aboutsummaryrefslogtreecommitdiff
#!/bin/sh
# Create the build system.

set -e -x

# Generate stubs for translations.
langs=`find po/doc -type f -name 'guix-manual*.po' \
        | sed -e 's,.*/guix-manual\.,,;s,\.po$,,'`
for lang in ${langs}; do
    if [ ! -e "doc/guix.${lang}.texi" ]; then
	echo "@setfilename guix.${lang}.info" > "doc/guix.${lang}.texi"
	echo "@include version-${lang}.texi" >> "doc/guix.${lang}.texi"
	# Ensure .po file is newer.
	touch "po/doc/guix-manual.${lang}.po"
    fi
done
langs=`find po/doc -type f -name 'guix-cookbook*.po' \
        | sed -e 's,.*/guix-cookbook\.,,;s,\.po$,,'`
for lang in ${langs}; do
    if [ ! -e "doc/guix-cookbook.${lang}.texi" ]; then
	echo "@setfilename guix-cookbook.${lang}.info" > "doc/guix-cookbook.${lang}.texi"
	# Ensure .po file is newer.
	touch "po/doc/guix-cookbook.${lang}.po"
    fi
done

autoreconf -vfi

# Replace Automake's build-aux/mdate-sh with build-aux/mdate-from-git, our
# own, reproducible version.
chmod +w build-aux/mdate-sh
rm -f build-aux/mdate-sh
ln -s mdate-from-git.scm build-aux/mdate-sh
eader'>Diffstat (limited to 'gnu')
-rw-r--r--gnu/installer/connman.scm2
-rw-r--r--gnu/installer/newt/keymap.scm2
-rw-r--r--gnu/installer/newt/page.scm2
-rw-r--r--gnu/installer/newt/timezone.scm5
-rw-r--r--gnu/installer/newt/utils.scm2
-rw-r--r--gnu/installer/newt/wifi.scm8
-rw-r--r--gnu/installer/parted.scm6
-rw-r--r--gnu/installer/timezone.scm10
-rw-r--r--gnu/local.mk26
-rw-r--r--gnu/packages.scm53
-rw-r--r--gnu/packages/admin.scm54
-rw-r--r--gnu/packages/aidc.scm29
-rw-r--r--gnu/packages/algebra.scm146
-rw-r--r--gnu/packages/assembly.scm12
-rw-r--r--gnu/packages/audio.scm38
-rw-r--r--gnu/packages/aux-files/chromium/master-preferences.json26
-rw-r--r--gnu/packages/backup.scm44
-rw-r--r--gnu/packages/base.scm5
-rw-r--r--gnu/packages/bioconductor.scm23
-rw-r--r--gnu/packages/bioinformatics.scm306
-rw-r--r--gnu/packages/bittorrent.scm22
-rw-r--r--gnu/packages/bootloaders.scm12
-rw-r--r--gnu/packages/busybox.scm6
-rw-r--r--gnu/packages/check.scm32
-rw-r--r--gnu/packages/chez.scm155
-rw-r--r--gnu/packages/chromium.scm705
-rw-r--r--gnu/packages/compression.scm77
-rw-r--r--gnu/packages/conky.scm18
-rw-r--r--gnu/packages/coq.scm81
-rw-r--r--gnu/packages/cran.scm150
-rw-r--r--gnu/packages/crypto.scm6
-rw-r--r--gnu/packages/cups.scm52
-rw-r--r--gnu/packages/curl.scm10
-rw-r--r--gnu/packages/databases.scm37
-rw-r--r--gnu/packages/debug.scm36
-rw-r--r--gnu/packages/dictionaries.scm2
-rw-r--r--gnu/packages/disk.scm32
-rw-r--r--gnu/packages/dlang.scm4
-rw-r--r--gnu/packages/dns.scm28
-rw-r--r--gnu/packages/docker.scm13
-rw-r--r--gnu/packages/documentation.scm13
-rw-r--r--gnu/packages/efi.scm10
-rw-r--r--gnu/packages/emacs-xyz.scm183
-rw-r--r--gnu/packages/engineering.scm9
-rw-r--r--gnu/packages/file-systems.scm4
-rw-r--r--gnu/packages/finance.scm168
-rw-r--r--gnu/packages/flashing-tools.scm20
-rw-r--r--gnu/packages/fonts.scm51
-rw-r--r--gnu/packages/ftp.scm8
-rw-r--r--gnu/packages/game-development.scm12
-rw-r--r--gnu/packages/games.scm74
-rw-r--r--gnu/packages/gd.scm11
-rw-r--r--gnu/packages/genimage.scm194
-rw-r--r--gnu/packages/geo.scm27
-rw-r--r--gnu/packages/gimp.scm16
-rw-r--r--gnu/packages/gl.scm6
-rw-r--r--gnu/packages/gnome.scm334
-rw-r--r--gnu/packages/gnupg.scm19
-rw-r--r--gnu/packages/gnuzilla.scm4
-rw-r--r--gnu/packages/gtk.scm29
-rw-r--r--gnu/packages/guile-xyz.scm101
-rw-r--r--gnu/packages/hardware.scm12
-rw-r--r--gnu/packages/ibus.scm145
-rw-r--r--gnu/packages/image-processing.scm8
-rw-r--r--gnu/packages/image-viewers.scm6
-rw-r--r--gnu/packages/image.scm42
-rw-r--r--gnu/packages/irc.scm8
-rw-r--r--gnu/packages/java.scm41
-rw-r--r--gnu/packages/kde-frameworks.scm337
-rw-r--r--gnu/packages/kde-plasma.scm228
-rw-r--r--gnu/packages/kde.scm101
-rw-r--r--gnu/packages/kodi.scm6
-rw-r--r--gnu/packages/libffi.scm6
-rw-r--r--gnu/packages/libreoffice.scm36
-rw-r--r--gnu/packages/linux.scm42
-rw-r--r--gnu/packages/lisp.scm15
-rw-r--r--gnu/packages/llvm.scm88
-rw-r--r--gnu/packages/lxqt.scm2
-rw-r--r--gnu/packages/machine-learning.scm3
-rw-r--r--gnu/packages/magic-wormhole.scm160
-rw-r--r--gnu/packages/mail.scm42
-rw-r--r--gnu/packages/maths.scm110
-rw-r--r--gnu/packages/maven.scm12
-rw-r--r--gnu/packages/mpi.scm27
-rw-r--r--gnu/packages/multiprecision.scm15
-rw-r--r--gnu/packages/music.scm18
-rw-r--r--gnu/packages/musl.scm12
-rw-r--r--gnu/packages/ncdu.scm6
-rw-r--r--gnu/packages/ncurses.scm8
-rw-r--r--gnu/packages/netpbm.scm4
-rw-r--r--gnu/packages/networking.scm46
-rw-r--r--gnu/packages/ocaml.scm228
