-zwave-hidapi.patch diff --git a/gnu/local.mk b/gnu/local.mk index da3245ea18..74d2bafa8d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1130,6 +1130,7 @@ dist_patch_DATA = \ %D%/packages/patches/openssl-1.1-c-rehash-in.patch \ %D%/packages/patches/openssl-c-rehash-in.patch \ %D%/packages/patches/openssl-CVE-2019-1559.patch \ + %D%/packages/patches/open-zwave-hidapi.patch \ %D%/packages/patches/orpheus-cast-errors-and-includes.patch \ %D%/packages/patches/osip-CVE-2017-7853.patch \ %D%/packages/patches/ots-no-include-missing-file.patch \ diff --git a/gnu/packages/patches/open-zwave-hidapi.patch b/gnu/packages/patches/open-zwave-hidapi.patch new file mode 100644 index 0000000000..fc50bfeade --- /dev/null +++ b/gnu/packages/patches/open-zwave-hidapi.patch @@ -0,0 +1,15 @@ +Build against the system's HIDAPI instead of the bundled one. + +--- open-zwave-1.6-checkout/cpp/build/support.mk 2019-06-16 15:15:34.258331628 +0200 ++++ open-zwave-1.6-checkout/cpp/build/support.mk 2019-06-16 15:15:54.698249462 +0200 +@@ -86,6 +86,10 @@ endif + endif + SED := sed + ++# Build against the system's HIDAPI. ++CPPFLAGS += $(shell pkg-config hidapi-libusb --cflags) ++LDFLAGS += $(shell pkg-config hidapi-libusb --libs) ++ + #determine if we are release or debug Build and set appropriate flags + ifeq ($(BUILD), release) + CFLAGS += -c $(RELEASE_CFLAGS) diff --git a/gnu/packages/zwave.scm b/gnu/packages/zwave.scm index 43d1747332..f07367d264 100644 --- a/gnu/packages/zwave.scm +++ b/gnu/packages/zwave.scm @@ -21,9 +21,12 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix git-download) #:use-module (guix build-system gnu) + #:use-module (gnu packages) #:use-module (gnu packages base) + #:use-module (gnu packages libusb) #:use-module (gnu packages linux) #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages xml)) (define-public open-zwave @@ -39,6 +42,7 @@ (sha256 (base32 "0xgs4mmr0480c269wx9xkk67ikjzxkh8xcssrdx0f5xcl1lyd333")) + (patches (search-patches "open-zwave-hidapi.patch")) (modules '((guix build utils))) (snippet '(begin @@ -52,6 +56,9 @@ (substitute* "cpp/build/Makefile" (("LIBS \\+= -ludev") "LIBS += -ludev -ltinyxml ")) + + ;; Delete the bundled HIDAPI. + (delete-file-recursively "cpp/hidapi") #t)))) (build-system gnu-build-system) (arguments @@ -70,9 +77,11 @@ ;; them. #:tests? #f)) (native-inputs `(("which" ,which) + ("pkg-config" ,pkg-config) ("perl" ,perl) ;for tests ("perl-xml-simple" ,perl-xml-simple))) (inputs `(("tinyxml" ,tinyxml) + ("hidapi" ,hidapi) ("eudev" ,eudev))) (home-page "http://www.openzwave.net/") (synopsis "Access Z-Wave devices from C++ programs") From ed504cafa23c34bfa1823a4d5abf3ad55205484b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 17 Jun 2019 10:51:49 +0200 Subject: [PATCH 095/224] vm: 'system-docker-image' builds in a UTF-8 locale. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . Reported by Björn Höfling . This is a followup to 9c941364bfc0120e3ab5c5c4cc71a9a302d59a2b. * gnu/system/vm.scm (system-docker-image)[build]: Set GUIX_LOCPATH and call 'setlocale'. --- gnu/system/vm.scm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index 0d4ed63eec..e7f7d8ca51 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -535,6 +535,11 @@ system." ;; Set the SQL schema location. (sql-schema #$schema) + ;; Allow non-ASCII file names--e.g., 'nss-certs'--to be decoded. + (setenv "GUIX_LOCPATH" + #+(file-append glibc-utf8-locales "/lib/locale")) + (setlocale LC_ALL "en_US.utf8") + (let* (;; This initializer requires elevated privileges that are ;; not normally available in the build environment (e.g., ;; it needs to create device nodes). In order to obtain From 73eacca85ec68100e08ab21a3732cabbd77a2dbd Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Tue, 11 Jun 2019 09:21:57 +0200 Subject: [PATCH 096/224] gnu: kakoune: Remove dependency on boost. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit kakoune builds without boost since a while already. * gnu/packages/text-editors.scm (kakoune)[inputs]: Remove boost. Signed-off-by: Ludovic Courtès --- gnu/packages/text-editors.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index 534934dfd1..731bbc5d16 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -140,8 +140,7 @@ based command language.") ("pkg-config" ,pkg-config) ("ruby" ,ruby))) (inputs - `(("ncurses" ,ncurses) - ("boost" ,boost))) + `(("ncurses" ,ncurses))) (synopsis "Vim-inspired code editor") (description "Kakoune is a code editor heavily inspired by Vim, as such most of its From f434664cc03b5217eacccab36698c8eeb1e7e10f Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Thu, 13 Jun 2019 18:25:30 +0200 Subject: [PATCH 097/224] gnu: oil-shell: Update to 0.6pre22. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit It turns out the currently packaged release fails to build for me. According to upstream, the 0.6 pre-releases are preferable to currently packaged 0.5. gnu/packages/shells.scm (oil-shell): Update to 0.6pre22. Signed-off-by: Ludovic Courtès --- gnu/packages/shells.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 49152dc3fd..f8c0fdf71f 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -749,14 +749,14 @@ Shell (pdksh).") (define-public oil-shell (package (name "oil-shell") - (version "0.5.0") + (version "0.6.pre22") (source (origin (method url-fetch) (uri (string-append "https://www.oilshell.org/download/oil-" version ".tar.xz")) (sha256 (base32 - "03zc7rhhpl0cybng2i3c33pky1knsnyvn526bn91hg6w4znvn66w")))) + "1kslycqa8rrzk9p2265dy045xd88q675w4baqiygcrnvxwn588c5")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; the tests are not distributed in the tarballs From 5cfc16320a870b5b006d65095564bf5188d4557a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 13:28:56 +0200 Subject: [PATCH 098/224] gnu: python-scipy: Update to 1.2.2. * gnu/packages/python-xyz.scm (python-scipy): Update to 1.2.2. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 284ecbd441..3efd18a72b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3974,14 +3974,14 @@ operators such as union, intersection, and difference.") (define-public python-scipy (package (name "python-scipy") - (version "1.1.0") + (version "1.2.2") (source (origin (method url-fetch) (uri (pypi-uri "scipy" version)) (sha256 (base32 - "1lfg686w6vv2m2dfs8v9d0bf2i18z7wz5vgzjnkgmpr4hi0550w7")))) + "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4")))) (build-system python-build-system) (propagated-inputs `(("python-numpy" ,python-numpy) From de2d14f2ff3577f521b6dc9c52f45924249c1949 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= Date: Mon, 17 Jun 2019 13:30:57 +0200 Subject: [PATCH 099/224] gnu: waybar: Add optional dependencies. * gnu/packages/wm.scm(waybar)[inputs]: Add libdbusmenu, libnl, libmpdclient and pulseaudio. --- gnu/packages/wm.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 5737fea8d9..0b15801633 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -1349,7 +1349,11 @@ modules for building a Wayland compositor.") (inputs `(("fmt" ,fmt) ("gtkmm" ,gtkmm) ("jsoncpp" ,jsoncpp) + ("libdbusmenu" ,libdbusmenu) ("libinput" ,libinput) + ("libmpdclent" ,libmpdclient) + ("libnl" ,libnl) + ("pulseaudio" ,pulseaudio) ("spdlog" ,spdlog) ("wayland" ,wayland))) (native-inputs `(("gcc-toolchain" ,gcc-toolchain-7) ; TODO remove when default gcc version >=7 From 505459d7cb139eaa3b73b4977d502a3acc400b3b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 17 Jun 2019 16:26:41 +0300 Subject: [PATCH 100/224] gnu: busybox: Don't install to usr. * gnu/packages/busybox.scm (busybox)[arguments]: Add a custom phase to prevent installing to %PREFIX/usr. --- gnu/packages/busybox.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/busybox.scm b/gnu/packages/busybox.scm index 182b8ac618..7bb677cdd0 100644 --- a/gnu/packages/busybox.scm +++ b/gnu/packages/busybox.scm @@ -54,6 +54,12 @@ #t)) (replace 'configure (lambda _ (invoke "make" "defconfig"))) + (add-after 'configure 'dont-install-to-usr + (lambda _ + (substitute* ".config" + (("# CONFIG_INSTALL_NO_USR is not set") + "CONFIG_INSTALL_NO_USR=y")) + #t)) (replace 'check (lambda _ (substitute* '("testsuite/du/du-s-works" From 20caeea4838ed0cf92452b6f7cf4cb9b42cd4ba8 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Mon, 17 Jun 2019 15:11:21 +0200 Subject: [PATCH 101/224] gnu: Add cliquer. * gnu/packages/sagemath.scm (cliquer): New variable. --- gnu/packages/sagemath.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index baa79ab1c0..42b2bbdb94 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -20,6 +20,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix build-system gnu) #:use-module (guix build-system python) #:use-module (gnu packages algebra) #:use-module (gnu packages compression) @@ -89,3 +90,29 @@ libraries GMO, MPFR and MPC.") (define-public python2-gmpy2 (package-with-python2 python-gmpy2)) + +(define-public cliquer + (package + (name "cliquer") + (version "1.21") + ;; The original source package is available from the home page and + ;; has not seen any release since 2010; it comes with only a Makefile + ;; without an "install" target. Instead, there is an autotoolized + ;; tarball available from the Sage project. + (source + (origin + (method url-fetch) + (uri "http://users.ox.ac.uk/~coml0531/sage/cliquer-1.21.tar.gz") + (sha256 + (base32 + "1hdzrmrx0nvvj8kbwxrs8swqgkd284khzl623jizixcv28xb77aq")))) + (build-system gnu-build-system) + (synopsis "C routines for finding cliques in weighted graphs") + (description "Cliquer is a set of reentrant C routines for finding +cliques in a weighted or unweighted graph. It uses an exact +branch-and-bound algorithm. It can search for maximum or maximum-weight +cliques or cliques with size or weight within a given range, restrict the +search to maximal cliques, store cliques in memory and call a user-defined +function for every found clique.") + (license license:gpl2+) + (home-page "https://users.aalto.fi/~pat/cliquer.html"))) From 1e1a65a63349d1d2bd272738304a1d9f3b128a84 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Mon, 17 Jun 2019 15:59:14 +0200 Subject: [PATCH 102/224] gnu: python-cypari2: Update to 2.1.1. * gnu/packages/sagemath.scm (python-cypari2): Update to 2.1.1. --- gnu/packages/sagemath.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 42b2bbdb94..f7d695049c 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -32,14 +32,14 @@ (define-public python-cypari2 (package (name "python-cypari2") - (version "2.0.3") + (version "2.1.1") (source (origin (method url-fetch) (uri (pypi-uri "cypari2" version)) (sha256 (base32 - "0mghbmilmy34xp1d50xdx76sijqxmpkm2bcgx2v1mdji2ff7n0yc")))) + "1nwkzgqvbw6361x0rpggy1q5nx663fswhpvg8md6xhqyfwpgc7nz")))) (build-system python-build-system) (native-inputs `(("python-cython" ,python-cython))) From 9f6065237d7be3672b9c48e0dfd89af85ff4eeec Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Mon, 17 Jun 2019 17:02:01 +0200 Subject: [PATCH 103/224] gnu: Add edge-addition-planarity-suite. * gnu/packages/maths.scm (edge-addition-planarity-suite): New variable. --- gnu/packages/maths.scm | 30 +++++++++++++++++++++++++++++- 1 file changed, 29 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 6d8fb9cec5..b4e4067101 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge +;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge ;;; Copyright © 2013 Nikita Karetnikov ;;; Copyright © 2014, 2016, 2017 John Darrington ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Eric Bavier @@ -5003,3 +5003,31 @@ command-line tools, and an Application Programming Interface (API). This package provides the static libraries required to run programs compiled against the nauty library.") (license license:asl2.0))) + +(define-public edge-addition-planarity-suite + (package + (name "edge-addition-planarity-suite") + (version "3.0.0.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url (string-append "https://github.com/graph-algorithms/" + name)) + (commit (string-append "Version_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (synopsis "Embedding of planar graphs") + (description "The package provides a reference implementation of the +linear time edge addition algorithm for embedding planar graphs and +isolating planarity obstructions.") + (license license:bsd-3) + (home-page + "https://github.com/graph-algorithms/edge-addition-planarity-suite"))) From 7658904a34f0114ee5160be6ec4858fbec9dbe4c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 17 Jun 2019 17:37:04 +0200 Subject: [PATCH 104/224] gnu: Fix freeorion build. * gnu/packages/games.scm (freeorion)[arguments]: Fix font unbundling. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index eed409135b..bf95bf735d 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -7492,9 +7492,9 @@ win.") (let ((roboto-dir (string-append (assoc-ref inputs "font-roboto") "/share/fonts/truetype/"))) (substitute* "UI/ClientUI.cpp" - (("\\(GetRootDataDir.*?\"Roboto-(Bold|Regular)\\.ttf\"\\)\\.string\\(\\)\\);" + (("\\(GetRootDataDir.*?Roboto-(Bold|Regular)\\.ttf\"\\)\\.string\\(\\)\\);" all type) - (string-append "\"" roboto-dir "Roboto-" type "\");"))) + (string-append "\"" roboto-dir "Roboto-" type ".ttf\");"))) #t)))))) (inputs `(("boost" ,boost) From f455d99dfaacd32411c224faa3020d594a7a24e9 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Mon, 17 Jun 2019 19:16:53 +0200 Subject: [PATCH 105/224] gnu: edge-addition-planarity-suite: Move to the (gnu packages graph) module. * gnu/packages/maths.scm (edge-addition-planarity-suite): Move from here... * gnu/packages/maths.scm (edge-addition-planarity-suite): ...to here. --- gnu/packages/graph.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/maths.scm | 30 +----------------------------- 2 files changed, 31 insertions(+), 29 deletions(-) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 36d0467175..abcb659456 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2019 Efraim Flashner +;;; Copyright © 2019 Andreas Enge ;;; ;;; This file is part of GNU Guix. ;;; @@ -31,6 +32,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages gcc) + #:use-module (gnu packages autotools) #:use-module (gnu packages bioconductor) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages check) @@ -446,3 +448,31 @@ they can fit in memory). The core function is @code{find_partition} which finds the optimal partition using the Leiden algorithm, which is an extension of the Louvain algorithm, for a number of different methods.") (license license:gpl3+))) + +(define-public edge-addition-planarity-suite + (package + (name "edge-addition-planarity-suite") + (version "3.0.0.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url (string-append "https://github.com/graph-algorithms/" + name)) + (commit (string-append "Version_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (synopsis "Embedding of planar graphs") + (description "The package provides a reference implementation of the +linear time edge addition algorithm for embedding planar graphs and +isolating planarity obstructions.") + (license license:bsd-3) + (home-page + "https://github.com/graph-algorithms/edge-addition-planarity-suite"))) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index b4e4067101..6d8fb9cec5 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge +;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge ;;; Copyright © 2013 Nikita Karetnikov ;;; Copyright © 2014, 2016, 2017 John Darrington ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Eric Bavier @@ -5003,31 +5003,3 @@ command-line tools, and an Application Programming Interface (API). This package provides the static libraries required to run programs compiled against the nauty library.") (license license:asl2.0))) - -(define-public edge-addition-planarity-suite - (package - (name "edge-addition-planarity-suite") - (version "3.0.0.5") - (source - (origin - (method git-fetch) - (uri (git-reference - (url (string-append "https://github.com/graph-algorithms/" - name)) - (commit (string-append "Version_" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8")))) - (build-system gnu-build-system) - (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) - (synopsis "Embedding of planar graphs") - (description "The package provides a reference implementation of the -linear time edge addition algorithm for embedding planar graphs and -isolating planarity obstructions.") - (license license:bsd-3) - (home-page - "https://github.com/graph-algorithms/edge-addition-planarity-suite"))) From bf473f0ca0b218e9a93b00234a8f25ba015b8bd3 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Mon, 17 Jun 2019 19:46:29 +0200 Subject: [PATCH 106/224] gnu: Add rw. * gnu/packages/graph.scm (rw): New variable. --- gnu/packages/graph.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index abcb659456..8b06aaa0e9 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -476,3 +476,27 @@ isolating planarity obstructions.") (license license:bsd-3) (home-page "https://github.com/graph-algorithms/edge-addition-planarity-suite"))) + +(define-public rw + (package + (name "rw") + ;; There is a version 0.8, but the tarball is broken with symlinks + ;; to /usr/share. + (version "0.7") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/rankwidth/" + "rw-" version ".tar.gz")) + (sha256 + (base32 + "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0")))) + (build-system gnu-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("igraph" ,igraph))) + (home-page "https://sourceforge.net/projects/rankwidth/") + (synopsis "Rank-width and rank-decomposition of graphs") + (description "rw computes rank-width and rank-decompositions +of graphs.") + (license license:gpl2+))) From a6f2ced34b873612e6caca719ed448af3ee92b7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 14:39:29 +0200 Subject: [PATCH 107/224] gnu: Add tbsp. * gnu/packages/bioinformatics.scm (tbsp): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 90f12f41ec..8002f24110 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14756,3 +14756,40 @@ spliced-in} (PSI) values of alternatively-spliced exons that were computed by vast-tools, an RNA-Seq pipeline for alternative splicing analysis. The plots are generated using @code{ggplot2}.") (license license:expat))) + +(define-public tbsp + (let ((commit "ec8fff4410cfb13a677dbbb95cbbc60217e64907") + (revision "1")) + (package + (name "tbsp") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/phoenixding/tbsp.git") + (commit commit))) + (sha256 + (base32 + "025ym14x8gbd6hb55lsinqj6f5qzw36i10klgs7ldzxxd7s39ki1")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; no tests included + (inputs + `(("python-matplotlib" ,python-matplotlib) + ("python-networkx" ,python-networkx) + ("python-numpy" ,python-numpy) + ("python-pybigwig" ,python-pybigwig) + ("python-biopython" ,python-biopython) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy))) + (home-page "https://github.com/phoenixding/tbsp/") + (synopsis "SNP-based trajectory inference") + (description + "Several studies focus on the inference of developmental and response +trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of +computational methods, often referred to as pseudo-time ordering, have been +developed for this task. CRISPR has also been used to reconstruct lineage +trees by inserting random mutations. The tbsp package implements an +alternative method to detect significant, cell type specific sequence +mutations from scRNA-Seq data.") + (license license:expat)))) From 27d6d24e6352012a9d8cf1a7828c557a4539f023 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 14:39:38 +0200 Subject: [PATCH 108/224] gnu: python-scikit-learn: Update to 0.20.3. * gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.20.3. --- gnu/packages/machine-learning.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index b330b2357f..370cfe1a30 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -792,7 +792,7 @@ computing environments.") (define-public python-scikit-learn (package (name "python-scikit-learn") - (version "0.20.1") + (version "0.20.3") (source (origin (method git-fetch) @@ -802,7 +802,7 @@ computing environments.") (file-name (git-file-name name version)) (sha256 (base32 - "0fkhwg3xn1s7ln9q1szq6kwc4jhwvjh8w4kmv9wcrqy7cq3lbv0d")))) + "08aaby5zphfxy83mggg35bwyka7wk91l2qijh8kk0bl08dikq8dl")))) (build-system python-build-system) (arguments `(#:phases From c8535731b883cbc41bf42e9dc566b896726f8b17 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Mon, 17 Jun 2019 22:52:09 +0200 Subject: [PATCH 109/224] gnu: python-flask-script: Fix tests. * gnu/packages/python-web.scm (python-flask-script)[arguments]<#:phases>[patch-tests]: New phase. --- gnu/packages/python-web.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index d78d97c883..6fe6d5ade8 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2499,6 +2499,14 @@ this it tries to be opinion-free and very extendable.") (base32 "0r8w2v89nj6b9p91p495cga5m72a673l2wc0hp0zqk05j4yrc9b4")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "tests.py" + (("flask\\.ext\\.script") "flask_script")) + #t))))) (propagated-inputs `(("python-flask" ,python-flask) ("python-argcomplete" ,python-argcomplete) From 1539156231205004993c9d9592039daa61021c50 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= Date: Mon, 17 Jun 2019 23:20:44 +0200 Subject: [PATCH 110/224] doc: Fix typo. * doc/guix.texi (Base Services)[guix-publish-service-type]: "guix-publish-configuration" instead of "guix-configuration". --- doc/guix.texi | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 033ad9ea8e..03f890c71d 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -58,7 +58,7 @@ Copyright @copyright{} 2018 Rutger Helling@* Copyright @copyright{} 2018 Oleg Pykhalov@* Copyright @copyright{} 2018 Mike Gerwitz@* Copyright @copyright{} 2018 Pierre-Antoine Rouby@* -Copyright @copyright{} 2018 Gábor Boskovits@* +Copyright @copyright{} 2018, 2019 Gábor Boskovits@* Copyright @copyright{} 2018, 2019 Florian Pelz@* Copyright @copyright{} 2018 Laura Lazzati@* Copyright @copyright{} 2018 Alex Vong@* @@ -12245,7 +12245,7 @@ The GPM package to use. @anchor{guix-publish-service-type} @deffn {Scheme Variable} guix-publish-service-type This is the service type for @command{guix publish} (@pxref{Invoking -guix publish}). Its value must be a @code{guix-configuration} +guix publish}). Its value must be a @code{guix-publish-configuration} object, as described below. This assumes that @file{/etc/guix} already contains a signing key pair as From 972ef8f591fcdbd5d5bb33d0f8dc6f6c40adf952 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 00:04:55 +0200 Subject: [PATCH 111/224] gnu: Add libbraiding. * gnu/packages/sagemath.scm (libbraiding): New variable. --- gnu/packages/sagemath.scm | 32 ++++++++++++++++++++++++++++++-- 1 file changed, 30 insertions(+), 2 deletions(-) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index f7d695049c..91b46a8890 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -18,11 +18,13 @@ (define-module (gnu packages sagemath) #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix packages) - #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system python) + #:use-module (guix download) + #:use-module (guix git-download) + #:use-module (guix packages) #:use-module (gnu packages algebra) + #:use-module (gnu packages autotools) #:use-module (gnu packages compression) #:use-module (gnu packages multiprecision) #:use-module (gnu packages python) @@ -116,3 +118,29 @@ search to maximal cliques, store cliques in memory and call a user-defined function for every found clique.") (license license:gpl2+) (home-page "https://users.aalto.fi/~pat/cliquer.html"))) + +(define-public libbraiding + (package + (name "libbraiding") + (version "1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url (string-append "https://github.com/miguelmarco/" + name)) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0l68rikfr7k2l547gb3pp3g8cj5zzxwipm79xrb5r8ffj466ydxg")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (synopsis "Computations with braid groups") + (description "libbraiding performs computations with braid groups, +in particular it computes normal forms of group elements.") + (license license:gpl2+) + (home-page "https://github.com/miguelmarco/libbraiding"))) From 4c32f116cd89d158960c93ada28c32f3738e7b16 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 00:12:36 +0200 Subject: [PATCH 112/224] gnu: Add libhomfly. * gnu/packages/sagemath.scm (libhomfly): New variable. --- gnu/packages/sagemath.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 91b46a8890..9736f79dc3 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -25,6 +25,7 @@ #:use-module (guix packages) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) + #:use-module (gnu packages bdw-gc) #:use-module (gnu packages compression) #:use-module (gnu packages multiprecision) #:use-module (gnu packages python) @@ -144,3 +145,31 @@ function for every found clique.") in particular it computes normal forms of group elements.") (license license:gpl2+) (home-page "https://github.com/miguelmarco/libbraiding"))) + +(define-public libhomfly + (package + (name "libhomfly") + (version "1.02r6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url (string-append "https://github.com/miguelmarco/" + name)) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0sv3cwrf9v9sb5a8wbhjmarxvya13ma3j8y8592f9ymxlk5y0ldk")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (inputs + `(("libgc" ,libgc))) + (synopsis "Computation of homfly polynomials of links") + (description "libhomfly computes homfly polynomials of links, +represented as strings.") + (license license:public-domain) + (home-page "https://github.com/miguelmarco/libhomfly"))) From 46dc940c9af3d8b48966d16e52273ba88e92f946 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= Date: Tue, 18 Jun 2019 00:22:46 +0200 Subject: [PATCH 113/224] gnu: Add mako. * gnu/packages/wm.scm (mako): New variable. --- gnu/packages/wm.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 0b15801633..90bc7fc883 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -1365,3 +1365,31 @@ modules for building a Wayland compositor.") (description "Waybar is a highly customisable Wayland bar for Sway and Wlroots based compositors.") (license license:expat))) ; MIT license + +(define-public mako + (package + (name "mako") + (version "1.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/mako.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "17azdc37xsbmx13fkfp23vg9lznrv9fh6nhagn64wdq3nhsxm3b6")))) + (build-system meson-build-system) + (inputs `(("cairo" ,cairo) + ("elogind" ,elogind) + ("gdk-pixbuf" ,gdk-pixbuf) + ("pango" ,pango) + ("wayland" ,wayland))) + (native-inputs `(("pkg-config" ,pkg-config) + ("scdoc" ,scdoc) + ("wayland-protocols" ,wayland-protocols))) + (home-page "https://wayland.emersion.fr/mako") + (synopsis "Lightweight Wayland notification daemon") + (description "Mako is a lightweight notification daemon for Wayland +compositors that support the layer-shell protocol.") + (license license:expat))) ; MIT license From 0ab5e91e1ced624c51cecc2693deb7c789fe1f07 Mon Sep 17 00:00:00 2001 From: Ivan Petkov Date: Wed, 22 May 2019 20:50:47 -0700 Subject: [PATCH 114/224] gnu: rust: Update to 1.35.0. * gnu/packages/rust.scm (rust): Rename to... (rust-1.34): ...this. (rust): New variable. --- gnu/packages/rust.scm | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm index 3f5ec590a9..9c8088b2f7 100644 --- a/gnu/packages/rust.scm +++ b/gnu/packages/rust.scm @@ -1048,7 +1048,7 @@ jemalloc = \"" jemalloc "/lib/libjemalloc_pic.a" "\" (setenv "RUST_TEST_THREADS" "2") #t))))))))) -(define-public rust +(define-public rust-1.34 (let ((base-rust (rust-bootstrapped-package rust-1.33 "1.34.1" "19s09k7y5j6g3y4d2rk6kg9pvq6ml94c49w6b72dmq8p9lk8bixh"))) @@ -1062,3 +1062,23 @@ jemalloc = \"" jemalloc "/lib/libjemalloc_pic.a" "\" (delete-file-recursively "src/llvm-project") (delete-file-recursively "vendor/jemalloc-sys/jemalloc") #t))))))) + +(define-public rust + (let ((base-rust + (rust-bootstrapped-package rust-1.34 "1.35.0" + "0bbizy6b7002v1rdhrxrf5gijclbyizdhkglhp81ib3bf5x66kas"))) + (package + (inherit base-rust) + (arguments + (substitute-keyword-arguments (package-arguments base-rust) + ((#:phases phases) + `(modify-phases ,phases + ;; The tidy test includes a pass which ensures large binaries + ;; don't accidentally get checked into the rust git repo. + ;; Unfortunately the test assumes that git is always available, + ;; so we'll comment out the invocation of this pass. + (add-after 'configure 'disable-tidy-bins-check + (lambda* _ + (substitute* "src/tools/tidy/src/main.rs" + (("bins::check") "//bins::check")) + #t))))))))) From 8dec0cdf6e552cd473b768e73c50cd3be3c042b4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 04:51:14 +0200 Subject: [PATCH 115/224] gnu: radare2: Update to 3.5.1. * gnu/packages/engineering.scm (radare2): Update to 3.5.1. --- gnu/packages/engineering.