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authorMarius Bakke <mbakke@fastmail.com>2018-11-14 21:20:46 +0100
committerMarius Bakke <mbakke@fastmail.com>2018-11-14 21:20:46 +0100
commit79ee97a144aaaa890be0724aaf796e2a771179d7 (patch)
treefddd2f20003d60e42eed7a614acea91a13d854d7
parent7d9d521fbcf1423f66d6f33208c03d5dacb7ba50 (diff)
parente921993c25626541385f191f0463cad8e5e5c5c7 (diff)
downloadguix-79ee97a144aaaa890be0724aaf796e2a771179d7.tar.gz
guix-79ee97a144aaaa890be0724aaf796e2a771179d7.zip
Merge branch 'master' into core-updates
Diffstat
-rw-r--r--doc/guix.texi47
-rw-r--r--gnu/local.mk2
-rw-r--r--gnu/packages/admin.scm4
-rw-r--r--gnu/packages/audio.scm192
-rw-r--r--gnu/packages/backup.scm19
-rw-r--r--gnu/packages/bioconductor.scm61
-rw-r--r--gnu/packages/bioinformatics.scm127
-rw-r--r--gnu/packages/compression.scm27
-rw-r--r--gnu/packages/cran.scm451
-rw-r--r--gnu/packages/crypto.scm53
-rw-r--r--gnu/packages/databases.scm21
-rw-r--r--gnu/packages/datastructures.scm24
-rw-r--r--gnu/packages/emacs.scm32
-rw-r--r--gnu/packages/embedded.scm13
-rw-r--r--gnu/packages/game-development.scm11
-rw-r--r--gnu/packages/geo.scm4
-rw-r--r--gnu/packages/gnustep.scm19
-rw-r--r--gnu/packages/gnuzilla.scm78
-rw-r--r--gnu/packages/golang.scm49
-rw-r--r--gnu/packages/gtk.scm8
-rw-r--r--gnu/packages/guile.scm74
-rw-r--r--gnu/packages/ibus.scm683
-rw-r--r--gnu/packages/image-viewers.scm4
-rw-r--r--gnu/packages/imagemagick.scm5
-rw-r--r--gnu/packages/linux.scm49
-rw-r--r--gnu/packages/llvm.scm23
-rw-r--r--gnu/packages/lxde.scm9
-rw-r--r--gnu/packages/mail.scm52
-rw-r--r--gnu/packages/messaging.scm62
-rw-r--r--gnu/packages/mtools.scm6
-rw-r--r--gnu/packages/music.scm126
-rw-r--r--gnu/packages/nano.scm4
-rw-r--r--gnu/packages/package-management.scm6
-rw-r--r--gnu/packages/patches/icecat-CVE-2018-12383.patch103
-rw-r--r--gnu/packages/patches/poppler-CVE-2018-19149.patch80
-rw-r--r--gnu/packages/pdf.scm34
-rw-r--r--gnu/packages/php.scm9
-rw-r--r--gnu/packages/python.scm19
-rw-r--r--gnu/packages/rdf.scm20
-rw-r--r--gnu/packages/samba.scm5
-rw-r--r--gnu/packages/serialization.scm8
-rw-r--r--gnu/packages/shells.scm7
-rw-r--r--gnu/packages/shellutils.scm5
-rw-r--r--gnu/packages/spice.scm2
-rw-r--r--gnu/packages/ssh.scm8
-rw-r--r--gnu/packages/statistics.scm50
-rw-r--r--gnu/packages/syncthing.scm31
-rw-r--r--gnu/packages/telephony.scm21
-rw-r--r--gnu/packages/textutils.scm51
-rw-r--r--gnu/packages/tls.scm6
-rw-r--r--gnu/packages/tor.scm9
-rw-r--r--gnu/packages/video.scm4
-rw-r--r--gnu/packages/vim.scm4
-rw-r--r--gnu/packages/web.scm6
-rw-r--r--gnu/packages/webkit.scm46
-rw-r--r--gnu/packages/wine.scm6
-rw-r--r--gnu/packages/xdisorg.scm16
-rw-r--r--gnu/packages/xorg.scm4
-rw-r--r--gnu/services/base.scm54
-rw-r--r--gnu/services/mail.scm51
-rw-r--r--gnu/services/mcron.scm2
-rw-r--r--gnu/tests/base.scm14
-rw-r--r--guix/build/go-build-system.scm3
-rw-r--r--guix/ci.scm74
-rw-r--r--guix/gexp.scm7
-rw-r--r--guix/gnu-maintenance.scm115
