Merge branch 'master' into core-updates
This commit is contained in:
Leo Famulari
commit
02c73adcdf
|
|
@ -21,9 +21,6 @@ AC_USE_SYSTEM_EXTENSIONS
|
|||
AM_GNU_GETTEXT([external])
|
||||
AM_GNU_GETTEXT_VERSION([0.18.1])
|
||||
|
||||
guilemoduledir="${datarootdir}/guile/site/2.0"
|
||||
AC_SUBST([guilemoduledir])
|
||||
|
||||
GUIX_SYSTEM_TYPE
|
||||
GUIX_ASSERT_SUPPORTED_SYSTEM
|
||||
|
||||
|
|
@ -77,7 +74,7 @@ m4_pattern_forbid([GUILE_MODULE_AVAILABLE])
|
|||
m4_pattern_forbid([^GUILE_P$])
|
||||
|
||||
dnl Search for 'guile' and 'guild'. Prefer 2.0 until the 2.2 upgrade is
|
||||
dnl complete.
|
||||
dnl complete. This macro defines 'GUILE_EFFECTIVE_VERSION'.
|
||||
GUILE_PKG([2.0 2.2])
|
||||
GUILE_PROGS
|
||||
if test "x$GUILD" = "x"; then
|
||||
|
|
@ -90,6 +87,10 @@ else
|
|||
AC_MSG_WARN([Guile $GUILE_EFFECTIVE_VERSION is not fully supported!])
|
||||
fi
|
||||
|
||||
dnl Installation directory for .scm and .go files.
|
||||
guilemoduledir="${datarootdir}/guile/site/$GUILE_EFFECTIVE_VERSION"
|
||||
AC_SUBST([guilemoduledir])
|
||||
|
||||
dnl guile-json is used for the PyPI package importer
|
||||
GUILE_MODULE_AVAILABLE([have_guile_json], [(json)])
|
||||
AM_CONDITIONAL([HAVE_GUILE_JSON], [test "x$have_guile_json" = "xyes"])
|
||||
|
|
|
|||
|
|
@ -27,7 +27,8 @@ Copyright @copyright{} 2016 Chris Marusich@*
|
|||
Copyright @copyright{} 2016 Efraim Flashner@*
|
||||
Copyright @copyright{} 2016 John Darrington@*
|
||||
Copyright @copyright{} 2016 ng0@*
|
||||
Copyright @copyright{} 2016 Jan Nieuwenhuizen
|
||||
Copyright @copyright{} 2016 Jan Nieuwenhuizen@*
|
||||
Copyright @copyright{} 2016 Julien Lepiller
|
||||
|
||||
Permission is granted to copy, distribute and/or modify this document
|
||||
under the terms of the GNU Free Documentation License, Version 1.3 or
|
||||
|
|
@ -11229,6 +11230,7 @@ The @code{(gnu services web)} module provides the following service:
|
|||
@deffn {Scheme Procedure} nginx-service [#:nginx nginx] @
|
||||
[#:log-directory ``/var/log/nginx''] @
|
||||
[#:run-directory ``/var/run/nginx''] @
|
||||
[#:vhost-list (list (nginx-vhost-configuration))] @
|
||||
[#:config-file]
|
||||
|
||||
Return a service that runs @var{nginx}, the nginx web server.
|
||||
|
|
@ -11239,8 +11241,54 @@ files are written to @var{run-directory}. For proper operation, these
|
|||
arguments should match what is in @var{config-file} to ensure that the
|
||||
directories are created when the service is activated.
|
||||
|
||||
As an alternative to using a @var{config-file}, @var{vhost-list} can be
|
||||
used to specify the list of @dfn{virtual hosts} required on the host. For
|
||||
this to work, use the default value for @var{config-file}.
|
||||
|
||||
@end deffn
|
||||
|
||||
@deftp {Data Type} nginx-vhost-configuration
|
||||
Data type representing the configuration of an nginx virtual host.
|
||||
This type has the following parameters:
|
||||
|
||||
@table @asis
|
||||
@item @code{http-port} (default: @code{80})
|
||||
Nginx will listen for HTTP connection on this port. Set it at @code{#f} if
|
||||
nginx should not listen for HTTP (non secure) connection for this
|
||||
@dfn{virtual host}.
|
||||
|
||||
@item @code{https-port} (default: @code{443})
|
||||
Nginx will listen for HTTPS connection on this port. Set it at @code{#f} if
|
||||
nginx should not listen for HTTPS (secure) connection for this @dfn{virtual host}.
|
||||
|
||||
Note that nginx can listen for HTTP and HTTPS connections in the same
|
||||
@dfn{virtual host}.
|
||||
|
||||
@item @code{server-name} (default: @code{(list 'default)})
|
||||
A list of server names this vhost represents. @code{'default} represents the
|
||||
default vhost for connections matching no other vhost.
|
||||
|
||||
@item @code{root} (default: @code{"/srv/http"})
|
||||
Root of the website nginx will serve.
|
||||
|
||||
@item @code{index} (default: @code{(list "index.html")})
|
||||
Index files to look for when clients ask for a directory. If it cannot be found,
|
||||
Nginx will send the list of files in the directory.
|
||||
|
||||
@item @code{ssl-certificate} (default: @code{"/etc/nginx/cert.pem"})
|
||||
Where to find the certificate for secure connections. Set it to @code{#f} if
|
||||
you don't have a certificate or you don't want to use HTTPS.
|
||||
|
||||
@item @code{ssl-certificate-key} (default: @code{"/etc/nginx/key.pem"})
|
||||
Where to find the private key for secure connections. Set it to @code{#f} if
|
||||
you don't have a key or you don't want to use HTTPS.
|
||||
|
||||
@item @code{server-tokens?} (default: @code{#f})
|
||||
Whether the server should add its configuration to response.
|
||||
|
||||
@end table
|
||||
@end deftp
|
||||
|
||||
@node Network File System
|
||||
@subsubsection Network File System
|
||||
@cindex NFS
|
||||
|
|
|
|||
|
|
@ -0,0 +1,71 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2015 Andy Wingo <wingo@igalia.com>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
||||
;;; under the terms of the GNU General Public License as published by
|
||||
;;; the Free Software Foundation; either version 3 of the License, or (at
|
||||
;;; your option) any later version.
|
||||
;;;
|
||||
;;; GNU Guix is distributed in the hope that it will be useful, but
|
||||
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
;;; GNU General Public License for more details.
|
||||
;;;
|
||||
;;; You should have received a copy of the GNU General Public License
|
||||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
(define-module (gnu build svg)
|
||||
#:use-module (srfi srfi-11)
|
||||
#:export (svg->png))
|
||||
|
||||
;; We need Guile-RSVG and Guile-Cairo. Load them lazily, at run time, to
|
||||
;; allow compilation to proceed. See also <http://bugs.gnu.org/12202>.
|
||||
(module-autoload! (current-module)
|
||||
'(rsvg) '(rsvg-handle-new-from-file))
|
||||
(module-autoload! (current-module)
|
||||
'(cairo) '(cairo-image-surface-create))
|
||||
|
||||
(define* (downscaled-surface surface
|
||||
#:key
|
||||
source-width source-height
|
||||
width height)
|
||||
"Return a new rendering context where SURFACE is scaled to WIDTH x HEIGHT."
|
||||
(let ((cr (cairo-create (cairo-image-surface-create 'argb32
|
||||
width height))))
|
||||
(cairo-scale cr (/ width source-width) (/ height source-height))
|
||||
(cairo-set-source-surface cr surface 0 0)
|
||||
(cairo-pattern-set-filter (cairo-get-source cr) 'best)
|
||||
(cairo-rectangle cr 0 0 source-width source-height)
|
||||
(cairo-fill cr)
|
||||
cr))
|
||||
|
||||
(define* (svg->png in-svg out-png
|
||||
#:key width height)
|
||||
"Render the file at IN-SVG as a PNG file in OUT-PNG. When WIDTH and HEIGHT
|
||||
are provided, use them as the dimensions of OUT-PNG; otherwise preserve the
|
||||
dimensions of IN-SVG."
|
||||
(define svg
|
||||
(rsvg-handle-new-from-file in-svg))
|
||||
|
||||
(let-values (((origin-width origin-height)
|
||||
(rsvg-handle-get-dimensions svg)))
|
||||
(let* ((surf (cairo-image-surface-create 'argb32
|
||||
origin-width origin-height))
|
||||
(cr (cairo-create surf)))
|
||||
(rsvg-handle-render-cairo svg cr)
|
||||
(cairo-surface-flush surf)
|
||||
(let ((cr (if (and width height
|
||||
(not (= width origin-width))
|
||||
(not (= height origin-height)))
|
||||
(downscaled-surface surf
|
||||
#:source-width origin-width
|
||||
#:source-height origin-height
|
||||
#:width width
|
||||
#:height height)
|
||||
cr)))
|
||||
(cairo-surface-write-to-png (cairo-get-target cr) out-png)))))
|
||||
|
||||
;;; svg.scm ends here
|
||||
12
gnu/local.mk
12
gnu/local.mk
|
|
@ -229,6 +229,7 @@ GNU_SYSTEM_MODULES = \
|
|||
%D%/packages/llvm.scm \
|
||||
%D%/packages/lout.scm \
|
||||
%D%/packages/logging.scm \
|
||||
%D%/packages/lolcode.scm \
|
||||
%D%/packages/lsof.scm \
|
||||
%D%/packages/lua.scm \
|
||||
%D%/packages/lxde.scm \
|
||||
|
|
@ -327,6 +328,7 @@ GNU_SYSTEM_MODULES = \
|
|||
%D%/packages/sdcc.scm \
|
||||
%D%/packages/sdl.scm \
|
||||
%D%/packages/search.scm \
|
||||
%D%/packages/security-token.scm \
|
||||
%D%/packages/serialization.scm \
|
||||
%D%/packages/serveez.scm \
|
||||
%D%/packages/shells.scm \
|
||||
|
|
@ -386,7 +388,6 @@ GNU_SYSTEM_MODULES = \
|
|||
%D%/packages/xdisorg.scm \
|
||||
%D%/packages/xorg.scm \
|
||||
%D%/packages/xfce.scm \
|
||||
%D%/packages/yubico.scm \
|
||||
%D%/packages/zile.scm \
|
||||
%D%/packages/zip.scm \
|
||||
\
|
||||
|
|
@ -433,6 +434,7 @@ GNU_SYSTEM_MODULES = \
|
|||
%D%/build/linux-initrd.scm \
|
||||
%D%/build/linux-modules.scm \
|
||||
%D%/build/marionette.scm \
|
||||
%D%/build/svg.scm \
|
||||
%D%/build/vm.scm \
|
||||
\
|
||||
%D%/tests.scm \
|
||||
|
|
@ -486,6 +488,7 @@ dist_patch_DATA = \
|
|||
%D%/packages/patches/clucene-pkgconfig.patch \
|
||||
%D%/packages/patches/clx-remove-demo.patch \
|
||||
%D%/packages/patches/cmake-fix-tests.patch \
|
||||
%D%/packages/patches/coda-use-system-libs.patch \
|
||||
%D%/packages/patches/cpio-CVE-2016-2037.patch \
|
||||
%D%/packages/patches/cpufrequtils-fix-aclocal.patch \
|
||||
%D%/packages/patches/cracklib-CVE-2016-6318.patch \
|
||||
|
|
@ -589,6 +592,9 @@ dist_patch_DATA = \
|
|||
%D%/packages/patches/hdf4-reproducibility.patch \
|
||||
%D%/packages/patches/hdf4-shared-fortran.patch \
|
||||
%D%/packages/patches/hdf5-config-date.patch \
|
||||
%D%/packages/patches/hdf-eos2-build-shared.patch \
|
||||
%D%/packages/patches/hdf-eos2-remove-gctp.patch \
|
||||
%D%/packages/patches/hdf-eos2-fortrantests.patch \
|
||||
%D%/packages/patches/hdf-eos5-build-shared.patch \
|
||||
%D%/packages/patches/hdf-eos5-remove-gctp.patch \
|
||||
%D%/packages/patches/hdf-eos5-fix-szip.patch \
|
||||
|
|
@ -671,7 +677,6 @@ dist_patch_DATA = \
|
|||
%D%/packages/patches/libwmf-CVE-2015-4696.patch \
|
||||
%D%/packages/patches/libxslt-generated-ids.patch \
|
||||
%D%/packages/patches/linux-pam-no-setfsuid.patch \
|
||||
%D%/packages/patches/linux-libre-4.1-CVE-2016-5195.patch \
|
||||
%D%/packages/patches/lirc-localstatedir.patch \
|
||||
%D%/packages/patches/llvm-for-extempore.patch \
|
||||
%D%/packages/patches/lm-sensors-hwmon-attrs.patch \
|
||||
|
|
@ -703,7 +708,9 @@ dist_patch_DATA = \
|
|||
%D%/packages/patches/mupdf-build-with-openjpeg-2.1.patch \
|
||||
%D%/packages/patches/mupdf-CVE-2016-6265.patch \
|
||||
%D%/packages/patches/mupdf-CVE-2016-6525.patch \
|
||||
%D%/packages/patches/mupdf-CVE-2016-8674.patch \
|
||||
%D%/packages/patches/mupen64plus-ui-console-notice.patch \
|
||||
%D%/packages/patches/musl-CVE-2016-8859.patch \
|
||||
%D%/packages/patches/mutt-store-references.patch \
|
||||
%D%/packages/patches/nasm-no-ps-pdf.patch \
|
||||
%D%/packages/patches/net-tools-bitrot.patch \
|
||||
|
|
@ -714,7 +721,6 @@ dist_patch_DATA = \
|
|||
%D%/packages/patches/ninja-tests.patch \
|
||||
%D%/packages/patches/ninja-zero-mtime.patch \
|
||||
%D%/packages/patches/node-9077.patch \
|
||||
%D%/packages/patches/notmuch-emacs-25-compatibility-fix.patch \
|
||||
%D%/packages/patches/nss-pkgconfig.patch \
|
||||
%D%/packages/patches/nvi-assume-preserve-path.patch \
|
||||
%D%/packages/patches/nvi-dbpagesize-binpower.patch \
|
||||
|
|
|
|||
|
|
@ -602,15 +602,19 @@ e.g. microbiome samples, genomes, metagenomes.")
|
|||
(map (compose package-transitive-target-inputs cadr) inputs))))))
|
||||
(package
|
||||
(name "bioperl-minimal")
|
||||
(version "1.6.924")
|
||||
(version "1.7.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-"
|
||||
version ".tar.gz"))
|
||||
(uri (string-append "https://github.com/bioperl/bioperl-live/"
|
||||
"archive/release-"
|
||||
(string-map (lambda (c)
|
||||
(if (char=? c #\.)
|
||||
#\- c)) version)
|
||||
".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1l3npcvvvwjlhkna9dndpfv1hklhrgva013kw96m0n1wpd37ask1"))))
|
||||
"12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06"))))
|
||||
(build-system perl-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
|
|
@ -5190,14 +5194,14 @@ data types as well.")
|
|||
(define-public r-annotate
|
||||
(package
|
||||
(name "r-annotate")
|
||||
(version "1.50.0")
|
||||
(version "1.52.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "annotate" version))
|
||||
(sha256
|
||||
(base32
|
||||
"00wnhbjp5i6a5vyvlq4f5hs8qngjxz7fm869kla1spmd0dp2ynsy"))))
|
||||
"1fd2csq7dcs2gwndgwdx2nwkymz8gsmlnqqzv3p0vjjsvvq5n2a8"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-annotationdbi" ,r-annotationdbi)
|
||||
|
|
@ -5216,14 +5220,14 @@ microarrays.")
|
|||
(define-public r-geneplotter
|
||||
(package
|
||||
(name "r-geneplotter")
|
||||
(version "1.50.0")
|
||||
(version "1.52.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "geneplotter" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0lvrywl0251g4y0h0qlgkbg4l83ja5544c85z1wj30qxiy77iqc2"))))
|
||||
"1p6yvxi243irhjxwm97hp73abhwampj0myyf8z00ij166674pc7h"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-annotate" ,r-annotate)
|
||||
|
|
@ -5241,14 +5245,14 @@ microarrays.")
|
|||
(define-public r-genefilter
|
||||
(package
|
||||
(name "r-genefilter")
|
||||
(version "1.54.2")
|
||||
(version "1.56.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "genefilter" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1hmz6as0njvrsrdbgmk72jyclnnqvfdvp6kqv456h43ldq2ajfv5"))))
|
||||
"1vzgciqd09csqcw9qync8blsv51ylrd86a65iadgyy6j26g01fwd"))))
|
||||
(build-system r-build-system)
|
||||
(native-inputs
|
||||
`(("gfortran" ,gfortran)))
|
||||
|
|
@ -5267,14 +5271,14 @@ high-throughput sequencing experiments.")
|
|||
(define-public r-deseq2
|
||||
(package
|
||||
(name "r-deseq2")
|
||||
(version "1.12.4")
|
||||
(version "1.14.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "DESeq2" version))
|
||||
(sha256
|
||||
(base32
|
||||
"12h77f0dpi5xaj7aqf50kkyn6lq9j7bcsly1r0ffmyfcszrp1sfx"))))
|
||||
"0kq06jy4xg5ii3a9l62f17kirsfx0gsiwq6mhiy985cqzpdn893g"))))
|
||||
(properties `((upstream-name . "DESeq2")))
|
||||
(build-system r-build-system)
|
||||
(arguments
|
||||
|
|
@ -5312,14 +5316,14 @@ distribution.")
|
|||
(define-public r-annotationforge
|
||||
(package
|
||||
(name "r-annotationforge")
|
||||
(version "1.14.2")
|
||||
(version "1.16.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "AnnotationForge" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1vkdd1qdv5g680ipw4vwjvn52xn66xpg6ngmwyknz77ckxnnpf4q"))))
|
||||
"02msyb9p3hywrryx00zpjkjl126mrv827i1ah1092s0cplm6xxvf"))))
|
||||
(properties
|
||||
`((upstream-name . "AnnotationForge")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -5328,6 +5332,7 @@ distribution.")
|
|||
("r-biobase" ,r-biobase)
|
||||
("r-biocgenerics" ,r-biocgenerics)
|
||||
("r-dbi" ,r-dbi)
|
||||
("r-rcurl" ,r-rcurl)
|
||||
("r-rsqlite" ,r-rsqlite)
|
||||
("r-s4vectors" ,r-s4vectors)
|
||||
("r-xml" ,r-xml)))
|
||||
|
|
@ -5341,14 +5346,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.")
|
|||
(define-public r-rbgl
|
||||
(package
|
||||
(name "r-rbgl")
|
||||
(version "1.48.1")
|
||||
(version "1.50.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "RBGL" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1k82zcbyfx3p9hc8r0hwq73krbhakjan8fgbfr6w8z2crfkv3zmz"))))
|
||||
"1q14m8w6ih56v680kf3d9wh1qbgp7af33kz3cxafdf1vvzx9km08"))))
|
||||
(properties `((upstream-name . "RBGL")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs `(("r-graph" ,r-graph)))
|
||||
|
|
@ -5362,14 +5367,14 @@ the graph algorithms contained in the Boost library.")
|
|||
(define-public r-gseabase
|
||||
(package
|
||||
(name "r-gseabase")
|
||||
(version "1.34.1")
|
||||
(version "1.36.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "GSEABase" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1mvgja8malrnbzfakzjl5mmi7g080kj8zgxwc5964hcmn33i937j"))))
|
||||
"0l2x7yj7lfb0m2dmsav5ib026dikpgl4crdckrnj776yy08lgxpj"))))
|
||||
(properties `((upstream-name . "GSEABase")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -5389,14 +5394,14 @@ Enrichment Analysis} (GSEA).")
|
|||
(define-public r-category
|
||||
(package
|
||||
(name "r-category")
|
||||
(version "2.38.0")
|
||||
(version "2.40.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "Category" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0c8px9ar589f3iqkbk9vfhwj30dpnxj81h8sfq20cl1cbmcx2a04"))))
|
||||
"16ncwz7b4y48k0p3fvbrbmvf7nfz63li9ysgcl8kp9kl4hg7llng"))))
|
||||
(properties `((upstream-name . "Category")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -5420,14 +5425,14 @@ analysis.")
|
|||
(define-public r-gostats
|
||||
(package
|
||||
(name "r-gostats")
|
||||
(version "2.38.1")
|
||||
(version "2.40.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "GOstats" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1hhw6vqr8f3g4jzq0v8f2za0r1h117j5s6av87zxs41cv7dq1wb3"))))
|
||||
"0g2czm94zhzx92z7y2r4mjfxhwml7bhab2db6820ks8nkw1zvr9n"))))
|
||||
(properties `((upstream-name . "GOstats")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -5450,14 +5455,14 @@ testing and other simple calculations.")
