diff options
Diffstat (limited to 'gnu/packages')
159 files changed, 3730 insertions, 2719 deletions
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 28961ecf88..d30c13d845 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -125,7 +125,9 @@ `(("libgcrypt" ,libgcrypt) ("libgpg-error" ,libgpg-error) ("libmhash" ,libmhash) + ("pcre:static" ,pcre "static") ("pcre" ,pcre) + ("zlib:static" ,zlib "static") ("zlib" ,zlib))) (synopsis "File and directory integrity checker") (description @@ -225,13 +227,15 @@ interface and is based on GNU Guile.") (modify-phases %standard-phases (add-after 'unpack 'chdir (lambda _ - (chdir ,(string-append name "-" version)))) + (chdir ,(string-append name "-" version)) + #t)) (delete 'configure) (add-before 'build 'patch (lambda _ (substitute* "src/error.h" (("extern int errno;") - "#include <errno.h>")))) + "#include <errno.h>")) + #t)) (replace 'build (lambda _ (invoke "package/compile"))) @@ -241,7 +245,8 @@ interface and is based on GNU Guile.") (bin (string-append out "/bin"))) (for-each (lambda (file) (install-file file bin)) - (find-files "command")))))))) + (find-files "command"))) + #t))))) (synopsis "Tools for managing UNIX style services") (description "@code{daemontools} is a collection of tools for managing UNIX @@ -963,7 +968,7 @@ at once based on a Perl regular expression.") #t)) (add-after 'install 'install-info (lambda _ - (zero? (system* "make" "install-info"))))))) + (invoke "make" "install-info")))))) (native-inputs `(("texinfo" ,texinfo) ("util-linux" ,util-linux))) ; for 'cal' (home-page "https://www.gnu.org/software/rottlog/") @@ -1094,7 +1099,8 @@ commands and their arguments.") CFLAGS += $(shell pkg-config libnl-3.0 --cflags) CONFIG_LIBNL32=y CONFIG_READLINE=y\n" port) - (close-port port)))) + (close-port port)) + #t)) (add-after 'install 'install-man-pages (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -1233,11 +1239,10 @@ This package provides the 'wpa_supplicant' daemon and the 'wpa_cli' command.") ;; It's an old configure script that doesn't understand ;; the extra options we pass. (setenv "CONFIG_SHELL" (which "bash")) - (zero? - (system* "./configure" - (string-append "--prefix=" out) - (string-append "--mandir=" out - "/share/man"))))))) + (invoke "./configure" + (string-append "--prefix=" out) + (string-append "--mandir=" out + "/share/man")))))) #:tests? #f)) (home-page "https://www.kernel.org") ; really, no home page (synopsis "Send a wake-on-LAN packet") @@ -1639,20 +1644,18 @@ things like zero-downtime rolling updates with load balancers.") (arguments `(#:phases (modify-phases %standard-phases (delete 'configure) - (replace - 'build - (lambda _ - (zero? (system* "make" "CC=gcc" "-Csrc")))) - (replace - 'check - (lambda _ - (zero? (system* "make" "CC=gcc" "-Ctests")))) - (replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (install-file "src/cpulimit" bin))))))) + (replace 'build + (lambda _ + (invoke "make" "CC=gcc" "-Csrc"))) + (replace 'check + (lambda _ + (invoke "make" "CC=gcc" "-Ctests"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (install-file "src/cpulimit" bin)) + #t))))) (home-page "https://github.com/opsengine/cpulimit") (synopsis "Limit CPU usage") (description @@ -1861,10 +1864,9 @@ done with the @code{auditctl} utility.") (replace 'install (lambda* (#:key outputs #:allow-other-keys) (define (make out . args) - (unless (zero? (apply system* "make" - (string-append "prefix=" out) - args)) - (error "make failed"))) + (apply invoke "make" + (string-append "prefix=" out) + args)) (define (python-path dir) (string-append dir "/lib/python2.7/site-packages")) (let ((out (assoc-ref outputs "out")) @@ -1878,13 +1880,14 @@ done with the @code{auditctl} utility.") (make ndiff "install-ndiff") (wrap-program (string-append ndiff "/bin/ndiff") `("PYTHONPATH" prefix - (,(python-path ndiff))))))) + (,(python-path ndiff))))) + #t)) ;; These are the tests that do not require network access. (replace 'check - (lambda _ (zero? (system* "make" - "check-nse" - "check-ndiff" - "check-dns"))))) + (lambda _ (invoke "make" + "check-nse" + "check-ndiff" + "check-dns")))) ;; Nmap can't cope with out-of-source building. #:out-of-source? #f)) (home-page "https://nmap.org/") @@ -2190,15 +2193,15 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.") #t)) (replace 'build (lambda* (#:key make-flags #:allow-other-keys) - (zero? (apply system* "make" "tools" "misc" make-flags)))) + (apply invoke "make" "tools" "misc" make-flags))) (add-after 'build 'build-armhf (lambda* (#:key make-flags #:allow-other-keys) (setenv "LIBRARY_PATH" #f) - (zero? (apply system* "make" "target-tools" make-flags)))) + (apply invoke "make" "target-tools" make-flags))) (replace 'install (lambda* (#:key make-flags #:allow-other-keys) - (zero? (apply system* "make" "install-all" "install-misc" - make-flags))))))) + (apply invoke "make" "install-all" "install-misc" + make-flags)))))) (home-page "https://github.com/linux-sunxi/sunxi-tools") (synopsis "Hardware management tools for Allwinner computers") (description "This package contains tools for Allwinner devices: diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index 6bb38aac4d..d2113555eb 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2018 Alex ter Weele <alex.ter.weele@gmail.com> ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -85,6 +86,7 @@ (lambda* (#:key outputs inputs tests? (configure-flags '()) #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) + (name-version (strip-store-file-name out)) (input-dirs (match inputs (((_ . dir) ...) dir) @@ -95,8 +97,7 @@ `(,(string-append "--bindir=" out "/bin")) `(,(string-append "--docdir=" out - "/share/doc/" ((@@ (guix build haskell-build-system) - package-name-version) out))) + "/share/doc/" name-version)) '("--libsubdir=$compiler/$pkg-$version") '("--package-db=../package.conf.d") '("--global") diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index cc1a8f25d0..8ee4bc4080 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -590,14 +590,14 @@ a C program.") (define-public fftw (package (name "fftw") - (version "3.3.7") + (version "3.3.8") (source (origin (method url-fetch) (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-" version".tar.gz")) (sha256 (base32 - "0wsms8narnbhfsa8chdflv2j9hzspvflblnqdn7hw8x5xdzrnq1v")))) + "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1")))) (build-system gnu-build-system) (arguments `(#:configure-flags diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 45d20ca46a..f9c1b4d434 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -797,7 +797,8 @@ language and software synthesizer.") (lambda _ (symlink "libclalsadrv.so" (string-append (assoc-ref %outputs "out") - "/lib/libclalsadrv.so.2")))) + "/lib/libclalsadrv.so.2")) + #t)) ;; no configure script (delete 'configure)))) (inputs @@ -1566,7 +1567,8 @@ synchronous execution of all clients, and low latency operation.") ((".*CFLAGS.*-Wall.*" m) (string-append m " conf.env.append_unique('LINKFLAGS'," - "'-Wl,-rpath=" %output "/lib')\n"))))) + "'-Wl,-rpath=" %output "/lib')\n"))) + #t)) (add-after 'install 'wrap-python-scripts (lambda* (#:key inputs outputs #:allow-other-keys) ;; Make sure 'jack_control' runs with the correct PYTHONPATH. @@ -1602,6 +1604,7 @@ synchronous execution of all clients, and low latency operation.") (build-system waf-build-system) (arguments `(#:tests? #f ; no check target + #:python ,python-2 #:phases (modify-phases %standard-phases (add-before @@ -1649,19 +1652,20 @@ plugin function as a JACK application.") (arguments `(#:tests? #f ; the "test" target is a listening test only #:phases - (alist-replace - 'configure - (lambda* (#:key inputs outputs #:allow-other-keys #:rest args) - (chdir "src") - (let ((out (assoc-ref outputs "out"))) - (substitute* "makefile" - (("/usr/lib/ladspa/") (string-append out "/lib/ladspa/")) - (("/usr/include/") (string-append out "/include/")) - (("/usr/bin/") (string-append out "/bin/")) - (("-mkdirhier") "mkdir -p") - (("^CC.*") "CC = gcc\n") - (("^CPP.*") "CPP = g++\n")))) - (alist-delete 'build %standard-phases)))) + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys #:rest args) + (chdir "src") + (let ((out (assoc-ref outputs "out"))) + (substitute* "makefile" + (("/usr/lib/ladspa/") (string-append out "/lib/ladspa/")) + (("/usr/include/") (string-append out "/include/")) + (("/usr/bin/") (string-append out "/bin/")) + (("-mkdirhier") "mkdir -p") + (("^CC.*") "CC = gcc\n") + (("^CPP.*") "CPP = g++\n"))) + #t)) + (delete 'build)))) ;; Since the home page is gone, we provide a link to the archived version. (home-page "https://web.archive.org/web/20140729190945/http://www.ladspa.org/") @@ -1876,6 +1880,8 @@ significantly faster and have minimal dependencies.") (build-system waf-build-system) (arguments `(#:tests? #f ; no check target + ;; XXX: The bundled waf does not work with Python 3.7. + #:python ,python-2 #:configure-flags '("--no-plugins"))) (inputs ;; Leaving off cairo and gtk+-2.0 which are needed for example plugins @@ -2434,6 +2440,7 @@ the Turtle syntax.") (build-system waf-build-system) (arguments `(#:tests? #f ; no check target + #:python ,python-2 ;XXX: The bundled waf does not work with Python 3.7.0. #:configure-flags '("CXXFLAGS=-std=gnu++11"))) (inputs @@ -2582,7 +2589,8 @@ analysis plugins or audio feature extraction plugins.") (symlink (string-append (assoc-ref inputs "automake") "/share/automake-" ,(package-version automake) "/ar-lib") - "ar-lib")))))) + "ar-lib") + #t))))) (home-page "http://sbsms.sourceforge.net/") (synopsis "Library for time stretching and pitch scaling of audio") (description @@ -2978,12 +2986,14 @@ result.") (substitute* "libs/Makefile" (("ldconfig") "true") (("^LIBDIR =.*") "LIBDIR = lib\n")) - (chdir "libs") #t)) + (chdir "libs") + #t)) (add-after 'install 'install-symlink (lambda _ (symlink "libzita-convolver.so" (string-append (assoc-ref %outputs "out") - "/lib/libzita-convolver.so.3")))) + "/lib/libzita-convolver.so.3")) + #t)) ;; no configure script (delete 'configure)))) (inputs `(("fftwf" ,fftwf))) @@ -3033,7 +3043,8 @@ engine.") (lambda _ (symlink "libzita-resampler.so" (string-append (assoc-ref %outputs "out") - "/lib/libzita-resampler.so.1")))) + "/lib/libzita-resampler.so.1")) + #t)) ;; no configure script (delete 'configure)))) (home-page "https://kokkinizita.linuxaudio.org/linuxaudio/zita-resampler/resampler.html") @@ -3074,7 +3085,8 @@ provide high-quality sample rate conversion.") (lambda _ (symlink "libzita-alsa-pcmi.so" (string-append (assoc-ref %outputs "out") - "/lib/libzita-alsa-pcmi.so.0")))) + "/lib/libzita-alsa-pcmi.so.0")) + #t)) ;; no configure script (delete 'configure)))) (inputs @@ -3259,7 +3271,8 @@ code, used in @code{libtoxcore}.") (mkdir-p (string-append out "/man/man1")) (mkdir-p (string-append out "/man/man3")) (mkdir-p (string-append out "/bin")) - (mkdir-p (string-append out "/lib"))))) + (mkdir-p (string-append out "/lib"))) + #t)) (add-after 'install 'post-install (lambda _ (let ((out (assoc-ref %outputs "out"))) @@ -3267,7 +3280,8 @@ code, used in @code{libtoxcore}.") (string-append out "/include")) (mkdir-p (string-append out "/include/gsm")) (copy-recursively "inc" - (string-append out "/include/gsm"))))) + (string-append out "/include/gsm"))) + #t)) (delete 'configure)))) ; no configure script (synopsis "GSM 06.10 lossy speech compression library") (description "This C library provides an encoder and a decoder for the GSM @@ -3543,14 +3557,16 @@ representations.") (invoke "sh" "autogen.sh"))) (add-before 'build 'make-cava-ldflags (lambda* (#:key outputs #:allow-other-keys) - (mkdir-p (string-append (assoc-ref outputs "out") "/lib")))) + (mkdir-p (string-append (assoc-ref outputs "out") "/lib")) + #t)) (add-after 'install 'data (lambda* (#:key outputs #:allow-other-keys) (for-each (lambda (file) (install-file file (string-append (assoc-ref outputs "out") "/share/doc/examples"))) - (find-files "example_files"))))))) + (find-files "example_files")) + #t))))) (home-page "https://karlstav.github.io/cava/") (synopsis "Console audio visualizer for ALSA, MPD, and PulseAudio") (description "C.A.V.A. is a bar audio spectrum visualizer for the terminal diff --git a/gnu/packages/authentication.scm b/gnu/packages/authentication.scm index a58eac9890..68a6459828 100644 --- a/gnu/packages/authentication.scm +++ b/gnu/packages/authentication.scm @@ -17,6 +17,7 @@ ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. (define-module (gnu packages authentication) + #:use-module (gnu packages) #:use-module (gnu packages linux) #:use-module (gnu packages pkg-config) #:use-module (guix build-system gnu) @@ -35,6 +36,7 @@ (method url-fetch) (uri (string-append "https://download.savannah.nongnu.org/releases/" name "/" name "-" version ".tar.gz")) + (patches (search-patches "oath-toolkit-glibc-compat.patch")) (sha256 (base32 "182ah8vfbg0yhv6mh1b6ap944d0na6x7lpfkwkmzb6jl9gx4cd5h")))) (build-system gnu-build-system) diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 4065af0abc..60f8051dc6 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -102,6 +102,15 @@ command-line arguments, multiple languages, and so on.") (arguments `(#:phases (modify-phases %standard-phases + (add-before 'check 'disable-failing-tests + (lambda _ + ;; These tests are expected to fail due to a glibc bug which has + ;; been fixed in 2.28, so they are unexpectedly passing. They + ;; should be fixed for grep versions > 3.1. + (substitute* "tests/Makefile.in" + (("^[[:blank:]]+backref-alt[[:blank:]]+\\\\") "\\") + (("^[[:blank:]]+triple-backref[[:blank:]]+\\\\") "\\")) + #t)) (add-after 'install 'fix-egrep-and-fgrep ;; Patch 'egrep' and 'fgrep' to execute 'grep' via its ;; absolute file name instead of searching for it in $PATH. @@ -289,7 +298,9 @@ interactive means to merge two files.") (base32 "178nn4dl7wbcw499czikirnkniwnx36argdnqgz4ik9i6zvwkm6y")) (patches (search-patches + "findutils-gnulib-libio.patch" "findutils-localstatedir.patch" + "findutils-makedev.patch" "findutils-test-xargs.patch")) (modules '((guix build utils))) (snippet @@ -326,14 +337,14 @@ used to apply commands with arbitrarily long arguments.") (define-public coreutils (package (name "coreutils") - (version "8.29") + (version "8.30") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/coreutils/coreutils-" version ".tar.xz")) (sha256 (base32 - "0plm1zs9il6bb5mk881qvbghq4glc8ybbgakk2lfzb0w64fgml4j")))) + "0mxhw43d4wpqmvg0l4znk1vm10fy92biyh90lzdnqjcic2lb6cg8")))) (build-system gnu-build-system) (inputs `(("acl" ,acl) ; TODO: add SELinux ("gmp" ,gmp) ;bignums in 'expr', yay! @@ -364,7 +375,17 @@ used to apply commands with arbitrarily long arguments.") (substitute* (find-files "gnulib-tests" "\\.c$") (("/bin/sh") (which "sh"))) (substitute* (find-files "tests" "\\.sh$") - (("#!/bin/sh") (which "sh"))) + (("#!/bin/sh") (string-append "#!" (which "sh")))) + #t)) + (add-before 'check 'disable-broken-test + (lambda _ + ;; This test hits the 127 character shebang limit in the build + ;; environment due to the way "env -S" splits arguments into + ;; shebangs. Note that "env-S-script.sh" works around this + ;; specific issue, but "env-S.pl" is not adjusted for build + ;; environments with long prefixes (/tmp/guix-build-...). + (substitute* "Makefile" + (("^.*tests/misc/env-S.pl.*$") "")) #t))) ;; Work around a cross-compilation bug whereby libcoreutils.a would @@ -435,14 +456,14 @@ change. GNU make offers many powerful extensions over the standard utility.") (define-public binutils (package (name "binutils") - (version "2.30") + (version "2.31.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/binutils/binutils-" version ".tar.bz2")) (sha256 (base32 - "028cklfqaab24glva1ks2aqa1zxa6w6xmc8q34zs1sb7h22dxspg")) + "1l34hn1zkmhr1wcrgf0d4z7r3najxnw3cx2y2fk7v55zjlk3ik7z")) (patches (search-patches "binutils-loongson-workaround.patch")))) (build-system gnu-build-system) @@ -480,17 +501,6 @@ included.") (license gpl3+) (home-page "https://www.gnu.org/software/binutils/"))) -(define-public binutils/fixed - ;; TODO: Incorporate this in binutils during the next rebuild cycle. - (hidden-package - (package - (inherit binutils) - (source (origin - (inherit (package-source binutils)) - (patches (append (origin-patches (package-source binutils)) - (search-patches - "binutils-aarch64-symbol-relocation.patch")))))))) - (define* (make-ld-wrapper name #:key (target (const #f)) binutils @@ -567,18 +577,20 @@ store.") (export make-ld-wrapper) -(define-public glibc/linux +(define-public glibc + ;; This is the GNU C Library, used on GNU/Linux and GNU/Hurd. Prior to + ;; version 2.28, GNU/Hurd used a different glibc branch. (package (name "glibc") ;; Note: Always use a dot after the minor version since various places rely ;; on "version-major+minor" to determine where locales are found. - (version "2.27") + (version "2.28") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/glibc/glibc-" version ".tar.xz")) (sha256 (base32 - "0wpwq7gsm7sd6ysidv0z575ckqdg13cr2njyfgrbgh4f65adwwji")) + "10iha5ynvdj5m62vgpgqbq4cwvc2yhyl2w9yyyjgfxmdmx8h145i")) (snippet ;; Disable 'ldconfig' and /etc/ld.so.cache. The latter is ;; required on LFS distros to avoid loading the distro's libc.so @@ -590,7 +602,7 @@ store.") #t)) (modules '((guix build utils))) (patches (search-patches "glibc-ldd-x86_64.patch" - "glibc-2.27-git-fixes.patch" + "glibc-2.28-git-fixes.patch" "glibc-hidden-visibility-ldconfig.patch" "glibc-versioned-locpath.patch" "glibc-allow-kernel-2.6.32.patch" @@ -598,8 +610,13 @@ store.") (build-system gnu-build-system) ;; Glibc's <limits.h> refers to <linux/limit.h>, for instance, so glibc - ;; users should automatically pull Linux headers as well. - (propagated-inputs `(("kernel-headers" ,linux-libre-headers))) + ;; users should automatically pull Linux headers as well. On GNU/Hurd, + ;; libc provides <hurd.h>, which includes a bunch of Hurd and Mach headers, + ;; so both should be propagated. + (propagated-inputs + (if (hurd-target?) + `(("hurd-core-headers" ,hurd-core-headers)) + `(("kernel-headers" ,linux-libre-headers)))) (outputs '("out" "debug" "static")) ;9 MiB of .a files @@ -654,7 +671,13 @@ store.") ;; Use our Bash instead of /bin/sh. (string-append "BASH_SHELL=" (assoc-ref %build-inputs "bash") - "/bin/bash")) + "/bin/bash") + + ;; On GNU/Hurd we get discarded-qualifiers warnings for + ;; 'device_write_inband' among other things. Ignore them. + ,@(if (hurd-target?) + '("--disable-werror") + '())) #:tests? #f ; XXX #:phases (modify-phases %standard-phases @@ -759,7 +782,18 @@ store.") (filter linker-script? (map (cut string-append slib "/" <>) files))) - #t)))))) + #t))) + + ,@(if (hurd-target?) + '((add-after 'install 'augment-libc.so + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (substitute* (string-append out "/lib/libc.so") + (("/[^ ]+/lib/libc.so.0.3") + (string-append out "/lib/libc.so.0.3" + " libmachuser.so libhurduser.so")))) + #t))) + '())))) (inputs `(("static-bash" ,static-bash))) @@ -768,7 +802,12 @@ store.") (native-inputs `(("texinfo" ,texinfo) ("perl" ,perl) ("bison" ,bison) - ("gettext" ,gettext-minimal))) + ("gettext" ,gettext-minimal) + + ,@(if (hurd-target?) + `(("mig" ,mig) + ("perl" ,perl)) + '()))) (native-search-paths ;; Search path for packages that provide locale data. This is useful @@ -790,108 +829,25 @@ with the Linux kernel.") (license lgpl2.0+) (home-page "https://www.gnu.org/software/libc/"))) -(define-public glibc/hurd - ;; The Hurd's libc variant. - (package (inherit glibc/linux) - (name "glibc-hurd") - (version "2.23") - (source (origin - (method url-fetch) - (uri (string-append "http://alpha.gnu.org/gnu/hurd/glibc-" - version "-hurd+libpthread-20161218" ".tar.gz")) - (sha256 - (base32 - "0vpdv05j6j3ria5bw8gp468i64gij94cslxkxj9xkfgi6p615b8p")))) - - ;; Libc provides <hurd.h>, which includes a bunch of Hurd and Mach headers, - ;; so both should be propagated. - (propagated-inputs `(("hurd-core-headers" ,hurd-core-headers))) - (native-inputs - `(,@(package-native-inputs glibc/linux) - ("mig" ,mig) - ("perl" ,perl))) +;; Below are old libc versions, which we use mostly to build locale data in +;; the old format (which the new libc cannot cope with.) - (arguments - (substitute-keyword-arguments (package-arguments glibc/linux) - ((#:phases original-phases) - ;; Add libmachuser.so and libhurduser.so to libc.so's search path. - ;; See <http://lists.gnu.org/archive/html/bug-hurd/2015-07/msg00051.html>. - `(modify-phases ,original-phases - (add-after 'install 'augment-libc.so - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out"))) - (substitute* (string-append out "/lib/libc.so") - (("/[^ ]+/lib/libc.so.0.3") - (string-append out "/lib/libc.so.0.3" " libmachuser.so" " libhurduser.so")))) - #t)) - (add-after 'pre-configure 'pre-configure-set-pwd - (lambda _ - ;; Use the right 'pwd'. - (substitute* "configure" - (("/bin/pwd") "pwd")) - #t)) - (replace 'build - (lambda _ - ;; Force mach/hurd/libpthread subdirs to build first in order to avoid - ;; linking errors. - ;; See <https://lists.gnu.org/archive/html/bug-hurd/2016-11/msg00045.html> - (let ((flags (list "-j" (number->string (parallel-job-count))))) - (define (make target) - (apply invoke "make" target flags)) - (make "mach/subdir_lib") - (make "hurd/subdir_lib") - (make "libpthread/subdir_lib") - (apply invoke "make" flags)))))) - ((#:configure-flags original-configure-flags) - `(append (list "--host=i586-pc-gnu" - - ;; We need this to get a working openpty() function. - "--enable-pt_chown" - - ;; <https://lists.gnu.org/archive/html/bug-hurd/2016-10/msg00033.html> - "--disable-werror" - - ;; nscd fails to build for GNU/Hurd: - ;; <https://lists.gnu.org/archive/html/bug-hurd/2014-07/msg00006.html>. - ;; Disable it. - "--disable-nscd") - (filter (lambda (flag) - (not (string-prefix? "--enable-kernel=" flag))) - ,original-configure-flags))))) - (synopsis "The GNU C Library (GNU Hurd variant)") - (supported-systems %hurd-systems))) - -(define* (glibc-for-target #:optional - (target (or (%current-target-system) - (%current-system)))) - "Return the glibc for TARGET, GLIBC/LINUX for a Linux host or -GLIBC/HURD for a Hurd host" - (match target - ((or "i586-pc-gnu" "i586-gnu") glibc/hurd) - (_ glibc/linux))) - -(define-syntax glibc - (identifier-syntax (glibc-for-target))) - -;; The "next" libc. Useful for populating locale data before reconfiguring the -;; entire system on it. Will be the default in the next rebuild cycle. -(define-public glibc-2.28 +(define-public glibc-2.27 (package (inherit glibc) - (version "2.28") + (version "2.27") (source (origin (inherit (package-source glibc)) (uri (string-append "mirror://gnu/glibc/glibc-" version ".tar.xz")) (sha256 (base32 - "10iha5ynvdj5m62vgpgqbq4cwvc2yhyl2w9yyyjgfxmdmx8h145i")) - (patches (search-patches "glibc-allow-kernel-2.6.32.patch" - "glibc-ldd-x86_64.patch" + "0wpwq7gsm7sd6ysidv0z575ckqdg13cr2njyfgrbgh4f65adwwji")) + (patches (search-patches "glibc-ldd-x86_64.patch" + "glibc-2.27-git-fixes.patch" "glibc-hidden-visibility-ldconfig.patch" - "glibc-versioned-locpath.patch")))))) - -;; Below are old libc versions, which we use mostly to build locale data in -;; the old format (which the new libc cannot cope with.) + "glibc-versioned-locpath.patch" + "glibc-allow-kernel-2.6.32.patch" + "glibc-reinstate-prlimit64-fallback.patch")))))) (define-public glibc-2.26 (package @@ -1111,18 +1067,17 @@ command.") (license gpl3+))) ; some files are under GPLv2+ (define-public glibc/hurd-headers - (package (inherit glibc/hurd) + (package (inherit glibc) (name "glibc-hurd-headers") (outputs '("out")) (propagated-inputs `(("gnumach-headers" ,gnumach-headers) ("hurd-headers" ,hurd-headers))) (arguments - (substitute-keyword-arguments (package-arguments glibc/hurd) + (substitute-keyword-arguments (package-arguments glibc) ;; We just pass the flags really needed to build the headers. ((#:configure-flags _) `(list "--enable-add-ons" - "--host=i586-pc-gnu" - "--enable-obsolete-rpc")) + "--host=i586-pc-gnu")) ((#:phases _) '(modify-phases %standard-phases (replace 'install @@ -1137,13 +1092,7 @@ command.") (open-output-file (string-append out "/include/gnu/stubs.h")))) #t)) - (delete 'build) ; nothing to build - (add-before 'configure 'patch-configure-script - (lambda _ - ;; Use the right 'pwd'. - (substitute* "configure" - (("/bin/pwd") "pwd")) - #t)))))))) + (delete 'build))))))) ; nothing to build (define-public tzdata (package diff --git a/gnu/packages/bash.scm b/gnu/packages/bash.scm index 121a459fa6..fb4e3f4be3 100644 --- a/gnu/packages/bash.scm +++ b/gnu/packages/bash.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2015, 2017 Leo Famulari <leo@famulari.name> -;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. @@ -79,7 +79,11 @@ (16 "1cgi1y6mifm8hsgv4avj5ih76535js3qba1sqwbfvp7si76927sh") (17 "0w6jpj2giakji1ir83rpkx1y7n7xqppah3j748m6dm38hywr0gvp") (18 "1k58h4wxbsg7r4rwhrvzx5hfbapba2nxjysbhh6qp6ki5ys99i2v") - (19 "07n1i5610lbs672x1s8g82qn3qfj06s0ip3z80sri0g8vxp0s5r7"))) + (19 "07n1i5610lbs672x1s8g82qn3qfj06s0ip3z80sri0g8vxp0s5r7") + (20 "0b2jk5n1af1vh590qfc52hv65mafb4vl1xv26s8j5a3byb5y4h0q") + (21 "1hblcd2xmqqlp0idnavw66570n7m0yv5rbbr873c2gkn982mk3xx") + (22 "0yfbjzr79vzjs2hyi5m8iy2b38fq7vikdfa4zqdvjsp36q4iycs5") + (23 "1dlism6qdx60nvzj0v7ndr7lfahl4a8zmzckp13hqgdx7xpj7v2g"))) (define (download-patches store count) "Download COUNT Bash patches into store. Return a list of diff --git a/gnu/packages/bdw-gc.scm b/gnu/packages/bdw-gc.scm index eba30217da..c7491f845f 100644 --- a/gnu/packages/bdw-gc.scm +++ b/gnu/packages/bdw-gc.scm @@ -30,14 +30,14 @@ (define-public libgc (package (name "libgc") - (version "7.6.4") + (version "7.6.6") (source (origin (method url-fetch) - (uri (string-append "http://www.hboehm.info/gc/gc_source/gc-" - version ".tar.gz")) + (uri (string-append "https://github.com/ivmai/bdwgc/releases" + "/download/v" version "/gc-" version ".tar.gz")) (sha256 (base32 - "076dzsqqyxd3nlzs0z277vvhqjp8nv5dqi763s0m90zr6ljiyk5r")))) + "1p1r015a7jbpvkkbgzv1y8nxrbbp6dg0mq3ksi6ji0qdz3wfss79")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -91,7 +91,7 @@ C or C++ programs, though that is not its primary goal.") (define-public libatomic-ops (package (name "libatomic-ops") - (version "7.6.4") + (version "7.6.6") (source (origin (method url-fetch) (uri (string-append @@ -99,7 +99,7 @@ C or C++ programs, though that is not its primary goal.") version "/libatomic_ops-" version ".tar.gz")) (sha256 (base32 - "0knxncsjhbknlyy6lx7ycxhpzfk3sykhvicgxyp0rmsxd1d3v0jv")))) + "0x7071z707msvyrv9dmgahd1sghbkw8fpbagvcag6xs8yp2spzlr")))) (build-system gnu-build-system) (outputs '("out" "debug")) (synopsis "Accessing hardware atomic memory update operations") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 782af294e0..a193e56ed9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -281,7 +281,8 @@ instance, it implements several methods to assess contig-wise read coverage.") (setenv "LDFLAGS" (string-append "-Wl,-rpath=" - (assoc-ref outputs "out") "/lib/bamtools"))))))) + (assoc-ref outputs "out") "/lib/bamtools")) + #t))))) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/pezmaster31/bamtools") (synopsis "C++ API and command-line toolkit for working with BAM data") @@ -496,7 +497,8 @@ BED, GFF/GTF, VCF.") '("create_annotations_files.bash" "create_metaplots.bash" "Ribotaper_ORF_find.sh" - "Ribotaper.sh")))))))) + "Ribotaper.sh"))) + #t))))) (inputs `(("bedtools" ,bedtools-2.18) ("samtools" ,samtools-0.1) @@ -591,7 +593,8 @@ independently with transcriptional regulation.") (man (string-append out "/share/man/man1"))) (mkdir-p man) (copy-file "awk.1" (string-append man "/bioawk.1")) - (install-file "bioawk" bin))))))) + (install-file "bioawk" bin)) + #t))))) (home-page "https://github.com/lh3/bioawk") (synopsis "AWK with bioinformatics extensions") (description "Bioawk is an extension to Brian Kernighan's awk, adding the @@ -1811,7 +1814,8 @@ databases.") (copy-recursively "QuarryFiles" (string-append out "/QuarryFiles")) (install-file "CodingQuarry" bin) - (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))))))) + (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)) + #t))))) (inputs `(("openmpi" ,openmpi))) (native-search-paths (list (search-path-specification @@ -2727,7 +2731,8 @@ Illumina, Roche 454, and the SOLiD platform.") (share (string-append out "/share/fraggenescan/train"))) (install-file "run_FragGeneScan.pl" bin) (install-file "FragGeneScan" bin) - (copy-recursively "train" share)))) + (copy-recursively "train" share)) + #t)) (delete 'check) (add-after 'install 'post-install-check ;; In lieu of 'make check', run one of the examples and check the @@ -4153,7 +4158,8 @@ probabilistic distances of genome abundance and tetranucleotide frequency.") "#!" (assoc-ref inputs "bash") "/bin/sh\n\n" (assoc-ref inputs "jre") "/bin/java -jar " bin "/minced.jar \"$@\"\n")))) - (chmod wrapper #o555))))))) + (chmod wrapper #o555)) + #t))))) (native-inputs `(("jdk" ,icedtea "jdk"))) (inputs @@ -4408,7 +4414,7 @@ downstream analysis.") #:phases (modify-phases %standard-phases (add-after 'unpack 'enter-scripts-dir - (lambda _ (chdir "scripts"))) + (lambda _ (chdir "scripts") #t)) (replace 'check (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)) (add-after 'install 'wrap-executables @@ -6019,7 +6025,8 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (lambda _ (substitute* "Makefile" (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post) - (string-append pre "Built with Guix" post))))) + (string-append pre "Built with Guix" post))) + #t)) (add-after 'enter-source-dir 'do-not-use-bundled-htslib (lambda _ (substitute* "Makefile" @@ -6103,7 +6110,8 @@ sequences.") (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (mkdir-p bin) - (copy-recursively "../bin" bin)))) + (copy-recursively "../bin" bin)) + #t)) ;; no "configure" script (delete 'configure)))) (inputs `(("zlib" ,zlib))) @@ -12007,11 +12015,13 @@ bytes of memory space, where n is the length of the string.") (add-after 'unpack 'do-not-look-for-boost (lambda* (#:key inputs #:allow-other-keys) (substitute* "CMakeLists.txt" - (("find_package\\(Boost 1\\.53\\.0") "#")))) + (("find_package\\(Boost 1\\.53\\.0") "#")) + #t)) (add-after 'unpack 'do-not-assign-to-macro (lambda _ (substitute* "include/spdlog/details/format.cc" - (("const unsigned CHAR_WIDTH = 1;") "")))) + (("const unsigned CHAR_WIDTH = 1;") "")) + #t)) (add-after 'unpack 'prepare-rapmap (lambda* (#:key inputs #:allow-other-keys) (let ((src "external/install/src/rapmap/") @@ -12027,7 +12037,8 @@ bytes of memory space, where n is the length of the string.") (for-each (lambda (file) (install-file file src)) (find-files "/tmp/rapmap/src" "\\.(c|cpp)")) - (copy-recursively "/tmp/rapmap/include" include)))) + (copy-recursively "/tmp/rapmap/include" include)) + #t)) (add-after 'unpack 'use-system-libraries (lambda* (#:key inputs #:allow-other-keys) (substitute* '("src/SailfishIndexer.cpp" @@ -12067,7 +12078,8 @@ bytes of memory space, where n is the length of the string.") (string-append (getenv "CPLUS_INCLUDE_PATH") ":" (assoc-ref inputs "eigen") - "/include/eigen3"))))))) + "/include/eigen3")) + #t))))) (inputs `(("boost" ,boost) ("eigen" ,eigen) @@ -12253,11 +12265,13 @@ performance as its primary goal.") (add-after 'unpack 'do-not-look-for-boost (lambda* (#:key inputs #:allow-other-keys) (substitute* "CMakeLists.txt" - (("find_package\\(Boost 1\\.53\\.0") "#")))) + (("find_package\\(Boost 1\\.53\\.0") "#")) + #t)) (add-after 'unpack 'do-not-phone-home (lambda _ (substitute* "src/Salmon.cpp" - (("getVersionMessage\\(\\)") "\"\"")))) + (("getVersionMessage\\(\\)") "\"\"")) + #t)) (add-after 'unpack 'prepare-rapmap (lambda* (#:key inputs #:allow-other-keys) (let ((src "external/install/src/rapmap/") @@ -12274,7 +12288,8 @@ performance as its primary goal.") "external/install/include/rapmap/concurrentqueue.h" "external/install/include/rapmap/FastxParserThreadUtils.hpp" "external/install/src/rapmap/FastxParser.cpp" - "external/install/src/rapmap/xxhash.c"))))) + "external/install/src/rapmap/xxhash.c"))) + #t)) (add-after 'unpack 'use-system-libraries (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/CMakeLists.txt" @@ -12385,8 +12400,7 @@ variational inference.") (propagated-inputs `(("python-h5py" ,python-h5py) ("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-typing" ,python-typing))) + ("python-scipy" ,python-scipy))) (home-page "https://github.com/linnarsson-lab/loompy") (synopsis "Work with .loom files for single-cell RNA-seq data") (description "The loom file format is an efficient format for very large @@ -13059,7 +13073,7 @@ expression report comparing samples in an easily configurable manner.") ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) - ("snakemake" ,snakemake-4) + ("snakemake" ,snakemake) ("samtools" ,samtools) ("bedtools" ,bedtools) ("kentutils" ,kentutils))) @@ -13120,7 +13134,7 @@ in an easily configurable manner.") ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) - ("snakemake" ,snakemake-4) + ("snakemake" ,snakemake) ("bismark" ,bismark) ("fastqc" ,fastqc) ("bowtie" ,bowtie) @@ -13170,7 +13184,7 @@ methylation and segmentation.") ("ghc-pandoc" ,ghc-pandoc) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("samtools" ,samtools) - ("snakemake" ,snakemake-4) + ("snakemake" ,snakemake) ("star" ,star) ("r-minimal" ,r-minimal) ("r-argparser" ,r-argparser) diff --git a/gnu/packages/bison.scm b/gnu/packages/bison.scm index 09c6481a16..71de47762d 100644 --- a/gnu/packages/bison.scm +++ b/gnu/packages/bison.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2012, 2013, 2015 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,7 +30,7 @@ (define-public bison (package (name "bison") - (version "3.0.4") + (version "3.0.5") (source (origin (method url-fetch) @@ -37,10 +38,10 @@ version ".tar.xz")) (sha256 (base32 - "1qbgf6q1n2z17k8g33444m0q68kf3fbiq65q7jlrzpvvj73jh957")))) + "0f7kjygrckkx8vas2nm673592jif0a9mw5g8207f6hj6h4pfyp07")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl) - ;; m4 is not present in PATH when cross-building + ;; m4 is not present in PATH when cross-building. ("m4" ,m4))) (inputs `(("flex" ,flex))) (propagated-inputs `(("m4" ,m4))) @@ -52,15 +53,3 @@ deterministic or generalized LR parser from an annotated, context-free grammar. It is versatile enough to have many applications, from parsers for simple tools through complex programming languages.") (license gpl3+))) - -(define-public bison-2.7 - (package (inherit bison) - (version "2.7") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://gnu/bison/bison-" - version ".tar.xz")) - (sha256 - (base32 - "1zd77ilmpv5mi3kr55jrj6ncqlcnyhpianhrwzak2q28cv2cbn23")))))) diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm index cf70a29775..897987f71c 100644 --- a/gnu/packages/boost.scm +++ b/gnu/packages/boost.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -27,6 +28,7 @@ (define-module (gnu packages boost) #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix utils) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) @@ -43,7 +45,7 @@ (define-public boost (package (name "boost") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (string-append @@ -52,7 +54,7 @@ ".tar.bz2")) (sha256 (base32 - "1aaw48cmimsskzgiclwn0iifp62a5iw9cbqrhfari876af1828ap")) + "1dyqsr9yb01y0nnjdq9b8q5s2kvhxbayk34832k5cpzn7jy30qbz")) (patches (search-patches "boost-fix-icu-build.patch")))) (build-system gnu-build-system) (inputs `(("icu4c" ,icu4c) @@ -78,7 +80,6 @@ (out (assoc-ref outputs "out"))) (substitute* '("libs/config/configure" "libs/spirit/classic/phoenix/test/runtest.sh" - "tools/build/doc/bjam.qbk" "tools/build/src/engine/execunix.c" "tools/build/src/engine/Jambase" "tools/build/src/engine/jambase.c") @@ -100,7 +101,18 @@ make-flags))) (replace 'install (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "./b2" "install" make-flags)))))) + (apply invoke "./b2" "install" make-flags))) + (add-after 'install 'provide-libboost_python + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + ;; Boost can build support for both Python 2 and Python 3 since + ;; version 1.67.0, and suffixes each library with the Python + ;; version. Many consumers only check for libboost_python + ;; however, so we provide it here as suggested in + ;; <https://github.com/boostorg/python/issues/203>. + (with-directory-excursion (string-append out "/lib") + (symlink "libboost_python27.so" "libboost_python.so")) + #t)))))) (home-page "https://www.boost.org") (synopsis "Peer-reviewed portable C++ source libraries") @@ -124,6 +136,15 @@ across a broad spectrum of applications.") (sha256 (base32 "1jj1aai5rdmd72g90a3pd8sw9vi32zad46xv5av8fhnr48ir6ykj")))) + (arguments (substitute-keyword-arguments (package-arguments boost) + ((#:phases phases) + `(modify-phases ,phases + ;; This was removed after boost-1.67. + (add-before 'configure 'more-bin-sh-patching + (lambda _ + (substitute* "tools/build/doc/bjam.qbk" + (("/bin/sh") (which "sh"))))) + (delete 'provide-libboost_python))))) (properties '((hidden? . #t))))) (define-public boost-sync diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 0c11639150..c155228b4d 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -87,7 +87,8 @@ (sha256 (base32 "03vvdfhdmf16121v7xs8is2krwnv15wpkhkf16a4yf8nsfc3f2w1")) - (patches (search-patches "grub-check-error-efibootmgr.patch")))) + (patches (search-patches "grub-check-error-efibootmgr.patch" + "grub-binutils-compat.patch")))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm index a52ee480ac..a34e7ebff4 100644 --- a/gnu/packages/build-tools.scm +++ b/gnu/packages/build-tools.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2017 Corentin Bocquillon <corentin@nybble.fr> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com> @@ -158,7 +158,7 @@ files and generates build instructions for the Ninja build system.") (define-public meson (package (name "meson") - (version "0.47.1") + (version "0.47.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/mesonbuild/meson/" @@ -166,7 +166,7 @@ files and generates build instructions for the Ninja build system.") version ".tar.gz")) (sha256 (base32 - "19mdap2ncvczajx220bd73xmwhd8x906382y18cn9c5syxwxwwyn")))) + "1swmycf6p9p0ag6yiywyyri42ffkxxj38r2ic7in24km47cszn4j")))) (build-system python-build-system) (arguments `(;; FIXME: Tests require many additional inputs, a fix for the RUNPATH diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm index d89b6ea00d..c5141451f0 100644 --- a/gnu/packages/c.scm +++ b/gnu/packages/c.scm @@ -185,8 +185,45 @@ compiler while still keeping it small, simple, fast and understandable.") "download/" version "/libbytesize-" version ".tar.gz")) (sha256 (base32 - "0bbqzln1nhjxl71aydq9k4jg3hvki9lqsb4w10s1i27jgibxqkdv")))) + "0bbqzln1nhjxl71aydq9k4jg3hvki9lqsb4w10s1i27jgibxqkdv")) + (modules '((guix build utils))) + (snippet + '(begin + ;; This Makefile hard-codes MSGMERGE et al. instead of + ;; honoring what 'configure' detected. Fix that. + (substitute* "po/Makefile.in" + (("^MSGMERGE = msgmerge") + "MSGMERGE = @MSGMERGE@\n")) + #t)))) (build-system gnu-build-system) + (arguments + ;; When running "make", the POT files are built with the build time as + ;; their "POT-Creation-Date". Later on, "make" notices that .pot + ;; files were updated and goes on to run "msgmerge"; as a result, the + ;; non-deterministic POT-Creation-Date finds its way into .po files, + ;; and then in .gmo files. To avoid that, simply make sure 'msgmerge' + ;; never runs. See <https://bugs.debian.org/792687>. + '(#:configure-flags '("ac_cv_path_MSGMERGE=true") + + #:phases (modify-phases %standard-phases + (add-after 'configure 'create-merged-po-files + (lambda _ + ;; Create "merged PO" (.mpo) files so that 'msgmerge' + ;; doesn't need to run. + (for-each (lambda (po-file) + (let ((merged-po + (string-append (dirname po-file) "/" + (basename po-file + ".po") + ".mpo"))) + (copy-file po-file merged-po))) + (find-files "po" "\\.po$")) + #t))) + + ;; One test fails because busctl (systemd only?) and python2-pocketlint + ;; are missing. Should we fix it, we would need the "python-2" , + ;; "python2-polib" and "python2-six" native-inputs. + #:tests? #f)) (native-inputs `(("gettext" ,gettext-minimal) ("pkg-config" ,pkg-config) @@ -194,10 +231,6 @@ compiler while still keeping it small, simple, fast and understandable.") (inputs `(("mpfr" ,mpfr) ("pcre" ,pcre))) - ;; One test fails because busctl (systemd only?) and python2-pocketlint - ;; are missing. Should we fix it, we would need the "python-2" , - ;; "python2-polib" and "python2-six" native-inputs. - (arguments `(#:tests? #f)) (home-page "https://github.com/storaged-project/libbytesize") (synopsis "Tiny C library for working with arbitrary big sizes in bytes") (description diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm index c2bbf139c1..24e19b472c 100644 --- a/gnu/packages/calendar.scm +++ b/gnu/packages/calendar.scm @@ -48,7 +48,7 @@ (define-public libical (package (name "libical") - (version "3.0.3") + (version "3.0.4") (source (origin (method url-fetch) (uri (string-append @@ -56,7 +56,7 @@ version "/libical-" version ".tar.gz")) (sha256 (base32 - "0hcjyf35b8rrvy8xziqxc4imi28mmkixb09gknisvp6jsa5fp4av")))) + "0ifisnh42cw5z53hp9p52l3ggc7k877zlqk0n06gdhrk0bhidckj")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; test suite appears broken diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm index d8dc9ee6f9..ccb276607a 100644 --- a/gnu/packages/cdrom.scm +++ b/gnu/packages/cdrom.scm @@ -291,17 +291,26 @@ images.") `(#:tests? #f ; No tests. #:phases (modify-phases %standard-phases + (add-after 'unpack 'fix-glibc-compatability + (lambda* (#:key inputs #:allow-other-keys) + ;; We use sed --in-place because substitute* cannot handle the + ;; character encoding used by growisofs.c. + (invoke "sed" "-i" "-e" + (string-append + "s,<sys/stat.h>," + "<sys/stat.h>\\\n#include <sys/sysmacros.h>,") + "growisofs.c"))) (replace 'configure (lambda _ (setenv "prefix" (assoc-ref %outputs "out")) #t)) (add-before 'build 'embed-mkisofs - (lambda* (#:key inputs #:allow-other-keys) + (lambda* (#:key inputs #:allow-other-keys) ;; We use sed --in-place because substitute* cannot handle the ;; character encoding used by growisofs.c. - (zero? (system* "sed" "-i" "-e" - (string-append - "s,\"mkisofs\"," - "\"" (which "mkisofs") "\",") - "growisofs.c"))))))) + (invoke "sed" "-i" "-e" + (string-append + "s,\"mkisofs\"," + "\"" (which "mkisofs") "\",") + "growisofs.c")))))) (home-page "http://fy.chalmers.se/~appro/linux/DVD+RW/") (synopsis "DVD and Blu-ray Disc burning tools") (description "dvd+rw-tools, mostly known for its command diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 40f341fb64..937e4e094c 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -26,7 +26,7 @@ ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is> ;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018 Marius Bakke <mbakke@fastmail.com> -;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com> ;;; ;;; This file is part of GNU Guix. @@ -51,6 +51,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages llvm) #:use-module (gnu packages golang) + #:use-module (gnu packages perl) #:use-module (gnu packages python) #:use-module (gnu packages python-web) #:use-module (gnu packages time) @@ -250,7 +251,7 @@ a multi-paradigm automated test framework for C++ and Objective-C.") ;; the build environment. Hence assuming-failure test fails. (delete-file "yarn.tests/assuming-failure.script") (delete-file "yarn.tests/assuming-failure.stdout") - (zero? (system* "python" "setup.py" "check"))))))) + (invoke "python" "setup.py" "check")))))) (native-inputs `(("python2-coverage-test-runner" ,python2-coverage-test-runner))) (propagated-inputs @@ -619,14 +620,14 @@ standard library.") (define-public python-pytest (package (name "python-pytest") - (version "3.5.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (pypi-uri "pytest" version)) (sha256 (base32 - "1q832zd07zak2lyxbycxjydh0jp7y3hvawjqzlvra6aghz8r3r7s")))) + "17grcfvd6ggvvqmprwv5y8g319nayam70hr43ssjwj40ws27z858")))) (build-system python-build-system) (arguments `(#:phases @@ -642,9 +643,11 @@ standard library.") (string-append "@pytest.mark.skip" "(reason=\"Assumes that /usr exists.\")\n " line))) - #t))))) + #t)) + (replace 'check (lambda _ (invoke "pytest" "-vv")))))) (propagated-inputs - `(("python-attrs" ,python-attrs-bootstrap) + `(("python-atomicwrites" ,python-atomicwrites) + ("python-attrs" ,python-attrs-bootstrap) ("python-more-itertools" ,python-more-itertools) ("python-pluggy" ,python-pluggy) ("python-py" ,python-py) @@ -655,6 +658,7 @@ standard library.") ("python-hypothesis" ,python-hypothesis) ("python-nose" ,python-nose) ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest-bootstrap) ("python-setuptools-scm" ,python-setuptools-scm))) (home-page "http://pytest.org") (synopsis "Python testing library") @@ -672,6 +676,7 @@ and many external plugins.") (inherit pytest) (propagated-inputs `(("python2-funcsigs" ,python2-funcsigs) + ("python2-pathlib2" ,python2-pathlib2) ,@(package-propagated-inputs pytest)))))) (define-public python-pytest-bootstrap @@ -688,19 +693,20 @@ and many external plugins.") (package (inherit pytest) (propagated-inputs `(("python2-funcsigs" ,python2-funcsigs-bootstrap) + ("python2-pathlib2" ,python2-pathlib2-bootstrap) ,@(package-propagated-inputs pytest)))))) (define-public python-pytest-cov (package (name "python-pytest-cov") - (version "2.4.0") + (version "2.5.1") (source (origin (method url-fetch) (uri (pypi-uri "pytest-cov" version)) (sha256 (base32 - "03c2qc42r4bczyw93gd7n0qi1h1jfhw7fnbhi33c3vp1hs81gm2k")))) + "0bbfpwdh9k3636bxc88vz9fa7vf4akchgn513ql1vd0xy4n7bah3")))) (build-system python-build-system) (arguments `(#:phases @@ -710,8 +716,8 @@ and many external plugins.") ;; options taken from tox.ini ;; TODO: make "--restructuredtext" tests pass. They currently fail ;; with "Duplicate implicit target name" - (zero? (system* "python" "./setup.py" "check" - "--strict" "--metadata"))))))) + (invoke "python" "./setup.py" "check" + "--strict" "--metadata")))))) (propagated-inputs `(("python-coverage" ,python-coverage) ("python-pytest" ,python-pytest))) @@ -729,26 +735,15 @@ supports coverage of subprocesses.") (define-public python-pytest-runner (package (name "python-pytest-runner") - (version "2.11.1") + (version "4.2") (source (origin (method url-fetch) (uri (pypi-uri "pytest-runner" version)) (sha256 (base32 - "1cw978kqqcq916b9gfns1qjqvg33c5ail5jhw9054dsynkm32flq")))) + "1gkpyphawxz38ni1gdq1fmwyqcg02m7ypzqvv46z06crwdxi2gyj")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; The fancy way of setting the version with setuptools_scm does not - ;; seem to work here. - (add-after 'unpack 'set-version - (lambda _ - (substitute* "docs/conf.py" - (("version = setuptools_scm\\.get_version\\(root='\\.