-rw-r--r--guix/grafts.scm8
-rw-r--r--guix/nar.scm13
-rw-r--r--guix/scripts/package.scm10
-rw-r--r--guix/scripts/system.scm7
-rw-r--r--guix/store.scm68
-rw-r--r--guix/store/database.scm6
-rw-r--r--guix/store/deduplication.scm12
-rw-r--r--guix/tests.scm34
-rw-r--r--tests/challenge.scm8
-rw-r--r--tests/debug-link.scm8
-rw-r--r--tests/gexp.scm5
-rw-r--r--tests/guix-package.sh4
-rw-r--r--tests/nar.scm47
-rw-r--r--tests/profiles.scm11
-rw-r--r--tests/size.scm8
81 files changed, 2463 insertions, 1005 deletions
diff --git a/doc/guix.texi b/doc/guix.texi
index 441b65bcaf..0ba034e822 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -10563,11 +10563,14 @@ Start,,, shepherd, The GNU Shepherd Manual}). For example:
The above command, run as @code{root}, lists the currently defined
services. The @command{herd doc} command shows a synopsis of the given
-service:
+service and its associated actions:
@example
# herd doc nscd
Run libc's name service cache daemon (nscd).
+
+# herd doc nscd action invalidate
+invalidate: Invalidate the given cache--e.g., 'hosts' for host name lookups.
@end example
The @command{start}, @command{stop}, and @command{restart} sub-commands
@@ -10965,6 +10968,27 @@ The Kmscon package to use.
Return a service that runs the libc name service cache daemon (nscd) with the
given @var{config}---an @code{<nscd-configuration>} object. @xref{Name
Service Switch}, for an example.
+
+For convenience, the Shepherd service for nscd provides the following actions:
+
+@table @code
+@item invalidate
+@cindex cache invalidation, nscd
+@cindex nscd, cache invalidation
+This invalidate the given cache. For instance, running:
+
+@example
+herd invalidate nscd hosts
+@end example
+
+@noindent
+invalidates the host name lookup cache of nscd.
+
+@item statistics
+Running @command{herd statistics nscd} displays information about nscd usage
+and caches.
+@end table
+
@end deffn
@defvr {Scheme Variable} %nscd-default-configuration
@@ -14349,11 +14373,30 @@ Defaults to @samp{#t}.
@end deftypevr
+@deftypevr {@code{service-configuration} parameter} non-negative-integer client-limit
+Maximum number of simultaneous client connections per process. Once
+this number of connections is received, the next incoming connection
+will prompt Dovecot to spawn another process. If set to 0,
+@code{default-client-limit} is used instead.
+
+Defaults to @samp{0}.
+
+@end deftypevr
+
@deftypevr {@code{service-configuration} parameter} non-negative-integer service-count
Number of connections to handle before starting a new process.
Typically the only useful values are 0 (unlimited) or 1. 1 is more
secure, but 0 is faster. <doc/wiki/LoginProcess.txt>.
Defaults to @samp{1}.
+
+@end deftypevr
+
+@deftypevr {@code{service-configuration} parameter} non-negative-integer process-limit
+Maximum number of processes that can exist for this service. If set to
+0, @code{default-process-limit} is used instead.
+
+Defaults to @samp{0}.