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index ad70c0878f..7d48414889 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -1248,17 +1248,17 @@ bindings for Python, Java, OCaml and more.") (define-public radare2 (package (name "radare2") - (version "2.5.0") + (version "3.5.1") (source (origin (method url-fetch) (uri (string-append "https://radare.mikelloc.com/get/" version "/" "radare2-" version ".tar.gz")) (sha256 (base32 - "17h4ba5qqahfi8mi4x2dcvq87cqpir5v2dlaqbvmay6vby4zh4v7")) + "174x5545fw2nyf000gd46hi7rx2bn3bw5bsnvizn9yi99pn7m4mw")) (modules '((guix build utils))) (snippet - '(begin + '(begin (substitute* "libr/asm/p/Makefile" (("LDFLAGS\\+=") "LDFLAGS+=-Wl,-rpath=$(LIBDIR) ")) (substitute* "libr/parse/p/Makefile" @@ -1268,7 +1268,7 @@ bindings for Python, Java, OCaml and more.") #t)))) (build-system gnu-build-system) (arguments - '(#:tests? #f; tests require git and network access + '(#:tests? #f ; tests require git and network access #:phases (modify-phases %standard-phases (add-before 'configure 'mklibdir From 23414a8efad59f19b4563a0464089ff64c676933 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 07:59:19 +0200 Subject: [PATCH 116/224] gnu: mpd-mpc: Update to 0.32. * gnu/packages/mpd.scm (mpd-mpc): Update to 0.32. --- gnu/packages/mpd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 1d75592795..ff4800c3ca 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -171,7 +171,7 @@ protocol.") (define-public mpd-mpc (package (name "mpd-mpc") - (version "0.31") + (version "0.32") (source (origin (method url-fetch) (uri @@ -180,7 +180,7 @@ protocol.") "/mpc-" version ".tar.xz")) (sha256 (base32 - "0b9bsn4sl26xc6wdcms51x9yxznkxkppaycn8gnv4rd1m21kwdv2")))) + "1irilgz64pny7b8zygy5i74nfmlhgsawz0djx9mrj6g0gidxjqbr")))) (build-system meson-build-system) (inputs `(("libmpdclient" ,libmpdclient))) (native-inputs From 6807d6a9855bcae88aca4c2434c14182ca1059ab Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 16:19:33 +0200 Subject: [PATCH 117/224] gnu: hcxtools: Update to 5.1.6. * gnu/packages/networking.scm (hcxtools): Update to 5.1.6. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 6ade8ed85d..83741e4572 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2255,7 +2255,7 @@ Ethernet and TAP interfaces is supported. Packet capture is also supported.") (define-public hcxtools (package (name "hcxtools") - (version "5.1.4") + (version "5.1.6") (source (origin (method git-fetch) @@ -2263,7 +2263,7 @@ Ethernet and TAP interfaces is supported. Packet capture is also supported.") (url "https://github.com/ZerBea/hcxtools.git") (commit version))) (sha256 - (base32 "1bkl0j6m5q091fas99s83aclcc5kfwacmkgmyg8565z2npvnj7nf")) + (base32 "05sjbmv2wq3nlmammrwxqc62c4sagjjgczzddr1jcqkf6kywzkl8")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (inputs From a0f2c945e3522141e7c9cb6eab4fa36e4afe0584 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 16:19:48 +0200 Subject: [PATCH 118/224] gnu: hcxdumptool: Update to 5.1.5. * gnu/packages/networking.scm (hcxdumptool): Update to 5.1.5. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 83741e4572..04e59ecf00 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2298,7 +2298,7 @@ packets from wireless devices for use with hashcat or John the Ripper.") (define-public hcxdumptool (package (name "hcxdumptool") - (version "5.1.4") + (version "5.1.5") (source (origin (method git-fetch) @@ -2306,7 +2306,7 @@ packets from wireless devices for use with hashcat or John the Ripper.") (url "https://github.com/ZerBea/hcxdumptool.git") (commit version))) (sha256 - (base32 "0h2cc2dfpc83325hwqkxwn0p8qfq5gh1dg0yb1nr8bnffy0b4r4v")) + (base32 "0xkzdvwpi6dq9wsrn882f2ljb7d5v2bvarq8gs6jm8znfx3y8hi2")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (arguments From 55c08305d6d0dee7c459449e0005d5f5309aff3b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 16:19:57 +0200 Subject: [PATCH 119/224] gnu: gandi.cli: Update to 1.5. * gnu/packages/networking.scm (gandi.cli): Update to 1.5. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 04e59ecf00..2cd000ec0a 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -685,13 +685,13 @@ fashion.") (define-public gandi.cli (package (name "gandi.cli") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (pypi-uri name version)) (sha256 - (base32 "1lfvb5npk99nz1lwhr5m67ia1kj35nqd6a2xp9mii28xgzsd5awk")))) + (base32 "110wc9zgxsrvw4yzp21p0ian5lcf7vhcpxhnmsc4fg9pzl2bwxd5")))) (build-system python-build-system) (arguments `(#:phases From ecd5c202b2722c4cdc0ea3353a45a4ebf4acd45e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 18:26:58 +0200 Subject: [PATCH 120/224] gnu: libnftnl: Update to 1.1.3. * gnu/packages/linux.scm (libnftnl): Update to 1.1.3. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index caa121c49a..936d8bec4c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -4788,14 +4788,14 @@ re-use code and to avoid re-inventing the wheel.") (define-public libnftnl (package (name "libnftnl") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (string-append "mirror://netfilter.org/libnftnl/" "libnftnl-" version ".tar.bz2")) (sha256 - (base32 "0pffmsv41alsn5ac7mwnb9fh3qpwzqk13jrzn6c5i71wq6kbgix5")))) + (base32 "03xszkcpqk3s1rqc6vh7g5j13kh3d3yjnvjhk5scds3an39rgp92")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) From f2c119a129d68567e5ff450c45f80bda89e073fb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 18:38:51 +0200 Subject: [PATCH 121/224] gnu: rtv: Update to 1.27.0. * gnu/packages/syndication.scm (rtv): Update to 1.27.0. --- gnu/packages/syndication.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm index bfcefb7270..a84281364f 100644 --- a/gnu/packages/syndication.scm +++ b/gnu/packages/syndication.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2019 Efraim Flashner -;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -97,14 +97,13 @@ It started life as a fork of the currently unmaintained Newsbeuter.") (define-public rtv (package (name "rtv") - (version "1.26.0") + (version "1.27.0") (source (origin (method url-fetch) (uri (pypi-uri "rtv" version)) (sha256 - (base32 - "1aamkli1mlq2vxixlva790y0l0cbvbkz07lknajin0841sdq0411")))) + (base32 "0hvw426y09l3yzwv2zkb9hifpfbg9wd1gg0y3z3pxcli6n3ii2wl")))) (build-system python-build-system) (arguments '(#:phases From 614f7df3ae435dc356053572095de35063ad912d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 18:50:22 +0200 Subject: [PATCH 122/224] gnu: mercurial: Update to 5.0.1. * gnu/packages/version-control.scm (mercurial): Update to 5.0.1. --- gnu/packages/version-control.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index c8773adc7b..8effe1d502 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1223,14 +1223,14 @@ control to Git repositories.") (define-public mercurial (package (name "mercurial") - (version "5.0") + (version "5.0.1") (source (origin (method url-fetch) (uri (string-append "https://www.mercurial-scm.org/" "release/mercurial-" version ".tar.gz")) (sha256 (base32 - "0akivl76sb4q2s42zncrm8jcsn86718wdcngfcw8i6wd2fh7dv2l")))) + "1kk27radafw2q18khg9mk52vny3bmki5wf7pbsmgx5amrpjai62c")))) (build-system python-build-system) (arguments `(;; Restrict to Python 2, as Python 3 would require From b37fa81d9bc9793f99ca0e90ba05f49960099cd9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 18:50:51 +0200 Subject: [PATCH 123/224] gnu: eternalterminal: Update to 5.1.10. * gnu/packages/terminals.scm (eternalterminal): Update to 5.1.10. --- gnu/packages/terminals.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index f742e86a6b..4d0e875012 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -1032,7 +1032,7 @@ comfortably in a pager or editor. (define-public eternalterminal (package (name "eternalterminal") - (version "5.1.9") + (version "5.1.10") (source (origin (method git-fetch) @@ -1041,8 +1041,7 @@ comfortably in a pager or editor. (commit (string-append "et-v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "07ynkcnk3z6wafdlnzdxcd308cw1rzabxyq47ybj79lyji3wsgk7")))) + (base32 "0jh89229bd9s82h3aj6faaybwr5xvnk8w2kgz47gq263pz021zpl")))) (build-system cmake-build-system) (arguments '(#:configure-flags '("-DBUILD_TEST=ON") From 90d537f833a1ce89878146665b668a9927626579 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 17 Jun 2019 19:11:10 +0200 Subject: [PATCH 124/224] gnu: gaupol: Update to 1.6. * gnu/packages/video.scm (gaupol): Update to 1.6. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 760c057ac0..643a40ed77 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -3488,7 +3488,7 @@ video from a Wayland session.") (define-public gaupol (package (name "gaupol") - (version "1.5") + (version "1.6") (source (origin (method git-fetch) (uri (git-reference @@ -3497,7 +3497,7 @@ video from a Wayland session.") (file-name (git-file-name name version)) (sha256 (base32 - "0dk44fmcs86ymfxfbpdbrr4x5nn5hnv57wkqjyw61g779xjhlrd2")))) + "164wlxxjiqvkzbqjzvqvz2zkn0kgqmhn52294xx4vc9b9ngdnn0m")))) (build-system python-build-system) (native-inputs `(("gettext" ,gettext-minimal) From 1e609b78c7f35fc6230638e2e24f57ab2715d9f2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 18 Jun 2019 00:29:28 +0200 Subject: [PATCH 125/224] gnu: stunnel: Update to 5.55. * gnu/packages/web.scm (stunnel): Update to 5.55. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 1ed113cd20..1d9190ef63 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4812,14 +4812,14 @@ tools like SSH (Secure Shell) to reach the outside world.") (define-public stunnel (package (name "stunnel") - (version "5.54") + (version "5.55") (source (origin (method url-fetch) (uri (string-append "https://www.stunnel.org/downloads/stunnel-" version ".tar.gz")) (sha256 - (base32 "00krr0h3vsyi93mqhrbgfgn8v47l4l3hzdg1ccfnpd3lqak8i1ay")))) + (base32 "0qjc0wkjf6bqz29fvwwsn9hnjhm6alsm10jcwx4jad2q3ks6kplh")))) (build-system gnu-build-system) (native-inputs ;; For tests. From eed81080dc6f552e381971ec11cec5de0c58a58d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 18 Jun 2019 12:47:37 +0200 Subject: [PATCH 126/224] gnu: python-pygments: Update to 2.4.2. * gnu/packages/python-xyz.scm (python-pygments): Update to 2.4.2. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e1d0b7f50a..466b2d8768 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2502,14 +2502,14 @@ reStructuredText.") (define-public python-pygments (package (name "python-pygments") - (version "2.4.0") + (version "2.4.2") (source (origin (method url-fetch) (uri (pypi-uri "Pygments" version)) (sha256 (base32 - "1xb5n3hvhk63kxypc03k7kfry20pny6gygi4bsl9kw1rnzzsdjri")))) + "15v2sqm5g12bqa0c7wikfh9ck2nl97ayizy1hpqhmws5gqalq748")))) (build-system python-build-system) (arguments ;; FIXME: Tests require sphinx, which depends on this. From dede052a2cb5f8e35ddb342c6d77b5784f46ed0b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 18 Jun 2019 14:13:48 +0200 Subject: [PATCH 127/224] gnu: Add python-backcall. * gnu/packages/python-xyz.scm (python-backcall): New variable. --- gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3efd18a72b..28ed440c78 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5062,6 +5062,28 @@ installing @code{kernelspec}s for use with Jupyter frontends.") (description "The package provides a PARI/GP kernel for Jupyter.") (license license:gpl3+))) +(define-public python-backcall + (package + (name "python-backcall") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "backcall" version)) + (sha256 + (base32 + "1r01dqch3f8fdj3n6fviw8hxqrs6w5v0qw4izmvqzry1w9dxiv1q")))) + (build-system python-build-system) + (home-page "https://github.com/takluyver/backcall/") + (synopsis "Specifications for callback functions passed in to an API") + (description + "If your code lets other people supply callback functions, it's important +to specify the function signature you expect, and check that functions support +that. Adding extra parameters later would break other peoples code unless +you're careful. The @code{backcall} package provides a way of specifying the +callback signature using a prototype function.") + (license license:bsd-3))) + ;; This is the latest release of the LTS version of ipython with support for ;; Python 2.7 and Python 3.x. Later non-LTS versions starting from 6.0 have ;; dropped support for Python 2.7. We may want to rename this package. From 0f3789477a79a4816ffdc8e1a232543909455d2c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 18 Jun 2019 14:14:07 +0200 Subject: [PATCH 128/224] gnu: python2-ipykernel: Split from python-ipykernel. * gnu/packages/python-xyz.scm (python2-ipykernel): Define without package-with-python2. --- gnu/packages/python-xyz.scm | 33 ++++++++++++++++++++++++++++++++- 1 file changed, 32 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 28ed440c78..a2abf36cbd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5034,8 +5034,39 @@ installing @code{kernelspec}s for use with Jupyter frontends.") "This package provides the IPython kernel for Jupyter.") (license license:bsd-3))) +;; Version 5.1.1 and above no longer support Python 2. (define-public python2-ipykernel - (package-with-python2 python-ipykernel)) + (package + (name "python2-ipykernel") + (version "5.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ipykernel" version)) + (sha256 + (base32 "0br95qhrd5k65g10djngiy27hs0642301hlf2q142i8djabvzh0g")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "HOME" "/tmp") + (invoke "pytest" "-v") + #t))))) + (propagated-inputs + `(("python2-ipython" ,python2-ipython) + ;; imported at runtime during connect + ("python2-jupyter-client" ,python2-jupyter-client))) + (native-inputs + `(("python2-pytest" ,python2-pytest) + ("python2-nose" ,python2-nose))) + (home-page "https://ipython.org") + (synopsis "IPython Kernel for Jupyter") + (description + "This package provides the IPython kernel for Jupyter.") + (license license:bsd-3))) (define-public python-pari-jupyter (package From 82110deadb52d5ae56eb177fde40fbe2caae95cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 18 Jun 2019 14:14:47 +0200 Subject: [PATCH 129/224] gnu: python-ipykernel: Update to 5.1.1. * gnu/packages/python-xyz.scm (python-ipykernel): Update to 5.1.1. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a2abf36cbd..0dd761cb3a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5005,13 +5005,13 @@ installing @code{kernelspec}s for use with Jupyter frontends.") (define-public python-ipykernel (package (name "python-ipykernel") - (version "5.1.0") + (version "5.1.1") (source (origin (method url-fetch) (uri (pypi-uri "ipykernel" version)) (sha256 - (base32 "0br95qhrd5k65g10djngiy27hs0642301hlf2q142i8djabvzh0g")))) + (base32 "173nm29g85w8cac3fg40b27qaq26g41wgg6qn79ql1hq4w2n5sgh")))) (build-system python-build-system) (arguments `(#:phases From 8b5f756ccbdd680926b5cce05d66c87b4042d0b4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 18 Jun 2019 14:15:19 +0200 Subject: [PATCH 130/224] gnu: python-ipython: Update to 7.5.0 * gnu/packages/python-xyz.scm (python2-ipython): Do not inherit from python-ipython. [outputs]: Remove separate "doc" output. [native-inputs]: Remove python-sphinx, python-sphinx-rtd-theme, texinfo, and the texlive-union consisting of texlive-fonts-amsfonts, texlive-fonts-ec, texlive-generic-ifxetex, texlive-generic-pdftex, texlive-latex-amsfonts, texlive-latex-capt-of, texlive-latex-cmap, texlive-latex-environ, texlive-latex-eqparbox, texlive-latex-etoolbox, texlive-latex-expdlist, texlive-latex-fancyhdr, texlive-latex-fancyvrb, texlive-latex-fncychap, texlive-latex-float, texlive-latex-framed, texlive-latex-geometry, texlive-latex-graphics, texlive-latex-hyperref, texlive-latex-mdwtools, texlive-latex-multirow, texlive-latex-oberdiek, texlive-latex-parskip, texlive-latex-preview, texlive-latex-tabulary, texlive-latex-threeparttable, texlive-latex-titlesec, texlive-latex-trimspaces, texlive-latex-ucs, texlive-latex-upquote, texlive-latex-url, texlive-latex-varwidth, and texlive-latex-wrapfig. [arguments]: Remove "install-doc" phase; rename "fix-tests" phase to "delete-broken-tests" and adjust. (python-ipython): Update to 7.5.0. [outputs]: Remove separate "doc" output. [propagated-inputs]: Add python-backcall and python-jedi; replace python-prompt-toolkit-1 with python-prompt-toolkit. [native-inputs]: Remove python-sphinx, python-sphinx-rtd-theme, texinfo, and the texlive-union consisting of texlive-fonts-amsfonts, texlive-fonts-ec, texlive-generic-ifxetex, texlive-generic-pdftex, texlive-latex-amsfonts, texlive-latex-capt-of, texlive-latex-cmap, texlive-latex-environ, texlive-latex-eqparbox, texlive-latex-etoolbox, texlive-latex-expdlist, texlive-latex-fancyhdr, texlive-latex-fancyvrb, texlive-latex-fncychap, texlive-latex-float, texlive-latex-framed, texlive-latex-geometry, texlive-latex-graphics, texlive-latex-hyperref, texlive-latex-mdwtools, texlive-latex-multirow, texlive-latex-oberdiek, texlive-latex-parskip, texlive-latex-preview, texlive-latex-tabulary, texlive-latex-threeparttable, texlive-latex-titlesec, texlive-latex-trimspaces, texlive-latex-ucs, texlive-latex-upquote, texlive-latex-url, texlive-latex-varwidth, and texlive-latex-wrapfig. [arguments]: Remove "install-doc" phase; simplify "fix-tests" phase. [properties]: Remove. (python-ipython-documentation): New variable. --- gnu/packages/python-xyz.scm | 245 ++++++++++++++++++++++-------------- 1 file changed, 150 insertions(+), 95 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0dd761cb3a..aca8a140e7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5117,10 +5117,10 @@ callback signature using a prototype function.") ;; This is the latest release of the LTS version of ipython with support for ;; Python 2.7 and Python 3.x. Later non-LTS versions starting from 6.0 have -;; dropped support for Python 2.7. We may want to rename this package. -(define-public python-ipython +;; dropped support for Python 2.7. +(define-public python2-ipython (package - (name "python-ipython") + (name "python2-ipython") (version "5.8.0") (source (origin @@ -5129,14 +5129,75 @@ callback signature using a prototype function.") (sha256 (base32 "01l93i4hspf0lvhmycvc8j378bslm9rw30mwfspsl6v1ayc69b2b")))) (build-system python-build-system) - (outputs '("out" "doc")) (propagated-inputs - `(("python-pyzmq" ,python-pyzmq) - ("python-prompt-toolkit" ,python-prompt-toolkit-1) + `(("python2-backports-shutil-get-terminal-size" + ,python2-backports-shutil-get-terminal-size) + ("python2-pathlib2" ,python2-pathlib2) + ("python2-pyzmq" ,python2-pyzmq) + ("python2-prompt-toolkit" ,python2-prompt-toolkit-1) + ("python2-terminado" ,python2-terminado) + ("python2-matplotlib" ,python2-matplotlib) + ("python2-numpy" ,python2-numpy) + ("python2-numpydoc" ,python2-numpydoc) + ("python2-jinja2" ,python2-jinja2) + ("python2-mistune" ,python2-mistune) + ("python2-pexpect" ,python2-pexpect) + ("python2-pickleshare" ,python2-pickleshare) + ("python2-simplegeneric" ,python2-simplegeneric) + ("python2-jsonschema" ,python2-jsonschema) + ("python2-traitlets" ,python2-traitlets) + ("python2-nbformat" ,python2-nbformat) + ("python2-pygments" ,python2-pygments))) + (inputs + `(("readline" ,readline) + ("which" ,which))) + (native-inputs + `(("graphviz" ,graphviz) + ("pkg-config" ,pkg-config) + ("python2-requests" ,python2-requests) ;; for tests + ("python2-testpath" ,python2-testpath) + ("python2-mock" ,python2-mock) + ("python2-nose" ,python2-nose))) + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (add-before 'check 'delete-broken-tests + (lambda* (#:key inputs #:allow-other-keys) + ;; These tests throw errors for unknown reasons. + (delete-file "IPython/core/tests/test_profile.py") + (delete-file "IPython/core/tests/test_interactiveshell.py") + (delete-file "IPython/core/tests/test_magic.py") + #t))))) + (home-page "https://ipython.org") + (synopsis "IPython is a tool for interactive computing in Python") + (description + "IPython provides a rich architecture for interactive computing with: +Powerful interactive shells, a browser-based notebook, support for interactive +data visualization, embeddable interpreters and tools for parallel +computing.") + (license license:bsd-3))) + +(define-public python-ipython + (package + (name "python-ipython") + (version "7.5.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ipython" version ".tar.gz")) + (sha256 + (base32 "09mbxq37mfn88xjnib7qfzaq9krr7gf1jxwy1p6mcjr254082h78")))) + (build-system python-build-system) + (propagated-inputs + `(("python-backcall" ,python-backcall) + ("python-pyzmq" ,python-pyzmq) + ("python-prompt-toolkit" ,python-prompt-toolkit) ("python-terminado" ,python-terminado) ("python-matplotlib" ,python-matplotlib) ("python-numpy" ,python-numpy) ("python-numpydoc" ,python-numpydoc) + ("python-jedi" ,python-jedi) ("python-jinja2" ,python-jinja2) ("python-mistune" ,python-mistune) ("python-pexpect" ,python-pexpect) @@ -5154,74 +5215,10 @@ callback signature using a prototype function.") ("pkg-config" ,pkg-config) ("python-requests" ,python-requests) ;; for tests ("python-testpath" ,python-testpath) - ("python-nose" ,python-nose) - ("python-sphinx" ,python-sphinx) - ("python-shpinx-rtd-theme" ,python-sphinx-rtd-theme) - ;; FIXME: It's possible that a smaller union would work just as well. - ("texlive" ,(texlive-union (list texlive-fonts-amsfonts - texlive-fonts-ec - texlive-generic-ifxetex - texlive-generic-pdftex - texlive-latex-amsfonts - texlive-latex-capt-of - texlive-latex-cmap - texlive-latex-environ - texlive-latex-eqparbox - texlive-latex-etoolbox - texlive-latex-expdlist - texlive-latex-fancyhdr - texlive-latex-fancyvrb - texlive-latex-fncychap - texlive-latex-float - texlive-latex-framed - texlive-latex-geometry - texlive-latex-graphics - texlive-latex-hyperref - texlive-latex-mdwtools - texlive-latex-multirow - texlive-latex-oberdiek - texlive-latex-parskip - texlive-latex-preview - texlive-latex-tabulary - texlive-latex-threeparttable - texlive-latex-titlesec - texlive-latex-trimspaces - texlive-latex-ucs - texlive-latex-upquote - texlive-latex-url - texlive-latex-varwidth - texlive-latex-wrapfig))) - ("texinfo" ,texinfo))) + ("python-nose" ,python-nose))) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'install 'install-doc - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "doc") "/share")) - (doc (string-append data "/doc/" ,name "-" ,version)) - (html (string-append doc "/html")) - (man1 (string-append data "/man/man1")) - (info (string-append data "/info")) - (examples (string-append doc "/examples")) - (python-arg (string-append "PYTHON=" (which "python")))) - (setenv "LANG" "en_US.utf8") - ;; Make installed package available for running the tests - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "docs" - ;; FIXME: pdf fails to build - ;;(system* "make" "pdf" "PAPER=a4") - (system* "make" python-arg "html") - (system* "make" python-arg "info")) - (copy-recursively "docs/man" man1) - (copy-recursively "examples" examples) - (copy-recursively "docs/build/html" html) - ;; (copy-file "docs/build/latex/ipython.pdf" - ;; (string-append doc "/ipython.pdf")) - (mkdir-p info) - (copy-file "docs/build/texinfo/ipython.info" - (string-append info "/ipython.info")) - (copy-file "COPYING.rst" (string-append doc "/COPYING.rst"))) - #t)) ;; Tests can only be run after the library has been installed and not ;; within the source directory. (delete 'check) @@ -5244,19 +5241,11 @@ callback signature using a prototype function.") (substitute* "./IPython/core/tests/test_inputtransformer.py" (("#!/usr/bin/env python") (string-append "#!" (which "python")))) - ;; Disable 1 failing test - (substitute* "./IPython/core/tests/test_magic.py" - (("def test_dirops\\(\\):" all) - (string-append "@dec.skipif(True)\n" all))) ;; This test introduces a circular dependency on ipykernel ;; (which depends on ipython). (delete-file "IPython/core/tests/test_display.py") - ;; These tests throw errors for unknown reasons. - (delete-file "IPython/extensions/tests/test_storemagic.py") - (delete-file "IPython/core/tests/test_displayhook.py") + ;; AttributeError: module 'IPython.core' has no attribute 'formatters' (delete-file "IPython/core/tests/test_interactiveshell.py") - (delete-file "IPython/core/tests/test_pylabtools.py") - (delete-file "IPython/core/tests/test_paths.py") #t))))) (home-page "https://ipython.org") (synopsis "IPython is a tool for interactive computing in Python") @@ -5265,22 +5254,88 @@ callback signature using a prototype function.") Powerful interactive shells, a browser-based notebook, support for interactive data visualization, embeddable interpreters and tools for parallel computing.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python2-ipython)))))) + (license license:bsd-3))) -(define-public python2-ipython - (let ((ipython (package-with-python2 (strip-python2-variant python-ipython)))) - (package - (inherit ipython) - ;; FIXME: add pyreadline once available. - (propagated-inputs - `(("python2-backports-shutil-get-terminal-size" - ,python2-backports-shutil-get-terminal-size) - ("python2-pathlib2" ,python2-pathlib2) - ,@(package-propagated-inputs ipython))) - (native-inputs - `(("python2-mock" ,python2-mock) - ,@(package-native-inputs ipython)))))) +(define-public python-ipython-documentation + (package + (inherit python-ipython) + (name "python-ipython-documentation") + (version (package-version python-ipython)) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'build) + (delete 'check) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((data (string-append (assoc-ref outputs "out") "/share")) + (doc (string-append data "/doc/" ,name "-" ,version)) + (html (string-append doc "/html")) + (man1 (string-append data "/man/man1")) + (info (string-append data "/info")) + (examples (string-append doc "/examples")) + (python-arg (string-append "PYTHON=" (which "python")))) + (setenv "LANG" "en_US.utf8") + (with-directory-excursion "docs" + ;; FIXME: pdf fails to build + ;;(system* "make" "pdf" "PAPER=a4") + (system* "make" python-arg "html") + ;; FIXME: the generated texi file contains ^@^@, which trips + ;; up the parser. + ;; (system* "make" python-arg "info") + ) + (copy-recursively "docs/man" man1) + (copy-recursively "examples" examples) + (copy-recursively "docs/build/html" html) + ;; (copy-file "docs/build/latex/ipython.pdf" + ;; (string-append doc "/ipython.pdf")) + (mkdir-p info) + ;; (copy-file "docs/build/texinfo/ipython.info" + ;; (string-append info "/ipython.info")) + (copy-file "COPYING.rst" (string-append doc "/COPYING.rst"))) + #t))))) + (inputs + `(("python-ipython" ,python-ipython) + ("python-ipykernel" ,python-ipykernel))) + (native-inputs + `(("python-sphinx" ,python-sphinx) + ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme) + ;; FIXME: It's possible that a smaller union would work just as well. + ("texlive" ,(texlive-union (list texlive-fonts-amsfonts + texlive-fonts-ec + texlive-generic-ifxetex + texlive-generic-pdftex + texlive-latex-amsfonts + texlive-latex-capt-of + texlive-latex-cmap + texlive-latex-environ + texlive-latex-eqparbox + texlive-latex-etoolbox + texlive-latex-expdlist + texlive-latex-fancyhdr + texlive-latex-fancyvrb + texlive-latex-fncychap + texlive-latex-float + texlive-latex-framed + texlive-latex-geometry + texlive-latex-graphics + texlive-latex-hyperref + texlive-latex-mdwtools + texlive-latex-multirow + texlive-latex-needspace + texlive-latex-oberdiek + texlive-latex-parskip + texlive-latex-preview + texlive-latex-tabulary + texlive-latex-threeparttable + texlive-latex-titlesec + texlive-latex-trimspaces + texlive-latex-ucs + texlive-latex-upquote + texlive-latex-url + texlive-latex-varwidth + texlive-latex-wrapfig))) + ("texinfo" ,texinfo))))) (define-public python-urwid (package From 55dae98f737b641aaf6e0b73ed343ae3be47545d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 18 Jun 2019 14:48:36 +0200 Subject: [PATCH 131/224] gnu: Add python-matplotlib-venn. * gnu/packages/python-xyz.scm (python-matplotlib-venn): New variable. --- gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index aca8a140e7..be9c58bb98 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3941,6 +3941,32 @@ toolkits.") (define-public python2-matplotlib-documentation (package-with-python2 python-matplotlib-documentation)) +(define-public python-matplotlib-venn + (package + (name "python-matplotlib-venn") + (version "0.11.