From 7eed584507738c11df178740bba2980f1e4d307e Mon Sep 17 00:00:00 2001 From: Giacomo Leidi Date: Sun, 16 Feb 2020 22:21:32 +0100 Subject: gnu: Add lodepng. * gnu/packages/image.scm (lodepng): New variable. Signed-off-by: Marius Bakke --- gnu/packages/image.scm | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index f9da1e9e89..106b733673 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 © 2020 Giacomo Leidi ;;; ;;; This file is part of GNU Guix. ;;; @@ -1844,3 +1845,58 @@ using only text tools. SNG is implemented by a compiler/decompiler called sng that losslessly translates between SNG and PNG.") (license license:zlib))) + +(define-public lodepng + ;; There are no tags in the repository, so we take the version as defined in + ;; lodepng.cpp. + (let ((commit "48e5364ef48ec2408f44c727657ac1b6703185f8") + (revision "1") + (version "20200215")) + (package + (name "lodepng") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/lvandeve/lodepng") + (commit commit))) + (sha256 + (base32 + "1a1x8ag2scanzb2066jm9hg2y9kaa3wmpgmz10l1x9bkpik612lw")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (setenv "CXXFLAGS" "-fPIC") + (invoke "make" "lodepng.o") + (invoke "make" "lodepng_util.o") + (invoke "g++" "-fPIC" "-O3" + "-o" "liblodepng.so" + "-shared" "lodepng.o" "lodepng_util.o") + #t)) + (replace 'check + (lambda _ + (invoke "make" "unittest") + (invoke "./unittest") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (doc (string-append out "/share/doc")) + (lib (string-append out "/lib")) + (include (string-append out "/include"))) + (install-file "lodepng.h" include) + (install-file "lodepng_util.h" include) + (install-file "liblodepng.so" lib) + (install-file "README.md" doc) + #t)))))) + (home-page "https://lodev.org/lodepng/") + (synopsis "PNG encoder and decoder in C and C++, without dependencies") + (description "LodePNG is a PNG image decoder and encoder, all in one, +no dependency or linkage required. It's made for C (ISO C90), and has a C++ +wrapper with a more convenient interface on top.") + (license license:zlib)))) -- cgit v1.2.3 From 2e0787a5750dc4682505e284f3a0b399c99985db Mon Sep 17 00:00:00 2001 From: Giacomo Leidi Date: Sun, 16 Feb 2020 22:42:42 +0100 Subject: gnu: Add libtcod. * gnu/packages/game-development.scm (libtcod): New variable. Signed-off-by: Marius Bakke --- gnu/packages/game-development.scm | 74 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 74 insertions(+) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 24527abae1..05e026a846 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2019 Jethro Cao ;;; Copyright © 2020 Nicolas Goaziou ;;; Copyright © 2020 Timotej Lazar +;;; Copyright © 2020 Giacomo Leidi ;;; ;;; This file is part of GNU Guix. ;;; @@ -88,6 +89,7 @@ #:use-module (gnu packages sphinx) #:use-module (gnu packages stb) #:use-module (gnu packages texinfo) + #:use-module (gnu packages textutils) #:use-module (gnu packages tls) #:use-module (gnu packages video) #:use-module (gnu packages web) @@ -2114,3 +2116,75 @@ computer games, 3D authoring tools and simulation tools.") (description "Chipmunk is a simple, lightweight, fast and portable 2D rigid body physics library written in C.") (license license:expat))) + +(define-public libtcod + (package + (name "libtcod") + (version "1.15.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/libtcod/libtcod.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0pzr8ajmbqvh43ldjajx962xirj3rf8ayh344p6mqlrmb8gxrfr5")) + (modules '((guix build utils))) + (snippet '(begin + (delete-file-recursively "src/vendor/utf8proc") + (delete-file-recursively "src/vendor/zlib") + (delete-file "src/vendor/stb_truetype.h") + (delete-file "src/vendor/stb_sprintf.h") + (delete-file "src/vendor/lodepng.cpp") + (delete-file "src/vendor/lodepng.h") + + (substitute* "buildsys/autotools/sources.am" + (("\\.\\./\\.\\./src/vendor/lodepng\\.cpp \\\\\n") "") + (("\\.\\./\\.\\./src/vendor/stb\\.c \\\\") + "../../src/vendor/stb.c") + (("\\.\\./\\.\\./src/vendor/utf8proc/utf8proc\\.c") "")) + + (substitute* "src/libtcod/sys_sdl_img_png.cpp" + (("\\.\\./vendor/") "")) + + (substitute* '("src/libtcod/color/canvas.cpp" + "src/libtcod/sys_sdl_img_png.cpp" + "src/libtcod/tileset/truetype.cpp" + "src/libtcod/tileset/tilesheet.cpp") + (("\\.\\./\\.\\./vendor/") "")) + + (substitute* "src/libtcod/console/printing.cpp" + (("\\.\\./\\.\\./vendor/utf8proc/") "")) + #t)))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags '("--with-gnu-ld" + "LIBS=-lutf8proc -llodepng") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'change-to-build-dir + (lambda _ + (chdir "buildsys/autotools") + (patch-shebang "get_version.py") + #t))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("python" ,python) + ("pkg-config" ,pkg-config) + ("stb-sprintf" ,stb-sprintf) + ("stb-truetype" ,stb-truetype))) + (inputs + `(("lodepng" ,lodepng) + ("sdl2" ,sdl2) + ("utf8proc" ,utf8proc) + ("zlib" ,zlib))) + (home-page "https://github.com/libtcod/libtcod") + (synopsis "Library specifically designed for writing roguelikes") + (description + "libtcod is a fast, portable and uncomplicated API for roguelike +developers providing an advanced true color console, input, and lots of other +utilities frequently used in roguelikes.") + (license license:bsd-3))) -- cgit v1.2.3 From 25590118ad1a9e93b9f438c668bf1de020fd36d2 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 24 Feb 2020 22:46:03 +0100 Subject: gnu: Add ld wrapper variant that supports quotes in response files. * gnu/packages/ld-wrapper-next.in: New file. * gnu/local.mk (MISC_DISTRO_FILES): Adjust accordingly. * gnu/packages/chromium.scm (ld-wrapper-next): New variable. --- gnu/local.mk | 3 +- gnu/packages/chromium.scm | 15 +- gnu/packages/ld-wrapper-next.in | 305 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 321 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/ld-wrapper-next.in diff --git a/gnu/local.mk b/gnu/local.mk index b85c289c4e..857345cfad 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1515,4 +1515,5 @@ dist_patch_DATA = \ %D%/packages/patches/xsane-tighten-default-umask.patch MISC_DISTRO_FILES = \ - %D%/packages/ld-wrapper.in + %D%/packages/ld-wrapper.in \ + %D%/packages/ld-wrapper-next.in diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index 49ad8de84c..06e259b985 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -70,7 +70,8 @@ #:use-module (gnu packages xml) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg) - #:use-module (ice-9 match)) + #:use-module (ice-9 match) + #:use-module (srfi srfi-1)) (define %preserved-third-party-files '("base/third_party/cityhash" ;Expat @@ -423,6 +424,18 @@ from forcing GEXP-PROMISE." `(cons "--enable-custom-modes" ,flags)))))) +;; Add a custom ld wrapper that supports quoted strings in response files. +;; To be merged with 'ld-wrapper' in a future rebuild cycle. +(define-public ld-wrapper-next + (let ((orig (car (assoc-ref (%final-inputs) "ld-wrapper")))) + (package + (inherit orig) + (name "ld-wrapper-next") + (inputs + `(("wrapper" ,(search-path %load-path + "gnu/packages/ld-wrapper-next.in")) + ,@(alist-delete "wrapper" (package-inputs orig))))))) + (define-public ungoogled-chromium (package (name "ungoogled-chromium") diff --git a/gnu/packages/ld-wrapper-next.in b/gnu/packages/ld-wrapper-next.in new file mode 100644 index 0000000000..5d5756f6a3 --- /dev/null +++ b/gnu/packages/ld-wrapper-next.in @@ -0,0 +1,305 @@ +#!@BASH@ +# -*- mode: scheme; coding: utf-8; -*- + +# XXX: We have to go through Bash because there's no command-line switch to +# augment %load-compiled-path, and because of the silly 127-byte limit for +# the shebang line in Linux. +# Use `load-compiled' because `load' (and `-l') doesn't otherwise load our +# .go file (see ). +# Unset 'GUILE_LOAD_COMPILED_PATH' to make sure we do not stumble upon +# incompatible .go files. See +# . + +unset GUILE_LOAD_COMPILED_PATH +main="(@ (gnu build-support ld-wrapper) ld-wrapper)" +exec @GUILE@ -c "(load-compiled \"@SELF@.go\") (apply $main (cdr (command-line)))" "$@" +!# +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2020 Marius Bakke +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu build-support ld-wrapper) + #:use-module (srfi srfi-1) + #:use-module (ice-9 match) + #:autoload (ice-9 rdelim) (read-delimited) + #:export (ld-wrapper)) + +;;; Commentary: +;;; +;;; This is a wrapper for the linker. Its purpose is to inspect the -L and +;;; -l switches passed to the linker, add corresponding -rpath arguments, and +;;; invoke the actual linker with this new set of arguments. +;;; +;;; The alternatives to this hack would be: +;;; +;;; 1. Using $LD_RUN_PATH. However, that would tend to include more than +;;; needed in the RPATH; for instance, given a package with `libfoo' as +;;; an input, all its binaries would have libfoo in their RPATH, +;;; regardless of whether they actually NEED it. +;;; +;;; 2. Use a GCC "lib" spec string such as `%{L*:-rpath %*}', which adds a +;;; `-rpath LIBDIR' argument for each occurrence of `-L LIBDIR'. +;;; However, this doesn't work when $LIBRARY_PATH is used, because the +;;; additional `-L' switches are not matched by the above rule, because +;;; the rule only matches explicit user-provided switches. See +;;; for details. +;;; +;;; As a bonus, this wrapper checks for "impurities"--i.e., references to +;;; libraries outside the store. +;;; +;;; Code: + +(define %real-ld + ;; Name of the linker that we wrap. + "@LD@") + +(define %store-directory + ;; File name of the store. + (or (getenv "NIX_STORE") "/gnu/store")) + +(define %temporary-directory + ;; Temporary directory. + (or (getenv "TMPDIR") "/tmp")) + +(define %build-directory + ;; Top build directory when run from a builder. + (getenv "NIX_BUILD_TOP")) + +(define %allow-impurities? + ;; Whether to allow references to libraries outside the store. + ;; Allow them by default for convenience. + (let ((value (getenv "GUIX_LD_WRAPPER_ALLOW_IMPURITIES"))) + (or (not value) + (let ((value (string-downcase value))) + (cond ((member value '("yes" "y" "t" "true" "1")) + #t) + ((member value '("no" "n" "f" "false" "0")) + #f) + (else + (format (current-error-port) + "ld-wrapper: ~s: invalid value for \ +'GUIX_LD_WRAPPER_ALLOW_IMPURITIES'~%" + value))))))) + +(define %debug? + ;; Whether to emit debugging output. + (getenv "GUIX_LD_WRAPPER_DEBUG")) + +(define %disable-rpath? + ;; Whether to disable automatic '-rpath' addition. + (getenv "GUIX_LD_WRAPPER_DISABLE_RPATH")) + +(define (readlink* file) + ;; Call 'readlink' until the result is not a symlink. + (define %max-symlink-depth 50) + + (let loop ((file file) + (depth 0)) + (define (absolute target) + (if (absolute-file-name? target) + target + (string-append (dirname file) "/" target))) + + (if (>= depth %max-symlink-depth) + file + (call-with-values + (lambda () + (catch 'system-error + (lambda () + (values #t (readlink file))) + (lambda args + (let ((errno (system-error-errno args))) + (if (or (= errno EINVAL) (= errno ENOENT)) + (values #f file) + (apply throw args)))))) + (lambda (success? target) + (if success? + (loop (absolute target) (+ depth 1)) + file)))))) + +(define (pure-file-name? file) + ;; Return #t when FILE is the name of a file either within the store + ;; (possibly via a symlink) or within the build directory. + (let ((file (readlink* file))) + (or (not (string-prefix? "/" file)) + (string-prefix? %store-directory file) + (string-prefix? %temporary-directory file) + (and %build-directory + (string-prefix? %build-directory file))))) + +(define (store-file-name? file) + ;; Return #t when FILE is a store file, possibly indirectly. + (string-prefix? %store-directory (readlink* file))) + +(define (shared-library? file) + ;; Return #t when FILE denotes a shared library. + (or (string-suffix? ".so" file) + (let ((index (string-contains file ".so."))) + ;; Since we cannot use regexps during bootstrap, roll our own. + (and index + (string-every (char-set-union (char-set #\.) char-set:digit) + (string-drop file (+ index 3))))))) + +(define (library-search-path args) + ;; Return the library search path as a list of directory names. The GNU ld + ;; manual notes that "[a]ll `-L' options apply to all `-l' options, + ;; regardless of the order in which the options appear", so we must compute + ;; the search path independently of the -l options. + (let loop ((args args) + (path '())) + (match args + (() + (reverse path)) + (("-L" directory . rest) + (loop rest (cons directory path))) + ((argument . rest) + (if (string-prefix? "-L" argument) ;augment the search path + (loop rest + (cons (string-drop argument 2) path)) + (loop rest path)))))) + +(define (library-files-linked args library-path) + ;; Return the absolute file names of shared libraries explicitly linked + ;; against via `-l' or with an absolute file name in ARGS, looking them up + ;; in LIBRARY-PATH. + (define files+args + (fold (lambda (argument result) + (match result + ((library-files ((and flag + (or "-dynamic-linker" "-plugin")) + . rest)) + ;; When passed '-dynamic-linker ld.so', ignore 'ld.so'; when + ;; passed '-plugin liblto_plugin.so', ignore + ;; 'liblto_plugin.so'. See . + (list library-files + (cons* argument flag rest))) + ((library-files previous-args) + (cond ((string-prefix? "-l" argument) ;add library + (let* ((lib (string-append "lib" + (string-drop argument 2) + ".so")) + (full (search-path library-path lib))) + (list (if full + (cons full library-files) + library-files) + (cons argument previous-args)))) + ((and (string-prefix? %store-directory argument) + (shared-library? argument)) ;add library + (list (cons argument library-files) + (cons argument previous-args))) + (else + (list library-files + (cons argument previous-args))))))) + (list '() '()) + args)) + + (match files+args + ((files arguments) + (reverse files)))) + +(define (rpath-arguments library-files) + ;; Return the `-rpath' argument list for each of LIBRARY-FILES, a list of + ;; absolute file names. + (fold-right (lambda (file args) + ;; Add '-rpath' if and only if FILE is in the store; we don't + ;; want to add '-rpath' for files under %BUILD-DIRECTORY or + ;; %TEMPORARY-DIRECTORY because that could leak to installed + ;; files. + (cond ((and (not %disable-rpath?) + (store-file-name? file)) + (cons* "-rpath" (dirname file) args)) + ((or %allow-impurities? + (pure-file-name? file)) + args) + (else + (begin + (format (current-error-port) + "ld-wrapper: error: attempt to use \ +library outside of ~a: ~s~%" + %store-directory file) + (exit 1))))) + '() + library-files)) + +(define (expand-arguments args) + ;; Expand ARGS such that "response file" arguments, such as "@args.txt", are + ;; expanded (info "(gcc) Overall Options"). + (define (response-file-arguments file) + (define (tokenize port) + ;; Return a list of all strings found in PORT. Quote characters are removed, + ;; but whitespaces within quoted strings are preserved. + (let loop ((words '())) + (let* ((word (read-delimited " '\"" port 'split)) + (token (car word)) + (delim (cdr word))) + (if (eof-object? delim) + (reverse words) + (case delim + ((#\") (loop (cons (read-delimited "\"" port) words))) + ((#\') (loop (cons (read-delimited "'" port) words))) + ((#\ ) (if (> 0 (string-length token)) + (loop (cons token words)) + (loop words))) + (else (loop words))))))) + + (when %debug? + (format (current-error-port) + "ld-wrapper: attempting to read arguments from '~a'~%" file)) + + (call-with-input-file file tokenize)) + + (define result + (fold-right (lambda (arg result) + (if (string-prefix? "@" arg) + (let ((file (string-drop arg 1))) + (append (catch 'system-error + (lambda () + (response-file-arguments file)) + (lambda args + ;; FILE doesn't exist or cannot be read so + ;; leave ARG as is. + (list arg))) + result)) + (cons arg result))) + '() + args)) + + ;; If there are "@" arguments in RESULT *and* we can expand them (they don't + ;; refer to nonexistent files), then recurse. + (if (equal? result args) + result + (expand-arguments result))) + +(define (ld-wrapper . args) + ;; Invoke the real `ld' with ARGS, augmented with `-rpath' switches. + (let* ((args (expand-arguments args)) + (path (library-search-path args)) + (libs (library-files-linked args path)) + (args (append args (rpath-arguments libs)))) + (when %debug? + (format (current-error-port) + "ld-wrapper: library search path: ~s~%" path) + (format (current-error-port) + "ld-wrapper: libraries linked: ~s~%" libs) + (format (current-error-port) + "ld-wrapper: invoking `~a' with ~s~%" + %real-ld args) + (force-output (current-error-port))) + (apply execl %real-ld (basename %real-ld) args))) + +;;; ld-wrapper.scm ends here -- cgit v1.2.3 From f613d459be9a91ca778d1a2d5ece941ee21469b5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 24 Feb 2020 22:56:30 +0100 Subject: gnu: ungoogled-chromium: Update to 80.0.3987.116-0.bb952f1. * gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for Chromium 80. (%chromium-version): Set to 80.0.3987.116. (%ungoogled-revision): Set to bb952f18c8c80c569583edd8dbb0b54443f49043. (%debian-revision): Set to debian/80.0.3987.116-1. (%chromium-origin, %ungoogled-origin, %debian-origin): Update hashes. (ungoogled-chromium)[arguments]: In #:configure-flags, add "is_cfi=false". Remove "is_clang", "enable_iterator_debugging", "exclude_unwind_tables", "use_jumbo_build", "jumbo_file_merge_limit". Adjust environment for building with Clang. [native-inputs]: Remove GCC-8. Add CLANG-9 and LD-WRAPPER-NEXT. --- gnu/packages/chromium.scm | 59 +++++++++++++++++++++++++---------------------- 1 file changed, 31 insertions(+), 28 deletions(-) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index 06e259b985..24879dfdcd 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -37,7 +37,6 @@ #:use-module (gnu packages curl) #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) - #:use-module (gnu packages gcc) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages glib) @@ -49,6 +48,7 @@ #:use-module (gnu packages libevent) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) + #:use-module (gnu packages llvm) #:use-module (gnu packages kerberos) #:use-module (gnu packages ninja) #:use-module (gnu packages node) @@ -107,10 +107,6 @@ "third_party/blink" ;BSD-3, LGPL2+ "third_party/boringssl" ;OpenSSL/ISC (Google additions are ISC) "third_party/boringssl/src/third_party/fiat" ;Expat - "third_party/boringssl/src/third_party/sike" ;Expat - ;; XXX: these files are generated by fp-$arch.pl in the above directory. - "third_party/boringssl/linux-aarch64/crypto/third_party/sike/asm/fp-armv8.S" - "third_party/boringssl/linux-x86_64/crypto/third_party/sike/asm/fp-x86_64.S" "third_party/breakpad" ;BSD-3 "third_party/brotli" ;Expat "third_party/cacheinvalidation" ;ASL2.0 @@ -118,11 +114,14 @@ "third_party/catapult/common/py_vulcanize/third_party/rcssmin" ;ASL2.0 "third_party/catapult/common/py_vulcanize/third_party/rjsmin" ;ASL2.0 "third_party/catapult/third_party/polymer" ;BSD-3 + ;; XXX: This is a minified version of . "third_party/catapult/tracing/third_party/d3" ;BSD-3 "third_party/catapult/tracing/third_party/gl-matrix" ;Expat + ;; XXX: Minified version of . "third_party/catapult/tracing/third_party/jszip" ;Expat or GPL3 "third_party/catapult/tracing/third_party/mannwhitneyu" ;Expat "third_party/catapult/tracing/third_party/oboe" ;BSD-2 + ;; XXX: Minified version of . "third_party/catapult/tracing/third_party/pako" ;Expat "third_party/ced" ;BSD-3 "third_party/cld_3" ;ASL2.0 @@ -135,6 +134,9 @@ "third_party/dav1d" ;BSD-2 "third_party/dawn" ;ASL2.0 "third_party/depot_tools/owners.py" ;BSD-3 + "third_party/devtools-frontend" ;BSD-3 + "third_party/devtools-frontend/src/third_party/axe-core" + "third_party/devtools-frontend/src/third_party/pyjson5" "third_party/dom_distiller_js" ;BSD-3 "third_party/emoji-segmenter" ;ASL2.0 "third_party/flatbuffers" ;ASL2.0 @@ -155,6 +157,7 @@ "third_party/libaom" ;BSD-2 or "Alliance for Open Media Patent License 1.0" "third_party/libaom/source/libaom/third_party/vector" ;Expat "third_party/libaom/source/libaom/third_party/x86inc" ;ISC + "third_party/libgifcodec" ;MPL1.1/GPL2+/LGPL2.1+, BSD-3, BSD-2 "third_party/libjingle_xmpp" ;BSD-3 "third_party/libphonenumber" ;ASL2.0 "third_party/libsecret" ;LGPL2.1+ @@ -182,6 +185,7 @@ "third_party/pdfium/third_party/bigint" ;Public domain, BSD-3 "third_party/pdfium/third_party/skia_shared" ;BSD-3 "third_party/pdfium/third_party/freetype/include/pstables.h" ;FreeType + "third_party/perfetto" "third_party/pffft" ;the "FFTPACK" license, similar to BSD-3 "third_party/ply" ;BSD-3 "third_party/polymer" ;BSD-3 @@ -195,7 +199,6 @@ "third_party/sfntly" ;ASL2.0 "third_party/skia" ;BSD-3 "third_party/skia/include/third_party/skcms" ;BSD-3 - "third_party/skia/third_party/gif" ;MPL1.1/GPL2+/LGPL2.1+ "third_party/skia/third_party/skcms" ;BSD-3 "third_party/skia/third_party/vulkanmemoryallocator" ;BSD-3, Expat "third_party/smhasher" ;Expat, public domain @@ -244,9 +247,9 @@ from forcing GEXP-PROMISE." #:system system #:guile-for-build guile))) -(define %chromium-version "79.0.3945.130") -(define %ungoogled-revision "e2fae994d786b6716fb473a47b0c880bcfdc2497") -(define %debian-revision "debian/79.0.3945.130-2") +(define %chromium-version "80.0.3987.116") +(define %ungoogled-revision "bb952f18c8c80c569583edd8dbb0b54443f49043") +(define %debian-revision "debian/80.0.3987.116-1") (define package-revision "0") (define %package-version (string-append %chromium-version "-" package-revision "." @@ -260,7 +263,7 @@ from forcing GEXP-PROMISE." %chromium-version ".tar.xz")) (sha256 (base32 - "183vz3lf1588cr9s5vlnj65qvbmz36s8cg8k7dvr64cxmcqk86an")))) + "00c9czjyk1h3i40lvmh2rshp1mq7pcxwsfh1qrq22w8ba6ydkib5")))) (define %ungoogled-origin (origin @@ -271,7 +274,7 @@ from forcing GEXP-PROMISE." (string-take %ungoogled-revision 7))) (sha256 (base32 - "15vmc07iba1zmzn4j7c5n2hyvyxzwwf9hc3kyym0m4jajlsyxr5f")))) + "0lvj3mjwnxvd3kjl2ikl5f0ddrwnp2xsycfx296nwnrimx0frcmg")))) (define %debian-origin (origin @@ -285,7 +288,7 @@ from forcing GEXP-PROMISE." (_ (string-take %debian-revision 7))))) (sha256 (base32 - "1rbzxcwfp7v0c6rkvn9jl9by7p363cnbdyqazwiak1z03kmw3nkz")))) + "1cc5sp566dd8f2grgr770xwbxgxf58dk1w7q3s8pmv4js5h3pwq8")))) ;; This is a "computed" origin that does the following: ;; *) Runs the Ungoogled scripts on a pristine Chromium tarball. @@ -345,7 +348,7 @@ from forcing GEXP-PROMISE." (with-directory-excursion chromium-dir - (format #t "applying Debian patches...~%") + (format #t "Applying Debian patches...