-rw-r--r--gnu/packages/package-management.scm87
-rw-r--r--gnu/packages/parallel.scm6
-rw-r--r--gnu/packages/patches/allegro4-mesa-18.2.5-and-later.patch41
-rw-r--r--gnu/packages/patches/clang-7.0-libc-search-path.patch82
-rw-r--r--gnu/packages/patches/dealii-mpi-deprecations.patch28
-rw-r--r--gnu/packages/patches/doxygen-test.patch8
-rw-r--r--gnu/packages/patches/gd-CVE-2019-6977.patch36
-rw-r--r--gnu/packages/patches/gd-CVE-2019-6978.patch301
-rw-r--r--gnu/packages/patches/glibc-CVE-2018-11236.patch149
-rw-r--r--gnu/packages/patches/glibc-CVE-2018-11237.patch55
-rw-r--r--gnu/packages/patches/kio-search-smbd-on-PATH.patch2
-rw-r--r--gnu/packages/patches/ledger-revert-boost-python-fix.patch39
-rw-r--r--gnu/packages/patches/mrustc-0.8.0-fix-variable-length-integer-receiving.patch15
-rw-r--r--gnu/packages/patches/pius.patch38
-rw-r--r--gnu/packages/patches/qtbase-old-kernel.patch25
-rw-r--r--gnu/packages/patches/red-eclipse-remove-gamma-name-hack.patch52
-rw-r--r--gnu/packages/patches/ruby-safe-yaml-add-require-time.patch19
-rw-r--r--gnu/packages/patches/runc-CVE-2019-5736.patch343
-rw-r--r--gnu/packages/patches/scalapack-blacs-mpi-deprecations.patch170
-rw-r--r--gnu/packages/patches/soundconverter-remove-gconf-dependency.patch104
-rw-r--r--gnu/packages/patches/tomsfastmath-constness.patch76
-rw-r--r--gnu/packages/patches/xf86-video-i128-remove-mibstore.patch23
-rw-r--r--gnu/packages/patches/xmodmap-asprintf.patch14
-rw-r--r--gnu/packages/pdf.scm17
-rw-r--r--gnu/packages/perl.scm17
-rw-r--r--gnu/packages/python-crypto.scm82
-rw-r--r--gnu/packages/python-web.scm116
-rw-r--r--gnu/packages/python-xyz.scm189
-rw-r--r--gnu/packages/python.scm62
-rw-r--r--gnu/packages/qt.scm33
-rw-r--r--gnu/packages/rails.scm372
-rw-r--r--gnu/packages/rdesktop.scm26
-rw-r--r--gnu/packages/rrdtool.scm6
-rw-r--r--gnu/packages/ruby.scm1777
-rw-r--r--gnu/packages/rust.scm16
-rw-r--r--gnu/packages/sagemath.scm59
-rw-r--r--gnu/packages/sdl.scm48
-rw-r--r--gnu/packages/search.scm6
-rw-r--r--gnu/packages/security-token.scm8
-rw-r--r--gnu/packages/simh.scm19
-rw-r--r--gnu/packages/skarnet.scm6
-rw-r--r--gnu/packages/statistics.scm23
-rw-r--r--gnu/packages/suckless.scm4
-rw-r--r--gnu/packages/sync.scm43
-rw-r--r--gnu/packages/terminals.scm55
-rw-r--r--gnu/packages/textutils.scm4
-rw-r--r--gnu/packages/tls.scm24
-rw-r--r--gnu/packages/tmux.scm23
-rw-r--r--gnu/packages/tor.scm7
-rw-r--r--gnu/packages/version-control.scm19
-rw-r--r--gnu/packages/video.scm62
-rw-r--r--gnu/packages/vim.scm12
-rw-r--r--gnu/packages/virtualization.scm16
-rw-r--r--gnu/packages/web-browsers.scm4
-rw-r--r--gnu/packages/web.scm103
-rw-r--r--gnu/packages/wine.scm6
-rw-r--r--gnu/packages/wm.scm66
-rw-r--r--gnu/packages/xdisorg.scm53
-rw-r--r--gnu/packages/xml.scm36
-rw-r--r--gnu/packages/xorg.scm123
-rw-r--r--gnu/services/desktop.scm109
-rw-r--r--gnu/services/xorg.scm121
-rw-r--r--gnu/system/vm.scm6
155 files changed, 8328 insertions, 2547 deletions
diff --git a/gnu/installer/connman.scm b/gnu/installer/connman.scm
index 740df7424a..ef8cca3952 100644
--- a/gnu/installer/connman.scm
+++ b/gnu/installer/connman.scm
@@ -299,7 +299,7 @@ to merge stdout and stderr using bash redirection. Then error messages are
extracted from connmanctl output using a regexp. This makes the whole
procedure even more unreliable.
-Raise &connman-connection-error if an error occured during connection. Raise
+Raise &connman-connection-error if an error occurred during connection. Raise
&connman-password-error if the given password is incorrect."
(define connman-error-regexp (make-regexp "Error[ ]*([^\n]+)\n"))
diff --git a/gnu/installer/newt/keymap.scm b/gnu/installer/newt/keymap.scm
index 6211af2bc5..3e765bfdd4 100644
--- a/gnu/installer/newt/keymap.scm
+++ b/gnu/installer/newt/keymap.scm
@@ -71,7 +71,7 @@
(cut append <> <>)))
(define (sort-variants variants)
- "Sort VARIANTS list by putting the internation variant ahead and return it."
+ "Sort VARIANTS list by putting the international variant ahead and return it."
(call-with-values
(lambda ()
(partition
diff --git a/gnu/installer/newt/page.scm b/gnu/installer/newt/page.scm
index edf0b8c999..23fbfcce76 100644
--- a/gnu/installer/newt/page.scm
+++ b/gnu/installer/newt/page.scm
@@ -188,7 +188,7 @@ If SORT-LISTBOX-ITEMS? is set to #t, the listbox items are sorted using
'string<=' procedure (after being converted to text).
If ALLOW-DELETE? is #t, the form will return if the <DELETE> key is pressed,
-otherwise nothing will happend.
+otherwise nothing will happen.