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "matplotlib-venn" version ".zip")) + (sha256 + (base32 + "13w3i1wih0mij08hrgppzg0g9z50y54rc28l6gdi1r5w45l7l0dy")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; tests are not included + (propagated-inputs + `(("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "https://github.com/konstantint/matplotlib-venn") + (synopsis "Plot area-proportional Venn diagrams") + (description + "This package provides tools for plotting area-proportional two- and +three-way Venn diagrams in @code{matplotlib}.") + (license license:expat))) + (define-public python2-pysnptools (package (name "python2-pysnptools") From 4e24e442f2c9629edf08bef30ec98959da950189 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 18 Jun 2019 15:21:14 +0200 Subject: [PATCH 132/224] gnu: python-freezegun: Update to 0.3.12. * gnu/packages/check.scm (python-freezegun): Update to 0.3.12. [native-inputs]: Remove PYTHON-NOSE and PYTHON-COVERAGE. Add PYTHON-PYTEST. [arguments]: Use "pytest" instead of "nosetests" for running tests. --- gnu/packages/check.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 82391ac5e1..e24f2713b4 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2043,18 +2043,17 @@ create data based on random numbers and yet remain repeatable.") (define-public python-freezegun (package (name "python-freezegun") - (version "0.3.11") + (version "0.3.12") (source (origin (method url-fetch) (uri (pypi-uri "freezegun" version)) (sha256 - (base32 "1nh0fzqjwg88n57k3qa8mxnmiwrr7lqyd5xvc96qn5g8zcxv8fg8")))) + (base32 "1rx57v8ryjncjimg8hys9kx1r3rknvwcl4y340g20jn0sf69qk9a")))) (build-system python-build-system) (native-inputs `(("python-mock" ,python-mock) - ("python-nose" ,python-nose) - ("python-coverage" ,python-coverage))) + ("python-pytest" ,python-pytest))) (propagated-inputs `(("python-six" ,python-six) ("python-dateutil" ,python-dateutil))) @@ -2065,7 +2064,7 @@ create data based on random numbers and yet remain repeatable.") ;; package does not include the Makefile. (replace 'check (lambda _ - (invoke "nosetests" "./tests/")))))) + (invoke "pytest" "-vv")))))) (home-page "https://github.com/spulec/freezegun") (synopsis "Test utility for mocking the datetime module") (description From 93253411d6a55ebdcd91de2c6eb80e1c9134d12a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 18 Jun 2019 15:21:21 +0200 Subject: [PATCH 133/224] gnu: python-babel: Update to 2.7.0. * gnu/packages/python-xyz.scm (python-babel): Update to 2.7.0. (python2-babel-2.6): New variable. * gnu/packages/sphinx.scm (python2-sphinx)[propagated-inputs]: Change PYTHON2-BABEL to PYTHON2-BABEL-2.6. --- gnu/packages/python-xyz.scm | 16 ++++++++++++++-- gnu/packages/sphinx.scm | 2 +- 2 files changed, 15 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 466b2d8768..c072cf574c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -311,14 +311,14 @@ by @code{binstar}, @code{binstar-build} and @code{chalmers}.") (define-public python-babel (package (name "python-babel") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) (uri (pypi-uri "Babel" version)) (sha256 (base32 - "08rxmbx2s4irp0w0gmn498vns5xy0fagm0fg33xa772jiks51flc")))) + "0a7wawx8vsg7igvz6p3x909fskhg4b2y1910xk4f4c8y22p3aqg8")))) (build-system python-build-system) (native-inputs `(("python-freezegun" ,python-freezegun) @@ -343,6 +343,18 @@ etc. ") (define-public python2-babel (package-with-python2 python-babel)) +;; Sphinx < 2.0 requires this version. Remove once no longer needed. +(define-public python2-babel-2.6 + (package + (inherit python2-babel) + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "Babel" version)) + (sha256 + (base32 + "08rxmbx2s4irp0w0gmn498vns5xy0fagm0fg33xa772jiks51flc")))))) + (define-public python2-backport-ssl-match-hostname (package (name "python2-backport-ssl-match-hostname") diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 0b86398a68..a9475ab87b 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -132,7 +132,7 @@ sources.") ("python2-imagesize" ,python2-imagesize) ("python2-sphinx-alabaster-theme" ,python2-sphinx-alabaster-theme) - ("python2-babel" ,python2-babel) + ("python2-babel" ,python2-babel-2.6) ("python2-snowballstemmer" ,python2-snowballstemmer) ("python2-docutils" ,python2-docutils) ("python2-jinja2" ,python2-jinja2) From 71c08ee60bb3f62bac0614888fb62405f7a388ab Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 18 Jun 2019 15:21:40 +0200 Subject: [PATCH 134/224] gnu: python-pytz: Update to 2019.1. * gnu/packages/time.scm (python-pytz): Update to 2019.1. --- gnu/packages/time.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index 747e4cf080..9bbfe07803 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -92,14 +92,14 @@ to a file.") (define-public python-pytz (package (name "python-pytz") - (version "2018.5") + (version "2019.1") (source (origin (method url-fetch) (uri (pypi-uri "pytz" version ".tar.gz")) (sha256 (base32 - "0xzj5gkpdn2da8m6j47chlp6zrzcypv9m0fjv4236q3jw4fyzfgz")))) + "0hg1r2c41gnmljdsdmdgy6kb1zkfmxsf49imd96g8znp4cyxsiyp")))) (build-system python-build-system) (home-page "http://pythonhosted.org/pytz") (synopsis "Python timezone library") From a32e3b90787ab3d221fb1b8d0bfd9c519a874230 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 18 Jun 2019 15:57:43 +0200 Subject: [PATCH 135/224] gnu: gemmlowp-for-tensorflow: Use SSE2. * gnu/packages/machine-learning.scm (gemmlowp-for-tensorflow)[arguments]: Only enable SSE2, not SSE4.1 on i686 and x86_64 architectures. --- gnu/packages/machine-learning.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 370cfe1a30..505cc88f4b 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -668,7 +668,7 @@ geometric models.") `(#:configure-flags (list ,@(match (%current-system) ((or "x86_64-linux" "i686-linux") - '("-DCMAKE_CXX_FLAGS=-msse4.1")) + '("-DCMAKE_CXX_FLAGS=-msse2")) (_ '()))) #:phases (modify-phases %standard-phases From 5c7f87881a52a6424fc6722376b990284a06de5a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 17 Jun 2019 22:48:44 +0200 Subject: [PATCH 136/224] tests: Avoid 'delete-paths' calls for 'derivation-prerequisites-to-build'. * tests/derivations.scm ("derivation-prerequisites-to-build when outputs already present"): Insert random text in BUILDER, and remove two calls to 'delete-paths'. Use 'derivation->output-path' for INPUT-PATH instead of an old idiom. --- tests/derivations.scm | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/tests/derivations.scm b/tests/derivations.scm index c421d094a4..93f4cdd8ee 100644 --- a/tests/derivations.scm +++ b/tests/derivations.scm @@ -816,20 +816,17 @@ (null? (derivation-prerequisites-to-build %store drv)))) (test-assert "derivation-prerequisites-to-build when outputs already present" - (let* ((builder '(begin (mkdir %output) #t)) + (let* ((builder `(begin ,(random-text) (mkdir %output) #t)) (input-drv (build-expression->derivation %store "input" builder)) - (input-path (derivation-output-path - (assoc-ref (derivation-outputs input-drv) - "out"))) + (input-path (derivation->output-path input-drv)) (drv (build-expression->derivation %store "something" builder #:inputs `(("i" ,input-drv)))) (output (derivation->output-path drv))) - ;; Make sure these things are not already built. - (when (valid-path? %store input-path) - (delete-paths %store (list input-path))) - (when (valid-path? %store output) - (delete-paths %store (list output))) + ;; Assume these things are not already built. + (when (or (valid-path? %store input-path) + (valid-path? %store output)) + (error "things already built" input-drv)) (and (equal? (map derivation-input-path (derivation-prerequisites-to-build %store drv)) From 9353b199c18caca4a429f20423e1a5e7bc26a8da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 18 Jun 2019 09:50:38 +0200 Subject: [PATCH 137/224] guix build: '--log-file' looks for build logs of equivalent derivations. Previously, '--log-file' would look for log files only for the current derivation, and thus wouldn't find log files of equivalent derivations that produce the same output. * guix/scripts/build.scm (guix-build) : Replace 'derivation-file-name' by 'derivation->output-path'. --- guix/scripts/build.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm index 8fa700c883..61ca4dca9f 100644 --- a/guix/scripts/build.scm +++ b/guix/scripts/build.scm @@ -935,9 +935,12 @@ needed." #:mode mode)) (cond ((assoc-ref opts 'log-file?) + ;; Pass 'show-build-log' the output file names, not the + ;; derivation file names, because there can be several + ;; derivations leading to the same output. (for-each (cut show-build-log store <> urls) (delete-duplicates - (append (map derivation-file-name drv) + (append (map derivation->output-path drv) items)))) ((assoc-ref opts 'derivations-only?) (format #t "~{~a~%~}" (map derivation-file-name drv)) From b95ccbaf61eb4108b00986f5d6996185e8887112 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 18 Jun 2019 12:27:46 +0200 Subject: [PATCH 138/224] doc: Replace invalid uses of @var with @code. * doc/guix.texi: Replace @var with @code in cases where we refer to a Scheme variable and not to a metasyntactic variable. --- doc/guix.texi | 46 +++++++++++++++++++++++----------------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 03f890c71d..65c3b8a7f1 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -6445,7 +6445,7 @@ Connect to the daemon over the Unix-domain socket at @var{uri} (a string). When extra space on the file system so that the garbage collector can still operate should the disk become full. Return a server object. -@var{file} defaults to @var{%default-socket-path}, which is the normal +@var{file} defaults to @code{%default-socket-path}, which is the normal location given the options that were passed to @command{configure}. @end deffn @@ -10357,7 +10357,7 @@ configuration options. The @code{packages} field lists packages that will be globally visible on the system, for all user accounts---i.e., in every user's @code{PATH} environment variable---in addition to the per-user profiles -(@pxref{Invoking guix package}). The @var{%base-packages} variable +(@pxref{Invoking guix package}). The @code{%base-packages} variable provides all the tools one would expect for basic user and administrator tasks---including the GNU Core Utilities, the GNU Networking Utilities, the GNU Zile lightweight text editor, @command{find}, @command{grep}, @@ -10418,7 +10418,7 @@ customize them. To do this, use @code{modify-services} (@pxref{Service Reference, @code{modify-services}}) to modify the list. For example, suppose you want to modify @code{guix-daemon} and Mingetty -(the console log-in) in the @var{%base-services} list (@pxref{Base +(the console log-in) in the @code{%base-services} list (@pxref{Base Services, @code{%base-services}}). To do that, you can write the following in your operating system declaration: @@ -10442,7 +10442,7 @@ following in your operating system declaration: This changes the configuration---i.e., the service parameters---of the @code{guix-service-type} instance, and that of all the -@code{mingetty-service-type} instances in the @var{%base-services} list. +@code{mingetty-service-type} instances in the @code{%base-services} list. Observe how this is accomplished: first, we arrange for the original configuration to be bound to the identifier @code{config} in the @var{body}, and then we write the @var{body} so that it evaluates to the @@ -10473,15 +10473,15 @@ This example refers to the @file{/boot/efi} file system by its UUID, as returned by the @command{blkid} command. @xref{Desktop Services}, for the exact list of services provided by -@var{%desktop-services}. @xref{X.509 Certificates}, for background +@code{%desktop-services}. @xref{X.509 Certificates}, for background information about the @code{nss-certs} package that is used here. -Again, @var{%desktop-services} is just a list of service objects. If +Again, @code{%desktop-services} is just a list of service objects. If you want to remove services from there, you can do so using the procedures for list filtering (@pxref{SRFI-1 Filtering and Partitioning,,, guile, GNU Guile Reference Manual}). For instance, the following expression returns a list that contains all the services in -@var{%desktop-services} minus the Avahi service: +@code{%desktop-services} minus the Avahi service: @example (remove (lambda (service) @@ -10600,7 +10600,7 @@ A procedure that returns an initial RAM disk for the Linux kernel. This field is provided to support low-level customization and should rarely be needed for casual use. @xref{Initial RAM Disk}. -@item @code{firmware} (default: @var{%base-firmware}) +@item @code{firmware} (default: @code{%base-firmware}) @cindex firmware List of firmware packages loadable by the operating system kernel. @@ -10635,7 +10635,7 @@ device, provided that the necessary device mapping and file system are also specified. @xref{Mapped Devices} and @ref{File Systems}. @item @code{users} (default: @code{%base-user-accounts}) -@itemx @code{groups} (default: @var{%base-groups}) +@itemx @code{groups} (default: @code{%base-groups}) List of user accounts and groups. @xref{User Accounts}. If the @code{users} list lacks a user account with UID@tie{}0, a @@ -10655,11 +10655,11 @@ For instance, a valid value may look like this: (activate-readline)"))) @end example -@item @code{issue} (default: @var{%default-issue}) +@item @code{issue} (default: @code{%default-issue}) A string denoting the contents of the @file{/etc/issue} file, which is displayed when users log in on a text console. -@item @code{packages} (default: @var{%base-packages}) +@item @code{packages} (default: @code{%base-packages}) The set of packages installed in the global profile, which is accessible at @file{/run/current-system/profile}. @@ -10678,7 +10678,7 @@ causes @command{guix system} to fail. The name of the default locale (@pxref{Locale Names,,, libc, The GNU C Library Reference Manual}). @xref{Locales}, for more information. -@item @code{locale-definitions} (default: @var{%default-locale-definitions}) +@item @code{locale-definitions} (default: @code{%default-locale-definitions}) The list of locale definitions to be compiled and that may be used at run time. @xref{Locales}. @@ -10687,12 +10687,12 @@ The list of GNU@tie{}libc packages whose locale data and tools are used to build the locale definitions. @xref{Locales}, for compatibility considerations that justify this option. -@item @code{name-service-switch} (default: @var{%default-nss}) +@item @code{name-service-switch} (default: @code{%default-nss}) Configuration of the libc name service switch (NSS)---a @code{} object. @xref{Name Service Switch}, for details. -@item @code{services} (default: @var{%base-services}) +@item @code{services} (default: @code{%base-services}) A list of service objects denoting system services. @xref{Services}. @cindex essential services @@ -11557,7 +11557,7 @@ more. This is the default value of the @code{services} field of @code{operating-system} declarations. Usually, when customizing a -system, you will want to append services to @var{%base-services}, like +system, you will want to append services to @code{%base-services}, like this: @example @@ -12054,7 +12054,7 @@ Whether to authorize the substitute keys listed in (@pxref{Substitutes}). @vindex %default-authorized-guix-keys -@item @code{authorized-keys} (default: @var{%default-authorized-guix-keys}) +@item @code{authorized-keys} (default: @code{%default-authorized-guix-keys}) The list of authorized key files for archive imports, as a list of string-valued gexps (@pxref{Invoking guix archive}). By default, it contains that of @code{@value{SUBSTITUTE-SERVER}} (@pxref{Substitutes}). @@ -12062,7 +12062,7 @@ contains that of @code{@value{SUBSTITUTE-SERVER}} (@pxref{Substitutes}). @item @code{use-substitutes?} (default: @code{#t}) Whether to use substitutes. -@item @code{substitute-urls} (default: @var{%default-substitute-urls}) +@item @code{substitute-urls} (default: @code{%default-substitute-urls}) The list of URLs where to look for substitutes by default. @item @code{max-silent-time} (default: @code{0}) @@ -12223,7 +12223,7 @@ allows users to use the mouse in the console, notably to select, copy, and paste text. The value for services of this type must be a @code{gpm-configuration} -(see below). This service is not part of @var{%base-services}. +(see below). This service is not part of @code{%base-services}. @end defvr @deftp {Data Type} gpm-configuration @@ -14732,7 +14732,7 @@ services that users typically expect on a machine with a graphical environment and networking: @defvr {Scheme Variable} %desktop-services -This is a list of services that builds upon @var{%base-services} and +This is a list of services that builds upon @code{%base-services} and adds or adjusts services for a typical ``desktop'' setup. In particular, it adds a graphical login manager (@pxref{X Window, @@ -14747,7 +14747,7 @@ name service switch service configured to be able to use @code{nss-mdns} (@pxref{Name Service Switch, mDNS}). @end defvr -The @var{%desktop-services} variable can be used as the @code{services} +The @code{%desktop-services} variable can be used as the @code{services} field of an @code{operating-system} declaration (@pxref{operating-system Reference, @code{services}}). @@ -16756,7 +16756,7 @@ Data type representing the configuration of opensmtpd. @item @code{package} (default: @var{opensmtpd}) Package object of the OpenSMTPD SMTP server. -@item @code{config-file} (default: @var{%default-opensmtpd-file}) +@item @code{config-file} (default: @code{%default-opensmtpd-file}) File-like object of the OpenSMTPD configuration file to use. By default it listens on the loopback network interface, and allows for mail from users and daemons on the local machine, as well as permitting email to @@ -24363,7 +24363,7 @@ to the @code{packages} field of the @code{operating-system} declaration @code{nss-certs}, which is a set of CA certificates provided as part of Mozilla's Network Security Services. -Note that it is @emph{not} part of @var{%base-packages}, so you need to +Note that it is @emph{not} part of @code{%base-packages}, so you need to explicitly add it. The @file{/etc/ssl/certs} directory, which is where most applications and libraries look for certificates by default, points to the certificates installed globally. @@ -24457,7 +24457,7 @@ want is to have @code{.local} host lookup working. Note that, in this case, in addition to setting the @code{name-service-switch} of the @code{operating-system} declaration, you also need to use @code{avahi-service-type} (@pxref{Networking Services, -@code{avahi-service-type}}), or @var{%desktop-services}, which includes it +@code{avahi-service-type}}), or @code{%desktop-services}, which includes it (@pxref{Desktop Services}). Doing this makes @code{nss-mdns} accessible to the name service cache daemon (@pxref{Base Services, @code{nscd-service}}). From 0c212811ac5cdfd6bcdfd4e7eb82571bbd6e33d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 18 Jun 2019 16:51:22 +0200 Subject: [PATCH 139/224] gnu: Add python-slurm-magic. * gnu/packages/parallel.scm (python-slurm-magic): New variable. --- gnu/packages/parallel.scm | 53 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 52 insertions(+), 1 deletion(-) diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index 94c844eec9..cdc35b4703 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2017, 2018 Rutger Helling ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018 Clément Lassieur +;;; Copyright © 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -26,8 +27,10 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages parallel) - #:use-module (guix build-system gnu) #:use-module (guix download) + #:use-module (guix git-download) + #:use-module (guix build-system gnu) + #:use-module (guix build-system python) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (gnu packages) @@ -40,6 +43,7 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) #:use-module (gnu packages tcl) #:use-module (gnu packages tls) @@ -188,3 +192,50 @@ to SLURM. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems.") (license license:gpl3+))) + +(define-public python-slurm-magic + (let ((commit "73dd1a2b85799f7dae4b3f1cd9027536eff0c4d7") + (revision "0")) + (package + (name "python-slurm-magic") + (version (git-version "0.0" revision commit)) + (home-page "https://github.com/NERSC/slurm-magic") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) + (commit commit))) + (sha256 + (base32 + "19pp2vs0wm8mx0arz9n6lw9wgyv70w9wyi4y6b91qc5j3bz5igfs")) + (file-name (git-file-name name version)))) + (build-system python-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (add-before 'build 'set-slurm-path + (lambda* (#:key inputs #:allow-other-keys) + ;; The '_execute' method tries to exec 'salloc' + ;; etc. from $PATH. Record the absolute file name + ;; instead. + (let ((slurm (assoc-ref inputs "slurm"))) + (substitute* "slurm_magic.py" + (("name = (.*)$" _ value) + (string-append "name = \"" + slurm "/bin/\" + " + value "\n"))) + #t)))))) + (inputs + `(("slurm" ,slurm))) + (propagated-inputs + `(("python-ipython" ,python-ipython) + ("python-pandas" ,python-pandas))) + (synopsis "Control the SLURM batch scheduler from Jupyter Notebook") + (description + "This package implements Jupyter/IPython +@uref{http://ipython.readthedocs.io/en/stable/interactive/magics.html, magic +commands} for interacting with the SLURM workload manager. SLURM magic simply +wraps command-line executables and the commands themselves should look like +their command-line counterparts. Commands are spawned via @code{subprocess} +and output captured in the notebook. Whatever arguments are accepted by a +SLURM command line executable are also accepted by the corresponding magic +command---e.g., @code{%salloc}, @code{%sbatch}, etc.") + (license license:bsd-3)))) From e6e2f4a08dce2bb2f8d1e1db58e49dfb1e55131a Mon Sep 17 00:00:00 2001 From: Zzull Date: Sat, 15 Jun 2019 20:48:43 +0200 Subject: [PATCH 140/224] gnu: Add emacs-gruvbox-theme MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-gruvbox-theme): New variable Signed-off-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3ef69ab9e0..719c729f62 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -48,6 +48,7 @@ ;;; Copyright © 2019 Gabriel Hondet ;;; Copyright © 2019 LaFreniere, Joseph ;;; Copyright © 2019 Amar Singh +;;; Copyright © 2019 Baptiste Strazzulla ;;; ;;; This file is part of GNU Guix. ;;; @@ -4081,6 +4082,33 @@ transparent background. If you load it from a GUI, it will default to a dark background.") (license license:gpl3+))) +(define-public emacs-gruvbox-theme + (package + (name "emacs-gruvbox-theme") + (version "1.28.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/greduan/emacs-theme-gruvbox.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00qq92gp1g55pzm97rh7k0dgxy44pxziridl8kqm4rbpi31r7k9p")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-autothemer" ,emacs-autothemer))) + (home-page "https://github.com/greduan/emacs-theme-gruvbox") + (synopsis "Gruvbox is a retro groove color scheme ported from Vim") + (description + "Gruvbox is heavily inspired by badwolf, jellybeans and solarized. + +Designed as a bright theme with pastel 'retro groove' colors and light/dark +mode switching in the way of solarized. The main focus when developing gruvbox +is to keep colors easily distinguishable, contrast enough and still pleasant +for the eyes.") + (license license:expat))) ; MIT license + (define-public emacs-2048-game (package (name "emacs-2048-game") From 2e8c912fdc1b17b7bd1cec0c346b401d3979928f Mon Sep 17 00:00:00 2001 From: Vasile Dumitrascu Date: Sun, 16 Jun 2019 01:15:14 +0200 Subject: [PATCH 141/224] gnu: aircrack-ng: Update to 1.5.2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/networking.scm (aircrack-ng): Update to 1.5.2. Signed-off-by: Ludovic Courtès --- gnu/packages/networking.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 2cd000ec0a..3281387253 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -27,6 +27,7 @@ ;;; Copyright © 2018 Oleg Pykhalov ;;; Copyright © 2018 Pierre Neidhardt ;;; Copyright © 2019 Maxim Cournoyer +;;; Copyright © 2019 Vasile Dumitrascu ;;; ;;; This file is part of GNU Guix. ;;; @@ -885,7 +886,7 @@ live network and disk I/O bandwidth monitor.") (define-public aircrack-ng (package (name "aircrack-ng") - (version "1.3") + (version "1.5.2") (source (origin (method url-fetch) @@ -893,7 +894,7 @@ live network and disk I/O bandwidth monitor.") version ".tar.gz")) (sha256 (base32 - "1jl30d0kibc82447fr3lgw75arik0l9729k94z76l7vl51y8mq4a")))) + "0hc2x17bxk2n00z8jj5jfwq3z41681fd19n018724il0cpkjyncy")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) From d60b064d47a1620754b24fd52722ca77a361b8aa Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 18 Jun 2019 17:58:31 +0200 Subject: [PATCH 142/224] gnu: Add python-iml. * gnu/packages/machine-learning.scm (python-iml): New variable. --- gnu/packages/machine-learning.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 505cc88f4b..245ccb999b 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2018 Fis Trivial ;;; Copyright © 2018 Julien Lepiller ;;; Copyright © 2018 Björn Höfling +;;; Copyright © 2019 Nicolas Goaziou ;;; ;;; This file is part of GNU Guix. ;;; @@ -1753,3 +1754,30 @@ API for beginners that allows users to build models quickly by plugging together building blocks and a subclassing API with an imperative style for advanced research.") (license license:asl2.0))) + +(define-public python-iml + (package + (name "python-iml") + (version "0.6.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "iml" version)) + (sha256 + (base32 + "1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l")))) + (build-system python-build-system) + (propagated-inputs + `(("ipython" ,python-ipython) + ("nose" ,python-nose) + ("numpy" ,python-numpy) + ("pandas" ,python-pandas) + ("scipy" ,python-scipy))) + (home-page "http://github.com/interpretable-ml/iml") + (synopsis "Interpretable Machine Learning (iML) package") + (description "Interpretable ML (iML) is a set of data type objects, +visualizations, and interfaces that can be used by any method designed to +explain the predictions of machine learning models (or really the output of +any function). It currently contains the interface and IO code from the Shap +project, and it will potentially also do the same for the Lime project.") + (license license:expat))) From 4088ae4270ca3918537eb560d5bd01f113519fdd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 18 Jun 2019 18:18:45 +0200 Subject: [PATCH 143/224] gnu: python-on-guile: Update to 0.1.0-2.058c596. * gnu/packages/guile-xyz.scm (python-on-guile): Update to 0.1.0-2.058c596. [source]: Fetch from fork at git.elephly.net. [arguments]: Remove phase "use-canonical-directory-for-go-files". --- gnu/packages/guile-xyz.scm | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 69fca334ca..c02606f919 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2163,20 +2163,20 @@ serializing continuations or delimited continuations.") (license license:lgpl2.0+)))) (define-public python-on-guile - (let ((commit "0cb7c2b2fff4338ca6153473f3f5c409a818f293") - (revision "1")) + (let ((commit "058c596cd3886447da31171e1026d4d19f5f5313") + (revision "2")) (package (name "python-on-guile") (version (git-version "0.1.