~%") (force-output) (let* ((debian #+debian-source) (patches (string-append debian "/debian/patches")) @@ -459,8 +462,10 @@ from forcing GEXP-PROMISE." ;; directory for an exhaustive list of supported flags. ;; (Note: The 'configure' phase will do that for you.) (list "is_debug=false" + "is_cfi=false" "use_gold=false" "use_lld=false" + "clang_use_chrome_plugins=false" "linux_use_bundled_binutils=false" "use_custom_libcxx=false" "use_sysroot=false" @@ -490,18 +495,6 @@ from forcing GEXP-PROMISE." ;; friends from the environment. "custom_toolchain=\"//build/toolchain/linux/unbundle:default\"" "host_toolchain=\"//build/toolchain/linux/unbundle:default\"" - ;; Don't assume it's clang. - "is_clang=false" - ;; Disable debugging features to save space. These are normally - ;; pulled in by "is_official_build", but that requires "is_clang". - "enable_iterator_debugging=false" - "exclude_unwind_tables=true" - ;; Optimize for building everything at once, as opposed to - ;; incrementally for development. See "docs/jumbo.md". - "use_jumbo_build=true" - ;; The default file merge limit of 50 requires huge amounts of RAM. - ;; Cap it to make sure the build succeeds on commodity hardware. - "jumbo_file_merge_limit=8" ;; Prefer system libraries. "use_system_freetype=true" @@ -597,6 +590,10 @@ from forcing GEXP-PROMISE." (substitute* "third_party/webrtc/rtc_base/strings/json.h" (("#include \"third_party/jsoncpp/") "#include \"json/")) + (substitute* "gpu/config/gpu_util.cc" + (("third_party/vulkan/include/") + "")) + (substitute* '("components/viz/common/gpu/vulkan_context_provider.h" "components/viz/common/resources/resource_format_utils.h") (("third_party/vulkan/include/") "")) @@ -649,14 +646,19 @@ from forcing GEXP-PROMISE." ;; Make sure the right build tools are used. (setenv "AR" "ar") (setenv "NM" "nm") - (setenv "CC" "gcc") (setenv "CXX" "g++") + (setenv "CC" "clang") (setenv "CXX" "clang++") - ;; Prevent GCC from optimizing away null pointer safety checks. + ;; Do not optimize away null pointer safety checks. (setenv "CXXFLAGS" "-fno-delete-null-pointer-checks") ;; TODO: pre-compile instead. Avoids a race condition. (setenv "PYTHONDONTWRITEBYTECODE" "1") + (substitute* + ;; From Debians 'system/node.patch'. + "third_party/devtools-frontend/src/scripts/devtools_paths.py" + (("/usr/bin/nodejs") (which "node"))) + ;; XXX: How portable is this. (mkdir-p "third_party/node/linux/node-linux-x64") (symlink (string-append (assoc-ref inputs "node") "/bin") @@ -761,9 +763,10 @@ from forcing GEXP-PROMISE." #t)))))) (native-inputs `(("bison" ,bison) - ("gcc" ,gcc-8) + ("clang" ,clang-9) ("gn" ,gn) ("gperf" ,gperf) + ("ld-wrapper" ,ld-wrapper-next) ("ninja" ,ninja) ("node" ,node) ("pkg-config" ,pkg-config) -- cgit v1.2.3 From c23b42dd55e014a5a79032cc0ef85e775cb02e8b Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 25 Feb 2020 00:26:16 +0100 Subject: guix: node-build-system: Do not symlink /bin. * guix/build/node-build-system.scm (install): Do not add a symlink for /bin. --- guix/build/node-build-system.scm | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/guix/build/node-build-system.scm b/guix/build/node-build-system.scm index 3c0ac2a12b..7799f03595 100644 --- a/guix/build/node-build-system.scm +++ b/guix/build/node-build-system.scm @@ -133,10 +133,7 @@ the @file{bin} directory." (symlink (string-append target "/node_modules/" modulename "/" value) (string-append binaries "/" key)))))) - binary-configuration)) - (else - (symlink (string-append target "/node_modules/" modulename "/bin") - binaries))) + binary-configuration))) (when dependencies (mkdir-p (string-append target "/node_modules/" modulename "/node_modules")) -- cgit v1.2.3 From 679d41b4406d30ec5805ee8015d2ffa446a4e334 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 25 Feb 2020 01:59:37 +0100 Subject: Revert "gnu: vim: Fix build on CoW file systems." This reverts commit b947ba77e60d3d3c5cc6a1c914096e7dab1f7db7. --- gnu/packages/vim.scm | 7 ------- 1 file changed, 7 deletions(-) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index 579b21524e..67f245b26d 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -84,12 +84,6 @@ #:parallel-tests? #f #:phases (modify-phases %standard-phases - (add-after 'unpack 'disable-CoW - ;; Disable copy-on-write (CoW) in the build directory. Tests fail on - ;; btrfs (and possibly other CoW file systems) for unclear reasons. - ;; This needs to be run early as it only affects newly-created files. - (lambda _ - (invoke "chattr" "-R" "+C" "."))) (add-after 'configure 'patch-config-files (lambda _ (substitute* "runtime/tools/mve.awk" @@ -134,7 +128,6 @@ `(("libtool" ,libtool) ;; For tests. - ("e2fsprogs" ,e2fsprogs) ; for chattr in disable-CoW above ("tzdata" ,tzdata-for-tests))) (home-page "https://www.vim.org/") (synopsis "Text editor based on vi") -- cgit v1.2.3 From 0d197a63d1c2751c562f44046b089017cd246574 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 8 Jan 2020 16:51:05 +0100 Subject: gnu: font-fantasque-sans: Update to 1.8.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fonts.scm (font-fantasque-sans): Update to 1.8.0. [native-inputs]: Remove ttf2eot. [arguments]: Rename the ‘xrange->range’ phase to ‘support-python@3’. Patch another Python twoism. --- gnu/packages/fonts.scm | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index b248b27ce2..186e1eecff 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -781,7 +781,7 @@ It contains the following fonts and styles: (define-public font-fantasque-sans (package (name "font-fantasque-sans") - (version "1.7.2") + (version "1.8.0") (source (origin (method git-fetch) @@ -790,26 +790,27 @@ It contains the following fonts and styles: (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "1gjranq7qf20rfxnpxsckv1hl35nzsal0rjs475nhfbpqy5wmly6")))) + (base32 "17l18488qyl9gdj80r8pcym3gp3jkgsdikwalnrp5rgvwidqx507")))) (build-system gnu-build-system) (native-inputs `(("ttfautohint" ,ttfautohint) ("woff-tools" ,woff-tools) ("fontforge" ,fontforge) ("woff2" ,woff2) - ("ttf2eot" ,ttf2eot) ("zip" ,zip))) (arguments `(#:tests? #f ;test target intended for visual inspection #:phases (modify-phases %standard-phases (delete 'configure) ;no configuration - (add-before 'build 'xrange->range - ;; Rather than use a python2 fontforge, just replace the - ;; offending function. + (add-before 'build 'support-python@3 + ;; Rather than use a Python 2 fontforge, replace Python-2- + ;; specific code with a passable Python 3 equivalent. (lambda _ (substitute* "Scripts/fontbuilder.py" (("xrange") "range")) + (substitute* "Scripts/features.py" + (("f\\.write\\(fea_code\\)") + "f.write(str.encode(fea_code))")) #t)) (replace 'install ;; 'make install' wants to install to ~/.fonts, install to -- cgit v1.2.3 From d70e74ce0eb036095bf7d9e06bbfe2bf669dd05a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 25 Feb 2020 08:53:50 +0200 Subject: gnu: datamash: Update to 1.6. * gnu/packages/datamash.scm (datamash): Update to 1.6. --- gnu/packages/datamash.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/datamash.scm b/gnu/packages/datamash.scm index ac1b71e63b..a61ee96fec 100644 --- a/gnu/packages/datamash.scm +++ b/gnu/packages/datamash.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2018 Eric Bavier -;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner +;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,7 +29,7 @@ (define-public datamash (package (name "datamash") - (version "1.5") + (version "1.6") (source (origin (method url-fetch) @@ -37,7 +37,7 @@ version ".tar.gz")) (sha256 (base32 - "1b91pbdarnfmbhid8aa2f50k0fln8n7pg62782b4y0jlzvaljqi2")))) + "1jvqxcyh0aghnqh3m2rk5av1x0038flcmfzd493vasv1k69vgfdr")))) (native-inputs `(("which" ,which) ;for tests ("perl" ,perl))) ;for help2man -- cgit v1.2.3 From 54a968258317df628a57d9cb739b81f45a8171da Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Mon, 20 Jan 2020 03:49:00 +0300 Subject: gnu: Add rust-color-quant-1.0. * gnu/packages/crates-io.scm (rust-color-quant-1.0): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 699fb52d11..f58745f199 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2122,6 +2122,27 @@ CMAKE environmental variable is set.") (license (list license:asl2.0 license:expat)))) +(define-public rust-color-quant-1.0 + (package + (name "rust-color-quant") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "color-quant" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1ga56jrafnjm80903nnqjkyii4bwd6a7visxh0g8hgi6cmrvbfqd")))) + (build-system cargo-build-system) + (home-page "https://github.com/PistonDevelopers/color_quant.git") + (synopsis + "Color quantization library to reduce n colors to 256 colors") + (description + "Color quantization library to reduce n colors to 256 colors.") + (license license:expat))) + ;; This package requires features which are unavailable ;; on the stable releases of Rust. (define-public rust-compiler-builtins-0.1 -- cgit v1.2.3 From c6f876c889561ea29cc9c1bf7b1a34bf7d839d1c Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Mon, 20 Jan 2020 03:53:25 +0300 Subject: gnu: Add rust-memmap-0.2. * gnu/packages/crates-io.scm (rust-memmap-0.2): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f58745f199..54e2e597b8 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -8200,6 +8200,29 @@ file IO.") (base32 "1zy6s0ni0lx9rjzq3gq2zz9r8zgjmbp02332g3gsj4fyhv4s5zz2")))))) +(define-public rust-memmap-0.2 + (package + (inherit rust-memmap-0.6) + (name "rust-memmap") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "memmap" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0li737lakqcbbgd87x7h8d4vp0r1fqcbn5lb5vi746i9jgnp43zj")))) + (arguments + `(#:cargo-inputs + (("rust-fs2" ,rust-fs2-0.2) + ("rust-kernel32-sys" ,rust-kernel32-sys-0.2) + ("rust-libc" ,rust-libc-0.2) + ("rust-winapi" ,rust-winapi-0.2)) + #:cargo-development-inputs + (("rust-tempdir" ,rust-tempdir-0.3)))))) + (define-public rust-memoffset-0.5 (package (name "rust-memoffset") -- cgit v1.2.3 From 519c7d056c9ff3f0219f8d9c100d4c57787cd473 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Mon, 20 Jan 2020 03:49:33 +0300 Subject: gnu: Add rust-gif-0.10. * gnu/packages/crates-io.scm (rust-gif-0.10): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 54e2e597b8..17269f6afe 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -5581,6 +5581,33 @@ API library @code{gdi32}.") retrieving random data from system source.") (license (list license:expat license:asl2.0)))) +(define-public rust-gif-0.10 + (package + (name "rust-gif") + (version "0.10.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "gif" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1bw174f7civdfgryvc8pvyhicpr96hzdajnda4s3y8iv3ch907a7")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; tests not included in release + #:cargo-inputs + (("rust-color-quant" ,rust-color-quant-1.0) + ("rust-libc" ,rust-libc-0.2) + ("rust-lzw" ,rust-lzw-0.10)) + #:cargo-development-inputs + (("rust-glob" ,rust-glob-0.3)))) + (home-page "https://github.com/image-rs/image-gif") + (synopsis "GIF decoder and encoder") + (description "This package provides a GIF decoder and encoder in Rust.") + (license (list license:expat license:asl2.0)))) + (define-public rust-gimli-0.18 (package (name "rust-gimli") -- cgit v1.2.3 From 8b2708a5660bd74a87c0247c43bdbba38632015a Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Mon, 20 Jan 2020 03:47:41 +0300 Subject: gnu: Add rust-expat-sys-2.1. * gnu/packages/crates-io.scm (rust-expat-sys-2.1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 17269f6afe..7756a4d997 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -38,6 +38,7 @@ #:use-module (gnu packages ssh) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) + #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) ;;; @@ -4245,6 +4246,36 @@ is configured via an environment variable.") (description "Geometry primitives written in Rust.") (license (list license:expat license:asl2.0)))) +(define-public rust-expat-sys-2.1 + (package + (name "rust-expat-sys") + (version "2.1.6") + (source + (origin + (method url-fetch) + (uri (crate-uri "expat-sys" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1yj5pqynds776ay8wg9mhi3hvna4fv7vf244yr1864r0i5r1k3v5")) + (modules '((guix build utils))) + (snippet + '(begin (delete-file-recursively "expat") #t)))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cmake" ,rust-cmake-0.1) + ("rust-pkg-config" ,rust-pkg-config-0.3)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("expat" ,expat))) + (home-page "http://www.libexpat.org/") + (synopsis "XML parser library written in C") + (description "XML parser library written in C") + (license license:expat))) + (define-public rust-fake-simd-0.1 (package (name "rust-fake-simd") -- cgit v1.2.3 From 3800d492caaf10b09f5d94d19025fafdb793c631 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Mon, 20 Jan 2020 03:55:45 +0300 Subject: gnu: Add rust-sema-0.1. * gnu/packages/crates-io.scm (rust-sema-0.1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 7756a4d997..515a7e5e9e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13432,6 +13432,38 @@ proven statistical guarantees.") (license (list license:asl2.0 license:expat)))) +(define-public rust-sema-0.1 + (package + (name "rust-sema") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "sema" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0ckq33sg84785p195m54h03jcn7fai8w08hjnb94nzaakgzibbz3")) + (modules '((guix build utils))) + (snippet + '(begin (substitute* "Cargo.toml" + (("libc.*") "libc = \"0.2\"\n")) + #t)))) + (build-system cargo-build-system) + (arguments + `( #:cargo-inputs + (("rust-libc" ,rust-libc-0.2) + ("rust-rand" ,rust-rand-0.3) + ("rust-time" ,rust-time-0.1)) + #:cargo-development-inputs + (("rust-lazy-static" ,rust-lazy-static-1) + ("rust-nix" ,rust-nix-0.15)))) + (home-page "https://github.com/cpjreynolds/sema") + (synopsis "Rust semaphore library") + (description "Rust semaphore library.") + (license license:expat))) + (define-public rust-semver-0.9 (package (name "rust-semver") -- cgit v1.2.3 From 2a7940e83ea7911788b76e25f7eb213db7c3d2b9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 25 Feb 2020 09:56:46 +0200 Subject: gnu: rust-nix-0.15: Don't skip build. * gnu/packages/crates-io.scm (rust-nix-0.15)[arguments]: Don't skip build. Skip tests. Move rust-cc-1.0 from cargo-development-inputs to cargo-inputs. Replace rust-rand-0.4 with 0.6, rust-sysctl-0.4 with 0.1 in cargo-development-inputs. --- gnu/packages/crates-io.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 515a7e5e9e..037e9981f3 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -8966,19 +8966,19 @@ release (fork of debug_unreachable)") "0aa2l7wg9pzx24ks4p97gdy09a4hhs1sr9drxnm75v906d7hnbiv")))) (build-system cargo-build-system) (arguments - `(#:skip-build? #t + `(#:tests? #f ; test suite hangs #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1) + ("rust-cc" ,rust-cc-1.0) ("rust-cfg-if" ,rust-cfg-if-0.1) ("rust-libc" ,rust-libc-0.2) ("rust-void" ,rust-void-1.0)) #:cargo-development-inputs (("rust-bytes" ,rust-bytes-0.4) ("rust-caps" ,rust-caps-0.3) - ("rust-cc" ,rust-cc-1.0) ("rust-lazy-static" ,rust-lazy-static-1) - ("rust-rand" ,rust-rand-0.4) - ("rust-sysctl" ,rust-sysctl-0.4) + ("rust-rand" ,rust-rand-0.6) + ("rust-sysctl" ,rust-sysctl-0.1) ("rust-tempfile" ,rust-tempfile-3.0)))) (home-page "https://github.com/nix-rust/nix") (synopsis "Rust friendly bindings to *nix APIs") -- cgit v1.2.3 From 448a63ee411b03a92fec7c2203b528be82bd80b6 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Mon, 20 Jan 2020 03:58:31 +0300 Subject: gnu: Add rust-servo-freetype-sys-4. * gnu/packages/crates-io.scm (rust-servo-freetype-sys-4): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 037e9981f3..9195528caa 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13843,6 +13843,37 @@ for the serde framework.") (description "YAML support for Serde.") (license (list license:asl2.0 license:expat)))) +(define-public rust-servo-freetype-sys-4 + (package + (name "rust-servo-freetype-sys") + (version "4.0.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "servo-freetype-sys" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1z0dvnakans4vn4vlpx4nxg984427lh8dskxxz9pglij1mnwnk1c")) + (modules '((guix build utils))) + (snippet + '(begin (delete-file-recursively "freetype2") #t)))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cmake" ,rust-cmake-0.1) + ("rust-pkg-config" ,rust-pkg-config-0.3)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("freetype" ,freetype))) + (home-page "http://www.freetype.org/") + (synopsis "Rust wrapper around freetype") + (description + "This package provides a Rust wrapper around the FreeType library.") + (license license:mpl2.0))) ; build.rs is mpl2.0 + (define-public rust-sha-1-0.8 (package (name "rust-sha-1") -- cgit v1.2.3 From 935cfbae63234211af31adb3c21213ed6dfa05bc Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Mon, 20 Jan 2020 03:58:55 +0300 Subject: gnu: Add rust-servo-fontconfig-sys-4. * gnu/packages/crates-io.scm (rust-servo-fontconfig-sys-4): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 9195528caa..5774a45ff5 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13874,6 +13874,41 @@ for the serde framework.") "This package provides a Rust wrapper around the FreeType library.") (license license:mpl2.0))) ; build.rs is mpl2.0 +(define-public rust-servo-fontconfig-sys-4 + (package + (name "rust-servo-fontconfig-sys") + (version "4.0.9") + (source + (origin + (method url-fetch) + (uri (crate-uri "servo-fontconfig-sys" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0v0mbicy74wd6cjd5jyqnm4nvrrr5lmg053cn16kylhg8mkf3cv2")) + (modules '((guix build utils))) + (snippet + '(begin + (for-each delete-file-recursively + (find-files "." "[^Cargo.toml,^build\\.rs]")) + #t)))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-expat-sys" ,rust-expat-sys-2.1) + ("rust-servo-freetype-sys" ,rust-servo-freetype-sys-4) + ("rust-pkg-config" ,rust-pkg-config-0.3)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("fontconfig" ,fontconfig))) + (home-page "https://crates.io/crates/servo-fontconfig-sys") + (synopsis "Rust wrapper around Fontconfig") + (description + "This package provides a Rust wrapper around Fontxonfig.") + (license license:mpl2.0))) ; build.rs is mpl2.0 + (define-public rust-sha-1-0.8 (package (name "rust-sha-1") -- cgit v1.2.3 From 753a43c2e8dd8f954e4d9bceccdd4d71a111af0a Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Mon, 20 Jan 2020 03:59:16 +0300 Subject: gnu: Add rust-servo-fontconfig-0.4. * gnu/packages/crates-io.scm (rust-servo-fontconfig-0.4): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 5774a45ff5..2f1106fc3d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13874,6 +13874,33 @@ for the serde framework.") "This package provides a Rust wrapper around the FreeType library.") (license license:mpl2.0))) ; build.rs is mpl2.0 +(define-public rust-servo-fontconfig-0.4 + (package + (name "rust-servo-fontconfig") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "servo-fontconfig" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1nach6s4hdf86jz5hlm4p5r7vin91cs7gg89mr533id5fpbzi250")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-libc" ,rust-libc-0.2) + ("rust-servo-fontconfig-sys" ,rust-servo-fontconfig-sys-4)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("fontconfig" ,fontconfig))) + (home-page "https://github.com/servo/rust-fontconfig/") + (synopsis "Rust bindings for fontconfig") + (description "This package provides Rust bindings for fontconfig.") + (license (list license:expat license:asl2.0)))) + (define-public rust-servo-fontconfig-sys-4 (package (name "rust-servo-fontconfig-sys") -- cgit v1.2.3 From c67c3a676c0f974882df65b42bdee1c4eadefa4a Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:20:29 +0300 Subject: gnu: Add rust-png-0.15. * gnu/packages/crates-io.scm (rust-png-0.15): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 2f1106fc3d..3179a0a0fa 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -10811,6 +10811,40 @@ used in Cargo build scripts.") "Lazily evaluated, order-independent plugins for extensible types.") (license license:expat))) +(define-public rust-png-0.15 + (package + (name "rust-png") + (version "0.15.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "png" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "10x2qkhyfnm3si5vgx77r2ik811gaap7ahi825wfxgsb0lirm1gg")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-bitflags" ,rust-bitflags-1) + ("rust-crc32fast" ,rust-crc32fast-1.2) + ("rust-deflate" ,rust-deflate-0.7) + ("rust-inflate" ,rust-inflate-0.4)) + #:cargo-development-inputs + (("rust-getopts" ,rust-getopts-0.2) + ;; TODO: glium has many cyclic dependencies with other packages + ;;("rust-glium" ,rust-glium-0.24) + ("rust-glob" ,rust-glob-0.3) + ("rust-rand" ,rust-rand-0.7) + ("rust-term" ,rust-term-0.6)))) + (home-page "https://github.com/image-rs/image-png.git") + (synopsis "PNG decoding and encoding library in pure Rust") + (description + "PNG decoding and encoding library in pure Rust.") + (license (list license:expat license:asl2.0)))) + (define-public rust-pocket-resources-0.3 (package (name "rust-pocket-resources") -- cgit v1.2.3 From b043a3404b659b926088fdfa09ce899afc579e6a Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:23:20 +0300 Subject: gnu: Add rust-png-0.14. * gnu/packages/crates-io.scm (rust-png-0.14): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 3179a0a0fa..de9a9b5ce2 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -10845,6 +10845,35 @@ used in Cargo build scripts.") "PNG decoding and encoding library in pure Rust.") (license (list license:expat license:asl2.0)))) +(define-public rust-png-0.14 + (package + (inherit rust-png-0.15) + (name "rust-png") + (version "0.14.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "png" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0nf3a8r9p9zrj4x30b48f7yv18dz9xkmrq9b3lnzmpnhzn0z9nk3")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-bitflags" ,rust-bitflags-1) + ("rust-deflate" ,rust-deflate-0.7) + ("rust-inflate" ,rust-inflate-0.4) + ("rust-num-iter" ,rust-num-iter-0.1)) + #:cargo-development-inputs + (("rust-getopts" ,rust-getopts-0.2) + ;; TODO: glium has many cyclic dependencies with other packages + ;; ("rust-glium" ,rust-glium-0.22) + ("rust-glob" ,rust-glob-0.2) + ("rust-rand" ,rust-rand-0.5) + ("rust-term" ,rust-term-0.4)))))) + (define-public rust-pocket-resources-0.3 (package (name "rust-pocket-resources") -- cgit v1.2.3 From 2a9521f7cc584caf65ef50b1d020722971a3b1e2 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:23:56 +0300 Subject: gnu: Add rust-png-0.12. * gnu/packages/crates-io.scm (rust-png-0.12): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index de9a9b5ce2..7966a5c9d2 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -10874,6 +10874,34 @@ used in Cargo build scripts.") ("rust-rand" ,rust-rand-0.5) ("rust-term" ,rust-term-0.4)))))) +(define-public rust-png-0.12 + (package + (inherit rust-png-0.14) + (name "rust-png") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "png" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0nqlc8lqf8ncv3kj0gzlxwli61dbbxcjlrp176kvilw4sl09cjzm")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-bitflags" ,rust-bitflags-1) + ("rust-deflate" ,rust-deflate-0.7) + ("rust-inflate" ,rust-inflate-0.4) + ("rust-num-iter" ,rust-num-iter-0.1)) + #:cargo-development-inputs + (("rust-getopts" ,rust-getopts-0.2) + ;; TODO: gluum has many cyclic dependencies with other packages + ;; ("rust-glium" ,rust-glium-0.21) + ("rust-glob" ,rust-glob-0.2) + ("rust-term" ,rust-term-0.4)))))) + (define-public rust-pocket-resources-0.3 (package (name "rust-pocket-resources") -- cgit v1.2.3 From 12f0aefd1418443823450fdd111259269ad3d9cb Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Tue, 18 Feb 2020 10:42:06 +0100 Subject: build-system/linux-module: Disable depmod. * guix/build/linux-module-build-system.scm (install): Disable depmod. --- guix/build/linux-module-build-system.