+
@end deftypevr
@deftypevr {@code{service-configuration} parameter} non-negative-integer process-min-avail
@@ -24197,7 +24240,7 @@ to be updated to refer to these binaries on the target platform. That
is, the hashes and URLs of the bootstrap tarballs for the new platform
must be added alongside those of the currently supported platforms. The
bootstrap Guile tarball is treated specially: it is expected to be
-available locally, and @file{gnu/local.mk} has rules do download it for
+available locally, and @file{gnu/local.mk} has rules to download it for
the supported architectures; a rule for the new platform must be added
as well.
diff --git a/gnu/local.mk b/gnu/local.mk
index 3e355ac9b3..c4299fcbe4 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -816,7 +816,6 @@ dist_patch_DATA = \
%D%/packages/patches/hplip-remove-imageprocessor.patch \
%D%/packages/patches/hydra-disable-darcs-test.patch \
%D%/packages/patches/icecat-avoid-bundled-libraries.patch \
- %D%/packages/patches/icecat-CVE-2018-12383.patch \
%D%/packages/patches/icecat-use-system-graphite2+harfbuzz.patch \
%D%/packages/patches/icecat-use-system-media-libs.patch \
%D%/packages/patches/icedtea-6-hotspot-gcc-segfault-workaround.patch \
@@ -1048,6 +1047,7 @@ dist_patch_DATA = \
%D%/packages/patches/plink-1.07-unclobber-i.patch \
%D%/packages/patches/plink-endian-detection.patch \
%D%/packages/patches/plotutils-libpng-jmpbuf.patch \
+ %D%/packages/patches/poppler-CVE-2018-19149.patch \
%D%/packages/patches/portaudio-audacity-compat.patch \
%D%/packages/patches/portmidi-modular-build.patch \
%D%/packages/patches/potrace-tests.patch \
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 3c65ce102c..0da35ea62e 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -981,7 +981,7 @@ system administrator.")
(define-public sudo
(package
(name "sudo")
- (version "1.8.25p1")
+ (version "1.8.26")
(source (origin
(method url-fetch)
(uri
@@ -991,7 +991,7 @@ system administrator.")
version ".tar.gz")))
(sha256
(base32
- "0nqri46d4dpycj96zin2f2wszmhm7q9mr68hhj9sp81pgmx9rjcx"))
+ "1qpyyfga8rs02p3186sns8qvh2bzwa48ka845nrcqh83dyd23nj0"))
(modules '((guix build utils)))
(snippet
'(begin
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 28447552f2..6dc0d82668 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -572,13 +572,14 @@ based on human speech recordings.")
(name "infamous-plugins")
(version "0.2.04")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/ssj71/infamousPlugins/"
- "archive/v" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ssj71/infamousPlugins.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1n6rhqsmvad7692w2h01niw5gqg5yk7a09wxl5ivs77zyp93vf7z"))))
+ "0hmqk80w4qxq09iag7b7srf2g0wigkyhzq0ywxvhz2iz0hq9k0dh"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; there are no tests
@@ -610,13 +611,14 @@ envelope follower, distortion effects, tape effects and more.")
(name "swh-plugins-lv2")
(version "1.0.16")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/swh/"
- "lv2/archive/v" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/swh/lv2.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0j1mih0lp4fds07knp5i32in515sh0df1qi6694pmyz2wqnm295w"))))
+ "0y7nnww864mm4k6ayy2lhcws3wlbhb2gkyjbrwk921fvc18qk9mz"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no check target
@@ -654,14 +656,14 @@ emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.")
(name "csound")
(version "6.11.0")
(source (origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/csound/csound/archive/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/csound/csound.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "072pk5h9w0vhw0ncc9dn90haw1yv18v04iwwjn8nsp6930w7dvxd"))))
+ "1hlkrnv3gghx4v382nl6v6k2k1dzm5ddk35m5g3q6pzc959726s7"))))
(build-system cmake-build-system)
(inputs
`(("alsa-lib" ,alsa-lib)
@@ -1174,19 +1176,15 @@ PS, and DAB+.")