\\.')") - (string-append "version = \"" ,version "\""))) - #t))))) (native-inputs `(("python-pytest" ,python-pytest-bootstrap) ("python-setuptools-scm" ,python-setuptools-scm))) @@ -765,14 +760,14 @@ supports coverage of subprocesses.") (define-public python-pytest-mock (package (name "python-pytest-mock") - (version "1.6.3") + (version "1.10.0") (source (origin (method url-fetch) (uri (pypi-uri "pytest-mock" version)) (sha256 (base32 - "075v7b2wm5f839r1a30n21wfk5rfqp3d05q7zb9jlb2wmxki23cj")))) + "1h6lgpmsvs9s8j2s80v06f9f3iaw1n1rc51mbrxk1f12sw4q56nq")))) (build-system python-build-system) (native-inputs `(("python-setuptools-scm" ,python-setuptools-scm))) @@ -885,7 +880,8 @@ subprocess and see the output as well as any file modifications.") (uri (pypi-uri "testtools" version)) (sha256 (base32 - "0n8519lk8aaa91vymz842831181wf7fss98hyllhygi3z1nfq9sq")))) + "0n8519lk8aaa91vymz842831181wf7fss98hyllhygi3z1nfq9sq")) + (patches (search-patches "python-testtools.patch")))) (build-system python-build-system) (arguments '(#:tests? #f)) (propagated-inputs @@ -1105,8 +1101,8 @@ python-fixtures package instead.") (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "python" "-m" "testtools.run" - "fixtures.test_suite"))))))) + (invoke "python" "-m" "testtools.run" + "fixtures.test_suite")))))) (propagated-inputs ;; Fixtures uses pbr at runtime to check versions, etc. `(("python-pbr" ,python-pbr) @@ -1346,20 +1342,20 @@ the last py.test invocation.") (define-public python-pytest-localserver (package (name "python-pytest-localserver") - (version "0.4.1") + (version "0.5.0") (source (origin - (method url-fetch) - (uri (pypi-uri "pytest-localserver" version)) - (sha256 - (base32 - "08f06rvj31wqf0vgmd1waya87r7vy6x8ck48lxl3dxy83q5gcam7")))) + (method url-fetch) + (uri (pypi-uri "pytest-localserver" version)) + (sha256 + (base32 + "1hpgpxrpfq5c731ndnsay2lc0y9nh2wy9fn1f83s3z8xkn82fm1s")))) (build-system python-build-system) (arguments - `(#:phases (modify-phases %standard-phases + '(#:phases + (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "py.test" "--genscript=runtests.py")) - (zero? (system* "py.test"))))))) + (invoke "py.test" "-v")))))) (native-inputs `(("python-pytest" ,python-pytest) ("python-requests" ,python-requests) @@ -1421,16 +1417,17 @@ normally the case.") (define-public python-hypothesis (package (name "python-hypothesis") - (version "3.52.0") + (version "3.70.3") (source (origin (method url-fetch) (uri (pypi-uri "hypothesis" version)) (sha256 (base32 - "0g54cypfi5qj6cgxfr7l1nb41r1cqhhngx4qxn4ga9h720rcsbr8")))) + "1rshs1japfmwgar98yrkq4hg4z2q76hlnq7w2n3lfbjnscn1jd9b")))) (build-system python-build-system) (native-inputs - `(("python-flake8" ,python-flake8) + `(;; FIXME: Change to python-flake8 in the next rebuild cycle. + ("python-flake8" ,python-flake8-3.5) ("python-pytest" ,python-pytest-bootstrap))) (propagated-inputs `(("python-attrs" ,python-attrs-bootstrap) @@ -1527,7 +1524,7 @@ failures.") ;; It's easier to run tests after install. ;; Make installed package available for running the tests (add-installed-pythonpath inputs outputs) - (zero? (system* "py.test" "-vv"))))))) + (invoke "py.test" "-vv")))))) (native-inputs `(("python-coverage" ,python-coverage) ("python-pytest" ,python-pytest) @@ -1564,7 +1561,7 @@ failures.") (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "./testrun"))))))) + (invoke "./testrun")))))) (propagated-inputs `(("python2-coverage" ,python2-coverage))) (home-page "https://liw.fi/coverage-test-runner/") @@ -1610,9 +1607,9 @@ statements in the module it tests.") (string-append (getenv "PYTHONPATH") ":" work)) (copy-recursively "." work) (with-directory-excursion "/tmp" - (zero? (system* "python" "-m" "unittest" "discover" - "-s" (string-append work "/pylint/test") - "-p" "*test_*.py"))))))))) + (invoke "python" "-m" "unittest" "discover" + "-s" (string-append work "/pylint/test") + "-p" "*test_*.py")))))))) (home-page "https://github.com/PyCQA/pylint") (synopsis "Python source code analyzer which looks for coding standard errors") @@ -1845,7 +1842,8 @@ tests written in a natural language style, backed up by Python code.") (lambda _ (substitute* "setup.py" (("'wheel'") "") ; We don't use it. - (("'ordereddict==1.1'") ""))))))) ; Python >= 2.7 has it built-in. + (("'ordereddict==1.1'") "")) ; Python >= 2.7 has it built-in. + #t))))) (propagated-inputs `(("behave" ,behave) ("python-requests" ,python-requests))) @@ -2091,3 +2089,42 @@ aspects of UnitTest++. UnitTest++ is mostly standard C++ and makes minimal use of advanced library and language features, which means it should be easily portable to just about any platform.") (license license:expat))) + +(define-public libfaketime + (package + (name "libfaketime") + (version "0.9.7") + (home-page "https://github.com/wolfcw/libfaketime") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (sha256 + (base32 + "1cin1pqwpsswcv7amiwijirvcg3x1zf2l00s1x84nxc5602fzr5c")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (setenv "CC" "gcc") + (setenv "PREFIX" out) + #t))) + (add-before 'check 'pre-check + (lambda _ + (substitute* "test/functests/test_exclude_mono.sh" + (("/bin/bash") (which "bash"))) + #t))) + #:test-target "test")) + (native-inputs + `(("perl" ,perl))) ;for tests + (synopsis "Fake the system time for single applications") + (description + "The libfaketime library allows users to modify the system time that an +application \"sees\". It is meant to be loaded using the dynamic linker's +@code{LD_PRELOAD} environment variable. The @command{faketime} command +provides a simple way to achieve this.") + (license license:gpl2))) diff --git a/gnu/packages/chez.scm b/gnu/packages/chez.scm index c8e76b8ab4..929e50ee9b 100644 --- a/gnu/packages/chez.scm +++ b/gnu/packages/chez.scm @@ -85,6 +85,7 @@ ("xorg-rgb" ,xorg-rgb) ("nanopass" ,nanopass) ("zlib" ,zlib) + ("zlib:static" ,zlib "static") ("stex" ,stex))) (native-inputs `(("texlive" ,texlive) @@ -128,6 +129,7 @@ (nanopass (assoc-ref inputs "nanopass")) (stex (assoc-ref inputs "stex")) (zlib (assoc-ref inputs "zlib")) + (zlib-static (assoc-ref inputs "zlib:static")) (unpack (assoc-ref %standard-phases 'unpack)) (patch-source-shebangs (assoc-ref %standard-phases 'patch-source-shebangs))) @@ -148,7 +150,7 @@ (("\\$\\{Kernel\\}: \\$\\{kernelobj\\} \\.\\./zlib/libz\\.a") "${Kernel}: ${kernelobj}") (("ld ([-a-zA-Z0-9_${} ]+) \\.\\./zlib/libz\\.a" all args) - (string-append "ld " args " " zlib "/lib/libz.a")) + (string-append "ld " args " " zlib-static "/lib/libz.a")) (("\\(cd \\.\\./zlib; ([-a-zA-Z0-9=./ ]+))") (which "true"))) (substitute* (find-files "mats" "Mf-.*") diff --git a/gnu/packages/cmake.scm b/gnu/packages/cmake.scm index 06b1cab82c..5abf087557 100644 --- a/gnu/packages/cmake.scm +++ b/gnu/packages/cmake.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -43,7 +44,7 @@ (define-public cmake (package (name "cmake") - (version "3.11.0") + (version "3.12.2") (source (origin (method url-fetch) (uri (string-append "https://www.cmake.org/files/v" @@ -51,7 +52,7 @@ "/cmake-" version ".tar.gz")) (sha256 (base32 - "0sv5k9q6braa8hhw0y3w19avqn0xn5czv5jf5fz5blnlf7ivw4y3")) + "19410mxgcyvk5q42phaclb1hz6rl08z4yj8iriq706p5k5bli5qg")) (modules '((guix build utils))) (snippet '(begin @@ -86,6 +87,13 @@ " --exclude-regex ^\\(" (string-join skipped-tests "\\|") "\\)$"))) #:phases (modify-phases %standard-phases + (add-after 'unpack 'split-package + ;; Remove files that have been packaged in other package recipes. + (lambda _ + (delete-file "Auxiliary/cmake-mode.el") + (substitute* "Auxiliary/CMakeLists.txt" + ((".*cmake-mode.el.*") "")) + #t)) (add-before 'configure 'patch-bin-sh (lambda _ ;; Replace "/bin/sh" by the right path in... a lot of diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm index 30a0ffcec9..0aa65fe638 100644 --- a/gnu/packages/commencement.scm +++ b/gnu/packages/commencement.scm @@ -186,12 +186,25 @@ ,cf))))) (inputs %boot0-inputs)))) +;; Use a "fixed" package source for this early libstdc++ variant so we can +;; update GCC 4.9 without triggering a full rebuild. +(define gcc-for-libstdc++ + (package + (inherit gcc-4.9) + (source (origin + (inherit (package-source gcc-4.9)) + (patches (search-patches "gcc-4.9-libsanitizer-fix.patch" + "gcc-arm-bug-71399.patch" + "gcc-asan-missing-include.patch" + "gcc-libvtv-runpath.patch" + "gcc-fix-texi2pod.patch")))))) + (define libstdc++-boot0 ;; GCC's libcc1 is always built as a shared library (the top-level ;; 'Makefile.def' forcefully adds --enable-shared) and thus needs to refer ;; to libstdc++.so. We cannot build libstdc++-5.3 because it relies on ;; C++14 features missing in some of our bootstrap compilers. - (let ((lib (package-with-bootstrap-guile (make-libstdc++ gcc-4.9)))) + (let ((lib (package-with-bootstrap-guile (make-libstdc++ gcc-for-libstdc++)))) (package (inherit lib) (name "libstdc++-boot0") diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index e775052b7a..32b92a976c 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2017, 2018 Leo Famulari <leo@famulari.name> ;;; Copyright © 2015 Jeff Mickey <j@codemac.net> -;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2016 Danny Milosavljevic <dannym@scratchpost.org> ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> @@ -85,6 +85,7 @@ (base32 "18dighcs333gsvajvvgqp8l4cx7h1x7yx9gd5xacnk80spyykrf3")))) (build-system gnu-build-system) + (outputs '("out" "static")) (arguments `(#:phases (modify-phases %standard-phases @@ -99,7 +100,15 @@ `((setenv "CHOST" ,(%current-target-system))) '()) (invoke "./configure" - (string-append "--prefix=" out)))))))) + (string-append "--prefix=" out))))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (static (assoc-ref outputs "static"))) + (with-directory-excursion (string-append out "/lib") + (install-file "libz.a" (string-append static "/lib")) + (delete-file "libz.a") + #t))))))) (home-page "https://zlib.net/") (synopsis "Compression library") (description @@ -208,6 +217,21 @@ adding and extracting files to/from a tar archive.") '(#:tests? #f #:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-for-glibc-2.28 + (lambda _ + ;; Adjust the bundled gnulib to work with glibc 2.28. See e.g. + ;; "m4-gnulib-libio.patch". This is a phase rather than patch + ;; or snippet to work around <https://bugs.gnu.org/32347>. + (substitute* (find-files "lib" "\\.c$") + (("#if defined _IO_ftrylockfile") + "#if defined _IO_EOF_SEEN")) + (substitute* "lib/stdio-impl.h" + (("^/\\* BSD stdio derived implementations") + (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n" + "# define _IO_IN_BACKUP 0x100\n" + "#endif\n\n" + "/* BSD stdio derived implementations"))) + #t)) (add-after 'unpack 'use-absolute-name-of-gzip (lambda* (#:key outputs #:allow-other-keys) (substitute* "gunzip.in" @@ -240,6 +264,7 @@ file; as a result, it is often used in conjunction with \"tar\", resulting in (arguments `(#:modules ((guix build gnu-build-system) (guix build utils) + (ice-9 ftw) (srfi srfi-1)) #:phases (modify-phases %standard-phases @@ -268,25 +293,32 @@ file; as a result, it is often used in conjunction with \"tar\", resulting in ;; it create all the (un)versioned symlinks, so we handle it here. (let* ((out (assoc-ref outputs "out")) (libdir (string-append out "/lib")) - ;; Find the actual library (e.g. "libbz2.so.1.0.6"). - (lib (string-drop - (car (find-files - "." - (lambda (file stat) - (and (string-prefix? "./libbz2.so" file) - (eq? 'regular (stat:type stat)))))) - 2)) - (soversion (string-drop lib (string-length "libbz2.so.")))) + (soname "libbz2.so") + ;; Locate the built library (e.g. "libbz2.so.1.0.6"). + (lib (car (scandir "." + (lambda (file) + (and (string-prefix? soname file) + (eq? 'regular + (stat:type (lstat file)))))))) + (soversion (string-drop lib (+ 1 (string-length soname))))) (install-file lib libdir) (with-directory-excursion libdir ;; Create symlinks libbz2.so.1 -> libbz2.so.1.0, etc. - (let loop ((base "libbz2.so") + (let loop ((base soname) (numbers (string-split soversion #\.))) (unless (null? numbers) (let ((so-file (string-append base "." (car numbers)))) (symlink so-file base) (loop so-file (cdr numbers)))))) #t))) + (add-after 'install-shared-lib 'move-static-lib + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (static (assoc-ref outputs "static"))) + (with-directory-excursion (string-append out "/lib") + (install-file "libbz2.a" (string-append static "/lib")) + (delete-file "libbz2.a") + #t)))) (add-after 'install-shared-lib 'patch-scripts (lambda* (#:key outputs inputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out"))) @@ -301,6 +333,7 @@ file; as a result, it is often used in conjunction with \"tar\", resulting in ,@(if (%current-target-system) '(#:tests? #f) '()))) + (outputs '("out" "static")) (synopsis "High-quality data compression program") (description "bzip2 is a freely available, patent free (see below), high-quality data @@ -322,7 +355,20 @@ decompression.") version ".tar.gz")) (sha256 (base32 - "1sahaqc5bw4i0iyri05syfza4ncf5cml89an033fspn97klmxis6")))) + "1sahaqc5bw4i0iyri05syfza4ncf5cml89an033fspn97klmxis6")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* (find-files "lib" "\\.c$") + (("#if defined _IO_ftrylockfile") + "#if defined _IO_EOF_SEEN")) + (substitute* "lib/stdio-impl.h" + (("^/\\* BSD stdio derived implementations") + (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n" + "# define _IO_IN_BACKUP 0x100\n" + "#endif\n\n" + "/* BSD stdio derived implementations"))) + #t)))) (build-system gnu-build-system) (synopsis "Parallel bzip2 compression utility") (description @@ -368,7 +414,7 @@ compressed with pbzip2 can be decompressed with bzip2).") (define-public xz (package (name "xz") - (version "5.2.3") + (version "5.2.4") (source (origin (method url-fetch) (uri (list (string-append "http://tukaani.org/xz/xz-" version @@ -377,7 +423,7 @@ compressed with pbzip2 can be decompressed with bzip2).") version ".tar.gz"))) (sha256 (base32 - "1jr8pxnz55ifc8cvp3ivgl79ph9iik5aypsc9cma228aglsqp4ki")))) + "0ibi2zsfaz6l756spjwc5rayf4ckgc9hwmy8qinppcyk4svz64mm")))) (build-system gnu-build-system) (synopsis "General-purpose data compression") (description @@ -543,7 +589,20 @@ decompressors when faced with corrupted input.") (patches (search-patches "sharutils-CVE-2018-1000097.patch")) (sha256 (base32 - "16isapn8f39lnffc3dp4dan05b7x6mnc76v6q5nn8ysxvvvwy19b")))) + "16isapn8f39lnffc3dp4dan05b7x6mnc76v6q5nn8ysxvvvwy19b")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* (find-files "lib" "\\.c$") + (("#if defined _IO_ftrylockfile") + "#if defined _IO_EOF_SEEN")) + (substitute* "lib/stdio-impl.h" + (("^/\\* BSD stdio derived implementations") + (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n" + "# define _IO_IN_BACKUP 0x100\n" + "#endif\n\n" + "/* BSD stdio derived implementations"))) + #t)))) (build-system gnu-build-system) (inputs `(("which" ,which))) @@ -701,7 +760,8 @@ INCLUDE = ~a/include LIB = ~:*~a/lib OLD_ZLIB = False GZIP_OS_CODE = AUTO_DETECT" - (assoc-ref inputs "zlib"))))))))) + (assoc-ref inputs "zlib")))) + #t))))) (home-page "https://metacpan.org/release/Compress-Raw-Zlib") (synopsis "Low-level interface to zlib compression library") (description "This module provides a Perl interface to the zlib @@ -834,8 +894,16 @@ the LZ4 frame format.") #:phases (modify-phases %standard-phases (replace 'configure - (lambda _ - (chdir "squashfs-tools")))))) + (lambda _ + (chdir "squashfs-tools") + #t)) + (add-after 'unpack 'fix-glibc-compatability + (lambda _ + (substitute* '("squashfs-tools/mksquashfs.c" + "squashfs-tools/unsquashfs.c") + (("<sys/sysinfo.h>") + "<sys/sysinfo.h>\n#include <sys/sysmacros.h>")) + #t))))) (inputs `(("lz4" ,lz4) ("lzo" ,lzo) @@ -1134,16 +1202,30 @@ well as bzip2.") (define-public bitshuffle (package (name "bitshuffle") - (version "0.3.4") + (version "0.3.5") (source (origin (method url-fetch) (uri (pypi-uri "bitshuffle" version)) (sha256 (base32 - "0ydawb01ghsvmw0lraczhrgvkjj97bpg98f1qqs1cnfp953mdd5v")))) + "1823x61kyax4dc2hjmc1xraskxi1193y8lvxd03vqv029jrj8cjy")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Remove generated Cython files. + (delete-file "bitshuffle/h5.c") + (delete-file "bitshuffle/ext.c") + #t)))) (build-system python-build-system) (arguments - `(#:tests? #f)) ; fail: https://github.com/h5py/h5py/issues/769 + `(#:tests? #f ; fail: https://github.com/h5py/h5py/issues/769 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'dont-build-native + (lambda _ + (substitute* "setup.py" + (("'-march=native', ") "")) + #t))))) (inputs `(("numpy" ,python-numpy) ("h5py" ,python-h5py) @@ -1161,14 +1243,15 @@ algorithm within the Numpy framework.") (package (name "snappy") (version "1.1.7") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/google/snappy/archive/" - version ".tar.gz")) - (file-name (string-append "snappy-" version ".tar.gz")) - (sha256 - (base32 - "1m7rcdqzkys5lspj8jcsaah8w33zh28s771bw0ga2lgzfgl05yix")))) + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/google/snappy/archive/" + version ".tar.gz")) + (file-name (string-append "snappy-" version ".tar.gz")) + (sha256 + (base32 "1m7rcdqzkys5lspj8jcsaah8w33zh28s771bw0ga2lgzfgl05yix")) + (patches (search-patches "snappy-add-O2-flag-in-CmakeLists.txt.patch")))) (build-system cmake-build-system) (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"))) @@ -1278,7 +1361,8 @@ install: libbitshuffle.so (add-after 'build-jni 'copy-jni (lambda _ (copy-recursively "src/main/resources/org/xerial/snappy/native" - "build/classes/org/xerial/snappy/native"))) + "build/classes/org/xerial/snappy/native") + #t)) (add-before 'check 'fix-failing (lambda _ (with-directory-excursion "src/test/java/org/xerial/snappy" @@ -1396,7 +1480,8 @@ compressor/decompressor.") class)) (invoke "ant" "compile-tests") (test "org.iq80.snappy.SnappyFramedStreamTest") - (test "org.iq80.snappy.SnappyStreamTest"))) + (test "org.iq80.snappy.SnappyStreamTest") + #t)) (add-before 'build 'remove-hadoop-dependency (lambda _ ;; We don't have hadoop @@ -1751,7 +1836,7 @@ speed.") `(#:phases (modify-phases %standard-phases (add-after 'unpack 'enter-subdirectory - (lambda _ (chdir "contrib/pzstd"))) + (lambda _ (chdir "contrib/pzstd") #t)) (delete 'configure) ; no configure script (add-before 'check 'compile-tests (lambda* (#:key make-flags #:allow-other-keys) @@ -2033,14 +2118,16 @@ type by using either Perl modules, or command-line tools on your system.") (lambda _ ;; Our build system enters the first directory in the archive, but ;; the package is not contained in a subdirectory - (chdir ".."))) + (chdir "..") + #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) ;; Do we want to install *Demo.jar? (install-file "build/jar/xz.jar" (string-append (assoc-ref outputs "out") - "/share/java/xz.jar"))))))) + "/share/java/xz.jar")) + #t))))) (native-inputs `(("unzip" ,unzip))) (home-page "https://tukaani.org") diff --git a/gnu/packages/cross-base.scm b/gnu/packages/cross-base.scm index bbd779ae4e..2fcb7fb36b 100644 --- a/gnu/packages/cross-base.scm +++ b/gnu/packages/cross-base.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org> ;;; Copyright © 2016 Manolis Fragkiskos Ragkousis <manolis837@gmail.com> @@ -356,7 +356,7 @@ target that libc." ,@(package-arguments glibc/hurd-headers)) ((#:phases phases) `(modify-phases ,phases - (add-before 'pre-configure 'set-cross-headers-path + (add-after 'unpack 'set-cross-headers-path (lambda* (#:key inputs #:allow-other-keys) (let* ((mach (assoc-ref inputs "gnumach-headers")) (hurd (assoc-ref inputs "hurd-headers")) @@ -426,17 +426,9 @@ target that libc." (xheaders (cross-kernel-headers target))) "Return a libc cross-built for TARGET, a GNU triplet. Use XGCC and XBINUTILS and the cross tool chain." - (define (cross-libc-for-target target) - "Return libc depending on TARGET." - (match target - ((or "i586-pc-gnu" "i586-gnu") glibc/hurd) - (_ glibc/linux))) - - ;; Use (cross-libc-for-target ...) to determine the correct libc to use. - (if (cross-newlib? target) (native-libc target) - (let ((libc (cross-libc-for-target target))) + (let ((libc glibc)) (package (inherit libc) (name (string-append "glibc-cross-" target)) (arguments @@ -457,7 +449,9 @@ XBINUTILS and the cross tool chain." ,@(package-arguments libc)) ((#:configure-flags flags) `(cons ,(string-append "--host=" target) - ,flags)) + ,(if (hurd-triplet? target) + `(cons "--disable-werror" ,flags) + flags))) ((#:phases phases) `(modify-phases ,phases (add-before 'configure 'set-cross-kernel-headers-path diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm index 04a533de02..4343910d59 100644 --- a/gnu/packages/cups.scm +++ b/gnu/packages/cups.scm @@ -53,7 +53,7 @@ (define-public cups-filters (package (name "cups-filters") - (version "1.20.1") + (version "1.21.0") (source(origin (method url-fetch) (uri @@ -61,7 +61,7 @@ "cups-filters-" version ".tar.xz")) (sha256 (base32 - "0qix1whz5n4ijnl6d44f1v8nzkpv99wqjyrby8vx6xnpskw5hsxk")) + "0fs90xx9i4h8gbpligf5kkh21llv4kf5g3bgfbx4z272xkm7bsfi")) (modules '((guix build utils))) (snippet ;; install backends, banners and filters to cups-filters output @@ -176,8 +176,7 @@ filters for the PDF-centric printing workflow introduced by OpenPrinting.") (define-public cups-minimal (package (name "cups-minimal") - (replacement cups-minimal-2.2.8) - (version "2.2.6") + (version "2.2.8") (source (origin (method url-fetch) @@ -185,7 +184,7 @@ filters for the PDF-centric printing workflow introduced by OpenPrinting.") version "/cups-" version "-source.tar.gz")) (sha256 (base32 - "16qn41b84xz6khrr2pa2wdwlqxr29rrrkjfi618gbgdkq9w5ff20")))) + "1r7r7b3nqpzc1a9dczqpj2mr8rkcwf01676v11sp4j7w4qfzqs1r")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -237,21 +236,8 @@ describe printer capabilities and features, and a wide variety of generic and device-specific programs to convert and print many types of files.") (license license:gpl2))) -(define-public cups-minimal-2.2.8 - (package - (inherit cups-minimal) - (version "2.2.8") - (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/apple/cups/releases/download/v" - version "/cups-" version "-source.tar.gz")) - (sha256 - (base32 - "1r7r7b3nqpzc1a9dczqpj2mr8rkcwf01676v11sp4j7w4qfzqs1r")))))) - (define-public cups - (package/inherit cups-minimal + (package (inherit cups-minimal) (name "cups") (arguments `(;; Three tests fail: diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm index 2fb87251f4..61313af7d2 100644 --- a/gnu/packages/curl.scm +++ b/gnu/packages/curl.scm @@ -50,7 +50,7 @@ (define-public curl (package (name "curl") - (version "7.59.0") + (version "7.61.1") (replacement curl-7.62.0) (source (origin (method url-fetch) @@ -58,7 +58,7 @@ version ".tar.xz")) (sha256 (base32 - "1z310hrjm2vmbcpkyp81dcmj9rk127zkjyawpy2pah0nz6yslkp4")))) + "148qv1f32290r9pwg07mccawihz4srznkzsdwdl2xllvlgb16n9x")))) (build-system gnu-build-system) (outputs '("out" "doc")) ;1.2 MiB of man3 pages @@ -85,7 +85,8 @@ (separator #f) ;single entry (files '("etc/ssl/certs/ca-certificates.crt"))))) (arguments - `(#:configure-flags '("--with-gnutls" "--with-gssapi") + `(#:configure-flags '("--with-gnutls" "--with-gssapi" + "--disable-static") ;; Add a phase to patch '/bin/sh' occurances in tests/runtests.pl #:phases (modify-phases %standard-phases diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 7258622f42..393b13a314 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -153,7 +153,7 @@ (modify-phases %standard-phases (add-after 'unpack 'generate-configure (lambda _ - (zero? (system* "sh" "autogen.sh"))))))) + (invoke "sh" "autogen.sh")))))) ;; http://www.4store.org has been down for a while now. (home-page "https://github.com/4store/4store") (synopsis "Clustered RDF storage and query engine") @@ -164,14 +164,14 @@ either single machines or networked clusters.") (define-public gdbm (package (name "gdbm") - (version "1.14.1") + (version "1.18") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/gdbm/gdbm-" version ".tar.gz")) (sha256 (base32 - "0pxwz3jlwvglq2mrbxvrjgr8pa0aj73p3v9sxmdlj570zw0gzknd")))) + "1kimnv12bzjjhaqk4c8w2j6chdj9c6bg21lchaf7abcyfss2r0mq")))) (arguments `(#:configure-flags '("--enable-libgdbm-compat"))) (build-system gnu-build-system) (home-page "http://www.gnu.org.ua/software/gdbm") @@ -207,14 +207,16 @@ and provides interfaces to the traditional file format.") (delete 'reset-gzip-timestamps) (add-before 'check 'start-mongodb (lambda* (#:key tests? #:allow-other-keys) - (or (not tests?) - (with-directory-excursion "src/gopkg.in/mgo.v2" - (invoke "make" "startdb"))))) + (when tests? + (with-directory-excursion "src/gopkg.in/mgo.v2" + (invoke "make" "startdb"))) + #t)) (add-after 'check 'stop'mongodb (lambda* (#:key tests? #:allow-other-keys) - (or (not tests?) - (with-directory-excursion "src/gopkg.in/mgo.v2" - (invoke "make" "stopdb")))))))) + (when tests? + (with-directory-excursion "src/gopkg.in/mgo.v2" + (invoke "make" "stopdb"))) + #t))))) (native-inputs `(("go-gopkg.in-check.v1" ,go-gopkg.in-check.v1) ("mongodb" ,mongodb) @@ -511,28 +513,27 @@ applications.") (setenv "TZDIR" (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo")) - (or (not tests?) - ;; Note that with the tests, especially the unittests, the - ;; build can take up to ~45GB of space, as many tests are - ;; individual executable files, with some being hundreds of - ;; megabytes in size. - (begin - (apply - invoke `("scons" ,@common-options "dbtest" "unittests")) - (substitute* "build/unittests.txt" - ;; TODO: Don't run the async_stream_test, as it hangs - (("^build\\/opt\\/mongo\\/executor\\/async\\_stream\\_test\n$") - "") - ;; TODO: This test fails - ;; Expected 0UL != disks.size() (0 != 0) @src/mongo/util/procparser_test.cpp:476 - (("^build\\/opt\\/mongo\\/util\\/procparser\\_test\n$") - "")) - (invoke "python" "buildscripts/resmoke.py" - "--suites=dbtest,unittests" - (format #f "--jobs=~a" (parallel-job-count))))))) + (when tests? + ;; Note that with the tests, especially the unittests, the + ;; build can take up to ~45GB of space, as many tests are + ;; individual executable files, with some being hundreds of + ;; megabytes in size. + (apply invoke `("scons" ,@common-options "dbtest" "unittests")) + (substitute* "build/unittests.txt" + ;; TODO: Don't run the async_stream_test, as it hangs + (("^build\\/opt\\/mongo\\/executor\\/async\\_stream\\_test\n$") + "") + ;; TODO: This test fails + ;; Expected 0UL != disks.size() (0 != 0) @src/mongo/util/procparser_test.cpp:476 + (("^build\\/opt\\/mongo\\/util\\/procparser\\_test\n$") + "")) + (invoke "python" "buildscripts/resmoke.py" + "--suites=dbtest,unittests" + (format #f "--jobs=~a" (parallel-job-count)))) + #t)) (replace 'install - (lambda _ - (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))) + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "mongod" bin) (install-file "mongos" bin) (install-file "mongo" bin)) @@ -620,7 +621,7 @@ Language.") (define-public mariadb (package (name "mariadb") - (version "10.1.35") + (version "10.1.36") (source (origin (method url-fetch) (uri (string-append "https://downloads.mariadb.org/f/" @@ -628,14 +629,20 @@ Language.") name "-" version ".tar.gz")) (sha256 (base32 - "0k9walaglwmwdwmkq48ir17g98n83vliyyg5wck22rjgxn2xk4cy")) - (patches (search-patches "mariadb-gcc-ice.patch" - "mariadb-client-test-32bit.patch")) + "0n5aj76mn9rxc21l2kjmfrg10bmsyy4cic68khjr94iby262wx5d")) + (patches (search-patches "mariadb-client-test-32bit.patch")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled snappy and xz. (delete-file-recursively "storage/tokudb/PerconaFT/third_party") + (substitute* "storage/tokudb/PerconaFT/CMakeLists.txt" + ;; This file checks that the bundled sources are present and + ;; declares build procedures for them. + (("^include\\(TokuThirdParty\\)") "")) + (substitute* "storage/tokudb/PerconaFT/ft/CMakeLists.txt" + ;; Don't attempt to use the procedures we just removed. + ((" build_lzma build_snappy") "")) ;; Preserve CMakeLists.txt for these. (for-each (lambda (file) @@ -679,7 +686,7 @@ Language.") "-DINSTALL_SHAREDIR=share") #:phases (modify-phases %standard-phases - (add-after 'unpack 'unbundle + (add-after 'unpack 'fix-pcre-detection (lambda _ ;; The bundled PCRE in MariaDB has a patch that was upstreamed ;; in version 8.34. Unfortunately the upstream patch behaves @@ -688,16 +695,6 @@ Language.") ;; XXX: Consider patching PCRE instead. (substitute* "cmake/pcre.cmake" ((" OR NOT PCRE_STACK_SIZE_OK") "")) - - (substitute* "storage/tokudb/PerconaFT/ft/CMakeLists.txt" - ;; Remove dependency on these CMake targets. - ((" build_lzma build_snappy") "")) - - (substitute* "storage/tokudb/PerconaFT/CMakeLists.txt" - ;; This file checks that the bundled sources are present and - ;; declares build procedures for them. We don't need that. - (("^include\\(TokuThirdParty\\)") "")) - #t)) (add-after 'unpack 'adjust-tests (lambda _ @@ -707,6 +704,7 @@ Language.") ;; See <https://jira.mariadb.org/browse/MDEV-7761>. "main.join_cache" "main.explain_non_select" + "main.stat_tables_innodb" "roles.acl_statistics" ;; FIXME: This test fails on i686: @@ -772,8 +770,8 @@ Language.") (for-each delete-file-recursively '("data" "mysql-test" "sql-bench" "share/man/man1/mysql-test-run.pl.1")) - ;; Delete huge mysqltest executables. - (for-each delete-file (find-files "bin" "test")) + ;; Delete huge and unnecessary executables. + (for-each delete-file (find-files "bin" "(test|embedded)")) ;; And static libraries. (for-each delete-file (find-files "lib" "\\.a$"))) #t)))))) @@ -785,11 +783,13 @@ Language.") ("libaio" ,libaio) ("libxml2" ,libxml2) ("ncurses" ,ncurses) - ("openssl" ,openssl) ("pcre" ,pcre) ("snappy" ,snappy) ("xz" ,xz) ("zlib" ,zlib))) + (propagated-inputs + ;; mariadb.pc says -lssl -lcrypto, so propagate it. + `(("openssl" ,openssl))) ;; The test suite is very resource intensive and can take more than three ;; hours on a x86_64 system. Give slow and busy machines some leeway. (properties '((timeout . 64800))) ;18 hours @@ -923,7 +923,23 @@ organized in a hash table or B+ tree.") version ".tar.gz")) (sha256 (base32 - "0cdwa4094x3yx7vn98xykvnlp9rngvd58d19vs3vh5hrvggccg93")))) + "0cdwa4094x3yx7vn98xykvnlp9rngvd58d19vs3vh5hrvggccg93")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Adjust the bundled gnulib to work with glibc 2.28. See e.g. + ;; "m4-gnulib-libio.patch". This is a phase rather than patch + ;; or snippet to work around <https://bugs.gnu.org/32347>. + (substitute* (find-files "lib" "\\.c$") + (("#if defined _IO_ftrylockfile") + "#if defined _IO_EOF_SEEN")) + (substitute* "lib/stdio-impl.h" + (("^/\\* BSD stdio derived implementations") + (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n" + "# define _IO_IN_BACKUP 0x100\n" + "#endif\n\n" + "/* BSD stdio derived implementations"))) + #t)))) (build-system gnu-build-system) ;; Running tests in parallel leads to test failures and crashes in @@ -973,15 +989,16 @@ types are supported, as is encryption.") (define-public rocksdb (package (name "rocksdb") - (version "5.12.4") + (version "5.15.10") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/facebook/rocksdb" - "/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/facebook/rocksdb") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1jcwgsjhk4hdfr2wf549blkgb89vwcdb5i2ahhqs6zf3mm20i3bf")) + "0q26frbj9pykarcfa0yxgwncxlvsqhjkby0jrbfs1a8srja688r4")) (modules '((guix build utils))) (snippet '(begin @@ -1102,7 +1119,8 @@ data in a single database. RocksDB is partially based on @code{LevelDB}.") (lambda _ (substitute* "Makefile" (("^gitrev :=.*$") - (string-append "gitrev = \"v" ,version "\""))))) + (string-append "gitrev = \"v" ,version "\""))) + #t)) ;; The install phase of the Makefile assumes $PREFIX/usr/local/bin. ;; This replacement does the same thing, except for using $PREFIX/bin ;; instead. @@ -1111,14 +1129,13 @@ data in a single database. RocksDB is partially based on @code{LevelDB}.") (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin"))) (install-file "sparql-query" bin) - (system* "ln" "--symbolic" - (string-append bin "/sparql-query") - (string-append bin "/sparql-update"))))) + (symlink (string-append bin "/sparql-query") + (string-append bin "/sparql-update"))) + #t)) (replace 'check (lambda* (#:key make-flags #:allow-other-keys) - (and - (zero? (apply system* "make" `(,@make-flags "scan-test"))) - (zero? (system "./scan-test")))))))) + (apply invoke "make" `(,@make-flags "scan-test")) + (invoke "./scan-test")))))) (home-page "https://github.com/tialaramex/sparql-query/") (synopsis "Command-line tool for accessing SPARQL endpoints over HTTP") (description "Sparql-query is a command-line tool for accessing SPARQL @@ -1166,7 +1183,7 @@ changes.") (define-public sqlite (package (name "sqlite") - (version "3.23.0") + (version "3.24.0") (source (origin (method url-fetch) (uri (let ((numeric-version @@ -1182,7 +1199,7 @@ changes.") numeric-version ".tar.gz"))) (sha256 (base32 - "0jbf78g3cm5wq77k7sfg8fb6rz44hnp9hs7p5d66fwd000c1lwdp")))) + "0jmprv2vpggzhy7ma4ynmv1jzn3pfiwzkld0kkg6hvgvqs44xlfr")))) (build-system gnu-build-system) (inputs `(("readline" ,readline))) (arguments @@ -1243,8 +1260,8 @@ is in the public domain.") (let ((out (assoc-ref outputs "out"))) ;; The 'configure' script is a wrapper for Waf and ;; doesn't recognize things like '--enable-fast-install'. - (zero? (system* "./configure" - (string-append "--prefix=" out))))))))) + (invoke "./configure" + (string-append "--prefix=" out)))))))) (native-inputs `(;; TODO: Build the documentation. ;; ("docbook-xsl" ,docbook-xsl) @@ -1609,7 +1626,7 @@ valid SQL query.") (define-public unixodbc (package (name "unixodbc") - (version "2.3.6") + (version "2.3.7") (source (origin (method url-fetch) (uri @@ -1617,7 +1634,7 @@ valid SQL query.") "ftp://ftp.unixodbc.org/pub/unixODBC/unixODBC-" version ".tar.gz")) (sha256 - (base32 "0sads5b8cmmj526gyjba7ccknl1vbhkslfqshv1yqln08zv3gdl8")))) + (base32 "0xry3sg497wly8f7715a7gwkn2k36bcap0mvzjw74jj53yx6kwa5")))) (build-system gnu-build-system) (synopsis "Data source abstraction library") (description "Unixodbc is a library providing an API with which to access @@ -1993,8 +2010,7 @@ can autogenerate peewee models using @code{pwiz}, a model generator.") (assoc-ref %standard-phases 'check)) (replace 'check (lambda _ - (zero? - (system* "./testfixture" "test/crypto.test"))))))) + (invoke "./testfixture" "test/crypto.test")))))) (home-page "https://www.zetetic.net/sqlcipher/") (synopsis "Library providing transparent encryption of SQLite database files") @@ -2250,9 +2266,6 @@ and web services platform functionality.") `(("pkg-config" ,pkg-config))) (inputs `(("mariadb" ,mariadb) - ;; FIXME: This should be propagated from MariaDB, but add it here - ;; for now to prevent a large rebuild. - ("openssl" ,openssl) ("zlib" ,zlib))) (propagated-inputs `(("r-dbi" ,r-dbi))) @@ -2321,7 +2334,7 @@ Database API 2.0T.") (define-public python-sqlalchemy (package (name "python-sqlalchemy") - (version "1.0.12") + (version "1.2.11") (source (origin (method url-fetch) @@ -2329,7 +2342,7 @@ Database API 2.0T.") "SQLAlchemy/SQLAlchemy-" version ".tar.gz")) (sha256 (base32 - "1l8qclhd0s90w3pvwhi5mjxdwr5j7gw7cjka2fx6f2vqmq7f4yb6")))) + "094mmbs4igrxplfyqd59j90jb83ixpbbzqc0w49yw81m82nnjrgg")))) (build-system python-build-system) (native-inputs `(("python-cython" ,python-cython) ;for c extensions @@ -2339,7 +2352,7 @@ Database API 2.0T.") `(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ (zero? (system* "py.test"))))))) + (lambda _ (invoke "py.test")))))) (home-page "http://www.sqlalchemy.org") (synopsis "Database abstraction library") (description @@ -2406,14 +2419,14 @@ You might also want to install the following optional dependencies: (define-public python-alembic (package (name "python-alembic") - (version "0.9.6") + (version "1.0.2") (source (origin (method url-fetch) (uri (pypi-uri "alembic" version)) (sha256 (base32 - "0cm73vabrqj92v7a0wwvldj8j7bc7dwv358kvkk7p87gx7mm2a04")))) + "0asqz9mwc4w8bsar1icv3ik9jslxrj3gv3yxgmhc6nc6r9qbkg04")))) (build-system python-build-system) (native-inputs `(("python-mock" ,python-mock) @@ -2731,13 +2744,13 @@ reasonable substitute.") (define-public python-rq (package (name "python-rq") - (version "0.7.1") + (version "0.12.0") (source (origin (method url-fetch) (uri (pypi-uri "rq" version)) (sha256 - (base32 "0gaq5pnh0zy46r8jvygi0ifbvz3pq6i7xla78ijcgjw0x77qzsdh")))) + (base32 "16d8kni57xlnah2hawy4xgw21xrv3f64j5q5shyp3zxx4yd9iibs")))) (build-system python-build-system) (propagated-inputs `(("python-click" ,python-click) @@ -2792,7 +2805,7 @@ is designed to have a low barrier to entry.") `(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ (zero? (system* "py.test"))))))) + (lambda _ (invoke "py.test")))))) (native-inputs `(("python-pytest" ,python-pytest))) (home-page "https://github.com/andialbrecht/sqlparse") @@ -2859,41 +2872,46 @@ transforms idiomatic python function calls to well-formed SQL queries.") (delete 'install-source) (replace 'build (lambda _ - (every (lambda (tool) - (let ((command - `("go" "build" - ;; This is where the tests expect to find the - ;; executables - "-o" ,(string-append - "src/github.com/mongodb/mongo-tools/bin/" - tool) - "-v" - "-tags=\"ssl sasl\"" - "-ldflags" - "-extldflags=-Wl,-z,now,-z,relro" - ,(string-append - "src/github.com/mongodb/mongo-tools/" - tool "/main/" tool ".go")))) - (simple-format #t "build: running ~A\n" - (string-join command)) - (apply invoke command))) - all-tools))) + (for-each (lambda (tool) + (let ((command + `("go" "build" + ;; This is where the tests expect to find the + ;; executables + "-o" ,(string-append + "src/github.com/mongodb/mongo-tools/bin/" + tool) + "-v" + "-tags=\"ssl sasl\"" + "-ldflags" + "-extldflags=-Wl,-z,now,-z,relro" + ,(string-append + "src/github.com/mongodb/mongo-tools/" + tool "/main/" tool ".go")))) + (simple-format #t "build: running ~A\n" + (string-join command)) + (apply invoke command))) + all-tools) + #t)) (replace 'check (lambda _ (with-directory-excursion "src" - (every (lambda (tool) - (invoke - "go" "test" "-v" - (string-append "github.com/mongodb/mongo-tools/" tool))) - all-tools)))) + (for-each (lambda (tool) + (invoke + "go" "test" "-v" + (string-append "github.com/mongodb/mongo-tools/" + tool))) + all-tools)) + #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (for-each (lambda (tool) (install-file - (string-append "src/github.com/mongodb/mongo-tools/bin/" tool) + (string-append "src/github.com/mongodb/mongo-tools/bin/" + tool) (string-append (assoc-ref outputs "out") "/bin"))) - all-tools))))))) + all-tools) + #t)))))) (native-inputs `(("go-github.com-howeyc-gopass" ,go-github.com-howeyc-gopass) ("go-github.com-jessevdk-go-flags" ,go-github.com-jessevdk-go-flags) diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index 2158da6a81..4c4a3b849f 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -76,6 +76,7 @@ (method url-fetch) (uri (string-append "mirror://gnu/parted/parted-" version ".tar.xz")) + (patches (search-patches "parted-glibc-compat.patch")) (sha256 (base32 "1r3qpg3bhz37mgvp9chsaa3k0csby3vayfvz8ggsqz194af5i2w5")))) diff --git a/gnu/packages/docbook.scm b/gnu/packages/docbook.scm index 1c00e56d6d..1e5379b020 100644 --- a/gnu/packages/docbook.scm +++ b/gnu/packages/docbook.scm @@ -138,11 +138,15 @@ by no means limited to these applications.) This package provides XML DTDs.") (method url-fetch) (uri (string-append "mirror://sourceforge/docbook/docbook-xsl/" version "/docbook-xsl-" version ".tar.bz2")) - ;; Note: If removing all patches, the XZ dependency is no longer needed. (patches (search-patches "docbook-xsl-nonrecursive-string-subst.patch")) (sha256 (base32 - "0s59lihif2fr7rznckxr2kfyrvkirv76r1zvidp9b5mj28p4apvj")))) + "0s59lihif2fr7rznckxr2kfyrvkirv76r1zvidp9b5mj28p4apvj")) + (modules '((guix build utils))) + (snippet + '(begin + (for-each delete-file (find-files "." "\\.jar$")) + #t)))) (build-system trivial-build-system) (arguments `(#:builder (let ((name-version (string-append ,name "-" ,version))) @@ -168,7 +172,7 @@ by no means limited to these applications.) This package provides XML DTDs.") #t)) #:modules ((guix build utils)))) (native-inputs `(("bzip2" ,bzip2) - ("xz" ,xz) + ("xz" ,xz) ;needed for repacked tarballs ("tar" ,tar))) (home-page "http://docbook.org") (synopsis "DocBook XSL style sheets for document authoring") diff --git a/gnu/packages/documentation.scm b/gnu/packages/documentation.scm index f533535f03..9425df707c 100644 --- a/gnu/packages/documentation.scm +++ b/gnu/packages/documentation.scm @@ -139,23 +139,10 @@ markup) can be customized and extended by the user.") ("libxml2" ,libxml2) ; provides xmllint for the tests ("python" ,python-2))) ; for creating the documentation (inputs - `(("bash" ,bash-minimal) - ,@(if (string-prefix? "armhf-" (%current-system)) - `(("gcc-ice-patch" ,@(search-patches "doxygen-gcc-ice.patch"))) - '()))) + `(("bash" ,bash-minimal))) (arguments `(#:test-target "tests" #:phases (modify-phases %standard-phases - ;; Work around an ICE that shows up on native compiles for - ;; armhf-linux. - ,@(if (string-prefix? "armhf-" (%current-system)) - `((add-after 'unpack 'apply-gcc-patch - (lambda* (#:key inputs #:allow-other-keys) - (let ((patch (assoc-ref inputs "gcc-ice-patch"))) - (invoke "patch" "-p1" "--force" - "--input" patch))))) - '()) - (add-before 'configure 'patch-sh (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/portable.cpp" diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 4e096ea8c5..fc036c07ba 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -1616,15 +1616,16 @@ filters, new key bindings and faces. It can be enabled by (package (name "emacs-pdf-tools") (version "0.80") + (home-page "https://github.com/politza/pdf-tools") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/politza/pdf-tools/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "06imydn3a92vr57azpn1zhqc14kxyyslmyi9ldsyphan9b724gb6")))) + "1i4647vax5na73basc5dz4lh9kprir00fh8ps4i0l1y3ippnjs2s")) + (patches (search-patches "emacs-pdf-tools-poppler.patch")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are no tests @@ -1649,6 +1650,8 @@ filters, new key bindings and faces. It can be enabled by (lambda _ (chdir "../lisp") #t)) (add-after 'enter-lisp-dir 'emacs-patch-variables (lambda* (#:key outputs #:allow-other-keys) + (for-each make-file-writable (find-files ".")) + ;; Set path to epdfinfo program. (emacs-substitute-variables "pdf-info.el" ("pdf-info-epdfinfo-program" @@ -1682,7 +1685,6 @@ filters, new key bindings and faces. It can be enabled by files. The key difference is that pages are not pre-rendered by e.g. ghostscript and stored in the file-system, but rather created on-demand and stored in memory.") - (home-page "https://github.com/politza/pdf-tools") (license license:gpl3+))) (define-public emacs-dash diff --git a/gnu/packages/file.scm b/gnu/packages/file.scm index 0473c519d5..78f0360c2e 100644 --- a/gnu/packages/file.scm +++ b/gnu/packages/file.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -28,14 +29,14 @@ (define-public file (package (name "file") - (version "5.32") + (version "5.33") (source (origin (method url-fetch) (uri (string-append "ftp://ftp.astron.com/pub/file/file-" version ".tar.gz")) (sha256 (base32 - "0l1bfa0icng9vdwya00ff48fhvjazi5610ylbhl35qi13d6xqfc6")))) + "1iipnwjkag7q04zjkaqic41r9nlw0ml6mhqian6qkkbisb1whlhw")))) (build-system gnu-build-system) ;; When cross-compiling, this package depends upon a native install of diff --git a/gnu/packages/flex.scm b/gnu/packages/flex.scm index 29c5c92766..e08b0c13db 100644 --- a/gnu/packages/flex.scm +++ b/gnu/packages/flex.scm @@ -45,22 +45,10 @@ (build-system gnu-build-system) (inputs (let ((bison-for-tests - ;; Work around an incompatibility with Bison 3.0: - ;; <http://lists.gnu.org/archive/html/bug-bison/2013-09/msg00014.html>. (package (inherit bison) - (version "2.7.1") - (source (origin - (method url-fetch) - (uri (string-append - "mirror://gnu/bison/" - "bison-" version ".tar.xz")) - (sha256 - (base32 - "1yx7isx67sdmyijvihgyra1f59fwdz7sqriginvavfj5yb5ss2dl")))) - - ;; Unlike Bison 3.0, this version did not need Flex for its - ;; tests, so it allows us to break the cycle. + ;; Disable tests, since they require flex. + (arguments '(#:tests? #f)) (inputs (alist-delete "flex" (package-inputs bison)))))) `(("bison" ,bison-for-tests) ("indent" ,indent)))) diff --git a/gnu/packages/fltk.scm b/gnu/packages/fltk.scm index a3c088c2e8..972506c8c5 100644 --- a/gnu/packages/fltk.scm +++ b/gnu/packages/fltk.scm @@ -115,6 +115,12 @@ UI builder called FLUID that can be used to create applications in minutes.") #:configure-flags '("--enable-gl") #:phases (modify-phases %standard-phases + (add-before 'configure 'setup-waf + (lambda* (#:key inputs #:allow-other-keys) + (let ((waf (assoc-ref inputs "waf"))) + (delete-file "waf") + (copy-file (string-append waf "/bin/waf") "waf")) + #t)) (add-before 'configure 'set-ldflags (lambda* (#:key outputs #:allow-other-keys) (setenv "LDFLAGS" @@ -123,7 +129,8 @@ UI builder called FLUID that can be used to create applications in minutes.") #t))))) (inputs `(("libjpeg" ,libjpeg) - ("glu" ,glu))) + ("glu" ,glu) + ("waf" ,python-waf))) ;; ntk.pc lists "x11" and "xft" in Requires.private, and "cairo" in ;; Requires. (propagated-inputs diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm index 09ba9b7e4a..2ff42945d7 100644 --- a/gnu/packages/fontutils.scm +++ b/gnu/packages/fontutils.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2017 Leo Famulari <leo@famulari.name> ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. @@ -55,15 +56,18 @@ (define-public freetype (package (name "freetype") - (version "2.9") + (version "2.9.1") (source (origin (method url-fetch) (uri (string-append "mirror://savannah/freetype/freetype-" version ".tar.bz2")) (sha256 (base32 - "12jcdz1in20yaa55izxalg3hm1pf7nydfrzps5bzb4zgihybmzz6")) - (patches (search-patches "freetype-CVE-2018-6942.patch")))) + "0kg8w6qyiizlyzh4a8lpzslipcbv96hcg3rqqpnxba8ffbm8g3fv")))) (build-system gnu-build-system) + (arguments + ;; The use of "freetype-config" is deprecated, but other packages still + ;; depend on it. + `(#:configure-flags (list "--enable-freetype-config"))) (native-inputs `(("pkg-config" ,pkg-config))) (propagated-inputs @@ -286,14 +290,14 @@ fonts to/from the WOFF2 format.") (define-public fontconfig (package (name "fontconfig") - (version "2.13.0") + (version "2.13.1") (source (origin (method url-fetch) (uri (string-append "https://www.freedesktop.org/software/fontconfig/release/fontconfig-" version ".tar.bz2")) (sha256 (base32 - "1fgf28zgsqh7x6dw30n6zi9z679gx6dyfyahp55z7dsm454yipci")))) + "0hb700a68kk0ip51wdlnjjc682kvlrmb6q920mzajykdk0mdsmgn")))) (build-system gnu-build-system) ;; In Requires or Requires.private of fontconfig.pc. (propagated-inputs `(("expat" ,expat) @@ -428,7 +432,7 @@ applications should be.") (define-public graphite2 (package (name "graphite2") - (version "1.3.11") + (version "1.3.12") (source (origin (method url-fetch) @@ -436,7 +440,7 @@ applications should be.") "download/" version "/" name "-" version ".tgz")) (sha256 (base32 - "0z5dcgh8r3678awq6fb8igik7xmar5m6z9xxwpkkhradhk8jxfds")))) + "1l1940d8fz67jm6a0x8cjb5p2dv48cvz3wcskwa83hamd70k15fd")))) (build-system cmake-build-system) (native-inputs `(("python" ,python-2) ; because of "import imap" in tests @@ -586,7 +590,10 @@ definitions.") ("libxml2" ,libxml2) ("pango" ,pango) ("potrace" ,potrace) - ("python" ,python-wrapper) + ;; FIXME: We use Python 2 here because there is a bug in Python + ;; 3.7 that is triggered when Py_Main is called after Py_Init, as + ;; is done by fontforge. This will be fixed in Python 3.7.1. + ("python" ,python-2) ("zlib" ,zlib))) (arguments '(#:phases diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 5cc2699ad8..8853ce1ceb 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -148,14 +148,14 @@ freedesktop.org project.") (define-public libinput (package (name "libinput") - (version "1.11.3") + (version "1.12.1") (source (origin (method url-fetch) (uri (string-append "https://freedesktop.org/software/libinput/" name "-" version ".tar.xz")) (sha256 (base32 - "01nb1shnl871d939wgfd7nc9svclcnfjfhlq64b4yns2dvcr24gk")))) + "14l6bvgq76ls63qc9c448r435q9xiig0rv8ilx6rnjvlgg64h32p")))) (build-system meson-build-system) (arguments `(#:configure-flags '("-Ddocumentation=false"))) @@ -437,14 +437,14 @@ Python.") (define-public wayland (package (name "wayland") - (version "1.15.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (string-append "https://wayland.freedesktop.org/releases/" name "-" version ".tar.xz")) (sha256 (base32 - "1c5fnys8hi71cnzjv5k7j0r8gx80p0yyqlrpmn06mmarhnxvwgzb")))) + "1xajhxad43izq9f7sbww1hlg42nayijy8xnp21kgpk09c6sw4wjf")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f)) diff --git a/gnu/packages/fribidi.scm b/gnu/packages/fribidi.scm index 0368779240..dfd2a77c20 100644 --- a/gnu/packages/fribidi.scm +++ b/gnu/packages/fribidi.scm @@ -27,7 +27,7 @@ (define-public fribidi (package (name "fribidi") - (version "1.0.2") + (version "1.0.5") (source (origin (method url-fetch) @@ -36,11 +36,8 @@ "/download/v" version "/fribidi-" version ".tar.bz2")) (sha256 - (base32 "0aw3i1g96axbr96flw4543dvhb8zlgb0w8314ks6cq2g1i9invdx")))) + (base32 "1kp4b1hpx2ky20ixgy2xhj5iygfl7ps5k9kglh1z5i7mhykg4r3a")))) (build-system gnu-build-system) - (arguments - `(#:configure-flags - (list "--disable-docs"))) ; TODO: enable; requires c2man (synopsis "Implementation of the Unicode bidirectional algorithm") (description "GNU FriBidi is an implementation of the Unicode Bidirectional diff --git a/gnu/packages/gcal.scm b/gnu/packages/gcal.scm index 425fa1f9a8..32d3849faa 100644 --- a/gnu/packages/gcal.scm +++ b/gnu/packages/gcal.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2013, 2018 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -32,7 +32,23 @@ version ".tar.xz")) (sha256 (base32 - "1av11zkfirbixn05hyq4xvilin0ncddfjqzc4zd9pviyp506rdci")))) + "1av11zkfirbixn05hyq4xvilin0ncddfjqzc4zd9pviyp506rdci")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Adjust the bundled gnulib to work with glibc 2.28. See e.g. + ;; "m4-gnulib-libio.patch". This is a phase rather than patch + ;; or snippet to work around <https://bugs.gnu.org/32347>. + (substitute* (find-files "lib" "\\.c$") + (("#if defined _IO_ftrylockfile") + "#if defined _IO_EOF_SEEN")) + (substitute* "lib/stdio-impl.h" + (("^/\\* BSD stdio derived implementations") + (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n" + "# define _IO_IN_BACKUP 0x100\n" + "#endif\n\n" + "/* BSD stdio derived implementations"))) + #t)))) (build-system gnu-build-system) (home-page "https://www.gnu.org/software/gcal/") (synopsis "Calculating and printing a wide variety of calendars") diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index 0dd5d64464..8207104174 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -398,6 +398,7 @@ Go. It also includes runtime support libraries for these languages.") (base32 "14l06m7nvcvb0igkbip58x59w3nq6315k6jcz3wr9ch1rn9d44bc")) (patches (search-patches "gcc-4.9-libsanitizer-fix.patch" + "gcc-4.9-libsanitizer-ustat.patch" "gcc-arm-bug-71399.patch" "gcc-asan-missing-include.patch" "gcc-libvtv-runpath.patch" @@ -432,6 +433,7 @@ Go. It also includes runtime support libraries for these languages.") (base32 "11zd1hgzkli3b2v70qsm2hyqppngd4616qc96lmm9zl2kl9yl32k")) (patches (search-patches "gcc-arm-bug-71399.patch" + "gcc-libsanitizer-ustat.patch" "gcc-strmov-store-file-names.patch" "gcc-5.0-libvtv-runpath.patch" "gcc-5-source-date-epoch-1.patch" @@ -452,7 +454,8 @@ Go. It also includes runtime support libraries for these languages.") "$OBJDUMP_FOR_TARGET -T")) #t)))) (inputs - `(("isl" ,isl) + `(;; GCC5 needs <isl/band.h> which is removed in later versions. + ("isl" ,isl-0.18) ,@(package-inputs gcc-4.7))))) (define-public gcc-6 @@ -467,6 +470,7 @@ Go. It also includes runtime support libraries for these languages.") (base32 "1m0lr7938lw5d773dkvwld90hjlcq2282517d1gwvrfzmwgg42w5")) (patches (search-patches "gcc-libsanitizer-fix.patch" + "gcc-libsanitizer-ustat.patch" "gcc-strmov-store-file-names.patch" "gcc-6-source-date-epoch-1.patch" "gcc-6-source-date-epoch-2.patch" @@ -511,6 +515,7 @@ Go. It also includes runtime support libraries for these languages.") (base32 "0p71bij6bfhzyrs8676a8jmpjsfz392s2rg862sdnsk30jpacb43")) (patches (search-patches "gcc-strmov-store-file-names.patch" + "gcc-libsanitizer-ustat.patch" "gcc-5.0-libvtv-runpath.patch")))) (description "GCC is the GNU Compiler Collection. It provides compiler front-ends @@ -854,7 +859,7 @@ as the 'native-search-paths' field." (define-public isl (package (name "isl") - (version "0.18") + (version "0.19") (source (origin (method url-fetch) (uri (list (string-append @@ -865,7 +870,7 @@ as the 'native-search-paths' field." name "-" version ".tar.gz"))) (sha256 (base32 - "06ybml6llhi4i56q90jnimbcgk1lpcdwhy9nxdxra2hxz3bhz2vb")))) + "1n4yz9rj24mv226hqbpw210ifvqkn8dgvpnkzf0s0lkq9zrjd5ym")))) (build-system gnu-build-system) (inputs `(("gmp" ,gmp))) (home-page "http://isl.gforge.inria.fr/") @@ -883,6 +888,20 @@ reduction, transitive closures on maps (which may encode infinite graphs), dependence analysis and bounds on piecewise step-polynomials.") (license lgpl2.1+))) +(define-public isl-0.18 + (package + (inherit isl) + (version "0.18") + (source (origin + (method url-fetch) + (uri (list (string-append "http://isl.gforge.inria.fr/isl-" + version ".tar.bz2") + (string-append %gcc-infrastructure + "isl-" version ".tar.gz"))) + (sha256 + (base32 + "06ybml6llhi4i56q90jnimbcgk1lpcdwhy9nxdxra2hxz3bhz2vb")))))) + (define-public isl-0.11 (package (inherit isl) diff --git a/gnu/packages/gd.scm b/gnu/packages/gd.scm index 327a1f1545..a53a4f2c2f 100644 --- a/gnu/packages/gd.scm +++ b/gnu/packages/gd.scm @@ -39,7 +39,6 @@ (define-public gd (package (name "gd") - (replacement gd/fixed) ;; Note: With libgd.org now pointing to github.com, genuine old ;; tarballs are no longer available. Notably, versions 2.0.x are ;; missing. @@ -52,7 +51,10 @@ (sha256 (base32 "0lfy5f241sbv8s3splm2zqiaxv7lxrcshh875xryryk7yk5jqc4c")) - (patches (search-patches "gd-fix-tests-on-i686.patch" + + (patches (search-patches "gd-CVE-2018-5711.patch" + "gd-CVE-2018-1000222.patch" + "gd-fix-tests-on-i686.patch" "gd-freetype-test-failure.patch")))) (build-system gnu-build-system) (arguments @@ -92,16 +94,6 @@ most common applications of GD involve website development.") "See COPYING file in the distribution.")) (properties '((cpe-name . "libgd"))))) -(define-public gd/fixed - (hidden-package - (package - (inherit gd) - (source (origin - (inherit (package-source gd)) - (patches (append (origin-patches (package-source gd)) - (search-patches "gd-CVE-2018-5711.patch" - "gd-CVE-2018-1000222.patch")))))))) - (define-public perl-gd (package (name "perl-gd") @@ -150,7 +142,7 @@ you can create PNG images on the fly or modify existing files.") '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-env - (lambda _ (setenv "PERL_USE_UNSAFE_INC" "1")))))) + (lambda _ (setenv "PERL_USE_UNSAFE_INC" "1") #t))))) (native-inputs `(("perl-module-build" ,perl-module-build))) (propagated-inputs diff --git a/gnu/packages/ghostscript.scm b/gnu/packages/ghostscript.scm index 518e18397b..b46451d94e 100644 --- a/gnu/packages/ghostscript.scm +++ b/gnu/packages/ghostscript.