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/guix/build/linux-module-build-system.scm b/guix/build/linux-module-build-system.scm index cd76df2de7..8145d5a724 100644 --- a/guix/build/linux-module-build-system.scm +++ b/guix/build/linux-module-build-system.scm @@ -60,15 +60,18 @@ ;; part. (define* (install #:key inputs native-inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) - (moddir (string-append out "/lib/modules")) - (kmod (assoc-ref (or native-inputs inputs) "kmod"))) + (moddir (string-append out "/lib/modules"))) ;; Install kernel modules (mkdir-p moddir) (invoke "make" "-C" (string-append (assoc-ref inputs "linux-module-builder") "/lib/modules/build") (string-append "M=" (getcwd)) - (string-append "DEPMOD=" kmod "/bin/depmod") + ;; Disable depmod because the Guix system's module directory + ;; is an union of potentially multiple packages. It is not + ;; possible to use depmod to usefully calculate a dependency + ;; graph while building only one of those packages. + "DEPMOD=true" (string-append "MODULE_DIR=" moddir) (string-append "INSTALL_PATH=" out) (string-append "INSTALL_MOD_PATH=" out) -- cgit v1.2.3 From 1fc47a9b491bcc6d3a216592f00f71468a2c80f0 Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Tue, 25 Feb 2020 13:47:40 +0100 Subject: gnu: plantuml: Update to 1.2020.1. * gnu/packages/uml.scm (plantuml): Update to 1.2020.1. [arguments]<#:phases>[delete-extra-from-classpath]: Modify. --- gnu/packages/uml.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/uml.scm b/gnu/packages/uml.scm index 41fb66c3b9..b3b4505938 100644 --- a/gnu/packages/uml.scm +++ b/gnu/packages/uml.scm @@ -30,14 +30,14 @@ (define-public plantuml (package (name "plantuml") - (version "1.2019.3") + (version "1.2020.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/plantuml/" version "/plantuml-" version ".tar.gz")) (sha256 (base32 - "0p2mqav0qfc6kmkhb2n1vjysffnvpsx4yal68nl0yrh5vd3bnmza")))) + "1mywv4m6v1y2wpfz9vqriw6cdq1d2md5k2vf244ldbd9s6j45467")))) (build-system ant-build-system) (arguments `(#:tests? #f ; no tests @@ -49,7 +49,7 @@ (substitute* "build.xml" (("1.6") "1.7") (("") "-->")) + (("ditaa0_9.jar\" />") "-->")) #t)) (add-after 'delete-extra-from-classpath 'patch-usr-bin-dot (lambda* (#:key inputs #:allow-other-keys) -- cgit v1.2.3 From c51c0033d00da046ff3fa573e99000b5b723cc05 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Tue, 25 Feb 2020 14:52:25 +0100 Subject: gnu: Add r-bsgenome-hsapiens-ncbi-grch38. * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ncbi-grch38): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e004560d58..e14f7bc93e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -224,6 +224,30 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") (license license:artistic2.0))) +(define-public r-bsgenome-hsapiens-ncbi-grch38 + (package + (name "r-bsgenome-hsapiens-ncbi-grch38") + (version "1.3.1000") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38" + version 'annotation)) + (sha256 + (base32 + "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) + (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) + (build-system r-build-system) + (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) + (home-page + "https://bioconductor.org/packages/release/data/annotation/html/\ +BSgenome.Hsapiens.NCBI.GRCh38.html") + (synopsis "Full genome sequences for Homo sapiens (GRCh38)") + (description + "This package provides full genome sequences for Homo sapiens (Human) as +provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") + (license license:artistic2.0))) + (define-public r-bsgenome-hsapiens-ucsc-hg19-masked (package (name "r-bsgenome-hsapiens-ucsc-hg19-masked") -- cgit v1.2.3 From 788de3aec8faa7b54ccb978860f1a6a57be6b8fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 25 Feb 2020 15:33:44 +0100 Subject: gnu: jamm: Update to 1.0.7.6. * gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6. --- 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 4adb3137e5..753b7fd0f5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13882,7 +13882,7 @@ absolute GSEA.") (define-public jamm (package (name "jamm") - (version "1.0.7.5") + (version "1.0.7.6") (source (origin (method git-fetch) @@ -13892,7 +13892,7 @@ absolute GSEA.") (file-name (git-file-name name version)) (sha256 (base32 - "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i")))) + "0bsa5mf9n9q5jz7mmacrra41l7r8rac5vgsn6wv1fb52ya58b970")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are none -- cgit v1.2.3 From def0676b0bbaa1fff2d5b0a18af172966bafbced Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:24:31 +0300 Subject: gnu: Add rust-jpeg-decoder-0.1. * gnu/packages/crates-io.scm (rust-jpeg-decoder-0.1): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 7966a5c9d2..07e40c36e7 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -7156,6 +7156,34 @@ primitives to an @code{io::Write}.") "An implementation of the GNU make jobserver for Rust.") (license (list license:expat license:asl2.0)))) +(define-public rust-jpeg-decoder-0.1 + (package + (name "rust-jpeg-decoder") + (version "0.1.18") + (source + (origin + (method url-fetch) + (uri (crate-uri "jpeg-decoder" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0lc428qgffh2a1agkq0p26mvf9rjaiswpywy5883j99mqypg0mh2")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; Some test files missing. + #:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1.3) + ("rust-rayon" ,rust-rayon-1.1)) + #:cargo-development-inputs + (("rust-criterion" ,rust-criterion-0.3) + ("rust-png" ,rust-png-0.14) + ("rust-walkdir" ,rust-walkdir-2.2)))) + (home-page "https://github.com/image-rs/jpeg-decoder") + (synopsis "JPEG decoder") + (description "JPEG decoder written in Rust.") + (license (list license:expat license:asl2.0)))) + (define-public rust-js-sys-0.3 (package (name "rust-js-sys") -- cgit v1.2.3 From 48748d53de47daae8f70595b8988bb7f711cf63a Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:25:57 +0300 Subject: gnu: Add rust-tiff-0.3. * gnu/packages/crates-io.scm (rust-tiff-0.3): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 07e40c36e7..f813ef4b6e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -16036,6 +16036,36 @@ fixed set of worker threads.") (license (list license:asl2.0 license:expat)))) +(define-public rust-tiff-0.3 + (package + (name "rust-tiff") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "tiff" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0zgmbny2f8rssqmjdfvnysy0vqwcvlwl6q9f5yixhavlqk7w5dyp")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; Tests images not included with release. + #:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1.3) + ("rust-lzw" ,rust-lzw-0.10) + ("rust-num-derive" ,rust-num-derive-0.2) + ("rust-num-traits" ,rust-num-traits-0.2)) + #:cargo-development-inputs + (("rust-tempfile" ,rust-tempfile-3.0)))) + (home-page "https://github.com/image-rs/image-tiff") + (synopsis + "TIFF decoding and encoding library in pure Rust") + (description + "TIFF decoding and encoding library in pure Rust.") + (license license:expat))) + (define-public rust-time-0.1 (package (name "rust-time") -- cgit v1.2.3 From 9fba0256cb6c5fcefc938dd6bf85071cde17cc9a Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:27:00 +0300 Subject: gnu: Add rust-tiff-0.2. * gnu/packages/crates-io.scm (rust-tiff-0.2): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f813ef4b6e..3fe0558ddc 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -16066,6 +16066,27 @@ fixed set of worker threads.") "TIFF decoding and encoding library in pure Rust.") (license license:expat))) +(define-public rust-tiff-0.2 + (package + (inherit rust-tiff-0.3) + (name "rust-tiff") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "tiff" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1kn7psgpacns337vvqh272rkqwnakmjd51rc7ygwnc03ibr38j0y")))) + (arguments + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1.3) + ("rust-lzw" ,rust-lzw-0.10) + ("rust-num-derive" ,rust-num-derive-0.2) + ("rust-num-traits" ,rust-num-traits-0.2)))))) + (define-public rust-time-0.1 (package (name "rust-time") -- cgit v1.2.3 From 4aaa7e13d9411b9c0187ea926065187abfd79f87 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:28:24 +0300 Subject: gnu: Add rust-image-0.22. * gnu/packages/crates-io.scm (rust-image-0.22): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 3fe0558ddc..26ae682657 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -6775,6 +6775,44 @@ SystemTime}}.") ignore files such as .gitignore against file paths.") (license (list license:unlicense license:expat)))) +(define-public rust-image-0.22 + (package + (name "rust-image") + (version "0.22.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "image" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0jpbd0p1q7xx6395ba9ikz2k4cfp26qczisa8m2v15w3hzd2mv88")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; Some test images are missing from the release. + #:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1.3) + ("rust-gif" ,rust-gif-0.10) + ("rust-jpeg-decoder" ,rust-jpeg-decoder-0.1) + ("rust-num-iter" ,rust-num-iter-0.1) + ("rust-num-rational" ,rust-num-rational-0.2) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-png" ,rust-png-0.15) + ("rust-scoped-threadpool" ,rust-scoped-threadpool-0.1) + ("rust-tiff" ,rust-tiff-0.3)) + #:cargo-development-inputs + (("rust-crc32fast" ,rust-crc32fast-1.2) + ("rust-glob" ,rust-glob-0.3) + ("rust-num-complex" ,rust-num-complex-0.2) + ("rust-quickcheck" ,rust-quickcheck-0.9)))) + (home-page "https://github.com/image-rs/image") + (synopsis "Imaging library written in Rust") + (description + "Imaging library written in Rust. Provides basic filters and decoders +for the most common image formats.") + (license license:expat))) + (define-public rust-indexmap-1.0 (package (name "rust-indexmap") -- cgit v1.2.3 From 4e832827e2b25aaf78c1d7a81bc396482c026ae0 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:29:21 +0300 Subject: gnu: Add rust-image-0.21. * gnu/packages/crates-io.scm (rust-image-0.21): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 26ae682657..b1325a421b 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -6813,6 +6813,37 @@ ignore files such as .gitignore against file paths.") for the most common image formats.") (license license:expat))) +(define-public rust-image-0.21 + (package + (inherit rust-image-0.22) + (name "rust-image") + (version "0.21.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "image" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1sv534xp8yyn7jj0q6yn2bgng1350f962g81sv8v7c6pgi31wdrm")))) + (arguments + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1.3) + ("rust-gif" ,rust-gif-0.10) + ("rust-jpeg-decoder" ,rust-jpeg-decoder-0.1) + ("rust-lzw" ,rust-lzw-0.10) + ("rust-num-iter" ,rust-num-iter-0.1) + ("rust-num-rational" ,rust-num-rational-0.2) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-png" ,rust-png-0.14) + ("rust-scoped-threadpool" ,rust-scoped-threadpool-0.1) + ("rust-tiff" ,rust-tiff-0.2)) + #:cargo-development-inputs + (("rust-glob" ,rust-glob-0.3) + ("rust-num-complex" ,rust-num-complex-0.2) + ("rust-quickcheck" ,rust-quickcheck-0.6)))))) + (define-public rust-indexmap-1.0 (package (name "rust-indexmap") -- cgit v1.2.3 From d899e93052644a3bc850ca0ee87d4cb539beece1 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:30:07 +0300 Subject: gnu: Add rust-image-0.20. * gnu/packages/crates-io.scm (rust-image-0.20): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b1325a421b..a14cf7a152 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -6844,6 +6844,37 @@ for the most common image formats.") ("rust-num-complex" ,rust-num-complex-0.2) ("rust-quickcheck" ,rust-quickcheck-0.6)))))) +(define-public rust-image-0.20 + (package + (inherit rust-image-0.21) + (name "rust-image") + (version "0.20.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "image" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "01058n0jcw25pq5shn7lkvywv8c28xsxb3nwwyb4r16ijm1mnrj4")))) + (arguments + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1.3) + ("rust-gif" ,rust-gif-0.10) + ("rust-jpeg-decoder" ,rust-jpeg-decoder-0.1) + ("rust-lzw" ,rust-lzw-0.10) + ("rust-num-iter" ,rust-num-iter-0.1) + ("rust-num-rational" ,rust-num-rational-0.2) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-png" ,rust-png-0.12) + ("rust-scoped-threadpool" ,rust-scoped-threadpool-0.1) + ("rust-tiff" ,rust-tiff-0.2)) + #:cargo-development-inputs + (("rust-glob" ,rust-glob-0.2) + ("rust-num-complex" ,rust-num-complex-0.2) + ("rust-quickcheck" ,rust-quickcheck-0.6)))))) + (define-public rust-indexmap-1.0 (package (name "rust-indexmap") -- cgit v1.2.3 From a36b06561f955d4bcafe4200bc27dcca0fbac1f9 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:30:49 +0300 Subject: gnu: Add rust-line-drawing-0.7. * gnu/packages/crates-io.scm (rust-line-drawing-0.7): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a14cf7a152..1b906d47c8 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -8980,6 +8980,36 @@ known as zlib).") (license (list license:asl2.0 license:expat)))) +(define-public rust-line-drawing-0.7 + (package + (name "rust-line-drawing") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "line_drawing" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1fcna7hq1g1kkkqy07hydscx5d2zgb6gskz3vnsvsif8h8ysvisw")))) + (build-system cargo-build-system) + (arguments + ;; This version does not specify any versions on dependants. + `(#:tests? #f ; Cannot compile line_drawing for the test suite. + #:cargo-inputs + (("rust-num-traits" ,rust-num-traits-0.2)) + #:cargo-development-inputs + (("rust-bresenham" ,rust-bresenham-0.1) + ("rust-image" ,rust-image-0.22) ; 0.17? + ("rust-rand" ,rust-rand-0.6)))) + (home-page "https://github.com/expenses/line_drawing") + (synopsis "Collection of line-drawing algorithms") + (description + "This package provides a collection of line-drawing algorithms for use in +graphics and video games.") + (license license:expat))) + (define-public rust-linked-hash-map-0.5 (package (name "rust-linked-hash-map") -- cgit v1.2.3 From b2ebcacd2d044d3dc9ba25ca15338386378c020b Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:33:47 +0300 Subject: gnu: Add rust-rusttype-0.8. * gnu/packages/crates-io.scm (rust-rusttype-0.8): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 1b906d47c8..595f82d8b7 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13273,6 +13273,42 @@ rustc compiler.") "Automatically apply the suggestions made by rustc.") (license (list license:expat license:asl2.0)))) +(define-public rust-rusttype-0.8 + (package + (name "rust-rusttype") + (version "0.8.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "rusttype" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "12hwfg85iii7sbgsyyr23yw862dzp7f8zwn9xv5iqydm5w1i3a8l")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; Artifacts for tests not included. + #:cargo-inputs + (("rust-approx" ,rust-approx-0.3) + ("rust-arrayvec" ,rust-arrayvec-0.5) + ("rust-crossbeam-deque" ,rust-crossbeam-deque-0.7) + ("rust-crossbeam-utils" ,rust-crossbeam-utils-0.7) + ("rust-libm" ,rust-libm-0.2) + ("rust-linked-hash-map" ,rust-linked-hash-map-0.5) + ("rust-num-cpus" ,rust-num-cpus-1.11) + ("rust-ordered-float" ,rust-ordered-float-1.0) + ("rust-rustc-hash" ,rust-rustc-hash-1.0) + ("rust-stb-truetype" ,rust-stb-truetype-0.3)))) + (home-page "https://gitlab.redox-os.org/redox-os/rusttype") + (synopsis "Pure Rust alternative to libraries like FreeType") + (description + "This package provides a pure Rust alternative to libraries like FreeType. +RustType provides an API for loading, querying and rasterising TrueType fonts. +It also provides an implementation of a dynamic GPU glyph cache for hardware +font rendering.") + (license (list license:expat license:asl2.0)))) + (define-public rust-rustversion-1.0 (package (name "rust-rustversion") -- cgit v1.2.3 From a836f50b46937949d68943bc922594dd2455c5c8 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:44:47 +0300 Subject: gnu: Add rust-cgmath-0.17. * gnu/packages/crates-io.scm (rust-cgmath-0.17): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 595f82d8b7..16937d7faf 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1847,6 +1847,39 @@ depending on a large number of #[cfg] parameters. Structured like an (("rust-gleam" ,rust-gleam-0.6) ("rust-libc" ,rust-libc-0.2)))))) +(define-public rust-cgmath-0.17 + (package + (name "rust-cgmath") + (version "0.17.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "cgmath" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1rvgila6ivr0dh1bxza450a4yfwdi2pwj3h1vnwg0jy4xk6l8f98")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t ; Crate won't build without glium. + #:cargo-inputs + (("rust-approx" ,rust-approx-0.3) + ("rust-mint" ,rust-mint-0.5) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-rand" ,rust-rand-0.6) + ("rust-serde" ,rust-serde-1.0) + ("rust-simd" ,rust-simd-0.2)) + #:cargo-development-inputs + (;("rust-glium" ,rust-glium-0.23) + ("rust-serde-json" ,rust-serde-json-1.0)))) + (home-page "https://github.com/brendanzab/cgmath") + (synopsis "Linear algebra and mathematics library") + (description + "This package provides a linear algebra and mathematics library +for computer graphics.") + (license license:asl2.0))) + (define-public rust-ci-info-0.3 (package (name "rust-ci-info") -- cgit v1.2.3 From ef6242415b4918a4efc70f35c960ea37c5d6b114 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:45:36 +0300 Subject: gnu: Add rust-cgmath-0.16. * gnu/packages/crates-io.scm (rust-cgmath-0.16): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 16937d7faf..035a747dc9 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1880,6 +1880,33 @@ depending on a large number of #[cfg] parameters. Structured like an for computer graphics.") (license license:asl2.0))) +(define-public rust-cgmath-0.16 + (package + (inherit rust-cgmath-0.17) + (name "rust-cgmath") + (version "0.16.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "cgmath" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "07754c03v3srzf64ghsl3fggrdi4kjy6l3vyq2d2wfjfixybb934")))) + (arguments + `(#:skip-build? #t ; Crate won't build without glium. + #:cargo-inputs + (("rust-approx" ,rust-approx-0.1) + ("rust-mint" ,rust-mint-0.5) + ("rust-num-traits" ,rust-num-traits-0.1) + ("rust-rand" ,rust-rand-0.4) + ("rust-serde" ,rust-serde-1.0) + ("rust-simd" ,rust-simd-0.2)) + #:cargo-development-inputs + (;("rust-glium" ,rust-glium-0.19) + ("rust-serde-json" ,rust-serde-json-1.0)))))) + (define-public rust-ci-info-0.3 (package (name "rust-ci-info") -- cgit v1.2.3 From 341069bac61ed83eab9771839cae0214a8c1ddd7 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:46:08 +0300 Subject: gnu: Add rust-genmesh-0.6. * gnu/packages/crates-io.scm (rust-genmesh-0.6): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 035a747dc9..98bcccaafe 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -5616,6 +5616,30 @@ API library @code{gdi32}.") (base32 "1v5jg7djicq34nbiv1dwaki71gkny002wyy9qfn3y0hfmrs053y6")))))) +(define-public rust-genmesh-0.6 + (package + (name "rust-genmesh") + (version "0.6.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "genmesh" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "17qybydyblf3hjiw7mq181jpi4vrbb8dmsj0wi347r8k0m354g89")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cgmath" ,rust-cgmath-0.16) + ("rust-mint" ,rust-mint-0.5)))) + (home-page "https://github.com/gfx-rs/genmesh") + (synopsis "Package for generating 3D meshes") + (description + "This package provides a package for generating 3D meshes/") + (license license:asl2.0))) + (define-public rust-getopts-0.2 (package (name "rust-getopts") -- cgit v1.2.3 From 2a7524304201da4a22eb007e310584b6e278b751 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 01:46:39 +0300 Subject: gnu: Add rust-obj-0.9. * gnu/packages/crates-io.scm (rust-obj-0.9): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 98bcccaafe..790425931d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -9759,6 +9759,28 @@ giga, kibi.") "This package can convert numbers into stack-allocated byte arrays.") (license (list license:expat license:asl2.0)))) +(define-public rust-obj-0.9 + (package + (name "rust-obj") + (version "0.9.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "obj" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "10z1r2r0xyhr4j1n07135kz4bc0zhqy98vabs99vz0x171bi8gy0")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs (("rust-genmesh" ,rust-genmesh-0.6)))) + (home-page "https://github.com/kvark/obj") + (synopsis "Package for loading Wavefront .obj files") + (description + "This package provides a package for loading Wavefront @code{.obj} files.") + (license license:asl2.0))) + (define-public rust-objc-0.2 (package (name "rust-objc") -- cgit v1.2.3 From d3237cd302ea9fb563336515e4cc2c4fe056437e Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 02:03:55 +0300 Subject: gnu: Add rust-regex-0.1 and its cyclic dependencies. * gnu/packages/crates-io.scm (rust-regex-0.1, rust-aho-corasick-0.5, rust-byteorder-0.5, rust-csv-0.14, rust-docopt-0.6, rust-memchr-0.1, rust-utf8-ranges-0.1): New variables. (rust-env-logger-0.3)[arguments]: Add missing input. (rust-quickcheck-0.2)[arguments]: Don't skip build. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 159 ++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 156 insertions(+), 3 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 790425931d..37b05db568 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -191,6 +191,31 @@ Rust, using gimli.") ("rust-serde" ,rust-serde-1.0) ("rust-serde-derive" ,rust-serde-derive-1.0)))))) +(define-public rust-aho-corasick-0.5 + (package + (inherit rust-aho-corasick-0.6) + (name "rust-aho-corasick") + (version "0.5.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "aho-corasick" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0rnvdmlajikq0i4zdy1p3pv699q6apvsxfc7av7byhppllp2r5ya")))) + (arguments + `(#:cargo-inputs + (("rust-memchr" ,rust-memchr-0.1)) + #:cargo-development-inputs + (("rust-csv" ,rust-csv-0.14) + ("rust-docopt" ,rust-docopt-0.6) + ("rust-memmap" ,rust-memmap-0.2) + ("rust-quickcheck" ,rust-quickcheck-0.2) + ("rust-rand" ,rust-rand-0.3) + ("rust-rustc-serialize" ,rust-rustc-serialize-0.3)))))) + (define-public rust-android-glue-0.2 (package (name "rust-android-glue") @@ -1443,6 +1468,26 @@ in a byte slice, fast.") little-endian.") (license (list license:expat license:unlicense)))) +(define-public rust-byteorder-0.5 + (package + (inherit rust-byteorder-1.3) + (name "rust-byteorder") + (version "0.5.