Each time the listbox current item changes, call SKIP-ITEM-PROCEDURE? with the
current listbox item as argument. If it returns #t, skip the element and jump
diff --git a/gnu/installer/newt/timezone.scm b/gnu/installer/newt/timezone.scm
index 6c96ee55b1..63b44af729 100644
--- a/gnu/installer/newt/timezone.scm
+++ b/gnu/installer/newt/timezone.scm
@@ -30,9 +30,6 @@
#:use-module (newt)
#:export (run-timezone-page))
-;; Heigth of the listbox displaying timezones.
-(define timezone-listbox-heigth (make-parameter 20))
-
;; Information textbox width.
(define info-textbox-width (make-parameter 40))
@@ -53,7 +50,7 @@ returned."
(define (run-page timezone-tree)
(define (loop path)
- (let ((timezones (locate-childrens timezone-tree path)))
+ (let ((timezones (locate-children timezone-tree path)))
(run-listbox-selection-page
#:title (G_ "Timezone")
#:info-text (G_ "Please select a timezone.")
diff --git a/gnu/installer/newt/utils.scm b/gnu/installer/newt/utils.scm
index 1c2ce4e628..dfb113e0c6 100644
--- a/gnu/installer/newt/utils.scm
+++ b/gnu/installer/newt/utils.scm
@@ -30,7 +30,7 @@
(define screen-rows (make-parameter 0))
(define (destroy-form-and-pop form)
- "Destory the given FORM and pop the current window."
+ "Destroy the given FORM and pop the current window."
(destroy-form form)
(pop-window))
diff --git a/gnu/installer/newt/wifi.scm b/gnu/installer/newt/wifi.scm
index 59e40e327e..4cf5c128e7 100644
--- a/gnu/installer/newt/wifi.scm
+++ b/gnu/installer/newt/wifi.scm
@@ -100,7 +100,7 @@ nmc_wifi_strength_bars."
"Run a page to inform user that a connection error happened."
(run-error-page
(format #f
- (G_ "An error occured while trying to connect to ~a, please retry.")
+ (G_ "An error occurred while trying to connect to ~a, please retry.")
service-name)
(G_ "Connection error")))
@@ -160,8 +160,8 @@ of <service-item> records present in LISTBOX."
;; Maximum length of a wifi service name.
(define service-name-max-length (make-parameter 20))
-;; Heigth of the listbox displaying wifi services.
-(define wifi-listbox-heigth (make-parameter 20))
+;; Height of the listbox displaying wifi services.
+(define wifi-listbox-height (make-parameter 20))
;; Information textbox width.
(define info-textbox-width (make-parameter 40))
@@ -188,7 +188,7 @@ network when the corresponding listbox entry is selected. A button allow to
force a wifi scan."
(let* ((listbox (make-listbox
-1 -1
- (wifi-listbox-heigth)
+ (wifi-listbox-height)
(logior FLAG-SCROLL FLAG-BORDER FLAG-RETURNEXIT)))
(form (make-form))
(buttons-grid (make-grid 1 1))
diff --git a/gnu/installer/parted.scm b/gnu/installer/parted.scm
index 187311e633..642b8c6d8a 100644
--- a/gnu/installer/parted.scm
+++ b/gnu/installer/parted.scm
@@ -677,7 +677,7 @@ otherwise."
(define* (mkpart disk user-partition
#:key (previous-partition #f))
"Create the given USER-PARTITION on DISK. The PREVIOUS-PARTITION argument as
-to be set to the partition preceeding USER-PARTITION if any."
+to be set to the partition preceding USER-PARTITION if any."
(define (parse-start-end start end)
"Parse start and end strings as positions on DEVICE expressed with a unit,
@@ -734,8 +734,8 @@ cause them to cross."
(< start-distance 3))
(+ start-sector start-offset)
start-sector)))
- ;; This is a hackery but parted almost always fails to create optimally
- ;; aligned partitions (unless specifiying percentages) because, the
+ ;; This is a hack. Parted almost always fails to create optimally
+ ;; aligned partitions (unless specifying percentages) because the
;; default range of 1MB centered on the start sector is not enough when
;; the optimal alignment is 2048 sectors of 512KB.
(extend-ranges! start-range end-range #:offset start-offset)
diff --git a/gnu/installer/timezone.scm b/gnu/installer/timezone.scm
index 32bc2ed6bb..c336b5f3ba 100644
--- a/gnu/installer/timezone.scm
+++ b/gnu/installer/timezone.scm
@@ -25,7 +25,7 @@
#:use-module (srfi srfi-35)
#:use-module (ice-9 match)
#:use-module (ice-9 receive)
- #:export (locate-childrens
+ #:export (locate-children
timezone->posix-tz
timezone-has-child?
zonetab->timezone-tree
@@ -94,15 +94,15 @@ timezones."
(loop (remove-first same-region))
(loop other-region))))))))
-(define (locate-childrens tree path)
- "Return the childrens of the timezone indicated by PATH in the given
+(define (locate-children tree path)
+ "Return the children of the timezone indicated by PATH in the given
TREE. Raise a condition if the PATH could not be found."
(let ((extract-proc (cut map car <>)))
(match path
(() (sort (extract-proc tree) string<?))
((region . rest)
(or (and=> (assoc-ref tree region)
- (cut locate-childrens <> rest))
+ (cut locate-children <> rest))
(raise
(condition
(&message
@@ -111,7 +111,7 @@ TREE. Raise a condition if the PATH could not be found."
(define (timezone-has-child? tree timezone)
"Return #t if the given TIMEZONE any child in TREE and #f otherwise."