(define-public faust-2
(package
(inherit faust)
- (version "2.1.0")
+ (version "2.5.23")
(source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/grame-cncm/faust.git")
- (commit (string-append "v"
- (string-map (lambda (c)
- (if (char=? c #\.) #\- c))
- version)))))
- (file-name (string-append "faust-" version "-checkout"))
+ (method url-fetch)
+ (uri (string-append "https://github.com/grame-cncm/faust/"
+ "releases/download/" version
+ "/faust-" version ".tar.gz"))
(sha256
(base32
- "06km0ygwxxwgw1lqldccqidxhmjfz8ck0wnbd95qk5sg8sbpc068"))))
+ "1yz5jnr76hh7rmxkpdi7gyrw1wp4gyqfpq8zyl97qdi5ga5gjznq"))))
(build-system gnu-build-system)
(arguments
(substitute-keyword-arguments (package-arguments faust)
@@ -1194,7 +1192,7 @@ PS, and DAB+.")
`(list (string-append "prefix=" (assoc-ref %outputs "out"))
"world"))))
(native-inputs
- `(("llvm" ,llvm-with-rtti)
+ `(("llvm" ,llvm-3.8-with-rtti)
("which" ,which)
("xxd" ,xxd)
("ctags" ,emacs-minimal) ; for ctags
@@ -1881,14 +1879,14 @@ software.")
(name "lvtk")
(version "1.2.0")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/lvtk/lvtk/archive/"
- version
- ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/lvtk/lvtk.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "03nbj2cqcklqwh50zj2gwm07crh5iwqbpxbpzwbg5hvgl4k4rnjd"))))
+ "1b01zvzl70ana6l1kn8fgyr7msnn3c7x61cgw7fdpp50322352p8"))))
(build-system waf-build-system)
(arguments
`(#:tests? #f ; no check target
@@ -2274,36 +2272,32 @@ tempo and pitch of an audio recording independently of one another.")
(name "rtmidi")
(version "2.1.0")
(source (origin
- (method url-fetch)
- (uri
- (string-append "https://github.com/powertab/rtmidi/archive/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/powertab/rtmidi.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0d49lapnmdgmjxh4vw57h6xk74nn5r0zwysv7jbd7m8kqhpq5rjj"))))
+ "106v177y3nrjv2l1yskch4phpqd8h97b67zj0jiq9pc3c69jr1ay"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no "check" target
- #:phases (modify-phases %standard-phases
- (add-after
- 'unpack 'autoconf
- (lambda _ (invoke "autoreconf" "-vfi")))
- (add-before
- 'build 'fix-makefile
- (lambda _
- (substitute* "Makefile"
- (("/bin/ln") "ln")
- (("RtMidi.h RtError.h") "RtMidi.h"))
- #t))
- (add-before
- 'install 'make-target-dirs
- (lambda _
- (let ((out (assoc-ref %outputs "out")))
- (mkdir-p (string-append out "/bin"))
- (mkdir (string-append out "/lib"))
- (mkdir (string-append out "/include")))
- #t)))))
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'fix-makefile
+ (lambda _
+ (substitute* "Makefile"
+ (("/bin/ln") "ln")
+ (("RtMidi.h RtError.h") "RtMidi.h"))
+ #t))
+ (add-before 'install 'make-target-dirs
+ (lambda _
+ (let ((out (assoc-ref %outputs "out")))
+ (mkdir-p (string-append out "/bin"))
+ (mkdir (string-append out "/lib"))
+ (mkdir (string-append out "/include")))
+ #t)))))
(inputs
`(("jack" ,jack-1)
("alsa-lib" ,alsa-lib)))
@@ -2754,20 +2748,14 @@ portions of LAME.")
;; TODO: Add ASIHPI.
`(("alsa-lib" ,alsa-lib)
("jack" ,jack-1)))
+ ;; Autoreconf is necessary because the audacity-compat patch modifies .in
+ ;; files.