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference - (url "https://gitlab.com/python-on-guile/python-on-guile.git") + (url "https://git.elephly.net/software/python-on-guile.git") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 - "0kpz08rrp5mwcf5ksc4flgrw992syham9x49dn9wq9w31bpcpnby")))) + "0ppyh5kkhsph5kc091p2b5a3alnj3wnlx8jr5xpyhrsj0vx9cqph")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -2185,12 +2185,7 @@ serializing continuations or delimited continuations.") #:phases (modify-phases %standard-phases (add-after 'unpack 'chdir - (lambda _ (chdir "modules") #t)) - (add-after 'chdir 'use-canonical-directory-for-go-files - (lambda _ - (substitute* "Makefile.am" - (("/ccache") "/site-ccache")) - #t))))) + (lambda _ (chdir "modules") #t))))) (inputs `(("guile" ,guile-2.2))) (propagated-inputs From cc908fde64799eaa60e1e63be75697a12f7cb017 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 18 Jun 2019 20:10:36 +0300 Subject: [PATCH 144/224] gnu: Remove hydra. Our copy of hydra hasn't built in years. * gnu/packages/ci.scm (hydra): Remove variable. --- gnu/packages/ci.scm | 141 -------------------------------------------- 1 file changed, 141 deletions(-) diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index 6533fb302d..eb5f665fc1 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -46,147 +46,6 @@ #:use-module (gnu packages xml) #:use-module (guix build-system gnu)) -(define-public hydra - (let ((commit "1ff48da3d3d4a425063f5b7dd0b89d35270f8932")) - (package - (name "hydra") - (version (string-append "20151030." (string-take commit 7))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/NixOS/hydra") - (commit commit))) - (file-name (string-append name "-" version)) - (patches (search-patches - ;; TODO: Remove once we have a darcs input - "hydra-disable-darcs-test.patch")) - (sha256 - (base32 - "0ni8i8v1nxxfr51rz8m6znwpbm77vr7i05k506hmgmg32r938lap")))) - (build-system gnu-build-system) - (native-inputs - `(("unzip" ,unzip) - ("pkg-config" ,pkg-config) - ;; For documentation - ("dblatex" ,dblatex) - ("xsltproc" ,libxslt) - ("docbook-xsl" ,docbook-xsl) - ;; For bootstrap - ("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ;; For tests - ("git" ,git) - ("subversion" ,subversion) - ("mercurial" ,mercurial) - ("bazaar" ,bazaar))) - (inputs - `(("libpqxx" ,libpqxx) - ("perl" ,perl) - ("guile" ,guile-2.0) - ("openssl" ,openssl) - ("bzip2" ,bzip2) - ("gzip" ,gzip) - ("sed" ,sed) - ("starman" ,starman) - ("git" ,git) - ("subversion" ,subversion) - ("mercurial" ,mercurial) - ("bazaar" ,bazaar) - ("nix" ,nix) - ;; Lots o' perl modules... - ("perl-catalyst-action-rest" ,perl-catalyst-action-rest) - ("perl-catalyst-authentication-store-dbix-class" - ,perl-catalyst-authentication-store-dbix-class) - ("perl-catalyst-devel" ,perl-catalyst-devel) - ("perl-catalyst-dispatchtype-regex" ,perl-catalyst-dispatchtype-regex) - ("perl-catalyst-plugin-accesslog" ,perl-catalyst-plugin-accesslog) - ("perl-catalyst-plugin-authorization-roles" - ,perl-catalyst-plugin-authorization-roles) - ("perl-catalyst-plugin-captcha" ,perl-catalyst-plugin-captcha) - ("perl-catalyst-plugin-session-state-cookie" - ,perl-catalyst-plugin-session-state-cookie) - ("perl-catalyst-plugin-session-store-fastmmap" - ,perl-catalyst-plugin-session-store-fastmmap) - ("perl-catalyst-plugin-stacktrace" ,perl-catalyst-plugin-stacktrace) - ("perl-catalyst-traitfor-request-proxybase" - ,perl-catalyst-traitfor-request-proxybase) - ("perl-catalyst-view-download" ,perl-catalyst-view-download) - ("perl-catalyst-view-json" ,perl-catalyst-view-json) - ("perl-catalyst-view-tt" ,perl-catalyst-view-tt) - ("perl-catalystx-roleapplicator" ,perl-catalystx-roleapplicator) - ("perl-catalystx-script-server-starman" - ,perl-catalystx-script-server-starman) - ("perl-crypt-randpasswd" ,perl-crypt-randpasswd) - ("perl-data-dump" ,perl-data-dump) - ("perl-datetime" ,perl-datetime) - ("perl-dbd-pg" ,perl-dbd-pg) - ("perl-dbd-sqlite" ,perl-dbd-sqlite) - ("perl-digest-sha1" ,perl-digest-sha1) - ("perl-email-mime" ,perl-email-mime) - ("perl-email-sender" ,perl-email-sender) - ("perl-file-slurp" ,perl-file-slurp) - ("perl-io-compress" ,perl-io-compress) - ("perl-ipc-run" ,perl-ipc-run) - ("perl-json-any" ,perl-json-any) - ("perl-json-xs" ,perl-json-xs) - ("perl-libwww" ,perl-libwww) - ("perl-lwp-protocol-https" ,perl-lwp-protocol-https) - ("perl-net-amazon-s3" ,perl-net-amazon-s3) - ("perl-net-statsd" ,perl-net-statsd) - ("perl-padwalker" ,perl-padwalker) - ("perl-readonly" ,perl-readonly) - ("perl-set-scalar" ,perl-set-scalar) - ("perl-sql-splitstatement" ,perl-sql-splitstatement) - ("perl-sys-hostname-long" ,perl-sys-hostname-long) - ("perl-text-diff" ,perl-text-diff) - ("perl-text-table" ,perl-text-table) - ("perl-xml-simple" ,perl-xml-simple))) - (arguments - `(#:configure-flags - (let ((docbook (assoc-ref %build-inputs "docbook-xsl"))) - (list (string-append "--with-docbook-xsl=" - docbook "/xml/xsl/docbook-xsl-" - ,(package-version docbook-xsl)) - (string-append "--docdir=" %output - "/doc/hydra-" ,version))) - #:phases (modify-phases %standard-phases - (add-before - 'check 'check-setup - (lambda _ (setenv "LOGNAME" "test.log"))) - (add-after - 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (for-each - (lambda (file) - (wrap-program file - `("PATH" ":" prefix - (,(string-append out "/bin") - ,@(map (lambda (i) - (string-append (assoc-ref inputs i) - "/bin")) - '("subversion" "git" "bazaar" - "mercurial" "coreutils" "gzip" - "sed" "unzip" "nix")))) - `("PERL5LIB" ":" prefix - (,(string-append out "/libexec/hydra/lib") - ,@(search-path-as-string->list - (getenv "PERL5LIB")))) - `("HYDRA_RELEASE" = (,,version)) - `("HYDRA_HOME" = - (,(string-append out "/libexec/hydra"))) - `("NIX_RELEASE" = (,,(package-version nix))))) - (find-files (string-append out "/bin") - ".*")))))))) - (home-page "https://nixos.org/hydra") - (synopsis "Continuous build system") - (description - "Hydra is a tool for continuous integration testing and software -release that uses a purely functional language to describe build jobs and -their dependencies.") - (license l:gpl3+)))) - (define-public cuirass (let ((commit "0b40dca734468e8b12b3ff58e3e779679f17d38e") (revision "21")) From f0fbb31d0175ec37f4c76addbfddf5a546361f6d Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 10:38:57 +0200 Subject: [PATCH 145/224] gnu: Add givaro. * gnu/packages/algebra.scm (givaro): New variable. --- gnu/packages/algebra.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 20ecc71b81..449ca7b189 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1094,3 +1094,43 @@ objects.") ;; means that the gpl2+ licence of GAP itself applies, but to be on the ;; safe side, we drop them for now. (license license:gpl2+))) + +(define-public givaro + (package + (name "givaro") + (version "4.1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/givaro") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (propagated-inputs + `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'bootstrap 'setenv + ;; Prevent the autogen.sh script to carry out the configure + ;; script, which has not yet been patched to replace /bin/sh. + (lambda _ + (setenv "NOCONFIGURE" "yes") + #t))))) + (synopsis "Algebraic computations with exact rings and fields") + (description + "Givaro is a C++ library implementing the basic arithmetic of various +algebraic objects: prime fields, extension fields, finite fields, finite +rings, polynomials, algebraic numbers, arbitrary precision integers and +rationals (C++ wrappers over gmp), fixed precision integers. It also +provides data-structures and templated classes for the manipulation of +compound objects, such as vectors, matrices and univariate polynomials.") + (license license:cecill-b) + (home-page "https://github.com/linbox-team/givaro"))) From 4bf9cb405358ab21be0a6d8650c51567dd8da0f2 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 13:08:07 +0200 Subject: [PATCH 146/224] gnu: Add fflas-ffpack. * gnu/packages/algebra.scm (fflas-ffpack): New variable. --- gnu/packages/algebra.scm | 51 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 449ca7b189..6b15df1e64 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -43,6 +43,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) @@ -1134,3 +1135,53 @@ provides data-structures and templated classes for the manipulation of compound objects, such as vectors, matrices and univariate polynomials.") (license license:cecill-b) (home-page "https://github.com/linbox-team/givaro"))) + +(define-public fflas-ffpack + (package + (name "fflas-ffpack") + (version "2.4.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/fflas-ffpack") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("openblas" ,openblas))) + (propagated-inputs + `(("givaro" ,givaro))) ; required according to the .pc file + (arguments + `(#:configure-flags + (list (string-append "--with-blas-libs=" + (assoc-ref %build-inputs "openblas") + "/lib/libopenblas.so")) + #:phases + (modify-phases %standard-phases + (add-before 'bootstrap 'setenv + ;; Prevent the autogen.sh script to carry out the configure + ;; script, which has not yet been patched to replace /bin/sh. + (lambda _ + (setenv "NOCONFIGURE" "yes") + #t))))) + (synopsis "C++ library for linear algebra over finite fields") + (description + "FFLAS-FFPACK is a C++ template library for basic linear algebra +operations over a finite field. +FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation +of a subset of routines of the numerical BLAS; it also supports sparse +matrix-vector products. +FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK +library to provide functionalities of higher level, using the kernel +of a BLAS. Additionally, it provides routines specific to exact linear +algebra, such as the row echelon form.") + (license license:lgpl2.1+) + (home-page "https://linbox-team.github.io/fflas-ffpack/"))) From a612f86684c5b93b2587fcfcf5ce52c1d6f23996 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 15:06:12 +0200 Subject: [PATCH 147/224] gnu: Add linbox. * gnu/packages/algebra.scm (linbox): New variable. --- gnu/packages/algebra.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 6b15df1e64..86c0a42758 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1185,3 +1185,41 @@ of a BLAS. Additionally, it provides routines specific to exact linear algebra, such as the row echelon form.") (license license:lgpl2.1+) (home-page "https://linbox-team.github.io/fflas-ffpack/"))) + +(define-public linbox + (package + (name "linbox") + (version "1.6.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/linbox") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("fflas-ffpack" ,fflas-ffpack))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'bootstrap 'setenv + ;; Prevent the autogen.sh script to carry out the configure + ;; script, which has not yet been patched to replace /bin/sh. + (lambda _ + (setenv "NOCONFIGURE" "yes") + #t))))) + (synopsis "C++ library for linear algebra over exact rings") + (description + "LinBox is a C++ template library for exact linear algebra computation +with dense, sparse, and structured matrices over the integers and over +finite fields.") + (license license:lgpl2.1+) + (home-page "https://linbox-team.github.io/linbox/"))) From 80a70da7fc6732341f184dbbbd50f2441d8cee3f Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 19:32:18 +0200 Subject: [PATCH 148/224] gnu: givaro: Add version 4.0.4. * gnu/packages/sagemath.scm (givaro-4.0.4): New variable. --- gnu/packages/sagemath.scm | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 9736f79dc3..4e1b51c023 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -173,3 +173,20 @@ in particular it computes normal forms of group elements.") represented as strings.") (license license:public-domain) (home-page "https://github.com/miguelmarco/libhomfly"))) + +;; The following three packages from the Linbox group are needed in +;; an outdated version for Sage. + +(define-public givaro-4.0.4 + (package (inherit givaro) + (name "givaro") + (version "4.0.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/givaro") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "199p8wyj5i63jbnk7j8qbdbfp5rm2lpmcxyk3mdjy9bz7ygx3hhy")))))) From 9fafb0d21fb584cdc7dd1a92ce6646e07d16efcd Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 19:48:41 +0200 Subject: [PATCH 149/224] gnu: fflas-ffpack: Add version 2.3.2. * gnu/packages/sagemath.scm (fflas-ffpack-2.3.2): New variable. --- gnu/packages/sagemath.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 4e1b51c023..b24f3411b1 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -23,6 +23,7 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix packages) + #:use-module (guix utils) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages bdw-gc) @@ -190,3 +191,24 @@ represented as strings.") (sha256 (base32 "199p8wyj5i63jbnk7j8qbdbfp5rm2lpmcxyk3mdjy9bz7ygx3hhy")))))) + +(define-public fflas-ffpack-2.3.2 + (package (inherit fflas-ffpack) + (name "fflas-ffpack") + (version "2.3.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/fflas-ffpack") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1cqhassj2dny3gx0iywvmnpq8ca0d6m82xl5rz4mb8gaxr2kwddl")))) + (propagated-inputs + `(("givaro" ,givaro-4.0.4))) + ;; A test fails, but since all tests pass in the latest version, + ;; there is not much point in investigating. + (arguments + (substitute-keyword-arguments (package-arguments fflas-ffpack) + ((#:tests? _ #f) #f))))) From e27ae2db008d081f2cfce14e14320b3b76a9fefb Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 19:54:59 +0200 Subject: [PATCH 150/224] gnu: linbox: Add version 1.5.2. * gnu/packages/sagemath.scm (linbox-1.5.2): New variable. --- gnu/packages/sagemath.scm | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index b24f3411b1..732011bf36 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -212,3 +212,19 @@ represented as strings.") (arguments (substitute-keyword-arguments (package-arguments fflas-ffpack) ((#:tests? _ #f) #f))))) + +(define-public linbox-1.5.2 + (package (inherit linbox) + (version "1.5.2") + (name "linbox") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/linbox") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1wfivlwp30mzdy1697w7rzb8caajim50mc8h27k82yipn2qc5n4i")))) + (inputs + `(("fflas-ffpack" ,fflas-ffpack-2.3.2))))) From cb13618b6d2293e39ab4722d541dd8720e4d1812 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 18 Jun 2019 21:01:54 +0300 Subject: [PATCH 151/224] gnu: python2: Add 'cpe-name' property. * gnu/packages/python.scm (python2)[properties]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 11f3aacf00..aa92e82ac2 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -261,6 +261,7 @@ introspection capabilities; intuitive object orientation; natural expression of procedural code; full modularity, supporting hierarchical packages; exception-based error handling; and very high level dynamic data types.") + (properties '((cpe-name . "python"))) (license license:psfl))) ;; Current 2.x version. From b84c4cda046589658c4d1ba4a9c0b292351fe5ca Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sat, 25 May 2019 11:49:42 +0530 Subject: [PATCH 152/224] linux-container: Remove networking service when network is shared with host. * gnu/system/linux-container.scm (dummy-networking-service-type): New variable. (containerized-operating-system): If network is shared with host, replace static-networking-service-type with dummy-networking-service-type. --- gnu/system/linux-container.scm | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/gnu/system/linux-container.scm b/gnu/system/linux-container.scm index c1e963d047..61248c62b9 100644 --- a/gnu/system/linux-container.scm +++ b/gnu/system/linux-container.scm @@ -30,6 +30,7 @@ #:use-module (gnu build linux-container) #:use-module (gnu services) #:use-module (gnu services base) + #:use-module (gnu services shepherd) #:use-module (gnu system) #:use-module (gnu system file-systems) #:export (system-container @@ -65,6 +66,16 @@ from OS that are needed on the bare metal and not in a container." files))) base))) +(define dummy-networking-service-type + (shepherd-service-type + 'dummy-networking + (const (shepherd-service + (documentation "Provide loopback and networking without actually +doing anything.") + (provision '(loopback networking)) + (start #~(const #t)))) + #f)) + (define* (containerized-operating-system os mappings #:key shared-network? @@ -96,7 +107,8 @@ containerized OS. EXTRA-FILE-SYSTEMS is a list of file systems to add to OS." agetty-service-type) ;; Remove nscd service if network is shared with the host. (if shared-network? - (list nscd-service-type) + (list nscd-service-type + static-networking-service-type) (list)))) (operating-system @@ -105,10 +117,17 @@ containerized OS. EXTRA-FILE-SYSTEMS is a list of file systems to add to OS." (essential-services (container-essential-services this-operating-system #:shared-network? shared-network?)) - (services (remove (lambda (service) - (memq (service-kind service) - useless-services)) - (operating-system-user-services os))) + (services (append (remove (lambda (service) + (memq (service-kind service) + useless-services)) + (operating-system-user-services os)) + ;; Many Guix services depend on a 'networking' shepherd + ;; service, so make sure to provide a dummy 'networking' + ;; service when we are sure that networking is already set up + ;; in the host and can be used. That prevents double setup. + (if shared-network? + (list (service dummy-networking-service-type)) + '()))) (file-systems (append (map mapping->fs (if shared-network? (append %network-file-mappings mappings) From cbc28ac133db5c0d35a1d900b8163279117eb6cb Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 18 Jun 2019 20:46:11 -0400 Subject: [PATCH 153/224] gnu: linux-libre@4.4: Update to 4.4.182. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.182. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 936d8bec4c..0eaafa5531 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -486,8 +486,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.181" - "1ird78a3pg8k6h60258g56ka86jpgiaj0q9r2jws770qgrmy324l" + (make-linux-libre "4.4.182" + "0ggs5pyjr7a9mldskfbsybzxlb3lmfbhxg5q2qpzxnh1c8wcn53h" '("x86_64-linux" "i686-linux") #:configuration-file kernel-config #:extra-options From 6bb60ba1ba7607ec65b2e14ce58c6fa5017265c3 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 18 Jun 2019 20:46:58 -0400 Subject: [PATCH 154/224] gnu: linux-libre@4.9: Update to 4.9.182. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.182. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 0eaafa5531..6a0daada1b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -480,8 +480,8 @@ It has been modified to remove all non-free binary blobs.") %linux-libre-4.14-hash)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.181" - "0fdqfd6z73q00nracrixliw0i0b60f4z352jmzabcwy431wszar5" + (make-linux-libre "4.9.182" + "1615v8ywwdm204bimq2cf6qv0zas14yagpr8lk9a5zqxas4p4rns" '("x86_64-linux" "i686-linux") #:configuration-file kernel-config)) From 4862957c603341b6e1b11019219930465d2316d4 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 18 Jun 2019 20:47:38 -0400 Subject: [PATCH 155/224] gnu: linux-libre@4.14: Update to 4.14.127. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.127. (%linux-libre-4.14-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 6a0daada1b..af5394f800 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -466,8 +466,8 @@ It has been modified to remove all non-free binary blobs.") (make-linux-libre-headers %linux-libre-4.19-version %linux-libre-4.19-hash)) -(define %linux-libre-4.14-version "4.14.126") -(define %linux-libre-4.14-hash "111whcprb72mdr4ivy49va1xx9qmnbqwgli4ql52g49ssfxkvc2c") +(define %linux-libre-4.14-version "4.14.127") +(define %linux-libre-4.14-hash "0dkzgxfzzc6n3k2x8nzzx98c6y3fhsr695rm46ahvg7fdg3vgcmi") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version From 999ab3807a0b2644e4b0f23a6c7c0e5875a165de Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 18 Jun 2019 20:48:29 -0400 Subject: [PATCH 156/224] gnu: linux-libre@4.19: Update to 4.19.52. * gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.52. (%linux-libre-4.19-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index af5394f800..3a4bef4c88 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -448,8 +448,8 @@ It has been modified to remove all non-free binary blobs.") (make-linux-libre-headers %linux-libre-version %linux-libre-hash)) -(define %linux-libre-4.19-version "4.19.51") -(define %linux-libre-4.19-hash "0xzgwv70inddbml8nvfknp2zaz5dvs00nzqa1r9iqmsxlmssipz7") +(define %linux-libre-4.19-version "4.19.52") +(define %linux-libre-4.19-hash "1wsrgrskmvipm7j4kzir93p9dp3iy49522163ghfxx71b1b2v4dg") (define %linux-libre-4.19-patches (list %boot-logo-patch From 5f7367cf8495f537b7b8ce42204ab14a3ed2e46b Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 18 Jun 2019 20:49:14 -0400 Subject: [PATCH 157/224] gnu: linux-libre: Update to 5.1.11. * gnu/packages/linux.scm (%linux-libre-version): Update to 5.1.11. (%linux-libre-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 3a4bef4c88..4f659e13f8 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -430,8 +430,8 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." It has been modified to remove all non-free binary blobs.") (license license:gpl2))) -(define %linux-libre-version "5.1.10") -(define %linux-libre-hash "0gpvp3p927wg31gmh4bakxcvzanx68s7d6dj6v89md7z146954k9") +(define %linux-libre-version "5.1.11") +(define %linux-libre-hash "15hmqycsggqd9bwrf229b7f0pfznzs03kpzcwrd9j867pvgwyl8c") (define %linux-libre-5.1-patches (list %boot-logo-patch From bf5929c5303511da338da894ce072c138fe8324f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 19 Jun 2019 11:48:31 +0200 Subject: [PATCH 158/224] tests: Fix opensmtpd test. * gnu/tests/mail.scm (run-opensmtpd-test) <"mail arrived">: Invoke smtpctl by its full file name. --- gnu/tests/mail.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/gnu/tests/mail.scm b/gnu/tests/mail.scm index 10e5be71d8..f064da5f53 100644 --- a/gnu/tests/mail.scm +++ b/gnu/tests/mail.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2018 Oleg Pykhalov ;;; Copyright © 2018 Clément Lassieur ;;; Copyright © 2019 Christopher Baines +;;; Copyright © 2019 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,6 +24,7 @@ (define-module (gnu tests mail) #:use-module (gnu tests) + #:use-module (gnu packages mail) #:use-module (gnu system) #:use-module (gnu system vm) #:use-module (gnu services) @@ -136,7 +138,9 @@ accept from any for local deliver to mbox (define (queue-empty?) (eof-object? (read-line - (open-input-pipe "smtpctl show queue")))) + (open-input-pipe + (string-append #$(file-append opensmtpd "/sbin/smtpctl") + " show queue"))))) (let wait () (if (queue-empty?) From 5d3675371c96fbda209b064fe3bef4a18592c3b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 19 Jun 2019 14:31:46 +0200 Subject: [PATCH 159/224] gnu: python-s3transfer: Update to 0.2.0. * gnu/packages/python-web.scm (python-s3transfer): Update to 0.2.0. [propagated-inputs]: Add python-urllib3. --- gnu/packages/python-web.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 6fe6d5ade8..cbcbe6c867 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2045,21 +2045,21 @@ Betamax.") (define-public python-s3transfer (package (name "python-s3transfer") - (version "0.1.13") + (version "0.2.0") (source (origin (method url-fetch) (uri (pypi-uri "s3transfer" version)) (sha256 (base32 - "1harvyn1s8v54n1w5h7c0lg4bgjh68aylhg28s8n174q53h1ip4h")))) + "08fhj73b1ai52hrs2q3nggshq3pswn1gq8ch3m009cb2v2vmqggj")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (replace 'check (lambda _ - ;; 7 of the 'integration' tests require network access or login - ;; credentials. + ;; Some of the 'integration' tests require network access or + ;; login credentials. (invoke "nosetests" "--exclude=integration") #t))))) (native-inputs @@ -2067,7 +2067,8 @@ Betamax.") ("python-mock" ,python-mock) ("python-nose" ,python-nose))) (propagated-inputs - `(("python-botocore" ,python-botocore))) + `(("python-botocore" ,python-botocore) + ("python-urllib3" ,python-urllib3))) (synopsis "Amazon S3 Transfer Manager") (description "S3transfer is a Python library for managing Amazon S3 transfers.") From 7bcf827c1d1a99097bea2dd309bdd5338e8de34a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 16 May 2019 17:46:33 +0200 Subject: [PATCH 160/224] gnu: python-botocore: Update to 1.12.149. * gnu/packages/python-xyz.scm (python-botocore): Update to 1.12.149. [native-inputs]: Add python-urllib3. --- gnu/packages/python-xyz.scm | 55 +++++++++++++++++++------------------ 1 file changed, 28 insertions(+), 27 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index be9c58bb98..2bf98222ae 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8428,34 +8428,35 @@ document.") (define-public python-botocore (package - (name "python-botocore") - (version "1.8.43") - (source - (origin - (method url-fetch) - (uri (pypi-uri "botocore" version)) - (sha256 - (base32 - "12cqpbnz3vfv41mp9admvciw7bc7hz57sjpqs2bxaw9wnfmbw5lg")))) - (build-system python-build-system) - (arguments - ;; FIXME: Many tests are failing. - '(#:tests? #f)) - (propagated-inputs - `(("python-dateutil" ,python-dateutil) - ("python-docutils" ,python-docutils) - ("python-jmespath" ,python-jmespath))) - (native-inputs - `(("python-mock" ,python-mock) - ("python-nose" ,python-nose) - ("behave" ,behave) - ("python-tox" ,python-tox) - ("python-wheel" ,python-wheel))) - (home-page "https://github.com/boto/botocore") - (synopsis "Low-level interface to AWS") - (description "Botocore is a Python library that provides a low-level + (name "python-botocore") + (version "1.12.149") + (source + (origin + (method url-fetch) + (uri (pypi-uri "botocore" version)) + (sha256 + (base32 + "12597f74khp3ngwr282cb949w0gcqj20rkfc3x275dijavyy5cmf")))) + (build-system python-build-system) + (arguments + ;; FIXME: Many tests are failing. + '(#:tests? #f)) + (propagated-inputs + `(("python-dateutil" ,python-dateutil) + ("python-docutils" ,python-docutils) + ("python-jmespath" ,python-jmespath))) + (native-inputs + `(("python-mock" ,python-mock) + ("python-nose" ,python-nose) + ("behave" ,behave) + ("python-tox" ,python-tox) + ("python-urllib3" ,python-urllib3) + ("python-wheel" ,python-wheel))) + (home-page "https://github.com/boto/botocore") + (synopsis "Low-level interface to AWS") + (description "Botocore is a Python library that provides a low-level interface to the Amazon Web Services (AWS) API.") - (license license:asl2.0))) + (license license:asl2.0))) (define-public python2-botocore (package-with-python2 python-botocore)) From d93ad19110efa665e6fe273c232733778a676970 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 19 Jun 2019 14:25:17 +0200 Subject: [PATCH 161/224] gnu: Add python-keras-applications. * gnu/packages/machine-learning.scm (python-keras-applications): New variable. --- gnu/packages/machine-learning.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 245ccb999b..e751d29b9b 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1781,3 +1781,32 @@ explain the predictions of machine learning models (or really the output of any function). It currently contains the interface and IO code from the Shap project, and it will potentially also do the same for the Lime project.") (license license:expat))) + +(define-public python-keras-applications + (package + (name "python-keras-applications") + (version "1.0.8") + (source + (origin + (method url-fetch) + (uri (pypi-uri "Keras_Applications" version)) + (sha256 + (base32 + "1rcz31ca4axa6kzhjx4lwqxbg4wvlljkj8qj9a7p9sfd5fhzjyam")))) + (build-system python-build-system) + ;; The tests require Keras, but this package is needed to build Keras. + (arguments '(#:tests? #f)) + (propagated-inputs + `(("python-h5py" ,python-h5py) + ("python-numpy" ,python-numpy))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-pep8" ,python-pytest-pep8) + ("python-pytest-xdist" ,python-pytest-xdist))) + (home-page "https://github.com/keras-team/keras-applications") + (synopsis "Reference implementations of popular deep learning models") + (description + "This package provides reference implementations of popular deep learning +models for use with the Keras deep learning framework.") + (license license:expat))) From 4abc50666e0a30baea3e3bf414e60d57916ab2c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 19 Jun 2019 14:25:26 +0200 Subject: [PATCH 162/224] gnu: Add python-keras-preprocessing. * gnu/packages/machine-learning.scm (python-keras-preprocessing): New variable. --- gnu/packages/machine-learning.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index e751d29b9b..aebbd1ac5d 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1810,3 +1810,33 @@ project, and it will potentially also do the same for the Lime project.") "This package provides reference implementations of popular deep learning models for use with the Keras deep learning framework.") (license license:expat))) + +(define-public python-keras-preprocessing + (package + (name "python-keras-preprocessing") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "Keras_Preprocessing" version)) + (sha256 + (base32 + "1r98nm4k1svsqjyaqkfk23i31bl1kcfcyp7094yyj3c43phfp3as")))) + (build-system python-build-system) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-six" ,python-six))) + (native-inputs + `(("python-pandas" ,python-pandas) + ("python-pillow" ,python-pillow) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-xdist" ,python-pytest-xdist) + ("tensorflow" ,tensorflow))) + (home-page "https://github.com/keras-team/keras-preprocessing/") + (synopsis "Data preprocessing and augmentation for deep learning models") + (description + "Keras Preprocessing is the data preprocessing and data augmentation +module of the Keras deep learning library. It provides utilities for working +with image data, text data, and sequence data.") + (license license:expat))) From 90afa80dd9f0e78a826c36b9bfa5f745e2290cd9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 19 Jun 2019 14:26:19 +0200 Subject: [PATCH 163/224] gnu: Add python-pytest-timeout. * gnu/packages/check.scm (python-pytest-timeout): New variable. --- gnu/packages/check.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 82391ac5e1..2a0da625fd 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -925,6 +925,27 @@ result back.") (define-public python2-pytest-xdist (package-with-python2 python-pytest-xdist)) +(define-public python-pytest-timeout + (package + (name "python-pytest-timeout") + (version "1.3.