- (not (null? (locate-childrens tree timezone))))
+ (not (null? (locate-children tree timezone))))
(define* (zonetab->timezone-tree zonetab)
"Return the timezone tree corresponding to the given ZONETAB file."
diff --git a/gnu/local.mk b/gnu/local.mk
index 3f66beac14..e239c76c7c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -100,6 +100,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/check.scm \
%D%/packages/chemistry.scm \
%D%/packages/chez.scm \
+ %D%/packages/chromium.scm \
%D%/packages/ci.scm \
%D%/packages/cinnamon.scm \
%D%/packages/clojure.scm \
@@ -191,6 +192,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/gcc.scm \
%D%/packages/gd.scm \
%D%/packages/gdb.scm \
+ %D%/packages/genimage.scm \
%D%/packages/geo.scm \
%D%/packages/gettext.scm \
%D%/packages/ghostscript.scm \
@@ -253,8 +255,9 @@ GNU_SYSTEM_MODULES = \
%D%/packages/jrnl.scm \
%D%/packages/jose.scm \
%D%/packages/julia.scm \
- %D%/packages/kde.scm \
+ %D%/packages/kde.scm \
%D%/packages/kde-frameworks.scm \
+ %D%/packages/kde-plasma.scm \
%D%/packages/kerberos.scm \
%D%/packages/key-mon.scm \
%D%/packages/kodi.scm \
@@ -294,6 +297,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/m4.scm \
%D%/packages/machine-learning.scm \
%D%/packages/man.scm \
+ %D%/packages/magic-wormhole.scm \
%D%/packages/mail.scm \
%D%/packages/make-bootstrap.scm \
%D%/packages/markup.scm \
@@ -635,7 +639,6 @@ dist_patch_DATA = \
%D%/packages/patches/aegisub-boost68.patch \
%D%/packages/patches/agg-am_c_prototype.patch \
%D%/packages/patches/allegro-mesa-18.2.5-and-later.patch \
- %D%/packages/patches/allegro4-mesa-18.2.5-and-later.patch \
%D%/packages/patches/amule-crypto-6.patch \
%D%/packages/patches/antiword-CVE-2014-8123.patch \
%D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch \
@@ -685,6 +688,7 @@ dist_patch_DATA = \
%D%/packages/patches/clang-3.5-libsanitizer-ustat-fix.patch \
%D%/packages/patches/clang-3.8-libc-search-path.patch \
%D%/packages/patches/clang-6.0-libc-search-path.patch \
+ %D%/packages/patches/clang-7.0-libc-search-path.patch \
%D%/packages/patches/clang-runtime-asan-build-fixes.patch \
%D%/packages/patches/clang-runtime-esan-build-fixes.patch \
%D%/packages/patches/classpath-aarch64-support.patch \
@@ -708,6 +712,7 @@ dist_patch_DATA = \
%D%/packages/patches/cursynth-wave-rand.patch \
%D%/packages/patches/cvs-2017-12836.patch \
%D%/packages/patches/dbus-helper-search-path.patch \
+ %D%/packages/patches/dealii-mpi-deprecations.patch \
%D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \
%D%/packages/patches/dfu-programmer-fix-libusb.patch \
%D%/packages/patches/diffutils-gets-undeclared.patch \
@@ -793,6 +798,8 @@ dist_patch_DATA = \
%D%/packages/patches/gcr-fix-collection-tests-to-work-with-gpg-21.patch \
%D%/packages/patches/gd-CVE-2018-5711.patch \
%D%/packages/patches/gd-CVE-2018-1000222.patch \
+ %D%/packages/patches/gd-CVE-2019-6977.patch \
+ %D%/packages/patches/gd-CVE-2019-6978.patch \
%D%/packages/patches/gd-fix-tests-on-i686.patch \
%D%/packages/patches/gd-freetype-test-failure.patch \
%D%/packages/patches/gdm-CVE-2018-14424.patch \
@@ -814,6 +821,8 @@ dist_patch_DATA = \
%D%/packages/patches/glibc-CVE-2017-1000366-pt1.patch \
%D%/packages/patches/glibc-CVE-2017-1000366-pt2.patch \
%D%/packages/patches/glibc-CVE-2017-1000366-pt3.patch \
+ %D%/packages/patches/glibc-CVE-2018-11236.patch \
+ %D%/packages/patches/glibc-CVE-2018-11237.patch \
%D%/packages/patches/glibc-allow-kernel-2.6.32.patch \
%D%/packages/patches/glibc-boot-2.16.0.patch \
%D%/packages/patches/glibc-boot-2.2.5.patch \
@@ -936,7 +945,6 @@ dist_patch_DATA = \
%D%/packages/patches/ldc-bootstrap-disable-tests.patch \
%D%/packages/patches/ldc-disable-phobos-tests.patch \
%D%/packages/patches/ledger-fix-uninitialized.patch \
- %D%/packages/patches/ledger-revert-boost-python-fix.patch \
%D%/packages/patches/liba52-enable-pic.patch \
%D%/packages/patches/liba52-link-with-libm.patch \
%D%/packages/patches/liba52-set-soname.patch \
@@ -1052,6 +1060,7 @@ dist_patch_DATA = \
%D%/packages/patches/mozjs38-tracelogger.patch \
%D%/packages/patches/mozjs38-version-detection.patch \
%D%/packages/patches/mrrescue-support-love-11.patch \
+ %D%/packages/patches/mrustc-0.8.0-fix-variable-length-integer-receiving.patch \
%D%/packages/patches/mumble-1.2.19-abs.patch \
%D%/packages/patches/mumps-build-parallelism.patch \
%D%/packages/patches/mupen64plus-ui-console-notice.patch \
@@ -1126,7 +1135,6 @@ dist_patch_DATA = \
%D%/packages/patches/pinentry-efl.patch \
%D%/packages/patches/pingus-boost-headers.patch \
%D%/packages/patches/pingus-sdl-libs-config.patch \
- %D%/packages/patches/pius.patch \
%D%/packages/patches/pixman-CVE-2016-5296.patch \
%D%/packages/patches/plink-1.07-unclobber-i.patch \
%D%/packages/patches/plink-endian-detection.patch \
@@ -1183,6 +1191,7 @@ dist_patch_DATA = \
%D%/packages/patches/qemu-CVE-2018-16872.patch \
%D%/packages/patches/qemu-CVE-2019-6778.patch \
%D%/packages/patches/qt4-ldflags.patch \
+ %D%/packages/patches/qtbase-old-kernel.patch \
%D%/packages/patches/qtbase-use-TZDIR.patch \
%D%/packages/patches/qtscript-disable-tests.patch \
%D%/packages/patches/quagga-reproducible-build.patch \
@@ -1199,6 +1208,7 @@ dist_patch_DATA = \
%D%/packages/patches/rct-add-missing-headers.patch \
%D%/packages/patches/readline-link-ncurses.patch \
%D%/packages/patches/readline-6.2-CVE-2014-2524.patch \
+ %D%/packages/patches/red-eclipse-remove-gamma-name-hack.patch \
%D%/packages/patches/reposurgeon-add-missing-docbook-files.patch \
%D%/packages/patches/reptyr-fix-gcc-7.patch \
%D%/packages/patches/ripperx-missing-file.patch \
@@ -1209,13 +1219,16 @@ dist_patch_DATA = \