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)
("pkg-config" ,pkg-config)))
- (arguments
- '(#:phases
- ;; Autoreconf is necessary because the audacity-compat patch modifies
- ;; .in files.
- (modify-phases %standard-phases
- (add-after 'unpack 'autoreconf
- (lambda _
- (invoke "autoreconf" "-vif"))))
- #:tests? #f)) ;no 'check' target
+ (arguments '(#:tests? #f)) ;no 'check' target
(home-page "http://www.portaudio.com/")
(synopsis "Audio I/O library")
(description
@@ -2813,12 +2801,13 @@ synthesizer written in C++.")
(version "1.1")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/Themaister/RSound/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Themaister/RSound.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "1wzs40c0k5zpkmm5ffl6c17xmr399sxli7ys0fbb9ib0fd334knx"))))
+ (base32 "0gspmr3klwnq98h17p5hc6ifygya4p80g4g8r7a1qavm3mv19waf"))))
(build-system gnu-build-system)
(inputs
`(("alsa-lib" ,alsa-lib)
@@ -2851,14 +2840,14 @@ with a much different focus than most other audio daemons.")
(name "xjackfreak")
(version "1.0")
(source (origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/johnhldavis/xjackfreak/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/johnhldavis/xjackfreak.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0xj6gpxfnw9jbdgwgm0x23xgfvj2kwmwb1nk0drw8lxgcchkq7d9"))))
+ "18c546qidbrj0f5wfiq5llii2192xpln0ab3r4vpr7i3wybxqjfz"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
@@ -3026,15 +3015,16 @@ point audio data.")
(name "cuetools")
(version "1.4.1")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/svend/cuetools/archive/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/svend/cuetools.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "01xi3rvdmil9nawsha04iagjylqr1l9v9vlzk99scs8c207l58i4"))))
+ "02ksv1ahf1v4cr2xbclsfv5x17m9ivzbssb5r8xjm97yh8a7spa3"))))
(build-system gnu-build-system)
- ;; The source tarball is not bootstrapped.
+ ;; The source checkout is not bootstrapped.
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
@@ -3075,13 +3065,14 @@ use them split WAVE data into multiple files.")
(name "dcadec")
(version "0.2.0")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/foo86/dcadec/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/foo86/dcadec.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0i0dpypgqkhhi4v1fmsp2way6w9kbcix3c7q79pmg39yvrzj17gd"))))
+ "07nd0ajizrp1w02bsyfcv18431r8m8rq8gjfmz9wmckpg7cxj2hs"))))
(build-system gnu-build-system)
(arguments
;; Test files are missing: https://github.com/foo86/dcadec/issues/53
@@ -3386,13 +3377,14 @@ the following features:
(version "1.6")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/dpayne/cli-visualizer/archive/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dpayne/cli-visualizer.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "07zkm87f2fr8kc6531zrkya7q81sdanm6813y2f54mg13g41y6hi"))))
+ "0mirp8bk398di5xyq95iprmdyvplfghxqmrfj7jdnpy554vx7ppc"))))
(build-system gnu-build-system)
(native-inputs
`(("which" ,which)))
@@ -3440,14 +3432,14 @@ representations.")
(name "cava")
(version "0.6.1")
(source (origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/karlstav/cava/archive/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/karlstav/cava.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "13d72swnjs894llf0paandmhf1lf90dz6ygkcdw4bv84wzkq1f4q"))))
+ "1kvhqgijs29909w3sq9m0bslx2zxxn4b3i07kdz4hb0dqkppxpjy"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 52afcbc676..c927a14673 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -11,6 +11,7 @@
;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -30,6 +31,7 @@
(define-module (gnu packages backup)
#:use-module (guix packages)
#:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix git-download)
#:use-module (guix download)
#:use-module (guix utils)
#:use-module (guix build-system gnu)
@@ -132,22 +134,18 @@ spying and/or modification by the server.")