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pytest-timeout" version)) + (sha256 + (base32 + "1cczcjhw4xx5sjkhxlhc5c1bkr7x6fcyx12wrnvwfckshdvblc2a")))) + (build-system python-build-system) + (propagated-inputs + `(("python-pytest" ,python-pytest))) + (home-page "http://bitbucket.org/pytest-dev/pytest-timeout/") + (synopsis "Plugin for py.test to abort hanging tests") + (description + "This package provides a py.test plugin that aborts hanging tests after a +timeout has been exceeded.") + (license license:expat))) + (define-public python-scripttest (package (name "python-scripttest") From f1765b57b8b4909fa99fab0cafd281ab31f78c94 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 19 Jun 2019 14:26:45 +0200 Subject: [PATCH 164/224] gnu: Add python-keras. * gnu/packages/machine-learning.scm (python-keras): New variable. --- gnu/packages/machine-learning.scm | 75 +++++++++++++++++++++++++++++++ 1 file changed, 75 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index aebbd1ac5d..2dc7dc81ef 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -54,6 +54,7 @@ #:use-module (gnu packages dejagnu) #:use-module (gnu packages gcc) #:use-module (gnu packages glib) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gstreamer) #:use-module (gnu packages image) #:use-module (gnu packages linux) @@ -68,6 +69,7 @@ #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages serialization) + #:use-module (gnu packages sphinx) #:use-module (gnu packages statistics) #:use-module (gnu packages sqlite) #:use-module (gnu packages swig) @@ -1840,3 +1842,76 @@ models for use with the Keras deep learning framework.") module of the Keras deep learning library. It provides utilities for working with image data, text data, and sequence data.") (license license:expat))) + +(define-public python-keras + (package + (name "python-keras") + (version "2.2.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "Keras" version)) + (sha256 + (base32 + "1j8bsqzh49vjdxy6l1k4iwax5vpjzniynyd041xjavdzvfii1dlh")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-tests-for-unavailable-features + (lambda _ + (delete-file "keras/backend/theano_backend.py") + (delete-file "keras/backend/cntk_backend.py") + (delete-file "tests/keras/backend/backend_test.py") + + ;; FIXME: This doesn't work because Tensorflow is missing the + ;; coder ops library. + (delete-file "tests/keras/test_callbacks.py") + #t)) + (replace 'check + (lambda _ + ;; These tests attempt to download data files from the internet. + (delete-file "tests/integration_tests/test_datasets.py") + (delete-file "tests/integration_tests/imagenet_utils_test.py") + + (setenv "PYTHONPATH" + (string-append (getcwd) "/build/lib:" + (getenv "PYTHONPATH"))) + (invoke "py.test" "-v" + "-p" "no:cacheprovider" + "--ignore" "keras/utils")))))) + (propagated-inputs + `(("python-h5py" ,python-h5py) + ("python-keras-applications" ,python-keras-applications) + ("python-keras-preprocessing" ,python-keras-preprocessing) + ("python-numpy" ,python-numpy) + ("python-pydot" ,python-pydot) + ("python-pyyaml" ,python-pyyaml) + ("python-scipy" ,python-scipy) + ("python-six" ,python-six) + ("tensorflow" ,tensorflow) + ("graphviz" ,graphviz))) + (native-inputs + `(("python-pandas" ,python-pandas) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-pep8" ,python-pytest-pep8) + ("python-pytest-timeout" ,python-pytest-timeout) + ("python-pytest-xdist" ,python-pytest-xdist) + ("python-sphinx" ,python-sphinx) + ("python-requests" ,python-requests))) + (home-page "https://github.com/keras-team/keras") + (synopsis "High-level deep learning framework") + (description "Keras is a high-level neural networks API, written in Python +and capable of running on top of TensorFlow. It was developed with a focus on +enabling fast experimentation. Use Keras if you need a deep learning library +that: + +@itemize +@item Allows for easy and fast prototyping (through user friendliness, + modularity, and extensibility). +@item Supports both convolutional networks and recurrent networks, as well as + combinations of the two. +@item Runs seamlessly on CPU and GPU. +@end itemize\n") + (license license:expat))) From 75b803ffa99072543577653c3b69c79f928c6c0e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 19 Jun 2019 13:43:38 +0200 Subject: [PATCH 165/224] gnu: libfilezilla: Update to 0.16.0. * gnu/packages/ftp.scm (libfilezilla): Update to 0.16.0. --- gnu/packages/ftp.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index 96953d6fd5..20f096b62a 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -170,15 +170,14 @@ as required.") (define-public libfilezilla (package (name "libfilezilla") - (version "0.15.1") + (version "0.16.0") (source (origin (method url-fetch) (uri (string-append "https://download.filezilla-project.org/" "libfilezilla/libfilezilla-" version ".tar.bz2")) (sha256 - (base32 - "17zlhw5b1a7jzh50cbpy2is3sps5lnzch5yf9qm7mwrviw9c8j10")))) + (base32 "1fd71vmllzvljff5l5ka5wnzbdsxx4i54dpxpklydmbsqpilnv1v")))) (build-system gnu-build-system) (native-inputs `(("cppunit" ,cppunit) From 68c138ffcec4758ebda95af388896332cc385a4c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 19 Jun 2019 13:43:46 +0200 Subject: [PATCH 166/224] gnu: filezilla: Update to 3.42.1. * gnu/packages/ftp.scm (filezilla): Update to 3.42.1. --- gnu/packages/ftp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index 20f096b62a..b2ab13d951 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -208,14 +208,14 @@ output. (define-public filezilla (package (name "filezilla") - (version "3.41.2") + (version "3.42.1") (source (origin (method url-fetch) (uri (string-append "https://download.filezilla-project.org/client/" "FileZilla_" version "_src.tar.bz2")) (sha256 - (base32 "05zhvzvzkbns0cdxmlswvasfa6031y22dhfj9y5p85gi654f4fy2")))) + (base32 "083ycsycwy1szhp3mzf998wsqa74hmdxdsy07x6k81vp2cxjxijg")))) (build-system gnu-build-system) (arguments ;; Don't let filezilla phone home to check for updates. From a6dc3cc197955708e16516926addbf5a617efee9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 19 Jun 2019 17:03:13 +0200 Subject: [PATCH 167/224] gnu: ansible: Update to 2.8.1. * gnu/packages/admin.scm (ansible): Update to 2.8.1. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 4ae0733fbb..fa1591a8ec 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1734,13 +1734,13 @@ of supported upstream metrics systems simultaneously.") (define-public ansible (package (name "ansible") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (pypi-uri "ansible" version)) (sha256 - (base32 "1bpk5r5x6vdgn839n74yv2chd2ja10yfrhav0fzwa38mi5yxsd3j")))) + (base32 "0ia4x17ywym3r1m96ar4h0wc2xlylhbjp6x4wzwkh4p2i0x1vmg1")))) (build-system python-build-system) (native-inputs `(("python-bcrypt" ,python-bcrypt) From bb3dc8025a7c98e95aa8a13537fb89ad3944685b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 19 Jun 2019 17:15:49 +0200 Subject: [PATCH 168/224] gnu: shadow: Update to 4.7. * gnu/packages/admin.scm (shadow): Update to 4.7. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index fa1591a8ec..6b4d657657 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -438,7 +438,7 @@ hostname.") (define-public shadow (package (name "shadow") - (version "4.6") + (version "4.7") (source (origin (method url-fetch) (uri (string-append @@ -446,7 +446,7 @@ hostname.") "download/" version "/shadow-" version ".tar.xz")) (sha256 (base32 - "10smy01km2bqjjvsd2jz17zvrxbzj89qczyb1amk38j28bcci609")))) + "0v71474rx38lg9kidrm4xbk35sg3icv3s5pk2b42icp3lyj9dqg5")))) (build-system gnu-build-system) (arguments `(;; Assume System V `setpgrp (void)', which is the default on GNU From 1f6dd7e9c2b1feb6339ed4eb8070e905a3afe9a6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 19 Jun 2019 17:16:46 +0200 Subject: [PATCH 169/224] gnu: shadow: Update home page. * gnu/packages/admin.scm (shadow)[home-page]: Update to new project home. --- gnu/packages/admin.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 6b4d657657..c6ed4c6d4a 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -482,7 +482,7 @@ hostname.") "-linux") `(("linux-pam" ,linux-pam)) '())) - (home-page "http://pkg-shadow.alioth.debian.org/") + (home-page "https://github.com/shadow-maint/shadow") (synopsis "Authentication-related tools such as passwd, su, and login") (description "Shadow provides a number of authentication-related tools, including: From 2dcde3c7338a11817ac7ad4ffc8587cc412a50e6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 19 Jun 2019 17:16:58 +0200 Subject: [PATCH 170/224] gnu: perl-xml-sax: Update to 1.02. * gnu/packages/xml.scm (perl-xml-sax): Update to 1.02. --- gnu/packages/xml.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 400dca9290..fc60758724 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -516,15 +516,14 @@ that allow you to generate HTML from an RSS, convert between 0.9, 0.91, and (define-public perl-xml-sax (package (name "perl-xml-sax") - (version "1.00") + (version "1.02") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/G/GR/GRANTM/" "XML-SAX-" version ".tar.gz")) (sha256 - (base32 - "1qra9k3wszjxvsgbragl55z3qba4nri0ipmjaxfib4l6xxj6bsj5")))) + (base32 "0am13vnv8qsjafr5ljakwnkhlwpk15sga02z8mxsg9is0j3w61j5")))) (build-system perl-build-system) (propagated-inputs `(("perl-xml-namespacesupport" ,perl-xml-namespacesupport) From 903bc2672d1f3cf412d914396e35644fe3ff560e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 19 Jun 2019 17:31:44 +0200 Subject: [PATCH 171/224] gnu: mpd: Update to 0.21.10. * gnu/packages/mpd.scm (mpd): Update to 0.21.10. --- gnu/packages/mpd.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index ff4800c3ca..7d46870c55 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -91,7 +91,7 @@ interfacing MPD in the C, C++ & Objective C languages.") (define-public mpd (package (name "mpd") - (version "0.21.9") + (version "0.21.10") (source (origin (method url-fetch) (uri @@ -100,10 +100,10 @@ interfacing MPD in the C, C++ & Objective C languages.") "/mpd-" version ".tar.xz")) (sha256 (base32 - "0ghda8g9q0bi6nrvl6n756d8f45spqpblkh77mnb4k9gmiv57qir")))) + "0fx9n6qmyb4ls17j7kl58i1ivg9wfx9zm9wyfnwzw7lcwdl56sqk")))) (build-system meson-build-system) (arguments - `(#:configure-flags '("-Ddocumentation=true") ; The default is 'false'... + `(#:configure-flags '("-Ddocumentation=true") ; the default is 'false'... #:phases (modify-phases %standard-phases (add-before 'configure 'expand-C++-include-path From 76472ed959cf9c6a15cea5102e32f656be27c384 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 19 Jun 2019 17:36:37 +0200 Subject: [PATCH 172/224] gnu: notmuch: Update to 0.29.1. * gnu/packages/mail.scm (notmuch): Update to 0.29.1. --- gnu/packages/mail.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 7f9dc8e13f..4be30d8fdb 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -847,14 +847,14 @@ invoking @command{notifymuch} from the post-new hook.") (define-public notmuch (package (name "notmuch") - (version "0.29") + (version "0.29.1") (source (origin (method url-fetch) (uri (string-append "https://notmuchmail.org/releases/notmuch-" version ".tar.xz")) (sha256 (base32 - "0rg4jp0wlsham76rx9fmlpmcbv3n9vsd81vrzqvh6jrwlnmjds88")))) + "0rg3rwghd3wivf3bmqcqpkkd5c779ld5hi363zjcw5fl6a7gqilq")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) @@ -863,7 +863,7 @@ invoking @command{notifymuch} from the post-new hook.") #:imported-modules (,@%gnu-build-system-modules (guix build emacs-build-system) (guix build emacs-utils)) - #:make-flags (list "V=1") ; Verbose test output. + #:make-flags (list "V=1") ; verbose test output #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-notmuch-lib.el (lambda _ @@ -894,7 +894,7 @@ invoking @command{notifymuch} from the post-new hook.") (assoc-ref emacs:%standard-phases 'make-autoloads))))) (native-inputs `(("bash-completion" ,bash-completion) - ("emacs" ,emacs-no-x) ; Minimal lacks libxml, needed for some tests. + ("emacs" ,emacs-no-x) ; -minimal lacks libxml, needed for some tests ("pkg-config" ,pkg-config) ("python" ,python) ("python-docutils" ,python-docutils) From c8a67f13c971bae72e9782cd5ab1b3f76c8a43a5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 19 Jun 2019 17:50:17 +0200 Subject: [PATCH 173/224] gnu: nano: Update to 4.3. * gnu/packages/nano.scm (nano): Update to 4.3. --- gnu/packages/nano.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm index e3710b2de5..6f79dd49fc 100644 --- a/gnu/packages/nano.scm +++ b/gnu/packages/nano.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2012 Nikita Karetnikov ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner ;;; Copyright © 2016 Rene Saavedra -;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,15 +30,13 @@ (define-public nano (package (name "nano") - (version "4.2") + (version "4.3") (source (origin (method url-fetch) - (uri (string-append "mirror://gnu/nano/nano-" - version ".tar.xz")) + (uri (string-append "mirror://gnu/nano/nano-" version ".tar.xz")) (sha256 - (base32 - "1yaxqk6f1awnny0ywikdwb7mdv8xbipdpzsj28j1nf9fwvydwhqi")))) + (base32 "108dzj6azqmini9bvgl26r0q1y59s3nnrw75hfzv91bs50davlq0")))) (build-system gnu-build-system) (inputs `(("gettext" ,gettext-minimal) From f58b10cb3067bc9c9681f214142ecd3e9f16709b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 19 Jun 2019 17:57:28 +0200 Subject: [PATCH 174/224] gnu: balsa: Update to 2.5.7. * gnu/packages/mail.scm (balsa): Update to 2.5.7. [inputs]: Build with gtksourceview@3. --- gnu/packages/mail.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 4be30d8fdb..bf35d943ce 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -2592,15 +2592,14 @@ tools and applications: (define-public balsa (package (name "balsa") - (version "2.5.6") + (version "2.5.7") (source (origin (method url-fetch) (uri (string-append "https://pawsa.fedorapeople.org/balsa/" name "-" version ".tar.bz2")) (sha256 - (base32 - "17k6wcsl8gki7cskr3hhmfj6n54rha8ca3b6fzd8blsl5shsankx")))) + (base32 "0yfqhfpwm1qnwmbpr6dfn2f5w8a8xxq51pn8ypgg0fw973l1c1nx")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -2622,7 +2621,7 @@ tools and applications: ("gnutls" ,gnutls) ("gpgme" ,gpgme) ("gtk+" ,gtk+) - ("gtksourceview" ,gtksourceview) + ("gtksourceview" ,gtksourceview-3) ("gtkspell3" ,gtkspell3) ("libcanberra" ,libcanberra) ("libesmtp" ,libesmtp) From 538230c9331b64844f1f2bdb884ae9a88d3ac537 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Wed, 19 Jun 2019 09:55:42 +0200 Subject: [PATCH 175/224] gnu: python-gmpy2: Update to 2.1.0b1. The gmpy2 package has become a standard package in sage-8.7, and the latest stable release is too old. * gnu/packages/sagemath.scm (python-gmpy2): Update to 2.1.0b1. --- gnu/packages/sagemath.scm | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 732011bf36..82b73d7811 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -65,18 +65,21 @@ but it can be used independently.") (package-with-python2 python-cypari2)) ;; The stable version of the following package is not young enough to be -;; used with Sage, since it does not support cython. One would need to -;; use an alpha release. On the other hand, Sage can be built without it. +;; used with Sage, since it does not support cython; so we use a beta +;; release. (define-public python-gmpy2 (package (name "python-gmpy2") - (version "2.0.8") + (version "2.1.0b1") (source (origin - (method url-fetch) - (uri (pypi-uri "gmpy2" version ".zip")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/aleaxit/gmpy") + (commit (string-append "gmpy2-" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0grx6zmi99iaslm07w6c2aqpnmbkgrxcqjrqpfq223xri0r3w8yx")))) + "0ljvnmhxqdfsp0yy4c2hynhk5sggm63kkqsq4iwq4k9vsnx2xm97")))) (build-system python-build-system) (native-inputs `(("unzip" ,unzip))) From 3923e9d9421f2608c900d7815896e5809b154fec Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Wed, 19 Jun 2019 15:33:01 +0200 Subject: [PATCH 176/224] gnu: Add pynac. * gnu/packages/sagemath.scm (pynac): New variable. --- gnu/packages/sagemath.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 82b73d7811..07c13582de 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -29,6 +29,7 @@ #:use-module (gnu packages bdw-gc) #:use-module (gnu packages compression) #:use-module (gnu packages multiprecision) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz)) @@ -231,3 +232,37 @@ represented as strings.") "1wfivlwp30mzdy1697w7rzb8caajim50mc8h27k82yipn2qc5n4i")))) (inputs `(("fflas-ffpack" ,fflas-ffpack-2.3.2))))) + +(define-public pynac + (package + (name "pynac") + (version "0.7.25") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pynac/pynac/") + (commit (string-append "pynac-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0nnifvg6kzx0lq6gz7znind8g30v3d2pjfwgsdiks3vv9kv9nbj3")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("flint" ,flint) + ("gmp" ,gmp) + ("python" ,python) + ("singular" ,singular))) + (synopsis "Sage fork of GiNaC") + (description "Pynac is a derivative of the C++ library GiNaC, which +allows manipulation of symbolic expressions. It currently provides the +backend for symbolic expressions in Sage. The main difference between +Pynac and GiNaC is that Pynac relies on Sage to provide the operations +on numerical types, while GiNaC depends on CLN for this purpose.") + (license license:gpl2+) + (home-page "http://pynac.org/"))) From 01822e3ebf24031d6438fc4e7ad3a869ea12fdf4 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Wed, 19 Jun 2019 16:54:09 +0200 Subject: [PATCH 177/224] gnu: Add zn_poly. * gnu/packages/sagemath.scm (zn_poly): New variable. --- gnu/packages/sagemath.scm | 47 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 07c13582de..6cf1badb3c 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -266,3 +266,50 @@ Pynac and GiNaC is that Pynac relies on Sage to provide the operations on numerical types, while GiNaC depends on CLN for this purpose.") (license license:gpl2+) (home-page "http://pynac.org/"))) + +;; Sage has become upstream of the following package. +(define-public zn_poly + (package + (name "zn_poly") + (version "0.9.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url (string-append "https://gitlab.com/sagemath/" + name ".git/")) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ra5vy585bqq7g3317iw6fp44iqgqvds3j0l1va6mswimypq4vxb")))) + (build-system gnu-build-system) + (native-inputs + `(("python" ,python-2))) + (inputs + `(("gmp" ,gmp))) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'configure + ;; The configure script chokes on --enable-fast-install. + (lambda* (#:key inputs outputs #:allow-other-keys) + (invoke "./configure" + (string-append "--prefix=" (assoc-ref outputs "out")) + "--cflags=-O3 -fPIC"))) + (add-before 'build 'prepare-build + (lambda _ + (setenv "CC" "gcc") + #t)) + (add-after 'build 'build-so + (lambda _ + (invoke "make" "libzn_poly.so"))) + (add-after 'install 'install-so + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) + (install-file "libzn_poly.so" lib))))))) + (synopsis "Arithmetic for polynomials over Z/NZ") + (description "zn_poly implements the arithmetic of polynomials the +coefficients of which are modular integers.") + (license (list license:gpl2 license:gpl3)) ; dual licensed + (home-page "https://gitlab.com/sagemath/zn_poly"))) From 7c5f623192d4d316ce62270cbdb9daa7848c323d Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Wed, 19 Jun 2019 18:54:52 +0200 Subject: [PATCH 178/224] gnu: Add gf2x. * gnu/packages/algebra.scm (gf2x): New variable. --- gnu/packages/algebra.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 86c0a42758..fefe712a33 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -93,6 +93,27 @@ multiplication routines such as Toom–Cook and the FFT.") (license license:lgpl3+) (home-page "http://mpfrcx.multiprecision.org/"))) +(define-public gf2x + (package + (name "gf2x") + (version "1.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-" + version ".tar.gz")) + (sha256 + (base32 + "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1")))) + (build-system gnu-build-system) + (synopsis "Arithmetic of polynomials over binary finite fields") + (description + "The gf2x library provides arithmetic of polynomials over finite fields +of characteristic 2. It implements the multiplication, squaring and +greatest common divisor operations.") + (license license:gpl3+) + (home-page "https://gforge.inria.fr/projects/gf2x/"))) + (define-public cm (package (name "cm") From 0c842e3a59da42d344f054b246e870eba708f779 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 19 Jun 2019 21:43:12 +0200 Subject: [PATCH 179/224] gnu: Add ratpoints. * gnu/packages/maths.scm (ratpoints): New variable. * gnu/packages/patches/ratpoints-sturm_and_rp_private.patch: New file. * gnu/local.mk (dist_patch_DATA): Reference patch. --- gnu/local.mk | 1 + gnu/packages/maths.scm | 41 ++++ .../ratpoints-sturm_and_rp_private.patch | 194 ++++++++++++++++++ 3 files changed, 236 insertions(+) create mode 100644 gnu/packages/patches/ratpoints-sturm_and_rp_private.patch diff --git a/gnu/local.mk b/gnu/local.mk index 74d2bafa8d..57552d206c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1233,6 +1233,7 @@ dist_patch_DATA = \ %D%/packages/patches/randomjungle-disable-static-build.patch \ %D%/packages/patches/rapicorn-isnan.patch \ %D%/packages/patches/raptor2-heap-overflow.patch \ + %D%/packages/patches/ratpoints-sturm_and_rp_private.patch \ %D%/packages/patches/ratpoison-shell.patch \ %D%/packages/patches/rcs-5.9.4-noreturn.patch \ %D%/packages/patches/rct-add-missing-headers.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 6d8fb9cec5..fc57801354 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5003,3 +5003,44 @@ command-line tools, and an Application Programming Interface (API). This package provides the static libraries required to run programs compiled against the nauty library.") (license license:asl2.0))) + +(define-public ratpoints + (package + (name "ratpoints") + (version "2.1.3") + (source (origin + (method url-fetch) + (uri (string-append + "http://www.mathe2.uni-bayreuth.de/stoll/programs/" + "ratpoints-" version ".tar.gz")) + (sha256 + (base32 + "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4")) + (patches + ;; Taken from + ;; + (search-patches "ratpoints-sturm_and_rp_private.patch")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:make-flags + (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure) ;no configure script + (add-before 'install 'create-install-directories + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (mkdir-p out) + (with-directory-excursion out + (for-each (lambda (d) (mkdir-p d)) + '("bin" "include" "lib")))) + #t))))) + (inputs + `(("gmp" ,gmp))) + (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/") + (synopsis "Find rational points on hyperelliptic curves") + (description "Ratpoints tries to find all rational points within +a given height bound on a hyperelliptic curve in a very efficient way, +by using an optimized quadratic sieve algorithm.") + (license license:gpl2+))) diff --git a/gnu/packages/patches/ratpoints-sturm_and_rp_private.patch b/gnu/packages/patches/ratpoints-sturm_and_rp_private.patch new file mode 100644 index 0000000000..664198c4de --- /dev/null +++ b/gnu/packages/patches/ratpoints-sturm_and_rp_private.patch @@ -0,0 +1,194 @@ +diff --git a/rp-private.h b/rp-private.h +index b4c7dad..0c7193e 100644 +--- a/rp-private.h ++++ b/rp-private.h +@@ -36,7 +36,7 @@ + #define LONG_SHIFT ((LONG_LENGTH == 16) ? 4 : \ + (LONG_LENGTH == 32) ? 5 : \ + (LONG_LENGTH == 64) ? 6 : 0) +-#define LONG_MASK (~(-1L<>1); ++static const long min = (long)(-(((unsigned long)(-1))>>1)); ++ /* recursive helper function */ ++static void iterate(long nl, long nr, long del, long der, long cleft, long cright, ++ long sl, long sr, long depth, ++ ratpoints_interval **iptr, const ratpoints_interval *ivlo, ++ const ratpoints_args *args, const long k, const long sturm_degs[], ++ const mpz_t sturm[][args->degree + 1]) ++ { /* nl/2^del, nr/2^der : interval left/right endpoints, ++ cleft, cright: sign change counts at endpoints, ++ sl, sr: signs at endpoints, ++ depth: iteration depth */ ++ long iter = args->sturm; ++ if(cleft == cright && sl < 0) { return; } ++ /* here we know the polynomial is negative on the interval */ ++ if((cleft == cright && sl > 0) || depth >= iter) ++ /* we have to add/extend an interval if we either know that ++ the polynomial is positive on the interval (first condition) ++ or the maximal iteration depth has been reached (second condition) */ ++ { double l = ((double)nl)/((double)(1<low = l; (*iptr)->up = u; (*iptr)++; } ++ else ++ { if(((*iptr)-1)->up == l) /* extend interval */ ++ { ((*iptr)-1)->up = u; } ++ else /* new interval */ ++ { (*iptr)->low = l; (*iptr)->up = u; (*iptr)++; } ++ } ++ return; ++ } ++ /* now we must split the interval and evaluate the sturm sequence ++ at the midpoint */ ++ { long nm, dem, s0, s1, s2, s, cmid = 0, n; ++ if(nl == min) ++ { if(nr == max) { nm = 0; dem = 0; } ++ else { nm = (nr == 0) ? -1 : 2*nr; dem = 0; } ++ } ++ else ++ { if(nr == max) { nm = (nl == 0) ? 1 : 2*nl; dem = 0; } ++ else /* "normal" case */ ++ { if(del == der) /* then both are zero */ ++ { if(((nl+nr) & 1) == 0) { nm = (nl+nr)>>1; dem = 0; } ++ else { nm = nl+nr; dem = 1; } ++ } ++ else /* here one de* is greater */ ++ { if(del > der) { nm = nl + (nr<<(del-der)); dem = del+1; } ++ else { nm = (nl<<(der-del)) + nr; dem = der+1; } ++ } ++ } ++ } ++ s0 = eval_sign(args, sturm[0], sturm_degs[0], nm, dem); ++ s1 = eval_sign(args, sturm[1], sturm_degs[1], nm, dem); ++ if(s0*s1 == -1) { cmid++; } ++ s = (s1 == 0) ? s0 : s1; ++ for(n = 2; n <= k; n++) ++ { s2 = eval_sign(args, sturm[n], sturm_degs[n], nm, dem); ++ if(s2 == -s) { cmid++; s = s2; } ++ else if(s2 != 0) { s = s2; } ++ } ++ /* now recurse */ ++ iterate(nl, nm, del, dem, cleft, (s0==0) ? (cmid+1) : cmid, ++ sl, (s0==0) ? -s1 : s0, depth+1, ++ iptr, ivlo, args, k, sturm_degs, sturm); ++ iterate(nm, nr, dem, der, cmid, cright, ++ (s0==0) ? s1 : s0, sr, depth+1, ++ iptr, ivlo, args, k, sturm_degs, sturm); ++ } ++ } /* end iterate() */ ++ + long _ratpoints_compute_sturm(ratpoints_args *args) + { + mpz_t *cofs = args->cof; + long degree = args->degree; +- long iter = args->sturm; + ratpoints_interval *ivlist = args->domain; + long num_iv = args->num_inter; + long n, m, k, new_num; +@@ -165,75 +233,12 @@ long _ratpoints_compute_sturm(ratpoints_args *args) + /* recall: typedef struct {double low; double up;} ratpoints_interval; */ + { ratpoints_interval ivlocal[1 + (degree>>1)]; + ratpoints_interval *iptr = &ivlocal[0]; +- long max = (long)(((unsigned long)(-1))>>1); +- long min = -max; + long num_intervals; + long slcf = mpz_cmp_si(cofs[degree], 0); + +- /* recursive helper function */ +- void iterate(long nl, long nr, long del, long der, long cleft, long cright, +- long sl, long sr, long depth) +- { /* nl/2^del, nr/2^der : interval left/right endpoints, +- cleft, cright: sign change counts at endpoints, +- sl, sr: signs at endpoints, +- depth: iteration depth */ +- if(cleft == cright && sl < 0) { return; } +- /* here we know the polynomial is negative on the interval */ +- if((cleft == cright && sl > 0) || depth >= iter) +- /* we have to add/extend an interval if we either know that +- the polynomial is positive on the interval (first condition) +- or the maximal iteration depth has been reached (second condition) */ +- { double l = ((double)nl)/((double)(1<low = l; iptr->up = u; iptr++; } +- else +- { if((iptr-1)->up == l) /* extend interval */ +- { (iptr-1)->up = u; } +- else /* new interval */ +- { iptr->low = l; iptr->up = u; iptr++; } +- } +- return; +- } +- /* now we must split the interval and evaluate the sturm sequence +- at the midpoint */ +- { long nm, dem, s0, s1, s2, s, cmid = 0, n; +- if(nl == min) +- { if(nr == max) { nm = 0; dem = 0; } +- else { nm = (nr == 0) ? -1 : 2*nr; dem = 0; } +- } +- else +- { if(nr == max) { nm = (nl == 0) ? 1 : 2*nl; dem = 0; } +- else /* "normal" case */ +- { if(del == der) /* then both are zero */ +- { if(((nl+nr) & 1) == 0) { nm = (nl+nr)>>1; dem = 0; } +- else { nm = nl+nr; dem = 1; } +- } +- else /* here one de* is greater */ +- { if(del > der) { nm = nl + (nr<<(del-der)); dem = del+1; } +- else { nm = (nl<<(der-del)) + nr; dem = der+1; } +- } +- } +- } +- s0 = eval_sign(args, sturm[0], sturm_degs[0], nm, dem); +- s1 = eval_sign(args, sturm[1], sturm_degs[1], nm, dem); +- if(s0*s1 == -1) { cmid++; } +- s = (s1 == 0) ? s0 : s1; +- for(n = 2; n <= k; n++) +- { s2 = eval_sign(args, sturm[n], sturm_degs[n], nm, dem); +- if(s2 == -s) { cmid++; s = s2; } +- else if(s2 != 0) { s = s2; } +- } +- /* now recurse */ +- iterate(nl, nm, del, dem, cleft, (s0==0) ? (cmid+1) : cmid, +- sl, (s0==0) ? -s1 : s0, depth+1); +- iterate(nm, nr, dem, der, cmid, cright, +- (s0==0) ? s1 : s0, sr, depth+1); +- } +- } /* end iterate() */ +- + iterate(min, max, 0, 0, count2, count1, +- (degree & 1) ? -slcf : slcf, slcf, 0); ++ (degree & 1) ? -slcf : slcf, slcf, 0, ++ &iptr, &ivlocal[0], args, k, sturm_degs, sturm); + num_intervals = iptr - &ivlocal[0]; + /* intersect with given intervals */ + { ratpoints_interval local_copy[num_iv]; From 74247b80e5f8e1b385dbcc82df4851c2ee5792f3 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 19 Jun 2019 22:01:53 +0200 Subject: [PATCH 180/224] gnu: Add python-pandocfilters. * gnu/packages/textutils.scm (python-pandocfilters): New variable. --- gnu/packages/textutils.