|
|||
(define-public r-shortread
|
||||
(package
|
||||
(name "r-shortread")
|
||||
(version "1.30.0")
|
||||
(version "1.32.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "ShortRead" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0qlxns4bhwfpafx3km2lnivgl2qyp7n4g1ardm6vrinpq8paxbjg"))))
|
||||
"0mjdlg92x5qw4x2djc4dv5lxwl7ai6ix56nnf86zr07jk8vc7yls"))))
|
||||
(properties `((upstream-name . "ShortRead")))
|
||||
(build-system r-build-system)
|
||||
(inputs
|
||||
|
|
@ -5492,14 +5497,14 @@ ungapped alignment formats.")
|
|||
(define-public r-systempiper
|
||||
(package
|
||||
(name "r-systempiper")
|
||||
(version "1.6.4")
|
||||
(version "1.8.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "systemPipeR" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0s2g46a5d5bvx45i3cgmib48wf8hrniyladhm0f7kgcbfx57248m"))))
|
||||
"0hyi841w8fm2yzpm6lwqi3jz5kc8ny8dy5p29dxynzaw5bpjw56d"))))
|
||||
(properties `((upstream-name . "systemPipeR")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -5538,14 +5543,14 @@ annotation infrastructure.")
|
|||
(define-public r-grohmm
|
||||
(package
|
||||
(name "r-grohmm")
|
||||
(version "1.6.0")
|
||||
(version "1.8.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "groHMM" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1l9mcyzyc548114ysb9r0q7hgzw3yy7gpiahrzkzj6hblc4f1jyp"))))
|
||||
"0d91nyhqbi5hv3mgmr2z0g29wg2md26g0hyv5mgapmz20cd9zi4y"))))
|
||||
(properties `((upstream-name . "groHMM")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -5852,13 +5857,13 @@ barplots or heatmaps.")
|
|||
(define-public r-biocgenerics
|
||||
(package
|
||||
(name "r-biocgenerics")
|
||||
(version "0.18.0")
|
||||
(version "0.20.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "BiocGenerics" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1jjp48vbph09w5bmc7368gjjywsa1lmzfybpiwlypr60b51vlkp6"))))
|
||||
"06szdz7dfs1iyv5zdl4fjzad18nnf1zf3wvglc6c6yd9mrqlf7vk"))))
|
||||
(properties
|
||||
`((upstream-name . "BiocGenerics")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -5872,13 +5877,13 @@ packages.")
|
|||
(define-public r-biocinstaller
|
||||
(package
|
||||
(name "r-biocinstaller")
|
||||
(version "1.22.3")
|
||||
(version "1.24.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "BiocInstaller" version))
|
||||
(sha256
|
||||
(base32
|
||||
"02qkfq6f2b7v9klri6d1nv21r54bywv1zd5x47ka0jhhp946cqpr"))))
|
||||
"0y1y5wmy6lzjqx3hdg15n91d417ccjj8dbvdkhmp99bs5aijwcpn"))))
|
||||
(properties
|
||||
`((upstream-name . "BiocInstaller")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6032,13 +6037,13 @@ that accept short and long options.")
|
|||
(define-public r-dnacopy
|
||||
(package
|
||||
(name "r-dnacopy")
|
||||
(version "1.46.0")
|
||||
(version "1.48.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "DNAcopy" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0vwv2mndfjpcjp4sybg75abc7xnx8zyw8zjk717k6xh8c33ymcip"))))
|
||||
"1idyvfvy7xx8k9vk00y4k3819qmip8iqm809j3vpxabmsn7r9zyh"))))
|
||||
(properties
|
||||
`((upstream-name . "DNAcopy")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6054,13 +6059,13 @@ abnormal copy number.")
|
|||
(define-public r-s4vectors
|
||||
(package
|
||||
(name "r-s4vectors")
|
||||
(version "0.10.3")
|
||||
(version "0.12.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "S4Vectors" version))
|
||||
(sha256
|
||||
(base32
|
||||
"09lrvy3d5q58hsgw9as4hyyx07k1vyy2zjn3xsvhyfd97yk6w6lv"))))
|
||||
"0m0npc0vhmcwcxws7v2f8k4hvvrjvnlrsr94klxf4a8m4xw2xzzk"))))
|
||||
(properties
|
||||
`((upstream-name . "S4Vectors")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6081,14 +6086,14 @@ S4Vectors package itself.")
|
|||
(define-public r-seqinr
|
||||
(package
|
||||
(name "r-seqinr")
|
||||
(version "3.3-1")
|
||||
(version "3.3-3")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "seqinr" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1al83y6m7739dz2j895yihksm0s5l45ialid4yw911ylbg3w6cm1"))))
|
||||
"0rk4yba8km26c0rh1f4h474zsb5n6kjmqsi55bnzr6p8pymp18hj"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-ade4" ,r-ade4)
|
||||
|
|
@ -6106,13 +6111,13 @@ utilities for sequence data management under the ACNUC system.")
|
|||
(define-public r-iranges
|
||||
(package
|
||||
(name "r-iranges")
|
||||
(version "2.6.1")
|
||||
(version "2.8.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "IRanges" version))
|
||||
(sha256
|
||||
(base32
|
||||
"06pyam3bjjfw2m3l86rda503lsz2jcg645lcnhvrz6qi0nv359yg"))))
|
||||
"0cdl1sfd3cvf93lnz91fdk64fbg1mnd5g958dwh1il8r358hqq3f"))))
|
||||
(properties
|
||||
`((upstream-name . "IRanges")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6135,13 +6140,13 @@ possible.")
|
|||
(define-public r-genomeinfodb
|
||||
(package
|
||||
(name "r-genomeinfodb")
|
||||
(version "1.8.7")
|
||||
(version "1.10.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "GenomeInfoDb" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1x96468bbjx7z3ikp1dgr2krnz9pwx86vmssfbfrsikaxfs4q829"))))
|
||||
"0nhg4bk38gzvf3mvnbqgisbbhfv1kzjld27z1z9knnlkplkiyyyv"))))
|
||||
(properties
|
||||
`((upstream-name . "GenomeInfoDb")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6161,17 +6166,18 @@ names in their natural, rather than lexicographic, order.")
|
|||
(define-public r-edger
|
||||
(package
|
||||
(name "r-edger")
|
||||
(version "3.14.0")
|
||||
(version "3.16.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "edgeR" version))
|
||||
(sha256
|
||||
(base32
|
||||
"14vrygy7rz5ngaap4kgkvr3j18y5l6m742n79h68plk6iqgmsskn"))))
|
||||
"1qr20j55m35dwzqyzzmla69gk5bzff8v1v2qjh7yd3362wq1ch49"))))
|
||||
(properties `((upstream-name . "edgeR")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-limma" ,r-limma)))
|
||||
`(("r-limma" ,r-limma)
|
||||
("r-locfit" ,r-locfit)))
|
||||
(home-page "http://bioinf.wehi.edu.au/edgeR")
|
||||
(synopsis "EdgeR does empirical analysis of digital gene expression data")
|
||||
(description "This package can do differential expression analysis of
|
||||
|
|
@ -6186,27 +6192,33 @@ CAGE.")
|
|||
(define-public r-variantannotation
|
||||
(package
|
||||
(name "r-variantannotation")
|
||||
(version "1.18.7")
|
||||
(version "1.20.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "VariantAnnotation" version))
|
||||
(sha256
|
||||
(base32
|
||||
"002kif2c66wbcng953m3g1jys7w1lgz7hh3zsk4jlnhc20jdv1vj"))))
|
||||
"1lwzfgahz8ipwli73kcfqb18y6adi129hap1gnycnj3980m54i8q"))))
|
||||
(properties
|
||||
`((upstream-name . "VariantAnnotation")))
|
||||
(inputs
|
||||
`(("zlib" ,zlib)))
|
||||
(propagated-inputs
|
||||
`(("r-annotationdbi" ,r-annotationdbi)
|
||||
("r-biobase" ,r-biobase)
|
||||
("r-biocgenerics" ,r-biocgenerics)
|
||||
("r-biostrings" ,r-biostrings)
|
||||
("r-bsgenome" ,r-bsgenome)
|
||||
("r-dbi" ,r-dbi)
|
||||
("r-genomeinfodb" ,r-genomeinfodb)
|
||||
("r-genomicfeatures" ,r-genomicfeatures)
|
||||
("r-genomicranges" ,r-genomicranges)
|
||||
("r-iranges" ,r-iranges)
|
||||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||||
("r-rsamtools" ,r-rsamtools)
|
||||
("r-rtracklayer" ,r-rtracklayer)
|
||||
("r-s4vectors" ,r-s4vectors)
|
||||
("r-xvector" ,r-xvector)
|
||||
("r-zlibbioc" ,r-zlibbioc)))
|
||||
(build-system r-build-system)
|
||||
(home-page "https://bioconductor.org/packages/VariantAnnotation")
|
||||
|
|
@ -6218,13 +6230,13 @@ coding changes and predict coding outcomes.")
|
|||
(define-public r-limma
|
||||
(package
|
||||
(name "r-limma")
|
||||
(version "3.28.21")
|
||||
(version "3.30.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "limma" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1dvisifd2rr7s1rrsqj5vrv2qcg4la4yi2ajbn0zkk5z81ffxv9f"))))
|
||||
"0d8wp7b7nymawf4czwsg27k4c61i4ij2lhv7phi6cb3hdd8c76yf"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://bioinf.wehi.edu.au/limma")
|
||||
(synopsis "Package for linear models for microarray and RNA-seq data")
|
||||
|
|
@ -6237,13 +6249,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
|
|||
(define-public r-xvector
|
||||
(package
|
||||
(name "r-xvector")
|
||||
(version "0.12.1")
|
||||
(version "0.14.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "XVector" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1kydy9f5y0ihn2mbkamr1kh0g1d3g1k9d7s4i09qgw9ysr6j414v"))))
|
||||
"09lbqxpqr80g0kw77mpz0p1a8cq706j33kz8194wp71il67cdzi7"))))
|
||||
(properties
|
||||
`((upstream-name . "XVector")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6273,19 +6285,21 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
|
|||
(define-public r-genomicranges
|
||||
(package
|
||||
(name "r-genomicranges")
|
||||
(version "1.24.3")
|
||||
(version "1.26.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "GenomicRanges" version))
|
||||
(sha256
|
||||
(base32
|
||||
"098a34hfgb5z120v6wpl5nv8v61nm65yg6xq0j7i9bigvxr7apg2"))))
|
||||
"039nxccg9i2an8q2wni79x8dr9p1fcfcqvih9hg9w243pczg2g3c"))))
|
||||
(properties
|
||||
`((upstream-name . "GenomicRanges")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-biocgenerics" ,r-biocgenerics)
|
||||
("r-genomeinfodb" ,r-genomeinfodb)
|
||||
("r-iranges" ,r-iranges)
|
||||
("r-s4vectors" ,r-s4vectors)
|
||||
("r-xvector" ,r-xvector)))
|
||||
(home-page "http://bioconductor.org/packages/GenomicRanges")
|
||||
(synopsis "Representation and manipulation of genomic intervals")
|
||||
|
|
@ -6300,13 +6314,13 @@ manipulating genomic intervals and variables defined along a genome.")
|
|||
(define-public r-biobase
|
||||
(package
|
||||
(name "r-biobase")
|
||||
(version "2.32.0")
|
||||
(version "2.34.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "Biobase" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0q4icv9n5rc2qfkv6k1wjhmfcpzcyr8f45m2z3xharbdv912kl1i"))))
|
||||
"0js9j9wqls8f571ifl9ylllbb9a9hwf7b7drf2grwb1fl31ldazl"))))
|
||||
(properties
|
||||
`((upstream-name . "Biobase")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6322,13 +6336,13 @@ on Bioconductor or which replace R functions.")
|
|||
(define-public r-annotationdbi
|
||||
(package
|
||||
(name "r-annotationdbi")
|
||||
(version "1.34.4")
|
||||
(version "1.36.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "AnnotationDbi" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1k3gfsjrivc7467vg0h705hh4dvzgdhknz62j7zmfxm67qk9r8rq"))))
|
||||
"0ydrqw1k1j5p6w76bwc753cx545c055x88q87wzya93858synj6r"))))
|
||||
(properties
|
||||
`((upstream-name . "AnnotationDbi")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6349,13 +6363,13 @@ annotation data packages using SQLite data storage.")
|
|||
(define-public r-biomart
|
||||
(package
|
||||
(name "r-biomart")
|
||||
(version "2.28.0")
|
||||
(version "2.30.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "biomaRt" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1g0w6an9hkflgyhvq6pmrs92s93qarv23v636b9a4bz771wjvm5v"))))
|
||||
"1x0flcghq71784q2l02j0g4f9jkmyb14f6i307n6c59d6ji7h7x6"))))
|
||||
(properties
|
||||
`((upstream-name . "biomaRt")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6379,13 +6393,13 @@ powerful online queries from gene annotation to database mining.")
|
|||
(define-public r-biocparallel
|
||||
(package
|
||||
(name "r-biocparallel")
|
||||
(version "1.6.6")
|
||||
(version "1.8.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "BiocParallel" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1l39zmvhjlvlczrk5wal4y2s4g0b2kmaczgq5biah9qn45y474mw"))))
|
||||
"0vz23i14f7wjygr5d4y1hp8ki6l6igwcsjscfpr6dcigmknyi55c"))))
|
||||
(properties
|
||||
`((upstream-name . "BiocParallel")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6403,13 +6417,13 @@ objects.")
|
|||
(define-public r-biostrings
|
||||
(package
|
||||
(name "r-biostrings")
|
||||
(version "2.40.2")
|
||||
(version "2.42.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "Biostrings" version))
|
||||
(sha256
|
||||
(base32
|
||||
"153rfws5sdha324p1nv7jp75ip6ny0f62jzhqcvs46l85h3i8zgh"))))
|
||||
"08z8lkz3axa94wkf144a931ry6vf6cc25avi1ywr84ln2k5czz9f"))))
|
||||
(properties
|
||||
`((upstream-name . "Biostrings")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6429,13 +6443,13 @@ biological sequences or sets of sequences.")
|
|||
(define-public r-rsamtools
|
||||
(package
|
||||
(name "r-rsamtools")
|
||||
(version "1.24.0")
|
||||
(version "1.26.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "Rsamtools" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0w0drs8cpk8nlazq64ag7nm1w5jd1m8riialivm01hz5zcra7scb"))))
|
||||
"0pf4f6brf4bl5zgjrah0f38qslazrs49ayqgyh0xfqgrh63yx4ck"))))
|
||||
(properties
|
||||
`((upstream-name . "Rsamtools")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6473,13 +6487,13 @@ files.")
|
|||
(define-public r-summarizedexperiment
|
||||
(package
|
||||
(name "r-summarizedexperiment")
|
||||
(version "1.2.3")
|
||||
(version "1.4.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "SummarizedExperiment" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0c43fsrha886sd0diislnlf8r5h5x7fbhphkzcm0rw3k2jz8wlyk"))))
|
||||
"1kbj8sg2ik9f8d6g95wz0py62jldg01qy5rsdpg1cxw95nf7dzi3"))))
|
||||
(properties
|
||||
`((upstream-name . "SummarizedExperiment")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6502,13 +6516,13 @@ samples.")
|
|||
(define-public r-genomicalignments
|
||||
(package
|
||||
(name "r-genomicalignments")
|
||||
(version "1.8.4")
|
||||
(version "1.10.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "GenomicAlignments" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1cccvalmm83ilk1kpq31ll8kdy9xclsr4pm4mlcc7bmp0rwkd2p2"))))
|
||||
"11vb0a0zd36i4yhg4mfijv787v0nihn6pkjj6q7rfy19gwy61xlc"))))
|
||||
(properties
|
||||
`((upstream-name . "GenomicAlignments")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6535,13 +6549,13 @@ alignments.")
|
|||
(define-public r-rtracklayer
|
||||
(package
|
||||
(name "r-rtracklayer")
|
||||
(version "1.32.2")
|
||||
(version "1.34.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "rtracklayer" version))
|
||||
(sha256
|
||||
(base32
|
||||
"190767zpwc7maqjpy0x5bpkm0jp1vfawy9991fifw0mc634cjkga"))))
|
||||
"0mix5k75j70mwplbdipqw71n8qic75ny6y8w2f5jj0pqg1k0327d"))))
|
||||
(build-system r-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
|
|
@ -6580,13 +6594,13 @@ as well as query and modify the browser state, such as the current viewport.")
|
|||
(define-public r-genomicfeatures
|
||||
(package
|
||||
(name "r-genomicfeatures")
|
||||
(version "1.24.5")
|
||||
(version "1.26.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "GenomicFeatures" version))
|
||||
(sha256
|
||||
(base32
|
||||
"17qpisdgqyjz2mnaiwc4dx7dg11pwq3mkvmkah9zn07g9rhh8f7p"))))
|
||||
"0z8spi2knwzwi10c38vr7xlvi3ah9faj7m1lka880mmxkl9cai4k"))))
|
||||
(properties
|
||||
`((upstream-name . "GenomicFeatures")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6621,7 +6635,7 @@ extracting the desired features in a convenient format.")
|
|||
(define-public r-go-db
|
||||
(package
|
||||
(name "r-go-db")
|
||||
(version "3.3.0")
|
||||
(version "3.4.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "http://www.bioconductor.org/packages/"
|
||||
|
|
@ -6629,7 +6643,7 @@ extracting the desired features in a convenient format.")
|
|||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0x2hkbhg9d8waw32hdn05887vv3zbs5aqff3mf5vfyzvl7xhgxy0"))))
|
||||
"02cj8kqi5w39jwcs8gp1dgj08sah262ppxnkz4h3qd0w191y8yyl"))))
|
||||
(properties
|
||||
`((upstream-name . "GO.db")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6645,13 +6659,13 @@ information about the latest version of the Gene Ontologies.")
|
|||
(define-public r-graph
|
||||
(package
|
||||
(name "r-graph")
|
||||
(version "1.50.0")
|
||||
(version "1.52.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "graph" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0ys5s19m5r30rlr0fnx2h0z2qw7n2xrad4l2yfb1bbrk8dwyf4pi"))))
|
||||
"0g3dk5vsdp489fmyg8mifczmzgqrjlakkkr8i96dj15gghp3l135"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-biocgenerics" ,r-biocgenerics)))
|
||||
|
|
@ -6664,18 +6678,19 @@ information about the latest version of the Gene Ontologies.")
|
|||
(define-public r-topgo
|
||||
(package
|
||||
(name "r-topgo")
|
||||
(version "2.24.0")
|
||||
(version "2.26.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "topGO" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1p4vsl32qhjw15yv9ym01ni63gjg73jaghlf17wc4zfn3iaz2zar"))))
|
||||
"0j6sgvam4lk9348ag6pypcbkv93x4fk0di8ivhr23mz2s2yqzwrx"))))
|
||||
(properties
|
||||
`((upstream-name . "topGO")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-annotationdbi" ,r-annotationdbi)
|
||||
("r-dbi" ,r-dbi)
|
||||
("r-biobase" ,r-biobase)
|
||||
("r-biocgenerics" ,r-biocgenerics)
|
||||
("r-go-db" ,r-go-db)
|
||||
|
|
@ -6695,13 +6710,13 @@ dependencies between GO terms can be implemented and applied.")
|
|||
(define-public r-bsgenome
|
||||
(package
|
||||
(name "r-bsgenome")
|
||||
(version "1.40.1")
|
||||
(version "1.42.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "BSgenome" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0zmlzlcwairka59is5wmkh6knh6j4d328z9fsw3v91fx6gavjl2n"))))
|
||||
"0hxwc02h5mzhkrk60d1jmlsfjf0ai9jxdc0128kj1sg4r2k1q94y"))))
|
||||
(properties
|
||||
`((upstream-name . "BSgenome")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6725,13 +6740,13 @@ genome data packages and support for efficient SNP representation.")
|
|||
(define-public r-impute
|
||||
(package
|
||||
(name "r-impute")
|
||||
(version "1.46.0")
|
||||
(version "1.48.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "impute" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0v9ibgv8kp8il52miz7b7z65mv6irqxylx6lfzkxgvxd970dgrz0"))))
|
||||
"1164zvnikbjd0ybdn9xwn520rlmdjd824vmhnl83zgv3v9lzp9bm"))))
|
||||
(inputs
|
||||
`(("gfortran" ,gfortran)))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6745,13 +6760,13 @@ microarray data, using nearest neighbor averaging.")
|
|||
(define-public r-seqpattern
|
||||
(package
|
||||
(name "r-seqpattern")
|
||||
(version "1.4.0")
|
||||
(version "1.6.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "seqPattern" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1dj9hfnbdj11yjxwd8jmxrdkj7n6gmaaj6244g2psgarhjcp4wfb"))))
|
||||
"0lsa5pz36xapi3yiv78k3z286a5md5sm5g21pgfyg8zmhmkxr7y8"))))
|
||||
(properties
|
||||
`((upstream-name . "seqPattern")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -6759,6 +6774,7 @@ microarray data, using nearest neighbor averaging.")