%D%/packages/patches/ruby-concurrent-ignore-broken-test.patch \
%D%/packages/patches/ruby-concurrent-test-arm.patch \
%D%/packages/patches/ruby-rack-ignore-failing-test.patch \
+ %D%/packages/patches/ruby-safe-yaml-add-require-time.patch \
%D%/packages/patches/ruby-tzinfo-data-ignore-broken-test.patch\
+ %D%/packages/patches/runc-CVE-2019-5736.patch \
%D%/packages/patches/rust-1.19-mrustc.patch \
%D%/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch \
%D%/packages/patches/rust-bootstrap-stage0-test.patch \
%D%/packages/patches/rust-coresimd-doctest.patch \
%D%/packages/patches/rust-reproducible-builds.patch \
%D%/packages/patches/rxvt-unicode-escape-sequences.patch \
+ %D%/packages/patches/scalapack-blacs-mpi-deprecations.patch \
%D%/packages/patches/scheme48-tests.patch \
%D%/packages/patches/scotch-build-parallelism.patch \
%D%/packages/patches/scotch-integer-declarations.patch \
@@ -1273,7 +1286,6 @@ dist_patch_DATA = \
%D%/packages/patches/tk-find-library.patch \
%D%/packages/patches/ttf2eot-cstddef.patch \
%D%/packages/patches/ttfautohint-source-date-epoch.patch \
- %D%/packages/patches/tomsfastmath-constness.patch \
%D%/packages/patches/totem-meson-easy-codec.patch \
%D%/packages/patches/tuxpaint-stamps-path.patch \
%D%/packages/patches/twinkle-include-qregexpvalidator.patch \
@@ -1332,7 +1344,6 @@ dist_patch_DATA = \
%D%/packages/patches/x265-arm-flags.patch \
%D%/packages/patches/xf86-video-ark-remove-mibstore.patch \
%D%/packages/patches/xf86-video-geode-glibc-2.20.patch \
- %D%/packages/patches/xf86-video-i128-remove-mibstore.patch \
%D%/packages/patches/xf86-video-mach64-glibc-2.20.patch \
%D%/packages/patches/xf86-video-savage-xorg-compat.patch \
%D%/packages/patches/xf86-video-siliconmotion-fix-ftbfs.patch \
@@ -1342,8 +1353,7 @@ dist_patch_DATA = \
%D%/packages/patches/xfce4-session-fix-xflock4.patch \
%D%/packages/patches/xfce4-settings-defaults.patch \
%D%/packages/patches/xinetd-fix-fd-leak.patch \
- %D%/packages/patches/xinetd-CVE-2013-4342.patch \
- %D%/packages/patches/xmodmap-asprintf.patch
+ %D%/packages/patches/xinetd-CVE-2013-4342.patch
MISC_DISTRO_FILES = \
%D%/packages/ld-wrapper.in
diff --git a/gnu/packages.scm b/gnu/packages.scm
index 9cd57fc704..e484d9754f 100644
--- a/gnu/packages.scm
+++ b/gnu/packages.scm
@@ -375,34 +375,41 @@ reducing the memory footprint."
(define cache-file
(string-append directory %package-cache-file))
- (define (expand-cache module symbol variable result)
+ (define (expand-cache module symbol variable result+seen)
(match (false-if-exception (variable-ref variable))
((? package? package)
- (if (hidden-package? package)
- result
- (cons `#(,(package-name package)
- ,(package-version package)
- ,(module-name module)
- ,symbol
- ,(package-outputs package)
- ,(->bool (member (%current-system)
- (package-supported-systems package)))
- ,(->bool (package-superseded package))
- ,@(let ((loc (package-location package)))
- (if loc
- `(,(location-file loc)
- ,(location-line loc)
- ,(location-column loc))
- '(#f #f #f))))
- result)))
+ (match result+seen
+ ((result . seen)
+ (if (or (vhash-assq package seen)
+ (hidden-package? package))
+ (cons result seen)
+ (cons (cons `#(,(package-name package)
+ ,(package-version package)
+ ,(module-name module)
+ ,symbol
+ ,(package-outputs package)
+ ,(->bool
+ (member (%current-system)
+ (package-supported-systems package)))
+ ,(->bool (package-superseded package))
+ ,@(let ((loc (package-location package)))
+ (if loc
+ `(,(location-file loc)
+ ,(location-line loc)
+ ,(location-column loc))
+ '(#f #f #f))))
+ result)
+ (vhash-consq package #t seen))))))
(_
- result)))
+ result+seen)))
(define exp
- (fold-module-public-variables* expand-cache '()
- (all-modules (%package-module-path)
- #:warn
- warn-about-load-error)))
+ (first
+ (fold-module-public-variables* expand-cache
+ (cons '() vlist-null)
+ (all-modules (%package-module-path)
+ #:warn
+ warn-about-load-error))))
(mkdir-p (dirname cache-file))
(call-with-output-file cache-file
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index f4c34e10fe..24486cec18 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -9,7 +9,7 @@
;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Peter Feigl <peter.feigl@nexoid.at>
;;; Copyright © 2016 John J. Foerch <jjfoerch@earthlink.net>
;;; Copyright © 2016, 2017 Nils Gillmann <ng0@n0.is>
@@ -285,26 +285,26 @@ graphs and can export its output to different formats.")
(define-public htop
(package
- (name "htop")
- (version "2.2.0")
- (source (origin
- (method url-fetch)
- (uri (string-append "http://hisham.hm/htop/releases/"
- version "/htop-" version ".tar.gz"))
- (sha256
- (base32
- "0mrwpb3cpn3ai7ar33m31yklj64c3pp576vh1naqff6f21pq5mnr"))))
- (build-system gnu-build-system)
- (inputs
- `(("ncurses" ,ncurses)))
- (native-inputs
- `(("python" ,python-minimal-wrapper))) ; for scripts/MakeHeader.py
- (home-page "https://hisham.hm/htop/")
- (synopsis "Interactive process viewer")
- (description
- "This is htop, an interactive process viewer. It is a text-mode
+ (name "htop")
+ (version "2.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://hisham.hm/htop/releases/"
+ version "/htop-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0mrwpb3cpn3ai7ar33m31yklj64c3pp576vh1naqff6f21pq5mnr"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("ncurses" ,ncurses)))
+ (native-inputs
+ `(("python" ,python-wrapper))) ;for scripts/MakeHeader.py
+ (home-page "https://hisham.hm/htop/")
+ (synopsis "Interactive process viewer")
+ (description
+ "This is htop, an interactive process viewer. It is a text-mode
application (for console or X terminals) and requires ncurses.")