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index c204fb9b92..79835e8578 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -851,3 +851,28 @@ Mainland China, Taiwan, and Hong-Kong.") hosts and terminals. It converts input kanji code to designated kanji code such as ISO-2022-JP, Shift_JIS, EUC-JP, UTF-8, UTF-16 or UTF-32.") (license license:zlib)))) + +(define-public python-pandocfilters + (package + (name "python-pandocfilters") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pandocfilters" version)) + (sha256 + (base32 + "1a8d9b7s48gmq9zj0pmbyv2sivn5i7m6mybgpkk4jm5vd7hp1pdk")))) + (build-system python-build-system) + (home-page "https://github.com/jgm/pandocfilters") + (synopsis "Python module for writing Pandoc filters") + (description "Pandoc is a powerful utility to transform various +input formats into a wide range of output formats. To alter the +exported output document, Pandoc allows the usage of filters, which +are pipes that read a JSON serialization of the Pandoc AST from stdin, +transform it in some way, and write it to stdout. It allows therefore +to alter the processing of Pandoc's supported input formats, for +instance one can add new syntax elements to markdown, etc. + +This package provides Python bindings.") + (license license:bsd-3))) From 2ef22a9f371276be0b1474c512f125d1f0d0c064 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 19 Jun 2019 21:49:22 +0200 Subject: [PATCH 181/224] derivations: Add 'derivation-input-derivation'. * guix/derivations.scm (derivation-input-derivation): New procedure. (derivation-prerequisites): Use it. --- guix/derivations.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/guix/derivations.scm b/guix/derivations.scm index cad77bdb06..8145d51143 100644 --- a/guix/derivations.scm +++ b/guix/derivations.scm @@ -62,6 +62,7 @@ derivation-input? derivation-input-path + derivation-input-derivation derivation-input-sub-derivations derivation-input-output-paths valid-derivation-input? @@ -152,6 +153,10 @@ (path derivation-input-path) ; store path (sub-derivations derivation-input-sub-derivations)) ; list of strings +(define (derivation-input-derivation input) + "Return the object INPUT refers to." + (read-derivation-from-file (derivation-input-path input))) + (set-record-type-printer! (lambda (drv port) (format port "# ~a ~a>" @@ -243,9 +248,7 @@ result is the set of prerequisites of DRV not already in valid." (fold2 loop (append inputs result) (fold set-insert input-set inputs) - (map (lambda (i) - (read-derivation-from-file (derivation-input-path i))) - inputs))))) + (map derivation-input-derivation inputs))))) (define (offloadable-derivation? drv) "Return true if DRV can be offloaded, false otherwise." From aad086d8717d8ee6fa0ec37dd7932b74fe6398c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 19 Jun 2019 21:50:45 +0200 Subject: [PATCH 182/224] grafts: Avoid 'query-valid-derivers' RPC. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Previously we'd make 502 'query-valid-derivers' RPCs for "guix build vim -d", and after this patch, we don't do any. Furthermore, the previous strategy was "stateful" in the sense that 'item->deriver' could return a derivation that is not the one that was actually computed by this process, but an "equivalent" one (due to fixed-output derivations); which one is chosen would depend on the state of the store. This in turn means that we'd have to call 'read-derivation-from-file' to actually read .drv files (as opposed to getting them from %DERIVATION-CACHE). This is costly and doesn't work with GUIX_DAEMON_SOCKET=ssh://…. * guix/grafts.scm (item->deriver): Remove. (reference-origin): New procedure. (cumulative-grafts): Use it instead of 'item->deriver'. --- guix/grafts.scm | 67 +++++++++++++++++++++++++++++-------------------- 1 file changed, 40 insertions(+), 27 deletions(-) diff --git a/guix/grafts.scm b/guix/grafts.scm index a3e12f6efd..3b43e11425 100644 --- a/guix/grafts.scm +++ b/guix/grafts.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -22,9 +22,9 @@ #:use-module (guix records) #:use-module (guix derivations) #:use-module ((guix utils) #:select (%current-system)) + #:use-module (guix sets) #:use-module (srfi srfi-1) #:use-module (srfi srfi-9 gnu) - #:use-module (srfi srfi-11) #:use-module (srfi srfi-26) #:use-module (srfi srfi-34) #:use-module (ice-9 match) @@ -151,21 +151,6 @@ are not recursively applied to dependencies of DRV." #:substitutable? #f #:properties properties))))) -(define (item->deriver store item) - "Return two values: the derivation that led to ITEM (a store item), and the -name of the output of that derivation ITEM corresponds to (for example -\"out\"). When ITEM has no deriver, for instance because it is a plain file, -#f and #f are returned." - (match (valid-derivers store item) - (() ;ITEM is a plain file - (values #f #f)) - ((drv-file _ ...) - (let ((drv (read-derivation-from-file drv-file))) - (values drv - (any (match-lambda - ((name . path) - (and (string=? item path) name))) - (derivation->output-paths drv))))))) (define (non-self-references references drv outputs) "Return the list of references of the OUTPUTS of DRV, excluding self @@ -230,6 +215,33 @@ available." (set-current-state (vhash-cons key result cache)) (return result))))))) +(define (reference-origin drv item) + "Return the derivation/output pair among the inputs of DRV, recursively, +that produces ITEM. Return #f if ITEM is not produced by a derivation (i.e., +it's a content-addressed \"source\"), or if it's not produced by a dependency +of DRV." + ;; Perform a breadth-first traversal of the dependency graph of DRV in + ;; search of the derivation that produces ITEM. + (let loop ((drv (list drv)) + (visited (setq))) + (match drv + (() + #f) + ((drv . rest) + (if (set-contains? visited drv) + (loop rest visited) + (let ((inputs (derivation-inputs drv))) + (or (any (lambda (input) + (let ((drv (derivation-input-derivation input))) + (any (match-lambda + ((output . file) + (and (string=? file item) + (cons drv output)))) + (derivation->output-paths drv)))) + inputs) + (loop (append rest (map derivation-input-derivation inputs)) + (set-insert drv visited))))))))) + (define* (cumulative-grafts store drv grafts references #:key @@ -257,16 +269,17 @@ derivations to the corresponding set of grafts." #f))) (define (dependency-grafts item) - (let-values (((drv output) (item->deriver store item))) - (if drv - ;; If GRAFTS already contains a graft from DRV, do not override it. - (if (find (cut graft-origin? drv <>) grafts) - (state-return grafts) - (cumulative-grafts store drv grafts references - #:outputs (list output) - #:guile guile - #:system system)) - (state-return grafts)))) + (match (reference-origin drv item) + ((drv . output) + ;; If GRAFTS already contains a graft from DRV, do not override it. + (if (find (cut graft-origin? drv <>) grafts) + (state-return grafts) + (cumulative-grafts store drv grafts references + #:outputs (list output) + #:guile guile + #:system system))) + (#f + (state-return grafts)))) (with-cache (cons (derivation-file-name drv) outputs) (match (non-self-references references drv outputs) From a7a31827619b23f71160e224f6ab658cd9419662 Mon Sep 17 00:00:00 2001 From: Giacomo Leidi Date: Tue, 18 Jun 2019 01:58:05 +0200 Subject: [PATCH 183/224] gnu: Add numix-theme. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnome.scm (numix-theme): New variable Signed-off-by: Ludovic Courtès --- gnu/packages/gnome.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 875d28caee..ad6b9203b9 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -36,6 +36,7 @@ ;;; Copyright © 2019 Danny Milosavljevic ;;; Copyright © 2019 Marius Bakke ;;; Copyright © 2019 Florian Pelz +;;; Copyright © 2019 Giacomo Leidi ;;; ;;; This file is part of GNU Guix. ;;; @@ -6880,6 +6881,38 @@ functionality and behavior.") (home-page "https://extensions.gnome.org/") (license license:gpl3+))) +(define-public numix-theme + (package + (name "numix-theme") + (version "2.6.7") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/numixproject/numix-gtk-theme.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "12mw0kr0kkvg395qlbsvkvaqccr90cmxw5rrsl236zh43kj8grb7")))) + (build-system gnu-build-system) + (arguments + '(#:make-flags (list (string-append "DESTDIR=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'check)))) + (native-inputs + `(("glib:bin" ,glib "bin") ; for glib-compile-schemas + ("gnome-shell" ,gnome-shell) + ("gtk+" ,gtk+) + ("xmllint" ,libxml2) + ("ruby-sass" ,ruby-sass))) + (synopsis "Flat theme with light and dark elements") + (description "Numix is a modern flat theme with a combination of light and +dark elements. It supports GNOME, Unity, Xfce, and Openbox.") + (home-page "https://numixproject.github.io") + (license license:gpl3+))) + (define-public arc-theme (package (name "arc-theme") From 8785a71faf45253819cb4fec9cb7e0155b18ceb0 Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Tue, 18 Jun 2019 06:48:35 +0200 Subject: [PATCH 184/224] gnu: emacs-unpackaged-el: Add patch for missing require statement. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-unpackaged-el)[source]: Add patch. * gnu/packages/patches/emacs-unpackaged-req.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/emacs-xyz.scm | 5 +++- .../patches/emacs-unpackaged-req.patch | 24 +++++++++++++++++++ 3 files changed, 29 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/emacs-unpackaged-req.patch diff --git a/gnu/local.mk b/gnu/local.mk index 57552d206c..ac5f0e9dbf 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -765,6 +765,7 @@ dist_patch_DATA = \ %D%/packages/patches/emacs-highlight-stages-add-gexp.patch \ %D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch \ %D%/packages/patches/emacs-source-date-epoch.patch \ + %D%/packages/patches/emacs-unpackaged-req.patch \ %D%/packages/patches/emacs-undohist-ignored.patch \ %D%/packages/patches/emacs-wordnut-require-adaptive-wrap.patch \ %D%/packages/patches/emacs-zones-called-interactively.patch \ diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 719c729f62..9bf101ab31 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -591,12 +591,15 @@ from within Emacs.") (file-name (git-file-name name version)) (sha256 (base32 - "1yf3zrgqfhnr0az8gn1kqqwnhfi3nc0vbjkcagwcqwk3sp1jda86")))) + "1yf3zrgqfhnr0az8gn1kqqwnhfi3nc0vbjkcagwcqwk3sp1jda86")) + (patches + (search-patches "emacs-unpackaged-req.patch")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) ("emacs-org" ,emacs-org) ("emacs-s" ,emacs-s) + ("emacs-hydra" ,emacs-hydra) ("emacs-use-package" ,emacs-use-package))) (home-page "https://github.com/alphapapa/unpackaged.el") (synopsis "Useful snippets of Emacs Lisp code") diff --git a/gnu/packages/patches/emacs-unpackaged-req.patch b/gnu/packages/patches/emacs-unpackaged-req.patch new file mode 100644 index 0000000000..ddb9277610 --- /dev/null +++ b/gnu/packages/patches/emacs-unpackaged-req.patch @@ -0,0 +1,24 @@ +From e5be173e201710538464c279335bef735a327a68 Mon Sep 17 00:00:00 2001 +From: Brian Leung +Date: Tue, 18 Jun 2019 06:37:46 +0200 +Subject: [PATCH] Add missing require. + +--- + unpackaged.el | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/unpackaged.el b/unpackaged.el +index 2d46b3c..e62184a 100644 +--- a/unpackaged.el ++++ b/unpackaged.el +@@ -38,6 +38,7 @@ + (require 'dash) + (require 's) + (require 'use-package) ++(require 'hydra) + + ;;; Faces, fonts + +-- +2.22.0 + From 3f9a027ce2016fdde41355f98ce44e66a2bb7980 Mon Sep 17 00:00:00 2001 From: Dan Frumin Date: Sat, 8 Jun 2019 15:30:33 +0200 Subject: [PATCH 185/224] gnu: Add crispy-doom. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/games.scm (crispy-doom): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/games.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index bf95bf735d..bf3ab94e68 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -41,6 +41,7 @@ ;;; Copyright © 2019 Pierre Langlois ;;; Copyright © 2019 Julien Lepiller ;;; Copyright © 2019 Jesse Gibbons +;;; Copyright © 2019 Dan Frumin ;;; ;;; This file is part of GNU Guix. ;;; @@ -5596,6 +5597,40 @@ affect gameplay).") (home-page "https://www.chocolate-doom.org/wiki/index.php/Chocolate_Doom") (license license:gpl2))) +(define-public crispy-doom + (package + (inherit chocolate-doom) + (name "crispy-doom") + (version "5.5.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fabiangreffrath/crispy-doom.git") + (commit (string-append "crispy-doom-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1a60ns0blhvml6gzj9qx18c18pbf02rq7vypaajd6nqy5h4fz3cn")))) + (native-inputs + (append + (package-native-inputs chocolate-doom) + `(("automake" ,automake) + ("autoreconf" ,autoconf)))) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'bootstrap + ;; the autogen.sh script in the source tree doesn't work + (lambda _ (invoke "autoreconf" "-vif")))))) + (synopsis "Limit-removing enhanced-resolution Doom source port based on +Chocolate Doom") + (description + "Crispy Doom is a friendly fork of Chocolate Doom that provides a higher +display resolution, removes the static limits of the Doom engine and offers +further optional visual, tactical and physical enhancements while remaining +entirely config file, savegame, netplay and demo compatible with the +original.") + (home-page "https://www.chocolate-doom.org/wiki/index.php/Crispy_Doom"))) + (define-public fortune-mod (package (name "fortune-mod") From 37edfb0f1cdff251b1231d687041dfe6e7ea92e5 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Wed, 19 Jun 2019 19:37:52 +0200 Subject: [PATCH 186/224] gnu: Add m4ri. * gnu/packages/algebra.scm (m4ri): New variable. --- gnu/packages/algebra.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index fefe712a33..05733fa405 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1244,3 +1244,33 @@ with dense, sparse, and structured matrices over the integers and over finite fields.") (license license:lgpl2.1+) (home-page "https://linbox-team.github.io/linbox/"))) + +(define-public m4ri + (package + (name "m4ri") + (version "20140914") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://bitbucket.org/malb/m4ri") + (commit (string-append "release-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("libpng" ,libpng))) + (synopsis "Arithmetic of dense matrices over F_2") + (description "M4RI is a library for fast arithmetic with dense matrices +over F2. The name M4RI comes from the first implemented algorithm: The +Method of the Four Russians inversion algorithm published by Gregory Bard. +This algorithm in turn is named after the Method of the Four Russians +multiplication algorithm.") + (license license:gpl2+) + (home-page "https://bitbucket.org/malb/m4ri/"))) From a1dcaacb7b790668fd8cce6ce29a004587f50218 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Wed, 19 Jun 2019 23:57:49 +0200 Subject: [PATCH 187/224] gnu: Add brial. * gnu/packages/sagemath.scm (brial): New variable. --- gnu/packages/sagemath.scm | 40 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 6cf1badb3c..8ae3cf77ff 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -27,7 +27,9 @@ #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages bdw-gc) + #:use-module (gnu packages boost) #:use-module (gnu packages compression) + #:use-module (gnu packages image) #:use-module (gnu packages multiprecision) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -313,3 +315,41 @@ on numerical types, while GiNaC depends on CLN for this purpose.") coefficients of which are modular integers.") (license (list license:gpl2 license:gpl3)) ; dual licensed (home-page "https://gitlab.com/sagemath/zn_poly"))) + +(define-public brial + (package + (name "brial") + (version "1.2.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BRiAl/BRiAl/") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1nv56fp3brpzanxj7vwvxqdafqfsfhdgq5imr3m94psw5gdfqwja")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("boost" ,boost) + ("libpng" ,libpng) + ("m4ri" ,m4ri))) + (arguments + ;; We are missing the boost unit test framework. + `(#:tests? #f + #:configure-flags (list "--without-boost-unit-test-framework"))) + (synopsis "Arithmetic of polynomials over boolean rings") + (description "BRiAl is the successor to PolyBoRi maintained by the +Sage community. Its core is a C++ library, which provides high-level data +types for Boolean polynomials and monomials, exponent vectors, as well as +for the underlying polynomial rings and subsets of the powerset of the +Boolean variables. As a unique approach, binary decision diagrams are +used as internal storage type for polynomial structures.") + (license license:gpl2+) + (home-page "https://gitlab.com/sagemath/zn_poly"))) From 80ee7c4a48cdab4afa4d8eb4b7b8873d47841830 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Thu, 20 Jun 2019 00:03:46 +0200 Subject: [PATCH 188/224] gnu: zn_poly: Rename to zn-poly, according to our naming conventions. Reported by Nicolas Goaziou . This is a follow-up to commit 01822e3ebf24031d6438fc4e7ad3a869ea12fdf4. * gnu/packages/sagemath.scm (zn_poly): Rename to... * gnu/packages/sagemath.scm (zn-poly): ...this. --- gnu/packages/sagemath.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 8ae3cf77ff..63d1281668 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -270,18 +270,18 @@ on numerical types, while GiNaC depends on CLN for this purpose.") (home-page "http://pynac.org/"))) ;; Sage has become upstream of the following package. -(define-public zn_poly +(define-public zn-poly (package - (name "zn_poly") + (name "zn-poly") (version "0.9.1") (source (origin (method git-fetch) (uri (git-reference (url (string-append "https://gitlab.com/sagemath/" - name ".git/")) + "zn_poly.git/")) (commit version))) - (file-name (git-file-name name version)) + (file-name (git-file-name "zn_poly" version)) (sha256 (base32 "0ra5vy585bqq7g3317iw6fp44iqgqvds3j0l1va6mswimypq4vxb")))) From c5c51bda0b8c087858183190a2aebe0c7ca811d1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 20 Jun 2019 00:26:50 +0200 Subject: [PATCH 189/224] gnu: bind: Update to 9.14.3 [fixes CVE-2019-6471]. * gnu/packages/dns.scm (isc-bind): Update to 9.14.3. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 3ff83bcadb..3eec104f50 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -108,7 +108,7 @@ and BOOTP/TFTP for network booting of diskless machines.") (define-public isc-bind (package (name "bind") - (version "9.14.2") + (version "9.14.3") (source (origin (method url-fetch) (uri (string-append @@ -116,7 +116,7 @@ and BOOTP/TFTP for network booting of diskless machines.") "/bind-" version ".tar.gz")) (sha256 (base32 - "033zqajnj5ys45g899132xkhh9f0hsh76ffv7302wl166xbjfh0f")))) + "1ymxr38c62w6961j8g2vllnv0s72z7zk4b2j2k8ixdh1rymqm1yf")))) (build-system gnu-build-system) (outputs `("out" "utils")) (inputs From 5543d3bb09e65107afe4f839c97285bb2106b70e Mon Sep 17 00:00:00 2001 From: Meiyo Peng Date: Tue, 18 Jun 2019 11:07:50 +0800 Subject: [PATCH 190/224] gnu: spdlog: Clarify license. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/logging.scm (spdlog): Clarify license of the bundled fmt library. Signed-off-by: Gábor Boskovits --- gnu/packages/logging.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/logging.scm b/gnu/packages/logging.scm index e936733136..24a47567d0 100644 --- a/gnu/packages/logging.scm +++ b/gnu/packages/logging.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2017 Eric Bavier ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2019 Gábor Boskovits +;;; Copyright © 2019 Meiyo Peng ;;; ;;; This file is part of GNU Guix. ;;; @@ -205,5 +206,8 @@ windows in a terminal, colorize, filter and merge.") (list "-DSPDLOG_BUILD_BENCH=OFF"))) (home-page "https://github.com/gabime/spdlog") (synopsis "Fast C++ logging library") - (description "Spdlog is a very fast header-only/compiled C++ logging library.") - (license license:expat))) ; MIT license + (description "Spdlog is a very fast header-only/compiled C++ logging +library.") + ;; spdlog is under Expat license, but the bundled fmt library in + ;; "include/spdlog/fmt/bundled" is under BSD 2 clause license. + (license (list license:expat license:bsd-2)))) From ab398380eb5b7b0f77c0895bfbb22232fcf5ace6 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 20 Jun 2019 09:20:29 +0200 Subject: [PATCH 191/224] gnu: Move ratpoints into a different module. * gnu/packages/maths.scm (ratpoints): Move... * gnu/packages/algebra.scm: ...here. --- gnu/packages/algebra.scm | 41 ++++++++++++++++++++++++++++++++++++++++ gnu/packages/maths.scm | 41 ---------------------------------------- 2 files changed, 41 insertions(+), 41 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 05733fa405..4dbf537af3 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1274,3 +1274,44 @@ This algorithm in turn is named after the Method of the Four Russians multiplication algorithm.") (license license:gpl2+) (home-page "https://bitbucket.org/malb/m4ri/"))) + +(define-public ratpoints + (package + (name "ratpoints") + (version "2.1.3") + (source (origin + (method url-fetch) + (uri (string-append + "http://www.mathe2.uni-bayreuth.de/stoll/programs/" + "ratpoints-" version ".tar.gz")) + (sha256 + (base32 + "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4")) + (patches + ;; Taken from + ;; + (search-patches "ratpoints-sturm_and_rp_private.patch")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:make-flags + (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure) ;no configure script + (add-before 'install 'create-install-directories + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (mkdir-p out) + (with-directory-excursion out + (for-each (lambda (d) (mkdir-p d)) + '("bin" "include" "lib")))) + #t))))) + (inputs + `(("gmp" ,gmp))) + (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/") + (synopsis "Find rational points on hyperelliptic curves") + (description "Ratpoints tries to find all rational points within +a given height bound on a hyperelliptic curve in a very efficient way, +by using an optimized quadratic sieve algorithm.") + (license license:gpl2+))) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index fc57801354..6d8fb9cec5 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5003,44 +5003,3 @@ command-line tools, and an Application Programming Interface (API). This package provides the static libraries required to run programs compiled against the nauty library.") (license license:asl2.0))) - -(define-public ratpoints - (package - (name "ratpoints") - (version "2.1.3") - (source (origin - (method url-fetch) - (uri (string-append - "http://www.mathe2.uni-bayreuth.de/stoll/programs/" - "ratpoints-" version ".tar.gz")) - (sha256 - (base32 - "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4")) - (patches - ;; Taken from - ;; - (search-patches "ratpoints-sturm_and_rp_private.patch")))) - (build-system gnu-build-system) - (arguments - `(#:test-target "test" - #:make-flags - (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out"))) - #:phases - (modify-phases %standard-phases - (delete 'configure) ;no configure script - (add-before 'install 'create-install-directories - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (mkdir-p out) - (with-directory-excursion out - (for-each (lambda (d) (mkdir-p d)) - '("bin" "include" "lib")))) - #t))))) - (inputs - `(("gmp" ,gmp))) - (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/") - (synopsis "Find rational points on hyperelliptic curves") - (description "Ratpoints tries to find all rational points within -a given height bound on a hyperelliptic curve in a very efficient way, -by using an optimized quadratic sieve algorithm.") - (license license:gpl2+))) From 059e4c9a15b52f7e4b262e3317eac238bf53103d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 20 Jun 2019 10:09:17 +0200 Subject: [PATCH 192/224] gnu: Add libgd. * gnu/packages/image.scm (libgd): New variable. --- gnu/packages/image.scm | 53 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index f9709e2b19..1f6327a762 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2018 Pierre-Antoine Rouby ;;; Copyright © 2018 Alex Vong ;;; Copyright © 2018 Rutger Helling +;;; Copyright © 2019 Nicolas Goaziou ;;; ;;; This file is part of GNU Guix. ;;; @@ -1648,3 +1649,55 @@ identical visual appearance.") to the standard output. It works well together with grim.") ;; MIT license. (license license:expat))) + +(define-public libgd + (package + (name "libgd") + (version "2.2.5") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/libgd/libgd.git") + (commit (string-append "gd-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "17p0dlmn9kigr5b7vgpcsq2323mrgv0rh69x4ysg8nrjl8n5l1nl")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DBUILD_TEST=1" + "-DENABLE_FONTCONFIG=1" + "-DENABLE_FREETYPE=1" + "-DENABLE_JPEG=1" + "-DENABLE_PNG=1" + "-DENABLE_WEBP=1" + "-DENABLE_XPM=1" + (string-append "-DFREETYPE_INCLUDE_DIRS=" + (assoc-ref %build-inputs "freetype") + "/include/freetype2")))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("fontconfig" ,fontconfig) + ("freetype" ,freetype) + ("libjpeg" ,libjpeg) + ("libpng" ,libpng) + ("libwebp" ,libwebp) + ("libxmp" ,libxpm) + ("zlib" ,zlib))) + (home-page "https://libgd.github.io/") + (synopsis "GD Graphics Library") + (description "gd is a graphics library. It allows your code to +quickly draw images complete with lines, arcs, text, multiple colors, +cut and paste from other images, and flood fills, and write out the +result as a PNG or JPEG file. This is particularly useful in World +Wide Web applications, where PNG and JPEG are two of the formats +accepted for inline images by most browsers.") + ;; The project is released under a free license, which require + ;; that its terms are present in "user-accessible supporting + ;; documentation". Some files (mainly related to CMake) use + ;; alternatively GPL2+ and BSD-3 licenses. + (license (list (license:non-copyleft "file:///COPYING") + license:gpl2+ + license:bsd-3)))) From a42cb6f1f18e33d0e8d54260ebe5ad23c5d3f2fe Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Wed, 19 Jun 2019 09:35:31 -0500 Subject: [PATCH 193/224] gnu: zathura: Install icons. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/pdf.scm (zathura)[native-inputs]: Add librsvg to build and install the application icons. Signed-off-by: Gábor Boskovits --- gnu/packages/pdf.