(name "par2cmdline")
(version "0.8.0")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/Parchive/par2cmdline/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Parchive/par2cmdline.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1jpshmmcr81mxly0md2rr231qz9c8c680bbvcmhh100dg9i4a6s6"))))
+ "0f1jsd5sw2wynjzi7yjqjaf13yhyjfdid91p8yh0jn32y03kjyrz"))))
(native-inputs
`(("automake" ,automake)
("autoconf" ,autoconf)))
(build-system gnu-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'autoreconf
- (lambda _ (invoke "autoreconf" "-vfi"))))))
(synopsis "File verification and repair tools")
(description "Par2cmdline uses Reed-Solomon error-correcting codes to
generate and verify PAR2 recovery files. These files can be distributed
@@ -889,6 +887,7 @@ is like a time machine for your data. ")
,version)
;; Disable 'restic self-update'. It makes little sense in Guix.
(substitute* "build.go" (("selfupdate") ""))
+ (setenv "HOME" (getcwd)) ; for $HOME/.cache/go-build
(invoke "go" "run" "build.go"))))
(replace 'check
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bab6b2b64d..95c722ac40 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -969,3 +969,64 @@ using pre-clustering with the k-means algorithm. Functions are also provided
to search for all neighbors within a given distance. Parallelization is
achieved for all methods using the BiocParallel framework.")
(license license:gpl3)))
+
+(define-public r-destiny
+ (package
+ (name "r-destiny")
+ (version "2.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "destiny" version))
+ (sha256
+ (base32
+ "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-fnn" ,r-fnn)
+ ("r-ggthemes" ,r-ggthemes)
+ ("r-hmisc" ,r-hmisc)
+ ("r-igraph" ,r-igraph)
+ ("r-matrix" ,r-matrix)
+ ("r-proxy" ,r-proxy)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-scales" ,r-scales)
+ ("r-scatterplot3d" ,r-scatterplot3d)
+ ("r-smoother" ,r-smoother)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-vim" ,r-vim)))
+ (home-page "https://bioconductor.org/packages/destiny/")
+ (synopsis "Create and plot diffusion maps")
+ (description "This package provides tools to create and plot diffusion
+maps.")
+ ;; Any version of the GPL
+ (license license:gpl3+)))
+
+(define-public r-savr
+ (package
+ (name "r-savr")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "savR" version))
+ (sha256
+ (base32
+ "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
+ (properties `((upstream-name . "savR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-reshape2" ,r-reshape2)
+ ("r-scales" ,r-scales)
+ ("r-xml" ,r-xml)))
+ (home-page "https://github.com/bcalder/savR")
+ (synopsis "Parse and analyze Illumina SAV files")
+ (description
+ "This package provides tools to parse Illumina Sequence Analysis
+Viewer (SAV) files, access data, and generate QC plots.")
+ (license license:agpl3+)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8820ba0d8e..58cee5cbbe 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7099,13 +7099,13 @@ Bioconductor, CRAN, and Github.")
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.50.1")
+ (version "1.50.5")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "0hjm3r58i0r9qhyar9pk250cx7sfijg0lnvi12a9s6brmmbip1a3"))))
+ "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
@@ -7268,13 +7268,13 @@ abnormal copy number.")
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.20.0")
+ (version "0.20.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "0qgiykjhnsvvpcp3zwmrnpx3bv3msvj0szchyvb1yb0fxw716xc5"))))
+ "18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
@@ -7349,7 +7349,7 @@ possible.")
(define-public r-genomeinfodbdata
(package
(name "r-genomeinfodbdata")
- (version "1.1.0")
+ (version "1.2.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -7359,7 +7359,7 @@ possible.")
version ".tar.gz"))
(sha256
(base32
- "0k1hsjx6n2i1sf14hyrgdhxqxm5mxk0bgnivhiax944whcicmzbf"))))
+ "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
(properties
`((upstream-name . "GenomeInfoDbData")))
(build-system r-build-system)
@@ -7657,13 +7657,13 @@ objects.")