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "byteorder" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0ma8pkyz1jbglr29m1yzlc9ghmv6672nvsrn7zd0yn5jqs60xh8g")))) + (arguments + `(#:tests? #f + #:cargo-development-inputs + (("rust-quickcheck" ,rust-quickcheck-0.2) + ("rust-rand" ,rust-rand-0.3)))))) + (define-public rust-bytes-0.4 (package (name "rust-bytes") @@ -3014,6 +3059,27 @@ Code} (MAC) algorithms.") "Fast CSV parsing with support for serde.") (license (list license:unlicense license:expat)))) +(define-public rust-csv-0.14 + (package + (inherit rust-csv-1.1) + (name "rust-csv") + (version "0.14.7") + (source + (origin + (method url-fetch) + (uri (crate-uri "csv" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1g0qvr9fj25fq1fy0p758glrb30yz7x46h18hsysaqyaswaihv16")))) + (arguments + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder-0.5) + ("rust-rustc-serialize" ,rust-rustc-serialize-0.3)) + #:cargo-development-inputs + (("rust-regex" ,rust-regex-0.1)))))) + (define-public rust-csv-core-0.1 (package (name "rust-csv-core") @@ -3608,6 +3674,27 @@ from macros.") ("rust-rustc-serialize" ,rust-rustc-serialize-0.3) ("rust-strsim" ,rust-strsim-0.6)))))) +(define-public rust-docopt-0.6 + (package + (inherit rust-docopt-0.7) + (name "rust-docopt") + (version "0.6.86") + (source + (origin + (method url-fetch) + (uri (crate-uri "docopt" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1nf4f4zf5yk0d0l4kl7hkii4na22fhn0l2hgfb46yzv08l2g6zja")))) + (arguments + `(#:cargo-inputs + (("rust-lazy-static" ,rust-lazy-static-0.2) + ("rust-regex" ,rust-regex-0.1) + ("rust-rustc-serialize" ,rust-rustc-serialize-0.3) + ("rust-strsim" ,rust-strsim-0.5)))))) + (define-public rust-downcast-rs-1.1 (package (name "rust-downcast-rs") @@ -4149,7 +4236,7 @@ is configured via an environment variable.") (arguments `(#:skip-build? #t ; Cannot find dependent crates. #:cargo-inputs - (;("rust-regex" ,rust-regex-0.1) + (("rust-regex" ,rust-regex-0.1) ("rust-log" ,rust-log-0.3)))))) (define-public rust-envmnt-0.6 @@ -8428,6 +8515,27 @@ for searching bytes.") (base32 "0yjyja34pzhipdl855q3m21w1lyih4lw79x2dp3czwdla4pap3ql")))))) +(define-public rust-memchr-0.1 + (package + (inherit rust-memchr-1.0) + (name "rust-memchr") + (version "0.1.11") + (source + (origin + (method url-fetch) + (uri (crate-uri "memchr" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "084d85hjfa3xf5kwdms2mhbkh78m1gl2254cp5swcxj3a7xjkdnq")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-libc" ,rust-libc-0.2)) + #:cargo-development-inputs + (("rust-quickcheck" ,rust-quickcheck-0.2)))))) + (define-public rust-memmap-0.7 (package (name "rust-memmap") @@ -11766,8 +11874,7 @@ integers, floats, tuples, booleans, lists, strings, options and results.") `(#:cargo-inputs (("rust-env-logger" ,rust-env-logger-0.3) ("rust-log" ,rust-log-0.3) - ("rust-rand" ,rust-rand-0.3)) - #:skip-build? #t)))) ; Package needs 'unicode' crate. + ("rust-rand" ,rust-rand-0.3)))))) (define-public rust-quickcheck-macros-0.8 (package @@ -12929,6 +13036,34 @@ uses finite automata and guarantees linear time matching on all inputs.") ("rust-quickcheck" ,rust-quickcheck-0.6) ("rust-rand" ,rust-rand-0.4)))))) +(define-public rust-regex-0.1 + (package + (inherit rust-regex-0.2) + (name "rust-regex") + (version "0.1.80") + (source + (origin + (method url-fetch) + (uri (crate-uri "regex" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0bs036h3vzc6pj5jj4vc909s9rppq7b808ic99qn0y6gm3karm2g")))) + (arguments + `(#:skip-build? #t ; Can't find dependent crates. + #:cargo-inputs + (("rust-aho-corasick" ,rust-aho-corasick-0.5) + ("rust-memchr" ,rust-memchr-0.1) + ("rust-regex-syntax" ,rust-regex-syntax-0.3) + ("rust-simd" ,rust-simd-0.2) ; 0.1? + ("rust-thread-local" ,rust-thread-local-0.2) + ("rust-utf8-ranges" ,rust-utf8-ranges-0.1)) + #:cargo-development-inputs + (("rust-lazy-static" ,rust-lazy-static-0.1) + ("rust-quickcheck" ,rust-quickcheck-0.2) + ("rust-rand" ,rust-rand-0.3)))))) + (define-public rust-regex-automata-0.1 (package (name "rust-regex-automata") @@ -17789,6 +17924,24 @@ Unix users and groups.") "Convert ranges of Unicode codepoints to UTF-8 byte ranges.") (license (list license:expat license:unlicense)))) +(define-public rust-utf8-ranges-0.1 + (package + (inherit rust-utf8-ranges-1.0) + (name "rust-utf8-ranges") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "utf8-ranges" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "03xf604b2v51ag3jgzw92l97xnb10kw9zv948bhc7ja1ik017jm1")))) + (arguments + `(#:cargo-development-inputs + (("rust-quickcheck" ,rust-quickcheck-0.2)))))) + (define-public rust-utf8parse-0.1 (package (name "rust-utf8parse") -- cgit v1.2.3 From ba8984cf3d5cc3c4017762574c347274a2d6616a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 25 Feb 2020 16:18:22 +0200 Subject: gnu: rust-conv-0.3: Don't skip build. * gnu/packages/crates-io.scm (rust-conv-0.3)[source]: Add snippet to relax version requirements. [arguments]: Don't skip build. --- gnu/packages/crates-io.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 37b05db568..3a384c5b8d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2451,11 +2451,15 @@ It is inspired by the Linux kernel's @code{crypto_memneq}.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "168j1npqrif1yqxbgbk0pdrx9shzhs5ylc5a4xw49b6hbxi11zvq")))) + "168j1npqrif1yqxbgbk0pdrx9shzhs5ylc5a4xw49b6hbxi11zvq")) + (modules '((guix build utils))) + (snippet + '(begin (substitute* "Cargo.toml" + (("0.2.21.*") "0.2.21\"\n")) + #t)))) (build-system cargo-build-system) (arguments - `(#:skip-build? #t ; Package needs 'unicode' crate. - #:cargo-inputs + `(#:cargo-inputs (("rust-custom-derive" ,rust-custom-derive-0.1)) #:cargo-development-inputs (("rust-quickcheck" ,rust-quickcheck-0.2) -- cgit v1.2.3 From 8d90f2c786b97cee66fcf26d86aced39faf71a3f Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 02:07:15 +0300 Subject: gnu: Add rust-quickcheck-0.4. * gnu/packages/crates-io.scm (rust-quickcheck-0.4): New variable. (rust-quickcheck-0.2): Inherit from rust-quickcheck-0.4. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 3a384c5b8d..c1f8570557 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -11861,25 +11861,40 @@ integers, floats, tuples, booleans, lists, strings, options and results.") ("rust-log" ,rust-log-0.3) ("rust-rand" ,rust-rand-0.3)))))) -(define-public rust-quickcheck-0.2 +(define-public rust-quickcheck-0.4 (package - (inherit rust-quickcheck-0.9) + (inherit rust-quickcheck-0.5) (name "rust-quickcheck") - (version "0.2.27") + (version "0.4.1") (source (origin (method url-fetch) (uri (crate-uri "quickcheck" version)) - (file-name (string-append name "-" version ".tar.gz")) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1vb4acppaavlnchzc1jmn5wlkgir9x9gmhgp97bavyxxqxgsg1nh")))) + "01hligcv1h4pvc8ykch65qjzi7jgcq2s462v69j27slc84fl3hh2")))) (arguments `(#:cargo-inputs (("rust-env-logger" ,rust-env-logger-0.3) ("rust-log" ,rust-log-0.3) ("rust-rand" ,rust-rand-0.3)))))) +(define-public rust-quickcheck-0.2 + (package + (inherit rust-quickcheck-0.4) + (name "rust-quickcheck") + (version "0.2.27") + (source + (origin + (method url-fetch) + (uri (crate-uri "quickcheck" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1vb4acppaavlnchzc1jmn5wlkgir9x9gmhgp97bavyxxqxgsg1nh")))))) + (define-public rust-quickcheck-macros-0.8 (package (name "rust-quickcheck-macros") -- cgit v1.2.3 From 40b4b6dfee241dbddc1f2b84e499e382431f2811 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 25 Feb 2020 16:28:05 +0200 Subject: gnu: rust-regex-syntax-0.3: Don't skip build. * gnu/packages/crates-io.scm (rust-regex-syntax-0.3)[arguments]: Don't skip build. --- gnu/packages/crates-io.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index c1f8570557..f108bd5b4c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13170,8 +13170,7 @@ uses finite automata and guarantees linear time matching on all inputs.") (base32 "0ms9hgdhhsxw9w920i7gipydvagf100bb56jbs192rz86ln01v7r")))) (arguments - `(#:skip-build? #t - #:cargo-development-inputs + `(#:cargo-development-inputs (("rust-quickcheck" ,rust-quickcheck-0.2) ("rust-rand" ,rust-rand-0.3)))))) -- cgit v1.2.3 From d489351cf801df0aeecbc5da42192521a34a23d9 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 15:58:49 +0300 Subject: gnu: Add rust-walkdir-1.0. * gnu/packages/crates-io.scm (rust-walkdir-1.0): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f108bd5b4c..ad29303059 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -18275,6 +18275,31 @@ specified across Unix and Windows platforms.") (license (list license:unlicense license:expat)))) +(define-public rust-walkdir-1.0 + (package + (inherit rust-walkdir-2.2) + (name "rust-walkdir") + (version "1.0.7") + (source + (origin + (method url-fetch) + (uri (crate-uri "walkdir" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1zw8safzqpsrvfn0256cngq2fr9d4lmwv5qb8ycn1f7sf3kgj25v")))) + (arguments + `(#:cargo-inputs + (("rust-kernel32-sys" ,rust-kernel32-sys-0.2) + ("rust-same-file" ,rust-same-file-0.1) + ("rust-winapi" ,rust-winapi-0.2)) + #:cargo-development-inputs + (("rust-docopt" ,rust-docopt-0.7) + ("rust-quickcheck" ,rust-quickcheck-0.4) + ("rust-rand" ,rust-rand-0.3) + ("rust-rustc-serialize" ,rust-rustc-serialize-0.3)))))) + (define-public rust-wasi-0.5 (package (name "rust-wasi") -- cgit v1.2.3 From f93a13c44adae9e3942cff2b1b4c8a449fa8442d Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:00:43 +0300 Subject: gnu: Add rust-syn-0.11 and rust-synom-0.11. * gnu/packages/crates-io.scm (rust-syn-0.11, rust-synom-0.11): New variables. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 65 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ad29303059..95ccbdfaa7 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -15609,6 +15609,71 @@ cryptographic implementations.") ("rust-walkdir" ,rust-walkdir-2.2)))) (properties '()))) +(define-public rust-syn-0.11 + (package + (inherit rust-syn-0.15) + (name "rust-syn") + (version "0.11.11") + (source + (origin + (method url-fetch) + (uri (crate-uri "syn" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1b8x8jdsmj6r9ck7n1pg371526n1q90kx6rv6ivcb22w06wr3f6k")))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'fixup-cargo-toml + (lambda _ + (substitute* "Cargo.toml" + ((", path =.*,") ",")) + #t))) + #:cargo-inputs + (("rust-quote" ,rust-quote-0.3) + ("rust-synom" ,rust-synom-0.11) + ("rust-unicode-xid" ,rust-unicode-xid-0.0)) + #:cargo-development-inputs + (("rust-syntex-pos" ,rust-syntex-pos-0.58) + ("rust-syntex-syntax" ,rust-syntex-syntax-0.58) + ("rust-tempdir" ,rust-tempdir-0.3) + ("rust-walkdir" ,rust-walkdir-1.0)))))) + +(define-public rust-synom-0.11 + (package + (name "rust-synom") + (version "0.11.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "synom" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1dj536sh5xxhan2h0znxhv0sl6sb7lvzmsmrc3nvl3h1v5p0d4x3")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; doc tests fail + #:phases + (modify-phases %standard-phases + (add-before 'build 'fixup-cargo-toml + (lambda _ + (substitute* "Cargo.toml" + (("^path =.*") "")) + #t))) + #:cargo-inputs + (("rust-unicode-xid" ,rust-unicode-xid-0.0)) + #:cargo-development-inputs + (("rust-syn" ,rust-syn-0.11)))) + (home-page "https://github.com/dtolnay/syn") + (synopsis "Stripped-down Nom parser used by Syn") + (description + "Stripped-down Nom parser used by Syn.") + (license (list license:expat license:asl2.0)))) + (define-public rust-synstructure-0.10 (package (name "rust-synstructure") -- cgit v1.2.3 From f5520827b53104901b7f4eb88ac64900b82400d4 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Tue, 25 Feb 2020 15:52:38 +0100 Subject: gnu: emacs-geiser: Update to 0.11.2. * gnu/packages/emacs-xyz.scm (emacs-geiser): Update to 0.11.2. --- 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 be0e6a84c2..0932c87e9a 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -165,7 +165,7 @@ (define-public emacs-geiser (package (name "emacs-geiser") - (version "0.11") + (version "0.11.2") (source (origin (method git-fetch) (uri (git-reference @@ -174,7 +174,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0fb2h984hn7bnyiziplp7kgk29zdzc9yainsv0k1li436irlp9dd")))) + "1khi1bghsjx6cs5acizmlbw9z19s4qycnji9krdbn42cbpv0rysv")))) (build-system gnu-build-system) (arguments '(#:phases -- cgit v1.2.3 From d64584cfb3f1d95749c9e3605a6e1079137a2e42 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 25 Feb 2020 16:14:23 +0100 Subject: gnu: ungoogled-chromium: Add license information about preserved files. This is a follow-up to commit f613d459be9a91ca778d1a2d5ece941ee21469b5. * gnu/packages/chromium.scm (%preserved-third-party-files): Annotate newly added entries with license information. --- gnu/packages/chromium.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index 24879dfdcd..5697c80ed1 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -135,8 +135,8 @@ "third_party/dawn" ;ASL2.0 "third_party/depot_tools/owners.py" ;BSD-3 "third_party/devtools-frontend" ;BSD-3 - "third_party/devtools-frontend/src/third_party/axe-core" - "third_party/devtools-frontend/src/third_party/pyjson5" + "third_party/devtools-frontend/src/third_party/axe-core" ;MPL2.0 + "third_party/devtools-frontend/src/third_party/pyjson5" ;ASL2.0 "third_party/dom_distiller_js" ;BSD-3 "third_party/emoji-segmenter" ;ASL2.0 "third_party/flatbuffers" ;ASL2.0 @@ -185,7 +185,7 @@ "third_party/pdfium/third_party/bigint" ;Public domain, BSD-3 "third_party/pdfium/third_party/skia_shared" ;BSD-3 "third_party/pdfium/third_party/freetype/include/pstables.h" ;FreeType - "third_party/perfetto" + "third_party/perfetto" ;ASL2.0 "third_party/pffft" ;the "FFTPACK" license, similar to BSD-3 "third_party/ply" ;BSD-3 "third_party/polymer" ;BSD-3 -- cgit v1.2.3 From bfce33cdff32ec9bbe163bbf7270fe7477e4fdde Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 25 Feb 2020 16:14:54 +0100 Subject: gnu: ungoogled-chromium-wayland: Fix build. * gnu/packages/chromium.scm (ungoogled-chromium/wayland)[arguments]: Add #:phases. --- gnu/packages/chromium.scm | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index 5697c80ed1..ae7691d26c 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -868,6 +868,16 @@ disabled in order to protect the users privacy.") ,@(package-inputs ungoogled-chromium))) (arguments (substitute-keyword-arguments (package-arguments ungoogled-chromium) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'add-ozone-patch + (lambda _ + ;; Add missing include statement required when using libstdc++, + ;; Clang and Ozone. Fixed in M81. + (substitute* "ui/base/cursor/ozone/bitmap_cursor_factory_ozone.cc" + (("#include \"base/logging\\.h" all) + (string-append "#include \n" all))) + #t)))) ((#:configure-flags flags) `(append (list "use_ozone=true" "ozone_platform_wayland=true" -- cgit v1.2.3 From adf323e0d76ce9da9c4e4b46ce9d92aa3dbdbbc6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 25 Feb 2020 16:28:59 +0100 Subject: gnu: ungoogled-chromium: Update to 80.0.3987.122-0.bb952f1 [security fixes]. This release fixes CVE-2020-6407 and CVE-2020-6418. * gnu/packages/chromium.scm (%chromium-version): Set to 80.0.3987.122. (%ungoogled-revision): Update to 6056988937eb. (%chromium-origin): Update hash. (%ungoogled-origin): Download from pull request, update hash. --- gnu/packages/chromium.scm | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index ae7691d26c..be33e5b363 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -247,8 +247,8 @@ from forcing GEXP-PROMISE." #:system system #:guile-for-build guile))) -(define %chromium-version "80.0.3987.116") -(define %ungoogled-revision "bb952f18c8c80c569583edd8dbb0b54443f49043") +(define %chromium-version "80.0.3987.122") +(define %ungoogled-revision "6056988937ebc32f14293809487dbaaa65939834") (define %debian-revision "debian/80.0.3987.116-1") (define package-revision "0") (define %package-version (string-append %chromium-version "-" @@ -263,18 +263,21 @@ from forcing GEXP-PROMISE." %chromium-version ".tar.xz")) (sha256 (base32 - "00c9czjyk1h3i40lvmh2rshp1mq7pcxwsfh1qrq22w8ba6ydkib5")))) + "0wr487drgd030d7p84rdz1cys0c87wbgh2qg3d7qd98gqbfcpss8")))) (define %ungoogled-origin (origin (method git-fetch) - (uri (git-reference (url "https://github.com/Eloston/ungoogled-chromium") + ;; XXX: Temporarily download from a third party because the main + ;; ungoogled-chromium repo is stale. Code taken from this pull + ;; request: https://github.com/Eloston/ungoogled-chromium/pull/942 + (uri (git-reference (url "https://github.com/Zoraver/ungoogled-chromium") (commit %ungoogled-revision))) (file-name (git-file-name "ungoogled-chromium" (string-take %ungoogled-revision 7))) (sha256 (base32 - "0lvj3mjwnxvd3kjl2ikl5f0ddrwnp2xsycfx296nwnrimx0frcmg")))) + "0s4bfj5lr49hknb6d7vp3zah70w9sq5cdhhlyihnl7f9jlrrnwsi")))) (define %debian-origin (origin -- cgit v1.2.3 From 1b01c103db1698cf2e71bc4a352e705d4527e7d5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 25 Feb 2020 16:33:02 +0100 Subject: gnu: mbedtls-apache: Update to 2.16.5. * gnu/packages/tls.scm (mbedtls-apache): Update to 2.16.5. --- gnu/packages/tls.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 673f23c20b..86910a63fd 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -858,7 +858,7 @@ then ported to the GNU / Linux environment.") (define-public mbedtls-apache (package (name "mbedtls-apache") - (version "2.16.4") + (version "2.16.5") (source (origin (method url-fetch) @@ -868,7 +868,7 @@ then ported to the GNU / Linux environment.") version "-apache.tgz")) (sha256 (base32 - "1yxj5wahaj87xhdi89zbk78ig77b166h464yrj5gb3lwv8mz6h9l")))) + "0kdhwy241xsk4isbadqx6z80m8sf76da5sbmqv8qy11yr37cdd35")))) (build-system cmake-build-system) (arguments `(#:configure-flags -- cgit v1.2.3 From eab27d227750a218bd88d778a3f601291516c45f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 25 Feb 2020 16:37:51 +0100 Subject: gnu: fluidsynth: Update to 2.1.1. * gnu/packages/audio.scm (fluidsynth): Update to 2.1.1. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 5b8c610882..ac486aabfb 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1193,7 +1193,7 @@ follower.") (define-public fluidsynth (package (name "fluidsynth") - (version "2.1.0") + (version "2.1.1") (source (origin (method git-fetch) (uri (git-reference @@ -1202,7 +1202,7 @@ follower.") (file-name (git-file-name name version)) (sha256 (base32 - "0jhla1641rx77va4b6n4shn8srj87rpwvp170byj1bg8z8g89ji1")))) + "09jq04hrasidf6b5gkk4aba13fq55z3bmn7bq35rdaikz26xiij4")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no check target -- cgit v1.2.3 From cbd8d8a879fcf656f0f596228e658e85a78aee39 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 25 Feb 2020 16:41:46 +0100 Subject: gnu: libgphoto2: Update to 2.5.24. * gnu/packages/photo.scm (libgphoto2): Update to 2.5.24. --- gnu/packages/photo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index 4688629172..069767e414 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -133,14 +133,14 @@ data as produced by digital cameras.") (define-public libgphoto2 (package (name "libgphoto2") - (version "2.5.23") + (version "2.5.24") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gphoto/libgphoto/" version "/libgphoto2-" version ".tar.bz2")) (sha256 (base32 - "0bc5x2bkqbfi4hbkz8ab5xc0bkks9vvks1vygxhdh3x498v27byq")))) + "0cgvsk06c4kcfj16plc27nm7g16r9ci0y4k83sf3iyphd63mfg7x")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) (inputs -- cgit v1.2.3 From cce590367280c54ec7abc087d30af09ee860edcf Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 25 Feb 2020 16:55:15 +0100 Subject: gnu: xapian: Update to 1.4.15. * gnu/packages/search.scm (xapian, python-xapian-bindings): Update to 1.4.15. --- gnu/packages/search.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/search.scm b/gnu/packages/search.scm index 3b7bc36889..d1b67a3943 100644 --- a/gnu/packages/search.scm +++ b/gnu/packages/search.scm @@ -49,14 +49,14 @@ (define-public xapian (package (name "xapian") - (version "1.4.14") + (version "1.4.15") ;; Note: When updating Xapian, remember to update xapian-bindings below. (source (origin (method url-fetch) (uri (string-append "https://oligarchy.co.uk/xapian/" version "/xapian-core-" version ".tar.xz")) (sha256 - (base32 "0ja95vn0lkf6qkjhg2blkx306i10hg4fr8wlrhalmly93307lnlp")))) + (base32 "1sjhz6vgql801rdgl6vrsjj0vy1mwlkcxjx6nr7h27m031cyjs5i")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib) ("util-linux" ,util-linux))) @@ -94,7 +94,7 @@ rich set of boolean query operators.") "/xapian-bindings-" version ".tar.xz")) (sha256 (base32 - "0qb17cw8n0g5gcg8dq5b3hs6i16w74rgxcryd0ja9n2h0rlda2an")))) + "0364nalvh13c7wzx52mz4gaf8wg1rm17lw75cs8a813rv091ci38")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-python3") -- cgit v1.2.3 From 93f71b29a5ae19ba943b05ed96cec8e2da8cd2be Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 25 Feb 2020 17:18:32 +0100 Subject: gnu: python-xmlschema: Update to 1.1.1. * gnu/packages/xml.scm (python-xmlschema): Update to 1.1.1. --- gnu/packages/xml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 5e40ba1ec2..704839e5f3 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -2108,7 +2108,7 @@ libxml2 and libxslt.") (define-public python-xmlschema (package (name "python-xmlschema") - (version "1.1.0") + (version "1.1.1") (source (origin ;; Unit tests are not distributed with the PyPI archive. (method git-fetch) @@ -2118,7 +2118,7 @@ libxml2 and libxslt.") (file-name (git-file-name name version)) (sha256 (base32 - "1h8321jb6q3dhlh3608y3f3sbbzfd3jg1psyirxkrm4w5xs3lbvy")))) + "0nqhqbvp0kpd1bz11b6gpkc0mkg068mqs56ww4k5ang1cl9d8gd6")))) (build-system python-build-system) (arguments '(#:phases -- cgit v1.2.3 From dcc3f2158678734555b0b8522e55673eb06b93ea Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 25 Feb 2020 17:40:43 +0100 Subject: gnu: libzip: Update to 1.6.1. * gnu/packages/compression.scm (libzip): Update to 1.6.1. [inputs]: Add XZ. --- gnu/packages/compression.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 0982173b66..ee10bd03ce 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1624,18 +1624,19 @@ recreates the stored directory structure by default.") (define-public libzip (package (name "libzip") - (version "1.5.2") + (version "1.6.1") (source (origin (method url-fetch) (uri (string-append "https://libzip.org/download/libzip-" version ".tar.xz")) (sha256 (base32 - "1d53shcy7nvls5db573bbdlm25lfz1iw2zshng5f00cssi5lvpmk")))) + "0h9nsgkw0dk4srsvmz6xy6f9l4h815xn07j8h40l8gqvcxxaqpbh")))) (native-inputs `(("perl" ,perl))) (inputs `(("gnutls" ,gnutls) + ("liblzma" ,xz) ("openssl" ,openssl) ("zlib" ,zlib))) (build-system cmake-build-system) -- cgit v1.2.3 From 6616b22b12f682955610bed800e3497e0cdc801b Mon Sep 17 00:00:00 2001 From: Alexandros Theodotou Date: Tue, 25 Feb 2020 15:22:53 +0000 Subject: gnu: zrythm: Update to 0.7.573. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/music.scm (zrythm): Update to 0.7.573. Signed-off-by: Jakub Kądziołka --- gnu/packages/music.scm | 31 ++++++++++++++++--------------- 1 file changed, 16 insertions(+), 15 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 16e69840df..eecc4f1626 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -5138,7 +5138,7 @@ and as an LV2 plugin.") (define-public zrythm (package (name "zrythm") - (version "0.7.474") + (version "0.7.573") (source (origin (method url-fetch) @@ -5146,7 +5146,7 @@ and as an LV2 plugin.") version ".tar.xz")) (sha256 (base32 - "0qq9v8y27zhamcb7nq7pl76874ws8x8cxhp5r685b8binvl9p0az")))) + "075gq478xbzz5ql4fsrgfzhgxi7z26k6034lhlkmm0klfcb8j9mg")))) (build-system meson-build-system) (arguments `(#:glib-or-gtk? #t @@ -5164,24 +5164,25 @@ and as an LV2 plugin.") (inputs `(("alsa-lib" ,alsa-lib) ("jack" ,jack-1) - ("font-dseg", font-dseg) - ("ffmpeg", ffmpeg) - ("fftw", fftw) - ("fftwf", fftwf) - ("gettext", gettext-minimal) - ("glibc", glibc) - ("gtk+", gtk+) + ("font-dseg" ,font-dseg) + ("ffmpeg" ,ffmpeg) + ("fftw" ,fftw) + ("fftwf" ,fftwf) + ("gettext" ,gettext-minimal) + ("glibc" ,glibc) + ("gtk+" ,gtk+) + ("libcyaml" ,libcyaml) ("libsamplerate" ,libsamplerate) ("libsndfile" ,libsndfile) ("libyaml" ,libyaml) - ("lilv", lilv) - ("xdg-utils", xdg-utils) - ("rubberband", rubberband))) + ("lilv" ,lilv) + ("xdg-utils" ,xdg-utils) + ("rubberband" ,rubberband))) (native-inputs - `(("pkg-config", pkg-config) - ("help2man", help2man) + `(("pkg-config" ,pkg-config) + ("help2man" ,help2man) ("libaudec" ,libaudec) - ("lv2", lv2) + ("lv2" ,lv2) ("glib" ,glib "bin"))) ;for 'glib-compile-resources' (synopsis "Digital audio workstation focusing on usability") (description "Zrythm is a digital audio workstation designed to be -- cgit v1.2.3 From 91f242357d0a3c42b0b32db24775949695546769 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 25 Feb 2020 22:07:51 +0100 Subject: gnu: Add r-packrat. * gnu/packages/cran.scm (r-packrat): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 67f14a3b88..c6514c7a94 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20238,3 +20238,24 @@ data for the same conditions. Interactivity can improve complex heatmaps by providing tooltips with information about each cell and enabling zooming into interesting features. iheatmapr uses the plotly library for interactivity.") (license license:expat))) + +(define-public r-packrat + (package + (name "r-packrat") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "packrat" version)) + (sha256 + (base32 + "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n")))) + (properties `((upstream-name . "packrat"))) + (build-system r-build-system) + (home-page "https://github.com/rstudio/packrat/") + (synopsis "Dependency management R projects") + (description + "This package provides a dependency manager for R projects that allows +you to manage the R packages your project depends on in an isolated, portable, +and reproducible way.") + (license license:gpl2))) -- cgit v1.2.3 From d2ebdb795d00ae57199491af678ba97a905abc55 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 25 Feb 2020 22:08:38 +0100 Subject: gnu: Add r-rsconnect. * gnu/packages/cran.scm (r-rsconnect): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c6514c7a94..39d80e08b4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20259,3 +20259,32 @@ interesting features. iheatmapr uses the plotly library for interactivity.") you to manage the R packages your project depends on in an isolated, portable, and reproducible way.") (license license:gpl2))) + +(define-public r-rsconnect + (package + (name "r-rsconnect") + (version "0.8.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "rsconnect" version)) + (sha256 + (base32 + "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz")))) + (properties `((upstream-name . "rsconnect"))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-digest" ,r-digest) + ("r-jsonlite" ,r-jsonlite) + ("r-openssl" ,r-openssl) + ("r-packrat" ,r-packrat) + ("r-rstudioapi" ,r-rstudioapi) + ("r-yaml" ,r-yaml))) + (home-page "https://github.com/rstudio/rsconnect") + (synopsis "Deployment interface for R Markdown documents and Shiny applications") + (description + "This package provides a programmatic deployment interface for RPubs, +shinyapps.io, and RStudio Connect. Supported content types include R Markdown +documents, Shiny applications, Plumber APIs, plots, and static web content.") + (license license:gpl2))) -- cgit v1.2.3 From 290b55c55a5cecd686bd294a33e97f023e04a85b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 25 Feb 2020 22:47:17 +0100 Subject: gnu: clang-runtime-3.5: Fix build. * gnu/packages/llvm.scm (clang-runtime-3.5) [inputs]: Add libtirpc. [arguments]: Add phase to find rpc headers. --- gnu/packages/llvm.scm | 35 +++++++++++++++++++++++++++++------ 1 file changed, 29 insertions(+), 6 deletions(-) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index e819625a46..38f2118173 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2015, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2016 Dennis Mungai -;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus +;;; Copyright © 2016, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2017 Roel Janssen ;;; Copyright © 2018, 2019, 2020 Marius Bakke ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice @@ -48,6 +48,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages libffi) #:use-module (gnu packages mpi) + #:use-module (gnu packages onc-rpc) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -553,11 +554,33 @@ output), and Binutils.") "0xf5q17kkxsrm2gsi93h4pwlv663kji73r2g4asb97klsmb626a4")))))) (define-public clang-runtime-3.5 - (clang-runtime-from-llvm - llvm-3.5 - "1hsdnzzdr5kglz6fnv3lcsjs222zjsy14y8ax9dy6zqysanplbal" - '("clang-runtime-asan-build-fixes.patch" - "clang-3.5-libsanitizer-ustat-fix.patch"))) + (let ((runtime (clang-runtime-from-llvm + llvm-3.5 + "1hsdnzzdr5kglz6fnv3lcsjs222zjsy14y8ax9dy6zqysanplbal" + '("clang-runtime-asan-build-fixes.patch" + "clang-3.5-libsanitizer-ustat-fix.patch")))) + (package + (inherit runtime) + (arguments + (substitute-keyword-arguments (package-arguments runtime) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + ;; glibc no longer includes rpc/xdr.h, so we use the headers from + ;; libtirpc. + (add-after 'unpack 'find-rpc-includes + (lambda* (#:key inputs #:allow-other-keys) + (setenv "CPATH" + (string-append (assoc-ref inputs "libtirpc") + "/include/tirpc/:" + (or (getenv "CPATH") ""))) + (setenv "CPLUS_INCLUDE_PATH" + (string-append (assoc-ref inputs "libtirpc") + "/include/tirpc/:" + (or (getenv "CPLUS_INCLUDE_PATH") ""))) + #t)))))) + (inputs + `(("libtirpc" ,libtirpc) + ("llvm" ,llvm-3.5)))))) (define-public clang-3.5 (clang-from-llvm llvm-3.5 clang-runtime-3.5 -- cgit v1.2.3 From 4f19106770e52a54c54640b8931fd0e3250bc3b8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 08:58:06 +0100 Subject: gnu: pigx-scrnaseq: Update to 1.1.3. * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.3. [arguments]: Remove. [inputs]: Remove dropseq-tools and java-picard; add flexbar, jellyfish, and r-seurat; replace python-loompy-for-pigx-scrnaseq with python-loompy. --- gnu/packages/bioinformatics.scm | 17 ++++++----------- 1 file changed, 6 insertions(+), 11 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 753b7fd0f5..e64842b9d6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12770,7 +12770,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "0.0.8") + (version "1.1.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -12778,27 +12778,21 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "0zv0sc5amivxhb95vx2gfx6l9bh7n80fh7h47dalnwxxnfvnzai4")))) + "0ga2jr4968qzwml6aycky4603q64lny3y7lzw6dmafch5pydl1qi")))) (build-system gnu-build-system) - (arguments - `(#:configure-flags - (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard") - "/share/java/picard.jar") - (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools") - "/share/java/dropseq.jar")))) (inputs `(("coreutils" ,coreutils) ("perl" ,perl) - ("dropseq-tools" ,dropseq-tools) ("fastqc" ,fastqc) - ("java-picard" ,java-picard-2.10.3) ; same as for dropseq + ("flexbar" ,flexbar) ("java" ,icedtea-8) + ("jellyfish" ,jellyfish) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) ("python-pandas" ,python-pandas) ("python-magic" ,python-magic) ("python-numpy" ,python-numpy) - ("python-loompy" ,python-loompy-for-pigx-scrnaseq) + ("python-loompy" ,python-loompy) ("ghc-pandoc" ,ghc-pandoc) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("samtools" ,samtools) @@ -12825,6 +12819,7 @@ methylation and segmentation.") ("r-rtsne" ,r-rtsne) ("r-scater" ,r-scater) ("r-scran" ,r-scran) + ("r-seurat" ,r-seurat) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-stringr" ,r-stringr) ("r-yaml" ,r-yaml))) -- cgit v1.2.3 From 59c5f85d06c9e540477270b035431de7825e32b0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 08:59:11 +0100 Subject: gnu: Remove python-loompy-for-pigx-scrnaseq. * gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove variable. --- gnu/packages/bioinformatics.scm | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e64842b9d6..97d766b053 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12010,23 +12010,6 @@ graphs. This library makes it easy to work with @file{.loom} files for single-cell RNA-seq data.") (license license:bsd-3))) -;; pigx-scrnaseq does not work with the latest version of loompy. -(define-public python-loompy-for-pigx-scrnaseq - (package (inherit python-loompy) - (name "python-loompy") - (version "2.0.3") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/linnarsson-lab/loompy.git") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0pjyl532pl8sbv71yci6h0agchn0naw2qjcwj50n6afrsahbsag3")))) - ;; There are none. - (arguments '(#:tests? #f)))) - ;; We cannot use the latest commit because it requires Java 9. (define-public java-forester (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6") -- cgit v1.2.3 From 0ecb3a8bb44d4287063b85174aeeaaf048a9ace3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 09:18:17 +0100 Subject: gnu: Add r-dygraphs. * gnu/packages/cran.scm (r-dygraphs): New variable. --- gnu/packages/cran.scm | 79 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 39d80e08b4..0ca3297304 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20288,3 +20288,82 @@ and reproducible way.") shinyapps.io, and RStudio Connect. Supported content types include R Markdown documents, Shiny applications, Plumber APIs, plots, and static web content.") (license license:gpl2))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-dygraphs + (package + (name "r-dygraphs") + (version "1.1.1.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "dygraphs" version)) + (sha256 + (base32 + "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3")))) + (properties `((upstream-name . "dygraphs"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/" + (call-with-values + (lambda () + (unzip2 + `(("dygraphs/dygraph-combined-dev.js" + "dygraph-combined.js") + (,(assoc-ref inputs "js-jquery") + "jquery/jquery.min.js") + (,(assoc-ref inputs "js-fquarter") + "fquarter/moment-fquarter.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (call-with-output-file target + (lambda (port) + (dump-port minified port))))) + sources targets)))) + #t))))) + (native-inputs + `(("uglify-js" ,uglify-js) + ;; They actually use version 1.11.1, but this more recent version + ;; should be just fine. + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.12.4.js") + (sha256 + (base32 + "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))) + ("js-fquarter" + ,(origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/robgallen/" + "moment-fquarter/1.0.1/moment-fquarter.js")) + (sha256 + (base32 + "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij")))))) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-magrittr" ,r-magrittr) + ("r-xts" ,r-xts) + ("r-zoo" ,r-zoo))) + (home-page "https://github.com/rstudio/dygraphs") + (synopsis "Interface to Dygraphs interactive time series charting library") + (description + "This package provides an R interface to the dygraphs JavaScript charting +library (a copy of which is included in the package). It provides rich +facilities for charting time-series data in R, including highly configurable +series- and axis-display and interactive features like zoom/pan and +series/point highlighting.") + (license license:expat))) -- cgit v1.2.3 From 410cfa78be1a47f5f280acb7195a0264c4ec2810 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 10:11:51 +0100 Subject: gnu: Add r-shinystan. * gnu/packages/cran.scm (r-shinystan): New variable. --- gnu/packages/cran.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0ca3297304..7d53e5e623 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20367,3 +20367,45 @@ facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.") (license license:expat))) + +(define-public r-shinystan + (package + (name "r-shinystan") + (version "2.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinystan" version)) + (sha256 + (base32 + "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5")))) + (properties `((upstream-name . "shinystan"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bayesplot" ,r-bayesplot) + ("r-colourpicker" ,r-colourpicker) + ("r-dt" ,r-dt) + ("r-dygraphs" ,r-dygraphs) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtools" ,r-gtools) + ("r-markdown" ,r-markdown) + ("r-reshape2" ,r-reshape2) + ("r-rsconnect" ,r-rsconnect) + ("r-rstan" ,r-rstan) + ("r-shiny" ,r-shiny) + ("r-shinyjs" ,r-shinyjs) + ("r-shinythemes" ,r-shinythemes) + ("r-threejs" ,r-threejs) + ("r-xtable" ,r-xtable) + ("r-xts" ,r-xts))) + (home-page "https://mc-stan.org/") + (synopsis "Interactive visual and numerical analysis for Bayesian models") + (description + "This package provides a graphical user interface for interactive +@dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful +for analyzing a posterior sample. The interface is powered by the Shiny web +application framework and works with the output of MCMC programs written in +any programming language (and has extended functionality for Stan models fit +using the @code{rstan} and @code{rstanarm} packages).") + (license license:gpl3+))) -- cgit v1.2.3 From 70af390f62262ca52173d908a9ffeb334f0e4589 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 10:12:02 +0100 Subject: gnu: Add r-rstantools. * gnu/packages/cran.scm (r-rstantools): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7d53e5e623..618f892cc9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20409,3 +20409,30 @@ application framework and works with the output of MCMC programs written in any programming language (and has extended functionality for Stan models fit using the @code{rstan} and @code{rstanarm} packages).") (license license:gpl3+))) + +(define-public r-rstantools + (package + (name "r-rstantools") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rstantools" version)) + (sha256 + (base32 + "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa")))) + (properties `((upstream-name . "rstantools"))) + (build-system r-build-system) + (inputs `(("pandoc" ,ghc-pandoc))) + (propagated-inputs + `(("r-desc" ,r-desc) + ("r-rcpp" ,r-rcpp))) + (home-page "https://mc-stan.org/rstantools/") + (synopsis "Tools for developing R packages interfacing with Stan") + (description + "This package provides various tools for developers of R packages +interfacing with @url{https://mc-stan.org, Stan}, including functions to set +up the required package structure, S3 generics and default methods to unify +function naming across Stan-based R packages, and vignettes with +recommendations for developers.") + (license license:gpl3+))) -- cgit v1.2.3 From 762d3ca3dd201e3a0ae15adf128354bf70c918a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 10:12:14 +0100 Subject: gnu: Add r-loo. * gnu/packages/cran.scm (r-loo): New variable. --- gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 618f892cc9..15a39c9cad 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20436,3 +20436,36 @@ up the required package structure, S3 generics and default methods to unify function naming across Stan-based R packages, and vignettes with recommendations for developers.") (license license:gpl3+))) + +(define-public r-loo + (package + (name "r-loo") + (version "2.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "loo" version)) + (sha256 + (base32 + "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6")))) + (properties `((upstream-name . "loo"))) + (build-system r-build-system) + (inputs + `(("pandoc" ,ghc-pandoc) + ("pandoc-citeproc" ,ghc-pandoc-citeproc))) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-matrixstats" ,r-matrixstats))) + (home-page "https://mc-stan.org/loo/") + (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models") + (description + "This package provides an implementation of efficient approximate +@dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using +Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}. +The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new +procedure for regularizing importance weights. As a byproduct of the +calculations, we also obtain approximate standard errors for estimated +predictive errors and for the comparison of predictive errors between models. +The package also provides methods for using stacking and other model weighting +techniques to average Bayesian predictive distributions.") + (license license:gpl3+))) -- cgit v1.2.3 From f3de8b6c8a5a7e1404b234de37cac5ef71484c24 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 10:12:28 +0100 Subject: gnu: Add r-rstan. * gnu/packages/cran.scm (r-rstan): New variable. --- gnu/packages/cran.scm | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 15a39c9cad..e6a350d07e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20469,3 +20469,54 @@ predictive errors and for the comparison of predictive errors between models. The package also provides methods for using stacking and other model weighting techniques to average Bayesian predictive distributions.") (license license:gpl3+))) + +(define-public r-rstan + (package + (name "r-rstan") + (version "2.19.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "rstan" version)) + (sha256 + (base32 + "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np")))) + (properties `((upstream-name . "rstan"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'set-timezone + ;; This package is picky about timezones. + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC+1") + (setenv "TZDIR" + (string-append (assoc-ref inputs "tzdata") + "/share/zoneinfo")) + #t))))) + (native-inputs + `(("tzdata" ,tzdata) + ("pandoc" ,ghc-pandoc))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-inline" ,r-inline) + ("r-loo" ,r-loo) + ("r-pkgbuild" ,r-pkgbuild) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-stanheaders" ,r-stanheaders))) + (home-page "https://discourse.mc-stan.org/") + (synopsis "R interface to Stan") + (description + "User-facing R functions are provided to parse, compile, test, estimate, +and analyze Stan models by accessing the header-only Stan library provided by +the StanHeaders package. The Stan project develops a probabilistic +programming language that implements full Bayesian statistical inference via +Markov Chain Monte Carlo, rough Bayesian inference via 'variational' +approximation, and (optionally penalized) maximum likelihood estimation via +optimization. In all three cases, automatic differentiation is used to +quickly and accurately evaluate gradients without burdening the user with the +need to derive the partial derivatives.") + (license license:gpl3+))) -- cgit v1.2.3 From 849f6bc20bcb3280b3dee9e5555224d32796b575 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 10:12:36 +0100 Subject: gnu: Add r-rstanarm. * gnu/packages/cran.scm (r-rstanarm): New variable. --- gnu/packages/cran.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e6a350d07e..7ff282bde1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20520,3 +20520,44 @@ optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.") (license license:gpl3+))) + +(define-public r-rstanarm + (package + (name "r-rstanarm") + (version "2.19.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "rstanarm" version)) + (sha256 + (base32 + "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s")))) + (properties `((upstream-name . "rstanarm"))) + (build-system r-build-system) + (inputs + `(("pandoc" ,ghc-pandoc) + ("pandoc-citeproc" ,ghc-pandoc-citeproc))) + (propagated-inputs + `(("r-bayesplot" ,r-bayesplot) + ("r-bh" ,r-bh) + ("r-ggplot2" ,r-ggplot2) + ("r-lme4" ,r-lme4) + ("r-loo" ,r-loo) + ("r-matrix" ,r-matrix) + ("r-nlme" ,r-nlme) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rstan" ,r-rstan) + ("r-rstantools" ,r-rstantools) + ("r-shinystan" ,r-shinystan) + ("r-stanheaders" ,r-stanheaders) + ("r-survival" ,r-survival))) + (home-page "https://mc-stan.org/rstanarm/") + (synopsis "Bayesian applied regression modeling via Stan") + (description + "This package estimates previously compiled regression models using the +@code{rstan} package, which provides the R interface to the Stan C++ library +for Bayesian estimation. Users specify models via the customary R syntax with +a formula and @code{data.frame} plus some additional arguments for priors.") + (license license:gpl3+))) -- cgit v1.2.3 From 8a6c0f55152f95dcff675960d5870b1acdfc9a34 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Tue, 25 Feb 2020 18:33:30 +0100 Subject: gnu: Add cl-mysql. * gnu/packages/lisp-xyz.scm (sbcl-cl-mysql, cl-mysql): New variables. --- gnu/packages/lisp-xyz.scm | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 7afd409e9e..c6610d8425 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -51,6 +51,7 @@ #:use-module (guix build-system trivial) #:use-module (gnu packages c) #:use-module (gnu packages compression) + #:use-module (gnu packages databases) #:use-module (gnu packages glib) #:use-module (gnu packages gtk) #:use-module (gnu packages imagemagick) @@ -10718,3 +10719,45 @@ approach to templating.") (define-public ecl-lquery (sbcl-package->ecl-package sbcl-lquery)) + +(define-public sbcl-cl-mysql + (let ((commit "ab56c279c1815aec6ca0bfe85164ff7e85cfb6f9") + (revision "1")) + (package + (name "sbcl-cl-mysql") + (version (git-version "0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hackinghat/cl-mysql.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0dg5ynx2ww94d0qfwrdrm7plkn43h64hs4iiq9mj2s1s4ixnp3lr")))) + (build-system asdf-build-system/sbcl) + (native-inputs + `(("stefil" ,sbcl-stefil))) + (inputs + `(("cffi" ,sbcl-cffi) + ("mariadb-lib" ,mariadb "lib"))) + (arguments + `(#:tests? #f ; TODO: Tests require a running server + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "system.lisp" + (("libmysqlclient_r" all) + (string-append (assoc-ref inputs "mariadb-lib") + "/lib/" + all))) + #t))))) + (synopsis "Common Lisp wrapper for MySQL") + (description + "@code{cl-mysql} is a Common Lisp implementation of a MySQL wrapper.") + (home-page "http://www.hackinghat.com/index.php/cl-mysql") + (license license:expat)))) + +(define-public cl-mysql + (sbcl-package->cl-source-package sbcl-cl-mysql)) -- cgit v1.2.3 From c79ea1a217691a337f7831d5a2fe6a94f6accd14 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Tue, 25 Feb 2020 19:00:58 +0100 Subject: gnu: Add cl-simple-date. * gnu/packages/lisp-xyz.scm (sbcl-simple-date, cl-simple-date, ecl-simple-date): New variables. --- gnu/packages/lisp-xyz.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index c6610d8425..1955c943e1 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10761,3 +10761,34 @@ approach to templating.") (define-public cl-mysql (sbcl-package->cl-source-package sbcl-cl-mysql)) + +(define-public sbcl-simple-date + (let ((commit "74469b25bbda990ec9b77e0d0eccdba0cd7e721a") + (revision "1")) + (package + (name "sbcl-simple-date") + (version (git-version "1.19" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/marijnh/Postmodern.