- (license license:gpl2)))
+ (license license:gpl2)))
(define-public pies
(package
@@ -880,7 +880,7 @@ over ssh connections.")
(define-public rename
(package
(name "rename")
- (version "1.00")
+ (version "1.10")
(source (origin
(method url-fetch)
(uri (string-append
@@ -888,7 +888,7 @@ over ssh connections.")
version ".tar.gz"))
(sha256
(base32
- "03yhf8nmqsb0zyliv501fdvwlp589jqfn44yqkrflmpzrbik3zxl"))))
+ "137m8s06r4n038ivlr5r1d9a7q9l7shmwpvnyx053r9ndhvbnkh5"))))
(build-system perl-build-system)
(arguments
`(#:phases
@@ -1602,14 +1602,14 @@ of supported upstream metrics systems simultaneously.")
(define-public ansible
(package
(name "ansible")
- (version "2.7.6")
+ (version "2.7.7")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ansible" version))
(sha256
(base32
- "0f7b2ghm34ql8yv90wr0ngd6w7wyvnlcxpc3snkj86kcjsnmx1bd"))))
+ "0l4id24jqi578xmybvwrz10sm2jhs90gk9gs1y04gfarz4vcj304"))))
(build-system python-build-system)
(native-inputs
`(("python-bcrypt" ,python-bcrypt)
@@ -2715,8 +2715,9 @@ Python loading in HPC environments.")
"1k9148xnfznch1443niaa3w1kmsw4vp0xpwna6npgmi7zqg06ymy"))))
(build-system trivial-build-system)
(inputs
- `(("bash" ,bash)
- ("perl" ,perl)))
+ `(("bash" ,bash-minimal)
+ ("perl" ,perl)
+ ("procps" ,procps)))
(native-inputs
`(("gzip" ,gzip)))
(arguments
@@ -2789,7 +2790,6 @@ support forum. It runs with the @code{/exec} command in most IRC clients.")
("lm-sensors" ,lm-sensors)
("mesa-utils" ,mesa-utils)
("pciutils" ,pciutils)
- ("procps" ,procps)
("tar" ,tar)
("tree" ,tree)
("util-linux" ,util-linux) ; lsblk
diff --git a/gnu/packages/aidc.scm b/gnu/packages/aidc.scm
index 64d26548c4..afcb33ad6d 100644
--- a/gnu/packages/aidc.scm
+++ b/gnu/packages/aidc.scm
@@ -2,7 +2,7 @@
;;; Copyright © 2014 John Darringon <jmd@gnu.org>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -24,6 +24,8 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
+ #:use-module (guix git-download)
+ #:use-module (gnu packages autotools)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages image)
#:use-module (guix build-system gnu))
@@ -75,21 +77,28 @@ characters, and is highly robust.")
(define-public libdmtx
(package
(name "libdmtx")
- (version "0.7.4")
+ (version "0.7.5")
(source
(origin
- (method url-fetch)
- (uri (string-append
- "mirror://sourceforge/libdmtx/" name "/" version "/"
- name "-" version ".tar.bz2"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dmtx/libdmtx.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "0xnxx075ycy58n92yfda2z9zgd41h3d4ik5d9l197lzsqim5hb5n"))))
+ (base32 "0wk3fkxzf9ip75v8ia54v6ywx72ajp5s6777j4ay8barpbv869rj"))))
(build-system gnu-build-system)
+ (arguments
+ ;; XXX Test suite is broken: https://github.com/dmtx/libdmtx/issues/22
+ `(#:tests? #f))
(native-inputs
- `(("pkg-config" ,pkg-config)))
- (home-page "http://libdmtx.sourceforge.net/")
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://github.com/dmtx")
(synopsis "Library for reading and writing Data Matrix 2D barcodes")
(description "libdmtx is software for reading and writing Data Matrix 2D
-barcodes on Linux and Unix. At its core libdmtx is a shared library, allowing
+barcodes of the modern ECC200 variety. libdmtx is a shared library, allowing
C/C++ programs to use its capabilities without restrictions or overhead.")
(license license:bsd-3)))
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 52eb6ee366..f9ae22b3f3 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
@@ -856,3 +856,147 @@ xtensor provides:
@item tools to manipulate array expressions and build upon xtensor.
@end itemize")
(license license:bsd-3)))
+
+(define-public gap
+ (package
+ (name "gap")
+ (version "4.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://www.gap-system.org/pub/gap/gap-"
+ (version-major+minor version)
+ "/tar.bz2/gap-"
+ version
+ ".tar.bz2"))
+ (sha256
+ (base32
+ "1dmb8v4p7j1nnf7sx8sg54b49yln36bi9acwp7w1d3a1nxj17ird"))
+ (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
+ (snippet
+ '(begin
+ ;; Delete the external gmp and zlib libraries
+ ;; and a subdirectory not needed for our build.
+ (for-each delete-file-recursively
+ '("extern" "hpcgap"))
+ ;; Delete a failing test.
+ ;; FIXME: This might be fixed in the next release, see
+ ;; https://github.com/gap-system/gap/issues/3292
+ (delete-file "tst/testinstall/dir.tst")
+ ;; Delete all packages except for a fixed list.
+ (with-directory-excursion "pkg"
+ (for-each delete-file-recursively
+ (lset-difference string=? (scandir ".")
+ '("." ".."
+ ;; Necessary packages.
+ "GAPDoc-1.6.2"
+ "primgrp-3.3.2"
+ "SmallGrp-1.3" ; artistic2.0
+ "transgrp" ; artistic2.0 for data,
+ ; gpl2 or gpl3 for code
+ ;; Recommanded package.
+ "io-4.5.4" ; gpl3+
+ ;; Optional packages, searched for at start,
+ ;; and their depedencies.
+ "alnuth-3.1.0"
+ "AutoDoc-2018.09.20"
+ "autpgrp-1.10"
+ "crisp-1.4.4" ; bsd-2
+ ; "ctbllib" ; no explicit license, drop
+ "FactInt-1.6.2"
+ "fga"
+ "irredsol-1.4" ; bsd-2
+ "laguna-3.9.0"
+ "polenta-1.3.8"
+ "polycyclic-2.14"
+ "radiroot-2.8"
+ "resclasses-4.7.1"
+ "sophus-1.24"
+ ; "tomlib-1.2.7" ; no explicit license, drop
+ "utils-0.59"))))
+ #t))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("gmp" ,gmp)
+ ("zlib" ,zlib)))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'build 'build-packages
+ ;; Compile all packages that have not been deleted by the
+ ;; code snippet above.