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.50.0")
+ (version "2.50.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "0zw0dj67fnpbz4iqnam5fxs92c1c8w8d7mzl0rkq4ksx0xl8vgg7"))))
+ "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
@@ -7910,7 +7910,7 @@ extracting the desired features in a convenient format.")
(define-public r-go-db
(package
(name "r-go-db")
- (version "3.6.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
(uri (string-append "https://www.bioconductor.org/packages/"
@@ -7918,7 +7918,7 @@ extracting the desired features in a convenient format.")
version ".tar.gz"))
(sha256
(base32
- "0fi2qywr9apg5lwfqfq9qq6bgrnv4rdhxx25656qn4bsy62i838j"))))
+ "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
(properties
`((upstream-name . "GO.db")))
(build-system r-build-system)
@@ -8121,7 +8121,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
(define-public r-genomationdata
(package
(name "r-genomationdata")
- (version "1.10.0")
+ (version "1.14.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8131,7 +8131,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
"genomationData_" version ".tar.gz"))
(sha256
(base32
- "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla"))))
+ "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7"))))
(build-system r-build-system)
;; As this package provides little more than large data files, it doesn't
;; make sense to build substitutes.
@@ -8149,7 +8149,7 @@ downloaded from Encode.")
(define-public r-org-hs-eg-db
(package
(name "r-org-hs-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8159,7 +8159,7 @@ downloaded from Encode.")
"org.Hs.eg.db_" version ".tar.gz"))
(sha256
(base32
- "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927"))))
+ "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
(properties
`((upstream-name . "org.Hs.eg.db")))
(build-system r-build-system)
@@ -8175,7 +8175,7 @@ on mapping using Entrez Gene identifiers.")
(define-public r-org-ce-eg-db
(package
(name "r-org-ce-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8185,7 +8185,7 @@ on mapping using Entrez Gene identifiers.")
"org.Ce.eg.db_" version ".tar.gz"))
(sha256
(base32
- "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9"))))
+ "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
(properties
`((upstream-name . "org.Ce.eg.db")))
(build-system r-build-system)
@@ -8201,7 +8201,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
(define-public r-org-dm-eg-db
(package
(name "r-org-dm-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8211,7 +8211,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
"org.Dm.eg.db_" version ".tar.gz"))
(sha256
(base32
- "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d"))))
+ "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
(properties
`((upstream-name . "org.Dm.eg.db")))
(build-system r-build-system)
@@ -8227,7 +8227,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
(define-public r-org-mm-eg-db
(package
(name "r-org-mm-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8237,7 +8237,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
"org.Mm.eg.db_" version ".tar.gz"))
(sha256
(base32
- "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g"))))
+ "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
(properties
`((upstream-name . "org.Mm.eg.db")))
(build-system r-build-system)
@@ -8368,7 +8368,7 @@ in Biostrings objects.")
(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
(package
(name "r-txdb-mmusculus-ucsc-mm10-knowngene")
- (version "3.4.0")
+ (version "3.4.4")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8379,7 +8379,7 @@ in Biostrings objects.")
version ".tar.gz"))
(sha256
(base32
- "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
+ "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
(properties
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
(build-system r-build-system)
@@ -10215,14 +10215,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
(define-public r-ensembldb
(package
(name "r-ensembldb")
- (version "2.6.0")
+ (version "2.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
- "12jqz9h6w4mxyfr43w5qbwmacn512aw0mnl0zvhsg5i7p4qj45ks"))))
+ "1js05dcv1dj4g2vj7lzlg0rgjcjlk2irdr9rxqpwxmivm8nbvf36"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -14118,6 +14118,85 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering.
absolute GSEA.")