|
|||
`(("r-biostrings" ,r-biostrings)
|
||||
("r-genomicranges" ,r-genomicranges)
|
||||
("r-iranges" ,r-iranges)
|
||||
("r-kernsmooth" ,r-kernsmooth)
|
||||
("r-plotrix" ,r-plotrix)))
|
||||
(home-page "http://bioconductor.org/packages/seqPattern")
|
||||
(synopsis "Visualising oligonucleotide patterns and motif occurrences")
|
||||
|
|
@ -6771,13 +6787,13 @@ reference point and sorted by a user defined feature.")
|
|||
(define-public r-genomation
|
||||
(package
|
||||
(name "r-genomation")
|
||||
(version "1.4.2")
|
||||
(version "1.6.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "genomation" version))
|
||||
(sha256
|
||||
(base32
|
||||
"017hxh3yhizlsswd2vw8504arkckrcgq5zraiw67lldq9wzs5qzg"))))
|
||||
"1m4mz7wihj8yqivwkzw68div8ybk4rjsai3ffki7xp7sh21ax03y"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-biostrings" ,r-biostrings)
|
||||
|
|
@ -6793,11 +6809,17 @@ reference point and sorted by a user defined feature.")
|
|||
("r-matrixstats" ,r-matrixstats)
|
||||
("r-plotrix" ,r-plotrix)
|
||||
("r-plyr" ,r-plyr)
|
||||
("r-rcpp" ,r-rcpp)
|
||||
("r-readr" ,r-readr)
|
||||
("r-reshape2" ,r-reshape2)
|
||||
("r-rhtslib" ,r-rhtslib)
|
||||
("r-rsamtools" ,r-rsamtools)
|
||||
("r-rtracklayer" ,r-rtracklayer)
|
||||
("r-runit" ,r-runit)
|
||||
("r-s4vectors" ,r-s4vectors)
|
||||
("r-seqpattern" ,r-seqpattern)))
|
||||
(inputs
|
||||
`(("zlib" ,zlib)))
|
||||
(home-page "http://bioinformatics.mdc-berlin.de/genomation/")
|
||||
(synopsis "Summary, annotation and visualization of genomic data")
|
||||
(description
|
||||
|
|
@ -6814,7 +6836,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
|
|||
(define-public r-genomationdata
|
||||
(package
|
||||
(name "r-genomationdata")
|
||||
(version "1.4.2")
|
||||
(version "1.6.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
;; We cannot use bioconductor-uri here because this tarball is
|
||||
|
|
@ -6824,7 +6846,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
|
|||
"genomationData_" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1zl7gg144fs7zfycsmq5492sm1bqy7l527xbc2zj04schd9wsan2"))))
|
||||
"16dqwb7wx1igx77zdbcskx5m1hs4g4gp2hl56zzm70hcagnlkz8y"))))
|
||||
(build-system r-build-system)
|
||||
;; As this package provides little more than large data files, it doesn't
|
||||
;; make sense to build substitutes.
|
||||
|
|
@ -6946,14 +6968,14 @@ annotations for the genome of the model mouse Mus musculus.")
|
|||
(define-public r-seqlogo
|
||||
(package
|
||||
(name "r-seqlogo")
|
||||
(version "1.38.0")
|
||||
(version "1.40.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "seqLogo" version))
|
||||
(sha256
|
||||
(base32
|
||||
"01jddx62nhi3r7czbh9hxy0wwpazbc9ax1fgagfxl6p4kx9xz9rb"))))
|
||||
"18bajdl75h3039559d81rgllqqvnq8ygsfxfx081xphxs0v6xggy"))))
|
||||
(properties `((upstream-name . "seqLogo")))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://bioconductor.org/packages/seqLogo")
|
||||
|
|
@ -7157,14 +7179,14 @@ Biostrings objects.")
|
|||
(define-public r-motifrg
|
||||
(package
|
||||
(name "r-motifrg")
|
||||
(version "1.16.0")
|
||||
(version "1.18.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "motifRG" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1ds22paqc0923y6z1fy0arw0wxvvmglfvfgarhywv1qywhq68mbq"))))
|
||||
"1pa97aj6c5f3gx4bgriw110764dj3m9h104ddi8rv2bpy41yd98d"))))
|
||||
(properties `((upstream-name . "motifRG")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -7209,13 +7231,13 @@ two-dimensional genome scans.")
|
|||
(define-public r-zlibbioc
|
||||
(package
|
||||
(name "r-zlibbioc")
|
||||
(version "1.18.0")
|
||||
(version "1.20.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "zlibbioc" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0m8l7zpx1l3qsk73k3ibkxxzzff938x3qhnwki1ymf3cnsg8cb36"))))
|
||||
"0hbk90q5hl0fycfvy5nxxa4hxgglag9lzp7i0fg849bqygg5nbyq"))))
|
||||
(properties
|
||||
`((upstream-name . "zlibbioc")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -7228,20 +7250,22 @@ libraries for systems that do not have these available via other means.")
|
|||
(define-public r-rhtslib
|
||||
(package
|
||||
(name "r-rhtslib")
|
||||
(version "1.4.3")
|
||||
(version "1.6.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "Rhtslib" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1wgpn9x8abjj7fc087pdavqc3fz0pl5xdh231mgjila18irwlhb3"))))
|
||||
"1vk3ng61dhi3pbia1lp3gl3mlr3i1vb2lkq83qb53i9dzz128wh9"))))
|
||||
(properties `((upstream-name . "Rhtslib")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-zlibbioc" ,r-zlibbioc)))
|
||||
(inputs
|
||||
`(("zlib" ,zlib)))
|
||||
(native-inputs
|
||||
`(("autoconf" ,autoconf)))
|
||||
(home-page "https://github.com/nhayden/Rhtslib")
|
||||
(synopsis "High-throughput sequencing library as an R package")
|
||||
(description
|
||||
|
|
@ -7253,14 +7277,14 @@ of other R packages who wish to make use of HTSlib.")
|
|||
(define-public r-bamsignals
|
||||
(package
|
||||
(name "r-bamsignals")
|
||||
(version "1.4.3")
|
||||
(version "1.6.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "bamsignals" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1xqiqvg52p6fcvhr4146djbz79r3j1kmh75mq7rndwglmiybpwmy"))))
|
||||
"1k42gvk5mgq4la1fp0in3an2zfdz69h6522jsqhmk0f6i75kg4mb"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-biocgenerics" ,r-biocgenerics)
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@
|
|||
(define-public elfutils
|
||||
(package
|
||||
(name "elfutils")
|
||||
(version "0.166")
|
||||
(version "0.167")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -38,7 +38,7 @@
|
|||
version "/elfutils-" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32
|
||||
"0c5s9klq1zyb0zkmrw636k97kz30p5ih8y8dpq8b4f54r0a6j19w"))
|
||||
"0lv5fz2h7j9362l5apbg9jff7309ni385d3325ckavrbqj3h0c1z"))
|
||||
(patches (search-patches "elfutils-tests-ptrace.patch"))))
|
||||
(build-system gnu-build-system)
|
||||
|
||||
|
|
|
|||
|
|
@ -955,7 +955,7 @@ light user interface.")
|
|||
(define-public emacs-emms-player-mpv
|
||||
(package
|
||||
(name "emacs-emms-player-mpv")
|
||||
(version "0.0.8")
|
||||
(version "0.0.10")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
|
@ -964,7 +964,7 @@ light user interface.")
|
|||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"01wj410dpx25b3i8781i2j9c6nlvzvvphy9qgh7zfpmyz6a3wsm4"))))
|
||||
"1q81fpmwr8hpdgq71vbdai2nml4yyqbmk4ffdyl4irlwph8gfjyq"))))
|
||||
(build-system emacs-build-system)
|
||||
(propagated-inputs
|
||||
`(("emms" ,emms)))
|
||||
|
|
|
|||
|
|
@ -56,7 +56,7 @@
|
|||
(define-public efl
|
||||
(package
|
||||
(name "efl")
|
||||
(version "1.18.1")
|
||||
(version "1.18.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -64,7 +64,7 @@
|
|||
version ".tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"08njx6wd505as1vn0yp4mnmf6mb2v28jsipxxx4zhf78v18d2sqc"))))
|
||||
"1vbvsrrpkvvrmvjavwnp5q77kw5i7vmbaj2vq5mnmrbzamvaybr9"))))
|
||||
(build-system gnu-build-system)
|
||||
(native-inputs
|
||||
`(("pkg-config" ,pkg-config)))
|
||||
|
|
|
|||
|
|
@ -2158,42 +2158,42 @@ http://lavachat.symlynx.com/unix/")
|
|||
|
||||
(define-public red-eclipse
|
||||
(let ((data-sources
|
||||
'(("acerspyro" "0s6q56i5marpm67lx70g5109lir5d6r45y45i8kbz6arc1spa7pp")
|
||||
("actors" "0jclmciz64i81ngxwbag8x5m8wvxkhraa9c7plix566y6rh28fv1")
|
||||
("appleflap" "1iz5igzdksamldhy0zh4vdjkxqhmg5c0n5g64pd3kan6h8vlbkq4")
|
||||
("blendbrush" "1hz3x5npp25dixcadp020xyahmd1i3ihs4cdf77iy84i9njbp7bv")
|
||||
("caustics" "05sbj46lrc6lkf7j6ls6jwc21n0qzxvfhfy9j7hdw482p9gvz54h")
|
||||
("crosshairs" "05vfxc6vm91dyf1kzig550fglgydp9szl9135q677lk4g60w5dfh")
|
||||
("elyvisions" "0fzdbxc40ggqmv4v1llx6sys2gjc6l1nxsbi5scpxqvm86dbddi9")
|
||||
("fonts" "0sbvnd96aip49dy1ja01s36p8fwwczibpic7myfw1frs110m0zgr")
|
||||
("freezurbern" "0k60dzzq42mfq360qf7bsf4alhy6k5gjfaidg2i1wsz5zssgmqwn")
|
||||
("john" "1ln9v8vfm0ggavvdyl438cy4mizzm1i87r9msx1sbja30q8f57c1")
|
||||
("jojo" "0cdgl82s4bm6qlv07fsq5l7anbywvvw13d0mng831yn6scf0hxb1")
|
||||
("jwin" "0yg5vriffyckgfjmi4487sw07hsp44b3gfw90f0v4jsgbjjm2v20")
|
||||
("luckystrike" "0f82caq09znsr9m08qnlbh3jl9j5w0ysga0b7d5ayqr5lpqxfk9k")
|
||||
("maps" "14m23h3mip12anhx7i9k5xlapwkjbw4n0l7lj1b7dfcimf71gjll")
|
||||
("mayhem" "0dxrr6craqi7ag724qfj9y0lb0pmwyrfpap02cndmjbbacdya0ra")
|
||||
("mikeplus64" "040giyrk3hdd26sxhdx37q4mk923g5v3jbrinq1fw2yfvsl6n1cs")
|
||||
("misc" "07xfs9hngshg27rl2vf65nyxilgnak3534h8msaan0fjgmzvlk0q")
|
||||
("nobiax" "1n3nghi5426r2zav4rsfih8gn37sfa85absvhdwhir8wycsvbkh6")
|
||||
("particles" "0yj0nykal3fgxx50278xl2zn2bfz09wbrjcvng56aa6hhfiwp8gd")
|
||||
("philipk" "1m3krkxq9hsknbmxg1g5sgnpcv7c8c2q7zpbizw2wb3dir8snvcj")
|
||||
("projectiles" "05swvalja7vzqc3dlk136n5b5kdzn3a8il6bg1h12alcaa0k9rba")
|
||||
("props" "1cqi6gw5s4z5pj06x6kiiilh4if0hm1yrbqys5dln23mcvw8f0ny")
|
||||
("skyboxes" "1mm6xl89b0l98l2h3qn99id7svmpwr940bydgjbcrvlx21yqdric")
|
||||
("sounds" "03q7jazf0chszyiaa9cxirbwdnckcp5fl812sj42lv0z4sqz222l")
|
||||
("textures" "1caqyxa9xkrwpyhac65akdv1l7nqychgz7zfivasnskk2yy6jani")
|
||||
("torley" "1hp8lkzqmdqyq3jn9rains32diw11gg1w3dxxlln5pc041cd7vil")
|
||||
("trak" "0wlczjax33q0hz75lgc4qnxlm592pcxgnbkin5qrglv59nrxzxyr")
|
||||
("ulukai" "0dkn7qxf92sidhsy4sm4v5z54n449a2z2w9qax5cfgzs78kb5c34")
|
||||
("unnamed" "0p9mmfp0vplmswyxh8qab33phcl8lzmzh3mms4f7i587hppdg6db")
|
||||
("vanities" "1w23853lmvj4kx5cbxvb5dk598jiqz7ml2bm0qiy7idkf5mcd2lv")
|
||||
("vegetation" "0jw1ljhmv62fzvklid6i8syiacmrs075cp7r3gc069bg4fg47cpn")
|
||||
("weapons" "1p64ry1s4y7hkgm6i2rdk2x78368359wvx8v81gg179p3sjnjkww")
|
||||
("wicked" "1kmpy2n15lyh50rqjspyfg3qrc72jf0n3dx2y3ian7pjfp6ldxd9"))))
|
||||
'(("acerspyro" "0hqwa3b65l8mz73mcdsvrwbc14mrx1qn52073p5zh69pqd0mlfi0")
|
||||
("actors" "0v87wifqwam5j6vsiidmcvw22i51h9h4skgwhi511mxkwryrp26h")
|
||||
("appleflap" "0bkh1v125dwd5jhb4rrc1sl0jdlbb2ib53ihbxa66x1p8l27aklw")
|
||||
("blendbrush" "1wh88fshsy492kjvadql2ik1q5pqgcj84jz0hc93ngag8xibxhfi")
|
||||
("caustics" "0pc5bnd4fmxh06cm3h8045wgiy894f9x5a943n28gymdyql7q4f6")
|
||||
("crosshairs" "1w9acqhxw5nm690862msl5jjbk8qlizxm1vv7p95lgm7q7pg0yxx")
|
||||
("elyvisions" "04q31lp5jm8b9crf81s6k1jvrn90i1ay3s6vk103iv8g4amsfhdx")
|
||||
("fonts" "1rsfk2d9xk0aaazvrcxk4z5n2cnys7pixadh521mv7zrxbx2d95x")
|
||||
("freezurbern" "0b2xg5x79yxanr30dhw3zr6dsc6x9w7v7aghbh9kp292j31l280m")
|
||||
("john" "07pgjg1rxl3bmwriy2yl3g63nnryjws8jl0ry1cza3p9wd59f8rz")
|
||||
("jojo" "0lkzd5pwfqan1gaaz22r5iz4z2nq8dkzycddwa0cxavmq8qmj281")
|
||||
("jwin" "0mnyp1inhabw56mw5wkhfd4k6z0lvyhr6cjj6hnj3bz2dip2y2zm")
|
||||
("luckystrike" "1d89xnvahmzlgm0bjh3zhf02vxx1q16b70x2cihbl05dic1v75pr")
|
||||
("maps" "19gy8kl7w2llsklym32hnlnd05z2dhq5dhdxhq5ss5na67skv5by")
|
||||
("mayhem" "1si2gnsf732ml8ygkhg27ckvic9wafqmkgq0ab1ifpfpy606sa8d")
|
||||
("mikeplus64" "0l48czyglbc0d4ack8xz9imarb6r4l29krq0mf3ld7yrxbc296vr")
|
||||
("misc" "0fri1l3i1s1pzvr7aah4a7d9h2i877c21x184z80v4jpqv4228f3")
|
||||
("nobiax" "1jv2yv2qj9qbxhaj1nd70v5142dpg074gkkh3bw2anchi8pzyhs8")
|
||||
("particles" "0gwj6m5197gpwddqb3pwlkaiafgfszqysaz2h1bx60qzh5crgsf9")
|
||||
("philipk" "0ngccscmvlgc2z96vira7phr87f65l4v7immbl697zmc5fda6k68")
|
||||
("projectiles" "1ig6dag5989rgwrhvmz7xz5q8gf5slgnda8h8zmiyhvrnal09hbp")
|
||||
("props" "0g3sgrlgmk9zrl67d9pa93hzb4xx3wwznfxa1h3wwilld0m7gzhx")
|
||||
("skyboxes" "0lvpzc741vkmy2rnra41ij91wq3pdl28xamy6vapq61mf44xmmvj")
|
||||
("sounds" "0jmvvixcx7kv34sxjs4x7vqsyhir6l5av6b3lm8m8rsfi0sdvqml")
|
||||
("textures" "1yx01k9yn2v1k79sa68wa51qw1zk03b8irkvxyd14ygibkicvgnb")
|
||||
("torley" "1286srp05nfjban6ca124njyil70gr7bm6aqn5p0vz0xr00l4dw5")
|
||||
("trak" "1079fg2cbm95psxic3r63i94z3cnbf04wlid2hqnw308s9l9q36c")
|
||||
("ulukai" "0yd80ivn51ya60m4cg4bw13wxgijkjagfgskdphy9adgsaqq9n7b")
|
||||
("unnamed" "0l21dhw7kbav59p7ysn6dr2sqzjivwxafml4023yznlhxx5fic4m")
|
||||
("vanities" "1aqi32lf7y64fv1y00mpixckjr9wj8p1prgyxjiv7s3hf5q7n2b3")
|
||||
("vegetation" "0253fdn5sxywrjb79krhvq2884almxpysn6dn0hi6ylpjzl78zrn")
|
||||
("weapons" "0y2zsx6g6k9izshgix9id3y01hsisd88mp5zrlm5x9v8y0sf6kf8")
|
||||
("wicked" "0ib0325dn6vzpx3p4cr6bhg9qhj8c5s20xyzy88xjc3y2pazbdvx"))))
|
||||
(package
|
||||
(name "red-eclipse")
|
||||
(version "1.5.5")
|
||||
(version "1.5.6")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/red-eclipse/base"
|
||||
|
|
@ -2201,7 +2201,7 @@ http://lavachat.symlynx.com/unix/")
|
|||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0xl3655876i8j5nixy0yp73s0yw9nwysj68fyhqs2agmvshryy96"))))
|
||||
"1sv3xhng18sl655sd46lpmqbqz32h32s7nwz68bdr9z9w3iwkf66"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; no check target
|
||||
|
|
|
|||
|
|
@ -1614,7 +1614,7 @@ Hints specification (EWMH).")
|
|||
(sha256
|
||||
(base32
|
||||
"1s3dxvdwzmppsp2dfg90rccilf4hknhwjdy7lazr9sys58zchyx0"))))
|
||||
(build-system gnu-build-system)
|
||||
(build-system glib-or-gtk-build-system)
|
||||
(arguments
|
||||
`(;; The gnumeric developers don't worry much about failing tests.
|
||||
;; See https://bugzilla.gnome.org/show_bug.cgi?id=732387
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@
|
|||
(define-public windowmaker
|
||||
(package
|
||||
(name "windowmaker")
|
||||
(version "0.95.6")
|
||||
(version "0.95.7")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -43,7 +43,7 @@
|
|||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1i3dw1yagsa3rs9x2na2ynqlgmbahayws0kz4vl00fla6550nns3"))))
|
||||
"1acph0nq6fsb452sl7j7a7kcc87zqqaw7qms1p8ijar19dn4hbc4"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:phases (alist-cons-before
|
||||
|
|
|
|||
|
|
@ -292,7 +292,7 @@ developers consider to have good quality code and correct functionality.")
|
|||
;; vo-amrwbenc, vo-aacenc, bs2b, chromaprint, directfb, daala, libdts,
|
||||
;; faac, flite, libgsm, libde265, libmms, libmimic, mjpegtools,
|
||||
;; mpeg2enc, libofa, opencv, openh264, openni2, libtimemmgr, wildmidi,
|
||||
;; openspc, gme, sbc, schroedinger, zbar, librtmp, spandsp, x265
|
||||
;; openspc, gme, sbc, schroedinger, zbar, librtmp, spandsp
|
||||
`(("bluez" ,bluez)
|
||||
("curl" ,curl)
|
||||
("faad2" ,faad2)
|
||||
|
|
@ -328,6 +328,7 @@ developers consider to have good quality code and correct functionality.")
|
|||
;("qtdeclarative" ,qtdeclarative)
|
||||
;("qtx11extras" ,qtx11extras)
|
||||
("soundtouch" ,soundtouch)
|
||||
("x265" ,x265)
|
||||
("wayland" ,wayland)))
|
||||
(home-page "http://gstreamer.freedesktop.org/")
|
||||
(synopsis "Plugins for the GStreamer multimedia library")
|
||||
|
|
|
|||
|
|
@ -566,7 +566,7 @@ is part of the GNOME accessibility project.")
|
|||
(define-public gtk+-2
|
||||
(package
|
||||
(name "gtk+")
|
||||
(version "2.24.30")
|
||||
(version "2.24.31")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://gnome/sources/" name "/"
|
||||
|
|
@ -574,7 +574,7 @@ is part of the GNOME accessibility project.")
|
|||
name "-" version ".tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0l6aqk86aw5w132ygy6hv6nlxvd1h6xg7c85qbm60p6mnv1ww58d"))
|
||||
"0n26jm09n03nqbd00d2ij63xrby3vik56sk5yj6w1vy768kr5hb8"))
|
||||
(patches (search-patches "gtk2-respect-GUIX_GTK2_PATH.patch"
|
||||
"gtk2-respect-GUIX_GTK2_IM_MODULE_FILE.patch"
|
||||
"gtk2-theme-paths.patch"))))
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@
|
|||
;;; Copyright © 2016 Eraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2016 Alex Kost <alezost@gmail.com>
|
||||
;;; Copyright © 2016 Adonay "adfeno" Felipe Nogueira <https://libreplanet.org/wiki/User:Adfeno> <adfeno@openmailbox.org>
|
||||
;;; Copyright © 2016 Amirouche <amirouche@hypermove.net>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -1292,4 +1293,84 @@ is no support for parsing block and inline level HTML.")
|
|||
(define-public guile2.2-commonmark
|
||||
(package-for-guile-2.2 guile-commonmark))
|
||||
|
||||
(define-public guile-bytestructures
|
||||
(package
|
||||
(name "guile-bytestructures")
|
||||
(version "20160726.53127f6")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/TaylanUB/scheme-bytestructures")
|
||||
(commit "53127f608caf64b34fa41c389b2743b546fbe9da")))
|
||||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"0l4nx1vp9fkrgrgwjiycj7nx6wfjfd39rqamv4pmq7issi8mrywq"))))
|
||||
(build-system trivial-build-system)
|
||||
(arguments
|
||||
`(#:modules ((guix build utils))
|
||||
#:builder
|
||||
(begin
|
||||
(use-modules (guix build utils)
|
||||
(ice-9 match)
|
||||
(ice-9 popen)
|
||||
(ice-9 rdelim))
|
||||
(let* ((out (assoc-ref %outputs "out"))
|
||||
(guile (assoc-ref %build-inputs "guile"))
|
||||
(effective (read-line
|
||||
(open-pipe* OPEN_READ
|
||||
(string-append guile "/bin/guile")
|
||||
"-c" "(display (effective-version))")))
|
||||
(module-dir (string-append out "/share/guile/site/"
|
||||
effective))
|
||||
(source (assoc-ref %build-inputs "source"))
|
||||
(doc (string-append out "/share/doc/scheme-bytestructures"))
|
||||
(scm-files (filter (lambda (path)
|
||||
(not (string-prefix? "bytestructures/r7" path)))
|
||||
(with-directory-excursion source
|
||||
(find-files "bytestructures" "\\.scm$"))))
|
||||
(guild (string-append (assoc-ref %build-inputs "guile")
|
||||
"/bin/guild")))
|
||||
;; Make installation directories.
|
||||
(mkdir-p doc)
|
||||
|
||||
;; Compile .scm files and install.
|
||||
(chdir source)
|
||||
(setenv "GUILE_AUTO_COMPILE" "0")
|
||||
(for-each (lambda (file)
|
||||
(let* ((dest-file (string-append module-dir "/"
|
||||
file))
|
||||
(go-file (string-append module-dir "/"
|
||||
(substring file 0
|
||||
(string-rindex file #\.))
|
||||
".go")))
|
||||
;; Install source module.
|
||||
(mkdir-p (dirname dest-file))
|
||||
(copy-file file dest-file)
|
||||
|
||||
;; Install compiled module.
|
||||
(mkdir-p (dirname go-file))
|
||||
(unless (zero? (system* guild "compile"
|
||||
"-L" source
|
||||
"-o" go-file
|
||||
file))
|
||||
(error (format #f "Failed to compile ~s to ~s!"
|
||||
file go-file)))))
|
||||
scm-files)
|
||||
|
||||
;; Also copy over the README.
|
||||
(install-file "README.md" doc)
|
||||
#t))))
|
||||
(inputs
|
||||
`(("guile" ,guile-2.0)))
|
||||
(home-page "https://github.com/TaylanUB/scheme-bytestructures")
|
||||
(synopsis "Structured access to bytevector contents for Guile")
|
||||
(description
|
||||
"Guile bytestructures offers a system imitating the type system
|
||||
of the C programming language, to be used on bytevectors. C's type
|
||||
system works on raw memory, and Guile works on bytevectors which are
|
||||
an abstraction over raw memory. It's also more powerful than the C
|
||||
type system, elevating types to first-class status.")
|
||||
(license gpl3+)))
|
||||
|
||||
;;; guile.scm ends here
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@
|
|||
;;; Copyright © 2014 Kevin Lemonnier <lemonnierk@ulrar.net>
|
||||
;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2016 ng0 <ngillmann@runbox.com>
|
||||
;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -139,14 +139,14 @@ SILC and ICB protocols via plugins.")
|
|||
(define-public weechat
|
||||
(package
|
||||
(name "weechat")
|
||||
(version "1.5")
|
||||
(version "1.6")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "http://weechat.org/files/src/weechat-"
|
||||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0w87w4wy61x705ama8h36z9mgdj2gmmzdfrsxvwyh2m2as2max1i"))
|
||||
"0lyqrymdjdvkzg8510l46c4zw8mjagnmri2i6m9y9qz0c1sfaq9h"))
|
||||
(patches (search-patches "weechat-python.patch"))))
|
||||
(build-system gnu-build-system)
|
||||
(native-inputs `(("autoconf" ,autoconf)
|
||||
|
|
|
|||
|
|
@ -335,13 +335,10 @@ It has been modified to remove all non-free binary blobs.")
|
|||
#:configuration-file kernel-config))
|
||||
|
||||
(define-public linux-libre-4.1
|
||||
(make-linux-libre "4.1.34"
|
||||
"0dajsb363p9lgga22ml8gp9k9lxd8mvrzxk9y3h9c6hpzfcmqdqr"
|
||||
(make-linux-libre "4.1.35"
|
||||
"05zvrld1digqwf9kqf5pxx0mxqmwpr5kamhnks6y4yfy7x7jynyk"
|
||||
%intel-compatible-systems
|
||||
#:configuration-file kernel-config
|
||||
#:patches (list %boot-logo-patch
|
||||
(search-patch
|
||||
"linux-libre-4.1-CVE-2016-5195.patch"))))
|
||||
#:configuration-file kernel-config))
|
||||
|
||||
;; Avoid rebuilding kernel variants when there is a minor version bump.
|
||||
(define %linux-libre-version "4.8.4")
|
||||
|
|
|
|||
|
|
@ -0,0 +1,58 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
||||
;;; under the terms of the GNU General Public License as published by
|
||||
;;; the Free Software Foundation; either version 3 of the License, or (at
|
||||
;;; your option) any later version.
|
||||
;;;
|
||||
;;; GNU Guix is distributed in the hope that it will be useful, but
|
||||
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
;;; GNU General Public License for more details.
|
||||
;;;
|
||||
;;; You should have received a copy of the GNU General Public License
|
||||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
(define-module (gnu packages lolcode)
|
||||
#:use-module (gnu packages)
|
||||
#:use-module (gnu packages python)
|
||||
#:use-module (gnu packages readline)
|
||||
#:use-module (guix build-system cmake)
|
||||
#:use-module (guix download)
|
||||
#:use-module ((guix licenses) #:prefix license:)
|
||||
#:use-module (guix packages))
|
||||
|
||||
(define-public lci
|
||||
(package
|
||||
(name "lci")
|
||||
(version "0.11.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/justinmeza/lci/archive/v"
|
||||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1li7ikcrs7wqah7gqkirg0k61n6pm12w7pydin966x1sdn9na46b"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))))
|
||||
(build-system cmake-build-system)
|
||||
(inputs
|
||||
`(("readline" ,readline)))
|
||||
(native-inputs
|
||||
`(("python-2" ,python-2))) ; for the tests
|
||||
(synopsis "LOLCODE interpreter written in C")
|
||||
(description
|
||||
"@code{lci} is a LOLCODE interpreter written in C and is designed to be
|
||||
correct, portable, fast, and precisely documented.
|
||||
@enumerate
|
||||
@item correct: Every effort has been made to test lci's conformance to the
|
||||
LOLCODE language specification. Unit tests come packaged with the lci source code.
|
||||
@item portable: lci follows the widely ported ANSI C specification allowing it
|
||||
to compile on a broad range of systems.
|
||||
@item fast: Much effort has gone into producing simple and efficient code
|
||||
whenever possible to the extent that the above points are not compromized.
|
||||
@end enumerate")
|
||||
(home-page "http://lolcode.org/")
|
||||
(license license:gpl3+)))
|
||||
|
|
@ -19,6 +19,7 @@
|
|||
;;; Copyright © 2016 Clément Lassieur <clement@lassieur.org>
|
||||
;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net>
|
||||
;;; Copyright © 2016 John Darrington <jmd@gnu.org>
|
||||
;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -47,6 +48,7 @@
|
|||
#:use-module (gnu packages databases)
|
||||
#:use-module (gnu packages dejagnu)
|
||||
#:use-module (gnu packages dns)
|
||||
#:use-module (gnu packages documentation)
|
||||
#:use-module (gnu packages emacs)
|
||||
#:use-module (gnu packages enchant)
|
||||
#:use-module (gnu packages ghostscript)
|
||||
|
|
@ -319,6 +321,9 @@ and corrections. It is based on a Bayesian filter.")
|
|||
(base32
|
||||
"0smxh5ag3cbn92kp49jq950j5m2pivs9kr04prpd1lw62hy7gnhr"))))
|
||||
(build-system python-build-system)
|
||||
(native-inputs
|
||||
`(("asciidoc" ,asciidoc)
|
||||
("libxslt" ,libxslt))) ; for xsltproc
|
||||
(inputs `(("python2-pysqlite" ,python2-pysqlite)
|
||||
("python2-six" ,python2-six)))
|
||||
(arguments
|
||||
|
|
@ -328,8 +333,21 @@ and corrections. It is based on a Bayesian filter.")
|
|||
#:tests? #f
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'install 'wrap-binary
|
||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
(add-after 'build 'build-documentation
|
||||
(lambda _
|
||||
(substitute* "docs/Makefile"
|
||||
;; Prevent xmllint and xsltproc from downloading a DTD file.
|
||||
(("a2x -v") "a2x --no-xmllint --xsltproc-opts=--nonet -v"))
|
||||
(zero? (system* "make" "-C" "docs" "man"))))
|
||||
(add-after 'install 'install-documentation
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let* ((out (assoc-ref outputs "out"))
|
||||
(man (string-append out "/share/man")))
|
||||
(install-file "docs/offlineimap.1" (string-append man "/man1"))
|
||||
(install-file "docs/offlineimapui.7" (string-append man "/man7"))
|
||||
#t)))
|
||||
(add-after 'install-documentation 'wrap-binary
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let* ((out (assoc-ref outputs "out"))
|
||||
(bin (string-append out "/bin/offlineimap")))
|
||||
(wrap-program bin
|
||||
|
|
@ -501,18 +519,14 @@ invoking @command{notifymuch} from the post-new hook.")
|
|||
(define-public notmuch
|
||||
(package
|
||||
(name "notmuch")
|
||||
(version "0.23")
|
||||
(version "0.23.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://notmuchmail.org/releases/notmuch-"
|
||||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1f51l34rdhjf8lvafrwybkxdsdwx8k9397m7qxd8rdg2irjmpry5"))
|
||||
(patches
|
||||
;; Remove this for the next release. See this thread for context:
|
||||
;; https://notmuchmail.org/pipermail/notmuch/2016/023227.html
|
||||
(search-patches "notmuch-emacs-25-compatibility-fix.patch"))))
|
||||
"106ijsnilqf8760z4cq99rqzjsvyaw86d0lgnzz7v95gm4d2l0g8"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:make-flags (list "V=1") ; Verbose test output.
|
||||
|
|
@ -1618,7 +1632,7 @@ some additional standard extensions. It allows ordinary machines to exchange
|
|||
e-mails with other systems speaking the SMTP protocol.")
|
||||
(home-page "https://www.opensmtpd.org")
|
||||
(license (list bsd-2 bsd-3 bsd-4 (non-copyleft "file://COPYING")
|
||||
public-domain isc openssl))))
|
||||
public-domain isc license:openssl))))
|
||||
|
||||
(define-public opensmtpd-extras
|
||||
(package
|
||||
|
|
@ -1681,8 +1695,8 @@ e-mails with other systems speaking the SMTP protocol.")
|
|||
(assoc-ref %build-inputs "python-2"))
|
||||
(string-append "--with-lua="
|
||||
(assoc-ref %build-inputs "lua")))))
|
||||
(license (list bsd-2 bsd-3 bsd-4 non-copyleft
|
||||
public-domain isc openssl))
|
||||
(license (list bsd-2 bsd-3 bsd-4
|
||||
public-domain isc license:openssl))
|
||||
(synopsis "Extra tables, filters, and various other addons for OpenSMTPD")
|
||||
(description
|
||||
"This package provides extra tables, filters, and various other addons
|
||||
|
|
|
|||
|
|
@ -113,6 +113,47 @@ interactive dialogs to guide them.")
|
|||
(license license:gpl3+)
|
||||
(home-page "http://www.gnu.org/software/c-graph/")))
|
||||
|
||||
(define-public coda
|
||||
(package
|
||||
(name "coda")
|
||||
(version "2.17.3")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/stcorp/coda/releases/download/"
|
||||
version "/coda-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h"))
|
||||
(patches (search-patches "coda-use-system-libs.patch"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
;; Make sure we don't use the bundled software.
|
||||
'(for-each (lambda (d)
|
||||
(delete-file-recursively (string-append "libcoda/" d)))
|
||||
'("zlib" "pcre" "expat")))))
|
||||
(native-inputs
|
||||
`(("fortran" ,gfortran)
|
||||
("python" ,python)
|
||||
("python-numpy" ,python-numpy)))
|
||||
(inputs
|
||||
`(("zlib" ,zlib)
|
||||
("pcre" ,pcre)
|
||||
("expat" ,expat)
|
||||
("hdf4" ,hdf4-alt)
|
||||
("hdf5" ,hdf5)))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
|
||||
"LIBS= -lz -lpcre -lexpat")))
|
||||
(synopsis "A common interface to various earth observation data formats")
|
||||
(description
|
||||
"The Common Data Access toolbox (CODA) provides a set of interfaces for
|
||||
reading remote sensing data from earth observation data files. It consists of
|
||||
command line applications and interfaces to the C, Fortran, Python, and Java
|
||||
programming languages.")
|
||||
(home-page "https://stcorp.nl/coda")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public units
|
||||
(package
|
||||
(name "units")
|
||||
|
|
@ -544,6 +585,41 @@ extremely large and complex data collections.")
|
|||
(license (license:x11-style
|
||||
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
|
||||
|
||||
(define-public hdf-eos2
|
||||
(package
|
||||
(name "hdf-eos2")
|
||||
(version "19.1.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri "ftp://edhs1.gsfc.nasa.gov\
|
||||
/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
|
||||
(sha256
|
||||
(base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
|
||||
(patches (search-patches "hdf-eos2-remove-gctp.patch"
|
||||
"hdf-eos2-build-shared.patch"
|
||||
"hdf-eos2-fortrantests.patch"))))
|
||||
(build-system gnu-build-system)
|
||||
(native-inputs
|
||||
`(("gfortran" ,gfortran)))
|
||||
(inputs
|
||||
`(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
|
||||
("zlib" ,zlib)
|
||||
("libjpeg" ,libjpeg)
|
||||
("gctp" ,gctp)))
|
||||
(arguments
|
||||
`( #:configure-flags '("--enable-install-include" "--enable-shared"
|
||||
"CC=h4cc -Df2cFortran" "LIBS=-lgctp")
|
||||
#:parallel-tests? #f))
|
||||
(home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
|
||||
(synopsis "HDF4-based data format for NASA's Earth Observing System")
|
||||
(description "HDF-EOS2 is a software library built on HDF4 which supports
|
||||
the construction of data structures used in NASA's Earth Observing
|
||||
System (Grid, Point and Swath).")
|
||||
|
||||
;; Source files carry a permissive license header.
|
||||
(license (license:non-copyleft home-page))))
|
||||
|
||||
(define-public hdf-eos5
|
||||
(package
|
||||
(name "hdf-eos5")
|
||||
|
|
@ -1911,14 +1987,14 @@ full text searching.")
|
|||
(define-public armadillo
|
||||
(package
|
||||
(name "armadillo")
|
||||
(version "6.700.7")
|
||||
(version "7.500.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://sourceforge/arma/armadillo-"
|
||||
version ".tar.gz"))
|
||||
version ".tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0xbidcxrvbq33xf7iysg2nic2ai9a043psl33kiv6ifkk7p8hcra"))))
|
||||
"1x98d32cgxbzbbma2ak6c37wnbpq13xxyxyd6jjvflv748mzi9ks"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments `(#:tests? #f)) ;no test target
|
||||
(inputs
|
||||
|
|
@ -1939,14 +2015,14 @@ associated functions (eg. contiguous and non-contiguous submatrix views).")
|
|||
|
||||
(define-public armadillo-for-rcpparmadillo
|
||||
(package (inherit armadillo)
|
||||
(version "7.400.2")
|
||||
(version "7.500.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://sourceforge/arma/armadillo-"
|
||||
version ".tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0xmpnqhm9mwr1lssjyarj0cl8b4svbqv6z1xa1dxlwd2ly1srkg4"))))))
|
||||
"1x98d32cgxbzbbma2ak6c37wnbpq13xxyxyd6jjvflv748mzi9ks"))))))
|
||||
|
||||
(define-public muparser
|
||||
;; When switching download sites, muparser re-issued a 2.2.5 release with a
|
||||
|
|
|
|||
|
|
@ -452,7 +452,7 @@ was initially a fork of xmpppy, but is using non-blocking sockets.")
|
|||
(define-public gajim
|
||||
(package
|
||||
(name "gajim")
|
||||
(version "0.16.5")
|
||||
(version "0.16.6")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://gajim.org/downloads/"
|
||||
|
|
@ -460,17 +460,10 @@ was initially a fork of xmpppy, but is using non-blocking sockets.")
|
|||
"/gajim-" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32
|
||||
"14fhcqnkqygh91132dnf1idayj4r3iqbwb44sd3mxv20n6ribh55"))))
|
||||
"1p3qwzy07f0wkika9yigyiq167l2k6wn12flqa7x55z4ihbysmqk"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(;; The only check done by gajim-0.16.x is to check that the
|
||||
;; translations are up-to-date, and in 0.16.5 they are not, so
|
||||
;; "make check" fails. Therefore, we disable tests for now.
|
||||
;;
|
||||
;; XXX TODO Try re-enabling tests in gajim-0.16.6 or later.
|
||||
;;
|
||||
#:tests? #f
|
||||
#:phases
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'install 'wrap-program
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
|
|
@ -504,7 +497,7 @@ Among its features are: a tabbed chat window and single window modes; support
|
|||
for group chat (with Multi-User Chat protocol), invitation, chat to group chat
|
||||
transformation; audio and video conferences; file transfer; TLS, GPG and
|
||||
end-to-end encryption support; XML console.")
|
||||
(license license:gpl3+)))
|
||||
(license license:gpl3)))
|
||||
|
||||
(define-public prosody
|
||||
(package
|
||||
|
|
|
|||
|
|
@ -32,6 +32,7 @@
|
|||
(method url-fetch)
|
||||
(uri (string-append "http://www.musl-libc.org/releases/"
|
||||
name "-" version ".tar.gz"))
|
||||
(patches (search-patches "musl-CVE-2016-8859.patch"))
|
||||
(sha256
|
||||
(base32
|
||||
"1ymhxkskivzph0q34zadwfglc5gyahqajm7chqqn2zraxv3lgr4p"))))
|
||||
|
|
|
|||
|
|
@ -48,6 +48,7 @@
|
|||
#:use-module (gnu packages gettext)
|
||||
#:use-module (gnu packages gnupg)
|
||||
#:use-module (gnu packages gtk)
|
||||
#:use-module (gnu packages libidn)
|
||||
#:use-module (gnu packages linux)
|
||||
#:use-module (gnu packages lua)
|
||||
#:use-module (gnu packages mit-krb5)
|
||||
|
|
@ -424,6 +425,44 @@ and up to 1 Mbit/s downstream.")
|
|||
;; src/md5.[ch] is released under the zlib license
|
||||
(license (list license:isc license:zlib))))
|
||||
|
||||
(define-public whois
|
||||
(package
|
||||
(name "whois")
|
||||
(version "5.2.12")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://debian/pool/main/w/whois/"
|
||||
name "_" version ".tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1wfdyqi64l5x56j259jrrlbh19b7q7i6r83a8q8rjzcqp0kl0vdj"))))
|
||||
(build-system gnu-build-system)
|
||||
;; TODO: unbundle mkpasswd binary + its po files.
|
||||
(arguments
|
||||
`(#:tests? #f ; Does not exist
|
||||
#:make-flags (list "CC=gcc"
|
||||
(string-append "prefix=" (assoc-ref %outputs "out")))
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure) ; No configure
|
||||
(add-before 'build 'setenv
|
||||
(lambda _
|
||||
(setenv "HAVE_ICONV" "1")
|
||||
(setenv "HAVE_LIBIDN" "1"))))))
|
||||
(inputs
|
||||
`(("libidn" ,libidn)))
|
||||
(native-inputs
|
||||
`(("gettext" ,gnu-gettext)
|
||||
("perl" ,perl)))
|
||||
(synopsis "Improved whois client")
|
||||
(description "This whois client is intelligent and can
|
||||
automatically select the appropriate whois server for most queries.
|
||||
Because of historical reasons this also includes a tool called mkpasswd
|
||||
which can be used to encrypt a password with @code{crypt(3)}.")
|
||||
(home-page "https://github.com/rfc1036/whois")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public wireshark
|
||||
(package
|
||||
(name "wireshark")
|
||||
|
|
|
|||
|
|
@ -0,0 +1,46 @@
|
|||
Remove dependencies on bundled zlib, pcre and expat.
|
||||
|
||||
diff --git a/Makefile.in b/Makefile.in
|
||||
index 4360a26..80f9f59 100644
|
||||
--- a/Makefile.in
|
||||
+++ b/Makefile.in
|
||||
@@ -210,8 +210,7 @@ coda_matlab_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
|
||||
@BUILD_MATLAB_TRUE@@SUBPACKAGE_MODE_FALSE@ -rpath \
|
||||
@BUILD_MATLAB_TRUE@@SUBPACKAGE_MODE_FALSE@ $(matlabmexexecdir)
|
||||
am__DEPENDENCIES_1 =
|
||||
-libcoda_la_DEPENDENCIES = @LTLIBOBJS@ libexpat_internal.la \
|
||||
- libpcre_internal.la libz_internal.la $(am__DEPENDENCIES_1) \
|
||||
+libcoda_la_DEPENDENCIES = @LTLIBOBJS@ $(am__DEPENDENCIES_1) \
|
||||
$(am__DEPENDENCIES_1)
|
||||
am__libcoda_la_SOURCES_DIST = libcoda/coda-ascbin-cursor.c \
|
||||
libcoda/coda-ascbin.h libcoda/coda-ascii-cursor.c \
|
||||
@@ -306,8 +305,7 @@ libcoda_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
|
||||
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
|
||||
$(libcoda_la_LDFLAGS) $(LDFLAGS) -o $@
|
||||
@SUBPACKAGE_MODE_FALSE@am_libcoda_la_rpath = -rpath $(libdir)
|
||||
-am__DEPENDENCIES_2 = @LTLIBOBJS@ libexpat_internal.la \
|
||||
- libpcre_internal.la libz_internal.la $(am__DEPENDENCIES_1) \
|
||||
+am__DEPENDENCIES_2 = @LTLIBOBJS@ $(am__DEPENDENCIES_1) \
|
||||
$(am__DEPENDENCIES_1)
|
||||
libcoda_internal_la_DEPENDENCIES = $(am__DEPENDENCIES_2)
|
||||
am__libcoda_internal_la_SOURCES_DIST = libcoda/coda-ascbin-cursor.c \
|
||||
@@ -898,8 +896,8 @@ INSTALL_DATA_HOOK_TARGETS = $(am__append_1)
|
||||
UNINSTALL_HOOK_TARGETS =
|
||||
CLEAN_LOCAL_TARGETS = $(am__append_11)
|
||||
ALL_LOCAL_TARGETS =
|
||||
-@SUBPACKAGE_MODE_FALSE@noinst_LTLIBRARIES = libcoda_internal.la libexpat_internal.la libpcre_internal.la libz_internal.la
|
||||
-@SUBPACKAGE_MODE_TRUE@noinst_LTLIBRARIES = libcoda_internal.la libexpat_internal.la libpcre_internal.la libz_internal.la
|
||||
+@SUBPACKAGE_MODE_FALSE@noinst_LTLIBRARIES = libcoda_internal.la
|
||||
+@SUBPACKAGE_MODE_TRUE@noinst_LTLIBRARIES = libcoda_internal.la
|
||||
|
||||
# libraries (+ related files)
|
||||
@SUBPACKAGE_MODE_FALSE@lib_LTLIBRARIES = libcoda.la
|
||||
@@ -1048,7 +1046,7 @@ libcoda_hdf5_files = \
|
||||
|
||||
libcoda_la_CPPFLAGS = -Ilibcoda/expat -I$(srcdir)/libcoda/expat -Ilibcoda/pcre -I$(srcdir)/libcoda/pcre -Ilibcoda/zlib -I$(srcdir)/libcoda/zlib $(AM_CPPFLAGS)
|
||||
libcoda_la_LDFLAGS = -no-undefined -version-info $(LIBCODA_CURRENT):$(LIBCODA_REVISION):$(LIBCODA_AGE)
|
||||
-libcoda_la_LIBADD = @LTLIBOBJS@ libexpat_internal.la libpcre_internal.la libz_internal.la $(HDF4LIBS) $(HDF5LIBS)
|
||||
+libcoda_la_LIBADD = @LTLIBOBJS@ $(HDF4LIBS) $(HDF5LIBS)
|
||||
libcoda_internal_la_SOURCES = libcoda/coda-ascbin-cursor.c \
|
||||
libcoda/coda-ascbin.h libcoda/coda-ascii-cursor.c \
|
||||
libcoda/coda-ascii-internal.h libcoda/coda-ascii.c \
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
Changes necessary for shared library linking to succeed.
|
||||
|
||||
diff --git a/src/Makefile.in b/src/Makefile.in
|
||||
index 9534473..12411bf 100644
|
||||
--- a/src/Makefile.in
|
||||
+++ b/src/Makefile.in
|
||||
@@ -73,7 +73,7 @@ LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) \
|
||||
$(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \
|
||||
$(AM_CFLAGS) $(CFLAGS)
|
||||
CCLD = $(CC)
|
||||
-LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
|
||||
+LINK = HDF4_USE_SHLIB=yes $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
|
||||
$(AM_LDFLAGS) $(LDFLAGS) -o $@
|
||||
SOURCES = $(libhdfeos_la_SOURCES)
|
||||
DIST_SOURCES = $(libhdfeos_la_SOURCES)
|
||||
@@ -125,8 +125,6 @@ INSTALL_PROGRAM = @INSTALL_PROGRAM@
|
||||
INSTALL_SCRIPT = @INSTALL_SCRIPT@
|
||||
INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
|
||||
|
||||
-# Set LDFLAGS to alow the HDF-EOS library to use extern variables from HDF4
|
||||
-LDFLAGS = -Wl,-single_module
|
||||
LIBOBJS = @LIBOBJS@
|
||||
LIBS = @LIBS@
|
||||
LIBTOOL = @LIBTOOL@
|
||||
|
||||
|
|
@ -0,0 +1,329 @@
|
|||
Fix multi-line string formatting in fortran test programs (reported upstream).
|
||||
|
||||
diff --git a/samples/appendfield.f b/samples/appendfield.f
|
||||
index 42c4b6b..58257f7 100644
|
||||
--- a/samples/appendfield.f
|
||||
+++ b/samples/appendfield.f
|
||||
@@ -22,8 +22,8 @@ c
|
||||
inarray(i) = i
|
||||
enddo
|
||||
|
||||
- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer_o
|
||||
- 1f_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
swid = swattach(swfid, "Swath1")
|
||||
|
||||
|
||||
diff --git a/samples/definefields.f b/samples/definefields.f
|
||||
index 89859e4..f3b3497 100644
|
||||
--- a/samples/definefields.f
|
||||
+++ b/samples/definefields.f
|
||||
@@ -24,8 +24,8 @@ c DFACC_RDWR accesscode in the open statement. The SWopen
|
||||
c routine returns the swath fileid, swfid, which is used to
|
||||
c identify the file in subsequent routines.
|
||||
|
||||
- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer
|
||||
- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
|
||||
|
||||
c
|
||||
diff --git a/samples/definegdflds.f b/samples/definegdflds.f
|
||||
index 177422e..1b7fcf6 100644
|
||||
--- a/samples/definegdflds.f
|
||||
+++ b/samples/definegdflds.f
|
||||
@@ -21,8 +21,8 @@
|
||||
fillval1=-7.0
|
||||
fillval2=-9999.0
|
||||
|
||||
- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_
|
||||
- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
|
||||
|
||||
gdid1 = gdattach(gdfid, "UTMGrid")
|
||||
diff --git a/samples/definelevels.f b/samples/definelevels.f
|
||||
index 2496d5f..64b2842 100644
|
||||
--- a/samples/definelevels.f
|
||||
+++ b/samples/definelevels.f
|
||||
@@ -32,8 +32,8 @@ c DFACC_RDWR access code in the open statement. The ptopen
|
||||
c routine returns the point fileid, ptfid, which is used to
|
||||
c identify the file in subsequent routines.
|
||||
|
||||
- ptfid = ptopen("PointFile_created_with_hadeos_sample_file_writer
|
||||
- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ ptfid = ptopen("PointFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1 "r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
|
||||
|
||||
c
|
||||
diff --git a/samples/inquiregrid.f b/samples/inquiregrid.f
|
||||
index 8110461..8ce71e4 100644
|
||||
--- a/samples/inquiregrid.f
|
||||
+++ b/samples/inquiregrid.f
|
||||
@@ -18,8 +18,8 @@
|
||||
|
||||
|
||||
|
||||
- gdfid = gdopen('GridFile_created_with_hadeos_sample_file_writer_
|
||||
- 1of_HDFEOS2_version_219_or_higher_release.hdf', DFACC_READ)
|
||||
+ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
|
||||
|
||||
if (gdfid .ne. -1) then
|
||||
diff --git a/samples/inquireswath.f b/samples/inquireswath.f
|
||||
index 899ee59..78c292b 100644
|
||||
--- a/samples/inquireswath.f
|
||||
+++ b/samples/inquireswath.f
|
||||
@@ -24,8 +24,8 @@ c
|
||||
c Open the Swath File for read only access
|
||||
c
|
||||
|
||||
- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer
|
||||
- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
+ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
|
||||
|
||||
if (swfid .NE. -1) then
|
||||
diff --git a/samples/readdimscalegrid.f b/samples/readdimscalegrid.f
|
||||
index fed5540..a0bb48a 100644
|
||||
--- a/samples/readdimscalegrid.f
|
||||
+++ b/samples/readdimscalegrid.f
|
||||
@@ -34,8 +34,8 @@
|
||||
! * id, gdfid, which is used to identify the file in subsequent routines.
|
||||
! */
|
||||
|
||||
- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_
|
||||
- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
|
||||
! /*
|
||||
! * If the grid file cannot be found, gdopen will return -1 for the file
|
||||
diff --git a/samples/readdimscaleswath.f b/samples/readdimscaleswath.f
|
||||
index 97b6264..1b61624 100644
|
||||
--- a/samples/readdimscaleswath.f
|
||||
+++ b/samples/readdimscaleswath.f
|
||||
@@ -33,8 +33,8 @@
|
||||
! * id, swfid, which is used to identify the file in subsequent routines.
|
||||
! */
|
||||
|
||||
- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer
|
||||
- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
|
||||
! /*
|
||||
! * If the swath file cannot be found, swopen will return -1 for the file
|
||||
diff --git a/samples/readfields.f b/samples/readfields.f
|
||||
index 873b30a..29d42f0 100644
|
||||
--- a/samples/readfields.f
|
||||
+++ b/samples/readfields.f
|
||||
@@ -21,8 +21,8 @@ c
|
||||
c Open the HDF swath file, "SwathFile.hdf"
|
||||
c
|
||||
|
||||
- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer
|
||||
- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
+ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
|
||||
|
||||
if (swfid .NE. -1) then
|
||||
diff --git a/samples/readgdflds.f b/samples/readgdflds.f
|
||||
index e5fe85f..ff2bd86 100644
|
||||
--- a/samples/readgdflds.f
|
||||
+++ b/samples/readgdflds.f
|
||||
@@ -9,8 +9,8 @@
|
||||
integer DFNT_FLOAT32
|
||||
parameter (DFNT_FLOAT32=5)
|
||||
|
||||
- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_
|
||||
- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
|
||||
if (gdfid .ne. -1) then
|
||||
|
||||
diff --git a/samples/readlevels.f b/samples/readlevels.f
|
||||
index a7fd033..f349398 100644
|
||||
--- a/samples/readlevels.f
|
||||
+++ b/samples/readlevels.f
|
||||
@@ -36,8 +36,8 @@ c
|
||||
c Open the HDF swath file, "PointFile.hdf".
|
||||
c
|
||||
|
||||
- ptfid = ptopen("PointFile_created_with_hadeos_sample_file_writer
|
||||
- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
+ ptfid = ptopen("PointFile_created_with_hadeos_sample_file_write"//
|
||||
+ + "r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
|
||||
c
|
||||
c Read Simple Point
|
||||
@@ -47,6 +47,8 @@ c
|
||||
status = ptlevinfo(ptid, 0, fldlist, fldtype, fldorder)
|
||||
n = ptnrecs(ptid, 0)
|
||||
|
||||
+ write(*,*) n
|
||||
+
|
||||
do 5 i=1,n
|
||||
recs(i) = i - 1
|
||||
5 continue
|
||||
diff --git a/samples/setupgrid.f b/samples/setupgrid.f
|
||||
index be5408c..cf4bd04 100644
|
||||
--- a/samples/setupgrid.f
|
||||
+++ b/samples/setupgrid.f
|
||||
@@ -34,8 +34,8 @@ c code in the open statement. The GDopen routine returns the grid
|
||||
c file id, gdfid, which is used to identify the file in subsequent
|
||||
c routines in the library.
|
||||
c
|
||||
- gdfid = gdopen('GridFile_created_with_hadeos_sample_file_writer_of
|
||||
- 1_HDFEOS2_version_219_or_higher_release.hdf',DFACC_CREATE)
|
||||
+ gdfid = gdopen('GridFile_created_with_hadeos_sample_file_writer_"//
|
||||
+ 1"of_HDFEOS2_version_219_or_higher_release.hdf',DFACC_CREATE)
|
||||
|
||||
c
|
||||
c Create UTM Grid
|
||||
diff --git a/samples/setupswath.f b/samples/setupswath.f
|
||||
index d0289d6..fbaa0bb 100644
|
||||
--- a/samples/setupswath.f
|
||||
+++ b/samples/setupswath.f
|
||||
@@ -22,8 +22,8 @@ c code in the open statement. The SWopen routine returns the swath
|
||||
c file id, swfid, which is used to identify the file in subsequent
|
||||
c routines in the library.
|
||||
c
|
||||
- swfid = swopen('SwathFile_created_with_hadeos_sample_file_writer_o
|
||||
- 1f_HDFEOS2_version_219_or_higher_release.hdf',DFACC_CREATE)
|
||||
+ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf",DFACC_CREATE)
|
||||
|
||||
c
|
||||
c The first of these, SWcreate, creates the swath, "Swath1", within the
|
||||
diff --git a/samples/subsetgrid.f b/samples/subsetgrid.f
|
||||
index c57e541..087e5b1 100644
|
||||
--- a/samples/subsetgrid.f
|
||||
+++ b/samples/subsetgrid.f
|
||||
@@ -22,8 +22,8 @@ c
|
||||
c Open the HDF grid file, "GridFile.hdf"
|
||||
c
|
||||
|
||||
- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_
|
||||
- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
+ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
|
||||
if (gdfid .NE. -1) then
|
||||
|
||||
diff --git a/samples/subsetpoint.f b/samples/subsetpoint.f
|
||||
index 9e72c5f..2e76d7d 100644
|
||||
--- a/samples/subsetpoint.f
|
||||
+++ b/samples/subsetpoint.f
|
||||
@@ -21,8 +21,8 @@ c
|
||||
c Open the HDF point file, "PointFile.hdf"
|
||||
c
|
||||
|
||||
- ptfid = ptopen("PointFile_created_with_hadeos_sample_file_writer
|
||||
- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
+ ptfid = ptopen("PointFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1 "r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
|
||||
if (ptfid .NE. -1) then
|
||||
|
||||
diff --git a/samples/subsetswath.f b/samples/subsetswath.f
|
||||
index dcee609..9af8a46 100644
|
||||
--- a/samples/subsetswath.f
|
||||
+++ b/samples/subsetswath.f
|
||||
@@ -28,8 +28,8 @@ c
|
||||
c Open the HDF swath file, "SwathFile.hdf"
|
||||
c
|
||||
|
||||
- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer
|
||||
- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
+ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_READ)
|
||||
|
||||
if (swfid .NE. -1) then
|
||||
|
||||
diff --git a/samples/writedimscalegrid.f b/samples/writedimscalegrid.f
|
||||
index 09688d8..42013fe 100644
|
||||
--- a/samples/writedimscalegrid.f
|
||||
+++ b/samples/writedimscalegrid.f
|
||||
@@ -29,8 +29,8 @@
|
||||
! * id, gdfid, which is used to identify the file in subsequent routines.
|
||||
! */
|
||||
|
||||
- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_
|
||||
- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
|
||||
! /*
|
||||
! * If the grid file cannot be found, gdopen will return -1 for the file
|
||||
diff --git a/samples/writedimscaleswath.f b/samples/writedimscaleswath.f
|
||||
index 1151671..1a911a6 100644
|
||||
--- a/samples/writedimscaleswath.f
|
||||
+++ b/samples/writedimscaleswath.f
|
||||
@@ -31,8 +31,8 @@
|
||||
! * id, swfid, which is used to identify the file in subsequent routines.
|
||||
! */
|
||||
|
||||
- swfid = swopen("SwathFile_created_with_hadeos_sample_file_write
|
||||
- 1r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
|
||||
! /*
|
||||
! * If the swath file cannot be found, swopen will return -1 for the file
|
||||
diff --git a/samples/writefields.f b/samples/writefields.f
|
||||
index a743661..862b96c 100644
|
||||
--- a/samples/writefields.f
|
||||
+++ b/samples/writefields.f
|
||||
@@ -31,8 +31,8 @@ c
|
||||
c Open the HDF swath file, "SwathFile.hdf"
|
||||
c
|
||||
|
||||
- swfid = swopen("SwathFile_created_with_hadeos_sample_file_writer
|
||||
- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ swfid = swopen("SwathFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
|
||||
|
||||
if (swfid .NE. -1) then
|
||||
diff --git a/samples/writegdflds.f b/samples/writegdflds.f
|
||||
index d1540b3..81aef75 100644
|
||||
--- a/samples/writegdflds.f
|
||||
+++ b/samples/writegdflds.f
|
||||
@@ -23,8 +23,8 @@
|
||||
enddo
|
||||
|
||||
|
||||
- gdfid = gdopen("GridFile_created_with_hadeos_sample_file_writer_
|
||||
- 1of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ gdfid = gdopen("GridFile_created_with_hadeos_sample_file_write"//
|
||||
+ 1"r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
|
||||
if (gdfid .ne. -1) then
|
||||
|
||||
diff --git a/samples/writelevels.f b/samples/writelevels.f
|
||||
index 88e7780..cb40c9e 100644
|
||||
--- a/samples/writelevels.f
|
||||
+++ b/samples/writelevels.f
|
||||
@@ -32,8 +32,8 @@ c
|
||||
c Open the HDF point file, "PointFile.hdf".
|
||||
c
|
||||
|
||||
- ptfid = ptopen("PointFile_created_with_hadeos_sample_file_writer
|
||||
- 1_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
+ ptfid = ptopen("PointFile_created_with_hadeos_sample_file_write"//
|
||||
+ + "r_of_HDFEOS2_version_219_or_higher_release.hdf", DFACC_RDWR)
|
||||
|
||||
|
||||
c
|
||||
--
|
||||
2.10.0
|
||||
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
Don't build the GCTP bundled with the source and link with the
|
||||
system's -lgctp instead. We also remove references to the
|
||||
"testdrivers" directory, which is not distributed together with the
|
||||
source, causing autoreconf to fail.