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 5c858510eb..b2eb81ef0f 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -14,6 +14,7 @@ ;;; Copyright © 2017 Alex Vong ;;; Copyright © 2017, 2018 Rene Saavedra ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2019 Alex Griffin ;;; ;;; This file is part of GNU Guix. ;;; @@ -514,6 +515,9 @@ by using the poppler rendering engine.") ;; For building documentation. ("python-sphinx" ,python-sphinx) + ;; For building icons. + ("librsvg" ,librsvg) + ;; For tests. ("check" ,check) ("xorg-server" ,xorg-server-for-tests))) From 75a73bb024c840dc7a917a527915ff8d8d918af8 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 19 Jun 2019 07:57:57 +0200 Subject: [PATCH 194/224] gnu: Add symmetrica. * gnu/packages/algebra.scm (symmetrica): New variable. * gnu/packages/patches/symmetrica-bruch.patch: * gnu/packages/patches/symmetrica-int32.patch: * gnu/packages/patches/symmetrica-return_values.patch: * gnu/packages/patches/symmetrica-sort_sum_rename.patch: New files. * gnu/local.mk (dist_patch_DATA): Add patches. --- gnu/local.mk | 6 +- gnu/packages/algebra.scm | 60 ++++ gnu/packages/patches/symmetrica-bruch.patch | 38 ++ gnu/packages/patches/symmetrica-int32.patch | 37 ++ .../patches/symmetrica-return_values.patch | 14 + .../patches/symmetrica-sort_sum_rename.patch | 340 ++++++++++++++++++ 6 files changed, 494 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/symmetrica-bruch.patch create mode 100644 gnu/packages/patches/symmetrica-int32.patch create mode 100644 gnu/packages/patches/symmetrica-return_values.patch create mode 100644 gnu/packages/patches/symmetrica-sort_sum_rename.patch diff --git a/gnu/local.mk b/gnu/local.mk index ac5f0e9dbf..336b5c89ed 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1282,6 +1282,7 @@ dist_patch_DATA = \ %D%/packages/patches/sssd-curl-compat.patch \ %D%/packages/patches/steghide-fixes.patch \ %D%/packages/patches/streamlink-update-test.patch \ + %D%/packages/patches/stumpwm-fix-broken-read-one-line.patch \ %D%/packages/patches/superlu-dist-awpm-grid.patch \ %D%/packages/patches/superlu-dist-fix-mpi-deprecations.patch \ %D%/packages/patches/superlu-dist-scotchmetis.patch \ @@ -1290,7 +1291,10 @@ dist_patch_DATA = \ %D%/packages/patches/swig-guile-gc.patch \ %D%/packages/patches/swish-e-search.patch \ %D%/packages/patches/swish-e-format-security.patch \ - %D%/packages/patches/stumpwm-fix-broken-read-one-line.patch \ + %D%/packages/patches/symmetrica-bruch.patch \ + %D%/packages/patches/symmetrica-int32.patch \ + %D%/packages/patches/symmetrica-return_values.patch \ + %D%/packages/patches/symmetrica-sort_sum_rename.patch \ %D%/packages/patches/t1lib-CVE-2010-2642.patch \ %D%/packages/patches/t1lib-CVE-2011-0764.patch \ %D%/packages/patches/t1lib-CVE-2011-1552+.patch \ diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 4dbf537af3..eeaee61755 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1315,3 +1315,63 @@ multiplication algorithm.") a given height bound on a hyperelliptic curve in a very efficient way, by using an optimized quadratic sieve algorithm.") (license license:gpl2+))) + +(define-public symmetrica + (package + (name "symmetrica") + (version "2.0") + (source (origin + (method url-fetch/tarbomb) + (uri (let ((v (string-join (string-split version #\.) "_"))) + (string-append "http://www.algorithm.uni-bayreuth.de/" + "en/research/SYMMETRICA/" + "SYM" v "_tar.gz"))) + (sha256 + (base32 + "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz")) + ;; Taken from + (patches (search-patches "symmetrica-bruch.patch" + "symmetrica-int32.patch" + "symmetrica-return_values.patch" + "symmetrica-sort_sum_rename.patch")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no test + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-makefile + (lambda _ + (substitute* "makefile" + (("cc -c") "gcc -c")) + #t)) + (add-after 'fix-makefile 'turn-off-banner + (lambda _ + (substitute* "de.c" + (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE"))) + #t)) + (delete 'configure) ;no configure script + (replace 'install ;no install target + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (inc (string-append out "/include/symmetrica")) + (doc (string-append out "/share/doc/symmetrica-" ,version)) + (static "libsymmetrica.a")) + ;; Build static library. + (apply invoke "ar" "crs" static (find-files "." "\\.o$")) + (invoke "ranlib" static) + ;; Install static library and headers. + (for-each (lambda (f) (install-file f inc)) + (find-files "." "\\.h$")) + (install-file "libsymmetrica.a" lib) + ;; Install documentation. + (for-each (lambda (f) (install-file f doc)) + (find-files "." "\\.doc$")) + #t)))))) + (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/") + (synopsis "Combinatoric C Library") + (description "Symmetrica is a library for combinatorics. It has support +for the representation theory of the symmetric group and related groups, +combinatorics of tableaux, symmetric functions and polynomials, Schubert +polynomials, and the representation theory of Hecke algebras of type A_n.") + (license license:public-domain))) diff --git a/gnu/packages/patches/symmetrica-bruch.patch b/gnu/packages/patches/symmetrica-bruch.patch new file mode 100644 index 0000000000..ae88b79206 --- /dev/null +++ b/gnu/packages/patches/symmetrica-bruch.patch @@ -0,0 +1,38 @@ +--- src/bruch.c 2007-12-06 11:30:00.000000000 -0500 ++++ b/bruch.c 2013-10-22 08:37:43.000000000 -0400 +@@ -975,14 +975,16 @@ + ggterg = ggt_i(S_B_UI(bruch),S_B_OI(bruch)); + + if (ggterg == S_B_UI(bruch)) { ++ INT tmp = S_B_OI(bruch); + freeself_bruch(bruch); +- M_I_I(S_B_OI(bruch) / ggterg,bruch); ++ M_I_I(tmp / ggterg,bruch); + goto ende; + } + + if (-ggterg == S_B_UI(bruch)) { ++ INT tmp = S_B_OI(bruch); + freeself_bruch(bruch); +- M_I_I(- S_B_OI(bruch) / ggterg,bruch); ++ M_I_I(- tmp / ggterg,bruch); + goto ende; + } + +@@ -1032,12 +1034,14 @@ + + if (S_O_K(S_B_U(bruch)) == INTEGER) + if (S_B_UI(bruch) == 1) { ++ INT tmp = S_B_OI(bruch); + freeself_bruch(bruch); +- M_I_I(S_B_OI(bruch),bruch); ++ M_I_I(tmp,bruch); + goto ende; } + else if (S_B_UI(bruch) == -1) { ++ INT tmp = S_B_OI(bruch); + freeself_bruch(bruch); +- M_I_I( - S_B_OI(bruch),bruch); ++ M_I_I( - tmp,bruch); + goto ende; } + if (NEGP(S_B_O(bruch)) && NEGP(S_B_U(bruch))) + { diff --git a/gnu/packages/patches/symmetrica-int32.patch b/gnu/packages/patches/symmetrica-int32.patch new file mode 100644 index 0000000000..b64f27d51e --- /dev/null +++ b/gnu/packages/patches/symmetrica-int32.patch @@ -0,0 +1,37 @@ +diff -ru src/def.h c/def.h +--- src/def.h 2007-12-06 17:30:56.000000000 +0100 ++++ c/def.h 2013-10-19 18:42:55.118745730 +0200 +@@ -2,14 +2,9 @@ + /* INT should always be 4 byte */ + #ifndef DEF_H + +- +-#ifdef __alpha +-typedef int INT; +-typedef unsigned int UINT; +-#else /* __alpha */ +-typedef long INT; +-typedef unsigned long UINT; +-#endif /* __alpha */ ++#include ++typedef int32_t INT; ++typedef uint32_t UINT; + + #include + #include +@@ -65,10 +60,13 @@ + + + /* definitionen fuer object.c */ +-typedef INT OBJECTKIND; /* 4 byte */ ++/* NOTE: partition code assumes that there is no unused space in the ++ * object struct when an INT is stored. This requires both OBJECTKIND ++ * and OBJECTSELF to have a size equal to a machine word. */ ++typedef intptr_t OBJECTKIND; + + typedef union { +- INT ob_INT; ++ intptr_t ob_INT; + INT * ob_INTpointer; + char *ob_charpointer; + struct bruch *ob_bruch; diff --git a/gnu/packages/patches/symmetrica-return_values.patch b/gnu/packages/patches/symmetrica-return_values.patch new file mode 100644 index 0000000000..e09c389337 --- /dev/null +++ b/gnu/packages/patches/symmetrica-return_values.patch @@ -0,0 +1,14 @@ +diff -ru src/part.c b/part.c +--- src/part.c Thu May 14 06:01:00 2009 -0400 ++++ b/part.c Thu May 14 06:01:00 2009 -0400 +@@ -1767,8 +1767,8 @@ + /* to compute number of partitions */ + { + INT erg = OK; +- if (ni<0) return; +- if (not EMPTYP(S_V_I(vec,ni))) return; ++ if (ni<0) return 0; ++ if (not EMPTYP(S_V_I(vec,ni))) return 0; + else if (ni<=1) M_I_I(1,S_V_I(vec,ni)); + else { + diff --git a/gnu/packages/patches/symmetrica-sort_sum_rename.patch b/gnu/packages/patches/symmetrica-sort_sum_rename.patch new file mode 100644 index 0000000000..2d9a2dae06 --- /dev/null +++ b/gnu/packages/patches/symmetrica-sort_sum_rename.patch @@ -0,0 +1,340 @@ +diff -r 5cd656a07aa5 src/bar.c +--- a/bar.c Thu May 14 06:01:00 2009 -0400 ++++ b/bar.c Thu May 14 07:38:17 2009 -0400 +@@ -237,7 +237,7 @@ + g = callocobject(); + e = S_V_I(a,0L); + f = S_V_I(a,1L); +- erg += sum(f,g); ++ erg += sym_sum(f,g); + j=0L; + for (i=0L;iob_kind = (OBJECTKIND)(b)) +--- a/nc.c Thu May 14 06:01:00 2009 -0400 ++++ b/nc.c Thu May 14 07:38:17 2009 -0400 +@@ -204,7 +204,7 @@ + erg += mult(S_NC_C(a),S_NC_C(b),d); + erg += m_gl_co(S_NC_GL(a),e); + erg += mult_apply(e,d); +- erg += sum(d,e); ++ erg += sym_sum(d,e); + erg += m_gl_go(S_NC_GL(a),d); + erg += div(e,d,c); + erg += freeall(e); +@@ -617,7 +617,7 @@ + erg += mult_nc_kranz(c,a,e); + erg += mult(S_V_I(e,1L),f,c); + erg += div(c,g,c); +- erg += sum(c,S_V_I(S_NC_C(b),S_I_I(d))); ++ erg += sym_sum(c,S_V_I(S_NC_C(b),S_I_I(d))); + } + erg += freeall(c); + erg += freeall(d); +@@ -712,7 +712,7 @@ + for(j = 0L; j=0;j--) +diff -r 5cd656a07aa5 src/perm.c +--- a/perm.c Thu May 14 06:01:00 2009 -0400 ++++ b/perm.c Thu May 14 07:38:17 2009 -0400 +@@ -833,9 +833,9 @@ + /* s = Anzahl der spalten */ + + s = S_V_LI(S_V_I(a,0L)); +- sum(S_V_I(a,0L),summe);/* composition ist vector */ ++ sym_sum(S_V_I(a,0L),summe);/* composition ist vector */ + z = S_I_I(summe); +- FREEALL(summe); ++ FREEALL(summe); + m_ilih_nm(s,z,b); + C_O_K(b,KRANZTYPUS); + for (i=0L;i Date: Thu, 20 Jun 2019 10:41:51 +0200 Subject: [PATCH 195/224] services: Fix typo in (gnu services mail) exports. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/mail.scm (define-module): Re-spell ‘%default-imap4d-config-file’. --- gnu/services/mail.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm index 216b2c80b0..0e85ada3d0 100644 --- a/gnu/services/mail.scm +++ b/gnu/services/mail.scm @@ -69,7 +69,7 @@ imap4d-configuration imap4d-configuration? imap4d-service-type - %defualt-imap4d-config-file)) + %default-imap4d-config-file)) ;;; Commentary: ;;; From 1de48e8f8afec23847458c533d2fae0d69d8942a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 20 Jun 2019 11:03:37 +0200 Subject: [PATCH 196/224] gnu: fplll: Update to 5.2.1. * gnu/packages/algebra.scm (fplll): Update to 5.2.1. [source]: Use Github tagged release: the original tarball no longer exists. [native-inputs]: Add Autoconf and al. [homepage]: Update it, the previous one no longer exists. [description]: Expound description. --- gnu/packages/algebra.scm | 62 ++++++++++++++++++++++++++++------------ 1 file changed, 44 insertions(+), 18 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index eeaee61755..8d7c9709d1 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -144,24 +144,50 @@ line applications.") (define-public fplll (package - (name "fplll") - (version "4.0.4") - (source (origin - (method url-fetch) - (uri (string-append - "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-" - version ".tar.gz")) - (sha256 (base32 - "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b")))) - (build-system gnu-build-system) - (inputs `(("gmp" ,gmp) - ("mpfr" ,mpfr))) - (synopsis "Library for LLL-reduction of euclidean lattices") - (description - "fplll LLL-reduces euclidean lattices. Since version 3, it can also -solve the shortest vector problem.") - (license license:lgpl2.1+) - (home-page "http://perso.ens-lyon.fr/damien.stehle/fplll/"))) + (name "fplll") + (version "5.2.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fplll/fplll.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (inputs + `(("gmp" ,gmp) + ("mpfr" ,mpfr))) + (home-page "https://github.com/fplll/fplll") + (synopsis "Library for LLL-reduction of euclidean lattices") + (description + "fplll contains implementations of several lattice algorithms. +The implementation relies on floating-point orthogonalization, and LLL +is central to the code, hence the name. + +It includes implementations of floating-point LLL reduction +algorithms, offering different speed/guarantees ratios. It contains +a @emph{wrapper} choosing the estimated best sequence of variants in +order to provide a guaranteed output as fast as possible. In the case +of the wrapper, the succession of variants is oblivious to the user. + +It includes an implementation of the BKZ reduction algorithm, +including the BKZ-2.0 improvements (extreme enumeration +pruning, pre-processing of blocks, early termination). Additionally, +Slide reduction and self dual BKZ are supported. + +It also includes a floating-point implementation of the +Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice +vector. For the same task, the GaussSieve algorithm is also available +in fplll. Finally, it contains a variant of the enumeration algorithm +that computes a lattice vector closest to a given vector belonging to +the real span of the lattice.") + (license license:lgpl2.1+))) (define-public pari-gp (package From 25cbaa9e705a4d8cde39b5a83c4c54114db45984 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 20 Jun 2019 11:07:12 +0200 Subject: [PATCH 197/224] gnu: Add python-fpylll. * gnu/packages/algebra.scm (python-fpylll): New variable. --- gnu/packages/algebra.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 8d7c9709d1..22d458d36d 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -189,6 +189,38 @@ that computes a lattice vector closest to a given vector belonging to the real span of the lattice.") (license license:lgpl2.1+))) +(define-public python-fpylll + (package + (name "python-fpylll") + (version "0.4.1") + (source + (origin + ;; Pypi contains and older release, so we use a tagged release from + ;; Github instead. + (method git-fetch) + (uri (git-reference + (url "https://github.com/fplll/fpylll.git") + (commit (string-append version "dev")))) + (sha256 + (base32 + "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w")))) + (build-system python-build-system) + (inputs + `(("fplll" ,fplll) + ("gmp" ,gmp) + ("mpfr" ,mpfr) + ("pari-gp" ,pari-gp))) + (propagated-inputs + `(("cysignals" ,python-cysignals) + ("cython" ,python-cython) + ("flake8" ,python-flake8) + ("numpy" ,python-numpy) + ("pytest" ,python-pytest))) + (home-page "https://github.com/fplll/fpylll") + (synopsis "Python interface for fplll") + (description "fpylll is a Python wrapper for fplll.") + (license license:gpl2+))) + (define-public pari-gp (package (name "pari-gp") From 9553a41dbee956aeece7631321fc52a264311541 Mon Sep 17 00:00:00 2001 From: Josh Holland Date: Wed, 19 Jun 2019 20:55:29 +0100 Subject: [PATCH 198/224] gnu: weechat: update to 2.5 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/irc.scm (weechat): update to 2.5 Signed-off-by: Gábor Boskovits --- gnu/packages/irc.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index d3b3a51294..851bea05bf 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -166,14 +166,14 @@ SILC and ICB protocols via plugins.") (define-public weechat (package (name "weechat") - (version "2.1") + (version "2.5") (source (origin (method url-fetch) (uri (string-append "https://weechat.org/files/src/weechat-" version ".tar.xz")) (sha256 (base32 - "0f7d2vdbxc5kgjl7lkamnbxvidgxwa8f9j3nr9fd4gr4z0gzi86d")) + "09sc5lf7z70x3iw87q4zh8rbyngsw89pwnzs5jk195zzqdspgj2j")) (patches (search-patches "weechat-python.patch")))) (build-system cmake-build-system) (native-inputs @@ -212,7 +212,7 @@ SILC and ICB protocols via plugins.") ((".*\\$\\{plugin.name\\} == (javascript|php|ruby)" all) (string-append "// SKIP" all))) (substitute* "tests/scripts/test-scripts.cpp" - ((".*\\{ \"(jvascript|php|ruby)\", " all) ; sic + ((".*\\{ \"(javascript|php|ruby)\", " all) (string-append "// SKIP" all))) #t)) (add-after 'install 'wrap From 6cbedbd2f25f7e4da057d226e0fa2ac21e2577b1 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Thu, 20 Jun 2019 11:15:37 +0200 Subject: [PATCH 199/224] gnu: Add m4rie. * gnu/packages/algebra.scm (m4rie): New variable. --- gnu/packages/algebra.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 22d458d36d..c1cbaca311 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1433,3 +1433,30 @@ for the representation theory of the symmetric group and related groups, combinatorics of tableaux, symmetric functions and polynomials, Schubert polynomials, and the representation theory of Hecke algebras of type A_n.") (license license:public-domain))) + +(define-public m4rie + (package + (name "m4rie") + (version "20150908") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://bitbucket.org/malb/m4rie") + (commit (string-append "release-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (inputs + `(("m4ri" ,m4ri))) + (synopsis "Arithmetic of dense matrices over F_{2^e}") + (description "M4RI is a library for fast arithmetic with dense matrices +over finite fields of characteristic 2. So it extends the functionality +of M4RI from F_2 to F_{2^e}.") + (license license:gpl2+) + (home-page "https://bitbucket.org/malb/m4rie/"))) From 66c67e7ba1b468dc3874fb9c84997992b7737181 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Thu, 20 Jun 2019 11:45:04 +0200 Subject: [PATCH 200/224] gnu: Add eclib. * gnu/packages/algebra.scm (eclib): New variable. --- gnu/packages/algebra.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index c1cbaca311..810e9ce12a 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1460,3 +1460,33 @@ over finite fields of characteristic 2. So it extends the functionality of M4RI from F_2 to F_{2^e}.") (license license:gpl2+) (home-page "https://bitbucket.org/malb/m4rie/"))) + +(define-public eclib + (package + (name "eclib") + (version "20190226") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JohnCremona/eclib/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1910np1xzyjzszay24xn4b81qhpsvhp5aix9vdpknplni2mq8kwb")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (inputs + `(("gmp" ,gmp) + ("ntl" ,ntl) + ("pari-gp" ,pari-gp))) + (synopsis "Ranks of elliptic curves and modular symbols") + (description "The eclib package includes mwrank (for 2-descent on +elliptic curves over Q) and modular symbol code; it has been written by +John Cremona to compute his elliptic curve database.") + (license license:gpl2+) + (home-page (string-append "http://homepages.warwick.ac.uk/staff/" + "J.E.Cremona/mwrank/index.html")))) From 197ebc36be1dd44f90bcfbbaddda8632cdeff3d2 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Thu, 20 Jun 2019 12:15:07 +0200 Subject: [PATCH 201/224] gnu: Add lrcalc. * gnu/packages/algebra.scm (lrcalc): New variable. --- gnu/packages/algebra.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 810e9ce12a..1b401f8e5b 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1490,3 +1490,39 @@ John Cremona to compute his elliptic curve database.") (license license:gpl2+) (home-page (string-append "http://homepages.warwick.ac.uk/staff/" "J.E.Cremona/mwrank/index.html")))) + +(define-public lrcalc + (package + (name "lrcalc") + (version "1.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://bitbucket.org/asbuch/lrcalc") + (commit (string-append "lrcalc-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'fix-permission + (lambda _ + (chmod "lrcalc.maple.src" #o644) + #t))))) + (synopsis "Littlewood-Richardson calculator in algebraic combinatorics") + (description "The Littlewood-Richardson Calculator (lrcalc) is a +program designed to compute Littlewood-Richardson coefficients. It computes +single Littlewood-Richardson coefficients, products of Schur functions, or +skew Schur functions. In addition it computes products in the small quantum +cohomology ring of a Grassmann variety. The software package also includes +a program that performs fast computation of the more general multiplicative +structure constants of Schubert polynomials.") + (license license:gpl2+) + (home-page "http://sites.math.rutgers.edu/~asbuch/lrcalc/"))) From e2ab228b46a879a3147d8f40d4d98d8ebb278b6b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 20 Jun 2019 12:39:21 +0200 Subject: [PATCH 202/224] Revert "gnu: Add libgd." This reverts commit 059e4c9a15b52f7e4b262e3317eac238bf53103d. --- gnu/packages/image.scm | 53 ------------------------------------------ 1 file changed, 53 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 1f6327a762..f9709e2b19 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -23,7 +23,6 @@ ;;; Copyright © 2018 Pierre-Antoine Rouby ;;; Copyright © 2018 Alex Vong ;;; Copyright © 2018 Rutger Helling -;;; Copyright © 2019 Nicolas Goaziou ;;; ;;; This file is part of GNU Guix. ;;; @@ -1649,55 +1648,3 @@ identical visual appearance.") to the standard output. It works well together with grim.") ;; MIT license. (license license:expat))) - -(define-public libgd - (package - (name "libgd") - (version "2.2.5") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/libgd/libgd.git") - (commit (string-append "gd-" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "17p0dlmn9kigr5b7vgpcsq2323mrgv0rh69x4ysg8nrjl8n5l1nl")))) - (build-system cmake-build-system) - (arguments - `(#:configure-flags - (list "-DBUILD_TEST=1" - "-DENABLE_FONTCONFIG=1" - "-DENABLE_FREETYPE=1" - "-DENABLE_JPEG=1" - "-DENABLE_PNG=1" - "-DENABLE_WEBP=1" - "-DENABLE_XPM=1" - (string-append "-DFREETYPE_INCLUDE_DIRS=" - (assoc-ref %build-inputs "freetype") - "/include/freetype2")))) - (native-inputs - `(("pkg-config" ,pkg-config))) - (inputs - `(("fontconfig" ,fontconfig) - ("freetype" ,freetype) - ("libjpeg" ,libjpeg) - ("libpng" ,libpng) - ("libwebp" ,libwebp) - ("libxmp" ,libxpm) - ("zlib" ,zlib))) - (home-page "https://libgd.github.io/") - (synopsis "GD Graphics Library") - (description "gd is a graphics library. It allows your code to -quickly draw images complete with lines, arcs, text, multiple colors, -cut and paste from other images, and flood fills, and write out the -result as a PNG or JPEG file. This is particularly useful in World -Wide Web applications, where PNG and JPEG are two of the formats -accepted for inline images by most browsers.") - ;; The project is released under a free license, which require - ;; that its terms are present in "user-accessible supporting - ;; documentation". Some files (mainly related to CMake) use - ;; alternatively GPL2+ and BSD-3 licenses. - (license (list (license:non-copyleft "file:///COPYING") - license:gpl2+ - license:bsd-3)))) From 8e590c81539a79ec19bf91d3e5f8a2c4f9a659bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 20 Jun 2019 13:12:23 +0200 Subject: [PATCH 203/224] gnu: python2-jupyter-console: Split from python-jupyter-console. * gnu/packages/python-xyz.scm (python2-jupyter-console): Implement without package-with-python2. --- gnu/packages/python-xyz.scm | 27 ++++++++++++++++++++++++++- 1 file changed, 26 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2bf98222ae..d3d3ef31d0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7593,7 +7593,32 @@ Jupyter kernels such as IJulia and IRKernel.") (license license:bsd-3))) (define-public python2-jupyter-console - (package-with-python2 python-jupyter-console)) + (package + (name "python2-jupyter-console") + (version "5.2.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "jupyter_console" version)) + (sha256 + (base32 + "1kam1qzgwr7srhm5r6aj90di5sws4bq0jmiw15452ddamb9yspal")))) + (build-system python-build-system) + ;; Tests only run in an TTY. + (arguments `(#:tests? #f)) + (propagated-inputs + `(("python2-ipykernel" ,python2-ipykernel) + ("python2-jupyter-client" ,python2-jupyter-client) + ("python2-prompt-toolkit" ,python2-prompt-toolkit-1) + ("python2-pygments" ,python2-pygments))) + (native-inputs + `(("python2-nose" ,python2-nose))) + (home-page "https://jupyter.org") + (synopsis "Jupyter terminal console") + (description "This package provides a terminal-based console frontend for +Jupyter kernels. It also allows for console-based interaction with non-Python +Jupyter kernels such as IJulia and IRKernel.") + (license license:bsd-3))) ;; The python-ipython and python-jupyter-console require each other. To get ;; the functionality in both packages working, strip down the From becb9cbfe1e2fb70da940e989f56be17abe31133 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 20 Jun 2019 13:13:00 +0200 Subject: [PATCH 204/224] gnu: python-jupyter-console: Update to 6.0.0. * gnu/packages/python-xyz.scm (python-jupyter-console): Update to 6.0.0. [arguments]: Enable tests. [propagated-inputs]: Replace python-prompt-toolkit-1 with python-prompt-toolkit. --- gnu/packages/python-xyz.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d3d3ef31d0..5e19cc9b5d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7567,21 +7567,19 @@ in the data.") (define-public python-jupyter-console (package (name "python-jupyter-console") - (version "5.2.0") + (version "6.0.0") (source (origin (method url-fetch) (uri (pypi-uri "jupyter_console" version)) (sha256 (base32 - "1kam1qzgwr7srhm5r6aj90di5sws4bq0jmiw15452ddamb9yspal")))) + "1xdjw11cppf1fxvwkw2bk13ckkwas3bdah8baingn9296mvfi31h")))) (build-system python-build-system) - ;; Tests only run in an TTY. - (arguments `(#:tests? #f)) (propagated-inputs `(("python-ipykernel" ,python-ipykernel) ("python-jupyter-client" ,python-jupyter-client) - ("python-prompt-toolkit" ,python-prompt-toolkit-1) + ("python-prompt-toolkit" ,python-prompt-toolkit) ("python-pygments" ,python-pygments))) (native-inputs `(("python-nose" ,python-nose))) From c050f1870016a6bf6e79aee8e5abe5da366fa210 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 20 Jun 2019 13:50:22 +0200 Subject: [PATCH 205/224] gnu: guile: Add 2.2.5. * gnu/packages/guile.scm (guile-2.2.5): New variable. --- gnu/packages/guile.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 67825ffc30..f0a53e7c39 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -286,6 +286,18 @@ without requiring the source code to be rewritten.") (max-silent-time . 36000))))) ;10 hours (needed on ARM ; when heavily loaded) +(define-public guile-2.2.5 + (package + (inherit guile-2.2) + (version "2.2.5") + (source (origin + (inherit (package-source guile-2.2)) + (uri (string-append "mirror://gnu/guile/guile-" version + ".tar.xz")) + (sha256 + (base32 + "19w5ws1jvs01dpv756qv2cgs37rsnwq1f4f07mj0wra35pqp6c7w")))))) + (define-public guile-next ;; This is the upcoming Guile 3.0, with JIT support. (let ((commit "6f3357b0df64c4be17e72079864c09a542f1c779") From 3149c002644b927e0245d237cdda3a6aeca00e4a Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Sun, 16 Jun 2019 16:18:29 +0200 Subject: [PATCH 206/224] utils: canonical-newline-port: Fix handling of carriage return at buffer end. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Prior to this change the added test fails for me locally at byte 1024. It might depend on some default buffer sizes. Fixes . * tests/utils.scm ("canonical-newline-port-1024"): Add test. * guix/utils.scm (canonical-newline-port): Correct comments on CR/LF. Remove CR even when they're at the end of the buffer. Signed-off-by: Ludovic Courtès --- guix/utils.scm | 6 +++--- tests/utils.scm | 6 ++++++ 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/guix/utils.scm b/guix/utils.scm index 709cdf9353..f480c3291f 100644 --- a/guix/utils.scm +++ b/guix/utils.scm @@ -718,7 +718,7 @@ environment variable name like \"XDG_CONFIG_HOME\"; SUFFIX is a suffix like (define (canonical-newline-port port) "Return an input port that wraps PORT such that all newlines consist - of a single carriage return." + of a single linefeed." (define (get-position) (if (port-has-port-position? port) (port-position port) #f)) (define (set-position! position) @@ -730,11 +730,11 @@ environment variable name like \"XDG_CONFIG_HOME\"; SUFFIX is a suffix like (let loop ((count 0) (byte (get-u8 port))) (cond ((eof-object? byte) count) + ;; XXX: consume all CRs even if not followed by LF. + ((eqv? byte (char->integer #\return)) (loop count (get-u8 port))) ((= count (- n 1)) (bytevector-u8-set! bv (+ start count) byte) n) - ;; XXX: consume all LFs even if not followed by CR. - ((eqv? byte (char->integer #\return)) (loop count (get-u8 port))) (else (bytevector-u8-set! bv (+ start count) byte) (loop (+ count 1) (get-u8 port)))))) diff --git a/tests/utils.scm b/tests/utils.scm index 44861384ab..f78ec356bd 100644 --- a/tests/utils.scm +++ b/tests/utils.scm @@ -230,6 +230,12 @@ skip these tests." "This is a journey\r\nInto the sound\r\nA journey ...\n"))) (get-string-all (canonical-newline-port port)))) +(test-equal "canonical-newline-port-1024" + (string-concatenate (make-list 100 "0123456789abcde\n")) + (let ((port (open-string-input-port + (string-concatenate + (make-list 100 "0123456789abcde\r\n"))))) + (get-string-all (canonical-newline-port port)))) (test-equal "edit-expression" "(display \"GNU Guix\")\n(newline)\n" From b46a9b9a5e833989396565c9d924cc97ce080703 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Sun, 16 Jun 2019 16:55:36 +0200 Subject: [PATCH 207/224] import: hackage: Add two expected failing test cases. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This adds failing test cases for two hackage import bugs: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=25138 https://debbugs.gnu.org/cgi/bugreport.cgi?bug=35743 * tests/hackage.scm: Make comment style consistent. Add two cabal parsing tests, marked as expected failures. Signed-off-by: Ludovic Courtès --- tests/hackage.scm | 52 +++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 50 insertions(+), 2 deletions(-) diff --git a/tests/hackage.scm b/tests/hackage.scm index 14176b2cf9..77e333cbfc 100644 --- a/tests/hackage.scm +++ b/tests/hackage.