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2013, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com> -;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017 Leo Famulari <leo@famulari.name> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> @@ -55,7 +55,7 @@ (sha256 (base32 "083xisy6z01zhm7p7rgk4bx9d6zlr8l20qkfv1g29ylnhgwzvij8")))) (build-system gnu-build-system) - (inputs `(("libjpeg-8" ,libjpeg-8) + (inputs `(("libjpeg" ,libjpeg) ("libtiff" ,libtiff) ("zlib" ,zlib))) (synopsis "Little CMS, a small-footprint colour management engine") @@ -135,8 +135,7 @@ printing, and psresize, for adjusting page sizes.") (define-public ghostscript (package (name "ghostscript") - (replacement ghostscript/fixed) - (version "9.23") + (version "9.24") (source (origin (method url-fetch) @@ -146,8 +145,9 @@ printing, and psresize, for adjusting page sizes.") "/ghostscript-" version ".tar.xz")) (sha256 (base32 - "1ng8d9fm5lza7k1f7ybc791275c07z5hcmpkrl2i226nshkxrkhz")) - (patches (search-patches "ghostscript-runpath.patch" + "1mk922rnml93w2g42yxiyn8xqanc50cm65irrgh0b6lp4kgifjfl")) + (patches (search-patches "ghostscript-CVE-2018-16509.patch" + "ghostscript-bug-699708.patch" "ghostscript-no-header-creationdate.patch" "ghostscript-no-header-id.patch" "ghostscript-no-header-uuid.patch")) @@ -166,7 +166,9 @@ printing, and psresize, for adjusting page sizes.") (arguments `(#:disallowed-references ("doc") #:configure-flags - (list "--with-system-libtiff" + (list (string-append "LDFLAGS=-Wl,-rpath=" + (assoc-ref %outputs "out") "/lib") + "--with-system-libtiff" "LIBS=-lz" (string-append "ZLIBDIR=" (assoc-ref %build-inputs "zlib") "/include") @@ -184,6 +186,12 @@ printing, and psresize, for adjusting page sizes.") '())) #:phases (modify-phases %standard-phases + (add-before 'configure 'create-output-directory + (lambda* (#:key outputs #:allow-other-keys) + ;; The configure script refuses to function if the directory + ;; specified as -rpath does not already exist. + (mkdir-p (string-append (assoc-ref outputs "out") "/lib")) + #t)) (add-after 'configure 'remove-doc-reference (lambda _ ;; Don't retain a reference to the 'doc' output in 'gs'. @@ -254,44 +262,6 @@ output file formats and printers.") (home-page "https://www.ghostscript.com/") (license license:agpl3+))) -(define-public ghostscript/fixed - (hidden-package - (package - (inherit ghostscript) - (version "9.24") - (source - (origin - (inherit (package-source ghostscript)) - (uri (string-append "https://github.com/ArtifexSoftware/" - "ghostpdl-downloads/releases/download/gs" - (string-delete #\. version) - "/ghostscript-" version ".tar.xz")) - (sha256 - (base32 - "1mk922rnml93w2g42yxiyn8xqanc50cm65irrgh0b6lp4kgifjfl")) - (patches (search-patches "ghostscript-CVE-2018-16509.patch" - "ghostscript-bug-699708.patch" - "ghostscript-no-header-creationdate.patch" - "ghostscript-no-header-id.patch" - "ghostscript-no-header-uuid.patch")))) - (arguments - (substitute-keyword-arguments (package-arguments ghostscript) - ((#:configure-flags flags) - ;; Notice that we removed the 'ghostscript-runpath' patch above. - ;; The reason is that it conflicts with an upstream change that - ;; takes LDFLAGS into account. - `(cons (string-append "LDFLAGS=-Wl,-rpath=" - (assoc-ref %outputs "out") "/lib") - ,flags)) - ((#:phases phases) - `(modify-phases ,phases - (add-before 'configure 'create-output-directory - (lambda* (#:key outputs #:allow-other-keys) - ;; Unfortunately the configure script refuses to function if - ;; the directory specified as -rpath does not already exist. - (mkdir-p (string-append (assoc-ref outputs "out") "/lib")) - #t))))))))) - (define-public ghostscript/x (package/inherit ghostscript (name (string-append (package-name ghostscript) "-with-x")) diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm index 11c89b3d88..851a31447b 100644 --- a/gnu/packages/gl.scm +++ b/gnu/packages/gl.scm @@ -224,7 +224,7 @@ also known as DXTn or DXTC) for Mesa.") (define-public mesa (package (name "mesa") - (version "18.1.5") + (version "18.1.8") (source (origin (method url-fetch) @@ -236,7 +236,7 @@ also known as DXTn or DXTC) for Mesa.") version "/mesa-" version ".tar.xz"))) (sha256 (base32 - "1sldv7l3g6jfx0yn16kvxlik1qiy037lypdqpvsqc0v6lvqydnv9")) + "06y28hpynb8w1qagznr85ml48hf8264w4ji6cmvm2fy7x5zyc6xx")) (patches (search-patches "mesa-skip-disk-cache-test.patch")))) (build-system gnu-build-system) @@ -252,7 +252,7 @@ also known as DXTn or DXTC) for Mesa.") ("xorgproto" ,xorgproto))) (inputs `(("expat" ,expat) - ("libelf" ,libelf) ;required for r600 when using llvm + ("libelf" ,elfutils) ;required for r600 when using llvm ("libva" ,(force libva-without-mesa)) ("libxml2" ,libxml2) ;; TODO: Add 'libxml2-python' for OpenGL ES 1.1 and 2.0 support diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index 703cd3f74e..491f688c8e 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -80,7 +80,7 @@ (define dbus (package (name "dbus") - (version "1.12.6") + (version "1.12.10") (source (origin (method url-fetch) (uri (string-append @@ -88,7 +88,7 @@ version ".tar.gz")) (sha256 (base32 - "05picaq8j60wlwyi84qvw5liw3nd0cws9va3krnc3pms0wm906v2")) + "1xywijmgfad4m3cxp0b4l6kvypwc53ckmhwwzbrc6n32jwj3ssab")) (patches (search-patches "dbus-helper-search-path.patch")))) (build-system gnu-build-system) (arguments @@ -150,7 +150,7 @@ shared NFS home directories.") (define glib (package (name "glib") - (version "2.56.0") + (version "2.56.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" @@ -158,7 +158,7 @@ shared NFS home directories.") name "-" version ".tar.xz")) (sha256 (base32 - "1iqgi90fmpl3l23jm2iv44qp7hqsxvnv7978s18933bvx4bnxvzc")) + "12d738n1wpvrn39zvy9xazg5h6vzyiwsw8z1qibcj09mh4bbsjnn")) (patches (search-patches "glib-tests-timer.patch")))) (build-system gnu-build-system) (outputs '("out" ; everything @@ -303,14 +303,14 @@ dynamic loading, and an object system.") (define gobject-introspection (package (name "gobject-introspection") - (version "1.56.0") + (version "1.56.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" "gobject-introspection/" (version-major+minor version) "/gobject-introspection-" version ".tar.xz")) (sha256 - (base32 "1y50pbn5qqbcv2h9rkz96wvv5jls2gma9bkqjq6wapmaszx5jw0d")) + (base32 "0jx2kryjd7l0vl5gb3qp1qjfy3cjiizvcd1snsm7pzwrzz67aa2v")) (modules '((guix build utils))) (snippet '(begin @@ -598,7 +598,7 @@ useful for C++.") (define-public python-pygobject (package (name "python-pygobject") - (version "3.28.2") + (version "3.28.3") (source (origin (method url-fetch) @@ -607,7 +607,7 @@ useful for C++.") "/pygobject-" version ".tar.xz")) (sha256 (base32 - "1jpjws4v17wv99lbhks0g0152w0f70mnwpdn8ibzzfgw2kykli5c")))) + "1c6h3brzlyvzbpdsammnd957azmp6cbzqrd65r400vnh2l8f5lrx")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 06ec28b342..e94779c482 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -124,6 +124,7 @@ #:use-module (gnu packages ssh) #:use-module (gnu packages xml) #:use-module (gnu packages gl) + #:use-module (gnu packages graphviz) #:use-module (gnu packages compression) #:use-module (gnu packages spice) #:use-module (gnu packages tex) @@ -942,14 +943,14 @@ guidelines.") (define-public shared-mime-info (package (name "shared-mime-info") - (version "1.8") + (version "1.9") (source (origin (method url-fetch) (uri (string-append "https://freedesktop.org/~hadess/" "shared-mime-info-" version ".tar.xz")) (sha256 (base32 - "1sc96lv9dp1lkvs8dh3ngm3hbjb274d363dl9avhb61il3qmxx9a")))) + "10ywzhzg8v1xmb9sz5xbqaci90id38knswigynyl33i29vn360aw")))) (build-system gnu-build-system) (arguments ;; The build system appears not to be parallel-safe. @@ -1180,7 +1181,7 @@ XML/CSS rendering engine.") (define-public libgsf (package (name "libgsf") - (version "1.14.43") + (version "1.14.44") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -1188,7 +1189,7 @@ XML/CSS rendering engine.") name "-" version ".tar.xz")) (sha256 (base32 - "05pf3h0dha3s20ddsrljbx7m94qyiqs5igwxx1ql0vlsdlylx50j")))) + "1ppzfk3zmmgrg9jh8vc4dacddbfngjslq2wpj94pcr3i0c8dxgk8")))) (build-system gnu-build-system) (native-inputs `(("intltool" ,intltool) @@ -2038,7 +2039,7 @@ passwords in the GNOME keyring.") (define-public vala (package (name "vala") - (version "0.36.3") + (version "0.40.9") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -2046,7 +2047,7 @@ passwords in the GNOME keyring.") name "-" version ".tar.xz")) (sha256 (base32 - "0706izk9prxqclm7gv4f63diwnlc1llvfl5sc9ghqbgn076lx2mc")))) + "0yvaijkpahzz26sa37cyzbj75a9vbcbgvxbqzzb7hbcvfy009zy7")))) (build-system gnu-build-system) (arguments '(#:phases @@ -2054,20 +2055,25 @@ passwords in the GNOME keyring.") (add-before 'check 'pre-check (lambda _ (setenv "CC" "gcc") + (substitute* "valadoc/tests/testrunner.sh" + (("export PKG_CONFIG_PATH=" m) + (string-append m "$PKG_CONFIG_PATH:"))) ;; For missing '/etc/machine-id'. (setenv "DBUS_FATAL_WARNINGS" "0") - #t))) - ;; Build the Vala API generator - #:configure-flags '("--enable-vapigen"))) + #t))))) (native-inputs `(("pkg-config" ,pkg-config) ("flex" ,flex) ("bison" ,bison) ("xsltproc" ,libxslt) + ("grep" ,grep) + ("sed" ,sed) ("dbus" ,dbus) ; for dbus tests ("gobject-introspection" ,gobject-introspection))) ; for gir tests + (inputs + `(("graphviz" ,graphviz))) (propagated-inputs - `(("glib" ,glib))) ; required by libvala-0.26.pc + `(("glib" ,glib))) ; required by libvala-0.40.pc (home-page "https://live.gnome.org/Vala/") (synopsis "Compiler for the GObject type system") (description @@ -5860,7 +5866,7 @@ is complete it provides a graphical representation of each selected folder.") (define-public gnome-backgrounds (package (name "gnome-backgrounds") - (version "3.26.2") + (version "3.28.0") (source (origin (method url-fetch) @@ -5869,8 +5875,8 @@ is complete it provides a graphical representation of each selected folder.") name "-" version ".tar.xz")) (sha256 (base32 - "0kzrh5h0cfby3rhsy31d1w1c0rr3wcc845kv6zibqw1x8v9si2rs")))) - (build-system glib-or-gtk-build-system) + "1qgim0yhzjgcq172y4vp5hqz4rh1ak38a7pgi6s7dq0wklyrcnxj")))) + (build-system meson-build-system) (native-inputs `(("intltool" ,intltool))) (home-page "https://git.gnome.org/browse/gnome-backgrounds") diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 46ca812a13..53fdc8200c 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -75,7 +75,7 @@ (define-public libgpg-error (package (name "libgpg-error") - (version "1.28") + (version "1.32") (source (origin (method url-fetch) @@ -83,8 +83,7 @@ version ".tar.bz2")) (sha256 (base32 - "0jfsfnh9bxlxiwxws60yah4ybjw2hshmvqp31pri4m4h8ivrbnry")) - (patches (search-patches "libgpg-error-aarch64-logging-fix.patch")))) + "1jj08ns4sh1hmafqp1giskvdicdz18la516va26jycy27kkwaif3")))) (build-system gnu-build-system) (home-page "https://gnupg.org") (synopsis "Library of error values for GnuPG components") @@ -97,32 +96,19 @@ Daemon and possibly more in the future.") (properties '((ftp-server . "ftp.gnupg.org") (ftp-directory . "/gcrypt/libgpg-error"))))) -;; Some packages (e.g. GPGME) require a newer libgpg-error to deal with -;; error codes from recent GnuPG. Remove this in the next rebuild cycle. -(define-public libgpg-error-1.31 - (package - (inherit libgpg-error) - (version "1.31") - (source (origin - (method url-fetch) - (uri (string-append "mirror://gnupg/libgpg-error/libgpg-error-" - version ".tar.bz2")) - (sha256 - (base32 - "1vx4nw6rxh2biy3h8n96fyr86q29h8gjl6837437i51jr4isil20")))))) - (define-public libgcrypt (package - (replacement libgcrypt/fixed) (name "libgcrypt") - (version "1.8.2") + (version "1.8.3") (source (origin (method url-fetch) (uri (string-append "mirror://gnupg/libgcrypt/libgcrypt-" version ".tar.bz2")) (sha256 (base32 - "01sca9m8hm6b5v8hmqsfdjhyz013869p1f0fxw9ln52qfnp4q1n8")))) + "0z5gs1khzyknyfjr19k8gk4q148s6q987ya85cpn0iv70fz91v36")) + (patches + (search-patches "libgcrypt-make-yat2m-reproducible.patch")))) (build-system gnu-build-system) (propagated-inputs `(("libgpg-error-host" ,libgpg-error))) @@ -148,19 +134,6 @@ generation.") (properties '((ftp-server . "ftp.gnupg.org") (ftp-directory . "/gcrypt/libgcrypt"))))) -(define libgcrypt/fixed - (package - (inherit libgcrypt) - (name "libgcrypt") - (version "1.8.3") - (source (origin - (method url-fetch) - (uri (string-append "mirror://gnupg/libgcrypt/libgcrypt-" - version ".tar.bz2")) - (sha256 - (base32 - "0z5gs1khzyknyfjr19k8gk4q148s6q987ya85cpn0iv70fz91v36")))))) - (define-public libassuan (package (name "libassuan") @@ -409,7 +382,7 @@ libskba (working with X.509 certificates and CMS data).") `(("gnupg" ,gnupg))) (propagated-inputs ;; Needs to be propagated because gpgme.h includes gpg-error.h. - `(("libgpg-error" ,libgpg-error-1.31))) + `(("libgpg-error" ,libgpg-error))) (inputs `(("libassuan" ,libassuan))) (home-page "https://www.gnupg.org/related_software/gpgme/") diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index e1abe8c2cd..d6b1f4c2d6 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -39,6 +39,7 @@ #:use-module (gnu packages audio) #:use-module (gnu packages autotools) #:use-module (gnu packages base) + #:use-module (gnu packages check) #:use-module (gnu packages databases) #:use-module (gnu packages glib) #:use-module (gnu packages gtk) @@ -417,7 +418,12 @@ in the Mozilla clients.") (setenv "DOMSUF" "(none)") (setenv "USE_IP" "TRUE") (setenv "IP_ADDRESS" "127.0.0.1") - (invoke "./nss/tests/all.sh"))) + + ;; The "PayPalEE.cert" certificate expires every six months, + ;; leading to test failures: + ;; <https://bugzilla.mozilla.org/show_bug.cgi?id=609734>. To + ;; work around that, set the time to roughly the release date. + (invoke "faketime" "2018-09-01" "./nss/tests/all.sh"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -453,7 +459,8 @@ in the Mozilla clients.") `(("sqlite" ,sqlite) ("zlib" ,zlib))) (propagated-inputs `(("nspr" ,nspr))) ; required by nss.pc. - (native-inputs `(("perl" ,perl))) + (native-inputs `(("perl" ,perl) + ("libfaketime" ,libfaketime))) ;for tests ;; The NSS test suite takes around 48 hours on Loongson 3A (MIPS) when ;; another build is happening concurrently on the same machine. diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 38df23a6c1..60890bf724 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -280,6 +280,15 @@ in the style of communicating sequential processes (@dfn{CSP}).") (string-append "\"-Wl,-rpath=" gcclib "\", \"-lgcc_s\", "))) + ;; XXX Commit 65fa2b615b72c1fa61a7 in the Go repo. We do this + ;; without a patch because ((guix packages) patch-and-repack) + ;; resets file mtimes, and parts of Go's test suite rely on + ;; those timestamps. + ;; <https://github.com/golang/go/issues/26369> + (substitute* "cmd/internal/objfile/elf.go" + (("PT_LOAD") + "PT_LOAD && p.Flags&elf.PF_X != 0")) + ;; Disable failing tests: these tests attempt to access ;; commands or network resources which are neither available ;; nor necessary for the build to succeed. diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index 435c3e5b3a..f43a0fc2f5 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -102,7 +102,7 @@ arrays of data.") (define-public gstreamer (package (name "gstreamer") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) @@ -111,7 +111,7 @@ arrays of data.") version ".tar.xz")) (sha256 (base32 - "029fi3v0vrravysgfwhfkrb3ndg64sjmigbb0iwr7wpkk5r15mjb")))) + "0mh4755an4gk0z3ygqhjpdjk0r2cwswbpwfgl0x6qmnln4757bhk")))) (build-system gnu-build-system) (outputs '("out" "doc")) (arguments @@ -150,7 +150,7 @@ This package provides the core library and elements.") (define-public gst-plugins-base (package (name "gst-plugins-base") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) @@ -158,7 +158,7 @@ This package provides the core library and elements.") name "-" version ".tar.xz")) (sha256 (base32 - "0z0wy0p0nxxqhsis3n517d6ykldm02g7rca9fhq9kxb9m05yidx4")))) + "0lkr1fm3bz21nqq9vi5v74mlxw6dd6i7piw00fhc5zz0dg1ikczh")))) (build-system gnu-build-system) (outputs '("out" "doc")) (propagated-inputs @@ -209,7 +209,7 @@ for the GStreamer multimedia library.") (define-public gst-plugins-good (package (name "gst-plugins-good") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) @@ -218,7 +218,7 @@ for the GStreamer multimedia library.") name "-" version ".tar.xz")) (sha256 (base32 - "1bfa4n6xhr4v4wga8pv1y00rm1aka498snw6kgszy2w624l5wmy0")))) + "0pgzgfqbfp8lz2ns68797xfxdr0cr5rpi93wd1h2grhbmzkbq4ji")))) (build-system gnu-build-system) (inputs `(("aalib" ,aalib) @@ -271,14 +271,14 @@ developers consider to have good quality code and correct functionality.") (define-public gst-plugins-bad (package (name "gst-plugins-bad") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) (uri (string-append "https://gstreamer.freedesktop.org/src/" name "/" name "-" version ".tar.xz")) (sha256 (base32 - "1bqy3dn7q4kdkd4lqznyly8fv854d0hhncv88jk6ai4rf3dbgyil")))) + "1mczcna91f3kkk3yv5fkfa8nmqdr9d93aq9z4d8sv18vkiflw8mj")))) (outputs '("out" "doc")) (build-system gnu-build-system) (arguments @@ -346,7 +346,7 @@ par compared to the rest.") (define-public gst-plugins-ugly (package (name "gst-plugins-ugly") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) @@ -354,7 +354,7 @@ par compared to the rest.") name "/" name "-" version ".tar.xz")) (sha256 (base32 - "0s9xrz8knfv06fj1nbv3iq4xj7dj4cnzj3xvgb7zs89rv7crgq2m")))) + "01i31g5rvw36rjlyi9w24n0g1xa6053d14vaiba6vqpas727z123")))) (build-system gnu-build-system) (inputs `(("gst-plugins-base" ,gst-plugins-base) @@ -381,7 +381,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.") (define-public gst-libav (package (name "gst-libav") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) (uri (string-append @@ -389,7 +389,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.") name "-" version ".tar.xz")) (sha256 (base32 - "1pknqpjxq1l3vlprdsmxxwk0lwqa555fqd543k9vphngqlwiqdca")) + "0xxnb80yhfa42x4wx1928zydaal35b2mcj0zdcdsv1apnjdm40wv")) (modules '((guix build utils))) (snippet '(begin @@ -417,7 +417,7 @@ compression formats through the use of the libav library.") (define-public python-gst (package (name "python-gst") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) (uri (string-append @@ -425,7 +425,7 @@ compression formats through the use of the libav library.") "gst-python-" version ".tar.xz")) (sha256 (base32 - "08nb011acyvlz48fqh8c084k0dlssz9b7wha7zzk797inidbwh6w")))) + "01w3mpimbm8drifhrkvpns79h15kd9h9v0dynr7yb12kjrnfghsg")))) (build-system gnu-build-system) (arguments ;; XXX: Factorize python-sitedir with python-build-system. diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 0d62b80833..08f92df96c 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com> ;;; Copyright © 2015 Andy Wingo <wingo@igalia.com> ;;; Copyright © 2015 David Hashe <david.hashe@dhashe.com> -;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> +;;; Coypright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Fabian Harfert <fhmgufs@web.de> ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net> @@ -113,15 +113,16 @@ tools have full access to view and control running applications.") (define-public cairo (package (name "cairo") - (version "1.14.10") + (version "1.14.12") (source (origin (method url-fetch) (uri (string-append "https://cairographics.org/releases/cairo-" version ".tar.xz")) (sha256 (base32 - "02banr0wxckq62nbhc3mqidfdh2q956i2r7w2hd9bjgjb238g1vy")) - (patches (search-patches "cairo-CVE-2016-9082.patch")))) + "05mzyxkvsfc1annjw2dja8vka01ampp9pp93lg09j8hba06g144c")) + (patches (search-patches "cairo-CVE-2016-9082.patch" + "cairo-setjmp-wrapper.patch")))) (build-system gnu-build-system) (propagated-inputs `(("fontconfig" ,fontconfig) @@ -179,7 +180,7 @@ affine transformation (scale, rotation, shear, etc.).") (define-public harfbuzz (package (name "harfbuzz") - (version "1.7.6") + (version "1.8.8") (source (origin (method url-fetch) (uri (string-append "https://www.freedesktop.org/software/" @@ -187,7 +188,7 @@ affine transformation (scale, rotation, shear, etc.).") version ".tar.bz2")) (sha256 (base32 - "16rf7qwgy1gza74v2ws79zdwwb1lpvgz2abwwm8ws9j82cwysyys")))) + "1ag3scnm1fcviqgx2p4858y433mr0ndqw6zccnccrqcr9mpcird8")))) (build-system gnu-build-system) (outputs '("out" "bin")) ; 160K, only hb-view depend on cairo @@ -218,8 +219,7 @@ affine transformation (scale, rotation, shear, etc.).") (define-public pango (package (name "pango") - (version "1.42.0") - (replacement pango-1.42.4) + (version "1.42.4") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/pango/" @@ -227,18 +227,18 @@ affine transformation (scale, rotation, shear, etc.).") name "-" version ".tar.xz")) (sha256 (base32 - "0illn78nfwpa8y5knh9ir74wa1skc2hi8f3ny19zgpyf7n5dh94r")))) + "17bwb7dgbncrfsmchlib03k9n3xaalirb39g3yb43gg8cg6p8aqx")))) (build-system gnu-build-system) (propagated-inputs ;; These are all in Requires or Requires.private of the '.pc' files. `(("cairo" ,cairo) + ("fribidi" ,fribidi) ("fontconfig" ,fontconfig) ("freetype" ,freetype) ("glib" ,glib) ("harfbuzz" ,harfbuzz))) (inputs - `(("fribidi" ,fribidi) - ("zlib" ,zlib) + `(("zlib" ,zlib) ;; Some packages, such as Openbox, expect Pango to be built with the ;; optional libxft support. @@ -255,19 +255,6 @@ used throughout the world.") (license license:lgpl2.0+) (home-page "https://developer.gnome.org/pango/"))) -(define-public pango-1.42.4 - (package - (inherit pango) - (version "1.42.4") - (source (origin - (method url-fetch) - (uri (string-append "mirror://gnome/sources/pango/" - (version-major+minor version) "/" - "pango-" version ".tar.xz")) - (sha256 - (base32 - "17bwb7dgbncrfsmchlib03k9n3xaalirb39g3yb43gg8cg6p8aqx")))))) - (define-public pangox-compat (package (name "pangox-compat") @@ -318,6 +305,7 @@ functions which were removed.") (string-append "-Wl,-rpath=" (assoc-ref outputs "out") "/lib")) #t))) + #:python ,python-2 ;XXX: The bundled waf fails with Python 3.7.0. #:tests? #f)) ; no check target (inputs `(("gtk" ,gtk+-2) @@ -457,7 +445,7 @@ highlighting and other features typical of a source code editor.") (define-public gdk-pixbuf (package (name "gdk-pixbuf") - (version "2.36.12") + (version "2.38.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -465,26 +453,39 @@ highlighting and other features typical of a source code editor.") name "-" version ".tar.xz")) (sha256 (base32 - "0d534ysa6n9prd17wwzisq7mj6qkhwh8wcf8qgin1ar3hbs5ry7z")))) - (build-system gnu-build-system) + "0ixfmnxjylx06mjaw116apymwi1a8rnkmkbbvqaxxg2pfwy9fl6x")))) + (build-system meson-build-system) (arguments - '(#:configure-flags '("--with-x11") + '(#:configure-flags '("-Dinstalled-tests=false") #:phases (modify-phases %standard-phases (add-after 'unpack 'disable-failing-tests (lambda _ - (substitute* "tests/Makefile.in" + (substitute* "tests/meson.build" ;; XXX FIXME: This test fails on armhf machines with: ;; SKIP Not enough memory to load bitmap image ;; ERROR: cve-2015-4491 - too few tests run (expected 4, got 2) - (("cve-2015-4491\\$\\(EXEEXT\\) ") "") + ((".*'cve-2015-4491'.*") "") ;; XXX FIXME: This test fails with: ;; ERROR:pixbuf-jpeg.c:74:test_type9_rotation_exif_tag: ;; assertion failed (error == NULL): Data differ ;; (gdk-pixbuf-error-quark, 0) - (("pixbuf-jpeg\\$\\(EXEEXT\\) ") "")) - #t))))) + ((".*'pixbuf-jpeg'.*") "") + ;; Extend the timeout of the test suite. + ;; TODO: Check upstreaming effort: + ;; https://gitlab.gnome.org/GNOME/gdk-pixbuf/merge_requests/21 + (("300") "1800")) + #t)) + (add-before 'configure 'aid-install-script + (lambda* (#:key outputs #:allow-other-keys) + ;; "build-aux/post-install.sh" invokes `gdk-pixbuf-query-loaders` + ;; for updating loader.cache, but it's not on PATH. Make it use + ;; the one we're installing. XXX: Won't work when cross-compiling. + (substitute* "build-aux/post-install.sh" + (("gdk-pixbuf-query-loaders" match) + (string-append (assoc-ref outputs "out") "/bin/" match))) + #t))))) (propagated-inputs `(;; Required by gdk-pixbuf-2.0.pc ("glib" ,glib) @@ -497,6 +498,7 @@ highlighting and other features typical of a source code editor.") ("libx11" ,libx11))) (native-inputs `(("pkg-config" ,pkg-config) + ("gettext" ,gettext-minimal) ("glib" ,glib "bin") ; glib-mkenums, etc. ("gobject-introspection" ,gobject-introspection))) ; g-ir-compiler, etc. (synopsis "GNOME image loading and manipulation library") @@ -516,7 +518,7 @@ in the GNOME project.") `(("librsvg" ,librsvg) ,@(package-inputs gdk-pixbuf))) (arguments - '(#:configure-flags '("--with-x11") + '(#:configure-flags '("-Dinstalled-tests=false") #:tests? #f ; tested by the gdk-pixbuf package already #:phases (modify-phases %standard-phases @@ -585,7 +587,7 @@ is part of the GNOME accessibility project.") (define-public at-spi2-atk (package (name "at-spi2-atk") - (version "2.26.1") + (version "2.26.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -593,7 +595,7 @@ is part of the GNOME accessibility project.") name "-" version ".tar.xz")) (sha256 (base32 - "0x9vc99ni46fg5dzlx67vbw0zqffr24gz8jvbdxbmzyvc5xw5w5l")))) + "0vkan52ab9vrkknnv8y4f1cspk8x7xd10qx92xk9ys71p851z2b1")))) (build-system gnu-build-system) (arguments '(#:phases @@ -686,7 +688,7 @@ application suites.") (name "gtk+") ;; NOTE: When updating the version of 'gtk+', the hash of 'mate-themes' in ;; mate.scm will also need to be updated. - (version "3.22.30") + (version "3.24.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -694,7 +696,7 @@ application suites.") name "-" version ".tar.xz")) (sha256 (base32 - "0rv5k8fyi2i19k4zncai6vf429s6zy3kncr8vb6f3m034z0sb951")) + "1a1jbsh9fg5ykmwrcl3svy7xfvx0b87d314qsx9n483pj8w93s82")) (patches (search-patches "gtk3-respect-GUIX_GTK3_PATH.patch" "gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch")))) (outputs '("out" "bin" "doc")) @@ -730,9 +732,9 @@ application suites.") ("python-wrapper" ,python-wrapper) ;; By using a special xorg-server for GTK+'s tests, we reduce the impact ;; of updating xorg-server directly on the master branch. - ("xorg-server" ,xorg-server-1.19.3))) + ("xorg-server" ,xorg-server-for-tests))) (arguments - `(#:disallowed-references (,xorg-server-1.19.3) + `(#:disallowed-references (,xorg-server-for-tests) ;; 47 MiB goes to "out" (24 of which is locale data!), and 26 MiB goes ;; to "doc". #:configure-flags (list (string-append "--with-html-dir=" @@ -1061,7 +1063,7 @@ toolkit.") (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) ("glib" ,glib "bin") ;for 'glib-compile-resources' - ("xorg-server" ,xorg-server-1.19.3))) + ("xorg-server" ,xorg-server-for-tests))) (propagated-inputs `(("pangomm" ,pangomm) ("cairomm" ,cairomm) @@ -1072,7 +1074,7 @@ toolkit.") `(;; XXX: Tests require C++14 or later. Remove this when the default ;; compiler is >= GCC6. #:configure-flags '("CXXFLAGS=-std=gnu++14") - #:disallowed-references (,xorg-server-1.19.3) + #:disallowed-references (,xorg-server-for-tests) #:phases (modify-phases %standard-phases (add-before 'check 'run-xvfb (lambda* (#:key inputs #:allow-other-keys) @@ -1153,7 +1155,7 @@ printing and other features typical of a source code editor.") (define-public python-pycairo (package (name "python-pycairo") - (version "1.16.3") + (version "1.17.1") (source (origin (method url-fetch) @@ -1161,7 +1163,7 @@ printing and other features typical of a source code editor.") version "/pycairo-" version ".tar.gz")) (sha256 (base32 - "1xq1bwhyi5imca5kvd28szh2rdzi8g0kaspwaqgsbczqskjj3csv")))) + "165n0g7gp2a0qi8558snvfans17x83jv2lv7bx4vr1rxjbn3a2hg")))) (build-system python-build-system) (native-inputs `(("pkg-config" ,pkg-config) @@ -1356,7 +1358,7 @@ and routines to assist in editing internationalized text.") ("check" ,check) ("gettext" ,gettext-minimal) ("glib:bin" ,glib "bin") - ("xorg-server" ,xorg-server-1.19.3))) + ("xorg-server" ,xorg-server-for-tests))) ;; Listed in 'Requires.private' of 'girara.pc'. (propagated-inputs `(("gtk+" ,gtk+))) (arguments diff --git a/gnu/packages/guile-wm.scm b/gnu/packages/guile-wm.scm index 364477be72..3755282403 100644 --- a/gnu/packages/guile-wm.scm +++ b/gnu/packages/guile-wm.scm @@ -56,7 +56,7 @@ (string-append "--with-guile-site-ccache-dir=" (assoc-ref %outputs "out") - "/share/guile/site/2.2")))) + "/lib/guile/2.2/site-ccache")))) (native-inputs `(("pkg-config" ,pkg-config) ("texinfo" ,texinfo))) (inputs `(("guile" ,guile-2.2) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index f95641ab13..022ac5ee24 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -214,8 +214,7 @@ without requiring the source code to be rewritten.") (files '("share/guile/site/2.0"))) (search-path-specification (variable "GUILE_LOAD_COMPILED_PATH") - (files '("lib/guile/2.0/site-ccache" - "share/guile/site/2.0"))))) + (files '("lib/guile/2.0/site-ccache"))))) (synopsis "Scheme implementation intended especially for extensions") (description @@ -244,7 +243,7 @@ without requiring the source code to be rewritten.") (define-public guile-2.2 (package (inherit guile-2.0) (name "guile") - (version "2.2.3") + (version "2.2.4") (source (origin (method url-fetch) @@ -254,7 +253,7 @@ without requiring the source code to be rewritten.") ".tar.xz")) (sha256 (base32 - "11j01agvnci2cx32wwpqs9078856yxmvs15gcsz7ganpkj2ahlw3")) + "07p3g0v2ba2vlfbfidqzlgbhnzdx46wh2rgc5gszq1mjyx5bks6r")) (modules '((guix build utils))) ;; Remove the pre-built object files. Instead, build everything @@ -273,8 +272,7 @@ without requiring the source code to be rewritten.") (files '("share/guile/site/2.2"))) (search-path-specification (variable "GUILE_LOAD_COMPILED_PATH") - (files '("lib/guile/2.2/site-ccache" - "share/guile/site/2.2"))))) + (files '("lib/guile/2.2/site-ccache"))))) (arguments (if (%current-target-system) @@ -303,35 +301,6 @@ without requiring the source code to be rewritten.") (max-silent-time . 36000))))) ;10 hours (needed on ARM ; when heavily loaded) -(define-public guile-2.2.2 - ;; Keep it so that, when 'guix' runs on 2.2.2, 'guix pull' compiles objects - ;; with 2.2.2, thereby avoiding the ABI incompatibility issues described in - ;; <https://bugs.gnu.org/29570>. - (package - (inherit guile-2.2) - (version "2.2.2") - (source (origin - (inherit (package-source guile-2.2)) - (uri (string-append "mirror://gnu/guile/guile-" version - ".tar.xz")) - (sha256 - (base32 - "1azm25zcmxif0skxfrp11d2wc89nrzpjaann9yxdw6pvjxhs948w")))))) - -(define-public guile-2.2.4 - ;; This version contains important bug fixes, in particular wrt. to crashes - ;; of multi-threaded code as used by 'guix pull' and grafting. - (package - (inherit guile-2.2) - (version "2.2.4") - (source (origin - (inherit (package-source guile-2.2)) - (uri (string-append "mirror://gnu/guile/guile-" version - ".tar.xz")) - (sha256 - (base32 - "07p3g0v2ba2vlfbfidqzlgbhnzdx46wh2rgc5gszq1mjyx5bks6r")))))) - (define-public guile-next ;; This is the upcoming Guile 3.0, with JIT support. (let ((commit "6f3357b0df64c4be17e72079864c09a542f1c779") @@ -1636,7 +1605,7 @@ you send to a FIFO file.") (define-public guile-commonmark (package (name "guile-commonmark") - (version "0.1") + (version "0.1.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/OrangeShark/" name @@ -1644,24 +1613,12 @@ you send to a FIFO file.") "/" name "-" version ".tar.gz")) (sha256 (base32 - "12cb5fqvvgc87f5xp0ih5az305wnjia89l5jba83d0r2p8bfy0b0")) - (modules '((guix build utils))) - (snippet - ;; Use the real effective version of Guile in directory names - ;; instead of a hard-coded "/2.0". - '(begin - (substitute* "configure" - (("ac_subst_vars='") - "ac_subst_vars='GUILE_EFFECTIVE_VERSION\n")) - (substitute* "Makefile.in" - (("moddir =.*") - "moddir = $(datadir)/guile/site/@GUILE_EFFECTIVE_VERSION@\n") - (("godir =.*") - "godir = $(libdir)/guile/@GUILE_EFFECTIVE_VERSION@/site-ccache\n")) - #t)))) + "0kzclwkfijj8xka3g9kfj53y67c34ndfy84swdbw3j7y962ndxq6")))) (build-system gnu-build-system) (inputs `(("guile" ,guile-2.2))) + (native-inputs + `(("pkg-config" ,pkg-config))) (synopsis "CommonMark parser for Guile") (description "guile-commonmark is a library for parsing CommonMark, a fully specified @@ -2295,7 +2252,7 @@ tracker's SOAP service, such as @url{https://bugs.gnu.org}.") ("autoconf" ,autoconf) ("automake" ,automake))) (inputs - `(("guile" ,guile-2.2.4))) + `(("guile" ,guile-2.2))) (home-page "https://git.systemreboot.net/guile-email") (synopsis "Guile email parser") (description "This package provides an email parser written in pure @@ -2324,7 +2281,7 @@ Guile.") ("automake" ,automake) ("texinfo" ,texinfo))) (inputs - `(("guile" ,guile-2.2.4) + `(("guile" ,guile-2.2) ("guile-email" ,guile-email)))))) ;; There has not been any release yet. diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 0a90ac523c..57435dca07 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -10619,6 +10619,7 @@ expose it from another module in the hierarchy. (lambda* (#:key outputs inputs tests? (configure-flags '()) #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) + (name-version (strip-store-file-name out)) (input-dirs (match inputs (((_ . dir) ...) dir) @@ -10629,8 +10630,7 @@ expose it from another module in the hierarchy. `(,(string-append "--bindir=" out "/bin")) `(,(string-append "--docdir=" out - "/share/doc/" ((@@ (guix build haskell-build-system) - package-name-version) out))) + "/share/doc/" name-version)) '("--libsubdir=$compiler/$pkg-$version") '("--package-db=../package.conf.d") '("--global") diff --git a/gnu/packages/hurd.scm b/gnu/packages/hurd.scm index d6c1fb5e64..938cb116ca 100644 --- a/gnu/packages/hurd.scm +++ b/gnu/packages/hurd.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2016, 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com> +;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -24,17 +25,25 @@ #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (guix build-system trivial) + #:use-module (gnu packages autotools) #:use-module (gnu packages flex) #:use-module (gnu packages bison) #:use-module (gnu packages perl) #:use-module (gnu packages base) #:use-module (guix git-download) - #:export (hurd-triplet?)) + #:export (hurd-triplet? + hurd-target?)) (define (hurd-triplet? triplet) (and (string-suffix? "-gnu" triplet) (not (string-contains triplet "linux")))) +(define (hurd-target?) + "Return true if the cross-compilation target or the current system is +GNU/Hurd." + (or (and=> (%current-target-system) hurd-triplet?) + (string-suffix? (%current-system) "-gnu"))) + (define (gnumach-source-url version) (string-append "mirror://gnu/gnumach/gnumach-" version ".tar.gz")) @@ -43,6 +52,10 @@ (string-append "mirror://gnu/hurd/hurd-" version ".tar.gz")) +(define (patch-url repository commit) + (string-append "https://git.savannah.gnu.org/cgit/hurd/" repository + ".git/patch/?id=" commit)) + (define-public gnumach-headers (package (name "gnumach-headers") @@ -53,7 +66,24 @@ (uri (gnumach-source-url version)) (sha256 (base32 - "02hygsfpd2dljl5lg1vjjg9pizi9jyxd4aiiqzjshz6jax62jm9f")))) + "02hygsfpd2dljl5lg1vjjg9pizi9jyxd4aiiqzjshz6jax62jm9f")) + (patches (list (origin + ;; This patch adds <mach/vm_wire.h>, which defines the + ;; VM_WIRE_* constants needed by glibc 2.28. + (method url-fetch) + (uri (patch-url "gnumach" "2b0f19f602e08fd9d37268233b962674fd592634")) + (sha256 + (base32 + "01iajnwsmka0w9hwjkxxijc4xfhwqbvlkw1w8n71hpnhfixd0y28")) + (file-name "gnumach-vm-wire-header.patch")))) + (modules '((guix build utils))) + (snippet + '(begin + ;; Actually install vm_wire.h. + (substitute* "Makefile.in" + (("^include_mach_HEADERS =") + "include_mach_HEADERS = include/mach/vm_wire.h")) + #t)))) (build-system gnu-build-system) (arguments `(#:phases @@ -110,56 +140,71 @@ communication.") (license gpl2+))) (define-public hurd-headers - (package - (name "hurd-headers") - (version "0.9") - (source (origin - (method url-fetch) - (uri (hurd-source-url version)) - (sha256 - (base32 - "1nw9gly0n7pyv3cpfm4mmxy4yccrx4g0lyrvd3vk2vil26jpbggw")))) - (build-system gnu-build-system) - (native-inputs - `(("mig" ,mig))) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'install - (lambda _ - (invoke "make" "install-headers" "no_deps=t"))) - (delete 'build)) + ;; Resort to a post-0.9 snapshot that provides the 'file_utimens' and + ;; 'file_exec_paths' RPCs that glibc 2.28 expects. + (let ((revision "0") + (commit "98b33905c89b7e5c309c74ae32302a5745901a6e")) + (package + (name "hurd-headers") + (version "0.9") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.savannah.gnu.org/git/hurd/hurd.git") + (commit commit))) + (sha256 + (base32 + "1mj22sxgscas2675vrbxr477mwbxdj68pqcrh65lbir8qlssrgrf")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (native-inputs + `(("mig" ,mig) + ("autoconf" ,autoconf) + ("automake" ,automake))) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'install + (lambda _ + (invoke "make" "install-headers" "no_deps=t"))) + (delete 'build)) - #:configure-flags '(;; Pretend we're on GNU/Hurd; 'configure' wants - ;; that. - ,@(if (%current-target-system) - '() - '("--host=i586-pc-gnu")) + #:configure-flags '( ;; Pretend we're on GNU/Hurd; 'configure' wants + ;; that. + ,@(if (%current-target-system) + '() + '("--host=i586-pc-gnu")) - ;; Reduce set of dependencies. - "--without-parted" - "--disable-ncursesw" - "--disable-test" - "--without-libbz2" - "--without-libz" - ;; Skip the clnt_create check because it expects - ;; a working glibc causing a circular dependency. - "ac_cv_search_clnt_create=no") + ;; Reduce set of dependencies. + "--without-parted" + "--disable-ncursesw" + "--disable-test" + "--without-libbz2" + "--without-libz" + ;; Skip the clnt_create check because it expects + ;; a working glibc causing a circular dependency. + "ac_cv_search_clnt_create=no" - #:tests? #f)) - (home-page "https://www.gnu.org/software/hurd/hurd.html") - (synopsis "GNU Hurd headers") - (description - "This package provides C headers of the GNU Hurd, used to build the GNU C + ;; Annihilate the checks for the 'file_exec_paths' + ;; & co. libc functions to avoid "link tests are + ;; not allowed after AC_NO_EXECUTABLES" error. + "ac_cv_func_file_exec_paths=no" + "ac_cv_func_exec_exec_paths=no" + "ac_cv_func__hurd_exec_paths=no" + "ac_cv_func_file_futimens=no") + + #:tests? #f)) + (home-page "https://www.gnu.org/software/hurd/hurd.html") + (synopsis "GNU Hurd headers") + (description + "This package provides C headers of the GNU Hurd, used to build the GNU C Library and other user programs.") - (license gpl2+))) + (license gpl2+)))) (define-public hurd-minimal (package (inherit hurd-headers) (name "hurd-minimal") (inputs `(("glibc-hurd-headers" ,glibc/hurd-headers))) - (native-inputs - `(("mig" ,mig))) (arguments (substitute-keyword-arguments (package-arguments hurd-headers) ((#:phases _) @@ -178,6 +223,11 @@ Library and other user programs.") #t))) (replace 'build (lambda _ + ;; Install <assert-backtrace.h> & co. + (invoke "make" "-Clibshouldbeinlibc" + "../include/assert-backtrace.h") + + ;; Build libihash. (invoke "make" "-Clibihash" "libihash.a"))))))) (home-page "https://www.gnu.org/software/hurd/hurd.html") (synopsis "GNU Hurd libraries") diff --git a/gnu/packages/icu4c.scm b/gnu/packages/icu4c.scm index c4d3703794..2d28107e81 100644 --- a/gnu/packages/icu4c.scm +++ b/gnu/packages/icu4c.scm @@ -32,7 +32,7 @@ (define-public icu4c (package (name "icu4c") - (version "61.1") + (version "62.1") (source (origin (method url-fetch) (uri (string-append @@ -42,7 +42,7 @@ (string-map (lambda (x) (if (char=? x #\.) #\_ x)) version) "-src.tgz")) (sha256 - (base32 "1vxgkx0cyvdy00a9yd5khkx14r5kcndkax2wa99klm52x2dgh1yh")))) + (base32 "18ssgnwzzpm1g1fvbm9h1fvryiwxvvn5wc3fdakdsl33cs6qdn9x")))) (build-system gnu-build-system) (inputs `(("perl" ,perl))) @@ -55,10 +55,24 @@ (string-prefix? "mips" s))) '("--with-data-packaging=archive") '())) + ,@(if (string-prefix? "i686" (or (%current-target-system) + (%current-system))) + ;; FIXME: Some tests are failing on i686: + ;; <https://unicode-org.atlassian.net/browse/ICU-20080>. + '(#:tests? #f) + '()) #:phases (modify-phases %standard-phases (add-after 'unpack 'chdir-to-source - (lambda _ (chdir "source") #t))))) + (lambda _ (chdir "source") #t)) + (add-after 'install 'avoid-coreutils-reference + ;; Don't keep a reference to the build tools. + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* (find-files (string-append out "/lib/icu") + "\\.inc$") + (("INSTALL_CMD=.*/bin/install") "INSTALL_CMD=install")) + #t)))))) (synopsis "International Components for Unicode") (description "ICU is a set of C/C++ and Java libraries providing Unicode and diff --git a/gnu/packages/idutils.scm b/gnu/packages/idutils.scm index abab0c16bf..81715591b4 100644 --- a/gnu/packages/idutils.scm +++ b/gnu/packages/idutils.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2012, 2013, 2015 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 208 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,7 +36,20 @@ (sha256 (base32 "1hmai3422iaqnp34kkzxdnywl7n7pvlxp11vrw66ybxn9wxg90c1")) - (patches (search-patches "diffutils-gets-undeclared.patch")))) + (patches (search-patches "diffutils-gets-undeclared.patch")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* (find-files "lib" "\\.c$") + (("#if defined _IO_ftrylockfile") + "#if defined _IO_EOF_SEEN")) + (substitute* "lib/stdio-impl.h" + (("^/\\* BSD stdio derived implementations") + (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n" + "# define _IO_IN_BACKUP 0x100\n" + "#endif\n\n" + "/* BSD stdio derived implementations"))) + #t)))) (build-system gnu-build-system) (native-inputs `(("emacs" ,emacs-minimal))) (home-page "https://www.gnu.org/software/idutils/") diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 8168a225fc..d03a0a287d 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -137,15 +137,15 @@ library. It supports almost all PNG features and is extensible.") (add-after 'unpack 'patch-apng (lambda* (#:key inputs #:allow-other-keys) (define (apply-patch file) - (zero? (system* "patch" "-p1" "--force" - "--input" file))) + (invoke "patch" "-p1" "--force" + "--input" file)) (let ((apng.gz (assoc-ref inputs "apng"))) (format #t "Applying APNG patch '~a'...~%" apng.gz) - (and - (zero? - (system (string-append "gunzip < " apng.gz " > the-patch"))) - (apply-patch "the-patch"))))) + (invoke "sh" "-c" + (string-append "gunzip < " apng.gz " > the-patch")) + (apply-patch "the-patch") + #t))) (add-before 'configure 'no-checks (lambda _ (substitute* "Makefile.in" @@ -240,7 +240,8 @@ in-memory raw vectors.") (string-append vardef (assoc-ref inputs "zlib") "/")) ;; The Makefile is written by hand and not using $PREFIX (("\\$\\(DESTDIR\\)/usr/") - (string-append (assoc-ref outputs "out") "/")))))))) + (string-append (assoc-ref outputs "out") "/"))) + #t))))) (inputs `(("libpng" ,libpng) ("zlib" , zlib))) @@ -312,13 +313,13 @@ Currently all documentation resides in @file{pnglite.h}.") (define-public libjpeg (package (name "libjpeg") - (version "9b") + (version "9c") (source (origin (method url-fetch) (uri (string-append "http://www.ijg.org/files/jpegsrc.v" version ".tar.gz")) (sha256 (base32 - "0lnhpahgdwlrkd41lx6cr90r199f8mc6ydlh7jznj5klvacd63r4")))) + "08kixcf3a7s9x91174abjnk1xbvj4v8crdc73zi4k9h3jfbm00k5")))) (build-system gnu-build-system) (synopsis "Library for handling JPEG files") (description @@ -460,7 +461,6 @@ extracting icontainer icon files.") (define-public libtiff (package (name "libtiff") - (replacement libtiff/fixed) (version "4.0.9") (source (origin @@ -471,7 +471,9 @@ extracting icontainer icon files.") (base32 "1kfg4q01r4mqn7dj63ifhi6pmqzbf4xax6ni6kkk81ri5kndwyvf")) (patches (search-patches "libtiff-CVE-2017-9935.patch" - "libtiff-CVE-2017-18013.patch")))) + "libtiff-CVE-2017-18013.patch" + "libtiff-CVE-2018-8905.patch" + "libtiff-CVE-2018-10963.patch")))) (build-system gnu-build-system) (outputs '("out" "doc")) ;1.3 MiB of HTML documentation @@ -493,17 +495,6 @@ collection of tools for doing simple manipulations of TIFF images.") "See COPYRIGHT in the distribution.")) (home-page "http://www.simplesystems.org/libtiff/"))) -(define libtiff/fixed - (package - (inherit libtiff) - (source - (origin - (inherit (package-source libtiff)) - (patches - (append (origin-patches (package-source libtiff)) - (search-patches "libtiff-CVE-2018-8905.patch" - "libtiff-CVE-2018-10963.patch"))))))) - (define-public leptonica (package (name "leptonica") @@ -539,14 +530,15 @@ collection of tools for doing simple manipulations of TIFF images.") (modify-phases %standard-phases (add-after 'unpack 'autogen (lambda _ - (zero? (system* "sh" "autobuild")))) + (invoke "sh" "autobuild"))) (add-after 'unpack 'patch-reg-wrapper (lambda _ (substitute* "prog/reg_wrapper.sh" ((" /bin/sh ") (string-append " " (which "sh") " ")) (("which gnuplot") - "true"))))))) + "true")) + #t))))) (home-page "http://www.leptonica.com/") (synopsis "Library and tools for image processing and analysis") (description @@ -561,18 +553,18 @@ arithmetic ops.") (define-public jbig2dec (package (name "jbig2dec") - (version "0.14") - (replacement jbig2dec-0.15) - (source - (origin - (method url-fetch) - (uri - (string-append "https://github.com/ArtifexSoftware/ghostpdl-downloads/" - "releases/download/gs922/" name "-" version ".tar.gz")) - (sha256 - (base32 "0k01hp0q4275fj4rbr1gy64svfraw5w7wvwl08yjhvsnpb1rid11")) - (patches (search-patches "jbig2dec-ignore-testtest.patch")))) + (version "0.15") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ArtifexSoftware" + "/ghostpdl-downloads/releases/download" + "/gs924/" name "-" version ".tar.gz")) + (sha256 + (base32 + "0m1qwpbjbirgw2fqznbajdhdhh35d6xa2csr64lpjz735pvimykb")) + (patches (search-patches "jbig2dec-ignore-testtest.patch")))) (build-system gnu-build-system) + (arguments '(#:configure-flags '("--disable-static"))) (synopsis "Decoder of the JBIG2 image compression format") (description "JBIG2 is designed for lossy or lossless encoding of 'bilevel' (1-bit @@ -587,21 +579,6 @@ work.") (home-page "https://jbig2dec.com") (license license:gpl2+))) -;; This is a bugfix release from an ongoing Ghostscript security audit. -;; It was released alongside Ghostscript 9.24. -(define-public jbig2dec-0.15 - (package - (inherit jbig2dec) - (version "0.15") - (source (origin - (inherit (package-source jbig2dec)) - (uri (string-append "https://github.com/ArtifexSoftware" - "/ghostpdl-downloads/releases/download/gs924/" - "jbig2dec-" version ".tar.gz")) - (sha256 - (base32 - "0m1qwpbjbirgw2fqznbajdhdhh35d6xa2csr64lpjz735pvimykb")))))) - (define-public openjpeg (package (name "openjpeg") @@ -908,11 +885,15 @@ graphics image formats like PNG, BMP, JPEG, TIFF and others.") `(#:test-target "check" #:phases (modify-phases %standard-phases - ;; See https://github.com/ukoethe/vigra/issues/432 - (add-after 'unpack 'disable-broken-test + (add-after 'unpack 'disable-broken-tests (lambda _ + ;; See https://github.com/ukoethe/vigra/issues/432 (substitute* "test/fourier/CMakeLists.txt" (("VIGRA_ADD_TEST.*") "")) + ;; This test fails with Numpy 1.15: + ;; <https://github.com/ukoethe/vigra/issues/436>. + (substitute* "vigranumpy/test/CMakeLists.txt" + (("test1\\.py") "")) #t))) #:configure-flags (list "-Wno-dev" ; suppress developer mode with lots of warnings @@ -1160,7 +1141,7 @@ ISO/IEC 15444-1).") (modify-phases %standard-phases (add-after 'unpack 'autogen (lambda _ - (zero? (system* "sh" "autogen.sh"))))))) + (invoke "sh" "autogen.sh")))))) (synopsis "Scaling, colorspace conversion, and dithering library") (description "Zimg implements the commonly required image processing basics of scaling, colorspace conversion, and depth conversion. A simple API enables @@ -1193,7 +1174,8 @@ the programmer.") ;; of the source tree, one level higher than expected (lambda _ (substitute* "test/run_tests.bash" - (("../build") "../../build"))))))) + (("../build") "../../build")) + #t))))) (home-page "https://github.com/myint/perceptualdiff") (synopsis "Perceptual image comparison utility") (description "PerceptualDiff visually compares two images to determine diff --git a/gnu/packages/inkscape.scm b/gnu/packages/inkscape.scm index de9940df1c..1673cc602e 100644 --- a/gnu/packages/inkscape.scm +++ b/gnu/packages/inkscape.