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0im7ymnyxjhn2w74jfg76k5gpr0gl33n31akx33hl28722ljd0hd")))) + (build-system asdf-build-system/sbcl) + (native-inputs + `(("fiveam" ,sbcl-fiveam))) + (synopsis "Basic date and time objects for Common Lisp") + (description + "@code{simple-date} is a very basic implementation of date and time +objects, used to support storing and retrieving time-related SQL types.") + (home-page "https://marijnhaverbeke.nl/postmodern/") + (license license:zlib)))) + +(define-public cl-simple-date + (sbcl-package->cl-source-package sbcl-simple-date)) + +(define-public ecl-simple-date + (sbcl-package->ecl-package sbcl-simple-date)) -- cgit v1.2.3 From f5203d25847c3ee1f094946362fd5d9e64838328 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Tue, 25 Feb 2020 19:11:58 +0100 Subject: gnu: Add cl-postgres. * gnu/packages/lisp-xyz.scm (sbcl-cl-postgres, cl-postgres): New variables. --- gnu/packages/lisp-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 1955c943e1..2f84ad2694 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10792,3 +10792,24 @@ objects, used to support storing and retrieving time-related SQL types.") (define-public ecl-simple-date (sbcl-package->ecl-package sbcl-simple-date)) + +(define-public sbcl-cl-postgres + (package + (inherit sbcl-simple-date) + (name "sbcl-cl-postgres") + (native-inputs + `(("fiveam" ,sbcl-fiveam) + ("simple-date" ,sbcl-simple-date))) + (inputs + `(("md5" ,sbcl-md5) + ("split-sequence" ,sbcl-split-sequence) + ("usocket" ,sbcl-usocket))) + (arguments + `(#:tests? #f)) ; TODO: Break simple-date/postgres-glue circular dependency + (synopsis "Common Lisp interface for PostgreSQL") + (description + "@code{cl-postgres} is a low-level library used for interfacing with +a PostgreSQL server over a socket."))) + +(define-public cl-postgres + (sbcl-package->cl-source-package sbcl-cl-postgres)) -- cgit v1.2.3 From acba62d9bd80a8fd4e9bd91073db037ba5094d09 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Tue, 25 Feb 2020 19:48:30 +0100 Subject: gnu: Add cl-simple-date-postgres-glue. * gnu/packages/lisp-xyz.scm (sbcl-simple-date-postgres-glue, cl-simple-date-postgres-glue): New variables. --- gnu/packages/lisp-xyz.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 2f84ad2694..736efc79f9 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10813,3 +10813,17 @@ a PostgreSQL server over a socket."))) (define-public cl-postgres (sbcl-package->cl-source-package sbcl-cl-postgres)) + +(define-public sbcl-simple-date-postgres-glue + (package + (inherit sbcl-simple-date) + (name "sbcl-simple-date-postgres-glue") + (inputs + `(("cl-postgres" ,sbcl-cl-postgres) + ("simple-date" ,sbcl-simple-date))) + (arguments + `(#:asd-file "simple-date.asd" + #:asd-system-name "simple-date/postgres-glue")))) + +(define-public cl-simple-date-postgres-glue + (sbcl-package->cl-source-package sbcl-simple-date-postgres-glue)) -- cgit v1.2.3 From 88dbe39b16a53d1f1fa7b4dad97f10bca22f7d02 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Tue, 25 Feb 2020 22:14:11 +0100 Subject: gnu: Add cl-s-sql. * gnu/packages/lisp-xyz.scm (sbcl-s-sql, cl-s-sql): New variables. --- gnu/packages/lisp-xyz.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 736efc79f9..0f5e995afa 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10827,3 +10827,21 @@ a PostgreSQL server over a socket."))) (define-public cl-simple-date-postgres-glue (sbcl-package->cl-source-package sbcl-simple-date-postgres-glue)) + +(define-public sbcl-s-sql + (package + (inherit sbcl-simple-date) + (name "sbcl-s-sql") + (inputs + `(("alexandria" ,sbcl-alexandria) + ("cl-postgres" ,sbcl-cl-postgres))) + (arguments + `(#:tests? #f)) ; TODO: Break postmodern circular dependency + (synopsis "Lispy DSL for SQL") + (description + "@code{s-sql} is a Common Lisp library that can be used to compile +s-expressions to strings of SQL code, escaping any Lisp values inside, and +doing as much as possible of the work at compile time."))) + +(define-public cl-s-sql + (sbcl-package->cl-source-package sbcl-s-sql)) -- cgit v1.2.3 From add1a3561f697df0ea8bbd0c9b1c11fdf7334352 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Tue, 25 Feb 2020 22:35:49 +0100 Subject: gnu: Add cl-postmodern. * gnu/packages/lisp-xyz.scm (sbcl-postmodern, cl-postmodern): New variables. --- gnu/packages/lisp-xyz.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 0f5e995afa..5d30446b43 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10845,3 +10845,40 @@ doing as much as possible of the work at compile time."))) (define-public cl-s-sql (sbcl-package->cl-source-package sbcl-s-sql)) + +(define-public sbcl-postmodern + (package + (inherit sbcl-simple-date) + (name "sbcl-postmodern") + (native-inputs + `(("fiveam" ,sbcl-fiveam) + ("simple-date" ,sbcl-simple-date) + ("simple-date-postgres-glue" ,sbcl-simple-date-postgres-glue))) + (inputs + `(("alexandria" ,sbcl-alexandria) + ("bordeaux-threads" ,sbcl-bordeaux-threads) + ("cl-postgres" ,sbcl-cl-postgres) + ("closer-mop" ,sbcl-closer-mop) + ("global-vars" ,sbcl-global-vars) + ("s-sql" ,sbcl-s-sql) + ("split-sequence" ,sbcl-split-sequence))) + (arguments + ;; TODO: Fix missing dependency errors for simple-date/postgres-glue, + ;; cl-postgres/tests and s-sql/tests. + `(#:tests? #f)) + (synopsis "Common Lisp library for interacting with PostgreSQL") + (description + "@code{postmodern} is a Common Lisp library for interacting with +PostgreSQL databases. It provides the following features: + +@itemize +@item Efficient communication with the database server without need for +foreign libraries. +@item Support for UTF-8 on Unicode-aware Lisp implementations. +@item A syntax for mixing SQL and Lisp code. +@item Convenient support for prepared statements and stored procedures. +@item A metaclass for simple database-access objects. +@end itemize\n"))) + +(define-public cl-postmodern + (sbcl-package->cl-source-package sbcl-postmodern)) -- cgit v1.2.3 From 47a6cde09c4c3b028ae7ec3b675579a9a369e8f7 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Tue, 25 Feb 2020 22:53:36 +0100 Subject: gnu: Add cl-dbi. * gnu/packages/lisp-xyz.scm (sbcl-dbi, cl-dbi): New variables. --- gnu/packages/lisp-xyz.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 5d30446b43..77323cb17b 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10882,3 +10882,33 @@ foreign libraries. (define-public cl-postmodern (sbcl-package->cl-source-package sbcl-postmodern)) + +(define-public sbcl-dbi + (package + (name "sbcl-dbi") + (version "0.9.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fukamachi/cl-dbi.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0m1fsravfaizamdak84adh3jxc4j91maqnrb4m08bfbmb04cdqhs")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("bordeaux-threads" ,sbcl-bordeaux-threads) + ("closer-mop" ,sbcl-closer-mop) + ("split-sequence" ,sbcl-split-sequence))) + (arguments + `(#:tests? #f)) ; TODO: Break circular dependency with dbd-* + (synopsis "Database independent interface for Common Lisp") + (description + "@code{dbi} is a Common Lisp library providing a database independent +interface for MySQL, PostgreSQL and SQLite.") + (home-page "https://github.com/fukamachi/cl-dbi") + (license license:llgpl))) + +(define-public cl-dbi + (sbcl-package->cl-source-package sbcl-dbi)) -- cgit v1.2.3 From 903d0e81a10444d377c5516e704a67b66695f895 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 26 Feb 2020 10:51:19 +0100 Subject: gnu: Add cl-dbd-mysql. * gnu/packages/lisp-xyz.scm (sbcl-dbd-mysql, cl-dbd-mysql): New variables. --- gnu/packages/lisp-xyz.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 77323cb17b..d0e7524e9b 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10912,3 +10912,15 @@ interface for MySQL, PostgreSQL and SQLite.") (define-public cl-dbi (sbcl-package->cl-source-package sbcl-dbi)) + +(define-public sbcl-dbd-mysql + (package + (inherit sbcl-dbi) + (name "sbcl-dbd-mysql") + (inputs + `(("cl-mysql" ,sbcl-cl-mysql) + ("dbi" ,sbcl-dbi))) + (synopsis "Database driver for MySQL"))) + +(define-public cl-dbd-mysql + (sbcl-package->cl-source-package sbcl-dbd-mysql)) -- cgit v1.2.3 From af469826e2579074f9f88099d0ec55c5ccac8e26 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 26 Feb 2020 11:00:25 +0100 Subject: gnu: Add cl-dbd-postgres. * gnu/packages/lisp-xyz.scm (sbcl-dbd-postgres, cl-dbd-postgres): New variables. --- gnu/packages/lisp-xyz.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index d0e7524e9b..a45f14e5e1 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10924,3 +10924,16 @@ interface for MySQL, PostgreSQL and SQLite.") (define-public cl-dbd-mysql (sbcl-package->cl-source-package sbcl-dbd-mysql)) + +(define-public sbcl-dbd-postgres + (package + (inherit sbcl-dbi) + (name "sbcl-dbd-postgres") + (inputs + `(("cl-postgres" ,sbcl-cl-postgres) + ("dbi" ,sbcl-dbi) + ("trivial-garbage" ,sbcl-trivial-garbage))) + (synopsis "Database driver for PostgreSQL"))) + +(define-public cl-dbd-postgres + (sbcl-package->cl-source-package sbcl-dbd-postgres)) -- cgit v1.2.3 From 0e9fc3d61f41d83775b74c6f81789cd840f68fc5 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 26 Feb 2020 11:07:13 +0100 Subject: gnu: Add cl-dbd-sqlite3. * gnu/packages/lisp-xyz.scm (sbcl-dbd-sqlite3, cl-dbd-sqlite3): New variables. --- gnu/packages/lisp-xyz.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index a45f14e5e1..292c9d7317 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -10937,3 +10937,16 @@ interface for MySQL, PostgreSQL and SQLite.") (define-public cl-dbd-postgres (sbcl-package->cl-source-package sbcl-dbd-postgres)) + +(define-public sbcl-dbd-sqlite3 + (package + (inherit sbcl-dbi) + (name "sbcl-dbd-sqlite3") + (inputs + `(("cl-sqlite" ,sbcl-cl-sqlite) + ("dbi" ,sbcl-dbi) + ("trivial-garbage" ,sbcl-trivial-garbage))) + (synopsis "Database driver for SQLite3"))) + +(define-public cl-dbd-sqlite3 + (sbcl-package->cl-source-package sbcl-dbd-sqlite3)) -- cgit v1.2.3 From 640d910427f3e7128be3702a261a1bb40264040b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 12:51:57 +0100 Subject: gnu: macs: Update to 2.2.6. * gnu/packages/bioinformatics.scm (macs): Update to 2.2.6. [source]: Fetch from git. [arguments]: Enable tests, build with default Python. [inputs]: Replace python2-numpy with python-numpy. [native-inputs]: Add python-pytest. --- gnu/packages/bioinformatics.scm | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 97d766b053..7f2a852fb0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4274,19 +4274,30 @@ experiments.") (define-public macs (package (name "macs") - (version "2.1.1.20160309") + (version "2.2.6") (source (origin - (method url-fetch) - (uri (pypi-uri "MACS2" version)) + ;; The PyPi tarball does not contain tests. + (method git-fetch) + (uri (git-reference + (url "https://github.com/taoliu/MACS.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "09ixspd1vcqmz1c81ih70xs4m7qml2iy5vyx1y74zww3iy1vl210")))) + "1c5gxr0mk6hkd4vclf0k00wvyvzw2vrmk52c85338p7aqjwg6n15")))) (build-system python-build-system) (arguments - `(#:python ,python-2 ; only compatible with Python 2.7 - #:tests? #f)) ; no test target + `(#:phases + (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-v")))))) (inputs - `(("python-numpy" ,python2-numpy))) + `(("python-numpy" ,python-numpy))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/taoliu/MACS/") (synopsis "Model based analysis for ChIP-Seq data") (description -- cgit v1.2.3 From 8119352ffaf5249a814f7ffc939ab811f2a5057a Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:03:07 +0300 Subject: gnu: Add rust-serde-codegen-internals-0.14. * gnu/packages/crates-io.scm (rust-serde-codegen-internals-0.14): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 95ccbdfaa7..eb73004ad9 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -14248,6 +14248,28 @@ proven statistical guarantees.") for the serde framework.") (license (list license:expat license:asl2.0)))) +(define-public rust-serde-codegen-internals-0.14 + (package + (name "rust-serde-codegen-internals") + (version "0.14.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde_codegen_internals" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0004s3wlc85vi6hq62hq84cv5b6qbbin1n6hdaqj095xhg98p25w")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs (("rust-syn" ,rust-syn-0.11)))) + (home-page "https://serde.rs") + (synopsis "AST representation used by Serde codegen") + (description + "Unstable AST representation used by Serde codegen.") + (license (list license:expat license:asl2.0)))) + (define-public rust-serde-derive-1.0 (package (name "rust-serde-derive") -- cgit v1.2.3 From 7881fc114efcd4c107d0d8cbb55729b67ec4e8b3 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:03:36 +0300 Subject: gnu: Add rust-serde-derive-0.9. * gnu/packages/crates-io.scm (rust-serde-derive-0.9): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index eb73004ad9..3a8c043a80 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -14298,6 +14298,33 @@ for the serde framework.") "Macros 1.1 implementation of #[derive(Serialize, Deserialize)]") (license (list license:expat license:asl2.0)))) +(define-public rust-serde-derive-0.9 + (package + (inherit rust-serde-derive-1.0) + (name "rust-serde-derive") + (version "0.9.15") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde-derive" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1fkldf0lnl6pwxs00qpyp79m30qmfpi3bk0wm22211ylyikdi3wp")))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-cargo-toml + (lambda _ + (substitute* "Cargo.toml" + ((", path =.*}") "}")) + #t))) + #:cargo-inputs + (("rust-quote" ,rust-quote-0.3) + ("rust-serde-codegen-internals" ,rust-serde-codegen-internals-0.14) + ("rust-syn" ,rust-syn-0.11)))))) + (define-public rust-serde-json-1.0 (package (name "rust-serde-json") -- cgit v1.2.3 From 1516f20a2708255ba694e33582b3592c8eb6991e Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:04:07 +0300 Subject: gnu: Add rust-serde-0.9. * gnu/packages/crates-io.scm (rust-serde-0.9): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 3a8c043a80..e1ca2bdac2 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -14097,6 +14097,33 @@ proven statistical guarantees.") "This package provides a generic serialization/deserialization framework.") (license (list license:expat license:asl2.0)))) +(define-public rust-serde-0.9 + (package + (inherit rust-serde-1.0) + (name "rust-serde") + (version "0.9.15") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1bsla8l5xr9pp5sirkal6mngxcq6q961km88jvf339j5ff8j7dil")))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-cargo-toml + (lambda _ + (substitute* "Cargo.toml" + ((", path =.*}") "}")) + #t))) + #:cargo-inputs + (("rust-serde-derive" ,rust-serde-derive-0.9)) + #:cargo-development-inputs + (("rust-serde-derive" ,rust-serde-derive-0.9)))))) + (define-public rust-serde-0.8 (package (inherit rust-serde-1.0) -- cgit v1.2.3 From 87c1e7f5c976ba729e8e3cf51a0acfc6d7639408 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:04:19 +0300 Subject: gnu: Add rust-serde-0.4. * gnu/packages/crates-io.scm (rust-serde-0.4): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index e1ca2bdac2..2005b81fd1 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -14142,6 +14142,24 @@ proven statistical guarantees.") (("rust-clippy" ,rust-clippy-0.0)) #:tests? #f)))) +(define-public rust-serde-0.4 + (package + (inherit rust-serde-0.9) + (name "rust-serde") + (version "0.4.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "06s2ayx1p5zzj4q7bfld60c9iprsk1256pnh8qj6h794mjinw11b")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs (("rust-num" ,rust-num-0.2)))))) + (define-public rust-serde-big-array-0.1 (package (name "rust-serde-big-array") -- cgit v1.2.3 From be9655d96d294e1ac9915c30e0d506ad3a8de4db Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:05:22 +0300 Subject: gnu: Add rust-serde-test-0.9. * gnu/packages/crates-io.scm (rust-serde-test-0.9): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 2005b81fd1..2041e0e3cb 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -14428,6 +14428,30 @@ for the serde framework.") "Token De/Serializer for testing De/Serialize implementations.") (license (list license:expat license:asl2.0)))) +(define-public rust-serde-test-0.9 + (package + (inherit rust-serde-test-1.0) + (name "rust-serde-test") + (version "0.9.15") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde_test" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "193mf0qkhvjywd06x6hhmkixlqcyfbpfwfmr75dp2b8xwzpsvxwf")))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-cargo-toml + (lambda _ + (substitute* "Cargo.toml" + ((", path =.*}") "}")) + #t))) + #:cargo-inputs (("rust-serde" ,rust-serde-0.9)))))) + (define-public rust-serde-test-0.8 (package (inherit rust-serde-test-1.0) -- cgit v1.2.3 From 537f998be7200adc59a200f8209e3514c120f099 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:06:46 +0300 Subject: gnu: Add rust-serde-macros-0.4. * gnu/packages/crates-io.scm (rust-serde-macros-0.4): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 2041e0e3cb..a68ddcd2ff 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -14400,6 +14400,42 @@ for the serde framework.") "This package provides a JSON serialization file format.") (license (list license:expat license:asl2.0)))) +(define-public rust-serde-macros-0.4 + (package + (name "rust-serde-macros") + (version "0.4.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde_macros" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1717rpncvvyvyrpb7hdjgxpiki9vdgygwv2r3d9aal5n8cm8xi8i")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-cargo-toml + (lambda _ + (substitute* "Cargo.toml" + ((", path =.*}") "}")) + #t))) + #:cargo-inputs + (("rust-serde-codegen" ,rust-serde-codegen-0.4)) + #:cargo-development-inputs + (("rust-num" ,rust-num-0.2) + ("rust-rustc-serialize" ,rust-rustc-serialize-0.3) + ("rust-serde" ,rust-serde-0.4)))) + (home-page "https://serde.rs") + (synopsis + "Macros to auto-generate implementations for the serde framework") + (description + "Macros to auto-generate implementations for the serde framework.") + (license (list license:expat license:asl2.0)))) + (define-public rust-serde-test-1.0 (package (name "rust-serde-test") -- cgit v1.2.3 From 6b11c1e401c242eea3d53cc40e314c017701836d Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:07:47 +0300 Subject: gnu: Add rust-linked-hash-map-0.4. * gnu/packages/crates-io.scm (rust-linked-hash-map-0.4): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a68ddcd2ff..edae31ce6c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -9237,6 +9237,27 @@ pairs in insertion order.") (license (list license:asl2.0 license:expat)))) +(define-public rust-linked-hash-map-0.4 + (package + (inherit rust-linked-hash-map-0.5) + (name "rust-linked-hash-map") + (version "0.4.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "linked-hash-map" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0fd958y02ggwpa2246kmjky9xmnww7vxg0ik3rxgy23hgwlyqq3q")))) + (arguments + `(#:cargo-inputs + (("rust-clippy" ,rust-clippy-0.0) + ("rust-heapsize" ,rust-heapsize-0.3) + ("rust-serde" ,rust-serde-0.9) + ("rust-serde-test" ,rust-serde-test-0.9)))))) + (define-public rust-linked-hash-map-0.3 (package (inherit rust-linked-hash-map-0.5) -- cgit v1.2.3 From c7d5b98dd9a593564a73ef3e1f532a77d473597d Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:09:06 +0300 Subject: gnu: Add rust-serde-json-0.9. * gnu/packages/crates-io.scm (rust-serde-json-0.9): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index edae31ce6c..a735df49d7 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -14421,6 +14421,31 @@ for the serde framework.") "This package provides a JSON serialization file format.") (license (list license:expat license:asl2.0)))) +(define-public rust-serde-json-0.9 + (package + (inherit rust-serde-json-1.0) + (name "rust-serde-json") + (version "0.9.10") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde_json" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "188nbf56m7p6mnh3xd71rwqxd4g95lqh8gsl7mfy3lp7gd4cz2xd")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-dtoa" ,rust-dtoa-0.4) + ("rust-itoa" ,rust-itoa-0.3) + ("rust-linked-hash-map" ,rust-linked-hash-map-0.4) + ("rust-num-traits" ,rust-num-traits-0.1) + ("rust-serde" ,rust-serde-0.9)) + #:cargo-development-inputs + (("rust-serde-derive" ,rust-serde-derive-0.9)))))) + (define-public rust-serde-macros-0.4 (package (name "rust-serde-macros") -- cgit v1.2.3 From f6a57eecbe4385c4dc33d9d6e1035a85c5a195e9 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:09:36 +0300 Subject: gnu: Add rust-target-build-utils-0.3. * gnu/packages/crates-io.scm (rust-target-build-utils-0.3): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a735df49d7..b41be6160a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -16127,6 +16127,32 @@ memory all at once.") "This package provides a small wrapper around option.") (license (list license:asl2.0 license:expat)))) +(define-public rust-target-build-utils-0.3 + (package + (name "rust-target-build-utils") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "target_build_utils" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0p7713x4bpbwi11l196z1mi8ym8qj1cdnab1mm2ffpm2wi516g81")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-phf" ,rust-phf-0.7) + ("rust-serde-json" ,rust-serde-json-0.9) + ("rust-phf-codegen" ,rust-phf-codegen-0.7)))) + (home-page "https://github.com/nagisa/target_build_utils.rs") + (synopsis "Rust utility to handle TARGET environment variable") + (description + "Utility crate to handle the @code{TARGET} environment variable passed into +@code{build.rs} scripts.") + (license (list license:isc license:asl2.0)))) + (define-public rust-tempdir-0.3 (package (name "rust-tempdir") -- cgit v1.2.3 From a83d31ef844ada117e21e803cadcacc8e9d6358e Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:11:32 +0300 Subject: gnu: Add rust-libloading-0.3. * gnu/packages/crates-io.scm (rust-libloading-0.3): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b41be6160a..9d2dab60ef 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -7970,6 +7970,29 @@ allows loading dynamic libraries (also known as shared libraries) as well as use functions and static variables these libraries contain.") (license license:isc))) +(define-public rust-libloading-0.3 + (package + (inherit rust-libloading-0.5) + (name "rust-libloading") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "libloading" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0risz19rllhdc0d7nkpwkf4pcbjjgg1iim0kkmzb6kkp874hl0ha")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; Some test libraries not included in release. + #:cargo-inputs + (("rust-kernel32-sys" ,rust-kernel32-sys-0.2) + ("rust-lazy-static" ,rust-lazy-static-0.2) + ("rust-winapi" ,rust-winapi-0.2) + ("rust-target-build-utils" ,rust-target-build-utils-0.3)))))) + (define-public rust-libm-0.2 (package (name "rust-libm") -- cgit v1.2.3 From 389f9ab6ab52d73cfd82b6ef1fc5e07098357ea5 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:12:40 +0300 Subject: gnu: Add rust-clang-sys-0.11. * gnu/packages/crates-io.scm (rust-clang-sys-0.11): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 9d2dab60ef..db52c144c9 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2068,6 +2068,38 @@ for computer graphics.") (string-append clang "/lib"))) #t))))))) +(define-public rust-clang-sys-0.11 + (package + (inherit rust-clang-sys-0.22) + (name "rust-clang-sys") + (version "0.11.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "clang-sys" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "17i47skqp1d9svil2m1wspnhz7ci1x0fipia70ns0qffciwiz48r")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bitflags" ,rust-bitflags-0.7) + ("rust-clippy" ,rust-clippy-0.0) + ("rust-glob" ,rust-glob-0.2) + ("rust-lazy-static" ,rust-lazy-static-0.2) + ("rust-libc" ,rust-libc-0.2) + ("rust-libloading" ,rust-libloading-0.3)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-environmental-variable + (lambda* (#:key inputs #:allow-other-keys) + (let ((clang (assoc-ref inputs "libclang"))) + (setenv "LIBCLANG_PATH" + (string-append clang "/lib"))) + #t))))))) + (define-public rust-clap-2 (package (name "rust-clap") -- cgit v1.2.3 From d1e647e3638e1c2bcedfc918ccbd34a7ad78315a Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:13:24 +0300 Subject: gnu: Add rust-cexpr-0.2. * gnu/packages/crates-io.scm (rust-cexpr-0.2): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index db52c144c9..39332dd78a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1789,6 +1789,37 @@ archive to be linked into Rustcode.") "This package provides a C expression parser and evaluator.") (license (list license:asl2.0 license:expat)))) +(define-public rust-cexpr-0.2 + (package + (inherit rust-cexpr-0.3) + (name "rust-cexpr") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "cexpr" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0v1xa3758czmj8h97gh548mr8g0v13ixxvrlm1s79nb7jmgc9aj2")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-nom" ,rust-nom-3)) + #:cargo-development-inputs + (("rust-clang-sys" ,rust-clang-sys-0.11)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-environmental-variable + (lambda* (#:key inputs #:allow-other-keys) + (let ((clang (assoc-ref inputs "libclang"))) + (setenv "LIBCLANG_PATH" + (string-append clang "/lib"))) + #t))))) + (inputs + `(("libclang" ,clang))))) + (define-public rust-chrono-0.4 (package (name "rust-chrono") -- cgit v1.2.3 From bb088feeff52db2069b1cb64745b0f6ff66caff0 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:14:43 +0300 Subject: gnu: Add rust-bindgen-0.33. * gnu/packages/crates-io.scm (rust-bindgen-0.33): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 39332dd78a..d403e387d4 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -985,6 +985,39 @@ Bresenham's line algorithm.") libraries.") (license license:bsd-3))) +(define-public rust-bindgen-0.33 + (package + (inherit rust-bindgen-0.50) + (name "rust-bindgen") + (version "0.33.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "bindgen" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0vnw5fb74gl9pgnimgbrkac1xgwrjz86pqilx20rbkia77cdhgk0")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cexpr" ,rust-cexpr-0.2) + ("rust-cfg-if" ,rust-cfg-if-0.1) + ("rust-clang-sys" ,rust-clang-sys-0.22) + ("rust-clap" ,rust-clap-2) + ("rust-env-logger" ,rust-env-logger-0.5) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-log" ,rust-log-0.4) + ("rust-peeking-take-while" ,rust-peeking-take-while-0.1) + ("rust-quote" ,rust-quote-0.3) + ("rust-regex" ,rust-regex-0.2) + ("rust-which" ,rust-which-1.0)) + #:cargo-development-inputs + (("rust-clap" ,rust-clap-2) + ("rust-diff" ,rust-diff-0.1) + ("rust-shlex" ,rust-shlex-0.1)))))) + (define-public rust-bit-set-0.5 (package (name "rust-bit-set") -- cgit v1.2.3 From 63502072bdc9b2408812b83a3157439743d52678 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:15:16 +0300 Subject: gnu: Add rust-winpty-sys-0.4. * gnu/packages/crates-io.scm (rust-winpty-sys-0.4): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d403e387d4..5799d953ee 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -19183,6 +19183,30 @@ color in a Windows console.") (license (list license:unlicense license:expat)))) +(define-public rust-winpty-sys-0.4 + (package + (name "rust-winpty-sys") + (version "0.4.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "winpty-sys" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0s5m2vvlw7wphc466s47zfmp08zk00wzj999l1w3ajqlxbnfgb9x")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-bindgen" ,rust-bindgen-0.33) + ("rust-cc" ,rust-cc-1.0)))) + (home-page "https://github.com/rprichard/winpty") + (synopsis "Rust winpty bindings") + (description "Rust winpty bindings.") + (license license:expat))) + (define-public rust-winreg-0.6 (package (name "rust-winreg") -- cgit v1.2.3 From 66d27f5d779507ac56e7f4df36b4d2e04bee41f6 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:27:15 +0300 Subject: gnu: Add rust-partial-io-0.2. * gnu/packages/crates-io.scm (rust-partial-io-0.2): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 5799d953ee..18b502b751 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -10763,6 +10763,36 @@ deserialization, and interpreter in Rust.") (license (list license:asl2.0 license:expat)))) +(define-public rust-partial-io-0.2 + (package + (name "rust-partial-io") + (version "0.2.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "partial-io" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "03iynvayh11a4mckhwflm5y1qmnkw5m3b20gzi1crpasndy3h8xx")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-futures" ,rust-futures-0.1) + ("rust-quickcheck" ,rust-quickcheck-0.4) + ("rust-tokio-io" ,rust-tokio-io-0.1)) + #:cargo-development-inputs + (("rust-lazy-static" ,rust-lazy-static-0.2) + ("rust-quickcheck" ,rust-quickcheck-0.4) + ("rust-tokio-core" ,rust-tokio-core-0.1)))) + (home-page "https://github.com/facebookincubator/rust-partial-io") + (synopsis + "Helpers to test partial, interrupted and would-block I/O operations") + (description + "Helpers to test partial, interrupted and would-block I/O operations.") + (license license:bsd-3))) + (define-public rust-paste-0.1 (package (name "rust-paste") -- cgit v1.2.3 From f4b8c2729793d61dfcd7b5533e55461598d035cd Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:27:58 +0300 Subject: gnu: Add rust-bzip2-0.3. * gnu/packages/crates-io.scm (rust-bzip2-0.3): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 18b502b751..b9ec9fcc29 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1570,6 +1570,39 @@ little-endian.") #:cargo-development-inputs (("rust-rand" ,rust-rand-0.3)))))) +(define-public rust-bzip2-0.3 + (package + (name "rust-bzip2") + (version "0.3.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "bzip2" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0fvfwanp42j1zpig880jhb5mc0na50bijmwd6211p77sy35w7ds2")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bzip2-sys" ,rust-bzip2-sys-0.1) + ("rust-futures" ,rust-futures-0.1) + ("rust-libc" ,rust-libc-0.2) + ("rust-tokio-io" ,rust-tokio-io-0.1)) + #:cargo-development-inputs + (("rust-partial-io" ,rust-partial-io-0.2) + ("rust-quickcheck" ,rust-quickcheck-0.4) + ("rust-rand" ,rust-rand-0.3) + ("rust-tokio-core" ,rust-tokio-core-0.1)))) + (home-page "https://github.com/alexcrichton/bzip2-rs") + (synopsis + "Rust bindings to libbzip2 for bzip2 compression and decompression") + (description + "Bindings to @code{libbzip2} for @code{bzip2} compression and decompression +exposed as Reader/Writer streams.") + (license (list license:expat license:asl2.0)))) + (define-public rust-bzip2-sys-0.1 (package (name "rust-bzip2-sys") -- cgit v1.2.3 From b7c40a971344dcf214f1fe9ae657130e55efe89b Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:29:32 +0300 Subject: gnu: Add rust-zip-0.5. * gnu/packages/crates-io.scm (rust-zip-0.5): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b9ec9fcc29..9cf62015ce 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -19566,6 +19566,38 @@ to XDG Base Directory specification") (("rust-clippy" ,rust-clippy-0.0) ("rust-linked-hash-map" ,rust-linked-hash-map-0.3)))))) +(define-public rust-zip-0.5 + (package + (name "rust-zip") + (version "0.5.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "zip" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1biv5kh4fl7wpjlsxfczvgrdjlybf0xjaw7s36didql8lxxz67z4")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bzip2" ,rust-bzip2-0.3) + ("rust-crc32fast" ,rust-crc32fast-1.2) + ("rust-flate2" ,rust-flate2-1.0) + ("rust-podio" ,rust-podio-0.1) + ("rust-time" ,rust-time-0.1)) + #:cargo-development-inputs + (("rust-bencher" ,rust-bencher-0.1) + ("rust-rand" ,rust-rand-0.4) + ("rust-walkdir" ,rust-walkdir-1.0)))) + (home-page "https://github.com/mvdnes/zip-rs.git") + (synopsis + "Library to support the reading and writing of zip files") + (description + "Library to support the reading and writing of zip files.") + (license license:expat))) + (define-public rust-zoneinfo-compiled-0.4 (package (name "rust-zoneinfo-compiled") -- cgit v1.2.3 From 754917c903c80429b29df657311c148cf8a846bf Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:34:41 +0300 Subject: gnu: Add rust-pnacl-build-helper-1.4. * gnu/packages/crates-io.scm (rust-pnacl-build-helper-1.4): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 9cf62015ce..2a4605d23f 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -11390,6 +11390,31 @@ used in Cargo build scripts.") "Lazily evaluated, order-independent plugins for extensible types.") (license license:expat))) +(define-public rust-pnacl-build-helper-1.4 + (package + (name "rust-pnacl-build-helper") + (version "1.4.11") + (source + (origin + (method url-fetch) + (uri (crate-uri "pnacl-build-helper" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "145hxz3m3sg8mm9sfqqqaarnna43v65l6whwswrvcvy0fzp17gnz")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-tempdir" ,rust-tempdir-0.3) + ("rust-walkdir" ,rust-walkdir-1.0)))) + (home-page "https://github.com/DiamondLovesYou/cargo-pnacl-helper") + (synopsis + "Build script helper for building PNaCl/NaCl C/CXX libraries from source") + (description + "Build script helper for building PNaCl/NaCl C/CXX libraries from source") + (license license:mpl2.0))) + (define-public rust-png-0.15 (package (name "rust-png") -- cgit v1.2.3 From a86fc40dc384ae237b10a1d401f984c6f277aa88 Mon Sep 17 00:00:00 2001 From: Valentin Ignatev Date: Sun, 26 Jan 2020 16:35:52 +0300 Subject: gnu: Add rust-libressl-pnacl-sys-2. * gnu/packages/crates-io.scm (rust-libressl-pnacl-sys-2): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 2a4605d23f..5b5c36525c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -8161,6 +8161,30 @@ functions and static variables these libraries contain.") (base32 "16pc0gx4gkg0q2s1ssq8268brn14j8344623vwhadmivc4lsmivz")))))) +(define-public rust-libressl-pnacl-sys-2 + (package + (name "rust-libressl-pnacl-sys") + (version "2.1.6") + (source + (origin + (method url-fetch) + (uri (crate-uri "libressl-pnacl-sys" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0w9yvgrf591phpr1222j0dj7x1n489v2sihnr8syz8xn3aamih6b")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-pnacl-build-helper" ,rust-pnacl-build-helper-1.4)))) + (home-page "https://github.com/DiamondLovesYou/libressl-pnacl-sys") + (synopsis "Openssl linking provider for PNaCl/NaCl targets") + (description + "This package provides an openssl linking provider for PNaCl/NaCl targets.") + (license license:expat))) + (define-public rust-libssh2-sys-0.2 (package (name "rust-libssh2-sys") -- cgit v1.2.3 From b38dd34f40ff9a779f9e8faf2c8d3739b6d6270f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 13:14:57 +0100 Subject: gnu: crossmap: Update to 0.3.8. * gnu/packages/bioinformatics.scm (crossmap): Update to 0.3.8. [arguments]: Remove to build with default Python. [inputs]: Add python-pybigwig; replace python2-bx-python, python2-numpy, and python2-pysam with their Python 3 variants. [native-inputs]: Replace python2-cython and python2-nose with their Python 3 variants. --- gnu/packages/bioinformatics.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7f2a852fb0..1f17c019f0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2272,23 +2272,23 @@ time.") (define-public crossmap (package (name "crossmap") - (version "0.2.9") + (version "0.3.8") (source (origin (method url-fetch) (uri (pypi-uri "CrossMap" version)) (sha256 (base32 - "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p")))) + "1sb2f2qbxya4fzw3yjl09vbrs8vfmw22zrygrvz004sf9gb1vkan")))) (build-system python-build-system) - (arguments `(#:python ,python-2)) (inputs - `(("python-bx-python" ,python2-bx-python) - ("python-numpy" ,python2-numpy) - ("python-pysam" ,python2-pysam) + `(("python-bx-python" ,python-bx-python) + ("python-numpy" ,python-numpy) + ("python-pybigwig" ,python-pybigwig) + ("python-pysam" ,python-pysam) ("zlib" ,zlib))) (native-inputs - `(("python-cython" ,python2-cython) - ("python-nose" ,python2-nose))) + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose))) (home-page "http://crossmap.sourceforge.net/") (synopsis "Convert genome coordinates between assemblies") (description -- cgit v1.2.3 From 920757566996f6a22b14074b92acd4bdf29a47cd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 14:05:12 +0100 Subject: gnu: diamond: Update to 0.9.30. * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30. --- 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 1f17c019f0..546be38ab0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2578,7 +2578,7 @@ accurately delineate genomic rearrangements throughout the genome.") (define-public diamond (package (name "diamond") - (version "0.9.22") + (version "0.9.30") (source (origin (method git-fetch) (uri (git-reference @@ -2587,7 +2587,7 @@ accurately delineate genomic rearrangements throughout the genome.") (file-name (git-file-name name version)) (sha256 (base32 - "0bky78v79g3wmdpsd706cscckgw1v09fg8vdd0z8z0d5b97aj9zl")))) + "0k6f3kb6cniw11xw6763kkbs1sl0yack7xsy7q5fl5v170ssphq4")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target -- cgit v1.2.3 From 146430ea0e0008ff91972f944920dfa01d1ab360 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 26 Feb 2020 14:05:36 +0100 Subject: gnu: proteinortho: Update to 6.0.14. * gnu/packages/bioinformatics.scm (proteinortho): Update to 6.0.14. [source]: Fetch from git; remove pre-built scripts. [arguments]: Set make-flags; update wrap-programs phase to wrap all scripts. [inputs]: Add guile-3.0, diamond, python-wrapper, lapack, and openblas; remove python-2. [native-inputs]: Add which. [license]: Update to GPLv3+ --- gnu/packages/bioinformatics.scm | 52 ++++++++++++++++++++++++++--------------- 1 file changed, 33 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 546be38ab0..8ed13b22e5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4921,20 +4921,26 @@ predicts the locations of structural units in the sequences.") (define-public proteinortho (package (name "proteinortho") - (version "5.16b") - (source - (origin - (method url-fetch) - (uri - (string-append - "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v" - version "_src.tar.gz")) - (sha256 - (base32 - "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j")))) + (version "6.0.14") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/paulklemm_PHD/proteinortho.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0pmy617zy2z2w6hjqxjhf3rzikf5n3mpia80ysq8233vfr7wrzff")) + (modules '((guix build utils))) + (snippet + '(begin + ;; remove pre-built scripts + (delete-file-recursively "src/BUILD/") + #t)))) (build-system gnu-build-system) (arguments `(#:test-target "test" + #:make-flags '("CC=gcc") #:phases (modify-phases %standard-phases (replace 'configure @@ -4952,15 +4958,23 @@ predicts the locations of structural units in the sequences.") #t)) (add-after 'install 'wrap-programs (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((path (getenv "PATH")) - (out (assoc-ref outputs "out")) - (binary (string-append out "/bin/proteinortho5.pl"))) - (wrap-program binary `("PATH" ":" prefix (,path)))) + (let ((path (getenv "PATH")) + (out (assoc-ref outputs "out"))) + (for-each (lambda (script) + (wrap-script script `("PATH" ":" prefix (,path)))) + (cons (string-append out "/bin/proteinortho") + (find-files out "\\.(pl|py)$")))) #t))))) (inputs - `(("perl" ,perl) - ("python" ,python-2) - ("blast+" ,blast+))) + `(("guile" ,guile-3.0) ; for wrap-script + ("diamond" ,diamond) + ("perl" ,perl) + ("python" ,python-wrapper) + ("blast+" ,blast+) + ("lapack" ,lapack) + ("openblas" ,openblas))) + (native-inputs + `(("which" ,which))) (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") (synopsis "Detect orthologous genes across species") (description @@ -4968,7 +4982,7 @@ predicts the locations of structural units in the sequences.") species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at once.") - (license license:gpl2+))) + (license license:gpl3+))) (define-public pyicoteo (package -- cgit v1.2.3 From b68f5a68f895307ee184da725882d6f243ccded6 Mon Sep 17 00:00:00 2001 From: Evan Straw Date: Sat, 22 Feb 2020 19:48:54 -0800 Subject: gnu: Add emacs-company-emoji. [[PGP Signed Part:No public key for F530C3B4A2A9F06D created at 2020-02-23T04:48:54+0100 using RSA]] From 6c23c5966a3c7ed01c784874e410d5fe3009bfc5 Mon Sep 17 00:00:00 2001 From: Evan Straw Date: Sat, 22 Feb 2020 19:47:19 -0800 Subject: [PATCH] gnu: Add emacs-company-emoji. * gnu/packages/emacs-xyz.scm (emacs-company-emoji): New variable. --- gnu/packages/emacs-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 0932c87e9a..1025529fd4 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -59,6 +59,7 @@ ;;; Copyright © 2019 David Wilson ;;; Copyright © 2020 Paul Garlick ;;; Copyright © 2020 Robert Smith +;;; Copyright © 2020 Evan Straw ;;; ;;; This file is part of GNU Guix. ;;; @@ -21536,3 +21537,26 @@ Values are stored in a directory in @code{user-emacs-directory}, using one file per value. This makes it easy to delete or remove unused variables.") (license license:gpl3+))) + +(define-public emacs-company-emoji + (package + (name "emacs-company-emoji") + (version "2.5.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dunn/company-emoji/") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0r9zcbm3nb3zw5cwrkl098v5b49jbga5404bj7j55g6k4rwkjar2")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-company" ,emacs-company))) + (home-page "https://github.com/dunn/company-emoji/") + (synopsis "Company completion back-end for emoji") + (description + "This library is a Company back-end providing auto-completion for +emoji.") + (license license:gpl3+))) -- cgit v1.2.3 From 6fda3a6cb421121d6ff600b9bc836e24c18a433a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 26 Feb 2020 17:00:21 +0100 Subject: gnu: pocl: Build with LLVM@9. * gnu/packages/opencl.scm (pocl)[inputs]: Change from LLVM-8 to LLVM. --- gnu/packages/opencl.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/opencl.scm b/gnu/packages/opencl.scm index 04b3cb0524..32eb360e04 100644 --- a/gnu/packages/opencl.scm +++ b/gnu/packages/opencl.scm @@ -315,7 +315,7 @@ back-end for the LLVM compiler framework.") (inputs `(("clang" ,clang) ("hwloc" ,hwloc-2 "lib") - ("llvm" ,llvm-8) + ("llvm" ,llvm) ("ocl-icd" ,ocl-icd))) (arguments `(#:configure-flags -- cgit v1.2.3 From ae9cfc647daea456823adecba28021896b51407e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 26 Feb 2020 16:15:18 +0100 Subject: gnu: LibUV: Add version 1.34.2. * gnu/packages/libevent.scm (libuv/latest): New public variable. --- gnu/packages/libevent.scm | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm index 338b2afd4e..3754a5c427 100644 --- a/gnu/packages/libevent.scm +++ b/gnu/packages/libevent.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2017 Mark H Weaver ;;; Copyright © 2015 Eric Dvorsak ;;; Copyright © 2016 David Thompson -;;; Copyright © 2017, 2019 Marius Bakke +;;; Copyright © 2017, 2019, 2020 Marius Bakke ;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019 Pierre Neidhardt @@ -130,6 +130,20 @@ resolution, asynchronous file system operations, and threading primitives.") ;; details. Documentation is CC-BY 4.0 as of 1.12.0; see 'LICENSE-docs'. (license (list expat cc-by4.0)))) +;; This newer version of LibUV is required by 'node'. Package it separately +;; to avoid massive rebuilds. +(define-public libuv/latest + (package/inherit + libuv + (version "1.34.2") + (source (origin + (method url-fetch) + (uri (string-append "https://dist.libuv.org/dist/v" version + "/libuv-v" version ".tar.gz")) + (sha256 + (base32 + "0inzk8qpw78im3fiazrc54qi1gcapbs8dhf0hk3kwpzg0i2kpnb5")))))) + (define-public perl-anyevent (package (name "perl-anyevent") -- cgit v1.2.3 From bbd804b29bbb9bc7739688bca192eb83d0edb882 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 26 Feb 2020 16:15:47 +0100 Subject: gnu: nghttp2: Add version 1.40.0. * gnu/packages/web.scm (nghttp2-1.40): New public variable. --- gnu/packages/web.scm | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 4976059203..2be3dfefe4 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -19,7 +19,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2016 Bake Timmons ;;; Copyright © 2017 Thomas Danckaert -;;; Copyright © 2017, 2018 Marius Bakke +;;; Copyright © 2017, 2018, 2020 Marius Bakke ;;; Copyright © 2017 Kei Kebreau ;;; Copyright © 2017 Petter ;;; Copyright © 2017 Pierre Langlois @@ -7025,6 +7025,20 @@ compressed JSON header blocks. (base32 "12yfsjghbaypp4w964d45ih9vs38g6anih80wbsflaxx192idlm2")))))) +;; 'Node' requires this newer version, to be removed on the next rebuild cycle. +(define-public nghttp2-1.40 + (package/inherit + nghttp2 + (version "1.40.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/nghttp2/nghttp2/" + "releases/download/v" version "/" + "nghttp2-" version ".tar.xz")) + (sha256 + (base32 + "0wwhwv7cvi1vxpdjwvg0kpa4jzhszclpnwrwfcw728zz53a47z09")))))) + (define-public hpcguix-web (let ((commit "f39c90b35e99e4122b0866ec4337020d61c81508") (revision "4")) -- cgit v1.2.3 From 458c3ff552005cbf69ed4a1daee3529214ae73cf Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 26 Feb 2020 16:16:29 +0100 Subject: gnu: node: Update to 10.19.0. * gnu/packages/node.scm (node): Update to 10.19.0. [inputs]: Remove LIBUV and NGHTTP2:LIB. Add LIBUV/LATEST and NGHTTP2-1.40:LIB. --- gnu/packages/node.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm index ee35d76852..296a5e1980 100644 --- a/gnu/packages/node.scm +++ b/gnu/packages/node.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2016 Ludovic Courtès ;;; Copyright © 2017 Mike Gerwitz ;;; Copyright © 2018 Tobias Geerinckx-Rice -;;; Copyright © 2018, 2019 Marius Bakke +;;; Copyright © 2018, 2019, 2020 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -45,14 +45,14 @@ (define-public node (package (name "node") - (version "10.16.0") + (version "10.19.0") (source (origin (method url-fetch) (uri (string-append "https://nodejs.org/dist/v" version "/node-v" version ".tar.xz")) (sha256 (base32 - "0236jlb1hxhzqjlmmlxipcycrndiq92c8434iyy7zshh3n4pzqqq")) + "0sginvcsf7lrlzsnpahj4bj1f673wfvby8kaxgvzlrbb7sy229v2")) (modules '((guix build utils))) (snippet `(begin @@ -170,8 +170,8 @@ `(("c-ares" ,c-ares) ("http-parser" ,http-parser) ("icu4c" ,icu4c) - ("libuv" ,libuv) - ("nghttp2" ,nghttp2 "lib") + ("libuv" ,libuv/latest) + ("nghttp2" ,nghttp2-1.40 "lib") ("openssl" ,openssl) ("zlib" ,zlib))) (synopsis "Evented I/O for V8 JavaScript") -- cgit v1.2.3 From 5cfc6a88e9fbb9f34855ebd43264266b0201ce50 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 26 Feb 2020 17:22:22 +0100 Subject: gnu: node: Disable failing tests on armhf-linux. * gnu/packages/node.scm (node)[arguments]: When building on armhf-linux, disable several zlib tests. --- gnu/packages/node.scm | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm index 296a5e1980..eb8c83d831 100644 --- a/gnu/packages/node.scm +++ b/gnu/packages/node.scm @@ -74,8 +74,7 @@ #t)))) (build-system gnu-build-system) (arguments - ;; TODO: Purge the bundled copies from the source. - '(#:configure-flags '("--shared-cares" + `(#:configure-flags '("--shared-cares" "--shared-http-parser" "--shared-libuv" "--shared-nghttp2" @@ -121,6 +120,20 @@ ;; https://github.com/nodejs/node/issues/31213 (delete-file "test/parallel/test-net-listen-after-destroying-stdin.js") + ;; FIXME: These tests fail on armhf-linux: + ;; https://github.com/nodejs/node/issues/31970 + ,@(if (string-prefix? "arm" (%current-system)) + '((for-each delete-file + '("test/parallel/test-zlib.js" + "test/parallel/test-zlib-brotli.js" + "test/parallel/test-zlib-brotli-flush.js" + "test/parallel/test-zlib-brotli-from-brotli.js" + "test/parallel/test-zlib-brotli-from-string.js" + "test/parallel/test-zlib-convenience-methods.js" + "test/parallel/test-zlib-random-byte-pipes.js" + "test/parallel/test-zlib-write-after-flush.js"))) + '()) + ;; These tests have an expiry date: they depend on the validity of ;; TLS certificates that are bundled with the source. We want this ;; package to be reproducible forever, so remove those. -- cgit v1.2.3 From f5cc5de8b6c542295b08c108d9a6f1ca52cdc37a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 26 Feb 2020 20:59:09 +0100 Subject: gnu: clang: Fix C++ search path handling on non-x86_64. * gnu/packages/llvm.scm (clang-from-llvm)[arguments]: Add phase 'add-missing-triplets'. --- gnu/packages/llvm.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index 38f2118173..4a1a1239d7 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -208,6 +208,24 @@ compiler. In LLVM this library is called \"compiler-rt\".") #:build-type "Release" #:phases (modify-phases %standard-phases + (add-after 'unpack 'add-missing-triplets + (lambda _ + ;; Clang iterates through known triplets to search for + ;; GCC's headers, but does not recognize some of the + ;; triplets that are used in Guix. + (substitute* ,@(if (version>=? version "6.0") + '("lib/Driver/ToolChains/Gnu.cpp") + '("lib/Driver/ToolChains.cpp")) + (("\"aarch64-linux-gnu\"," all) + (string-append "\"aarch64-unknown-linux-gnu\", " + all)) + (("\"arm-linux-gnueabihf\"," all) + (string-append all + " \"arm-unknown-linux-gnueabihf\",")) + (("\"i686-pc-linux-gnu\"," all) + (string-append "\"i686-unknown-linux-gnu\", " + all))) + #t)) (add-after 'unpack 'set-glibc-file-names (lambda* (#:key inputs #:allow-other-keys) -- cgit v1.2.3 From 5041cc28cb33a714ea40c91e14e55706d6dbb9dc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 26 Feb 2020 21:06:01 +0100 Subject: gnu: clang: Move version conditionals out of the builder. * gnu/packages/llvm.scm (clang-from-llvm)[arguments]: Rewrite phase 'set-glibc-file-names' to use VERSION>=? from (guix utils) and splice in the relevant build code, instead of doing the comparison at build time. --- gnu/packages/llvm.scm | 107 ++++++++++++++++++++++++-------------------------- 1 file changed, 51 insertions(+), 56 deletions(-) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index 4a1a1239d7..41217d14f0 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -226,64 +226,59 @@ compiler. In LLVM this library is called \"compiler-rt\".") (string-append "\"i686-unknown-linux-gnu\", " all))) #t)) - (add-after - 'unpack 'set-glibc-file-names - (lambda* (#:key inputs #:allow-other-keys) - (let ((libc (assoc-ref inputs "libc")) - (compiler-rt (assoc-ref inputs "clang-runtime")) - (gcc (assoc-ref inputs "gcc")) - (version - (string->number - ,(version-major (package-version clang-runtime))))) - (cond - ((> version 3) - ;; Link to libclang_rt files from clang-runtime. - (substitute* "lib/Driver/ToolChain.cpp" - (("getDriver\\(\\)\\.ResourceDir") - (string-append "\"" compiler-rt "\""))) - - ;; Make "LibDir" refer to /lib so that it - ;; uses the right dynamic linker file name. - (substitute* "lib/Driver/ToolChains/Linux.cpp" - (("(^[[:blank:]]+LibDir = ).*" _ declaration) - (string-append declaration "\"" libc "/lib\";\n")) - - ;; Make clang look for libstdc++ in the right - ;; location. - (("LibStdCXXIncludePathCandidates\\[\\] = \\{") - (string-append - "LibStdCXXIncludePathCandidates[] = { \"" gcc "/include/c++\",")) - - ;; Make sure libc's libdir is on the search path, to - ;; allow crt1.o & co. to be found. - (("@GLIBC_LIBDIR@") - (string-append libc "/lib")))) - (else - (substitute* "lib/Driver/Tools.cpp" - ;; Patch the 'getLinuxDynamicLinker' function so that - ;; it uses the right dynamic linker file name. - (("/lib64/ld-linux-x86-64.so.2") - (string-append libc - ,(glibc-dynamic-linker)))) - - ;; Link to libclang_rt files from clang-runtime. - ;; This substitution needed slight adjustment in 3.8. - (if (< 3.8 (string->number ,(version-major+minor - (package-version - clang-runtime)))) - (substitute* "lib/Driver/Tools.cpp" - (("TC\\.getDriver\\(\\)\\.ResourceDir") - (string-append "\"" compiler-rt "\""))) + (add-after 'unpack 'set-glibc-file-names + (lambda* (#:key inputs #:allow-other-keys) + (let ((libc (assoc-ref inputs "libc")) + (compiler-rt (assoc-ref inputs "clang-runtime")) + (gcc (assoc-ref inputs "gcc"))) + ,@(cond + ((version>=? version "6.0") + `(;; Link to libclang_rt files from clang-runtime. (substitute* "lib/Driver/ToolChain.cpp" (("getDriver\\(\\)\\.ResourceDir") - (string-append "\"" compiler-rt "\"")))) - - ;; Make sure libc's libdir is on the search path, to - ;; allow crt1.o & co. to be found. - (substitute* "lib/Driver/ToolChains.cpp" - (("@GLIBC_LIBDIR@") - (string-append libc "/lib"))))) - #t))) + (string-append "\"" compiler-rt "\""))) + + ;; Make "LibDir" refer to /lib so that it + ;; uses the right dynamic linker file name. + (substitute* "lib/Driver/ToolChains/Linux.cpp" + (("(^[[:blank:]]+LibDir = ).*" _ declaration) + (string-append declaration "\"" libc "/lib\";\n")) + + ;; Make clang look for libstdc++ in the right + ;; location. + (("LibStdCXXIncludePathCandidates\\[\\] = \\{") + (string-append + "LibStdCXXIncludePathCandidates[] = { \"" gcc + "/include/c++\",")) + + ;; Make sure libc's libdir is on the search path, to + ;; allow crt1.o & co. to be found. + (("@GLIBC_LIBDIR@") + (string-append libc "/lib"))))) + (else + `((substitute* "lib/Driver/Tools.cpp" + ;; Patch the 'getLinuxDynamicLinker' function so that + ;; it uses the right dynamic linker file name. + (("/lib64/ld-linux-x86-64.so.2") + (string-append libc + ,(glibc-dynamic-linker)))) + + ;; Link to libclang_rt files from clang-runtime. + ;; This substitution needed slight adjustment in 3.8. + ,@(if (version>=? version "3.8") + '((substitute* "lib/Driver/Tools.cpp" + (("TC\\.getDriver\\(\\)\\.ResourceDir") + (string-append "\"" compiler-rt "\"")))) + '((substitute* "lib/Driver/ToolChain.cpp" + (("getDriver\\(\\)\\.ResourceDir") + (string-append "\"" compiler-rt "\""))))) + + ;; Make sure libc's libdir is on the search path, to + ;; allow crt1.o & co. to be found. + (substitute* "lib/Driver/ToolChains.cpp" + (("@GLIBC_LIBDIR@") + (string-append libc "/lib")))))) + #t))) (add-after 'install 'install-clean-up-/share/clang (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) -- cgit v1.2.3 From 66ed570a05c0363b8aa856469bddf0775a4554ee Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Sat, 22 Feb 2020 16:48:02 -0500 Subject: gnu: emacs-elixir-mode: Fix capitalization in description. * gnu/packages/emacs-xyz.scm (emacs-elixir-mode)[description]: Downcase incorrectly capitalized word. Signed-off-by: Marius Bakke --- gnu/packages/emacs-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1025529fd4..cfc92cecc5 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20371,7 +20371,7 @@ color. Designed for 256-color terminals. Comes in light and dark!") "https://github.com/elixir-editors/emacs-elixir") (synopsis "Major mode for editing Elixir files") (description - "Elixir-Mode Provides font-locking, indentation and navigation support + "Elixir-Mode provides font-locking, indentation and navigation support for the Elixir programming language.") (license license:gpl3+))) -- cgit v1.2.3 From b18d3c526834a58d71566be6f0f0453dc55881e2 Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Sat, 22 Feb 2020 16:49:00 -0500 Subject: gnu: emacs-eacl: Fix typo in description. * gnu/packages/emacs-xyz.scm (emacs-eacl)[description]: Correct misspelling of "commands". Signed-off-by: Marius Bakke --- gnu/packages/emacs-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index cfc92cecc5..b61eb19069 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -19361,7 +19361,7 @@ with passwords for paths matching regexps.") `(("emacs-ivy" ,emacs-ivy))) (home-page "https://github.com/redguardtoo/eacl") (synopsis "Auto-complete lines by using @code{grep} on a project") - (description "This package provides auto-completion cammands for single + (description "This package provides auto-completion commands for single and multiple lines of code in a project.") (license license:gpl3+))) -- cgit v1.2.3 From 176dd26b38410b371a6283813698d6d7a419ada3 Mon Sep 17 00:00:00 2001 From: Vincent Legoll Date: Sat, 22 Feb 2020 00:37:23 +0100 Subject: gnu: benchmark: Add bonnie++. * gnu/packages/benchmark.scm (bonnie++): New variable. Signed-off-by: Marius Bakke --- gnu/packages/benchmark.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index 602681ac86..9ae30eefc8 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2019 Eric Bavier ;;; Copyright © 2019 Gábor Boskovits ;;; Copyright © 2019 Ludovic Courtès +;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,6 +36,7 @@ #:use-module (gnu packages linux) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) + #:use-module (gnu packages perl) #:use-module (gnu packages python) #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) @@ -231,3 +233,28 @@ This can give a much better understanding of the command's performance.") "Benchmark is a library to benchmark code snippets, similar to unit tests.") (license license:asl2.0))) + +(define-public bonnie++ + (package + (name "bonnie++") + (version "1.98") + (source (origin + (method url-fetch) + (uri (string-append "https://www.coker.com.au/bonnie++/bonnie++-" + version ".tgz")) + (sha256 + (base32 + "010bmlmi0nrlp3aq7p624sfaj5a65lswnyyxk3cnz1bqig0cn2vf")))) + (build-system gnu-build-system) + (native-inputs + `(("perl" ,perl))) + (arguments '(#:tests? #f)) ; there are no tests + (home-page "https://doc.coker.com.au/projects/bonnie/") + (synopsis "Hard drive and file system benchmark suite") + (description + "Bonnie++ is a benchmark suite that is aimed at performing a number of +simple tests of hard drive and file system performance. Bonnie++ allows you to +benchmark how your file systems perform with respect to data read and write +speed, the number of seeks that can be performed per second, and the number of +file metadata operations that can be performed per second.") + (license license:gpl2))) ;GPL 2 only, see copyright.txt -- cgit v1.2.3 From 233332c2e9cb76927dd7573b24bd7cdf7afca993 Mon Sep 17 00:00:00 2001 From: Vincent Legoll Date: Mon, 24 Feb 2020 23:42:35 +0100 Subject: gnu: musl: Update to 1.2.0. * gnu/packages/musl (musl): Update to 1.2.0. Signed-off-by: Marius Bakke --- gnu/packages/musl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/musl.scm b/gnu/packages/musl.scm index 7e4e27d00d..44c39750d6 100644 --- a/gnu/packages/musl.scm +++ b/gnu/packages/musl.scm @@ -28,14 +28,14 @@ (define-public musl (package (name "musl") - (version "1.1.24") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://www.musl-libc.org/releases/" "musl-" version ".tar.gz")) (sha256 (base32 - "18r2a00k82hz0mqdvgm7crzc7305l36109c0j9yjmkxj2alcjw0k")))) + "1s6lix02k1ijm4nmhzpmwzk5w6xfkhn70nvvk8zjs51r24cpppn6")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; musl has no tests -- cgit v1.2.3 From cae3b3774ea9905bbf6a7299c3cd964cfa48a705 Mon Sep 17 00:00:00 2001 From: Jack Hill Date: Tue, 25 Feb 2020 14:16:07 -0500 Subject: gnu: vim-full: Describe differences from vim. * gnu/packages/vim.scm (vim-full)[description]: New field. Explain what vim-full provides over vim. Signed-off-by: Marius Bakke --- gnu/packages/vim.scm | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index 67f245b26d..a94a677b25 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2019 HiPhish ;;; Copyright © 2019 Julien Lepiller ;;; Copyright © 2019, 2020 Jakub Kądziołka +;;; Copyright © 2020 Jack Hill ;;; ;;; This file is part of GNU Guix. ;;; @@ -131,6 +132,8 @@ ("tzdata" ,tzdata-for-tests))) (home-page "https://www.vim.org/") (synopsis "Text editor based on vi") + ;; The description shares language with the vim-full package. When making + ;; changes, check if the other description also needs to be updated. (description "Vim is a highly configurable text editor built to enable efficient text editing. It is an improved version of the vi editor distributed with most UNIX @@ -254,7 +257,21 @@ with the editor vim."))) ("python-3" ,python) ("ruby" ,ruby) ("tcl" ,tcl) - ,@(package-inputs vim))))) + ,@(package-inputs vim))) + ;; The description shares language with the vim package. When making + ;; changes, check if the other description also needs to be updated. + (description "Vim is a highly configurable text editor built to enable efficient text +editing. It is an improved version of the vi editor distributed with most UNIX +systems. + +Vim is often called a \"programmer's editor,\" and so useful for programming +that many consider it an entire IDE. It's not just for programmers, though. +Vim is perfect for all kinds of text editing, from composing email to editing +configuration files. + +This package provides a version of Vim with many optional features enabled. +It includes a graphical interface, @command{gvim}, and support for plugins +written in the Python 3, Perl, Ruby, Tcl, and Lua programming languages."))) (define-public vim-neocomplete (package -- cgit v1.2.3 From e524b57740cd6ac51613b5072b6e43b4c5aab281 Mon Sep 17 00:00:00 2001 From: Evan Straw Date: Tue, 25 Feb 2020 11:27:16 -0800 Subject: gnu: awscli: Update to 1.18.6. * gnu/packages/python-web.scm (awscli): Update to 1.18.6. Signed-off-by: Marius Bakke --- gnu/packages/python-web.scm | 73 +++++++++++++++++++++++---------------------- 1 file changed, 37 insertions(+), 36 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index f9981454fb..310fec4edf 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -32,6 +32,7 @@ ;;; Copyright © 2019 Pierre Langlois ;;; Copyright © 2019 Tanguy Le Carrour ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2020 Evan Straw ;;; ;;; This file is part of GNU Guix. ;;; @@ -1600,43 +1601,43 @@ supports url redirection and retries, and also gzip and deflate decoding.") (define-public awscli (package - (name "awscli") - (version "1.14.41") - (source - (origin - (method url-fetch) - (uri (pypi-uri name version)) - (sha256 - (base32 - "0sispclx263lybbk19zp1n9yhg8xxx4jddypzgi24vpjaqnsbwlc")))) - (build-system python-build-system) - (arguments - ;; FIXME: The 'pypi' release does not contain tests. - '(#:tests? #f - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-reference-to-groff - (lambda _ - (substitute* "awscli/help.py" - (("if not self._exists_on_path\\('groff'\\):") "") - (("raise ExecutableNotFoundError\\('groff'\\)") "") - (("cmdline = \\['groff'") - (string-append "cmdline = ['" (which "groff") "'"))) - #t))))) - (propagated-inputs - `(("python-colorama" ,python-colorama) - ("python-botocore" ,python-botocore) - ("python-s3transfer" ,python-s3transfer) - ("python-docutils" ,python-docutils) - ("python-pyyaml" ,python-pyyaml) - ("python-rsa" ,python-rsa))) - (inputs - `(("groff" ,groff))) - (home-page "https://aws.amazon.com/cli/") - (synopsis "Command line client for AWS") - (description "AWS CLI provides a unified command line interface to the + (name "awscli") + (version "1.18.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri name version)) + (sha256 + (base32 + "0p479mfs9r0m82a217pap8156ijwvhv6r3kqa4k267gd05wgvygm")))) + (build-system python-build-system) + (arguments + ;; FIXME: The 'pypi' release does not contain tests. + '(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-reference-to-groff + (lambda _ + (substitute* "awscli/help.py" + (("if not self._exists_on_path\\('groff'\\):") "") + (("raise ExecutableNotFoundError\\('groff'\\)") "") + (("cmdline = \\['groff'") + (string-append "cmdline = ['" (which "groff") "'"))) + #t))))) + (propagated-inputs + `(("python-colorama" ,python-colorama) + ("python-botocore" ,python-botocore) + ("python-s3transfer" ,python-s3transfer) + ("python-docutils" ,python-docutils) + ("python-pyyaml" ,python-pyyaml) + ("python-rsa" ,python-rsa))) + (native-inputs + `(("groff" ,groff))) + (home-page "https://aws.amazon.com/cli/") + (synopsis "Command line client for AWS") + (description "AWS CLI provides a unified command line interface to the Amazon Web Services (AWS) API.") - (license license:asl2.0))) + (license license:asl2.0))) (define-public python-wsgiproxy2 (package -- cgit v1.2.3 From 513c0a0f4602018a49d8fd2dfa24670a3fa08ac9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 26 Feb 2020 21:44:48 +0100 Subject: daemon: Drop 'AT_STATX_DONT_SYNC' flag upon EINVAL. Fixes . Reported by Paul Garlick . * nix/libstore/gc.cc (LocalStore::removeUnusedLinks) [HAVE_STATX]: Add 'statx_flags' static variables. Clear 'AT_STATX_DONT_SYNC' flag from 'statx_flags' when 'statx' returns EINVAL. --- nix/libstore/gc.cc | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/nix/libstore/gc.cc b/nix/libstore/gc.cc index 77d7fa2dc7..8bc4e01eb0 100644 --- a/nix/libstore/gc.cc +++ b/nix/libstore/gc.cc @@ -581,15 +581,27 @@ void LocalStore::removeUnusedLinks(const GCState & state) #ifdef HAVE_STATX # define st_size stx_size # define st_nlink stx_nlink + static int statx_flags = AT_SYMLINK_NOFOLLOW | AT_STATX_DONT_SYNC; struct statx st; - if (statx(AT_FDCWD, path.c_str(), - AT_SYMLINK_NOFOLLOW | AT_STATX_DONT_SYNC, - STATX_SIZE | STATX_NLINK, &st) == -1) + + if (statx(AT_FDCWD, path.c_str(), statx_flags, + STATX_SIZE | STATX_NLINK, &st) == -1) { + if (errno == EINVAL) { + /* Old 3.10 kernels (CentOS 7) don't support + AT_STATX_DONT_SYNC, so try again without it. */ + statx_flags &= ~AT_STATX_DONT_SYNC; + if (statx(AT_FDCWD, path.c_str(), statx_flags, + STATX_SIZE | STATX_NLINK, &st) == -1) + throw SysError(format("statting `%1%'") % path); + } else { + throw SysError(format("statting `%1%'") % path); + } + } #else struct stat st; if (lstat(path.c_str(), &st) == -1) -#endif throw SysError(format("statting `%1%'") % path); +#endif if (st.st_nlink != 1) { actualSize += st.st_size; -- cgit v1.2.3 From fb7eec3a84afd7464027d2492a8b551a61df2725 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Tue, 25 Feb 2020 11:23:30 +0100 Subject: scripts: Emit GC hint if free space is lower than absolute and relative threshold. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * guix/scripts.scm (%disk-space-warning-absolute): New variable. (warn-about-disk-space): Test against %disk-space-warning-absolute. Fix error in display-hint due to extraneous 'profile' argument. Signed-off-by: Ludovic Courtès --- guix/scripts.scm | 65 ++++++++++++++++++++++++++++++++++++++++++++------------ 1 file changed, 51 insertions(+), 14 deletions(-) diff --git a/guix/scripts.scm b/guix/scripts.scm index 77cbf12350..7ad1d5194c 100644 --- a/guix/scripts.scm +++ b/guix/scripts.scm @@ -181,32 +181,69 @@ Show what and how will/would be built." (newline (guix-warning-port)))) (define %disk-space-warning - ;; The fraction (between 0 and 1) of free disk space below which a warning - ;; is emitted. - (make-parameter (match (and=> (getenv "GUIX_DISK_SPACE_WARNING") - string->number) - (#f .05) ;5% - (threshold (/ threshold 100.))))) + ;; Return a pair of absolute threshold (number of bytes) and relative + ;; threshold (fraction between 0 and 1) for the free disk space below which + ;; a warning is emitted. + ;; GUIX_DISK_SPACE_WARNING can contain both thresholds. A value in [0;100) + ;; is a relative threshold, otherwise it's absolute. The following + ;; example values are valid: + ;; - 1GiB;10% ;1 GiB absolute, and 10% relative. + ;; - 15G ;15 GiB absolute, and default relative. + ;; - 99% ;99% relative, and default absolute. + ;; - 99 ;Same. + ;; - 100 ;100 absolute, and default relative. + (let* ((default-absolute-threshold (size->number "5GiB")) + (default-relative-threshold 0.05) + (percentage->float (lambda (percentage) + (or (and=> (string->number + (car (string-split percentage #\%))) + (lambda (n) (/ n 100.0))) + default-relative-threshold))) + (size->number* (lambda (size) + (or (false-if-exception (size->number size)) + default-absolute-threshold))) + (absolute? (lambda (size) + (not (or (string-suffix? "%" size) + (false-if-exception (< (size->number size) 100))))))) + (make-parameter + (match (getenv "GUIX_DISK_SPACE_WARNING") + (#f (list default-absolute-threshold + default-relative-threshold)) + (env-string (match (string-split env-string #\;) + ((threshold) + (if (absolute? threshold) + (list (size->number* threshold) + default-relative-threshold) + (list default-absolute-threshold + (percentage->float threshold)))) + ((threshold1 threshold2) + (if (absolute? threshold1) + (list (size->number* threshold1) + (percentage->float threshold2)) + (list (size->number* threshold2) + (percentage->float threshold1)))))))))) (define* (warn-about-disk-space #:optional profile #:key - (threshold (%disk-space-warning))) + (thresholds (%disk-space-warning))) "Display a hint about 'guix gc' if less than THRESHOLD of /gnu/store is -available." +available. +THRESHOLD is a pair of (ABSOLUTE-THRESHOLD RELATIVE-THRESHOLD)." (let* ((stats (statfs (%store-prefix))) (block-size (file-system-block-size stats)) (available (* block-size (file-system-blocks-available stats))) (total (* block-size (file-system-block-count stats))) - (ratio (/ available total 1.))) - (when (< ratio threshold) - (warning (G_ "only ~,1f% of free space available on ~a~%") - (* ratio 100) (%store-prefix)) + (relative-threshold-in-bytes (* total (cadr thresholds))) + (absolute-threshold-in-bytes (* 1024 1024 1024 (car thresholds)))) + (when (< available (min relative-threshold-in-bytes + absolute-threshold-in-bytes)) + (warning (G_ "only ~,1f GiB of free space available on ~a~%") + available (%store-prefix)) (display-hint (format #f (G_ "Consider deleting old profile generations and collecting garbage, along these lines: @example guix gc --delete-generations=1m -@end example\n") - profile))))) +@end example\n")))))) ;;; scripts.scm ends here -- cgit v1.2.3 From a73a530df2b5bac3d82f074b13fe41cc1ea8ba12 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 26 Feb 2020 22:09:44 +0100 Subject: git-authenticate: Add sub-key for thomasd. This is a followup to commit 7dc0f1d5a8c248addfcaadf76e45bf601bc51411, signed with sub-key "3D2C DA58 819C 08C2 A649 D43D 5C3B 064C 724A 5726". * build-aux/git-authenticate.scm (%committers): Provide fingerprint of subkey for thomasd. --- build-aux/git-authenticate.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/build-aux/git-authenticate.scm b/build-aux/git-authenticate.scm index 8d05f0ee40..4f9ef7c886 100644 --- a/build-aux/git-authenticate.scm +++ b/build-aux/git-authenticate.scm @@ -193,7 +193,8 @@ ;; https://lists.gnu.org/archive/html/guix-devel/2017-03/msg00826.html ("thomasd" - "1DD1 681F E285 E07F 11DC 0C59 2E15 A6BC D77D 54FD") + ;; primary: "1DD1 681F E285 E07F 11DC 0C59 2E15 A6BC D77D 54FD" + "3D2C DA58 819C 08C2 A649 D43D 5C3B 064C 724A 5726") ("thomasd (old)" "A5C5 92EA 606E 7106 A6A3 BC08 98B2 1575 91E1 2B08") -- cgit v1.2.3 From 2e4011465b6c0757c45ddf118c9f406df045b376 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 26 Feb 2020 22:11:19 +0100 Subject: git-authenticate: Remove duplicate entry. * build-aux/git-authenticate.scm (%committers): Remove duplicate of snape. --- build-aux/git-authenticate.scm | 2 -- 1 file changed, 2 deletions(-) diff --git a/build-aux/git-authenticate.scm b/build-aux/git-authenticate.scm index 4f9ef7c886..640dedbff5 100644 --- a/build-aux/git-authenticate.scm +++ b/build-aux/git-authenticate.scm @@ -184,8 +184,6 @@ "77DD AD2D 97F5 31BB C0F3 C7FD DFB5 EB09 AA62 5423") ("snape" "F494 72F4 7A59 00D5 C235 F212 89F9 6D48 08F3 59C7") - ("snape" - "F494 72F4 7A59 00D5 C235 F212 89F9 6D48 08F3 59C7") ("steap" "4E26 CCE9 578E 0828 9855 BDD4 1C79 95D2 D5A3 8336") ("taylanub" -- cgit v1.2.3