(license license:gpl2)))
+(define-public jamm
+ (package
+ (name "jamm")
+ (version "1.0.7.5")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mahmoudibrahim/JAMM.git")
+ (commit (string-append "JAMMv" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are none
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "JAMM.sh"
+ (("^sPath=.*")
+ (string-append "")))
+ #t))
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (libexec (string-append out "/libexec/jamm"))
+ (bin (string-append out "/bin")))
+ (substitute* '("JAMM.sh"
+ "SignalGenerator.sh")
+ (("^sPath=.*")
+ (string-append "sPath=\"" libexec "\"\n")))
+ (for-each (lambda (file)
+ (install-file file libexec))
+ (list "bincalculator.r"
+ "peakfinder.r"
+ "peakhelper.r"
+ "signalmaker.r"
+ "xcorr.r"
+ "xcorrhelper.r"
+ ;; Perl scripts
+ "peakfilter.pl"
+ "readshifter.pl"))
+
+ (for-each
+ (lambda (script)
+ (chmod script #o555)
+ (install-file script bin)
+ (wrap-program (string-append bin "/" script)
+ `("PATH" ":" prefix
+ (,(string-append (assoc-ref inputs "coreutils") "/bin")
+ ,(string-append (assoc-ref inputs "gawk") "/bin")
+ ,(string-append (assoc-ref inputs "perl") "/bin")
+ ,(string-append (assoc-ref inputs "r-minimal") "/bin")))
+ `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
+ `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
+ (list "JAMM.sh" "SignalGenerator.sh")))
+ #t)))))
+ (inputs
+ `(("bash" ,bash)
+ ("coreutils" ,coreutils)
+ ("gawk" ,gawk)
+ ("perl" ,perl)
+ ("r-minimal" ,r-minimal)
+ ;;("r-parallel" ,r-parallel)
+ ("r-signal" ,r-signal)
+ ("r-mclust" ,r-mclust)))
+ (home-page "https://github.com/mahmoudibrahim/JAMM")
+ (synopsis "Peak finder for NGS datasets")
+ (description
+ "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq,
+ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak
+boundaries accurately. JAMM is applicable to both broad and narrow
+datasets.")
+ (license license:gpl3+)))
+
(define-public ngless
(package
(name "ngless")
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 7f6857d260..6c3d88e7cb 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -133,10 +133,7 @@ in compression.")
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-source
- (lambda _ (chdir "contrib/minizip") #t))
- (add-after 'enter-source 'autoreconf
- (lambda _
- (invoke "autoreconf" "-vif"))))))
+ (lambda _ (chdir "contrib/minizip") #t)))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
@@ -188,12 +185,7 @@ utility. Instead of being written in Java, FastJar is written in C.")
"02cihzl77ia0dcz7z2cga2412vyhhs5pa2355q4wpwbyga2lrwjh"))
(patches (search-patches "libtar-CVE-2013-4420.patch"))))
(build-system gnu-build-system)
- (arguments
- `(#:tests? #f ;no "check" target
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'autoconf
- (lambda _ (invoke "sh" "autoreconf" "-vfi"))))))
+ (arguments `(#:tests? #f)) ; no "check" target
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
@@ -1122,13 +1114,14 @@ smaller than those produced by @code{Xdelta}.")
(version "3.1.0")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/jmacd/xdelta/archive/v"
- version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jmacd/xdelta.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "17g2pbbqy6h20qgdjq7ykib7kg5ajh8fwbsfgyjqg8pwg19wy5bm"))
- (file-name (string-append name "-" version ".tar.gz"))
+ "09mmsalc7dwlvgrda56s2k927rpl3a5dzfa88aslkqcjnr790wjy"))
(snippet
;; This file isn't freely distributable and has no effect on building.
'(begin
@@ -1142,9 +1135,7 @@ smaller than those produced by @code{Xdelta}.")
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-build-directory
- (lambda _ (chdir "xdelta3") #t))
- (add-after 'enter-build-directory 'autoconf
- (lambda _ (invoke "autoreconf" "-vfi"))))))
+ (lambda _ (chdir "xdelta3") #t)))))
(home-page "http://xdelta.org")
(synopsis "Delta encoder for binary files")
(description "xdelta encodes only the differences between two binary files
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ec950ce0ac..6ce9bdd16f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm