From 6324727770ef4b5d1579ea1be2de5a05552d76db Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 10 Mar 2019 20:16:09 +0100 Subject: gnu: pugixml is a regular input. * gnu/packages/emulators.scm (mame)[native-inputs]: Move PUGIXML ... [inputs]: ... here. * gnu/packages/ftp.scm (filezilla)[native-inputs, inputs]: Likewise. --- gnu/packages/emulators.scm | 2 +- gnu/packages/ftp.scm | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 53d4662588..04a510cdcf 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -1339,7 +1339,6 @@ play them on systems for which they were never designed!") #t)))))) (native-inputs `(("pkg-config" ,pkg-config) - ("pugixml" ,pugixml) ("python-sphinx" ,python-sphinx) ("texinfo" ,texinfo))) (inputs @@ -1354,6 +1353,7 @@ play them on systems for which they were never designed!") ("lua" ,lua) ("portaudio" ,portaudio) ("portmidi" ,portmidi) + ("pugixml" ,pugixml) ("python-wrapper" ,python-wrapper) ("qtbase" ,qtbase) ("rapidjson" ,rapidjson) diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index 916f8f6b0e..605b92d6e7 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -224,7 +224,6 @@ output. (native-inputs `(("gettext" ,gettext-minimal) ("pkg-config" ,pkg-config) - ("pugixml" ,pugixml) ("xdg-utils" ,xdg-utils))) (inputs `(("dbus" ,dbus) @@ -233,6 +232,7 @@ output. ("libfilezilla" ,libfilezilla) ("libidn" ,libidn) ("nettle" ,nettle) + ("pugixml" ,pugixml) ("sqlite" ,sqlite) ("wxwidgets" ,wxwidgets))) (home-page "https://filezilla-project.org") -- cgit v1.2.3 From e2bdf60982311a28f5643bebc4cc4cc47a2f9171 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 10 Mar 2019 20:21:14 +0100 Subject: gnu: FileZilla: Update to 3.41.1. * gnu/packages/ftp.scm (filezilla): Update to 3.41.1. --- gnu/packages/ftp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index 605b92d6e7..3651b92e5d 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -209,14 +209,14 @@ output. (define-public filezilla (package (name "filezilla") - (version "3.40.0") + (version "3.41.1") (source (origin (method url-fetch) (uri (string-append "https://download.filezilla-project.org/client/" "FileZilla_" version "_src.tar.bz2")) (sha256 - (base32 "11b0410fcwrahq5dd7ph10bc09m62sxra4bjp0kj5gph822s0v63")))) + (base32 "0mlv21054fk11rspbnig0q4gph1iqsqm4rpya3wl5is50p33vg5w")))) (build-system gnu-build-system) (arguments ;; Don't let filezilla phone home to check for updates. -- cgit v1.2.3 From 7fda7b8fad5ed47ef36d7d00d8e0652d6c43c268 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 10 Mar 2019 20:43:54 +0100 Subject: gnu: pugixml: Build as shared library. * gnu/packages/patches/pugixml-versioned-libdir.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/xml.scm (pugixml)[source](patches): New field. [arguments]: Instruct the build system to create a shared rather than static library. [native-inputs]: Add PKG-CONFIG. --- .../patches/pugixml-versioned-libdir.patch | 61 ++++++++++++++++++++++ gnu/packages/xml.scm | 8 +-- 2 files changed, 66 insertions(+), 3 deletions(-) create mode 100644 gnu/packages/patches/pugixml-versioned-libdir.patch (limited to 'gnu/packages') diff --git a/gnu/packages/patches/pugixml-versioned-libdir.patch b/gnu/packages/patches/pugixml-versioned-libdir.patch new file mode 100644 index 0000000000..7cd23b1a71 --- /dev/null +++ b/gnu/packages/patches/pugixml-versioned-libdir.patch @@ -0,0 +1,61 @@ +This patch makes pugixml install its headers to a standard location when +built as a shared library. + +Taken from this upstream commit: +https://github.com/zeux/pugixml/commit/daeb8013b20f9c47e85730faaa4131064a1f9c2e + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 90fa6793..d7bc1b20 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -4,7 +4,7 @@ project(pugixml) + + option(BUILD_SHARED_LIBS "Build shared instead of static library" OFF) + option(BUILD_TESTS "Build tests" OFF) +-option(BUILD_PKGCONFIG "Build in PKGCONFIG mode" OFF) ++option(USE_VERSIONED_LIBDIR "Use a private subdirectory to install the headers and libs" OFF) + + set(BUILD_DEFINES "" CACHE STRING "Build defines") + +@@ -55,7 +55,7 @@ endif() + set_target_properties(pugixml PROPERTIES VERSION 1.9 SOVERSION 1) + get_target_property(PUGIXML_VERSION_STRING pugixml VERSION) + +-if(BUILD_PKGCONFIG) ++if(USE_VERSIONED_LIBDIR) + # Install library into its own directory under LIBDIR + set(INSTALL_SUFFIX /pugixml-${PUGIXML_VERSION_STRING}) + endif() +@@ -71,10 +71,8 @@ install(TARGETS pugixml EXPORT pugixml-config + install(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}${INSTALL_SUFFIX}) + install(EXPORT pugixml-config DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/pugixml) + +-if(BUILD_PKGCONFIG) +- configure_file(scripts/pugixml.pc.in ${PROJECT_BINARY_DIR}/pugixml.pc @ONLY) +- install(FILES ${PROJECT_BINARY_DIR}/pugixml.pc DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/pkgconfig) +-endif() ++configure_file(scripts/pugixml.pc.in ${PROJECT_BINARY_DIR}/pugixml.pc @ONLY) ++install(FILES ${PROJECT_BINARY_DIR}/pugixml.pc DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/pkgconfig) + + if(BUILD_TESTS) + file(GLOB TEST_SOURCES tests/*.cpp) +diff --git a/scripts/pugixml.pc.in b/scripts/pugixml.pc.in +index 3c97c28d..804c4d38 100644 +--- a/scripts/pugixml.pc.in ++++ b/scripts/pugixml.pc.in +@@ -1,11 +1,11 @@ + prefix=@CMAKE_INSTALL_PREFIX@ + exec_prefix=${prefix} +-includedir=${prefix}/include/pugixml-@PUGIXML_VERSION_STRING@ +-libdir=${exec_prefix}/lib/pugixml-@PUGIXML_VERSION_STRING@ ++includedir=${prefix}/include@INSTALL_SUFFIX@ ++libdir=${exec_prefix}/lib@INSTALL_SUFFIX@ + + Name: pugixml + Description: Light-weight, simple and fast XML parser for C++ with XPath support. + URL: http://pugixml.org/ + Version: @PUGIXML_VERSION_STRING@ + Cflags: -I${includedir} +-Libs: -L${libdir} -lpugixml +\ No newline at end of file ++Libs: -L${libdir} -lpugixml diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index c80dfb1eac..0ba23bcba4 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -861,14 +861,16 @@ the form of functions.") (method url-fetch) (uri (string-append "https://github.com/zeux/pugixml/releases/download/v" version "/pugixml-" version ".tar.gz")) + (patches (search-patches "pugixml-versioned-libdir.patch")) (sha256 (base32 "19nv3zhik3djp4blc4vrjwrl8dfhzmal8b21sq7y907nhddx6mni")))) (build-system cmake-build-system) (arguments - `(#:configure-flags '("-DCMAKE_CXX_FLAGS=-shared -fPIC" - "-DCMAKE_C_FLAGS=-shared -fPIC") - #:tests? #f)) ; no tests + `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON") + #:tests? #f)) ;no tests + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "https://pugixml.org") (synopsis "Light-weight, simple and fast XML parser for C++ with XPath support") (description -- cgit v1.2.3 From 5ae5932b2f84b58f51f220f5d3103f96a8ef09e8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Mar 2019 22:54:43 +0100 Subject: gnu: ansible: Update to 2.7.8 [fixes CVE-2019-3828]. * gnu/packages/admin.scm (ansible): Update to 2.7.8. --- gnu/packages/admin.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index e26bf030cc..48b8582d52 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1598,14 +1598,13 @@ of supported upstream metrics systems simultaneously.") (define-public ansible (package (name "ansible") - (version "2.7.7") + (version "2.7.8") (source (origin (method url-fetch) (uri (pypi-uri "ansible" version)) (sha256 - (base32 - "0l4id24jqi578xmybvwrz10sm2jhs90gk9gs1y04gfarz4vcj304")))) + (base32 "11yx7vd0mp5gkq428af141dwnrwf8f9cp3f65243qbs9icjxnrrx")))) (build-system python-build-system) (native-inputs `(("python-bcrypt" ,python-bcrypt) -- cgit v1.2.3 From 45fef894eb5b39029633cd0cd907e8ce8c5ab379 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 10 Mar 2019 23:29:39 +0100 Subject: gnu: gnome-shell: Avoid top-level reference to inkscape. Fixes . Reported by Marius Bakke . * gnu/packages/gnome.scm (gnome-shell)[source](snippet): Remove reference to INKSCAPE. Instead, simply copy the SVG file to data/theme. [arguments]: Add 'convert-logo-to-png' phase. [native-inputs]: Add INKSCAPE. --- gnu/packages/gnome.scm | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 12ce39cb4a..0344e42444 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -5695,10 +5695,9 @@ properties, screen resolution, and other GNOME parameters.") (copy-file #$(file-append %artwork-repository "/slim/0.x/background.png") "data/theme/guix-background.png") - (invoke #+(file-append inkscape "/bin/inkscape") - "--export-png=data/theme/guix-logo.png" - #$(file-append %artwork-repository - "/logo/Guix-horizontal-white.svg")) + (copy-file #$(file-append %artwork-repository + "/logo/Guix-horizontal-white.svg") + "data/theme/guix-logo.svg") #t)))) (build-system glib-or-gtk-build-system) (arguments @@ -5711,6 +5710,11 @@ properties, screen resolution, and other GNOME parameters.") (invoke "make" "-C" "data" "theme/gnome-shell.css" "theme/gnome-shell-high-contrast.css"))) + (add-before 'build 'convert-logo-to-png + (lambda* (#:key inputs #:allow-other-keys) + ;; Convert the logo from SVG to PNG. + (invoke "inkscape" "--export-png=data/theme/guix-logo.png" + "data/theme/guix-logo.svg"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -5741,7 +5745,8 @@ properties, screen resolution, and other GNOME parameters.") ("pkg-config" ,pkg-config) ("python" ,python) ("xsltproc" ,libxslt) - ("ruby-sass" ,ruby-sass))) + ("ruby-sass" ,ruby-sass) + ("inkscape" ,inkscape))) (inputs `(("accountsservice" ,accountsservice) ("caribou" ,caribou) -- cgit v1.2.3 From 0189045904e9c29ee112091f7e51f9086a385ab2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Mar 2019 23:19:50 +0100 Subject: gnu: snd: Update to 19.2. * gnu/packages/audio.scm (snd): Update to 19.2. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 395cdfed0d..d77ad3d1c4 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -3361,14 +3361,14 @@ on the ALSA software PCM plugin.") (define-public snd (package (name "snd") - (version "17.7") + (version "19.2") (source (origin (method url-fetch) (uri (string-append "ftp://ccrma-ftp.stanford.edu/pub/Lisp/" "snd-" version ".tar.gz")) (sha256 (base32 - "1vm0dy5qlycqkima7y5ajzvazyjybifa803fabjcpncjz08c26vp")))) + "1a6ls2hyvggss12idca22hq5vsq4jw2xkwrx22dx29i9926gdr6h")))) (build-system glib-or-gtk-build-system) (arguments `(#:tests? #f ; no tests -- cgit v1.2.3 From c170080689cb9fe361ec1597794646783ae92a5e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Mar 2019 23:26:08 +0100 Subject: gnu: console-setup: Update to 1.190. * gnu/packages/xorg.scm (console-setup): Update to 1.190. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 9bc23c4279..3434fbee2f 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -6370,7 +6370,7 @@ output.") (define-public console-setup (package (name "console-setup") - (version "1.189") + (version "1.190") (source (origin (method git-fetch) @@ -6378,7 +6378,7 @@ output.") (url "https://salsa.debian.org/installer-team/console-setup.git") (commit version))) (sha256 - (base32 "09rfnnhwjm98im711v6jrgl49iy5n1b26x12zzk5rw6g1667mz86")) + (base32 "0qklm9ww1wap2bs7hp31xkfjyhdrirg2mk4hiv7h6fiqckzmdwvd")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (arguments -- cgit v1.2.3 From 77ad8ec4fcbad17d246b3a50076d82cfac1218a2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Mar 2019 23:31:14 +0100 Subject: gnu: xf86-video-amdgpu: Update to 19.0.0. * gnu/packages/xorg.scm (xf86-video-amdgpu): Update to 19.0.0. [source]: Re-indent. --- gnu/packages/xorg.scm | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 3434fbee2f..17a8b1414b 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -2624,17 +2624,14 @@ as USB mice.") (define-public xf86-video-amdgpu (package (name "xf86-video-amdgpu") - (version "18.1.0") + (version "19.0.0") (source - (origin - (method url-fetch) - (uri (string-append - "mirror://xorg/individual/driver/xf86-video-amdgpu-" - version - ".tar.bz2")) - (sha256 - (base32 - "0wlnb929l3yqj4hdkzyxyhbaph13ac4villajgmbh66pa6xja7z1")))) + (origin + (method url-fetch) + (uri (string-append "mirror://xorg/individual/driver/" + "xf86-video-amdgpu-" version ".tar.bz2")) + (sha256 + (base32 "0lag9jxd752ja7m7ngz3dmqffb5wbx4crdwjw74qx42m8xyi8dl8")))) (build-system gnu-build-system) (inputs `(("xorg-server" ,xorg-server))) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From 0330d6b2bfe98f5331b8761dc80083be80d3cf78 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Mar 2019 23:31:25 +0100 Subject: gnu: xf86-video-ati: Update to 19.0.0. * gnu/packages/xorg.scm (xf86-video-ati): Update to 19.0.0. [source]: Re-indent. --- gnu/packages/xorg.scm | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 17a8b1414b..a029d23953 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -2691,17 +2691,14 @@ X server.") (define-public xf86-video-ati (package (name "xf86-video-ati") - (version "18.0.1") + (version "19.0.0") (source - (origin - (method url-fetch) - (uri (string-append - "mirror://xorg/individual/driver/xf86-video-ati-" - version - ".tar.bz2")) - (sha256 - (base32 - "180l2yw8c63cbcs3zk729vx439aig1d7yicpyxj0nmfl4y0kpskj")))) + (origin + (method url-fetch) + (uri (string-append "mirror://xorg/individual/driver/" + "xf86-video-ati-" version ".tar.bz2")) + (sha256 + (base32 "0mzl7yp3qkvankh22758sgpaw9mg6jxsfbg6wy0nxfw4i0qpv46x")))) (build-system gnu-build-system) (inputs `(("mesa" ,mesa) ("xorgproto" ,xorgproto) -- cgit v1.2.3 From fd46742dd2191c7762590a15bc054bbfd1feb3fc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 00:08:04 +0100 Subject: gnu: nginx: Update to 1.15.9. * gnu/packages/web.scm (nginx): Update to 1.15.9. --- gnu/packages/web.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index d9b7def67b..e6f339f7b7 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -194,16 +194,18 @@ Interface} specification.") (define-public nginx (package (name "nginx") - ;; Consider updating the nginx-documentation package if the nginx package is - ;; updated. - (version "1.14.2") + ;; Track the ‘mainline’ branch. Upstream considers it more reliable than + ;; ’stable’ and recommends that “in general you deploy the NGINX mainline + ;; branch at all times” (https://www.nginx.com/blog/nginx-1-6-1-7-released/) + ;; Consider updating the nginx-documentation package together with this one. + (version "1.15.9") (source (origin (method url-fetch) (uri (string-append "https://nginx.org/download/nginx-" version ".tar.gz")) (sha256 (base32 - "15wppq12qmq8acjs35xfj61czhf9cdc0drnl5mm8hcg3aihryb80")))) + "0hxfsz1117r91b9fb5hjddyrf1czvb36lh1z7zalqqdskfcbmkz4")))) (build-system gnu-build-system) (inputs `(("openssl" ,openssl) ("pcre" ,pcre) -- cgit v1.2.3 From 266cd19eb93ed5e2430a3280666cb13128821749 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 00:23:53 +0100 Subject: gnu: nginx-documentation: Update to 2019-03-01-2345-7ef11708457e. * gnu/packages/web.scm (nginx-documentation): Update to 2019-03-01-2345-7ef11708457e. [arguments]: Simplify substitution. --- gnu/packages/web.scm | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index e6f339f7b7..0d15981a56 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -329,13 +329,13 @@ documentation.") (license l:bsd-2)))) (define-public nginx-documentation - ;; This documentation should be relevant for nginx@1.13.11. - (let ((revision 2131) - (changeset "dbaf3950f8e9")) + ;; This documentation should be relevant for nginx@1.15.9. + (let ((revision 2345) + (changeset "7ef11708457e")) (package (name "nginx-documentation") (version - (simple-format #f "2018-04-04-~A-~A" revision changeset)) + (simple-format #f "2019-03-01-~A-~A" revision changeset)) (source (origin (method hg-fetch) (uri (hg-reference @@ -344,7 +344,7 @@ documentation.") (file-name (string-append name "-" version)) (sha256 (base32 - "0acdjsdaqixzh9g9s6db552v4pan4nqrllyqapay9ns9yzh1hrp7")))) + "15975jvh53mnsgi4hhgrwdwy3by23v4kxnhy2vnkziq8v7wkmy4y")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no test suite @@ -362,8 +362,7 @@ documentation.") ;; banner. (substitute* "xslt/style.xslt" (("#banner \\{ background: black;") - "#banner { background: black; - display: none;")) + "#banner { display: none;")) (invoke "make") #t))) (replace 'install -- cgit v1.2.3 From a9644c5a4925a6bb7836216ab7a3bb32e8c2611f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 00:53:07 +0100 Subject: gnu: you-get: Update to 0.4.1270. * gnu/packages/video.scm (you-get): Update to 0.4.1270. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index d5dc3d29e1..851b2127bf 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1531,7 +1531,7 @@ other site that youtube-dl supports.") (define-public you-get (package (name "you-get") - (version "0.4.1256") + (version "0.4.1270") (source (origin (method git-fetch) (uri (git-reference @@ -1540,7 +1540,7 @@ other site that youtube-dl supports.") (file-name (git-file-name name version)) (sha256 (base32 - "1hzr7ha1jvbc0v2bwl7s08ymwdmvb0f2jz4xp1fi6agq5y3ca1iv")))) + "123g6x8sh32v4yn4ss55lfw7j79hgl3l6aiwgrk4ndq7dzhnz46q")))) (build-system python-build-system) (inputs `(("ffmpeg" ,ffmpeg))) ; for multi-part and >=1080p videos -- cgit v1.2.3 From dbfb24824bfc7f5cfe6913ff2ec06f7a33e49895 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 00:56:04 +0100 Subject: gnu: stunnel: Update to 5.50. * gnu/packages/web.scm (stunnel): Update to 5.50. --- gnu/packages/web.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 0d15981a56..463f18b7f0 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4764,15 +4764,14 @@ tools like SSH (Secure Shell) to reach the outside world.") (define-public stunnel (package (name "stunnel") - (version "5.48") + (version "5.50") (source (origin (method url-fetch) (uri (string-append "https://www.stunnel.org/downloads/stunnel-" version ".tar.gz")) (sha256 - (base32 - "1pxqn9ixl80nrhfq12igyi874653jclji56hh9w24snf0aixa48h")))) + (base32 "0j811iakljjxw39qchmqf235jdkwixb0i4xxjyi55f08558947cm")))) (build-system gnu-build-system) (native-inputs ;; For tests. -- cgit v1.2.3 From 585be42f46543d04f51153071f7610e5835c8a27 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 01:08:22 +0100 Subject: gnu: texmaker: Update to 5.0.3. * gnu/packages/tex.scm (texmaker): Update to 5.0.3. --- gnu/packages/tex.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index a0eeb23950..584b2bcfa5 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -9,7 +9,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2017 Leo Famulari ;;; Copyright © 2017 Marius Bakke -;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018 Danny Milosavljevic ;;; Copyright © 2018 Arun Isaac ;;; @@ -5457,14 +5457,14 @@ PDF documents.") (define-public texmaker (package (name "texmaker") - (version "5.0.2") + (version "5.0.3") (source (origin (method url-fetch) (uri (string-append "http://www.xm1math.net/texmaker/texmaker-" version ".tar.bz2")) (sha256 (base32 - "0y81mjm89b99pr9svcwpaf4iz2q9pc9hjas5kiwd1pbgl5vqskm9")))) + "0vrj9w5lk3vf6138n5bz8phmy3xp5kv4dq1rgirghcf4hbxdyx30")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit v1.2.3 From 129294e7483e22f60d1fb67db6ac482dd1346d68 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 01:10:09 +0100 Subject: gnu: youtube-dl: Update to 2019.03.09. * gnu/packages/video.scm (youtube-dl): Update to 2019.03.09. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 851b2127bf..6d17f920ea 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1412,7 +1412,7 @@ access to mpv's powerful playback capabilities.") (define-public youtube-dl (package (name "youtube-dl") - (version "2019.03.01") + (version "2019.03.09") (source (origin (method url-fetch) (uri (string-append "https://github.com/rg3/youtube-dl/releases/" @@ -1420,7 +1420,7 @@ access to mpv's powerful playback capabilities.") version ".tar.gz")) (sha256 (base32 - "0bxk6adyppdv50jnp5cika8wc6wfgd6d8zbg1njgmcs1pxskllmf")))) + "1g46mrmzr31b2r6x0g6wmg3j00qc8l6cbzmdik0l5vwjfcrdvghf")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion -- cgit v1.2.3 From 7d3ac6c08e165d60cabe343c44ffb520b0306142 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 01:10:53 +0100 Subject: gnu: avidemux: Don't use NAME in source URI. * gnu/packages/video.scm (avidemux)[source]: Hard-code NAME. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 6d17f920ea..ef7376597f 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1820,8 +1820,8 @@ for use with HTML5 video.") (source (origin (method url-fetch) (uri (string-append - "mirror://sourceforge/" name "/" name "/" version "/" - name "_" version ".tar.gz")) + "mirror://sourceforge/avidemux/avidemux/" version "/" + "avidemux_" version ".tar.gz")) (sha256 (base32 "15g9h791qbnmycabbbl7s2b3n3xpvygm88qrfk35g2cw6957ik9w")) -- cgit v1.2.3 From 642de36b9eded5d4bbcb06560ce963b60e933cec Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 01:28:21 +0100 Subject: gnu: avidemux: Factorise ffmpeg version. * gnu/packages/video.scm (avidemux)[arguments]: Move oft-repeated hard-coded ffmpeg version number to a single let-bound variable. --- gnu/packages/video.scm | 135 +++++++++++++++++++++++++------------------------ 1 file changed, 68 insertions(+), 67 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index ef7376597f..9d47f6d903 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1857,73 +1857,74 @@ for use with HTML5 video.") #:phases ;; Make sure files inside the included ffmpeg tarball are ;; patch-shebanged. - (modify-phases %standard-phases - (add-before 'patch-source-shebangs 'unpack-ffmpeg - (lambda _ - (with-directory-excursion "avidemux_core/ffmpeg_package" - (invoke "tar" "xf" "ffmpeg-3.3.7.tar.bz2") - (delete-file "ffmpeg-3.3.7.tar.bz2")) - #t)) - (add-after 'patch-source-shebangs 'repack-ffmpeg - (lambda _ - (with-directory-excursion "avidemux_core/ffmpeg_package" - (substitute* "ffmpeg-3.3.7/configure" - (("#! /bin/sh") (string-append "#!" (which "sh")))) - (invoke "tar" "cjf" "ffmpeg-3.3.7.tar.bz2" "ffmpeg-3.3.7" - ;; avoid non-determinism in the archive - "--sort=name" "--mtime=@0" - "--owner=root:0" "--group=root:0") - (delete-file-recursively "ffmpeg-3.3.7")) - #t)) - (replace 'configure - (lambda _ - ;; Copy-paste settings from the cmake build system. - (setenv "CMAKE_LIBRARY_PATH" (getenv "LIBRARY_PATH")) - (setenv "CMAKE_INCLUDE_PATH" (getenv "C_INCLUDE_PATH")) - #t)) - (replace 'build - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib")) - (top (getcwd)) - (sdl (assoc-ref inputs "sdl")) - (build_component - (lambda* (component srcdir #:optional (args '())) - (let ((builddir (string-append "build_" component))) - (mkdir builddir) - (with-directory-excursion builddir - (apply invoke "cmake" - "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" - (string-append "-DCMAKE_INSTALL_PREFIX=" out) - (string-append "-DCMAKE_INSTALL_RPATH=" lib) - (string-append "-DCMAKE_SHARED_LINKER_FLAGS=" - "\"-Wl,-rpath=" lib "\"") - (string-append "-DAVIDEMUX_SOURCE_DIR=" top) - (string-append "-DSDL_INCLUDE_DIR=" - sdl "/include/SDL") - (string-append "../" srcdir) - "-DENABLE_QT5=True" - args) - (invoke "make" "-j" - (number->string (parallel-job-count))) - (invoke "make" "install")))))) - (mkdir out) - (build_component "core" "avidemux_core") - (build_component "cli" "avidemux/cli") - (build_component "qt4" "avidemux/qt4") - (build_component "plugins_common" "avidemux_plugins" - '("-DPLUGIN_UI=COMMON")) - (build_component "plugins_cli" "avidemux_plugins" - '("-DPLUGIN_UI=CLI")) - (build_component "plugins_qt4" "avidemux_plugins" - '("-DPLUGIN_UI=QT4")) - (build_component "plugins_settings" "avidemux_plugins" - '("-DPLUGIN_UI=SETTINGS")) - ;; Remove .exe and .dll file. - (delete-file-recursively - (string-append out "/share/ADM6_addons")) - #t))) - (delete 'install)))) + (let ((ffmpeg "ffmpeg-3.3.7")) + (modify-phases %standard-phases + (add-before 'patch-source-shebangs 'unpack-ffmpeg + (lambda _ + (with-directory-excursion "avidemux_core/ffmpeg_package" + (invoke "tar" "xf" (string-append ffmpeg ".tar.bz2")) + (delete-file (string-append ffmpeg ".tar.bz2"))) + #t)) + (add-after 'patch-source-shebangs 'repack-ffmpeg + (lambda _ + (with-directory-excursion "avidemux_core/ffmpeg_package" + (substitute* (string-append ffmpeg "/configure") + (("#! /bin/sh") (string-append "#!" (which "sh")))) + (invoke "tar" "cjf" (string-append ffmpeg ".tar.bz2") ffmpeg + ;; avoid non-determinism in the archive + "--sort=name" "--mtime=@0" + "--owner=root:0" "--group=root:0") + (delete-file-recursively ffmpeg)) + #t)) + (replace 'configure + (lambda _ + ;; Copy-paste settings from the cmake build system. + (setenv "CMAKE_LIBRARY_PATH" (getenv "LIBRARY_PATH")) + (setenv "CMAKE_INCLUDE_PATH" (getenv "C_INCLUDE_PATH")) + #t)) + (replace 'build + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (top (getcwd)) + (sdl (assoc-ref inputs "sdl")) + (build_component + (lambda* (component srcdir #:optional (args '())) + (let ((builddir (string-append "build_" component))) + (mkdir builddir) + (with-directory-excursion builddir + (apply invoke "cmake" + "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" + (string-append "-DCMAKE_INSTALL_PREFIX=" out) + (string-append "-DCMAKE_INSTALL_RPATH=" lib) + (string-append "-DCMAKE_SHARED_LINKER_FLAGS=" + "\"-Wl,-rpath=" lib "\"") + (string-append "-DAVIDEMUX_SOURCE_DIR=" top) + (string-append "-DSDL_INCLUDE_DIR=" + sdl "/include/SDL") + (string-append "../" srcdir) + "-DENABLE_QT5=True" + args) + (invoke "make" "-j" + (number->string (parallel-job-count))) + (invoke "make" "install")))))) + (mkdir out) + (build_component "core" "avidemux_core") + (build_component "cli" "avidemux/cli") + (build_component "qt4" "avidemux/qt4") + (build_component "plugins_common" "avidemux_plugins" + '("-DPLUGIN_UI=COMMON")) + (build_component "plugins_cli" "avidemux_plugins" + '("-DPLUGIN_UI=CLI")) + (build_component "plugins_qt4" "avidemux_plugins" + '("-DPLUGIN_UI=QT4")) + (build_component "plugins_settings" "avidemux_plugins" + '("-DPLUGIN_UI=SETTINGS")) + ;; Remove .exe and .dll file. + (delete-file-recursively + (string-append out "/share/ADM6_addons")) + #t))) + (delete 'install))))) (home-page "http://fixounet.free.fr/avidemux/") (synopsis "Video editor") (description "Avidemux is a video editor designed for simple cutting, -- cgit v1.2.3 From 4d34fe46810b41601af82af181c257dbaa999acd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 01:34:03 +0100 Subject: gnu: avidemux: Update to 2.7.2. * gnu/packages/video.scm (avidemux): Update to 2.7.2. [arguments]: Update version of included ffmpeg. --- gnu/packages/video.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 9d47f6d903..c8fd6c1a34 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1816,7 +1816,7 @@ for use with HTML5 video.") (define-public avidemux (package (name "avidemux") - (version "2.7.1") + (version "2.7.2") (source (origin (method url-fetch) (uri (string-append @@ -1824,7 +1824,7 @@ for use with HTML5 video.") "avidemux_" version ".tar.gz")) (sha256 (base32 - "15g9h791qbnmycabbbl7s2b3n3xpvygm88qrfk35g2cw6957ik9w")) + "07fdz3y4iln7cizikdjj96dqvp2f8zzhs31ncxxwzdkngn5v8138")) (patches (search-patches "avidemux-install-to-lib.patch")))) (build-system cmake-build-system) (native-inputs @@ -1857,7 +1857,7 @@ for use with HTML5 video.") #:phases ;; Make sure files inside the included ffmpeg tarball are ;; patch-shebanged. - (let ((ffmpeg "ffmpeg-3.3.7")) + (let ((ffmpeg "ffmpeg-4.1.1")) (modify-phases %standard-phases (add-before 'patch-source-shebangs 'unpack-ffmpeg (lambda _ -- cgit v1.2.3 From d05c14dfc9f41d7aa07a64b22ad7bf0ecf5a1725 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 02:04:36 +0100 Subject: gnu: python-acme, certbot: Update to 0.32.0. * gnu/packages/tls.scm (python-acme): Update to 0.32.0. (certbot)[source]: Update hash. [native-inputs]: Replace python-nose with python-pytest. [propagated-inputs]: Add python-cryptography. --- gnu/packages/tls.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 26a2eaa2a7..bdfbc003d3 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -533,13 +533,13 @@ netcat implementation that supports TLS.") (package (name "python-acme") ;; Remember to update the hash of certbot when updating python-acme. - (version "0.31.0") + (version "0.32.0") (source (origin (method url-fetch) (uri (pypi-uri "acme" version)) (sha256 (base32 - "1gxjv09c695lj8swspa390nch117i60qkrgy135383vfk00jsp3y")))) + "1v0skyrjnbxq0lfmia5k6jy29iig4sxbi9j9q367xsw0g25wxvqf")))) (build-system python-build-system) (arguments `(#:phases @@ -590,7 +590,7 @@ netcat implementation that supports TLS.") (uri (pypi-uri name version)) (sha256 (base32 - "0wq4jgyzli684h154w26xplp0fzyks2vlrnmhafhyb0h1bw9cc8c")))) + "1j63i0j019q0d3l5rx14fv4nxy01nplhk7q2k2fq10vxl0jlxff0")))) (build-system python-build-system) (arguments `(,@(substitute-keyword-arguments (package-arguments python-acme) @@ -608,8 +608,8 @@ netcat implementation that supports TLS.") #t)))))))) ;; TODO: Add optional inputs for testing. (native-inputs - `(("python-nose" ,python-nose) - ("python-mock" ,python-mock) + `(("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) ;; For documentation ("python-sphinx" ,python-sphinx) ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme) @@ -618,6 +618,7 @@ netcat implementation that supports TLS.") ("texinfo" ,texinfo))) (propagated-inputs `(("python-acme" ,python-acme) + ("python-cryptography" ,python-cryptography) ("python-zope-interface" ,python-zope-interface) ("python-pyrfc3339" ,python-pyrfc3339) ("python-pyopenssl" ,python-pyopenssl) -- cgit v1.2.3 From 93a72fa7c92e49f74066856aa4e6dcf0830d4668 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 02:05:50 +0100 Subject: gnu: xvid: Update to 1.3.5. * gnu/packages/video.scm (xvid): Update to 1.3.5. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index c8fd6c1a34..c97dbbe204 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1984,7 +1984,7 @@ format changes.") (define-public xvid (package (name "xvid") - (version "1.3.4") + (version "1.3.5") (source (origin (method url-fetch) (uri (string-append @@ -1992,7 +1992,7 @@ format changes.") version ".tar.bz2")) (sha256 (base32 - "1xwbmp9wqshc0ckm970zdpi0yvgqxlqg0s8bkz98mnr8p2067bsz")))) + "1d0hy1w9sn6491a3vhyf3vmhq4xkn6yd4ralx1191s6qz5wz483w")))) (build-system gnu-build-system) (native-inputs `(("yasm" ,yasm))) (arguments -- cgit v1.2.3 From a5c8460a6d8141e48ef839656932dc389a9ed499 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 11 Mar 2019 10:06:05 +0200 Subject: gnu: crawl: Build without SSE only on some architecures. This is a follow-up to b89284407fd5d865ca7cc8622459692cec9297cf. * gnu/packages/games.scm (crawl)[arguments]: Remove custom 'patch-flags phase, add make-flag on non-x86* architectures to build without SSE. --- gnu/packages/games.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 295007319d..0a8c3e9452 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4441,12 +4441,17 @@ fish. The whole game is accompanied by quiet, comforting music.") ("python-pyyaml" ,python-pyyaml) ("pkg-config" ,pkg-config))) (arguments - '(#:make-flags + `(#:make-flags (let* ((sqlite (assoc-ref %build-inputs "sqlite")) (out (assoc-ref %outputs "out"))) (list (string-append "SQLITE_INCLUDE_DIR=" sqlite "/include") (string-append "prefix=" out) "SAVEDIR=~/.crawl" + ;; Don't compile with SSE on systems which don't use it + ,@(match (%current-system) + ((or "i686-linux" "x86_64-linux") + '()) + (_ '("NOSSE=TRUE"))) ;; don't build any bundled dependencies "BUILD_LUA=" "BUILD_SQLITE=" @@ -4454,11 +4459,6 @@ fish. The whole game is accompanied by quiet, comforting music.") "-Csource")) #:phases (modify-phases %standard-phases - (add-after 'unpack 'patch-flags - (lambda _ - (substitute* "source/Makefile" - (("-mfpmath=sse -msse2") "")) - #t)) (add-after 'unpack 'find-SDL-image (lambda _ (substitute* "source/windowmanager-sdl.cc" -- cgit v1.2.3 From 2206f236796002bb120baf0777d002005fd09a6f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 5 Mar 2019 21:18:08 +0200 Subject: gnu: Add eternalterminal. * gnu/packages/terminals.scm (eternalterminal): New variable. --- gnu/packages/terminals.scm | 52 +++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 51 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index b3979d8a41..2961d61604 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner +;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner ;;; Copyright © 2016 Mckinley Olsen ;;; Copyright © 2016, 2017 Alex Griffin ;;; Copyright © 2016 David Craven @@ -44,6 +44,7 @@ #:use-module (gnu packages autotools) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages crypto) #:use-module (gnu packages docbook) #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) @@ -60,6 +61,8 @@ #:use-module (gnu packages perl) #:use-module (gnu packages perl-check) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages popt) + #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) @@ -1015,3 +1018,50 @@ arbitrary programs of your choice. This is useful for browsing the history comfortably in a pager or editor. @end itemize") (license license:gpl3+))) + +(define-public eternalterminal + (package + (name "eternalterminal") + (version "5.1.9") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/MisterTea/EternalTerminal.git") + (commit (string-append "et-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "07ynkcnk3z6wafdlnzdxcd308cw1rzabxyq47ybj79lyji3wsgk7")))) + (build-system cmake-build-system) + (arguments + '(#:configure-flags '("-DBUILD_TEST=ON") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'insert-googletests + (lambda* (#:key inputs #:allow-other-keys) + (let ((tests (assoc-ref inputs "googletest"))) + (invoke "tar" "xvf" tests "-C" "external/googletest" + "--strip-components=1")))) + (add-after 'install 'dont-provide-gtest-libraries + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (delete-file-recursively (string-append out "/include")) + (delete-file-recursively (string-append out "/lib"))) + #t))))) + (inputs + `(("gflags" ,gflags) + ("libsodium" ,libsodium) + ("protobuf" ,protobuf))) + (native-inputs + `(("googletest" ,(package-source googletest)))) + (home-page "https://mistertea.github.io/EternalTerminal/") + (synopsis "Remote shell that reconnects without interrupting the session") + (description "@dfn{Eternal Terminal} (ET) is a remote shell that +automatically reconnects without interrupting the session. ET uses SSH to +initialize a secure connection. Unlike SSH sessions, which must be killed and +reconnected after a network outage an ET session will survive network outages +and IP roaming. ET provides the same core functionality as @command{mosh}, +while also supporting native scrolling and @command{tmux} control mode +(@code{tmux -CC}).") + (license license:asl2.0))) -- cgit v1.2.3 From 32ede5bbf9e9d6b118bf595af9d1ecf4a9693e1a Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 11 Mar 2019 07:14:01 -0400 Subject: gnu: linux-libre@4.19: Update to 4.19.28. * gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.28. (%linux-libre-4.19-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 3b7a769fac..e746b0a534 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -428,8 +428,8 @@ It has been modified to remove all non-free binary blobs.") #:patches %linux-libre-5.0-patches #:configuration-file kernel-config)) -(define %linux-libre-4.19-version "4.19.27") -(define %linux-libre-4.19-hash "055n4s4yrkcrwkdsxbf1q1zyxmpabf7kba8d0phpfadian3wr4s0") +(define %linux-libre-4.19-version "4.19.28") +(define %linux-libre-4.19-hash "0j65gp9z3qrygx67mkhm4ri3pj1pz0gdwcdlds2ypg53rh12jc0a") (define %linux-libre-4.19-patches (list %boot-logo-patch -- cgit v1.2.3 From 3edd7a3f4c8d6faeb6c8229ff053f66947459a71 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 11 Mar 2019 07:14:58 -0400 Subject: gnu: linux-libre: Update to 5.0.1. * gnu/packages/linux.scm (%linux-libre-version): Update to 5.0.1. (%linux-libre-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index e746b0a534..e4a58834a9 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -414,8 +414,8 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." It has been modified to remove all non-free binary blobs.") (license license:gpl2))) -(define %linux-libre-version "5.0") -(define %linux-libre-hash "18gs0kl5xvbmh725m7crg6iyqw3p8qq421aql7z0nlk035fh5xbx") +(define %linux-libre-version "5.0.1") +(define %linux-libre-hash "0izbdpml170g5jg87ccnf2q1hc01gsyiy1gqxnqzzi3pri00dfyz") (define %linux-libre-5.0-patches (list %boot-logo-patch -- cgit v1.2.3 From 0234f4af2709baa62822a84d12e543c203922590 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 10:32:36 +0100 Subject: gnu: perl-image-exiftool: Add upstream URL. * gnu/packages/photo.scm (perl-image-exiftool)[source]: Also download from the home page. --- gnu/packages/photo.scm | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index 15857c6cad..88b9ea023f 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -208,14 +208,17 @@ MTP, and much more.") (package (name "perl-image-exiftool") (version "11.11") - (source (origin - (method url-fetch) - (uri (string-append - "mirror://cpan/authors/id/E/EX/EXIFTOOL/Image-ExifTool-" - version ".tar.gz")) - (sha256 - (base32 - "1szg1k82nz88pp5n7lg71ja7q3hh5i5f9bcbb7m482dwrmsywkp6")))) + (source + (origin + (method url-fetch) + (uri (list + (string-append "mirror://cpan/authors/id/E/EX/EXIFTOOL/" + "Image-ExifTool-" version ".tar.gz") + ;; New releases may take a while to hit CPAN. + (string-append "https://www.sno.phy.queensu.ca/~phil/exiftool/" + "Image-ExifTool-" version ".tar.gz"))) + (sha256 + (base32 "1szg1k82nz88pp5n7lg71ja7q3hh5i5f9bcbb7m482dwrmsywkp6")))) (build-system perl-build-system) (arguments '(#:phases -- cgit v1.2.3 From 130c12c9b9a61ec6863307c55cf7685527684b7e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 10:34:44 +0100 Subject: gnu: perl-image-exiftool: Update to 11.31. * gnu/packages/photo.scm (perl-image-exiftool): Update to 11.31. --- gnu/packages/photo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index 88b9ea023f..ec693d72b3 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -207,7 +207,7 @@ MTP, and much more.") (define-public perl-image-exiftool (package (name "perl-image-exiftool") - (version "11.11") + (version "11.31") (source (origin (method url-fetch) @@ -218,7 +218,7 @@ MTP, and much more.") (string-append "https://www.sno.phy.queensu.ca/~phil/exiftool/" "Image-ExifTool-" version ".tar.gz"))) (sha256 - (base32 "1szg1k82nz88pp5n7lg71ja7q3hh5i5f9bcbb7m482dwrmsywkp6")))) + (base32 "1kplb7hvhrhqxkr4ddc44q7a3fs0r8svv2jlh325nwkfi7aa5kz5")))) (build-system perl-build-system) (arguments '(#:phases -- cgit v1.2.3 From 33238b552000aa730d6e306df4fadbac2ad2db02 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 11:05:45 +0100 Subject: gnu: picocom: Update to 3.1. * gnu/packages/terminals.scm (picocom): Update to 3.1. --- gnu/packages/terminals.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index 2961d61604..1217088491 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -341,7 +341,7 @@ combining, and so on, with a simple interface.") (define-public picocom (package (name "picocom") - (version "2.2") + (version "3.1") (source (origin (method git-fetch) (uri (git-reference @@ -350,15 +350,16 @@ combining, and so on, with a simple interface.") (file-name (git-file-name name version)) (sha256 (base32 - "06b2ic34dnxc73cprc5imi3iamlhsv623sbg9vj5h5rvs586dwjx")))) + "1vvjydqf0ax47nvdyyl67jafw5b3sfsav00xid6qpgia1gs2r72n")))) (build-system gnu-build-system) (arguments `(#:make-flags '("CC=gcc") - #:tests? #f ; No tests + #:tests? #f ; no tests #:phases (modify-phases %standard-phases - (delete 'configure) + (delete 'configure) ; no configure script (replace 'install + ;; The Makefile lacks an ‘install’ target. (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin")) -- cgit v1.2.3 From 5e5bd818437f325ca4f6f9e44578bedbc4067e85 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 11:07:11 +0100 Subject: gnu: picocom: Fix description. * gnu/packages/terminals.scm (picocom)[synopsis]: Shorten. [description]: Properly introduce. --- gnu/packages/terminals.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index 1217088491..536a48986f 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -367,11 +367,12 @@ combining, and so on, with a simple interface.") (install-file "picocom" bin) (install-file "picocom.1" man))))))) (home-page "https://github.com/npat-efault/picocom") - (synopsis "Minimal dumb-terminal emulation program") - (description "It was designed to serve as a simple, manual, modem -configuration, testing, and debugging tool. It has also serves well -as a low-tech serial communications program to allow access to all -types of devices that provide serial consoles.") + (synopsis "Minimal dumb-terminal emulator") + (description + "Picocom is a minimal dumb-terminal emulation program. It was designed to +serve as a simple and manual modem configuration, testing, and debugging tool. +It also serves well as a low-tech serial communications program to allow access +to all types of devices that provide serial consoles.") (license license:gpl2+))) (define-public beep -- cgit v1.2.3 From a699a81b84ba314e10c60a62a52468695b64bfbc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 12:09:09 +0100 Subject: gnu: skalibs: Update to 2.8.0.1. * gnu/packages/skarnet.scm (skalibs): Update to 2.8.0.1. --- gnu/packages/skarnet.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 9ba37b0f19..0b1bd470b1 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -29,15 +29,14 @@ (define-public skalibs (package (name "skalibs") - (version "2.7.0.0") + (version "2.8.0.1") (source (origin (method url-fetch) (uri (string-append "http://skarnet.org/software/skalibs/skalibs-" version ".tar.gz")) (sha256 - (base32 - "0mnprdf4w4ami0db22rwd111m037cdmn2p8xa4i8cbwxcrv4sjcn")))) + (base32 "00mh15jx3p4xzhkslxzpgi1c0xglywck1ik7ffi0hfwcq092wla7")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no tests exist -- cgit v1.2.3 From 5c9bf737c40fe64c773cd54828e632d30a0cde83 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 12:23:18 +0100 Subject: gnu: execline: Update to 2.5.1.0. * gnu/packages/skarnet.scm (execline): Update to 2.5.1.0. --- gnu/packages/skarnet.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 0b1bd470b1..23998d7ced 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -61,15 +61,14 @@ and file system operations. It is used by all skarnet.org software.") (define-public execline (package (name "execline") - (version "2.5.0.1") + (version "2.5.1.0") (source (origin (method url-fetch) (uri (string-append "http://skarnet.org/software/execline/execline-" version ".tar.gz")) (sha256 - (base32 - "0j8hwdw8wn0rv8njdza8fbgmvyjg7hqp3qlbw00i7fwskr7d21wd")))) + (base32 "0xr6yb50wm6amj1wc7jmxyv7hvlx2ypbnww1vc288j275625d9xi")))) (build-system gnu-build-system) (inputs `(("skalibs" ,skalibs))) (arguments -- cgit v1.2.3 From 6954594d5cf13e9c9935194d743c3362cd4a966d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 12:23:33 +0100 Subject: gnu: s6: Update to 2.8.0.0. * gnu/packages/skarnet.scm (s6): Update to 2.8.0.0. --- gnu/packages/skarnet.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 23998d7ced..ee6d225ff1 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -103,15 +103,14 @@ complexity."))) (define-public s6 (package (name "s6") - (version "2.7.2.2") + (version "2.8.0.0") (source (origin (method url-fetch) (uri (string-append "http://skarnet.org/software/s6/s6-" version ".tar.gz")) (sha256 - (base32 - "0psjmfidjdciswakw9agzzniqfmhrr21765m0q77kwxg7iisgpsq")))) + (base32 "01milx5shixvniaxxmanfzz54vcymjfi86433w62rk5ypvc94ir8")))) (build-system gnu-build-system) (inputs `(("skalibs" ,skalibs) ("execline" ,execline))) -- cgit v1.2.3 From ce3262e9a3c58263cc927f15fa7d131431bab5a3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 12:23:50 +0100 Subject: gnu: s6-dns: Update to 2.3.0.2. * gnu/packages/skarnet.scm (s6-dns): Update to 2.3.0.2. --- gnu/packages/skarnet.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index ee6d225ff1..c101c980d2 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -141,15 +141,14 @@ functionality with a very small amount of code."))) (define-public s6-dns (package (name "s6-dns") - (version "2.3.0.1") + (version "2.3.0.2") (source (origin (method url-fetch) (uri (string-append "http://skarnet.org/software/s6-dns/s6-dns-" version ".tar.gz")) (sha256 - (base32 - "16ymalc4yxbwc0kapwmissxlw2bdk4sx3b33zp1gwx3n6hkcgh8c")))) + (base32 "1y9bhvx8bqsb2xq5lmlfnc1hw2b3jyqg11i9r4lj0n6vvaqwh1j8")))) (build-system gnu-build-system) (inputs `(("skalibs" ,skalibs))) (arguments -- cgit v1.2.3 From 8722fd43d484c4bfefd2a2d1082408fe74864ba2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 12:24:08 +0100 Subject: gnu: s6-networking: Update to 2.3.0.4. * gnu/packages/skarnet.scm (s6-networking): Update to 2.3.0.4. --- gnu/packages/skarnet.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index c101c980d2..bf520491f8 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -170,15 +170,14 @@ as an alternative to the BIND, djbdns or other DNS clients."))) (define-public s6-networking (package (name "s6-networking") - (version "2.3.0.3") + (version "2.3.0.4") (source (origin (method url-fetch) (uri (string-append "http://skarnet.org/software/s6-networking/s6-networking-" version ".tar.gz")) (sha256 - (base32 - "1kfjl7da6wkmyq1mvq9irkbzk2wbi0axjfbcw5cym5y11mqswsjs")))) + (base32 "00kqp0mcp8c7f0z5s4399rd1haxasxkqgd6ds0j0607hvi56mqqa")))) (build-system gnu-build-system) (inputs `(("skalibs" ,skalibs) ("execline" ,execline) -- cgit v1.2.3 From 0953b09aa895537f401dbc55757cd5ebb3eb6285 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 12:24:22 +0100 Subject: gnu: s6-rc: Update to 0.5.0.0. * gnu/packages/skarnet.scm (s6-rc): Update to 0.5.0.0. --- gnu/packages/skarnet.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index bf520491f8..ddb263fea3 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -213,15 +213,14 @@ clock synchronization."))) (define-public s6-rc (package (name "s6-rc") - (version "0.4.1.0") + (version "0.5.0.0") (source (origin (method url-fetch) (uri (string-append "http://skarnet.org/software/s6-rc/s6-rc-" version ".tar.gz")) (sha256 - (base32 - "1xl37xi509pcm5chcvn8l7gb952sr5mkpxhpkbsxhsllj791bfa2")))) + (base32 "0p97p49i8m44lfiffycgn7xi08yzxkrs5dyb03svdhd6clwh6zyb")))) (build-system gnu-build-system) (inputs `(("skalibs" ,skalibs) ("execline" ,execline) -- cgit v1.2.3 From b673d2d793d2a1b45d6ce4193c03c31bf6129219 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 12:25:02 +0100 Subject: gnu: s6-portable-utils: Update to 2.2.1.3. * gnu/packages/skarnet.scm (s6-portable-utils): Update to 2.2.1.3. --- gnu/packages/skarnet.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index ddb263fea3..a5babf7c21 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -254,7 +254,7 @@ environment."))) (define-public s6-portable-utils (package (name "s6-portable-utils") - (version "2.2.1.2") + (version "2.2.1.3") (source (origin (method url-fetch) @@ -262,8 +262,7 @@ environment."))) "http://skarnet.org/software/s6-portable-utils/s6-portable-utils-" version ".tar.gz")) (sha256 - (base32 - "0if77z07rfygd1yk9d2abxkdbx3dg52vcjhb20isb8kvqxhkg8ih")))) + (base32 "1ibjns1slyg1p7jl9irzlrjz8b01f506iw87g3s7db5arhf17vv2")))) (build-system gnu-build-system) (inputs `(("skalibs" ,skalibs))) (arguments -- cgit v1.2.3 From 8dc458bb18fba40cdc5d75addbd10e4946b9664d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 12:25:13 +0100 Subject: gnu: s6-linux-init: Update to 0.4.0.1. * gnu/packages/skarnet.scm (s6-linux-init): Update to 0.4.0.1. --- gnu/packages/skarnet.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index a5babf7c21..37e702428e 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -286,7 +286,7 @@ systems and other constrained environments, but they work everywhere."))) (define-public s6-linux-init (package (name "s6-linux-init") - (version "0.4.0.0") + (version "0.4.0.1") (source (origin (method url-fetch) @@ -294,8 +294,7 @@ systems and other constrained environments, but they work everywhere."))) "http://skarnet.org/software/s6-linux-init/s6-linux-init-" version ".tar.gz")) (sha256 - (base32 - "0zpd6n30cf8847240f658gw40sh64lm1mbaxr19q6rryvs5rpb6l")))) + (base32 "0i79b0r3amhsf1xqr9k9v9bxmm4imlakfpsybviwhlj8dlawldxm")))) (build-system gnu-build-system) (inputs `(("skalibs" ,skalibs))) -- cgit v1.2.3 From e445bd1607ca5aefcaac5ef2608b0073ae657143 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 12:25:34 +0100 Subject: gnu: s6-linux-utils: Update to 2.5.0.1. * gnu/packages/skarnet.scm (s6-linux-utils): Update to 2.5.0.1. --- gnu/packages/skarnet.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 37e702428e..b0c19f2664 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -323,7 +323,7 @@ all the details."))) (define-public s6-linux-utils (package (name "s6-linux-utils") - (version "2.5.0.0") + (version "2.5.0.1") (source (origin (method url-fetch) @@ -331,8 +331,7 @@ all the details."))) "http://skarnet.org/software/s6-linux-utils/s6-linux-utils-" version ".tar.gz")) (sha256 - (base32 - "04q2z71dkzahd2ppga2zikclz2qk014c23gm7rigqxjc8rs1amvq")))) + (base32 "0bpcaah3rbz4i013bkarr7wxmfvisjyxg0z78xg5zfbgajpgjxx1")))) (build-system gnu-build-system) (inputs `(("skalibs" ,skalibs))) (arguments -- cgit v1.2.3 From 4948c23677be81c8ca061aadd37ba6537aa51c2c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 11 Mar 2019 15:24:42 +0100 Subject: gnu: r-with-tests: Update to 3.5.3. * gnu/packages/statistics.scm (r-with-tests): Update to 3.5.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index eaca034366..e017d60767 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -177,7 +177,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "3.5.1") + (version "3.5.3") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -185,7 +185,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "1vap2k8kj5icy9naw61f9zyphf4rs0c9rxvil0zxkwx0xvsvyqq4")))) + "1337irx9y0r3jm1rcq1dcwnxsgfhnvgjs5wadcyh17vhpnvkgyib")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) -- cgit v1.2.3 From 34e3d028b9d180535108432a46b9569be6ab4dc5 Mon Sep 17 00:00:00 2001 From: Oleg Pykhalov Date: Sun, 10 Mar 2019 00:10:51 +0300 Subject: gnu: emacs-json-reformat: Fix test. This patch deletes a test which tries to compare JSON objects order. * gnu/packages/emacs-xyz.scm (emacs-json-reformat): Delete 'json-reformat-test:json-reformat-region' test. --- gnu/packages/emacs-xyz.scm | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 30248f673a..b359777923 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -26,7 +26,7 @@ ;;; Copyright © 2017 George Clemmer ;;; Copyright © 2017, 2018 Feng Shu ;;; Copyright © 2017 Jan Nieuwenhuizen -;;; Copyright © 2017, 2018 Oleg Pykhalov +;;; Copyright © 2017, 2018, 2019 Oleg Pykhalov ;;; Copyright © 2017 Mekeor Melire ;;; Copyright © 2017 Peter Mikkelsen ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice @@ -7032,7 +7032,19 @@ running a customisable handler command (@code{ignore} by default). ") ("ert-runner" ,emacs-ert-runner))) (arguments `(#:tests? #t - #:test-command '("ert-runner"))) + #:test-command '("ert-runner") + #:phases + (modify-phases %standard-phases + (add-before 'check 'delete-json-objects-order-test + (lambda _ + (emacs-batch-edit-file "test/json-reformat-test.el" + `(progn (progn (goto-char (point-min)) + (re-search-forward + "ert-deftest json-reformat-test:json-reformat-region") + (beginning-of-line) + (kill-sexp)) + (basic-save-buffer))) + #t))))) (home-page "https://github.com/gongo/json-reformat") (synopsis "Reformatting tool for JSON") (description "@code{json-reformat} provides a reformatting tool for -- cgit v1.2.3 From 842e66c573c74da5bd01204c590fea667b64498c Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 11 Mar 2019 18:46:25 +0100 Subject: gnu: Add emacs-lorem-ipsum. * gnu/packages/emacs-xyz.scm (emacs-lorem-ipsum): New variable. --- gnu/packages/emacs-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index b359777923..7807f97c45 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13247,3 +13247,25 @@ provides several enhancements over the ordinary in the completion list and showing keyboard shortcuts, and it supports several completion systems for selecting commands, such as ido and ivy.") (license license:gpl3+))) + +(define-public emacs-lorem-ipsum + (let ((commit "4b39f6fed455d67f635b3837cf5668bf74d0f6cd")) + (package + (name "emacs-lorem-ipsum") + (version (git-version "0.2" "1" commit)) + (home-page "https://github.com/jschaf/emacs-lorem-ipsum/") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0a3b18p3vdjci89prsgdzjnfxsl8p67vjhf8ai4qdng7zvh50lir")))) + (build-system emacs-build-system) + (synopsis "Insert dummy pseudo Latin text in Emacs") + (description "This package provides convenience functions to insert +dummy Latin text into a buffer. This can be useful if you need to produce +paragraphs or pages of text for testing purposes.") + (license license:gpl3+)))) -- cgit v1.2.3 From 684626763fa1fc66f4d7f7d909bf85a52d769b02 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 11 Mar 2019 19:01:49 +0100 Subject: gnu: emacs-magit: Fix perl path in dedicated variable. * gnu/packages/emacs-xyz.scm (emacs-magit)[arguments]: Do it. --- gnu/packages/emacs-xyz.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 7807f97c45..b7e2167d53 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -278,7 +278,12 @@ on stdout instead of using a socket as the Emacsclient does.") ("magit-popup" ,emacs-magit-popup) ("with-editor" ,emacs-with-editor))) (arguments - `(#:test-target "test" + `(#:modules ((guix build gnu-build-system) + (guix build utils) + (guix build emacs-utils)) + #:imported-modules (,@%gnu-build-system-modules + (guix build emacs-utils)) + #:test-target "test" #:tests? #f ; tests are not included in the release #:make-flags @@ -317,8 +322,9 @@ on stdout instead of using a socket as the Emacsclient does.") 'build 'patch-exec-paths (lambda* (#:key inputs #:allow-other-keys) (let ((perl (assoc-ref inputs "perl"))) - (substitute* "lisp/magit-sequence.el" - (("perl") (string-append perl "/bin/perl"))) + (make-file-writable "lisp/magit-sequence.el") + (emacs-substitute-variables "lisp/magit-sequence.el" + ("magit-perl-executable" (string-append perl "/bin/perl"))) #t)))))) (home-page "https://magit.vc/") (synopsis "Emacs interface for the Git version control system") -- cgit v1.2.3 From eea969cf8da5f85cd197032bb965cafbe18c0408 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Mon, 11 Mar 2019 20:12:48 +0100 Subject: gnu: Add wlroots. * gnu/packages/wm.scm (wlroots): New variable. --- gnu/packages/wm.scm | 49 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 96ef06bc15..68a737dbab 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -18,6 +18,7 @@ ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018 Pierre-Antoine Rouby ;;; Copyright © 2018 Meiyo Peng +;;; Copyright © 2019 Rutger Helling ;;; ;;; This file is part of GNU Guix. ;;; @@ -42,6 +43,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system haskell) + #:use-module (guix build-system meson) #:use-module (guix build-system perl) #:use-module (guix build-system python) #:use-module (gnu packages haskell) @@ -77,6 +79,8 @@ #:use-module (gnu packages linux) #:use-module (gnu packages suckless) #:use-module (gnu packages mpd) + #:use-module (gnu packages gl) + #:use-module (gnu packages video) #:use-module (guix download) #:use-module (guix git-download)) @@ -1102,3 +1106,48 @@ its size customizable status bars for their desktop environment. It has built-in functionality to display information about the most commonly used services.") (license license:expat))) + +(define-public wlroots + (package + (name "wlroots") + (version "0.5.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/swaywm/wlroots.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1phiidyddzgaxy4gbqwmykxn0y8za6y5mp66l9dpd9i6fml153yq")))) + (build-system meson-build-system) + (arguments + `(#:configure-flags '("-Dlogind-provider=elogind") + #:phases + (modify-phases %standard-phases + (add-before 'configure 'hardcode-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "xwayland/xwayland.c" + (("Xwayland") (string-append (assoc-ref inputs + "xorg-server-xwayland") + "/bin/Xwayland"))) + #t))))) + (inputs `(("elogind" ,elogind) + ("eudev" ,eudev) + ("libinput" ,libinput) + ("libxkbcommon" ,libxkbcommon) + ("mesa" ,mesa) + ("pixman" ,pixman) + ("wayland" ,wayland) + ("xorg-server-xwayland" ,xorg-server-xwayland))) + (native-inputs `(("ffmpeg" ,ffmpeg) + ("libcap" ,libcap) + ("libpng" ,libpng) + ("pkg-config" ,pkg-config) + ("wayland-protocols" ,wayland-protocols))) + (home-page "https://github.com/swaywm/wlroots") + (synopsis "Pluggable, composable, unopinionated modules for building a +Wayland compositor") + (description "wlroots is a set of pluggable, composable, unopinionated +modules for building a Wayland compositor.") + (license license:expat))) ; MIT license -- cgit v1.2.3 From 2ff844f0900be711be2322258beadeaa68e7b8b7 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Mon, 11 Mar 2019 20:17:34 +0100 Subject: gnu: Add sway. * gnu/packages/wm.scm (sway): New variable. --- gnu/packages/wm.scm | 47 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 68a737dbab..fedea67cc4 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -81,6 +81,8 @@ #:use-module (gnu packages mpd) #:use-module (gnu packages gl) #:use-module (gnu packages video) + #:use-module (gnu packages version-control) + #:use-module (gnu packages man) #:use-module (guix download) #:use-module (guix git-download)) @@ -1151,3 +1153,48 @@ Wayland compositor") (description "wlroots is a set of pluggable, composable, unopinionated modules for building a Wayland compositor.") (license license:expat))) ; MIT license + +(define-public sway + (package + (name "sway") + (version "1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/swaywm/sway.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "09cndc2nl39d3l7g5634xp0pxcz60pvc5277mfw89r22mh0j78rx")))) + (build-system meson-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'configure 'hardcode-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "meson.build" + (("scdoc.get_pkgconfig_variable..scdoc..") + (string-append "'" (assoc-ref inputs "scdoc") + "/bin/scdoc'"))) + #t))))) + (inputs `(("cairo" ,cairo) + ("elogind" ,elogind) + ("gdk-pixbuf" ,gdk-pixbuf) + ("json-c" ,json-c) + ("libinput" ,libinput) + ("libxkbcommon" ,libxkbcommon) + ("pango" ,pango) + ("wayland" ,wayland) + ("wlroots" ,wlroots))) + (native-inputs `(("git" ,git) + ("libcap" ,libcap) + ("linux-pam" ,linux-pam) + ("mesa" ,mesa) + ("pkg-config" ,pkg-config) + ("scdoc" ,scdoc) + ("wayland-protocols" ,wayland-protocols))) + (home-page "https://github.com/swaywm/sway") + (synopsis "Wayland compositor compatible with i3") + (description "Sway is a i3-compatible Wayland compositor.") + (license license:expat))) ; MIT license -- cgit v1.2.3 From 06ae5efcf385312faec3e6280786bc7b4aa63978 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Mon, 11 Mar 2019 20:19:41 +0100 Subject: gnu: Add swayidle. * gnu/packages/wm.scm (swayidle): New variable. --- gnu/packages/wm.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index fedea67cc4..fe4e0f404f 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -1198,3 +1198,26 @@ modules for building a Wayland compositor.") (synopsis "Wayland compositor compatible with i3") (description "Sway is a i3-compatible Wayland compositor.") (license license:expat))) ; MIT license + +(define-public swayidle + (package + (name "swayidle") + (version "1.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/swaywm/swayidle.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0b65flajwn2i6k2kdxxgw25w7ikzzmm595f4j5x1wac1rb0yah9w")))) + (build-system meson-build-system) + (inputs `(("wayland" ,wayland))) + (native-inputs `(("pkg-config" ,pkg-config) + ("scdoc" ,scdoc) + ("wayland-protocols" ,wayland-protocols))) + (home-page "https://github.com/swaywm/sway") + (synopsis "Idle management daemon for Wayland compositors") + (description "Swayidle is a idle management daemon for Wayland compositors.") + (license license:expat))) ; MIT license -- cgit v1.2.3 From b0805973cd1c08fe031bfed312e570697a665494 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Mon, 11 Mar 2019 20:22:00 +0100 Subject: gnu: Add swaylock. * gnu/packages/wm.scm (swaylock): New variable. --- gnu/packages/wm.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index fe4e0f404f..27848ea161 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -1221,3 +1221,33 @@ modules for building a Wayland compositor.") (synopsis "Idle management daemon for Wayland compositors") (description "Swayidle is a idle management daemon for Wayland compositors.") (license license:expat))) ; MIT license + +(define-public swaylock + (package + (name "swaylock") + (version "1.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/swaywm/swaylock.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "093nv1y9wyg48rfxhd36qdljjry57v1vkzrlc38mkf6zvsq8j7wb")))) + (build-system meson-build-system) + (inputs `(("cairo" ,cairo) + ("gdk-pixbuf" ,gdk-pixbuf) + ("libxkbcommon" ,libxkbcommon) + ;("linux-pam" ,linux-pam) ; FIXME: Doesn't work. + ("wayland" ,wayland))) + (native-inputs `( + ("git" ,git) + ("pango" ,pango) + ("pkg-config" ,pkg-config) + ("scdoc" ,scdoc) + ("wayland-protocols" ,wayland-protocols))) + (home-page "https://github.com/swaywm/sway") + (synopsis "Screen locking utility for Wayland compositors") + (description "Swaylock is a screen locking utility for Wayland compositors.") + (license license:expat))) ; MIT license -- cgit v1.2.3 From 7959ccac3f311c310f117b89e643f4d845557841 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Mon, 11 Mar 2019 20:30:27 +0100 Subject: gnu: swaylock: Fix indentation. * gnu/packages/wm.scm (swaylock): Fix indentation. --- gnu/packages/wm.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 27848ea161..4a6fc62069 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -1241,8 +1241,7 @@ modules for building a Wayland compositor.") ("libxkbcommon" ,libxkbcommon) ;("linux-pam" ,linux-pam) ; FIXME: Doesn't work. ("wayland" ,wayland))) - (native-inputs `( - ("git" ,git) + (native-inputs `(("git" ,git) ("pango" ,pango) ("pkg-config" ,pkg-config) ("scdoc" ,scdoc) -- cgit v1.2.3 From e1c61029070e07db1735a8510f4e5d90eb324fab Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Mar 2019 21:22:01 +0100 Subject: gnu: libxcursor: Update to 1.2.0. * gnu/packages/xorg.scm (libxcursor): Update to 1.2.0. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 27005e768b..78c67fb9e8 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5279,7 +5279,7 @@ draggable titlebars and borders.") (define-public libxcursor (package (name "libxcursor") - (version "1.1.15") + (version "1.2.0") (source (origin (method url-fetch) @@ -5289,7 +5289,7 @@ draggable titlebars and borders.") ".tar.bz2")) (sha256 (base32 - "0syzlfvh29037p0vnlc8f3jxz8nl55k65blswsakklkwsc6nfki9")))) + "10l7c9fm0jmpkm9ab9dz8r6m1pr87vvgqjnbx1psz50h4pwfklrs")))) (build-system gnu-build-system) (propagated-inputs `(("libx11" ,libx11) -- cgit v1.2.3 From e440a7564084c84658c1af9ff424b1cc4df32b7b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Mar 2019 21:22:24 +0100 Subject: gnu: libxcomposite: Update to 0.4.5. * gnu/packages/xorg.scm (libxcomposite): Update to 0.4.5. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 78c67fb9e8..bc4e052937 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -1271,7 +1271,7 @@ with the Cygwin XWin server when running X11 in a rootless mode.") (define-public libxcomposite (package (name "libxcomposite") - (version "0.4.4") + (version "0.4.5") (source (origin (method url-fetch) @@ -1281,7 +1281,7 @@ with the Cygwin XWin server when running X11 in a rootless mode.") ".tar.bz2")) (sha256 (base32 - "0y21nfpa5s8qmx0srdlilyndas3sgl0c6rc26d5fx2vx436m1qpd")))) + "13sfcglvz87vl58hd9rszwr73z0z4nwga3c12rfh7f5s2ln8l8dk")))) (build-system gnu-build-system) (propagated-inputs ;; xcomposite.pc refers to all these. -- cgit v1.2.3 From 6f93b525d3159675478c78541c95452d1b12e5a3 Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Mon, 4 Mar 2019 01:39:57 +0100 Subject: gnu: Add emacs-xml-rpc. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-xml-rpc): New variable. Co-authored-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index b7e2167d53..673a490752 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11376,6 +11376,33 @@ Org-mode. It features: @end itemize\n") (license license:gpl3+)))) +(define-public emacs-xml-rpc + (let ((commit "8f624f8b964e9145acb504e4457c9510e87dd93c") + (revision "1")) + (package + (name "emacs-xml-rpc") + (version (git-version "1.6.12" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hexmode/xml-rpc-el") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xa54z52rsfl3n0xgmbycj4zazp8ksgdwcq56swzs6wp72zlalmj")))) + (build-system emacs-build-system) + (home-page "https://github.com/hexmode/xml-rpc-el") + (synopsis "XML-RPC client for Emacs") + (description "This package provides an XML-RPC client for Emacs capable +of both synchronous and asynchronous method calls using the @code{url} +package's async retrieval functionality. @file{xml-rpc.el} represents XML-RPC +datatypes as Lisp values, automatically converting to and from the XML +datastructures as needed, both for method parameters and return values, making +using XML-RPC methods fairly transparent to the Lisp code.") + (license license:gpl3+)))) + (define-public emacs-fish-completion (package (name "emacs-fish-completion") -- cgit v1.2.3 From 1bc24bbf00e21a26d9eb71e5c89d941812dcdad7 Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Mon, 4 Mar 2019 01:40:38 +0100 Subject: gnu: Add emacs-debpaste. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-debpaste): New variable. Co-authored-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 673a490752..543cfaea3d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11376,6 +11376,29 @@ Org-mode. It features: @end itemize\n") (license license:gpl3+)))) +(define-public emacs-debpaste + (package + (name "emacs-debpaste") + (version "0.1.5") + (home-page "https://github.com/alezost/debpaste.el") + (source + (origin + (method git-fetch) + (uri (git-reference (url home-page) + (commit (string-append "v" version)))) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1wi70r56pd5z0x4dp4m58p9asq03j74kdm4fi9vai83vsl2z9amq")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-xml-rpc" ,emacs-xml-rpc))) + (synopsis "Manipulate pastes from the Debian Pastezone") + (description "Debpaste is an Emacs interface for the Debian Pastezone, +allowing you to receive, post, and delete pastes. It communicates with the +server using XML-RPC.") + (license license:gpl3+))) + (define-public emacs-xml-rpc (let ((commit "8f624f8b964e9145acb504e4457c9510e87dd93c") (revision "1")) -- cgit v1.2.3 From 1340ce2899acebf0ff5eec64c7db881497427016 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 12 Mar 2019 01:52:50 +0100 Subject: gnu: guile-colorized: Don't use unstable tarball. * gnu/packages/guile-xyz.scm (guile-colorized)[source]: Use GIT-FETCH and GIT-FILE-NAME. --- gnu/packages/guile-xyz.scm | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 1ef523d9ce..60f3325e67 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -605,14 +605,15 @@ using Guile's foreign function interface.") (package (name "guile-colorized") (version "0.1") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/NalaGinrut/guile-colorized/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "16xhc3an6aglnca8xl3mvgi8hsqzqn68vsl5ga4bz8bvbap5fn4p")))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/NalaGinrut/guile-colorized.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "10mv8c63159r3qvwwdvsgnsvdg7nc2ghak85zapwqpv4ywrqp9zc")))) (build-system guile-build-system) (native-inputs `(("guile" ,guile-2.2))) -- cgit v1.2.3 From 55f4282e0ce4f7ab071ddd544ad9486d59e85292 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 12 Mar 2019 02:01:44 +0100 Subject: gnu: guile-colorized: Move project home. * gnu/packages/guile-xyz.scm (guile-colorized)[source, home-page]: Update. --- gnu/packages/guile-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 60f3325e67..e758d44966 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -609,7 +609,7 @@ using Guile's foreign function interface.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/NalaGinrut/guile-colorized.git") + (url "https://gitlab.com/NalaGinrut/guile-colorized.git") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -617,7 +617,7 @@ using Guile's foreign function interface.") (build-system guile-build-system) (native-inputs `(("guile" ,guile-2.2))) - (home-page "https://github.com/NalaGinrut/guile-colorized") + (home-page "https://gitlab.com/NalaGinrut/guile-colorized") (synopsis "Colorized REPL for Guile") (description "Guile-colorized provides you with a colorized REPL for GNU Guile.") -- cgit v1.2.3 From 2f813be342cccc1cc20be09e608b5e310e0b0861 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 20:46:24 +0100 Subject: gnu: perl-sql-abstract: Update to 1.86. * gnu/packages/databases.scm (perl-sql-abstract): Update to 1.86. --- gnu/packages/databases.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 482d399a97..3d901fe3da 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1335,15 +1335,14 @@ module, and nothing else.") (define-public perl-sql-abstract (package (name "perl-sql-abstract") - (version "1.85") + (version "1.86") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/I/IL/ILMARI/" "SQL-Abstract-" version ".tar.gz")) (sha256 - (base32 - "1aycggrvppy2zgkwwn85jkdz93n5gsx4dambrjk67k5067hayi4z")))) + (base32 "1pwcm8hwxcgidyyrak37lx69d85q728jxsb0b14jz93gbvdgg9z7")))) (build-system perl-build-system) (native-inputs `(("perl-module-install" ,perl-module-install) -- cgit v1.2.3 From 49596a54133f6b0702f22518c84bdd6fc2c8d9ff Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 20:54:34 +0100 Subject: gnu: perl-dbd-mysql: Update to 4.050. * gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.050. --- gnu/packages/databases.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 3d901fe3da..2665024fa2 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1274,15 +1274,14 @@ columns, primary keys, unique constraints and relationships.") (define-public perl-dbd-mysql (package (name "perl-dbd-mysql") - (version "4.048") + (version "4.050") (source (origin (method url-fetch) - (uri (string-append "mirror://cpan/authors/id/M/MI/MICHIELB/" + (uri (string-append "mirror://cpan/authors/id/D/DV/DVEEDEN/" "DBD-mysql-" version ".tar.gz")) (sha256 - (base32 - "1zqmch6c9gq06z90mkmk1skajk2kaggriw19ym5w04l7wv5gydqp")))) + (base32 "0y4djb048i09dk19av7mzfb3khr72vw11p3ayw2p82jsy4gm8j2g")))) (build-system perl-build-system) (arguments `(#:phases -- cgit v1.2.3 From d49bdbca5c3984a17b750bc60e5f276bcd4eaaa3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 21:03:09 +0100 Subject: gnu: perl-dbd-sqlite: Update to 1.62. * gnu/packages/databases.scm (perl-dbd-sqlite): Update to 1.62. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 2665024fa2..ea660b8b3a 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1311,7 +1311,7 @@ columns, primary keys, unique constraints and relationships.") (define-public perl-dbd-sqlite (package (name "perl-dbd-sqlite") - (version "1.58") + (version "1.62") (source (origin (method url-fetch) (uri (string-append @@ -1319,7 +1319,7 @@ columns, primary keys, unique constraints and relationships.") version ".tar.gz")) (sha256 (base32 - "0fqx386jgs9mmrknr7smmzapf07izgivza7x08lfm39ks2cxs83i")))) + "0p78ri1q6xpc1i98i6mlriv8n66iz8r5r11dlsknjm4y58rfz0mx")))) (build-system perl-build-system) (inputs `(("sqlite" ,sqlite))) (propagated-inputs `(("perl-dbi" ,perl-dbi))) -- cgit v1.2.3 From 72b7de49b44b8394a9e009dd71e45d63830d42ea Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 21:10:52 +0100 Subject: gnu: python-psycopg2: Update to 2.7.7. * gnu/packages/databases.scm (python-psycopg2): Update to 2.7.7. --- gnu/packages/databases.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index ea660b8b3a..6c34a5b8d8 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2332,14 +2332,13 @@ designed to be easy and intuitive to use.") (define-public python-psycopg2 (package (name "python-psycopg2") - (version "2.7.5") + (version "2.7.7") (source (origin (method url-fetch) (uri (pypi-uri "psycopg2" version)) (sha256 - (base32 - "17klx964gw8z0znl0raz3by8vdc7cq5gxj4pdcrfcina84nrdkzc")))) + (base32 "0zjbabb4qjx9dm07imhf8y5a9rpa06d5zah80myiimgdi83nslpl")))) (build-system python-build-system) (arguments ;; Tests would require a postgresql database "psycopg2_test" -- cgit v1.2.3 From 99e690a59abc09445ef6853af19c11cb8e9cf4d2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 21:14:51 +0100 Subject: gnu: python-pyodbc: Update to 4.0.25. * gnu/packages/databases.scm (python-pyodbc): Update to 4.0.25. --- gnu/packages/databases.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 6c34a5b8d8..aead84c1b7 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1844,14 +1844,13 @@ for ODBC.") (define-public python-pyodbc (package (name "python-pyodbc") - (version "4.0.24") + (version "4.0.25") (source (origin (method url-fetch) (uri (pypi-uri "pyodbc" version)) (sha256 - (base32 - "1m311vi7vpay1j7rkq71fpsk0gb7454k4lldk5b63hyy6yvsn9j3")) + (base32 "1bbwrb812w5i0x56jfn0l86mxc2ck904hl8y87mziay96znwia0f")) (file-name (string-append name "-" version ".tar.gz")))) (build-system python-build-system) (inputs -- cgit v1.2.3 From 909404b5718786756dbb2d2d18f75869d15b1084 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 21:23:10 +0100 Subject: gnu: python-sql: Update to 1.0.0. * gnu/packages/databases.scm (python-sql): Update to 1.0.0. --- gnu/packages/databases.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index aead84c1b7..98fb6f9093 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2575,14 +2575,13 @@ provides support for parsing, splitting and formatting SQL statements.") (define-public python-sql (package (name "python-sql") - (version "0.9") + (version "1.0.0") (source (origin (method url-fetch) (uri (pypi-uri "python-sql" version)) (sha256 - (base32 - "0p6kaqj02vz0habmdx37zjk6hjxdfm8aw737zs059vvpr70ird87")))) + (base32 "05ni936y0ia9xmryl7mlhbj9i80nnvq1bi4zxhb96rv7yvpb3fqb")))) (build-system python-build-system) (home-page "https://python-sql.tryton.org/") (synopsis "Library to write SQL queries in a pythonic way") -- cgit v1.2.3 From 96ec46047ba772162cc46a7a3e60770229269b9b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 21:50:47 +0100 Subject: gnu: gcompris-qt: Update to 0.96. * gnu/packages/education.scm (gcompris-qt): Update to 0.96. [inputs]: Add openssl. --- gnu/packages/education.scm | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 5b899f4e78..c54005ccf9 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2016, 2017 Ricardo Wurmus ;;; Copyright © 2016 Hartmut Goebel ;;; Copyright © 2017, 2018 Efraim Flashner -;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018 Nicolas Goaziou ;;; ;;; This file is part of GNU Guix. @@ -41,6 +41,7 @@ #:use-module (gnu packages sdl) #:use-module (gnu packages sqlite) #:use-module (gnu packages texinfo) + #:use-module (gnu packages tls) #:use-module (gnu packages xorg) #:use-module (gnu packages xml) #:use-module ((guix licenses) #:prefix license:) @@ -116,16 +117,15 @@ of categories with some of the activities available in that category. (define-public gcompris-qt (package (name "gcompris-qt") - (version "0.95") + (version "0.96") (source - (origin - (method url-fetch) - (uri (string-append - "https://gcompris.net/download/qt/src/gcompris-qt-" - version ".tar.xz")) - (sha256 - (base32 - "1aaijjx2b7k1cyx59jhs64hlp1sppw1faa81qxl5lxc79vifrlrl")))) + (origin + (method url-fetch) + (uri (string-append + "https://gcompris.net/download/qt/src/gcompris-qt-" + version ".tar.xz")) + (sha256 + (base32 "06483il59l46ny2w771sg45dgzjwv1ph7vidzzbj0wb8wbk2rg52")))) (build-system cmake-build-system) (arguments `(#:phases @@ -162,7 +162,8 @@ of categories with some of the activities available in that category. ("qttools" ,qttools) ("xorg-server" ,xorg-server))) (inputs - `(("python-2" ,python-2) + `(("openssl" ,openssl) + ("python-2" ,python-2) ("qtbase" ,qtbase) ("qtdeclarative" ,qtdeclarative) ("qtgraphicaleffects" ,qtgraphicaleffects) -- cgit v1.2.3 From 6d04f694dc29f23833a48b9f114c42670e12d168 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 22:01:37 +0100 Subject: gnu: python-sqlalchemy: Update to 1.3.1. * gnu/packages/databases.scm (python-sqlalchemy): Update to 1.3.1. --- gnu/packages/databases.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 98fb6f9093..5dbcd92477 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2091,19 +2091,18 @@ Database API 2.0T.") (define-public python-sqlalchemy (package (name "python-sqlalchemy") - (version "1.2.11") + (version "1.3.1") (source (origin (method url-fetch) (uri (pypi-uri "SQLAlchemy" version)) (sha256 - (base32 - "094mmbs4igrxplfyqd59j90jb83ixpbbzqc0w49yw81m82nnjrgg")))) + (base32 "12sr36646sipf9ac3n2xh8z0w5pz4d3dvw5qjv2kzvcls6wvf7vq")))) (build-system python-build-system) (native-inputs - `(("python-cython" ,python-cython) ;for c extensions + `(("python-cython" ,python-cython) ; for C extensions ("python-pytest" ,python-pytest) - ("python-mock" ,python-mock))) ;for tests + ("python-mock" ,python-mock))) ; for tests (arguments `(#:phases (modify-phases %standard-phases -- cgit v1.2.3 From 5cfe650b9d7d2179a9a7676745ddd78cee674978 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 22:02:38 +0100 Subject: gnu: python-sqlalchemy: Use HTTPS home page. * gnu/packages/databases.scm (python-sqlalchemy)[home-page]: Use HTTPS. --- gnu/packages/databases.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 5dbcd92477..be02b79efa 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2108,7 +2108,7 @@ Database API 2.0T.") (modify-phases %standard-phases (replace 'check (lambda _ (invoke "py.test")))))) - (home-page "http://www.sqlalchemy.org") + (home-page "https://www.sqlalchemy.org") (synopsis "Database abstraction library") (description "SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that -- cgit v1.2.3 From 3d21f1ea0f68a8741f168ea32368c68b57269f5b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 22:30:55 +0100 Subject: gnu: gtkwave: Update to 3.3.99. * gnu/packages/fpga.scm (gtkwave): Update to 3.3.99. --- gnu/packages/fpga.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/fpga.scm b/gnu/packages/fpga.scm index f6bb3280f0..24a1219ce5 100644 --- a/gnu/packages/fpga.scm +++ b/gnu/packages/fpga.scm @@ -301,14 +301,14 @@ Includes the actual FTDI connector.") (define-public gtkwave (package (name "gtkwave") - (version "3.3.91") + (version "3.3.99") (source (origin (method url-fetch) (uri (string-append "http://gtkwave.sourceforge.net/" name "-" version ".tar.gz")) (sha256 (base32 - "1vp9qj3wyfwm36jk3pajvi09xvc1m1crf3d4gphfbs6nkyx2z942")))) + "0lc4y2vizrbxldjk5yw2i4y7pyprjdjqx3iafzjfnin694zp2630")))) (build-system gnu-build-system) (native-inputs `(("gperf" ,gperf) -- cgit v1.2.3 From 23df8f35785c7843d8b7fb549fd78c0b85a24c16 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 22:45:54 +0100 Subject: gnu: kicad: Update to 5.0.2. * gnu/packages/engineering.scm (kicad): Update to 5.0.2. --- gnu/packages/engineering.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 6b7dc3f595..51236d8a31 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -734,7 +734,7 @@ language.") (define-public kicad (package (name "kicad") - (version "5.0.0") + (version "5.0.2") (source (origin (method url-fetch) @@ -743,7 +743,7 @@ language.") "https://launchpad.net/kicad/" (version-major+minor version) "/" version "/+download/" name "-" version ".tar.xz")) (sha256 - (base32 "17nqjszyvd25wi6550j981whlnb1wxzmlanljdjihiki53j84x9p")))) + (base32 "10605rr10x0353n6yk2z095ydnkd1i6j1ncbq64pfxdn5vkhcd1g")))) (build-system cmake-build-system) (arguments `(#:out-of-source? #t -- cgit v1.2.3 From b13b7143d72d0bc37a0f945d9560872c1c918dae Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 22:46:02 +0100 Subject: gnu: kicad: Don't use NAME in source URI. * gnu/packages/engineering.scm (kicad)[source]: Hard-code NAME. --- gnu/packages/engineering.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 51236d8a31..aa0fd166a8 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -741,7 +741,7 @@ language.") (file-name (string-append name "-" version ".tar.xz")) (uri (string-append "https://launchpad.net/kicad/" (version-major+minor version) - "/" version "/+download/" name "-" version ".tar.xz")) + "/" version "/+download/kicad-" version ".tar.xz")) (sha256 (base32 "10605rr10x0353n6yk2z095ydnkd1i6j1ncbq64pfxdn5vkhcd1g")))) (build-system cmake-build-system) -- cgit v1.2.3 From 65bab0120b9feb1fc1570062f0de98440417ebff Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 22:46:36 +0100 Subject: gnu: kicad-symbols: Update to 5.0.2. * gnu/packages/engineering.scm (kicad-symbols): Update to 5.0.2. --- gnu/packages/engineering.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index aa0fd166a8..28cba37c4f 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -888,7 +888,7 @@ render model libraries.") (define-public kicad-symbols (package (name "kicad-symbols") - (version "5.0.1") + (version "5.0.2") (source (origin (method git-fetch) (uri (git-reference @@ -897,7 +897,7 @@ render model libraries.") (file-name (string-append "kicad-symbols-" version "-checkout")) (sha256 (base32 - "18z5vpdq7hy2mpvm5vz1dz3ra3a5iybavvlzi8q2bmmdb6gsvf64")))) + "1rjh2pjcrc3bhcgyyskj5pssm7vffrjk0ymwr70fb7sjpmk96yjk")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; No tests exist -- cgit v1.2.3 From a55446212321deaa07d82edc9889168dd7fdd8a2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 22:47:21 +0100 Subject: gnu: kicad-symbols: Use GIT-FILE-NAME. * packages/engineering.scm (kicad-symbols)[source]: Use GIT-FILE-NAME. --- gnu/packages/engineering.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 28cba37c4f..8bed5795a0 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -894,7 +894,7 @@ render model libraries.") (uri (git-reference (url "https://github.com/KiCad/kicad-symbols.git") (commit version))) - (file-name (string-append "kicad-symbols-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 "1rjh2pjcrc3bhcgyyskj5pssm7vffrjk0ymwr70fb7sjpmk96yjk")))) -- cgit v1.2.3 From 98704a8133b65491a08e788331204ce5f1cba1cb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 22:58:14 +0100 Subject: gnu: libmanette: Update to 0.2.2. * gnu/packages/games.scm (libmanette): Update to 0.2.2. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 0a8c3e9452..ae50858bc5 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -5864,7 +5864,7 @@ when packaged in Blorb container files or optionally from individual files.") (define-public libmanette (package (name "libmanette") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -5872,7 +5872,7 @@ when packaged in Blorb container files or optionally from individual files.") name "-" version ".tar.xz")) (sha256 (base32 - "14vqz30p4693yy3yxs0gj858x25sl2kawib1g9lj8g5frgl0hd82")))) + "1lpprk2qz1lsqf9xj6kj2ciyc1zmjhj5lwd584qkh7jgz2x9y6wb")))) (build-system meson-build-system) (native-inputs `(("glib" ,glib "bin") ; for glib-compile-resources -- cgit v1.2.3 From 2ee05bb9d4a3939cdece4ffea9b1156527f12229 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 12 Mar 2019 01:48:46 +0100 Subject: gnu: freedink-engine: Update to 109.6. * gnu/packages/games.scm (freedink-engine): Update to 109.6. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index ae50858bc5..46b58e352c 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -1403,14 +1403,14 @@ interface or via an external visual interface such as GNU XBoard.") (define freedink-engine (package (name "freedink-engine") - (version "109.4") + (version "109.6") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/freedink/freedink-" version ".tar.gz")) (sha256 (base32 - "0iaagwnyfgm3mqzkj550q60hrsjr13gykg5vfn2nz2ia520bb52g")))) + "00hhk1bjdrc1np2qz44sa5n1mb62qzwxbvsnws3vpms6iyn3a2sy")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--disable-embedded-resources") -- cgit v1.2.3 From a922b2aee220647398bc9215ce1e0b3a5f75a8d9 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Tue, 12 Mar 2019 08:06:50 +0100 Subject: gnu: emacs-helm: Update to 3.1. * gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 543cfaea3d..7e3fe9145f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4957,7 +4957,7 @@ ack, ag, helm and pt.") (define-public emacs-helm (package (name "emacs-helm") - (version "3.0") + (version "3.1") (source (origin (method url-fetch) (uri (string-append @@ -4966,7 +4966,7 @@ ack, ag, helm and pt.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0k2r0ccppaqfjvyszaxa16vf7g2qzj1clhfr6v646ncsy17laciw")))) + "0ymykcsbcgq2kskqc0ddigg0kfznxx3j02mkd5r3c3n8gn3kgz84")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-async" ,emacs-async) -- cgit v1.2.3 From b6180f93bd256ec3e2b12c91ac7884f82313dd3b Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Tue, 12 Mar 2019 09:24:31 +0100 Subject: gnu: emacs-suggest: Update to 0.7. * gnu/packages/emacs-xyz.scm (emacs-suggest): Update to 0.7. --- gnu/packages/emacs-xyz.scm | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 7e3fe9145f..a82d6e9ea5 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10161,23 +10161,26 @@ and doesn't require memorisation of commands. (define-public emacs-suggest (package (name "emacs-suggest") - (version "0.4") + (version "0.7") + (home-page "https://github.com/Wilfred/suggest.el") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/Wilfred/suggest.el/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1760fm3j19w8xxcawq6s859h86q1rdg69pg9yz48n76kwfk3vlgp")))) + "01v8plska5d3g19sb1m4ph1i3ayprfzk8mi6mpabjy6zad397xjl")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-loop" ,emacs-loop) ("emacs-dash" ,emacs-dash) ("emacs-s" ,emacs-s) - ("emacs-f" ,emacs-f))) - (home-page "https://github.com/Wilfred/suggest.el") + ("emacs-f" ,emacs-f) + ("emacs-spinner" ,emacs-spinner) + ("emacs-shut-up" ,emacs-shut-up))) (synopsis "Suggest Elisp functions that give the output requested") (description "Suggest.el will find functions that give the output requested. It's a great way of exploring list, string and arithmetic -- cgit v1.2.3 From 75dabac633bb9a33efbebf859f8aa4bb3b9582b2 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Tue, 12 Mar 2019 09:28:01 +0100 Subject: gnu: Add emacs-lisp-extra-font-lock. * gnu/packages/emacs-xyz.scm (emacs-lisp-extra-font-lock): New variable. --- gnu/packages/emacs-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a82d6e9ea5..064b8cb054 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13328,3 +13328,25 @@ completion systems for selecting commands, such as ido and ivy.") dummy Latin text into a buffer. This can be useful if you need to produce paragraphs or pages of text for testing purposes.") (license license:gpl3+)))) + +(define-public emacs-lisp-extra-font-lock + (let ((commit "4605eccbe1a7fcbd3cacf5b71249435413b4db4f")) + (package + (name "emacs-lisp-extra-font-lock") + (version (git-version "0.0.6" "1" commit)) + (home-page "https://github.com/Lindydancer/lisp-extra-font-lock") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "152vcp3mdlv33jf5va4rinl1d0k960gnfhbrqqrafazgx9j3ya8w")))) + (build-system emacs-build-system) + (synopsis "Highlight bound variables and quoted expressions in Emacs") + (description "This package highlight the location where local variables +is created (bound, for example, by let) as well as quoted and backquoted +constant expressions.") + (license license:gpl3+)))) -- cgit v1.2.3 From 47b3eed821cf86c350dc4b0fdbe75647cdc275b0 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Tue, 12 Mar 2019 11:18:17 +0100 Subject: gnu: vulkan-headers: Update to 1.103. * gnu/packages/vulkan.scm (vulkan-headers): Update to 1.1.103. * gnu/packages/vulkan.scm (vulkan-loader): Adjust version. * gnu/packages/vulkan.scm (vulkan-tools): Adjust version. --- gnu/packages/vulkan.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm index 98a0523ee7..7517d24b69 100644 --- a/gnu/packages/vulkan.scm +++ b/gnu/packages/vulkan.scm @@ -163,7 +163,7 @@ interpretation of the specifications for these languages.") (define-public vulkan-headers (package (name "vulkan-headers") - (version "1.1.102") + (version "1.1.103") (source (origin (method git-fetch) @@ -173,7 +173,7 @@ interpretation of the specifications for these languages.") (file-name (git-file-name name version)) (sha256 (base32 - "1dkjg48l7dfpq16bq1w9c3y9dwpj2hhv7b3njvj52lpgpa14s0f9")))) + "1q3c79rf3mma0vqmwnxwps588pnyzap4nn49hk41m39k79vniaz8")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; No tests. @@ -187,7 +187,7 @@ interpretation of the specifications for these languages.") (define-public vulkan-loader (package (name "vulkan-loader") - (version (package-version vulkan-headers)) + (version "1.1.102") (source (origin (method git-fetch) @@ -244,7 +244,7 @@ and the ICD.") (define-public vulkan-tools (package (name "vulkan-tools") - (version (package-version vulkan-headers)) + (version "1.1.102") (source (origin (method git-fetch) -- cgit v1.2.3 From e3df159edca975baa3ae10576be8ecf4c323c854 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 22:56:43 +0100 Subject: gnu: geos: Update to 3.7.1. * gnu/packages/geo.scm (geos): Update to 3.7.1. --- gnu/packages/geo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 884f57eabd..cf4fcee8dd 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -63,7 +63,7 @@ (define-public geos (package (name "geos") - (version "3.7.0") + (version "3.7.1") (source (origin (method url-fetch) (uri (string-append "http://download.osgeo.org/geos/geos-" @@ -71,7 +71,7 @@ ".tar.bz2")) (sha256 (base32 - "1mrz778m6bd1x9k6sha5kld43kalhq79h2lynlx2jx7xjakl3gsg")))) + "1312m02xk4sp6f1xdpb9w0ic0zbxg90p5y66qnwidl5fksscf1h0")))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases -- cgit v1.2.3 From b4ed7c3e8d7b2915ab9ea7e369bc1bdd05f41ad1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 11 Mar 2019 22:51:27 +0100 Subject: gnu: libinput: Don't use NAME in source URI. * gnu/packages/freedesktop.scm (libinput)[source]: Hard-code NAME. --- gnu/packages/freedesktop.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 93fc02cd4b..d90e75352e 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -152,7 +152,7 @@ freedesktop.org project.") (source (origin (method url-fetch) (uri (string-append "https://freedesktop.org/software/libinput/" - name "-" version ".tar.xz")) + "libinput-" version ".tar.xz")) (sha256 (base32 "0mg2zqbjcgj0aq7d9nwawvyhx43vakilahrc83hrfyif3a3gyrpj")))) -- cgit v1.2.3 From 8dbd8e426c7d7e4c14f9e787e68fd9d00edccb1e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 12 Mar 2019 13:14:53 +0100 Subject: gnu: aspell-dict-it: Update to 2.4-20070901-0. * gnu/packages/aspell.scm (aspell-dict-it): Update to 2.4-20070901-0. --- gnu/packages/aspell.scm | 26 ++++++++++++++++++++------ 1 file changed, 20 insertions(+), 6 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/aspell.scm b/gnu/packages/aspell.scm index ca9fc8eda5..dd006e8184 100644 --- a/gnu/packages/aspell.scm +++ b/gnu/packages/aspell.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2016, 2017, 2019 Efraim Flashner ;;; Copyright © 2016 Christopher Andersson ;;; Copyright © 2016 Theodoros Foradis -;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice +;;; Copyright © 2016, 2017, 2019 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -197,11 +197,25 @@ dictionaries, including personal ones.") "13bhbghx5b8g0119g3wxd4n8mlf707y41vlf59irxjj0kynankfn"))) (define-public aspell-dict-it - (aspell-dictionary "it" "Italian" - #:version "2.2_20050523-0" - #:sha256 - (base32 - "1gdf7bc1a0kmxsmphdqq8pl01h667mjsj6hihy6kqy14k5qdq69v"))) + (let ((version "2.4-20070901-0") + (sha256 + (base32 "0d6ypii3jblprpibazb6ypady536jz62rwxlss1x1raq07rhvvqn"))) + (package + (inherit (aspell-dictionary "it" "Italian" + #:version version + #:sha256 sha256)) + + ;; The version hosted at is even + ;; more out of date. + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/linguistico/" + "Dizionario%20italiano%20per%20Aspell/" version "/" + "aspell6-it-" version ".tar.bz2")) + (sha256 sha256))) + (home-page + "http://linguistico.sourceforge.net/pages/dizionario_italiano.html")))) (define-public aspell-dict-nl (aspell-dictionary "nl" "Dutch" -- cgit v1.2.3 From 737300be4bbd4a1d8df047035b836f5eeaaec92f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 12 Mar 2019 13:19:47 +0100 Subject: gnu: aide: Move project home. * gnu/packages/admin.scm (aide)[source, home-page]: Update. --- gnu/packages/admin.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 48b8582d52..ade16c1fca 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -114,13 +114,13 @@ (package (name "aide") (version "0.16") - (source (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/aide/aide/" - version "/aide-" version ".tar.gz")) - (sha256 - (base32 - "0ibkv4z2gk14fn014kq13rp2ysiq6nn2cflv2q5i7zf466hm6758")))) + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/aide/aide/releases/download/v" + version "/aide-" version ".tar.gz")) + (sha256 + (base32 "0ibkv4z2gk14fn014kq13rp2ysiq6nn2cflv2q5i7zf466hm6758")))) (build-system gnu-build-system) (native-inputs `(("bison" ,bison) @@ -141,7 +141,7 @@ that it finds from its configuration files. Once this database is initialized it can be used to verify the integrity of the files. It has several message digest algorithms that are used to check the integrity of files. All of the usual file attributes can be checked for inconsistencies.") - (home-page "http://aide.sourceforge.net/") + (home-page "https://aide.github.io/") (license license:gpl2+))) (define-public progress -- cgit v1.2.3 From 2f805e97f28f2403459dfb8297cf4981cc628f74 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 12 Mar 2019 13:26:13 +0100 Subject: gnu: aide: Update to 0.16.1. * gnu/packages/admin.scm (aide): Update to 0.16.1. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index ade16c1fca..568402f2fc 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -113,14 +113,14 @@ (define-public aide (package (name "aide") - (version "0.16") + (version "0.16.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/aide/aide/releases/download/v" version "/aide-" version ".tar.gz")) (sha256 - (base32 "0ibkv4z2gk14fn014kq13rp2ysiq6nn2cflv2q5i7zf466hm6758")))) + (base32 "1dqhc0c24wa4zid06pfy61k357yvzh28ij86bk9jf6hcqzn7qaqg")))) (build-system gnu-build-system) (native-inputs `(("bison" ,bison) -- cgit v1.2.3 From 17ab1e43a640d0d70db88336e139e55f78d3a37c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 12 Mar 2019 13:53:53 +0100 Subject: gnu: perl-anyevent: Update to 7.15. * gnu/packages/libevent.scm (perl-anyevent): Update to 7.15. --- gnu/packages/libevent.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm index b3a5471527..b5d67cd581 100644 --- a/gnu/packages/libevent.scm +++ b/gnu/packages/libevent.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2016 David Thompson ;;; Copyright © 2017 Marius Bakke ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019 Pierre Neidhardt ;;; ;;; This file is part of GNU Guix. @@ -170,14 +170,14 @@ resolution, asynchronous file system operations, and threading primitives.") (define-public perl-anyevent (package (name "perl-anyevent") - (version "7.14") + (version "7.15") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/M/ML/MLEHMANN/" "AnyEvent-" version ".tar.gz")) (sha256 (base32 - "0akxr9y0q9yjkl614x4clbiiayvh5a67y8gmci54plxs4p95i4sk")))) + "0m73r67ah9xmcwzxs50jxf8ncd8h71mi4wf2mvnqkxvibhrv478i")))) (build-system perl-build-system) (native-inputs `(("perl-canary-stability" ,perl-canary-stability))) -- cgit v1.2.3 From 49fb2d0922f6642d88f038aece2d30ec88e8e655 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 12 Mar 2019 15:15:05 +0100 Subject: gnu: inxi-minimal: Update to 3.0.22-1. * gnu/packages/admin.scm (inxi-minimal): Update to 3.0.22-1. --- gnu/packages/admin.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 568402f2fc..0dd2bee124 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2699,7 +2699,7 @@ Python loading in HPC environments.") (let ((real-name "inxi")) (package (name "inxi-minimal") - (version "3.0.20-1") + (version "3.0.22-1") (source (origin (method git-fetch) @@ -2707,8 +2707,7 @@ Python loading in HPC environments.") (url "https://github.com/smxi/inxi") (commit version))) (sha256 - (base32 - "1k9148xnfznch1443niaa3w1kmsw4vp0xpwna6npgmi7zqg06ymy")))) + (base32 "1br392s3xc2nwqmfx4nwb3i97wjwasvkq8ayr8jq72mi5qzsgizn")))) (build-system trivial-build-system) (inputs `(("bash" ,bash-minimal) -- cgit v1.2.3 From 7458ceaca8f207924f35cdf8bebaa537d88261b2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 12 Mar 2019 17:29:19 +0200 Subject: gnu: inxi-minimal: Declare source-file-name. * gnu/packages/admin.scm (inxi-minimal)[source]: Add missing field. --- gnu/packages/admin.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 0dd2bee124..f3052953cf 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2706,6 +2706,7 @@ Python loading in HPC environments.") (uri (git-reference (url "https://github.com/smxi/inxi") (commit version))) + (file-name (git-file-name real-name version)) (sha256 (base32 "1br392s3xc2nwqmfx4nwb3i97wjwasvkq8ayr8jq72mi5qzsgizn")))) (build-system trivial-build-system) -- cgit v1.2.3 From 2ffec22eeb5cdc7d95472aaf1a402c831be1f407 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 12 Mar 2019 18:50:59 +0100 Subject: gnu: python-pygit2: Update to 0.27.4. * gnu/packages/python-xyz.scm (python-pygit2): Update to 0.27.4. (python-pygit2)[arguments]: Disable tests. --- gnu/packages/python-xyz.scm | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8406e33591..1f8e00fdfd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3220,26 +3220,19 @@ color scales, and color space conversion easy. It has support for: (define-public python-pygit2 (package (name "python-pygit2") - (version "0.27.3") + (version "0.27.4") (source (origin (method url-fetch) (uri (pypi-uri "pygit2" version)) (sha256 (base32 - "046ahvsb7a20sgvscqfm3cb32sp3sii4gim9vz7zzrkf7yz16xlv")))) + "15c1mhwwjc7nr8hn5gm21hcfhw61jmwb0vngpjhlm3y5565wg2pz")))) (build-system python-build-system) (arguments - '(#:phases + '(#:tests? #f; tests don't run correctly in our environment + #:phases (modify-phases %standard-phases - ;; Remove after the next update. See: - ;; https://github.com/libgit2/pygit2/pull/851 - (add-after 'unpack 'compile-with-cffi - (lambda _ - (substitute* "setup.py" - (("install_requires") - "setup_requires=['cffi'],\n install_requires")) - #t)) (add-after 'unpack 'fix-dependency-versioning (lambda _ (substitute* "setup.py" -- cgit v1.2.3 From 94a33ab899cddeda3b577cc968cd905623a692f1 Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Tue, 12 Mar 2019 09:45:00 +0100 Subject: gnu: Add emacs-eshell-bookmark. * gnu/packages/emacs-xyz.scm (emacs-eshell-bookmark): New variable. Signed-off-by: Oleg Pykhalov --- gnu/packages/emacs-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 064b8cb054..d3b2fc8ec6 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11176,6 +11176,29 @@ systems.") filters, highlighting of regexp group levels, and more.") (license license:gpl2+)))) +(define-public emacs-eshell-bookmark + (package + (name "emacs-eshell-bookmark") + (version "2.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Fuco1/eshell-bookmark") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "14dmsnixf9vqdhsixw693sml0fn80zcf0b37z049fb40cmppqxdw")))) + (build-system emacs-build-system) + (home-page "https://github.com/Fuco1/eshell-bookmark") + (synopsis "Provide @file{bookmark.el} integration for @code{eshell}") + (description + "This package allows for bookmarking @code{eshell} buffers. Upon +visiting the bookmark, a new @code{eshell} session will be opened in the +appropriate directory if no @code{eshell} session is active.") + (license license:gpl3+))) + (define-public emacs-esh-autosuggest (package (name "emacs-esh-autosuggest") -- cgit v1.2.3 From e80a809f1fca1bc8580a9ab24fc071b822f65e7e Mon Sep 17 00:00:00 2001 From: Oleg Pykhalov Date: Sun, 10 Mar 2019 18:30:12 +0300 Subject: gnu: Add tmux-xpanes. * gnu/packages/tmux.scm (tmux-xpanes): New variable. --- gnu/packages/tmux.scm | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/tmux.scm b/gnu/packages/tmux.scm index e09e6c1fbe..7dbe2128a5 100644 --- a/gnu/packages/tmux.scm +++ b/gnu/packages/tmux.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2017 Vasile Dumitrascu ;;; Copyright © 2017 Stefan Reichör ;;; Copyright © 2019 Tobias Geerinckx-Rice +;;; Copyright © 2019 Oleg Pykhalov ;;; ;;; This file is part of GNU Guix. ;;; @@ -27,7 +28,9 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system gnu) + #:use-module (guix build-system trivial) #:use-module (gnu packages) + #:use-module (gnu packages bash) #:use-module (gnu packages libevent) #:use-module (gnu packages ncurses)) @@ -134,3 +137,50 @@ continue running in the background, then later reattached.") command and helper commands provided by tmuxifier to manage Tmux sessions and windows.") (license expat))) + +(define-public tmux-xpanes + (package + (name "tmux-xpanes") + (version "4.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/greymd/tmux-xpanes.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0px164ikhnzfls6dld4xhiyd9j5jp2rbmwfg11b1pxzm9mp7qk6r")))) + (build-system trivial-build-system) + (inputs + `(("bash" ,bash))) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (setenv "PATH" (string-append (assoc-ref %build-inputs "bash") "/bin")) + (copy-recursively (assoc-ref %build-inputs "source") ".") + (substitute* "bin/xpanes" + (("/bin/bash") (which "bash"))) + (install-file "bin/xpanes" (string-append %output "/bin")) + (install-file "man/xpanes.1" (string-append %output "/man/man1")) + #t))) + (home-page "https://github.com/greymd/tmux-xpanes") + (synopsis "Tmux based terminal divider") + (description "This package provides tmux-based terminal divider. + +@code{xpanes} or @code{tmux-xpanes} (alias of @code{xpanes}) commands have +following features: + +@itemize +@item Split tmux window into multiple panes. +@item Build command lines & execute them on the panes. +@item Runnable from outside of tmux session. +@item Runnable from inside of tmux session. +@item Record operation log. +@item Flexible layout arrangement for panes. +@item Display pane title on each pane. +@item Generate command lines from standard input (Pipe mode). +@end itemize") + (license expat))) -- cgit v1.2.3 From 12d73f9c3c809a948046a750e0e88e2a6036bae7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 12:18:30 +0100 Subject: gnu: Add guile-persist. * gnu/packages/guile-xyz.scm (guile-persist): New variable. --- gnu/packages/guile-xyz.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index e758d44966..a9fb96d407 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2098,3 +2098,54 @@ supports backtracking and a small logical framework. The idea is to build up chunks that are memoized and there is no clear scanner/parser separation, chunks can be expressions as well as simple tokens.") (license license:lgpl2.0+)))) + +(define-public guile-persist + (let ((commit "b14927b0368af51c024560aee5f55724aee35233") + (revision "1")) + (package + (name "guile-persist") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/tampe/guile-persist") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0z5nf377wh8yj6n3sx2ddn4bdx1qrqnw899dlqjhg0q69qzil522")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-prefix + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "src/Makefile.am" + (("/usr/local/lib/guile") + (string-append (assoc-ref outputs "out") "/lib/guile")) + (("/usr/local/include/guile") + (string-append (assoc-ref inputs "guile") "/include/guile")) + (("-L/usr/local/lib") + (string-append "-L" (assoc-ref inputs "guile") "/lib"))) + #t)) + (add-after 'unpack 'patch-library-reference + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* "persist/persistance.scm" + (("\"libguile-persist\"") + (format #f "\"~a/lib/guile/2.2/extensions/libguile-persist\"" out))) + #t)))))) + (inputs + `(("guile" ,guile-2.2))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (home-page "https://gitlab.com/tampe/guile-persist") + (synopsis "Persistance programming framework for Guile") + (description + "This is a serialization library for serializing objects like classes +and objects, closures and structs. This currently does not support +serializing continuations or delimited continuations.") + (license license:lgpl2.0+)))) -- cgit v1.2.3 From 557a1089c634198b5aee20afb330f92ec204e876 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 21:30:47 +0100 Subject: gnu: Add r-hsmmsinglecell. * gnu/packages/bioconductor.scm (r-hsmmsinglecell): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8df065a60c..329bacb190 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -33,6 +33,9 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages web)) + +;;; Annotations + (define-public r-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") @@ -647,6 +650,44 @@ based on the knownGene track.") (license license:artistic2.0))) +;;; Experiment data + +(define-public r-hsmmsinglecell + (package + (name "r-hsmmsinglecell") + (version "1.2.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/experiment/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/experiment/src/contrib/" + "HSMMSingleCell_" version ".tar.gz")) + (sha256 + (base32 + "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) + (properties + `((upstream-name . "HSMMSingleCell"))) + (build-system r-build-system) + (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") + (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") + (description + "Skeletal myoblasts undergo a well-characterized sequence of +morphological and transcriptional changes during differentiation. In this +experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded +under high mitogen conditions (GM) and then differentiated by switching to +low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several +hundred cells taken over a time-course of serum-induced differentiation. +Between 49 and 77 cells were captured at each of four time points (0, 24, 48, +72 hours) following serum switch using the Fluidigm C1 microfluidic system. +RNA from each cell was isolated and used to construct mRNA-Seq libraries, +which were then sequenced to a depth of ~4 million reads per library, +resulting in a complete gene expression profile for each cell.") + (license license:artistic2.0))) + + +;;; Packages + (define-public r-biocgenerics (package (name "r-biocgenerics") -- cgit v1.2.3 From 4dc2ecc27933a1c1f41f04ca9f3b6940f592f49b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:06:05 +0100 Subject: gnu: r-qvalue: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-qvalue): Move from here... * gnu/packages/bioconductor.scm (r-qvalue): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 329bacb190..44b81b0704 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -807,6 +807,35 @@ region sets and other genomic features.") "This package provides functions for plotting genomic data.") (license license:artistic2.0))) +(define-public r-qvalue + (package + (name "r-qvalue") + (version "2.14.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "qvalue" version)) + (sha256 + (base32 + "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-reshape2" ,r-reshape2))) + (home-page "http://github.com/jdstorey/qvalue") + (synopsis "Q-value estimation for false discovery rate control") + (description + "This package takes a list of p-values resulting from the simultaneous +testing of many hypotheses and estimates their q-values and local @dfn{false +discovery rate} (FDR) values. The q-value of a test measures the proportion +of false positives incurred when that particular test is called significant. +The local FDR measures the posterior probability the null hypothesis is true +given the test's p-value. Various plots are automatically generated, allowing +one to make sensible significance cut-offs. The software can be applied to +problems in genomics, brain imaging, astrophysics, and data mining.") + ;; Any version of the LGPL. + (license license:lgpl3+))) + (define-public r-diffbind (package (name "r-diffbind") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 26fcc3a41a..e29f2a7a39 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10293,35 +10293,6 @@ quality controls, normalization, visualization, and further analysis are also provided.") (license license:artistic2.0))) -(define-public r-qvalue - (package - (name "r-qvalue") - (version "2.14.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "qvalue" version)) - (sha256 - (base32 - "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc")))) - (build-system r-build-system) - (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2))) - (home-page "http://github.com/jdstorey/qvalue") - (synopsis "Q-value estimation for false discovery rate control") - (description - "This package takes a list of p-values resulting from the simultaneous -testing of many hypotheses and estimates their q-values and local @dfn{false -discovery rate} (FDR) values. The q-value of a test measures the proportion -of false positives incurred when that particular test is called significant. -The local FDR measures the posterior probability the null hypothesis is true -given the test's p-value. Various plots are automatically generated, allowing -one to make sensible significance cut-offs. The software can be applied to -problems in genomics, brain imaging, astrophysics, and data mining.") - ;; Any version of the LGPL. - (license license:lgpl3+))) - (define-public r-hdf5array (package (name "r-hdf5array") -- cgit v1.2.3 From c691c607d7682d08b079e4e168b9392de234b3fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:08:03 +0100 Subject: gnu: Add r-dorng. * gnu/packages/cran.scm (r-dorng): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5bd5c60d49..67a1950756 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10839,3 +10839,32 @@ using @code{S3}.") for model selection. The calibration methods available are based on the slope heuristics.") (license license:gpl2+))) + +(define-public r-dorng + (package + (name "r-dorng") + (version "1.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "doRNG" version)) + (sha256 + (base32 + "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7")))) + (properties `((upstream-name . "doRNG"))) + (build-system r-build-system) + (propagated-inputs + `(("r-foreach" ,r-foreach) + ("r-iterators" ,r-iterators) + ("r-pkgmaker" ,r-pkgmaker) + ("r-rngtools" ,r-rngtools))) + (home-page "https://renozao.github.io/doRNG/") + (synopsis "Generic reproducible parallel backend for foreach loops") + (description + "This package provides functions to perform reproducible parallel +@code{foreach} loops, using independent random streams as generated by +L'Ecuyer's combined multiple-recursive generator. It enables to easily +convert standard @code{%dopar%} loops into fully reproducible loops, +independently of the number of workers, the task scheduling strategy, or the +chosen parallel environment and associated foreach backend.") + (license license:gpl2+))) -- cgit v1.2.3 From f3233beec5c403e95e0ab102fd4d109dffd59219 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:08:59 +0100 Subject: gnu: Add r-blockmodeling. * gnu/packages/cran.scm (r-blockmodeling): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 67a1950756..ac0d497e90 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10868,3 +10868,30 @@ convert standard @code{%dopar%} loops into fully reproducible loops, independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.") (license license:gpl2+))) + +(define-public r-blockmodeling + (package + (name "r-blockmodeling") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "blockmodeling" version)) + (sha256 + (base32 + "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-doparallel" ,r-doparallel) + ("r-dorng" ,r-dorng) + ("r-foreach" ,r-foreach) + ("r-matrix" ,r-matrix))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/blockmodeling") + (synopsis "Generalized and classical blockmodeling of valued networks") + (description + "This package is primarily meant as an implementation of generalized +blockmodeling for valued networks. In addition, measures of similarity or +dissimilarity based on structural equivalence and regular equivalence (REGE +algorithms) can be computed and partitioned matrices can be plotted.") + (license license:gpl2+))) -- cgit v1.2.3 From 4af186a96321d4245560d3d8dc315376eba5797b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:09:21 +0100 Subject: gnu: Add r-upsetr. * gnu/packages/cran.scm (r-upsetr): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ac0d497e90..7e7a3af1ce 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10895,3 +10895,30 @@ blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted.") (license license:gpl2+))) + +(define-public r-upsetr + (package + (name "r-upsetr") + (version "1.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "UpSetR" version)) + (sha256 + (base32 + "08vj7l92b8fpqyqwxshll2mhk3yhgyr74axvr2lf29z78bapymhz")))) + (properties `((upstream-name . "UpSetR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-plyr" ,r-plyr) + ("r-scales" ,r-scales))) + (home-page "https://github.com/hms-dbmi/UpSetR") + (synopsis "Visualize intersecting sets") + (description + "This package provides a more scalable alternative to Venn and Euler +diagrams for visualizing intersecting sets. Create visualizations of +intersecting sets using a novel matrix design, along with visualizations of +several common set, element and attribute related tasks.") + (license license:expat))) -- cgit v1.2.3 From 1901a53241708f64a4c97df5f12c6412a49e697a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:09:57 +0100 Subject: gnu: Add r-outliers. * gnu/packages/cran.scm (r-outliers): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7e7a3af1ce..7a49beee4e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10922,3 +10922,22 @@ diagrams for visualizing intersecting sets. Create visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.") (license license:expat))) + +(define-public r-outliers + (package + (name "r-outliers") + (version "0.14") + (source + (origin + (method url-fetch) + (uri (cran-uri "outliers" version)) + (sha256 + (base32 + "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/outliers/index.html") + (synopsis "Tests for outliers") + (description + "This package provides a collection of some tests commonly used for +identifying outliers.") + (license license:gpl2+))) -- cgit v1.2.3 From 8cd3f49d464935d2b266de112aa4b69e7609fae0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:12:44 +0100 Subject: gnu: Add r-bayesm. * gnu/packages/cran.scm (r-bayesm): New variable. --- gnu/packages/cran.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7a49beee4e..877ddea19b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10941,3 +10941,38 @@ several common set, element and attribute related tasks.") "This package provides a collection of some tests commonly used for identifying outliers.") (license license:gpl2+))) + +(define-public r-bayesm + (package + (name "r-bayesm") + (version "3.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "bayesm" version)) + (sha256 + (base32 + "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "http://www.perossi.org/home/bsm-1") + (synopsis "Bayesian inference for marketing/micro-econometrics") + (description + "This package covers many important models used in marketing and +micro-econometrics applications, including Bayes Regression (univariate or +multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and +Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), +Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate +Mixtures of Normals (including clustering), Dirichlet Process Prior Density +Estimation with normal base, Hierarchical Linear Models with normal prior and +covariates, Hierarchical Linear Models with a mixture of normals prior and +covariates, Hierarchical Multinomial Logits with a mixture of normals prior +and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior +and covariates, Hierarchical Negative Binomial Regression Models, Bayesian +analysis of choice-based conjoint data, Bayesian treatment of linear +instrumental variables models, Analysis of Multivariate Ordinal survey data +with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random +Coefficient Logit Models.") + (license license:gpl2+))) -- cgit v1.2.3 From 262ab4b17cd75e51b60ee34e6303722b654d3e09 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:17:41 +0100 Subject: gnu: Add r-tensora. * gnu/packages/cran.scm (r-tensora): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 877ddea19b..32505a1208 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10976,3 +10976,26 @@ instrumental variables models, Analysis of Multivariate Ordinal survey data with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random Coefficient Logit Models.") (license license:gpl2+))) + +(define-public r-tensora + (package + (name "r-tensora") + (version "0.36.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tensorA" version)) + (sha256 + (base32 + "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7")))) + (properties `((upstream-name . "tensorA"))) + (build-system r-build-system) + (home-page "http://www.stat.boogaart.de/tensorA") + (synopsis "Advanced tensor arithmetic with named indices") + (description + "This package provides convenience functions for advanced linear algebra +with tensors and computation with datasets of tensors on a higher level +abstraction. It includes Einstein and Riemann summing conventions, dragging, +co- and contravariate indices, and parallel computations on sequences of +tensors.") + (license license:gpl2+))) -- cgit v1.2.3 From 7d779142ab663f898aae316b12cee3b52840ec38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:18:42 +0100 Subject: gnu: Add r-rarpack. * gnu/packages/cran.scm (r-rarpack): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 32505a1208..6d200d0768 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10999,3 +10999,27 @@ abstraction. It includes Einstein and Riemann summing conventions, dragging, co- and contravariate indices, and parallel computations on sequences of tensors.") (license license:gpl2+))) + +(define-public r-rarpack + (package + (name "r-rarpack") + (version "0.11-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rARPACK" version)) + (sha256 + (base32 + "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63")))) + (properties `((upstream-name . "rARPACK"))) + (build-system r-build-system) + (propagated-inputs `(("r-rspectra" ,r-rspectra))) + (home-page "https://github.com/yixuan/rARPACK") + (synopsis "Solvers for large scale eigenvalue and SVD problems") + (description + "This package was previously an R wrapper of the ARPACK library, and now +a shell of the R package RSpectra, an R interface to the Spectra library for +solving large scale eigenvalue/vector problems. The current version of +rARPACK simply imports and exports the functions provided by RSpectra. New +users of rARPACK are advised to switch to the RSpectra package.") + (license license:bsd-3))) -- cgit v1.2.3 From 5fde35b3859b23b2063750bcb569efdb63c2ac52 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:19:37 +0100 Subject: gnu: Add r-compositions. * gnu/packages/cran.scm (r-compositions): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6d200d0768..07a6da3c01 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11023,3 +11023,28 @@ solving large scale eigenvalue/vector problems. The current version of rARPACK simply imports and exports the functions provided by RSpectra. New users of rARPACK are advised to switch to the RSpectra package.") (license license:bsd-3))) + +(define-public r-compositions + (package + (name "r-compositions") + (version "1.40-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "compositions" version)) + (sha256 + (base32 + "12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bayesm" ,r-bayesm) + ("r-energy" ,r-energy) + ("r-robustbase" ,r-robustbase) + ("r-tensora" ,r-tensora))) + (home-page "http://www.stat.boogaart.de/compositions") + (synopsis "Compositional data analysis") + (description + "This package provides functions for the consistent analysis of +compositional data (e.g. portions of substances) and positive +numbers (e.g. concentrations).") + (license license:gpl2+))) -- cgit v1.2.3 From 5f673e2c1c6d0af1475f97dca087c6ccb2dd4d4f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:20:38 +0100 Subject: gnu: Add r-cobs. * gnu/packages/cran.scm (r-cobs): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 07a6da3c01..85b75dead7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11048,3 +11048,25 @@ users of rARPACK are advised to switch to the RSpectra package.") compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations).") (license license:gpl2+))) + +(define-public r-cobs + (package + (name "r-cobs") + (version "1.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "cobs" version)) + (sha256 + (base32 + "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-quantreg" ,r-quantreg) + ("r-sparsem" ,r-sparsem))) + (home-page "https://cran.r-project.org/web/packages/cobs") + (synopsis "Constrained B-Splines (sparse matrix based)") + (description + "This package provides qualitatively constrained (regression) smoothing +splines via linear programming and sparse matrices.") + (license license:gpl2+))) -- cgit v1.2.3 From c60e3e10f3b26629b4468b357a6b0e2761872941 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:21:08 +0100 Subject: gnu: Add r-drimpute. * gnu/packages/cran.scm (r-drimpute): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 85b75dead7..2cfa277e69 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11070,3 +11070,28 @@ numbers (e.g. concentrations).") "This package provides qualitatively constrained (regression) smoothing splines via linear programming and sparse matrices.") (license license:gpl2+))) + +(define-public r-drimpute + (package + (name "r-drimpute") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "DrImpute" version)) + (sha256 + (base32 + "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b")))) + (properties `((upstream-name . "DrImpute"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://github.com/ikwak2/DrImpute") + (synopsis "Imputing dropout events in single-cell RNA-Seq data") + (description + "This is an R package for imputing dropout events. Many statistical +methods in cell type identification, visualization and lineage reconstruction +do not account for dropout events. DrImpute can improve the performance of +such software by imputing dropout events.") + (license license:gpl3))) -- cgit v1.2.3 From 061a4b68500a7aa002a89b2eea5bea8374ed905d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:22:53 +0100 Subject: gnu: Add r-gamlss-dist. * gnu/packages/cran.scm (r-gamlss-dist): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2cfa277e69..f3f964d70e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11095,3 +11095,30 @@ methods in cell type identification, visualization and lineage reconstruction do not account for dropout events. DrImpute can improve the performance of such software by imputing dropout events.") (license license:gpl3))) + +(define-public r-gamlss-dist + (package + (name "r-gamlss-dist") + (version "5.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gamlss.dist" version)) + (sha256 + (base32 + "1cd0vl9klcb849i8xwyjm8ihb1da92631j1rxdbnflgffkzrkya4")))) + (properties `((upstream-name . "gamlss.dist"))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "http://www.gamlss.org/") + (synopsis "Distributions for Generalized Additive Models for location scale and shape") + (description + "This package provides a set of distributions which can be used for +modelling the response variables in Generalized Additive Models for Location +Scale and Shape. The distributions can be continuous, discrete or mixed +distributions. Extra distributions can be created, by transforming, any +continuous distribution defined on the real line, to a distribution defined on +ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit} +transformation, respectively.") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) -- cgit v1.2.3 From 4fd994432f032446fbf3654ddd55c738e145e0ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:23:36 +0100 Subject: gnu: Add r-minpack-lm. * gnu/packages/cran.scm (r-minpack-lm): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f3f964d70e..921a33fb26 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11122,3 +11122,27 @@ ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit} transformation, respectively.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) + +(define-public r-minpack-lm + (package + (name "r-minpack-lm") + (version "1.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "minpack.lm" version)) + (sha256 + (base32 + "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql")))) + (properties `((upstream-name . "minpack.lm"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/minpack.lm") + (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm") + (description + "The @code{nls.lm} function provides an R interface to @code{lmder} and +@code{lmdif} from the MINPACK library, for solving nonlinear least-squares +problems by a modification of the Levenberg-Marquardt algorithm, with support +for lower and upper parameter bounds. The implementation can be used via +@rode{nls}-like calls using the @code{nlsLM} function.") + (license license:gpl3))) -- cgit v1.2.3 From 01fe44cbdca1f59e993ff6fceeaa410df0fed27d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:24:01 +0100 Subject: gnu: Add r-moments. * gnu/packages/cran.scm (r-moments): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 921a33fb26..2b5c2b021e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11146,3 +11146,23 @@ problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and upper parameter bounds. The implementation can be used via @rode{nls}-like calls using the @code{nlsLM} function.") (license license:gpl3))) + +(define-public r-moments + (package + (name "r-moments") + (version "0.14") + (source + (origin + (method url-fetch) + (uri (cran-uri "moments" version)) + (sha256 + (base32 + "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/moments") + (synopsis "Moments, cumulants, skewness, kurtosis and related tests") + (description + "This package provides functions to calculate: moments, Pearson's +kurtosis, Geary's kurtosis and skewness; it also includes tests related to +them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") + (license license:gpl2+))) -- cgit v1.2.3 From 9e2ff342aa0d6e870267441f3ba4c6d6de16d366 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:24:23 +0100 Subject: gnu: Add r-msir. * gnu/packages/cran.scm (r-msir): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2b5c2b021e..3f2c80d3f0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11166,3 +11166,25 @@ for lower and upper parameter bounds. The implementation can be used via kurtosis, Geary's kurtosis and skewness; it also includes tests related to them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") (license license:gpl2+))) + +(define-public r-msir + (package + (name "r-msir") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "msir" version)) + (sha256 + (base32 + "1ipzgdffsqly3dp91pw7yp3h5cwn08l9qsj7cdmrykd42jc98950")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mclust" ,r-mclust) + ("r-rgl" ,r-rgl))) + (home-page "https://cran.r-project.org/web/packages/msir") + (synopsis "Model-based sliced inverse regression") + (description + "This is an R package for dimension reduction based on finite Gaussian +mixture modeling of inverse regression.") + (license license:gpl2+))) -- cgit v1.2.3 From e8be5a00983c05b2dd9199cc3e3c752630a5a65d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:24:44 +0100 Subject: gnu: Add r-pbivnorm. * gnu/packages/cran.scm (r-pbivnorm): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3f2c80d3f0..d619c576fb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11188,3 +11188,23 @@ them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") "This is an R package for dimension reduction based on finite Gaussian mixture modeling of inverse regression.") (license license:gpl2+))) + +(define-public r-pbivnorm + (package + (name "r-pbivnorm") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "pbivnorm" version)) + (sha256 + (base32 + "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://github.com/brentonk/pbivnorm") + (synopsis "Vectorized bivariate normal CDF") + (description + "This package provides a vectorized R function for calculating +probabilities from a standard bivariate normal CDF.") + (license license:gpl2+))) -- cgit v1.2.3 From ca3f13704ac1f5c6fcc1e0efaec851453ad973d1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:25:36 +0100 Subject: gnu: Add r-lavaan. * gnu/packages/cran.scm (r-lavaan): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d619c576fb..0d9b721f94 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11208,3 +11208,28 @@ mixture modeling of inverse regression.") "This package provides a vectorized R function for calculating probabilities from a standard bivariate normal CDF.") (license license:gpl2+))) + +(define-public r-lavaan + (package + (name "r-lavaan") + (version "0.6-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "lavaan" version)) + (sha256 + (base32 + "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-mnormt" ,r-mnormt) + ("r-numderiv" ,r-numderiv) + ("r-pbivnorm" ,r-pbivnorm))) + (home-page "http://lavaan.ugent.be") + (synopsis "Latent variable analysis") + (description + "This package provides tools to fit a variety of latent variable models, +including confirmatory factor analysis, structural equation modeling and +latent growth curve models.") + (license license:gpl2+))) -- cgit v1.2.3 From 4d1f19e02c99ca13de95fa57afa8e1e2a0702384 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:26:46 +0100 Subject: gnu: Add r-nonnest2. * gnu/packages/cran.scm (r-nonnest2): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0d9b721f94..d087ffd26e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11233,3 +11233,30 @@ probabilities from a standard bivariate normal CDF.") including confirmatory factor analysis, structural equation modeling and latent growth curve models.") (license license:gpl2+))) + +(define-public r-nonnest2 + (package + (name "r-nonnest2") + (version "0.5-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "nonnest2" version)) + (sha256 + (base32 + "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6")))) + (build-system r-build-system) + (propagated-inputs + `(("r-compquadform" ,r-compquadform) + ("r-lavaan" ,r-lavaan) + ("r-mvtnorm" ,r-mvtnorm) + ("r-sandwich" ,r-sandwich))) + (home-page "https://cran.r-project.org/web/packages/nonnest2/") + (synopsis "Tests of non-nested models") + (description + "This package allows for testing of non-nested models. It includes tests +of model distinguishability and of model fit that can be applied to both +nested and non-nested models. The package also includes functionality to +obtain confidence intervals associated with AIC and BIC.") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) -- cgit v1.2.3 From be0777ba865550e3bc80d6ef962e230233bae45f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:27:10 +0100 Subject: gnu: Add r-penalized. * gnu/packages/cran.scm (r-penalized): New variable. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d087ffd26e..0c789dd69f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11260,3 +11260,31 @@ nested and non-nested models. The package also includes functionality to obtain confidence intervals associated with AIC and BIC.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) + +(define-public r-penalized + (package + (name "r-penalized") + (version "0.9-51") + (source + (origin + (method url-fetch) + (uri (cran-uri "penalized" version)) + (sha256 + (base32 + "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/penalized/") + (synopsis "Penalized estimation in GLMs and in the Cox model") + (description + "This package provides tools for fitting possibly high dimensional +penalized regression models. The penalty structure can be any combination of +an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity +constraint on the regression coefficients. The supported regression models +are linear, logistic and Poisson regression and the Cox Proportional Hazards +model. Cross-validation routines allow optimization of the tuning +parameters.") + (license license:gpl2+))) -- cgit v1.2.3 From 5570804a69f6cf8a69f6da24411c99b129130893 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:27:29 +0100 Subject: gnu: Add r-zim. * gnu/packages/cran.scm (r-zim): New variable. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0c789dd69f..b41e456735 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11288,3 +11288,31 @@ are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.") (license license:gpl2+))) + +(define-public r-zim + (package + (name "r-zim") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ZIM" version)) + (sha256 + (base32 + "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig")))) + (properties `((upstream-name . "ZIM"))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "https://github.com/biostatstudio/ZIM") + (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros") + (description + "Analyze count time series with excess zeros. Two types of statistical +models are supported: Markov regression and state-space models. They are also +known as observation-driven and parameter-driven models respectively in the +time series literature. The functions used for Markov regression or +observation-driven models can also be used to fit ordinary regression models +with independent data under the zero-inflated Poisson (ZIP) or zero-inflated +negative binomial (ZINB) assumption. The package also contains miscellaneous +functions to compute density, distribution, quantile, and generate random +numbers from ZIP and ZINB distributions.") + (license license:gpl3))) -- cgit v1.2.3 From 173c99601a9f7a0ac650c9b78213d98628319e24 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:46:51 +0100 Subject: gnu: Add r-deds. * gnu/packages/bioconductor.scm (r-deds): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 44b81b0704..4fc7fcbf32 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1764,3 +1764,28 @@ estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).") (license license:gpl3+))) + +(define-public r-deds + (package + (name "r-deds") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DEDS" version)) + (sha256 + (base32 + "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c")))) + (properties `((upstream-name . "DEDS"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/DEDS/") + (synopsis "Differential expression via distance summary for microarray data") + (description + "This library contains functions that calculate various statistics of +differential expression for microarray data, including t statistics, fold +change, F statistics, SAM, moderated t and F statistics and B statistics. It +also implements a new methodology called DEDS (Differential Expression via +Distance Summary), which selects differentially expressed genes by integrating +and summarizing a set of statistics using a weighted distance approach.") + ;; Any version of the LGPL. + (license license:lgpl3+))) -- cgit v1.2.3 From 29e76f07223bed1520a19d273ada5fc48fba141d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Mar 2019 22:48:40 +0100 Subject: gnu: guile-stis-parser: Override source file name. * gnu/packages/guile-xyz.scm (guile-stis-parser)[source]: Provide file name for git checkout. --- gnu/packages/guile-xyz.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages') diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index a9fb96d407..8e371c62f4 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2070,6 +2070,7 @@ completion, a simple mode line, etc.") (uri (git-reference (url "https://gitlab.com/tampe/stis-parser") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "0v4hvq7rlpbra1ni73lf8k6sdmjlflr50yi3p1f24g85h77pc7c0")))) -- cgit v1.2.3 From c9c51ac39aae7a4a49c8125916740f340fdfd4f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 12 Mar 2019 17:07:04 +0100 Subject: Revert "packages: 'package-input-rewriting' can take a promise." This reverts commit 7d2be1277b44de9d0528d9d3015443b40cb3b104, which turned out to be unhelpful for the problem at hand: https://lists.gnu.org/archive/html/guix-devel/2019-01/msg00486.html --- gnu/packages/guile.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index eb32e596d3..daeadca610 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -391,7 +391,7 @@ GNU@tie{}Guile. Use the @code{(ice-9 readline)} module and call its (define package-for-guile-2.0 ;; A procedure that rewrites the dependency tree of the given package to use ;; GUILE-2.0 instead of GUILE-2.2. - (package-input-rewriting (delay `((,guile-2.2 . ,guile-2.0))) + (package-input-rewriting `((,guile-2.2 . ,guile-2.0)) (guile-variant-package-name "guile2.0"))) (define-public guile-for-guile-emacs -- cgit v1.2.3 From a269c89457c511a05a7b993a5f738de3f1f359d9 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 12 Mar 2019 23:52:53 +0100 Subject: gnu: musescore: Update to 3.0.5. * gnu/packages/music.scm (musescore): Update to 3.0.5. --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 7d3020469f..095d485d1c 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3667,7 +3667,7 @@ audio samples and various soft sythesizers. It can receive input from a MIDI ke (define-public musescore (package (name "musescore") - (version "3.0.4") + (version "3.0.5") (source (origin (method git-fetch) (uri (git-reference @@ -3676,7 +3676,7 @@ audio samples and various soft sythesizers. It can receive input from a MIDI ke (file-name (git-file-name name version)) (sha256 (base32 - "05cn4j5f7xr438lgl0by3lrc7wckdgicdn4jrvxfqic8hv81sca7")) + "1inf6zdyh6yspjv1i7g6rw9wn90vki1s2qgilkp0j4aphayj4mic")) (modules '((guix build utils))) (snippet ;; Un-bundle OpenSSL and remove unused libraries. -- cgit v1.2.3 From 0d5101c3a341d28b5f2277c2f0087674e162ba65 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 12 Mar 2019 23:57:40 +0100 Subject: gnu: rosegarden: Update to 18.12. * gnu/packages/music.scm (rosegarden): Update to 18.12. [arguments]: Remove unused flag. --- gnu/packages/music.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 095d485d1c..05fdc1428f 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3835,7 +3835,7 @@ specification and header.") (define-public rosegarden (package (name "rosegarden") - (version "18.06") + (version "18.12") (source (origin (method url-fetch) (uri (string-append @@ -3843,10 +3843,10 @@ specification and header.") version "/rosegarden-" version ".tar.bz2")) (sha256 (base32 - "04qc80sqb2ji42pq3mayhvqqn39hlxzymsywpbpzfpchr19chxx7")))) + "15i9fm0vkn3wsgahaxqi1j5zs0wc0j3wdwml0x49084gk2p328vb")))) (build-system cmake-build-system) (arguments - `(#:configure-flags '("-DUSE_QT5=1") ; "-DCMAKE_BUILD_TYPE=Release" + `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release") #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-tests -- cgit v1.2.3 From 2f041a4cef82fa339ec0b86b3538e05e2c9705c4 Mon Sep 17 00:00:00 2001 From: Jack Hill Date: Tue, 12 Mar 2019 23:27:39 -0400 Subject: gnu: r-minpack-lm: Fix typo in description. * gnu/packages/cran.scm (r-minpack-lm)[description]: Fix typo. Signed-off-by: Leo Famulari --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b41e456735..d6301f1a89 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11144,7 +11144,7 @@ transformation, respectively.") @code{lmdif} from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and upper parameter bounds. The implementation can be used via -@rode{nls}-like calls using the @code{nlsLM} function.") +@code{nls}-like calls using the @code{nlsLM} function.") (license license:gpl3))) (define-public r-moments -- cgit v1.2.3 From 77f3d3036406b1d1ceaeba8017ae5f597f2a0fb4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tom=C3=A1=C5=A1=20=C4=8Cech?= Date: Sat, 9 Mar 2019 14:53:41 +0100 Subject: gnu: python-py3status: Update to 3.16. * gnu/packages/python-xyz.scm (python-py3status): Update to 3.16. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1f8e00fdfd..1f48c33222 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8993,14 +8993,14 @@ to occurrences in strings and comments.") (define-public python-py3status (package (name "python-py3status") - (version "3.7") + (version "3.16") (source (origin (method url-fetch) (uri (pypi-uri "py3status" version)) (sha256 (base32 - "0shxcfz4wcczj0mhwp4w0dvwd2fdd9bgprq8slim1519iiqzgwhq")))) + "1xrfph277bgjln3jbpzpgkhxad04fjvj7s3xfil42q1sxi4s3q3g")))) (build-system python-build-system) (inputs `(("file" ,file))) -- cgit v1.2.3 From 2b6ab17f7d61bcee92194d8b155a709481a95244 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 3 Mar 2019 01:33:44 +0100 Subject: gnu: wireshark: Update to 3.0.0. * gnu/packages/networking.scm (wireshark): Update to 3.0.0. --- gnu/packages/networking.scm | 101 ++++++++++++++++++++++---------------------- 1 file changed, 50 insertions(+), 51 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index f7477230a6..ce775a3a0f 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -591,7 +591,7 @@ of the same name.") (define-public wireshark (package (name "wireshark") - (version "2.6.6") + (version "3.0.0") (source (origin (method url-fetch) @@ -599,59 +599,58 @@ of the same name.") version ".tar.xz")) (sha256 (base32 - "0qz8a1ays63712pq1v7nnw7c57zlqkcifq7himfv5nsv0zm36ya8")))) - (build-system gnu-build-system) - (inputs `(("c-ares" ,c-ares) - ("glib" ,glib) - ("gnutls" ,gnutls) - ("libcap" ,libcap) - ("libgcrypt" ,libgcrypt) - ("libnl" ,libnl) - ("libpcap" ,libpcap) - ("libssh" ,libssh) - ("libxml2" ,libxml2) - ("lz4" ,lz4) - ("lua" ,lua-5.2) ;Lua 5.3 unsupported - ("krb5" ,mit-krb5) - ("portaudio" ,portaudio) - ("qtbase" ,qtbase) - ("qtmultimedia" ,qtmultimedia) - ("sbc" ,sbc) - ("snappy" ,snappy) - ("zlib" ,zlib))) - (native-inputs `(("perl" ,perl) - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper) - ("qttools" ,qttools))) + "17h0ixq7yr6scscjkidaj3dh5x6dfd3f97ggdxlklkz9nbsk0kxw")))) + (build-system cmake-build-system) (arguments - `(#:configure-flags - (list (string-append "--with-c-ares=" (assoc-ref %build-inputs "c-ares")) - (string-append "--with-krb5=" (assoc-ref %build-inputs "krb5")) - (string-append "--with-libcap=" (assoc-ref %build-inputs "libcap")) - (string-append "--with-libssh=" (assoc-ref %build-inputs "libssh")) - (string-append "--with-lua=" (assoc-ref %build-inputs "lua")) - (string-append "--with-lz4=" (assoc-ref %build-inputs "lz4")) - (string-append "--with-pcap=" (assoc-ref %build-inputs "libpcap")) - (string-append "--with-portaudio=" - (assoc-ref %build-inputs "portaudio")) - (string-append "--with-sbc=" (assoc-ref %build-inputs "sbc")) - (string-append "--with-snappy=" (assoc-ref %build-inputs "snappy")) - (string-append "--with-zlib=" (assoc-ref %build-inputs "zlib"))) - #:phases + `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'patch-source + (add-after 'unpack 'remove-failing-test + ;; Test 31/32 fails with errors like "Program reassemble_test is + ;; not available". Skipping it for now. (lambda _ - ;; Fix build against Qt 5.11. - (substitute* "ui/qt/packet_format_group_box.cpp" - (("#include ") "#include -#include ")) - (substitute* "ui/qt/time_shift_dialog.cpp" - (("#include ") "#include -#include ")) - (substitute* "ui/qt/wireless_frame.cpp" - (("#include ") "#include -#include ")) - #t))))) + (substitute* "CMakeLists.txt" + (("suite_unittests" all) (string-append "# " all))) + #t))) + ;; Build process chokes during `validate-runpath' phase. + ;; + ;; Errors are like the following: + ;; "/gnu/store/...wireshark-3.0.0/lib/wireshark/plugins/3.0/epan/ethercat.so: + ;; error: depends on 'libwireshark.so.12', which cannot be found in + ;; RUNPATH". That is, "/gnu/store/...wireshark-3.0.0./lib" doesn't + ;; belong to RUNPATH. + ;; + ;; That’s not a problem in practice because "ethercat.so" is a plugin, + ;; so it’s dlopen’d by a process that already provides "libwireshark". + ;; For now, we disable this phase. + #:validate-runpath? #f)) + (inputs + `(("c-ares" ,c-ares) + ("glib" ,glib) + ("gnutls" ,gnutls) + ("libcap" ,libcap) + ("libgcrypt" ,libgcrypt) + ("libnl" ,libnl) + ("libpcap" ,libpcap) + ("libssh" ,libssh) + ("libxml2" ,libxml2) + ("lz4" ,lz4) + ("lua" ,lua-5.2) ;Lua 5.3 unsupported + ("krb5" ,mit-krb5) + ("qtbase" ,qtbase) + ("qtmultimedia" ,qtmultimedia) + ("qtsvg" ,qtsvg) + ("sbc" ,sbc) + ("snappy" ,snappy) + ("zlib" ,zlib))) + (native-inputs + `(("bison" ,bison) + ("doxygen" ,doxygen) + ("flex" ,flex) + ("gettext" ,gettext-minimal) + ("perl" ,perl) + ("pkg-config" ,pkg-config) + ("python" ,python-wrapper) + ("qttools" ,qttools))) (synopsis "Network traffic analyzer") (description "Wireshark is a network protocol analyzer, or @dfn{packet sniffer}, that lets you capture and interactively browse the contents of -- cgit v1.2.3 From 7ed869f7962a07473af7f3e6671cda2f87792b77 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 09:08:22 +0100 Subject: gnu: Add r-nbpseq. * gnu/packages/bioconductor.scm (r-nbpseq): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4fc7fcbf32..7127e963bb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1789,3 +1789,27 @@ Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.") ;; Any version of the LGPL. (license license:lgpl3+))) + +;; This is a CRAN package, but since it depends on a Bioconductor package we +;; put it here. +(define-public r-nbpseq + (package + (name "r-nbpseq") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "NBPSeq" version)) + (sha256 + (base32 + "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) + (properties `((upstream-name . "NBPSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-qvalue" ,r-qvalue))) + (home-page "https://cran.r-project.org/web/packages/NBPSeq") + (synopsis "Negative binomial models for RNA-Seq data") + (description + "This package provides negative binomial models for two-group comparisons +and regression inferences from RNA-sequencing data.") + (license license:gpl2))) -- cgit v1.2.3 From 3087a2f37b5588deac54351fe4f240160b5d57b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 09:09:00 +0100 Subject: gnu: Add r-ebseq. * gnu/packages/bioconductor.scm (r-ebseq): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7127e963bb..899b06aa34 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1813,3 +1813,27 @@ and summarizing a set of statistics using a weighted distance approach.") "This package provides negative binomial models for two-group comparisons and regression inferences from RNA-sequencing data.") (license license:gpl2))) + +(define-public r-ebseq + (package + (name "r-ebseq") + (version "1.22.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EBSeq" version)) + (sha256 + (base32 + "1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0")))) + (properties `((upstream-name . "EBSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-blockmodeling" ,r-blockmodeling) + ("r-gplots" ,r-gplots) + ("r-testthat" ,r-testthat))) + (home-page "https://bioconductor.org/packages/EBSeq") + (synopsis "Differential expression analysis of RNA-seq data") + (description + "This package provides tools for differential expression analysis at both +gene and isoform level using RNA-seq data") + (license license:artistic2.0))) -- cgit v1.2.3 From 2cb71d81a47279db14e441eb37cad022c03535e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 09:34:39 +0100 Subject: gnu: Add r-lpsymphony. * gnu/packages/bioconductor.scm (r-lpsymphony): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 899b06aa34..a08ad46110 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -30,6 +30,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages maths) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web)) @@ -1837,3 +1838,33 @@ and regression inferences from RNA-sequencing data.") "This package provides tools for differential expression analysis at both gene and isoform level using RNA-seq data") (license license:artistic2.0))) + +(define-public r-lpsymphony + (package + (name "r-lpsymphony") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "lpsymphony" version)) + (sha256 + (base32 + "0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y")))) + (build-system r-build-system) + (inputs + `(("gfortran" ,gfortran) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://r-forge.r-project.org/projects/rsymphony") + (synopsis "Symphony integer linear programming solver in R") + (description + "This package was derived from Rsymphony. The package provides an R +interface to SYMPHONY, a linear programming solver written in C++. The main +difference between this package and Rsymphony is that it includes the solver +source code, while Rsymphony expects to find header and library files on the +users' system. Thus the intention of @code{lpsymphony} is to provide an easy +to install interface to SYMPHONY.") + ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. + ;; lpsimphony is released under the same terms. + (license license:epl1.0))) -- cgit v1.2.3 From 704de8f5eeee67402648cc6624defa79600d1d75 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 11:18:27 +0100 Subject: gnu: Add r-ihw. * gnu/packages/bioconductor.scm (r-ihw): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a08ad46110..0e26033d44 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1868,3 +1868,33 @@ to install interface to SYMPHONY.") ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. ;; lpsimphony is released under the same terms. (license license:epl1.0))) + +(define-public r-ihw + (package + (name "r-ihw") + (version "1.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "IHW" version)) + (sha256 + (base32 + "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n")))) + (properties `((upstream-name . "IHW"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-fdrtool" ,r-fdrtool) + ("r-lpsymphony" ,r-lpsymphony) + ("r-slam" ,r-slam))) + (home-page "https://bioconductor.org/packages/IHW") + (synopsis "Independent hypothesis weighting") + (description + "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing +procedure that increases power compared to the method of Benjamini and +Hochberg by assigning data-driven weights to each hypothesis. The input to +IHW is a two-column table of p-values and covariates. The covariate can be +any continuous-valued or categorical variable that is thought to be +informative on the statistical properties of each hypothesis test, while it is +independent of the p-value under the null hypothesis.") + (license license:artistic2.0))) -- cgit v1.2.3 From 849350fbce49950348516f702a351cf7e0216af7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 12:06:36 +0100 Subject: gnu: Add r-shinybs. * gnu/packages/cran.scm (r-shinybs): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d6301f1a89..5b6546e51c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10923,6 +10923,33 @@ intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.") (license license:expat))) +;; This package includes a JavaScript file, which is not minified. When +;; upgrading please check that there are no new minified JavaScript files. +(define-public r-shinybs + (package + (name "r-shinybs") + (version "0.61") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyBS" version)) + (sha256 + (base32 + "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji")))) + (properties `((upstream-name . "shinyBS"))) + (build-system r-build-system) + ;; The tests spawn Shiny browser apps. They cannot be run + ;; non-interactively. + (arguments '(#:tests? #f)) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-shiny" ,r-shiny))) + (home-page "https://ebailey78.github.io/shinyBS/") + (synopsis "Twitter Bootstrap components for Shiny") + (description + "This package adds additional Twitter Bootstrap components to Shiny.") + (license license:gpl3))) + (define-public r-outliers (package (name "r-outliers") -- cgit v1.2.3 From 5146a24ece569f8b0fc772deb096857188568cdf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 12:11:14 +0100 Subject: gnu: Add r-shinyjs. * gnu/packages/cran.scm (r-shinyjs): New variable. --- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5b6546e51c..a204389f9c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11150,6 +11150,36 @@ transformation, respectively.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) +;; This package includes JavaScript files, which are not minified. When +;; upgrading please check that there are no new minified JavaScript files. +(define-public r-shinyjs + (package + (name "r-shinyjs") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyjs" version)) + (sha256 + (base32 + "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-shiny" ,r-shiny))) + (home-page "https://deanattali.com/shinyjs") + (synopsis "Improve the user experience of your Shiny apps") + (description + "Perform common useful JavaScript operations in Shiny apps that will +greatly improve your apps without having to know any JavaScript. Examples +include: hiding an element, disabling an input, resetting an input back to its +original value, delaying code execution by a few seconds, and many more useful +functions for both the end user and the developer. Shinyjs can also be used +to easily call your own custom JavaScript functions from R.") + (license license:agpl3+))) + (define-public r-minpack-lm (package (name "r-minpack-lm") -- cgit v1.2.3 From c27927dbf5f55c088a017df6fb3976e4b4419e0e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 12:39:39 +0100 Subject: gnu: Add r-colourpicker. * gnu/packages/cran.scm (r-colourpicker): New variable. --- gnu/packages/cran.scm | 79 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a204389f9c..c44749f252 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11180,6 +11180,85 @@ functions for both the end user and the developer. Shinyjs can also be used to easily call your own custom JavaScript functions from R.") (license license:agpl3+))) +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-colourpicker + (package + (name "r-colourpicker") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "colourpicker" version)) + (sha256 + (base32 + "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi")))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-salvattore") + "examples/colourInput/www/salvattore.min.js") + (,(assoc-ref inputs "js-jquery") + "htmlwidgets/lib/jquery/jquery.min.js") + ("www/shared/colourpicker/js/colourpicker.js" + "www/shared/colourpicker/js/colourpicker.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (delete-file target) + (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (call-with-output-file target + (lambda (port) + (dump-port minified port))))) + sources targets)))) + #t))))) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jsonlite" ,r-jsonlite) + ("r-miniui" ,r-miniui) + ("r-shiny" ,r-shiny) + ("r-shinyjs" ,r-shinyjs))) + (native-inputs + `(("uglify-js" ,uglify-js) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-3.3.1.js") + (sha256 + (base32 + "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) + ("js-salvattore" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js") + (sha256 + (base32 + "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5")))))) + (home-page "https://github.com/daattali/colourpicker") + (synopsis "Color picker tool for Shiny and for selecting colors in plots") + (description + "This package provides a color picker that can be used as an input in +Shiny apps or Rmarkdown documents. The color picker supports alpha opacity, +custom color palettes, and many more options. A plot color helper tool is +available as an RStudio Addin, which helps you pick colors to use in your +plots. A more generic color picker RStudio Addin is also provided to let you +select colors to use in your R code.") + (license license:expat))) + (define-public r-minpack-lm (package (name "r-minpack-lm") -- cgit v1.2.3 From 30f53ec86d536e96ba5d61c526004d9dd1d7b370 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 12:40:14 +0100 Subject: gnu: Add r-ggextra. * gnu/packages/cran.scm (r-ggextra): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c44749f252..79753eb8d3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11259,6 +11259,35 @@ plots. A more generic color picker RStudio Addin is also provided to let you select colors to use in your R code.") (license license:expat))) +(define-public r-ggextra + (package + (name "r-ggextra") + (version "0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggExtra" version)) + (sha256 + (base32 + "1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b")))) + (properties `((upstream-name . "ggExtra"))) + (build-system r-build-system) + (propagated-inputs + `(("r-colourpicker" ,r-colourpicker) + ("r-ggplot2" ,r-ggplot2) + ("r-gtable" ,r-gtable) + ("r-miniui" ,r-miniui) + ("r-scales" ,r-scales) + ("r-shiny" ,r-shiny) + ("r-shinyjs" ,r-shinyjs))) + (home-page "https://github.com/daattali/ggExtra") + (synopsis "Marginal histograms for ggplot2 and other enhancements") + (description + "This package is a collection of functions and layers to enhance ggplot2. +The flagship function is @code{ggMarginal()}, which can be used to add +marginal histograms/boxplots/density plots to ggplot2 scatterplots.") + (license license:expat))) + (define-public r-minpack-lm (package (name "r-minpack-lm") -- cgit v1.2.3 From 026dd77c636c33a7ef3e5d7116bd824c6d2c5415 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 12:43:20 +0100 Subject: gnu: Add r-nor1mix. * gnu/packages/cran.scm (r-nor1mix): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 79753eb8d3..a00c71ae7f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11481,3 +11481,24 @@ negative binomial (ZINB) assumption. The package also contains miscellaneous functions to compute density, distribution, quantile, and generate random numbers from ZIP and ZINB distributions.") (license license:gpl3))) + +(define-public r-nor1mix + (package + (name "r-nor1mix") + (version "1.2-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "nor1mix" version)) + (sha256 + (base32 + "1bvk888qml9qr7q703s7qzgm0sqfchcjdjqwqllm5vrjx0cnapj3")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/nor1mix/") + (synopsis "Normal (1-d) mixture models") + (description + "This package provides S3 classes and methods for one-dimensional normal +mixture models, for, e.g., density estimation or clustering algorithms +research and teaching; it provides the widely used Marron-Wand densities. It +also provides tools for efficient random number generation and graphics.") + (license license:gpl2+))) -- cgit v1.2.3 From 648dbd2702da24a777757413c53c45a9364a8463 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 12:43:35 +0100 Subject: gnu: Add r-beanplot. * gnu/packages/cran.scm (r-beanplot): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a00c71ae7f..cebc92a627 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11502,3 +11502,23 @@ mixture models, for, e.g., density estimation or clustering algorithms research and teaching; it provides the widely used Marron-Wand densities. It also provides tools for efficient random number generation and graphics.") (license license:gpl2+))) + +(define-public r-beanplot + (package + (name "r-beanplot") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "beanplot" version)) + (sha256 + (base32 + "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/beanplot/") + (synopsis "Visualization via beanplots") + (description + "This package provides beanplots, an alternative to +boxplot/stripchart/violin plots. It can be used to plot univariate comparison +graphs.") + (license license:gpl2))) -- cgit v1.2.3 From 251e08301a514fa035feb17fbb0173f9a0914015 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 12:51:48 +0100 Subject: gnu: Add r-icobra. * gnu/packages/bioconductor.scm (r-icobra): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0e26033d44..adc0e846d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1898,3 +1898,37 @@ any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.") (license license:artistic2.0))) + +(define-public r-icobra + (package + (name "r-icobra") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "iCOBRA" version)) + (sha256 + (base32 + "0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld")))) + (properties `((upstream-name . "iCOBRA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-dt" ,r-dt) + ("r-ggplot2" ,r-ggplot2) + ("r-limma" ,r-limma) + ("r-reshape2" ,r-reshape2) + ("r-rocr" ,r-rocr) + ("r-scales" ,r-scales) + ("r-shiny" ,r-shiny) + ("r-shinybs" ,r-shinybs) + ("r-shinydashboard" ,r-shinydashboard) + ("r-upsetr" ,r-upsetr))) + (home-page "https://bioconductor.org/packages/iCOBRA") + (synopsis "Comparison and visualization of ranking and assignment methods") + (description + "This package provides functions for calculation and visualization of +performance metrics for evaluation of ranking and binary +classification (assignment) methods. It also contains a Shiny application for +interactive exploration of results.") + (license license:gpl2+))) -- cgit v1.2.3 From 925fcdbb7943f04e1f0a8ac79c236d3543a9945b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 12:53:03 +0100 Subject: gnu: Add r-mast. * gnu/packages/bioconductor.scm (r-mast): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index adc0e846d2..782b769225 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1932,3 +1932,36 @@ performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a Shiny application for interactive exploration of results.") (license license:gpl2+))) + +(define-public r-mast + (package + (name "r-mast") + (version "1.8.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MAST" version)) + (sha256 + (base32 + "0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix")))) + (properties `((upstream-name . "MAST"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) + ("r-ggplot2" ,r-ggplot2) + ("r-plyr" ,r-plyr) + ("r-progress" ,r-progress) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://github.com/RGLab/MAST/") + (synopsis "Model-based analysis of single cell transcriptomics") + (description + "This package provides methods and models for handling zero-inflated +single cell assay data.") + (license license:gpl2+))) -- cgit v1.2.3 From 2d7627cfff63fad03f43e63234ce0d8e37f3d8d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 12:59:55 +0100 Subject: gnu: Add r-monocle. * gnu/packages/bioconductor.scm (r-monocle): New variable. --- gnu/packages/bioconductor.scm | 55 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 782b769225..af7259330c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1965,3 +1965,58 @@ interactive exploration of results.") "This package provides methods and models for handling zero-inflated single cell assay data.") (license license:gpl2+))) + +(define-public r-monocle + (package + (name "r-monocle") + (version "2.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "monocle" version)) + (sha256 + (base32 + "0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocviews" ,r-biocviews) + ("r-cluster" ,r-cluster) + ("r-combinat" ,r-combinat) + ("r-ddrtree" ,r-ddrtree) + ("r-densityclust" ,r-densityclust) + ("r-dplyr" ,r-dplyr) + ("r-fastica" ,r-fastica) + ("r-ggplot2" ,r-ggplot2) + ("r-hsmmsinglecell" ,r-hsmmsinglecell) + ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-limma" ,r-limma) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-pheatmap" ,r-pheatmap) + ("r-plyr" ,r-plyr) + ("r-proxy" ,r-proxy) + ("r-qlcmatrix" ,r-qlcmatrix) + ("r-rann" ,r-rann) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2) + ("r-rtsne" ,r-rtsne) + ("r-slam" ,r-slam) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-vgam" ,r-vgam) + ("r-viridis" ,r-viridis))) + (home-page "https://bioconductor.org/packages/monocle") + (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") + (description + "Monocle performs differential expression and time-series analysis for +single-cell expression experiments. It orders individual cells according to +progress through a biological process, without knowing ahead of time which +genes define progress through that process. Monocle also performs +differential expression analysis, clustering, visualization, and other useful +tasks on single cell expression data. It is designed to work with RNA-Seq and +qPCR data, but could be used with other types as well.") + (license license:artistic2.0))) -- cgit v1.2.3 From 6213e4418557dfece72c8aa12468490e68618d3b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:04:11 +0100 Subject: gnu: Add r-noiseq. * gnu/packages/bioconductor.scm (r-noiseq): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index af7259330c..15173e1659 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2020,3 +2020,30 @@ differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.") (license license:artistic2.0))) + +(define-public r-noiseq + (package + (name "r-noiseq") + (version "2.26.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "NOISeq" version)) + (sha256 + (base32 + "1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn")))) + (properties `((upstream-name . "NOISeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-matrix" ,r-matrix))) + (home-page "https://bioconductor.org/packages/NOISeq") + (synopsis "Exploratory analysis and differential expression for RNA-seq data") + (description + "This package provides tools to support the analysis of RNA-seq +expression data or other similar kind of data. It provides exploratory plots +to evaluate saturation, count distribution, expression per chromosome, type of +detected features, features length, etc. It also supports the analysis of +differential expression between two experimental conditions with no parametric +assumptions.") + (license license:artistic2.0))) -- cgit v1.2.3 From b409c3570ffc0b1ab1c124347ba6886d9aad898f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:13:18 +0100 Subject: gnu: Add r-scdd. * gnu/packages/bioconductor.scm (r-scdd): New variable. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 15173e1659..dfc43acc95 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2047,3 +2047,39 @@ detected features, features length, etc. It also supports the analysis of differential expression between two experimental conditions with no parametric assumptions.") (license license:artistic2.0))) + +(define-public r-scdd + (package + (name "r-scdd") + (version "1.6.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scDD" version)) + (sha256 + (base32 + "0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8")))) + (properties `((upstream-name . "scDD"))) + (build-system r-build-system) + (propagated-inputs + `(("r-arm" ,r-arm) + ("r-biocparallel" ,r-biocparallel) + ("r-ebseq" ,r-ebseq) + ("r-fields" ,r-fields) + ("r-ggplot2" ,r-ggplot2) + ("r-mclust" ,r-mclust) + ("r-outliers" ,r-outliers) + ("r-s4vectors" ,r-s4vectors) + ("r-scran" ,r-scran) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://github.com/kdkorthauer/scDD") + (synopsis "Mixture modeling of single-cell RNA-seq data") + (description + "This package implements a method to analyze single-cell RNA-seq data +utilizing flexible Dirichlet Process mixture models. Genes with differential +distributions of expression are classified into several interesting patterns +of differences between two conditions. The package also includes functions +for simulating data with these patterns from negative binomial +distributions.") + (license license:gpl2))) -- cgit v1.2.3 From f088775799f4470d8c7e2c16380f83eea4f24e0e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:14:40 +0100 Subject: gnu: Add r-scone. * gnu/packages/bioconductor.scm (r-scone): New variable. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dfc43acc95..a95fbbf3eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2083,3 +2083,43 @@ of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.") (license license:gpl2))) + +(define-public r-scone + (package + (name "r-scone") + (version "1.6.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scone" version)) + (sha256 + (base32 + "0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p")))) + (build-system r-build-system) + (propagated-inputs + `(("r-aroma-light" ,r-aroma-light) + ("r-biocparallel" ,r-biocparallel) + ("r-boot" ,r-boot) + ("r-class" ,r-class) + ("r-cluster" ,r-cluster) + ("r-compositions" ,r-compositions) + ("r-diptest" ,r-diptest) + ("r-edger" ,r-edger) + ("r-fpc" ,r-fpc) + ("r-gplots" ,r-gplots) + ("r-hexbin" ,r-hexbin) + ("r-limma" ,r-limma) + ("r-matrixstats" ,r-matrixstats) + ("r-mixtools" ,r-mixtools) + ("r-rarpack" ,r-rarpack) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rhdf5" ,r-rhdf5) + ("r-ruvseq" ,r-ruvseq) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/scone") + (synopsis "Single cell overview of normalized expression data") + (description + "SCONE is an R package for comparing and ranking the performance of +different normalization schemes for single-cell RNA-seq and other +high-throughput analyses.") + (license license:artistic2.0))) -- cgit v1.2.3 From f9201d670406e1256ef1876f7a765b21faf224bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:15:24 +0100 Subject: gnu: Add r-geoquery. * gnu/packages/bioconductor.scm (r-geoquery): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a95fbbf3eb..c9d5755963 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2123,3 +2123,34 @@ distributions.") different normalization schemes for single-cell RNA-seq and other high-throughput analyses.") (license license:artistic2.0))) + +(define-public r-geoquery + (package + (name "r-geoquery") + (version "2.50.5") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GEOquery" version)) + (sha256 + (base32 + "074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6")))) + (properties `((upstream-name . "GEOquery"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-limma" ,r-limma) + ("r-magrittr" ,r-magrittr) + ("r-readr" ,r-readr) + ("r-tidyr" ,r-tidyr) + ("r-xml2" ,r-xml2))) + (home-page "https://github.com/seandavi/GEOquery/") + (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") + (description + "The NCBI Gene Expression Omnibus (GEO) is a public repository of +microarray data. Given the rich and varied nature of this resource, it is +only natural to want to apply BioConductor tools to these data. GEOquery is +the bridge between GEO and BioConductor.") + (license license:gpl2))) -- cgit v1.2.3 From eed6ff0358dc510e3d71bfe72aba4620de7d3418 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:15:42 +0100 Subject: gnu: Add r-illuminaio. * gnu/packages/bioconductor.scm (r-illuminaio): New variable. --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c9d5755963..c188dacfbd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2154,3 +2154,24 @@ microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.") (license license:gpl2))) + +(define-public r-illuminaio + (package + (name "r-illuminaio") + (version "0.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "illuminaio" version)) + (sha256 + (base32 + "1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns")))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64" ,r-base64))) + (home-page "https://github.com/HenrikBengtsson/illuminaio/") + (synopsis "Parse Illumina microarray output files") + (description + "This package provides tools for parsing Illumina's microarray output +files, including IDAT.") + (license license:gpl2))) -- cgit v1.2.3 From f4eac09653ddebbe57e16824da42aad04af35632 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:16:22 +0100 Subject: gnu: Add r-siggenes. * gnu/packages/bioconductor.scm (r-siggenes): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c188dacfbd..b29ae9d607 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2175,3 +2175,28 @@ the bridge between GEO and BioConductor.") "This package provides tools for parsing Illumina's microarray output files, including IDAT.") (license license:gpl2))) + +(define-public r-siggenes + (package + (name "r-siggenes") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "siggenes" version)) + (sha256 + (base32 + "0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-multtest" ,r-multtest))) + (home-page "https://bioconductor.org/packages/siggenes/") + (synopsis + "Multiple testing using SAM and Efron's empirical Bayes approaches") + (description + "This package provides tools for the identification of differentially +expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using +both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical +Bayes Analyses of Microarrays} (EBAM).") + (license license:lgpl2.0+))) -- cgit v1.2.3 From 34a24f95ece7be7e5174513091ecd3c4974ce631 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:16:48 +0100 Subject: gnu: Add r-bumphunter. * gnu/packages/bioconductor.scm (r-bumphunter): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b29ae9d607..34f5ceb5aa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2200,3 +2200,37 @@ expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical Bayes Analyses of Microarrays} (EBAM).") (license license:lgpl2.0+))) + +(define-public r-bumphunter + (package + (name "r-bumphunter") + (version "1.24.5") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bumphunter" version)) + (sha256 + (base32 + "1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dorng" ,r-dorng) + ("r-foreach" ,r-foreach) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-iterators" ,r-iterators) + ("r-limma" ,r-limma) + ("r-locfit" ,r-locfit) + ("r-matrixstats" ,r-matrixstats) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/ririzarr/bumphunter") + (synopsis "Find bumps in genomic data") + (description + "This package provides tools for finding bumps in genomic data in order +to identify differentially methylated regions in epigenetic epidemiology +studies.") + (license license:artistic2.0))) -- cgit v1.2.3 From 0fbaf1956b090d63cb21aa45dd213ea81ac34d00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:17:11 +0100 Subject: gnu: Add r-minfi. * gnu/packages/bioconductor.scm (r-minfi): New variable. --- gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 34f5ceb5aa..79eab6b67d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2234,3 +2234,52 @@ Bayes Analyses of Microarrays} (EBAM).") to identify differentially methylated regions in epigenetic epidemiology studies.") (license license:artistic2.0))) + +(define-public r-minfi + (package + (name "r-minfi") + (version "1.28.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "minfi" version)) + (sha256 + (base32 + "1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r")))) + (build-system r-build-system) + (propagated-inputs + `(("r-beanplot" ,r-beanplot) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bumphunter" ,r-bumphunter) + ("r-data-table" ,r-data-table) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-genefilter" ,r-genefilter) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-geoquery" ,r-geoquery) + ("r-hdf5array" ,r-hdf5array) + ("r-illuminaio" ,r-illuminaio) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma) + ("r-mass" ,r-mass) + ("r-mclust" ,r-mclust) + ("r-nlme" ,r-nlme) + ("r-nor1mix" ,r-nor1mix) + ("r-preprocesscore" ,r-preprocesscore) + ("r-quadprog" ,r-quadprog) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape" ,r-reshape) + ("r-s4vectors" ,r-s4vectors) + ("r-siggenes" ,r-siggenes) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://github.com/hansenlab/minfi") + (synopsis "Analyze Illumina Infinium DNA methylation arrays") + (description + "This package provides tools to analyze and visualize Illumina Infinium +methylation arrays.") + (license license:artistic2.0))) -- cgit v1.2.3 From 86fded86c2cef1801b1f4a51a9766807512cda4c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:19:06 +0100 Subject: gnu: portaudio: Build position independent code and install more headers. * gnu/packages/audio.scm (portaudio)[arguments]: Pass "--with-pic" and initialize libtool in new build phase "build-only-position-independent-code"; install extra header in new build phase "install-missing-headers". --- gnu/packages/audio.scm | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index d77ad3d1c4..91bb467de6 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2834,7 +2834,26 @@ portions of LAME.") ("automake" ,automake) ("libtool" ,libtool) ("pkg-config" ,pkg-config))) - (arguments '(#:tests? #f)) ;no 'check' target + (arguments + '(#:tests? #f ;no 'check' target + #:configure-flags '("--with-pic") + #:phases + (modify-phases %standard-phases + ;; This is needed for linking the static libraries + (add-after 'unpack 'build-only-position-independent-code + (lambda _ + (substitute* "configure.in" + (("AC_PROG_LIBTOOL" m) + (string-append m "\nAM_PROG_AR\nLT_INIT([pic-only])"))) + (delete-file "configure") + #t)) + ;; Some headers are not installed by default, but are needed by + ;; packages like Kaldi. + (add-after 'install 'install-missing-headers + (lambda* (#:key outputs #:allow-other-keys) + (install-file "src/common/pa_ringbuffer.h" + (string-append (assoc-ref outputs "out") "/include")) + #t))))) (home-page "http://www.portaudio.com/") (synopsis "Audio I/O library") (description -- cgit v1.2.3 From 0f5c9cec502e0b4c8b4a8aa5b9c42474920c3e03 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:35:18 +0100 Subject: gnu: Add r-fdb-infiniummethylation-hg19. * gnu/packages/bioconductor.scm (r-fdb-infiniummethylation-hg19): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 79eab6b67d..39eb705a02 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -650,6 +650,38 @@ the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) based on the knownGene track.") (license license:artistic2.0))) +(define-public r-fdb-infiniummethylation-hg19 + (package + (name "r-fdb-infiniummethylation-hg19") + (version "2.2.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "FDb.InfiniumMethylation.hg19_" + version ".tar.gz")) + (sha256 + (base32 + "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) + (properties + `((upstream-name . "FDb.InfiniumMethylation.hg19"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-annotationdbi" ,r-annotationdbi) + ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) + (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") + (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") + (description + "This is an annotation package for Illumina Infinium DNA methylation +probes. It contains the compiled HumanMethylation27 and HumanMethylation450 +annotations.") + (license license:artistic2.0))) + ;;; Experiment data -- cgit v1.2.3 From 5ec5ba027208f0028009a5e0b9b1dcb97ffe520e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:35:33 +0100 Subject: gnu: Add r-methylumi. * gnu/packages/bioconductor.scm (r-methylumi): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 39eb705a02..c0dbbebea6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2315,3 +2315,47 @@ studies.") "This package provides tools to analyze and visualize Illumina Infinium methylation arrays.") (license license:artistic2.0))) + +(define-public r-methylumi + (package + (name "r-methylumi") + (version "2.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "methylumi" version)) + (sha256 + (base32 + "14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) + ("r-genefilter" ,r-genefilter) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-illuminaio" ,r-illuminaio) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-matrixstats" ,r-matrixstats) + ("r-minfi" ,r-minfi) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/methylumi") + (synopsis "Handle Illumina methylation data") + (description + "This package provides classes for holding and manipulating Illumina +methylation data. Based on eSet, it can contain MIAME information, sample +information, feature information, and multiple matrices of data. An +\"intelligent\" import function, methylumiR can read the Illumina text files +and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from +HumanMethylation27 and HumanMethylation450 microarrays. Normalization, +background correction, and quality control features for GoldenGate, Infinium, +and Infinium HD arrays are also included.") + (license license:gpl2))) -- cgit v1.2.3 From 09605cb2d16623649064fcd7b26dc7d7e0ae5f88 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:35:40 +0100 Subject: gnu: Add r-lumi. * gnu/packages/bioconductor.scm (r-lumi): New variable. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c0dbbebea6..f2572b45c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2359,3 +2359,42 @@ HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.") (license license:gpl2))) + +(define-public r-lumi + (package + (name "r-lumi") + (version "2.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "lumi" version)) + (sha256 + (base32 + "1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-dbi" ,r-dbi) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-kernsmooth" ,r-kernsmooth) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-methylumi" ,r-methylumi) + ("r-mgcv" ,r-mgcv) + ("r-nleqslv" ,r-nleqslv) + ("r-preprocesscore" ,r-preprocesscore) + ("r-rsqlite" ,r-rsqlite))) + (home-page "https://bioconductor.org/packages/lumi") + (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") + (description + "The lumi package provides an integrated solution for the Illumina +microarray data analysis. It includes functions of Illumina +BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific +variance stabilization, normalization and gene annotation at the probe level. +It also includes the functions of processing Illumina methylation microarrays, +especially Illumina Infinium methylation microarrays.") + (license license:lgpl2.0+))) -- cgit v1.2.3 From 9475a248fcceaaf12733e24aeaa4c9f8cef1cec0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 13:49:20 +0100 Subject: gnu: Add r-illuminahumanmethylationepicmanifest. * gnu/packages/bioconductor.scm (r-illuminahumanmethylationepicmanifest): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f2572b45c2..45711ab6b6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -682,6 +682,32 @@ probes. It contains the compiled HumanMethylation27 and HumanMethylation450 annotations.") (license license:artistic2.0))) +(define-public r-illuminahumanmethylationepicmanifest + (package + (name "r-illuminahumanmethylationepicmanifest") + (version "0.3.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "IlluminaHumanMethylationEPICmanifest_" + version ".tar.gz")) + (sha256 + (base32 + "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) + (properties + `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) + (build-system r-build-system) + (propagated-inputs + `(("r-minfi" ,r-minfi))) + (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") + (synopsis "Manifest for Illumina's EPIC methylation arrays") + (description + "This is a manifest package for Illumina's EPIC methylation arrays.") + (license license:artistic2.0))) + ;;; Experiment data -- cgit v1.2.3 From f313baf0c890f69bf2db6ee9a9934024edb81f09 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 14:26:08 +0100 Subject: gnu: Add r-pbdzmq. * gnu/packages/cran.scm (r-pbdzmq): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cebc92a627..2702e62a9a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -58,6 +58,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) + #:use-module (gnu packages networking) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -11522,3 +11523,31 @@ also provides tools for efficient random number generation and graphics.") boxplot/stripchart/violin plots. It can be used to plot univariate comparison graphs.") (license license:gpl2))) + +(define-public r-pbdzmq + (package + (name "r-pbdzmq") + (version "0.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "pbdZMQ" version)) + (sha256 + (base32 + "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf")))) + (properties `((upstream-name . "pbdZMQ"))) + (build-system r-build-system) + (inputs + `(("zeromq" ,zeromq) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://pbdr.org/") + (synopsis "R interface to ZeroMQ") + (description + "ZeroMQ is a well-known library for high-performance asynchronous +messaging in scalable, distributed applications. This package provides high +level R wrapper functions to easily utilize ZeroMQ. The main focus is on +interactive client/server programming frameworks. A few wrapper functions +compatible with @code{rzmq} are also provided.") + (license license:gpl3))) -- cgit v1.2.3 From d17186d626c06d1bf2da1d0e03773dbb799cbb99 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 14:26:25 +0100 Subject: gnu: Add r-repr. * gnu/packages/cran.scm (r-repr): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2702e62a9a..afa56f0e89 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11551,3 +11551,26 @@ level R wrapper functions to easily utilize ZeroMQ. The main focus is on interactive client/server programming frameworks. A few wrapper functions compatible with @code{rzmq} are also provided.") (license license:gpl3))) + +(define-public r-repr + (package + (name "r-repr") + (version "0.19.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "repr" version)) + (sha256 + (base32 + "1mhhzakkagb8z568yx3p2ixs8fcifm7f8l2yq285zrz8jmnpckfx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite))) + (home-page "https://cran.r-project.org/web/packages/repr/") + (synopsis "Serializable representations") + (description + "This package provides string and binary representations of objects for +several formats and MIME types.") + (license license:gpl3))) -- cgit v1.2.3 From 664dedd52485e543623e30ef7c06a8cc1dd4dc96 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 14:26:34 +0100 Subject: gnu: Add r-irdisplay. * gnu/packages/cran.scm (r-irdisplay): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index afa56f0e89..a61a7c71f4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11574,3 +11574,26 @@ compatible with @code{rzmq} are also provided.") "This package provides string and binary representations of objects for several formats and MIME types.") (license license:gpl3))) + +(define-public r-irdisplay + (package + (name "r-irdisplay") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "IRdisplay" version)) + (sha256 + (base32 + "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli")))) + (properties `((upstream-name . "IRdisplay"))) + (build-system r-build-system) + (propagated-inputs + `(("r-repr" ,r-repr))) + (home-page "https://cran.r-project.org/web/packages/IRdisplay/") + (synopsis "Jupyter display machinery") + (description + "This package provides an interface to the rich display capabilities of +Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a +running IRkernel session.") + (license license:expat))) -- cgit v1.2.3 From 984a8aa64462b6ecf197f756260e0f83016ac575 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 14:26:45 +0100 Subject: gnu: Add r-irkernel. * gnu/packages/cran.scm (r-irkernel): New variable. --- gnu/packages/cran.scm | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a61a7c71f4..f2fd741fb6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -62,6 +62,7 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages statistics) #:use-module (gnu packages tls) #:use-module (gnu packages web) @@ -11597,3 +11598,47 @@ several formats and MIME types.") Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a running IRkernel session.") (license license:expat))) + +(define-public r-irkernel + (package + (name "r-irkernel") + (version "0.8.15") + (source + (origin + (method url-fetch) + (uri (cran-uri "IRkernel" version)) + (sha256 + (base32 + "1n0nc3paij8fgbp7l2b4405zk9k4y3gdi2bz6z8x6j0h5mi6k6a6")))) + (properties `((upstream-name . "IRkernel"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'install-kernelspec + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (setenv "HOME" "/tmp") + (invoke "jupyter" "kernelspec" "install" + "--name" "ir" + "--prefix" out + (string-append out "/site-library/IRkernel/kernelspec")) + #t)))))) + (inputs + `(("jupyter" ,jupyter))) + (propagated-inputs + `(("r-crayon" ,r-crayon) + ("r-digest" ,r-digest) + ("r-evaluate" ,r-evaluate) + ("r-irdisplay" ,r-irdisplay) + ("r-jsonlite" ,r-jsonlite) + ("r-pbdzmq" ,r-pbdzmq) + ("r-repr" ,r-repr) + ("r-uuid" ,r-uuid))) + (home-page "https://cran.r-project.org/web/packages/IRkernel/") + (synopsis "Native R kernel for Jupyter") + (description + "The R kernel for the Jupyter environment executes R code which the +front-end (Jupyter Notebook or other front-ends) submits to the kernel via the +network.") + (license license:expat))) -- cgit v1.2.3 From 0b5d12ccdfdbfe9820e1236420288d1380ed87a3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 15:14:10 +0100 Subject: gnu: Add tetoolkit. * gnu/packages/bioinformatics.scm (tetoolkit): New variable. --- gnu/packages/bioinformatics.scm | 66 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e29f2a7a39..97d2404bf3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1752,6 +1752,72 @@ high-throughput sequencing data – with an emphasis on simplicity.") (define-public python2-plastid (package-with-python2 python-plastid)) +(define-public tetoolkit + (package + (name "tetoolkit") + (version "2.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mhammell-laboratory/tetoolkit.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1yzi0kfpzip8zpjb82x1ik6h22yzfyjiz2dv85v6as2awwqvk807")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 ; not guaranteed to work with Python 3 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-writable + (lambda _ + (for-each make-file-writable (find-files ".")) + #t)) + (add-after 'unpack 'patch-invocations + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("bin/TEtranscripts" + "bin/TEcount") + (("'sort ") + (string-append "'" (which "sort") " ")) + (("'rm -f ") + (string-append "'" (which "rm") " -f ")) + (("'Rscript'") (string-append "'" (which "Rscript") "'"))) + (substitute* "TEToolkit/IO/ReadInputs.py" + (("BamToBED") (which "bamToBed"))) + (substitute* "TEToolkit/Normalization.py" + (("\"Rscript\"") + (string-append "\"" (which "Rscript") "\""))) + #t)) + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure the executables find R packages. + (let ((out (assoc-ref outputs "out"))) + (for-each + (lambda (script) + (wrap-program (string-append out "/bin/" script) + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) + '("TEtranscripts" + "TEcount"))) + #t))))) + (inputs + `(("coreutils" ,coreutils) + ("bedtools" ,bedtools) + ("python-argparse" ,python2-argparse) + ("python-pysam" ,python2-pysam) + ("r-minimal" ,r-minimal) + ("r-deseq2" ,r-deseq2))) + (home-page "https://github.com/mhammell-laboratory/tetoolkit") + (synopsis "Transposable elements in differential enrichment analysis") + (description + "This is package for including transposable elements in differential +enrichment analysis of sequencing datasets. TEtranscripts and TEcount take +RNA-seq (and similar data) and annotates reads to both genes and transposable +elements. TEtranscripts then performs differential analysis using DESeq2. +Note that TEtranscripts and TEcount rely on specially curated GTF files, which +are not included due to their size.") + (license license:gpl3+))) + (define-public cd-hit (package (name "cd-hit") -- cgit v1.2.3 From 51df43408b040effb83526e1342ce336e6ee90e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 17:10:41 +0100 Subject: gnu: Add r-gmodels. * gnu/packages/cran.scm (r-gmodels): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f2fd741fb6..82a39da6a9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11642,3 +11642,24 @@ running IRkernel session.") front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network.") (license license:expat))) + +(define-public r-gmodels + (package + (name "r-gmodels") + (version "2.18.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gmodels" version)) + (sha256 + (base32 + "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-gdata" ,r-gdata) + ("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/gmodels/") + (synopsis "Various R programming tools for model fitting") + (description + "This package provides various R programming tools for model fitting.") + (license license:gpl2))) -- cgit v1.2.3 From 3942bf5e4ca175313102a24570212aadc3d1337e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 17:10:53 +0100 Subject: gnu: Add r-apcluster. * gnu/packages/cran.scm (r-apcluster): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 82a39da6a9..4baf0307ba 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11663,3 +11663,28 @@ network.") (description "This package provides various R programming tools for model fitting.") (license license:gpl2))) + +(define-public r-apcluster + (package + (name "r-apcluster") + (version "1.4.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "apcluster" version)) + (sha256 + (base32 + "188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/apcluster/") + (synopsis "Affinity propagation clustering") + (description + "This package implements affinity propagation clustering introduced by +Frey and Dueck (2007). The package further provides leveraged affinity +propagation and an algorithm for exemplar-based agglomerative clustering that +can also be used to join clusters obtained from affinity propagation. Various +plotting functions are available for analyzing clustering results.") + (license license:gpl2+))) -- cgit v1.2.3 From 70daf82f2835fbcb9da61818a167c302ec6c0512 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 17:11:09 +0100 Subject: gnu: Add python2-argparse. * gnu/packages/python-xyz.scm (python2-argparse): New variable. --- gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1f48c33222..8be5f390a9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11649,6 +11649,27 @@ applications in seconds while maintaining all the flexibility.") (define-public python2-mando (package-with-python2 python-mando)) +(define-public python2-argparse + (package + (name "python2-argparse") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "argparse" version)) + (sha256 + (base32 + "1r6nznp64j68ih1k537wms7h57nvppq0szmwsaf99n71bfjqkc32")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2)) + (home-page "https://github.com/ThomasWaldmann/argparse/") + (synopsis "Python command-line parsing library") + (description + "This package is mostly for people who want to have @code{argparse} on +older Pythons because it was not part of the standard library back then.") + (license license:psfl))) + (define-public python-fudge (package (name "python-fudge") -- cgit v1.2.3 From 4291f36a22081e25fad1346178d14f3a3c9df1c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 17:13:21 +0100 Subject: gnu: Add r-linnorm. * gnu/packages/bioconductor.scm (r-linnorm): New variable. --- gnu/packages/bioconductor.scm | 59 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 45711ab6b6..251ad1e1ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2424,3 +2424,62 @@ variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.") (license license:lgpl2.0+))) + +(define-public r-linnorm + (package + (name "r-linnorm") + (version "2.6.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Linnorm" version)) + (sha256 + (base32 + "1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6")))) + (properties `((upstream-name . "Linnorm"))) + (build-system r-build-system) + (propagated-inputs + `(("r-amap" ,r-amap) + ("r-apcluster" ,r-apcluster) + ("r-ellipse" ,r-ellipse) + ("r-fastcluster" ,r-fastcluster) + ("r-fpc" ,r-fpc) + ("r-ggdendro" ,r-ggdendro) + ("r-ggplot2" ,r-ggplot2) + ("r-gmodels" ,r-gmodels) + ("r-igraph" ,r-igraph) + ("r-limma" ,r-limma) + ("r-mass" ,r-mass) + ("r-mclust" ,r-mclust) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rtsne" ,r-rtsne) + ("r-statmod" ,r-statmod) + ("r-vegan" ,r-vegan) + ("r-zoo" ,r-zoo))) + (home-page "http://www.jjwanglab.org/Linnorm/") + (synopsis "Linear model and normality based transformation method") + (description + "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq +count data or any large scale count data. It transforms such datasets for +parametric tests. In addition to the transformtion function (@code{Linnorm}), +the following pipelines are implemented: + +@enumerate +@item Library size/batch effect normalization (@code{Linnorm.Norm}) +@item Cell subpopluation analysis and visualization using t-SNE or PCA K-means + clustering or hierarchical clustering (@code{Linnorm.tSNE}, + @code{Linnorm.PCA}, @code{Linnorm.HClust}) +@item Differential expression analysis or differential peak detection using + limma (@code{Linnorm.limma}) +@item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) +@item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) +@item Stable gene selection for scRNA-seq data; for users without or who do + not want to rely on spike-in genes (@code{Linnorm.SGenes}) +@item Data imputation (@code{Linnorm.DataImput}). +@end enumerate + +Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the +@code{RnaXSim} function is included for simulating RNA-seq data for the +evaluation of DEG analysis methods.") + (license license:expat))) -- cgit v1.2.3 From a97796cd5333e7ec0cb07bc480b435c22f8d58fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 17:19:58 +0100 Subject: gnu: Add r-valr. * gnu/packages/cran.scm (r-valr): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4baf0307ba..b04a69d5c1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11688,3 +11688,32 @@ propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.") (license license:gpl2+))) + +(define-public r-valr + (package + (name "r-valr") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "valr" version)) + (sha256 + (base32 + "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika")))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-rcpp" ,r-rcpp) + ("r-readr" ,r-readr) + ("r-rlang" ,r-rlang) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble))) + (home-page "http://github.com/rnabioco/valr") + (synopsis "Genome interval arithmetic in R") + (description + "This package enables you to read and manipulate genome intervals and +signals. It provides functionality similar to command-line tool suites within +R, enabling interactive analysis and visualization of genome-scale data.") + (license license:expat))) -- cgit v1.2.3 From b9445d0b76dfc05dc64e2b72427f43da65869595 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 19:30:19 +0100 Subject: gnu: Add kaldi. * gnu/packages/machine-learning.scm (kaldi): New variable. --- gnu/packages/machine-learning.scm | 103 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 103 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 1db5f4a256..4067b4b1ea 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -40,14 +40,19 @@ #:use-module (guix git-download) #:use-module (gnu packages) #:use-module (gnu packages algebra) + #:use-module (gnu packages audio) #:use-module (gnu packages autotools) + #:use-module (gnu packages base) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cran) #:use-module (gnu packages dejagnu) #:use-module (gnu packages gcc) + #:use-module (gnu packages glib) + #:use-module (gnu packages gstreamer) #:use-module (gnu packages image) + #:use-module (gnu packages linux) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages ocaml) @@ -924,3 +929,101 @@ interactive learning.") Models, is a program for performing both single-SNP and SNP-set genome-wide association studies (GWAS) on extremely large data sets.") (license license:asl2.0))) + +;; There have been no proper releases yet. +(define-public kaldi + (let ((commit "2f95609f0bb085bd3a1dc5eb0a39f3edea59e606") + (revision "1")) + (package + (name "kaldi") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kaldi-asr/kaldi.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "src") #t)) + (replace 'configure + (lambda* (#:key build system inputs outputs #:allow-other-keys) + (when (not (or (string-prefix? "x86_64" system) + (string-prefix? "i686" system))) + (substitute* "makefiles/linux_openblas.mk" + (("-msse -msse2") ""))) + (substitute* "makefiles/default_rules.mk" + (("/bin/bash") (which "bash"))) + (substitute* "Makefile" + (("ext_depend: check_portaudio") + "ext_depend:")) + (substitute* '("online/Makefile" + "onlinebin/Makefile" + "gst-plugin/Makefile") + (("../../tools/portaudio/install") + (assoc-ref inputs "portaudio"))) + + ;; This `configure' script doesn't support variables passed as + ;; arguments, nor does it support "prefix". + (let ((out (assoc-ref outputs "out")) + (openblas (assoc-ref inputs "openblas")) + (openfst (assoc-ref inputs "openfst"))) + (substitute* "configure" + (("check_for_slow_expf;") "") + ;; This affects the RPATH and also serves as the installation + ;; directory. + (("KALDILIBDIR=`pwd`/lib") + (string-append "KALDILIBDIR=" out "/lib"))) + (mkdir-p out) ; must exist + (setenv "CONFIG_SHELL" (which "bash")) + (setenv "OPENFST_VER" ,(package-version openfst)) + (invoke "./configure" + "--use-cuda=no" + "--shared" + (string-append "--openblas-root=" openblas) + (string-append "--fst-root=" openfst))))) + (add-after 'build 'build-ext-and-gstreamer-plugin + (lambda _ + (invoke "make" "-C" "online" "depend") + (invoke "make" "-C" "online") + (invoke "make" "-C" "onlinebin" "depend") + (invoke "make" "-C" "onlinebin") + (invoke "make" "-C" "gst-plugin" "depend") + (invoke "make" "-C" "gst-plugin") + #t)) + ;; TODO: also install the executables. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib"))) + (mkdir-p lib) + (install-file "gst-plugin/libgstonlinegmmdecodefaster.so" lib) + #t)))))) + (inputs + `(("alsa-lib" ,alsa-lib) + ("gfortran" ,gfortran "lib") + ("glib" ,glib) + ("gstreamer" ,gstreamer) + ("jack" ,jack-1) + ("openblas" ,openblas) + ("openfst" ,openfst) + ("portaudio" ,portaudio) + ("python" ,python))) + (native-inputs + `(("glib" ,glib "bin") ; glib-genmarshal + ("grep" ,grep) + ("sed" ,sed) + ("pkg-config" ,pkg-config) + ("which" ,which))) + (home-page "https://kaldi-asr.org/") + (synopsis "Speech recognition toolkit") + (description "Kaldi is an extensible toolkit for speech recognition +written in C++.") + (license license:asl2.0)))) -- cgit v1.2.3 From 8318b3ed8c04ef73f042816fca9bbe884eadc00c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 20:41:41 +0100 Subject: gnu: guile-stis-parser: Install go files to canonical directory. * gnu/packages/guile-xyz.scm (guile-stis-parser)[arguments]: Add build phase "use-canonical-directory-for-go-files". --- gnu/packages/guile-xyz.scm | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 8e371c62f4..48bfa46c7e 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2081,6 +2081,11 @@ completion, a simple mode line, etc.") (modify-phases %standard-phases (add-after 'unpack 'chdir (lambda _ (chdir "modules") #t)) + (add-after 'chdir 'use-canonical-directory-for-go-files + (lambda _ + (substitute* "Makefile.am" + (("/ccache") "/site-ccache")) + #t)) (add-after 'chdir 'delete-broken-symlink (lambda _ (delete-file "parser/stis-parser/lang/.#calc.scm") -- cgit v1.2.3 From 8f05252862080e6b4a1723f26fc08e1b6ad1c7ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 20:42:23 +0100 Subject: gnu: guile-persist: Install go files to canonical directory. * gnu/packages/guile-xyz.scm (guile-persist)[arguments]: Patch target directory for go files in build phase "patch-prefix". --- gnu/packages/guile-xyz.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 48bfa46c7e..27230ddc3c 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2132,7 +2132,9 @@ chunks can be expressions as well as simple tokens.") (("/usr/local/include/guile") (string-append (assoc-ref inputs "guile") "/include/guile")) (("-L/usr/local/lib") - (string-append "-L" (assoc-ref inputs "guile") "/lib"))) + (string-append "-L" (assoc-ref inputs "guile") "/lib")) + ;; Use canonical directory for go files. + (("/ccache") "/site-ccache")) #t)) (add-after 'unpack 'patch-library-reference (lambda* (#:key outputs #:allow-other-keys) -- cgit v1.2.3 From 6d37301bd53ca55f6a2fa73d80b6d3892effd30b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 20:43:35 +0100 Subject: gnu: Add python-on-guile. * gnu/packages/guile-xyz.scm (python-on-guile): New variable. --- gnu/packages/guile-xyz.scm | 47 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 27230ddc3c..a64a54323a 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2157,3 +2157,50 @@ chunks can be expressions as well as simple tokens.") and objects, closures and structs. This currently does not support serializing continuations or delimited continuations.") (license license:lgpl2.0+)))) + +(define-public python-on-guile + (let ((commit "0cb7c2b2fff4338ca6153473f3f5c409a818f293") + (revision "1")) + (package + (name "python-on-guile") + (version (git-version "0.1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/python-on-guile/python-on-guile.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0kpz08rrp5mwcf5ksc4flgrw992syham9x49dn9wq9w31bpcpnby")))) + (build-system gnu-build-system) + (arguments + `(#:parallel-build? #f ; not supported + #:make-flags + '("GUILE_AUTO_COMPILE=0") ; to prevent guild errors + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "modules") #t)) + (add-after 'chdir 'use-canonical-directory-for-go-files + (lambda _ + (substitute* "Makefile.am" + (("/ccache") "/site-ccache")) + #t))))) + (inputs + `(("guile" ,guile-2.2))) + (propagated-inputs + `(("guile-persist" ,guile-persist) + ("guile-readline" ,guile-readline) + ("guile-stis-parser" ,guile-stis-parser))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (home-page "https://gitlab.com/python-on-guile/python-on-guile/") + (synopsis "Python implementation in Guile") + (description + "This package allows you to compile a Guile Python file to any target +from @code{tree-il}.") + (license license:lgpl2.0+)))) -- cgit v1.2.3 From f9325407737bfc1ebad0914067e01a5babab9b43 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 20:43:55 +0100 Subject: gnu: python-llvmlite: Update to 0.27.1. * gnu/packages/llvm.scm (python-llvmlite): Update to 0.27.1. [inputs]: Update patch for custom LLVM variant. --- gnu/packages/llvm.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index bb5a4a141c..8ae646d87e 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -451,14 +451,14 @@ use with Clang, targeting C++11, C++14 and above.") (define-public python-llvmlite (package (name "python-llvmlite") - (version "0.24.0") + (version "0.27.1") (source (origin (method url-fetch) (uri (pypi-uri "llvmlite" version)) (sha256 (base32 - "01zwjlc3c5mhrwmv4b73zgbskwqps9ly0nrh54bbj1f1l72f839j")))) + "1aq003zbyjnz4q1118h6qx5lfimc8s5fvgskl75j12gxd6pc78a8")))) (build-system python-build-system) (inputs `(("llvm" @@ -472,10 +472,10 @@ use with Clang, targeting C++11, C++14 and above.") (method url-fetch) (uri (string-append "https://raw.githubusercontent.com/numba/" "llvmlite/v" version "/conda-recipes/" - "D47188-svml.patch")) + "D47188-svml-VF.patch")) (sha256 (base32 - "0mrj24jvkv3hjcmyg98zmvmyl1znlh2j63rdr69f6g7s96d2pfv1"))) + "0wxhgb61k17f0zg2m0726sf3hppm41f8jar2kkg2n8sl5cnjj9mr"))) (origin (method url-fetch) (uri (string-append "https://raw.githubusercontent.com/numba/" -- cgit v1.2.3 From 7757e6d8b989bd62b300c0b9f2bb4f135344962a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 20:44:25 +0100 Subject: gnu: python-numba: Update to 0.42.0. * gnu/packages/python-xyz.scm (python-numba): Update to 0.42.0. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8be5f390a9..ab8e543295 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14382,14 +14382,14 @@ validation testing and application logic.") (define-public python-numba (package (name "python-numba") - (version "0.39.0") + (version "0.42.0") (source (origin (method url-fetch) (uri (pypi-uri "numba" version)) (sha256 (base32 - "1bibvkwga1v8293i9ivl469d8bzgabn3vgr2ig7c1i68v8frsx07")))) + "03rqdfx0512lcri2bcpngx5k3jwfbqnanqj3n19c7d6h6hqxvq9x")))) (build-system python-build-system) (arguments `(#:modules ((guix build utils) -- cgit v1.2.3 From 3899ae891cfc7763a1e6201b212010ea8f64d038 Mon Sep 17 00:00:00 2001 From: Oleg Pykhalov Date: Mon, 11 Mar 2019 20:42:18 +0300 Subject: gnu: Add emacs-docker-tramp. * gnu/packages/emacs-xyz.scm (emacs-docker-tramp): New variable. --- gnu/packages/emacs-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d3b2fc8ec6..45dab3cd5d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13373,3 +13373,24 @@ paragraphs or pages of text for testing purposes.") is created (bound, for example, by let) as well as quoted and backquoted constant expressions.") (license license:gpl3+)))) + +(define-public emacs-docker-tramp + (package + (name "emacs-docker-tramp") + (version "0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-pe/docker-tramp.el") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0lxvzmfg52fhxrhbvp92zwp7cv4i1rlxnkyyzgngj3sjm7y60yvg")))) + (build-system emacs-build-system) + (home-page "https://github.com/emacs-pe/docker-tramp.el") + (synopsis "TRAMP integration for docker containers") + (description + "This package provides a TRAMP method for Docker containers.") + (license license:gpl3+))) -- cgit v1.2.3 From 18964a6029e0800277ca115886518f20303c12a9 Mon Sep 17 00:00:00 2001 From: Oleg Pykhalov Date: Mon, 11 Mar 2019 20:44:35 +0300 Subject: gnu: Add emacs-docker. * gnu/packages/emacs-xyz.scm (emacs-docker): New variable. --- gnu/packages/emacs-xyz.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 45dab3cd5d..ab45956e63 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13394,3 +13394,35 @@ constant expressions.") (description "This package provides a TRAMP method for Docker containers.") (license license:gpl3+))) + +(define-public emacs-docker + (package + (name "emacs-docker") + (version "1.2.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Silex/docker.el") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "15kd86kaq1x6giz855q9w6zvnyc742j309j0pmm86rwx398g4rq1")))) + (inputs + `(("emacs-undercover" ,emacs-undercover))) + (propagated-inputs + `(("emacs-dash" ,emacs-dash) + ("emacs-docker-tramp" ,emacs-docker-tramp) + ("emacs-magit-popup" ,emacs-magit-popup) + ("emacs-s" ,emacs-s) + ("emacs-tablist" ,emacs-tablist) + ("emacs-json-mode" ,emacs-json-mode))) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'check)))) ;no tests + (build-system emacs-build-system) + (home-page "https://github.com/Silex/docker.el") + (synopsis "Manage docker from Emacs") + (description "This package provides an Emacs interface for Docker.") + (license license:gpl3+))) -- cgit v1.2.3 From 1f058eced3a4dad4fe0c7f46a1abcc621ffe4ce3 Mon Sep 17 00:00:00 2001 From: Oleg Pykhalov Date: Mon, 11 Mar 2019 20:47:02 +0300 Subject: gnu: Add emacs-dockerfile-mode. * gnu/packages/emacs-xyz.scm (emacs-dockerfile-mode): New variable. --- gnu/packages/emacs-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ab45956e63..5896060a76 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13426,3 +13426,29 @@ constant expressions.") (synopsis "Manage docker from Emacs") (description "This package provides an Emacs interface for Docker.") (license license:gpl3+))) + +(define-public emacs-dockerfile-mode + ;; Latest upstream release is too old. + (let ((commit "7223d92718f78fa3ab15667cdb2ed90cfeb579e7")) + (package + (name "emacs-dockerfile-mode") + (version (git-version "1.2" "1" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/spotify/dockerfile-mode.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0hmipgl4rk6aih11i8mnspwdijjiwk2y0wns6lzs8bgkvy3c064r")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-s" ,emacs-s))) + (home-page "https://github.com/spotify/dockerfile-mode") + (synopsis "Major mode for editing Dockerfile") + (description + "This package provides a major mode @code{dockerfile-mode} for use with +the standard @code{Dockerfile} file format.") + (license license:asl2.0)))) -- cgit v1.2.3 From 55a0a3c853dc9177afeb9d438f3e4bdc1a1379e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 22:43:43 +0100 Subject: gnu: python-loompy: Update to 2.0.17. * gnu/packages/bioinformatics.scm (python-loompy): Update to 2.0.17. [source]: Fetch via git. [arguments]: Enable tests, replace "check" phase. [propagated-inputs]: Add python-pandas. [native-inputs]: Add python-pytest. --- gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++---------- 1 file changed, 24 insertions(+), 10 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 97d2404bf3..da0edcdf40 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11945,21 +11945,35 @@ variational inference.") (define-public python-loompy (package (name "python-loompy") - (version "2.0.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "loompy" version)) - (sha256 - (base32 - "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51")))) + (version "2.0.17") + ;; The tarball on Pypi does not include the tests. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linnarsson-lab/loompy.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "12a5kjgiikapv93wahfw0frszx1lblnppyz3vs5gy8fgmgngra07")))) (build-system python-build-system) - ;; There are no tests - (arguments '(#:tests? #f)) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" + (getenv "PYTHONPATH"))) + (invoke "pytest" "tests") + #t))))) (propagated-inputs `(("python-h5py" ,python-h5py) ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/linnarsson-lab/loompy") (synopsis "Work with .loom files for single-cell RNA-seq data") (description "The loom file format is an efficient format for very large -- cgit v1.2.3 From fd4c7a098a508c1de7a8513c0f3d88d5a0df12e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Mar 2019 22:48:10 +0100 Subject: gnu: Add python-velocyto. * gnu/packages/bioinformatics.scm (python-velocyto): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index da0edcdf40..9b0a4314b9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14209,3 +14209,34 @@ short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs.") (license license:gpl2+))) + +(define-public python-velocyto + (package + (name "python-velocyto") + (version "0.17.17") + (source + (origin + (method url-fetch) + (uri (pypi-uri "velocyto" version)) + (sha256 + (base32 + "0fgygyzqgrq32dv6a00biq1p1cwi6kbl5iqblxq1kklj6b2mzmhs")))) + (build-system python-build-system) + (propagated-inputs + `(("python-click" ,python-click) + ("python-cython" ,python-cython) + ("python-h5py" ,python-h5py) + ("python-loompy" ,python-loompy) + ("python-matplotlib" ,python-matplotlib) + ("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-pysam" ,python-pysam) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy))) + (home-page "https://github.com/velocyto-team/velocyto.py") + (synopsis "RNA velocity analysis for single cell RNA-seq data") + (description + "Velocyto is a library for the analysis of RNA velocity. Velocyto +includes a command line tool and an analysis pipeline.") + (license license:bsd-2))) -- cgit v1.2.3 From 59e80445882f8b0379e54916f89510c0deda6698 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 13 Mar 2019 16:44:02 +0100 Subject: Remove traces of "GuixSD". * gnu/bootloader/extlinux.scm (extlinux-configuration-file): Remove mentions of "GuixSD". * gnu/bootloader/grub.scm (install-grub-efi): Likewise. * gnu/build/vm.scm (make-iso9660-image): Change default #:volume-id to "Guix_image". (initialize-hard-disk): Search for the "Guix_image" label. * gnu/ci.scm (system-test-jobs, tarball-jobs): Remove "GuixSD". * gnu/installer/newt/welcome.scm (run-welcome-page): Likewise. * gnu/packages/audio.scm (supercollider)[description]: Likewise. * gnu/packages/curl.scm (curl): Likewise. * gnu/packages/emacs.scm (emacs): Likewise. * gnu/packages/gnome.scm (network-manager): Likewise. * gnu/packages/julia.scm (julia): Likewise. * gnu/packages/linux.scm (alsa-plugins): Likewise. (powertop, wireless-regdb): Likewise. * gnu/packages/package-management.scm (guix): Likewise. * gnu/packages/polkit.scm (polkit): Likewise. * gnu/packages/tex.scm (texlive-bin): Likewise. * gnu/services/base.scm (file-systems->fstab): Likewise. * gnu/services/cups.scm (%cups-activation): Likewise. * gnu/services/mail.scm (%dovecot-activation): Likewise. * gnu/services/messaging.scm (prosody-configuration)[log]: Likewise. * gnu/system/examples/vm-image.tmpl (vm-image-motd): Likewise. * gnu/system/install.scm (installation-os)[file-systems]: Change root file system label to "Guix_image". * gnu/system/mapped-devices.scm (check-device-initrd-modules): Remove "GuixSD". * gnu/system/vm.scm (system-docker-image): Likewise. (system-disk-image)[root-label]: Change to "Guix_image". * gnu/tests/install.scm (run-install): Remove "GuixSD". * guix/modules.scm (guix-module-name?): Likewise. * nix/libstore/optimise-store.cc: Likewise. --- gnu/packages/audio.scm | 2 +- gnu/packages/curl.scm | 2 +- gnu/packages/emacs.scm | 2 +- gnu/packages/gnome.scm | 2 +- gnu/packages/julia.scm | 2 +- gnu/packages/kde-frameworks.scm | 2 +- gnu/packages/linux.scm | 6 +++--- gnu/packages/package-management.scm | 4 ++-- gnu/packages/polkit.scm | 2 +- gnu/packages/tex.scm | 2 +- 10 files changed, 13 insertions(+), 13 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 91bb467de6..8bcd3c4b85 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2270,7 +2270,7 @@ for experimenting with sound synthesis and algorithmic composition. SuperCollider requires jackd to be installed in your user profile and your user must be allowed to access the realtime features of the kernel. Search for \"realtime\" in the index of the Guix manual to learn how to achieve this -using GuixSD.") +using Guix System.") (license license:gpl2+))) (define-public raul diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm index 822fe17036..456a18012d 100644 --- a/gnu/packages/curl.scm +++ b/gnu/packages/curl.scm @@ -108,7 +108,7 @@ (("/bin/sh") (which "sh"))) ;; XXX FIXME: Test #1510 seems to work on some machines and not - ;; others, possibly based on the kernel version. It works on GuixSD + ;; others, possibly based on the kernel version. It works on Guix System ;; on x86_64 with linux-libre-4.1, but fails on Hydra for both i686 ;; and x86_64 with the following error: ;; diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 1e76f0821c..74005972db 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -92,7 +92,7 @@ '("eshell/esh-groups.el"))) ;; Make sure Tramp looks for binaries in the right places on - ;; remote GuixSD machines, where 'getconf PATH' returns + ;; remote Guix System machines, where 'getconf PATH' returns ;; something bogus. (substitute* "net/tramp-sh.el" ;; Patch the line after "(defcustom tramp-remote-path". diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 0344e42444..3d67b7b9c1 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -5161,7 +5161,7 @@ users.") (doc (assoc-ref %outputs "doc")) (dhclient (string-append (assoc-ref %build-inputs "isc-dhcp") "/sbin/dhclient"))) - (list "--with-systemd-logind=yes" ;In GuixSD, this is provided by elogind. + (list "--with-systemd-logind=yes" ;In Guix System, this is provided by elogind. "--with-consolekit=no" "--with-crypto=gnutls" "--disable-config-plugin-ibft" diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index a2e1264503..fa9709c40c 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -148,7 +148,7 @@ (use-modules (ice-9 match)) (substitute* "src/runtime_ccall.cpp" ;; Patch out invocations of '/sbin/ldconfig' to avoid getting - ;; error messages about missing '/sbin/ldconfig' on GuixSD. + ;; error messages about missing '/sbin/ldconfig' on Guix System. (("popen\\(.*ldconfig.*\\);") "NULL;\n") diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 2ae5feaf52..10a1dfe0d1 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -3487,7 +3487,7 @@ workspace.") ("qtsvg" ,qtsvg) ("qttools" ,qttools) ("qtx11extras" ,qtx11extras))) - ;; FIXME: Use GuixSD ca-bundle.crt in etc/xdg/ksslcalist and + ;; FIXME: Use Guix ca-bundle.crt in etc/xdg/ksslcalist and ;; share/kf5/kssl/ca-bundle.crt ;; TODO: NixOS has nix-kde-include-dir.patch to change std-dir "include" ;; into "@dev@/include/". Think about whether this is needed for us, too. diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index e4a58834a9..1cdffb8c79 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1112,7 +1112,7 @@ MIDI functionality to the Linux-based operating system.") (outputs '("out" "pulseaudio" "jack")) (arguments `(#:configure-flags '(;; Do not install a "local" configuration targeted - ;; for /etc/alsa. On GuixSD plugins are loaded from + ;; for /etc/alsa. On Guix System plugins are loaded from ;; the ALSA service, and other distributions likely ;; won't use these files. "--with-alsalconfdir=/tmp/noop") @@ -1579,7 +1579,7 @@ devices. It replaces @code{iwconfig}, which is deprecated.") '(#:phases (modify-phases %standard-phases ;; TODO: Patch some hardcoded "wlan0" in calibrate/calibrate.cpp to - ;; allow calibrating the network interface in GuixSD. + ;; allow calibrating the network interface in Guix System. (add-after 'unpack 'patch-absolute-file-names (lambda* (#:key inputs #:allow-other-keys) (let ((kmod (assoc-ref inputs "kmod"))) @@ -2379,7 +2379,7 @@ compliance.") #:tests? #f ;no tests #:make-flags (let ((out (assoc-ref %outputs "out"))) (list (string-append "PREFIX=" out) - (string-append "LSB_ID=GuixSD") + (string-append "LSB_ID=Guix") (string-append "DISTRO_PUBKEY=/dev/null") (string-append "DISTRO_PRIVKEY=/dev/null") (string-append "REGDB_PUBKEY=/dev/null") diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 1244cf2fc3..86e8fce1dc 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -142,8 +142,8 @@ ;; Set 'DOT_USER_PROGRAM' to the empty string so ;; we don't keep a reference to Graphviz, whose - ;; closure is pretty big (too big for the GuixSD - ;; installation image.) + ;; closure is pretty big (too big for the Guix + ;; system installation image.) "ac_cv_path_DOT_USER_PROGRAM=dot" ;; To avoid problems with the length of shebangs, diff --git a/gnu/packages/polkit.scm b/gnu/packages/polkit.scm index 0433b423eb..ba74a5c905 100644 --- a/gnu/packages/polkit.scm +++ b/gnu/packages/polkit.scm @@ -73,7 +73,7 @@ (substitute* "src/polkitbackend/polkitbackendjsauthority.cpp" (("systemd") "elogind")) - ;; GuixSD's polkit service stores actions under + ;; Guix System's polkit service stores actions under ;; /etc/polkit-1/actions. (substitute* "src/polkitbackend/polkitbackendinteractiveauthority.c" (("PACKAGE_DATA_DIR \"/polkit-1/actions\"") diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 584b2bcfa5..5b29937672 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -185,7 +185,7 @@ ;; ps2eps.pl uses the "gswin32c" ghostscript executable on Windows, ;; and the "gs" ghostscript executable on Unix. It detects Unix by ;; checking for the existence of the /usr/bin directory. Since - ;; GuixSD does not have /usr/bin, it is also detected as Windows. + ;; Guix System does not have /usr/bin, it is also detected as Windows. (lambda* (#:key inputs #:allow-other-keys) (substitute* "utils/ps2eps/ps2eps-src/bin/ps2eps.pl" (("gswin32c") "gs")) -- cgit v1.2.3 From 8a55c38915c55b36054cfbc34adf04e63d3f4dd0 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 13 Mar 2019 20:05:45 -0400 Subject: gnu: w3m: Update to 0.5.3+git20190105. * gnu/packages/w3m.scm (w3m): Update to 0.5.3+git20190105. --- gnu/packages/w3m.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/w3m.scm b/gnu/packages/w3m.scm index a8761ec602..b88bbd39bb 100644 --- a/gnu/packages/w3m.scm +++ b/gnu/packages/w3m.scm @@ -39,7 +39,7 @@ (define-public w3m (package (name "w3m") - (version "0.5.3+git20180125") + (version "0.5.3+git20190105") (source (origin (method git-fetch) ;; Debian's fork of w3m is the only one that is still maintained. @@ -49,7 +49,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0dafdfx1yhrvhbqzslkcapj09dvf64m2jadz3wl2icni0k4msq90")))) + "1fbg2p8qh2gvi3g4iz4q6vc0k70pf248r4yndi5lcn2m3mzvjx0i")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no check target -- cgit v1.2.3 From 100f56024e72ad5effff340d34cd7a91a34a830a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=B2=20Balzarotti?= Date: Thu, 14 Mar 2019 10:53:25 +0100 Subject: gnu: Add r-rematch2. * gnu/packages/cran.scm (r-rematch2): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b04a69d5c1..eac6293fc9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14,6 +14,7 @@ ;;; Copyright © 2018 Leo Famulari ;;; Copyright © 2018 Marius Bakke ;;; Copyright © 2018, 2019 Brett Gilio +;;; Copyright © 2019 Nicolò Balzarotti ;;; ;;; This file is part of GNU Guix. ;;; @@ -11717,3 +11718,24 @@ plotting functions are available for analyzing clustering results.") signals. It provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data.") (license license:expat))) + +(define-public r-rematch2 + (package + (name "r-rematch2") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "rematch2" version)) + (sha256 + (base32 + "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6")))) + (build-system r-build-system) + (propagated-inputs + `(("r-tibble" ,r-tibble))) + (home-page "https://github.com/r-lib/rematch2") + (synopsis "Tidy output from regular expression matching") + (description + "This package provides wrappers on @code{regexpr} and @code{gregexpr} to +return the match results in tidy data frames.") + (license license:expat))) -- cgit v1.2.3 From bb2f114de945451da979b06d33c34d0b929e5e90 Mon Sep 17 00:00:00 2001 From: Meiyo Peng Date: Thu, 14 Mar 2019 11:36:56 +0800 Subject: gnu: fish: Update to 3.0.2. * gnu/packages/shells.scm (fish): Update to 3.0.2. Signed-off-by: Ricardo Wurmus --- gnu/packages/shells.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index d0561559e9..4c832c0702 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -91,7 +91,7 @@ direct descendant of NetBSD's Almquist Shell (@command{ash}).") (define-public fish (package (name "fish") - (version "3.0.0") + (version "3.0.2") (source (origin (method url-fetch) @@ -99,7 +99,7 @@ direct descendant of NetBSD's Almquist Shell (@command{ash}).") "releases/download/" version "/" name "-" version ".tar.gz")) (sha256 - (base32 "1kzjd0n0sfslkd36lzrvvvgy3qwkd9y466bkrqlnhd5h9dhx77ga")))) + (base32 "03j3jl9jzlnhq4p86zj8wqsh5sx45j1d1fvfa80ks1cfdg68qwhl")))) (build-system gnu-build-system) (inputs `(("fish-foreign-env" ,fish-foreign-env) -- cgit v1.2.3 From 8cd10b22f9e993cf9375fff10fb937c92ff71017 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Wed, 13 Mar 2019 15:50:22 -0700 Subject: gnu: Update dtc to 1.5.0. * gnu/packages/bootloaders (dtc): Update to 1.5.0. [native-inputs]: Add libyaml and pkg-config. Signed-off-by: Ricardo Wurmus --- gnu/packages/bootloaders.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 15953ab75e..d6ef7d52b5 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -340,7 +340,7 @@ menu to select one of the installed operating systems.") (define-public dtc (package (name "dtc") - (version "1.4.7") + (version "1.5.0") (source (origin (method url-fetch) (uri (string-append @@ -348,11 +348,13 @@ menu to select one of the installed operating systems.") "dtc-" version ".tar.xz")) (sha256 (base32 - "1rydi5jvhlhsr110h6n0pavv3daqa0cb4m5vcps50qzq1zqfhhv6")))) + "0wh10p42hf5403ipvs0dsxddb6kzfyk2sq4fgid9zqzpr51y8wn6")))) (build-system gnu-build-system) (native-inputs `(("bison" ,bison) ("flex" ,flex) + ("libyaml" ,libyaml) + ("pkg-config" ,pkg-config) ("swig" ,swig) ("valgrind" ,valgrind))) (inputs -- cgit v1.2.3 From 3490212a413c8f5f28b574f9b692bb28e081c7d0 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Tue, 19 Feb 2019 22:02:38 -0600 Subject: gnu: emacs-dash: Update to 2.15.0. * gnu/packages/emacs-xyz.scm (emacs-dash): Update to 2.15.0. Signed-off-by: Ricardo Wurmus --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 5896060a76..428be7f7ad 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1616,7 +1616,7 @@ and stored in memory.") (define-public emacs-dash (package (name "emacs-dash") - (version "2.14.1") + (version "2.15.0") (source (origin (method git-fetch) (uri (git-reference @@ -1625,7 +1625,7 @@ and stored in memory.") (file-name (git-file-name name version)) (sha256 (base32 - "1kzijmjxjxgr7p8clphzvmm47vczckbs8mza9an77c25bn627ywl")))) + "0dx8q3jr8fh73cfl7mqi5dq0012ambpvc74d2c71fsv9rfw85693")))) (build-system emacs-build-system) (arguments `(#:tests? #t -- cgit v1.2.3 From 60adaae0cfaeaeebacf703c8d021d6130fa5df59 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Tue, 19 Feb 2019 22:02:29 -0600 Subject: gnu: Add emacs-lsp-mode. * gnu/packages/emacs-xyz.scm (emacs-lsp-mode): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/emacs-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 428be7f7ad..d296c5e639 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13452,3 +13452,30 @@ constant expressions.") "This package provides a major mode @code{dockerfile-mode} for use with the standard @code{Dockerfile} file format.") (license license:asl2.0)))) + +(define-public emacs-lsp-mode + (package + (name "emacs-lsp-mode") + (version "6.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-lsp/lsp-mode.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1v1mq6ixzlgiazj8fmg4xaqhsqn3l89iqy74yndhvzh2rdf0pbkl")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-dash" ,emacs-dash) + ("emacs-f" ,emacs-f) + ("emacs-ht" ,emacs-ht) + ("emacs-spinner" ,emacs-spinner))) + (home-page "https://github.com/emacs-lsp/lsp-mode") + (synopsis "Emacs client and library for the Language Server Protocol") + (description "@code{LSP-mode} is a client and library implmentation for +the Language Server Protocol. This mode aims to provide an IDE-like +experience by providing optional integration with other popular Emacs packages +like @code{company}, @code{flycheck}, and @code{projectile}.") + (license license:gpl3+))) -- cgit v1.2.3 From 209393a0033ae6ad127b5fd3f124cf7bce5314f9 Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Tue, 19 Feb 2019 22:02:12 -0600 Subject: gnu: Add emacs-lsp-ui. * gnu/packages/emacs-xyz.scm (emacs-lsp-ui): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/emacs-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d296c5e639..e998ded897 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13479,3 +13479,30 @@ the Language Server Protocol. This mode aims to provide an IDE-like experience by providing optional integration with other popular Emacs packages like @code{company}, @code{flycheck}, and @code{projectile}.") (license license:gpl3+))) + +(define-public emacs-lsp-ui + (package + (name "emacs-lsp-ui") + (version "6.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-lsp/lsp-ui.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1r4327fd8cvjxfwkddp5c4bdskyncbs4sx9m3z2w4d773y2jrakc")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-dash" ,emacs-dash) + ("emacs-lsp-mode" ,emacs-lsp-mode) + ("emacs-markdown-mode" ,emacs-markdown-mode) + ("emacs-flycheck" ,emacs-flycheck))) + (home-page "https://github.com/emacs-lsp/lsp-ui") + (synopsis "User interface extensions for @code{lsp-mode}") + (description + "@code{LSP-ui} contains several enhancements and integrations for +@code{lsp-mode}, such as visual flychecking, displaying references in-line, +and code peeking.") + (license license:gpl3+))) -- cgit v1.2.3 From 1f2e06014890e7ac94558f0595f2b699711cdde2 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 10 Mar 2019 21:53:00 +0100 Subject: gnu: Add waylandpp. * gnu/packages/freedesktop.scm (waylandpp): New public variable. --- gnu/packages/freedesktop.scm | 30 +++++++++++++++++++++++++++++- 1 file changed, 29 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index d90e75352e..4750450f68 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2016, 2017 Efraim Flashner ;;; Copyright © 2016 Kei Kebreau ;;; Copyright © 2017, 2018 Mark H Weaver -;;; Copyright © 2017, 2018 Marius Bakke +;;; Copyright © 2017, 2018, 2019 Marius Bakke ;;; Copyright © 2017, 2018 Rutger Helling ;;; Copyright © 2017 Brendan Tildesley ;;; Copyright © 2018 Tobias Geerinckx-Rice @@ -36,6 +36,7 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system meson) #:use-module (guix build-system perl) @@ -452,6 +453,33 @@ applications, X servers (rootless or fullscreen) or other display servers.") (home-page "https://wayland.freedesktop.org") (license license:expat))) +(define-public waylandpp + (package + (name "waylandpp") + (version "0.2.5") + (home-page "https://github.com/NilsBrause/waylandpp") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit version))) + (sha256 + (base32 + "16h57hzd688664qcyznzhjp3hxipdkzgv46x82yhkww24av8b55n")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f)) ;no tests + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("mesa" ,mesa) + ("pugixml" ,pugixml))) + (propagated-inputs + `(;; In Requires of the .pc files. + ("wayland" ,wayland))) + (synopsis "Wayland C++ bindings") + (description + "This package provides C++ bindings for the Wayland display protocol.") + (license license:bsd-2))) + (define-public weston (package (name "weston") -- cgit v1.2.3 From b165fe61dc6eaf96997973bee7d1bb98ca3e264b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 10 Mar 2019 22:38:19 +0100 Subject: gnu: Kodi: Add Wayland variant. * gnu/packages/kodi.scm (kodi/wayland): New public variable. --- gnu/packages/kodi.scm | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm index 776f9c970e..3929909d10 100644 --- a/gnu/packages/kodi.scm +++ b/gnu/packages/kodi.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 David Thompson -;;; Copyright © 2017 Marius Bakke +;;; Copyright © 2017, 2019 Marius Bakke ;;; Copyright © 2017 Oleg Pykhalov ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018 Efraim Flashner @@ -43,6 +43,7 @@ #:use-module (gnu packages databases) #:use-module (gnu packages documentation) #:use-module (gnu packages fontutils) + #:use-module (gnu packages freedesktop) #:use-module (gnu packages fribidi) #:use-module (gnu packages gettext) #:use-module (gnu packages ghostscript) @@ -462,6 +463,23 @@ plug-in system.") license:bsd-3 ;misc, gtest license:bsd-2)))) ;xbmc/freebsd +(define-public kodi/wayland + (package/inherit kodi + (name "kodi-wayland") + (arguments + (substitute-keyword-arguments (package-arguments kodi) + ((#:configure-flags flags) + `(append '("-DCORE_PLATFORM_NAME=wayland" + "-DWAYLAND_RENDER_SYSTEM=gl") + ,flags)))) + (inputs + `(("libinput" ,libinput) + ("libxkbcommon" ,libxkbcommon) + ("waylandpp" ,waylandpp) + ("waylandp-protocols" ,wayland-protocols) + ,@(package-inputs kodi))) + (synopsis "Kodi with Wayland rendering backend"))) + (define-public kodi-cli (let ((commit "104dc23b2a993c8e6db8c46f4f8bec24b146549b") ; Add support for (revision "1")) ; `$HOME/.kodirc'. -- cgit v1.2.3 From eccaa8bf8deafbce7bf65b9d3b2822add00219c0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 13 Mar 2019 14:03:57 +0100 Subject: gnu: libsoup: Update to 2.66.0. * gnu/packages/gnome.scm (libsoup): Update to 2.66.0. [build-system]: Change to MESON-BUILD-SYSTEM. [arguments]: Adjust accordingly. [native-inputs]: Add GTK-DOC. [inputs]: Add MIT-KRB5. Move SQLITE and LIBPSL ... [propagated-inputs]: ... here. --- gnu/packages/gnome.scm | 55 ++++++++++++++++++++------------------------------ 1 file changed, 22 insertions(+), 33 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 3d67b7b9c1..2697beebca 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -2561,7 +2561,7 @@ libxml to ease remote use of the RESTful API.") (define-public libsoup (package (name "libsoup") - (version "2.64.2") + (version "2.66.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/libsoup/" @@ -2569,38 +2569,23 @@ libxml to ease remote use of the RESTful API.") name "-" version ".tar.xz")) (sha256 (base32 - "1il6lyrmfi0hfh3ysw8w1qzc1rdz0igkb7dv6d8g5mmilnac3pbm")))) - (build-system gnu-build-system) + "08c9kkdhzy504gv23pfdm4sq3dd3j20sikwz6gv0qrwcdjnw5bai")))) + (build-system meson-build-system) (outputs '("out" "doc")) (arguments `(#:modules ((guix build utils) - (guix build gnu-build-system) + (guix build meson-build-system) (ice-9 popen)) - #:configure-flags - (list (string-append "--with-html-dir=" - (assoc-ref %outputs "doc") - "/share/gtk-doc/html") - (string-append "--with-apache-module-dir=" - (assoc-ref %build-inputs "httpd") - "/modules")) + #:configure-flags '("-Ddoc=true") #:phases (modify-phases %standard-phases - (add-before 'configure 'disable-unconnected-socket-test - ;; This test fails due to missing /etc/nsswitch.conf - ;; in the build environment. + (add-after 'unpack 'adjust-tests (lambda _ + ;; This test fails due to missing /etc/nsswitch.conf + ;; in the build environment. (substitute* "tests/socket-test.c" ((".*/sockets/unconnected.*") "")) - #t)) - (add-before 'check 'pre-check - (lambda _ - ;; The 'check-local' target runs 'env LANG=C sort -u', - ;; unset 'LC_ALL' to make 'LANG' working. - (unsetenv "LC_ALL") - ;; HTTPD in Guix uses mod_event and does not build prefork. - (substitute* "tests/httpd.conf" - (("^LoadModule mpm_prefork_module.*$") "\n")) ;; Generate a self-signed certificate that has "localhost" as its ;; 'dnsName'. Failing to do that, and starting with GnuTLS @@ -2646,16 +2631,19 @@ libxml to ease remote use of the RESTful API.") )) (close-pipe pipe)) #t)) - (replace 'install - (lambda _ - (invoke "make" - ;; Install vala bindings into $out. - (string-append "vapidir=" %output - "/share/vala/vapi") - "install")))))) + (add-after 'install 'move-doc + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (doc (assoc-ref outputs "doc"))) + (mkdir-p (string-append doc "/share")) + (copy-recursively (string-append out "/share/gtk-doc") + (string-append doc "/share/gtk-doc")) + (delete-file-recursively (string-append out "/share/gtk-doc")) + #t)))))) (native-inputs `(("glib:bin" ,glib "bin") ; for glib-mkenums ("gobject-introspection" ,gobject-introspection) + ("gtk-doc" ,gtk-doc) ("intltool" ,intltool) ("pkg-config" ,pkg-config) ("python" ,python-wrapper) @@ -2668,11 +2656,12 @@ libxml to ease remote use of the RESTful API.") (propagated-inputs ;; libsoup-2.4.pc refers to all these. `(("glib" ,glib) - ("libxml2" ,libxml2))) - (inputs - `(("glib-networking" ,glib-networking) ("libpsl" ,libpsl) + ("libxml2" ,libxml2) ("sqlite" ,sqlite))) + (inputs + `(("glib-networking" ,glib-networking) + ("mit-krb5" ,mit-krb5))) (home-page "https://live.gnome.org/LibSoup/") (synopsis "GLib-based HTTP Library") (description -- cgit v1.2.3 From 72663b48221668f30b7bdcc502c299757a647156 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 13 Mar 2019 15:00:30 +0100 Subject: gnu: WebKitGTK: Update to 2.24.0. * gnu/packages/webkit.scm (webkitgtk-2.22): Rename to ... (webkitgtk-2.24): ... this. Update to 2.24.0. [inputs]: Add OPENJPEG. * gnu/packages/gnome.scm (eolie, epiphany)[inputs]: Adjust accordingly. * gnu/packages/web-browsers.scm (next-gtk-webkit)[inputs]: Likewise. --- gnu/packages/gnome.scm | 4 ++-- gnu/packages/web-browsers.scm | 2 +- gnu/packages/webkit.scm | 9 ++++++--- 3 files changed, 9 insertions(+), 6 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 2697beebca..ea6d255c88 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4235,7 +4235,7 @@ work and the interface is well tested.") ("libsecret" ,libsecret) ("gtkspell3" ,gtkspell3) ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) - ("webkitgtk" ,webkitgtk-2.22))) + ("webkitgtk" ,webkitgtk-2.24))) (home-page "https://wiki.gnome.org/Apps/Eolie") (synopsis "Web browser for GNOME") (description @@ -4294,7 +4294,7 @@ a secret password store, an adblocker, and a modern UI.") ("libxslt" ,libxslt) ("nettle" ,nettle) ; for hogweed ("sqlite" ,sqlite) - ("webkitgtk" ,webkitgtk-2.22))) + ("webkitgtk" ,webkitgtk-2.24))) (home-page "https://wiki.gnome.org/Apps/Web") (synopsis "GNOME web browser") (description diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index a19a0dc7c3..b6af572778 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -397,7 +397,7 @@ driven and does not detract you from your daily work.") (inputs `(("glib-networking" ,glib-networking) ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) - ("webkitgtk" ,webkitgtk-2.22))) + ("webkitgtk" ,webkitgtk-2.24))) (native-inputs `(("gcc-7" ,gcc-7) ; needed because webkitgtk-2.22 is compiled with gcc-7 ("pkg-config" ,pkg-config))) diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index 7a4818609e..14c374dd3e 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -165,20 +165,23 @@ HTML/CSS applications to full-fledged web browsers.") ;; newer version of GCC than our default compiler, and this causes problems ;; when linked with C++ libraries built using our default compiler. For now, ;; we use this newer webkitgtk only for selected packages, e.g. epiphany. -(define-public webkitgtk-2.22 +(define-public webkitgtk-2.24 (package/inherit webkitgtk (name "webkitgtk") - (version "2.22.7") + (version "2.24.0") (source (origin (method url-fetch) (uri (string-append "https://www.webkitgtk.org/releases/" name "-" version ".tar.xz")) (sha256 (base32 - "1zrhmz90sn30zgyflj4i86fsscws10xsi2kfs87nj2nd0pbggrjb")))) + "01s446lmjk7y8il4snjm32vpxws2rp4hmxrwm2swx0p47x8d2jif")))) (native-inputs `(("gcc" ,gcc-7) ; webkitgtk-2.22 requires gcc-6 or newer ,@(package-native-inputs webkitgtk))) + (inputs + `(("openjpeg" ,openjpeg) + ,@(package-inputs webkitgtk))) (arguments (substitute-keyword-arguments (package-arguments webkitgtk) ((#:phases phases) -- cgit v1.2.3 From 66fea0c4d95e471ba9d4a011bdaf5f8022029b05 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 14 Mar 2019 14:16:52 +0100 Subject: gnu: libzip: Don't use NAME in source URI. * gnu/packages/compression.scm (libzip)[source](uri): Hard-code NAME. --- gnu/packages/compression.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 090c164e18..de208b6802 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1567,7 +1567,7 @@ recreates the stored directory structure by default.") (source (origin (method url-fetch) (uri (string-append - "https://libzip.org/download/" name "-" version ".tar.xz")) + "https://libzip.org/download/libzip-" version ".tar.xz")) (sha256 (base32 "0wnkkvkq90wyawj9221i77sf3nix1vj3ygzdy59k8yvcjnv3bsh4")))) -- cgit v1.2.3 From dd10c0adad6d3606639eebd029cea6f37104a79c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 14 Mar 2019 14:17:33 +0100 Subject: gnu: libzip: Update to 1.5.2. * gnu/packages/compression.scm (libzip): Update to 1.5.2. --- gnu/packages/compression.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index de208b6802..23a8f997f0 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1563,14 +1563,14 @@ recreates the stored directory structure by default.") (define-public libzip (package (name "libzip") - (version "1.5.1") + (version "1.5.2") (source (origin (method url-fetch) (uri (string-append "https://libzip.org/download/libzip-" version ".tar.xz")) (sha256 (base32 - "0wnkkvkq90wyawj9221i77sf3nix1vj3ygzdy59k8yvcjnv3bsh4")))) + "1d53shcy7nvls5db573bbdlm25lfz1iw2zshng5f00cssi5lvpmk")))) (native-inputs `(("perl" ,perl))) (inputs -- cgit v1.2.3 From 84ff7821ffac2ee123447701fcb927834752484e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 14 Mar 2019 14:19:13 +0100 Subject: gnu: samba: Update to 4.9.5. * gnu/packages/samba.scm (samba): Update to 4.9.5. --- gnu/packages/samba.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm index d90d12e665..d10c6ebc9c 100644 --- a/gnu/packages/samba.scm +++ b/gnu/packages/samba.scm @@ -151,14 +151,14 @@ anywhere.") (define-public samba (package (name "samba") - (version "4.9.4") + (version "4.9.5") (source (origin (method url-fetch) (uri (string-append "https://download.samba.org/pub/samba/stable/" "samba-" version ".tar.gz")) (sha256 (base32 - "0kqbzywlnh1skg6g78qilyn12qv7wri66h5v9f77igncpkcai63d")))) + "001p896z609vb0qs196bgl362j7y3qibgm5gcl9028lfv795d287")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit v1.2.3 From 22656b24d817944aa12af1444243a3f52bc00a84 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 14 Mar 2019 14:28:02 +0100 Subject: gnu: rapidjson: Update home page. * gnu/packages/web.scm (rapidjson)[source, home-page]: Follow redirected URL. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 463f18b7f0..3c126bb941 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -751,7 +751,7 @@ current version of any major web browser.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/miloyip/rapidjson.git") + (url "https://github.com/Tencent/rapidjson.git") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -776,7 +776,7 @@ current version of any major web browser.") (("native") "armv8-a")) #t)))) '()))) - (home-page "https://github.com/miloyip/rapidjson") + (home-page "https://github.com/Tencent/rapidjson") (synopsis "JSON parser/generator for C++ with both SAX/DOM style API") (description "RapidJSON is a fast JSON parser/generator for C++ with both SAX/DOM -- cgit v1.2.3 From 8cc3983a4d02a15ad4a863671c1a5a8b2b542625 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 14 Mar 2019 14:31:29 +0100 Subject: gnu: jasper: Update to 2.0.16. * gnu/packages/image.scm (jasper): Update to 2.0.16. --- gnu/packages/image.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 9f25578050..941b991695 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1101,7 +1101,7 @@ convert, manipulate, filter and display a wide variety of image formats.") (define-public jasper (package (name "jasper") - (version "2.0.14") + (version "2.0.16") (source (origin (method git-fetch) (uri (git-reference @@ -1110,7 +1110,7 @@ convert, manipulate, filter and display a wide variety of image formats.") (file-name (git-file-name name version)) (sha256 (base32 - "0aarg8nbik9wrm7fx0451sbm5ypfdfr6i169pxzi354mpdp8gg7f")))) + "05l75yd1zsxwv25ykwwwjs8961szv7iywf16nc6vc6qpby27ckv6")))) (build-system cmake-build-system) (inputs `(("libjpeg" ,libjpeg))) (synopsis "JPEG-2000 library") -- cgit v1.2.3 From 4d9ebc62ba61c45e5212c73158fe852ea802a87b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 14 Mar 2019 14:36:24 +0100 Subject: gnu: gtk+: Update to 3.24.7. * gnu/packages/gtk.scm (gtk+): Update to 3.24.7. --- gnu/packages/gtk.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 713bb85430..f93bd819e5 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -731,7 +731,7 @@ application suites.") (name "gtk+") ;; NOTE: When updating the version of 'gtk+', the hash of 'mate-themes' in ;; mate.scm will also need to be updated. - (version "3.24.5") + (version "3.24.7") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -739,7 +739,7 @@ application suites.") name "-" version ".tar.xz")) (sha256 (base32 - "0bxhvnixc1hjxbzx063lghmix0wmv282khsqmckdxhrb606zpr8b")) + "080m925dyhiidlhsxqzx040l4iha2gg38pzbfpnsnjyzl92124jj")) (patches (search-patches "gtk3-respect-GUIX_GTK3_PATH.patch" "gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch")) (modules '((guix build utils))) -- cgit v1.2.3 From c958c31caefb20c32cf89caea7d4668d7021a92b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 14 Mar 2019 14:37:57 +0100 Subject: gnu: double-conversion: Update to 3.1.4. * gnu/packages/maths.scm (double-conversion): Update to 3.1.4. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 687fa3b61a..2781761474 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -324,7 +324,7 @@ enough to be used effectively as a scientific calculator.") (define-public double-conversion (package (name "double-conversion") - (version "3.1.3") + (version "3.1.4") (home-page "https://github.com/google/double-conversion") (source (origin (method git-fetch) @@ -333,7 +333,7 @@ enough to be used effectively as a scientific calculator.") (file-name (git-file-name name version)) (sha256 (base32 - "082w15xq8f4c422a71phvcahgc8vmqrig97av9g9628q5n2ybbgg")))) + "13xwcqk2c0q8c1siw566clxcpvp0xrxvb72mra42wa3nvq9wlsv6")))) (build-system cmake-build-system) (arguments '(#:test-target "test" -- cgit v1.2.3