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Merge branch 'master' into core-updates

master
Leo Famulari 2016-10-26 18:59:28 -04:00
parent a19da40630 5d73e30000
commit 02c73adcdf
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44 changed files with 2442 additions and 1045 deletions
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9
configure.ac
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@ -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"])

50
doc/guix.texi
View File

@ -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

71
gnu/build/svg.scm Normal file
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@ -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
View File

@ -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 \

222
gnu/packages/bioinformatics.scm
View File

@ -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)

4
gnu/packages/elf.scm
View File

@ -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)

4
gnu/packages/emacs.scm
View File

@ -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)))

4
gnu/packages/enlightenment.scm
View File

@ -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)))

70
gnu/packages/games.scm
View File

@ -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

2
gnu/packages/gnome.scm
View File

@ -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

4
gnu/packages/gnustep.scm
View File

@ -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

3
gnu/packages/gstreamer.scm
View File

@ -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")

4
gnu/packages/gtk.scm
View File

@ -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"))))

81
gnu/packages/guile.scm
View File

@ -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

6
gnu/packages/irc.scm
View File

@ -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)

9
gnu/packages/linux.scm
View File

@ -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")

58
gnu/packages/lolcode.scm Normal file
View File

@ -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+)))

36
gnu/packages/mail.scm
View File

@ -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

86
gnu/packages/maths.scm
View File

@ -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

45
gnu/packages/messaging.scm
View File

@ -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/"
@ -460,34 +460,27 @@ 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)
;; Make sure all Python scripts run with the correct PYTHONPATH.
(let ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
(for-each (lambda (name)
(let ((file (string-append out "/bin/" name)))
;; Wrapping destroys identification of intended
;; application, so we need to override "APP".
(substitute* file
(("APP=`basename \\$0`")
(string-append "APP=" name)))
(wrap-program file
`("PYTHONPATH" ":" prefix (,path)))))
'("gajim" "gajim-remote" "gajim-history-manager")))
#t)))))
(lambda* (#:key outputs #:allow-other-keys)
;; Make sure all Python scripts run with the correct PYTHONPATH.
(let ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
(for-each (lambda (name)
(let ((file (string-append out "/bin/" name)))
;; Wrapping destroys identification of intended
;; application, so we need to override "APP".
(substitute* file
(("APP=`basename \\$0`")
(string-append "APP=" name)))
(wrap-program file
`("PYTHONPATH" ":" prefix (,path)))))
'("gajim" "gajim-remote" "gajim-history-manager")))
#t)))))
(native-inputs
`(("intltool" ,intltool)))
(propagated-inputs
@ -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

1
gnu/packages/musl.scm
View File

@ -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"))))

39
gnu/packages/networking.scm
View File

@ -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")

46
gnu/packages/patches/coda-use-system-libs.patch Normal file
View File

@ -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 \

25
gnu/packages/patches/hdf-eos2-build-shared.patch Normal file
View File

@ -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@

329
gnu/packages/patches/hdf-eos2-fortrantests.patch Normal file
View File

@ -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

55
gnu/packages/patches/hdf-eos2-remove-gctp.patch Normal file
View File

@ -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

99
gnu/packages/patches/linux-libre-4.1-CVE-2016-5195.patch
View File

@ -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

165
gnu/packages/patches/mupdf-CVE-2016-8674.patch Normal file
View File

@ -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

81
gnu/packages/patches/musl-CVE-2016-8859.patch Normal file
View File

@ -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

46
gnu/packages/patches/notmuch-emacs-25-compatibility-fix.patch
View File

@ -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

3
gnu/packages/pdf.scm
View File

@ -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

82
gnu/packages/psyc.scm
View File

@ -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))))

4
gnu/packages/python.scm
View File

@ -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)))

8
gnu/packages/yubico.scm → gnu/packages/security-token.scm
View File

@ -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)))

26
gnu/packages/ssh.scm
View File

@ -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"))))

94
gnu/packages/statistics.scm
View File

@ -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")

34
gnu/packages/video.scm
View File

@ -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

8
gnu/packages/web.scm
View File

@ -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

92
gnu/services/web.scm
View File

@ -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

39
gnu/system/grub.scm
View File

@ -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)))))

4
guix/import/cran.scm
View File

@ -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/"))

18
guix/scripts/package.scm
View File

@ -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
View File

@ -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."

1381
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