+ (lambda _
+ (setenv "CONFIG_SHELL" (which "bash"))
+ (with-directory-excursion "pkg"
+ (invoke "../bin/BuildPackages.sh")
+ #t)))
+ (add-after 'build-packages 'build-doc
+ ;; The documentation is bundled, but we create it from source.
+ (lambda _
+ (with-directory-excursion "doc"
+ (invoke "./make_doc"))
+ #t))
+ (replace 'check
+ (lambda _
+ ;; "make check" is expected to appear in gap-4.10.1
+ (invoke "./gap" "tst/testinstall.g")
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (prog (string-append bin "/gap"))
+ (prog-real (string-append bin "/.gap-real"))
+ (share (string-append out "/share/gap"))
+ (include (string-append out "/include/gap")))
+ ;; Install only the gap binary; the gac compiler is left
+ ;; for maybe later. "Wrap" it in a shell script that calls
+ ;; the binary with the correct parameter.
+ (mkdir-p bin)
+ (copy-file "gap" prog-real)
+ (call-with-output-file prog
+ (lambda (port)
+ (format port
+ "#!~a~%exec ~a -l ~a \"$@\"~%"
+ (which "bash")
+ prog-real
+ share)))
+ (chmod prog #o755)
+ ;; Install the headers and the library, which are needed by
+ ;; Sage. The Makefile targets are available in gap-4.10.0,
+ ;; but planned to be removed in gap-4.10.1.
+ (invoke "make" "install-headers")
+ (invoke "make" "install-libgap")
+ (install-file "gen/config.h" include)
+ ;; Install a certain number of files and directories to
+ ;; SHARE, where the wrapped shell script expects them.
+ ;; Remove information on the build directory from sysinfo.gap.
+ (substitute* "sysinfo.gap"
+ (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
+ (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
+ (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
+ (install-file "sysinfo.gap" share)
+ (copy-recursively "grp" (string-append share "/grp"))
+ (copy-recursively "pkg" (string-append share "/pkg"))
+ ;; The following is not the C library libgap.so, but a
+ ;; library of GAP code.
+ (copy-recursively "lib" (string-append share "/lib"))
+ ;; The gap binary looks for documentation inside SHARE.
+ (copy-recursively "doc" (string-append share "/doc")))
+ #t)))))
+ (home-page "https://www.gap-system.org/")
+ (synopsis
+ "System for computational group theory")
+ (description
+ "GAP is a system for computational discrete algebra, with particular
+emphasis on computational group theory. It provides a programming language,
+a library of thousands of functions implementing algebraic algorithms
+written in the GAP language as well as large data libraries of algebraic
+objects.")
+ ;; Some packages have different licenses (effectively forcing the
+ ;; combined work to be licensed as gpl3+); if this is the case, this
+ ;; is mentioned above next to their name.
+ ;; Some packages have no license mentioned explicitly; supposedly this
+ ;; means that the gpl2+ licence of GAP itself applies, but to be on the
+ ;; safe side, we drop them for now.
+ (license license:gpl2+)))
diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm
index 9b8ef562d3..0de2183b88 100644
--- a/gnu/packages/assembly.scm
+++ b/gnu/packages/assembly.scm
@@ -3,7 +3,7 @@
;;; Copyright © 2013, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Guy Fleury Iteriteka <hoonandon@gmail.com>
;;;
;;; This file is part of GNU Guix.
@@ -129,7 +129,7 @@ to the clients.")
(define-public fasm
(package
(name "fasm")
- (version "1.73.06")
+ (version "1.73.08")
(source
(origin
(method url-fetch)
@@ -137,14 +137,14 @@ to the clients.")
version ".tgz"))
(sha256
(base32
- "02wqkqxpn3p0iwcagsm92qd9cdfcnbx8a09qg03b3pjppp30hmp6"))))
+ "1l4my3fran06h5jiygswx4fsj53dvpfgg9ksfbdzsdg20r672997"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ; No tests exist
- #:strip-binaries? #f ; fasm has no sections
+ `(#:tests? #f ; no tests exist
+ #:strip-binaries? #f ; fasm has no sections
#:phases
(modify-phases %standard-phases
- (delete 'configure) ; no "configure" script exists
+ (delete 'configure) ; no "configure" script
(replace 'build
(lambda _
(chdir "source/Linux/")
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 12755dd7a7..ae0dddeb66 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -19,6 +19,7 @@
;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2018 Brendan Tildesley <brendan.tildesley@openmailbox.org>
;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
+;;; Copyright © 2019 Leo Famulari <leo@famulari.name>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -1374,7 +1375,20 @@ patches that can be used with softsynths such as Timidity and WildMidi.")
(list
;; Add the output lib directory to the RUNPATH.
(string-append "--ldflags=-Wl,-rpath=" %output "/lib")
- "--cxxflags=-std=c++11")))
+ "--cxxflags=-std=c++11")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-boost-includes
+ (lambda _
+ (substitute* "src/headers/gx_internal_plugins.h"
+ (("namespace gx_jack" m)
+ (string-append "#include <boost/noncopyable.hpp>\n" m)))
+ (substitute* '("src/headers/gx_system.h"
+ "src/headers/gx_parameter.h"
+ "src/headers/gx_json.h")
+ (("namespace gx_system" m)
+ (string-append "#include <boost/noncopyable.hpp>\n" m)))
+ #t)))))
(inputs
`(("libsndfile" ,libsndfile)
("boost" ,boost)
@@ -2446,18 +2460,17 @@ the Turtle syntax.")
(define-public suil
(package
(name "suil")
- (version "0.10.0")
+ (version "0.10.2")
(source (origin
(method url-fetch)
(uri (string-append "https://download.drobilla.net/suil-"
version ".tar.bz2"))
(sha256
(base32
- "0j489gm3fhnmwmbgw30bvd4byw1vsy4yazdlnji8jzhcz0qwb5cq"))))
+ "00d43m0nai63ajb7rkm9v084jcih206y17ib3160zcvzc885ji4z"))))
(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.
+ `(#:tests? #f ; no check target
#:configure-flags
'("CXXFLAGS=-std=gnu++11")))
(inputs
@@ -3207,7 +3220,7 @@ with support for HD extensions.")
(define-public bs1770gain
(package
(name "bs1770gain")
- (version "0.5.1")
+ (version "0.5.2")
(source
(origin
(method url-fetch)
@@ -3215,11 +3228,20 @@ with support for HD extensions.")
version "/bs1770gain-" version ".tar.gz"))
(sha256
(base32
- "0r4fbajgfmnwgl63hcm56f1j8m5f135q6j5jkzdvrrhpcj39yx06"))))
+ "1p6yz5q7czyf9ard65sp4kawdlkg40cfscr3b24znymmhs3p7rbk"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; XXX
+ (substitute* "bs1770gain/bs1770gain.c"
+ (("\"N.*\"") "\"\""))
+ (substitute* "configure"
+ (("URL=.*$")
+ "https://manpages.debian.org/sid/bs1770gain/bs1770gain.1.en.html\n"))))))
(build-system gnu-build-system)
(inputs `(("ffmpeg" ,ffmpeg)
("sox" ,sox)))
- (home-page "http://bs1770gain.sourceforge.net/")
+ (home-page "https://manpages.debian.org/sid/bs1770gain/bs1770gain.1.en.html")
(synopsis "Tool to adjust loudness of media files")
(description
"BS1770GAIN is a loudness scanner compliant with ITU-R BS.1770 and its
diff --git a/gnu/packages/aux-files/chromium/master-preferences.json b/gnu/packages/aux-files/chromium/master-preferences.json
new file mode 100644
index 0000000000..5a2049fa72
--- /dev/null
+++ b/gnu/packages/aux-files/chromium/master-preferences.json
@@ -0,0 +1,26 @@
+{
+ "distribution": {
+ "import_bookmarks": false,
+ "make_chrome_default": false,
+ "make_chrome_default_for_user": false,
+ "verbose_logging": true,
+ "skip_first_run_ui": true,
+ "suppress_first_run_default_browser_prompt": true
+ },
+ "browser": {
+ "has_seen_welcome_page" : true,
+ "check_default_browser" : false
+ },
+ "dns_prefetching": {
+ "enabled": false
+ },
+ "alternate_error_pages": {
+ "enabled": false
+ },
+ "hardware": {
+ "audio_capture_enabled": false
+ },
+ "default_apps": "noinstall",
+ "hide_web_store_icon": true,
+ "homepage": "https://www.gnu.org/software/guix/"
+}
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 45b1be2413..5da7475150 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -46,6 +46,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages crypto)
#:use-module (gnu packages databases)
+ #:use-module (gnu packages datastructures)
#:use-module (gnu packages dbm)
#:use-module (gnu packages dejagnu)
#:use-module (gnu packages ftp)
@@ -495,14 +496,14 @@ detection, and lossless compression.")
(define-public borg
(package
(name "borg")
- (version "1.1.8")
+ (version "1.1.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "borgbackup" version))
(sha256
(base32
- "0qqvcscn1l4y83x4sh3izdpmr8zq38j8chjkpfq4q4d01i470hqb"))
+ "0x95nhv4h34m8cxycbwc4xdz350saaxlgh727b23bgn4ci7gh3vx"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -548,11 +549,6 @@ detection, and lossless compression.")
;; HOME=/homeless-shelter.
(setenv "HOME" "/tmp")
#t)))
- (add-after 'unpack 'remove-documentation-timestamps ; reproducibility
- (lambda _
- (substitute* "setup.py"
- (("write\\(':Date:'.*") "\n"))
- #t))
;; The tests need to be run after Borg is installed.
(delete 'check)
(add-after 'install 'check
@@ -589,17 +585,12 @@ detection, and lossless compression.")
'("docs/misc/create_chunker-params.txt"
"docs/misc/internals-picture.txt"
"docs/misc/prune-example.txt"))
- (add-installed-pythonpath inputs outputs)
- (invoke "python3" "setup.py" "build_man")
(copy-recursively "docs/man" man)
#t))))))
(native-inputs
`(("python-cython" ,python-cython)
("python-setuptools-scm" ,python-setuptools-scm)
- ("python-pytest" ,python-pytest)
- ;; For generating the documentation.
- ("python-sphinx" ,python-sphinx)
- ("python-guzzle-sphinx-theme" ,python-guzzle-sphinx-theme)))
+ ("python-pytest" ,python-pytest)))
(inputs
`(("acl" ,acl)
("libb2" ,libb2)
@@ -985,3 +976,30 @@ de-duplicated before it is actually written to the storage back end to save
precious backup space.
@end itemize")
(license license:bsd-2)))
+
+(define-public burp
+ (package
+ (name "burp")
+ (version "2.3.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/burp/burp-" version
+ "/burp-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "0in49c0ir7lb7jli0fcphdq1nh5rclhans4ngm7z7hzyxa4jrgri"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("librsync" ,librsync)
+ ("openssl" ,openssl)
+ ("uthash" ,uthash)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("check" ,check)
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://burp.grke.org")
+ (synopsis "Differential backup and restore")
+ (description "Burp is a network backup and restore program. It attempts
+to reduce network traffic and the amount of space that is used by each
+backup.")
+ (license license:agpl3)))
diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index c3db665e98..289631acee 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -860,7 +860,10 @@ with the Linux kernel.")
"glibc-versioned-locpath.patch"
"glibc-allow-kernel-2.6.32.patch"
"glibc-reinstate-prlimit64-fallback.patch"
- "glibc-supported-locales.patch"))))))
+ "glibc-supported-locales.patch"
+ "glibc-CVE-2018-11236.patch"
+ "glibc-CVE-2018-11237.patch"))))
+ (properties `((lint-hidden-cve . ("CVE-2017-18269")))))) ; glibc-2.27-git-fixes
(define-public glibc-2.26
(package
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 20aabb0be4..9057158cde 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -27,6 +27,7 @@
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
#:use-module (gnu packages maths)
#:use-module (gnu packages statistics)
@@ -1176,3 +1177,25 @@ Viewer (SAV) files, access data, and generate QC plots.")
"This package provides a quality control pipeline for ChIP-exo/nexus
sequencing data.")
(license license:gpl2+)))
+
+(define-public r-dnacopy
+ (package
+ (name "r-dnacopy")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DNAcopy" version))
+ (sha256
+ (base32
+ "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
+ (properties `((upstream-name . "DNAcopy")))
+ (build-system r-build-system)
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "https://bioconductor.org/packages/DNAcopy")
+ (synopsis "DNA copy number data analysis")
+ (description
+ "This package implements the @dfn{circular binary segmentation} (CBS)
+algorithm to segment DNA copy number data and identify genomic regions with
+abnormal copy number.")
+ (license license:gpl2+)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 02cafb2358..5dc3945035 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm