From 38fe6449c0d1fac6f64fcbabfbc94943752830b9 Mon Sep 17 00:00:00 2001 From: Benjamin Slade Date: Mon, 3 Sep 2018 23:19:30 +0200 Subject: gnu: Add transset-df. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/xorg.scm (transset-df): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/xorg.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 3875765d25..c89661272b 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Kei Kebreau ;;; Copyright © 2018 Oleg Pykhalov +;;; Copyright © 2018 Benjamin Slade ;;; ;;; This file is part of GNU Guix. ;;; @@ -6196,3 +6197,44 @@ and embedded platforms.") cursor to any point on the screen with a few key strokes. It also simulates mouse click. You can do everything mouse can do with a keyboard.") (license license:bsd-3))) + +(define-public transset-df + (package + (name "transset-df") + (version "6") + (source (origin + (method url-fetch) + (uri (string-append "http://forchheimer.se/" name "/" name "-" version + ".tar.gz")) + (sha256 + (base32 + "1vnykwwrv75miigbhmcwxniw8xnhsdyzhqydip2m9crxi2lwhqs5")))) + (build-system gnu-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'setenv + (lambda _ + (setenv "CC" (which "gcc")) + #t)) + (delete 'configure) + (delete 'check) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (install-file "transset-df" bin) + #t)))))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs `(("libxcomposite" ,libxcomposite) + ("libxdamager" ,libxdamage) + ("libxrender" ,libxrender))) + (synopsis "Set the transparency of X11 windows") + (description "The @command{transset-df} command allows you to set the +opacity of X11 windows. This patched version of X.Org's @command{transset} +adds functionality, including: selecting window by clicking (as transset), +selecting windows by pointing select actual focused X11 window, selecting by +window name or id, forcing toggle, increase or decrease opacity.") + (home-page "http://forchheimer.se/transset-df/") + (license license:x11))) -- cgit v1.2.3 From 5108c18e7e163c3b45568f1f4c3416581a2cea19 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rapha=C3=ABl=20M=C3=A9lotte?= Date: Mon, 3 Sep 2018 10:20:06 +0200 Subject: gnu: perl: Add support for cross-compilation MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/perl.scm (perl): use cross-libc when cross-compiling Signed-off-by: Ludovic Courtès --- gnu/packages/perl.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 4d70e019b9..b10be9567d 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -48,6 +48,7 @@ #:use-module (guix utils) ;substitute-keyword-arguments for perl-5.26.2 #:use-module (gnu packages base) #:use-module (gnu packages compression) + #:use-module (gnu packages cross-base) #:use-module (gnu packages freedesktop) #:use-module (gnu packages perl-check) #:use-module (gnu packages perl-web) @@ -79,7 +80,7 @@ "perl-reproducible-build-date.patch")))) (build-system gnu-build-system) (arguments - '(#:tests? #f + `(#:tests? #f #:configure-flags (let ((out (assoc-ref %outputs "out")) (libc (assoc-ref %build-inputs "libc"))) @@ -128,7 +129,10 @@ (add-after 'install 'remove-extra-references (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) - (libc (assoc-ref inputs "libc")) + (libc (assoc-ref inputs + (if ,(%current-target-system) + "cross-libc" + "libc"))) (config1 (car (find-files (string-append out "/lib/perl5") "^Config_heavy\\.pl$"))) (config2 (find-files (string-append out "/lib/perl5") -- cgit v1.2.3 From fd95f37f361ad9444fb13faebda29662d3bf7be6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 3 Sep 2018 23:49:06 +0200 Subject: Revert "gnu: perl: Add support for cross-compilation" This reverts commit 5108c18e7e163c3b45568f1f4c3416581a2cea19, which was accidentally committed. --- gnu/packages/perl.scm | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index b10be9567d..4d70e019b9 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -48,7 +48,6 @@ #:use-module (guix utils) ;substitute-keyword-arguments for perl-5.26.2 #:use-module (gnu packages base) #:use-module (gnu packages compression) - #:use-module (gnu packages cross-base) #:use-module (gnu packages freedesktop) #:use-module (gnu packages perl-check) #:use-module (gnu packages perl-web) @@ -80,7 +79,7 @@ "perl-reproducible-build-date.patch")))) (build-system gnu-build-system) (arguments - `(#:tests? #f + '(#:tests? #f #:configure-flags (let ((out (assoc-ref %outputs "out")) (libc (assoc-ref %build-inputs "libc"))) @@ -129,10 +128,7 @@ (add-after 'install 'remove-extra-references (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) - (libc (assoc-ref inputs - (if ,(%current-target-system) - "cross-libc" - "libc"))) + (libc (assoc-ref inputs "libc")) (config1 (car (find-files (string-append out "/lib/perl5") "^Config_heavy\\.pl$"))) (config2 (find-files (string-append out "/lib/perl5") -- cgit v1.2.3 From 9c4b522f1572db2c5dab81976982b95d5da51e6e Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 24 Aug 2018 00:36:15 +0530 Subject: gnu: Add ghc-wcwidth. * gnu/packages/haskell.scm (ghc-wcwidth): New variable. --- gnu/packages/haskell.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index a07bb049a2..6e19cd67ee 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -10152,4 +10152,29 @@ tools are not needed to actually run Gtk2Hs programs.") backends provided by the @code{Cairo} and @code{Diagrams} libraries.") (license license:bsd-3))) +(define-public ghc-wcwidth + (package + (name "ghc-wcwidth") + (version "0.0.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/wcwidth/wcwidth-" + version ".tar.gz")) + (sha256 + (base32 + "1n1fq7v64b59ajf5g50iqj9sa34wm7s2j3viay0kxpmvlcv8gipz")))) + (build-system haskell-build-system) + (inputs + `(("ghc-setlocale" ,ghc-setlocale) + ("ghc-utf8-string" ,ghc-utf8-string) + ("ghc-attoparsec" ,ghc-attoparsec))) + (home-page "https://github.com/solidsnack/wcwidth/") + (synopsis "Haskell bindings to wcwidth") + (description "This package provides Haskell bindings to your system's +native wcwidth and a command line tool to examine the widths assigned by it. +The command line tool can compile a width table to Haskell code that assigns +widths to the Char type.") + (license license:bsd-3))) + ;;; haskell.scm ends here -- cgit v1.2.3 From 3ad6b8909025a8f4d3e1f1f5ea16bcd0cace557c Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 24 Aug 2018 12:14:17 +0530 Subject: gnu: ghc-tasty: Update to 1.1.0.3. * gnu/packages/haskell-check.scm (ghc-tasty): Update to 1.1.0.3. [inputs]: Add ghc-wcwidth. (ghc-attoparsec-bootstrap, ghc-integer-logarithms-bootstrap, ghc-scientific-bootstrap): New variables. (ghc-wcwidth)[inputs]: Replace ghc-attoparsec with ghc-attoparsec-bootstrap. (ghc-scientific)[inputs]: Replace ghc-integer-logarithms with ghc-integer-logarithms-bootstrap. (ghc-attoparsec)[inputs]: Replace ghc-scientific with ghc-scientific-bootstrap. --- gnu/packages/haskell-check.scm | 7 ++++--- gnu/packages/haskell.scm | 27 ++++++++++++++++++++++++--- 2 files changed, 28 insertions(+), 6 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm index c3ef85f3f0..1064872fec 100644 --- a/gnu/packages/haskell-check.scm +++ b/gnu/packages/haskell-check.scm @@ -183,7 +183,7 @@ timer functions of different operating systems via a unified API.") (define-public ghc-tasty (package (name "ghc-tasty") - (version "0.11.0.4") + (version "1.1.0.3") (source (origin (method url-fetch) @@ -193,7 +193,7 @@ timer functions of different operating systems via a unified API.") ".tar.gz")) (sha256 (base32 - "05pxjzgbgjdn7477xry0ssjrnmnsydqiq6nm6ck8n2da1baliqp0")))) + "14riid753hjqr6lca1kgxpnvq0wykf0k3qc5jpag42hh8bszav22")))) (build-system haskell-build-system) (inputs `(("ghc-stm" ,ghc-stm) @@ -205,7 +205,8 @@ timer functions of different operating systems via a unified API.") ("ghc-unbounded-delays" ,ghc-unbounded-delays) ("ghc-async" ,ghc-async) ("ghc-ansi-terminal" ,ghc-ansi-terminal) - ("ghc-clock-bootstrap" ,ghc-clock-bootstrap))) + ("ghc-clock-bootstrap" ,ghc-clock-bootstrap) + ("ghc-wcwidth" ,ghc-wcwidth))) (home-page "http://documentup.com/feuerbach/tasty") (synopsis "Modern and extensible testing framework") (description "Tasty is a modern testing framework for Haskell. It lets diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 6e19cd67ee..70929ddae6 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -2866,7 +2866,7 @@ with slicing and Clang-style colored diagnostics.") ;; re-enable them. (arguments `(#:tests? #f)) (inputs - `(("ghc-scientific" ,ghc-scientific) + `(("ghc-scientific-bootstrap" ,ghc-scientific-bootstrap) ("ghc-text" ,ghc-text))) (native-inputs `(("ghc-tasty" ,ghc-tasty) @@ -2881,6 +2881,13 @@ aimed particularly at dealing efficiently with network protocols and complicated text/binary file formats.") (license license:bsd-3))) +(define ghc-attoparsec-bootstrap + (package + (inherit ghc-attoparsec) + (name "ghc-attoparsec-bootstrap") + (arguments '(#:tests? #f)) + (native-inputs '()))) + (define-public ghc-zip-archive (package (name "ghc-zip-archive") @@ -5208,6 +5215,13 @@ occurrences of a substring (the first in case of overlaps) with another.") in migrated modules.") (license license:expat))) +(define ghc-integer-logarithms-bootstrap + (package + (inherit ghc-integer-logarithms) + (name "ghc-integer-logarithms-bootstrap") + (arguments `(#:tests? #f)) + (native-inputs '()))) + (define-public ghc-scientific (package (name "ghc-scientific") @@ -5224,7 +5238,7 @@ in migrated modules.") "03ql2f0ac8bsl524idy9xxa3kxisb2sj3avflzw580j5hzy0m397")))) (build-system haskell-build-system) (inputs - `(("ghc-integer-logarithms" ,ghc-integer-logarithms) + `(("ghc-integer-logarithms-bootstrap" ,ghc-integer-logarithms-bootstrap) ("ghc-text" ,ghc-text) ("ghc-hashable" ,ghc-hashable) ("ghc-primitive" ,ghc-primitive))) @@ -5245,6 +5259,13 @@ and space efficient. They are represented using notation}.") (license license:bsd-3))) +(define ghc-scientific-bootstrap + (package + (inherit ghc-scientific) + (name "ghc-scientific-bootstrap") + (arguments `(#:tests? #f)) + (native-inputs '()))) + (define-public ghc-boxes (package (name "ghc-boxes") @@ -10168,7 +10189,7 @@ backends provided by the @code{Cairo} and @code{Diagrams} libraries.") (inputs `(("ghc-setlocale" ,ghc-setlocale) ("ghc-utf8-string" ,ghc-utf8-string) - ("ghc-attoparsec" ,ghc-attoparsec))) + ("ghc-attoparsec-bootstrap" ,ghc-attoparsec-bootstrap))) (home-page "https://github.com/solidsnack/wcwidth/") (synopsis "Haskell bindings to wcwidth") (description "This package provides Haskell bindings to your system's -- cgit v1.2.3 From 8374cc4b051e31905581250fbc0697b1513db60a Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 4 Sep 2018 15:21:56 +0530 Subject: gnu: ghc-tasty-ant-xml: Update to 1.1.4. * gnu/packages/haskell-check.scm (ghc-tasty-ant-xml): Update to 1.1.4. --- gnu/packages/haskell-check.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm index 1064872fec..65333f8269 100644 --- a/gnu/packages/haskell-check.scm +++ b/gnu/packages/haskell-check.scm @@ -39,7 +39,7 @@ (define-public ghc-tasty-ant-xml (package (name "ghc-tasty-ant-xml") - (version "1.0.2") + (version "1.1.4") (source (origin (method url-fetch) @@ -49,7 +49,7 @@ ".tar.gz")) (sha256 (base32 - "0pgz2lclg2hp72ykljcbxd88pjanfdfk8m5vb2qzcyjr85kwrhxv")))) + "0v0gsb90kh6hwlgxbclzawsskywc6yf7n8xhiifia97l4y0yx2m8")))) (build-system haskell-build-system) (inputs `(("ghc-generic-deriving" ,ghc-generic-deriving) -- cgit v1.2.3 From 6300ba5b6669e6e1a3864144390a358b8c260296 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 4 Sep 2018 15:24:32 +0530 Subject: gnu: ghc-integer-logarithms: Allow building with newer tasty. * gnu/packages/haskell.scm (ghc-integer-logarithms)[arguments]: Allow building with newer tasty. --- gnu/packages/haskell.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 70929ddae6..e7072633de 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -5197,6 +5197,8 @@ occurrences of a substring (the first in case of overlaps) with another.") (base32 "1wj8kgjg5bn2yrs4zh9qfjv85cx6w998j9pi39yrbv305944mb9j")))) (build-system haskell-build-system) + (arguments + `(#:configure-flags (list "--allow-newer=tasty"))) (native-inputs `(("ghc-quickcheck" ,ghc-quickcheck) ("ghc-smallcheck" ,ghc-smallcheck) -- cgit v1.2.3 From 906a396bff28ba46b37014a0efc5d4fbf417dc82 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 4 Sep 2018 17:26:14 +0530 Subject: gnu: ghc-zlib: Enable tests. * gnu/packages/haskell.scm (ghc-zlib)[arguments]: Enable tests. Allow building with newer tasty. [native-inputs]: Add ghc-quickcheck, ghc-tasty, ghc-tasty-hunit and ghc-tasty-quickcheck. --- gnu/packages/haskell.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index e7072633de..b8ae26346e 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -2078,9 +2078,13 @@ literals.") (base32 "1vbzf0awb6zb456xf48za1kl22018646cfzq4frvxgb9ay97vk0d")))) (build-system haskell-build-system) - ;; Tests require older versions of testy. - (arguments `(#:tests? #f)) + (arguments `(#:configure-flags (list "--allow-newer=tasty"))) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("ghc-quickcheck" ,ghc-quickcheck) + ("ghc-tasty" ,ghc-tasty) + ("ghc-tasty-hunit" ,ghc-tasty-hunit) + ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck))) (home-page "https://hackage.haskell.org/package/zlib") (synopsis "Compression and decompression in the gzip and zlib formats") -- cgit v1.2.3 From b50658fe8ac898544a5c481f232a454c485524b9 Mon Sep 17 00:00:00 2001 From: Jonathan Brielmaier Date: Thu, 16 Aug 2018 13:33:48 +0200 Subject: gnu: kicad: Update to 5.0.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/engineering.scm (kicad): Update to 5.0.0. [source]: Change from git to url-fetch. [arguments]: Remove now unneeded build version parameter. [inputs]: Add opencascade-oce. Signed-off-by: Ludovic Courtès --- gnu/packages/engineering.scm | 25 ++++++++++--------------- 1 file changed, 10 insertions(+), 15 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index d53b25cff9..ee524ec78e 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2017 Julien Lepiller ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Clément Lassieur +;;; Copyright © 2018 Jonathan Brielmaier ;;; ;;; This file is part of GNU Guix. ;;; @@ -680,24 +681,19 @@ language.") (define-public ao (deprecated-package "ao-cad" libfive)) -;; We use kicad from a git commit, because support for boost 1.61.0 has been -;; recently added. (define-public kicad - (let ((commit "5f4599fb56da4dd748845ab10abec02961d477f3") - (revision "2")) (package (name "kicad") - (version (string-append "4.0-" revision "." - (string-take commit 7))) + (version "5.0.0") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://git.launchpad.net/kicad") - (commit commit))) + (method url-fetch) + (file-name (string-append name "-" version ".tar.xz")) + (uri (string-append + "https://launchpad.net/kicad/5.0/" version "/+download/" name + "-" version ".tar.xz")) (sha256 - (base32 "1833pln2975gmc5s18xf7s8m9vg834lmxxdjk0wlk3lq7bvjjnff")) - (file-name (string-append name "-" version "-checkout")))) + (base32 "17nqjszyvd25wi6550j981whlnb1wxzmlanljdjihiki53j84x9p")))) (build-system cmake-build-system) (arguments `(#:out-of-source? #t @@ -706,8 +702,6 @@ language.") #:configure-flags (list "-DKICAD_STABLE_VERSION=ON" "-DKICAD_REPO_NAME=stable" - ,(string-append "-DKICAD_BUILD_VERSION=4.0-" - (string-take commit 7)) "-DKICAD_SKIP_BOOST=ON"; Use our system's boost library. "-DKICAD_SCRIPTING=ON" "-DKICAD_SCRIPTING_MODULES=ON" @@ -754,6 +748,7 @@ language.") ("libngspice" ,libngspice) ("libsm" ,libsm) ("mesa" ,mesa) + ("opencascade-oce" ,opencascade-oce) ("openssl" ,openssl) ("python" ,python-2) ("wxwidgets" ,wxwidgets-gtk2) @@ -764,7 +759,7 @@ language.") boards and electrical circuits. The software has a number of programs that perform specific functions, for example, pcbnew (Editing PCB), eeschema (editing electrical diagrams), gerbview (viewing Gerber files) and others.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public kicad-library (let ((version "4.0.7")) -- cgit v1.2.3 From 71ca16b58d20aa26157acc4c345c0af80ec8df5d Mon Sep 17 00:00:00 2001 From: Paul Garlick Date: Mon, 3 Sep 2018 11:57:38 +0100 Subject: gnu: petsc-openmpi: Configure with support for hdf5 data format. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add hdf5-parallel-openmpi. [arguments]: Add '--with-hdf5-include' and '--with-hdf5-lib' flags. Add 'set-test-environment' phase. Signed-off-by: Ludovic Courtès --- gnu/packages/maths.scm | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 50c0a320e0..42136f65ea 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -15,7 +15,7 @@ ;;; Copyright © 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2016 Leo Famulari ;;; Copyright © 2016, 2017 Thomas Danckaert -;;; Copyright © 2017 Paul Garlick +;;; Copyright © 2017, 2018 Paul Garlick ;;; Copyright © 2017 Nils Gillmann ;;; Copyright © 2017 Ben Woodcroft ;;; Copyright © 2017 Theodoros Foradis @@ -1685,6 +1685,7 @@ scientific applications modeled by partial differential equations.") (name "petsc-openmpi") (inputs `(("openmpi" ,openmpi) + ("hdf5" ,hdf5-parallel-openmpi) ,@(package-inputs petsc))) (arguments (substitute-keyword-arguments (package-arguments petsc) @@ -1692,7 +1693,21 @@ scientific applications modeled by partial differential equations.") ``("--with-mpiexec=mpirun" ,(string-append "--with-mpi-dir=" (assoc-ref %build-inputs "openmpi")) - ,@(delete "--with-mpi=0" ,cf))))) + ,(string-append "--with-hdf5-include=" + (assoc-ref %build-inputs "hdf5") "/include") + ,(string-append "--with-hdf5-lib=" + (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a") + ,@(delete "--with-mpi=0" ,cf))) + ((#:phases phases) + `(modify-phases ,phases + (add-before 'check 'set-test-environment + (lambda _ + ;; By default, running the test suite would fail because 'ssh' + ;; could not be found in $PATH. Define this variable to + ;; placate Open MPI without adding a dependency on OpenSSH (the + ;; agent isn't used anyway.) + (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) + #t)))))) (synopsis "Library to solve PDEs (with MPI support)"))) (define-public petsc-complex-openmpi -- cgit v1.2.3 From 1bf758767d1553594b6d7534ca8c38a2171b5afe Mon Sep 17 00:00:00 2001 From: Alex Vong Date: Mon, 3 Sep 2018 02:25:31 +0800 Subject: gnu: Add emacs-picpocket. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs.scm (emacs-picpocket): New public variable. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs.scm | 39 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 8f0c564f88..957b72f4e7 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -15,7 +15,7 @@ ;;; Copyright © 2016, 2017 Nils Gillmann ;;; Copyright © 2016 Alex Griffin ;;; Copyright © 2016, 2017, 2018 Nicolas Goaziou -;;; Copyright © 2016, 2017 Alex Vong +;;; Copyright © 2016, 2017, 2018 Alex Vong ;;; Copyright © 2016, 2017, 2018 Arun Isaac ;;; Copyright © 2017 Christopher Baines ;;; Copyright © 2017, 2018 Mathieu Othacehe @@ -11315,6 +11315,43 @@ e.g. the package dependencies it requires. See function file.") (license license:gpl3+)))) +(define-public emacs-picpocket + (let ((version "20180610.1059") ; taken from melpa + (commit "ce4b6ed088384f2414af82e8e4eae5b92c2874bf")) + (package + (name "emacs-picpocket") + (version version) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/johanclaesson/picpocket") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "15vpbcv83mc4j1pvrk7xic0klh2bl9gzg2xxs7c2lmnix52hy8mv")))) + (build-system emacs-build-system) + (arguments ; needed for running tests + `(#:tests? #t + #:emacs ,emacs + #:test-command '("emacs" "--batch" + "-l" "picpocket-test.el" + "-f" "ert-run-tests-batch-and-exit"))) + (home-page "https://github.com/johanclaesson/picpocket") + (synopsis "Image viewer for Emacs") + (description + "Picpocket is an image viewer for GNU Emacs. It has commands for: + +@itemize +@item File operations on the picture files (delete, move, copy, hardlink). +@item Scale and rotate the picture. +@item Associate pictures with tags which are saved to disk. +@item Filter pictures according to tags. +@item Customizing keystrokes for quick tagging and file operations. +@item Undo and browse history of undoable commands. +@end itemize") + (license license:gpl3+)))) + (define-public emacs-wgrep-helm ;; `emacs-wgrep-helm' was mistakenly added. (deprecated-package "emacs-wgrep-helm" emacs-wgrep)) -- cgit v1.2.3 From ca719424455465fca4b872c371daf2a46de88b33 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 31 Aug 2018 17:07:07 +0200 Subject: Switch to Guile-Gcrypt. This removes (guix hash) and (guix pk-crypto), which now live as part of Guile-Gcrypt (version 0.1.0.) * guix/gcrypt.scm, guix/hash.scm, guix/pk-crypto.scm, tests/hash.scm, tests/pk-crypto.scm: Remove. * configure.ac: Test for Guile-Gcrypt. Remove LIBGCRYPT and LIBGCRYPT_LIBDIR assignments. * m4/guix.m4 (GUIX_ASSERT_LIBGCRYPT_USABLE): Remove. * README: Add Guile-Gcrypt to the dependencies; move libgcrypt as "required unless --disable-daemon". * doc/guix.texi (Requirements): Likewise. * gnu/packages/bash.scm, guix/derivations.scm, guix/docker.scm, guix/git.scm, guix/http-client.scm, guix/import/cpan.scm, guix/import/cran.scm, guix/import/crate.scm, guix/import/elpa.scm, guix/import/gnu.scm, guix/import/hackage.scm, guix/import/texlive.scm, guix/import/utils.scm, guix/nar.scm, guix/pki.scm, guix/scripts/archive.scm, guix/scripts/authenticate.scm, guix/scripts/download.scm, guix/scripts/hash.scm, guix/scripts/pack.scm, guix/scripts/publish.scm, guix/scripts/refresh.scm, guix/scripts/substitute.scm, guix/store.scm, guix/store/deduplication.scm, guix/tests.scm, tests/base32.scm, tests/builders.scm, tests/challenge.scm, tests/cpan.scm, tests/crate.scm, tests/derivations.scm, tests/gem.scm, tests/nar.scm, tests/opam.scm, tests/pki.scm, tests/publish.scm, tests/pypi.scm, tests/store-deduplication.scm, tests/store.scm, tests/substitute.scm: Adjust imports. * gnu/system/vm.scm: Likewise. (guile-sqlite3&co): Rename to... (gcrypt-sqlite3&co): ... this. Add GUILE-GCRYPT. (expression->derivation-in-linux-vm)[config]: Remove. (iso9660-image)[config]: Remove. (qemu-image)[config]: Remove. (system-docker-image)[config]: Remove. * guix/scripts/pack.scm: Adjust imports. (guile-sqlite3&co): Rename to... (gcrypt-sqlite3&co): ... this. Add GUILE-GCRYPT. (self-contained-tarball)[build]: Call 'make-config.scm' without #:libgcrypt argument. (squashfs-image)[libgcrypt]: Remove. [build]: Call 'make-config.scm' without #:libgcrypt. (docker-image)[config, json]: Remove. [build]: Add GUILE-GCRYPT to the extensions Remove (guix config) from the imported modules. * guix/self.scm (specification->package): Remove "libgcrypt", add "guile-gcrypt". (compiled-guix): Remove #:libgcrypt. [guile-gcrypt]: New variable. [dependencies]: Add it. [*core-modules*]: Remove #:libgcrypt from 'make-config.scm' call. Add #:extensions. [*config*]: Remove #:libgcrypt from 'make-config.scm' call. (%dependency-variables): Remove %libgcrypt. (make-config.scm): Remove #:libgcrypt. * build-aux/build-self.scm (guile-gcrypt): New variable. (make-config.scm): Remove #:libgcrypt. (build-program)[fake-gcrypt-hash]: New variable. Add (gcrypt hash) to the imported modules. Adjust load path assignments. * gnu/packages/package-management.scm (guix)[propagated-inputs]: Add GUILE-GCRYPT. [arguments]: In 'wrap-program' phase, add GUILE-GCRYPT to the search path. --- gnu/packages/bash.scm | 2 +- gnu/packages/package-management.scm | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bash.scm b/gnu/packages/bash.scm index 64f7782f58..121a459fa6 100644 --- a/gnu/packages/bash.scm +++ b/gnu/packages/bash.scm @@ -36,7 +36,7 @@ #:use-module (guix store) #:use-module (guix build-system gnu) #:autoload (guix gnupg) (gnupg-verify*) - #:autoload (guix hash) (port-sha256) + #:autoload (gcrypt hash) (port-sha256) #:autoload (guix base32) (bytevector->nix-base32-string) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 78db0abfa8..e40a94a844 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -213,6 +213,7 @@ ;; Guile-JSON, and Guile-Git automatically. (let* ((out (assoc-ref outputs "out")) (guile (assoc-ref inputs "guile")) + (gcrypt (assoc-ref inputs "guile-gcrypt")) (json (assoc-ref inputs "guile-json")) (sqlite (assoc-ref inputs "guile-sqlite3")) (git (assoc-ref inputs "guile-git")) @@ -220,7 +221,8 @@ "guile-bytestructures")) (ssh (assoc-ref inputs "guile-ssh")) (gnutls (assoc-ref inputs "gnutls")) - (deps (list json sqlite gnutls git bs ssh)) + (deps (list gcrypt json sqlite gnutls + git bs ssh)) (effective (read-line (open-pipe* OPEN_READ @@ -279,6 +281,7 @@ '()))) (propagated-inputs `(("gnutls" ,gnutls) + ("guile-gcrypt" ,guile-gcrypt) ("guile-json" ,guile-json) ("guile-sqlite3" ,guile-sqlite3) ("guile-ssh" ,guile-ssh) -- cgit v1.2.3 From 95681e55862991a5303449a4eb3961441b337033 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 4 Sep 2018 15:08:13 -0400 Subject: gnu: Zsh: Update to 5.6 [fixes CVE-2018-{0502,13259}]. * gnu/packages/shells.scm (zsh): Update to 5.6. [arguments]: Skip some tests. --- gnu/packages/shells.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 6dbe1c4db7..c3647221aa 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -292,7 +292,7 @@ history mechanism, job control and a C-like syntax.") (define-public zsh (package (name "zsh") - (version "5.5.1") + (version "5.6") (source (origin (method url-fetch) (uri (list (string-append @@ -303,7 +303,7 @@ history mechanism, job control and a C-like syntax.") ".tar.xz"))) (sha256 (base32 - "105aqkdfsdxc4531anrj2zis2ywz6icagjam9lsc235yzh48ihz1")))) + "1mp6h2452z2029n12mxipjv4b0cc8i8sb72g8p8jklg8275iysvl")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-tcsetpgrp" "--enable-pcre") #:phases @@ -336,6 +336,11 @@ history mechanism, job control and a C-like syntax.") (("command -pv") "command -v") (("command -p") "command ") (("'command' -p") "'command' ")) + ;; Several of these tests fail spuriously in the Guix + ;; build environment due to assumptions about PATH and + ;; the location of the test files. It was easier to just + ;; skip them than try to make them work. + (delete-file "Test/A05execution.ztst") #t))))) (native-inputs `(("autoconf" ,autoconf))) (inputs `(("ncurses" ,ncurses) -- cgit v1.2.3 From fcf4841c0ee16631e8330d797cf3788dac0eca05 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 4 Sep 2018 18:33:06 -0400 Subject: gnu: Zsh: Patch some tests that began failing in 5.6. * gnu/packages/shells.scm (zsh)[arguments]: Patch the tests rather than deleting them. --- gnu/packages/shells.scm | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index c3647221aa..900c8ec686 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -336,11 +336,19 @@ history mechanism, job control and a C-like syntax.") (("command -pv") "command -v") (("command -p") "command ") (("'command' -p") "'command' ")) - ;; Several of these tests fail spuriously in the Guix - ;; build environment due to assumptions about PATH and - ;; the location of the test files. It was easier to just - ;; skip them than try to make them work. - (delete-file "Test/A05execution.ztst") + ;; This file is ISO-8859-1 encoded. + (with-fluids ((%default-port-encoding #f)) + (substitute* "Test/A05execution.ztst" + ;; Help it find `sh` + (("PATH=/bin:\\$\\{ZTST_testdir\\}/command.tmp/ tstcmd-slashless") + (string-append "PATH=/bin:" + (assoc-ref %build-inputs "bash") "/bin:" + "${ZTST_testdir}/command.tmp/ tstcmd-slashless")) + ;; Help it find `echo` + (("PATH=/bin:\\$\\{ZTST_testdir\\}/command.tmp tstcmd-arg") + (string-append "PATH=/bin:" + (assoc-ref %build-inputs "coreutils") "/bin:" + "PATH=/bin:${ZTST_testdir}/command.tmp tstcmd-arg")))) #t))))) (native-inputs `(("autoconf" ,autoconf))) (inputs `(("ncurses" ,ncurses) -- cgit v1.2.3 From fefe17b0888b467383ea91fed73a9586295c49f0 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Wed, 5 Sep 2018 10:19:25 +0200 Subject: gnu: dolphin-emu: Update to commit 5f0d825. * gnu/packages/emulators.scm (dolphin-emu): Update to commit 5f0d825. --- gnu/packages/emulators.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 8e68c676ef..e02339af62 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -117,8 +117,8 @@ ;; Building from recent Git because the official 5.0 release no longer builds. (define-public dolphin-emu - (let ((commit "806c1ee8f0ed824008185212bfab2658d400b576") - (revision "2")) + (let ((commit "5f0d825f40b8aabe13eaef32d44ab667ff8e8c28") + (revision "3")) (package (name "dolphin-emu") (version (git-version "5.0" revision commit)) @@ -144,7 +144,7 @@ #t)) (sha256 (base32 - "1sdc7rh6z7gjx4kxg18jrv7srfpx1vgf936zg5y43radnlscrh1j")))) + "0dh7mih16aif9ynbgcsn7n10f89g8d232i86xqfp2rijsdggcmzl")))) (build-system cmake-build-system) (arguments '(#:tests? #f -- cgit v1.2.3 From ca1dc4c76a81d289360c0601fed16a7852833d9b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 11:44:15 +0200 Subject: gnu: nss-pam-ldapd: Update to 0.9.10. * gnu/packages/openldap.scm (nss-pam-ldapd): Update to 0.9.10. --- gnu/packages/openldap.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm index 12964e302a..4b615b5d32 100644 --- a/gnu/packages/openldap.scm +++ b/gnu/packages/openldap.scm @@ -108,14 +108,14 @@ (define-public nss-pam-ldapd (package (name "nss-pam-ldapd") - (version "0.9.9") + (version "0.9.10") (source (origin (method url-fetch) (uri (string-append "https://arthurdejong.org/nss-pam-ldapd/" "nss-pam-ldapd-" version ".tar.gz")) (sha256 (base32 - "1lj7qkjlg3bshwdc5x5r1ny37rly4wgm1c8b6w6b5f4wa11nmji0")))) + "1cqamcr6qpgwxijlr6kg7jspjamjra8w0haan0qssn0yxn95d7c0")))) (build-system gnu-build-system) (arguments `(#:configure-flags -- cgit v1.2.3 From 0d7974c376c4b84dd26096ba0c53ed2535afcbc9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 11:07:26 +0200 Subject: gnu: libbigwig: Update to 0.4.2. * gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.2. [source]: Fetch from git. [arguments]: Disable tests; remove build phases "disable-curl-test" and "create-target-dirs". [native-inputs]: Add python-2. --- gnu/packages/bioinformatics.scm | 33 ++++++++++++--------------------- 1 file changed, 12 insertions(+), 21 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f60fc4c84c..7f865ae878 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1887,42 +1887,33 @@ other types of unwanted sequence from high-throughput sequencing reads.") (define-public libbigwig (package (name "libbigwig") - (version "0.1.4") + (version "0.4.2") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/dpryan79/libBigWig/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dpryan79/libBigWig.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1")))) + "0h2smg24v5srdcqzrmz2g23cmlp4va465mgx8r2z571sfz8pv454")))) (build-system gnu-build-system) (arguments `(#:test-target "test" + #:tests? #f ; tests require access to the web #:make-flags (list "CC=gcc" (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (modify-phases %standard-phases - (delete 'configure) - (add-before 'check 'disable-curl-test - (lambda _ - (substitute* "Makefile" - (("./test/testRemote.*") "")) - #t)) - ;; This has been fixed with the upstream commit 4ff6959cd8a0, but - ;; there has not yet been a release containing this change. - (add-before 'install 'create-target-dirs - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (mkdir-p (string-append out "/lib")) - (mkdir-p (string-append out "/include")) - #t)))))) + (delete 'configure)))) (inputs `(("zlib" ,zlib) ("curl" ,curl))) (native-inputs - `(("doxygen" ,doxygen))) + `(("doxygen" ,doxygen) + ;; Need for tests + ("python" ,python-2))) (home-page "https://github.com/dpryan79/libBigWig") (synopsis "C library for handling bigWig files") (description -- cgit v1.2.3 From 8afdeb87518f09383d93cf0dc9b86bde237ba561 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 11:08:25 +0200 Subject: gnu: python-pybigwig: Update to 0.3.12. * gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12. [propagated-inputs]: Add python-numpy. --- gnu/packages/bioinformatics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7f865ae878..05d516165e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1924,13 +1924,13 @@ files.") (define-public python-pybigwig (package (name "python-pybigwig") - (version "0.2.5") + (version "0.3.12") (source (origin (method url-fetch) (uri (pypi-uri "pyBigWig" version)) (sha256 (base32 - "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d")) + "00w4kfnm2c5l7wdwr2nj1z5djv8kzgf7h1zhsgv6njff1rwr26g0")) (modules '((guix build utils))) (snippet '(begin @@ -1946,6 +1946,8 @@ files.") (substitute* "setup.py" (("libs=\\[") "libs=[\"BigWig\", ")) #t))))) + (propagated-inputs + `(("python-numpy" ,python-numpy))) (inputs `(("libbigwig" ,libbigwig) ("zlib" ,zlib) -- cgit v1.2.3 From 4fd2622df8615ce3e4d081124bee824315f00f85 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 11:09:01 +0200 Subject: gnu: python-tables: Update to 3.4.4. * gnu/packages/python.scm (python-tables): Update to 3.4.4. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8cf5550f81..8c7c9d3c33 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6297,14 +6297,14 @@ printing of sub-tables by specifying a row range.") (define-public python-tables (package (name "python-tables") - (version "3.2.2") + (version "3.4.4") (source (origin (method url-fetch) (uri (pypi-uri "tables" version)) (sha256 (base32 - "117s6w7s3yxafpmf3zz3svana7xfrsviw01va1xp7h8ylx8v6r1m")) + "0affz7k8babh8wdmsgrz5jxrd569by2w8ffimcxs9wiaf5rw1idx")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From 185948b8a83f583135de050698cff983e46c8145 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 5 Sep 2018 13:57:43 +0200 Subject: gnu: xorg: Fix typo. * gnu/packages/xorg.scm: Fix typo in Benjamin's email address. --- gnu/packages/xorg.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index c89661272b..30e46fac7c 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -17,7 +17,7 @@ ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Kei Kebreau ;;; Copyright © 2018 Oleg Pykhalov -;;; Copyright © 2018 Benjamin Slade +;;; Copyright © 2018 Benjamin Slade ;;; ;;; This file is part of GNU Guix. ;;; -- cgit v1.2.3 From 53166aec987957efba917c83f093817d6cf6e943 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 5 Sep 2018 14:31:48 +0200 Subject: gnu: guix: Update to 3d43017. * gnu/packages/package-management.scm (guix): Update to 3d43017. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index e40a94a844..b0941b50de 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -101,8 +101,8 @@ ;; Note: the 'update-guix-package.scm' script expects this definition to ;; start precisely like this. (let ((version "0.15.0") - (commit "8bbb79cf95a07a40950448a8a09d888254404ed4") - (revision 2)) + (commit "3d43017026f9995ad128915db8ca5eafe061bf75") + (revision 3)) (package (name "guix") @@ -118,7 +118,7 @@ (commit commit))) (sha256 (base32 - "0h83l91v2cg9bb78c7vqx9wj71ckz22jbjmm2fy4vqs9216jnvc0")) + "167rzz2h33xmmchkplwzfq94s5jwdn5nabsq2lb84s54ps0sm89m")) (file-name (string-append "guix-" version "-checkout")))) (build-system gnu-build-system) (arguments -- cgit v1.2.3 From 998100e6e8be64d4cc14e6509f744d3f5c37cf27 Mon Sep 17 00:00:00 2001 From: Alex Vong Date: Wed, 5 Sep 2018 02:10:48 +0800 Subject: gnu: eyed3: Update home page. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/mp3.scm (eyed3)[home-page]: Update to redirected HTTPS URL. Signed-off-by: 宋文武 --- gnu/packages/mp3.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/mp3.scm b/gnu/packages/mp3.scm index 579127d06e..fb919c6e6c 100644 --- a/gnu/packages/mp3.scm +++ b/gnu/packages/mp3.scm @@ -491,7 +491,7 @@ specifically mp3 files containing ID3 metadata (i.e. song info). It provides a command-line tool (eyeD3) and a Python library (import eyed3) that can be used to write your own applications or plugins that are callable from the command-line tool.") - (home-page "http://eyed3.nicfit.net/") + (home-page "https://eyed3.readthedocs.io/en/latest/") (license license:gpl2+))) (define-public chromaprint -- cgit v1.2.3 From 296f091b4879679cf970e1526d919c671c80a473 Mon Sep 17 00:00:00 2001 From: Alex Vong Date: Wed, 5 Sep 2018 02:16:53 +0800 Subject: gnu: packages: mp3: Use HTTPS where possible. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/mp3.scm (libmad)[home-page]: Use HTTPS. (libid3tag)[home-page]: Likewise. (mp3info)[source, home-page]: Likewise. (mpg123)[source]: Likewise. (libmpcdec)[source, home-page]: Likewise. Signed-off-by: 宋文武 --- gnu/packages/mp3.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/mp3.scm b/gnu/packages/mp3.scm index fb919c6e6c..c9effbafa3 100644 --- a/gnu/packages/mp3.scm +++ b/gnu/packages/mp3.scm @@ -84,7 +84,7 @@ fully implemented. This package contains the library.") (license license:gpl2+) - (home-page "http://www.underbit.com/products/mad/"))) + (home-page "https://www.underbit.com/products/mad/"))) (define-public libid3tag (package @@ -105,7 +105,7 @@ This package contains the library.") "Libid3tag is a library for reading ID3 tags, both ID3v1 and the various versions of ID3v2.") (license license:gpl2+) - (home-page "http://www.underbit.com/products/mad/"))) + (home-page "https://www.underbit.com/products/mad/"))) (define-public id3lib (package @@ -184,7 +184,7 @@ Speex, WavPack TrueAudio, WAV, AIFF, MP4 and ASF files.") (source (origin (method url-fetch) (uri (string-append - "http://ibiblio.org" + "https://ibiblio.org" "/pub/linux/apps/sound/mp3-utils/mp3info/mp3info-" version ".tgz")) (sha256 @@ -231,7 +231,7 @@ Speex, WavPack TrueAudio, WAV, AIFF, MP4 and ASF files.") (inputs `(("gtk+" ,gtk+-2) ("ncurses" ,ncurses))) - (home-page "http://www.ibiblio.org/mp3info/") + (home-page "https://www.ibiblio.org/mp3info/") (synopsis "MP3 technical info viewer and ID3 1.x tag editor") (description "MP3Info is a little utility used to read and modify the ID3 tags of MP3 @@ -309,7 +309,7 @@ This package contains the binary.") (uri (list (string-append "mirror://sourceforge/mpg123/mpg123/" version "/mpg123-" version ".tar.bz2") (string-append - "http://www.mpg123.org/download/mpg123-" + "https://www.mpg123.org/download/mpg123-" version ".tar.bz2"))) (sha256 (base32 @@ -413,7 +413,7 @@ for album and track information.") (source (origin (method url-fetch) (uri (string-append - "http://files.musepack.net/source/libmpcdec-" + "https://files.musepack.net/source/libmpcdec-" version ".tar.bz2")) (sha256 (base32 @@ -424,7 +424,7 @@ for album and track information.") "This library supports decoding of the Musepack (MPC) audio compression format.") (license license:bsd-3) - (home-page "http://musepack.net"))) + (home-page "https://musepack.net"))) (define-public mpc123 (package -- cgit v1.2.3 From b26e4f26ff0bfede3dc17db48dce2936ecd0c129 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Tue, 31 Jul 2018 11:04:19 -0500 Subject: gnu: Add SUNDIALS. * gnu/packages/maths.scm (sundials, sundials-openmpi): New variables. --- gnu/packages/maths.scm | 77 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 42136f65ea..c6bcec844b 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4042,3 +4042,80 @@ terminal do calculations simply and quickly. The formula to be calculated can be fed to @command{tcalc} through the command line.") (home-page "https://sites.google.com/site/mohammedisam2000/tcalc") (license license:gpl3+))) + +(define-public sundials + (package + (name "sundials") + (version "3.1.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://computation.llnl.gov/projects/sundials/download/" + "sundials-" version ".tar.gz")) + (sha256 + (base32 + "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2")))) + (build-system cmake-build-system) + (native-inputs + `(("python" ,python-2))) ;for tests; syntax incompatible with python 3 + (inputs + `(("fortran" ,gfortran) ;for fcmix + ("blas" ,openblas) + ("suitesparse" ,suitesparse))) ;TODO: Add hypre + (arguments + `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON" + "-DEXAMPLES_ENABLE_CXX:BOOL=ON" + "-DEXAMPLES_ENABLE_F77:BOOL=ON" + "-DEXAMPLES_ENABLE_F90:BOOL=ON" + "-DEXAMPLES_INSTALL:BOOL=OFF" + + "-DFCMIX_ENABLE:BOOL=ON" + + "-DKLU_ENABLE:BOOL=ON" + ,(string-append "-DKLU_INCLUDE_DIR=" + (assoc-ref %build-inputs "suitesparse") + "/include") + ,(string-append "-DKLU_LIBRARY_DIR=" + (assoc-ref %build-inputs "suitesparse") + "/lib")))) + (home-page "https://computation.llnl.gov/projects/sundials") + (synopsis "Suite of nonlinear and differential/algebraic equation solvers") + (description "SUNDIALS is a family of software packages implemented with +the goal of providing robust time integrators and nonlinear solvers that can +easily be incorporated into existing simulation codes.") + (license license:bsd-3))) + +(define-public sundials-openmpi + (package (inherit sundials) + (name "sundials-openmpi") + (inputs + `(("mpi" ,openmpi) + ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI + ,@(package-inputs sundials))) + (arguments + (substitute-keyword-arguments (package-arguments sundials) + ((#:configure-flags flags '()) + `(cons* "-DMPI_ENABLE:BOOL=ON" + "-DPETSC_ENABLE:BOOL=ON" + (string-append "-DPETSC_INCLUDE_DIR=" + (assoc-ref %build-inputs "petsc") + "/include") + (string-append "-DPETSC_LIBRARY_DIR=" + (assoc-ref %build-inputs "petsc") + "/lib") + ,flags)) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (add-before 'check 'set-test-environment + (lambda _ + ;; By default, running the test suite would fail because 'ssh' + ;; could not be found in $PATH. Define this variable to + ;; placate Open MPI without adding a dependency on OpenSSH (the + ;; agent isn't used anyway.) + (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) + ;; Allow oversubscription in case there are less + ;; physical cores available in the build environment + ;; than SUNDIALS wants while testing. + (setenv "OMPI_MCA_rmaps_base_oversubscribe" "yes") + #t)))))) + (synopsis "SUNDIALS with OpenMPI support"))) -- cgit v1.2.3 From a3a99e27bb727b0407da13955ef47566a1919629 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Tue, 31 Jul 2018 11:31:59 -0500 Subject: petsc: Move example code to "examples" output. * gnu/packages/maths.scm (petsc)[arguments]: New 'move-examples' phase. --- gnu/packages/maths.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index c6bcec844b..ba39531bdb 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1589,6 +1589,8 @@ September 2004}") "petsc-lite-" version ".tar.gz")) (sha256 (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s")))) + (outputs '("out" ;libraries and headers + "examples")) ;~24MiB of examples (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) @@ -1662,6 +1664,15 @@ September 2004}") "PETScBuildInternal.cmake" ;; Once installed, should uninstall with Guix "uninstall.py")) + #t))) + (add-after 'install 'move-examples + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (examples (assoc-ref outputs "examples")) + (exdir (string-append out "/share/petsc/examples")) + (exdir' (string-append examples "/share/petsc/examples"))) + (copy-recursively exdir exdir') + (delete-file-recursively exdir) #t)))))) (home-page "http://www.mcs.anl.gov/petsc") (synopsis "Library to solve PDEs") -- cgit v1.2.3 From c15be1280e103c781f8c57bb621e92124e8e2cc5 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Tue, 31 Jul 2018 11:32:57 -0500 Subject: petsc: Upgrade to 3.9.3. * gnu/packages/maths.scm (petsc): Upgrade to 3.9.3. [arguments]: Remove unnecessary configure flags. --- gnu/packages/maths.scm | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ba39531bdb..ef20f239e5 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1580,7 +1580,7 @@ September 2004}") (define-public petsc (package (name "petsc") - (version "3.8.0") + (version "3.9.3") (source (origin (method url-fetch) @@ -1588,9 +1588,9 @@ September 2004}") (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" "petsc-lite-" version ".tar.gz")) (sha256 - (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s")))) + (base32 "1fwkbwv4g7zf2lc8fw865xd0bl9anb6jaczfis5dff7h449gwa48")))) (outputs '("out" ;libraries and headers - "examples")) ;~24MiB of examples + "examples")) ;~30MiB of examples (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) @@ -1607,11 +1607,7 @@ September 2004}") #:configure-flags `("--with-mpi=0" "--with-openmp=1" - "--with-superlu=1" - ,(string-append "--with-superlu-include=" - (assoc-ref %build-inputs "superlu") "/include") - ,(string-append "--with-superlu-lib=" - (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) + "--with-superlu=1") #:make-flags ;; Honor (parallel-job-count) for build. Do not use --with-make-np, ;; whose value is dumped to $out/lib/petsc/conf/petscvariables. -- cgit v1.2.3 From 3f5e6ccf9be46381b21f63638f89853ee81bfb64 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Tue, 31 Jul 2018 12:14:54 -0500 Subject: slepc: Upgrade to 3.9.2. * gnu/packages/maths.scm (slepc): Upgrade to 3.9.2. --- 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 ef20f239e5..d2b9df01a7 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1760,7 +1760,7 @@ savings are consistently > 5x.") (define-public slepc (package (name "slepc") - (version "3.8.2") + (version "3.9.2") (source (origin (method url-fetch) @@ -1768,7 +1768,7 @@ savings are consistently > 5x.") version ".tar.gz")) (sha256 (base32 - "04zd48p43rnvg68p6cp28zll0px5whglc5v0sc3s6vdj1v920z8y")))) + "0gmhdqac8zm3jx43h935z7bflazjnpvqxjv4jh5za2y1z2rqax94")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) -- cgit v1.2.3 From 5e3082df1c8eb07f7c7cd02f118cd9975eb32bb8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 5 Sep 2018 15:33:25 +0200 Subject: =?UTF-8?q?gnu:=20guile-fibers:=20Install=20.go=20files=20to=20"?= =?UTF-8?q?=E2=80=A6/site-ccache".?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/guile.scm (guile-fibers)[arguments]: New field. --- gnu/packages/guile.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index a585dd6dc8..f594cd13ed 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -1817,6 +1817,20 @@ Note that 8sync is only available for Guile 2.2.") (base32 "0vjkg72ghgdgphzbjz9ig8al8271rq8974viknb2r1rg4lz92ld0")))) (build-system gnu-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (add-after 'install 'mode-guile-objects + (lambda* (#:key outputs #:allow-other-keys) + ;; .go files are installed to "lib/guile/X.Y/cache". + ;; This phase moves them to "…/site-ccache". + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib/guile")) + (old (car (find-files lib "^ccache$" + #:directories? #t))) + (new (string-append (dirname old) + "/site-ccache"))) + (rename-file old new) + #t)))))) (native-inputs `(("texinfo" ,texinfo) ("pkg-config" ,pkg-config))) -- cgit v1.2.3 From 7903f00a74871ac4ecd41878ac9846fdae91e276 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 5 Sep 2018 14:46:28 +0200 Subject: gnu: cuirass: Add dependency on Guile-Gcrypt. This is a followup to 53166aec987957efba917c83f093817d6cf6e943, which added a hard dependency of Guix on Guile-Gcrypt. * gnu/packages/ci.scm (cuirass)[inputs]: Add GUILE-GCRYPT. [arguments]: In 'wrap-program' phase, use 'string-join' to compute 'mods'. Define 'objs' for use in GUILE_LOAD_COMPILED_PATH, and take objects from lib/guile/X.Y/site-ccache. --- gnu/packages/ci.scm | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index e26983da3b..067a288004 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -32,6 +32,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages databases) #:use-module (gnu packages guile) + #:use-module (gnu packages gnupg) #:use-module (gnu packages mail) #:use-module (gnu packages package-management) #:use-module (gnu packages perl) @@ -223,39 +224,42 @@ their dependencies.") (lambda* (#:key inputs outputs #:allow-other-keys) ;; Wrap the 'cuirass' command to refer to the right modules. (let* ((out (assoc-ref outputs "out")) + (gcrypt (assoc-ref inputs "guile-gcrypt")) (json (assoc-ref inputs "guile-json")) (sqlite (assoc-ref inputs "guile-sqlite3")) (git (assoc-ref inputs "guile-git")) (bytes (assoc-ref inputs "guile-bytestructures")) (fibers (assoc-ref inputs "guile-fibers")) (guix (assoc-ref inputs "guix")) + (deps (list gcrypt json sqlite git bytes fibers guix)) (guile (assoc-ref %build-inputs "guile")) (effective (read-line (open-pipe* OPEN_READ (string-append guile "/bin/guile") "-c" "(display (effective-version))"))) - (mods (string-append json "/share/guile/site/" - effective ":" - git "/share/guile/site/" - effective ":" - bytes "/share/guile/site/" - effective ":" - sqlite "/share/guile/site/" - effective ":" - fibers "/share/guile/site/" - effective ":" - guix "/share/guile/site/" - effective))) + (mods (string-drop-right ;drop trailing colon + (string-join deps + (string-append "/share/guile/site/" + effective ":") + 'suffix) + 1)) + (objs (string-drop-right + (string-join deps + (string-append "/lib/guile/" effective + "/site-ccache:") + 'suffix) + 1))) ;; Make sure 'cuirass' can find the 'evaluate' command, as ;; well as the relevant Guile modules. (wrap-program (string-append out "/bin/cuirass") `("PATH" ":" prefix (,(string-append out "/bin"))) `("GUILE_LOAD_PATH" ":" prefix (,mods)) - `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,mods))) + `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,objs))) #t)))))) (inputs `(("guile" ,guile-2.2) ("guile-fibers" ,guile-fibers) + ("guile-gcrypt" ,guile-gcrypt) ("guile-json" ,guile-json) ("guile-sqlite3" ,guile-sqlite3) ("guile-git" ,guile-git) -- cgit v1.2.3 From 3b0153bd828f68804f7226ca655d26aaa1a0c065 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 5 Sep 2018 15:48:04 +0200 Subject: gnu: guix-daemon: Add dependency on Guile-Gcrypt. This is a followup to 53166aec987957efba917c83f093817d6cf6e943, which made Guile-Gcrypt a hard dependency. * gnu/packages/package-management.scm (guix-daemon)[inputs]: Add GUILE-GCRYPT. --- gnu/packages/package-management.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index b0941b50de..529d2943c4 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -317,6 +317,7 @@ the Nix package manager.") (inputs `(("gnutls" ,gnutls) ("guile-git" ,guile-git) + ("guile-gcrypt" ,guile-gcrypt) ,@(fold alist-delete (package-inputs guix) '("boot-guile" "boot-guile/i686" "util-linux")))) -- cgit v1.2.3 From 356230da4a77eef1345e4b2079db7020df98cdc6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 12:26:56 +0200 Subject: gnu: Add r-fansi. * gnu/packages/cran.scm (r-fansi): 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 016d1b1e41..be64aa3a98 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4424,6 +4424,27 @@ packages. It contains also functions for simplifying some clustering analysis steps and provides ggplot2-based elegant data visualization.") (license license:gpl2))) +(define-public r-fansi + (package + (name "r-fansi") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "fansi" version)) + (sha256 + (base32 + "135qj7bcc3mwn0vg55hiiadf66lx6zaxvkicfmfw9x0zr7ah2r6x")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://github.com/brodieG/fansi") + (synopsis "ANSI control sequence aware string functions") + (description + "This package provides counterparts to R string manipulation functions +that account for the effects of ANSI text formatting control sequences.") + (license license:gpl2+))) + (define-public r-nbclust (package (name "r-nbclust") -- cgit v1.2.3 From 53718658d20388f47fcf3747264f454c944c451e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 12:56:40 +0200 Subject: gnu: Add r-polynom. * gnu/packages/cran.scm (r-polynom): 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 be64aa3a98..a142e9f1c7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4516,6 +4516,25 @@ patterned after functions in the Python @code{itertools} module, and others patterned after functions in the snow package.") (license license:gpl2))) +(define-public r-polynom + (package + (name "r-polynom") + (version "1.3-9") + (source + (origin + (method url-fetch) + (uri (cran-uri "polynom" version)) + (sha256 + (base32 + "1s4xxv5rvpigawknvq27v9vzvs83phfsj5h8mim2lmf5bj950nnk")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/polynom/") + (synopsis "Functions for univariate polynomial manipulations") + (description + "This package provides a collection of functions to implement a class for +univariate polynomial manipulations.") + (license license:gpl2))) + (define-public r-writexl (package (name "r-writexl") -- cgit v1.2.3 From dd954dd7436b47494c8708cefd0856bf6719ac68 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:38:39 +0200 Subject: gnu: Add r-gbrd. * gnu/packages/cran.scm (r-gbrd): 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 a142e9f1c7..64dba2c9de 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4535,6 +4535,27 @@ patterned after functions in the snow package.") univariate polynomial manipulations.") (license license:gpl2))) +(define-public r-gbrd + (package + (name "r-gbrd") + (version "0.4-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "gbRd" version)) + (sha256 + (base32 + "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82")))) + (properties `((upstream-name . "gbRd"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/gbRd/") + (synopsis "Utilities for processing Rd objects and files") + (description + "This package provides utilities for processing Rd objects and files. +Extract argument descriptions and other parts of the help pages of +functions.") + (license license:gpl2+))) + (define-public r-writexl (package (name "r-writexl") -- cgit v1.2.3 From 6a8469755cd63a2fd9deb617962bff22f8542485 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:38:51 +0200 Subject: gnu: Add r-rdpack. * gnu/packages/cran.scm (r-rdpack): 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 64dba2c9de..f09bdbd06f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4556,6 +4556,33 @@ Extract argument descriptions and other parts of the help pages of functions.") (license license:gpl2+))) +(define-public r-rdpack + (package + (name "r-rdpack") + (version "0.9-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rdpack" version)) + (sha256 + (base32 + "067w0w6kza0hkzcnx58danl83yfvl9yjacr47mnid2bg856gdd1b")))) + (properties `((upstream-name . "Rdpack"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bibtex" ,r-bibtex) + ("r-gbrd" ,r-gbrd))) + (home-page "https://github.com/GeoBosh/Rdpack") + (synopsis "Update and manipulate Rd documentation objects") + (description + "This package provides functions for manipulation of R documentation +objects, including functions @code{reprompt()} and @code{ereprompt()} for +updating Rd documentation for functions, methods and classes; it also includes +Rd macros for citations and import of references from bibtex files for use in +Rd files and roxygen2 comments, as well as many functions for manipulation of +references and Rd files.") + (license license:gpl2+))) + (define-public r-writexl (package (name "r-writexl") -- cgit v1.2.3 From 88e4ed55d68ffeaf67e5dad128f0e762e5814d26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:41:11 +0200 Subject: gnu: Add r-clipr. * gnu/packages/cran.scm (r-clipr): 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 f09bdbd06f..2082378aae 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -43,6 +43,25 @@ #:use-module (gnu packages tls) #:use-module (gnu packages web)) +(define-public r-clipr + (package + (name "r-clipr") + (version "0.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "clipr" version)) + (sha256 + (base32 + "061x84ildc7g1p91yw5iyj8lpqdf4hqv36as85lw8c6qv9ywbsqv")))) + (build-system r-build-system) + (home-page "https://github.com/mdlincoln/clipr") + (synopsis "Read and write from the system clipboard") + (description + "This package provides simple utility functions to read from and write to +the system clipboards.") + (license license:gpl3))) + (define-public r-tidyverse (package (name "r-tidyverse") -- cgit v1.2.3 From 65050163e01d40d197f57748dc82072026676445 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:42:00 +0200 Subject: gnu: r-chippeakanno: Update to 3.14.1. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7e993189d6..1ff86779e8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -363,14 +363,14 @@ expressed genes in DNA microarray experiments.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.14.0") + (version "3.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0")))) + "1cn1hfc3nvsf2n3563lkmvwjxfbiygx7f84zk683p89gy7zi1gyj")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ce0e762bf926bcd6f126466c3556a820833621ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:44:42 +0200 Subject: gnu: r-annotationforge: Update to 1.22.2. * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 05d516165e..6028311b3c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6371,14 +6371,14 @@ exploration of the results.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.22.0") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65")))) + "17kmy7nvpyyj6w5jyrjciw87rydmmmc8q6cnwqjv1j7li9bp09gr")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) -- cgit v1.2.3 From 3c0437561401986d90de358a8d5fae50d6593261 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:46:03 +0200 Subject: gnu: r-biocviews: Update to 1.48.3. * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6028311b3c..e900bd6194 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6957,13 +6957,13 @@ Bioconductor, CRAN, and Github.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.48.2") + (version "1.48.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "01yiafayl1m5704xdd2cn3zjc78rs10dqyz66lr3qkf6d8w66938")))) + "1rxvwikqivsgxjjcazlszy8xgz346lfh5rw4llxw6fz38fjgb0k5")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) -- cgit v1.2.3 From 5728d9c6c081b7a0eeb6d29ec221d4638f6dd083 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:46:20 +0200 Subject: gnu: r-iranges: Update to 2.14.11. * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e900bd6194..5aec3cc6ae 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7176,13 +7176,13 @@ utilities for sequence data management under the ACNUC system.") (define-public r-iranges (package (name "r-iranges") - (version "2.14.10") + (version "2.14.11") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6")))) + "0wz63hysspyjihqadg91dbvllc5a61zzjrsz0b9498lihqc6m1la")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 1adf4596a6d268c3d2a249d235569631f8df306f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:48:36 +0200 Subject: gnu: r-edger: Update to 3.22.3. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5aec3cc6ae..b6b6e7267c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7256,13 +7256,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.22.2") + (version "3.22.3") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3")))) + "0w3jv29n0kkaiig8dbbdqy2dkng8xfaihch82mj9ci5hphrx3nng")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 33a103a54393f4e8994b2cb46f6be7d8942cc42e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:51:48 +0200 Subject: gnu: r-variantannotation: Update to 1.26.1. * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b6b6e7267c..6efb6f1c1b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7284,13 +7284,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7")))) + "1r55ki951dj81qvy73knfcy69ik5vzkd56wnk3f6vvf9vngqb8jr")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs -- cgit v1.2.3 From 688cb0852706d1e2d0cc03c707a04098ab59b98b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:52:03 +0200 Subject: gnu: r-limma: Update to 3.36.3. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6efb6f1c1b..29558768c0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7322,13 +7322,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.36.1") + (version "3.36.3") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm")))) + "0iiifszr6hcqih6kszdsbkx3gacfg3d7v8hdx0lbjqnjqgqz7pwk")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") -- cgit v1.2.3 From 1d56c79f86cd0c776e76a1bece26622f56c28f12 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:52:53 +0200 Subject: gnu: r-genomicranges: Update to 1.32.6. * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 29558768c0..2b467145d0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7377,13 +7377,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.32.3") + (version "1.32.6") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni")))) + "0p58yk2i5gqvjlkx548mnrr49wvs0xfcl06l9rqj2hi6hkkbvnp3")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit v1.2.3 From a02340058c15a22cf8c942c96d0053b8e0881452 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:58:33 +0200 Subject: gnu: r-biocparallel: Update to 1.14.2. * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2b467145d0..9d55198f4f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7488,13 +7488,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.14.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "00qg1kg2l9qqpyjaw5q910cmf84vwfiw1fhsx3ig784gwinwgj6n")))) + "1llb5a62hn4yxpdgqdh2l7i5zd06mjkk8hagsna69cq65wv6iifm")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.2.3 From 3e61c2a8b1dfbc03f9506aaf10df57651728a7d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:58:44 +0200 Subject: gnu: r-rsamtools: Update to 1.32.3. * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9d55198f4f..c682399ace 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7539,13 +7539,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "1.32.0") + (version "1.32.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1s65y5wn4d0x8zsljg2kmhcl6r9884h95kr041j7hp49bmxg3an6")))) + "1hpjr22h33pf4fgv0sj83rqzv6l5l7s6fpmmqvchh45ikks1mnhq")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) -- cgit v1.2.3 From aea1b6fb8a9b48b35139e146faffaf27463091b8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:59:06 +0200 Subject: gnu: r-delayedarray: Update to 0.6.5. * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c682399ace..d9d70ea97b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7583,13 +7583,13 @@ files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.6.1") + (version "0.6.5") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0sjwszxdi0vkj2i2di5i46gh9chc660yr3gs5nk9qnqp77713zds")))) + "10b03zrnvz5isfh4z55hasya2m71lrfx10l5lm2sdmqs0gwkanrd")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) -- cgit v1.2.3 From f2e79823c697843afd880e79e7f810ad69411722 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:59:25 +0200 Subject: gnu: r-rtracklayer: Update to 1.40.6. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d9d70ea97b..3610f823dc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7678,13 +7678,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.40.3") + (version "1.40.6") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0kvsjdaypn1jnxbnsxpycildwdyxwnjkigfq8qm8mlyfc4ahdgy3")))) + "1wxxxlyps19dw3i0pw4mlm3kinnswsc35rgvlnbwvpnpjbca6w4l")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From ad2ed8d01fa3a5486072f0f484beb74129928796 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:59:44 +0200 Subject: gnu: r-genomicfeatures: Update to 1.32.2. * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3610f823dc..0631d59651 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7725,13 +7725,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.32.0") + (version "1.32.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1cqcl72q0k5wylw1brn4g4h7xzys1v06piry19cvp0gjcvm5sp7a")))) + "0kfyyg1ib8fkq2hxraal10z4bx3rg8figdskw4yhn1mbh6l42q5f")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.2.3 From 48b21f8b6b7fcd6d0857fc1ac75dddb52bbabdf4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:00:00 +0200 Subject: gnu: r-seqminer: Update to 6.1. * gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0631d59651..878f5723da 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9321,14 +9321,14 @@ unmodeled, or latent sources of noise.") (define-public r-seqminer (package (name "r-seqminer") - (version "6.0") + (version "6.1") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l")))) + "15yhg4vfc7jg1jnqb3371j00pgbmbyc9l1xx63hq1l3p34lazq2l")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From 4ee8c37cca305dd7c581a7bf0fcf82fa351104a8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:00:56 +0200 Subject: gnu: r-maldiquant: Update to 1.18. * gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 878f5723da..5b8a1a23b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9375,14 +9375,14 @@ trait.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.17") + (version "1.18") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z")))) + "18nl214xjsxkcpbg79jkmw0yznwm5szyh2qb84n7ip46mm779ha6")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/MALDIquant") -- cgit v1.2.3 From 07bd90ce90784eb6803c581a18d8b335ce49e1bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:01:19 +0200 Subject: gnu: r-msnbase: Update to 2.6.3. * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5b8a1a23b0..01603d2937 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9619,14 +9619,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.6.1") + (version "2.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0zrpx9r93q5ca2zdak5rs2m9sjm0wjdra1xfj3d3sx6p5gzfyg6n")))) + "15jhqg02ypmznc0wxksw56yij02csy678vqy531fdv86fsmypwa0")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6f6aef80e3def1ffa7c8e4b0f75b22bd2ececc74 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:20:56 +0200 Subject: gnu: r-seurat: Update to 2.3.4. * gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4. [source]: Remove snippet. [arguments]: Remove. [native-inputs]: Remove. [propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger, r-stringr, r-tclust, and rvgam; add r-httr. --- gnu/packages/bioinformatics.scm | 39 ++++----------------------------------- 1 file changed, 4 insertions(+), 35 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 01603d2937..c29122b0cf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9701,58 +9701,31 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.3.2") + (version "2.3.4") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1sjpy5rrpvlpm6hs7qy7qpglgbp7zrgfybcsalpmjb51rhxhgcg1")) - ;; Delete pre-built jar. - (snippet - '(begin (delete-file "inst/java/ModularityOptimizer.jar") - #t)))) + "0l8bv4i9nzz26mirnva10mq6pimibj24vk7vpvfypgn7xk4942hd")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'build-jar - (lambda* (#:key inputs #:allow-other-keys) - (let ((classesdir "tmp-classes")) - (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) - (mkdir classesdir) - (with-output-to-file "manifest" - (lambda _ - (display "Manifest-Version: 1.0 -Main-Class: ModularityOptimizer\n"))) - (and (zero? (apply system* `("javac" "-d" ,classesdir - ,@(find-files "java" "\\.java$")))) - (zero? (system* "jar" - "-cmf" "manifest" - "inst/java/ModularityOptimizer.jar" - "-C" classesdir "."))))))))) - (native-inputs - `(("jdk" ,icedtea "jdk"))) (propagated-inputs `(("r-ape" ,r-ape) - ("r-caret" ,r-caret) ("r-cluster" ,r-cluster) ("r-cowplot" ,r-cowplot) - ("r-diffusionmap" ,r-diffusionmap) ("r-dosnow" ,r-dosnow) ("r-dplyr" ,r-dplyr) ("r-dtw" ,r-dtw) ("r-fitdistrplus" ,r-fitdistrplus) - ("r-fnn" ,r-fnn) ("r-foreach" ,r-foreach) ("r-fpc" ,r-fpc) - ("r-gdata" ,r-gdata) ("r-ggplot2" ,r-ggplot2) ("r-ggridges" ,r-ggridges) ("r-gplots" ,r-gplots) ("r-hdf5r" ,r-hdf5r) ("r-hmisc" ,r-hmisc) + ("r-httr" ,r-httr) ("r-ica" ,r-ica) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) @@ -9765,7 +9738,6 @@ Main-Class: ModularityOptimizer\n"))) ("r-pbapply" ,r-pbapply) ("r-plotly" ,r-plotly) ("r-png" ,r-png) - ("r-ranger" ,r-ranger) ("r-rann" ,r-rann) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) @@ -9776,11 +9748,8 @@ Main-Class: ModularityOptimizer\n"))) ("r-rocr" ,r-rocr) ("r-rtsne" ,r-rtsne) ("r-sdmtools" ,r-sdmtools) - ("r-stringr" ,r-stringr) - ("r-tclust" ,r-tclust) ("r-tidyr" ,r-tidyr) - ("r-tsne" ,r-tsne) - ("r-vgam" ,r-vgam))) + ("r-tsne" ,r-tsne))) (home-page "http://www.satijalab.org/seurat") (synopsis "Seurat is an R toolkit for single cell genomics") (description -- cgit v1.2.3 From c273bcdfce1f1cac53990e6c26455fb6a749763f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:22:33 +0200 Subject: gnu: r-diffusionmap: Update to 1.1-0.1. * gnu/packages/graph.scm (r-diffusionmap): Update to 1.1-0.1. --- gnu/packages/graph.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index b393919e66..998e4ead46 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -130,14 +130,14 @@ more.") (define-public r-diffusionmap (package (name "r-diffusionmap") - (version "1.1-0") + (version "1.1-0.1") (source (origin (method url-fetch) (uri (cran-uri "diffusionMap" version)) (sha256 (base32 - "1l985q2hfc8ss5afajik4p25dx628yikvhdimz5s0pql800q2yv3")))) + "11l4kbciawvli5nlsi4qaf8afmgk5xgqiqpdyhvaqri5mx0zhk5j")))) (properties `((upstream-name . "diffusionMap"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From eb251fe524127e5490b26e86a4c826bb6c79003c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:22:44 +0200 Subject: gnu: r-igraph: Update to 1.2.2. * gnu/packages/graph.scm (r-igraph): Update to 1.2.2. --- gnu/packages/graph.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 998e4ead46..3b222d6ee8 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -98,14 +98,14 @@ more.") (define-public r-igraph (package (name "r-igraph") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "1hcr6b1lz030lgay1bz8y8sxaf2j93ds8n8gsqr6qhssz141hd2m")))) + "1bggm7b8v3bh7q2589w26qvd7sgs69m4qiij7d0rbm0ykkgxm8lx")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From 3c553046888943842d953012759aacde255c4e0c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:27:26 +0200 Subject: gnu: r-edaseq: Update to 2.14.1. * gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c29122b0cf..0860d85bab 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9822,14 +9822,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.14.0") + (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "1832pb3jkim4vrqzb8lajwx9r482bhww5n9nz3s6crvyamlp2dj0")))) + "0970w9d5ddqw1qxqqafdidkxh6hmcv9j5djwgnpz3fgl05kmysg8")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ff7c7d62f464d0a8d5e91ef058579ad03247d817 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:29:51 +0200 Subject: gnu: r-keggrest: Update to 1.20.1. * gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0860d85bab..eb7d2b840a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9949,14 +9949,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1349vidgl9m10l1rbrp3pkwwgi2xcbsw9h9z2xqbvg97lmqc4r8j")))) + "1ss0xd5570x570v01r6lp64rr1apjrzp0j62520pvm3g8knjhfvs")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 70daf9362b328079886ed7854e6afe4d96181323 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:30:16 +0200 Subject: gnu: r-biovizbase: Update to 1.28.2. * gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2. [propagated-inputs]: Add r-rlang. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eb7d2b840a..f65dad5f96 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10169,14 +10169,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.28.0") + (version "1.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "0lkiqdr3ics6hgv47lwkykcy761823bbkhffbn4ykyfzyqwl4p67")))) + "0wc45j3hfn01i44bkkxjj3n8b8xzbkkcdv35mrkzb1f9yprkf8gq")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -10193,6 +10193,7 @@ the fact that each of these packages implements a select methods.") ("r-hmisc" ,r-hmisc) ("r-iranges" ,r-iranges) ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) -- cgit v1.2.3 From 16527f1cbc8af73b1034ddce2edf9e2bce094564 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:31:06 +0200 Subject: gnu: r-ggbio: Update to 1.28.5. * gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5. [propagated-inputs]: Add r-rlang. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f65dad5f96..9882356a08 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10211,14 +10211,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.28.0") + (version "1.28.5") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0wszh3w8yia5zw758h837i1q35k99sn444y2hahcxqbdmmlbf7in")))) + "19s2v40fycwf44fl3lm791y635xzw67b30sq2g0qq4a6phjik42d")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10241,6 +10241,7 @@ effort and encourages consistency.") ("r-iranges" ,r-iranges) ("r-organismdbi" ,r-organismdbi) ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) -- cgit v1.2.3 From e69c07e61a870861f5c9d9f114e2783cba213934 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:32:25 +0200 Subject: gnu: r-hdf5array: Update to 1.8.1. * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9882356a08..53bf86180f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10696,14 +10696,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1l0276qxkhgdxsfck3jmi8jvnsr20g10gjki53g0mqa45wnhm3ck")))) + "1s44zgm9jg82bk4b8k3dh7xw7mxychlfm3grs8516mxnw91zpvy5")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8e44ff0c0de2ee752ccaf9189d882735d3185c65 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:37:02 +0200 Subject: gnu: r-scater: Update to 1.8.4. * gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 53bf86180f..687cb131d2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10842,13 +10842,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.8.0") + (version "1.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0bhpikgz3b9f510dawsay4zry9rlp8vjx5n6zvwbcpwrd94p3903")))) + "173lfpas2fqsp4xxsw01wkxd4496c5p8himw9b4r9z4npxkfyv16")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) -- cgit v1.2.3 From f0771741781ff75af42ea59027a592ac159bcf98 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:41:37 +0200 Subject: gnu: r-scran: Update to 1.8.4. * gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 687cb131d2..760b716408 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10886,14 +10886,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.8.2") + (version "1.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0nbn5x75gf9d0p18w7vpkbv30cpdqvp5bz8xvila0h7jla7xdyih")))) + "17vq9vb9ak7n4mcqpwnm9x3z91vmr7xnsgj8f45b8dbj7m0v126j")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) -- cgit v1.2.3 From 1ec1989f8007d0b90cc3b5ac379bb2f7133e299f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:42:01 +0200 Subject: gnu: r-httpuv: Update to 1.4.5. * gnu/packages/web.scm (r-httpuv): Update to 1.4.5. [native-inputs]: Add pkg-config. --- gnu/packages/web.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 0d27fa0054..918548513d 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3823,15 +3823,17 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.4.4.1") + (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "12kwq10xa8glrip7rai9xb4hnpysng00g2l0rw7swfzq5lk4z966")))) + "1ddpcarzf694h0gy5pdz7l5glqfv4hr9dmxb4vw7yqd0bga174gi")))) (build-system r-build-system) - (native-inputs `(("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-rcpp" ,r-rcpp) + ("pkg-config" ,pkg-config))) (propagated-inputs `(("r-bh" ,r-bh) ("r-later" ,r-later) -- cgit v1.2.3 From 4f8247b54b4bb95fc58b3c4f0c30d635909496e2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:46:33 +0200 Subject: gnu: Add r-pkgbuild. * gnu/packages/cran.scm (r-pkgbuild): 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 2082378aae..ae51844dab 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -499,6 +499,33 @@ print, summary, plot, update, etc. processes. Most of its code is based on the @code{psutil} Python package.") (license license:bsd-3))) +(define-public r-pkgbuild + (package + (name "r-pkgbuild") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "pkgbuild" version)) + (sha256 + (base32 + "10iz8057mixl9j73pq2cbp4ib6dadfsgi3fcsjjm7l3wwb9issd9")))) + (build-system r-build-system) + (propagated-inputs + `(("r-callr" ,r-callr) + ("r-crayon" ,r-crayon) + ("r-desc" ,r-desc) + ("r-r6" ,r-r6) + ("r-rprojroot" ,r-rprojroot) + ("r-withr" ,r-withr))) + (home-page "https://github.com/r-pkgs/pkgbuild") + (synopsis "Find tools needed to build R packages") + (description + "This package provides functions used to build R packages. It locates +compilers needed to build R packages on various platforms and ensures the PATH +is configured appropriately so R can use them.") + (license license:gpl3))) + (define-public r-rcpp (package (name "r-rcpp") -- cgit v1.2.3 From e362be8e899707fa85e7ae3102cbb5013d51bb69 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:46:49 +0200 Subject: gnu: Add r-pkgload. * gnu/packages/cran.scm (r-pkgload): 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 ae51844dab..9d736d4d6e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -526,6 +526,33 @@ compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use them.") (license license:gpl3))) +(define-public r-pkgload + (package + (name "r-pkgload") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "pkgload" version)) + (sha256 + (base32 + "1rjj229nq9fsl4ki4m75ybsavjgpqqhsr1zjzapwicsrxv6212px")))) + (build-system r-build-system) + (propagated-inputs + `(("r-desc" ,r-desc) + ("r-pkgbuild" ,r-pkgbuild) + ("r-rlang" ,r-rlang) + ("r-rprojroot" ,r-rprojroot) + ("r-rstudioapi" ,r-rstudioapi) + ("r-withr" ,r-withr))) + (home-page "https://github.com/r-lib/pkgload") + (synopsis "Simulate package installation and attach") + (description + "This package simulates the process of installing a package and then +attaching it. This is a key part of the @code{devtools} package as it allows +you to rapidly iterate while developing a package.") + (license license:gpl3))) + (define-public r-rcpp (package (name "r-rcpp") -- cgit v1.2.3 From 97c81cc174b31fe898263cf4e802e00e95f76ef3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:52:33 +0200 Subject: gnu: r-stringi: Update to 1.2.4. * gnu/packages/statistics.scm (r-stringi): Update to 1.2.4. --- 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 97246dc31d..1f03649fa5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -960,14 +960,14 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.2.3") + (version "1.2.4") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "1sgg4krw03qkz1n4dwiya0djggk7giwd0w21qlp0pfjqi0rxq6qx")))) + "1y46xab7g1lsjmilp4hbl7pjad6pcxp66hdj8wnfdg9518h0lmq1")))) (build-system r-build-system) (inputs `(("icu4c" ,icu4c))) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From 3bf390279d9fce490fcfbab21330a0009a4d178c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:52:53 +0200 Subject: gnu: r-scales: Update to 1.0.0. * gnu/packages/statistics.scm (r-scales): Update to 1.0.0. [propagated-inputs]: Remove r-dichromat and r-plyr. --- gnu/packages/statistics.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1f03649fa5..35f89f2dc5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1033,19 +1033,17 @@ using just two functions: melt and dcast (or acast).") (define-public r-scales (package (name "r-scales") - (version "0.5.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "scales" version)) (sha256 - (base32 "0zg9wfzmsdjxpbld0nzv7hcpq5r0wazqxmn7grvvif2agj0w1z6v")))) + (base32 "0353dkh3d7x78463c6ds80hcml59lrqwr8rlv82a8dnkxla4l7qc")))) (build-system r-build-system) (propagated-inputs - `(("r-dichromat" ,r-dichromat) - ("r-labeling" ,r-labeling) + `(("r-labeling" ,r-labeling) ("r-munsell" ,r-munsell) - ("r-plyr" ,r-plyr) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-r6" ,r-r6) -- cgit v1.2.3 From 2a96a093ec9a812bf7ccb6e095b3377df81d75aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:53:36 +0200 Subject: gnu: r-evaluate: Update to 0.11. * gnu/packages/statistics.scm (r-evaluate): Update to 0.11. --- 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 35f89f2dc5..09470fa0a0 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1249,13 +1249,13 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.10.1") + (version "0.11") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "070vvmnbdlp7sz2zhza7fhd2a6mlwiln8fn4hyzhsiizbn4n79y9")))) + "1k8vcd4vsgg0hf7kdz8rlqp1dx4ygvg35aj4n3ay50kdnpzhaj5h")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr))) -- cgit v1.2.3 From 3299bc1c5e43a146ba1ea380fc905b2c096f9174 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:53:49 +0200 Subject: gnu: r-yaml: Update to 2.2.0. * gnu/packages/statistics.scm (r-yaml): Update to 2.2.0. --- 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 09470fa0a0..b7118b672a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1354,13 +1354,13 @@ syntax that can be converted to XHTML or other formats.") (define-public r-yaml (package (name "r-yaml") - (version "2.1.19") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "yaml" version)) (sha256 (base32 - "04bzrnfgbpk0rhkvzwp3k3ip7jpq26bjxz71bx5mwxmcjdb07nz5")))) + "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/yaml/") (synopsis "Methods to convert R data to YAML and back") -- cgit v1.2.3 From 6b02569f1db9a3943305afcdea3f5970f80ecf74 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:54:02 +0200 Subject: gnu: r-dbplyr: Update to 1.2.2. * gnu/packages/statistics.scm (r-dbplyr): Update to 1.2.2. --- 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 b7118b672a..ac0d5d613c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1654,14 +1654,14 @@ database.") (define-public r-dbplyr (package (name "r-dbplyr") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "dbplyr" version)) (sha256 (base32 - "1nwrls9c3kc9q7405jp6b9sh23642sz13yw55iikgw134shffj5k")))) + "0j5w6a1qim972kv4vmvinp3j50yr4idmm9cd3w7y3zsz0nq0nhcx")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit v1.2.3 From 7f38b31ecbeab97f3efdc633504c4caa1a3a0621 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:54:19 +0200 Subject: gnu: r-xtable: Update to 1.8-3. * gnu/packages/statistics.scm (r-xtable): Update to 1.8-3. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ac0d5d613c..88b9ee6037 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1787,17 +1787,17 @@ and fast file reading.") (define-public r-xtable (package (name "r-xtable") - (version "1.8-2") + (version "1.8-3") (source (origin (method url-fetch) (uri (cran-uri "xtable" version)) (sha256 (base32 - "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn")))) + "09f311gq9g7dzf8jdvcx72j11xb7p00jlg066jjbpa6pz3zv1cjk")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "http://xtable.r-forge.r-project.org/") (synopsis "Export R tables to LaTeX or HTML") (description -- cgit v1.2.3 From 9b7e8df85bc8f06a662f0a9631231bd56939cfb2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:54:35 +0200 Subject: gnu: r-ade4: Update to 1.7-13. * gnu/packages/statistics.scm (r-ade4): Update to 1.7-13. --- 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 88b9ee6037..c74e198449 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1934,14 +1934,14 @@ chain.") (define-public r-ade4 (package (name "r-ade4") - (version "1.7-11") + (version "1.7-13") (source (origin (method url-fetch) (uri (cran-uri "ade4" version)) (sha256 (base32 - "0wm54wcpn87rdh6vyw04cr8vgba899y6jsl61f22bmlvx6d7kkac")))) + "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) -- cgit v1.2.3 From 2848c52c5ec537e9d4ee23bedd6658c610ff02fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:54:52 +0200 Subject: gnu: r-roxygen2: Update to 6.1.0. * gnu/packages/statistics.scm (r-roxygen2): Update to 6.1.0. [propagated-inputs]: Add r-pkgload and r-purrr. [native-inputs]: Add r-knitr. --- gnu/packages/statistics.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c74e198449..43d0197395 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2235,24 +2235,28 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "6.0.1") + (version "6.1.0") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "0xpzziminf225kjwhyl51kgkzhplyzhk5farhf5s822krl2xqbfj")))) + "0ji9k4s1bvfbl8wimfqj1lqr33h1claaz30vb5pgksxyg77j5xaa")))) (build-system r-build-system) (propagated-inputs `(("r-brew" ,r-brew) ("r-commonmark" ,r-commonmark) ("r-desc" ,r-desc) ("r-digest" ,r-digest) + ("r-pkgload" ,r-pkgload) + ("r-purrr" ,r-purrr) ("r-r6" ,r-r6) ("r-rcpp" ,r-rcpp) ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/klutometis/roxygen") (synopsis "In-source documentation system for R") (description -- cgit v1.2.3 From 19cb93be55e4cffab4b48542835d9b18ef74d949 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:58:00 +0200 Subject: gnu: r-git2r: Update to 0.23.0. * gnu/packages/statistics.scm (r-git2r): Update to 0.23.0. [native-inputs]: Add pkg-config. --- gnu/packages/statistics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 43d0197395..164e0b5851 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2322,13 +2322,13 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.21.0") + (version "0.23.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "11xgddmxzh9cy85k8fb90il43qswpvryz0h9r0j1gbclfg2f9004")))) + "01250jz255fnyy2ap90nskvzhd8nhlmbhwgpvb43mk1fax077lrz")))) (build-system r-build-system) ;; This R package contains modified sources of libgit2. This modified ;; version of libgit2 is built as the package is built. Hence libgit2 is @@ -2337,6 +2337,8 @@ functions make it easy to control additional request components.") `(("libssh2" ,libssh2) ("openssl" ,openssl) ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "https://github.com/ropensci/git2r") (synopsis "Access Git repositories with R") (description -- cgit v1.2.3 From 41f6685388da9e2258ababbdb5e16be56993e949 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:58:39 +0200 Subject: gnu: r-rcpparmadillo: Update to 0.9.100.5.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.100.5.0. --- 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 164e0b5851..2e8bfb33fa 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2518,13 +2518,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.8.500.0") + (version "0.9.100.5.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1sh36dx6inmb56m40nigy94gxlgjva816qnlmjwg7y2bdvqj8vsi")))) + "1iyjqhfjip1nxrkllzh7r1m01jjnx7cahqkf3s557w34p987f2l1")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From 2aafa73a94daa2ea0399ba0873b87fdfb9d03ff0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:59:01 +0200 Subject: gnu: r-xml: Update to 3.98-1.16. * gnu/packages/statistics.scm (r-xml): Update to 3.98-1.16. --- 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 2e8bfb33fa..f02c40b43a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2803,13 +2803,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.98-1.11") + (version "3.98-1.16") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "18izvlg2x9mzr6yb3yf02ghwbyn00frki3av4lpc44r22m4djnsh")))) + "0nl1kk354r8snhj6p9mc74m7awvqc6akmd4y3a46y78yv3g15njp")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) -- cgit v1.2.3 From e926159eb3fd006c6c688729e03043741a456bf9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:59:24 +0200 Subject: gnu: r-e1071: Update to 1.7-0. * gnu/packages/statistics.scm (r-e1071): Update to 1.7-0. --- 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 f02c40b43a..0bdf0783d0 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3285,14 +3285,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") (define-public r-e1071 (package (name "r-e1071") - (version "1.6-8") + (version "1.7-0") (source (origin (method url-fetch) (uri (cran-uri "e1071" version)) (sha256 (base32 - "08n6i26nfckjpxjkzi8phhanc3ahsrirkv5rz38y2jcv7ds031pn")))) + "0fk4pw67cw1663d0n9rf1qfdqzz8k5nqkjgp3hi5jr422qp9lsck")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class))) -- cgit v1.2.3 From eefa7c7f3dc48a144e39d9167d3befa74f4f8645 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 14:59:45 +0200 Subject: gnu: r-r-utils: Update to 2.7.0. * gnu/packages/statistics.scm (r-r-utils): Update to 2.7.0. --- 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 0bdf0783d0..9d03d5df1f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3463,13 +3463,13 @@ maintenance for package developers.") (define-public r-r-utils (package (name "r-r-utils") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) (uri (cran-uri "R.utils" version)) (sha256 (base32 - "03j7hrs03kyj9qrjxyp5kqv4lpqqpk6xwbkzx6j15d8928yrjr2x")))) + "0cxhn14a57x4gcyrwpfz1d6dw4xh0jcpqkb33hx8imnr340blh7n")))) (properties `((upstream-name . "R.utils"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e2a2c3378ecba09fc94ad2114c3e21df3460050e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 15:00:00 +0200 Subject: gnu: r-r-rsp: Update to 0.43.0. * gnu/packages/statistics.scm (r-r-rsp): Update to 0.43.0. --- 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 9d03d5df1f..4b1001a0cd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3511,13 +3511,13 @@ persistent (on the file system).") (define-public r-r-rsp (package (name "r-r-rsp") - (version "0.42.0") + (version "0.43.0") (source (origin (method url-fetch) (uri (cran-uri "R.rsp" version)) (sha256 (base32 - "1zcq0hzi0j7fvj2rs796a1i120wbr0387vck17rrd644awwbsbm0")))) + "0ax6781kfylx0acz0i3sqnpkxmrq73x29wwfic59ng7vj0ws0gyd")))) (properties `((upstream-name . "R.rsp"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 195eec737c13a871c39f9ebfeb3641a5e7b9d583 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 15:00:16 +0200 Subject: gnu: r-matrixstats: Update to 0.54.0. * gnu/packages/statistics.scm (r-matrixstats): Update to 0.54.0. --- 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 4b1001a0cd..a5c44b485f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3562,13 +3562,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.53.1") + (version "0.54.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "0bkiz5fm09d3512mfr2ymj9qsb1b8aic5l5m6fkaf5j7nsgvqw6z")))) + "0vx00ldsg2zvdrjn49jxczk2c9iaabgvzgpdka5j02ihh7hv83cg")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From 88cb7aa9e7d18db3c7266424f6efc356a575c0f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 15:00:41 +0200 Subject: gnu: r-plotly: Update to 4.8.0. * gnu/packages/statistics.scm (r-plotly): Update to 4.8.0. [propagated-inputs]: Add r-promises and r-rlang. --- gnu/packages/statistics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a5c44b485f..68255ccf3a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3743,13 +3743,13 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.7.1") + (version "4.8.0") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "0wj9lw7w28z8w9ip9vadv6sydjhqyg65kfiai9m3bndzz50b1m3w")))) + "19p8pa03q9mw5vaan7r56xgd13d90ssiz0flbrkvpfrir2105ybq")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -3765,8 +3765,10 @@ features present in other programming languages.") ("r-jsonlite" ,r-jsonlite) ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) + ("r-promises" ,r-promises) ("r-purrr" ,r-purrr) ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) -- cgit v1.2.3 From 5dbe7aa92026ef7143d36036570e7e027ab85b64 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 15:01:09 +0200 Subject: gnu: r-googlesheets: Update to 0.3.0. * gnu/packages/statistics.scm (r-googlesheets): Update to 0.3.0. [propagated-inputs]: Add r-tibble. --- gnu/packages/statistics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 68255ccf3a..dd7494db49 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3850,14 +3850,14 @@ character vector.") (define-public r-googlesheets (package (name "r-googlesheets") - (version "0.2.2") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "googlesheets" version)) (sha256 (base32 - "18q0xmxn09b52rmky7gr5flp0awndcnsgb7zcvkzvkrkvmwad52b")))) + "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8")))) (build-system r-build-system) (propagated-inputs `(("r-cellranger" ,r-cellranger) @@ -3867,6 +3867,7 @@ character vector.") ("r-purrr" ,r-purrr) ("r-readr" ,r-readr) ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-xml2" ,r-xml2))) (home-page "https://github.com/jennybc/googlesheets") -- cgit v1.2.3 From c183fa26881d363c2c078dad534c9098e05456cd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 15:12:31 +0200 Subject: gnu: Add r-officer. * gnu/packages/cran.scm (r-officer): 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 9d736d4d6e..a7a42573ae 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4656,6 +4656,41 @@ Rd files and roxygen2 comments, as well as many functions for manipulation of references and Rd files.") (license license:gpl2+))) +(define-public r-officer + (package + (name "r-officer") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "officer" version)) + (sha256 + (base32 + "14b6ii9h3fi5g8ja929mfhxps9r7x78flqjdy437y9aygkhmiz2i")))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-digest" ,r-digest) + ("r-htmltools" ,r-htmltools) + ("r-magrittr" ,r-magrittr) + ("r-r6" ,r-r6) + ("r-rcpp" ,r-rcpp) + ("r-uuid" ,r-uuid) + ("r-xml2" ,r-xml2) + ("r-zip" ,r-zip))) + (home-page "https://davidgohel.github.io/officer") + (synopsis "Manipulation of Word and PowerPoint documents") + (description + "This package provides tools to access and manipulate Word and PowerPoint +documents from R. The package focuses on tabular and graphical reporting from +R; it also provides two functions that let users get document content into +data objects. A set of functions lets add and remove images, tables and +paragraphs of text in new or existing documents. When working with PowerPoint +presentations, slides can be added or removed; shapes inside slides can also +be added or removed. When working with Word documents, a cursor can be used +to help insert or delete content at a specific location in the document.") + (license license:gpl3))) + (define-public r-writexl (package (name "r-writexl") -- cgit v1.2.3 From bfee9ce88f3c6bd49a1dfc003128d1cb3b7aa421 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 15:12:47 +0200 Subject: gnu: Add r-snakecase. * gnu/packages/cran.scm (r-snakecase): 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 a7a42573ae..e26deabd6e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4691,6 +4691,28 @@ be added or removed. When working with Word documents, a cursor can be used to help insert or delete content at a specific location in the document.") (license license:gpl3))) +(define-public r-snakecase + (package + (name "r-snakecase") + (version "0.9.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "snakecase" version)) + (sha256 + (base32 + "1g6xai53dl24ws0mwhqrkcv583ziaq505cv3z8v5dhjgy98kilyj")))) + (build-system r-build-system) + (propagated-inputs + `(("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/Tazinho/snakecase") + (synopsis "Convert strings into any case") + (description + "This package provides a consistent, flexible and easy to use tool to +parse and convert strings into cases like snake or camel among others.") + (license license:gpl3))) + (define-public r-writexl (package (name "r-writexl") -- cgit v1.2.3 From de059e4bd3dce2937a4ac7853731f7f65e950475 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 15:12:57 +0200 Subject: gnu: Add r-prediction. * gnu/packages/cran.scm (r-prediction): 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 e26deabd6e..64156f5aa6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4713,6 +4713,30 @@ to help insert or delete content at a specific location in the document.") parse and convert strings into cases like snake or camel among others.") (license license:gpl3))) +(define-public r-prediction + (package + (name "r-prediction") + (version "0.3.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "prediction" version)) + (sha256 + (base32 + "19d7312f5lkqfglfvlgssnvyw7gl161s0xradcry44r1i6qp05j1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table))) + (home-page "https://github.com/leeper/prediction") + (synopsis "Tidy, type-safe prediction methods") + (description + "This package provides the @code{prediction()} function, a type-safe +alternative to @code{predict()} that always returns a data frame. The package +currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"}) +from the @code{stats} package, as well as numerous other model classes from +other add-on packages.") + (license license:expat))) + (define-public r-writexl (package (name "r-writexl") -- cgit v1.2.3 From cfc06314334933f0045e1851449722a612e28f5b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 15:14:17 +0200 Subject: gnu: Add r-sjlabelled. * gnu/packages/cran.scm (r-sjlabelled): New variable. --- gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 64156f5aa6..bf942f03f6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4737,6 +4737,39 @@ from the @code{stats} package, as well as numerous other model classes from other add-on packages.") (license license:expat))) +(define-public r-sjlabelled + (package + (name "r-sjlabelled") + (version "1.0.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "sjlabelled" version)) + (sha256 + (base32 + "0xizj7mrhnbn8kwjgm076si9w68a7lgrx4vj1sbqmv9jx055h8wv")))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-haven" ,r-haven) + ("r-magrittr" ,r-magrittr) + ("r-prediction" ,r-prediction) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-snakecase" ,r-snakecase) + ("r-tibble" ,r-tibble) + ("r-tidyselect" ,r-tidyselect))) + (home-page "https://github.com/strengejacke/sjlabelled") + (synopsis "Labelled data utility functions") + (description + "This package provides a collection of functions dealing with labelled +data, like reading and writing data between R and other statistical software +packages. This includes easy ways to get, set or change value and variable +label attributes, to convert labelled vectors into factors or numeric (and +vice versa), or to deal with multiple declared missing values.") + (license license:gpl3))) + (define-public r-writexl (package (name "r-writexl") -- cgit v1.2.3 From 1f560b9cdb820569e796caa9949557d9a18f8549 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 15:14:33 +0200 Subject: gnu: Add r-sjmisc. * gnu/packages/cran.scm (r-sjmisc): New variable. --- gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bf942f03f6..65474d8f8b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4770,6 +4770,43 @@ label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.") (license license:gpl3))) +(define-public r-sjmisc + (package + (name "r-sjmisc") + (version "2.7.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "sjmisc" version)) + (sha256 + (base32 + "11cy09k1d2y5wwqvafqxr01hzk4x68ji2pqlwj7fnpw27i3ap4q4")))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-crayon" ,r-crayon) + ("r-dplyr" ,r-dplyr) + ("r-haven" ,r-haven) + ("r-magrittr" ,r-magrittr) + ("r-pillar" ,r-pillar) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-sjlabelled" ,r-sjlabelled) + ("r-stringdist" ,r-stringdist) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect))) + (home-page "https://github.com/strengejacke/sjmisc") + (synopsis "Data and variable transformation functions") + (description + "This package is a collection of miscellaneous utility functions, +supporting data transformation tasks like recoding, dichotomizing or grouping +variables, setting and replacing missing values. The data transformation +functions also support labelled data, and all integrate seamlessly into a +tidyverse workflow.") + (license license:gpl3))) + (define-public r-writexl (package (name "r-writexl") -- cgit v1.2.3 From aaed237d1bcae69bd3c65f06633a8a4c88f2e382 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 15:14:45 +0200 Subject: gnu: Add r-nortest. * gnu/packages/cran.scm (r-nortest): 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 65474d8f8b..4d6bd269b1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4807,6 +4807,25 @@ functions also support labelled data, and all integrate seamlessly into a tidyverse workflow.") (license license:gpl3))) +(define-public r-nortest + (package + (name "r-nortest") + (version "1.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "nortest" version)) + (sha256 + (base32 + "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/nortest/") + (synopsis "Tests for normality") + (description + "This package provides five omnibus tests for testing the composite +hypothesis of normality.") + (license license:gpl2+))) + (define-public r-writexl (package (name "r-writexl") -- cgit v1.2.3 From 0fd7d59dc387eea437482f7584d03c5a20399faa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 15:14:56 +0200 Subject: gnu: Add r-moonbook. * gnu/packages/cran.scm (r-moonbook): 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 4d6bd269b1..1025ff093a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4826,6 +4826,35 @@ tidyverse workflow.") hypothesis of normality.") (license license:gpl2+))) +(define-public r-moonbook + (package + (name "r-moonbook") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "moonBook" version)) + (sha256 + (base32 + "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6")))) + (properties `((upstream-name . "moonBook"))) + (build-system r-build-system) + (propagated-inputs + `(("r-magrittr" ,r-magrittr) + ("r-nortest" ,r-nortest) + ("r-purrr" ,r-purrr) + ("r-sjmisc" ,r-sjmisc) + ("r-stringr" ,r-stringr) + ("r-survival" ,r-survival))) + (home-page "https://github.com/cardiomoon/moonBook") + (synopsis "Functions and datasets for the book by Keon-Woong Moon") + (description + "This package provides several analysis-related functions for the book +entitled \"R statistics and graph for medical articles\" (written in Korean), +version 1, by Keon-Woong Moon with Korean demographic data with several plot +functions.") + (license license:gpl2))) + (define-public r-writexl (package (name "r-writexl") -- cgit v1.2.3 From 90708323a13c94bf36a56735da9c21a2203e9fde Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 18:39:43 +0200 Subject: Revert "gnu: ghc-base-compat: Update to 0.10.4." This reverts commit 0fa2c552fcd5176b0484b77b7f7c94d82d46415e. We may not upgrade base-compat at this point because we haven't upgraded the default GHC yet. --- gnu/packages/haskell.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index b8ae26346e..31a0d6d7ee 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -4231,7 +4231,7 @@ system.") (define-public ghc-base-compat (package (name "ghc-base-compat") - (version "0.10.4") + (version "0.9.3") (source (origin (method url-fetch) @@ -4241,7 +4241,7 @@ system.") ".tar.gz")) (sha256 (base32 - "0ksp990gxs731mq19rzbxrbs43nazfljjc8krlx5bjqblw3kfs8d")))) + "0452l6zf6fjhy4kxqwv6i6hhg6yfx4wcg450k3axpyj30l7jnq3x")))) (build-system haskell-build-system) (native-inputs `(("ghc-quickcheck" ,ghc-quickcheck) -- cgit v1.2.3 From f9f4578ba0c4b5b22cdac86e8183dc542d66cc85 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 18:43:11 +0200 Subject: Revert "gnu: ghc-tasty: Update to 1.1.0.3." This reverts commit 3ad6b8909025a8f4d3e1f1f5ea16bcd0cace557c. --- gnu/packages/haskell-check.scm | 7 +++---- gnu/packages/haskell.scm | 27 +++------------------------ 2 files changed, 6 insertions(+), 28 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm index 65333f8269..31407ca259 100644 --- a/gnu/packages/haskell-check.scm +++ b/gnu/packages/haskell-check.scm @@ -183,7 +183,7 @@ timer functions of different operating systems via a unified API.") (define-public ghc-tasty (package (name "ghc-tasty") - (version "1.1.0.3") + (version "0.11.0.4") (source (origin (method url-fetch) @@ -193,7 +193,7 @@ timer functions of different operating systems via a unified API.") ".tar.gz")) (sha256 (base32 - "14riid753hjqr6lca1kgxpnvq0wykf0k3qc5jpag42hh8bszav22")))) + "05pxjzgbgjdn7477xry0ssjrnmnsydqiq6nm6ck8n2da1baliqp0")))) (build-system haskell-build-system) (inputs `(("ghc-stm" ,ghc-stm) @@ -205,8 +205,7 @@ timer functions of different operating systems via a unified API.") ("ghc-unbounded-delays" ,ghc-unbounded-delays) ("ghc-async" ,ghc-async) ("ghc-ansi-terminal" ,ghc-ansi-terminal) - ("ghc-clock-bootstrap" ,ghc-clock-bootstrap) - ("ghc-wcwidth" ,ghc-wcwidth))) + ("ghc-clock-bootstrap" ,ghc-clock-bootstrap))) (home-page "http://documentup.com/feuerbach/tasty") (synopsis "Modern and extensible testing framework") (description "Tasty is a modern testing framework for Haskell. It lets diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 31a0d6d7ee..eb629cf138 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -2870,7 +2870,7 @@ with slicing and Clang-style colored diagnostics.") ;; re-enable them. (arguments `(#:tests? #f)) (inputs - `(("ghc-scientific-bootstrap" ,ghc-scientific-bootstrap) + `(("ghc-scientific" ,ghc-scientific) ("ghc-text" ,ghc-text))) (native-inputs `(("ghc-tasty" ,ghc-tasty) @@ -2885,13 +2885,6 @@ aimed particularly at dealing efficiently with network protocols and complicated text/binary file formats.") (license license:bsd-3))) -(define ghc-attoparsec-bootstrap - (package - (inherit ghc-attoparsec) - (name "ghc-attoparsec-bootstrap") - (arguments '(#:tests? #f)) - (native-inputs '()))) - (define-public ghc-zip-archive (package (name "ghc-zip-archive") @@ -5221,13 +5214,6 @@ occurrences of a substring (the first in case of overlaps) with another.") in migrated modules.") (license license:expat))) -(define ghc-integer-logarithms-bootstrap - (package - (inherit ghc-integer-logarithms) - (name "ghc-integer-logarithms-bootstrap") - (arguments `(#:tests? #f)) - (native-inputs '()))) - (define-public ghc-scientific (package (name "ghc-scientific") @@ -5244,7 +5230,7 @@ in migrated modules.") "03ql2f0ac8bsl524idy9xxa3kxisb2sj3avflzw580j5hzy0m397")))) (build-system haskell-build-system) (inputs - `(("ghc-integer-logarithms-bootstrap" ,ghc-integer-logarithms-bootstrap) + `(("ghc-integer-logarithms" ,ghc-integer-logarithms) ("ghc-text" ,ghc-text) ("ghc-hashable" ,ghc-hashable) ("ghc-primitive" ,ghc-primitive))) @@ -5265,13 +5251,6 @@ and space efficient. They are represented using notation}.") (license license:bsd-3))) -(define ghc-scientific-bootstrap - (package - (inherit ghc-scientific) - (name "ghc-scientific-bootstrap") - (arguments `(#:tests? #f)) - (native-inputs '()))) - (define-public ghc-boxes (package (name "ghc-boxes") @@ -10195,7 +10174,7 @@ backends provided by the @code{Cairo} and @code{Diagrams} libraries.") (inputs `(("ghc-setlocale" ,ghc-setlocale) ("ghc-utf8-string" ,ghc-utf8-string) - ("ghc-attoparsec-bootstrap" ,ghc-attoparsec-bootstrap))) + ("ghc-attoparsec" ,ghc-attoparsec))) (home-page "https://github.com/solidsnack/wcwidth/") (synopsis "Haskell bindings to wcwidth") (description "This package provides Haskell bindings to your system's -- cgit v1.2.3 From 78f2c08c0b780dd2fe72548b901df7eb887da7f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:22:20 +0200 Subject: gnu: r-rmarkdown: Use latest version of Pandoc. * gnu/packages/statistics.scm (r-rmarkdown)[propagated-inputs]: Replace "ghc-pandoc-1" with "ghc-pandoc". --- gnu/packages/statistics.scm | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index dd7494db49..69c72541a7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2633,11 +2633,7 @@ certain criterion, e.g., it contains a certain regular file.") ("r-stringr" ,r-stringr) ("r-tinytex" ,r-tinytex) ("r-yaml" ,r-yaml) - ;; rmarkdown works with the 2.x release of Pandoc, but with degraded - ;; functionality. For example, tabbed plots do not currently work with - ;; Pandoc 2. The authors of rmarkdown recommend the use of Pandoc 1 - ;; for the time being. - ("ghc-pandoc" ,ghc-pandoc-1))) + ("ghc-pandoc" ,ghc-pandoc))) (home-page "http://rmarkdown.rstudio.com") (synopsis "Convert R Markdown documents into a variety of formats") (description -- cgit v1.2.3 From 589bd1c4260a429536d3a69a4b7c0a7bcd2e4357 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:23:51 +0200 Subject: gnu: Add r-flextable. * gnu/packages/cran.scm (r-flextable): New variable. --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1025ff093a..ea3f1c4981 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4855,6 +4855,37 @@ version 1, by Keon-Woong Moon with Korean demographic data with several plot functions.") (license license:gpl2))) +(define-public r-flextable + (package + (name "r-flextable") + (version "0.4.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "flextable" version)) + (sha256 + (base32 + "09j2y0z7rkc0w1cl9pp1cpk6fnzzfr6245mxa3ca42z9k2cy2jfl")))) + (build-system r-build-system) + (propagated-inputs + `(("r-gdtools" ,r-gdtools) + ("r-htmltools" ,r-htmltools) + ("r-knitr" ,r-knitr) + ("r-officer" ,r-officer) + ("r-r6" ,r-r6) + ("r-rmarkdown" ,r-rmarkdown) + ("r-stringr" ,r-stringr) + ("r-xml2" ,r-xml2))) + (home-page "https://davidgohel.github.io/flextable") + (synopsis "Functions for tabular reporting") + (description + "This package provides tools to create pretty tables for HTML documents +and other formats. Functions are provided to let users create tables, modify +and format their content. It extends the @code{officer} package and can be +used within R markdown documents when rendering to HTML and to Word +documents.") + (license license:gpl3))) + (define-public r-writexl (package (name "r-writexl") -- cgit v1.2.3 From cb96d81be47ac5e553dc7b14ce64823a9b6f99a5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:24:12 +0200 Subject: gnu: r-doby: Update to 4.6-2. * gnu/packages/cran.scm (r-doby): Update to 4.6-2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ea3f1c4981..56b6462fae 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5079,14 +5079,14 @@ Group (Non-)Overlap considerations.") (define-public r-doby (package (name "r-doby") - (version "4.6-1") + (version "4.6-2") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "1y02awzid23bxz8hx6j8pxd6i7jaq8pdw3k60rag8y6m69incrw5")))) + "02vbv9nfgywg6lsiialkmfnax5z3rkyb9nr8j9l2cp8xi6ml95mb")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2cdd9d4f832bf11d9b419e15fdfcdcf49ec99520 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:24:41 +0200 Subject: gnu: r-reticulate: Update to 1.10. * gnu/packages/cran.scm (r-reticulate): Update to 1.10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 56b6462fae..9033fac0a6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4236,14 +4236,14 @@ obtain a better initial configuration in non-metric MDS.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.8") + (version "1.10") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "0zwb4ikf021nw7axdn7qlr6bq4xkph3anfy314idkspy1iil4nmr")))) + "0bz3lxbisjwn6cv23090zivpy0bxcncr82g5qja13l37i8xnvqsq")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs -- cgit v1.2.3 From e3c1e93e35f25fc746476226e3c7b8c633eb2b8e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:25:04 +0200 Subject: gnu: r-reprex: Update to 0.2.0. * gnu/packages/cran.scm (r-reprex): Update to 0.2.0. [propagated-inputs]: Add r-clipr, r-rlang, and r-withr. --- gnu/packages/cran.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9033fac0a6..2c6de3ddd2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -162,20 +162,23 @@ package is a port of the Python package @code{cssselect}.") (define-public r-reprex (package (name "r-reprex") - (version "0.1.2") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 - "105d9vsmqfilgpw8psfb2wyiz1hvcycvh4cqhb3ab37lm3rcavvs")))) + "1l44pxjiz3g0jkk3v6rg5jps3llihfiah0qyv40s0bxvxa6gm8v9")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) + ("r-clipr" ,r-clipr) ("r-knitr" ,r-knitr) + ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) - ("r-whisker" ,r-whisker))) + ("r-whisker" ,r-whisker) + ("r-withr" ,r-withr))) (home-page "https://github.com/tidyverse/reprex") (synopsis "Prepare reproducible R code examples for sharing") (description -- cgit v1.2.3 From b72de5b3f674e3b360f1d7c5032d9fb47e0992d7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:25:42 +0200 Subject: gnu: r-callr: Update to 3.0.0. * gnu/packages/cran.scm (r-callr): Update to 3.0.0. [propagated-inputs]: Add r-base64enc. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2c6de3ddd2..5c3c7ed821 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -193,17 +193,18 @@ such as copy/paste from an R session.") (define-public r-callr (package (name "r-callr") - (version "2.0.4") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "1053qqq632z94pqq2v5dynjpgyv1b1c8zvidmcllw7zn8zha8gqf")))) + "1rxbxy6kn7dj90z9hpppr9cnpvnxzknba2dwrdp0lrk5dh462qz3")))) (build-system r-build-system) (propagated-inputs - `(("r-r6" ,r-r6) + `(("r-base64enc" ,r-base64enc) + ("r-r6" ,r-r6) ("r-processx" ,r-processx))) (home-page "https://github.com/r-lib/callr#readme") (synopsis "Call R from R") -- cgit v1.2.3 From b00e8ae77105d8fe398f5b9d47812844aa21b5dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:26:04 +0200 Subject: gnu: r-glue: Update to 1.3.0. * gnu/packages/cran.scm (r-glue): Update to 1.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5c3c7ed821..6ef31e09dd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -392,14 +392,14 @@ colors are provided.") (define-public r-glue (package (name "r-glue") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 - "0vi9y8ix95g6hjqdz9c9y4119apbdjcypdv0ag8cl6vaxqs5n9qr")))) + "1vhw5497lpfr4m8lcx9bs0fgdp4ax0sycrk6n8yksp33qd25m7kq")))) (build-system r-build-system) (home-page "https://github.com/tidyverse/glue") (synopsis "Interpreted string literals") -- cgit v1.2.3 From c73752cac5e74691d9f28c3c8c29a2fbb8291f4c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:26:18 +0200 Subject: gnu: r-pls: Update to 2.7-0. * gnu/packages/cran.scm (r-pls): Update to 2.7-0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6ef31e09dd..c6f4f73f53 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -453,14 +453,14 @@ error stream.") (define-public r-pls (package (name "r-pls") - (version "2.6-0") + (version "2.7-0") (source (origin (method url-fetch) (uri (cran-uri "pls" version)) (sha256 (base32 - "15j59p5x0rkdrk7iqzkipsy50rsyjl31w8zxc4w3v1j5gzxhi1rx")))) + "0xaqqgmdvfh7g7v1m4bcwjqzph68b9cq3bn4kjisfsadl54i5p2x")))) (build-system r-build-system) (home-page "http://mevik.net/work/software/pls.html") (synopsis "Partial Least Squares and Principal Component Regression") -- cgit v1.2.3 From 2d2b95d15141f55f747b785ca0094aeaf3001268 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:26:33 +0200 Subject: gnu: r-ipred: Update to 0.9-7. * gnu/packages/cran.scm (r-ipred): Update to 0.9-7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c6f4f73f53..b2768cc403 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1755,14 +1755,14 @@ provided.") (define-public r-ipred (package (name "r-ipred") - (version "0.9-6") + (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 - "1vrw1pqcpnc04x1r2h9grdfm6bivs358sww5gg90jwlvxcw69lxq")))) + "0q53cqs46501wsd4cmfsmr78l8nv1hkbamk9m0ns5qy02df5r254")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) -- cgit v1.2.3 From 45c156bf812e227b07e94b0420d41ed57ae10220 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:26:58 +0200 Subject: gnu: r-broom: Update to 0.5.0. * gnu/packages/cran.scm (r-broom): Update to 0.5.0. [propagated-inputs]: Add r-backports, r-dplyr, r-purrr, and r-tibble; remove r-plyr and r-psych. --- gnu/packages/cran.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b2768cc403..4cf7d6295e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1816,22 +1816,23 @@ created using basic graphics.") (define-public r-broom (package (name "r-broom") - (version "0.4.5") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1mrrqqw1bmjf2v88ziqwb5y86g29h0a3rsx2jpw0hrzrzb8i5kcb")))) + "1r3831vq0fd5sh5841xr844sghg88z7ws91hg4jgnzbbkxfjp4ag")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) + `(("r-backports" ,r-backports) + ("r-dplyr" ,r-dplyr) ("r-nlme" ,r-nlme) - ("r-plyr" ,r-plyr) - ("r-psych" ,r-psych) + ("r-purrr" ,r-purrr) ("r-reshape2" ,r-reshape2) ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (home-page "https://github.com/tidyverse/broom") (synopsis "Convert statistical analysis objects into tidy data frames") -- cgit v1.2.3 From dc66835226858236c12c498cc9de0e98c8c86e18 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:32:40 +0200 Subject: gnu: Add r-ucminf. * gnu/packages/cran.scm (r-ucminf): 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 4cf7d6295e..f64b48da5f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1981,6 +1981,30 @@ can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.") (license license:gpl3+))) +(define-public r-ucminf + (package + (name "r-ucminf") + (version "1.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "ucminf" version)) + (sha256 + (base32 + "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/ucminf/") + (synopsis "General-purpose unconstrained non-linear optimization") + (description + "This package provides an implementation of an algorithm for +general-purpose unconstrained non-linear optimization. The algorithm is of +quasi-Newton type with BFGS updating of the inverse Hessian and soft line +search with a trust region type monitoring of the input to the line search +algorithm. The interface of @code{ucminf} is designed for easy interchange +with the package @code{optim}.") + (license license:gpl2+))) + (define-public r-jomo (package (name "r-jomo") -- cgit v1.2.3 From b8f6e2f82a733759017269170e7b8813f04a9425 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:32:50 +0200 Subject: gnu: Add r-ordinal. * gnu/packages/cran.scm (r-ordinal): 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 f64b48da5f..590d2c90d3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2005,6 +2005,33 @@ algorithm. The interface of @code{ucminf} is designed for easy interchange with the package @code{optim}.") (license license:gpl2+))) +(define-public r-ordinal + (package + (name "r-ordinal") + (version "2018.8-25") + (source + (origin + (method url-fetch) + (uri (cran-uri "ordinal" version)) + (sha256 + (base32 + "03cv9hcrw8j3lhamzhz8sk2p3ns4cw9z41x49h301k2b3pajv43h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-numderiv" ,r-numderiv) + ("r-ucminf" ,r-ucminf))) + (home-page "https://github.com/runehaubo/ordinal") + (synopsis "Regression models for ordinal data") + (description + "This package provides an implementation of cumulative link (mixed) +models also known as ordered regression models, proportional odds models, +proportional hazards models for grouped survival times and ordered models. +Estimation is via maximum likelihood and mixed models are fitted with the +Laplace approximation and adaptive Gauss-Hermite quadrature.") + (license license:gpl2+))) + (define-public r-jomo (package (name "r-jomo") -- cgit v1.2.3 From e7630cc93182f38b486c1c6825bf7a9ca5c3a6b0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:27:42 +0200 Subject: gnu: r-jomo: Update to 2.6-4. * gnu/packages/cran.scm (r-jomo): Update to 2.6-4. [propagated-inputs]: Add r-ordinal. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 590d2c90d3..8f9a463a0f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2035,17 +2035,18 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.") (define-public r-jomo (package (name "r-jomo") - (version "2.6-3") + (version "2.6-4") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 - "14s8q0j5zgl1g1pfxg3a4y1jzvs0wl61ir4992wsj7safskj7zvi")))) + "05g2rj9g7rgyb22b0gybw042nydyqsqsb31v05hifzavri8ij01x")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) + ("r-ordinal" ,r-ordinal) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/jomo/") (synopsis "Multilevel Joint Modelling Multiple Imputation") -- cgit v1.2.3 From a7265593d3385423adc2dbeaeb4827db586b2e34 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:33:37 +0200 Subject: gnu: r-pan: Update to 1.6. * gnu/packages/cran.scm (r-pan): Update to 1.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8f9a463a0f..46cb3e16a5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2062,14 +2062,14 @@ impute compatibly with the substantive model.") (define-public r-pan (package (name "r-pan") - (version "1.4") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "pan" version)) (sha256 (base32 - "1p3nigmhrnlch86g89hn7l0wvkifx3k9n59g0psi95yck43kza76")))) + "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/pan/") -- cgit v1.2.3 From 1b3b2a72eeaa5a134e0db8928f43e42340df36f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:33:48 +0200 Subject: gnu: r-mice: Update to 3.3.0. * gnu/packages/cran.scm (r-mice): Update to 3.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 46cb3e16a5..3865ffa150 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2107,14 +2107,14 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.1.0") + (version "3.3.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "0xpn215yfzib4hw09cwilnyg9zbvq460njavfvm84mvgwbm25byi")))) + "1p0ipbqk5aqdi7iikw3qrjyvdi9sdhpnw1h5mwakwvv0yl0pzbyx")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) -- cgit v1.2.3 From 69bf449bf10fe3c6ea5fc643ee49ed6ee8e50b84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:34:29 +0200 Subject: gnu: r-xts: Update to 0.11-0. * gnu/packages/cran.scm (r-xts): Update to 0.11-0. [native-inputs]: Remove. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3865ffa150..afba068dd6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2312,17 +2312,16 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.10-2") + (version "0.11-0") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "1i11fczks4lh8rpi6xbm9bm7f3jpcp6xw03kv178g3n3361qhmc1")))) + "1v50yn4bsjzdyk7r90isn6dxmpkapillrhpx3gqsshd180vwzqk9")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) - (native-inputs `(("gfortran" ,gfortran))) (home-page "https://github.com/joshuaulrich/xts") (synopsis "Extensible time series") (description -- cgit v1.2.3 From 6f5b157e3dab1ee7db0e62552ba6350b91c66d1e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:34:57 +0200 Subject: gnu: r-pillar: Update to 1.3.0. * gnu/packages/cran.scm (r-pillar): Update to 1.3.0. [propagated-inputs]: Add r-fansi. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index afba068dd6..7d2f93a394 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2798,18 +2798,19 @@ display.") (define-public r-pillar (package (name "r-pillar") - (version "1.2.3") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1rzhssprqgam1nq3s0f5rzxhxsq02azcghvxf6k8kmsmddf1n7f8")))) + "1q6arybmfqxhp5zqj1fri5pb8v7ywcv7bmgf81rrmgl892p4bn5f")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-crayon" ,r-crayon) + ("r-fansi" ,r-fansi) ("r-rlang" ,r-rlang) ("r-utf8" ,r-utf8))) (home-page "https://github.com/r-lib/pillar") -- cgit v1.2.3 From d97d98e142e40820807b050c656df40a33e8d020 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:35:24 +0200 Subject: gnu: r-tinytex: Update to 0.8. * gnu/packages/cran.scm (r-tinytex): Update to 0.8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7d2f93a394..b7827931c1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2843,14 +2843,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.6") + (version "0.8") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "16y9dldaff2kx1fkm92p7zlph0dcrdmlmavpdgf5y9jbhmc8g83f")))) + "1bgpr5i5399jf9n6pg2mm4aamisbhppg082ad0wv1j4g0rlxf1gy")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) -- cgit v1.2.3 From e32368c130893da22b35b4318f06606baacd5056 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:35:46 +0200 Subject: gnu: r-metap: Update to 1.0. * gnu/packages/cran.scm (r-metap): Update to 1.0. [propagated-inputs]: Add r-rdpack. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b7827931c1..784f476145 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2867,17 +2867,18 @@ automatically.") (define-public r-metap (package (name "r-metap") - (version "0.9") + (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 - "03vg0mb6q7j2z0pkxykbak0hcp6dcak7zxs1lw9hswz9kqrq5jhz")))) + "18rzvqfzyk8fn54gjvy2qd21nk9w69j7ihww477ma3f3ab6i982h")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + `(("r-lattice" ,r-lattice) + ("r-rdpack" ,r-rdpack))) (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") (synopsis "Meta-analysis of significance values") (description -- cgit v1.2.3 From be5642eb69d3b0dba1685742291b5d635f004c66 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:36:12 +0200 Subject: gnu: r-statnet-common: Update to 4.1.4. * gnu/packages/cran.scm (r-statnet-common): Update to 4.1.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 784f476145..fb398f56b8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2912,14 +2912,14 @@ supports arbitrary vertex/edge/graph attributes.") (define-public r-statnet-common (package (name "r-statnet-common") - (version "4.1.2") + (version "4.1.4") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 - "0h3g687214rlycca0fjrpy1lqbqsrginxqhmhl2mb2jinqqxcfgd")))) + "14dydm4c4dzc4v6ldxpn04q551nczzfablwibrd8lzgja8x9ksic")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) -- cgit v1.2.3 From 1fe9919a575b5d2d97dc7dee65251a2689709ed4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:36:31 +0200 Subject: gnu: r-tsa: Update to 1.2. * gnu/packages/cran.scm (r-tsa): Update to 1.2. [propagated-inputs]: Remove r-tseries. --- gnu/packages/cran.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fb398f56b8..478df95eaf 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3141,21 +3141,20 @@ University Press, 2000.") (define-public r-tsa (package (name "r-tsa") - (version "1.01") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "TSA" version)) (sha256 (base32 - "0cm97hwxm6vfgy9mc3kgwq6dnmn86p8a4avnfjbai048qnwrn6hx")))) + "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q")))) (properties `((upstream-name . "TSA"))) (build-system r-build-system) (propagated-inputs `(("r-leaps" ,r-leaps) ("r-locfit" ,r-locfit) - ("r-mgcv" ,r-mgcv) - ("r-tseries" ,r-tseries))) + ("r-mgcv" ,r-mgcv))) (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm") (synopsis "Time series analysis") (description -- cgit v1.2.3 From 19950821d74e5ae008919f28511bb8caa8c516ce Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:37:05 +0200 Subject: gnu: r-heatmaply: Update to 0.15.2. * gnu/packages/cran.scm (r-heatmaply): Update to 0.15.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 478df95eaf..706f612344 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3407,14 +3407,14 @@ exponentiation.") (define-public r-heatmaply (package (name "r-heatmaply") - (version "0.14.1") + (version "0.15.2") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 - "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc")))) + "0h8s5djzj4mrmaswlcaap6jbwxrkbzc43bbqik3qf8vrqz335w04")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit v1.2.3 From 7a96c4e0a00e0c527862df289aa48cab231380dc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:39:09 +0200 Subject: gnu: r-fnn: Update to 1.1.2.1. * gnu/packages/cran.scm (r-fnn): Update to 1.1.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 706f612344..9e7cb04f91 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3763,14 +3763,14 @@ multivariate plot methods.") (define-public r-fnn (package (name "r-fnn") - (version "1.1") + (version "1.1.2.1") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 - "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj")))) + "1n61jrcmakqif8f827x4qnlhm2jqpj5fgjj65c4p0kdd8lzw8pqp")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") -- cgit v1.2.3 From 12132229b0c9c57b1f99db158e02a81922a1aabf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:39:23 +0200 Subject: gnu: r-maptools: Update to 0.9-3. * gnu/packages/cran.scm (r-maptools): Update to 0.9-3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9e7cb04f91..116fdf42cb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4055,14 +4055,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "0.9-2") + (version "0.9-3") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "075lmb3b62171cw2dg8fv1vwmvfzg39r1ji7jwb8s5k9dz88ry1v")))) + "0hxbv01im9zk1qrwgigpc510w6x0kzdzip4gx2jzfqmmwr8m17r8")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) -- cgit v1.2.3 From 2e6909baf0512cb5f4de9553e6dad3329db7e47c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:39:46 +0200 Subject: gnu: r-later: Update to 0.7.4. * gnu/packages/cran.scm (r-later): Update to 0.7.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 116fdf42cb..82111ff96e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4083,14 +4083,14 @@ exchanging spatial objects with other R packages.") (define-public r-later (package (name "r-later") - (version "0.7.3") + (version "0.7.4") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 - "04j2phymxgkk4hv9pfa5w3s98w5d7fvm11blrdhxmray4n618msw")))) + "125zc499gj702x2bch95lsfzk2qb4dzv3604x9afym2i3ylrmm64")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) -- cgit v1.2.3 From a9b02ddd73adf938d5ef68658c2873dac64b7f04 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:39:58 +0200 Subject: gnu: r-codedepends: Update to 0.6.5. * gnu/packages/cran.scm (r-codedepends): Update to 0.6.5. [propagated-inputs]: Add r-graph. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 82111ff96e..8eac103109 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4180,18 +4180,19 @@ it.") (define-public r-codedepends (package (name "r-codedepends") - (version "0.5-3") + (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "CodeDepends" version)) (sha256 (base32 - "03p82s0abca2jimzqvxdzykfzca7c7fhm5xsjxybcksr4gggr5sc")))) + "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) (properties `((upstream-name . "CodeDepends"))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) + ("r-graph" ,r-graph) ("r-xml" ,r-xml))) (home-page "http://cran.r-project.org/web/packages/CodeDepends") (synopsis "Analysis of R code for reproducible research and code comprehension") -- cgit v1.2.3 From caaec8865117a15392a5220fe29f0acacef1a318 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:40:20 +0200 Subject: gnu: r-ggpubr: Update to 0.1.8. * gnu/packages/cran.scm (r-ggpubr): Update to 0.1.8. [propagated-inputs]: Add r-glue and r-polynom. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8eac103109..9f3d1bfd09 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4411,14 +4411,14 @@ and adds the annotation to the plot.") (define-public r-ggpubr (package (name "r-ggpubr") - (version "0.1.7") + (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 - "110ny8p41kmbz0a5rl0mv9cqpjkx6yr3ybflp1r0fmcvhwv7cr3i")))) + "0psl2zndm4wk6nnj1nv305islpxfvfgd87gjh2ph8yqn4mxpnfi1")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) @@ -4427,8 +4427,10 @@ and adds the annotation to the plot.") ("r-ggrepel" ,r-ggrepel) ("r-ggsci" ,r-ggsci) ("r-ggsignif" ,r-ggsignif) + ("r-glue" ,r-glue) ("r-gridextra" ,r-gridextra) ("r-magrittr" ,r-magrittr) + ("r-polynom" ,r-polynom) ("r-purrr" ,r-purrr) ("r-scales" ,r-scales) ("r-tidyr" ,r-tidyr))) -- cgit v1.2.3 From 5dfe491290b14a1ee7efd70f9cd083969c24e1c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:46:12 +0200 Subject: gnu: r-graph: Move from bioinformatics to bioconductor. * gnu/packages/bioinformatics.scm (r-graph): Move from here... * gnu/packages/bioconductor.scm (r-graph): ...to here. --- gnu/packages/bioconductor.scm | 19 +++++++++++++++++++ gnu/packages/bioinformatics.scm | 19 ------------------- 2 files changed, 19 insertions(+), 19 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1ff86779e8..fc01c2283b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -360,6 +360,25 @@ cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.") (license license:lgpl3))) +(define-public r-graph + (package + (name "r-graph") + (version "1.58.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "graph" version)) + (sha256 + (base32 + "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/graph") + (synopsis "Handle graph data structures in R") + (description + "This package implements some simple graph handling capabilities for R.") + (license license:artistic2.0))) + (define-public r-chippeakanno (package (name "r-chippeakanno") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 760b716408..a03d37c5b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7787,25 +7787,6 @@ extracting the desired features in a convenient format.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-graph - (package - (name "r-graph") - (version "1.58.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "graph" version)) - (sha256 - (base32 - "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) - (home-page "https://bioconductor.org/packages/graph") - (synopsis "Handle graph data structures in R") - (description - "This package implements some simple graph handling capabilities for R.") - (license license:artistic2.0))) - (define-public r-topgo (package (name "r-topgo") -- cgit v1.2.3 From a207bca2adf5371aabe41f28203c0e3e7bfbacad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:47:19 +0200 Subject: gnu: r-codedepends: Move from cran to bioconductor. * gnu/packages/cran.scm (r-codedepends): Move from here... * gnu/packages/bioconductor.scm (r-codedepends): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/cran.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fc01c2283b..a47a5aad05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -379,6 +379,34 @@ expressed genes in DNA microarray experiments.") "This package implements some simple graph handling capabilities for R.") (license license:artistic2.0))) +(define-public r-codedepends + (package + (name "r-codedepends") + (version "0.6.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "CodeDepends" version)) + (sha256 + (base32 + "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) + (properties `((upstream-name . "CodeDepends"))) + (build-system r-build-system) + (propagated-inputs + `(("r-codetools" ,r-codetools) + ("r-graph" ,r-graph) + ("r-xml" ,r-xml))) + (home-page "http://cran.r-project.org/web/packages/CodeDepends") + (synopsis "Analysis of R code for reproducible research and code comprehension") + (description + "This package provides tools for analyzing R expressions or blocks of +code and determining the dependencies between them. It focuses on R scripts, +but can be used on the bodies of functions. There are many facilities +including the ability to summarize or get a high-level view of code, +determining dependencies between variables, code improvement suggestions.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-chippeakanno (package (name "r-chippeakanno") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9f3d1bfd09..447be5657a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4177,34 +4177,6 @@ to the cluster management tool @code{sfCluster}, but can also used without it.") (license license:gpl2+))) -(define-public r-codedepends - (package - (name "r-codedepends") - (version "0.6.5") - (source - (origin - (method url-fetch) - (uri (cran-uri "CodeDepends" version)) - (sha256 - (base32 - "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) - (properties `((upstream-name . "CodeDepends"))) - (build-system r-build-system) - (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-xml" ,r-xml))) - (home-page "http://cran.r-project.org/web/packages/CodeDepends") - (synopsis "Analysis of R code for reproducible research and code comprehension") - (description - "This package provides tools for analyzing R expressions or blocks of -code and determining the dependencies between them. It focuses on R scripts, -but can be used on the bodies of functions. There are many facilities -including the ability to summarize or get a high-level view of code, -determining dependencies between variables, code improvement suggestions.") - ;; Any version of the GPL - (license (list license:gpl2+ license:gpl3+)))) - (define-public r-rappdirs (package (name "r-rappdirs") -- cgit v1.2.3 From c0608f815c4706ede4e7533409f3e7da127b767f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:49:33 +0200 Subject: gnu: r-adaptivesparsity: Update to 1.6. * gnu/packages/machine-learning.scm (r-adaptivesparsity): Update to 1.6. [propagated-inputs]: Add r-mass and r-matrix. --- gnu/packages/machine-learning.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index a86bdcb5ed..ec917e4442 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -560,13 +560,13 @@ I/O.") (define-public r-adaptivesparsity (package (name "r-adaptivesparsity") - (version "1.4") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "AdaptiveSparsity" version)) (sha256 (base32 - "1az7isvalf3kmdiycrfl6s9k9xqk22k1mc6rh8v0jmcz402qyq8z")))) + "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91")))) (properties `((upstream-name . "AdaptiveSparsity"))) (build-system r-build-system) @@ -579,7 +579,9 @@ I/O.") (("PKG_LIBS=" prefix) (string-append prefix "-larmadillo")))))))) (propagated-inputs - `(("r-rcpp" ,r-rcpp) + `(("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo))) (inputs `(("armadillo" ,armadillo))) -- cgit v1.2.3 From c28d8d8db06e165faa168a8e197651d941bbb9ee Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:50:14 +0200 Subject: gnu: r-kernlab: Update to 0.9-27. * gnu/packages/machine-learning.scm (r-kernlab): Update to 0.9-27. --- gnu/packages/machine-learning.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index ec917e4442..7790e78779 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -596,14 +596,14 @@ geometric models.") (define-public r-kernlab (package (name "r-kernlab") - (version "0.9-26") + (version "0.9-27") (source (origin (method url-fetch) (uri (cran-uri "kernlab" version)) (sha256 (base32 - "0xv0slf3ggw3sswsi34416lb1g3h1pqkrr2h7r1n1kvgii3l0jcm")))) + "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/kernlab") (synopsis "Kernel-based machine learning tools") -- cgit v1.2.3 From 8da236a377f4c0c6679334bcc76704d858ae088f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:50:43 +0200 Subject: gnu: r-gtools: Update to 3.8.1. * gnu/packages/statistics.scm (r-gtools): Update to 3.8.1. --- 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 69c72541a7..4fefdcd7f2 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4091,14 +4091,14 @@ Zurich, including many that are related to graphics.") (define-public r-gtools (package (name "r-gtools") - (version "3.5.0") + (version "3.8.1") (source (origin (method url-fetch) (uri (cran-uri "gtools" version)) (sha256 (base32 - "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6")))) + "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From f0519c8faec872b599debde5f2f91d6dbf57a5b4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:50:59 +0200 Subject: gnu: r-zoo: Update to 1.8-3. * gnu/packages/statistics.scm (r-zoo): Update to 1.8-3. --- 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 4fefdcd7f2..eb4063c984 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4231,13 +4231,13 @@ mechanism.") (define-public r-zoo (package (name "r-zoo") - (version "1.8-2") + (version "1.8-3") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 - "1lpwigxmi5sc23xrha4gcsccsm4yfsg0sa97y6vac3pg1lliblvx")))) + "15jmkgwvq2mm9f09vijgx7sff8pszh90fndcwhk2vw9i0p183di0")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) -- cgit v1.2.3 From e5db6890adb1b842d4ad5dc3313a65f6628ec3bf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:51:15 +0200 Subject: gnu: r-ztable: Update to 0.2.0. * gnu/packages/statistics.scm (r-ztable): Update to 0.2.0. [propagated-inputs]: Add r-flextable, r-magrittr, r-moonbook, r-officer, r-rcolorbrewer, r-scales, and r-stringr. --- gnu/packages/statistics.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index eb4063c984..ccff5fc293 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4251,14 +4251,22 @@ series of numeric vectors/matrices and factors.") (define-public r-ztable (package (name "r-ztable") - (version "0.1.8") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "ztable" version)) (sha256 (base32 - "1hk5k9614n52dpfrhdws06w4gvwhnz8q47x4cwxx88qmrzm8z2m3")))) + "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy")))) (build-system r-build-system) + (propagated-inputs + `(("r-flextable" ,r-flextable) + ("r-magrittr" ,r-magrittr) + ("r-moonbook" ,r-moonbook) + ("r-officer" ,r-officer) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr))) (home-page "https://cran.r-project.org/web/packages/ztable") (synopsis "Zebra-striped tables in LaTeX and HTML formats for R") (description -- cgit v1.2.3 From 314e8e763f9a2b3a3d5f98e8e435691f9dc01501 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:52:05 +0200 Subject: gnu: r-ggthemes: Update to 4.0.1. * gnu/packages/statistics.scm (r-ggthemes): Update to 4.0.1. [propagated-inputs]: Remove r-assertthat and r-colorspace; add r-purrr, r-stringr, and r-tibble. --- gnu/packages/statistics.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ccff5fc293..51a3c1fada 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4361,19 +4361,20 @@ data at that region, and avoids over-plotting.") (define-public r-ggthemes (package (name "r-ggthemes") - (version "3.5.0") + (version "4.0.1") (source (origin (method url-fetch) (uri (cran-uri "ggthemes" version)) (sha256 (base32 - "0drbzzb4i5jq1579fx1wmgh87ybnswjn7srak2l8g771ip49xwb8")))) + "0y6570wv135sf7pv57l7bqilzw47rziaqx4vsk45pf1w4lmj0w8b")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-colorspace" ,r-colorspace) - ("r-ggplot2" ,r-ggplot2) - ("r-scales" ,r-scales))) + `(("r-ggplot2" ,r-ggplot2) + ("r-purrr" ,r-purrr) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble))) (home-page "https://cran.rstudio.com/web/packages/ggthemes") (synopsis "Extra themes, scales and geoms for @code{ggplot2}") (description "This package provides extra themes and scales for -- cgit v1.2.3 From 8e499d756a4a7c5f875e023da2500536bdc10258 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:53:17 +0200 Subject: gnu: r-rann: Update to 2.6. * gnu/packages/statistics.scm (r-rann): Update to 2.6. --- 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 51a3c1fada..d832003791 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4413,13 +4413,13 @@ dispersion modeling and Tweedie power-law families.") (define-public r-rann (package (name "r-rann") - (version "2.5.1") + (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "RANN" version)) (sha256 (base32 - "0il5i99vbcagnxvb15af5n37g04a4q1x96bz73zh3jhki9fpw9vm")))) + "1r6rivh9ba4gwnzryip0aiwsbm46zma7nvd9z5y456p2dgzp9lii")))) (properties `((upstream-name . "RANN"))) (build-system r-build-system) -- cgit v1.2.3 From 0d279d607aeccc2365a4502db4c58ec247724bb4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:53:34 +0200 Subject: gnu: r-robustbase: Update to 0.93-2. * gnu/packages/statistics.scm (r-robustbase): Update to 0.93-2. --- 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 d832003791..07e180cf53 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4735,14 +4735,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.93-0") + (version "0.93-2") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "130pzibn5cb8mycv8byc6npzcpddghz8m7jqwk15qmx4g3cj8zgy")))) + "1632p73iv9iqqm0v3k9rfv9way0him3fl35si1nly9wi5kpq5ci7")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From f33a4748b7343a0f2ae3e560047b6eeca0f95235 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:53:52 +0200 Subject: gnu: r-modelmetrics: Update to 1.2.0. * gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.0. [propagated-inputs]: Add r-data-table. --- gnu/packages/statistics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 07e180cf53..ce7335619b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5011,18 +5011,19 @@ decompositions of such matrices, and solutions of linear systems.") (define-public r-modelmetrics (package (name "r-modelmetrics") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "ModelMetrics" version)) (sha256 (base32 - "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8")))) + "1sgdyrf6fbsn18gk8slir4a1yhv133kfhyg2crfs759nff4aw89h")))) (properties `((upstream-name . "ModelMetrics"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + `(("r-rcpp" ,r-rcpp) + ("r-data-table" ,r-data-table))) (home-page "https://cran.r-project.org/web/packages/ModelMetrics") (synopsis "Rapid calculation of model metrics") (description -- cgit v1.2.3 From dff5640a59da533fc91fa285b6d7d7fec2f7e60a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:55:00 +0200 Subject: gnu: r-rcas: Use standard version of ghc-pandoc-citeproc. * gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc". --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a03d37c5b0..028643aeb4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8518,7 +8518,7 @@ paired-end data.") `(("r-testthat" ,r-testthat) ;; During vignette building knitr checks that "pandoc-citeproc" ;; is in the PATH. - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1))) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biomart" ,r-biomart) -- cgit v1.2.3 From ca248f1db90c2e7b01d734aaa51d330a29fe0937 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:55:56 +0200 Subject: gnu: pigx-rnaseq: Use latest version of Pandoc. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc". --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 028643aeb4..99313824e9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12830,8 +12830,8 @@ once. This package provides tools to perform Drop-seq analyses.") ("r-rtracklayer" ,r-rtracklayer) ("r-rjson" ,r-rjson) ("salmon" ,salmon) - ("ghc-pandoc" ,ghc-pandoc-1) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml))) (home-page "http://bioinformatics.mdc-berlin.de/pigx/") -- cgit v1.2.3 From 7cd40c8c5dee1b323117ec85787566505be2d9ad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:56:38 +0200 Subject: gnu: pigx-chipseq: Use latest version of Pandoc. * gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc". --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 99313824e9..e1d953561b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12892,8 +12892,8 @@ expression report comparing samples in an easily configurable manner.") ("macs" ,macs) ("multiqc" ,multiqc) ("perl" ,perl) - ("ghc-pandoc" ,ghc-pandoc-1) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) -- cgit v1.2.3 From c2b4f81e51bab9a3ca6f2d1ba81ab1ff3b573ab4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:56:53 +0200 Subject: gnu: pigx-bsseq: Use latest version of Pandoc. * gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc". --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e1d953561b..7c25a71c6b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12954,8 +12954,8 @@ in an easily configurable manner.") ("r-bookdown" ,r-bookdown) ("r-ggplot2" ,r-ggplot2) ("r-ggbio" ,r-ggbio) - ("ghc-pandoc" ,ghc-pandoc-1) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) ("snakemake" ,snakemake-4) -- cgit v1.2.3 From 00a43cb81cecb30d40f9940407c9f1ba08d3d38e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:57:09 +0200 Subject: gnu: pigx-scrnaseq: Use latest version of Pandoc. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc". --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7c25a71c6b..92b6e7d50c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13005,8 +13005,8 @@ methylation and segmentation.") ("python-magic" ,python-magic) ("python-numpy" ,python-numpy) ("python-loompy" ,python-loompy) - ("ghc-pandoc" ,ghc-pandoc-1) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("samtools" ,samtools) ("snakemake" ,snakemake-4) ("star" ,star) -- cgit v1.2.3 From a5c70c2e0e91ede6061ba130c27e5fdedbcbf2d8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 6 Sep 2018 02:29:48 +0200 Subject: gnu: libmpdclient: Update to 2.15. * gnu/packages/mpd.scm (libmpdclient): Update to 2.15. --- gnu/packages/mpd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 2554ec9efd..5c82bf9ba1 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -56,7 +56,7 @@ (define-public libmpdclient (package (name "libmpdclient") - (version "2.14") + (version "2.15") (source (origin (method url-fetch) (uri @@ -65,7 +65,7 @@ "/libmpdclient-" version ".tar.xz")) (sha256 (base32 - "0whk0qw0lsd3kaimdznz0c45bfym0p4885zf4b7pfc7y3dwy510a")))) + "1la60ar6i4ghpscrlgm45kci9b74bvkpsfybhg0ygs4rzpwzdnxl")))) (build-system meson-build-system) (native-inputs `(("pkg-config" ,pkg-config) -- cgit v1.2.3 From d83477adf92f18bd3a19b1ab2d22a0312bbaf294 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 6 Sep 2018 02:23:49 +0200 Subject: gnu: font-fira-code: Update to 1.205. * gnu/packages/fonts.scm (font-fira-code): Update to 1.205. --- gnu/packages/fonts.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 4d02b4bc62..ce07d3ad4c 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -887,7 +887,7 @@ designed to work well in user interface environments.") (define-public font-fira-code (package (name "font-fira-code") - (version "1.204") + (version "1.205") (source (origin (method url-fetch/zipbomb) (uri (string-append "https://github.com/tonsky/FiraCode/releases/" @@ -895,7 +895,7 @@ designed to work well in user interface environments.") "/FiraCode_" version ".zip")) (sha256 (base32 - "17wky221b3igrqhmxgmqiyv1xdfn0nw471vzhpkrvv1w2w1w1k18")))) + "13bxgf59g6fw5191xclcjzn22hj8jk9k5jjwf7vz07mpjbgadcl5")))) (build-system font-build-system) (home-page "https://mozilla.github.io/Fira/") (synopsis "Monospaced font with programming ligatures") -- cgit v1.2.3 From 79b283e433be171c7917fd5d9f10fa2185862a36 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 6 Sep 2018 02:21:26 +0200 Subject: gnu: ccache: Update to 3.4.3. * gnu/packages/ccache.scm (ccache): Update to 3.4.3. [arguments]: Remove obsolete 'munge-failing-test' phase. --- gnu/packages/ccache.scm | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/ccache.scm b/gnu/packages/ccache.scm index af06b741a7..af29cee565 100644 --- a/gnu/packages/ccache.scm +++ b/gnu/packages/ccache.scm @@ -30,7 +30,7 @@ (define-public ccache (package (name "ccache") - (version "3.4.2") + (version "3.4.3") (source (origin (method url-fetch) @@ -38,7 +38,7 @@ version ".tar.xz")) (sha256 (base32 - "1qpy6k9f06kpr6bxy26ncdxcszqv1skcncvczcvksgfncx1v3a0q")))) + "0jjzq5340qw3jm5gkajjkkb5wd0yqqy1dyjw3mf3jy15cakmazi9")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl) ; for test.sh ("which" ,(@ (gnu packages base) which)))) @@ -49,13 +49,6 @@ (lambda _ (substitute* '("unittest/test_hashutil.c" "test/suites/base.bash") (("#!/bin/sh") (string-append "#!" (which "sh")))) - #t)) - (add-before 'check 'munge-failing-test - (lambda _ - ;; XXX The new ‘Multiple -fdebug-prefix-map’ test added in - ;; 3.3.5 fails (why?). Force it to report success instead. - (substitute* "test/suites/debug_prefix_map.bash" - (("grep \"name\"") "true")) #t))))) (home-page "https://ccache.samba.org/") (synopsis "Compiler cache") -- cgit v1.2.3 From d53aeeafccb91fd03c6c540153720717eceb92a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 6 Sep 2018 04:53:32 +0200 Subject: Add missing use-modules clause. This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2. Sorry! * gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages bioconductor). --- gnu/packages/bioinformatics.scm | 1 + gnu/packages/graph.scm | 1 + 2 files changed, 2 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 92b6e7d50c..2d5ec6d170 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -51,6 +51,7 @@ #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bison) + #:use-module (gnu packages bioconductor) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 3b222d6ee8..245ee8f956 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -28,6 +28,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages gcc) + #:use-module (gnu packages bioconductor) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages compression) #:use-module (gnu packages cran) -- cgit v1.2.3 From 96d6c41dfa5d69d4f25c8b53cb74e2ee621165d6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 6 Sep 2018 10:43:01 +0200 Subject: gnu: guile-commonmark: Install .go files to libdir. * gnu/packages/guile.scm (guile-commonmark)[source](snippet): Change the "modir = " and "godir = " line separately, allowing .go files to be installed to $(libdir). --- gnu/packages/guile.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index f594cd13ed..335bd6219f 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -1612,8 +1612,10 @@ you send to a FIFO file.") (("ac_subst_vars='") "ac_subst_vars='GUILE_EFFECTIVE_VERSION\n")) (substitute* "Makefile.in" - (("/site/2.0") - "/site/@GUILE_EFFECTIVE_VERSION@")) + (("moddir =.*") + "moddir = $(datadir)/guile/site/@GUILE_EFFECTIVE_VERSION@\n") + (("godir =.*") + "godir = $(libdir)/guile/@GUILE_EFFECTIVE_VERSION@/site-ccache\n")) #t)))) (build-system gnu-build-system) (inputs -- cgit v1.2.3 From b3ca2d8883f7aa5c8505e04427f2d892148f61e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 6 Sep 2018 10:46:07 +0200 Subject: gnu: hpcguix-web: Update to 9ff40fc. * gnu/packages/web.scm (hpcguix-web): Update to 9ff40fc. [arguments]: In 'wrap-program' phase, add guile-gcrypt, guile-git, and guile-bytestructures to DEPS. --- gnu/packages/web.scm | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 918548513d..9567254424 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6708,10 +6708,11 @@ compressed JSON header blocks. (license l:expat))) (define-public hpcguix-web - (let ((commit "87cb51611c0f1fd3863b830614ab1364599cf1ca")) + (let ((commit "9ff40fcc77f248901d861756dbbddc80270c380c") + (revision "2")) (package (name "hpcguix-web") - (version (git-version "0.0.1" "1" commit)) + (version (git-version "0.0.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -6720,7 +6721,7 @@ compressed JSON header blocks. (file-name (git-file-name name version)) (sha256 (base32 - "0p66fl8r3v73v13fqg9rbqbzbdzvyznchxbq2s1jwq6qfsn2w3gr")))) + "0lxcj9s3wxrv1l7lrxxx374jwzx7h60gxwkbgr46lzcbgvb3k26s")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) @@ -6741,10 +6742,13 @@ compressed JSON header blocks. (let* ((out (assoc-ref outputs "out")) (guix (assoc-ref inputs "guix")) (guile (assoc-ref inputs "guile")) + (gcrypt (assoc-ref inputs "guile-gcrypt")) + (git (assoc-ref inputs "guile-git")) + (bs (assoc-ref inputs "guile-bytestructures")) (json (assoc-ref inputs "guile-json")) (guile-cm (assoc-ref inputs "guile-commonmark")) - (deps (list guile guile-cm guix json)) + (deps (list guile gcrypt git bs guile-cm guix json)) (effective (read-line (open-pipe* OPEN_READ -- cgit v1.2.3 From 89874fd15610bc35c586b38a0d575522140ff5b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 6 Sep 2018 10:48:44 +0200 Subject: gnu: guile-charting: Install .go files to libdir. * gnu/packages/plotutils.scm (guile-charting)[source](modules, snippet): Remove. --- gnu/packages/plotutils.scm | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/plotutils.scm b/gnu/packages/plotutils.scm index 0e65cb319f..2a330695c6 100644 --- a/gnu/packages/plotutils.scm +++ b/gnu/packages/plotutils.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2015 Eric Bavier ;;; Copyright © 2016, 2017 Nicolas Goaziou ;;; Copyright © 2018 Tobias Geerinckx-Rice @@ -93,15 +93,7 @@ scientific data.") "guile-charting-" version ".tar.gz")) (sha256 (base32 - "0w5qiyv9v0ip5li22x762bm48g8xnw281w66iyw094zdw611pb2m")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Use the standard location for modules. - (substitute* "Makefile.in" - (("godir = .*$") - "godir = $(moddir)\n")) - #t)))) + "0w5qiyv9v0ip5li22x762bm48g8xnw281w66iyw094zdw611pb2m")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("guile" ,guile-2.2))) -- cgit v1.2.3 From b290a631a0f9ee9a52095be66c843780dc0366f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 6 Sep 2018 10:49:42 +0200 Subject: gnu: guile-present: Install .go files to libdir. * gnu/packages/plotutils.scm (guile-present)[source](modules, snippet): Remove. --- gnu/packages/gtk.scm | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 6c43a3ab56..4daaad0ebc 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -903,14 +903,7 @@ images onto Cairo surfaces.") (sha256 (base32 "1qam447m05sxxv6x8dlzg7qnyfc4dh8apjw1idpfhpns671gfr6m")) - (patches (search-patches "guile-present-coding.patch")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "Makefile.in" - (("godir = .*$") - "godir = $(moddir)\n")) - #t)))) + (patches (search-patches "guile-present-coding.patch")))) (build-system gnu-build-system) (arguments '(#:phases -- cgit v1.2.3 From f66be84d08b90a9ecf08f79c8156d072ad359c36 Mon Sep 17 00:00:00 2001 From: Eric Brown Date: Sun, 2 Sep 2018 09:27:56 -0500 Subject: gnu: gfortran, gcc-objc, gcc-objc++: Add version 8. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gcc.scm (gfortran-8, gcc-objc-8, gcc-objc++-8): New variables. Signed-off-by: Ludovic Courtès --- gnu/packages/gcc.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index bdff2ddada..0dd5d64464 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -663,6 +663,10 @@ as the 'native-search-paths' field." (custom-gcc gcc-7 "gfortran" '("fortran") %generic-search-paths)) +(define-public gfortran-8 + (custom-gcc gcc-8 "gfortran" '("fortran") + %generic-search-paths)) + (define-public gfortran ;; Note: Update this when GCC changes! We cannot use ;; (custom-gcc gcc "fortran" …) because that would lead to a package object @@ -723,6 +727,15 @@ as the 'native-search-paths' field." (variable "LIBRARY_PATH") (files '("lib" "lib64")))))) +(define-public gcc-objc-8 + (custom-gcc gcc-8 "gcc-objc" '("objc") + (list (search-path-specification + (variable "OBJC_INCLUDE_PATH") + (files '("include"))) + (search-path-specification + (variable "LIBRARY_PATH") + (files '("lib" "lib64")))))) + (define-public gcc-objc gcc-objc-5) (define-public gcc-objc++-4.8 @@ -770,6 +783,15 @@ as the 'native-search-paths' field." (variable "LIBRARY_PATH") (files '("lib" "lib64")))))) +(define-public gcc-objc++-8 + (custom-gcc gcc-8 "gcc-objc++" '("obj-c++") + (list (search-path-specification + (variable "OBJCPLUS_INCLUDE_PATH") + (files '("include"))) + (search-path-specification + (variable "LIBRARY_PATH") + (files '("lib" "lib64")))))) + (define-public gcc-objc++ gcc-objc++-5) (define (make-libstdc++-doc gcc) -- cgit v1.2.3 From 21f5f351fb4a21a8051cdb2b747fef57aa2fa8d4 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Thu, 6 Sep 2018 10:55:21 -0400 Subject: gnu: libgme: Update to 0.6.2. * gnu/packages/music.scm (libgme): Update to 0.6.2. [native-inputs]: Add gcc-4.9. --- gnu/packages/music.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index ba21e5da2b..e39478e794 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -786,18 +786,23 @@ interface. It is implemented as a frontend to @code{klick}.") (define-public libgme (package (name "libgme") - (version "0.6.1") + (version "0.6.2") (source (origin (method url-fetch) (uri (string-append "https://bitbucket.org/mpyne/game-music-emu/" "downloads/game-music-emu-" version - ".tar.bz2")) + ".tar.xz")) (sha256 (base32 - "08fk7zddpn7v93d0fa7fcypx7hvgwx9b5psj9l6m8b87k2hbw4fw")))) + "0hkkmxbaas2sirlb5i4r10mgbbiaapjx8pazifabwba23m3wnijh")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no check target + (native-inputs + `(;; Use gcc-4.9 to work around an internal compiler error that happens + ;; when using gcc-5.5.0. FIXME: Try removing this when the default + ;; compiler is no longer gcc-5.5.0. + ("gcc" ,gcc-4.9))) (home-page "https://bitbucket.org/mpyne/game-music-emu") (synopsis "Video game music file playback library") (description -- cgit v1.2.3 From 1e066f070611b64d24af4544efe8075bb1999d30 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 6 Sep 2018 16:43:10 -0400 Subject: gnu: curl: Update replacement to 7.61.1 [fixes CVE-2018-14618]. * gnu/packages/curl.scm (curl)[replacement]: Update to 7.61.1. (curl-7.61.0): Replace variable with ... (curl-7.61.1): ... new variable. --- gnu/packages/curl.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm index 1907d2dc3d..6d45dc0cc5 100644 --- a/gnu/packages/curl.scm +++ b/gnu/packages/curl.scm @@ -51,7 +51,7 @@ (package (name "curl") (version "7.59.0") - (replacement curl-7.61.0) + (replacement curl-7.61.1) (source (origin (method url-fetch) (uri (string-append "https://curl.haxx.se/download/curl-" @@ -141,10 +141,10 @@ tunneling, and so on.") "See COPYING in the distribution.")) (home-page "https://curl.haxx.se/"))) -(define-public curl-7.61.0 +(define-public curl-7.61.1 (package (inherit curl) - (version "7.61.0") + (version "7.61.1") (source (origin (method url-fetch) @@ -152,7 +152,7 @@ tunneling, and so on.") version ".tar.xz")) (sha256 (base32 - "080p9r2kln8cbfj0rqfn6wqp5kdn9k5wp720nirkcw845lcmavpg")))))) + "148qv1f32290r9pwg07mccawihz4srznkzsdwdl2xllvlgb16n9x")))))) (define-public kurly (package -- cgit v1.2.3 From 91cc2a38ded0f9a637c37d83d72fa514a13fe6bd Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 6 Sep 2018 16:46:08 -0400 Subject: gnu: Wireshark: Update to 2.6.3 [fixes CVE-2018-{14994,16056,16057,16058}]. * gnu/packages/networking.scm (wireshark): Update to 2.6.3. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 61c0ad7fba..acf523d366 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -580,7 +580,7 @@ of the same name.") (define-public wireshark (package (name "wireshark") - (version "2.6.2") + (version "2.6.3") (source (origin (method url-fetch) @@ -588,7 +588,7 @@ of the same name.") version ".tar.xz")) (sha256 (base32 - "153h6prxamv5a62f3pfadkry0y57696xrgxfy2gfy5xswdg8kcj9")))) + "1v538h02y8avwy3cr11xz6wkyf9xd8qva4ng4sl9f2fw4skahn6i")))) (build-system gnu-build-system) (inputs `(("c-ares" ,c-ares) ("glib" ,glib) -- cgit v1.2.3 From 0012e0dd5642fbbb8ee40a68f65afc184952fc98 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 7 Sep 2018 02:57:28 +0200 Subject: gnu: knot: Update to 2.7.2. * gnu/packages/dns.scm (knot): Update to 2.7.2. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 7a80e1bd9b..29c3d9b923 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -498,14 +498,14 @@ Extensions} (DNSSEC).") (define-public knot (package (name "knot") - (version "2.7.1") + (version "2.7.2") (source (origin (method url-fetch) (uri (string-append "https://secure.nic.cz/files/knot-dns/" name "-" version ".tar.xz")) (sha256 (base32 - "108k6x3hjsnyf06pv5rlxqhynjbbz13pzwax1mqff3hgv85f4skx")) + "0cc4wgb02ch09x99a1fnr7vsdik8k920q7jafzcamjvy3kpb4w6b")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From 12498b59e76c0285f0d9babb0107e8e82855aa60 Mon Sep 17 00:00:00 2001 From: Alex Branham Date: Thu, 6 Sep 2018 18:35:36 +0200 Subject: gnu: emacs-ess: Update to 17.11. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs.scm (emacs-ess): Update to 17.11 [url]: Use github for https [snippet]: update julia-mode substitution, only build info doc, bypass failing test [propagated-inputs]: Add emacs-julia-mode [description]: Mention that ESS supports Julia and JAGS (which replaces OpenBUGS) [arguments]: Remove 'set-home' phase. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs.scm | 39 +++++++++++++++++++++++---------------- 1 file changed, 23 insertions(+), 16 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 957b72f4e7..1f64a5e84a 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -38,6 +38,7 @@ ;;; Copyright © 2018 Tim Gesthuizen ;;; Copyright © 2018 Jack Hill ;;; Copyright © 2018 Pierre-Antoine Rouby +;;; Copyright © 2018 Alex Branham ;;; ;;; This file is part of GNU Guix. ;;; @@ -4123,22 +4124,34 @@ programming language.") (define-public emacs-ess (package (name "emacs-ess") - (version "16.10") + (version "17.11") (source (origin (method url-fetch) - (uri (string-append "http://ess.r-project.org/downloads/ess/ess-" - version ".tgz")) + (uri (string-append "https://github.com/emacs-ess/ESS/archive/v" + version ".tar.gz")) (sha256 (base32 - "04m8lwp3ylh2vl7k2bjjs7mxbm64j4sdckqpvnm9k0qhaqf02pjk")) + "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c")) + (file-name (string-append name "-" version ".tar.gz")) (modules '((guix build utils))) (snippet '(begin ;; Stop ESS from trying to bundle an external julia-mode.el. (substitute* "lisp/Makefile" (("^\tjulia-mode.elc\\\\\n") "") - (("^all: \\$\\(ELC\\) ess-custom.el julia-mode.el") - "all: $(ELC) ess-custom.el")) + (("^dist: all julia-mode.el") + "dist: all")) + ;; No need to build docs in so many formats. Also, skipping + ;; pdf lets us not pull in texlive. + (substitute* "doc/Makefile" + (("all : info text html pdf") + "all : info") + (("install: install-info install-other-docs") + "install: install-info")) + ;; Test fails upstream + (substitute* "test/ess-r-tests.el" + (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()") + "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed")) #t)))) (build-system gnu-build-system) (arguments @@ -4157,10 +4170,6 @@ programming language.") (("SHELL = /bin/sh") (string-append "SHELL = " (which "sh")))) #t)) - ;; FIXME: the texlive-union insists on regenerating fonts. It stores - ;; them in HOME, so it needs to be writeable. - (add-before 'build 'set-HOME - (lambda _ (setenv "HOME" "/tmp") #t)) (replace 'check (lambda _ (invoke "make" "test"))))))) @@ -4169,16 +4178,14 @@ programming language.") ("r-minimal" ,r-minimal))) (native-inputs `(("perl" ,perl) - ("texinfo" ,texinfo) - ("texlive" ,(texlive-union (list texlive-latex-natbib - texlive-latex-seminar - texlive-latex-hyperref - texlive-tex-texinfo))))) + ("texinfo" ,texinfo))) + (propagated-inputs + `(("emacs-julia-mode" ,emacs-julia-mode))) (home-page "https://ess.r-project.org/") (synopsis "Emacs mode for statistical analysis programs") (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU Emacs. It is designed to support editing of scripts and interaction with -various statistical analysis programs such as R and OpenBUGS.") +various statistical analysis programs such as R, Julia, and JAGS.") (license license:gpl2+))) (define-public emacs-smex -- cgit v1.2.3 From 40c10917bc3b8df853001c193da882d643db1bd1 Mon Sep 17 00:00:00 2001 From: pimi Date: Wed, 29 Aug 2018 09:24:34 +0200 Subject: gnu: Add r-abcp2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/cran.scm (r-abcp2): New variable. Signed-off-by: Ludovic Courtès --- 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 447be5657a..c713a9904b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5411,3 +5411,24 @@ maximum cycle number. The @code{r-abcoptim} implements the Artificial bee colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}. This version is a work-in-progress and is written in R code.") (license license:expat))) + +(define-public r-abcp2 + (package + (name "r-abcp2") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABCp2" version)) + (sha256 + (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) + (properties `((upstream-name . "ABCp2"))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ABCp2/") + (synopsis "Approximate Bayesian Computational Model for Estimating P2") + (description + "This package tests the goodness of fit of a distribution of offspring to the Normal, +Poisson, and Gamma distribution and estimates the proportional paternity of the +second male (P2) based on the best fit distribution.") + (license license:gpl2))) -- cgit v1.2.3 From cadc10a513af2624c9233fb2cffb4c4ff5471197 Mon Sep 17 00:00:00 2001 From: pimi Date: Wed, 29 Aug 2018 09:32:45 +0200 Subject: gnu: Add r-abcrf. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/cran.scm (r-abcrf): New variable. Signed-off-by: Ludovic Courtès --- 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 c713a9904b..93c111bccc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5432,3 +5432,31 @@ colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pd Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the best fit distribution.") (license license:gpl2))) + +(define-public r-abcrf + (package + (name "r-abcrf") + (version "1.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abcrf" version)) + (sha256 + (base32 "06vy3inikrr9hv36q4djhrgzi9zizdfnhz17wpra8kadmr7qj441")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-ranger" ,r-ranger) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-readr" ,r-readr) + ("r-stringr" ,r-stringr))) + (home-page "https://cran.r-project.org/web/packages/abcrf/") + (synopsis "Approximate bayesian computation via random forests") + (description + "This package performs approximate bayesian computation (ABC) model choice and +parameter inference via random forests. This machine learning tool named random +forests (RF) can conduct selection among the highly complex models covered by +ABC algorithms.") + (license license:gpl2+))) -- cgit v1.2.3 From 12da2a5e58c6f518892376df5e1af4a511f12e6b Mon Sep 17 00:00:00 2001 From: pimi Date: Wed, 29 Aug 2018 09:39:17 +0200 Subject: gnu: Add r-abctools. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/cran.scm (r-abctools): New variable. Signed-off-by: Ludovic Courtès --- 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 93c111bccc..aa58efce7c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5460,3 +5460,28 @@ parameter inference via random forests. This machine learning tool named random forests (RF) can conduct selection among the highly complex models covered by ABC algorithms.") (license license:gpl2+))) + +(define-public r-abctools + (package + (name "r-abctools") + (version "1.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "abctools" version)) + (sha256 + (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abc" ,r-abc) + ("r-abind" ,r-abind) + ("r-hmisc" ,r-hmisc) + ("r-plyr" ,r-plyr))) + (home-page "https://github.com/dennisprangle/abctools/") + (synopsis "Tools for ABC analyses") + (description + "This @code{r-abctools} package provides tools for approximate Bayesian computation +including summary statistic selection and assessing coverage. This includes +recent dimension reduction algorithms to tune the choice of summary statistics, +and coverage methods to tune the choice of threshold.") + (license license:gpl2+))) -- cgit v1.2.3 From 77b33e0ede4bd015d863f0b1f63f492c62fb1943 Mon Sep 17 00:00:00 2001 From: pimi Date: Wed, 29 Aug 2018 10:09:12 +0200 Subject: gnu: Add r-ggstance. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit gnu/packages/cran.scm (r-ggstance): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index aa58efce7c..8026f99736 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5485,3 +5485,29 @@ including summary statistic selection and assessing coverage. This includes recent dimension reduction algorithms to tune the choice of summary statistics, and coverage methods to tune the choice of threshold.") (license license:gpl2+))) + +(define-public r-ggstance + (package + (name "r-ggstance") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggstance" version)) + (sha256 + (base32 "0v7f3xdaaridw6d4jvnsfwxmpjrasvx5vl555wsrn50aah17fkvh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-plyr" ,r-plyr) + ("r-rlang" ,r-rlang) + ("r-withr" ,r-withr))) + (home-page "https://cran.r-project.org/web/packages/ggstance/") + (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") + (description + "This package is a @code{r-ggplot2} extension that provides flipped components: +@enumerate +@item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms; +@item vertical versions of @code{r-ggplot2} positions. +@end enumerate") + (license license:gpl3))) -- cgit v1.2.3 From c61f7bc543d98781d9c24989edbfde39af7e7320 Mon Sep 17 00:00:00 2001 From: pimi Date: Wed, 29 Aug 2018 10:16:11 +0200 Subject: gnu: Add r-mosaiccore. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/cran.scm (r-mosaiccore): New variable. Signed-off-by: Ludovic Courtès --- 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 8026f99736..3be7fd7d62 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5511,3 +5511,27 @@ and coverage methods to tune the choice of threshold.") @item vertical versions of @code{r-ggplot2} positions. @end enumerate") (license license:gpl3))) + +(define-public r-mosaiccore + (package + (name "r-mosaiccore") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mosaicCore" version)) + (sha256 + (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z")))) + (properties `((upstream-name . "mosaicCore"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-lazyeval" ,r-lazyeval) + ("r-mass" ,r-mass) + ("r-rlang" ,r-rlang) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/ProjectMOSAIC/mosaicCore/") + (synopsis "Common utilities for mosaic family packages") + (description + "Common utilities used in other Mosaic family packages are collected here.") + (license license:gpl2+))) -- cgit v1.2.3 From 214452ffd339491f63560d19d2aeab4e668029a4 Mon Sep 17 00:00:00 2001 From: pimi Date: Wed, 29 Aug 2018 10:19:55 +0200 Subject: gnu: Add r-ggformula. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/cran.scm (r-ggformula): New variable. Signed-off-by: Ludovic Courtès --- 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 3be7fd7d62..8144391729 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5535,3 +5535,32 @@ and coverage methods to tune the choice of threshold.") (description "Common utilities used in other Mosaic family packages are collected here.") (license license:gpl2+))) + +(define-public r-ggformula + (package + (name "r-ggformula") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggformula" version)) + (sha256 + (base32 "1pmpdfjfbrc6kcpq70cr1kbj2qy711hw940g2aiis6l443z706kh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-ggstance" ,r-ggstance) + ("r-magrittr" ,r-magrittr) + ("r-mosaiccore" ,r-mosaiccore) + ("r-rlang" ,r-rlang) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/ProjectMOSAIC/ggformula/") + (synopsis "Formula interface for the @code{r-ggplot2}") + (description + "The @code{r-ggformula} introduces a family of graphics functions, gf_point(), +gf_density(), and so on, bring the formula interface to ggplot(). This captures +and extends the excellent simplicity of the lattice-graphics formula interface, +while providing the intuitive capabilities of @code{r-ggplot2}.") + (license license:expat))) -- cgit v1.2.3 From 15214828a52b66f95890ee29f7fb25dec3c5b065 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 7 Sep 2018 17:03:49 +0200 Subject: gnu: guile-json: Update to 1.2.0. * gnu/packages/guile.scm (guile-json): Update to 1.2.0. [license]: Change to GPL3+. --- gnu/packages/guile.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 335bd6219f..05d9315214 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -897,7 +897,7 @@ for Guile\".") (define-public guile-json (package (name "guile-json") - (version "1.1.1") + (version "1.2.0") (home-page "https://github.com/aconchillo/guile-json") (source (origin (method url-fetch) @@ -906,7 +906,7 @@ for Guile\".") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "12jqkn9qgwdlxbasy2n25a2a7apf30dww1nnxqfam5735k3jdngv")))) + "02kqv0q98fmchn7i4y7ycmrjlh4b2c93ij0z7k036qwpp204w4gh")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -924,7 +924,9 @@ specification. These are the main features: @item Unicode support for strings. @item Allows JSON pretty printing. @end itemize\n") - (license license:lgpl3+))) + + ;; Version 1.2.0 switched to GPLv3+ (from LGPLv3+). + (license license:gpl3+))) (define-public guile2.2-json (deprecated-package "guile2.2-json" guile-json)) -- cgit v1.2.3 From 6b4f99102c4e3f57cc657c14ff196b211654f88b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 7 Sep 2018 17:38:08 +0200 Subject: gnu: gdb: Update to 8.2. * gnu/packages/gdb.scm (gdb): Update to 8.2. --- gnu/packages/gdb.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/gdb.scm b/gnu/packages/gdb.scm index f0c4c8b804..74eb0f8994 100644 --- a/gnu/packages/gdb.scm +++ b/gnu/packages/gdb.scm @@ -37,14 +37,14 @@ (define-public gdb (package (name "gdb") - (version "8.1.1") + (version "8.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/gdb/gdb-" version ".tar.xz")) (sha256 (base32 - "0g6hv9xk12aa58w77fydaldqr9a6b0a6bnwsq87jfc6lkcbc7p4p")))) + "0fbw6j4z7kmvywwgavn7w3knp860i5i9qnjffc5p52bwkji43963")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; FIXME "make check" fails on single-processor systems. -- cgit v1.2.3 From afdd1555c4639dbd378fddffdee702933d14a1b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 7 Sep 2018 17:57:04 +0200 Subject: gnu: indent: Add version 2.2.12. * gnu/packages/code.scm (indent-2.2.12): New variable. --- gnu/packages/code.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index be178a5f99..85ee6c2877 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -651,6 +651,19 @@ extensions over the standard utility.") (license license:gpl3+) (home-page "https://www.gnu.org/software/indent/"))) +(define-public indent-2.2.12 + (package + (inherit indent) + (version "2.2.12") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnu/indent/indent-" version + ".tar.gz")) + (sha256 + (base32 + "12xvcd16cwilzglv9h7sgh4h1qqjd1h8s48ji2dla58m4706hzg7")))) + (native-inputs `(("texinfo" ,texinfo))))) + (define-public amalgamate (let* ((commit "c91f07eea1133aa184f652b8f1398eaf03586208") (revision "0") -- cgit v1.2.3 From 9f1f200c0462d5fa798e4d7b8c3c09294f8bfb95 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 7 Sep 2018 17:59:16 +0200 Subject: gnu: diffoscope: Update to 100. * gnu/packages/package-management.scm (diffoscope): Update to 100. --- gnu/packages/package-management.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 529d2943c4..5edfb5dffb 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -568,13 +568,13 @@ transactions from C or Python.") (define-public diffoscope (package (name "diffoscope") - (version "96") + (version "100") (source (origin (method url-fetch) (uri (pypi-uri name version)) (sha256 (base32 - "1x66f2x8miy3giff14higpcs70c0zb5d3gj6yn8ac6p183sngl72")))) + "0sh7g26i5ndpa8l7xq6rnijbi3jz5izjn0b98zcnm6wpgghszw48")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases -- cgit v1.2.3 From 48d17ba1d333109876bc53fe6ede6f8b3f519609 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 7 Sep 2018 21:01:48 -0400 Subject: gnu: linux-libre@4.4: Update to 4.4.154. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.154. --- 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 02d723316d..1670cf7a3c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -452,8 +452,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.153" - "195vzkkmjiicqfzd38hgf381rlz665rl06abzf8cww0gbnzvrf72" + (make-linux-libre "4.4.154" + "08i9fvrmswkydj538wg6c7ggxmhll0ff0bjkw8rnyslqwilfwr1i" %intel-compatible-systems #:configuration-file kernel-config)) -- cgit v1.2.3 From ddb419ce046f6ef7732b71af9f145c46d4aa42de Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 7 Sep 2018 21:02:30 -0400 Subject: gnu: linux-libre@4.9: Update to 4.9.125. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.125. --- 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 1670cf7a3c..cabc34b0df 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -446,8 +446,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.124" - "0p78gx5jiqvaf2cadf5jp40lzgarrg0m0ybf9w2499v28vjsp30q" + (make-linux-libre "4.9.125" + "1saihk61l1kk42jf8yfsfkm77zalq31f0bdlam3c1g7yw702wj9g" %intel-compatible-systems #:configuration-file kernel-config)) -- cgit v1.2.3 From 4be8fdd3ccb5d41438812d6781379457800345bd Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 7 Sep 2018 21:03:03 -0400 Subject: gnu: linux-libre@4.14: Update to 4.14.68. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.68. (%linux-libre-4.14-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 cabc34b0df..2b02870a73 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -436,8 +436,8 @@ It has been modified to remove all non-free binary blobs.") #:patches %linux-libre-4.18-patches #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.67") -(define %linux-libre-4.14-hash "050zvdxjy6sc64q75pr1gxsmh49chwav2pwxz8xlif39bvahnrpg") +(define %linux-libre-4.14-version "4.14.68") +(define %linux-libre-4.14-hash "05l5y0vbbl60jxdbqglqr9c99a8g8lfsp4mcqfpcx1pkh5br7i3l") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version -- cgit v1.2.3 From 090e3768e8a3157d440f6fdf513b4bf058328b0f Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 7 Sep 2018 21:05:14 -0400 Subject: gnu: linux-libre: Update to 4.18.6. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.6. (%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 2b02870a73..7d5b3aed86 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -405,8 +405,8 @@ It has been modified to remove all non-free binary blobs.") ;; supports qemu "virt" machine and possibly a large number of ARM boards. ;; See : https://wiki.debian.org/DebianKernel/ARMMP. -(define %linux-libre-version "4.18.5") -(define %linux-libre-hash "1y52ns34vh9p4pfj08xsycv8p0xywm6dbpdi0wwpkll1xgpqikvf") +(define %linux-libre-version "4.18.6") +(define %linux-libre-hash "1l5caid77vbfb54zrfxkk7qj7lrf9ck9kpn96kr45spkwl51wm8m") (define %linux-libre-4.18-patches (list %boot-logo-patch -- cgit v1.2.3 From 39b5d8fd9d0383124c93b85fd22c6d35545f694f Mon Sep 17 00:00:00 2001 From: Benjamin Slade Date: Fri, 7 Sep 2018 21:08:15 -0600 Subject: gnu: Add frotz, frotz-dumb-terminal, and frotz-sdl. * gnu/packages/games.scm (frotz, frotz-dumb-terminal, frotz-sdl): New variables. Signed-off-by: Kei Kebreau --- gnu/packages/games.scm | 157 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 157 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 728f763806..2015e3ce47 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -34,6 +34,7 @@ ;;; Copyright © 2018 okapi ;;; Copyright © 2018 Tim Gesthuizen ;;; Copyright © 2018 Madalin Ionel-Patrascu +;;; Copyright © 2018 Benjamin Slade ;;; ;;; This file is part of GNU Guix. ;;; @@ -5553,3 +5554,159 @@ open-source FPS of its kind.") (license (list license:gpl2+ license:bsd-3 ; /source/d0_blind_id folder and others (license:x11-style "" "See file rcon.pl."))))) + +(define-public frotz + (package + (name "frotz") + (version "2.44") + (source (origin + (method url-fetch) + (uri (list (string-append + "http://www.ifarchive.org/if-archive/infocom/interpreters/" + name "/" name "-" version ".tar.gz") + (string-append + "ftp://ftp.ifarchive.org/if-archive/infocom/interpreters/" + name "/" name "-" version ".tar.gz"))) + (sha256 + (base32 + "1v735xr3blznac8fnwa27s1vhllx4jpz7kw7qdw1bsfj6kq21v3k")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'curses + (lambda _ + (substitute* "Makefile" + (("lcurses") "lncurses")) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man6"))) + (install-file "frotz" bin) + (mkdir-p man) + (install-file "doc/frotz.6" man) + #t)))))) + (inputs `(("libmodplug" ,libmodplug) + ("libsamplerate" ,libsamplerate) + ("libsndfile" ,libsndfile) + ("libvorbis" ,libvorbis) + ("ncurses" ,ncurses))) + (synopsis "Portable Z-machine interpreter (ncurses version) for text adventure games") + (description "Frotz is an interpreter for Infocom games and other Z-machine +games in the text adventure/interactive fiction genre. This version of Frotz +complies with standard 1.0 of Graham Nelson's specification. It plays all +Z-code games V1-V8, including V6, with sound support through libao, and uses +ncurses for text display.") + (home-page "http://frotz.sourceforge.net") + (license license:gpl2+))) + +(define-public frotz-dumb-terminal + (package + (name "frotz-dumb-terminal") + (version "2.44") + (source (origin + (method url-fetch) + (uri (list (string-append + "http://www.ifarchive.org/if-archive/infocom/interpreters/" + "frotz" "/" "frotz" "-" version ".tar.gz") + (string-append + "ftp://ftp.ifarchive.org/if-archive/infocom/interpreters/" + "frotz" "/" "frotz" "-" version ".tar.gz"))) + (sha256 + (base32 + "1v735xr3blznac8fnwa27s1vhllx4jpz7kw7qdw1bsfj6kq21v3k")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "make" "dumb"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man6"))) + (install-file "dfrotz" bin) + (mkdir-p man) + (install-file "doc/dfrotz.6" man) + #t)))))) + (synopsis "Portable Z-machine dumb interpreter for text adventure games") + (description "Frotz is an interpreter for Infocom games and +other Z-machine games in the text adventure/interactive fiction genre. +dfrotz is the dumb interface version. You get no screen control; everything +is just printed to the terminal line by line. The terminal handles all the +scrolling. Maybe you'd like to experience what it's like to play Adventure on +a teletype. A much cooler use for compiling Frotz with the dumb interface is +that it can be wrapped in CGI scripting, PHP, and the like to allow people +to play games on webpages. It can also be made into a chat bot.") + (home-page "http://frotz.sourceforge.net") + (license license:gpl2+))) + +(define-public frotz-sdl + (let* ((commit "4de8c34f2116fff554af6216c30ec9d41bf50b24")) + (package + (name "frotz-sdl") + (version "2.45pre") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/DavidGriffith/frotz") + (commit commit))) + (sha256 + (base32 + "18ms21pcrl7ipcnyqnf8janamkryzx78frsgd9kfk67jvbj0z2k8")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'patch-makefile + (lambda _ + (substitute* "Makefile" + (("lcurses") "lncurses") + (("^BUILD_DATE_TIME =.*$") + "BUILD_DATE_TIME = \"2.45pre-20180907.00000\"\n")) + #t)) + (replace 'build + (lambda _ + (invoke "make" "sdl"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man6"))) + (install-file "sfrotz" bin) + (mkdir-p man) + (install-file "doc/sfrotz.6" man) + #t)))))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("which" ,which) + ("perl" ,perl))) + (inputs `(("sdl2" ,sdl2) + ("sdl2-mixer" ,sdl2-mixer) + ("libmodplug" ,libmodplug) + ("libsamplerate" ,libsamplerate) + ("libsndfile" ,libsndfile) + ("libvorbis" ,libvorbis) + ("ncurses" ,ncurses) + ("freetype" ,freetype) + ("libjpeg-turbo" ,libjpeg-turbo))) + (synopsis "Portable Z-machine interpreter (SDL port) for text adventure games") + (description "Frotz is an interpreter for Infocom games and other Z-machine +games in the text adventure/interactive fiction genre. This version of Frotz +using SDL fully supports all these versions of the Z-Machine including the +graphical version 6. Graphics and sound are created through the use of the SDL +libraries. AIFF sound effects and music in MOD and OGG formats are supported +when packaged in Blorb container files or optionally from individual files.") + (home-page "http://frotz.sourceforge.net") + (license license:gpl2+)))) -- cgit v1.2.3 From 445ecce92307aa7ab70cf02b70078e860de17dc0 Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Sat, 8 Sep 2018 16:55:32 +0200 Subject: gnu: nyacc: Update to 0.86.0. * gnu/packages/patches/nyacc-binary-literals.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/mes.scm (nyacc): Update to 0.86.0, add patch. --- gnu/packages/mes.scm | 6 ++--- gnu/packages/patches/nyacc-binary-literals.patch | 29 ++++++++++++++++++++++++ 2 files changed, 32 insertions(+), 3 deletions(-) create mode 100644 gnu/packages/patches/nyacc-binary-literals.patch (limited to 'gnu/packages') diff --git a/gnu/packages/mes.scm b/gnu/packages/mes.scm index 81d4145439..7bdad5e32f 100644 --- a/gnu/packages/mes.scm +++ b/gnu/packages/mes.scm @@ -39,15 +39,15 @@ (define-public nyacc (package (name "nyacc") - (version "0.83.3") + (version "0.86.0") (source (origin (method url-fetch) (uri (string-append "mirror://savannah/nyacc/" name "-" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (patches (search-patches "nyacc-binary-literals.patch")) (sha256 (base32 - "0120n0mdb6r58c4jc024dhwqy5s8a20waknijfhqjc59a884lrd6")))) + "0lkd9lyspvhxlfs0496gsllwinh62jk9wij6gpadvx9gwz6yavd9")))) (build-system gnu-build-system) (native-inputs `(("guile" ,guile-2.2))) diff --git a/gnu/packages/patches/nyacc-binary-literals.patch b/gnu/packages/patches/nyacc-binary-literals.patch new file mode 100644 index 0000000000..8159d74032 --- /dev/null +++ b/gnu/packages/patches/nyacc-binary-literals.patch @@ -0,0 +1,29 @@ +From 6a08014b77bf435f025ecdac08396580b85f159a Mon Sep 17 00:00:00 2001 +From: Jan Nieuwenhuizen +Date: Sat, 8 Sep 2018 20:22:45 +0200 +Subject: [PATCH] fix binary literals. + +--- + module/nyacc/lex.scm | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/module/nyacc/lex.scm b/module/nyacc/lex.scm +index 2ec9895..b205212 100644 +--- a/module/nyacc/lex.scm ++++ b/module/nyacc/lex.scm +@@ -345,10 +345,11 @@ + ((char-numeric? ch) (iter chl '$fixed ba 1 ch)) + ((char=? #\. ch) (iter (cons ch chl) #f ba 15 (read-char))) + (else #f))) +- ((10) ;; allow x after 0 ++ ((10) ;; allow x, b after 0 + (cond + ((eof-object? ch) (iter chl ty ba 5 ch)) + ((char=? #\x ch) (iter (cons ch chl) ty 16 1 (read-char))) ++ ((char=? #\b ch) (iter (cons ch chl) ty 2 1 (read-char))) + (else (iter chl ty ba 1 ch)))) + ((15) ;; got `.' only + (cond +-- +2.18.0 + -- cgit v1.2.3 From c665774a1ca9431746b1d559b06e24c1b05625d8 Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Sat, 8 Sep 2018 16:58:37 +0200 Subject: gnu: mes: Update to 0.17.1. * gnu/packages/patches/mes-nyacc-0.86.0.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/mes.scm (mes): Update to 0.17.1, depend on latest Nyacc 0.86.0. (nyacc-for-mes): Remove. --- gnu/packages/mes.scm | 20 +-- gnu/packages/patches/mes-nyacc-0.86.0.patch | 197 ++++++++++++++++++++++++++++ 2 files changed, 201 insertions(+), 16 deletions(-) create mode 100644 gnu/packages/patches/mes-nyacc-0.86.0.patch (limited to 'gnu/packages') diff --git a/gnu/packages/mes.scm b/gnu/packages/mes.scm index 7bdad5e32f..63a8db449a 100644 --- a/gnu/packages/mes.scm +++ b/gnu/packages/mes.scm @@ -59,36 +59,24 @@ extensive examples, including parsers for the Javascript and C99 languages.") (home-page "https://savannah.nongnu.org/projects/nyacc") (license (list gpl3+ lgpl3+)))) -(define-public nyacc-for-mes - (package - (inherit nyacc) - (version "0.80.42") - (source (origin - (method url-fetch) - (uri (string-append "https://gitlab.com/janneke/nyacc" - "/-/archive/v" version - "/nyacc-" version ".tar.gz")) - (sha256 - (base32 - "0c8c8kxir0h2d4nxr131xbkfs7c80haipmkp2g6677sh14wn0b3y")))))) - (define-public mes (let ((triplet "i686-unknown-linux-gnu")) (package (name "mes") - (version "0.17") + (version "0.17.1") (source (origin (method url-fetch) (uri (string-append "http://alpha.gnu.org/gnu/mes/" "mes-" version ".tar.gz")) + (patches (search-patches "mes-nyacc-0.86.0.patch")) (sha256 (base32 - "1j32x4zqy2cqjlg9m35f2411mwac2b0p5ch4hm99gddmfbxzgyhg")))) + "02g8zig53ffd0ai8kqhv2zj7bj2366a8hr6ydkwakmi2d1amyrna")))) (build-system gnu-build-system) (supported-systems '("i686-linux" "x86_64-linux")) (propagated-inputs `(("mescc-tools" ,mescc-tools) - ("nyacc" ,nyacc-for-mes))) + ("nyacc" ,nyacc))) (native-inputs `(("guile" ,guile-2.2) ,@(if (not (string-prefix? "i686-linux" (or (%current-target-system) diff --git a/gnu/packages/patches/mes-nyacc-0.86.0.patch b/gnu/packages/patches/mes-nyacc-0.86.0.patch new file mode 100644 index 0000000000..58dfc5a46b --- /dev/null +++ b/gnu/packages/patches/mes-nyacc-0.86.0.patch @@ -0,0 +1,197 @@ +From 9e610736bf779f3295c1192e748cd19cbbe3be28 Mon Sep 17 00:00:00 2001 +From: Jan Nieuwenhuizen +Date: Wed, 5 Sep 2018 20:28:06 +0200 +Subject: [PATCH 1/2] mes: Support Nyacc 0.85.3: Add char-set-copy. + +* mes/module/srfi/srfi-14.mes (char-set-copy): New function> +--- + mes/module/srfi/srfi-14.mes | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/mes/module/srfi/srfi-14.mes b/mes/module/srfi/srfi-14.mes +index 0be39b1e..a16d16ce 100644 +--- a/mes/module/srfi/srfi-14.mes ++++ b/mes/module/srfi/srfi-14.mes +@@ -52,3 +52,6 @@ + + (define (char-whitespace? c) + (char-set-contains? char-set:whitespace c)) ++ ++(define (char-set-copy cs) ++ (map identity cs)) +-- +2.18.0 + +From b952bdf44f11edbfc277600dc35236aae1769b54 Mon Sep 17 00:00:00 2001 +From: Jan Nieuwenhuizen +Date: Wed, 5 Sep 2018 22:14:34 +0200 +Subject: [PATCH 2/2] mes: Support Nyacc 0.85.3: Integrate progress. + +* mes/module/nyacc/lang/sx-util.mes: New file. +* mes/module/nyacc/version.mes: New file. +* mes/module/nyacc/lang/c99/cpp.mes (nyacc): Include them. +* mes/module/nyacc/lang/c99/parser.mes (nyacc): Include them. +* module/mescc/preprocess.scm (need-progress): New function. +(progress): New function. +(insert-progress-monitors): Use them to Integrate progress. +--- + mes/module/mescc/preprocess.mes | 1 + + mes/module/nyacc/lang/c99/cpp.mes | 1 + + mes/module/nyacc/lang/c99/parser.mes | 1 + + mes/module/nyacc/lang/sx-util.mes | 27 +++++++++++++++++++++ + mes/module/nyacc/version.mes | 26 +++++++++++++++++++++ + module/mescc/preprocess.scm | 35 ++++++++++++++++++++++++++++ + 6 files changed, 91 insertions(+) + create mode 100644 mes/module/nyacc/lang/sx-util.mes + create mode 100644 mes/module/nyacc/version.mes + +diff --git a/mes/module/mescc/preprocess.mes b/mes/module/mescc/preprocess.mes +index c7c5fcaa..022a372c 100644 +--- a/mes/module/mescc/preprocess.mes ++++ b/mes/module/mescc/preprocess.mes +@@ -24,4 +24,5 @@ + (mes-use-module (srfi srfi-13)) + (mes-use-module (srfi srfi-26)) + (mes-use-module (nyacc lang c99 parser)) ++(mes-use-module (nyacc version)) + (include-from-path "mescc/preprocess.scm") +diff --git a/mes/module/nyacc/lang/c99/cpp.mes b/mes/module/nyacc/lang/c99/cpp.mes +index fad1dc55..b25c4a93 100644 +--- a/mes/module/nyacc/lang/c99/cpp.mes ++++ b/mes/module/nyacc/lang/c99/cpp.mes +@@ -28,5 +28,6 @@ + + (mes-use-module (nyacc parse)) + (mes-use-module (nyacc lex)) ++(mes-use-module (nyacc lang sx-util)) + (mes-use-module (nyacc lang util)) + (include-from-path "nyacc/lang/c99/cpp.scm") +diff --git a/mes/module/nyacc/lang/c99/parser.mes b/mes/module/nyacc/lang/c99/parser.mes +index c51552d6..1a9aaf73 100644 +--- a/mes/module/nyacc/lang/c99/parser.mes ++++ b/mes/module/nyacc/lang/c99/parser.mes +@@ -32,6 +32,7 @@ + + (mes-use-module (nyacc lex)) + (mes-use-module (nyacc parse)) ++(mes-use-module (nyacc lang sx-util)) + (mes-use-module (nyacc lang util)) + (mes-use-module (nyacc lang c99 cpp)) + +diff --git a/mes/module/nyacc/lang/sx-util.mes b/mes/module/nyacc/lang/sx-util.mes +new file mode 100644 +index 00000000..41ac5b4a +--- /dev/null ++++ b/mes/module/nyacc/lang/sx-util.mes +@@ -0,0 +1,27 @@ ++;;; -*-scheme-*- ++ ++;;; GNU Mes --- Maxwell Equations of Software ++;;; Copyright © 2018 Jan (janneke) Nieuwenhuizen ++;;; ++;;; This file is part of GNU Mes. ++;;; ++;;; GNU Mes is free software; you can redistribute it and/or modify it ++;;; under the terms of the GNU General Public License as published by ++;;; the Free Software Foundation; either version 3 of the License, or (at ++;;; your option) any later version. ++;;; ++;;; GNU Mes is distributed in the hope that it will be useful, but ++;;; WITHOUT ANY WARRANTY; without even the implied warranty of ++;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++;;; GNU General Public License for more details. ++;;; ++;;; You should have received a copy of the GNU General Public License ++;;; along with GNU Mes. If not, see . ++ ++;;; Commentary: ++ ++;;; Code: ++ ++(mes-use-module (srfi srfi-1)) ++(mes-use-module (srfi srfi-16)) ++(include-from-path "nyacc/lang/sx-util.scm") +diff --git a/mes/module/nyacc/version.mes b/mes/module/nyacc/version.mes +new file mode 100644 +index 00000000..b9db628e +--- /dev/null ++++ b/mes/module/nyacc/version.mes +@@ -0,0 +1,26 @@ ++;;; -*-scheme-*- ++ ++;;; GNU Mes --- Maxwell Equations of Software ++;;; Copyright © 2018 Jan (janneke) Nieuwenhuizen ++;;; ++;;; This file is part of GNU Mes. ++;;; ++;;; GNU Mes is free software; you can redistribute it and/or modify it ++;;; under the terms of the GNU General Public License as published by ++;;; the Free Software Foundation; either version 3 of the License, or (at ++;;; your option) any later version. ++;;; ++;;; GNU Mes is distributed in the hope that it will be useful, but ++;;; WITHOUT ANY WARRANTY; without even the implied warranty of ++;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++;;; GNU General Public License for more details. ++;;; ++;;; You should have received a copy of the GNU General Public License ++;;; along with GNU Mes. If not, see . ++ ++;;; Commentary: ++ ++;;; Code: ++ ++(include-from-path "nyacc/version.scm") ++(display "nyacc version\n") +diff --git a/module/mescc/preprocess.scm b/module/mescc/preprocess.scm +index 9e341cba..c2efb32c 100644 +--- a/module/mescc/preprocess.scm ++++ b/module/mescc/preprocess.scm +@@ -26,9 +26,44 @@ + #:use-module (srfi srfi-1) + #:use-module (srfi srfi-26) + #:use-module (nyacc lang c99 parser) ++ #:use-module (nyacc lang c99 parser) ++ #:use-module (nyacc version) + #:use-module (mes guile) + #:export (c99-input->ast)) + ++(format (current-error-port) "*nyacc-version*=~a\n" *nyacc-version*) ++;; list of which rules you want progress reported ++(define need-progress ++ (assoc-ref ++ '(("0.85.3" (1 2 3)) ++ ("0.86.0" (1 2 3))) ++ *nyacc-version*)) ++ ++(define (progress o) ++ (when (and o (getenv "NYACC_DEBUG")) ++ (display " :" (current-error-port)) ++ (display o (current-error-port)) ++ (display "\n" (current-error-port)))) ++ ++(define (insert-progress-monitors act-v len-v) ++ (let ((n (vector-length act-v))) ++ (let loop ((ix 0)) ++ (when (< ix n) ++ (if (memq ix need-progress) ++ (vector-set ++ act-v ix ++ (lambda args ++ (progress (list-ref args (1- (vector-ref len-v ix)))) ++ (apply (vector-ref act-v ix) args)))) ++ (loop (1+ ix)))))) ++ ++(cond-expand ++ (guile ++ (insert-progress-monitors (@@ (nyacc lang c99 parser) c99-act-v) ++ (@@ (nyacc lang c99 parser) c99-len-v))) ++ (mes ++ (insert-progress-monitors c99-act-v c99-len-v))) ++ + (define (logf port string . rest) + (apply format (cons* port string rest)) + (force-output port) +-- +2.18.0 + -- cgit v1.2.3 From d7f99b3b767e50e73afbe041a2887aa1c878d990 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= Date: Sun, 9 Sep 2018 18:56:18 +0800 Subject: gnu: perl: Improve description. Fixes . * gnu/packages/perl.scm (perl)[description]: Use description from 'perlintro'. --- gnu/packages/perl.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 4d70e019b9..1bf4cb15fe 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -156,8 +156,10 @@ (files '("lib/perl5/site_perl"))))) (synopsis "Implementation of the Perl programming language") (description - "Perl 5 is a highly capable, feature-rich programming language with over -24 years of development.") + "Perl is a general-purpose programming language originally developed for +text manipulation and now used for a wide range of tasks including system +administration, web development, network programming, GUI development, and +more.") (home-page "http://www.perl.org/") (license gpl1+))) ; or "Artistic" -- cgit v1.2.3 From 6930ea33c979b3d4713c9a1c59bd24ca0f642980 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 17 Aug 2018 16:09:33 +0200 Subject: gnu: aircrack-ng: Use HTTPS. * gnu/packages/networking.scm (aircrack-ng)[source, home-page]: Use HTTPS. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index acf523d366..5a85a9d40d 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -766,7 +766,7 @@ live network and disk I/O bandwidth monitor.") (source (origin (method url-fetch) - (uri (string-append "http://download.aircrack-ng.org/aircrack-ng-" + (uri (string-append "https://download.aircrack-ng.org/aircrack-ng-" version ".tar.gz")) (sha256 (base32 @@ -807,7 +807,7 @@ live network and disk I/O bandwidth monitor.") (("\\$\\(ethtool") (string-append "$(" ethtool))) #t)))))) - (home-page "http://www.aircrack-ng.org") + (home-page "https://www.aircrack-ng.org") (synopsis "Assess WiFi network security") (description "Aircrack-ng is a complete suite of tools to assess WiFi network -- cgit v1.2.3 From b9114ccbad64db553b88d2b17206a34585b60e37 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 17 Aug 2018 16:13:51 +0200 Subject: gnu: aircrack-ng: Update to 1.3. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/networking.scm (aircrack-ng): Update to 1.3. [native-inputs]: Add autoconf, automake, libtool, and which. [inputs]: Add libpcap. [arguments]: Use conventional --options in #:configure-flags. Restore ‘configure’ phase. Add ‘patch-evalrev’ and customise ‘bootstrap’ phases. Simplify ‘absolutize-tools’ phase. --- gnu/packages/networking.scm | 48 +++++++++++++++++++++++++-------------------- 1 file changed, 27 insertions(+), 21 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 5a85a9d40d..abc616de3c 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -762,7 +762,7 @@ live network and disk I/O bandwidth monitor.") (define-public aircrack-ng (package (name "aircrack-ng") - (version "1.2-rc4") + (version "1.3") (source (origin (method url-fetch) @@ -770,42 +770,48 @@ live network and disk I/O bandwidth monitor.") version ".tar.gz")) (sha256 (base32 - "0dpzx9kddxpgzmgvdpl3rxn0jdaqhm5wxxndp1xd7d75mmmc2fnr")))) + "1jl30d0kibc82447fr3lgw75arik0l9729k94z76l7vl51y8mq4a")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config) + ("which" ,which))) (inputs `(("libgcrypt" ,libgcrypt) ("libnl" ,libnl) + ("libpcap" ,libpcap) ("ethtool" ,ethtool) ("pcre" ,pcre) ("sqlite" ,sqlite) ("zlib" ,zlib))) (arguments - `(#:make-flags `("sqlite=true" - "gcrypt=true" - "libnl=true" - "pcre=true" - "experimental=true" ;build wesside-ng, etc. - "AVX2FLAG=N" "AVX1FLAG=N" - ,,@(match (%current-system) - ((or "x86_64-linux" "i686-linux") - `("SSEFLAG=Y")) - (_ - `("NEWSSE=false"))) - ,(string-append "prefix=" %output)) + `(#:configure-flags + (list "--with-experimental=yes" ; build wesside-ng, etc. + "--with-gcrypt") ; openssl's the default #:phases (modify-phases %standard-phases - (delete 'configure) ;no configure phase + (add-before 'bootstrap 'patch-evalrev + (lambda _ + ;; Called by ./autogen.sh below, before the default + ;; ‘patch-shebangs’ phase has had a chance to run. + (substitute* "evalrev" + (("/bin/sh") + (which "sh"))) + #t)) + (replace 'bootstrap + (lambda _ + ;; Patch shebangs in generated files before running + ;; ./configure. + (setenv "NOCONFIGURE" "please") + (invoke "bash" "./autogen.sh"))) (add-after 'build 'absolutize-tools (lambda* (#:key inputs #:allow-other-keys) (let ((ethtool (string-append (assoc-ref inputs "ethtool") "/sbin/ethtool"))) (substitute* "scripts/airmon-ng" - (("\\[ ! -x \"\\$\\(command -v ethtool 2>&1)\" \\]") - (string-append "! " ethtool " --version " - ">/dev/null 2>&1")) - (("\\$\\(ethtool") - (string-append "$(" ethtool))) + (("ethtool ") + (string-append ethtool " "))) #t)))))) (home-page "https://www.aircrack-ng.org") (synopsis "Assess WiFi network security") -- cgit v1.2.3 From a0fad0374e583d44a73d6f76ead3bfeefc6d6b08 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 9 Sep 2018 14:59:49 +0200 Subject: gnu: links: Update to 2.17. * gnu/packages/web-browsers.scm (links): Update to 2.17. --- gnu/packages/web-browsers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index 45252c933d..2c2767dbbc 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -86,14 +86,14 @@ older or slower computers and embedded systems.") (define-public links (package (name "links") - (version "2.16") + (version "2.17") (source (origin (method url-fetch) (uri (string-append "http://links.twibright.com/download/" name "-" version ".tar.bz2")) (sha256 (base32 - "0gsa2gpb1grhssl5jzpc5pa0zi21mxi8g25rh5bacl70slw31w42")))) + "0dh2gbzcw8kxy81z4ggsynibnqs56b83vy8qgz7illsag1irff6q")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit v1.2.3 From 2d32a6572ddcd23aa1ae598a5d9b6e36f7f87b09 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 9 Sep 2018 14:38:44 +0200 Subject: gnu: perl-params-validate: Update to 1.29. * gnu/packages/perl.scm (perl-params-validate): Update to 1.29. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 1bf4cb15fe..8dea2051a6 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -6744,7 +6744,7 @@ checking parameters easier.") (define-public perl-params-validate (package (name "perl-params-validate") - (version "1.26") + (version "1.29") (source (origin (method url-fetch) @@ -6752,7 +6752,7 @@ checking parameters easier.") "Params-Validate-" version ".tar.gz")) (sha256 (base32 - "1vbj78qd46ip09i06dsbb62jfwpzp4bg7yi617v98nvim77w66l2")))) + "0cwpf8yxwyxbnwhf6rx4wnaq1q38j38i34a78a005shb8gxqv9j9")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build) -- cgit v1.2.3 From 49e63e38846977342c6b6cb44349db0b070f2a84 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 9 Sep 2018 14:38:35 +0200 Subject: gnu: perl-datetime: Update to 1.50. * gnu/packages/perl.scm (perl-datetime): Update to 1.50. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 8dea2051a6..a3f899fdb3 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -2180,7 +2180,7 @@ hours, minutes, seconds, and time zones.") (define-public perl-datetime (package (name "perl-datetime") - (version "1.49") + (version "1.50") (source (origin (method url-fetch) @@ -2188,7 +2188,7 @@ hours, minutes, seconds, and time zones.") "DateTime-" version ".tar.gz")) (sha256 (base32 - "0hbw4zq1562slnz7g7hyhfhyq98dzkk3i5g21x3xra5cvfix93kh")))) + "165iqk1xvhs5j0kzsipa7aqycx3h37wqsl2r4jl104yqvmqhqszd")))) (build-system perl-build-system) (native-inputs `(("perl-cpan-meta-check" ,perl-cpan-meta-check) -- cgit v1.2.3 From 04fc0b9489e97e55914d0e1f9b1439a5b7964854 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 9 Sep 2018 14:13:51 +0200 Subject: gnu: perl-namespace-clean: Update to 0.27. * gnu/packages/perl.scm (perl-namespace-clean): Update to 0.27. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index a3f899fdb3..c81829165e 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -6364,7 +6364,7 @@ anything that looks like a method.") (define-public perl-namespace-clean (package (name "perl-namespace-clean") - (version "0.25") + (version "0.27") (source (origin (method url-fetch) @@ -6372,7 +6372,7 @@ anything that looks like a method.") "namespace-clean-" version ".tar.gz")) (sha256 (base32 - "016dds70ql1mp18b07chkxiy4drn976ibnbshqc2hmhrh9xjnsll")))) + "17dg64pd4bwi2ad3p8ykwys1zha7kg8a8ykvks7wfg8q7qyah44a")))) (build-system perl-build-system) (propagated-inputs `(("perl-package-stash" ,perl-package-stash) -- cgit v1.2.3 From 748e6e1271750319cfa1096f28f9c8588356bcf5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 9 Sep 2018 14:13:43 +0200 Subject: gnu: perl-getopt-long-descriptive: Update to 0.103. * gnu/packages/perl.scm (perl-getopt-long-descriptive): Update to 0.103. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index c81829165e..1c6b251198 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -3812,7 +3812,7 @@ single-letter approach, is provided but not enabled by default.") (define-public perl-getopt-long-descriptive (package (name "perl-getopt-long-descriptive") - (version "0.102") + (version "0.103") (source (origin (method url-fetch) @@ -3820,7 +3820,7 @@ single-letter approach, is provided but not enabled by default.") "Getopt-Long-Descriptive-" version ".tar.gz")) (sha256 (base32 - "0ii8xafvlph5vzcqp3dpc83lg7nkg3l1l2hmqdf5382a567vkm4s")))) + "1cpl240qxmh7jf85ai9sfkp3nzm99syya4jxidizp7aa83kvmqbh")))) (build-system perl-build-system) (native-inputs `(("perl-cpan-meta-check" ,perl-cpan-meta-check) -- cgit v1.2.3 From 4e77b75e114d8ab50ead5e28ae04556abc6c6883 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 9 Sep 2018 14:13:32 +0200 Subject: gnu: perl-extutils-helpers: Update to 0.026. * gnu/packages/perl.scm (perl-extutils-helpers): Update to 0.026. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 1c6b251198..0de597ca59 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -3232,7 +3232,7 @@ XS interface besides the perl one.") (define-public perl-extutils-helpers (package (name "perl-extutils-helpers") - (version "0.022") + (version "0.026") (source (origin (method url-fetch) @@ -3240,7 +3240,7 @@ XS interface besides the perl one.") "ExtUtils-Helpers-" version ".tar.gz")) (sha256 (base32 - "15dalfwmpfmifw312i5pwiai8134pxf7b2804shlqhdk1xqczy6k")))) + "05ilqcj1rg5izr09dsqmy5di4fvq6ph4k0chxks7qmd4j1kip46y")))) (build-system perl-build-system) (home-page "https://metacpan.org/release/ExtUtils-Helpers") (synopsis "Various portability utilities for module builders") -- cgit v1.2.3 From 15dbc911f6deb7c30e7fde2e9bb17e3b671183e5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 9 Sep 2018 14:13:22 +0200 Subject: gnu: perl-extutils-installpaths: Update to 0.012. * gnu/packages/perl.scm (perl-extutils-installpaths): Update to 0.012. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 0de597ca59..54dd29deec 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -3168,7 +3168,7 @@ only about 40% as many lines of code and with zero non-core dependencies.") (define-public perl-extutils-installpaths (package (name "perl-extutils-installpaths") - (version "0.011") + (version "0.012") (source (origin (method url-fetch) @@ -3176,7 +3176,7 @@ only about 40% as many lines of code and with zero non-core dependencies.") "ExtUtils-InstallPaths-" version ".tar.gz")) (sha256 (base32 - "0z06y0fhx9hy9x01abb7s2xdbqrh9x4ps7avmlf4bwfwih2gl2bn")))) + "1v9lshfhm9ck4p0v77arj5f7haj1mmkqal62lgzzvcds6wq5www4")))) (build-system perl-build-system) (propagated-inputs `(("perl-extutils-config" ,perl-extutils-config))) -- cgit v1.2.3 From 9ad80992d0111afeedfb47cd3594397e844517ba Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 9 Sep 2018 14:13:12 +0200 Subject: gnu: perl-config-autoconf: Update to 0.317. * gnu/packages/perl.scm (perl-config-autoconf): Update to 0.317. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 54dd29deec..fc0553798b 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -1409,7 +1409,7 @@ supports XML, YAML, JSON, Apache-style configuration, and Perl code.") (define-public perl-config-autoconf (package (name "perl-config-autoconf") - (version "0.315") + (version "0.317") (source (origin (method url-fetch) @@ -1417,7 +1417,7 @@ supports XML, YAML, JSON, Apache-style configuration, and Perl code.") "Config-AutoConf-" version ".tar.gz")) (sha256 (base32 - "0h39x9rzrhhilpg8yxlzpka269qrzsjg0iy0c1b9xflqlvhx2g2b")))) + "1qcwib4yaml5z2283qy5khjcydyibklsnk8zrk9wzdzc5wnv5r01")))) (build-system perl-build-system) (propagated-inputs `(("perl-capture-tiny" ,perl-capture-tiny))) -- cgit v1.2.3 From bb5e06a35e55d687cbc5c64299d039e5de7d9c8c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 9 Sep 2018 13:23:03 +0200 Subject: gnu: perl-pegex: Update to 0.67. * gnu/packages/perl.scm (perl-pegex): Update to 0.67. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index fc0553798b..c4c3b665db 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -6937,7 +6937,7 @@ for correctness.") (define-public perl-pegex (package (name "perl-pegex") - (version "0.64") + (version "0.67") (source (origin (method url-fetch) @@ -6946,7 +6946,7 @@ for correctness.") version ".tar.gz")) (sha256 (base32 - "1kb7y2cc3nibbn8i8y3vrzz1f9h3892nbf8jj88c5fdgpmj05q17")))) + "149015ra2figalxrnj72fz02qc5cm96xg6x8d6kmyanfmrrxzf9w")))) (build-system perl-build-system) (native-inputs `(("perl-file-sharedir-install" ,perl-file-sharedir-install) -- cgit v1.2.3 From bb105673b88cea5c290ea9a16094ce29fcf0f475 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 9 Sep 2018 13:17:08 +0200 Subject: gnu: musl: Update to 1.1.20. * gnu/packages/musl.scm (musl): Update to 1.1.20. --- gnu/packages/musl.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/musl.scm b/gnu/packages/musl.scm index ff789b8c6f..357372becd 100644 --- a/gnu/packages/musl.scm +++ b/gnu/packages/musl.scm @@ -28,17 +28,17 @@ (define-public musl (package (name "musl") - (version "1.1.19") + (version "1.1.20") (source (origin (method url-fetch) (uri (string-append "http://www.musl-libc.org/releases/" name "-" version ".tar.gz")) (sha256 (base32 - "1nf1wh44bhm8gdcfr75ayib29b99vpq62zmjymrq7f96h9bshnfv")))) + "0q8dsjxl41dccscv9a0r78bs7jap57mn4mni5pwbbip6s1qqggj4")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; Musl has no tests + `(#:tests? #f ; Musl has no tests #:configure-flags (list "--disable-gcc-wrapper"))) (synopsis "Small C standard library") -- cgit v1.2.3 From c2311644a5432eb118d5e789288a0ddf43990684 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 8 Sep 2018 14:56:54 +0200 Subject: gnu: signify: Update to 24. * gnu/packages/crypto.scm (signify): Update to 24. --- gnu/packages/crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index e070ef61ac..d9111135e8 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -126,7 +126,7 @@ communication, encryption, decryption, signatures, etc.") (define-public signify (package (name "signify") - (version "23") + (version "24") (source (origin (method url-fetch) (uri (string-append "https://github.com/aperezdc/signify/" @@ -134,7 +134,7 @@ communication, encryption, decryption, signatures, etc.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0c70mzawgahsvmsv4xdrass4pgyynd67ipd9lij0fgi8wkq0ns8w")))) + "0594vyvkq176xxzaz9xbq8qs0xdnr8s9gkd1prblwpdvnzmw0xvc")))) (build-system gnu-build-system) ;; TODO Build with libwaive (described in README.md), to implement something ;; like OpenBSD's pledge(). -- cgit v1.2.3 From b64e67ad40f7cf6d4867cd38eee0e4ec16cd6e9a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 8 Sep 2018 14:55:12 +0200 Subject: gnu: cloc: Update to 1.78. * gnu/packages/code.scm (cloc): Update to 1.78. [source]: Update URI. --- gnu/packages/code.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 85ee6c2877..b3fbea0b38 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -211,16 +211,16 @@ COCOMO model or user-provided parameters.") (define-public cloc (package (name "cloc") - (version "1.76") + (version "1.78") (source (origin (method url-fetch) (uri (string-append - "https://github.com/AlDanial/cloc/releases/download/v" version + "https://github.com/AlDanial/cloc/releases/download/" version "/cloc-" version ".tar.gz")) (sha256 (base32 - "05srlvzwisr7y7ymvzb5yfdsrspja27ysqdmkwhiiivy84mq2gnl")))) + "176xklr2qsgxh9zdb565gib6pp4gsm585rz5fvyphgjy4i679wkv")))) (build-system gnu-build-system) (inputs `(("coreutils" ,coreutils) -- cgit v1.2.3 From 81bf0fd0d4a7e78febb394576ea849285fc2d329 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 4 Sep 2018 18:53:13 +0200 Subject: gnu: julia: Update objconv input. * gnu/packages/julia.scm (julia)[inputs]: Update the hash of "objconv", which does not have a stable URL. Add a file name and use HTTPS while at it. --- gnu/packages/julia.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 39e2322739..fb9b0eeedf 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -355,10 +355,12 @@ ("objconv" ,(origin (method url-fetch) - (uri "http://www.agner.org/optimize/objconv.zip") + ;; No versioned URL, see for updates. + (uri "https://www.agner.org/optimize/objconv.zip") + (file-name "objconv-2018-08-15.zip") (sha256 (base32 - "1fi7qa2sd9vb35dvkgripjf0fayzg2qmff215f8agfqfiwd1g8qs")))) + "09y4pwxfs6fl47cyingbf95i2rxx74wmycl9fd4ldcgvpx9bzdrx")))) ("dsfmt" ,(origin (method url-fetch) -- cgit v1.2.3 From 617cf5de922e54042e93696d341350149942c6c4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 6 Sep 2018 19:14:39 +0200 Subject: gnu: mpfr: Update home page. * gnu/packages/multiprecision.scm (mpfr)[home-page]: Use HTTPS. --- gnu/packages/multiprecision.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/multiprecision.scm b/gnu/packages/multiprecision.scm index e185a98359..4f5eac16b9 100644 --- a/gnu/packages/multiprecision.scm +++ b/gnu/packages/multiprecision.scm @@ -108,7 +108,7 @@ algebra.") library for performing multiple-precision, floating-point computations with correct rounding.") (license lgpl3+) - (home-page "http://www.mpfr.org/"))) + (home-page "https://www.mpfr.org/"))) (define-public mpc (package -- cgit v1.2.3 From 249846bfdee20e28cc38425aa454ce2f932441f9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 7 Sep 2018 13:28:20 +0200 Subject: gnu: libsoup: Update to 2.64.0. * gnu/packages/gnome.scm (libsoup): Update to 2.64.0. [inputs]: Add LIBPSL. --- gnu/packages/gnome.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 13eb41e055..1a0cc9cc11 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -2455,7 +2455,7 @@ libxml to ease remote use of the RESTful API.") (define-public libsoup (package (name "libsoup") - (version "2.62.3") + (version "2.64.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/libsoup/" @@ -2463,7 +2463,7 @@ libxml to ease remote use of the RESTful API.") name "-" version ".tar.xz")) (sha256 (base32 - "0whi8p03kpbp68kg6fg3vb7rhykjp7wn3nlbzy9j0p298zjss4nk")))) + "09z7g3spww3f84y8jmicdd6lqp360mbggpg5h1fq1v4p5ihcjnyr")))) (build-system gnu-build-system) (outputs '("out" "doc")) (arguments @@ -2567,6 +2567,7 @@ libxml to ease remote use of the RESTful API.") ("libxml2" ,libxml2))) (inputs `(("glib-networking" ,glib-networking) + ("libpsl" ,libpsl) ("sqlite" ,sqlite))) (home-page "https://live.gnome.org/LibSoup/") (synopsis "GLib-based HTTP Library") -- cgit v1.2.3 From 37f9cfae43d8614904335434c91ea1c0d9d69508 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 7 Sep 2018 13:34:31 +0200 Subject: gnu: msmtp: Update to 1.8.0. * gnu/packages/mail.scm (msmtp): Update to 1.8.0. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 4944dd7622..91a8822cfd 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1071,7 +1071,7 @@ which can add many functionalities to the base client.") (define-public msmtp (package (name "msmtp") - (version "1.6.8") + (version "1.8.0") (source (origin (method url-fetch) @@ -1079,7 +1079,7 @@ which can add many functionalities to the base client.") "/msmtp-" version ".tar.xz")) (sha256 (base32 - "1ysrnshvwhzwmvb2walw5i9jdzlvmckj7inr0xnvb26q0jirbzsm")))) + "1k9wwlapkxk9ql3xq05y6vwn6ziqk9b1v8lyhj1866qd02zhqwxx")))) (build-system gnu-build-system) (inputs `(("libidn" ,libidn) -- cgit v1.2.3 From 91b3a6d4db848ae5de65ca511dc2deb27c7cb7dc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 7 Sep 2018 13:39:31 +0200 Subject: gnu: msmtp: Remove unneeded input. * gnu/packages/mail.scm (msmtp)[inputs]: Remove LIBIDN, which is only required when using OpenSSL (or GnuTLS sans IDN support). --- gnu/packages/mail.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 91a8822cfd..024e75aaa1 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1082,8 +1082,7 @@ which can add many functionalities to the base client.") "1k9wwlapkxk9ql3xq05y6vwn6ziqk9b1v8lyhj1866qd02zhqwxx")))) (build-system gnu-build-system) (inputs - `(("libidn" ,libidn) - ("libsecret" ,libsecret) + `(("libsecret" ,libsecret) ("gnutls" ,gnutls) ("zlib" ,zlib) ("gsasl" ,gsasl))) -- cgit v1.2.3 From e9c1492f66b0ca5c86d6f23655b713978a4d7644 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 7 Sep 2018 13:58:31 +0200 Subject: gnu: glm: Update to 0.9.9.1. * gnu/packages/maths.scm (glm): Update to 0.9.9.1. --- 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 d2b9df01a7..ebbe2b0294 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3253,7 +3253,7 @@ Failure to do so will result in a library with poor performance.") (define-public glm (package (name "glm") - (version "0.9.9.0") + (version "0.9.9.1") (source (origin (method url-fetch) @@ -3261,7 +3261,7 @@ Failure to do so will result in a library with poor performance.") version "/glm-" version ".zip")) (sha256 (base32 - "0ihjadp2sb8w312a276skfjsljm3y41bjscbxf79wn23gi00giz1")))) + "042a23hmxfs429czkmlg5ixf28aikzfbw18780prj2gcd4flgw8h")))) (build-system cmake-build-system) (native-inputs `(("unzip" ,unzip))) -- cgit v1.2.3 From 1448fa254732a76fc138059043a6b5f12c71367b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 7 Sep 2018 19:29:00 +0200 Subject: gnu: openal: Update to 1.19.0. * gnu/packages/audio.scm (openal): Update to 1.19.0. --- 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 e731569ae1..3b898c024a 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1908,7 +1908,7 @@ lv2-c++-tools.") (define-public openal (package (name "openal") - (version "1.18.2") + (version "1.19.0") (source (origin (method url-fetch) (uri (string-append @@ -1916,7 +1916,7 @@ lv2-c++-tools.") version ".tar.bz2")) (sha256 (base32 - "10kydm8701a2kppiss9sdidn1820cmzhqgx1b2bsa5dsgzic32lz")))) + "1mhf5bsb58s1xk6hvxl7ly7rd4rpl9z8h07xl1q94brywykg7bgi")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; no check target -- cgit v1.2.3 From a617fd55df0fbdae951ec82b81ad512436e972ed Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 7 Sep 2018 20:01:57 +0200 Subject: gnu: OpenBLAS: Update source URI. * gnu/packages/maths.scm (openblas)[source](uri): Use the more stable SourceForge mirror. --- 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 ebbe2b0294..01bd03c600 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2846,8 +2846,8 @@ parts of it.") (source (origin (method url-fetch) - (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v" - version)) + (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20" + version "%20version.tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 -- cgit v1.2.3 From 910a20e2b8ac6d1c331ff79535831cce6222b3a3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 8 Sep 2018 07:59:06 +0200 Subject: gnu: jbig2dec: Replace with 0.15 [security fixes]. * gnu/packages/image.scm (jbig2dec-0.15): New public variable. (jbig2dec)[replacement]: New field. --- gnu/packages/image.scm | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 81d22ed42d..78fb30c279 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Fis Trivial ;;; Copyright © 2018 Pierre Neidhardt +;;; Copyright © 2018 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -495,6 +496,7 @@ arithmetic ops.") (package (name "jbig2dec") (version "0.14") + (replacement jbig2dec-0.15) (source (origin (method url-fetch) @@ -519,6 +521,21 @@ work.") (home-page "https://jbig2dec.com") (license license:gpl2+))) +;; This is a bugfix release from an ongoing Ghostscript security audit. +;; It was released alongside Ghostscript 9.24. +(define-public jbig2dec-0.15 + (package + (inherit jbig2dec) + (version "0.15") + (source (origin + (inherit (package-source jbig2dec)) + (uri (string-append "https://github.com/ArtifexSoftware" + "/ghostpdl-downloads/releases/download/gs924/" + "jbig2dec-" version ".tar.gz")) + (sha256 + (base32 + "0m1qwpbjbirgw2fqznbajdhdhh35d6xa2csr64lpjz735pvimykb")))))) + (define-public openjpeg (package (name "openjpeg") -- cgit v1.2.3 From 0084744b3af0a6f8e125120143f57567902339a8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 8 Sep 2018 12:46:22 +0200 Subject: gnu: ghostscript: Update replacement to 9.24 [security fixes]. The following CVEs are fixed with this release: CVE-2018-15908, CVE-2018-15909, CVE-2018-15910, CVE-2018-15911, CVE-2018-16509, CVE-2018-16510, CVE-2018-16511, CVE-2018-16513, CVE-2018-16539, CVE-2018-16540, CVE-2018-16541, CVE-2018-16542, CVE-2018-16543. * gnu/packages/patches/ghostscript-CVE-2018-10194.patch: Delete file. * gnu/packages/patches/ghostscript-CVE-2018-16509.patch, gnu/packages/patches/ghostscript-bug-699708.patch: New files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/ghostscript.scm (ghostscript/fixed): Update to 9.24. [source](patches): Remove 'ghostscript-CVE-2018-10194.patch' and 'ghostscript-runpath.patch'. Add 'ghostscript-CVE-2018-16509.patch' and 'ghostscript-bug-699708.patch'. [arguments]: Add LDFLAGS to #:configure-flags, and a phase to create output directory. --- gnu/packages/ghostscript.scm | 37 +++- .../patches/ghostscript-CVE-2018-10194.patch | 52 ------ .../patches/ghostscript-CVE-2018-16509.patch | 193 +++++++++++++++++++++ gnu/packages/patches/ghostscript-bug-699708.patch | 160 +++++++++++++++++ 4 files changed, 387 insertions(+), 55 deletions(-) delete mode 100644 gnu/packages/patches/ghostscript-CVE-2018-10194.patch create mode 100644 gnu/packages/patches/ghostscript-CVE-2018-16509.patch create mode 100644 gnu/packages/patches/ghostscript-bug-699708.patch (limited to 'gnu/packages') diff --git a/gnu/packages/ghostscript.scm b/gnu/packages/ghostscript.scm index 1240b1dc16..518e18397b 100644 --- a/gnu/packages/ghostscript.scm +++ b/gnu/packages/ghostscript.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2017 Leo Famulari ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -38,8 +39,10 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix utils) #:use-module (guix build-system gnu) - #:use-module (guix build-system trivial)) + #:use-module (guix build-system trivial) + #:use-module (srfi srfi-1)) (define-public lcms (package @@ -255,11 +258,39 @@ output file formats and printers.") (hidden-package (package (inherit ghostscript) + (version "9.24") (source (origin (inherit (package-source ghostscript)) - (patches (append (origin-patches (package-source ghostscript)) - (search-patches "ghostscript-CVE-2018-10194.patch")))))))) + (uri (string-append "https://github.com/ArtifexSoftware/" + "ghostpdl-downloads/releases/download/gs" + (string-delete #\. version) + "/ghostscript-" version ".tar.xz")) + (sha256 + (base32 + "1mk922rnml93w2g42yxiyn8xqanc50cm65irrgh0b6lp4kgifjfl")) + (patches (search-patches "ghostscript-CVE-2018-16509.patch" + "ghostscript-bug-699708.patch" + "ghostscript-no-header-creationdate.patch" + "ghostscript-no-header-id.patch" + "ghostscript-no-header-uuid.patch")))) + (arguments + (substitute-keyword-arguments (package-arguments ghostscript) + ((#:configure-flags flags) + ;; Notice that we removed the 'ghostscript-runpath' patch above. + ;; The reason is that it conflicts with an upstream change that + ;; takes LDFLAGS into account. + `(cons (string-append "LDFLAGS=-Wl,-rpath=" + (assoc-ref %outputs "out") "/lib") + ,flags)) + ((#:phases phases) + `(modify-phases ,phases + (add-before 'configure 'create-output-directory + (lambda* (#:key outputs #:allow-other-keys) + ;; Unfortunately the configure script refuses to function if + ;; the directory specified as -rpath does not already exist. + (mkdir-p (string-append (assoc-ref outputs "out") "/lib")) + #t))))))))) (define-public ghostscript/x (package/inherit ghostscript diff --git a/gnu/packages/patches/ghostscript-CVE-2018-10194.patch b/gnu/packages/patches/ghostscript-CVE-2018-10194.patch deleted file mode 100644 index 242e57c27c..0000000000 --- a/gnu/packages/patches/ghostscript-CVE-2018-10194.patch +++ /dev/null @@ -1,52 +0,0 @@ -Fix CVE-2018-10194: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-10194 -https://bugs.ghostscript.com/show_bug.cgi?id=699255 - -Patch copied from upstream source repository: - -https://git.ghostscript.com/?p=ghostpdl.git;a=commit;h=39b1e54b2968620723bf32e96764c88797714879 - -From 39b1e54b2968620723bf32e96764c88797714879 Mon Sep 17 00:00:00 2001 -From: Ken Sharp -Date: Wed, 18 Apr 2018 15:46:32 +0100 -Subject: [PATCH] pdfwrite - Guard against trying to output an infinite number - -Bug #699255 " Buffer overflow on pprintg1 due to mishandle postscript file data to pdf" - -The file uses an enormous parameter to xyxhow, causing an overflow in -the calculation of text positioning (value > 1e39). - -Since this is basically a nonsense value, and PostScript only supports -real values up to 1e38, this patch follows the same approach as for -a degenerate CTM, and treats it as 0. - -Adobe Acrobat Distiller throws a limitcheck error, so we could do that -instead if this approach proves to be a problem. ---- - devices/vector/gdevpdts.c | 7 ++++++- - 1 file changed, 6 insertions(+), 1 deletion(-) - -diff --git a/devices/vector/gdevpdts.c b/devices/vector/gdevpdts.c -index 848ad781f..172fe6bc3 100644 ---- a/devices/vector/gdevpdts.c -+++ b/devices/vector/gdevpdts.c -@@ -103,9 +103,14 @@ append_text_move(pdf_text_state_t *pts, double dw) - static int - set_text_distance(gs_point *pdist, double dx, double dy, const gs_matrix *pmat) - { -- int code = gs_distance_transform_inverse(dx, dy, pmat, pdist); -+ int code; - double rounded; - -+ if (dx > 1e38 || dy > 1e38) -+ code = gs_error_undefinedresult; -+ else -+ code = gs_distance_transform_inverse(dx, dy, pmat, pdist); -+ - if (code == gs_error_undefinedresult) { - /* The CTM is degenerate. - Can't know the distance in user space. --- -2.18.0 - diff --git a/gnu/packages/patches/ghostscript-CVE-2018-16509.patch b/gnu/packages/patches/ghostscript-CVE-2018-16509.patch new file mode 100644 index 0000000000..50ffa3cb98 --- /dev/null +++ b/gnu/packages/patches/ghostscript-CVE-2018-16509.patch @@ -0,0 +1,193 @@ +Ghostscript 9.24 was released with an incomplete fix for CVE-2018-16509: +https://nvd.nist.gov/vuln/detail/CVE-2018-16509 +https://bugs.chromium.org/p/project-zero/issues/detail?id=1640#c19 +https://bugs.ghostscript.com/show_bug.cgi?id=699718 + +The reproducers no longer work after applying these commits: + +https://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=5812b1b78fc4d36fdc293b7859de69241140d590 +https://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=e914f1da46e33decc534486598dc3eadf69e6efb +https://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=3e5d316b72e3965b7968bb1d96baa137cd063ac6 +https://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=643b24dbd002fb9c131313253c307cf3951b3d47 + +This patch is a "squashed" version of those. + +diff --git a/Resource/Init/gs_setpd.ps b/Resource/Init/gs_setpd.ps +index bba3c8c0e..8fa7c51df 100644 +--- a/Resource/Init/gs_setpd.ps ++++ b/Resource/Init/gs_setpd.ps +@@ -95,27 +95,41 @@ level2dict begin + { % Since setpagedevice doesn't create new device objects, + % we must (carefully) reinstall the old parameters in + % the same device. +- .currentpagedevice pop //null currentdevice //null .trysetparams ++ .currentpagedevice pop //null currentdevice //null ++ { .trysetparams } .internalstopped ++ { ++ //null ++ } if + dup type /booleantype eq + { pop pop } +- { % This should never happen! ++ { + SETPDDEBUG { (Error in .trysetparams!) = pstack flush } if +- cleartomark pop pop pop ++ {cleartomark pop pop pop} .internalstopped pop ++ % if resetting the entire device state failed, at least put back the ++ % security related key ++ currentdevice //null //false mark /.LockSafetyParams ++ currentpagedevice /.LockSafetyParams .knownget not ++ {systemdict /SAFER .knownget not {//false} } if ++ .putdeviceparamsonly + /.installpagedevice cvx /rangecheck signalerror + } + ifelse pop pop + % A careful reading of the Red Book reveals that an erasepage + % should occur, but *not* an initgraphics. + erasepage .beginpage +- } bind def ++ } bind executeonly def + + /.uninstallpagedevice +- { 2 .endpage { .currentnumcopies //false .outputpage } if ++ { ++ {2 .endpage { .currentnumcopies //false .outputpage } if} .internalstopped pop + nulldevice + } bind def + + (%grestorepagedevice) cvn +- { .uninstallpagedevice grestore .installpagedevice ++ { ++ .uninstallpagedevice ++ grestore ++ .installpagedevice + } bind def + + (%grestoreallpagedevice) cvn +diff --git a/psi/zdevice2.c b/psi/zdevice2.c +index 0c7080d57..159a0c0d9 100644 +--- a/psi/zdevice2.c ++++ b/psi/zdevice2.c +@@ -251,8 +251,8 @@ z2currentgstate(i_ctx_t *i_ctx_p) + /* ------ Wrappers for operators that reset the graphics state. ------ */ + + /* Check whether we need to call out to restore the page device. */ +-static bool +-restore_page_device(const gs_gstate * pgs_old, const gs_gstate * pgs_new) ++static int ++restore_page_device(i_ctx_t *i_ctx_p, const gs_gstate * pgs_old, const gs_gstate * pgs_new) + { + gx_device *dev_old = gs_currentdevice(pgs_old); + gx_device *dev_new; +@@ -260,9 +260,10 @@ restore_page_device(const gs_gstate * pgs_old, const gs_gstate * pgs_new) + gx_device *dev_t2; + bool samepagedevice = obj_eq(dev_old->memory, &gs_int_gstate(pgs_old)->pagedevice, + &gs_int_gstate(pgs_new)->pagedevice); ++ bool LockSafetyParams = dev_old->LockSafetyParams; + + if ((dev_t1 = (*dev_proc(dev_old, get_page_device)) (dev_old)) == 0) +- return false; ++ return 0; + /* If we are going to putdeviceparams in a callout, we need to */ + /* unlock temporarily. The device will be re-locked as needed */ + /* by putdeviceparams from the pgs_old->pagedevice dict state. */ +@@ -271,23 +272,51 @@ restore_page_device(const gs_gstate * pgs_old, const gs_gstate * pgs_new) + dev_new = gs_currentdevice(pgs_new); + if (dev_old != dev_new) { + if ((dev_t2 = (*dev_proc(dev_new, get_page_device)) (dev_new)) == 0) +- return false; +- if (dev_t1 != dev_t2) +- return true; ++ samepagedevice = true; ++ else if (dev_t1 != dev_t2) ++ samepagedevice = false; ++ } ++ ++ if (LockSafetyParams && !samepagedevice) { ++ const int required_ops = 512; ++ const int required_es = 32; ++ ++ /* The %grestorepagedevice must complete: the biggest danger ++ is operand stack overflow. As we use get/putdeviceparams ++ that means pushing all the device params onto the stack, ++ pdfwrite having by far the largest number of parameters ++ at (currently) 212 key/value pairs - thus needing (currently) ++ 424 entries on the op stack. Allowing for working stack ++ space, and safety margin..... ++ */ ++ if (required_ops + ref_stack_count(&o_stack) >= ref_stack_max_count(&o_stack)) { ++ gs_currentdevice(pgs_old)->LockSafetyParams = LockSafetyParams; ++ return_error(gs_error_stackoverflow); ++ } ++ /* We also want enough exec stack space - 32 is an overestimate of ++ what we need to complete the Postscript call out. ++ */ ++ if (required_es + ref_stack_count(&e_stack) >= ref_stack_max_count(&e_stack)) { ++ gs_currentdevice(pgs_old)->LockSafetyParams = LockSafetyParams; ++ return_error(gs_error_execstackoverflow); ++ } + } + /* + * The current implementation of setpagedevice just sets new + * parameters in the same device object, so we have to check + * whether the page device dictionaries are the same. + */ +- return !samepagedevice; ++ return samepagedevice ? 0 : 1; + } + + /* - grestore - */ + static int + z2grestore(i_ctx_t *i_ctx_p) + { +- if (!restore_page_device(igs, gs_gstate_saved(igs))) ++ int code = restore_page_device(i_ctx_p, igs, gs_gstate_saved(igs)); ++ if (code < 0) return code; ++ ++ if (code == 0) + return gs_grestore(igs); + return push_callout(i_ctx_p, "%grestorepagedevice"); + } +@@ -297,7 +326,9 @@ static int + z2grestoreall(i_ctx_t *i_ctx_p) + { + for (;;) { +- if (!restore_page_device(igs, gs_gstate_saved(igs))) { ++ int code = restore_page_device(i_ctx_p, igs, gs_gstate_saved(igs)); ++ if (code < 0) return code; ++ if (code == 0) { + bool done = !gs_gstate_saved(gs_gstate_saved(igs)); + + gs_grestore(igs); +@@ -328,11 +359,15 @@ z2restore(i_ctx_t *i_ctx_p) + if (code < 0) return code; + + while (gs_gstate_saved(gs_gstate_saved(igs))) { +- if (restore_page_device(igs, gs_gstate_saved(igs))) ++ code = restore_page_device(i_ctx_p, igs, gs_gstate_saved(igs)); ++ if (code < 0) return code; ++ if (code > 0) + return push_callout(i_ctx_p, "%restore1pagedevice"); + gs_grestore(igs); + } +- if (restore_page_device(igs, gs_gstate_saved(igs))) ++ code = restore_page_device(i_ctx_p, igs, gs_gstate_saved(igs)); ++ if (code < 0) return code; ++ if (code > 0) + return push_callout(i_ctx_p, "%restorepagedevice"); + + code = dorestore(i_ctx_p, asave); +@@ -355,9 +390,12 @@ static int + z2setgstate(i_ctx_t *i_ctx_p) + { + os_ptr op = osp; ++ int code; + + check_stype(*op, st_igstate_obj); +- if (!restore_page_device(igs, igstate_ptr(op))) ++ code = restore_page_device(i_ctx_p, igs, igstate_ptr(op)); ++ if (code < 0) return code; ++ if (code == 0) + return zsetgstate(i_ctx_p); + return push_callout(i_ctx_p, "%setgstatepagedevice"); + } diff --git a/gnu/packages/patches/ghostscript-bug-699708.patch b/gnu/packages/patches/ghostscript-bug-699708.patch new file mode 100644 index 0000000000..1567be1c6f --- /dev/null +++ b/gnu/packages/patches/ghostscript-bug-699708.patch @@ -0,0 +1,160 @@ +Additional security fix that missed 9.24. + +Taken from upstream: +http://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=fb713b3818b52d8a6cf62c951eba2e1795ff9624 + +From fb713b3818b52d8a6cf62c951eba2e1795ff9624 Mon Sep 17 00:00:00 2001 +From: Chris Liddell +Date: Thu, 6 Sep 2018 09:16:22 +0100 +Subject: [PATCH] Bug 699708 (part 1): 'Hide' non-replaceable error handlers + for SAFER + +We already had a 'private' dictionary for non-standard errors: gserrordict. + +This now includes all the default error handlers, the dictionary is made +noaccess and all the prodedures are bound and executeonly. + +When running with -dSAFER, in the event of a Postscript error, instead of +pulling the handler from errordict, we'll pull it from gserrordict - thus +malicious input cannot trigger problems by the use of custom error handlers. + +errordict remains open and writeable, so files such as the Quality Logic tests +that install their own handlers will still 'work', with the exception that the +custom error handlers will not be called. + +This is a 'first pass', 'sledgehammer' approach: a nice addition would to allow +an integrator to specify a list of errors that are not to be replaced (for +example, embedded applications would probably want to ensure that VMerror is +always handled as they intend). +--- + Resource/Init/gs_init.ps | 29 ++++++++++++++++++----------- + psi/interp.c | 30 +++++++++++++++++++++--------- + 2 files changed, 39 insertions(+), 20 deletions(-) + +diff --git a/Resource/Init/gs_init.ps b/Resource/Init/gs_init.ps +index 071c39205..bc8b7951c 100644 +--- a/Resource/Init/gs_init.ps ++++ b/Resource/Init/gs_init.ps +@@ -881,7 +881,7 @@ userdict /.currentresourcefile //null put + { not exch pop exit } { pop } ifelse + } + for exch pop .quit +- } bind def ++ } bind executeonly def + /.errorhandler % .errorhandler - + { % Detect an internal 'stopped'. + 1 .instopped { //null eq { pop pop stop } if } if +@@ -926,7 +926,7 @@ userdict /.currentresourcefile //null put + $error /globalmode get $error /.nosetlocal get and .setglobal + $error /.inerror //false put + stop +- } bind def ++ } bind executeonly def + % Define the standard handleerror. We break out the printing procedure + % (.printerror) so that it can be extended for binary output + % if the Level 2 facilities are present. +@@ -976,7 +976,7 @@ userdict /.currentresourcefile //null put + ifelse % newerror + end + flush +- } bind def ++ } bind executeonly def + /.printerror_long % long error printout, + % $error is on the dict stack + { % Push the (anonymous) stack printing procedure. +@@ -1053,14 +1053,14 @@ userdict /.currentresourcefile //null put + { (Current file position is ) print position = } + if + +- } bind def ++ } bind executeonly def + % Define a procedure for clearing the error indication. + /.clearerror + { $error /newerror //false put + $error /errorname //null put + $error /errorinfo //null put + 0 .setoserrno +- } bind def ++ } bind executeonly def + + % Define $error. This must be in local VM. + .currentglobal //false .setglobal +@@ -1086,11 +1086,15 @@ end + /errordict ErrorNames length 3 add dict + .forcedef % errordict is local, systemdict is global + .setglobal % back to global VM +-% For greater Adobe compatibility, we put all non-standard errors in a +-% separate dictionary, gserrordict. It does not need to be in local VM, +-% because PostScript programs do not access it. ++% gserrordict contains all the default error handling methods, but unlike ++% errordict it is noaccess after creation (also it is in global VM). ++% When running 'SAFER', we'll ignore the contents of errordict, which ++% may have been tampered with by the running job, and always use gserrordict ++% gserrordict also contains any non-standard errors, for better compatibility ++% with Adobe. ++% + % NOTE: the name gserrordict is known to the interpreter. +-/gserrordict 5 dict def ++/gserrordict ErrorNames length 3 add dict def + % Register an error in errordict. We make this a procedure because we only + % register the Level 1 errors here: the rest are registered by "feature" + % files. However, ErrorNames contains all of the error names regardless of +@@ -1119,8 +1123,11 @@ errordict begin + } bind def + end % errordict + +-% Put non-standard errors in gserrordict. +-gserrordict /unknownerror errordict /unknownerror get put ++% Put all the default handlers in gserrordict ++gserrordict ++errordict {2 index 3 1 roll put} forall ++noaccess pop ++% remove the non-standard errors from errordict + errordict /unknownerror .undef + % Define a stable private copy of handleerror that we will always use under + % JOBSERVER mode. +diff --git a/psi/interp.c b/psi/interp.c +index c27b70dca..d41a9d3f5 100644 +--- a/psi/interp.c ++++ b/psi/interp.c +@@ -661,16 +661,28 @@ again: + return code; + if (gs_errorname(i_ctx_p, code, &error_name) < 0) + return code; /* out-of-range error code! */ +- /* +- * For greater Adobe compatibility, only the standard PostScript errors +- * are defined in errordict; the rest are in gserrordict. ++ ++ /* If LockFilePermissions is true, we only refer to gserrordict, which ++ * is not accessible to Postcript jobs + */ +- if (dict_find_string(systemdict, "errordict", &perrordict) <= 0 || +- (dict_find(perrordict, &error_name, &epref) <= 0 && +- (dict_find_string(systemdict, "gserrordict", &perrordict) <= 0 || +- dict_find(perrordict, &error_name, &epref) <= 0)) +- ) +- return code; /* error name not in errordict??? */ ++ if (i_ctx_p->LockFilePermissions) { ++ if (((dict_find_string(systemdict, "gserrordict", &perrordict) <= 0 || ++ dict_find(perrordict, &error_name, &epref) <= 0)) ++ ) ++ return code; /* error name not in errordict??? */ ++ } ++ else { ++ /* ++ * For greater Adobe compatibility, only the standard PostScript errors ++ * are defined in errordict; the rest are in gserrordict. ++ */ ++ if (dict_find_string(systemdict, "errordict", &perrordict) <= 0 || ++ (dict_find(perrordict, &error_name, &epref) <= 0 && ++ (dict_find_string(systemdict, "gserrordict", &perrordict) <= 0 || ++ dict_find(perrordict, &error_name, &epref) <= 0)) ++ ) ++ return code; /* error name not in errordict??? */ ++ } + doref = *epref; + epref = &doref; + /* Push the error object on the operand stack if appropriate. */ +-- +2.18.0 + -- cgit v1.2.3