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Federico Beffa +;;; Copyright © 2019 Robert Vollmert ;;; ;;; This file is part of GNU Guix. ;;; @@ -236,7 +237,7 @@ library (test-assert "hackage->guix-package test 6" (eval-test-with-cabal test-cabal-6 match-ghc-foo-6)) -;; Check multi-line layouted description +;; Check multi-line layouted description. (define test-cabal-multiline-layout "name: foo version: 1.0.0 @@ -254,7 +255,7 @@ executable cabal (test-assert "hackage->guix-package test multiline desc (layout)" (eval-test-with-cabal test-cabal-multiline-layout match-ghc-foo)) -;; Check multi-line braced description +;; Check multi-line braced description. (define test-cabal-multiline-braced "name: foo version: 1.0.0 @@ -274,6 +275,53 @@ executable cabal (test-assert "hackage->guix-package test multiline desc (braced)" (eval-test-with-cabal test-cabal-multiline-braced match-ghc-foo)) +;; Check mixed layout. Compare e.g. warp. +(define test-cabal-mixed-layout + "name: foo +version: 1.0.0 +homepage: http://test.org +synopsis: synopsis +description: description +license: BSD3 +executable cabal + build-depends: + HTTP >= 4000.2.5 && < 4000.3, + mtl >= 2.0 && < 3 + ghc-options: -Wall +") + +;; Fails: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=35743 +(test-expect-fail 1) +(test-assert "hackage->guix-package test mixed layout" + (eval-test-with-cabal test-cabal-mixed-layout match-ghc-foo)) + +;; Check flag executable. Compare e.g. darcs. +(define test-cabal-flag-executable + "name: foo +version: 1.0.0 +homepage: http://test.org +synopsis: synopsis +description: description +license: BSD3 +flag executable + description: Build executable + default: True +executable cabal + if !flag(executable) + buildable: False + else + buildable: True + + build-depends: + HTTP >= 4000.2.5 && < 4000.3, + mtl >= 2.0 && < 3 +") + +;; Fails: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=25138 +(test-expect-fail 1) +(test-assert "hackage->guix-package test flag executable" + (eval-test-with-cabal test-cabal-flag-executable match-ghc-foo)) + ;; Check Hackage Cabal revisions. (define test-cabal-revision "name: foo From 7cb44fb5718c748a80e05a673f9b5faaa7586137 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 20 Jun 2019 14:02:27 +0200 Subject: [PATCH 208/224] gnu: ncbi-vdb: Update to 2.9.6. * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.6. [arguments]: Pass HAVE_HDF5 make flag; add build phase "patch-krypto-flags". --- gnu/packages/bioinformatics.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8002f24110..2862cb1187 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5582,7 +5582,7 @@ simultaneously.") (define-public ncbi-vdb (package (name "ncbi-vdb") - (version "2.9.3") + (version "2.9.6") (source (origin (method git-fetch) (uri (git-reference @@ -5591,11 +5591,12 @@ simultaneously.") (file-name (git-file-name name version)) (sha256 (base32 - "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm")))) + "0knkj1sq34hlivgv5qd6jlczqrs3ldmfgn6vbbw7p4mqxvb9mirk")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported #:tests? #f ; no "check" target + #:make-flags '("HAVE_HDF5=1") #:phases (modify-phases %standard-phases (add-after 'unpack 'make-files-writable @@ -5607,6 +5608,13 @@ simultaneously.") (string-append (getcwd) "/setup:" (getenv "PERL5LIB"))) #t)) + ;; See https://github.com/ncbi/ncbi-vdb/issues/14 + (add-after 'unpack 'patch-krypto-flags + (lambda _ + (substitute* "libs/krypto/Makefile" + (("-Wa,-march=generic64\\+aes") "") + (("-Wa,-march=generic64\\+sse4") "")) + #t)) (replace 'configure (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) From 20874b7044ec3ee28dc8302dc79e3623f6aae53b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 20 Jun 2019 14:30:24 +0200 Subject: [PATCH 209/224] gnu: sra-tools: Update to 2.9.6. * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2862cb1187..c30b12dfab 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5941,7 +5941,7 @@ sequence itself can be retrieved from these databases.") (define-public sra-tools (package (name "sra-tools") - (version "2.9.3") + (version "2.9.6") (source (origin (method git-fetch) @@ -5951,7 +5951,7 @@ sequence itself can be retrieved from these databases.") (file-name (git-file-name name version)) (sha256 (base32 - "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b")))) + "0vqzap68v81k0zif2mnqfy8pnw2nrhsg87p6mgq8qk3nk2jv2rgy")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported From 30adfd36007884695d792eb78886d42e69266270 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 20 Jun 2019 14:33:45 +0200 Subject: [PATCH 210/224] gnu: ngs-sdk: Update to 2.9.6. * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c30b12dfab..8cbb2e10d0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5516,7 +5516,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (define-public ngs-sdk (package (name "ngs-sdk") - (version "2.9.3") + (version "2.9.6") (source (origin (method git-fetch) (uri (git-reference @@ -5525,7 +5525,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (file-name (git-file-name name version)) (sha256 (base32 - "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3")))) + "0d5k5kabgl15as37kj9x65xc92j4gcqms86hvihw3yb6wag0r0q3")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported From ace8e269a40b31a9c6f413c0674529880da6a48e Mon Sep 17 00:00:00 2001 From: Kristofer Buffington Date: Wed, 12 Jun 2019 16:34:30 -0400 Subject: [PATCH 211/224] services: opensmtpd: Extend the PAM service. * gnu/services/mail.scm (%opensmtpd-pam-services): New variable. (opensmtpd-service-type)[extensions]: Add it, extending PAM-ROOT-SERVICE-TYPE. Signed-off-by: Tobias Geerinckx-Rice --- gnu/services/mail.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm index 0e85ada3d0..3de0b4c2f3 100644 --- a/gnu/services/mail.scm +++ b/gnu/services/mail.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2017, 2018 Clément Lassieur ;;; Copyright © 2017 Carlo Zancanaro ;;; Copyright © 2017 Tobias Geerinckx-Rice +;;; Copyright © 2019 Kristofer Buffington ;;; ;;; This file is part of GNU Guix. ;;; @@ -1667,6 +1668,9 @@ accept from local for any relay (mkdir-p "/var/spool/smtpd") (chmod "/var/spool/smtpd" #o711)))))) +(define %opensmtpd-pam-services + (list (unix-pam-service "smtpd"))) + (define opensmtpd-service-type (service-type (name 'opensmtpd) @@ -1675,6 +1679,8 @@ accept from local for any relay (const %opensmtpd-accounts)) (service-extension activation-service-type opensmtpd-activation) + (service-extension pam-root-service-type + (const %opensmtpd-pam-services)) (service-extension profile-service-type (compose list opensmtpd-configuration-package)) (service-extension shepherd-root-service-type From 264334716f0ecc41d022a72cdaa7e737106d546f Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Thu, 20 Jun 2019 16:44:53 +0200 Subject: [PATCH 212/224] gnu: Add ppl. * gnu/packages/maths.scm (ppl): New variable. --- gnu/packages/maths.scm | 41 ++++++++++++++++++++++++++++++++++++++++- 1 file changed, 40 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 6d8fb9cec5..c2c7a57d75 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge +;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge ;;; Copyright © 2013 Nikita Karetnikov ;;; Copyright © 2014, 2016, 2017 John Darrington ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Eric Bavier @@ -5003,3 +5003,42 @@ command-line tools, and an Application Programming Interface (API). This package provides the static libraries required to run programs compiled against the nauty library.") (license license:asl2.0))) + +(define-public ppl + (package + (name "ppl") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://www.bugseng.com/products/ppl/download/" + "ftp/releases/" version + "/ppl-" version ".tar.gz")) + (sha256 + (base32 + "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb")))) + (build-system gnu-build-system) + (native-inputs + `(("m4", m4))) + (inputs + `(("glpk" ,glpk) + ("gmp", gmp))) + (home-page "https://www.bugseng.com/parma-polyhedra-library") + (synopsis + "Parma Polyhedra Library for computations with polyhedra") + (description + "The Parma Polyhedra Library (PPL) provides numerical abstractions +especially targeted at applications in the field of analysis and +verification of complex systems. These abstractions include convex +polyhedra, defined as the intersection of a finite number of (open or +closed) halfspaces, each described by a linear inequality (strict or +non-strict) with rational coefficients; some special classes of polyhedra +shapes that offer interesting complexity/precision tradeoffs; and grids +which represent regularly spaced points that satisfy a set of linear +congruence relations. The library also supports finite powersets and +products of (any kind of) polyhedra and grids, a mixed integer linear +programming problem solver using an exact-arithmetic version of the simplex +algorithm, a parametric integer programming solver, and primitives for +termination analysis via the automatic synthesis of linear ranking +functions.") + (license license:gpl3+))) From eacf29835dac41240fc63e080572998cd5982775 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Thu, 20 Jun 2019 17:36:39 +0200 Subject: [PATCH 213/224] gnu: Add iml. * gnu/packages/algebra.scm (iml): New variable. --- gnu/packages/algebra.scm | 56 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 1b401f8e5b..561347ad98 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1526,3 +1526,59 @@ a program that performs fast computation of the more general multiplicative structure constants of Schubert polynomials.") (license license:gpl2+) (home-page "http://sites.math.rutgers.edu/~asbuch/lrcalc/"))) + +(define-public iml + (package + (name "iml") + (version "1.0.5") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-" + version ".tar.bz2")) + (sha256 + (base32 + "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x")))) + (build-system gnu-build-system) + (inputs + `(("gmp", gmp) + ("cblas" ,openblas))) ; or any other BLAS library; the documentation + ; mentions ATLAS in particular + (arguments + `(#:configure-flags + (list + (string-append "--with-gmp-include=" + (assoc-ref %build-inputs "gmp") "/include") + (string-append "--with-gmp-lib=" + (assoc-ref %build-inputs "gmp") "/lib") + "--with-cblas=-lopenblas" + (string-append "--with-cblas-include=" + (assoc-ref %build-inputs "cblas") "/include") + (string-append "--with-cblas-lib=" + (assoc-ref %build-inputs "cblas") "/lib")))) + (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html") + (synopsis + "Solver for systems of linear equations over the integers") + (description + "IML is a C library implementing algorithms for computing exact +solutions to dense systems of linear equations over the integers. +Currently, IML provides the following functionality: + +@itemize +@item Nonsingular rational system solving: +compute the unique rational solution X to the system AX=B, where A and B +are integer matrices, A nonsingular. +@item Compute the right nullspace or kernel of an integer matrix. +@item Certified linear system solving: +compute a minimal denominator solution x to a system Ax=b, where b is an +integer vector and A is an integer matrix with arbitrary shape and +rank profile. +@end itemize + +In addition, IML provides some low level routines for a variety of mod p +matrix operations: computing the row-echelon form, determinant, rank +profile, and inverse of a mod p matrix. These mod p routines are not +general purpose; they require that p satisfy some preconditions based on +the dimension of the input matrix (usually p should be prime and should be +no more than about 20 bits long).") + (license license:bsd-3))) From 78407a27cf69ef5bbc4facbb5b483a7e62de1b84 Mon Sep 17 00:00:00 2001 From: Giovanni Biscuolo Date: Wed, 19 Jun 2019 18:47:36 +0200 Subject: [PATCH 214/224] licenses: Add Historical Permission Notice and Disclaimer license * gnu/licenses.scm (hpnd): New variable. --- guix/licenses.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/guix/licenses.scm b/guix/licenses.scm index 65d9c3da13..41d4fefad2 100644 --- a/guix/licenses.scm +++ b/guix/licenses.scm @@ -94,6 +94,7 @@ fsf-free wtfpl2 wxwindows3.1+ + hpnd fsdg-compatible)) (define-record-type @@ -628,6 +629,11 @@ which may be a file:// URI pointing the package's tree." "http://www.gzip.org/zlib/zlib_license.html" "https://www.gnu.org/licenses/license-list#ZLib")) +(define hpnd + (license "HPND" + "https://directory.fsf.org/wiki/License:HPND" + "https://www.gnu.org/licenses/license-list#HPND")) + (define* (fsf-free uri #:optional (comment "")) "Return a license that does not fit any of the ones above or a collection of licenses, approved as free by the FSF. More details can be found at URI." From 28618b05f002720bc56bae76659717a0eba4dd8b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 20 Jun 2019 22:29:07 +0200 Subject: [PATCH 215/224] gnu: pigx-rnaseq: Update to 0.0.7. * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7. [inputs]: Add coreutils and sed. --- gnu/packages/bioinformatics.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8cbb2e10d0..f1a73bca7e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12544,15 +12544,15 @@ once. This package provides tools to perform Drop-seq analyses.") (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.6") + (version "0.0.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" - "releases/download/v." version + "releases/download/v" version "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "1w7cwbbz1sbvbyqh5c60iqcjfs3qsppmdgxqa1i0w5wwb9mkh27m")))) + "013inbh22bjvwg2w0kx5i42k66w1zl4310ldip2ax6msgprs2ydj")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported @@ -12567,7 +12567,9 @@ once. This package provides tools to perform Drop-seq analyses.") (("^ test.sh") "")) #t))))) (inputs - `(("gzip" ,gzip) + `(("coreutils" ,coreutils) + ("sed" ,sed) + ("gzip" ,gzip) ("snakemake" ,snakemake) ("fastqc" ,fastqc) ("multiqc" ,multiqc) From 377bd155ea4d8de5dc0bf6ee6cd46d8aff16a769 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 15 Jun 2019 13:48:46 +0200 Subject: [PATCH 216/224] gnu: dbus: Fix CVE-2019-12749. * gnu/packages/patches/dbus-CVE-2019-12749.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/glib.scm (dbus)[replacement]: New field. (dbus/fixed): New variable. --- gnu/local.mk | 1 + gnu/packages/glib.scm | 9 ++ .../patches/dbus-CVE-2019-12749.patch | 116 ++++++++++++++++++ 3 files changed, 126 insertions(+) create mode 100644 gnu/packages/patches/dbus-CVE-2019-12749.patch diff --git a/gnu/local.mk b/gnu/local.mk index 336b5c89ed..649d901bf3 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -740,6 +740,7 @@ dist_patch_DATA = \ %D%/packages/patches/cursynth-wave-rand.patch \ %D%/packages/patches/cvs-2017-12836.patch \ %D%/packages/patches/dbus-helper-search-path.patch \ + %D%/packages/patches/dbus-CVE-2019-12749.patch \ %D%/packages/patches/dealii-mpi-deprecations.patch \ %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \ %D%/packages/patches/dfu-programmer-fix-libusb.patch \ diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index 7af7c86853..d75b963794 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -80,6 +80,7 @@ (package (name "dbus") (version "1.12.12") + (replacement dbus/fixed) (source (origin (method url-fetch) (uri (string-append @@ -146,6 +147,14 @@ or through unencrypted TCP/IP suitable for use behind a firewall with shared NFS home directories.") (license license:gpl2+))) ; or Academic Free License 2.1 +(define dbus/fixed + (package + (inherit dbus) + (source (origin + (inherit (package-source dbus)) + (patches (append (search-patches "dbus-CVE-2019-12749.patch") + (origin-patches (package-source dbus)))))))) + (define glib (package (name "glib") diff --git a/gnu/packages/patches/dbus-CVE-2019-12749.patch b/gnu/packages/patches/dbus-CVE-2019-12749.patch new file mode 100644 index 0000000000..12106f4589 --- /dev/null +++ b/gnu/packages/patches/dbus-CVE-2019-12749.patch @@ -0,0 +1,116 @@ +From 47b1a4c41004bf494b87370987b222c934b19016 Mon Sep 17 00:00:00 2001 +From: Simon McVittie +Date: Thu, 30 May 2019 12:53:03 +0100 +Subject: [PATCH] auth: Reject DBUS_COOKIE_SHA1 for users other than the server + owner + +The DBUS_COOKIE_SHA1 authentication mechanism aims to prove ownership +of a shared home directory by having the server write a secret "cookie" +into a .dbus-keyrings subdirectory of the desired identity's home +directory with 0700 permissions, and having the client prove that it can +read the cookie. This never actually worked for non-malicious clients in +the case where server uid != client uid (unless the server and client +both have privileges, such as Linux CAP_DAC_OVERRIDE or traditional +Unix uid 0) because an unprivileged server would fail to write out the +cookie, and an unprivileged client would be unable to read the resulting +file owned by the server. + +Additionally, since dbus 1.7.10 we have checked that ~/.dbus-keyrings +is owned by the uid of the server (a side-effect of a check added to +harden our use of XDG_RUNTIME_DIR), further ruling out successful use +by a non-malicious client with a uid differing from the server's. + +Joe Vennix of Apple Information Security discovered that the +implementation of DBUS_COOKIE_SHA1 was susceptible to a symbolic link +attack: a malicious client with write access to its own home directory +could manipulate a ~/.dbus-keyrings symlink to cause the DBusServer to +read and write in unintended locations. In the worst case this could +result in the DBusServer reusing a cookie that is known to the +malicious client, and treating that cookie as evidence that a subsequent +client connection came from an attacker-chosen uid, allowing +authentication bypass. + +This is mitigated by the fact that by default, the well-known system +dbus-daemon (since 2003) and the well-known session dbus-daemon (in +stable releases since dbus 1.10.0 in 2015) only accept the EXTERNAL +authentication mechanism, and as a result will reject DBUS_COOKIE_SHA1 +at an early stage, before manipulating cookies. As a result, this +vulnerability only applies to: + +* system or session dbus-daemons with non-standard configuration +* third-party dbus-daemon invocations such as at-spi2-core (although + in practice at-spi2-core also only accepts EXTERNAL by default) +* third-party uses of DBusServer such as the one in Upstart + +Avoiding symlink attacks in a portable way is difficult, because APIs +like openat() and Linux /proc/self/fd are not universally available. +However, because DBUS_COOKIE_SHA1 already doesn't work in practice for +a non-matching uid, we can solve this vulnerability in an easier way +without regressions, by rejecting it early (before looking at +~/.dbus-keyrings) whenever the requested identity doesn't match the +identity of the process hosting the DBusServer. + +Signed-off-by: Simon McVittie +Closes: https://gitlab.freedesktop.org/dbus/dbus/issues/269 +Closes: CVE-2019-12749 +--- + dbus/dbus-auth.c | 32 ++++++++++++++++++++++++++++++++ + 1 file changed, 32 insertions(+) + +diff --git a/dbus/dbus-auth.c b/dbus/dbus-auth.c +index 37d8d4c9..7390a9d5 100644 +--- a/dbus/dbus-auth.c ++++ b/dbus/dbus-auth.c +@@ -529,6 +529,7 @@ sha1_handle_first_client_response (DBusAuth *auth, + DBusString tmp2; + dbus_bool_t retval = FALSE; + DBusError error = DBUS_ERROR_INIT; ++ DBusCredentials *myself = NULL; + + _dbus_string_set_length (&auth->challenge, 0); + +@@ -565,6 +566,34 @@ sha1_handle_first_client_response (DBusAuth *auth, + return FALSE; + } + ++ myself = _dbus_credentials_new_from_current_process (); ++ ++ if (myself == NULL) ++ goto out; ++ ++ if (!_dbus_credentials_same_user (myself, auth->desired_identity)) ++ { ++ /* ++ * DBUS_COOKIE_SHA1 is not suitable for authenticating that the ++ * client is anyone other than the user owning the process ++ * containing the DBusServer: we probably aren't allowed to write ++ * to other users' home directories. Even if we can (for example ++ * uid 0 on traditional Unix or CAP_DAC_OVERRIDE on Linux), we ++ * must not, because the other user controls their home directory, ++ * and could carry out symlink attacks to make us read from or ++ * write to unintended locations. It's difficult to avoid symlink ++ * attacks in a portable way, so we just don't try. This isn't a ++ * regression, because DBUS_COOKIE_SHA1 never worked for other ++ * users anyway. ++ */ ++ _dbus_verbose ("%s: client tried to authenticate as \"%s\", " ++ "but that doesn't match this process", ++ DBUS_AUTH_NAME (auth), ++ _dbus_string_get_const_data (data)); ++ retval = send_rejected (auth); ++ goto out; ++ } ++ + /* we cache the keyring for speed, so here we drop it if it's the + * wrong one. FIXME caching the keyring here is useless since we use + * a different DBusAuth for every connection. +@@ -679,6 +708,9 @@ sha1_handle_first_client_response (DBusAuth *auth, + _dbus_string_zero (&tmp2); + _dbus_string_free (&tmp2); + ++ if (myself != NULL) ++ _dbus_credentials_unref (myself); ++ + return retval; + } + From bd9d72067e1469a1530a4b04427f25e93b37caac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 17 Jun 2019 18:26:21 +0200 Subject: [PATCH 217/224] gnu: python-unidecode: Update to 1.1.0. * gnu/packages/python-xyz.scm (python-unidecode): Update to 1.1.0. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5e19cc9b5d..c329a2cfbb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2063,13 +2063,13 @@ cutting and pasting that code over and over.") (define-public python-unidecode (package (name "python-unidecode") - (version "1.0.23") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "Unidecode" version)) (sha256 (base32 - "1ysjbr3nqfqj97h8zyj3v9pya413vkv7a1mzml80w37xx15kb1cb")))) + "00pi0czzwvbf7djhkkjyvimj60wqdx0llbddzfnax650g9b8yscc")))) (build-system python-build-system) (home-page "https://pypi.python.org/pypi/Unidecode") (synopsis "ASCII transliterations of Unicode text") From b549a053531539c15c2d3d321c180e8feb3890be Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 18 Jun 2019 18:28:04 +0200 Subject: [PATCH 218/224] gnu: Use HTTPS for sphinx-doc.org. * gnu/packages/sphinx.scm (python-sphinx, python-sphinxcontrib-websupport)[home-page]: Use HTTPS. --- gnu/packages/sphinx.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 1bc7149c24..0a7fc9606a 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -90,7 +90,7 @@ ("python-mock" ,python-mock) ("python-nose" ,python-nose) ("python-pytest" ,python-pytest))) - (home-page "http://sphinx-doc.org/") + (home-page "https://sphinx-doc.org/") (synopsis "Python documentation generator") (description "Sphinx is a tool that makes it easy to create documentation for Python projects or other documents consisting of multiple reStructuredText @@ -341,7 +341,7 @@ SVG images natively (e.g. LaTeX).") (arguments ;; FIXME: Tests depend on Sphinx, which depends on this. `(#:tests? #f)) - (home-page "http://sphinx-doc.org/") + (home-page "https://sphinx-doc.org/") (synopsis "Sphinx API for web applications") (description "This package provides a Python API to easily integrate Sphinx documentation into your web application. It provides tools to From 3df7b15e6c9a11cedba1451f0459c715b8ce3ca1 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Tue, 18 Jun 2019 14:55:30 -0500 Subject: [PATCH 219/224] gnu: ungoogled-chromium: Install icons. * gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Install icons. Signed-off-by: Marius Bakke --- gnu/packages/chromium.scm | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index 2127e402d7..3a242220f6 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019 Marius Bakke +;;; Copyright © 2019 Alex Griffin ;;; ;;; This file is part of GNU Guix. ;;; @@ -650,12 +651,6 @@ from forcing GEXP-PROMISE." (scandir "." (cut regexp-exec install-regexp <>))) (copy-file "chrome" (string-append lib "/chromium")) - ;; TODO: Install icons from "../../chrome/app/themes" into - ;; "out/share/icons/hicolor/$size". - (install-file - "product_logo_48.png" - (string-append out "/share/icons/48x48/chromium.png")) - (copy-recursively "locales" locales) (copy-recursively "resources" resources) @@ -669,8 +664,18 @@ from forcing GEXP-PROMISE." (,(string-append lib ":" nss "/lib/nss:" mesa "/lib:" udev "/lib"))) ;; Avoid file manager crash. See . - `("XDG_DATA_DIRS" ":" prefix (,(string-append gtk+ "/share")))) - #t))))))) + `("XDG_DATA_DIRS" ":" prefix (,(string-append gtk+ "/share"))))) + + (with-directory-excursion "chrome/app/theme/chromium" + (for-each + (lambda (size) + (let ((icons (string-append out "/share/icons/hicolor/" + size "x" size "/apps"))) + (mkdir-p icons) + (copy-file (string-append "product_logo_" size ".png") + (string-append icons "/chromium.png")))) + '("22" "24" "48" "64" "128" "256"))) + #t)))))) (native-inputs `(("bison" ,bison) ("gcc" ,gcc-8) From e4386b334a45bef32567de1a6b92e3079f79e3ef Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 20 Jun 2019 13:22:57 +0200 Subject: [PATCH 220/224] gnu: openh264: Update to 2.0.0. * gnu/packages/video.scm (openh264): Update to 2.0.0. [source](uri): Adjust file name. --- gnu/packages/video.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 643a40ed77..028a3b786f 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2678,16 +2678,16 @@ of modern, widely supported codecs.") (define-public openh264 (package (name "openh264") - (version "1.8.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/cisco/" name "/releases/download/v" - version "/Source.Code.tar.gz.gz")) + version "/Source.Code.tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0niha3wnn1jsndvz9vfwy2wyql8mp9j6v75vjsipy0idwan5yzgf")))) + "0iq802xfsfkskg6q1j0kg90xh04vv1sxf61mrmahgynz5d7hx2ii")))) (build-system gnu-build-system) (native-inputs `(("nasm" ,nasm) From cee835897b298bb51d2ee7ea1dabc350d5fabcfe Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 20 Jun 2019 13:23:25 +0200 Subject: [PATCH 221/224] gnu: ungoogled-chromium: Update to 75.0.3770.100-0.5d8abc3. * gnu/packages/chromium.scm (%chromium-version): Set to 75.0.3770.100. (%chromium-origin): Update hash. --- gnu/packages/chromium.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index 3a242220f6..f3f91cc603 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -227,7 +227,7 @@ from forcing GEXP-PROMISE." #:system system #:guile-for-build guile))) -(define %chromium-version "75.0.3770.90") +(define %chromium-version "75.0.3770.100") (define %ungoogled-revision "5d8abc38b43a62f379615a0dc972b29d9aebb4b4") (define %debian-revision "debian/75.0.3770.90-1") (define package-revision "0") @@ -243,7 +243,7 @@ from forcing GEXP-PROMISE." %chromium-version ".tar.xz")) (sha256 (base32 - "0f9qjhxvk8sajj7qa061crfmln65q7sniylrgp0qijwyw6xrmddi")))) + "187wfdxw6ji4302pbn0kyi9b859ydri7gns0wlsrd7vd3c8604wy")))) (define %ungoogled-origin (origin From 0605d939a91e9aa945bb09c2f41d4421dc1c6c0b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 20 Jun 2019 13:27:32 +0200 Subject: [PATCH 222/224] gnu: samba: Update to 4.10.5 [fixes CVE-2019-12435, CVE-2019-12436]. * gnu/packages/samba.scm (samba): Update to 4.10.5. --- gnu/packages/samba.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm index 7803a1c8d1..812a36ca9a 100644 --- a/gnu/packages/samba.scm +++ b/gnu/packages/samba.scm @@ -153,14 +153,14 @@ anywhere.") (define-public samba (package (name "samba") - (version "4.10.4") + (version "4.10.5") (source (origin (method url-fetch) (uri (string-append "https://download.samba.org/pub/samba/stable/" "samba-" version ".tar.gz")) (sha256 (base32 - "0xhfbh42dihccc85ffx243lyhf3jnphhi6xfcsr3a6mhsm7w1p26")))) + "0xb3mz38hcayqxchk0ws9mxn10vswsn97jbxl4gcwi4cbrnjc43c")))) (build-system gnu-build-system) (arguments `(#:phases From 9a2e5fe5fdcc6ea848ceeefa0f70147dfb360639 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 20 Jun 2019 22:47:36 +0200 Subject: [PATCH 223/224] gnu: ungoogled-chromium: Disable parallel build. * gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Set #:parallel-build? #f. Adjust 'build' phase to account for it. --- gnu/packages/chromium.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index f3f91cc603..a1e40b9ba0 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -404,6 +404,9 @@ from forcing GEXP-PROMISE." (build-system gnu-build-system) (arguments `(#:tests? #f + ;; Chromiums build processes may consume up to 8GiB of memory per core. + ;; Disable parallel builds to avoid thrashing end user systems. + #:parallel-build? #f ;; FIXME: Chromiums RUNPATH lacks entries for some libraries, so ;; we have to disable validation and add a wrapper below. #:validate-runpath? #f @@ -605,9 +608,11 @@ from forcing GEXP-PROMISE." (format #t "Dumping configure flags...\n") (invoke "gn" "args" "out/Release" "--list")))) (replace 'build - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key (parallel-build? #t) #:allow-other-keys) (invoke "ninja" "-C" "out/Release" - "-j" (number->string (parallel-job-count)) + "-j" (if parallel-build? + (number->string (parallel-job-count)) + "1") "chrome" "chromedriver"))) (replace 'install From 010689e7067df1288af29176f4a8639de816b1ef Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 20 Jun 2019 23:19:09 +0200 Subject: [PATCH 224/224] gnu: python-sphinx: Update to 2.1.2. * gnu/packages/sphinx.scm (python-sphinx): Update to 2.1.2. --- gnu/packages/sphinx.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index a5773c21e5..5ec769388a 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -45,14 +45,14 @@ (define-public python-sphinx (package (name "python-sphinx") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (pypi-uri "Sphinx" version)) (sha256 (base32 - "1ym150xpzc2nsv8zy77q3q4gxgwfnfvd7459dykzmiw6wxk3250m")))) + "09y4mjmbxz94pmfr2lzf1hkx2xk0khcpb8xsqfmir4l7dds9x9zr")))) (build-system python-build-system) (arguments `(#:phases