|
||||
|
||||
diff --git a/Makefile.in b/Makefile.in
|
||||
index d468af2..90428a7 100644
|
||||
--- a/Makefile.in
|
||||
+++ b/Makefile.in
|
||||
@@ -206,7 +206,7 @@ LIBGCTP = $(top_builddir)/gctp/src/libGctp.la
|
||||
@TESTDRIVERS_CONDITIONAL_TRUE@TESTDRIVERS = testdrivers
|
||||
@INSTALL_INCLUDE_CONDITIONAL_FALSE@INCLUDE =
|
||||
@INSTALL_INCLUDE_CONDITIONAL_TRUE@INCLUDE = include
|
||||
-SUBDIRS = gctp src $(INCLUDE) samples $(TESTDRIVERS)
|
||||
+SUBDIRS = src $(INCLUDE) samples $(TESTDRIVERS)
|
||||
all: all-recursive
|
||||
|
||||
.SUFFIXES:
|
||||
diff --git a/include/Makefile.in b/include/Makefile.in
|
||||
index 9938b23..afb7f40 100644
|
||||
--- a/include/Makefile.in
|
||||
+++ b/include/Makefile.in
|
||||
@@ -190,7 +190,7 @@ LIBGCTP = $(top_builddir)/gctp/src/libGctp.la
|
||||
# Boilerplate include
|
||||
|
||||
# Headers to install
|
||||
-include_HEADERS = HE2_config.h HdfEosDef.h HDFEOSVersion.h cfortHdf.h ease.h
|
||||
+include_HEADERS = HdfEosDef.h HDFEOSVersion.h cfortHdf.h ease.h
|
||||
all: HE2_config.h
|
||||
$(MAKE) $(AM_MAKEFLAGS) all-am
|
||||
|
||||
diff --git a/samples/Makefile.in b/samples/Makefile.in
|
||||
index 9da6e28..6a6186c 100644
|
||||
--- a/samples/Makefile.in
|
||||
+++ b/samples/Makefile.in
|
||||
@@ -108,7 +108,6 @@ AppendField_SOURCES = AppendField.c
|
||||
AppendField_OBJECTS = AppendField.$(OBJEXT)
|
||||
AppendField_LDADD = $(LDADD)
|
||||
am__DEPENDENCIES_1 = $(top_builddir)/src/libhdfeos.la
|
||||
-am__DEPENDENCIES_2 = $(top_builddir)/gctp/src/libGctp.la
|
||||
AppendField_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_2)
|
||||
DefineFields_SOURCES = DefineFields.c
|
||||
DefineFields_OBJECTS = DefineFields.$(OBJEXT)
|
||||
@@ -481,7 +480,7 @@ sharedstatedir = @sharedstatedir@
|
||||
sysconfdir = @sysconfdir@
|
||||
target_alias = @target_alias@
|
||||
LIBHDFEOS2 = $(top_builddir)/src/libhdfeos.la
|
||||
-LIBGCTP = $(top_builddir)/gctp/src/libGctp.la
|
||||
+LIBGCTP =
|
||||
|
||||
# Boilerplate definitions file
|
||||
|
||||
--
|
||||
2.10.0
|
||||
|
||||
|
|
@ -1,99 +0,0 @@
|
|||
Fix CVE-2016-5195, a.k.a. Dirty COW.
|
||||
Backported to linux-libre-4.1.x by Mark H Weaver <mhw@netris.org>.
|
||||
|
||||
From 18652320ea99913c95e7130d654be7f1da6b694f Mon Sep 17 00:00:00 2001
|
||||
From: Linus Torvalds <torvalds@linux-foundation.org>
|
||||
Date: Thu, 13 Oct 2016 13:07:36 -0700
|
||||
Subject: [PATCH] mm: remove gup_flags FOLL_WRITE games from __get_user_pages()
|
||||
|
||||
commit 19be0eaffa3ac7d8eb6784ad9bdbc7d67ed8e619 upstream.
|
||||
|
||||
This is an ancient bug that was actually attempted to be fixed once
|
||||
(badly) by me eleven years ago in commit 4ceb5db9757a ("Fix
|
||||
get_user_pages() race for write access") but that was then undone due to
|
||||
problems on s390 by commit f33ea7f404e5 ("fix get_user_pages bug").
|
||||
|
||||
In the meantime, the s390 situation has long been fixed, and we can now
|
||||
fix it by checking the pte_dirty() bit properly (and do it better). The
|
||||
s390 dirty bit was implemented in abf09bed3cce ("s390/mm: implement
|
||||
software dirty bits") which made it into v3.9. Earlier kernels will
|
||||
have to look at the page state itself.
|
||||
|
||||
Also, the VM has become more scalable, and what used a purely
|
||||
theoretical race back then has become easier to trigger.
|
||||
|
||||
To fix it, we introduce a new internal FOLL_COW flag to mark the "yes,
|
||||
we already did a COW" rather than play racy games with FOLL_WRITE that
|
||||
is very fundamental, and then use the pte dirty flag to validate that
|
||||
the FOLL_COW flag is still valid.
|
||||
|
||||
Reported-and-tested-by: Phil "not Paul" Oester <kernel@linuxace.com>
|
||||
Acked-by: Hugh Dickins <hughd@google.com>
|
||||
Reviewed-by: Michal Hocko <mhocko@suse.com>
|
||||
Cc: Andy Lutomirski <luto@kernel.org>
|
||||
Cc: Kees Cook <keescook@chromium.org>
|
||||
Cc: Oleg Nesterov <oleg@redhat.com>
|
||||
Cc: Willy Tarreau <w@1wt.eu>
|
||||
Cc: Nick Piggin <npiggin@gmail.com>
|
||||
Cc: Greg Thelen <gthelen@google.com>
|
||||
Signed-off-by: Linus Torvalds <torvalds@linux-foundation.org>
|
||||
Signed-off-by: Greg Kroah-Hartman <gregkh@linuxfoundation.org>
|
||||
---
|
||||
include/linux/mm.h | 1 +
|
||||
mm/gup.c | 14 ++++++++++++--
|
||||
2 files changed, 13 insertions(+), 2 deletions(-)
|
||||
|
||||
diff --git a/include/linux/mm.h b/include/linux/mm.h
|
||||
index 6b85ec6..7cadf0a 100644
|
||||
--- a/include/linux/mm.h
|
||||
+++ b/include/linux/mm.h
|
||||
@@ -2064,6 +2064,7 @@ static inline struct page *follow_page(struct vm_area_struct *vma,
|
||||
#define FOLL_NUMA 0x200 /* force NUMA hinting page fault */
|
||||
#define FOLL_MIGRATION 0x400 /* wait for page to replace migration entry */
|
||||
#define FOLL_TRIED 0x800 /* a retry, previous pass started an IO */
|
||||
+#define FOLL_COW 0x4000 /* internal GUP flag */
|
||||
|
||||
typedef int (*pte_fn_t)(pte_t *pte, pgtable_t token, unsigned long addr,
|
||||
void *data);
|
||||
diff --git a/mm/gup.c b/mm/gup.c
|
||||
index 6297f6b..e6de9e7 100644
|
||||
--- a/mm/gup.c
|
||||
+++ b/mm/gup.c
|
||||
@@ -32,6 +32,16 @@ static struct page *no_page_table(struct vm_area_struct *vma,
|
||||
return NULL;
|
||||
}
|
||||
|
||||
+/*
|
||||
+ * FOLL_FORCE can write to even unwritable pte's, but only
|
||||
+ * after we've gone through a COW cycle and they are dirty.
|
||||
+ */
|
||||
+static inline bool can_follow_write_pte(pte_t pte, unsigned int flags)
|
||||
+{
|
||||
+ return pte_write(pte) ||
|
||||
+ ((flags & FOLL_FORCE) && (flags & FOLL_COW) && pte_dirty(pte));
|
||||
+}
|
||||
+
|
||||
static struct page *follow_page_pte(struct vm_area_struct *vma,
|
||||
unsigned long address, pmd_t *pmd, unsigned int flags)
|
||||
{
|
||||
@@ -66,7 +76,7 @@ retry:
|
||||
}
|
||||
if ((flags & FOLL_NUMA) && pte_protnone(pte))
|
||||
goto no_page;
|
||||
- if ((flags & FOLL_WRITE) && !pte_write(pte)) {
|
||||
+ if ((flags & FOLL_WRITE) && !can_follow_write_pte(pte, flags)) {
|
||||
pte_unmap_unlock(ptep, ptl);
|
||||
return NULL;
|
||||
}
|
||||
@@ -315,7 +325,7 @@ static int faultin_page(struct task_struct *tsk, struct vm_area_struct *vma,
|
||||
* reCOWed by userspace write).
|
||||
*/
|
||||
if ((ret & VM_FAULT_WRITE) && !(vma->vm_flags & VM_WRITE))
|
||||
- *flags &= ~FOLL_WRITE;
|
||||
+ *flags |= FOLL_COW;
|
||||
return 0;
|
||||
}
|
||||
|
||||
--
|
||||
2.10.1
|
||||
|
||||
|
|
@ -0,0 +1,165 @@
|
|||
Fix CVE-2016-8674 (use-after-free in pdf_to_num()).
|
||||
|
||||
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-8674
|
||||
https://security-tracker.debian.org/tracker/CVE-2016-8674
|
||||
|
||||
Patch adapted from upstream source repository:
|
||||
http://git.ghostscript.com/?p=mupdf.git;h=1e03c06456d997435019fb3526fa2d4be7dbc6ec
|
||||
|
||||
diff --git a/include/mupdf/pdf/document.h b/include/mupdf/pdf/document.h
|
||||
index f8ef0cd..e8345b7 100644
|
||||
--- a/include/mupdf/pdf/document.h
|
||||
+++ b/include/mupdf/pdf/document.h
|
||||
@@ -258,6 +258,10 @@ struct pdf_document_s
|
||||
fz_font **type3_fonts;
|
||||
|
||||
pdf_resource_tables *resources;
|
||||
+
|
||||
+ int orphans_max;
|
||||
+ int orphans_count;
|
||||
+ pdf_obj **orphans;
|
||||
};
|
||||
|
||||
/*
|
||||
diff --git a/include/mupdf/pdf/object.h b/include/mupdf/pdf/object.h
|
||||
index 346a2f1..02d4119 100644
|
||||
--- a/include/mupdf/pdf/object.h
|
||||
+++ b/include/mupdf/pdf/object.h
|
||||
@@ -109,6 +109,7 @@ pdf_obj *pdf_dict_gets(fz_context *ctx, pdf_obj *dict, const char *key);
|
||||
pdf_obj *pdf_dict_getsa(fz_context *ctx, pdf_obj *dict, const char *key, const char *abbrev);
|
||||
void pdf_dict_put(fz_context *ctx, pdf_obj *dict, pdf_obj *key, pdf_obj *val);
|
||||
void pdf_dict_put_drop(fz_context *ctx, pdf_obj *dict, pdf_obj *key, pdf_obj *val);
|
||||
+void pdf_dict_get_put_drop(fz_context *ctx, pdf_obj *dict, pdf_obj *key, pdf_obj *val, pdf_obj **old_val);
|
||||
void pdf_dict_puts(fz_context *ctx, pdf_obj *dict, const char *key, pdf_obj *val);
|
||||
void pdf_dict_puts_drop(fz_context *ctx, pdf_obj *dict, const char *key, pdf_obj *val);
|
||||
void pdf_dict_putp(fz_context *ctx, pdf_obj *dict, const char *path, pdf_obj *val);
|
||||
diff --git a/source/pdf/pdf-object.c b/source/pdf/pdf-object.c
|
||||
index f2e4551..a0d0d8e 100644
|
||||
--- a/source/pdf/pdf-object.c
|
||||
+++ b/source/pdf/pdf-object.c
|
||||
@@ -1240,9 +1240,13 @@ pdf_dict_geta(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *abbrev)
|
||||
return pdf_dict_get(ctx, obj, abbrev);
|
||||
}
|
||||
|
||||
-void
|
||||
-pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val)
|
||||
+static void
|
||||
+pdf_dict_get_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val, pdf_obj **old_val)
|
||||
{
|
||||
+
|
||||
+ if (old_val)
|
||||
+ *old_val = NULL;
|
||||
+
|
||||
RESOLVE(obj);
|
||||
if (obj >= PDF_OBJ__LIMIT)
|
||||
{
|
||||
@@ -1282,7 +1286,10 @@ pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val)
|
||||
{
|
||||
pdf_obj *d = DICT(obj)->items[i].v;
|
||||
DICT(obj)->items[i].v = pdf_keep_obj(ctx, val);
|
||||
- pdf_drop_obj(ctx, d);
|
||||
+ if (old_val)
|
||||
+ *old_val = d;
|
||||
+ else
|
||||
+ pdf_drop_obj(ctx, d);
|
||||
}
|
||||
}
|
||||
else
|
||||
@@ -1305,10 +1312,27 @@ pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val)
|
||||
}
|
||||
|
||||
void
|
||||
+pdf_dict_put(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val)
|
||||
+{
|
||||
+ pdf_dict_get_put(ctx, obj, key, val, NULL);
|
||||
+}
|
||||
+
|
||||
+void
|
||||
pdf_dict_put_drop(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val)
|
||||
{
|
||||
fz_try(ctx)
|
||||
- pdf_dict_put(ctx, obj, key, val);
|
||||
+ pdf_dict_get_put(ctx, obj, key, val, NULL);
|
||||
+ fz_always(ctx)
|
||||
+ pdf_drop_obj(ctx, val);
|
||||
+ fz_catch(ctx)
|
||||
+ fz_rethrow(ctx);
|
||||
+}
|
||||
+
|
||||
+void
|
||||
+pdf_dict_get_put_drop(fz_context *ctx, pdf_obj *obj, pdf_obj *key, pdf_obj *val, pdf_obj **old_val)
|
||||
+{
|
||||
+ fz_try(ctx)
|
||||
+ pdf_dict_get_put(ctx, obj, key, val, old_val);
|
||||
fz_always(ctx)
|
||||
pdf_drop_obj(ctx, val);
|
||||
fz_catch(ctx)
|
||||
diff --git a/source/pdf/pdf-repair.c b/source/pdf/pdf-repair.c
|
||||
index fdd4648..212c8b7 100644
|
||||
--- a/source/pdf/pdf-repair.c
|
||||
+++ b/source/pdf/pdf-repair.c
|
||||
@@ -259,6 +259,27 @@ pdf_repair_obj_stm(fz_context *ctx, pdf_document *doc, int num, int gen)
|
||||
}
|
||||
}
|
||||
|
||||
+static void
|
||||
+orphan_object(fz_context *ctx, pdf_document *doc, pdf_obj *obj)
|
||||
+{
|
||||
+ if (doc->orphans_count == doc->orphans_max)
|
||||
+ {
|
||||
+ int new_max = (doc->orphans_max ? doc->orphans_max*2 : 32);
|
||||
+
|
||||
+ fz_try(ctx)
|
||||
+ {
|
||||
+ doc->orphans = fz_resize_array(ctx, doc->orphans, new_max, sizeof(*doc->orphans));
|
||||
+ doc->orphans_max = new_max;
|
||||
+ }
|
||||
+ fz_catch(ctx)
|
||||
+ {
|
||||
+ pdf_drop_obj(ctx, obj);
|
||||
+ fz_rethrow(ctx);
|
||||
+ }
|
||||
+ }
|
||||
+ doc->orphans[doc->orphans_count++] = obj;
|
||||
+}
|
||||
+
|
||||
void
|
||||
pdf_repair_xref(fz_context *ctx, pdf_document *doc)
|
||||
{
|
||||
@@ -520,12 +541,13 @@ pdf_repair_xref(fz_context *ctx, pdf_document *doc)
|
||||
/* correct stream length for unencrypted documents */
|
||||
if (!encrypt && list[i].stm_len >= 0)
|
||||
{
|
||||
+ pdf_obj *old_obj = NULL;
|
||||
dict = pdf_load_object(ctx, doc, list[i].num, list[i].gen);
|
||||
|
||||
length = pdf_new_int(ctx, doc, list[i].stm_len);
|
||||
- pdf_dict_put(ctx, dict, PDF_NAME_Length, length);
|
||||
- pdf_drop_obj(ctx, length);
|
||||
-
|
||||
+ pdf_dict_get_put_drop(ctx, dict, PDF_NAME_Length, length, &old_obj);
|
||||
+ if (old_obj)
|
||||
+ orphan_object(ctx, doc, old_obj);
|
||||
pdf_drop_obj(ctx, dict);
|
||||
}
|
||||
}
|
||||
diff --git a/source/pdf/pdf-xref.c b/source/pdf/pdf-xref.c
|
||||
index 3de1cd2..6682741 100644
|
||||
--- a/source/pdf/pdf-xref.c
|
||||
+++ b/source/pdf/pdf-xref.c
|
||||
@@ -1626,6 +1626,12 @@ pdf_close_document(fz_context *ctx, pdf_document *doc)
|
||||
|
||||
pdf_drop_resource_tables(ctx, doc);
|
||||
|
||||
+ for (i = 0; i < doc->orphans_count; i++)
|
||||
+ {
|
||||
+ pdf_drop_obj(ctx, doc->orphans[i]);
|
||||
+ }
|
||||
+ fz_free(ctx, doc->orphans);
|
||||
+
|
||||
fz_free(ctx, doc);
|
||||
}
|
||||
|
||||
--
|
||||
2.10.1
|
||||
|
||||
|
|
@ -0,0 +1,81 @@
|
|||
Fix CVE-2016-8859:
|
||||
|
||||
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-8859
|
||||
|
||||
Patch copied from upstream source repository:
|
||||
|
||||
http://git.musl-libc.org/cgit/musl/commit/?id=c3edc06d1e1360f3570db9155d6b318ae0d0f0f7
|
||||
|
||||
From c3edc06d1e1360f3570db9155d6b318ae0d0f0f7 Mon Sep 17 00:00:00 2001
|
||||
From: Rich Felker <dalias@aerifal.cx>
|
||||
Date: Thu, 6 Oct 2016 18:34:58 -0400
|
||||
Subject: [PATCH] fix missing integer overflow checks in regexec buffer size
|
||||
computations
|
||||
|
||||
most of the possible overflows were already ruled out in practice by
|
||||
regcomp having already succeeded performing larger allocations.
|
||||
however at least the num_states*num_tags multiplication can clearly
|
||||
overflow in practice. for safety, check them all, and use the proper
|
||||
type, size_t, rather than int.
|
||||
|
||||
also improve comments, use calloc in place of malloc+memset, and
|
||||
remove bogus casts.
|
||||
---
|
||||
src/regex/regexec.c | 23 ++++++++++++++++++-----
|
||||
1 file changed, 18 insertions(+), 5 deletions(-)
|
||||
|
||||
diff --git a/src/regex/regexec.c b/src/regex/regexec.c
|
||||
index 16c5d0a..dd52319 100644
|
||||
--- a/src/regex/regexec.c
|
||||
+++ b/src/regex/regexec.c
|
||||
@@ -34,6 +34,7 @@
|
||||
#include <wchar.h>
|
||||
#include <wctype.h>
|
||||
#include <limits.h>
|
||||
+#include <stdint.h>
|
||||
|
||||
#include <regex.h>
|
||||
|
||||
@@ -206,11 +207,24 @@ tre_tnfa_run_parallel(const tre_tnfa_t *tnfa, const void *string,
|
||||
|
||||
/* Allocate memory for temporary data required for matching. This needs to
|
||||
be done for every matching operation to be thread safe. This allocates
|
||||
- everything in a single large block from the stack frame using alloca()
|
||||
- or with malloc() if alloca is unavailable. */
|
||||
+ everything in a single large block with calloc(). */
|
||||
{
|
||||
- int tbytes, rbytes, pbytes, xbytes, total_bytes;
|
||||
+ size_t tbytes, rbytes, pbytes, xbytes, total_bytes;
|
||||
char *tmp_buf;
|
||||
+
|
||||
+ /* Ensure that tbytes and xbytes*num_states cannot overflow, and that
|
||||
+ * they don't contribute more than 1/8 of SIZE_MAX to total_bytes. */
|
||||
+ if (num_tags > SIZE_MAX/(8 * sizeof(int) * tnfa->num_states))
|
||||
+ goto error_exit;
|
||||
+
|
||||
+ /* Likewise check rbytes. */
|
||||
+ if (tnfa->num_states+1 > SIZE_MAX/(8 * sizeof(*reach_next)))
|
||||
+ goto error_exit;
|
||||
+
|
||||
+ /* Likewise check pbytes. */
|
||||
+ if (tnfa->num_states > SIZE_MAX/(8 * sizeof(*reach_pos)))
|
||||
+ goto error_exit;
|
||||
+
|
||||
/* Compute the length of the block we need. */
|
||||
tbytes = sizeof(*tmp_tags) * num_tags;
|
||||
rbytes = sizeof(*reach_next) * (tnfa->num_states + 1);
|
||||
@@ -221,10 +235,9 @@ tre_tnfa_run_parallel(const tre_tnfa_t *tnfa, const void *string,
|
||||
+ (rbytes + xbytes * tnfa->num_states) * 2 + tbytes + pbytes;
|
||||
|
||||
/* Allocate the memory. */
|
||||
- buf = xmalloc((unsigned)total_bytes);
|
||||
+ buf = calloc(total_bytes, 1);
|
||||
if (buf == NULL)
|
||||
return REG_ESPACE;
|
||||
- memset(buf, 0, (size_t)total_bytes);
|
||||
|
||||
/* Get the various pointers within tmp_buf (properly aligned). */
|
||||
tmp_tags = (void *)buf;
|
||||
--
|
||||
2.10.1
|
||||
|
||||
|
|
@ -1,46 +0,0 @@
|
|||
This fixes a test failure with emacs-25. Picked from
|
||||
https://git.notmuchmail.org/git?p=notmuch;a=commit;h=f575a346df09c82691bb9e7c462836d982fe31f7
|
||||
|
||||
From f575a346df09c82691bb9e7c462836d982fe31f7 Mon Sep 17 00:00:00 2001
|
||||
From: David Bremner <david@tethera.net>
|
||||
Date: Sun, 9 Oct 2016 19:30:44 -0300
|
||||
Subject: [PATCH] emacs/show: force notmuch-show-buttonise-links to act on
|
||||
lines
|
||||
|
||||
This seems to fix a problem with emacs 25 creating partial buttons by
|
||||
calling n-s-b-l with a region that does not include the whole button.
|
||||
I'm not 100% sure it's legit to act outside the region passed by
|
||||
jit-lock, but goto-address-fontify-region (where I borrowed the code
|
||||
from) already does this, so this patch to not make things worse.
|
||||
---
|
||||
emacs/notmuch-show.el | 12 +++++++-----
|
||||
1 file changed, 7 insertions(+), 5 deletions(-)
|
||||
|
||||
diff --git a/emacs/notmuch-show.el b/emacs/notmuch-show.el
|
||||
index 641398d..e7d16f8 100644
|
||||
--- a/emacs/notmuch-show.el
|
||||
+++ b/emacs/notmuch-show.el
|
||||
@@ -1174,13 +1174,15 @@ This also turns id:\"<message id>\"-parts and mid: links into
|
||||
buttons for a corresponding notmuch search."
|
||||
(goto-address-fontify-region start end)
|
||||
(save-excursion
|
||||
- (let (links)
|
||||
- (goto-char start)
|
||||
- (while (re-search-forward notmuch-id-regexp end t)
|
||||
+ (let (links
|
||||
+ (beg-line (progn (goto-char start) (line-beginning-position)))
|
||||
+ (end-line (progn (goto-char end) (line-end-position))))
|
||||
+ (goto-char beg-line)
|
||||
+ (while (re-search-forward notmuch-id-regexp end-line t)
|
||||
(push (list (match-beginning 0) (match-end 0)
|
||||
(match-string-no-properties 0)) links))
|
||||
- (goto-char start)
|
||||
- (while (re-search-forward notmuch-mid-regexp end t)
|
||||
+ (goto-char beg-line)
|
||||
+ (while (re-search-forward notmuch-mid-regexp end-line t)
|
||||
(let* ((mid-cid (match-string-no-properties 1))
|
||||
(mid (save-match-data
|
||||
(string-match "^[^/]*" mid-cid)
|
||||
--
|
||||
2.10.1
|
||||
|
||||
|
|
@ -489,7 +489,8 @@ extracting content or merging files.")
|
|||
"1k64pdapyj8a336jw3j61fhn0rp4q6az7d0dqp9r5n3d9rgwa5c0"))
|
||||
(patches (search-patches "mupdf-build-with-openjpeg-2.1.patch"
|
||||
"mupdf-CVE-2016-6265.patch"
|
||||
"mupdf-CVE-2016-6525.patch"))
|
||||
"mupdf-CVE-2016-6525.patch"
|
||||
"mupdf-CVE-2016-8674.patch"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
;; Delete all the bundled libraries except for mujs, which is
|
||||
|
|
|
|||
|
|
@ -18,15 +18,24 @@
|
|||
|
||||
(define-module (gnu packages psyc)
|
||||
#:use-module (guix download)
|
||||
#:use-module (guix git-download)
|
||||
#:use-module ((guix licenses) #:prefix license:)
|
||||
#:use-module (guix packages)
|
||||
#:use-module (guix build-system perl)
|
||||
#:use-module (guix build-system gnu)
|
||||
#:use-module (gnu packages)
|
||||
#:use-module (gnu packages admin)
|
||||
#:use-module (gnu packages autotools)
|
||||
#:use-module (gnu packages bison)
|
||||
#:use-module (gnu packages compression)
|
||||
#:use-module (gnu packages gettext)
|
||||
#:use-module (gnu packages linux)
|
||||
#:use-module (gnu packages man)
|
||||
#:use-module (gnu packages ncurses)
|
||||
#:use-module (gnu packages perl)
|
||||
#:use-module (gnu packages pcre)
|
||||
#:use-module (gnu packages pkg-config)
|
||||
#:use-module (gnu packages tls)
|
||||
#:use-module (gnu packages web))
|
||||
|
||||
(define-public perl-net-psyc
|
||||
|
|
@ -143,3 +152,76 @@ core aspects of PSYC, useful for all kinds of clients and servers
|
|||
including psyced.")
|
||||
(synopsis "PSYC library in C")
|
||||
(license license:agpl3+)))
|
||||
|
||||
;; This commit removes the historic bundled pcre, not released as a tarball so far.
|
||||
(define-public psyclpc
|
||||
(let* ((commit "8bd51f2a4847860ba8b82dc79348ab37d516011e")
|
||||
(revision "1"))
|
||||
(package
|
||||
(name "psyclpc")
|
||||
(version (string-append "20160821-" revision "." (string-take commit 7)))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "git://git.psyced.org/git/psyclpc")
|
||||
(commit commit)))
|
||||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"10w4kx9ygcv1lcmd7j4knvjiy8dac1y3hjfv3lhp67jpv6w3iagz"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; There are no tests/checks.
|
||||
#:configure-flags
|
||||
;; If you have questions about this part, look at
|
||||
;; "src/settings/psyced" and the ebuild.
|
||||
(list
|
||||
"--enable-use-tls=yes"
|
||||
"--enable-use-mccp" ; Mud Client Compression Protocol, leave this enabled.
|
||||
(string-append "--prefix="
|
||||
(assoc-ref %outputs "out"))
|
||||
;; src/Makefile: Set MUD_LIB to the directory which contains
|
||||
;; the mud data. defaults to MUD_LIB = @libdir@
|
||||
(string-append "--libdir="
|
||||
(assoc-ref %outputs "out")
|
||||
"/opt/psyced/world")
|
||||
(string-append "--bindir="
|
||||
(assoc-ref %outputs "out")
|
||||
"/opt/psyced/bin")
|
||||
;; src/Makefile: Set ERQ_DIR to directory which contains the
|
||||
;; stuff which ERQ can execute (hopefully) savely. Was formerly
|
||||
;; defined in config.h. defaults to ERQ_DIR= @libexecdir@
|
||||
(string-append "--libexecdir="
|
||||
(assoc-ref %outputs "out")
|
||||
"/opt/psyced/run"))
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-before 'configure 'chdir-to-src
|
||||
;; We need to pass this as env variables
|
||||
;; and manually change the directory.
|
||||
(lambda _
|
||||
(chdir "src")
|
||||
(setenv "CONFIG_SHELL" (which "sh"))
|
||||
(setenv "SHELL" (which "sh"))
|
||||
#t)))
|
||||
#:make-flags (list "install-all")))
|
||||
(inputs
|
||||
`(("zlib" ,zlib)
|
||||
("openssl" ,openssl)
|
||||
("pcre" ,pcre)))
|
||||
(native-inputs
|
||||
`(("pkg-config" ,pkg-config)
|
||||
("bison" ,bison)
|
||||
("gnu-gettext" ,gnu-gettext)
|
||||
("help2man" ,help2man)
|
||||
("autoconf" ,autoconf)
|
||||
("automake" ,automake)))
|
||||
(home-page "http://lpc.psyc.eu/")
|
||||
(synopsis "psycLPC is a multi-user network server programming language")
|
||||
(description
|
||||
"LPC is a bytecode language, invented to specifically implement
|
||||
multi user virtual environments on the internet. This technology is used for
|
||||
MUDs and also the psyced implementation of the Protocol for SYnchronous
|
||||
Conferencing (PSYC). psycLPC is a fork of LDMud with some new features and
|
||||
many bug fixes.")
|
||||
(license license:gpl2))))
|
||||
|
|
|
|||
|
|
@ -2298,13 +2298,13 @@ files.")
|
|||
(define-public python-certifi
|
||||
(package
|
||||
(name "python-certifi")
|
||||
(version "2015.11.20.1")
|
||||
(version "2016.8.31")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "certifi" version))
|
||||
(sha256
|
||||
(base32
|
||||
"05lgwf9rz1kn465azy2bpb3zmpnsn9gkypbhnjlclchv98ssgc1h"))))
|
||||
"06c9dcyv8ss050gkv5xjivbxhm6qm0s9vzy4r33wqabgv118lw7p"))))
|
||||
(build-system python-build-system)
|
||||
(inputs
|
||||
`(("python-setuptools" ,python-setuptools)))
|
||||
|
|
|
|||
|
|
@ -17,9 +17,9 @@
|
|||
;;; You should have received a copy of the GNU General Public License
|
||||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
(define-module (gnu packages yubico)
|
||||
(define-module (gnu packages security-token)
|
||||
#:use-module (gnu packages)
|
||||
#:use-module (guix licenses)
|
||||
#:use-module ((guix licenses) #:prefix license:)
|
||||
#:use-module (guix packages)
|
||||
#:use-module (guix download)
|
||||
#:use-module (guix build-system gnu)
|
||||
|
|
@ -45,7 +45,7 @@
|
|||
"This package contains a C library and command-line tools that make up
|
||||
the low-level development kit for the Yubico YubiKey authentication device.")
|
||||
(home-page "https://developers.yubico.com/yubico-c/")
|
||||
(license bsd-2)))
|
||||
(license license:bsd-2)))
|
||||
|
||||
(define-public ykclient
|
||||
(package
|
||||
|
|
@ -74,4 +74,4 @@ the low-level development kit for the Yubico YubiKey authentication device.")
|
|||
one-time-password (OTP) YubiKey against Yubico’s servers. See the Yubico
|
||||
website for more information about Yubico and the YubiKey.")
|
||||
(home-page "https://developers.yubico.com/yubico-c-client/")
|
||||
(license bsd-2)))
|
||||
(license license:bsd-2)))
|
||||
|
|
@ -5,6 +5,7 @@
|
|||
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
|
||||
;;; Copyright © 2016 Nicolas Goaziou <mail@nicolasgoaziou.fr>
|
||||
;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -506,3 +507,28 @@ manipulating key files.")
|
|||
authentication with SSH's so-called @dfn{interactive keyboard password
|
||||
authentication}.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public autossh
|
||||
(package
|
||||
(name "autossh")
|
||||
(version "1.4e")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"http://www.harding.motd.ca/autossh/autossh-"
|
||||
version ".tgz"))
|
||||
(sha256
|
||||
(base32 "0mlicw28vq2jxa0jf0dys5ja75v0fxpjavlq9dpif6bnknji13ly"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments `(#:tests? #f)) ; There is no "make check" or anything similar
|
||||
(inputs `(("openssh" ,openssh)))
|
||||
(synopsis "Automatically restart SSH sessions and tunnels")
|
||||
(description "autossh is a program to start a copy of @command{ssh} and
|
||||
monitor it, restarting it as necessary should it die or stop passing traffic.")
|
||||
(home-page "http://www.harding.motd.ca/autossh/")
|
||||
(license
|
||||
;; Why point to a source file? Well, all the individual files have a
|
||||
;; copy of this license in their headers, but there's no separate file
|
||||
;; with that information.
|
||||
(license:non-copyleft "file://autossh.c"))))
|
||||
|
|
|
|||
|
|
@ -200,13 +200,13 @@ available, greatly increasing its breadth and scope.")
|
|||
(define-public r-colorspace
|
||||
(package
|
||||
(name "r-colorspace")
|
||||
(version "1.2-6")
|
||||
(version "1.2-7")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "colorspace" version))
|
||||
(sha256
|
||||
(base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds"))))
|
||||
(base32 "0flw97iwwpkxy6si9cn982jhl61wb1rxi3r0nz2xxf0c3fzw18d5"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/colorspace")
|
||||
(synopsis "Color space manipulation")
|
||||
|
|
@ -410,14 +410,14 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
|
|||
(define-public r-matrix
|
||||
(package
|
||||
(name "r-matrix")
|
||||
(version "1.2-7")
|
||||
(version "1.2-7.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "Matrix" version))
|
||||
(sha256
|
||||
(base32
|
||||
"18x3mdq5cdhbk1lw5cj7vbr41lk8w9p4i5kzh8wslgq6p3d9ac3c"))))
|
||||
"09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa"))))
|
||||
(properties `((upstream-name . "Matrix")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -558,14 +558,14 @@ solution for sending email, including attachments, from within R.")
|
|||
(define-public r-stringi
|
||||
(package
|
||||
(name "r-stringi")
|
||||
(version "1.1.1")
|
||||
(version "1.1.2")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "stringi" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0rg14hga1g2havd3imhk04iyh1dnisnmxf7yhiiwhs7y72hphc94"))))
|
||||
"13i1p6j8mx31hsw2s4c2phm2llrrdakzixkm6i0axsxprri722z5"))))
|
||||
(build-system r-build-system)
|
||||
(inputs `(("icu4c" ,icu4c)))
|
||||
(native-inputs `(("pkg-config" ,pkg-config)))
|
||||
|
|
@ -608,13 +608,13 @@ the input of another.")
|
|||
(define-public r-reshape2
|
||||
(package
|
||||
(name "r-reshape2")
|
||||
(version "1.4.1")
|
||||
(version "1.4.2")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "reshape2" version))
|
||||
(sha256
|
||||
(base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v"))))
|
||||
(base32 "0swvjmc9f8cvkrsz463cp6snd8bncbv6q8yrfrb4rgkr0dhq6dvd"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-plyr" ,r-plyr)
|
||||
|
|
@ -811,13 +811,13 @@ for template use among CRAN packages.")
|
|||
(define-public r-evaluate
|
||||
(package
|
||||
(name "r-evaluate")
|
||||
(version "0.9")
|
||||
(version "0.10")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "evaluate" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1bn6bympg9prr8d16g1g530bddii8i04hf4i2bkw0yf4dsfqq4g8"))))
|
||||
"0mwna7rjyrmc76651a1fm7c76ippdsc2wsp3sj3iwb1c73mvlqv1"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-stringr" ,r-stringr)))
|
||||
|
|
@ -1131,13 +1131,13 @@ flexible and easy to set up.")
|
|||
(define-public r-r6
|
||||
(package
|
||||
(name "r-r6")
|
||||
(version "2.1.3")
|
||||
(version "2.2.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "R6" version))
|
||||
(sha256
|
||||
(base32
|
||||
"19qrkgxvssyi51fm80h93sabzz0n2vgqgv1w8xjqbsap0nx379vy"))))
|
||||
"1ir51pb0y6yj05qaxsflk4a6hv8n73cwlb0qajcskbrz632dsyvx"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "https://github.com/wch/R6/")
|
||||
(synopsis "Classes with reference semantics in R")
|
||||
|
|
@ -1209,14 +1209,14 @@ database.")
|
|||
(define-public r-acepack
|
||||
(package
|
||||
(name "r-acepack")
|
||||
(version "1.3-3.3")
|
||||
(version "1.4.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "acepack" version))
|
||||
(sha256
|
||||
(base32
|
||||
"13ry3vyys12iplb14jfhmkrl9g5fxg3iijiggq4s4zb5m5436b1y"))))
|
||||
"0brivhr0imf2qq1flc9qxibybg1zi5m8pxz8cjn5a8gb42bcv96n"))))
|
||||
(build-system r-build-system)
|
||||
(inputs
|
||||
`(("gfortran" ,gfortran)))
|
||||
|
|
@ -1230,14 +1230,14 @@ transformations.")
|
|||
(define-public r-cluster
|
||||
(package
|
||||
(name "r-cluster")
|
||||
(version "2.0.4")
|
||||
(version "2.0.5")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "cluster" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1r669aaaia05i8sv8hxiig1ddah7hm8qw869wgig5i0zzk22bnfl"))))
|
||||
"1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b"))))
|
||||
(build-system r-build-system)
|
||||
(inputs
|
||||
`(("gfortran" ,gfortran)))
|
||||
|
|
@ -1252,14 +1252,14 @@ Groups in Data\".")
|
|||
(define-public r-foreign
|
||||
(package
|
||||
(name "r-foreign")
|
||||
(version "0.8-66")
|
||||
(version "0.8-67")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "foreign" version))
|
||||
(sha256
|
||||
(base32
|
||||
"19278jm85728zb20800w6hq9q8jy8ywdn81mgmlnxkmrr9giwh6p"))))
|
||||
"1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/foreign")
|
||||
(synopsis "Read data stored by other statistics software in R")
|
||||
|
|
@ -1615,14 +1615,14 @@ limited to R.")
|
|||
(define-public r-backports
|
||||
(package
|
||||
(name "r-backports")
|
||||
(version "1.0.3")
|
||||
(version "1.0.4")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "backports" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0s04mbb7imqc00jl37i081y4yf7qdimk687dyrkvb20nixvjvjyh"))))
|
||||
"0fssh5rnnvpp8wm0ml9gk765idwrgj07xyxpkhpidl9zwydxzif2"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/backports")
|
||||
(synopsis "Reimplementations of functions introduced since R 3.0.0")
|
||||
|
|
@ -2051,13 +2051,13 @@ well as additional utilities such as panel and axis annotation functions.")
|
|||
(define-public r-rcpparmadillo
|
||||
(package
|
||||
(name "r-rcpparmadillo")
|
||||
(version "0.7.400.2.0")
|
||||
(version "0.7.500.0.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "RcppArmadillo" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0g2658iy43higy1cay00ljibgnwh0zv5gcwvbhckjs48y8z1a2pb"))
|
||||
"06qb6877c5qd8lvnc4b27z8fwb5r5pyylkj0g6kj1rn868zkh5ps"))
|
||||
(modules '((guix build utils)))
|
||||
;; Remove bundled armadillo sources
|
||||
(snippet
|
||||
|
|
@ -2135,14 +2135,14 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.")
|
|||
(define-public r-rmarkdown
|
||||
(package
|
||||
(name "r-rmarkdown")
|
||||
(version "1.0")
|
||||
(version "1.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "rmarkdown" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0c7gs9c8xdjfxviw0syh13pf3vys2b2ssixmnyqbji64xdscn7pz"))))
|
||||
"1czvkaz1ji3jyj6qrvbswisqs9d05ljqc4vjkfdrf6hygix7azd0"))))
|
||||
(properties `((upstream-name . "rmarkdown")))
|
||||
(build-system r-build-system)
|
||||
(arguments
|
||||
|
|
@ -2161,6 +2161,8 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.")
|
|||
#t)))))
|
||||
(propagated-inputs
|
||||
`(("r-catools" ,r-catools)
|
||||
("r-evaluate" ,r-evaluate)
|
||||
("r-tibble" ,r-tibble)
|
||||
("r-htmltools" ,r-htmltools)
|
||||
("r-jsonlite" ,r-jsonlite)
|
||||
("r-base64enc" ,r-base64enc)
|
||||
|
|
@ -2413,13 +2415,13 @@ multiple breakpoints are allowed.")
|
|||
(define-public r-snow
|
||||
(package
|
||||
(name "r-snow")
|
||||
(version "0.4-1")
|
||||
(version "0.4-2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "snow" version))
|
||||
(sha256
|
||||
(base32
|
||||
"19r2yq8aqw99vwyx81p6ay4afsfqffal1wzvizk3dj882s2n4j8w"))))
|
||||
"1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/snow")
|
||||
(synopsis "Support for simple parallel computing in R")
|
||||
|
|
@ -2477,14 +2479,14 @@ data.")
|
|||
(define-public r-codetools
|
||||
(package
|
||||
(name "r-codetools")
|
||||
(version "0.2-14")
|
||||
(version "0.2-15")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "codetools" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397"))))
|
||||
"0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/codetools")
|
||||
(synopsis "Code analysis tools for R")
|
||||
|
|
@ -2621,14 +2623,14 @@ flexible than the orphaned \"base64\" package.")
|
|||
(define-public r-irlba
|
||||
(package
|
||||
(name "r-irlba")
|
||||
(version "2.1.1")
|
||||
(version "2.1.2")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "irlba" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0yb8b8g6f3cb0f56r702fn2px8nf5rx8cyy2scq36xai9w7f25jj"))))
|
||||
"1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/irlba")
|
||||
(synopsis "Methods for eigendecomposition of large matrices")
|
||||
|
|
@ -2897,13 +2899,13 @@ maintenance for package developers.")
|
|||
(define-public r-r-utils
|
||||
(package
|
||||
(name "r-r-utils")
|
||||
(version "2.3.0")
|
||||
(version "2.4.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "R.utils" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0f4z7ka1wb7bgxc5wyqihqxsnqwgyyzbglwvfwmx0gn8i0wzi647"))))
|
||||
"0cn0wlmgwclmqak05825wrk9q894xa4qjqa7rn0i9p4ss7k6vifj"))))
|
||||
(properties `((upstream-name . "R.utils")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -2995,13 +2997,13 @@ t-probabilities, quantiles, random deviates and densities.")
|
|||
(define-public r-matrixstats
|
||||
(package
|
||||
(name "r-matrixstats")
|
||||
(version "0.50.2")
|
||||
(version "0.51.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "matrixStats" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0zj27xxx9cyrq16rn4g3l0krqg68p8f2qp18w1w4i767j87amlbj"))))
|
||||
"0bsalx605kgb9nl7mfnq1qinkyd9s97p8plymsyfja1gmcnjrcpj"))))
|
||||
(properties `((upstream-name . "matrixStats")))
|
||||
(build-system r-build-system)
|
||||
(native-inputs
|
||||
|
|
@ -3280,6 +3282,30 @@ conversion of R objects to LaTeX code, and recoding variables.")
|
|||
framework, with additional code inspection and report generation tools.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-kernsmooth
|
||||
(package
|
||||
(name "r-kernsmooth")
|
||||
(version "2.23-15")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "KernSmooth" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
|
||||
(properties `((upstream-name . "KernSmooth")))
|
||||
(build-system r-build-system)
|
||||
(inputs
|
||||
`(("gfortran" ,gfortran)))
|
||||
(home-page "http://cran.r-project.org/web/packages/KernSmooth")
|
||||
(synopsis "Functions for kernel smoothing")
|
||||
(description
|
||||
"This package provides functions for kernel smoothing (and density
|
||||
estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
|
||||
\"Kernel Smoothing\".")
|
||||
;; Unlimited use and distribution
|
||||
(license (license:non-copyleft "file://LICENSE.note"))))
|
||||
|
||||
(define-public r-zoo
|
||||
(package
|
||||
(name "r-zoo")
|
||||
|
|
|
|||
|
|
@ -250,6 +250,37 @@ H.264 (MPEG-4 AVC) video streams.")
|
|||
"file://extras/cl.h"
|
||||
"See extras/cl.h in the distribution.")))))
|
||||
|
||||
(define-public x265
|
||||
(package
|
||||
(name "x265")
|
||||
(version "2.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://download.videolan.org/videolan/x265/"
|
||||
"x265_" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0hx6sr9l7586gs4qds2sj0i1m5brxkaqq3cwmibhfb559fpvkz48"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(delete-file-recursively "source/compat/getopt"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; tests are skipped if cpu-optimized code isn't built
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-before 'configure 'prepare-build
|
||||
(lambda _
|
||||
(delete-file-recursively "build")
|
||||
(chdir "source")
|
||||
#t)))))
|
||||
(home-page "http://x265.org/")
|
||||
(synopsis "Library for encoding h.265/HEVC video streams")
|
||||
(description "x265 is a H.265 / HEVC video encoder application library,
|
||||
designed to encode video or images into an H.265 / HEVC encoded bitstream.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public libass
|
||||
(package
|
||||
(name "libass")
|
||||
|
|
@ -435,6 +466,7 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).")
|
|||
("soxr" ,soxr)
|
||||
("speex" ,speex)
|
||||
("twolame" ,twolame)
|
||||
("x265" ,x265)
|
||||
("xvid" ,xvid)
|
||||
("zlib" ,zlib)))
|
||||
(native-inputs
|
||||
|
|
@ -518,6 +550,7 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).")
|
|||
"--enable-libvpx"
|
||||
"--enable-libxvid"
|
||||
"--enable-libx264"
|
||||
"--enable-libx265"
|
||||
"--enable-openal"
|
||||
"--enable-opengl"
|
||||
"--enable-x11grab"
|
||||
|
|
@ -647,6 +680,7 @@ audio/video codec library.")
|
|||
("sdl" ,sdl)
|
||||
("sdl-image" ,sdl-image)
|
||||
("speex" ,speex)
|
||||
("x265" ,x265)
|
||||
("xcb-util-keysyms" ,xcb-util-keysyms)))
|
||||
(arguments
|
||||
`(#:configure-flags
|
||||
|
|
|
|||
|
|
@ -3205,13 +3205,13 @@ particularly easy to create complete web applications using httpuv alone.")
|
|||
(define-public r-jsonlite
|
||||
(package
|
||||
(name "r-jsonlite")
|
||||
(version "1.0")
|
||||
(version "1.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "jsonlite" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0bcnzzycvwwkm0lv0ka9xf55z5c1795b7c2vhmf53z73cxixsmnp"))))
|
||||
"0mrfzh0mxxrhqdmxai434wvyd7skkw28vxr7pyls19yrg941g6r3"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://arxiv.org/abs/1403.2805")
|
||||
(synopsis "Robust, high performance JSON parser and generator for R")
|
||||
|
|
@ -3311,13 +3311,13 @@ applications.")
|
|||
(define-public r-curl
|
||||
(package
|
||||
(name "r-curl")
|
||||
(version "1.2")
|
||||
(version "2.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "curl" version))
|
||||
(sha256
|
||||
(base32
|
||||
"04fwasg400v8dvkcn1fcha1jzdz8lbyxi0679q7flsyrp57b3jrf"))))
|
||||
"0hyvyjzf5ja7kfhzmlfgp86hg1lxrriiwbnr6pxabwwslswj3cmj"))))
|
||||
(build-system r-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
;;; Copyright © 2015 David Thompson <davet@gnu.org>
|
||||
;;; Copyright © 2015, 2016 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is>
|
||||
;;; Copyright © 2016 Julien Lepiller <julien@lepiller.eu>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -29,6 +30,8 @@
|
|||
#:use-module (ice-9 match)
|
||||
#:export (nginx-configuration
|
||||
nginx-configuration?
|
||||
nginx-vhost-configuration
|
||||
nginx-vhost-configuration?
|
||||
nginx-service
|
||||
nginx-service-type))
|
||||
|
||||
|
|
@ -38,6 +41,26 @@
|
|||
;;;
|
||||
;;; Code:
|
||||
|
||||
(define-record-type* <nginx-vhost-configuration>
|
||||
nginx-vhost-configuration make-nginx-vhost-configuration
|
||||
nginx-vhost-configuration?
|
||||
(http-port nginx-vhost-configuration-http-port
|
||||
(default 80))
|
||||
(https-port nginx-vhost-configuration-https-port
|
||||
(default 443))
|
||||
(server-name nginx-vhost-configuration-server-name
|
||||
(default (list 'default)))
|
||||
(root nginx-vhost-configuration-root
|
||||
(default "/srv/http"))
|
||||
(index nginx-vhost-configuration-index
|
||||
(default (list "index.html")))
|
||||
(ssl-certificate nginx-vhost-configuration-ssl-certificate
|
||||
(default "/etc/nginx/cert.pem"))
|
||||
(ssl-certificate-key nginx-vhost-configuration-ssl-certificate-key
|
||||
(default "/etc/nginx/key.pem"))
|
||||
(server-tokens? nginx-vhost-configuration-server-tokens?
|
||||
(default #f)))
|
||||
|
||||
(define-record-type* <nginx-configuration>
|
||||
nginx-configuration make-nginx-configuration
|
||||
nginx-configuration?
|
||||
|
|
@ -46,16 +69,70 @@
|
|||
(run-directory nginx-configuration-run-directory) ;string
|
||||
(file nginx-configuration-file)) ;string | file-like
|
||||
|
||||
(define (default-nginx-config log-directory run-directory)
|
||||
(define (config-domain-strings names)
|
||||
"Return a string denoting the nginx config representation of NAMES, a list
|
||||
of domain names."
|
||||
(string-concatenate
|
||||
(map (match-lambda
|
||||
('default "_")
|
||||
((? string? str) str))
|
||||
names)))
|
||||
|
||||
(define (config-index-strings names)
|
||||
"Return a string denoting the nginx config representation of NAMES, a list
|
||||
of index files."
|
||||
(string-concatenate
|
||||
(map (match-lambda
|
||||
((? string? str) str))
|
||||
names)))
|
||||
|
||||
(define (default-nginx-vhost-config vhost)
|
||||
(string-append
|
||||
" server {\n"
|
||||
(if (nginx-vhost-configuration-http-port vhost)
|
||||
(string-append " listen "
|
||||
(number->string (nginx-vhost-configuration-http-port vhost))
|
||||
";\n")
|
||||
"")
|
||||
(if (nginx-vhost-configuration-https-port vhost)
|
||||
(string-append " listen "
|
||||
(number->string (nginx-vhost-configuration-https-port vhost))
|
||||
" ssl;\n")
|
||||
"")
|
||||
" server_name " (config-domain-strings
|
||||
(nginx-vhost-configuration-server-name vhost))
|
||||
";\n"
|
||||
(if (nginx-vhost-configuration-ssl-certificate vhost)
|
||||
(string-append " ssl_certificate "
|
||||
(nginx-vhost-configuration-ssl-certificate vhost) ";\n")
|
||||
"")
|
||||
(if (nginx-vhost-configuration-ssl-certificate-key vhost)
|
||||
(string-append " ssl_certificate_key "
|
||||
(nginx-vhost-configuration-ssl-certificate-key vhost) ";\n")
|
||||
"")
|
||||
" root " (nginx-vhost-configuration-root vhost) ";\n"
|
||||
" index " (config-index-strings (nginx-vhost-configuration-index vhost)) ";\n"
|
||||
" server_tokens " (if (nginx-vhost-configuration-server-tokens? vhost)
|
||||
"on" "off") ";\n"
|
||||
" }\n"))
|
||||
|
||||
(define (default-nginx-config log-directory run-directory vhost-list)
|
||||
(plain-file "nginx.conf"
|
||||
(string-append
|
||||
"user nginx nginx;\n"
|
||||
"pid " run-directory "/pid;\n"
|
||||
"error_log " log-directory "/error.log info;\n"
|
||||
"http {\n"
|
||||
" client_body_temp_path " run-directory "/client_body_temp;\n"
|
||||
" proxy_temp_path " run-directory "/proxy_temp;\n"
|
||||
" fastcgi_temp_path " run-directory "/fastcgi_temp;\n"
|
||||
" uwsgi_temp_path " run-directory "/uwsgi_temp;\n"
|
||||
" scgi_temp_path " run-directory "/scgi_temp;\n"
|
||||
" access_log " log-directory "/access.log;\n"
|
||||
" root /var/www;\n"
|
||||
" server {}\n"
|
||||
(let ((http (map default-nginx-vhost-config vhost-list)))
|
||||
(do ((http http (cdr http))
|
||||
(block "" (string-append (car http) "\n" block )))
|
||||
((null? http) block)))
|
||||
"}\n"
|
||||
"events {}\n")))
|
||||
|
||||
|
|
@ -79,6 +156,12 @@
|
|||
(mkdir-p #$log-directory)
|
||||
(format #t "creating nginx run directory '~a'~%" #$run-directory)
|
||||
(mkdir-p #$run-directory)
|
||||
(format #t "creating nginx temp directories '~a/{client_body,proxy,fastcgi,uwsgi,scgi}_temp'~%" #$run-directory)
|
||||
(mkdir-p (string-append #$run-directory "/client_body_temp"))
|
||||
(mkdir-p (string-append #$run-directory "/proxy_temp"))
|
||||
(mkdir-p (string-append #$run-directory "/fastcgi_temp"))
|
||||
(mkdir-p (string-append #$run-directory "/uwsgi_temp"))
|
||||
(mkdir-p (string-append #$run-directory "/scgi_temp"))
|
||||
;; Check configuration file syntax.
|
||||
(system* (string-append #$nginx "/sbin/nginx")
|
||||
"-c" #$config-file "-t")))))
|
||||
|
|
@ -114,8 +197,9 @@
|
|||
(define* (nginx-service #:key (nginx nginx)
|
||||
(log-directory "/var/log/nginx")
|
||||
(run-directory "/var/run/nginx")
|
||||
(vhost-list (list (nginx-vhost-configuration)))
|
||||
(config-file
|
||||
(default-nginx-config log-directory run-directory)))
|
||||
(default-nginx-config log-directory run-directory vhost-list)))
|
||||
"Return a service that runs NGINX, the nginx web server.
|
||||
|
||||
The nginx daemon loads its runtime configuration from CONFIG-FILE, stores log
|
||||
|
|
|
|||
|
|
@ -27,9 +27,8 @@
|
|||
#:use-module (gnu artwork)
|
||||
#:use-module (gnu system file-systems)
|
||||
#:autoload (gnu packages grub) (grub)
|
||||
#:autoload (gnu packages inkscape) (inkscape)
|
||||
#:autoload (gnu packages imagemagick) (imagemagick)
|
||||
#:autoload (gnu packages compression) (gzip)
|
||||
#:autoload (gnu packages gtk) (guile-cairo guile-rsvg)
|
||||
#:use-module (ice-9 match)
|
||||
#:use-module (ice-9 regex)
|
||||
#:use-module (srfi srfi-1)
|
||||
|
|
@ -132,25 +131,23 @@ object denoting a file name."
|
|||
;;; Background image & themes.
|
||||
;;;
|
||||
|
||||
(define (svg->png svg)
|
||||
"Build a PNG from SVG."
|
||||
;; Don't use #:local-build? so that it's substitutable.
|
||||
(define* (svg->png svg #:key width height)
|
||||
"Build a PNG of HEIGHT x WIDTH from SVG."
|
||||
(gexp->derivation "grub-image.png"
|
||||
#~(zero?
|
||||
(system* (string-append #$inkscape "/bin/inkscape")
|
||||
"--without-gui"
|
||||
(string-append "--export-png=" #$output)
|
||||
#$svg))))
|
||||
(with-imported-modules '((gnu build svg))
|
||||
#~(begin
|
||||
;; We need these two libraries.
|
||||
(add-to-load-path (string-append #$guile-rsvg
|
||||
"/share/guile/site/"
|
||||
(effective-version)))
|
||||
(add-to-load-path (string-append #$guile-cairo
|
||||
"/share/guile/site/"
|
||||
(effective-version)))
|
||||
|
||||
(define (resize-image image width height)
|
||||
"Resize IMAGE to WIDTHxHEIGHT."
|
||||
;; Don't use #:local-build? so that it's substitutable.
|
||||
(let ((size (string-append (number->string width)
|
||||
"x" (number->string height))))
|
||||
(gexp->derivation "grub-image.resized.png"
|
||||
#~(zero?
|
||||
(system* (string-append #$imagemagick "/bin/convert")
|
||||
"-resize" #$size #$image #$output)))))
|
||||
(use-modules (gnu build svg))
|
||||
(svg->png #$svg #$output
|
||||
#:width #$width
|
||||
#:height #$height)))))
|
||||
|
||||
(define* (grub-background-image config #:key (width 1024) (height 768))
|
||||
"Return the GRUB background image defined in CONFIG with a ratio of
|
||||
|
|
@ -160,8 +157,8 @@ WIDTH/HEIGHT, or #f if none was found."
|
|||
(= (grub-image-aspect-ratio image) ratio))
|
||||
(grub-theme-images (grub-configuration-theme config)))))
|
||||
(if image
|
||||
(mlet %store-monad ((png (svg->png (grub-image-file image))))
|
||||
(resize-image png width height))
|
||||
(svg->png (grub-image-file image)
|
||||
#:width width #:height height)
|
||||
(with-monad %store-monad
|
||||
(return #f)))))
|
||||
|
||||
|
|
|
|||
|
|
@ -111,11 +111,11 @@ package definition."
|
|||
(define %cran-url "http://cran.r-project.org/web/packages/")
|
||||
(define %bioconductor-url "http://bioconductor.org/packages/")
|
||||
|
||||
;; The latest Bioconductor release is 3.3. Bioconductor packages should be
|
||||
;; The latest Bioconductor release is 3.4. Bioconductor packages should be
|
||||
;; updated together.
|
||||
(define %bioconductor-svn-url
|
||||
(string-append "https://readonly:readonly@"
|
||||
"hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/"
|
||||
"hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/"
|
||||
"madman/Rpacks/"))
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -3,6 +3,8 @@
|
|||
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
|
||||
;;; Copyright © 2013, 2015 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2014, 2016 Alex Kost <alezost@gmail.com>
|
||||
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
|
||||
;;; Copyright © 2016 Benz Schenk <benz.schenk@uzh.ch>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -667,24 +669,30 @@ processed, #f otherwise."
|
|||
((head tail ...) head))))
|
||||
(match (assoc-ref opts 'query)
|
||||
(('list-generations pattern)
|
||||
(define (list-generation number)
|
||||
(define (list-generation display-function number)
|
||||
(unless (zero? number)
|
||||
(display-generation profile number)
|
||||
(display-profile-content profile number)
|
||||
(display-function profile number)
|
||||
(newline)))
|
||||
|
||||
(define (diff-profiles profile numbers)
|
||||
(unless (null-list? (cdr numbers))
|
||||
(display-profile-content-diff profile (car numbers) (cadr numbers))
|
||||
(diff-profiles profile (cdr numbers))))
|
||||
(cond ((not (file-exists? profile)) ; XXX: race condition
|
||||
(raise (condition (&profile-not-found-error
|
||||
(profile profile)))))
|
||||
((string-null? pattern)
|
||||
(for-each list-generation (profile-generations profile)))
|
||||
(list-generation display-profile-content
|
||||
(car (profile-generations profile)))
|
||||
(diff-profiles profile (profile-generations profile)))
|
||||
((matching-generations pattern profile)
|
||||
=>
|
||||
(lambda (numbers)
|
||||
(if (null-list? numbers)
|
||||
(exit 1)
|
||||
(leave-on-EPIPE
|
||||
(for-each list-generation numbers)))))
|
||||
(list-generation display-profile-content (car numbers))
|
||||
(diff-profiles profile numbers)))))
|
||||
(else
|
||||
(leave (_ "invalid syntax: ~a~%")
|
||||
pattern)))
|
||||
|
|
|
|||
28
guix/ui.scm
28
guix/ui.scm
|
|
@ -7,6 +7,8 @@
|
|||
;;; Copyright © 2014, 2015 Alex Kost <alezost@gmail.com>
|
||||
;;; Copyright © 2015 David Thompson <davet@gnu.org>
|
||||
;;; Copyright © 2015, 2016 Mathieu Lirzin <mthl@gnu.org>
|
||||
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
|
||||
;;; Copyright © 2016 Benz Schenk <benz.schenk@uzh.ch>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -87,6 +89,7 @@
|
|||
matching-generations
|
||||
display-generation
|
||||
display-profile-content
|
||||
display-profile-content-diff
|
||||
roll-back*
|
||||
switch-to-generation*
|
||||
delete-generation*
|
||||
|
|
@ -1070,6 +1073,31 @@ DURATION-RELATION with the current time."
|
|||
(format #t (_ "~a\t(current)~%") header)
|
||||
(format #t "~a~%" header)))))
|
||||
|
||||
(define (display-profile-content-diff profile gen1 gen2)
|
||||
"Display the changed packages in PROFILE GEN2 compared to generation GEN2."
|
||||
|
||||
(define (equal-entry? first second)
|
||||
(string= (manifest-entry-item first) (manifest-entry-item second)))
|
||||
|
||||
(define (display-entry entry prefix)
|
||||
(match entry
|
||||
(($ <manifest-entry> name version output location _)
|
||||
(format #t " ~a ~a\t~a\t~a\t~a~%" prefix name version output location))))
|
||||
|
||||
(define (list-entries number)
|
||||
(manifest-entries (profile-manifest (generation-file-name profile number))))
|
||||
|
||||
(define (display-diff profile old new)
|
||||
(display-generation profile new)
|
||||
(let ((added (lset-difference
|
||||
equal-entry? (list-entries new) (list-entries old)))
|
||||
(removed (lset-difference
|
||||
equal-entry? (list-entries old) (list-entries new))))
|
||||
(for-each (cut display-entry <> "+") added)
|
||||
(for-each (cut display-entry <> "-") removed)))
|
||||
|
||||
(display-diff profile gen1 gen2))
|
||||
|
||||
(define (display-profile-content profile number)
|
||||
"Display the packages in PROFILE, generation NUMBER, in a human-readable
|
||||
way."
|
||||
|
|
|
|||
1369
po/guix/fr.po
1369
po/guix/fr.po
File diff suppressed because it is too large
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Reference in New Issue