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 John Darrington <jmd@gnu.org> ;;; Copyright © 2014, 2016 Mark H Weaver <mhw@netris.org> -;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2016, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; @@ -54,7 +54,24 @@ "inkscape-" version ".tar.bz2")) (sha256 (base32 - "1chng2yw8dsjxc9gf92aqv7plj11cav8ax321wmakmv5bb09cch6")))) + "1chng2yw8dsjxc9gf92aqv7plj11cav8ax321wmakmv5bb09cch6")) + (patches + (list (origin + (method url-fetch) + (uri (string-append "https://gitlab.com/inkscape/inkscape/commit/" + "a600c6438fef2f4c06f9a4a7d933d99fb054a973.diff")) + (file-name "inkscape-poppler-compat.patch") + (sha256 + (base32 + "19dam5vsy571xszgjddl5g0958dmcsv0wvgxidp4bhj2lban222i"))) + (origin + (method url-fetch) + (uri (string-append "https://gitlab.com/inkscape/inkscape/commit/" + "fa1c469aa8c005e07bb8676d72af9f7c16fae3e0.diff")) + (file-name "inkscape-poppler-compat2.patch") + (sha256 + (base32 + "14k9yrfjz4nx3bz9dk91q74mc0i7rvl2qzkwhcy1br71yqjvngn5"))))))) (build-system cmake-build-system) (inputs `(("aspell" ,aspell) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 0c7b9a9855..9af22146ed 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -46,6 +46,7 @@ #:use-module (gnu packages cpio) #:use-module (gnu packages cups) #:use-module (gnu packages compression) + #:use-module (gnu packages elf) #:use-module (gnu packages fontutils) #:use-module (gnu packages gawk) #:use-module (gnu packages gettext) @@ -1672,6 +1673,190 @@ new Date();")) '("jdk" "openjdk-src" "corba-drop" "jaxp-drop" "jaxws-drop" "jdk-drop" "langtools-drop" "hotspot-drop"))))))) +(define-public openjdk9 + (package + (name "openjdk") + (version "9.181") + (source (origin + (method url-fetch) + (uri "https://hg.openjdk.java.net/jdk/jdk/archive/3cc80be736f2.tar.bz2") + (file-name (string-append name "-" version ".tar.bz2")) + (sha256 + (base32 + "01ihmyf7k5z17wbr7xig7y40l9f01d5zjgkcmawn1102hw5kchpq")) + (modules '((guix build utils))) + (snippet + `(begin + (for-each delete-file (find-files "." ".*.bin$")) + (for-each delete-file (find-files "." ".*.exe$")) + (for-each delete-file (find-files "." ".*.jar$")) + #t)))) + (build-system gnu-build-system) + (outputs '("out" "jdk" "doc")) + (arguments + `(#:tests? #f; require jtreg + #:imported-modules + ((guix build syscalls) + ,@%gnu-build-system-modules) + #:phases + (modify-phases %standard-phases + (add-after 'patch-source-shebangs 'fix-java-shebangs + (lambda _ + ;; This file was "fixed" by patch-source-shebangs, but it requires + ;; this exact first line. + (substitute* "jdk/make/data/blacklistedcertsconverter/blacklisted.certs.pem" + (("^#!.*") "#! java BlacklistedCertsConverter SHA-256\n")) + #t)) + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; TODO: unbundle libpng and lcms + (invoke "bash" "./configure" + (string-append "--with-freetype=" (assoc-ref inputs "freetype")) + "--disable-freetype-bundling" + "--disable-warnings-as-errors" + "--disable-hotspot-gtest" + "--with-giflib=system" + "--with-libjpeg=system" + (string-append "--prefix=" (assoc-ref outputs "out"))) + #t)) + (replace 'build + (lambda _ + (with-output-to-file ".src-rev" + (lambda _ + (display ,version))) + (setenv "GUIX_LD_WRAPPER_ALLOW_IMPURITIES" "yes") + (invoke "make" "all") + #t)) + ;; Some of the libraries in the lib/ folder link to libjvm.so. + ;; But that shared object is located in the server/ folder, so it + ;; cannot be found. This phase creates a symbolic link in the + ;; lib/ folder so that the other libraries can find it. + ;; + ;; See: + ;; https://lists.gnu.org/archive/html/guix-devel/2017-10/msg00169.html + ;; + ;; FIXME: Find the bug in the build system, so that this symlink is + ;; not needed. + (add-after 'install 'install-libjvm + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((lib-out (string-append (assoc-ref outputs "out") + "/lib")) + (lib-jdk (string-append (assoc-ref outputs "jdk") + "/lib"))) + (symlink (string-append lib-jdk "/server/libjvm.so") + (string-append lib-jdk "/libjvm.so")) + (symlink (string-append lib-out "/server/libjvm.so") + (string-append lib-out "/libjvm.so"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (jdk (assoc-ref outputs "jdk")) + (doc (assoc-ref outputs "doc")) + (images (car (find-files "build" ".*-server-release" + #:directories? #t)))) + (copy-recursively (string-append images "/images/jdk") jdk) + (copy-recursively (string-append images "/images/jre") out) + (copy-recursively (string-append images "/images/docs") doc)) + #t)) + (add-after 'install 'strip-zip-timestamps + (lambda* (#:key outputs #:allow-other-keys) + (use-modules (guix build syscalls)) + (for-each (lambda (zip) + (let ((dir (mkdtemp! "zip-contents.XXXXXX"))) + (with-directory-excursion dir + (invoke "unzip" zip)) + (delete-file zip) + (for-each (lambda (file) + (let ((s (lstat file))) + (unless (eq? (stat:type s) 'symlink) + (format #t "reset ~a~%" file) + (utime file 0 0 0 0)))) + (find-files dir #:directories? #t)) + (with-directory-excursion dir + (let ((files (find-files "." ".*" #:directories? #t))) + (apply invoke "zip" "-0" "-X" zip files))))) + (find-files (assoc-ref outputs "doc") ".*.zip$")) + #t))))) + (inputs + `(("alsa-lib" ,alsa-lib) + ("cups" ,cups) + ("fontconfig" ,fontconfig) + ("freetype" ,freetype) + ("giflib" ,giflib) + ("lcms" ,lcms) + ("libelf" ,libelf) + ("libjpeg" ,libjpeg) + ("libice" ,libice) + ("libpng" ,libpng) + ("libx11" ,libx11) + ("libxcomposite" ,libxcomposite) + ("libxi" ,libxi) + ("libxinerama" ,libxinerama) + ("libxrender" ,libxrender) + ("libxt" ,libxt) + ("libxtst" ,libxtst))) + (native-inputs + `(("icedtea-8" ,icedtea-8) + ("icedtea-8:jdk" ,icedtea-8 "jdk") + ("unzip" ,unzip) + ("which" ,which) + ("zip" ,zip))) + (home-page "https://openjdk.java.net/projects/jdk9/") + (synopsis "Java development kit") + (description + "This package provides the Java development kit OpenJDK.") + (license license:gpl2+))) + +(define-public openjdk10 + (package + (inherit openjdk9) + (name "openjdk") + (version "10.46") + (source (origin + (method url-fetch) + (uri "http://hg.openjdk.java.net/jdk/jdk/archive/6fa770f9f8ab.tar.bz2") + (file-name (string-append name "-" version ".tar.bz2")) + (sha256 + (base32 + "0zywq2203b4hx4jms9vbwvjcj1d3k2v3qpx4s33729fkpmid97r4")) + (modules '((guix build utils))) + (snippet + `(begin + (for-each delete-file (find-files "." ".*.bin$")) + (for-each delete-file (find-files "." ".*.exe$")) + (for-each delete-file (find-files "." ".*.jar$")) + #t)))) + (arguments + (substitute-keyword-arguments (package-arguments openjdk9) + ((#:phases phases) + `(modify-phases ,phases + (replace 'fix-java-shebangs + (lambda _ + ;; This file was "fixed" by patch-source-shebangs, but it requires + ;; this exact first line. + (substitute* "make/data/blacklistedcertsconverter/blacklisted.certs.pem" + (("^#!.*") "#! java BlacklistedCertsConverter SHA-256\n")) + #t)) + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (invoke "bash" "./configure" + (string-append "--with-freetype=" (assoc-ref inputs "freetype")) + "--disable-freetype-bundling" + "--disable-warnings-as-errors" + "--disable-hotspot-gtest" + "--with-giflib=system" + "--with-libjpeg=system" + "--with-native-debug-symbols=zipped" + (string-append "--prefix=" (assoc-ref outputs "out"))) + #t)))))) + (native-inputs + `(("openjdk9" ,openjdk9) + ("openjdk9:jdk" ,openjdk9 "jdk") + ("unzip" ,unzip) + ("which" ,which) + ("zip" ,zip))))) + (define-public icedtea icedtea-8) diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm index 5086df7a1b..cb870208e4 100644 --- a/gnu/packages/jemalloc.scm +++ b/gnu/packages/jemalloc.scm @@ -32,7 +32,7 @@ (define-public jemalloc (package (name "jemalloc") - (version "5.0.1") + (version "5.1.0") (source (origin (method url-fetch) (uri (string-append @@ -40,8 +40,7 @@ version "/jemalloc-" version ".tar.bz2")) (sha256 (base32 - "1sf3lzgb0y8nnyzmp4zrca3sngdxw3kfh20sna9z03jv74fph528")) - (patches (search-patches "jemalloc-arm-address-bits.patch")))) + "0s3jpcyhzia8d4k0xyc67is78kg416p9yc3c2f9w6fhhqqffd5jk")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/kerberos.scm b/gnu/packages/kerberos.scm index 22d74d32df..508f9c4bd2 100644 --- a/gnu/packages/kerberos.scm +++ b/gnu/packages/kerberos.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2012, 2013 Nikita Karetnikov <nikita@karetnikov.org> ;;; Copyright © 2012, 2017 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com> ;;; ;;; This file is part of GNU Guix. @@ -47,7 +48,7 @@ (define-public mit-krb5 (package (name "mit-krb5") - (version "1.16") + (version "1.16.1") (source (origin (method url-fetch) (uri (list @@ -59,7 +60,7 @@ "/krb5-" version ".tar.gz"))) (sha256 (base32 - "024yjr15ij0qdnay0bcqfpclgfri0qa8iw4r5zdlryxhhdgi5szs")))) + "05qis9l93hhxaknbp0a2v5cr24fsy52fqx20aqqcgl1s9qwzwkr1")))) (build-system gnu-build-system) (native-inputs `(("bison" ,bison) @@ -116,7 +117,7 @@ cryptography.") '(;; This is required since we patch some of the build scripts. ;; Remove for the next Shishi release after 1.0.2 or when ;; removing 'shishi-fix-libgcrypt-detection.patch'. - #:configure-flags '("ac_cv_libgcrypt=yes"))) + #:configure-flags '("ac_cv_libgcrypt=yes" "--disable-static"))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("gnutls" ,gnutls) diff --git a/gnu/packages/libbsd.scm b/gnu/packages/libbsd.scm index 58b0be872c..a616de70bd 100644 --- a/gnu/packages/libbsd.scm +++ b/gnu/packages/libbsd.scm @@ -25,14 +25,14 @@ (define-public libbsd (package (name "libbsd") - (version "0.8.7") + (version "0.9.1") (source (origin (method url-fetch) (uri (string-append "https://libbsd.freedesktop.org/releases/" "libbsd-" version ".tar.xz")) (sha256 (base32 - "0c9bl49zs0xdddcwj5dh0lay9sxi2m1yi74848g8p87mb87g2j7m")))) + "1957w2wi7iqar978qlfsm220dwywnrh5m58nrnn9zmi74ds3bn2n")))) (build-system gnu-build-system) (synopsis "Utility functions from BSD systems") (description "This library provides useful functions commonly found on BSD diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm index a7752dc5f0..2de29707ca 100644 --- a/gnu/packages/libevent.scm +++ b/gnu/packages/libevent.scm @@ -122,24 +122,17 @@ limited support for fork events.") (define-public libuv (package (name "libuv") - (version "1.19.2") + (version "1.23.0") (source (origin (method url-fetch) (uri (string-append "https://dist.libuv.org/dist/v" version "/libuv-v" version ".tar.gz")) (sha256 (base32 - "1msk9ac1z69whww88ibrwjqkd1apdla6l77cm2fwy5kigq0z5g3w")))) + "09yf7c71n8b80nbsv4lsmq5nqmb0rylhpx3z9jgkv5za9lr6sx6i")))) (build-system gnu-build-system) (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack 'autogen - (lambda _ - ;; Fashionable people don't run 'make dist' these days, so - ;; we need to do that ourselves. - (invoke "sh" "autogen.sh")))) - - ;; XXX: Some tests want /dev/tty, attempt to make connections, etc. + '(;; XXX: Some tests want /dev/tty, attempt to make connections, etc. #:tests? #f)) (native-inputs `(("autoconf" ,autoconf-wrapper) ("automake" ,automake) @@ -159,6 +152,19 @@ 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 version is required for Node versions < 10. +(define-public libuv-1.19 + (package + (inherit libuv) + (version "1.19.2") + (source (origin + (method url-fetch) + (uri (string-append "https://dist.libuv.org/dist/v" version + "/libuv-v" version ".tar.gz")) + (sha256 + (base32 + "1msk9ac1z69whww88ibrwjqkd1apdla6l77cm2fwy5kigq0z5g3w")))))) + (define-public perl-anyevent (package (name "perl-anyevent") diff --git a/gnu/packages/libffi.scm b/gnu/packages/libffi.scm index 0d54c305b2..01a5ea2049 100644 --- a/gnu/packages/libffi.scm +++ b/gnu/packages/libffi.scm @@ -50,7 +50,10 @@ (patches (search-patches "libffi-3.2.1-complex-alpha.patch")))) (build-system gnu-build-system) (arguments - `(#:phases + `(;; Prevent the build system from passing -march and -mtune to the + ;; compiler. See "ax_cc_maxopt.m4" and "ax_gcc_archflag.m4". + #:configure-flags '("--enable-portable-binary" "--without-gcc-arch") + #:phases (modify-phases %standard-phases (add-after 'install 'post-install (lambda* (#:key outputs #:allow-other-keys) @@ -79,13 +82,14 @@ conversions for values passed between the two languages.") (define-public python-cffi (package (name "python-cffi") - (version "1.11.4") + (version "1.11.5") (source (origin (method url-fetch) (uri (pypi-uri "cffi" version)) (sha256 - (base32 "07fiy4wqg8g08x38r04ydjr8n6g0g74gb8si8b6jhymijalq746z")))) + (base32 "1x3lrj928dcxx1k8k9gf3s4s3jwvzv8mc3kkyg1g7c3a1sc1f3z9")) + (patches (search-patches "python-cffi-x87-stack-clean.patch")))) (build-system python-build-system) (outputs '("out" "doc")) (inputs diff --git a/gnu/packages/libidn.scm b/gnu/packages/libidn.scm index 249c3f8458..719a0f0b4b 100644 --- a/gnu/packages/libidn.scm +++ b/gnu/packages/libidn.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2017 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org> +;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -32,26 +33,18 @@ (define-public libidn (package (name "libidn") - (version "1.34") + (version "1.35") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/libidn/libidn-" version ".tar.gz")) (sha256 (base32 - "0g3fzypp0xjcgr90c5cyj57apx1cmy0c6y9lvw2qdcigbyby469p")) - (modules '((guix build utils))) - (snippet - '(begin - ;; The gnulib test-lock test is prone to writer starvation - ;; with our glibc@2.25, which prefers readers, so disable it. - ;; The gnulib commit b20e8afb0b2 should fix this once - ;; incorporated here. - (substitute* "lib/gltests/Makefile.in" - (("test-lock\\$\\(EXEEXT\\) ") "")) - #t)))) + "07pyy0afqikfq51z5kbzbj9ldbd12mri0zvx0mfv3ds6bc0g26pi")))) (build-system gnu-build-system) -;; FIXME: No Java and C# libraries are currently built. + ;; FIXME: No Java and C# libraries are currently built. + (arguments + `(#:configure-flags '("--disable-static"))) (synopsis "Internationalized string processing library") (description "libidn is a library implementing of the Stringprep, Punycode and IDNA @@ -66,19 +59,21 @@ Java libraries.") (define-public libidn2 (package (name "libidn2") - (version "2.0.4") + (version "2.0.5") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/libidn/" name "-" version ".tar.lz")) (sha256 (base32 - "00f2fyw5kwr9is3cdn5h9arzxp0lnvg0z9bb9zyfs0dq81gaqim4")))) + "0s4nkazy1xbs6bbq4farby1xhmhzk5bdclbil5gqdwyzxsgabxqg")))) (native-inputs `(("lzip" ,lzip))) (inputs `(("libunistring" ,libunistring))) (build-system gnu-build-system) + (arguments + `(#:configure-flags '("--disable-static"))) (synopsis "Internationalized domain name library for IDNA2008") (description "Libidn2 is an internationalized domain library implementing the IDNA2008 specifications. Libidn2 is believed to be a complete IDNA2008 diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index abf16acb3d..2e05820f72 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -318,7 +318,16 @@ working with graphics in the WPG (WordPerfect Graphics) format.") ;; During configure, the boost headers are found, but linking ;; fails without the following flag. (string-append "--with-boost=" - (assoc-ref %build-inputs "boost"))))) + (assoc-ref %build-inputs "boost"))) + #:phases (modify-phases %standard-phases + (add-before 'build 'fix-boost-include + (lambda _ + ;; This library moved in Boost and the compatibility + ;; redirect is no longer available since version 1.68.0. + (substitute* "src/libcmis/xml-utils.cxx" + (("boost/uuid/sha1.hpp") + "boost/uuid/detail/sha1.hpp")) + #t))))) (home-page "https://github.com/tdf/libcmis") (synopsis "CMIS client library") (description "LibCMIS is a C++ client library for the CMIS interface. It diff --git a/gnu/packages/libsigsegv.scm b/gnu/packages/libsigsegv.scm index 7f63bb26c4..927a12f4cf 100644 --- a/gnu/packages/libsigsegv.scm +++ b/gnu/packages/libsigsegv.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2012, 2013, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. @@ -38,20 +38,23 @@ (home-page "https://www.gnu.org/software/libsigsegv/") (synopsis "Library for handling page faults") (arguments - ;; On MIPS, work around this error: - ;; - ;; In file included from fault-linux-mips-old.h:18:0, - ;; [...] - ;; linux-libre-headers-cross-mips64el-linux-gnu-3.3.8/include/asm/sigcontext.h:57:8: error: redefinition of 'struct sigcontext' - (if (string-contains (or (%current-target-system) (%current-system)) - "mips64el") - `(#:phases (modify-phases %standard-phases - (add-before 'configure 'patch-mips-old-h - (lambda _ - (substitute* "src/fault-linux-mips-old.h" - (("#include <asm/sigcontext\\.h>") "")) - #t)))) - '())) + `(;; The shared library isn't built by default but some packages need it. + #:configure-flags '("--enable-shared") + + ;; On MIPS, work around this error: + ;; + ;; In file included from fault-linux-mips-old.h:18:0, + ;; [...] + ;; linux-libre-headers-cross-mips64el-linux-gnu-3.3.8/include/asm/sigcontext.h:57:8: error: redefinition of 'struct sigcontext' + ,@(if (string-contains (or (%current-target-system) (%current-system)) + "mips64el") + `(#:phases (modify-phases %standard-phases + (add-before 'configure 'patch-mips-old-h + (lambda _ + (substitute* "src/fault-linux-mips-old.h" + (("#include <asm/sigcontext\\.h>") "")) + #t)))) + '()))) (description "GNU libsigsegv is a library to handle page faults, which occur when a program tries to access an unavailable region of memory, in user mode. By diff --git a/gnu/packages/libunistring.scm b/gnu/packages/libunistring.scm index 6a3afd4f05..fda839be54 100644 --- a/gnu/packages/libunistring.scm +++ b/gnu/packages/libunistring.scm @@ -5,6 +5,8 @@ ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org> ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com> ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org> +;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -32,7 +34,7 @@ (define-public libunistring (package (name "libunistring") - (version "0.9.9") + (version "0.9.10") (source (origin (method url-fetch) (uri (string-append @@ -40,24 +42,25 @@ version ".tar.xz")) (sha256 (base32 - "0cx8v6862w7vvacbkcvg49kfx731ckdgaybmzw1zav71zkn97nd4")) - (modules '((guix build utils))) - (snippet - '(begin - ;; The gnulib test-lock test is prone to writer starvation - ;; with our glibc@2.25, which prefers readers, so disable it. - ;; The gnulib commit b20e8afb0b2 should fix this once - ;; incorporated here. - (substitute* "tests/Makefile.in" - (("test-lock\\$\\(EXEEXT\\) ") "")) - #t)))) + "1mq57h06622m6qc5cv347fc3qk5mj840axw3c0vd7qmnwk1v53zb")))) (propagated-inputs (libiconv-if-needed)) + (outputs '("out" "static")) (build-system gnu-build-system) (arguments ;; Work around parallel build issue whereby C files may be compiled before ;; config.h is built: see <http://hydra.gnu.org/build/59381/nixlog/2/raw> and ;; <http://lists.openembedded.org/pipermail/openembedded-core/2012-April/059850.html>. - '(#:parallel-build? #f)) + '(#:parallel-build? #f + #:phases (modify-phases %standard-phases + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (static (assoc-ref outputs "static"))) + (with-directory-excursion (string-append out "/lib") + (install-file "libunistring.a" + (string-append static "/lib")) + (delete-file "libunistring.a") + #t))))))) (synopsis "C library for manipulating Unicode strings") (description "GNU libunistring is a library providing functions to manipulate diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 5f5d55b691..661b7ed2ca 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -165,13 +165,13 @@ defconfig. Return the appropriate make target if applicable, otherwise return (define-public linux-libre-headers (package (name "linux-libre-headers") - (version "4.14.26") + (version "4.14.67") (source (origin (method url-fetch) (uri (linux-libre-urls version)) (sha256 (base32 - "1m2zr17wpasg5riysbaa4g5i492jzr93py2jm088ki818s4a9cm3")))) + "050zvdxjy6sc64q75pr1gxsmh49chwav2pwxz8xlif39bvahnrpg")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl))) (arguments @@ -300,12 +300,6 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." (or (%current-target-system) (%current-system))) ((or "x86_64" "i386") `(("gcc" ,gcc-7))) - ("arm64" - ;; Work around a binutils 2.30 bug where some kernel symbols would - ;; be incorrectly marked as relocatable: - ;; <https://sourceware.org/bugzilla/show_bug.cgi?id=22764>. - `(("ld-wrapper" ,(make-ld-wrapper "ld-wrapper" - #:binutils binutils/fixed)))) (_ '())) ,@(match (and configuration-file @@ -488,17 +482,17 @@ It has been modified to remove all non-free binary blobs.") (define-public linux-pam (package (name "linux-pam") - (version "1.3.0") + (version "1.3.1") (source (origin - (method url-fetch) - (uri (string-append - "http://www.linux-pam.org/library/" - "Linux-PAM-" version ".tar.bz2")) - (sha256 - (base32 - "1fyi04d5nsh8ivd0rn2y0z83ylgc0licz7kifbb6xxi2ylgfs6i4")) - (patches (search-patches "linux-pam-no-setfsuid.patch")))) + (method url-fetch) + (uri (string-append + "https://github.com/linux-pam/linux-pam/releases/download/v" + version "/Linux-PAM-" version ".tar.xz")) + (sha256 + (base32 + "1nyh9kdi3knhxcbv5v4snya0g3gff0m671lnvqcbygw3rm77mx7g")) + (patches (search-patches "linux-pam-no-setfsuid.patch")))) (build-system gnu-build-system) (native-inputs @@ -580,7 +574,7 @@ providing the system administrator with some help in common tasks.") (define-public util-linux (package (name "util-linux") - (version "2.32") + (version "2.32.1") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/linux/utils/" @@ -588,7 +582,7 @@ providing the system administrator with some help in common tasks.") name "-" version ".tar.xz")) (sha256 (base32 - "0d2758kjll5xqm5fpp3sww1h66aahx161sf2b60jxqv4qymrfwvc")) + "1ck7d8srw5szpjq7v0gpmjahnjs6wgqzm311ki4gazww6xx71rl6")) (patches (search-patches "util-linux-tests.patch")) (modules '((guix build utils))) (snippet @@ -644,7 +638,14 @@ providing the system administrator with some help in common tasks.") (rename-file file (string-append static "/" file))) - (find-files "lib" "\\.a$"))) + (find-files "lib" "\\.a$")) + + ;; Remove references to the static library from the '.la' + ;; files so that Libtool does the right thing when both + ;; the shared and static library is available. + (substitute* (find-files "lib" "\\.la$") + (("old_library=.*") "old_library=''\n"))) + #t)))))) (inputs `(("zlib" ,zlib) ("ncurses" ,ncurses) @@ -1250,7 +1251,8 @@ that the Ethernet protocol is much simpler than the IP protocol.") (lambda _ ;; Don't attempt to create /var/lib/arpd. (substitute* "Makefile" - (("^.*ARPDDIR.*$") ""))))))) + (("^.*ARPDDIR.*$") "")) + #t))))) (inputs `(("iptables" ,iptables) ("db4" ,bdb))) @@ -2533,9 +2535,7 @@ in a digital read-out.") (package (name "perf") (version (package-version linux-libre)) - (source (origin - (inherit (package-source linux-libre)) - (patches (search-patches "perf-gcc-ice.patch")))) + (source (package-source linux-libre)) (build-system gnu-build-system) (arguments '(#:phases @@ -3298,6 +3298,7 @@ and copy/paste text in the console and in xterm.") ("libuuid:static" ,util-linux "static") ("lzo" ,lzo) ("zlib" ,zlib) + ("zlib:static" ,zlib "static") ("zstd" ,zstd))) (native-inputs `(("pkg-config" ,pkg-config) ("asciidoc" ,asciidoc) @@ -3539,7 +3540,8 @@ from userspace.") (let* ((out (assoc-ref outputs "out")) (sbin (string-append out "/sbin"))) (symlink "mount.ntfs-3g" - (string-append sbin "/mount.ntfs")))))))) + (string-append sbin "/mount.ntfs"))) + #t))))) (home-page "https://www.tuxera.com/community/open-source-ntfs-3g/") (synopsis "Read-write access to NTFS file systems") (description @@ -3696,7 +3698,8 @@ from that to the system kernel's @file{/dev/random} machinery.") '(#:phases (modify-phases %standard-phases (add-after 'unpack 'enter-subdirectory (lambda _ - (chdir "tools/power/cpupower"))) + (chdir "tools/power/cpupower") + #t)) (delete 'configure) (add-before 'build 'fix-makefiles (lambda _ @@ -3704,7 +3707,8 @@ from that to the system kernel's @file{/dev/random} machinery.") (("/usr/") "/") (("/bin/(install|pwd)" _ command) command)) (substitute* "bench/Makefile" - (("\\$\\(CC\\) -o") "$(CC) $(LDFLAGS) -o"))))) + (("\\$\\(CC\\) -o") "$(CC) $(LDFLAGS) -o")) + #t))) #:make-flags (let ((out (assoc-ref %outputs "out"))) (list (string-append "DESTDIR=" out) (string-append "LDFLAGS=-Wl,-rpath=" out "/lib") @@ -4016,9 +4020,11 @@ developers.") ;; getver.sh uses ‘git --describe’, isn't worth an extra git ;; dependency, and doesn't even work on release(!) tarballs. (add-after 'unpack 'report-correct-version - (lambda _ (substitute* "getver.sh" - (("ver=unknown") - (string-append "ver=" ,version))))) + (lambda _ + (substitute* "getver.sh" + (("ver=unknown") + (string-append "ver=" ,version))) + #t)) (delete 'configure)) ; no configure script #:make-flags (list "CC=gcc" (string-append "PREFIX=" %output)) @@ -4245,8 +4251,7 @@ Light is the successor of lightscript.") #t)) (replace 'install (lambda _ - (invoke "make" "install-tlp" "install-man") - #t)) + (invoke "make" "install-tlp" "install-man"))) (add-after 'install 'wrap (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((bin (string-append (assoc-ref outputs "out") "/bin")) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index d237a05a84..0d3bff9476 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2017 Roel Janssen <roel@gnu.org> ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -280,7 +281,8 @@ code analysis tools.") llvm-3.9.1 "16gc2gdmp5c800qvydrdhsp0bzb97s8wrakl6i8a4lgslnqnf2fk" '("clang-runtime-asan-build-fixes.patch" - "clang-runtime-esan-build-fixes.patch"))) + "clang-runtime-esan-build-fixes.patch" + "clang-3.5-libsanitizer-ustat-fix.patch"))) (define-public clang-3.9.1 (clang-from-llvm llvm-3.9.1 clang-runtime-3.9.1 @@ -304,7 +306,8 @@ code analysis tools.") (clang-runtime-from-llvm llvm-3.8 "0p0y85c7izndbpg2l816z7z7558axq11d5pwkm4h11sdw7d13w0d" - '("clang-runtime-asan-build-fixes.patch"))) + '("clang-runtime-asan-build-fixes.patch" + "clang-3.5-libsanitizer-ustat-fix.patch"))) (define-public clang-3.8 (clang-from-llvm llvm-3.8 clang-runtime-3.8 @@ -327,7 +330,8 @@ code analysis tools.") (clang-runtime-from-llvm llvm-3.7 "10c1mz2q4bdq9bqfgr3dirc6hz1h3sq8573srd5q5lr7m7j6jiwx" - '("clang-runtime-asan-build-fixes.patch"))) + '("clang-runtime-asan-build-fixes.patch" + "clang-3.5-libsanitizer-ustat-fix.patch"))) (define-public clang-3.7 (clang-from-llvm llvm-3.7 clang-runtime-3.7 diff --git a/gnu/packages/lsof.scm b/gnu/packages/lsof.scm index 8b3ebe2945..311e244608 100644 --- a/gnu/packages/lsof.scm +++ b/gnu/packages/lsof.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -77,6 +78,12 @@ #t)) (add-before 'check 'disable-failing-tests (lambda _ + ;; In libc 2.28, the 'major' and 'minor' macros are provided by + ;; <sys/sysmacros.h> only so include it. + (substitute* "tests/LTlib.c" + (("#ifndef lint") + "#include <sys/sysmacros.h>\n\n#ifndef lint")) + (substitute* "tests/Makefile" ;; Fails with ‘ERROR!!! client gethostbyaddr() failure’. (("(STDTST=.*) LTsock" _ prefix) prefix) diff --git a/gnu/packages/m4.scm b/gnu/packages/m4.scm index b223ce91d1..090f5578e3 100644 --- a/gnu/packages/m4.scm +++ b/gnu/packages/m4.scm @@ -32,6 +32,7 @@ (method url-fetch) (uri (string-append "mirror://gnu/m4/m4-" version ".tar.xz")) + (patches (search-patches "m4-gnulib-libio.patch")) (sha256 (base32 "01sfjd5a4waqw83bibvmn522g69qfqvwig9i2qlgy154l1nfihgj")))) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 09c525ff20..4b2447ece0 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -706,7 +706,7 @@ computing environments.") (define-public python-scikit-learn (package (name "python-scikit-learn") - (version "0.19.2") + (version "0.20.1") (source (origin (method git-fetch) @@ -716,9 +716,7 @@ computing environments.") (file-name (git-file-name name version)) (sha256 (base32 - "1dk9hdj01c0bny4ps78b7869fjw9gr6qklxf6wyql8h6nh4k19xm")) - (patches (search-patches - "python-scikit-learn-fix-test-non-determinism.patch")))) + "0qv7ir1fy9vjar3llc72yxmfja3gxm5icdf0y3q57vsn3wcdglkz")))) (build-system python-build-system) (arguments `(#:phases @@ -729,11 +727,11 @@ computing environments.") (lambda _ ;; Restrict OpenBLAS threads to prevent segfaults while testing! (setenv "OPENBLAS_NUM_THREADS" "1") - ;; Disable tests that require network access - (delete-file "sklearn/datasets/tests/test_mldata.py") - (delete-file "sklearn/datasets/tests/test_rcv1.py") - (invoke "pytest" "sklearn") - #t)) + + ;; Some tests require write access to $HOME. + (setenv "HOME" "/tmp") + + (invoke "pytest" "sklearn" "-m" "not network"))) ;; FIXME: This fails with permission denied (delete 'reset-gzip-timestamps)))) (inputs @@ -753,24 +751,7 @@ data analysis.") (license license:bsd-3))) (define-public python2-scikit-learn - (let ((parent (package-with-python2 python-scikit-learn))) - (package (inherit parent) - (arguments - (substitute-keyword-arguments (package-arguments parent) - ((#:phases phases) - `(modify-phases ,phases - (replace 'check - (lambda _ - ;; Restrict OpenBLAS threads to prevent segfaults while testing! - (setenv "OPENBLAS_NUM_THREADS" "1") - ;; Some tests expect to be able to write to HOME. - (setenv "HOME" "/tmp") - ;; Disable tests that require network access - (delete-file "sklearn/datasets/tests/test_kddcup99.py") - (delete-file "sklearn/datasets/tests/test_mldata.py") - (delete-file "sklearn/datasets/tests/test_rcv1.py") - (invoke "pytest" "sklearn") - #t))))))))) + (package-with-python2 python-scikit-learn)) (define-public python-autograd (let* ((commit "442205dfefe407beffb33550846434baa90c4de7") diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index fa545da3b2..74b1d489a3 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -2681,7 +2681,7 @@ replacement for the @code{urlview} program.") ("guile-fibers" ,guile-fibers) ("guile-json" ,guile-json) ("guile-syntax-highlight" ,guile-syntax-highlight) - ("guile" ,guile-2.2.4))) + ("guile" ,guile-2.2))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) diff --git a/gnu/packages/make-bootstrap.scm b/gnu/packages/make-bootstrap.scm index 475749bbf6..65d632f64e 100644 --- a/gnu/packages/make-bootstrap.scm +++ b/gnu/packages/make-bootstrap.scm @@ -22,7 +22,7 @@ (define-module (gnu packages make-bootstrap) #:use-module (guix utils) #:use-module (guix packages) - #:use-module (guix licenses) + #:use-module ((guix licenses) #:select (gpl3+)) #:use-module (guix build-system trivial) #:use-module (guix build-system gnu) #:use-module ((gnu packages) #:select (search-patch)) @@ -34,6 +34,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages guile) #:use-module (gnu packages bdw-gc) + #:use-module (gnu packages libunistring) #:use-module (gnu packages linux) #:use-module (gnu packages hurd) #:use-module (gnu packages multiprecision) @@ -440,6 +441,9 @@ for `sh' in $PATH, and without nscd, and with static NSS modules." "^gnu-user.*\\.h$")) ((" -lgcc_s}}") "}}")) #t))))))) + (inputs + `(("zlib:static" ,zlib "static") + ,@(package-inputs gcc))) (native-inputs (if (%current-target-system) `(;; When doing a Canadian cross, we need GMP/MPFR/MPC both @@ -525,6 +529,10 @@ for `sh' in $PATH, and without nscd, and with static NSS modules." ;; Remove the 'debug' output (see above for the reason.) (outputs (delete "debug" (package-outputs guile-2.2))) + (inputs + `(("libunistring:static" ,libunistring "static") + ,@(package-inputs guile-2.2))) + (propagated-inputs `(("bdw-gc" ,libgc) ,@(alist-delete "bdw-gc" diff --git a/gnu/packages/markup.scm b/gnu/packages/markup.scm index cdcfbc7898..20da258029 100644 --- a/gnu/packages/markup.scm +++ b/gnu/packages/markup.scm @@ -173,7 +173,8 @@ convert it to structurally valid XHTML (or HTML).") (string-append "OTHERLDFLAGS = -lmarkdown -Wl,-rpath=" (assoc-ref inputs "discount") - "/lib")))))))) + "/lib"))) + #t))))) (inputs `(("discount" ,discount))) (home-page diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 0cf8916abe..009b82f824 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -322,15 +322,15 @@ enough to be used effectively as a scientific calculator.") (define-public double-conversion (package (name "double-conversion") - (version "3.0.0") + (version "3.1.0") (home-page "https://github.com/google/double-conversion") (source (origin - (method url-fetch) - (uri (string-append home-page "/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference (url home-page) (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "059r1czs28ljjd388pn6l3njg1ghbf1cv3q9nkxv3dj2a8siabqm")))) + "123rb2p4snqagrybw66vnapchqdwn2rfpr1wcq0ya9gwbyl7xccx")))) (build-system cmake-build-system) (arguments '(#:test-target "test" @@ -2600,15 +2600,16 @@ YACC = bison -pscotchyy -y -b y (replace 'build (lambda _ - (and - (zero? (system* "make" - (format #f "-j~a" (parallel-job-count)) - "ptscotch" "ptesmumps")) - ;; Install the serial metis compatibility library - (zero? (system* "make" "-C" "libscotchmetis" "install"))))) - (replace - 'check - (lambda _ (zero? (system* "make" "ptcheck")))))))) + (invoke "make" (format #f "-j~a" (parallel-job-count)) + "ptscotch" "ptesmumps") + + ;; Install the serial metis compatibility library + (invoke "make" "-C" "libscotchmetis" "install"))) + (add-before 'check 'mpi-setup + ,%openmpi-setup) + (replace 'check + (lambda _ + (invoke "make" "ptcheck"))))))) (synopsis "Programs and libraries for graph algorithms (with MPI)"))) (define-public pt-scotch32 @@ -2622,15 +2623,15 @@ YACC = bison -pscotchyy -y -b y `(modify-phases ,scotch32-phases (replace 'build (lambda _ - (and - (zero? (system* "make" - (format #f "-j~a" (parallel-job-count)) - "ptscotch" "ptesmumps")) - ;; Install the serial metis compatibility library - (zero? (system* "make" "-C" "libscotchmetis" "install"))))) + (invoke "make" (format #f "-j~a" (parallel-job-count)) + "ptscotch" "ptesmumps") + ;; Install the serial metis compatibility library + (invoke "make" "-C" "libscotchmetis" "install"))) + (add-before 'check 'mpi-setup + ,%openmpi-setup) (replace 'check (lambda _ - (zero? (system* "make" "ptcheck")))))))) + (invoke "make" "ptcheck"))))))) (synopsis "Programs and libraries for graph algorithms (with MPI and 32-bit integers)"))) @@ -2971,7 +2972,7 @@ parts of it.") (define-public openblas (package (name "openblas") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) @@ -2980,7 +2981,7 @@ parts of it.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0b20km2jv7m6qiylrlvhq2vnmkmilb633mr8rhqmgbn1wqrp58jq")))) + "0cvlixnpc3cdvvn3f30phfvsgnqljqix6wn72ps9rj7xdhvw06jg")))) (build-system gnu-build-system) (arguments `(#:test-target "test" diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index b789d67f7f..fca26edcbb 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -716,6 +716,7 @@ audio and video).") (build-system scons-build-system) (arguments `(#:scons-flags (list (string-append "PREFIX=" %output)) + #:scons ,scons-python2 #:tests? #f)) ;no "check" target (inputs `(("boost" ,boost) diff --git a/gnu/packages/nettle.scm b/gnu/packages/nettle.scm index 67a3062a5a..1212f32812 100644 --- a/gnu/packages/nettle.scm +++ b/gnu/packages/nettle.scm @@ -44,8 +44,22 @@ ;; $libdir, which is not the case by default. Work around it. '(#:configure-flags (list (string-append "LDFLAGS=-Wl,-rpath=" (assoc-ref %outputs "out") - "/lib")))) - (outputs '("out" "debug")) + "/lib")) + #:phases (modify-phases %standard-phases + (add-after 'install 'move-static-libraries + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (slib (string-append (assoc-ref outputs "static") + "/lib"))) + (mkdir-p slib) + (with-directory-excursion (string-append out "/lib") + (for-each (lambda (ar) + (rename-file ar (string-append + slib "/" + (basename ar)))) + (find-files "." "\\.a$"))) + #t)))))) + (outputs '("out" "debug" "static")) (native-inputs `(("m4" ,m4))) (propagated-inputs `(("gmp" ,gmp))) (home-page "https://www.lysator.liu.se/~nisse/nettle/") diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 5504742fa8..a9e1576733 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -144,7 +144,8 @@ or, more generally, MAC addresses of the same category of hardware.") 'check 'disable-checkconf-test (lambda _ (substitute* "src/Makefile" - (("^TESTS = .*") "TESTS = \n"))))))) + (("^TESTS = .*") "TESTS = \n")) + #t))))) (home-page "http://www.remlab.net/miredo/") (synopsis "Teredo IPv6 tunneling software") (description @@ -216,7 +217,7 @@ libwrap.so: $(LIB_OBJ)\n (substitute* "scaffold.c" (("extern char .malloc.*;") "")) ;; This, believe it or not, is the recommended way to build! - (zero? (system* "make" "REAL_DAEMON_DIR=/etc" "linux")))) + (invoke "make" "REAL_DAEMON_DIR=/etc" "linux"))) ;; There is no make install stage, so we have to do it ourselves. (replace 'install (lambda _ @@ -251,7 +252,8 @@ libwrap.so: $(LIB_OBJ)\n (for-each (lambda (x) (install-file x (string-append out "/bin/"))) - bins))))))) + bins)) + #t))))) (home-page "http://www.porcupine.org") (synopsis "Monitor and filter incoming requests for network services") (description "With this package you can monitor and filter incoming requests for @@ -373,8 +375,8 @@ files contain direct mappings of the abstractions provided by the ØMQ C API.") ;; librdkafka++.so lacks RUNPATH for librdkafka.so (setenv "LDFLAGS" (string-append "-Wl,-rpath=" out "/lib")) - (zero? (system* "./configure" - (string-append "--prefix=" out))))))))) + (invoke "./configure" + (string-append "--prefix=" out)))))))) (native-inputs `(("python" ,python-wrapper))) (propagated-inputs @@ -457,7 +459,8 @@ Ethernet devices.") (bin (string-append out "/bin"))) (mkdir-p bin) (copy-file "ifstatus" - (string-append bin "/ifstatus")))))))) + (string-append bin "/ifstatus"))) + #t))))) (inputs `(("ncurses" ,ncurses))) (home-page "http://ifstatus.sourceforge.net/graphic/index.html") (synopsis "Text based network interface status monitor") @@ -511,14 +514,16 @@ and min/max network usage.") (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/tun.c" (("PATH=[^ ]* ") - (string-append (assoc-ref inputs "net-tools") "/bin/"))))) + (string-append (assoc-ref inputs "net-tools") "/bin/"))) + #t)) (add-before 'check 'delete-failing-tests ;; Avoid https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=802105. (lambda _ (substitute* "tests/common.c" (("tcase_add_test\\(tc, \ test_parse_format_ipv(4(|_listen_all|_mapped_ipv6)|6)\\);") - ""))))) + "")) + #t))) #:make-flags (list "CC=gcc" (string-append "prefix=" (assoc-ref %outputs "out"))) #:test-target "test")) @@ -779,7 +784,8 @@ application stack itself.") (("ENV_CURL_BIN.get\\('curl'\\)") (string-append "ENV_CURL_BIN.get('" (assoc-ref inputs "curl") - "/bin/curl')")))))))) + "/bin/curl')"))) + #t))))) (home-page "https://github.com/reorx/httpstat") (synopsis "Visualize curl statistics") (description @@ -949,7 +955,7 @@ private (reserved).") ,(string-append "PREFIX=" out) "INSTALLDIRS=site"))) (setenv "CONFIG_SHELL" (which "sh")) - (zero? (apply system* "perl" args)))))))) + (apply invoke "perl" args))))))) (home-page "https://metacpan.org/release/Socket6") (synopsis "IPv6 related part of the C socket.h defines and structure manipulators for Perl") @@ -1009,7 +1015,7 @@ offline emulation of DNS.") ,(string-append "PREFIX=" out) "INSTALLDIRS=site"))) (setenv "CONFIG_SHELL" (which "sh")) - (zero? (apply system* "perl" args)))))))) + (apply invoke "perl" args))))))) (home-page "https://metacpan.org/release/NetAddr-IP") (synopsis @@ -1145,7 +1151,7 @@ sockets in Perl.") (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "ctest" "-E" "url-test"))))))) + (invoke "ctest" "-E" "url-test")))))) (synopsis "Library providing automatic proxy configuration management") (description "Libproxy handles the details of HTTP/HTTPS proxy configuration for applications across all scenarios. Applications using @@ -1416,13 +1422,13 @@ procedure calls (RPCs).") (modify-phases %standard-phases (replace 'install (lambda _ - (zero? (system* "make" - ;; Don't try to create directories under /var. - "RUNDIR=/tmp" - "PKIDIR=/tmp" - "LOGDIR=/tmp" - "DBDIR=/tmp" - "install"))))))) + (invoke "make" + ;; Don't try to create directories under /var. + "RUNDIR=/tmp" + "PKIDIR=/tmp" + "LOGDIR=/tmp" + "DBDIR=/tmp" + "install")))))) (native-inputs `(("perl" ,perl) ("pkg-config" ,pkg-config) @@ -1723,8 +1729,8 @@ interface and a programmable text output for scripting.") (lambda _ (chdir "libnet") #t)) (add-before 'build 'build-doc (lambda* (#:key make-flags #:allow-other-keys) - (zero? (apply system* "make" "-C" "doc" "doc" - make-flags))))))) + (apply invoke "make" "-C" "doc" "doc" + make-flags)))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) diff --git a/gnu/packages/nfs.scm b/gnu/packages/nfs.scm index f6bb5b3b71..bdb36d272b 100644 --- a/gnu/packages/nfs.scm +++ b/gnu/packages/nfs.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 John Darrington <jmd@gnu.org> ;;; Copyright © 2017, 2018 Leo Famulari <leo@famulari.name> +;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -60,6 +61,13 @@ ,(string-append "--with-krb5=" (assoc-ref %build-inputs "mit-krb5"))) #:phases (modify-phases %standard-phases + (add-after 'unpack 'fix-glibc-compatability + (lambda _ + (substitute* '("utils/blkmapd/device-discovery.c" + "utils/blkmapd/dm-device.c") + (("<sys/stat.h>") + "<sys/stat.h>\n#include <sys/sysmacros.h>")) + #t)) (add-before 'configure 'adjust-command-file-names (lambda _ ;; Remove assumptions of FHS from start-statd script diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm index b525804bdb..a0221601dd 100644 --- a/gnu/packages/node.scm +++ b/gnu/packages/node.scm @@ -184,7 +184,7 @@ `(("c-ares" ,c-ares) ("http-parser" ,http-parser) ("icu4c" ,icu4c) - ("libuv" ,libuv) + ("libuv" ,libuv-1.19) ("nghttp2" ,nghttp2 "lib") ("openssl" ,openssl) ("zlib" ,zlib))) diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm index 962a9c8cfe..850223cd4c 100644 --- a/gnu/packages/openldap.scm +++ b/gnu/packages/openldap.scm @@ -84,11 +84,9 @@ (native-inputs `(("libtool" ,libtool))) (arguments `(#:tests? #f + #:configure-flags '("--disable-static") #:phases (modify-phases %standard-phases - (add-after 'configure 'provide-libtool - (lambda _ (copy-file (which "libtool") "libtool") - #t)) (add-after 'install 'patch-sasl-path ;; Give -L arguments for cyrus-sasl to avoid propagation. (lambda* (#:key inputs outputs #:allow-other-keys) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 64e05c4b0e..c07f011c9d 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -182,7 +182,7 @@ guidelines}.") ("python-pbr" ,python-pbr))) (native-inputs `(("python-openstackdocstheme" ,python-openstackdocstheme) - ("python-sphinx" ,python-sphinx-1.6) + ("python-sphinx" ,python-sphinx) ("python-subunit" ,python-subunit) ("python-testrepository" ,python-testrepository) ("python-testtools" ,python-testtools))) @@ -216,7 +216,7 @@ with mox as possible, but small enhancements have been made.") `(("python-dulwich" ,python-dulwich) ("python-pbr" ,python-pbr))) (native-inputs - `(("python-sphinx" ,python-sphinx-1.6))) + `(("python-sphinx" ,python-sphinx))) (home-page "https://docs.openstack.org/openstackdocstheme/latest/") (synopsis "OpenStack Docs Theme") (description @@ -313,7 +313,7 @@ to docs.openstack.org and developer.openstack.org.") ("python-six" ,python-six))) (native-inputs `(("python-mock" ,python-mock) - ("python-sphinx" ,python-sphinx-1.6) + ("python-sphinx" ,python-sphinx) ("python-testrepository" ,python-testrepository))) (home-page "https://github.com/dreamhost/stevedore") (synopsis "Manage dynamic plugins for Python applications") @@ -405,7 +405,7 @@ common features used in Tempest.") ("python-openstackdocstheme" ,python-openstackdocstheme) ("python-oslotest" ,python-oslotest) ("python-reno" ,python-reno) - ("python-sphinx" ,python-sphinx-1.6) + ("python-sphinx" ,python-sphinx) ("python-testrepository" ,python-testrepository) ("python-testscenarios" ,python-testscenarios) ("python-testtools" ,python-testtools))) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index dd83d75874..471a08b799 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -267,9 +267,7 @@ ("sqlite" ,sqlite) ("libgcrypt" ,libgcrypt) - ;; Use 2.2.4 to avoid various thread-safety issues while building - ;; code in parallel. - ("guile" ,guile-2.2.4) + ("guile" ,guile-2.2) ;; Many tests rely on the 'guile-bootstrap' package, which is why we ;; have it here. diff --git a/gnu/packages/patches/binutils-aarch64-symbol-relocation.patch b/gnu/packages/patches/binutils-aarch64-symbol-relocation.patch deleted file mode 100644 index fbd596862b..0000000000 --- a/gnu/packages/patches/binutils-aarch64-symbol-relocation.patch +++ /dev/null @@ -1,36 +0,0 @@ -Fix a regression in Binutils 2.30 where some symbols are incorrectly assumed -to be addresses: - -https://sourceware.org/bugzilla/show_bug.cgi?id=22764 - -Patch taken from upstream (with ChangeLog entries and tests omitted): - -https://sourceware.org/git/gitweb.cgi?p=binutils-gdb.git;a=commitdiff;h=279b2f94168ee91e02ccd070d27c983fc001fe12 - -diff --git a/bfd/elfnn-aarch64.c b/bfd/elfnn-aarch64.c -index af448f9..2737773 100644 ---- a/bfd/elfnn-aarch64.c -+++ b/bfd/elfnn-aarch64.c -@@ -7189,10 +7189,19 @@ elfNN_aarch64_check_relocs (bfd *abfd, struct bfd_link_info *info, - #if ARCH_SIZE == 64 - case BFD_RELOC_AARCH64_32: - #endif -- if (bfd_link_pic (info) -- && (sec->flags & SEC_ALLOC) != 0 -- && (sec->flags & SEC_READONLY) != 0) -+ if (bfd_link_pic (info) && (sec->flags & SEC_ALLOC) != 0) - { -+ if (h != NULL -+ /* This is an absolute symbol. It represents a value instead -+ of an address. */ -+ && ((h->root.type == bfd_link_hash_defined -+ && bfd_is_abs_section (h->root.u.def.section)) -+ /* This is an undefined symbol. */ -+ || h->root.type == bfd_link_hash_undefined)) -+ break; -+ -+ /* For local symbols, defined global symbols in a non-ABS section, -+ it is assumed that the value is an address. */ - int howto_index = bfd_r_type - BFD_RELOC_AARCH64_RELOC_START; - _bfd_error_handler - /* xgettext:c-format */ diff --git a/gnu/packages/patches/cairo-setjmp-wrapper.patch b/gnu/packages/patches/cairo-setjmp-wrapper.patch new file mode 100644 index 0000000000..bffac6e041 --- /dev/null +++ b/gnu/packages/patches/cairo-setjmp-wrapper.patch @@ -0,0 +1,78 @@ +Revert faulty commit to avoid undefined behaviour: +https://bugs.freedesktop.org/show_bug.cgi?id=104325 + +Taken from this upstream commit: +https://cgit.freedesktop.org/cairo/commit/?h=1.14&id=2acc4382c54bd8239361ceed14423412a343d311 + +diff --git a/src/cairo-bentley-ottmann-rectangular.c b/src/cairo-bentley-ottmann-rectangular.c +index cb2e30c..5541bdc 100644 +--- a/src/cairo-bentley-ottmann-rectangular.c ++++ b/src/cairo-bentley-ottmann-rectangular.c +@@ -593,12 +593,6 @@ sweep_line_insert (sweep_line_t *sweep, rectangle_t *rectangle) + pqueue_push (sweep, rectangle); + } + +-static int +-sweep_line_setjmp (sweep_line_t *sweep_line) +-{ +- return setjmp (sweep_line->unwind); +-} +- + static cairo_status_t + _cairo_bentley_ottmann_tessellate_rectangular (rectangle_t **rectangles, + int num_rectangles, +@@ -615,7 +609,7 @@ _cairo_bentley_ottmann_tessellate_rectangular (rectangle_t **rectangles, + rectangles, num_rectangles, + fill_rule, + do_traps, container); +- if ((status = sweep_line_setjmp (&sweep_line))) ++ if ((status = setjmp (sweep_line.unwind))) + return status; + + rectangle = rectangle_pop_start (&sweep_line); +diff --git a/src/cairo-png.c b/src/cairo-png.c +index e64b14a..068617d 100644 +--- a/src/cairo-png.c ++++ b/src/cairo-png.c +@@ -158,14 +158,6 @@ png_simple_warning_callback (png_structp png, + */ + } + +-static int +-png_setjmp (png_struct *png) +-{ +-#ifdef PNG_SETJMP_SUPPORTED +- return setjmp (png_jmpbuf (png)); +-#endif +- return 0; +-} + + /* Starting with libpng-1.2.30, we must explicitly specify an output_flush_fn. + * Otherwise, we will segfault if we are writing to a stream. */ +@@ -237,8 +229,10 @@ write_png (cairo_surface_t *surface, + goto BAIL4; + } + +- if (png_setjmp (png)) ++#ifdef PNG_SETJMP_SUPPORTED ++ if (setjmp (png_jmpbuf (png))) + goto BAIL4; ++#endif + + png_set_write_fn (png, closure, write_func, png_simple_output_flush_fn); + +@@ -577,11 +571,12 @@ read_png (struct png_read_closure_t *png_closure) + png_set_read_fn (png, png_closure, stream_read_func); + + status = CAIRO_STATUS_SUCCESS; +- +- if (png_setjmp (png)) { ++#ifdef PNG_SETJMP_SUPPORTED ++ if (setjmp (png_jmpbuf (png))) { + surface = _cairo_surface_create_in_error (status); + goto BAIL; + } ++#endif + + png_read_info (png, info); + diff --git a/gnu/packages/patches/casync-renameat2-declaration.patch b/gnu/packages/patches/casync-renameat2-declaration.patch new file mode 100644 index 0000000000..74c2ca7b3c --- /dev/null +++ b/gnu/packages/patches/casync-renameat2-declaration.patch @@ -0,0 +1,27 @@ +Fix build failure on glibc 2.28 where 'renameat2' would end up being +declared twice: <https://github.com/systemd/casync/issues/166>. + +From 625244ca47e8ee1375d2d0092271bfd13b0913ea Mon Sep 17 00:00:00 2001 +From: Daniel Mack <daniel@zonque.org> +Date: Tue, 13 Nov 2018 17:52:48 +0100 +Subject: [PATCH] meson.build: pass -D_GNU_SOURCE when checking for functions + +As described in #166, -D_GNU_SOURCE needs to be passed to the meson function +availability checker. h/t to @tomeon for providing a link to the solution as +well. +--- + meson.build | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/meson.build b/meson.build +index f42ed16..c0f741e 100644 +--- a/meson.build ++++ b/meson.build +@@ -78,6 +78,6 @@ foreach ident : [ + ['copy_file_range', '''#include <sys/syscall.h> + #include <unistd.h>'''], + ] +- have = cc.has_function(ident[0], prefix : ident[1]) ++ have = cc.has_function(ident[0], args : '-D_GNU_SOURCE', prefix : ident[1]) + conf.set10('HAVE_' + ident[0].to_upper(), have) + endforeach diff --git a/gnu/packages/patches/ceph-detect-rocksdb.patch b/gnu/packages/patches/ceph-detect-rocksdb.patch new file mode 100644 index 0000000000..badad6d1b9 --- /dev/null +++ b/gnu/packages/patches/ceph-detect-rocksdb.patch @@ -0,0 +1,24 @@ +Help the build system find system RocksDB. + +Taken from this upstream commit: +https://github.com/ceph/ceph/commit/2ac26bd0e01fd6c82bd59936cf25c25173f7775a + +diff --git a/cmake/modules/Findrocksdb.cmake b/cmake/modules/Findrocksdb.cmake +index f8369f73fc..5926647348 100644 +--- a/cmake/modules/Findrocksdb.cmake ++++ b/cmake/modules/Findrocksdb.cmake +@@ -15,11 +15,11 @@ find_library(ROCKSDB_LIBRARIES rocksdb) + + if(ROCKSDB_INCLUDE_DIR AND EXISTS "${ROCKSDB_INCLUDE_DIR}/rocksdb/version.h") + foreach(ver "MAJOR" "MINOR" "PATCH") +- file(STRINGS "${ROCKSDB_INCLUDE_DIR}/version.h" ROCKSDB_VER_${ver}_LINE ++ file(STRINGS "${ROCKSDB_INCLUDE_DIR}/rocksdb/version.h" ROCKSDB_VER_${ver}_LINE + REGEX "^#define[ \t]+ROCKSDB_${ver}[ \t]+[0-9]+$") + string(REGEX REPLACE "^#define[ \t]+ROCKSDB_${ver}[ \t]+([0-9]+)$" +- "\\1" ROCKSDB_VERSION_${ver} "${ROCKDB_VER_${ver}_LINE}") +- unset(${ROCKDB_VER_${ver}_LINE}) ++ "\\1" ROCKSDB_VERSION_${ver} "${ROCKSDB_VER_${ver}_LINE}") ++ unset(${ROCKSDB_VER_${ver}_LINE}) + endforeach() + set(ROCKSDB_VERSION_STRING + "${ROCKSDB_VERSION_MAJOR}.${ROCKSDB_VERSION_MINOR}.${ROCKSDB_VERSION_PATCH}") diff --git a/gnu/packages/patches/ceph-rocksdb-compat.patch b/gnu/packages/patches/ceph-rocksdb-compat.patch deleted file mode 100644 index 1a3c6b0b23..0000000000 --- a/gnu/packages/patches/ceph-rocksdb-compat.patch +++ /dev/null @@ -1,63 +0,0 @@ -Fix compatibility with newer versions of RocksDB. - -Adapted from this upstream patch, with some additional changes for 12.2: -https://github.com/ceph/ceph/commit/9d73a7121fdb1ae87cb1aa6f7d9d7a13f329ae68 - -diff --git a/src/kv/RocksDBStore.cc b/src/kv/RocksDBStore.cc -index 8660afe1886d..bc0de79e23cb 100644 ---- a/src/kv/RocksDBStore.cc -+++ b/src/kv/RocksDBStore.cc -@@ -505,7 +505,7 @@ - // considering performance overhead, default is disabled - if (g_conf->rocksdb_perf) { - rocksdb::SetPerfLevel(rocksdb::PerfLevel::kEnableTimeExceptForMutex); -- rocksdb::perf_context.Reset(); -+ rocksdb::get_perf_context()->Reset(); - } - - RocksDBTransactionImpl * _t = -@@ -532,13 +532,13 @@ - utime_t write_wal_time; - utime_t write_pre_and_post_process_time; - write_wal_time.set_from_double( -- static_cast<double>(rocksdb::perf_context.write_wal_time)/1000000000); -+ static_cast<double>(rocksdb::get_perf_context()->write_wal_time)/1000000000); - write_memtable_time.set_from_double( -- static_cast<double>(rocksdb::perf_context.write_memtable_time)/1000000000); -+ static_cast<double>(rocksdb::get_perf_context()->write_memtable_time)/1000000000); - write_delay_time.set_from_double( -- static_cast<double>(rocksdb::perf_context.write_delay_time)/1000000000); -+ static_cast<double>(rocksdb::get_perf_context()->write_delay_time)/1000000000); - write_pre_and_post_process_time.set_from_double( -- static_cast<double>(rocksdb::perf_context.write_pre_and_post_process_time)/1000000000); -+ static_cast<double>(rocksdb::get_perf_context()->write_pre_and_post_process_time)/1000000000); - logger->tinc(l_rocksdb_write_memtable_time, write_memtable_time); - logger->tinc(l_rocksdb_write_delay_time, write_delay_time); - logger->tinc(l_rocksdb_write_wal_time, write_wal_time); -@@ -558,7 +558,7 @@ - // considering performance overhead, default is disabled - if (g_conf->rocksdb_perf) { - rocksdb::SetPerfLevel(rocksdb::PerfLevel::kEnableTimeExceptForMutex); -- rocksdb::perf_context.Reset(); -+ rocksdb::get_perf_context()->Reset(); - } - - RocksDBTransactionImpl * _t = -@@ -586,13 +586,13 @@ - utime_t write_wal_time; - utime_t write_pre_and_post_process_time; - write_wal_time.set_from_double( -- static_cast<double>(rocksdb::perf_context.write_wal_time)/1000000000); -+ static_cast<double>(rocksdb::get_perf_context()->write_wal_time)/1000000000); - write_memtable_time.set_from_double( -- static_cast<double>(rocksdb::perf_context.write_memtable_time)/1000000000); -+ static_cast<double>(rocksdb::get_perf_context()->write_memtable_time)/1000000000); - write_delay_time.set_from_double( -- static_cast<double>(rocksdb::perf_context.write_delay_time)/1000000000); -+ static_cast<double>(rocksdb::get_perf_context()->write_delay_time)/1000000000); - write_pre_and_post_process_time.set_from_double( -- static_cast<double>(rocksdb::perf_context.write_pre_and_post_process_time)/1000000000); -+ static_cast<double>(rocksdb::get_perf_context()->write_pre_and_post_process_time)/1000000000); - logger->tinc(l_rocksdb_write_memtable_time, write_memtable_time); - logger->tinc(l_rocksdb_write_delay_time, write_delay_time); - logger->tinc(l_rocksdb_write_wal_time, write_wal_time); diff --git a/gnu/packages/patches/ceph-skip-unittest_blockdev.patch b/gnu/packages/patches/ceph-skip-unittest_blockdev.patch index 43b9984862..407bd93278 100644 --- a/gnu/packages/patches/ceph-skip-unittest_blockdev.patch +++ b/gnu/packages/patches/ceph-skip-unittest_blockdev.patch @@ -4,25 +4,21 @@ This test tries to walk a sysfs path and hits a null pointer exception. Expected: (dir) != (nullptr), actual: NULL vs 8-byte object <00-00 00-00 00-00 00-00> diff --git a/src/test/common/CMakeLists.txt b/src/test/common/CMakeLists.txt -index 5172663898..ac84085eaa 100644 --- a/src/test/common/CMakeLists.txt +++ b/src/test/common/CMakeLists.txt -@@ -12,15 +12,6 @@ target_link_libraries(get_command_descriptions +@@ -12,15 +12,6 @@ ${CMAKE_DL_LIBS} ) -if(HAVE_BLKID) --# unittest_blkdev --add_executable(unittest_blkdev -- test_blkdev.cc -- ) --add_ceph_unittest(unittest_blkdev ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/unittest_blkdev) --target_link_libraries(unittest_blkdev global ${BLKID_LIBRARIES}) --endif(HAVE_BLKID) +- # unittest_blkdev +- add_executable(unittest_blkdev +- test_blkdev.cc +- ) +- add_ceph_unittest(unittest_blkdev) +- target_link_libraries(unittest_blkdev ceph-common ${BLKID_LIBRARIES}) +-endif() - # unittest_bloom_filter add_executable(unittest_bloom_filter test_bloom_filter.cc --- -2.11.1 - diff --git a/gnu/packages/patches/ceph-volume-respect-PATH.patch b/gnu/packages/patches/ceph-volume-respect-PATH.patch new file mode 100644 index 0000000000..08a9a15ddd --- /dev/null +++ b/gnu/packages/patches/ceph-volume-respect-PATH.patch @@ -0,0 +1,22 @@ +Look for required tools in $PATH instead of just a handful locations. + +diff --git a/src/ceph-volume/ceph_volume/util/system.py b/src/ceph-volume/ceph_volume/util/system.py +index b637f023a4..14516e1c65 100644 +--- a/src/ceph-volume/ceph_volume/util/system.py ++++ b/src/ceph-volume/ceph_volume/util/system.py +@@ -33,14 +33,7 @@ def generate_uuid(): + + def which(executable): + """find the location of an executable""" +- locations = ( +- '/usr/local/bin', +- '/bin', +- '/usr/bin', +- '/usr/local/sbin', +- '/usr/sbin', +- '/sbin', +- ) ++ locations = os.getenv('PATH').split(':') + + for location in locations: + executable_path = os.path.join(location, executable) diff --git a/gnu/packages/patches/clang-3.5-libsanitizer-ustat-fix.patch b/gnu/packages/patches/clang-3.5-libsanitizer-ustat-fix.patch new file mode 100644 index 0000000000..cfb09a8ce3 --- /dev/null +++ b/gnu/packages/patches/clang-3.5-libsanitizer-ustat-fix.patch @@ -0,0 +1,46 @@ +From d9d97cac3702b99a00cd113de98c41eb535d47ed Mon Sep 17 00:00:00 2001 +From: Efraim Flashner <efraim@flashner.co.il> +Date: Sun, 14 Oct 2018 12:11:30 +0300 +Subject: [PATCH] patch modified from the gcc patch series, also dealing with + ustat. + +--- + .../sanitizer_platform_limits_posix.cc | 15 +++++++++++++-- + 1 file changed, 13 insertions(+), 2 deletions(-) + +diff --git a/lib/sanitizer_common/sanitizer_platform_limits_posix.cc b/lib/sanitizer_common/sanitizer_platform_limits_posix.cc +index 29fea6e..570b9a5 100644 +--- a/lib/sanitizer_common/sanitizer_platform_limits_posix.cc ++++ b/lib/sanitizer_common/sanitizer_platform_limits_posix.cc +@@ -129,7 +129,6 @@ + #include <sys/statvfs.h> + #include <sys/timex.h> + #include <sys/user.h> +-#include <sys/ustat.h> + #include <linux/cyclades.h> + #include <linux/if_eql.h> + #include <linux/if_plip.h> +@@ -222,7 +221,19 @@ namespace __sanitizer { + #endif // SANITIZER_LINUX || SANITIZER_FREEBSD + + #if SANITIZER_LINUX && !SANITIZER_ANDROID +- unsigned struct_ustat_sz = sizeof(struct ustat); ++ // Use pre-computed size of struct ustat to avoid <sys/ustat.h> which ++ // has been removed from glibc 2.28. ++#if defined(__aarch64__) || defined(__s390x__) || defined (__mips64) \ ++ || defined(__powerpc64__) || defined(__arch64__) || defined(__sparcv9) \ ++ || defined(__x86_64__) ++#define SIZEOF_STRUCT_USTAT 32 ++#elif defined(__arm__) || defined(__i386__) || defined(__mips__) \ ++ || defined(__powerpc__) || defined(__s390__) ++#define SIZEOF_STRUCT_USTAT 20 ++#else ++#error Unknown size of struct ustat ++#endif ++ unsigned struct_ustat_sz = SIZEOF_STRUCT_USTAT; + unsigned struct_rlimit64_sz = sizeof(struct rlimit64); + unsigned struct_statvfs64_sz = sizeof(struct statvfs64); + #endif // SANITIZER_LINUX && !SANITIZER_ANDROID +-- +2.19.1 + diff --git a/gnu/packages/patches/doxygen-gcc-ice.patch b/gnu/packages/patches/doxygen-gcc-ice.patch deleted file mode 100644 index fbfedcb7ab..0000000000 --- a/gnu/packages/patches/doxygen-gcc-ice.patch +++ /dev/null @@ -1,25 +0,0 @@ -Work around this GCC ICE: <https://bugs.gnu.org/31708>. It shows up -only when doing native compiles on armhf-linux. - -Yes it's a terrible patch, but it does the job. - ---- doxygen-1.8.13/qtools/qutfcodec.cpp 1970-01-01 01:00:00.000000000 +0100 -+++ doxygen-1.8.13/qtools/qutfcodec.cpp 2018-06-08 14:14:29.614009929 +0200 -@@ -189,7 +189,7 @@ int QUtf16Codec::heuristicContentMatch(c - } - - -- -+volatile const void *bomPointer = &QChar::byteOrderMark; - - class QUtf16Encoder : public QTextEncoder { - bool headerdone; -@@ -209,7 +209,7 @@ public: - headerdone = TRUE; - len_in_out = (1+uc.length())*(int)sizeof(QChar); - QCString d(len_in_out); -- memcpy(d.rawData(),&QChar::byteOrderMark,sizeof(QChar)); -+ memcpy(d.rawData(),(void *)bomPointer,sizeof(QChar)); - memcpy(d.rawData()+sizeof(QChar),uc.unicode(),uc.length()*sizeof(QChar)); - return d; - } diff --git a/gnu/packages/patches/emacs-pdf-tools-poppler.patch b/gnu/packages/patches/emacs-pdf-tools-poppler.patch new file mode 100644 index 0000000000..0477508fa9 --- /dev/null +++ b/gnu/packages/patches/emacs-pdf-tools-poppler.patch @@ -0,0 +1,41 @@ +Fix build issue with recent Poppler: + <https://github.com/politza/pdf-tools/issues/372>. + +This combines upstream commits +6cd76dec9aece2a8daa90f17ab77fbf773157a1d..50a5297b82e26cfd52f6c00645ddc1057099d6a7 +for this file. + +diff --git a/server/poppler-hack.cc b/server/poppler-hack.cc +index 0c62f73..427f9df 100644 +--- a/server/poppler-hack.cc ++++ b/server/poppler-hack.cc +@@ -51,7 +51,10 @@ GType poppler_annot_markup_get_type (void) G_GNUC_CONST; + double y2; + }; + +- char *_xpoppler_goo_string_to_utf8(GooString *s) ++ // This function does not modify its argument s, but for ++ // compatibility reasons (e.g. getLength in GooString.h before 2015) ++ // with older poppler code, it can't be declared as such. ++ char *_xpoppler_goo_string_to_utf8(/* const */ GooString *s) + { + char *result; + +@@ -85,7 +88,7 @@ GType poppler_annot_markup_get_type (void) G_GNUC_CONST; + // Set the rectangle of an annotation. It was first added in v0.26. + void xpoppler_annot_set_rectangle (PopplerAnnot *a, PopplerRectangle *rectangle) + { +- GooString *state = a->annot->getAppearState (); ++ GooString *state = (GooString*) a->annot->getAppearState (); + char *ustate = _xpoppler_goo_string_to_utf8 (state); + + a->annot->setRect (rectangle->x1, rectangle->y1, +@@ -105,7 +108,7 @@ GType poppler_annot_markup_get_type (void) G_GNUC_CONST; + g_return_val_if_fail (POPPLER_IS_ANNOT_MARKUP (poppler_annot), NULL); + + annot = static_cast<AnnotMarkup *>(POPPLER_ANNOT (poppler_annot)->annot); +- text = annot->getDate (); ++ text = (GooString*) annot->getDate (); + + return text ? _xpoppler_goo_string_to_utf8 (text) : NULL; + } diff --git a/gnu/packages/patches/findutils-gnulib-libio.patch b/gnu/packages/patches/findutils-gnulib-libio.patch new file mode 100644 index 0000000000..79f9fd914d --- /dev/null +++ b/gnu/packages/patches/findutils-gnulib-libio.patch @@ -0,0 +1,114 @@ +Adjust to removal of libio interface in glibc 2.28. + +Based on this gnulib commit: +https://git.savannah.gnu.org/cgit/gnulib.git/commit/?id=4af4a4a71827c0bc5e0ec67af23edef4f15cee8e + +diff --git a/gl/lib/fflush.c b/gl/lib/fflush.c +index 5ae3e41..7a82470 100644 +--- a/gl/lib/fflush.c ++++ b/gl/lib/fflush.c +@@ -33,7 +33,7 @@ + #undef fflush + + +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + + /* Clear the stream's ungetc buffer, preserving the value of ftello (fp). */ + static void +@@ -72,7 +72,7 @@ clear_ungetc_buffer (FILE *fp) + + #endif + +-#if ! (defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */) ++#if ! (defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */) + + # if (defined __sferror || defined __DragonFly__ || defined __ANDROID__) && defined __SNPT + /* FreeBSD, NetBSD, OpenBSD, DragonFly, Mac OS X, Cygwin, Android */ +@@ -148,7 +148,7 @@ rpl_fflush (FILE *stream) + if (stream == NULL || ! freading (stream)) + return fflush (stream); + +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + + clear_ungetc_buffer_preserving_position (stream); + +diff --git a/gl/lib/fpurge.c b/gl/lib/fpurge.c +index f313b22..ecdf82d 100644 +--- a/gl/lib/fpurge.c ++++ b/gl/lib/fpurge.c +@@ -62,7 +62,7 @@ fpurge (FILE *fp) + /* Most systems provide FILE as a struct and the necessary bitmask in + <stdio.h>, because they need it for implementing getc() and putc() as + fast macros. */ +-# if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++# if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + fp->_IO_read_end = fp->_IO_read_ptr; + fp->_IO_write_ptr = fp->_IO_write_base; + /* Avoid memory leak when there is an active ungetc buffer. */ +diff --git a/gl/lib/freadahead.c b/gl/lib/freadahead.c +index 094daab..3f8101e 100644 +--- a/gl/lib/freadahead.c ++++ b/gl/lib/freadahead.c +@@ -25,7 +25,7 @@ + size_t + freadahead (FILE *fp) + { +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + if (fp->_IO_write_ptr > fp->_IO_write_base) + return 0; + return (fp->_IO_read_end - fp->_IO_read_ptr) +diff --git a/gl/lib/freading.c b/gl/lib/freading.c +index 0512b19..8c48fe4 100644 +--- a/gl/lib/freading.c ++++ b/gl/lib/freading.c +@@ -31,7 +31,7 @@ freading (FILE *fp) + /* Most systems provide FILE as a struct and the necessary bitmask in + <stdio.h>, because they need it for implementing getc() and putc() as + fast macros. */ +-# if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++# if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + return ((fp->_flags & _IO_NO_WRITES) != 0 + || ((fp->_flags & (_IO_NO_READS | _IO_CURRENTLY_PUTTING)) == 0 + && fp->_IO_read_base != NULL)); +diff --git a/gl/lib/fseeko.c b/gl/lib/fseeko.c +index 1c65d2a..9026408 100644 +--- a/gl/lib/fseeko.c ++++ b/gl/lib/fseeko.c +@@ -47,7 +47,7 @@ fseeko (FILE *fp, off_t offset, int whence) + #endif + + /* These tests are based on fpurge.c. */ +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + if (fp->_IO_read_end == fp->_IO_read_ptr + && fp->_IO_write_ptr == fp->_IO_write_base + && fp->_IO_save_base == NULL) +@@ -123,7 +123,7 @@ fseeko (FILE *fp, off_t offset, int whence) + return -1; + } + +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + fp->_flags &= ~_IO_EOF_SEEN; + fp->_offset = pos; + #elif defined __sferror || defined __DragonFly__ || defined __ANDROID__ +diff --git a/gl/lib/stdio-impl.h b/gl/lib/stdio-impl.h +index 502d891..ea38ee2 100644 +--- a/gl/lib/stdio-impl.h ++++ b/gl/lib/stdio-impl.h +@@ -18,6 +18,12 @@ + the same implementation of stdio extension API, except that some fields + have different naming conventions, or their access requires some casts. */ + ++/* Glibc 2.28 made _IO_IN_BACKUP private. For now, work around this ++ problem by defining it ourselves. FIXME: Do not rely on glibc ++ internals. */ ++#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN ++# define _IO_IN_BACKUP 0x100 ++#endif + + /* BSD stdio derived implementations. */ + diff --git a/gnu/packages/patches/findutils-makedev.patch b/gnu/packages/patches/findutils-makedev.patch new file mode 100644 index 0000000000..2f16c625d8 --- /dev/null +++ b/gnu/packages/patches/findutils-makedev.patch @@ -0,0 +1,22 @@ +Include <sys/sysmacros.h> for "makedev". + +Taken from this gnulib commit: +https://git.savannah.gnu.org/cgit/gnulib.git/commit/?id=4da63c5881f60f71999a943612da9112232b9161 + +diff --git a/gl/lib/mountlist.c b/gl/lib/mountlist.c +index bb4e4ee21..cf4020e2a 100644 +--- a/gl/lib/mountlist.c ++++ b/gl/lib/mountlist.c +@@ -37,6 +37,12 @@ + # include <sys/param.h> + #endif + ++#if MAJOR_IN_MKDEV ++# include <sys/mkdev.h> ++#elif MAJOR_IN_SYSMACROS ++# include <sys/sysmacros.h> ++#endif ++ + #if defined MOUNTED_GETFSSTAT /* OSF_1 and Darwin1.3.x */ + # if HAVE_SYS_UCRED_H + # include <grp.h> /* needed on OSF V4.0 for definition of NGROUPS, diff --git a/gnu/packages/patches/freetype-CVE-2018-6942.patch b/gnu/packages/patches/freetype-CVE-2018-6942.patch deleted file mode 100644 index 680f357765..0000000000 --- a/gnu/packages/patches/freetype-CVE-2018-6942.patch +++ /dev/null @@ -1,31 +0,0 @@ -Fix CVE-2018-6942: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-6942 -https://people.canonical.com/~ubuntu-security/cve/2018/CVE-2018-6942.html - -Copied from upstream (ChangeLog section removed): -https://git.savannah.gnu.org/cgit/freetype/freetype2.git/commit/?id=29c759284e305ec428703c9a5831d0b1fc3497ef - -diff --git a/src/truetype/ttinterp.c b/src/truetype/ttinterp.c -index d855aaa..551f14a 100644 ---- a/src/truetype/ttinterp.c -+++ b/src/truetype/ttinterp.c -@@ -7532,8 +7532,16 @@ - return; - } - -- for ( i = 0; i < num_axes; i++ ) -- args[i] = coords[i] >> 2; /* convert 16.16 to 2.14 format */ -+ if ( coords ) -+ { -+ for ( i = 0; i < num_axes; i++ ) -+ args[i] = coords[i] >> 2; /* convert 16.16 to 2.14 format */ -+ } -+ else -+ { -+ for ( i = 0; i < num_axes; i++ ) -+ args[i] = 0; -+ } - } - - diff --git a/gnu/packages/patches/gcc-4.9-libsanitizer-ustat.patch b/gnu/packages/patches/gcc-4.9-libsanitizer-ustat.patch new file mode 100644 index 0000000000..795881ab9b --- /dev/null +++ b/gnu/packages/patches/gcc-4.9-libsanitizer-ustat.patch @@ -0,0 +1,37 @@ +Remove use of deprecated ustat interface in glibc 2.28: +https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85835 + +Adapted to GCC 4 series from this upstream patch: +https://gcc.gnu.org/viewcvs/gcc?view=revision&revision=260684 + +--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc ++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc +@@ -81,7 +81,6 @@ + #include <sys/statvfs.h> + #include <sys/timex.h> + #include <sys/user.h> +-#include <sys/ustat.h> + #include <linux/cyclades.h> + #include <linux/if_eql.h> + #include <linux/if_plip.h> +@@ -163,7 +162,19 @@ + unsigned struct_old_utsname_sz = sizeof(struct old_utsname); + unsigned struct_oldold_utsname_sz = sizeof(struct oldold_utsname); + unsigned struct_itimerspec_sz = sizeof(struct itimerspec); +- unsigned struct_ustat_sz = sizeof(struct ustat); ++ // Use pre-computed size of struct ustat to avoid <sys/ustat.h> which ++ // has been removed from glibc 2.28. ++#if defined(__aarch64__) || defined(__s390x__) || defined (__mips64) \ ++ || defined(__powerpc64__) || defined(__arch64__) || defined(__sparcv9) \ ++ || defined(__x86_64__) ++#define SIZEOF_STRUCT_USTAT 32 ++#elif defined(__arm__) || defined(__i386__) || defined(__mips__) \ ++ || defined(__powerpc__) || defined(__s390__) ++#define SIZEOF_STRUCT_USTAT 20 ++#else ++#error Unknown size of struct ustat ++#endif ++ unsigned struct_ustat_sz = SIZEOF_STRUCT_USTAT; + #endif // SANITIZER_LINUX + + #if SANITIZER_LINUX && !SANITIZER_ANDROID diff --git a/gnu/packages/patches/gcc-libsanitizer-ustat.patch b/gnu/packages/patches/gcc-libsanitizer-ustat.patch new file mode 100644 index 0000000000..a4e0c6affa --- /dev/null +++ b/gnu/packages/patches/gcc-libsanitizer-ustat.patch @@ -0,0 +1,41 @@ +Remove use of deprecated ustat interface in glibc 2.28: + +https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85835 + +Taken from upstream: + +https://gcc.gnu.org/viewcvs/gcc?view=revision&revision=260684 + +diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc +index 858bb2184505..de18e56d11cf 100644 +--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc ++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc +@@ -157,7 +157,6 @@ typedef struct user_fpregs elf_fpregset_t; + # include <sys/procfs.h> + #endif + #include <sys/user.h> +-#include <sys/ustat.h> + #include <linux/cyclades.h> + #include <linux/if_eql.h> + #include <linux/if_plip.h> +@@ -250,7 +249,19 @@ namespace __sanitizer { + #endif // SANITIZER_LINUX || SANITIZER_FREEBSD + + #if SANITIZER_LINUX && !SANITIZER_ANDROID +- unsigned struct_ustat_sz = sizeof(struct ustat); ++ // Use pre-computed size of struct ustat to avoid <sys/ustat.h> which ++ // has been removed from glibc 2.28. ++#if defined(__aarch64__) || defined(__s390x__) || defined (__mips64) \ ++ || defined(__powerpc64__) || defined(__arch64__) || defined(__sparcv9) \ ++ || defined(__x86_64__) ++#define SIZEOF_STRUCT_USTAT 32 ++#elif defined(__arm__) || defined(__i386__) || defined(__mips__) \ ++ || defined(__powerpc__) || defined(__s390__) ++#define SIZEOF_STRUCT_USTAT 20 ++#else ++#error Unknown size of struct ustat ++#endif ++ unsigned struct_ustat_sz = SIZEOF_STRUCT_USTAT; + unsigned struct_rlimit64_sz = sizeof(struct rlimit64); + unsigned struct_statvfs64_sz = sizeof(struct statvfs64); + #endif // SANITIZER_LINUX && !SANITIZER_ANDROID diff --git a/gnu/packages/patches/gcc-strmov-store-file-names.patch b/gnu/packages/patches/gcc-strmov-store-file-names.patch index 9f9162855d..7358de3326 100644 --- a/gnu/packages/patches/gcc-strmov-store-file-names.patch +++ b/gnu/packages/patches/gcc-strmov-store-file-names.patch @@ -15,7 +15,7 @@ and <https://bugs.gnu.org/30395>. --- gcc-5.3.0/gcc/builtins.c 2016-10-18 10:50:46.080616285 +0200 +++ gcc-5.3.0/gcc/builtins.c 2016-11-09 15:26:43.693042737 +0100 -@@ -3192,6 +3192,54 @@ determine_block_size (tree len, rtx len_ +@@ -3192,6 +3192,58 @@ determine_block_size (tree len, rtx len_ GET_MODE_MASK (GET_MODE (len_rtx))); } @@ -35,9 +35,13 @@ and <https://bugs.gnu.org/30395>. + if (TREE_CODE (str) == VAR_DECL + && TREE_STATIC (str) + && TREE_READONLY (str)) -+ /* STR may be a 'static const' variable whose initial value -+ is a string constant. See <https://bugs.gnu.org/30395>. */ -+ str = DECL_INITIAL (str); ++ { ++ /* STR may be a 'static const' variable whose initial value ++ is a string constant. See <https://bugs.gnu.org/30395>. */ ++ str = DECL_INITIAL (str); ++ if (str == NULL_TREE) ++ return false; ++ } + + if (TREE_CODE (str) != STRING_CST) + return false; diff --git a/gnu/packages/patches/ghostscript-runpath.patch b/gnu/packages/patches/ghostscript-runpath.patch deleted file mode 100644 index 9f161e45b3..0000000000 --- a/gnu/packages/patches/ghostscript-runpath.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/base/unix-dll.mak b/base/unix-dll.mak -index 9d57a99..36ef1ff 100644 ---- a/base/unix-dll.mak -+++ b/base/unix-dll.mak -@@ -171,11 +171,11 @@ gpdl-so-links-subtarget: $(GPDL_SO) $(UNIX_DLL_MAK) $(MAKEDIRS) - # Build the small Ghostscript loaders, with Gtk+ and without - $(GSSOC_XE): gs-so-links-subtarget $(PSSRC)$(SOC_LOADER) $(UNIX_DLL_MAK) $(MAKEDIRS) - $(GLCC) -g -o $(GSSOC_XE) $(PSSRC)dxmainc.c \ -- -L$(BINDIR) -l$(GS_SO_BASE) -+ -L$(BINDIR) -l$(GS_SO_BASE) -Wl,-rpath=$(libdir) - - $(GSSOX_XE): gs-so-links-subtarget $(PSSRC)$(SOC_LOADER) $(UNIX_DLL_MAK) $(MAKEDIRS) - $(GLCC) -g $(SOC_CFLAGS) -o $(GSSOX_XE) $(PSSRC)$(SOC_LOADER) \ -- -L$(BINDIR) -l$(GS_SO_BASE) $(SOC_LIBS) -+ -L$(BINDIR) -l$(GS_SO_BASE) $(SOC_LIBS) -Wl,-rpath=$(libdir) - - $(PCLSOC_XE): gpcl6-so-links-subtarget $(PLSRC)$(REALMAIN_SRC).c $(UNIX_DLL_MAK) $(MAKEDIRS) - $(GLCC) -g -o $(PCLSOC_XE) $(PLSRC)$(REALMAIN_SRC).c -L$(BINDIR) -l$(PCL_SO_BASE) diff --git a/gnu/packages/patches/glibc-2.28-git-fixes.patch b/gnu/packages/patches/glibc-2.28-git-fixes.patch new file mode 100644 index 0000000000..7e370ef0b1 --- /dev/null +++ b/gnu/packages/patches/glibc-2.28-git-fixes.patch @@ -0,0 +1,248 @@ +This file contains fixes from the "release/2.28/master" branch: +https://sourceware.org/git/?p=glibc.git;a=shortlog;h=refs/heads/release/2.28/master + +Currently we have these commits (sans tests and ChangeLog updates): +7f11842e7483da7aa9fa3031be122021978ef600 +726e1554ce4db5e35af41cb0110c54c5e1232054 +4b25485f03158959cff45379eecc1d73c7dcdd11 +d05b05d1570ba3ae354a2f5a3cfeefb373b09979 +bfcfa22589f2b4277a65e60c6b736b6bbfbd87d0 +2f498f3d140ab5152bd784df2be7af7d9c5e63ed + +diff --git a/htl/Versions b/htl/Versions +index 6a63a1b8a1..c5a616da10 100644 +--- a/htl/Versions ++++ b/htl/Versions +@@ -150,6 +150,8 @@ libpthread { + __cthread_keycreate; + __cthread_getspecific; + __cthread_setspecific; ++ __pthread_getspecific; ++ __pthread_setspecific; + __pthread_getattr_np; + __pthread_attr_getstack; + } + +diff --git a/sysdeps/htl/pt-getspecific.c b/sysdeps/htl/pt-getspecific.c +index a0227a67f6..64ddf9551a 100644 +--- a/sysdeps/htl/pt-getspecific.c ++++ b/sysdeps/htl/pt-getspecific.c +@@ -36,3 +36,4 @@ __pthread_getspecific (pthread_key_t key) + return self->thread_specifics[key]; + } + strong_alias (__pthread_getspecific, pthread_getspecific); ++hidden_def (__pthread_getspecific) +diff --git a/sysdeps/htl/pt-setspecific.c b/sysdeps/htl/pt-setspecific.c +index a46a12f157..02aff417ef 100644 +--- a/sysdeps/htl/pt-setspecific.c ++++ b/sysdeps/htl/pt-setspecific.c +@@ -48,3 +48,4 @@ __pthread_setspecific (pthread_key_t key, const void *value) + return 0; + } + strong_alias (__pthread_setspecific, pthread_setspecific); ++hidden_def (__pthread_setspecific) +diff --git a/sysdeps/htl/pthreadP.h b/sysdeps/htl/pthreadP.h +index 132ac1718e..71c2fcd9c6 100644 +--- a/sysdeps/htl/pthreadP.h ++++ b/sysdeps/htl/pthreadP.h +@@ -68,6 +68,8 @@ struct __pthread_cancelation_handler **___pthread_get_cleanup_stack (void) attri + + #if IS_IN (libpthread) + hidden_proto (__pthread_key_create) ++hidden_proto (__pthread_getspecific) ++hidden_proto (__pthread_setspecific) + hidden_proto (_pthread_mutex_init) + #endif + +diff --git a/sysdeps/unix/sysv/linux/getdents64.c b/sysdeps/unix/sysv/linux/getdents64.c +index 3bde0cf4f0..bc140b5a7f 100644 +--- a/sysdeps/unix/sysv/linux/getdents64.c ++++ b/sysdeps/unix/sysv/linux/getdents64.c +@@ -33,41 +33,80 @@ strong_alias (__getdents64, __getdents) + # include <shlib-compat.h> + + # if SHLIB_COMPAT(libc, GLIBC_2_1, GLIBC_2_2) +-# include <olddirent.h> ++# include <olddirent.h> ++# include <unistd.h> + +-/* kernel definition of as of 3.2. */ +-struct compat_linux_dirent ++static ssize_t ++handle_overflow (int fd, __off64_t offset, ssize_t count) + { +- /* Both d_ino and d_off are compat_ulong_t which are defined in all +- architectures as 'u32'. */ +- uint32_t d_ino; +- uint32_t d_off; +- unsigned short d_reclen; +- char d_name[1]; +-}; ++ /* If this is the first entry in the buffer, we can report the ++ error. */ ++ if (count == 0) ++ { ++ __set_errno (EOVERFLOW); ++ return -1; ++ } ++ ++ /* Otherwise, seek to the overflowing entry, so that the next call ++ will report the error, and return the data read so far.. */ ++ if (__lseek64 (fd, offset, SEEK_SET) != 0) ++ return -1; ++ return count; ++} + + ssize_t + __old_getdents64 (int fd, char *buf, size_t nbytes) + { +- ssize_t retval = INLINE_SYSCALL_CALL (getdents, fd, buf, nbytes); ++ /* We do not move the individual directory entries. This is only ++ possible if the target type (struct __old_dirent64) is smaller ++ than the source type. */ ++ _Static_assert (offsetof (struct __old_dirent64, d_name) ++ <= offsetof (struct dirent64, d_name), ++ "__old_dirent64 is larger than dirent64"); ++ _Static_assert (__alignof__ (struct __old_dirent64) ++ <= __alignof__ (struct dirent64), ++ "alignment of __old_dirent64 is larger than dirent64"); + +- /* The kernel added the d_type value after the name. Change this now. */ +- if (retval != -1) ++ ssize_t retval = INLINE_SYSCALL_CALL (getdents64, fd, buf, nbytes); ++ if (retval > 0) + { +- union +- { +- struct compat_linux_dirent k; +- struct dirent u; +- } *kbuf = (void *) buf; +- +- while ((char *) kbuf < buf + retval) ++ char *p = buf; ++ char *end = buf + retval; ++ while (p < end) + { +- char d_type = *((char *) kbuf + kbuf->k.d_reclen - 1); +- memmove (kbuf->u.d_name, kbuf->k.d_name, +- strlen (kbuf->k.d_name) + 1); +- kbuf->u.d_type = d_type; ++ struct dirent64 *source = (struct dirent64 *) p; ++ ++ /* Copy out the fixed-size data. */ ++ __ino_t ino = source->d_ino; ++ __off64_t offset = source->d_off; ++ unsigned int reclen = source->d_reclen; ++ unsigned char type = source->d_type; ++ ++ /* Check for ino_t overflow. */ ++ if (__glibc_unlikely (ino != source->d_ino)) ++ return handle_overflow (fd, offset, p - buf); ++ ++ /* Convert to the target layout. Use a separate struct and ++ memcpy to side-step aliasing issues. */ ++ struct __old_dirent64 result; ++ result.d_ino = ino; ++ result.d_off = offset; ++ result.d_reclen = reclen; ++ result.d_type = type; ++ ++ /* Write the fixed-sized part of the result to the ++ buffer. */ ++ size_t result_name_offset = offsetof (struct __old_dirent64, d_name); ++ memcpy (p, &result, result_name_offset); ++ ++ /* Adjust the position of the name if necessary. Copy ++ everything until the end of the record, including the ++ terminating NUL byte. */ ++ if (result_name_offset != offsetof (struct dirent64, d_name)) ++ memmove (p + result_name_offset, source->d_name, ++ reclen - offsetof (struct dirent64, d_name)); + +- kbuf = (void *) ((char *) kbuf + kbuf->k.d_reclen); ++ p += reclen; + } + } + return retval; + +diff --git a/misc/error.c b/misc/error.c +index b4e8b6c938..03378e2f2a 100644 +--- a/misc/error.c ++++ b/misc/error.c +@@ -319,6 +319,7 @@ error (int status, int errnum, const char *message, ...) + + va_start (args, message); + error_tail (status, errnum, message, args); ++ va_end (args); + + #ifdef _LIBC + _IO_funlockfile (stderr); +@@ -390,6 +391,7 @@ error_at_line (int status, int errnum, const char *file_name, + + va_start (args, message); + error_tail (status, errnum, message, args); ++ va_end (args); + + #ifdef _LIBC + _IO_funlockfile (stderr); + +diff --git a/nscd/nscd_conf.c b/nscd/nscd_conf.c +index 265a02434d..7293b795b6 100644 +--- a/nscd/nscd_conf.c ++++ b/nscd/nscd_conf.c +@@ -190,7 +190,10 @@ nscd_parse_file (const char *fname, struct database_dyn dbs[lastdb]) + if (!arg1) + error (0, 0, _("Must specify user name for server-user option")); + else +- server_user = xstrdup (arg1); ++ { ++ free ((char *) server_user); ++ server_user = xstrdup (arg1); ++ } + } + else if (strcmp (entry, "stat-user") == 0) + { +@@ -198,6 +201,7 @@ nscd_parse_file (const char *fname, struct database_dyn dbs[lastdb]) + error (0, 0, _("Must specify user name for stat-user option")); + else + { ++ free ((char *) stat_user); + stat_user = xstrdup (arg1); + + struct passwd *pw = getpwnam (stat_user); + +diff --git a/nss/nss_files/files-alias.c b/nss/nss_files/files-alias.c +index cfd34b66b9..35b0bfc5d2 100644 +--- a/nss/nss_files/files-alias.c ++++ b/nss/nss_files/files-alias.c +@@ -221,6 +221,13 @@ get_next_alias (FILE *stream, const char *match, struct aliasent *result, + { + while (! feof_unlocked (listfile)) + { ++ if (room_left < 2) ++ { ++ free (old_line); ++ fclose (listfile); ++ goto no_more_room; ++ } ++ + first_unused[room_left - 1] = '\xff'; + line = fgets_unlocked (first_unused, room_left, + listfile); +@@ -229,6 +236,7 @@ get_next_alias (FILE *stream, const char *match, struct aliasent *result, + if (first_unused[room_left - 1] != '\xff') + { + free (old_line); ++ fclose (listfile); + goto no_more_room; + } + +@@ -256,6 +264,7 @@ get_next_alias (FILE *stream, const char *match, struct aliasent *result, + + __alignof__ (char *))) + { + free (old_line); ++ fclose (listfile); + goto no_more_room; + } + room_left -= ((first_unused - cp) + diff --git a/gnu/packages/patches/grub-binutils-compat.patch b/gnu/packages/patches/grub-binutils-compat.patch new file mode 100644 index 0000000000..2107869314 --- /dev/null +++ b/gnu/packages/patches/grub-binutils-compat.patch @@ -0,0 +1,53 @@ +Fix a relocation issue that shows up with recent binutils. + +Patch taken from upstream: +https://git.sv.gnu.org/cgit/grub.git/commit/?id=842c390469e2c2e10b5aa36700324cd3bde25875 + +diff --git a/grub-core/efiemu/i386/loadcore64.c b/grub-core/efiemu/i386/loadcore64.c +index e49d0b6..18facf4 100644 +--- a/grub-core/efiemu/i386/loadcore64.c ++++ b/grub-core/efiemu/i386/loadcore64.c +@@ -98,6 +98,7 @@ grub_arch_efiemu_relocate_symbols64 (grub_efiemu_segment_t segs, + break; + + case R_X86_64_PC32: ++ case R_X86_64_PLT32: + err = grub_efiemu_write_value (addr, + *addr32 + rel->r_addend + + sym.off +diff --git a/grub-core/kern/x86_64/dl.c b/grub-core/kern/x86_64/dl.c +index 4406906..3a73e6e 100644 +--- a/grub-core/kern/x86_64/dl.c ++++ b/grub-core/kern/x86_64/dl.c +@@ -70,6 +70,7 @@ grub_arch_dl_relocate_symbols (grub_dl_t mod, void *ehdr, + break; + + case R_X86_64_PC32: ++ case R_X86_64_PLT32: + { + grub_int64_t value; + value = ((grub_int32_t) *addr32) + rel->r_addend + sym->st_value - +diff --git a/util/grub-mkimagexx.c b/util/grub-mkimagexx.c +index a2bb054..39d7efb 100644 +--- a/util/grub-mkimagexx.c ++++ b/util/grub-mkimagexx.c +@@ -841,6 +841,7 @@ SUFFIX (relocate_addresses) (Elf_Ehdr *e, Elf_Shdr *sections, + break; + + case R_X86_64_PC32: ++ case R_X86_64_PLT32: + { + grub_uint32_t *t32 = (grub_uint32_t *) target; + *t32 = grub_host_to_target64 (grub_target_to_host32 (*t32) +diff --git a/util/grub-module-verifier.c b/util/grub-module-verifier.c +index 9179285..a79271f 100644 +--- a/util/grub-module-verifier.c ++++ b/util/grub-module-verifier.c +@@ -19,6 +19,7 @@ struct grub_module_verifier_arch archs[] = { + -1 + }, (int[]){ + R_X86_64_PC32, ++ R_X86_64_PLT32, + -1 + } + }, diff --git a/gnu/packages/patches/jemalloc-arm-address-bits.patch b/gnu/packages/patches/jemalloc-arm-address-bits.patch deleted file mode 100644 index f2ef24c25a..0000000000 --- a/gnu/packages/patches/jemalloc-arm-address-bits.patch +++ /dev/null @@ -1,39 +0,0 @@ -From 8cfc9dec37b312a2686f602bbcdd102ca07cca99 Mon Sep 17 00:00:00 2001 -From: David Goldblatt <davidgoldblatt@fb.com> -Date: Fri, 29 Sep 2017 13:54:08 -0700 -Subject: [PATCH] ARM: Don't extend bit LG_VADDR to compute high address bits. - -In userspace ARM on Linux, zero-ing the high bits is the correct way to do this. -This doesn't fix the fact that we currently set LG_VADDR to 48 on ARM, when in -fact larger virtual address sizes are coming soon. We'll cross that bridge when -we come to it. ---- - include/jemalloc/internal/rtree.h | 12 ++++++++++++ - 1 file changed, 12 insertions(+) - -diff --git a/include/jemalloc/internal/rtree.h b/include/jemalloc/internal/rtree.h -index b5d4db39..4563db23 100644 ---- a/include/jemalloc/internal/rtree.h -+++ b/include/jemalloc/internal/rtree.h -@@ -178,9 +178,21 @@ rtree_leaf_elm_bits_read(tsdn_t *tsdn, rtree_t *rtree, rtree_leaf_elm_t *elm, - - JEMALLOC_ALWAYS_INLINE extent_t * - rtree_leaf_elm_bits_extent_get(uintptr_t bits) { -+# ifdef __aarch64__ -+ /* -+ * aarch64 doesn't sign extend the highest virtual address bit to set -+ * the higher ones. Instead, the high bits gets zeroed. -+ */ -+ uintptr_t high_bit_mask = ((uintptr_t)1 << LG_VADDR) - 1; -+ /* Mask off the slab bit. */ -+ uintptr_t low_bit_mask = ~(uintptr_t)1; -+ uintptr_t mask = high_bit_mask & low_bit_mask; -+ return (extent_t *)(bits & mask); -+# else - /* Restore sign-extended high bits, mask slab bit. */ - return (extent_t *)((uintptr_t)((intptr_t)(bits << RTREE_NHIB) >> - RTREE_NHIB) & ~((uintptr_t)0x1)); -+# endif - } - - JEMALLOC_ALWAYS_INLINE szind_t diff --git a/gnu/packages/patches/libgcrypt-make-yat2m-reproducible.patch b/gnu/packages/patches/libgcrypt-make-yat2m-reproducible.patch new file mode 100644 index 0000000000..3056f0baad --- /dev/null +++ b/gnu/packages/patches/libgcrypt-make-yat2m-reproducible.patch @@ -0,0 +1,32 @@ +Make yat2m in libgcrypt respect SOURCE_DATE_EPOCH, making +the build reproducible. + +This was already fixed upstream in GnuPG: +https://dev.gnupg.org/rG139de02b93773615bdd95e04a7f0c1ad73b4f6fb + +and in libgpg-error: +https://dev.gnupg.org/rE5494a5728418938d2e42158bb646b07124184e64 + + +--- a/doc/yat2m.c 2017-11-23 19:16:58.000000000 +0100 ++++ b/doc/yat2m.c 2017-08-28 12:22:54.000000000 +0200 +@@ -1475,6 +1484,7 @@ + main (int argc, char **argv) + { + int last_argc = -1; ++ const char *s; + + opt_source = "GNU"; + opt_release = ""; +@@ -1608,6 +1618,11 @@ + if (argc > 1) + die ("usage: " PGM " [OPTION] [FILE] (try --help for more information)\n"); + ++ /* Take care of supplied timestamp for reproducible builds. See ++ * https://reproducible-builds.org/specs/source-date-epoch/ */ ++ if (!opt_date && (s = getenv ("SOURCE_DATE_EPOCH")) && *s) ++ opt_date = s; ++ + /* Start processing. */ + if (argc && strcmp (*argv, "-")) + { diff --git a/gnu/packages/patches/libgpg-error-aarch64-logging-fix.patch b/gnu/packages/patches/libgpg-error-aarch64-logging-fix.patch deleted file mode 100644 index d848d639b2..0000000000 --- a/gnu/packages/patches/libgpg-error-aarch64-logging-fix.patch +++ /dev/null @@ -1,58 +0,0 @@ -https://git.gnupg.org/cgi-bin/gitweb.cgi?p=libgpg-error.git;a=patch;h=791177de023574223eddf7288eb7c5a0721ac623 - -From 791177de023574223eddf7288eb7c5a0721ac623 Mon Sep 17 00:00:00 2001 -From: Werner Koch <wk@gnupg.org> -Date: Sun, 18 Mar 2018 17:39:43 +0100 -Subject: [PATCH] core: Fix regression on arm64 due to invalid use of va_list. - -* src/logging.c (_gpgrt_log_printhex): Provide a dummy arg instead of -NULL. --- - -Fix -Suggested-by: Jakub Wilk <jwilk@jwilk.net> - -Signed-off-by: Werner Koch <wk@gnupg.org> ---- - src/logging.c | 18 ++++++++++++++---- - 1 file changed, 14 insertions(+), 4 deletions(-) - -diff --git a/src/logging.c b/src/logging.c -index 1a4f620..d01f974 100644 ---- a/src/logging.c -+++ b/src/logging.c -@@ -1090,9 +1090,10 @@ _gpgrt_log_flush (void) - - - /* Print a hexdump of (BUFFER,LENGTH). With FMT passed as NULL print -- * just the raw dump, with FMT being an empty string, print a trailing -- * linefeed, otherwise print an entire debug line with the expanded -- * FMT followed by a possible wrapped hexdump and a final LF. */ -+ * just the raw dump (in this case ARG_PTR is not used), with FMT -+ * being an empty string, print a trailing linefeed, otherwise print -+ * an entire debug line with the expanded FMT followed by a possible -+ * wrapped hexdump and a final LF. */ - void - _gpgrt_logv_printhex (const void *buffer, size_t length, - const char *fmt, va_list arg_ptr) -@@ -1150,7 +1151,16 @@ _gpgrt_log_printhex (const void *buffer, size_t length, - va_end (arg_ptr); - } - else -- _gpgrt_logv_printhex (buffer, length, NULL, NULL); -+ { -+ /* va_list is not necessary a pointer and thus we can't use NULL -+ * because that would conflict with platforms using a straight -+ * struct for it (e.g. arm64). We use a dummy variable instead; -+ * the static is a simple way zero it out so to not get -+ * complains about uninitialized use. */ -+ static va_list dummy_argptr; -+ -+ _gpgrt_logv_printhex (buffer, length, NULL, dummy_argptr); -+ } - } - - --- -2.8.0.rc3 - diff --git a/gnu/packages/patches/m4-gnulib-libio.patch b/gnu/packages/patches/m4-gnulib-libio.patch new file mode 100644 index 0000000000..a26622ccf3 --- /dev/null +++ b/gnu/packages/patches/m4-gnulib-libio.patch @@ -0,0 +1,128 @@ +Adjust the bundled gnulib to cope with removal of libio interface in +glibc 2.28. + +Based on this upstream patch, without hunks that do not apply to m4: +https://git.savannah.gnu.org/cgit/gnulib.git/commit/?id=4af4a4a71827c0bc5e0ec67af23edef4f15cee8e + +diff --git a/lib/fflush.c b/lib/fflush.c +index 983ade0..a6edfa1 100644 +--- a/lib/fflush.c ++++ b/lib/fflush.c +@@ -33,7 +33,7 @@ + #undef fflush + + +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + + /* Clear the stream's ungetc buffer, preserving the value of ftello (fp). */ + static void +@@ -72,7 +72,7 @@ clear_ungetc_buffer (FILE *fp) + + #endif + +-#if ! (defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */) ++#if ! (defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */) + + # if (defined __sferror || defined __DragonFly__ || defined __ANDROID__) && defined __SNPT + /* FreeBSD, NetBSD, OpenBSD, DragonFly, Mac OS X, Cygwin, Minix 3, Android */ +@@ -148,7 +148,7 @@ rpl_fflush (FILE *stream) + if (stream == NULL || ! freading (stream)) + return fflush (stream); + +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + + clear_ungetc_buffer_preserving_position (stream); + +diff --git a/lib/fpending.c b/lib/fpending.c +index c84e3a5..789f50e 100644 +--- a/lib/fpending.c ++++ b/lib/fpending.c +@@ -32,7 +32,7 @@ __fpending (FILE *fp) + /* Most systems provide FILE as a struct and the necessary bitmask in + <stdio.h>, because they need it for implementing getc() and putc() as + fast macros. */ +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + return fp->_IO_write_ptr - fp->_IO_write_base; + #elif defined __sferror || defined __DragonFly__ || defined __ANDROID__ + /* FreeBSD, NetBSD, OpenBSD, DragonFly, Mac OS X, Cygwin, Minix 3, Android */ +diff --git a/lib/fpurge.c b/lib/fpurge.c +index b1d417c..3aedcc3 100644 +--- a/lib/fpurge.c ++++ b/lib/fpurge.c +@@ -62,7 +62,7 @@ fpurge (FILE *fp) + /* Most systems provide FILE as a struct and the necessary bitmask in + <stdio.h>, because they need it for implementing getc() and putc() as + fast macros. */ +-# if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++# if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + fp->_IO_read_end = fp->_IO_read_ptr; + fp->_IO_write_ptr = fp->_IO_write_base; + /* Avoid memory leak when there is an active ungetc buffer. */ +diff --git a/lib/freadahead.c b/lib/freadahead.c +index c2ecb5b..23ec76e 100644 +--- a/lib/freadahead.c ++++ b/lib/freadahead.c +@@ -30,7 +30,7 @@ extern size_t __sreadahead (FILE *); + size_t + freadahead (FILE *fp) + { +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + if (fp->_IO_write_ptr > fp->_IO_write_base) + return 0; + return (fp->_IO_read_end - fp->_IO_read_ptr) +diff --git a/lib/freading.c b/lib/freading.c +index 73c28ac..c24d0c8 100644 +--- a/lib/freading.c ++++ b/lib/freading.c +@@ -31,7 +31,7 @@ freading (FILE *fp) + /* Most systems provide FILE as a struct and the necessary bitmask in + <stdio.h>, because they need it for implementing getc() and putc() as + fast macros. */ +-# if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++# if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + return ((fp->_flags & _IO_NO_WRITES) != 0 + || ((fp->_flags & (_IO_NO_READS | _IO_CURRENTLY_PUTTING)) == 0 + && fp->_IO_read_base != NULL)); +diff --git a/lib/fseeko.c b/lib/fseeko.c +index 0101ab5..193f4e8 100644 +--- a/lib/fseeko.c ++++ b/lib/fseeko.c +@@ -47,7 +47,7 @@ fseeko (FILE *fp, off_t offset, int whence) + #endif + + /* These tests are based on fpurge.c. */ +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + if (fp->_IO_read_end == fp->_IO_read_ptr + && fp->_IO_write_ptr == fp->_IO_write_base + && fp->_IO_save_base == NULL) +@@ -123,7 +123,7 @@ fseeko (FILE *fp, off_t offset, int whence) + return -1; + } + +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + fp->_flags &= ~_IO_EOF_SEEN; + fp->_offset = pos; + #elif defined __sferror || defined __DragonFly__ || defined __ANDROID__ +diff --git a/lib/stdio-impl.h b/lib/stdio-impl.h +index 78d896e..05c5752 100644 +--- a/lib/stdio-impl.h ++++ b/lib/stdio-impl.h +@@ -18,6 +18,12 @@ + the same implementation of stdio extension API, except that some fields + have different naming conventions, or their access requires some casts. */ + ++/* Glibc 2.28 made _IO_IN_BACKUP private. For now, work around this ++ problem by defining it ourselves. FIXME: Do not rely on glibc ++ internals. */ ++#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN ++# define _IO_IN_BACKUP 0x100 ++#endif + + /* BSD stdio derived implementations. */ + diff --git a/gnu/packages/patches/mariadb-gcc-ice.patch b/gnu/packages/patches/mariadb-gcc-ice.patch deleted file mode 100644 index 59b188f45a..0000000000 --- a/gnu/packages/patches/mariadb-gcc-ice.patch +++ /dev/null @@ -1,24 +0,0 @@ -Work around this GCC ICE: <https://bugs.gnu.org/31708>. It shows up -only when doing native compiles on armhf-linux. - ---- mariadb-10.1.33/plugin/semisync/semisync_master.cc 2018-07-28 02:13:12.604020250 +0200 -+++ mariadb-10.1.33/plugin/semisync/semisync_master.cc 2018-07-28 02:14:11.907753417 +0200 -@@ -847,6 +847,8 @@ - return function_exit(kWho, 0); - } - -+volatile const void *kSyncHeaderPtr = &ReplSemiSyncMaster::kSyncHeader; -+ - int ReplSemiSyncMaster::reserveSyncHeader(unsigned char *header, - unsigned long size) - { -@@ -873,7 +875,7 @@ - /* Set the magic number and the sync status. By default, no sync - * is required. - */ -- memcpy(header, kSyncHeader, sizeof(kSyncHeader)); -+ memcpy(header, (void *)kSyncHeaderPtr, sizeof(kSyncHeader)); - hlen= sizeof(kSyncHeader); - } - return function_exit(kWho, hlen); - diff --git a/gnu/packages/patches/meson-for-build-rpath.patch b/gnu/packages/patches/meson-for-build-rpath.patch index 59249e294d..ef9a73f07c 100644 --- a/gnu/packages/patches/meson-for-build-rpath.patch +++ b/gnu/packages/patches/meson-for-build-rpath.patch @@ -2,10 +2,10 @@ This patch removes a part of meson that clears the rpath upon installation. This will only be applied to a special version of meson, used for the meson-build-system. -Patch by Peter Mikkelsen <petermikkelsen10@gmail.com> +Original patch for Meson 0.42.0 by Peter Mikkelsen <petermikkelsen10@gmail.com> ---- meson-0.42.0/mesonbuild/minstall.py.orig 2017-09-09 01:49:39.147374148 +0200 -+++ meson-0.42.0/mesonbuild/minstall.py 2017-09-09 01:51:01.209134717 +0200 +--- meson-0.47.1/mesonbuild/minstall.py.old 2018-08-10 11:01:27.812327013 +0200 ++++ meson-0.47.1/mesonbuild/minstall.py 2018-08-10 11:01:51.940368505 +0200 @@ -436,15 +436,6 @@ print("Symlink creation does not work on this platform. " "Skipping all symlinking.") diff --git a/gnu/packages/patches/oath-toolkit-glibc-compat.patch b/gnu/packages/patches/oath-toolkit-glibc-compat.patch new file mode 100644 index 0000000000..22814599e5 --- /dev/null +++ b/gnu/packages/patches/oath-toolkit-glibc-compat.patch @@ -0,0 +1,90 @@ +Adjust the bundled Gnulib to cope with removal of libio interface in Glibc 2.28. + +Based on this upstream gnulib patch: +https://git.savannah.gnu.org/cgit/gnulib.git/commit/?id=4af4a4a71827c0bc5e0ec67af23edef4f15cee8e + +--- a/liboath/gl/fflush.c ++++ b/liboath/gl/fflush.c +@@ -33,7 +33,7 @@ + #undef fflush + + +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + + /* Clear the stream's ungetc buffer, preserving the value of ftello (fp). */ + static void +@@ -72,7 +72,7 @@ + + #endif + +-#if ! (defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */) ++#if ! (defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */) + + # if (defined __sferror || defined __DragonFly__ || defined __ANDROID__) && defined __SNPT + /* FreeBSD, NetBSD, OpenBSD, DragonFly, Mac OS X, Cygwin, Android */ +@@ -148,7 +148,7 @@ + if (stream == NULL || ! freading (stream)) + return fflush (stream); + +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + + clear_ungetc_buffer_preserving_position (stream); + +--- a/liboath/gl/fpurge.c ++++ b/liboath/gl/fpurge.c +@@ -62,7 +62,7 @@ + /* Most systems provide FILE as a struct and the necessary bitmask in + <stdio.h>, because they need it for implementing getc() and putc() as + fast macros. */ +-# if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + fp->_IO_read_end = fp->_IO_read_ptr; + fp->_IO_write_ptr = fp->_IO_write_base; + /* Avoid memory leak when there is an active ungetc buffer. */ +--- a/libaoth/gl/freading.c ++++ b/liboath/gl/freading.c +@@ -31,7 +31,7 @@ + /* Most systems provide FILE as a struct and the necessary bitmask in + <stdio.h>, because they need it for implementing getc() and putc() as + fast macros. */ +-# if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + return ((fp->_flags & _IO_NO_WRITES) != 0 + || ((fp->_flags & (_IO_NO_READS | _IO_CURRENTLY_PUTTING)) == 0 + && fp->_IO_read_base != NULL)); +--- a/liboath/gl/fseeko.c ++++ b/liboath/gl/fseeko.c +@@ -47,7 +47,7 @@ + #endif + + /* These tests are based on fpurge.c. */ +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + if (fp->_IO_read_end == fp->_IO_read_ptr + && fp->_IO_write_ptr == fp->_IO_write_base + && fp->_IO_save_base == NULL) +@@ -123,7 +123,7 @@ + return -1; + } + +-#if defined _IO_ftrylockfile || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ ++#if defined _IO_EOF_SEEN || __GNU_LIBRARY__ == 1 /* GNU libc, BeOS, Haiku, Linux libc5 */ + fp->_flags &= ~_IO_EOF_SEEN; + fp->_offset = pos; + #elif defined __sferror || defined __DragonFly__ || defined __ANDROID__ +--- a/liboath/gl/stdio-impl.h ++++ b/liboath/gl/stdio-impl.h +@@ -18,6 +18,11 @@ + the same implementation of stdio extension API, except that some fields + have different naming conventions, or their access requires some casts. */ + ++/* Glibc 2.28 made _IO_IN_BACKUP private, so define it here for now. */ ++#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN ++# define _IO_IN_BACKUP 0x100 ++#endif ++ + /* BSD stdio derived implementations. */ + + #if defined __NetBSD__ /* NetBSD */ diff --git a/gnu/packages/patches/openssl-1.0.2-CVE-2018-0495.patch b/gnu/packages/patches/openssl-1.0.2-CVE-2018-0495.patch deleted file mode 100644 index 2d54ed03b9..0000000000 --- a/gnu/packages/patches/openssl-1.0.2-CVE-2018-0495.patch +++ /dev/null @@ -1,215 +0,0 @@ -Fix CVE-2018-0495: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-0495 -https://www.nccgroup.trust/us/our-research/technical-advisory-return-of-the-hidden-number-problem/ - -Patch copied from upstream source repository: - -https://github.com/openssl/openssl/commit/949ff36623eafc3523a9f91784992965018ffb05 - -From 949ff36623eafc3523a9f91784992965018ffb05 Mon Sep 17 00:00:00 2001 -From: Matt Caswell <matt@openssl.org> -Date: Fri, 25 May 2018 12:10:13 +0100 -Subject: [PATCH] Add blinding to an ECDSA signature - -Keegan Ryan (NCC Group) has demonstrated a side channel attack on an -ECDSA signature operation. During signing the signer calculates: - -s:= k^-1 * (m + r * priv_key) mod order - -The addition operation above provides a sufficient signal for a -flush+reload attack to derive the private key given sufficient signature -operations. - -As a mitigation (based on a suggestion from Keegan) we add blinding to -the operation so that: - -s := k^-1 * blind^-1 (blind * m + blind * r * priv_key) mod order - -Since this attack is a localhost side channel only no CVE is assigned. - -Reviewed-by: Rich Salz <rsalz@openssl.org> ---- - CHANGES | 4 ++ - crypto/ecdsa/ecdsatest.c | 9 ++++- - crypto/ecdsa/ecs_ossl.c | 82 ++++++++++++++++++++++++++++++++-------- - 3 files changed, 79 insertions(+), 16 deletions(-) - -diff --git a/crypto/ecdsa/ecdsatest.c b/crypto/ecdsa/ecdsatest.c -index 0f301f86d9..a130fc9117 100644 ---- a/crypto/ecdsa/ecdsatest.c -+++ b/crypto/ecdsa/ecdsatest.c -@@ -137,7 +137,7 @@ int restore_rand(void) - return 1; - } - --static int fbytes_counter = 0; -+static int fbytes_counter = 0, use_fake = 0; - static const char *numbers[8] = { - "651056770906015076056810763456358567190100156695615665659", - "6140507067065001063065065565667405560006161556565665656654", -@@ -158,6 +158,11 @@ int fbytes(unsigned char *buf, int num) - int ret; - BIGNUM *tmp = NULL; - -+ if (use_fake == 0) -+ return old_rand->bytes(buf, num); -+ -+ use_fake = 0; -+ - if (fbytes_counter >= 8) - return 0; - tmp = BN_new(); -@@ -199,11 +204,13 @@ int x9_62_test_internal(BIO *out, int nid, const char *r_in, const char *s_in) - /* create the key */ - if ((key = EC_KEY_new_by_curve_name(nid)) == NULL) - goto x962_int_err; -+ use_fake = 1; - if (!EC_KEY_generate_key(key)) - goto x962_int_err; - BIO_printf(out, "."); - (void)BIO_flush(out); - /* create the signature */ -+ use_fake = 1; - signature = ECDSA_do_sign(digest, 20, key); - if (signature == NULL) - goto x962_int_err; -diff --git a/crypto/ecdsa/ecs_ossl.c b/crypto/ecdsa/ecs_ossl.c -index 16d4f59b9b..1d37551803 100644 ---- a/crypto/ecdsa/ecs_ossl.c -+++ b/crypto/ecdsa/ecs_ossl.c -@@ -252,6 +252,7 @@ static ECDSA_SIG *ecdsa_do_sign(const unsigned char *dgst, int dgst_len, - { - int ok = 0, i; - BIGNUM *kinv = NULL, *s, *m = NULL, *tmp = NULL, *order = NULL; -+ BIGNUM *blind = NULL, *blindm = NULL; - const BIGNUM *ckinv; - BN_CTX *ctx = NULL; - const EC_GROUP *group; -@@ -269,14 +270,25 @@ static ECDSA_SIG *ecdsa_do_sign(const unsigned char *dgst, int dgst_len, - } - - ret = ECDSA_SIG_new(); -- if (!ret) { -+ if (ret == NULL) { - ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, ERR_R_MALLOC_FAILURE); - return NULL; - } - s = ret->s; - -- if ((ctx = BN_CTX_new()) == NULL || (order = BN_new()) == NULL || -- (tmp = BN_new()) == NULL || (m = BN_new()) == NULL) { -+ ctx = BN_CTX_new(); -+ if (ctx == NULL) { -+ ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, ERR_R_MALLOC_FAILURE); -+ goto err; -+ } -+ -+ BN_CTX_start(ctx); -+ order = BN_CTX_get(ctx); -+ tmp = BN_CTX_get(ctx); -+ m = BN_CTX_get(ctx); -+ blind = BN_CTX_get(ctx); -+ blindm = BN_CTX_get(ctx); -+ if (blindm == NULL) { - ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, ERR_R_MALLOC_FAILURE); - goto err; - } -@@ -315,26 +327,70 @@ static ECDSA_SIG *ecdsa_do_sign(const unsigned char *dgst, int dgst_len, - } - } - -- if (!BN_mod_mul(tmp, priv_key, ret->r, order, ctx)) { -+ /* -+ * The normal signature calculation is: -+ * -+ * s := k^-1 * (m + r * priv_key) mod order -+ * -+ * We will blind this to protect against side channel attacks -+ * -+ * s := k^-1 * blind^-1 * (blind * m + blind * r * priv_key) mod order -+ */ -+ -+ /* Generate a blinding value */ -+ do { -+ if (!BN_rand(blind, BN_num_bits(order) - 1, -1, 0)) -+ goto err; -+ } while (BN_is_zero(blind)); -+ BN_set_flags(blind, BN_FLG_CONSTTIME); -+ BN_set_flags(blindm, BN_FLG_CONSTTIME); -+ BN_set_flags(tmp, BN_FLG_CONSTTIME); -+ -+ /* tmp := blind * priv_key * r mod order */ -+ if (!BN_mod_mul(tmp, blind, priv_key, order, ctx)) { -+ ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, ERR_R_BN_LIB); -+ goto err; -+ } -+ if (!BN_mod_mul(tmp, tmp, ret->r, order, ctx)) { -+ ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, ERR_R_BN_LIB); -+ goto err; -+ } -+ -+ /* blindm := blind * m mod order */ -+ if (!BN_mod_mul(blindm, blind, m, order, ctx)) { -+ ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, ERR_R_BN_LIB); -+ goto err; -+ } -+ -+ /* s : = (blind * priv_key * r) + (blind * m) mod order */ -+ if (!BN_mod_add_quick(s, tmp, blindm, order)) { -+ ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, ERR_R_BN_LIB); -+ goto err; -+ } -+ -+ /* s:= s * blind^-1 mod order */ -+ if (BN_mod_inverse(blind, blind, order, ctx) == NULL) { - ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, ERR_R_BN_LIB); - goto err; - } -- if (!BN_mod_add_quick(s, tmp, m, order)) { -+ if (!BN_mod_mul(s, s, blind, order, ctx)) { - ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, ERR_R_BN_LIB); - goto err; - } -+ -+ /* s := s * k^-1 mod order */ - if (!BN_mod_mul(s, s, ckinv, order, ctx)) { - ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, ERR_R_BN_LIB); - goto err; - } -+ - if (BN_is_zero(s)) { - /* - * if kinv and r have been supplied by the caller don't to - * generate new kinv and r values - */ - if (in_kinv != NULL && in_r != NULL) { -- ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, -- ECDSA_R_NEED_NEW_SETUP_VALUES); -+ ECDSAerr(ECDSA_F_ECDSA_DO_SIGN, ECDSA_R_NEED_NEW_SETUP_VALUES); - goto err; - } - } else -@@ -349,15 +405,11 @@ static ECDSA_SIG *ecdsa_do_sign(const unsigned char *dgst, int dgst_len, - ECDSA_SIG_free(ret); - ret = NULL; - } -- if (ctx) -+ if (ctx != NULL) { -+ BN_CTX_end(ctx); - BN_CTX_free(ctx); -- if (m) -- BN_clear_free(m); -- if (tmp) -- BN_clear_free(tmp); -- if (order) -- BN_free(order); -- if (kinv) -+ } -+ if (kinv != NULL) - BN_clear_free(kinv); - return ret; - } --- -2.17.1 - diff --git a/gnu/packages/patches/openssl-1.0.2-CVE-2018-0732.patch b/gnu/packages/patches/openssl-1.0.2-CVE-2018-0732.patch deleted file mode 100644 index 50b95306a5..0000000000 --- a/gnu/packages/patches/openssl-1.0.2-CVE-2018-0732.patch +++ /dev/null @@ -1,50 +0,0 @@ -Fix CVE-2018-0732: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-0732 - -Patch copied from upstream source repository: - -https://github.com/openssl/openssl/commit/3984ef0b72831da8b3ece4745cac4f8575b19098 - -From 3984ef0b72831da8b3ece4745cac4f8575b19098 Mon Sep 17 00:00:00 2001 -From: Guido Vranken <guidovranken@gmail.com> -Date: Mon, 11 Jun 2018 19:38:54 +0200 -Subject: [PATCH] Reject excessively large primes in DH key generation. - -CVE-2018-0732 - -Signed-off-by: Guido Vranken <guidovranken@gmail.com> - -(cherry picked from commit 91f7361f47b082ae61ffe1a7b17bb2adf213c7fe) - -Reviewed-by: Tim Hudson <tjh@openssl.org> -Reviewed-by: Matt Caswell <matt@openssl.org> -(Merged from https://github.com/openssl/openssl/pull/6457) ---- - crypto/dh/dh_key.c | 7 ++++++- - 1 file changed, 6 insertions(+), 1 deletion(-) - -diff --git a/crypto/dh/dh_key.c b/crypto/dh/dh_key.c -index 387558f146..f235e0d682 100644 ---- a/crypto/dh/dh_key.c -+++ b/crypto/dh/dh_key.c -@@ -130,10 +130,15 @@ static int generate_key(DH *dh) - int ok = 0; - int generate_new_key = 0; - unsigned l; -- BN_CTX *ctx; -+ BN_CTX *ctx = NULL; - BN_MONT_CTX *mont = NULL; - BIGNUM *pub_key = NULL, *priv_key = NULL; - -+ if (BN_num_bits(dh->p) > OPENSSL_DH_MAX_MODULUS_BITS) { -+ DHerr(DH_F_GENERATE_KEY, DH_R_MODULUS_TOO_LARGE); -+ return 0; -+ } -+ - ctx = BN_CTX_new(); - if (ctx == NULL) - goto err; --- -2.17.1 - diff --git a/gnu/packages/patches/parted-glibc-compat.patch b/gnu/packages/patches/parted-glibc-compat.patch new file mode 100644 index 0000000000..edf4afb0d1 --- /dev/null +++ b/gnu/packages/patches/parted-glibc-compat.patch @@ -0,0 +1,17 @@ +Include <sys/sysmacros.h> for "major" and "minor". + +Taken from upstream: +https://git.savannah.gnu.org/cgit/parted.git/commit/?id=ba5e0451b51c983e40afd123b6e0d3eddb55e610 + +diff --git a/libparted/arch/linux.c b/libparted/arch/linux.c +index 31b98ab..7e86b51 100644 +--- a/libparted/arch/linux.c ++++ b/libparted/arch/linux.c +@@ -41,6 +41,7 @@ + #include <sys/utsname.h> /* for uname() */ + #include <scsi/scsi.h> + #include <assert.h> ++#include <sys/sysmacros.h> + #ifdef ENABLE_DEVICE_MAPPER + #include <libdevmapper.h> + #endif diff --git a/gnu/packages/patches/perf-gcc-ice.patch b/gnu/packages/patches/perf-gcc-ice.patch deleted file mode 100644 index 58ab5359c2..0000000000 --- a/gnu/packages/patches/perf-gcc-ice.patch +++ /dev/null @@ -1,13 +0,0 @@ -Work around this GCC ICE: <https://bugs.gnu.org/31708>. - ---- linux-4.16.13/tools/perf/util/header.c 2018-06-04 11:30:39.368146035 +0200 -+++ linux-4.16.13/tools/perf/util/header.c 2018-06-04 11:34:04.667212378 +0200 -@@ -135,7 +135,7 @@ int do_write(struct feat_fd *ff, const v - int write_padded(struct feat_fd *ff, const void *bf, - size_t count, size_t count_aligned) - { -- static const char zero_buf[NAME_ALIGN]; -+ static const char zero_buf[NAME_ALIGN] = { 0 }; - int err = do_write(ff, bf, count); - - if (!err) diff --git a/gnu/packages/patches/perl-archive-tar-CVE-2018-12015.patch b/gnu/packages/patches/perl-archive-tar-CVE-2018-12015.patch deleted file mode 100644 index 6460cf5855..0000000000 --- a/gnu/packages/patches/perl-archive-tar-CVE-2018-12015.patch +++ /dev/null @@ -1,36 +0,0 @@ -Fix CVE-2018-12015: - -https://security-tracker.debian.org/tracker/CVE-2018-12015 -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-12015 -https://rt.cpan.org/Ticket/Display.html?id=125523 - -Patch taken from this upstream commit and adapted to apply to -the bundled copy in the Perl distribution: - -https://github.com/jib/archive-tar-new/commit/ae65651eab053fc6dc4590dbb863a268215c1fc5 - -diff --git a/cpan/Archive-Tar/lib/Archive/Tar.pm b/cpan/Archive-Tar/lib/Archive/Tar.pm -index 6244369..a83975f 100644 ---- a/cpan/Archive-Tar/lib/Archive/Tar.pm -+++ b/cpan/Archive-Tar/lib/Archive/Tar.pm -@@ -845,6 +845,20 @@ sub _extract_file { - return; - } - -+ ### If a file system already contains a block device with the same name as -+ ### the being extracted regular file, we would write the file's content -+ ### to the block device. So remove the existing file (block device) now. -+ ### If an archive contains multiple same-named entries, the last one -+ ### should replace the previous ones. So remove the old file now. -+ ### If the old entry is a symlink to a file outside of the CWD, the new -+ ### entry would create a file there. This is CVE-2018-12015 -+ ### <https://rt.cpan.org/Ticket/Display.html?id=125523>. -+ if (-l $full || -e _) { -+ if (!unlink $full) { -+ $self->_error( qq[Could not remove old file '$full': $!] ); -+ return; -+ } -+ } - if( length $entry->type && $entry->is_file ) { - my $fh = IO::File->new; - $fh->open( $full, '>' ) or ( diff --git a/gnu/packages/patches/perl-deterministic-ordering.patch b/gnu/packages/patches/perl-deterministic-ordering.patch index 92e33ef135..be63d5cde3 100644 --- a/gnu/packages/patches/perl-deterministic-ordering.patch +++ b/gnu/packages/patches/perl-deterministic-ordering.patch @@ -12,10 +12,10 @@ reproducibility. cpan/Devel-PPPort/PPPort_xs.PL | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) -diff --git a/cpan/Devel-PPPort/PPPort_xs.PL b/cpan/Devel-PPPort/PPPort_xs.PL +diff --git a/dist/Devel-PPPort/PPPort_xs.PL b/dist/Devel-PPPort/PPPort_xs.PL index 5f18940..149f2fe 100644 ---- a/cpan/Devel-PPPort/PPPort_xs.PL -+++ b/cpan/Devel-PPPort/PPPort_xs.PL +--- a/dist/Devel-PPPort/PPPort_xs.PL ++++ b/dist/Devel-PPPort/PPPort_xs.PL @@ -38,7 +38,7 @@ END my $file; my $sec; diff --git a/gnu/packages/patches/perl-file-path-CVE-2017-6512.patch b/gnu/packages/patches/perl-file-path-CVE-2017-6512.patch deleted file mode 100644 index 28ab067599..0000000000 --- a/gnu/packages/patches/perl-file-path-CVE-2017-6512.patch +++ /dev/null @@ -1,173 +0,0 @@ -Fix CVE-2017-6512: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-6512 -https://rt.cpan.org/Public/Bug/Display.html?id=121951 - -Patch copied from Debian, adapted to apply to the copy of File::Path in Perl -5.24.0. - -https://github.com/jkeenan/File-Path/commit/e5ef95276ee8ad471c66ee574a5d42552b3a6af2 -https://anonscm.debian.org/cgit/perl/perl.git/diff/debian/patches/fixes/file_path_chmod_race.diff?id=e7b50f8fb6413f8ddfbbfda2d531615fb029e2d3 - -From d760748be0efca7c05454440e24f3df77bf7cf5d Mon Sep 17 00:00:00 2001 -From: John Lightsey <john@nixnuts.net> -Date: Tue, 2 May 2017 12:03:52 -0500 -Subject: Prevent directory chmod race attack. - -CVE-2017-6512 is a race condition attack where the chmod() of directories -that cannot be entered is misused to change the permissions on other -files or directories on the system. This has been corrected by limiting -the directory-permission loosening logic to systems where fchmod() is -supported. - -[Backported (whitespace adjustments) to File-Path 2.12 / perl 5.24 by -Dominic Hargreaves for Debian.] - -Bug: https://rt.cpan.org/Public/Bug/Display.html?id=121951 -Bug-Debian: https://bugs.debian.org/863870 -Patch-Name: fixes/file_path_chmod_race.diff ---- - cpan/File-Path/lib/File/Path.pm | 39 +++++++++++++++++++++++++-------------- - cpan/File-Path/t/Path.t | 40 ++++++++++++++++++++++++++-------------- - 2 files changed, 51 insertions(+), 28 deletions(-) - -diff --git a/cpan/File-Path/lib/File/Path.pm b/cpan/File-Path/lib/File/Path.pm -index 034da1e..a824cc8 100644 ---- a/cpan/File-Path/lib/File/Path.pm -+++ b/cpan/File-Path/lib/File/Path.pm -@@ -354,21 +354,32 @@ sub _rmtree { - - # see if we can escalate privileges to get in - # (e.g. funny protection mask such as -w- instead of rwx) -- $perm &= oct '7777'; -- my $nperm = $perm | oct '700'; -- if ( -- !( -- $arg->{safe} -- or $nperm == $perm -- or chmod( $nperm, $root ) -- ) -- ) -- { -- _error( $arg, -- "cannot make child directory read-write-exec", $canon ); -- next ROOT_DIR; -+ # This uses fchmod to avoid traversing outside of the proper -+ # location (CVE-2017-6512) -+ my $root_fh; -+ if (open($root_fh, '<', $root)) { -+ my ($fh_dev, $fh_inode) = (stat $root_fh )[0,1]; -+ $perm &= oct '7777'; -+ my $nperm = $perm | oct '700'; -+ local $@; -+ if ( -+ !( -+ $arg->{safe} -+ or $nperm == $perm -+ or !-d _ -+ or $fh_dev ne $ldev -+ or $fh_inode ne $lino -+ or eval { chmod( $nperm, $root_fh ) } -+ ) -+ ) -+ { -+ _error( $arg, -+ "cannot make child directory read-write-exec", $canon ); -+ next ROOT_DIR; -+ } -+ close $root_fh; - } -- elsif ( !chdir($root) ) { -+ if ( !chdir($root) ) { - _error( $arg, "cannot chdir to child", $canon ); - next ROOT_DIR; - } -diff --git a/cpan/File-Path/t/Path.t b/cpan/File-Path/t/Path.t -index ff52fd6..956ca09 100644 ---- a/cpan/File-Path/t/Path.t -+++ b/cpan/File-Path/t/Path.t -@@ -3,7 +3,7 @@ - - use strict; - --use Test::More tests => 127; -+use Test::More tests => 126; - use Config; - use Fcntl ':mode'; - use lib 't/'; -@@ -18,6 +18,13 @@ BEGIN { - - my $Is_VMS = $^O eq 'VMS'; - -+my $fchmod_supported = 0; -+if (open my $fh, curdir()) { -+ my ($perm) = (stat($fh))[2]; -+ $perm &= 07777; -+ eval { $fchmod_supported = chmod( $perm, $fh); }; -+} -+ - # first check for stupid permissions second for full, so we clean up - # behind ourselves - for my $perm (0111,0777) { -@@ -299,16 +306,19 @@ is($created[0], $dir, "created directory (old style 3 mode undef) cross-check"); - - is(rmtree($dir, 0, undef), 1, "removed directory 3 verbose undef"); - --$dir = catdir($tmp_base,'G'); --$dir = VMS::Filespec::unixify($dir) if $Is_VMS; -+SKIP: { -+ skip "fchmod of directories not supported on this platform", 3 unless $fchmod_supported; -+ $dir = catdir($tmp_base,'G'); -+ $dir = VMS::Filespec::unixify($dir) if $Is_VMS; - --@created = mkpath($dir, undef, 0200); -+ @created = mkpath($dir, undef, 0400); - --is(scalar(@created), 1, "created write-only dir"); -+ is(scalar(@created), 1, "created read-only dir"); - --is($created[0], $dir, "created write-only directory cross-check"); -+ is($created[0], $dir, "created read-only directory cross-check"); - --is(rmtree($dir), 1, "removed write-only dir"); -+ is(rmtree($dir), 1, "removed read-only dir"); -+} - - # borderline new-style heuristics - if (chdir $tmp_base) { -@@ -450,26 +460,28 @@ SKIP: { - } - - SKIP : { -- my $skip_count = 19; -+ my $skip_count = 18; - # this test will fail on Windows, as per: - # http://perldoc.perl.org/perlport.html#chmod - - skip "Windows chmod test skipped", $skip_count - if $^O eq 'MSWin32'; -+ skip "fchmod() on directories is not supported on this platform", $skip_count -+ unless $fchmod_supported; - my $mode; - my $octal_mode; - my @inputs = ( -- 0777, 0700, 0070, 0007, -- 0333, 0300, 0030, 0003, -- 0111, 0100, 0010, 0001, -- 0731, 0713, 0317, 0371, 0173, 0137, -- 00 ); -+ 0777, 0700, 0470, 0407, -+ 0433, 0400, 0430, 0403, -+ 0111, 0100, 0110, 0101, -+ 0731, 0713, 0317, 0371, -+ 0173, 0137); - my $input; - my $octal_input; -- $dir = catdir($tmp_base, 'chmod_test'); - - foreach (@inputs) { - $input = $_; -+ $dir = catdir($tmp_base, sprintf("chmod_test%04o", $input)); - # We can skip from here because 0 is last in the list. - skip "Mode of 0 means assume user defaults on VMS", 1 - if ($input == 0 && $Is_VMS); diff --git a/gnu/packages/patches/podofo-cmake-3.12.patch b/gnu/packages/patches/podofo-cmake-3.12.patch new file mode 100644 index 0000000000..0a3c19b21a --- /dev/null +++ b/gnu/packages/patches/podofo-cmake-3.12.patch @@ -0,0 +1,19 @@ +The build fails with cmake 3.12.0. This patch will be obsolete with the next +release. + +https://sourceforge.net/p/podofo/tickets/24/attachment/podofo-cmake-3.12.patch + + +--- a/test/TokenizerTest/CMakeLists.txt 2018-07-20 18:26:02.921494293 +0200 ++++ b/test/TokenizerTest/CMakeLists.txt 2018-07-20 18:34:53.727136443 +0200 +@@ -2,10 +2,3 @@ + TARGET_LINK_LIBRARIES(TokenizerTest ${PODOFO_LIB} ${PODOFO_LIB_DEPENDS}) + SET_TARGET_PROPERTIES(TokenizerTest PROPERTIES COMPILE_FLAGS "${PODOFO_CFLAGS}") + ADD_DEPENDENCIES(TokenizerTest ${PODOFO_DEPEND_TARGET}) +- +-# Copy the test samples over to the build tree +-ADD_CUSTOM_COMMAND( +- TARGET TokenizerTest +- POST_BUILD +- COMMAND "${CMAKE_COMMAND}" -E copy_directory "${CMAKE_CURRENT_SOURCE_DIR}/objects" "${CMAKE_CURRENT_BINARY_DIR}/objects" +- ) diff --git a/gnu/packages/patches/python-cffi-x87-stack-clean.patch b/gnu/packages/patches/python-cffi-x87-stack-clean.patch new file mode 100644 index 0000000000..50243505ee --- /dev/null +++ b/gnu/packages/patches/python-cffi-x87-stack-clean.patch @@ -0,0 +1,29 @@ +Fix test that fails on i686: + +https://bitbucket.org/cffi/cffi/issues/382 + +This is a squashed version of these commits: +https://bitbucket.org/cffi/cffi/commits/ef09637b2314 +https://bitbucket.org/cffi/cffi/commits/7a76a3815340 + +diff -r 99940f1f5402 testing/cffi0/test_function.py +--- a/testing/cffi0/test_function.py Tue Feb 27 21:18:33 2018 +0100 ++++ b/testing/cffi0/test_function.py Sun Nov 11 16:26:23 2018 +0100 +@@ -45,14 +45,14 @@ + assert x != math.sin(1.23) # rounding effects + assert abs(x - math.sin(1.23)) < 1E-6 + +- def test_sin_no_return_value(self): ++ def test_lround_no_return_value(self): + # check that 'void'-returning functions work too + ffi = FFI(backend=self.Backend()) + ffi.cdef(""" +- void sin(double x); ++ void lround(double x); + """) + m = ffi.dlopen(lib_m) +- x = m.sin(1.23) ++ x = m.lround(1.23) + assert x is None + + def test_dlopen_filename(self): diff --git a/gnu/packages/patches/python-networkx2-reproducible-build.patch b/gnu/packages/patches/python-networkx2-reproducible-build.patch deleted file mode 100644 index 8274767ab8..0000000000 --- a/gnu/packages/patches/python-networkx2-reproducible-build.patch +++ /dev/null @@ -1,29 +0,0 @@ -From c065b972ed294769a41936d6b9feb336473af5d1 Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= <boskovits@gmail.com> -Date: Sat, 4 Nov 2017 15:28:47 +0100 -Subject: Fix SOURCE_DATE_EPOCH ignored bug (#2735) - -* Fix SOURCE_DATE_EPOCH ignored bug - -Fix a bug in networkx/release.py that makes build -non-reproducible. ---- - networkx/release.py | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/networkx/release.py b/networkx/release.py -index e81fc0c0..6322cf0d 100644 ---- a/networkx/release.py -+++ b/networkx/release.py -@@ -135,7 +135,7 @@ def get_revision(): - - def get_info(dynamic=True): - # Date information -- date_info = datetime.datetime.now() -+ date_info = datetime.datetime.utcfromtimestamp(int(os.environ.get('SOURCE_DATE_EPOCH', time.time()))) - date = time.asctime(date_info.timetuple()) - - revision, version, version_info, vcs_info = None, None, None, None --- -2.14.2 - diff --git a/gnu/packages/patches/python-paste-remove-website-test.patch b/gnu/packages/patches/python-paste-remove-website-test.patch deleted file mode 100644 index 93417fbe75..0000000000 --- a/gnu/packages/patches/python-paste-remove-website-test.patch +++ /dev/null @@ -1,21 +0,0 @@ -Remove the test to see if the Python Paste website is up. - -Obviously without network access there is no way for us to check this, and -it's pretty strange to test a project's website when you really mean to test -the project anyhow... - ---- a/tests/test_proxy.py 2016-02-22 19:13:04.040117767 -0800 -+++ b/tests/test_proxy.py 2016-02-22 19:13:04.040117767 -0800 -@@ -1,12 +1,3 @@ - from paste import proxy - from paste.fixture import TestApp - --def test_paste_website(): -- # Not the most robust test... -- # need to test things like POSTing to pages, and getting from pages -- # that don't set content-length. -- app = proxy.Proxy('http://pythonpaste.org') -- app = TestApp(app) -- res = app.get('/') -- assert 'documentation' in res -- diff --git a/gnu/packages/patches/python-pillow-fix-failing-tests.patch b/gnu/packages/patches/python-pillow-fix-failing-tests.patch Binary files differdeleted file mode 100644 index 2575d6f612..0000000000 --- a/gnu/packages/patches/python-pillow-fix-failing-tests.patch +++ /dev/null diff --git a/gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch b/gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch deleted file mode 100644 index 90328cc0eb..0000000000 --- a/gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch +++ /dev/null @@ -1,25 +0,0 @@ -This patch stops a test sometimes failing because of non-determinism. See -https://github.com/scikit-learn/scikit-learn/pull/9542 - -From ff9f6db6e8b59c2b3528c8137ed4054f57c1d7c4 Mon Sep 17 00:00:00 2001 -From: Hanmin Qin <qinhanmin2005@sina.com> -Date: Sun, 13 Aug 2017 22:13:49 +0800 -Subject: [PATCH] add random_state - ---- - sklearn/tests/test_kernel_ridge.py | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/sklearn/tests/test_kernel_ridge.py b/sklearn/tests/test_kernel_ridge.py -index 4750a096ac6..979875870b6 100644 ---- a/sklearn/tests/test_kernel_ridge.py -+++ b/sklearn/tests/test_kernel_ridge.py -@@ -10,7 +10,7 @@ - from sklearn.utils.testing import assert_array_almost_equal - - --X, y = make_regression(n_features=10) -+X, y = make_regression(n_features=10, random_state=0) - Xcsr = sp.csr_matrix(X) - Xcsc = sp.csc_matrix(X) - Y = np.array([y, y]).T diff --git a/gnu/packages/patches/python-testtools.patch b/gnu/packages/patches/python-testtools.patch new file mode 100644 index 0000000000..42536e50f9 --- /dev/null +++ b/gnu/packages/patches/python-testtools.patch @@ -0,0 +1,57 @@ +https://github.com/testing-cabal/testtools/commit/29004731f9c480b7c44a9c2605513d50d372898f.patch +Should be fixed in the next release + +From 29004731f9c480b7c44a9c2605513d50d372898f Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Miro=20Hron=C4=8Dok?= <miro@hroncok.cz> +Date: Thu, 17 May 2018 17:52:26 +0200 +Subject: [PATCH] Fix the tests on Python 3.7 + +Exception's repr got changed not to include trailing comma + +Fixes https://github.com/testing-cabal/testtools/issues/270 +--- + .travis.yml | 1 + + testtools/tests/matchers/test_exception.py | 11 +++++++++-- + 2 files changed, 10 insertions(+), 2 deletions(-) + +diff --git a/.travis.yml b/.travis.yml +index 7f1f4db7..784608e0 100644 +--- a/.travis.yml ++++ b/.travis.yml +@@ -5,6 +5,7 @@ python: + - "3.4" + - "3.5" + - "3.6" ++ - "3.7-dev" + - "pypy" + + install: +diff --git a/testtools/tests/matchers/test_exception.py b/testtools/tests/matchers/test_exception.py +index 6cd80af1..acd39252 100644 +--- a/testtools/tests/matchers/test_exception.py ++++ b/testtools/tests/matchers/test_exception.py +@@ -32,15 +32,22 @@ class TestMatchesExceptionInstanceInterface(TestCase, TestMatchersInterface): + matches_matches = [error_foo] + matches_mismatches = [error_bar, error_base_foo] + ++ if sys.version_info >= (3, 7): ++ # exception's repr has changed ++ _e = '' ++ else: ++ _e = ',' ++ + str_examples = [ +- ("MatchesException(Exception('foo',))", ++ ("MatchesException(Exception('foo'%s))" % _e, + MatchesException(Exception('foo'))) + ] + describe_examples = [ + ("%r is not a %r" % (Exception, ValueError), + error_base_foo, + MatchesException(ValueError("foo"))), +- ("ValueError('bar',) has different arguments to ValueError('foo',).", ++ ("ValueError('bar'%s) has different arguments to ValueError('foo'%s)." ++ % (_e, _e), + error_bar, + MatchesException(ValueError("foo"))), + ] diff --git a/gnu/packages/patches/python2-CVE-2018-1060.patch b/gnu/packages/patches/python2-CVE-2018-1060.patch deleted file mode 100644 index 5eb7ccfbc9..0000000000 --- a/gnu/packages/patches/python2-CVE-2018-1060.patch +++ /dev/null @@ -1,20 +0,0 @@ -Fix CVE-2018-1060: -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-1060 - -Taken from upstream commit (sans test and NEWS): -https://github.com/python/cpython/commit/e052d40cea15f582b50947f7d906b39744dc62a2 - -diff --git a/Lib/poplib.py b/Lib/poplib.py -index b91e5f72d2ca..a238510b38fc 100644 ---- a/Lib/poplib.py -+++ b/Lib/poplib.py -@@ -274,7 +274,7 @@ def rpop(self, user): - return self._shortcmd('RPOP %s' % user) - - -- timestamp = re.compile(r'\+OK.*(<[^>]+>)') -+ timestamp = re.compile(br'\+OK.[^<]*(<.*>)') - - def apop(self, user, secret): - """Authorisation - diff --git a/gnu/packages/patches/python2-CVE-2018-1061.patch b/gnu/packages/patches/python2-CVE-2018-1061.patch deleted file mode 100644 index 6caab24b4d..0000000000 --- a/gnu/packages/patches/python2-CVE-2018-1061.patch +++ /dev/null @@ -1,20 +0,0 @@ -Fix CVE-2018-1061: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-1061 - -Taken from upstream commit (sans test and NEWS): -https://github.com/python/cpython/commit/e052d40cea15f582b50947f7d906b39744dc62a2 - -diff --git a/Lib/difflib.py b/Lib/difflib.py -index 1c6fbdbedcb7..788a92df3f89 100644 ---- a/Lib/difflib.py -+++ b/Lib/difflib.py -@@ -1103,7 +1103,7 @@ def _qformat(self, aline, bline, atags, btags): - - import re - --def IS_LINE_JUNK(line, pat=re.compile(r"\s*#?\s*$").match): -+def IS_LINE_JUNK(line, pat=re.compile(r"\s*(?:#\s*)?$").match): - r""" - Return 1 for ignorable line: iff `line` is blank or contains a single '#'. - diff --git a/gnu/packages/patches/qt-5-renameat2.patch b/gnu/packages/patches/qt-5-renameat2.patch new file mode 100644 index 0000000000..036070c7ff --- /dev/null +++ b/gnu/packages/patches/qt-5-renameat2.patch @@ -0,0 +1,35 @@ +Avoid conflicting declaration of 'renameat2' on glibc 2.28 +(see <https://github.com/meta-qt5/meta-qt5/issues/94>.) + +Patch from <https://github.com/meta-qt5/meta-qt5/pull/95> +by Andreas Müller <schnitzeltony@gmail.com>. + +--- + src/corelib/io/qfilesystemengine_unix.cpp | 11 ++++++++++++ + 1 file changed, 11 insertions(+) + +diff --git a/src/corelib/io/qfilesystemengine_unix.cpp b/src/corelib/io/qfilesystemengine_unix.cpp +index be6ce48d0cb..1bf1bebc7f1 100644 +--- a/qtbase/src/corelib/io/qfilesystemengine_unix.cpp ++++ b/qtbase/src/corelib/io/qfilesystemengine_unix.cpp +@@ -98,6 +98,17 @@ extern "C" NSString *NSTemporaryDirectory(); + # define FICLONE _IOW(0x94, 9, int) + #endif + ++// renameat2/statx features for non bootstrapped build ++#ifndef QT_BOOTSTRAPPED ++#ifdef __GLIBC_PREREQ ++# define QT_FEATURE_renameat2 (__GLIBC_PREREQ(2, 28) ? 1 : -1) ++# define QT_FEATURE_statx (__GLIBC_PREREQ(2, 28) ? 1 : -1) ++#else ++# define QT_FEATURE_renameat2 -1 ++# define QT_FEATURE_statx -1 ++#endif ++#endif ++ + # if defined(Q_OS_ANDROID) + // renameat2() and statx() are disabled on Android because quite a few systems + // come with sandboxes that kill applications that make system calls outside a +-- +2.14.4 + diff --git a/gnu/packages/patches/snappy-add-O2-flag-in-CmakeLists.txt.patch b/gnu/packages/patches/snappy-add-O2-flag-in-CmakeLists.txt.patch new file mode 100644 index 0000000000..561763dabe --- /dev/null +++ b/gnu/packages/patches/snappy-add-O2-flag-in-CmakeLists.txt.patch @@ -0,0 +1,36 @@ +From: Tobias Geerinckx-Rice <me@tobias.gr> +Date: Sun, 26 Aug 2018 17:24:42 +0200 +Subject: [PATCH] snappy: Add O2 flag in CmakeLists.txt. + +Use ‘-O2’ optimisation when building with CMake, as is already done when +using the Makefile. This patch was copied verbatim from the Snappy +mailing list[0]. + +[0]: <snappy-compression@googlegroups.com> + +From 903c72fb29b2db07b4abc38a5feb83d88f739d80 Mon Sep 17 00:00:00 2001 +From: huangwenjun <huangwenjun-hf@loongson.cn> +Date: Fri, 10 Aug 2018 17:17:35 +0800 +Subject: [PATCH] Add O2 optimize flag in CmakeLists.txt. + +--- + CMakeLists.txt | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 62ecd09..29e0cdc 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -6,6 +6,9 @@ set(CMAKE_CXX_STANDARD 11) + set(CMAKE_CXX_STANDARD_REQUIRED ON) + set(CMAKE_CXX_EXTENSIONS OFF) + ++SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O2") ++SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2") ++ + # BUILD_SHARED_LIBS is a standard CMake variable, but we declare it here to make + # it prominent in the GUI. + option(BUILD_SHARED_LIBS "Build shared libraries(DLLs)." OFF) +-- +2.1.0 + diff --git a/gnu/packages/patches/swig-guile-gc.patch b/gnu/packages/patches/swig-guile-gc.patch new file mode 100644 index 0000000000..0e745a6247 --- /dev/null +++ b/gnu/packages/patches/swig-guile-gc.patch @@ -0,0 +1,76 @@ +Fix garbage collection for Guile versions >= 2.0.12. This issue showed +up when running the tests on i686-linux. + +Taken from this upstream commit: +https://github.com/swig/swig/commit/38f2ab0c30e369e63bbd0a6152108488d0de68e1 + +diff --git a/Lib/guile/guile_scm_run.swg b/Lib/guile/guile_scm_run.swg +index 274f197158..0d04cb7c62 100644 +--- a/Lib/guile/guile_scm_run.swg ++++ b/Lib/guile/guile_scm_run.swg +@@ -99,6 +99,7 @@ SWIG_Guile_scm2newstr(SCM str, size_t *len) { + static int swig_initialized = 0; + static scm_t_bits swig_tag = 0; + static scm_t_bits swig_collectable_tag = 0; ++static scm_t_bits swig_finalized_tag = 0; + static scm_t_bits swig_destroyed_tag = 0; + static scm_t_bits swig_member_function_tag = 0; + static SCM swig_make_func = SCM_EOL; +@@ -163,7 +164,19 @@ SWIG_Guile_PointerType(SCM object) + } + else scm_wrong_type_arg("SWIG-Guile-PointerType", 1, object); + } +- ++ ++SWIGINTERN int ++SWIG_Guile_IsValidSmob(SCM smob) ++{ ++ /* We do not accept smobs representing destroyed pointers, but we have to ++ allow finalized smobs because Guile >= 2.0.12 sets all smob instances ++ to the 'finalized' type before calling their 'free' function. This change ++ was introduced to Guile in commit 8dff3af087c6eaa83ae0d72aa8b22aef5c65d65d */ ++ return SCM_SMOB_PREDICATE(swig_tag, smob) ++ || SCM_SMOB_PREDICATE(swig_collectable_tag, smob) ++ || SCM_SMOB_PREDICATE(swig_finalized_tag, smob); ++} ++ + SWIGINTERN int + SWIG_Guile_ConvertPtr(SCM s, void **result, swig_type_info *type, int flags) + { +@@ -179,8 +192,7 @@ SWIG_Guile_ConvertPtr(SCM s, void **result, swig_type_info *type, int flags) + *result = SCM_POINTER_VALUE(s); + return SWIG_OK; + #endif /* if SCM_MAJOR_VERSION >= 2 */ +- } else if (SCM_SMOB_PREDICATE(swig_tag, smob) || SCM_SMOB_PREDICATE(swig_collectable_tag, smob)) { +- /* we do not accept smobs representing destroyed pointers */ ++ } else if (SWIG_Guile_IsValidSmob(smob)) { + from = (swig_type_info *) SCM_CELL_WORD_2(smob); + if (!from) return SWIG_ERROR; + if (type) { +@@ -239,7 +251,7 @@ SWIG_Guile_MarkPointerNoncollectable(SCM s) + { + SCM smob = SWIG_Guile_GetSmob(s); + if (!SCM_NULLP(smob)) { +- if (SCM_SMOB_PREDICATE(swig_tag, smob) || SCM_SMOB_PREDICATE(swig_collectable_tag, smob)) { ++ if (SWIG_Guile_IsValidSmob(smob)) { + SCM_SET_CELL_TYPE(smob, swig_tag); + } + else scm_wrong_type_arg(NULL, 0, s); +@@ -252,7 +264,7 @@ SWIG_Guile_MarkPointerDestroyed(SCM s) + { + SCM smob = SWIG_Guile_GetSmob(s); + if (!SCM_NULLP(smob)) { +- if (SCM_SMOB_PREDICATE(swig_tag, smob) || SCM_SMOB_PREDICATE(swig_collectable_tag, smob)) { ++ if (SWIG_Guile_IsValidSmob(smob)) { + SCM_SET_CELL_TYPE(smob, swig_destroyed_tag); + } + else scm_wrong_type_arg(NULL, 0, s); +@@ -419,6 +431,8 @@ SWIG_Guile_Init () + scm_set_smob_print(swig_collectable_tag, print_collectable_swig); + scm_set_smob_equalp(swig_collectable_tag, equalp_swig); + scm_set_smob_free(swig_collectable_tag, free_swig); ++ /* For Guile >= 2.0.12. See libguile/smob.c:clear_smobnum */ ++ swig_finalized_tag = swig_collectable_tag & ~0xff00; + } + if (ensure_smob_tag(swig_module, &swig_destroyed_tag, + "destroyed-swig-pointer", "destroyed-swig-pointer-tag")) { diff --git a/gnu/packages/patches/texinfo-5-perl-compat.patch b/gnu/packages/patches/texinfo-5-perl-compat.patch new file mode 100644 index 0000000000..f16d6b4da8 --- /dev/null +++ b/gnu/packages/patches/texinfo-5-perl-compat.patch @@ -0,0 +1,19 @@ +Fix a deprecation warning with newer Perl that breaks some tests. + +--- a/tp/Texinfo/Parser.pm ++++ b/tp/Texinfo/Parser.pm +@@ -5438,12 +5438,12 @@ + } + } elsif ($command eq 'clickstyle') { + # REMACRO +- if ($line =~ /^\s+@([[:alnum:]][[:alnum:]\-]*)({})?\s*/) { ++ if ($line =~ /^\s+@([[:alnum:]][[:alnum:]\-]*)(\{})?\s*/) { + $args = ['@'.$1]; + $self->{'clickstyle'} = $1 + unless(_ignore_global_commands($self)); + $remaining = $line; +- $remaining =~ s/^\s+@([[:alnum:]][[:alnum:]\-]*)({})?\s*(\@(c|comment)((\@|\s+).*)?)?//; ++ $remaining =~ s/^\s+@([[:alnum:]][[:alnum:]\-]*)(\{})?\s*(\@(c|comment)((\@|\s+).*)?)?//; + $has_comment = 1 if (defined($4)); + } else { + $self->line_error (sprintf($self->__( diff --git a/gnu/packages/patches/texinfo-perl-compat.patch b/gnu/packages/patches/texinfo-perl-compat.patch new file mode 100644 index 0000000000..a7348fde0d --- /dev/null +++ b/gnu/packages/patches/texinfo-perl-compat.patch @@ -0,0 +1,51 @@ +Fix compatibility with newer Perls. + +The first patch is taken from upstream: +https://svn.savannah.gnu.org/viewvc/texinfo?view=revision&revision=8008 + +The second gets rid of a deprecation warning that breaks some tests. +Taken from Fedora: <https://bugzilla.redhat.com/show_bug.cgi?id=1590308>. + +--- trunk/tp/Texinfo/Convert/XSParagraph/xspara.c 2017/04/30 14:57:26 7765 ++++ trunk/tp/Texinfo/Convert/XSParagraph/xspara.c 2018/07/13 15:39:29 8008 +@@ -248,6 +248,11 @@ + + dTHX; + ++#if PERL_VERSION > 27 || (PERL_VERSION == 27 && PERL_SUBVERSION > 8) ++ /* needed due to thread-safe locale handling in newer perls */ ++ switch_to_global_locale(); ++#endif ++ + if (setlocale (LC_CTYPE, "en_US.UTF-8") + || setlocale (LC_CTYPE, "en_US.utf8")) + goto success; +@@ -320,6 +325,10 @@ + { + success: ; + free (utf8_locale); ++#if PERL_VERSION > 27 || (PERL_VERSION == 27 && PERL_SUBVERSION > 8) ++ /* needed due to thread-safe locale handling in newer perls */ ++ sync_locale(); ++#endif + /* + fprintf (stderr, "tried to set LC_CTYPE to UTF-8.\n"); + fprintf (stderr, "character encoding is: %s\n", + +diff -up texinfo-6.5/tp/Texinfo/Parser.pm.orig texinfo-6.5/tp/Texinfo/Parser.pm +--- texinfo-6.5/tp/Texinfo/Parser.pm.orig 2018-06-12 13:40:29.356030136 +0200 ++++ texinfo-6.5/tp/Texinfo/Parser.pm 2018-06-12 13:41:28.357725639 +0200 +@@ -5478,11 +5478,11 @@ sub _parse_special_misc_command($$$$) + } + } elsif ($command eq 'clickstyle') { + # REMACRO +- if ($line =~ /^\s+@([[:alnum:]][[:alnum:]\-]*)({})?\s*/) { ++ if ($line =~ /^\s+@([[:alnum:]][[:alnum:]\-]*)(\{})?\s*/) { + $args = ['@'.$1]; + $self->{'clickstyle'} = $1; + $remaining = $line; +- $remaining =~ s/^\s+@([[:alnum:]][[:alnum:]\-]*)({})?\s*(\@(c|comment)((\@|\s+).*)?)?//; ++ $remaining =~ s/^\s+@([[:alnum:]][[:alnum:]\-]*)(\{})?\s*(\@(c|comment)((\@|\s+).*)?)?//; + $has_comment = 1 if (defined($4)); + } else { + $self->line_error (sprintf($self->__( diff --git a/gnu/packages/pcre.scm b/gnu/packages/pcre.scm index 5719b7bb45..564a23d012 100644 --- a/gnu/packages/pcre.scm +++ b/gnu/packages/pcre.scm @@ -35,7 +35,7 @@ (define-public pcre (package (name "pcre") - (version "8.41") + (version "8.42") (source (origin (method url-fetch) (uri (list @@ -46,11 +46,12 @@ version "/pcre-" version ".tar.bz2"))) (sha256 (base32 - "0c5m469p5pd7jip621ipq6hbgh7128lzh7xndllfgh77ban7wb76")))) + "00ckpzlgyr16bnqx8fawa3afjgqxw5yxgs2l081vw23qi1y4pl1c")))) (build-system gnu-build-system) (outputs '("out" ;library & headers "bin" ;depends on Readline (adds 20MiB to the closure) - "doc")) ;1.8 MiB of HTML + "doc" ;1.8 MiB of HTML + "static")) ;1.8 MiB static libraries (inputs `(("bzip2" ,bzip2) ("readline" ,readline) ("zlib" ,zlib))) @@ -63,7 +64,19 @@ "--enable-unicode-properties" "--enable-pcre16" "--enable-pcre32" - "--enable-jit"))) + "--enable-jit") + #:phases (modify-phases %standard-phases + (add-after 'install 'move-static-libs + (lambda* (#:key outputs #:allow-other-keys) + (let ((source (string-append (assoc-ref outputs "out") "/lib")) + (static (string-append (assoc-ref outputs "static") "/lib"))) + (mkdir-p static) + (for-each (lambda (lib) + (link lib (string-append static "/" + (basename lib))) + (delete-file lib)) + (find-files source "\\.a$")) + #t)))))) (synopsis "Perl Compatible Regular Expressions") (description "The PCRE library is a set of functions that implement regular expression diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 9ffc5cb9bb..b89d49fd52 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -83,20 +83,20 @@ (package (name "poppler") (replacement poppler/fixed) - (version "0.63.0") + (version "0.68.0") (source (origin (method url-fetch) (uri (string-append "https://poppler.freedesktop.org/poppler-" version ".tar.xz")) (sha256 (base32 - "04d1z1ygyb3llzc6s6c99wxafvljj2sc5b76djif34f7mzfqmk17")))) + "0n0f7mv24lzv9p3dlzakpdhqg7ygcvl6l40grcz95xldzgq083gr")))) (build-system cmake-build-system) ;; FIXME: ;; use libcurl: no (inputs `(("fontconfig" ,fontconfig) ("freetype" ,freetype) - ("libjpeg" ,libjpeg) + ("libjpeg" ,libjpeg-turbo) ("libpng" ,libpng) ("libtiff" ,libtiff) ("lcms" ,lcms) @@ -107,8 +107,12 @@ ;; GLib. But of course, that Cairo must not depend on Poppler. ("cairo" ,(package (inherit cairo) (inputs (alist-delete "poppler" - (package-inputs cairo))))) - ("glib" ,glib))) + (package-inputs cairo))))))) + (propagated-inputs + ;; As per poppler-cairo and poppler-glib.pc. + ;; XXX: Ideally we'd propagate Cairo too, but that would require a + ;; different solution to the circular dependency mentioned above. + `(("glib" ,glib))) (native-inputs `(("pkg-config" ,pkg-config) ("glib" ,glib "bin") ; glib-mkenums, etc. @@ -509,7 +513,7 @@ by using the poppler rendering engine.") ;; For tests. ("check" ,check) - ("xorg-server" ,xorg-server-1.19.3))) + ("xorg-server" ,xorg-server-for-tests))) (inputs `(("sqlite" ,sqlite))) ;; Listed in 'Requires.private' of 'zathura.pc'. (propagated-inputs `(("cairo" ,cairo) @@ -553,7 +557,8 @@ interaction.") "/podofo-" version ".tar.gz")) (sha256 (base32 - "0wj0y4zcmj4q79wrn3vv3xq4bb0vhhxs8yifafwy9f2sjm83c5p9")))) + "0wj0y4zcmj4q79wrn3vv3xq4bb0vhhxs8yifafwy9f2sjm83c5p9")) + (patches (search-patches "podofo-cmake-3.12.patch")))) (build-system cmake-build-system) (native-inputs `(("cppunit" ,cppunit) @@ -656,14 +661,14 @@ line tools for batch rendering @command{pdfdraw}, rewriting files (define-public qpdf (package (name "qpdf") - (version "8.1.0") + (version "8.2.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/qpdf/qpdf/" version "/qpdf-" version ".tar.gz")) (sha256 (base32 - "1m3hcgip6bzjx4gd7wq1328p8zi3pq5savzncdyln6l0lcklh7vx")) + "1jdb0jj72fjdp6xip4m7yz31r5x13zs7h4smnxsycgw3vbmx6igl")) (modules '((guix build utils))) (snippet ;; Replace shebang with the bi-lingual shell/Perl trick to remove diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm index 98b4e392c7..d0abb39254 100644 --- a/gnu/packages/perl-check.scm +++ b/gnu/packages/perl-check.scm @@ -82,7 +82,7 @@ lexically, just dynamically.") '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-env - (lambda _ (setenv "PERL_USE_UNSAFE_INC" "1")))))) + (lambda _ (setenv "PERL_USE_UNSAFE_INC" "1") #t))))) (propagated-inputs `(("perl-importer" ,perl-importer) ("perl-term-table" ,perl-term-table) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index cbdf070e89..8c854e88df 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -43,9 +43,9 @@ #:use-module (gnu packages) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (guix build-system perl) - #:use-module (guix utils) ;substitute-keyword-arguments for perl-5.26.2 #:use-module (gnu packages base) #:use-module (gnu packages compression) #:use-module (gnu packages freedesktop) @@ -62,17 +62,15 @@ ;; Yeah, Perl... It is required early in the bootstrap process by Linux. (package (name "perl") - (version "5.26.1") - (replacement perl/fixed) + (version "5.28.0") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/src/5.0/perl-" version ".tar.gz")) (sha256 (base32 - "1p81wwvr5jb81m41d07kfywk5gvbk0axdrnvhc2aghcdbr4alqz7")) + "1a3f822lcl8dr8v0hk80yyhpzqlljg49z9flb48rs3nbsij9z4ky")) (patches (search-patches - "perl-file-path-CVE-2017-6512.patch" "perl-no-sys-dirs.patch" "perl-autosplit-default-time.patch" "perl-deterministic-ordering.patch" @@ -163,41 +161,6 @@ more.") (home-page "http://www.perl.org/") (license gpl1+))) ; or "Artistic" -;; Fixes CVE-2018-6797, CVE-2018-6798, and CVE-2018-6913. -;; See <https://metacpan.org/changes/release/SHAY/perl-5.26.2>. -(define perl-5.26.2 - (package - (inherit perl) - (version "5.26.2") - (source (origin - (inherit (package-source perl)) - (uri (string-append "mirror://cpan/src/5.0/perl-" - version ".tar.gz")) - (patches (append (origin-patches (package-source perl)) - (search-patches "perl-archive-tar-CVE-2018-12015.patch"))) - (sha256 - (base32 - "03gpnxx1g6hvlh0v4aqx00580h787sfywp1vlvw64q2xcbm9qbsp")))))) - -;; When grafting perl, complications arise when the replacement perl has a -;; different version number than the original. So, here we create a version -;; of perl-5.26.2 that thinks it is version 5.26.1. See -;; <https://bugs.gnu.org/31210> and <https://bugs.gnu.org/31216>. -(define perl/fixed - (package - (inherit perl-5.26.2) - (version "5.26.1") - (arguments - (substitute-keyword-arguments (package-arguments perl-5.26.2) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'revert-perl-subversion - (lambda _ - (substitute* "patchlevel.h" - (("^#define PERL_SUBVERSION 2") - "#define PERL_SUBVERSION 1")) - #t)))))))) - (define-public perl-algorithm-c3 (package (name "perl-algorithm-c3") @@ -2914,7 +2877,8 @@ interface for the RFC 2104 HMAC mechanism.") (add-after 'build 'set-permissions (lambda _ ;; Make MD5.so read-write so it can be stripped. - (chmod "blib/arch/auto/Digest/MD5/MD5.so" #o755)))))) + (chmod "blib/arch/auto/Digest/MD5/MD5.so" #o755) + #t))))) (home-page "https://metacpan.org/release/Digest-MD5") (synopsis "Perl interface to the MD-5 algorithm") (description @@ -3040,7 +3004,7 @@ also known as JIS 2000.") '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-env - (lambda _ (setenv "PERL_USE_UNSAFE_INC" "1")))))) + (lambda _ (setenv "PERL_USE_UNSAFE_INC" "1") #t))))) (home-page "https://metacpan.org/release/Encode-HanExtra") (synopsis "Additional Chinese encodings") (description "This Perl module provides Chinese encodings that are not @@ -4315,7 +4279,8 @@ run interactively. It also has an option to capture output/error buffers.") (lambda _ ;; This test fails, and we're not really interested in ;; it, so disable it. - (delete-file "t/win32_compile.t")))))) + (delete-file "t/win32_compile.t") + #t))))) (home-page "https://metacpan.org/release/IPC-Run") (synopsis "Run system() and background procs w/ piping, redirs, ptys") (description "IPC::Run allows you run and interact with child processes @@ -5286,7 +5251,7 @@ examine the contents, and perform some simple tasks. It can also load the (define-public perl-module-runtime (package (name "perl-module-runtime") - (version "0.014") + (version "0.016") (source (origin (method url-fetch) @@ -5294,7 +5259,7 @@ examine the contents, and perform some simple tasks. It can also load the "Module-Runtime-" version ".tar.gz")) (sha256 (base32 - "19326f094jmjs6mgpwkyisid54k67w34br8yfh0gvaaml87gwi2c")))) + "097hy2czwkxlppri32m599ph0xfvfsbf0a5y23a4fdc38v32wc38")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build))) (home-page "https://metacpan.org/release/Module-Runtime") @@ -6904,7 +6869,8 @@ directory specifications in a cross-platform manner.") (substitute* "Cwd.pm" (("'/bin/pwd'") (string-append "'" (assoc-ref inputs "coreutils") - "/bin/pwd'")))))))) + "/bin/pwd'"))) + #t))))) (inputs `(("coreutils" ,coreutils))) (home-page "https://metacpan.org/release/PathTools") @@ -9036,6 +9002,9 @@ defined by Annex #11 is used to determine breaking positions.") (base32 "1xnhazbdvpyfpnxd90krzhxkvabf8fa2ji6xzlrf75j6nz8251zs")))) (build-system perl-build-system) + ;; FIXME: Tests fail on 32-bit architectures: + ;; <https://rt.cpan.org/Public/Bug/Display.html?id=127007>. + (arguments `(#:tests? ,(target-64bit?))) (native-inputs `(("perl-test-fatal" ,perl-test-fatal) ("perl-test-leaktrace" ,perl-test-leaktrace) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index afa5022c37..aa9c93622f 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -227,7 +227,8 @@ MTP, and much more.") (pm (find-files out "^ExifTool\\.pm$")) (lib (dirname (dirname (car pm))))) (wrap-program (string-append out "/bin/exiftool") - `("PERL5LIB" prefix (,lib))))))))) + `("PERL5LIB" prefix (,lib))) + #t)))))) (home-page "https://metacpan.org/release/Image-ExifTool") (synopsis "Program and Perl library to manipulate EXIF and other metadata") (description "This package provides the @code{exiftool} command and the diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm index a22591d377..a28cb31e5c 100644 --- a/gnu/packages/php.scm +++ b/gnu/packages/php.scm @@ -50,16 +50,6 @@ #:use-module (guix build-system gnu) #:use-module ((guix licenses) #:prefix license:)) -(define gd-for-php - (package - (inherit gd) - (source (origin - (inherit (package-source gd)) - (patches (search-patches "gd-fix-tests-on-i686.patch" - "gd-freetype-test-failure.patch" - "gd-CVE-2018-5711.patch" - "gd-CVE-2018-1000222.patch")))))) - (define-public php (package (name "php") @@ -318,7 +308,7 @@ ("curl" ,curl) ("cyrus-sasl" ,cyrus-sasl) ("freetype" ,freetype) - ("gd" ,gd-for-php) + ("gd" ,gd) ("gdbm" ,gdbm) ("glibc" ,glibc) ("gmp" ,gmp) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 1d08578c3d..1c7640ac5f 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -341,13 +341,13 @@ password storage.") (define-public python-certifi (package (name "python-certifi") - (version "2017.1.23") + (version "2018.8.13") (source (origin (method url-fetch) (uri (pypi-uri "certifi" version)) (sha256 (base32 - "1klrzl3hgvcf2mjk00g0k3kk1p2z27vzwnxivwar4vhjmjvpz1w1")))) + "1x7jy10rz3100g9iw7c2czcw2z4lqfaalsd8yg991l4d82hnh7ac")))) (build-system python-build-system) (home-page "https://certifi.io/") (synopsis "Python CA certificate bundle") diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 55b8942ac9..03db842531 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr> -;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017 Christopher Baines <mail@cbaines.net> ;;; Copyright © 2016, 2017 Danny Milosavljevic <dannym+a@scratchpost.org> ;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr> @@ -1405,14 +1405,14 @@ authenticated session objects providing things like keep-alive.") (define-public python-urllib3 (package (name "python-urllib3") - (version "1.18.1") + (version "1.23") (source (origin (method url-fetch) (uri (pypi-uri "urllib3" version)) (sha256 (base32 - "1wb8aqnq53vzh2amrv8kc66f3h6fx217y0q62y6n30a64p2yqmam")))) + "1bvbd35q3zdcd7gsv38fwpizy7p06dr0154g5gfybrvnbvhwb2m6")))) (build-system python-build-system) (arguments `(#:tests? #f)) (native-inputs @@ -2672,19 +2672,25 @@ available in Django, but is a standalone package.") (define-public python-paste (package (name "python-paste") - (version "2.0.3") + (version "3.0.4") (source (origin (method url-fetch) (uri (pypi-uri "Paste" version)) (sha256 (base32 - "062jk0nlxf6lb2wwj6zc20rlvrwsnikpkh90y0dn8cjch93s6ii3")) - (patches (search-patches "python-paste-remove-website-test.patch" - "python-paste-remove-timing-test.patch")))) + "01w26w9jyfkh0mfydhfz3dwy3pj3fw7mzvj0lna3vs8hyx1hwl0n")) + (patches (search-patches "python-paste-remove-timing-test.patch")) + (modules '((guix build utils))) + (snippet + '(begin + ;; This test calls out to the internet. + (delete-file "tests/test_proxy.py") #t)))) (build-system python-build-system) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner) + ("python-nose" ,python-nose))) (propagated-inputs `(("python-six" ,python-six))) (home-page "http://pythonpaste.org") diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 868fa70e19..c68aa31173 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -143,12 +143,13 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system python) #:use-module (guix build-system trivial) - #:use-module (srfi srfi-1)) + #:use-module (srfi srfi-1) + #:use-module (srfi srfi-26)) (define-public python-2.7 (package (name "python2") - (version "2.7.14") + (version "2.7.15") (replacement python-2/fixed) (source (origin @@ -157,7 +158,7 @@ version "/Python-" version ".tar.xz")) (sha256 (base32 - "0rka541ys16jwzcnnvjp2v12m4cwgd2jp6wj4kj511p715pb5zvi")) + "0x2mvz9dp11wj7p5ccvmk9s0hzjk2fa1m462p395l4r6bfnb3n92")) (patches (search-patches "python-2.7-search-paths.patch" "python-2-deterministic-build-info.patch" "python-2.7-site-prefixes.patch" @@ -182,23 +183,7 @@ "tk")) ;tkinter; adds 50 MiB to the closure (build-system gnu-build-system) (arguments - `(;; 356 tests OK. - ;; 6 tests failed: - ;; test_compileall test_distutils test_import test_shutil test_socket - ;; test_subprocess - ;; 39 tests skipped: - ;; test_aepack test_al test_applesingle test_bsddb test_bsddb185 - ;; test_bsddb3 test_cd test_cl test_codecmaps_cn test_codecmaps_hk - ;; test_codecmaps_jp test_codecmaps_kr test_codecmaps_tw test_curses - ;; test_dl test_gdb test_gl test_imageop test_imgfile test_ioctl - ;; test_kqueue test_linuxaudiodev test_macos test_macostools - ;; test_msilib test_ossaudiodev test_scriptpackages test_smtpnet - ;; test_socketserver test_startfile test_sunaudiodev test_timeout - ;; test_tk test_ttk_guionly test_urllib2net test_urllibnet - ;; test_winreg test_winsound test_zipfile64 - ;; 4 skips unexpected on linux2: - ;; test_bsddb test_bsddb3 test_gdb test_ioctl - #:test-target "test" + `(#:test-target "test" #:configure-flags (list "--enable-shared" ;allow embedding "--with-system-ffi" ;build ctypes @@ -223,11 +208,6 @@ "Lib/test/support/__init__.py" "Lib/test/test_subprocess.py")) (("/bin/sh") (which "sh"))) - - ;; Use zero as the timestamp in .pyc files so that builds are - ;; deterministic. TODO: Remove it when this variable is set in - ;; gnu-build-system.scm. - (setenv "SOURCE_DATE_EPOCH" "1") #t)) (add-before 'configure 'do-not-record-configure-flags (lambda* (#:key configure-flags #:allow-other-keys) @@ -285,15 +265,6 @@ file)))))) (call-with-output-file "__init__.py" (const #t)) #t))))))) - (add-before 'strip 'make-libraries-writable - (lambda* (#:key outputs #:allow-other-keys) - ;; Make .so files writable so they can be stripped. - (let ((out (assoc-ref outputs "out"))) - (for-each (lambda (file) - (chmod file #o755)) - (find-files (string-append out "/lib") - "\\.so")) - #t))) (add-after 'install 'move-tk-inter (lambda* (#:key outputs #:allow-other-keys) ;; When Tkinter support is built move it to a separate output so @@ -353,9 +324,7 @@ data types.") (inherit (package-source python-2)) (patches (append (origin-patches (package-source python-2)) - (search-patches "python2-CVE-2018-1060.patch" - "python2-CVE-2018-1061.patch" - "python2-CVE-2018-14647.patch" + (search-patches "python2-CVE-2018-14647.patch" "python2-CVE-2018-1000802.patch"))))))) (define-public python2-called-python @@ -367,10 +336,10 @@ data types.") (name "python") (properties `((superseded . ,python-2))))) -(define-public python-3.6 +(define-public python-3.7 (package (inherit python-2) (name "python") - (version "3.6.5") + (version "3.7.0") (replacement python-3/fixed) (source (origin (method url-fetch) @@ -384,66 +353,39 @@ data types.") (patch-flags '("-p0")) (sha256 (base32 - "19l7inxm056jjw33zz97z0m02hsi7jnnx5kyb76abj5ml4xhad7l")) + "0j9mic5c9lbd2b20wka7hily7szz740wy9ilfrczxap63rnrk0h3")) (snippet '(begin (for-each delete-file - '("Lib/ctypes/test/test_structures.py" ; fails on aarch64 - "Lib/ctypes/test/test_win32.py" ; fails on aarch64 - "Lib/test/test_fcntl.py")) ; fails on aarch64 + '(;; This test may hang and eventually run out of + ;; memory on some systems: + ;; <https://bugs.python.org/issue34587> + "Lib/test/test_socket.py" + + ;; These tests fail on AArch64. + "Lib/ctypes/test/test_win32.py" + "Lib/test/test_fcntl.py" + "Lib/test/test_posix.py")) #t)))) (arguments (substitute-keyword-arguments (package-arguments python-2) - ((#:tests? _) #t) ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'patch-timestamp-for-pyc-files - (lambda _ - ;; We set DETERMINISTIC_BUILD to only override the mtime when - ;; building with Guix, lest we break auto-compilation in - ;; environments. - (setenv "DETERMINISTIC_BUILD" "1") - (substitute* "Lib/py_compile.py" - (("source_stats\\['mtime'\\]") - "(1 if 'DETERMINISTIC_BUILD' in os.environ else source_stats['mtime'])")) - - ;; Use deterministic hashes for strings, bytes, and datetime - ;; objects. - (setenv "PYTHONHASHSEED" "0") - - ;; Reset mtime when validating bytecode header. - (substitute* "Lib/importlib/_bootstrap_external.py" - (("source_mtime = int\\(source_stats\\['mtime'\\]\\)") - "source_mtime = 1")) - #t)) - ;; These tests fail because of our change to the bytecode - ;; validation. They fail because expected exceptions do not get - ;; thrown. This seems to be no problem. - (add-after 'unpack 'disable-broken-bytecode-tests - (lambda _ - (substitute* "Lib/test/test_importlib/source/test_file_loader.py" - (("test_bad_marshal") - "disable_test_bad_marshal") - (("test_no_marshal") - "disable_test_no_marshal") - (("test_non_code_marshal") - "disable_test_non_code_marshal")) - #t)) - ;; Unset DETERMINISTIC_BUILD to allow for tests that check that - ;; stale pyc files are rebuilt. - (add-before 'check 'allow-non-deterministic-compilation - (lambda _ (unsetenv "DETERMINISTIC_BUILD") #t)) - ;; We need to rebuild all pyc files for three different - ;; optimization levels to replace all files that were not built - ;; deterministically. - - ;; FIXME: Without this phase we have close to 2000 files that + `(modify-phases ,phases + ;; Unset SOURCE_DATE_EPOCH while running the test-suite and set it + ;; again afterwards. See <https://bugs.python.org/issue34022>. + (add-before 'check 'unset-SOURCE_DATE_EPOCH + (lambda _ (unsetenv "SOURCE_DATE_EPOCH") #t)) + (add-after 'check 'reset-SOURCE_DATE_EPOCH + (lambda _ (setenv "SOURCE_DATE_EPOCH" "1") #t)) + ;; FIXME: Without this phase we have close to 400 files that ;; differ across different builds of this package. With this phase - ;; there are about 500 files left that differ. - (add-after 'install 'rebuild-bytecode + ;; there are 44 files left that differ. + (add-after 'remove-tests 'rebuild-bytecode (lambda* (#:key outputs #:allow-other-keys) - (setenv "DETERMINISTIC_BUILD" "1") (let ((out (assoc-ref outputs "out"))) + ;; Disable hash randomization to ensure the generated .pycs + ;; are reproducible. + (setenv "PYTHONHASHSEED" "0") (for-each (lambda (opt) (format #t "Compiling with optimization level: ~a\n" @@ -455,8 +397,7 @@ data types.") "-m" "compileall" "-f" ; force rebuild ;; Don't build lib2to3, because it's Python 2 code. - ;; Also don't build obviously broken test code. - "-x" "(lib2to3|test/bad.*)" + "-x" "lib2to3/.*" ,file))) (find-files out "\\.py$"))) (list '() '("-O") '("-OO"))) @@ -469,7 +410,7 @@ data types.") "/site-packages")))))))) ;; Current 3.x version. -(define-public python-3 python-3.6) +(define-public python-3 python-3.7) (define python-3/fixed (package @@ -477,17 +418,7 @@ data types.") (source (origin (inherit (package-source python-3)) (patches (append (origin-patches (package-source python-3)) - (search-patches "python-CVE-2018-14647.patch"))))) - (arguments - (substitute-keyword-arguments (package-arguments python-3) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'delete-broken-test - (lambda _ - ;; Delete test which fails on recent kernels: - ;; <https://bugs.python.org/issue34587>. - (delete-file "Lib/test/test_socket.py") - #t)))))))) + (search-patches "python-CVE-2018-14647.patch"))))))) ;; Current major version. (define-public python python-3) @@ -715,18 +646,24 @@ by @code{binstar}, @code{binstar-build} and @code{chalmers}.") (define-public python-babel (package (name "python-babel") - (version "2.3.4") + (version "2.6.0") (source (origin (method url-fetch) (uri (pypi-uri "Babel" version)) (sha256 (base32 - "0x98qqqw35xllpcama013a9788ly84z8dm1w2wwfpxh2710c8df5")))) + "08rxmbx2s4irp0w0gmn498vns5xy0fagm0fg33xa772jiks51flc")))) (build-system python-build-system) + (native-inputs + `(("python-freezegun" ,python-freezegun) + ("python-pytest" ,python-pytest))) (propagated-inputs `(("python-pytz" ,python-pytz))) - (arguments `(#:tests? #f)) ; no test target + (arguments + `(#:phases (modify-phases %standard-phases + (replace 'check + (lambda _ (invoke "pytest" "-vv")))))) (home-page "http://babel.pocoo.org/") (synopsis "Tools for internationalizing Python applications") @@ -970,14 +907,14 @@ version identifier.") (define-public python-setuptools (package (name "python-setuptools") - (version "31.0.0") + (version "40.0.0") (source (origin (method url-fetch) - (uri (pypi-uri "setuptools" version)) + (uri (pypi-uri "setuptools" version ".zip")) (sha256 (base32 - "0ypybh4hx3bv4vhg2dc74xpj1g56ggnaffm87k4abhwjwq6wq608")) + "0pq116lr14gnc62v76nk0npkm6krb2mpp7p9ab369zgv4n7dnah1")) (modules '((guix build utils))) (snippet '(begin @@ -1273,13 +1210,13 @@ human-friendly syntax.") (define-public python-pandas (package (name "python-pandas") - (version "0.23.1") + (version "0.23.4") (source (origin (method url-fetch) (uri (pypi-uri "pandas" version)) (sha256 - (base32 "142nvwb01r2wv42y2cz40bx33hd8ffh6s6gynapg859fmzr2mdah")))) + (base32 "1x54pd7hr3y7qahx6b5bf2wzj54xvl8r3s1h4pl254pnmi3wl92v")))) (build-system python-build-system) (arguments `(#:modules ((guix build utils) @@ -1294,18 +1231,23 @@ human-friendly syntax.") (getcwd) "/build/" (car (scandir "build" (cut string-prefix? "lib." <>)))))) + ;; Disable the "strict data files" option which causes + ;; the build to error out if required data files are not + ;; available (as is the case with PyPI archives). + (substitute* "setup.cfg" + (("addopts = --strict-data-files") "addopts = ")) (with-directory-excursion build-directory ;; Delete tests that require "moto" which is not yet in Guix. (for-each delete-file '("pandas/tests/io/conftest.py" "pandas/tests/io/json/test_compression.py" + "pandas/tests/io/parser/test_network.py" "pandas/tests/io/test_excel.py" "pandas/tests/io/test_parquet.py")) - (invoke "pytest" "-v" "pandas" "-k" - (string-append - "not network and not disabled" - ;; XXX: Due to the deleted tests above. - " and not test_read_s3_jsonl"))))))))) + (invoke "pytest" "-vv" "pandas" "--skip-slow" + "--skip-network" "-k" + ;; XXX: Due to the deleted tests above. + "not test_read_s3_jsonl")))))))) (propagated-inputs `(("python-numpy" ,python-numpy) ("python-pytz" ,python-pytz) @@ -1816,14 +1758,14 @@ matching them against a list of media-ranges.") (define-public python-py (package (name "python-py") - (version "1.5.3") + (version "1.5.4") (source (origin (method url-fetch) (uri (pypi-uri "py" version)) (sha256 (base32 - "10gq2lckvgwlk9w6yzijhzkarx44hsaknd0ypa08wlnpjnsgmj99")))) + "1xxvwfn82457djf55f5n2c94699rfqnk43br8fif2r2q8gvrmm9z")))) (build-system python-build-system) (arguments ;; FIXME: "ImportError: 'test' module incorrectly imported from @@ -1831,7 +1773,9 @@ matching them against a list of media-ranges.") ;; Expected '/tmp/guix-build-python-py-1.4.31.drv-0/py-1.4.31/py'. ;; Is this module globally installed?" '(#:tests? #f)) - (home-page "https://pylib.readthedocs.io/") + (native-inputs + `(("python-setuptools-scm" ,python-setuptools-scm))) + (home-page "https://github.com/pytest-dev/py") (synopsis "Python library for parsing, I/O, instrospection, and logging") (description "Py is a Python library for file name parsing, .ini file parsing, I/O, @@ -2233,6 +2177,42 @@ easier to build concurrent applications.") (define-public python2-pykka (package-with-python2 python-pykka)) +(define-public python-pympler + (package + (name "python-pympler") + (home-page "https://pythonhosted.org/Pympler/") + (version "0.5") + (source (origin + (method url-fetch) + (uri (pypi-uri "Pympler" version)) + (sha256 + (base32 + "03qwsbilqgvnbl3a1jmpgixbr2kq6m3fvdlzyr3wdp01bwlc85kx")))) + (build-system python-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "python" "setup.py" "test")))))) + (synopsis "Measure, monitor and analyze memory behavior") + (description + "Pympler is a development tool to measure, monitor and analyze +the memory behavior of Python objects in a running Python application. + +By pympling a Python application, detailed insight in the size and the +lifetime of Python objects can be obtained. Undesirable or unexpected +runtime behavior like memory bloat and other @samp{pymples} can easily +be identified. + +A web profiling frontend exposes process statistics, garbage +visualisation and class tracker statistics.") + (license license:asl2.0))) + +(define-public python2-pympler + (package-with-python2 python-pympler)) + (define-public python-itsdangerous (package (name "python-itsdangerous") @@ -2321,7 +2301,7 @@ object.") (define-public python-markupsafe (package (name "python-markupsafe") - (version "0.23") + (version "1.0") (source (origin (method url-fetch) @@ -2330,7 +2310,7 @@ object.") version ".tar.gz")) (sha256 (base32 - "1hvip33wva3fnmvfp9x5klqri7hpl1hkgqmjbss18nmrb7zimv54")))) + "0rdn1s8x9ni7ss8rfiacj7x1085lx8mh2zdwqslnw8xc3l4nkgm6")))) (build-system python-build-system) (home-page "https://github.com/mitsuhiko/markupsafe") (synopsis "XML/HTML/XHTML markup safe string implementation for Python") @@ -2345,14 +2325,14 @@ for Python.") (define-public python-jinja2 (package (name "python-jinja2") - (version "2.9.6") + (version "2.10") (source (origin (method url-fetch) (uri (pypi-uri "Jinja2" version)) (sha256 (base32 - "1zzrkywhziqffrzks14kzixz7nd4yh2vc0fb04a68vfd2ai03anx")))) + "190l36hfw3wb2n3n68yacjabxyb1pnxwn7vjx96cmjj002xy2jzq")))) (build-system python-build-system) (propagated-inputs `(("python-markupsafe" ,python-markupsafe))) @@ -2482,26 +2462,17 @@ reStructuredText.") (define-public python-sphinxcontrib-websupport (package (name "python-sphinxcontrib-websupport") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "sphinxcontrib-websupport" version)) (sha256 (base32 - "1f9f0wjpi9nhikbyaz6d19s7qvzdf1nq2g5dsh640fma4q9rd1bs")))) + "1ff3ix76xi1y6m99qxhaq5161ix9swwzydilvdya07mgbcvpzr4x")))) (build-system python-build-system) - (propagated-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest) - ("python-xapian-bindings" ,python-xapian-bindings))) - ;; Needed for running the test suite - (native-inputs - `(("python-six" ,python-six) - ("python-jinja2" ,python-jinja2) - ("python-docutils" ,python-docutils) - ("python-sphinx" ,python-sphinx) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-whoosh" ,python-whoosh))) + (arguments + ;; FIXME: Tests depend on Sphinx, which depends on this. + `(#:tests? #f)) (home-page "http://sphinx-doc.org/") (synopsis "Sphinx API for web applications") (description "This package provides a Python API to easily integrate @@ -2509,17 +2480,20 @@ Sphinx documentation into your web application. It provides tools to integrate Sphinx documents in web templates and to handle searches.") (license license:bsd-3))) +(define-public python2-sphinxcontrib-websupport + (package-with-python2 python-sphinxcontrib-websupport)) + (define-public python-sphinx (package (name "python-sphinx") - (version "1.5.1") + (version "1.7.7") (source (origin (method url-fetch) (uri (pypi-uri "Sphinx" version)) (sha256 (base32 - "1i8p9idnli4gr0y4x67yakbdk5w6a0xjzhrg6bg51y9d1fi7fslf")))) + "0pkkbfj7cl157q550gcs45am5y78ps0h7q6455d64s1zmw01jlvi")))) (build-system python-build-system) (arguments `(#:phases @@ -2528,7 +2502,15 @@ integrate Sphinx documents in web templates and to handle searches.") (lambda _ ;; Requires Internet access. (delete-file "tests/test_build_linkcheck.py") - (zero? (system* "make" "test"))))))) + (substitute* "tests/test_build_latex.py" + (("@pytest.mark.sphinx\\('latex', testroot='images'\\)") + "@pytest.mark.skip()")) + (when (which "python") + ;; XXX: These tests are broken when using Python2: + ;; <https://github.com/sphinx-doc/sphinx/issues/4710>. + (delete-file "tests/test_api_translator.py") + (delete-file "tests/test_setup_command.py")) + (invoke "make" "test")))))) (propagated-inputs `(("python-imagesize" ,python-imagesize) ("python-sphinx-alabaster-theme" @@ -2537,14 +2519,18 @@ integrate Sphinx documents in web templates and to handle searches.") ("python-snowballstemmer" ,python-snowballstemmer) ("python-docutils" ,python-docutils) ("python-jinja2" ,python-jinja2) + ("python-packaging" ,python-packaging) ("python-pygments" ,python-pygments) ("python-requests" ,python-requests) - ("python-six" ,python-six))) + ("python-six" ,python-six) + ("python-sphinxcontrib-websupport" ,python-sphinxcontrib-websupport))) (native-inputs `(("graphviz" ,graphviz) + ("imagemagick" ,imagemagick) ;for "convert" ("python-html5lib" ,python-html5lib) ("python-mock" ,python-mock) - ("python-nose" ,python-nose))) + ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest))) (home-page "http://sphinx-doc.org/") (synopsis "Python documentation generator") (description "Sphinx is a tool that makes it easy to create documentation @@ -2553,62 +2539,6 @@ sources.") (license license:bsd-3) (properties `((python2-variant . ,(delay python2-sphinx)))))) -(define-public python-sphinx-1.6 - (package (inherit python-sphinx) - (name "python-sphinx") - (version "1.6.4") - (source (origin - (method url-fetch) - (uri (pypi-uri "Sphinx" version)) - (sha256 - (base32 - "0gjakw9fv5pwqb5yyclxycs36sapxizk1vx6mkcdizmzgzcfy0gi")))) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - ;; Requires Internet access. - (delete-file "tests/test_build_linkcheck.py") - (substitute* "tests/test_build_latex.py" - (("@pytest.mark.sphinx\\('latex', testroot='images'\\)") - "@pytest.mark.skip()")) - (zero? (system* "make" "test"))))))) - (propagated-inputs - `(("python-sphinxcontrib-websupport" ,python-sphinxcontrib-websupport) - ,@(package-propagated-inputs python-sphinx))) - (native-inputs - `(("python-pytest" ,python-pytest) - ("imagemagick" ,imagemagick) ; for "convert" - ,@(package-native-inputs python-sphinx))) - (properties `((python2-variant . ,(delay python2-sphinx-1.6)))))) - -(define-public python2-sphinx-1.6 - (let ((base (package-with-python2 (strip-python2-variant python-sphinx-1.6)))) - (package - (inherit base) - (propagated-inputs - `(("python2-typing" ,python2-typing) - ,@(package-propagated-inputs base))) - (native-inputs `(("python2-enum34" ,python2-enum34) - ,@(package-native-inputs base)))))) - -(define-public python-sphinx-1.5.3 - (package - (inherit python-sphinx) - (name "python-sphinx") - (version "1.5.3") - (source - (origin - (method url-fetch) - (uri (pypi-uri "Sphinx" version)) - (sha256 - (base32 - "0kw1axswbvaavr8ggyf4qr6hnisnrzlbkkcdada69vk1x9xjassg")))) - (native-inputs - `(("python-pytest" ,python-pytest) - ,@(package-native-inputs python-sphinx))))) - (define-public python2-sphinx (let ((base (package-with-python2 (strip-python2-variant python-sphinx)))) (package @@ -2617,6 +2547,7 @@ sources.") ("python2-enum34" ,python2-enum34) ,@(package-native-inputs base))) (propagated-inputs `(("python2-pytz" ,python2-pytz) + ("python2-typing" ,python2-typing) ,@(package-propagated-inputs base)))))) (define-public python-sphinx-gallery @@ -2960,7 +2891,11 @@ and is very extensible.") '()) (replace 'check - (lambda _ (invoke "python" "runtests.py" "-vv")))))) + (lambda _ + ;; The "with_outer_raising" test fails with Python 3.7. See + ;; https://github.com/cython/cython/issues/2454 + (delete-file "tests/run/generators_py.py") + (invoke "python" "runtests.py" "-vv")))))) (home-page "http://cython.org/") (synopsis "C extensions for Python") (description "Cython is an optimising static compiler for both the Python @@ -3004,7 +2939,7 @@ between language specification and implementation aspects.") (define-public python-numpy (package (name "python-numpy") - (version "1.14.6") + (version "1.15.4") (source (origin (method url-fetch) @@ -3013,14 +2948,14 @@ between language specification and implementation aspects.") version "/numpy-" version ".tar.gz")) (sha256 (base32 - "1k426vnmmd4pds09zgn75g6w92823ry75zrzwjhzjvg7s63ipc31")))) + "102vcl2qq4pjbm7a3d67vkkvn4466ngia1d8wi5avqwqh8j0jvkn")))) (build-system python-build-system) (inputs `(("openblas" ,openblas) ("lapack" ,lapack))) (native-inputs `(("python-cython" ,python-cython) - ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest) ("gfortran" ,gfortran))) (arguments `(#:phases @@ -3065,9 +3000,12 @@ include_dirs = ~a/include (lambda* (#:key outputs inputs #:allow-other-keys) ;; Make installed package available for running the tests (add-installed-pythonpath inputs outputs) + ;; Make sure "f2py" etc is found. + (setenv "PATH" (string-append (assoc-ref outputs "out") "/bin" + ":" (getenv "PATH"))) (with-directory-excursion "/tmp" - (zero? (system* "python" "-c" - "import numpy; numpy.test(verbose=2)")))))))) + (invoke "python" "-c" + "import numpy; numpy.test(verbose=2)"))))))) (home-page "http://www.numpy.org/") (synopsis "Fundamental package for scientific computing with Python") (description "NumPy is the fundamental package for scientific computing @@ -3432,25 +3370,14 @@ that client code uses to construct the grammar directly in Python code.") (define-public python-numpydoc (package (name "python-numpydoc") - (version "0.5") + (version "0.8.0") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/n/numpydoc/numpydoc-" - version ".tar.gz")) + (uri (pypi-uri "numpydoc" version)) (sha256 (base32 - "0d4dnifaxkll50jx6czj05y8cb4ny60njd2wz299sj2jxfy51w4k")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Drop a test requiring matplotlib, which we cannot add as an - ;; input since it would create a circular dependency: Extend the - ;; test for Python 3, where it is already dropped, to Python 2. - (substitute* "numpydoc/tests/test_plot_directive.py" - (("3") "2")) - #t)))) + "1zazxg3m8j4fksv3f7v7vpf4bj9qb1vj3r326am0vdip141vzx31")))) (build-system python-build-system) (propagated-inputs `(("python-sphinx" ,python-sphinx))) @@ -3670,7 +3597,7 @@ toolkits.") (native-inputs `(("python-matplotlib" ,python-matplotlib) ("python-colorspacious" ,python-colorspacious) - ("python-sphinx" ,python-sphinx-1.6) + ("python-sphinx" ,python-sphinx) ("python-sphinx-gallery" ,python-sphinx-gallery) ("python-numpydoc" ,python-numpydoc) ("python-ipython" ,python-ipython) @@ -3819,14 +3746,14 @@ functions.") (define-public python-scipy (package (name "python-scipy") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "scipy" version)) (sha256 (base32 - "1fj0r7bg0cfk5clvl57ga06y9bfh05iwlv1dqqs1r6pd89wccfc7")))) + "1lfg686w6vv2m2dfs8v9d0bf2i18z7wz5vgzjnkgmpr4hi0550w7")))) (build-system python-build-system) (propagated-inputs `(("python-numpy" ,python-numpy) @@ -3957,14 +3884,14 @@ as the original project seems to have been abandoned circa 2007.") (define-public python-pycodestyle (package (name "python-pycodestyle") - (version "2.3.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (pypi-uri "pycodestyle" version)) (sha256 (base32 - "0rk78b66p57ala26mdldl9lafr48blv5s659sah9q50qnfjmc8k8")))) + "0fhy4vnlgpjq4qd1wdnl6pvdw7rah0ypmn8c9mkhz8clsndskz6b")))) (build-system python-build-system) (home-page "https://pycodestyle.readthedocs.io/") (synopsis "Python style guide checker") @@ -4117,7 +4044,7 @@ services for your Python modules and applications.") (define-public python-olefile (package (name "python-olefile") - (version "0.44") + (version "0.45.1") (source (origin (method url-fetch) @@ -4126,7 +4053,7 @@ services for your Python modules and applications.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1wmxbrhyqjry2000zx0zdhqdqxhgi06nz7sbzjlh222q2zjv1gpj")))) + "18ai19zwagm6nli14k8bii31ipbab2rp7plrvsm6gmfql551a8ai")))) (build-system python-build-system) (home-page "https://www.decalage.info/python/olefileio") @@ -4143,19 +4070,17 @@ the OleFileIO module from PIL, the Python Image Library.") (define-public python-pillow (package (name "python-pillow") - (version "4.3.0") + (version "5.2.0") (source (origin (method url-fetch) (uri (pypi-uri "Pillow" version)) (sha256 (base32 - "09xmn7rl6840sli2iz1k3fgxfgmri2nqz6vkinmb9mgg8ifp2z59")) - (patch-flags '("-p1" "--binary")) - (patches (search-patches "python-pillow-fix-failing-tests.patch")))) + "1ary9mj2ddllq3lkxgn6aac7qxqiwbcg2pacrl94py58ql9x9czq")))) (build-system python-build-system) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-pytest" ,python-pytest))) (inputs `(("freetype" ,freetype) ("lcms" ,lcms) @@ -4176,9 +4101,8 @@ the OleFileIO module from PIL, the Python Image Library.") ;; Make installed package available for running the ;; tests (add-installed-pythonpath inputs outputs) - (and (zero? (system* "python" "selftest.py" - "--installed")) - (zero? (system* "python" "test-installed.py")))))) + (invoke "python" "selftest.py" "--installed") + (invoke "python" "-m" "pytest" "-vv")))) (delete 'check)))) (home-page "https://pypi.python.org/pypi/Pillow") (synopsis "Fork of the Python Imaging Library") @@ -4199,14 +4123,14 @@ a general image processing tool.") (define-public python-pycparser (package (name "python-pycparser") - (version "2.17") + (version "2.18") (source (origin (method url-fetch) (uri (pypi-uri "pycparser" version)) (sha256 (base32 - "1dkkjri0miidqb1zcqhqljfa34fcy9k5akasgwsv6k622zlk3b0a")))) + "09mjyw82ibqzl449g7swy8bfxnfpmas0815d2rkdjlcqw81wma4r")))) (outputs '("out" "doc")) (build-system python-build-system) (native-inputs @@ -4243,14 +4167,14 @@ a front-end for C compilers or analysis tools.") (define-public python-xcffib (package (name "python-xcffib") - (version "0.5.1") + (version "0.6.0") (source (origin (method url-fetch) (uri (pypi-uri "xcffib" version)) (sha256 (base32 - "09gbnmr5vn58mm8xi3fmd7fz6743cks6c46dphnxzwax6zsxmy60")))) + "04k91yxyb3pgc5lvxmivh8w71yjrap2g57yk3s73x4rm4nvjq51n")))) (build-system python-build-system) (inputs `(("libxcb" ,libxcb))) @@ -4289,17 +4213,14 @@ support for Python 3 and PyPy. It is based on cffi.") (define-public python-cairocffi (package (name "python-cairocffi") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) - ;; The archive on pypi is missing the 'utils' directory! - (uri (string-append "https://github.com/Kozea/cairocffi/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (pypi-uri "cairocffi" version)) (sha256 (base32 - "1rk2dvy3fxrga6bvvxc2fi5lbaynm5h4a0w0aaxyn3bc77rszjg9")) + "0dq3k4zhqd8cwsf3nyjqvjqm8wkvrjn1wjf44rl3v0h8kqx6qf0m")) (patches (search-patches "python-cairocffi-dlopen-path.patch")))) (build-system python-build-system) (outputs '("out" "doc")) @@ -4312,14 +4233,14 @@ support for Python 3 and PyPy. It is based on cffi.") (native-inputs `(("pkg-config" ,pkg-config) ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-runner" ,python-pytest-runner) ("python-sphinx" ,python-sphinx) ("python-docutils" ,python-docutils))) (propagated-inputs `(("python-xcffib" ,python-xcffib))) ; used at run time (arguments - `(;; FIXME: Tests cannot find 'libcairo.so.2'. - #:tests? #t - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'patch-paths (lambda* (#:key inputs outputs #:allow-other-keys) @@ -4535,13 +4456,13 @@ displayed.") (define-public python-pexpect (package (name "python-pexpect") - (version "4.2.1") + (version "4.6.0") (source (origin (method url-fetch) (uri (pypi-uri "pexpect" version)) (sha256 - (base32 "14ls7k99pwvl21zqv65kzrhccv50j89m5ij1hf0slmsvlxjj84rx")))) + (base32 "1fla85g47iaxxpjhp9vkxdnv4pgc7rplfy6ja491smrrk0jqi3ia")))) (build-system python-build-system) (arguments `(#:phases @@ -4584,13 +4505,13 @@ child application and control it as if a human were typing commands.") (define-public python-setuptools-scm (package (name "python-setuptools-scm") - (version "1.15.6") + (version "3.1.0") (source (origin (method url-fetch) (uri (pypi-uri "setuptools_scm" version)) (sha256 (base32 - "0pzvfmx8s20yrgkgwfbxaspz2x1g38qv61jpm0ns91lrb22ldas9")))) + "0h4bglwfz8b9prqljv8z3w9rgydfyxzaj05bm1y6zs5m6shz548i")))) (build-system python-build-system) (home-page "https://github.com/pypa/setuptools_scm/") (synopsis "Manage Python package versions in SCM metadata") @@ -4713,25 +4634,25 @@ away.") (define-public python-traitlets (package (name "python-traitlets") - (version "4.2.0") + (version "4.3.2") (source (origin (method url-fetch) (uri (pypi-uri "traitlets" version)) (sha256 (base32 - "1afy08sa5n9gnkvh3da49c16zkyv598vchv0p1hp7zzjy8895hz4")))) + "0dbq7sx26xqz5ixs711k5nc88p8a0nqyz6162pwks5dpcz9d4jww")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (replace 'check (lambda _ (zero? (system* "nosetests"))))))) + (replace 'check (lambda _ (invoke "pytest" "-vv" "traitlets")))))) (propagated-inputs `(("python-ipython-genutils" ,python-ipython-genutils) - ("python-decorator" ,python-decorator))) + ("python-decorator" ,python-decorator))) ;not needed for >4.3.2 (native-inputs - `(("python-mock" ,python-mock) - ("python-nose" ,python-nose))) + `(("python-pytest" ,python-pytest))) + (properties `((python2-variant . ,(delay python2-traitlets)))) (home-page "https://ipython.org") (synopsis "Configuration system for Python applications") (description @@ -4744,7 +4665,12 @@ without using the configuration machinery.") (license license:bsd-3))) (define-public python2-traitlets - (package-with-python2 python-traitlets)) + (let ((traitlets (package-with-python2 (strip-python2-variant python-traitlets)))) + (package + (inherit traitlets) + (propagated-inputs + `(("python2-enum34" ,python2-enum34) + ,@(package-propagated-inputs traitlets)))))) (define-public python-jupyter-core (package @@ -5094,15 +5020,15 @@ parsing (browser/HTTP) user agent strings.") (define-public python-dbus (package (name "python-dbus") - (version "1.2.0") + (version "1.2.8") (source (origin (method url-fetch) - (uri (string-append - "https://dbus.freedesktop.org/releases/dbus-python/dbus-python-" - version ".tar.gz")) + (uri (string-append "https://dbus.freedesktop.org/releases/dbus-python/" + "dbus-python-" version ".tar.gz")) (sha256 - (base32 "1py62qir966lvdkngg0v8k1khsqxwk5m4s8nflpk1agk5f5nqb71")))) + (base32 + "0vvvjmiwnc9cjlks3gcdk43ap7llhlpz7cm1wbw0nc2yfsxjpwdb")))) (build-system gnu-build-system) (arguments '(#:phases @@ -5118,7 +5044,7 @@ parsing (browser/HTTP) user agent strings.") (native-inputs `(("pkg-config" ,pkg-config))) (inputs - `(("python" ,python) + `(("python" ,python-wrapper) ("dbus-glib" ,dbus-glib))) (synopsis "Python bindings for D-bus") (description "python-dbus provides bindings for libdbus, the reference @@ -5140,14 +5066,14 @@ implementation of D-Bus.") (define-public python-lxml (package (name "python-lxml") - (version "3.8.0") + (version "4.2.4") (source (origin (method url-fetch) (uri (pypi-uri "lxml" version)) (sha256 (base32 - "15nvf6n285n282682qyw3wihsncb0x5amdhyi4b83bfa2nz74vvk")))) + "1jk336k0kw616gfhqk1wwxsjjwz0flld0n294lz8kxch610bxbz2")))) (build-system python-build-system) (inputs `(("libxml2" ,libxml2) @@ -5168,14 +5094,14 @@ libxml2 and libxslt.") (define-public python-beautifulsoup4 (package (name "python-beautifulsoup4") - (version "4.5.3") + (version "4.6.3") (source (origin (method url-fetch) (uri (pypi-uri "beautifulsoup4" version)) (sha256 (base32 - "0glaw1vyxnbp03fni7h5496n6iib0n5iim4gax1n0ngscs9s075j")))) + "041dhalzjciw6qyzzq7a2k4h1yvyk76xigp35hv5ibnn448ydy4h")))) (build-system python-build-system) (arguments `(#:phases @@ -5256,25 +5182,6 @@ of the structure, dynamics, and functions of complex networks.") (define-public python2-networkx (package-with-python2 python-networkx)) -;; Define new package, because the current version of python-colormath does -;; not build against 2.0. -(define-public python-networkx2 - (package (inherit python-networkx) - (name "python-networkx2") - (version "2.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "networkx" version ".zip")) - (sha256 - (base32 - "1ajl2jp8qry9nyjzzkqpy0vmsr14d23z1qk7y0vr5iwjbpvzhpyd")) - (patches - (search-patches "python-networkx2-reproducible-build.patch")))))) - -(define-public python2-networkx2 - (package-with-python2 python-networkx2)) - (define-public python-datrie (package (name "python-datrie") @@ -5287,6 +5194,14 @@ of the structure, dynamics, and functions of complex networks.") (base32 "08r0if7dry2q7p34gf7ffyrlnf4bdvnprxgydlfxgfnvq8f3f4bs")))) (build-system python-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (add-before 'build 'cythonize + (lambda _ + ;; Regenerate Cython classes to solve ABI issues with Python + ;; 3.7.0. See <https://github.com/pytries/datrie/issues/52>. + (invoke "cython" "src/datrie.pyx" "src/cdatrie.pxd" + "src/stdio_ext.pxd" "-a")))))) (native-inputs `(("python-cython" ,python-cython) ("python-hypothesis" ,python-hypothesis) @@ -5673,14 +5588,14 @@ so it might be a tiny bit slower.") (define-public python-waf (package (name "python-waf") - (version "1.9.8") + (version "2.0.11") (source (origin (method url-fetch) (uri (string-append "https://waf.io/" "waf-" version ".tar.bz2")) (sha256 (base32 - "0wl4cnmp06lfxqjxaan58bqxn27smhydz0sg5prrfbl3bsw4gv6q")))) + "13zrniwkmfqgsgzi9v5m1367fppp9yzrz6z2ny6hy8dmpb8mj4z4")))) (build-system python-build-system) (arguments '(#:phases @@ -5711,13 +5626,13 @@ applications.") (define-public python-pyzmq (package (name "python-pyzmq") - (version "15.1.0") + (version "17.1.2") (source (origin (method url-fetch) (uri (pypi-uri "pyzmq" version)) (sha256 - (base32 "13fhwnlvsvxv72kfhqbpn6qi7msh8mc8377mpabv32skk2cjfnxx")))) + (base32 "1pyxxrz60f88ffm0y6vpbx3q8jcr9ybz8fcilihwzwhh36n84ax7")))) (build-system python-build-system) (arguments `(#:configure-flags @@ -5767,14 +5682,14 @@ PEP 8.") (define-public python-pyflakes (package (name "python-pyflakes") - (version "1.5.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (pypi-uri "pyflakes" version)) (sha256 (base32 - "1x1pcca4a24k4pw8x1c77sgi58cg1wl2k38mp8a25k608pzls3da")))) + "0jba28czyvimdc72llms3f17swp3i8jdcabf5w0j00adfbn64xls")))) (build-system python-build-system) (home-page "https://github.com/pyflakes/pyflakes") @@ -5869,52 +5784,93 @@ complexity of Python source code.") (define-public python2-pyflakes-0.8.1 (package-with-python2 python-pyflakes-0.8.1)) -(define-public python-flake8 +;; This package is used by hypothesis which has thousands of dependent packages. +;; FIXME: Consolidate this with "python-flake8" below in the next rebuild cycle. +(define-public python-flake8-3.5 (package (name "python-flake8") - (version "3.4.1") + (version "3.5.0") (source (origin (method url-fetch) (uri (pypi-uri "flake8" version)) (sha256 (base32 - "1n0i38592vy3q0x2a9bf8z6rhhn04i30wsn5i5zzcj7qkxvl8062")))) + "184b33grvvjmiwlv9kyd7yng9qv5ld24154j70z332xxg9gjclvj")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases + ;; Two errors don't seem to have assigned codes. + (add-after 'unpack 'delete-broken-test + (lambda _ (delete-file "tests/unit/test_pyflakes_codes.py") #t)) + (add-after 'unpack 'fix-problem-with-pycodestyle + (lambda _ + ;; See https://gitlab.com/pycqa/flake8/merge_requests/230 + ;; This should no longer be needed with the next release. + (substitute* "setup.py" + (("PEP8_PLUGIN\\('break_around_binary_operator'\\),") + "PEP8_PLUGIN('break_after_binary_operator'),\ +PEP8_PLUGIN('break_before_binary_operator'),")) + #t)) (delete 'check) (add-after 'install 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (zero? (system* "pytest" "-v"))))))) + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-v") + #t))))) (propagated-inputs - `(("python-pycodestyle" ,python-pycodestyle) - ("python-pyflakes" ,python-pyflakes) - ;; flake8 depends on a newer setuptools than provided by python. - ("python-setuptools" ,python-setuptools) - ("python-mccabe" ,python-mccabe))) + `(("python-pycodestyle" ,python-pycodestyle) + ("python-pyflakes" ,python-pyflakes) + ("python-mccabe" ,python-mccabe))) (native-inputs - `(("python-mock" ,python-mock) ; TODO: only required for < 3.3 - ("python-pytest" ,python-pytest-bootstrap) - ("python-pytest-runner" ,python-pytest-runner))) + `(("python-mock" ,python-mock) + ("python-pytest" ,python-pytest-bootstrap) + ("python-pytest-runner" ,python-pytest-runner))) (home-page "https://gitlab.com/pycqa/flake8") (synopsis "The modular source code checker: pep8, pyflakes and co") (description "Flake8 is a wrapper around PyFlakes, pep8 and python-mccabe.") - (properties `((python2-variant . ,(delay python2-flake8)))) + (properties `((python2-variant . ,(delay python2-flake8-3.5)))) (license license:expat))) -(define-public python2-flake8 - (let ((base (package-with-python2 (strip-python2-variant python-flake8)))) +(define-public python2-flake8-3.5 + (let ((base (package-with-python2 (strip-python2-variant python-flake8-3.5)))) (package (inherit base) (propagated-inputs `(("python2-configparser" ,python2-configparser) ("python2-enum34" ,python2-enum34) ,@(package-propagated-inputs base)))))) +;; Version 3.5.0 has compatibility issues with Pyflakes 2.0, so we need +;; this newer version. Keep it as a separate variable for now to avoid +;; rebuilding "python-hypothesis"; this should be removed in the next +;; rebuild cycle. +(define-public python-flake8 + (package + (inherit python-flake8-3.5) + (version "3.6.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "flake8" version)) + (sha256 + (base32 + "0w0nprx22rbvrrkbfx9v5jc5gskbm08g219l7r8wai8zfswgadba")))) + (arguments + (substitute-keyword-arguments (package-arguments python-flake8-3.5) + ((#:phases phases) + `(modify-phases ,phases + (delete 'delete-broken-test) + (delete 'fix-problem-with-pycodestyle))))) + (properties `((python2-variant . ,(delay python2-flake8)))))) + +(define-public python2-flake8 + (let ((base (package-with-python2 (strip-python2-variant python-flake8)))) + (package (inherit base) + (propagated-inputs + (package-propagated-inputs python2-flake8-3.5))))) + ;; python-hacking requires flake8 <2.6.0. (define-public python-flake8-2.5 (package @@ -6143,28 +6099,18 @@ add functionality and customization to your projects with their own plugins.") (define-public python-fonttools (package (name "python-fonttools") - (version "3.15.1") + (version "3.28.0") (source (origin (method url-fetch) (uri (pypi-uri "fonttools" version ".zip")) (sha256 (base32 - "1hhj97izwliy0vybmza72d90l5d4mcn50y8akq7kyccfl82vdx4d")))) + "0vsvjhidpb5kywpjgz1j3fywzkddxkb0afqai18qa3h6lqjyxwpb")))) (build-system python-build-system) - (arguments - '(#:test-target "check" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-setuppy - ;; Remove the undocumented "extra_path" argument, which adds an - ;; intervening directories between site-packages and the package - ;; directory. - (lambda _ - (substitute* "setup.py" - (("^[ \t]*extra_path *= *'FontTools',") "")) - #t))))) (native-inputs - `(("unzip" ,unzip))) + `(("unzip" ,unzip) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) (home-page "https://github.com/behdad/fonttools") (synopsis "Tools to manipulate font files") (description @@ -6173,9 +6119,7 @@ supports reading and writing of TrueType/OpenType fonts, reading and writing of AFM files, reading (and partially writing) of PS Type 1 fonts. The package also contains a tool called “TTX” which converts TrueType/OpenType fonts to and from an XML-based format.") - (license (license:non-copyleft - "file://LICENSE.txt" - "See LICENSE.txt in the distribution.")))) + (license license:expat))) (define-public python2-fonttools (package-with-python2 python-fonttools)) @@ -6228,13 +6172,13 @@ should be stored on various operating systems.") (define-public python-llfuse (package (name "python-llfuse") - (version "1.3.3") + (version "1.3.5") (source (origin (method url-fetch) (uri (pypi-uri "llfuse" version ".tar.bz2")) (sha256 (base32 - "1rqww632y2zz71xmr6ch7yq80kvza9mhqr2z773k0d8l1lwzl575")))) + "1n7a90jww3ly49fm7x27m3xw3la3qfrnykcakga654g6kcyjlhbf")))) (build-system python-build-system) (inputs `(("fuse" ,fuse) @@ -6547,13 +6491,13 @@ implementations of ASN.1-based codecs and protocols.") (define-public python-ipaddress (package (name "python-ipaddress") - (version "1.0.19") + (version "1.0.22") (source (origin (method url-fetch) (uri (pypi-uri "ipaddress" version)) (sha256 (base32 - "10agaa1cys1bk1ycpl2w8lky9vjx8h1xh1z29mg0niqx0638c390")))) + "0b570bm6xqpjwqis15pvdy6lyvvzfndjvkynilcddjj5x98wfimi")))) (build-system python-build-system) (home-page "https://github.com/phihag/ipaddress") (synopsis "IP address manipulation library") @@ -6599,14 +6543,14 @@ versions of Python.") (define-public python-idna (package (name "python-idna") - (version "2.6") + (version "2.7") (source (origin (method url-fetch) (uri (pypi-uri "idna" version)) (sha256 (base32 - "13qaab6d0s15gknz8v3zbcfmbj6v86hn9pjxgkdf62ch13imssic")))) + "05jam7d31767dr12x0rbvvs8lxnpb1mhdb2zdlfxgh83z6k3hjk8")))) (build-system python-build-system) (home-page "https://github.com/kjd/idna") (synopsis "Internationalized domain names in applications") @@ -7407,25 +7351,26 @@ be set via config files and/or environment variables.") @code{ArgumentParser} object.") (license license:asl2.0))) -(define-public python-contextlib2 +(define-public python2-contextlib2 (package - (name "python-contextlib2") - (version "0.4.0") + (name "python2-contextlib2") + (version "0.5.5") (source (origin (method url-fetch) (uri (pypi-uri "contextlib2" version)) (sha256 (base32 - "0cmp131dlh0d0zvw0aza1zd13glvngzk8lb4avks0hm7yxwdr9am")))) + "0j6ad6lwwyc9kv71skj098v5l7x5biyj2hs4lc5x1kcixqcr97sh")))) (build-system python-build-system) (arguments - `(#:phases + `(#:python ,python-2 + #:phases (modify-phases %standard-phases (replace 'check - (lambda _ (zero? - (system* - "python" "test_contextlib2.py" "-v"))))))) + (lambda _ (invoke "python" "test_contextlib2.py" "-v")))))) + (native-inputs + `(("python2-unittest2" ,python2-unittest2))) (home-page "http://contextlib2.readthedocs.org/") (synopsis "Tools for decorators and context managers") (description "This module is primarily a backport of the Python @@ -7435,9 +7380,6 @@ managers. It also contains additional features that are not part of the standard library.") (license license:psfl))) -(define-public python2-contextlib2 - (package-with-python2 python-contextlib2)) - (define-public python-texttable (package (name "python-texttable") @@ -7581,13 +7523,13 @@ minimal and fast API targeting the following uses: (define-public python-icalendar (package (name "python-icalendar") - (version "4.0.2") + (version "4.0.3") (source (origin (method url-fetch) (uri (pypi-uri "icalendar" version)) (sha256 (base32 - "13003kw2vbas1ha146vv3x2rdg9k7w38rdzxj63vi1i67jgjldl0")))) + "0mk3dk1dxkcm46jy48v27j2w2349iv4sbimqj1yb5js43mx49hh7")))) (build-system python-build-system) (propagated-inputs `(("python-dateutil" ,python-dateutil) @@ -7916,15 +7858,17 @@ library as well as on the command line.") (define-public python-pluggy (package (name "python-pluggy") - (version "0.6.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (pypi-uri "pluggy" version)) (sha256 (base32 - "1zqckndfn85l1cd8pndw212zg1bq9fkg1nnj32kp2mppppsyg2kz")))) + "1qbn70mksmr03hac6jgp6fiqc4l7859z8dchx2x950vhlij87swm")))) (build-system python-build-system) + (native-inputs + `(("python-setuptools-scm" ,python-setuptools-scm))) (synopsis "Plugin and hook calling mechanism for Python") (description "Pluggy is an extraction of the plugin manager as used by Pytest but stripped of Pytest specific details.") @@ -8632,6 +8576,15 @@ ambiguities (forward vs. backward slashes, etc.). @end enumerate") (license license:expat))) +(define-public python2-pathlib2-bootstrap + (hidden-package + (package + (inherit python2-pathlib2) + (name "python2-pathlib2-bootstrap") + (propagated-inputs + `(("python2-scandir" ,python2-scandir) + ("python2-six" ,python2-six-bootstrap)))))) + (define-public python-jellyfish (package (name "python-jellyfish") @@ -8880,23 +8833,10 @@ LDFLAGS and parse the output to build extensions with setup.py.") files. It contains a drop-in replacement for the I/O interface in the standard library's @code{bz2} module, including features from the latest development version of CPython that are not available in older releases.") - (license license:asl2.0) - (properties `((python2-variant . ,(delay python2-bz2file)))))) + (license license:asl2.0))) (define-public python2-bz2file - (let ((base (package-with-python2 - (strip-python2-variant python-bz2file)))) - (package - (inherit base) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - ;; 'python setup.py test' does not work as of 0.98. - ;; There is only the one test file, so we run it directly. - (replace 'check - (lambda _ (zero? (system* "python" - "test_bz2file.py")))))))))) + (package-with-python2 python-bz2file)) (define-public python-future (package @@ -9081,6 +9021,14 @@ own code, responding to click events and updating clock every second.") (arguments `(#:phases (modify-phases %standard-phases + (add-before 'check 'adjust-tests + (lambda _ + (when (which "python3") + ;; Adjust the example output to match that of Python 3.7: + ;; <https://github.com/ionelmc/python-tblib/issues/36>. + (substitute* "README.rst" + (("Exception\\('fail',") "Exception('fail'")) + #t))) (replace 'check (lambda _ ;; Upstream runs tests after installation and the package itself @@ -9113,13 +9061,13 @@ multiple processes (imagine multiprocessing, billiard, futures, celery etc). (define-public python-greenlet (package (name "python-greenlet") - (version "0.4.11") + (version "0.4.14") (source (origin (method url-fetch) (uri (pypi-uri "greenlet" version)) (sha256 (base32 - "1xhik26j4f3kc4qw9xmj0c567rb5h1zryb4ijwqnqwwjvfhbv59h")))) + "1bsij3bwdhz2chq4ar2v6jqbh69yc7k9ymh41jd8vrdd2n52dk7i")))) (build-system python-build-system) (home-page "https://greenlet.readthedocs.io/") (synopsis "Lightweight in-process concurrent programming") @@ -9133,16 +9081,40 @@ are synchronized with data exchanges on \"channels\".") (define-public python2-greenlet (package-with-python2 python-greenlet)) +(define-public python-objgraph + (package + (name "python-objgraph") + (version "3.4.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "objgraph" version)) + (sha256 + (base32 + "184m09am5gpbqfaiy7l0hwh476mczbrly1dffs0rw2p1d1i2q32a")))) + (build-system python-build-system) + (propagated-inputs + `(("python-graphviz" ,python-graphviz))) + (native-inputs + `(("python-mock" ,python-mock) + ("graphviz" ,graphviz))) + (home-page "https://mg.pov.lt/objgraph/") + (synopsis "Draw Python object reference graphs with graphviz") + (description + "This package provides tools to draw Python object reference graphs with +graphviz.") + (license license:expat))) + (define-public python-gevent (package (name "python-gevent") - (version "1.2.2") + (version "1.3.7") (source (origin (method url-fetch) (uri (pypi-uri "gevent" version)) (sha256 (base32 - "0bbbjvi423y9k9xagrcsimnayaqymg6f2dj76m9z3mjpkjpci4a7")) + "0b0fr04qdk1p4sniv87fh8z5psac60x01pv054kpgi94520g81iz")) (modules '((guix build utils))) (snippet '(begin @@ -9174,11 +9146,14 @@ are synchronized with data exchanges on \"channels\".") (find-files "src/greentest" "\\.py$")) #t)) (add-before 'build 'do-not-use-bundled-sources - (lambda _ + (lambda* (#:key inputs #:allow-other-keys) (setenv "CONFIG_SHELL" (which "bash")) (setenv "LIBEV_EMBED" "false") (setenv "CARES_EMBED" "false") (setenv "EMBED" "false") + (setenv "CPATH" + (string-append (assoc-ref inputs "python-greenlet") + "/include/python3.7m")) #t)) (replace 'check (lambda _ @@ -9199,7 +9174,8 @@ are synchronized with data exchanges on \"channels\".") (make-regexp "test_+(subprocess|core)") <>))))))))) (propagated-inputs - `(("python-greenlet" ,python-greenlet))) + `(("python-greenlet" ,python-greenlet) + ("python-objgraph" ,python-objgraph))) (native-inputs `(("libev-source" ,(package-source libev)) ("python-six" ,python-six))) @@ -9847,32 +9823,25 @@ etc.") (define-public python-stem (package (name "python-stem") - (version "1.6.0") + (version "1.7.0") (source (origin (method url-fetch) (uri (pypi-uri "stem" version)) (sha256 (base32 - "1va9p3ij7lxg6ixfsvaql06dn11l3fgpxmss1dhlvafm7sqizznp")))) + "1awiglfiajnx2hva9aqpj3fmdvdb4qg7cwnlfyih827m68y3cq8v")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-before 'check 'fix-test-environment - (lambda _ - ;; Fixes: FileNotFoundError: [Errno 2] No such file or directory: - ;; '/tmp/guix-build-python-stem-1.6.0.drv-0/stem-1.6.0/.gitignore'. - (with-output-to-file ".gitignore" - (lambda _ (format #t "%"))) - #t)) (replace 'check (lambda _ (invoke "./run_tests.py" "--unit") #t))))) (native-inputs `(("python-mock" ,python-mock) - ("python-pep8" ,python-pep8) + ("python-pycodestyle" ,python-pycodestyle) ("python-pyflakes" ,python-pyflakes))) (home-page "https://stem.torproject.org/") (synopsis @@ -10629,21 +10598,17 @@ Record Format (DWARF).") (define-public python-imagesize (package (name "python-imagesize") - (version "0.7.1") + (version "1.0.0") (source (origin (method url-fetch) (uri (pypi-uri "imagesize" version)) (sha256 (base32 - "0qk07k0z4241lkzzjji7z4da04pcvg7bfc4xz1934zlqhwmwdcha")))) + "05b3p62r7rbcvvbk5vknr3bhcq9b2airysn6ric534mng136wcjv")))) (build-system python-build-system) - (arguments - '(;; Test files are not distributed on PyPi: - ;; https://github.com/shibukawa/imagesize_py/issues/7 - #:tests? #f)) (home-page "https://github.com/shibukawa/imagesize_py") - (synopsis "Gets image size of files in variaous formats in Python") + (synopsis "Gets image size of files in various formats in Python") (description "This package allows determination of image size from PNG, JPEG, JPEG2000 and GIF files in pure Python.") @@ -11110,6 +11075,32 @@ projects.") (define-public python2-incremental (package-with-python2 python-incremental)) +(define-public python-invoke + (package + (name "python-invoke") + (home-page "http://www.pyinvoke.org/") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "invoke" version)) + (sha256 + (base32 + "0aiy1xvk1f91246zxd1zqrm679vdvd10h843a2na41cqr3cflpi6")))) + (build-system python-build-system) + (arguments + ;; XXX: Requires many dependencies that are not yet in Guix. + `(#:tests? #f)) + (synopsis "Pythonic task execution") + (description + "Invoke is a Python task execution tool and library, drawing inspiration +from various sources to arrive at a powerful and clean feature set. It is +evolved from the Fabric project, but focuses on local and abstract concerns +instead of servers and network commands.") + (license license:bsd-3))) + +(define-public python2-invoke + (package-with-python2 python-invoke)) + (define-public python-automat (package (name "python-automat") @@ -11193,17 +11184,36 @@ and bit flag values.") (define-public python-attrs (package (name "python-attrs") - (version "17.4.0") + (version "18.2.0") (source (origin (method url-fetch) (uri (pypi-uri "attrs" version)) (sha256 (base32 - "1jafnn1kzd6qhxgprhx6y6ik1r5m2rilx25syzcmq03azp660y8w")))) + "0s9ydh058wmmf5v391pym877x4ahxg45dw6a0w4c7s5wgpigdjqh")))) (build-system python-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build python-build-system) + (ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26)) + #:phases (modify-phases %standard-phases + (replace 'check + (lambda _ + (let ((cwd (getcwd))) + (setenv "PYTHONPATH" + (string-append + cwd "/build/" + (find (cut string-prefix? "lib" <>) + (scandir (string-append cwd "/build"))) + ":" + (getenv "PYTHONPATH"))) + (invoke "python" "-m" "pytest"))))))) (native-inputs `(("python-coverage" ,python-coverage) ("python-hypothesis" ,python-hypothesis) + ("python-pympler" ,python-pympler) ("python-pytest" ,python-pytest) ("python-six" ,python-six) ("python-sphinx" ,python-sphinx) @@ -11222,6 +11232,15 @@ protocols.") (package (inherit python-attrs) (name "python-attrs-bootstrap") + ;; Keep this on a fixed version so python-attrs can be updated without + ;; triggering a mass-rebuild. FIXME: Update this in the next rebuild cycle. + (version "17.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "attrs" version)) + (sha256 + (base32 + "1jafnn1kzd6qhxgprhx6y6ik1r5m2rilx25syzcmq03azp660y8w")))) (native-inputs `()) (arguments `(#:tests? #f)))) @@ -11381,28 +11400,37 @@ clone, while other processes access the original tree.") (define-public python-astroid (package (name "python-astroid") - (version "1.5.3") + (version "2.0.4") (source (origin (method url-fetch) - (uri (string-append - "https://github.com/PyCQA/astroid/archive/astroid-" - version ".tar.gz")) + (uri (pypi-uri "astroid" version)) (sha256 (base32 - "0isn5p7f9n48hmksgbrj7dkm9dyglnayzn5jngk37qywg8a74ngn")))) + "138svbm88w5k0y2nvl4svyas1jfhcc5iy0d2ywkbcpn9kq8ks0f7")))) (build-system python-build-system) (propagated-inputs `(("python-lazy-object-proxy" ,python-lazy-object-proxy) ("python-six" ,python-six) ("python-wrapt" ,python-wrapt))) + (native-inputs + `(("python-dateutil" ,python-dateutil) + ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) (arguments `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'remove-spurious-test + (lambda _ + ;; This can be removed after upgrading from python-3.7 + ;; https://github.com/PyCQA/astroid/issues/593 + ;; https://bugs.python.org/issue34056 + (delete-file "astroid/tests/unittest_modutils.py") + #t)) (replace 'check - (lambda _ - (zero? (system* "python" "-m" "unittest" "discover" - "-p" "unittest*.py"))))))) + (lambda _ + (invoke "pytest" "astroid")))))) (home-page "https://github.com/PyCQA/astroid") (synopsis "Common base representation of python source code for pylint and other projects") @@ -11422,12 +11450,35 @@ builds partial trees by inspecting living objects.") (let ((base (package-with-python2 (strip-python2-variant python-astroid)))) (package (inherit base) - (propagated-inputs - `(("python2-backports-functools-lru-cache" - ,python2-backports-functools-lru-cache) - ("python2-enum34" ,python2-enum34) - ("python2-singledispatch" ,python2-singledispatch) - ,@(package-propagated-inputs base)))))) + ;; Version 2.x removes python2 support. + (version "1.6.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "astroid" version)) + (sha256 + (base32 + "0fir4b67sm7shcacah9n61pvq313m523jb4q80sycrh3p8nmi6zw")))) + (arguments + (substitute-keyword-arguments (package-arguments base) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'remove-spurious-test + (lambda _ + ;; https://github.com/PyCQA/astroid/issues/276 + (delete-file "astroid/tests/unittest_brain.py") + #t)) + (replace 'check + (lambda _ + (invoke"python" "-m" "unittest" "discover" + "-p" "unittest*.py"))))))) + (native-inputs `()) + (propagated-inputs + `(("python2-backports-functools-lru-cache" + ,python2-backports-functools-lru-cache) + ("python2-enum34" ,python2-enum34) + ("python2-singledispatch" ,python2-singledispatch) + ,@(package-propagated-inputs base)))))) (define-public python-isort (package @@ -11724,13 +11775,13 @@ It supports both normal and Unicode strings.") (define-public python-scandir (package (name "python-scandir") - (version "1.7") + (version "1.9.0") (source (origin (method url-fetch) (uri (pypi-uri "scandir" version)) (sha256 - (base32 "0gbnhjzg42rj87ljv9kb648rfxph69ly3c8r9841dxy4d7l5pmdj")))) + (base32 "0r3hvf1a9jm1rkqgx40gxkmccknkaiqjavs8lccgq9s8khh5x5s4")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -11850,15 +11901,19 @@ several utilities, as well as an API for building localization tools.") (define-public python-packaging (package (name "python-packaging") - (version "16.8") + (version "17.1") (source (origin (method url-fetch) (uri (pypi-uri "packaging" version)) (sha256 (base32 - "17k1xbjshackwvbsnxqixbph8rbqhz4bf4g3al5xyzhavxgq6l2x")))) + "0nrpayk8kij1zm9sjnk38ldz3a6705ggvw8ljylqbrb4vmqbf6gh")))) (build-system python-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (replace 'check + (lambda _ (invoke "py.test" "-vv")))))) (native-inputs `(("python-pretend" ,python-pretend) ("python-pytest" ,python-pytest))) @@ -12899,26 +12954,40 @@ belong to tagged versions.") (define-public python-pyclipper (package (name "python-pyclipper") - (version "1.0.6") + (version "1.1.0.post1") (source (origin (method url-fetch) (uri (pypi-uri "pyclipper" version ".zip")) (sha256 (base32 - "1zpmwv3bya3j984y5cf9x9d5108kf6mxldcba68wiq0frv5qrssw")))) + "0ldbkbnx94an4zzrwb1sxmg6k0jgk4cwmvcdyy8y5k1zslc612wa")) + (modules '((guix build utils))) + (snippet + '(begin + ;; This file is generated by Cython. + (delete-file "pyclipper/pyclipper.cpp") #t)))) (build-system python-build-system) (arguments - `(#:tests? #f)); 8 Tests fail, 37 succeed + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'cythonize-sources + (lambda _ + (with-directory-excursion "pyclipper" + (invoke "cython" "--cplus" "pyclipper.pyx"))))))) (propagated-inputs `(("python-setuptools-scm-git-archive" ,python-setuptools-scm-git-archive))) (native-inputs - `(("unzip" ,unzip))) + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner) + ("python-unittest2" ,python-unittest2) + ("unzip" ,unzip))) (home-page "https://github.com/greginvm/pyclipper") (synopsis "Wrapper for Angus Johnson's Clipper library") (description "Pyclipper is a Cython wrapper for the C++ translation of the - Angus Johnson's polygon clipping Clipper library (ver. 6.2.1).") +Angus Johnson's polygon clipping Clipper library (ver. 6.4.2).") (license license:expat))) (define-public python2-pyclipper @@ -13261,14 +13330,14 @@ user's @file{~/Trash} directory.") (define-public python-yapf (package (name "python-yapf") - (version "0.21.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (pypi-uri "yapf" version)) (sha256 (base32 - "144gc7d6b1415vh02409rnb8qd5kxi6mxlr7y64d5cizgxbf72kx")))) + "0anwby0ydmyzcsgjc5dn1ryddwvii4dq61vck447q0n96npnzfyf")))) (build-system python-build-system) (home-page "https://github.com/google/yapf") (synopsis "Formatter for Python code") @@ -13658,15 +13727,29 @@ file system events on Linux.") (define-public python-more-itertools (package (name "python-more-itertools") - (version "4.1.0") + (version "4.3.0") (source (origin (method url-fetch) (uri (pypi-uri "more-itertools" version)) (sha256 (base32 - "0i3ch700g5fyjp692gprlnzbysl8w0sa2vijbp3s40drvk67xkn9")))) + "17h3na0rdh8xq30w4b9pizgkdxmm51896bxw600x84jflg9vaxn4")))) (build-system python-build-system) + (arguments + `(,@(if (any (cute string-prefix? <> (or (%current-system) + (%current-target-system))) + '("armhf" "i686")) + '(#:phases + (modify-phases %standard-phases + ;; This is required for 32-bit hardware. + ;; TODO: Try to remove this when upgrading. + (add-after 'unpack 'patch-test + (lambda _ + (substitute* "more_itertools/tests/test_more.py" + (("10 \\*\\* 10") "9 ** 9")) + #t)))) + '()))) (propagated-inputs `(("python-six" ,python-six-bootstrap))) (home-page "https://github.com/erikrose/more-itertools") diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index d487699827..c4407fea29 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com> -;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2015, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2017 Nils Gillmann <ng0@n0.is> ;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be> @@ -121,6 +121,7 @@ system, and the core design of Django is reused in Grantlee.") (sha256 (base32 "10faac59jvz6dxxljdkaknlxazpnaxgvqdcszabfbbkc1f24n466")) + (patches (search-patches "qt-5-renameat2.patch")) (modules '((guix build utils))) (snippet '(begin @@ -623,7 +624,6 @@ system, and the core design of Django is reused in Grantlee.") ;; kernels that the glibc supports, including the RHEL6 ;; (2.6.32) and RHEL7 (3.10) kernels. "-no-feature-getentropy" ; requires Linux 3.17 - "-no-feature-renameat2" ; requires Linux 3.16 ;; Do not build examples; if desired, these could go ;; into a separate output, but for the time being, we diff --git a/gnu/packages/readline.scm b/gnu/packages/readline.scm index 4695e9fc71..59fa8af8af 100644 --- a/gnu/packages/readline.scm +++ b/gnu/packages/readline.scm @@ -48,7 +48,9 @@ (patch-series (1 "0xm3sxvwmss7ddyfb11n6pgcqd1aglnpy15g143vzcf75snb7hcs") (2 "0n1dxmqsbjgrfxb1hgk5c6lsraw4ncbnzxlsx7m35nym6lncjiw7") - (3 "1027kmymniizcy0zbdlrczxfx3clxcdln5yq05q9yzlc6y9slhwy"))) + (3 "1027kmymniizcy0zbdlrczxfx3clxcdln5yq05q9yzlc6y9slhwy") + (4 "0r3bbaf12iz8m02z6p3fzww2m365fhn71xmzab2p62gj54s6h9gr") + (5 "0lxpa4f72y2nsgj6fgrhjk2nmmxvccys6aciwfxwchb5f21rq5fa"))) (define-public readline (package diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm index ff237c96ce..b927bbbf9b 100644 --- a/gnu/packages/samba.scm +++ b/gnu/packages/samba.scm @@ -397,6 +397,18 @@ key-value pair databases and a real LDAP database.") (method url-fetch) (uri (string-append "https://www.samba.org/ftp/ppp/ppp-" version ".tar.gz")) + (patches + (list (origin + ;; Use OpenSSL for cryptography instead of the obsolete glibc + ;; crypto functions that were removed in glibc 2.28. + (method url-fetch) + (uri (string-append "https://github.com/paulusmack/ppp/commit/" + "3c7b86229f7bd2600d74db14b1fe5b3896be3875" + ".patch")) + (file-name "ppp-use-openssl-crypto.patch") + (sha256 + (base32 + "0qlbi247lx3injpy8a1gcij9yilik0vfaibkpvdp88k3sa1rs69z"))))) (sha256 (base32 "0c7vrjxl52pdwi4ckrvfjr08b31lfpgwf3pp0cqy76a77vfs7q02")))) @@ -409,15 +421,19 @@ key-value pair databases and a real LDAP database.") (add-before 'configure 'patch-Makefile (lambda* (#:key inputs #:allow-other-keys) (let ((libc (assoc-ref inputs "libc")) + (openssl (assoc-ref inputs "openssl")) (libpcap (assoc-ref inputs "libpcap"))) (substitute* "pppd/Makefile.linux" (("/usr/include/crypt\\.h") (string-append libc "/include/crypt.h")) + (("/usr/include/openssl") + (string-append openssl "/include/openssl")) (("/usr/include/pcap-bpf.h") (string-append libpcap "/include/pcap-bpf.h"))) #t)))))) (inputs - `(("libpcap" ,libpcap))) + `(("libpcap" ,libpcap) + ("openssl" ,(@ (gnu packages tls) openssl)))) (synopsis "Implementation of the Point-to-Point Protocol") (home-page "https://ppp.samba.org/") (description diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm index fb121a0581..94e6aa8438 100644 --- a/gnu/packages/spice.scm +++ b/gnu/packages/spice.scm @@ -211,6 +211,10 @@ which allows users to view a desktop computing environment.") `(#:configure-flags '("--enable-lz4" "--enable-automated-tests") + + ;; Several tests appear to be opening the same sockets concurrently. + #:parallel-tests? #f + #:phases (modify-phases %standard-phases (add-before 'check 'use-empty-ssl-cert-file (lambda _ (setenv "SSL_CERT_FILE" "/dev/null") #t))))) diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm index 5ea5148cbc..5c954eae35 100644 --- a/gnu/packages/ssh.scm +++ b/gnu/packages/ssh.scm @@ -116,23 +116,10 @@ applications.") (propagated-inputs `(("libgcrypt" ,libgcrypt) ("zlib" ,zlib))) (arguments `(#:configure-flags `("--with-libgcrypt") - #:phases - ;; FIXME: In the next core-updates cycle, replace the entire - ;; following ,(...) form with its first 'modify-phases' - ;; subform. The change made here is only strictly needed on - ;; MIPS, but should work on any system. For now, we apply it - ;; only to MIPS to avoid forcing thousands of rebuilds on - ;; other systems. - ,(if (string-prefix? "mips" (or (%current-target-system) - (%current-system))) - '(modify-phases %standard-phases - (replace 'bootstrap - (lambda _ - (invoke "autoreconf" "-v")))) - '(modify-phases %standard-phases - (add-before 'configure 'autoreconf - (lambda _ - (invoke "autoreconf" "-v"))))))) + #:phases (modify-phases %standard-phases + (replace 'bootstrap + (lambda _ + (invoke "autoreconf" "-v")))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake))) (synopsis "Client-side C library implementing the SSH2 protocol") diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2e75981de3..66f57ac879 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -248,9 +248,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ "/share/zoneinfo")) #t)) (add-after 'build 'make-info - (lambda _ (invoke "make" "info") #t)) + (lambda _ (invoke "make" "info"))) (add-after 'build 'install-info - (lambda _ (invoke "make" "install-info") #t))) + (lambda _ (invoke "make" "install-info")))) #:configure-flags `(;; We build the recommended packages here, because they are needed in ;; order to run the test suite. We disable them in the r-minimal diff --git a/gnu/packages/storage.scm b/gnu/packages/storage.scm index 11f6f9d7e8..5051ccd986 100644 --- a/gnu/packages/storage.scm +++ b/gnu/packages/storage.scm @@ -26,6 +26,7 @@ #:use-module (gnu packages) #:use-module (gnu packages admin) #:use-module (gnu packages assembly) + #:use-module (gnu packages authentication) #:use-module (gnu packages bdw-gc) #:use-module (gnu packages boost) #:use-module (gnu packages check) @@ -35,6 +36,7 @@ #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages disk) + #:use-module (gnu packages gcc) #:use-module (gnu packages gnuzilla) #:use-module (gnu packages gperf) #:use-module (gnu packages jemalloc) @@ -51,18 +53,19 @@ (define-public ceph (package (name "ceph") - (version "12.2.5") + (version "13.2.2") (source (origin (method url-fetch) (uri (string-append "https://download.ceph.com/tarballs/ceph-" version ".tar.gz")) (sha256 (base32 - "1ydc3mfvc0vpnpfnfmissvsrsj4jyxgzc2pcl1a4vdr3bwkcglp3")) + "0h483n9iy0fkbqrhf7k0dzspwdpcaswkjwmc5n5c600fr6s1v9pk")) (patches (search-patches "ceph-skip-unittest_blockdev.patch" "ceph-skip-collect-sys-info-test.patch" - "ceph-rocksdb-compat.patch" + "ceph-detect-rocksdb.patch" + "ceph-volume-respect-PATH.patch" "ceph-disable-cpu-optimizations.patch")) (modules '((guix build utils))) (snippet @@ -76,7 +79,7 @@ ;"src/zstd" ;"src/civetweb" "src/test/downloads" - "src/dpdk" + "src/rapidjson" "src/spdk" "src/rocksdb" "src/boost")) @@ -100,13 +103,14 @@ (assoc-ref %build-inputs "keyutils") "/include") "-DCMAKE_INSTALL_LOCALSTATEDIR=/var" "-DENABLE_SHARED=ON" - "-DWITH_EMBEDDED=OFF" "-DWITH_SYSTEM_ROCKSDB=ON" "-DWITH_SYSTEM_BOOST=ON" "-DWITH_PYTHON3=ON" ;; TODO: Enable these when available in Guix. + "-DWITH_MGR_DASHBOARD_FRONTEND=OFF" ;requires node + nodeenv "-DWITH_BABELTRACE=OFF" "-DWITH_LTTNG=OFF" + "-DWITH_SPDK=OFF" "-DWITH_XFS=OFF" "-DWITH_XIO=OFF" ;; Use jemalloc instead of tcmalloc. @@ -184,9 +188,6 @@ ;; /tmp/ceph-disk-virtualenv/bin/ceph-disk, but somehow ;; src/ceph-disk/CMakeLists.txt fails to create it. (substitute* "src/test/CMakeLists.txt" - ;; FIXME: "create cannot load compressor of type zlib" - ;; "libceph_zlib.so: undefined symbol: isal_deflate" - (("^add_subdirectory\\(compressor\\)") "") ;; FIXME: These tests fails because `ceph-disk' ;; is not available. (("^add_ceph_test\\(test-ceph-helpers\\.sh.*$") "\n") @@ -235,6 +236,11 @@ (("^add_ceph_test\\(osd-copy-from\\.sh.*$") "\n") (("^add_ceph_test\\(osd-fast-mark-down\\.sh.*$") "\n")) #t))) + (add-before 'configure 'gcc-workaround + (lambda _ + (unsetenv "C_INCLUDE_PATH") + (unsetenv "CPLUS_INCLUDE_PATH") + #t)) (add-before 'check 'set-check-environment (lambda _ ;; Run tests in parallel. @@ -262,28 +268,28 @@ (add-after 'install 'wrap-python-scripts (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) - (ceph (string-append out "/bin/ceph")) - (ceph-disk (string-append out "/bin/ceph-disk")) - (ceph-detect-init (string-append - out "/bin/ceph-detect-init")) - + (scripts '("ceph" "ceph-mgr" "ceph-volume" + "ceph-detect-init" + "ceph-disk")) ;deprecated (prettytable (assoc-ref inputs "python2-prettytable")) - + (six (assoc-ref inputs "python2-six")) (sitedir (lambda (package) (string-append package "/lib/python2.7/site-packages"))) (PYTHONPATH (string-append (sitedir out) ":" + (sitedir six) ":" (sitedir prettytable)))) (for-each (lambda (executable) - (wrap-program executable + (wrap-program (string-append out "/bin/" executable) `("PYTHONPATH" ":" prefix (,PYTHONPATH)))) - (list ceph ceph-disk ceph-detect-init)) + scripts) #t)))))) (outputs '("out" "lib")) (native-inputs - `(("gperf" ,gperf) + `(("gcc" ,gcc-7) ;7 or later is required + ("gperf" ,gperf) ("pkg-config" ,pkg-config) ("python-cython" ,python-cython) ("python-sphinx" ,python-sphinx) @@ -329,13 +335,16 @@ ("libatomic-ops" ,libatomic-ops) ("lua" ,lua) ("lz4" ,lz4) + ("oath-toolkit" ,oath-toolkit) ("openldap" ,openldap) ("openssl" ,openssl) ("nss" ,nss) ("parted" ,parted) ("python@2" ,python-2) ("python2-prettytable" ,python2-prettytable) ;used by ceph_daemon.py + ("python2-six" ,python2-six) ;for ceph-mgr + plugins ("python@3" ,python-3) + ("rapidjson" ,rapidjson) ("rocksdb" ,rocksdb) ("snappy" ,snappy) ("udev" ,eudev) diff --git a/gnu/packages/swig.scm b/gnu/packages/swig.scm index b931db412b..61f6a8ccfe 100644 --- a/gnu/packages/swig.scm +++ b/gnu/packages/swig.scm @@ -22,6 +22,7 @@ #:use-module (guix download) #:use-module (guix licenses) #:use-module (guix build-system gnu) + #:use-module (gnu packages) #:use-module (gnu packages pcre) #:use-module (gnu packages guile) #:use-module (gnu packages boost) @@ -37,6 +38,7 @@ (uri (string-append "mirror://sourceforge/" name "/" name "/" name "-" version "/" name "-" version ".tar.gz")) + (patches (search-patches "swig-guile-gc.patch")) (sha256 (base32 "0kf99ygrjs5616gsqhz1l7bib3a12izmxi7g48bwblbymr3z9ybw")))) diff --git a/gnu/packages/sync.scm b/gnu/packages/sync.scm index e0b0af3d96..60e66437a8 100644 --- a/gnu/packages/sync.scm +++ b/gnu/packages/sync.scm @@ -214,7 +214,8 @@ and does not hamper local file system performance.") (sha256 (base32 "0znkp3fcksrykcsv06y2mjvf2lbwmin25snmvfa8i5qfm3f4rm88")) - (file-name (string-append name "-" version "-checkout")))) + (file-name (string-append name "-" version "-checkout")) + (patches (search-patches "casync-renameat2-declaration.patch")))) (build-system meson-build-system) (native-inputs `(("pkg-config" ,pkg-config) diff --git a/gnu/packages/tcl.scm b/gnu/packages/tcl.scm index f7d3e0ec7d..b8c85eb844 100644 --- a/gnu/packages/tcl.scm +++ b/gnu/packages/tcl.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org> -;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org> ;;; Copyright © 2017 Kei Kebreau <kkebreau@posteo.net> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> @@ -25,6 +25,7 @@ (define-module (gnu packages tcl) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (guix build-system perl) #:use-module (gnu packages) @@ -145,13 +146,22 @@ X11 GUIs.") (patches (search-patches "tk-find-library.patch")))) (build-system gnu-build-system) (arguments - '(#:phases (modify-phases %standard-phases + `(#:phases (modify-phases %standard-phases (add-before 'configure 'pre-configure (lambda _ (chdir "unix") #t)) (add-after + 'install 'create-wish-symlink + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (symlink (string-append out "/bin/wish" + ,(version-major+minor + (package-version tk))) + (string-append out "/bin/wish"))) + #t)) + (add-after 'install 'add-fontconfig-flag (lambda* (#:key inputs outputs #:allow-other-keys) ;; Add the missing -L flag for Fontconfig in 'tk.pc' and @@ -179,7 +189,7 @@ X11 GUIs.") (propagated-inputs `(("libx11" ,libx11) ("libxext" ,libxext))) - (home-page "http://www.tcl.tk/") + (home-page "https://www.tcl.tk/") (synopsis "Graphical user interface toolkit for Tcl") (description "Tk is a graphical toolkit for building graphical user diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index f8b11f7e1a..916aa54d58 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -76,42 +76,41 @@ (define texlive-extra-src (origin (method url-fetch) - (uri "ftp://tug.org/historic/systems/texlive/2017/texlive-20170524-extra.tar.xz") + (uri "ftp://tug.org/historic/systems/texlive/2018/texlive-20180414-extra.tar.xz") (sha256 (base32 - "0zvd2zskk78ig114mfj24g15qys41hzqv59fmqpirdbgq9c9gr5g")))) + "0a83kymxc8zmlxjb0y1gf6mx7qnf0hxffwkivwh5yh138y2rfhsv")))) (define texlive-texmf-src (origin (method url-fetch) - (uri "ftp://tug.org/historic/systems/texlive/2017/texlive-20170524-texmf.tar.xz") + (uri "ftp://tug.org/historic/systems/texlive/2018/texlive-20180414-texmf.tar.xz") (sha256 (base32 - "1v69y3kgkbk24f7s4dfkknwd317mqmck5jgpyb35wqgqfy5p0qrz")))) + "1b8zigzg8raxkhhzphcmynf84rbdbj2ym2qkz24v8n0qx82zmqms")))) (define-public texlive-bin (package (name "texlive-bin") - (version "20170524") + (version "20180414") (source (origin - (method url-fetch) - (uri (string-append "ftp://tug.org/historic/systems/texlive/2017/" + (method url-fetch) + (uri (string-append "ftp://tug.org/historic/systems/texlive/2018/" "texlive-" version "-source.tar.xz")) + (sha256 + (base32 + "0khyi6h015r2zfqgg0a44a2j7vmr1cy42knw7jbss237yvakc07y")) (patches (list - ;; This is required for compatibility with Poppler >= 0.58. - ;; See <http://tutex.tug.org/pipermail/tex-k/2017-September/002809.html> - ;; and <https://bugs.archlinux.org/task/55720> for some discussion. + ;; This is required for compatibility with Poppler 0.64.0 and to fix a + ;; segmentation fault in dvipdfm-x from XeTeX. (origin (method url-fetch) - (uri (string-append "https://git.archlinux.org/svntogit/packages.git/plain" - "/trunk/texlive-poppler-0.59.patch?h=packages/texlive-bin" - "&id=ba2de374e2b21ecc4b85cc9777f2f15c4d356c61")) + (uri (string-append "http://www.linuxfromscratch.org/patches/blfs/" + "svn/texlive-" version "-source-upstream_fixes-1.patch")) (file-name "texlive-poppler-compat.patch") (sha256 (base32 - "1c4ikq4kxw48bi3i33bzpabrjvbk01fwjr2lz20gkc9kv8l0bg3n"))))) - (sha256 (base32 - "1amjrxyasplv4alfwcxwnw4nrx7dz2ydmddkq16k6hg90i9njq81")))) + "0f8vhyj167y4xj0jx47vkybrcacfpxw0wdn1b777yq3xmhlahhlg"))))))) (build-system gnu-build-system) (inputs `(("texlive-extra-src" ,texlive-extra-src) @@ -175,47 +174,62 @@ (not (or (string-prefix? "aarch64" s) (string-prefix? "mips64" s)))) #:phases - (modify-phases %standard-phases - (add-after 'unpack 'configure-ghostscript-executable - ;; ps2eps.pl uses the "gswin32c" ghostscript executable on Windows, - ;; and the "gs" ghostscript executable on Unix. It detects Unix by - ;; checking for the existence of the /usr/bin directory. Since - ;; GuixSD does not have /usr/bin, it is also detected as Windows. - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "utils/ps2eps/ps2eps-src/bin/ps2eps.pl" - (("gswin32c") "gs")) - (substitute* "texk/texlive/linked_scripts/epstopdf/epstopdf.pl" - (("\"gs\"") - (string-append "\"" (assoc-ref inputs "ghostscript") "/bin/gs\""))) - #t)) - (add-after 'install 'postint - (lambda* (#:key inputs outputs #:allow-other-keys #:rest args) - (let* ((out (assoc-ref outputs "out")) - (share (string-append out "/share")) - (texlive-extra (assoc-ref inputs "texlive-extra-src")) - (unpack (assoc-ref %standard-phases 'unpack)) - (patch-source-shebangs - (assoc-ref %standard-phases 'patch-source-shebangs))) - ;; Create symbolic links for the latex variants and their - ;; man pages. - (with-directory-excursion (string-append out "/bin/") - (for-each symlink - '("pdftex" "pdftex" "xetex" "luatex") - '("latex" "pdflatex" "xelatex" "lualatex"))) - (with-directory-excursion (string-append share "/man/man1/") - (symlink "luatex.1" "lualatex.1")) - ;; Unpack texlive-extra and install tlpkg. - (mkdir "texlive-extra") - (with-directory-excursion "texlive-extra" - (apply unpack (list #:source texlive-extra)) - (apply patch-source-shebangs (list #:source texlive-extra)) - (invoke "mv" "tlpkg" share)) - ;; texlua shebangs are not patched by the patch-source-shebangs - ;; phase because the texlua executable does not exist at that - ;; time. - (setenv "PATH" (string-append (getenv "PATH") ":" out "/bin")) - (with-directory-excursion out - (patch-source-shebangs)))))))) + (modify-phases %standard-phases + (add-after 'unpack 'configure-ghostscript-executable + ;; ps2eps.pl uses the "gswin32c" ghostscript executable on Windows, + ;; and the "gs" ghostscript executable on Unix. It detects Unix by + ;; checking for the existence of the /usr/bin directory. Since + ;; GuixSD does not have /usr/bin, it is also detected as Windows. + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "utils/ps2eps/ps2eps-src/bin/ps2eps.pl" + (("gswin32c") "gs")) + (substitute* "texk/texlive/linked_scripts/epstopdf/epstopdf.pl" + (("\"gs\"") + (string-append "\"" (assoc-ref inputs "ghostscript") "/bin/gs\""))) + #t)) + (add-after 'unpack 'use-code-for-new-poppler + (lambda _ + (copy-file "texk/web2c/pdftexdir/pdftoepdf-newpoppler.cc" + "texk/web2c/pdftexdir/pdftoepdf.cc") + (copy-file "texk/web2c/pdftexdir/pdftosrc-newpoppler.cc" + "texk/web2c/pdftexdir/pdftosrc.cc") + #t)) + (add-after 'unpack 'disable-failing-test + (lambda _ + ;; FIXME: This test fails on 32-bit architectures since Glibc 2.28: + ;; <https://bugzilla.redhat.com/show_bug.cgi?id=1631847>. + (substitute* "texk/web2c/omegafonts/check.test" + (("^\\./omfonts -ofm2opl \\$srcdir/tests/check tests/xcheck \\|\\| exit 1") + "./omfonts -ofm2opl $srcdir/tests/check tests/xcheck || exit 77")) + #t)) + (add-after 'install 'postint + (lambda* (#:key inputs outputs #:allow-other-keys #:rest args) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share")) + (texlive-extra (assoc-ref inputs "texlive-extra-src")) + (unpack (assoc-ref %standard-phases 'unpack)) + (patch-source-shebangs + (assoc-ref %standard-phases 'patch-source-shebangs))) + ;; Create symbolic links for the latex variants and their + ;; man pages. + (with-directory-excursion (string-append out "/bin/") + (for-each symlink + '("pdftex" "pdftex" "xetex" "luatex") + '("latex" "pdflatex" "xelatex" "lualatex"))) + (with-directory-excursion (string-append share "/man/man1/") + (symlink "luatex.1" "lualatex.1")) + ;; Unpack texlive-extra and install tlpkg. + (mkdir "texlive-extra") + (with-directory-excursion "texlive-extra" + (apply unpack (list #:source texlive-extra)) + (apply patch-source-shebangs (list #:source texlive-extra)) + (invoke "mv" "tlpkg" share)) + ;; texlua shebangs are not patched by the patch-source-shebangs + ;; phase because the texlua executable does not exist at that + ;; time. + (setenv "PATH" (string-append (getenv "PATH") ":" out "/bin")) + (with-directory-excursion out + (patch-source-shebangs)))))))) (synopsis "TeX Live, a package of the TeX typesetting system") (description "TeX Live provides a comprehensive TeX document production system. @@ -3995,7 +4009,7 @@ directly generate PDF documents instead of DVI.") (define texlive-texmf (package (name "texlive-texmf") - (version "2017") + (version "20180414") (source texlive-texmf-src) (build-system gnu-build-system) (inputs @@ -4067,7 +4081,7 @@ This package contains the complete tree of texmf-dist data.") (define-public texlive (package (name "texlive") - (version "2017") + (version "20180414") (source #f) (build-system trivial-build-system) (inputs `(("bash" ,bash) ; for wrap-program diff --git a/gnu/packages/texinfo.scm b/gnu/packages/texinfo.scm index 109a24bf62..fa98bd56b8 100644 --- a/gnu/packages/texinfo.scm +++ b/gnu/packages/texinfo.scm @@ -37,6 +37,7 @@ (method url-fetch) (uri (string-append "mirror://gnu/texinfo/texinfo-" version ".tar.xz")) + (patches (search-patches "texinfo-perl-compat.patch")) (sha256 (base32 "0qjzvbvnv9003xdrcpi3jp7y68j4hq2ciw9frh2hghh698zlnxvp")))) @@ -68,6 +69,7 @@ is on expressing the content semantically, avoiding physical markup commands.") (method url-fetch) (uri (string-append "mirror://gnu/texinfo/texinfo-" version ".tar.xz")) + (patches (search-patches "texinfo-5-perl-compat.patch")) (sha256 (base32 "1njfwh2z34r2c4r0iqa7v24wmjzvsfyz4vplzry8ln3479lfywal")))) diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index e9a4ab3d68..cda79231f1 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -198,6 +198,11 @@ encoding, supporting Unicode version 9.0.0.") (sha256 (base32 "0jiybkb2z58wa2msvllnphr4js2hvjvh988pavb3mzkgr6ihwbkr")))) (build-system gnu-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'bootstrap + (lambda _ (invoke "sh" "reconf")))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index 69aff5efaa..895cf6ac3b 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -88,17 +88,15 @@ to a file.") (define-public python-pytz (package (name "python-pytz") - (version "2017.3") + (version "2018.5") (source (origin (method url-fetch) - (uri (pypi-uri "pytz" version ".zip")) + (uri (pypi-uri "pytz" version ".tar.gz")) (sha256 (base32 - "1dw5l527vcafvdqq4wadwl7ikhb2sssz0v0cssibh8890kyczr7s")))) + "0xzj5gkpdn2da8m6j47chlp6zrzcypv9m0fjv4236q3jw4fyzfgz")))) (build-system python-build-system) - (native-inputs - `(("unzip" ,unzip))) (home-page "http://pythonhosted.org/pytz") (synopsis "Python timezone library") (description "This library brings the Olson tz database into Python. It @@ -143,15 +141,17 @@ Pendulum instances.") (define-public python-dateutil (package (name "python-dateutil") - (version "2.6.1") + (version "2.7.3") (source (origin (method url-fetch) (uri (pypi-uri "python-dateutil" version)) (sha256 (base32 - "1jkahssf0ir5ssxc3ydbp8cpv77limn8d4s77szb2nrgl2r3h749")))) + "1f7h54lg0w2ckch7592xpjkh8dg87k2br256h0iw49zn6bg02w72")))) (build-system python-build-system) + (native-inputs + `(("python-setuptools-scm" ,python-setuptools-scm))) (propagated-inputs `(("python-six" ,python-six))) (home-page "https://dateutil.readthedocs.io/en/stable/") @@ -159,7 +159,10 @@ Pendulum instances.") (description "The dateutil module provides powerful extensions to the standard datetime module, available in Python 2.3+.") - (license bsd-3))) + ;; The license was changed from the three-clause BSD license to a dual + ;; Apache 2.0/BSD-3 variant at 2017-12-01. Some code is only available as + ;; BSD-3 still; but all new code is dual licensed (the user can choose). + (license (list bsd-3 asl2.0)))) (define-public python2-dateutil (package-with-python2 python-dateutil)) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 2da4874e79..01c68d2e35 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -80,6 +80,8 @@ (base32 "1jlc1iahj8k3haz28j55nzg7sgni5h41vqy461i1bpbx6668wlky")))) (build-system gnu-build-system) + (arguments + `(#:configure-flags '("--disable-static"))) (native-inputs `(("perl" ,perl))) (home-page "https://www.gnu.org/software/libtasn1/") (synopsis "ASN.1 library") @@ -260,8 +262,7 @@ required structures.") (define-public openssl (package (name "openssl") - (replacement openssl/fixed) - (version "1.0.2o") + (version "1.0.2p") (source (origin (method url-fetch) (uri (list (string-append "https://www.openssl.org/source/openssl-" @@ -273,7 +274,7 @@ required structures.") "/" name "-" version ".tar.gz"))) (sha256 (base32 - "0kcy13l701054nhpbd901mz32v1kn4g311z0nifd83xs2jbmqgzc")) + "003xh9f898i56344vpvpxxxzmikivxig4xwlm7vbi7m8n43qxaah")) (patches (search-patches "openssl-runpath.patch" "openssl-c-rehash-in.patch")))) (build-system gnu-build-system) @@ -316,15 +317,7 @@ required structures.") (string-append "--openssldir=" out "/share/openssl-" ,version) - (string-append "--prefix=" out) - - ;; XXX FIXME: Work around a code generation bug in GCC - ;; 4.9.3 on ARM when compiled with -mfpu=neon. See: - ;; <https://gcc.gnu.org/bugzilla/show_bug.cgi?id=66917> - ,@(if (and (not (%current-target-system)) - (string-prefix? "armhf" (%current-system))) - '("-mfpu=vfpv3") - '()))))) + (string-append "--prefix=" out))))) (add-after 'install 'make-libraries-writable (lambda* (#:key outputs #:allow-other-keys) @@ -397,15 +390,6 @@ required structures.") (license license:openssl) (home-page "https://www.openssl.org/"))) -(define openssl/fixed - (package - (inherit openssl) - (source (origin - (inherit (package-source openssl)) - (patches (append (origin-patches (package-source openssl)) - (search-patches "openssl-1.0.2-CVE-2018-0495.patch" - "openssl-1.0.2-CVE-2018-0732.patch"))))))) - (define-public openssl-next (package (inherit openssl) @@ -616,7 +600,7 @@ netcat implementation that supports TLS.") `(("python-nose" ,python-nose) ("python-mock" ,python-mock) ;; For documentation - ("python-sphinx" ,python-sphinx-1.6) + ("python-sphinx" ,python-sphinx) ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme) ("python-sphinx-repoze-autointerface" ,python-sphinx-repoze-autointerface) ("python-sphinxcontrib-programoutput" ,python-sphinxcontrib-programoutput) diff --git a/gnu/packages/tv.scm b/gnu/packages/tv.scm index ef67ad37f2..2196162956 100644 --- a/gnu/packages/tv.scm +++ b/gnu/packages/tv.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018 Alex Kost <alezost@gmail.com> +;;; Copyright © 208 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -43,6 +44,15 @@ (base32 "1367rl3n6qxwf30lqyz234zpb43s9xjhig3hrvbg7cbqcl8g4fs0")))) (build-system gnu-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-glibc-compatability + (lambda _ + (substitute* "src/get_media_devices.c" + (("<sys/stat.h>") + "<sys/stat.h>\n#include <sys/sysmacros.h>")) + #t))))) (inputs `(("alsa-lib" ,alsa-lib) ("libx11" ,libx11) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index e9a49df787..8a5e730bd5 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1372,7 +1372,8 @@ YouTube.com and many more sites.") (("os\\.path\\.join\\('/usr', 'share'") (string-append "os.path.join('" (assoc-ref %outputs "out") - "', 'share'")))))))) + "', 'share'"))) + #t))))) (inputs `(("python2-wxpython" ,python2-wxpython) ("youtube-dl" ,youtube-dl))) @@ -1710,67 +1711,68 @@ for use with HTML5 video.") (add-before 'patch-source-shebangs 'unpack-ffmpeg (lambda _ (with-directory-excursion "avidemux_core/ffmpeg_package" - (system* "tar" "xf" "ffmpeg-2.7.6.tar.bz2") - (delete-file "ffmpeg-2.7.6.tar.bz2")))) + (invoke "tar" "xf" "ffmpeg-2.7.6.tar.bz2") + (delete-file "ffmpeg-2.7.6.tar.bz2")) + #t)) (add-after 'patch-source-shebangs 'repack-ffmpeg (lambda _ (with-directory-excursion "avidemux_core/ffmpeg_package" (substitute* "ffmpeg-2.7.6/configure" (("#! /bin/sh") (string-append "#!" (which "sh")))) - (system* "tar" "cjf" "ffmpeg-2.7.6.tar.bz2" "ffmpeg-2.7.6" - ;; avoid non-determinism in the archive - "--sort=name" "--mtime=@0" - "--owner=root:0" "--group=root:0") - (delete-file-recursively "ffmpeg-2.7.6")))) + (invoke "tar" "cjf" "ffmpeg-2.7.6.tar.bz2" "ffmpeg-2.7.6" + ;; avoid non-determinism in the archive + "--sort=name" "--mtime=@0" + "--owner=root:0" "--group=root:0") + (delete-file-recursively "ffmpeg-2.7.6")) + #t)) (replace 'configure (lambda _ ;; Copy-paste settings from the cmake build system. (setenv "CMAKE_LIBRARY_PATH" (getenv "LIBRARY_PATH")) - (setenv "CMAKE_INCLUDE_PATH" (getenv "C_INCLUDE_PATH")))) + (setenv "CMAKE_INCLUDE_PATH" (getenv "C_INCLUDE_PATH")) + #t)) (replace 'build (lambda* (#:key inputs outputs #:allow-other-keys) - (let* - ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib")) - (top (getcwd)) - (sdl (assoc-ref inputs "sdl")) - (build_component - (lambda* (component srcdir #:optional (args '())) - (let ((builddir (string-append "build_" component))) - (mkdir builddir) - (with-directory-excursion builddir - (zero? - (and - (apply system* "cmake" - "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" - (string-append "-DCMAKE_INSTALL_PREFIX=" out) - (string-append "-DCMAKE_INSTALL_RPATH=" lib) - (string-append "-DCMAKE_SHARED_LINKER_FLAGS=" - "\"-Wl,-rpath=" lib "\"") - (string-append "-DAVIDEMUX_SOURCE_DIR=" top) - (string-append "-DSDL_INCLUDE_DIR=" - sdl "/include/SDL") - (string-append "../" srcdir) - "-DENABLE_QT5=True" - args) - (system* "make" "-j" + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (top (getcwd)) + (sdl (assoc-ref inputs "sdl")) + (build_component + (lambda* (component srcdir #:optional (args '())) + (let ((builddir (string-append "build_" component))) + (mkdir builddir) + (with-directory-excursion builddir + (apply invoke "cmake" + "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" + (string-append "-DCMAKE_INSTALL_PREFIX=" out) + (string-append "-DCMAKE_INSTALL_RPATH=" lib) + (string-append "-DCMAKE_SHARED_LINKER_FLAGS=" + "\"-Wl,-rpath=" lib "\"") + (string-append "-DAVIDEMUX_SOURCE_DIR=" top) + (string-append "-DSDL_INCLUDE_DIR=" + sdl "/include/SDL") + (string-append "../" srcdir) + "-DENABLE_QT5=True" + args) + (invoke "make" "-j" (number->string (parallel-job-count))) - (system* "make" "install")))))))) + (invoke "make" "install")))))) (mkdir out) - (and (build_component "core" "avidemux_core") - (build_component "cli" "avidemux/cli") - (build_component "qt4" "avidemux/qt4") - (build_component "plugins_common" "avidemux_plugins" - '("-DPLUGIN_UI=COMMON")) - (build_component "plugins_cli" "avidemux_plugins" - '("-DPLUGIN_UI=CLI")) - (build_component "plugins_qt4" "avidemux_plugins" - '("-DPLUGIN_UI=QT4")) - (build_component "plugins_settings" "avidemux_plugins" - '("-DPLUGIN_UI=SETTINGS"))) + (build_component "core" "avidemux_core") + (build_component "cli" "avidemux/cli") + (build_component "qt4" "avidemux/qt4") + (build_component "plugins_common" "avidemux_plugins" + '("-DPLUGIN_UI=COMMON")) + (build_component "plugins_cli" "avidemux_plugins" + '("-DPLUGIN_UI=CLI")) + (build_component "plugins_qt4" "avidemux_plugins" + '("-DPLUGIN_UI=QT4")) + (build_component "plugins_settings" "avidemux_plugins" + '("-DPLUGIN_UI=SETTINGS")) ;; Remove .exe and .dll file. (delete-file-recursively - (string-append out "/share/ADM6_addons"))))) + (string-append out "/share/ADM6_addons")) + #t))) (delete 'install)))) (home-page "http://fixounet.free.fr/avidemux/") (synopsis "Video editor") @@ -1850,7 +1852,8 @@ format changes.") (lambda _ (chdir "build/generic") (substitute* "configure" - (("#! /bin/sh") (string-append "#!" (which "sh"))))))) + (("#! /bin/sh") (string-append "#!" (which "sh")))) + #t))) ;; No 'check' target. #:tests? #f)) (home-page "https://www.xvid.com/") @@ -1923,7 +1926,8 @@ from sites like Twitch.tv and pipes them into a video player of choice.") (lambda* (#:key outputs #:allow-other-keys) (install-file "plugins/rofi-twitchy" (string-append (assoc-ref outputs "out") - "/bin"))))))) + "/bin")) + #t))))) (inputs `(("python-requests" ,python-requests) ("streamlink" ,streamlink))) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index eeaaa85702..7f95748276 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -509,7 +509,7 @@ libraries for working with JNLP applets.") (define-public jansson (package (name "jansson") - (version "2.10") + (version "2.11") (source (origin (method url-fetch) (uri @@ -517,7 +517,7 @@ libraries for working with JNLP applets.") version ".tar.gz")) (sha256 (base32 - "0iv4rxsnamqm3ldpg7dyhjq0x9cp023nc7ac820jdd3pwb8ml8bq")))) + "1x5jllzzqamq6kahx9d9a5mrarm9m3f30vfxvcqpi6p4mcnz91bf")))) (build-system gnu-build-system) (home-page "http://www.digip.org/jansson/") (synopsis "JSON C library") @@ -5803,6 +5803,7 @@ Instagram and YouTube.") (uri (git-reference (url "https://github.com/linkchecker/linkchecker") (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 "03ihjmc4bqxxqv71bb43r2f23sx0xnbq1k2fsg9fw05qa5s9x187")))) @@ -6693,7 +6694,7 @@ derivation by David Revoy from the original MonsterID by Andreas Gohr.") (define-public nghttp2 (package (name "nghttp2") - (version "1.31.1") + (version "1.32.0") (source (origin (method url-fetch) @@ -6702,7 +6703,7 @@ derivation by David Revoy from the original MonsterID by Andreas Gohr.") name "-" version ".tar.xz")) (sha256 (base32 - "00z1687m4wi2gbgkijbv099l9hs1sjlyzbhh8jhn0xssx4xcifb5")))) + "0zbgp8f80h2zlfn8cd2ldrmgl81jzcdh1141n71aqmfckzaqj2kh")))) (build-system gnu-build-system) (outputs (list "out" "lib")) ; only libnghttp2 diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index c54282b985..966847e245 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -157,14 +157,14 @@ avoiding password prompts when X11 forwarding has already been setup.") (define-public libxkbcommon (package (name "libxkbcommon") - (version "0.8.0") + (version "0.8.2") (source (origin (method url-fetch) (uri (string-append "https://xkbcommon.org/download/" name "-" version ".tar.xz")) (sha256 (base32 - "0vgy84vfbig5bqznr137h5arjidnfwrxrdli0pxyn2jfn1fjcag8")))) + "136mdq11lrwg6rjmm44lmysxxgb9c35p4sq6k0cd129x82rw9f3s")))) (build-system gnu-build-system) (inputs `(("libx11" ,libx11) @@ -243,7 +243,8 @@ X11 (yet).") (mkdir-p (string-append out "/lib")) (setenv "PREFIX" out) (setenv "LDFLAGS" (string-append "-Wl,-rpath=" out "/lib")) - (setenv "CC" "gcc"))))))) + (setenv "CC" "gcc") + #t)))))) (native-inputs `(("perl" ,perl))) ; for pod2man (inputs `(("libx11" ,libx11) ("libxext" ,libxext) @@ -316,7 +317,7 @@ rasterisation.") (define-public libdrm (package (name "libdrm") - (version "2.4.92") + (version "2.4.93") (source (origin (method url-fetch) @@ -326,7 +327,7 @@ rasterisation.") ".tar.bz2")) (sha256 (base32 - "1yirzx8hmlvv6r0l7lb3zxmgy5la2mri9al0k16xqfg19pdqzr79")) + "0g6d9wsnb7lx8r1m4kq8js0wsc5jl20cz1csnlh6z9s8jpfd313f")) (patches (search-patches "libdrm-symbol-check.patch")))) (build-system gnu-build-system) (arguments @@ -477,7 +478,7 @@ move windows, switch between desktops, etc.).") (doc (string-append out "/share/doc/scrot"))) (mkdir-p doc) (invoke "make" "install" - (string-append "docsdir=" doc)))))))) + (string-append "docsdir=" doc)))))))) (inputs `(("libx11" ,libx11) ("giblib" ,giblib))) @@ -1004,7 +1005,8 @@ color temperature should be set to match the lamps in your room.") (lambda _ (substitute* '("driver/Makefile.in" "po/Makefile.in.in") (("@GTK_DATADIR@") "@datadir@") - (("@PO_DATADIR@") "@datadir@"))))) + (("@PO_DATADIR@") "@datadir@")) + #t))) #:configure-flags '("--with-pam" "--with-proc-interrupts" "--without-readdisplay") #:make-flags (list (string-append "AD_DIR=" @@ -1164,7 +1166,8 @@ by name.") (add-after 'unpack 'fix-installation-prefix (lambda _ (substitute* "CMakeLists.txt" - (("/etc") "${CMAKE_INSTALL_PREFIX}/etc"))))))) + (("/etc") "${CMAKE_INSTALL_PREFIX}/etc")) + #t))))) (inputs `(("gtk+" ,gtk+-2) ("imlib2" ,imlib2) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 347ac878a3..3ac01133e5 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -66,14 +66,14 @@ (define-public expat (package (name "expat") - (version "2.2.5") + (version "2.2.6") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/expat/expat/" version "/expat-" version ".tar.bz2")) (sha256 (base32 - "1xpd78sp7m34jqrw5x13bz7kgz0n6aj15wn4zj4gfx3ypbpk5p6r")))) + "1wl1x93b5w457ddsdgj0lh7yjq4q6l7wfbgwhagkc8fm2qkkrd0p")))) (build-system gnu-build-system) (home-page "https://libexpat.github.io/") (synopsis "Stream-oriented XML parser library written in C") @@ -131,8 +131,23 @@ hierarchical form with variable field lengths.") (base32 "0ci7is75bwqqw2p32vxvrk6ds51ik7qgx73m920rakv5jlayax0b")))) (build-system gnu-build-system) + (outputs '("out" "static")) + (arguments + `(#:phases (modify-phases %standard-phases + (add-after 'install 'move-static-libs + (lambda* (#:key outputs #:allow-other-keys) + (let ((src (string-append (assoc-ref outputs "out") "/lib")) + (dst (string-append (assoc-ref outputs "static") + "/lib"))) + (mkdir-p dst) + (for-each (lambda (ar) + (rename-file ar (string-append dst "/" + (basename ar)))) + (find-files src "\\.a$")) + #t)))))) (home-page "http://www.xmlsoft.org/") (synopsis "C parser for XML") + (inputs `(("xz" ,xz))) (propagated-inputs `(("zlib" ,zlib))) ; libxml2.la says '-lz'. (native-inputs `(("perl" ,perl))) ;; $XML_CATALOG_FILES lists 'catalog.xml' files found in under the 'xml' @@ -153,6 +168,7 @@ project (but it is usable outside of the Gnome platform).") (package/inherit libxml2 (name "python-libxml2") (build-system python-build-system) + (outputs '("out")) (arguments `(;; XXX: Tests are specified in 'Makefile.am', but not in 'setup.py'. #:tests? #f @@ -171,7 +187,8 @@ project (but it is usable outside of the Gnome platform).") (format #f "ROOT = r'~a'" libxml2)) ;; For 'iconv.h'. (("/opt/include") - (string-append glibc "/include"))))))))) + (string-append glibc "/include")))) + #t))))) (inputs `(("libxml2" ,libxml2))) (synopsis "Python bindings for the libxml2 library"))) @@ -536,7 +553,8 @@ that allow you to generate HTML from an RSS, convert between 0.9, 0.91, and (setenv "PERL5LIB" (string-append (getenv "PERL5LIB") ":" (assoc-ref outputs "out") - "/lib/perl5/site_perl"))))))) + "/lib/perl5/site_perl")) + #t))))) (home-page "https://metacpan.org/release/XML-SAX") (synopsis "Perl API for XML") (description "XML::SAX consists of several framework classes for using and @@ -1204,7 +1222,7 @@ elements to their parents (substitute* "test/run" ;; Run tests with `python' only (("^(PYTHON_VERSIONS = ).*" all m) (string-append m "['']"))) - (zero? (system* "test/run"))))))) + (invoke "test/run")))))) (home-page "https://github.com/dilshod/xlsx2csv") (synopsis "XLSX to CSV converter") (description @@ -1253,7 +1271,7 @@ files. It is designed to be fast and to handle large input files.") ;; Bootstrapping is required in order to fix the test driver script. (replace 'bootstrap (lambda _ - (zero? (system* "bash" "bootstrap"))))))) + (invoke "bash" "bootstrap")))))) (native-inputs `(("unzip" ,unzip) ("autoconf" ,autoconf) @@ -1854,7 +1872,8 @@ low memory footprint.") (modify-phases %standard-phases (add-before 'build 'copy-resources (lambda _ - (copy-recursively "src/main/resources" "build/classes")))))) + (copy-recursively "src/main/resources" "build/classes") + #t))))) (inputs `(("java-xpp3" ,java-xpp3))) (native-inputs diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 1b54296dc1..9aa65291b9 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -3829,7 +3829,7 @@ extension to the X11 protocol. It includes: (define-public xkeyboard-config (package (name "xkeyboard-config") - (version "2.23.1") + (version "2.24") (source (origin (method url-fetch) @@ -3839,7 +3839,7 @@ extension to the X11 protocol. It includes: ".tar.bz2")) (sha256 (base32 - "1wq27cs1c9y7d1d7zp5yhq29paj9smajdb68lyvm28d2zq2vqjra")))) + "1my4786pd7iv5x392r9skj3qclmbd26nqzvh2fllwkkbyj08bcci")))) (build-system gnu-build-system) (inputs `(("gettext" ,gettext-minimal) @@ -5193,21 +5193,10 @@ draggable titlebars and borders.") ;; This package is intended to be used when building GTK+. ;; Note: It's currently marked as "hidden" to avoid having two non-eq? ;; packages with the same name and version. -(define-public xorg-server-1.19.3 +(define-public xorg-server-for-tests (hidden-package (package - (inherit xorg-server) - (name "xorg-server") - (version "1.19.3") - (source - (origin - (method url-fetch) - (uri (string-append - "mirror://xorg/individual/xserver/" - name "-" version ".tar.bz2")) - (sha256 - (base32 - "162s1v901djr57gxmmk4airk8hiwcz79dqyz72972x1lw1k82yk7"))))))) + (inherit xorg-server)))) (define-public xorg-server-xwayland (package @@ -5233,8 +5222,7 @@ draggable titlebars and borders.") (define-public libx11 (package (name "libx11") - (version "1.6.5") - (replacement libx11-1.6.6) + (version "1.6.6") (source (origin (method url-fetch) @@ -5244,7 +5232,7 @@ draggable titlebars and borders.") ".tar.bz2")) (sha256 (base32 - "0pa3cfp6h9rl2vxmkph65250gfqyki0ccqyaan6bl9d25gdr0f2d")))) + "0ks1mxlda7nxfmffihi15ljsn50q8dknl33i2xag8xzc80fiizk5")))) (build-system gnu-build-system) (outputs '("out" "doc")) ;8 MiB of man pages + XML @@ -5264,20 +5252,6 @@ draggable titlebars and borders.") (description "Xorg Core X11 protocol client library.") (license license:x11))) -;; Replacement package to fix multiple security bugs: -;; <http://seclists.org/oss-sec/2018/q3/146>. -(define-public libx11-1.6.6 - (package - (inherit libx11) - (version "1.6.6") - (source (origin - (method url-fetch) - (uri (string-append "mirror://xorg/individual/lib/libX11-" - version ".tar.bz2")) - (sha256 - (base32 - "0ks1mxlda7nxfmffihi15ljsn50q8dknl33i2xag8xzc80fiizk5")))))) - ;; packages of height 5 in the propagated-inputs tree (define-public libxcursor @@ -5965,7 +5939,7 @@ Conventions Manual) and some of the @dfn{EWMH} (add-after 'unpack 'autogen (lambda _ (setenv "NOCONFIGURE" "t") - (zero? (system* "sh" "autogen.sh"))))))) + (invoke "sh" "autogen.sh")))))) (native-inputs `(("pkg-config" ,pkg-config) ("autoconf" ,autoconf) |