From 0991fd53367907908fbd901a9fbe79540e4e4527 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 6 Jan 2019 21:54:08 +0100 Subject: [PATCH 001/300] build: Require Guile 2.2. * configure.ac: Require Guile 2.2. * README: Adjust accordingly. * doc/guix.texi (Requirements): Likewise. * gnu/packages/package-management.scm (guile2.0-guix): Deprecate. (guix-minimal): Inherit from GUIX, not from GUILE2.0-GUIX. --- README | 2 +- configure.ac | 6 +---- doc/guix.texi | 5 ++-- gnu/packages/package-management.scm | 39 ++++++++++------------------- 4 files changed, 17 insertions(+), 35 deletions(-) diff --git a/README b/README index e7871917f2..296df41516 100644 --- a/README +++ b/README @@ -20,7 +20,7 @@ Guix is based on the [[https://nixos.org/nix/][Nix]] package manager. GNU Guix currently depends on the following packages: - - [[https://gnu.org/software/guile/][GNU Guile 2.2.x or 2.0.x]], version 2.0.13 or later + - [[https://gnu.org/software/guile/][GNU Guile 2.2.x]] - [[https://notabug.org/cwebber/guile-gcrypt][Guile-Gcrypt]] 0.1.0 or later - [[https://www.gnu.org/software/make/][GNU Make]] - [[https://www.gnutls.org][GnuTLS]] compiled with guile support enabled diff --git a/configure.ac b/configure.ac index 2817e6e24d..891fce28ae 100644 --- a/configure.ac +++ b/configure.ac @@ -93,16 +93,12 @@ m4_pattern_forbid([^GUIX_]) dnl Search for 'guile' and 'guild'. This macro defines dnl 'GUILE_EFFECTIVE_VERSION'. -GUILE_PKG([2.2 2.0]) +GUILE_PKG([2.2]) GUILE_PROGS if test "x$GUILD" = "x"; then AC_MSG_ERROR(['guild' binary not found; please check your guile-2.x installation.]) fi -if test "x$GUILE_EFFECTIVE_VERSION" = "x2.0"; then - PKG_CHECK_MODULES([GUILE], [guile-2.0 >= 2.0.13]) -fi - dnl Installation directories for .scm and .go files. guilemoduledir="${datarootdir}/guile/site/$GUILE_EFFECTIVE_VERSION" guileobjectdir="${libdir}/guile/$GUILE_EFFECTIVE_VERSION/site-ccache" diff --git a/doc/guix.texi b/doc/guix.texi index 96654165bb..7c6a714830 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -17,7 +17,7 @@ @set SUBSTITUTE-SERVER ci.guix.info @copying -Copyright @copyright{} 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès@* +Copyright @copyright{} 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès@* Copyright @copyright{} 2013, 2014, 2016 Andreas Enge@* Copyright @copyright{} 2013 Nikita Karetnikov@* Copyright @copyright{} 2014, 2015, 2016 Alex Kost@* @@ -645,8 +645,7 @@ GNU Guix is available for download from its website at GNU Guix depends on the following packages: @itemize -@item @url{http://gnu.org/software/guile/, GNU Guile}, version 2.0.13 or -later, including 2.2.x; +@item @url{http://gnu.org/software/guile/, GNU Guile}, version 2.2.x; @item @url{https://notabug.org/cwebber/guile-gcrypt, Guile-Gcrypt}, version 0.1.0 or later; @item diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 85c95a75e9..8eb4e2eefe 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2015, 2017 Ricardo Wurmus ;;; Copyright © 2017 Muriithi Frederick Muriuki ;;; Copyright © 2017, 2018 Oleg Pykhalov @@ -362,36 +362,23 @@ the Nix package manager.") (delete 'wrap-program))))))) (define-public guile2.0-guix - (package - (inherit guix) - (name "guile2.0-guix") - (inputs - `(("guile" ,guile-2.0) - ,@(alist-delete "guile" (package-inputs guix)))) - (propagated-inputs - `(("gnutls" ,gnutls/guile-2.0) - ("guile-gcrypt" ,guile2.0-gcrypt) - ("guile-json" ,guile2.0-json) - ("guile-sqlite3" ,guile2.0-sqlite3) - ("guile-ssh" ,guile2.0-ssh) - ("guile-git" ,guile2.0-git))))) + (deprecated-package "guile2.0-guix" guix)) (define-public guix-minimal ;; A version of Guix which is built with the minimal set of dependencies, as ;; outlined in the README "Requirements" section. Intended as a CI job, so ;; marked as hidden. - (let ((guix guile2.0-guix)) - (hidden-package - (package - (inherit guix) - (name "guix-minimal") - (inputs - `(("guile" ,guile-2.0.13) - ,@(alist-delete "guile" (package-inputs guix)))) - (propagated-inputs - (fold alist-delete - (package-propagated-inputs guix) - '("guile-ssh"))))))) + (hidden-package + (package + (inherit guix) + (name "guix-minimal") + (inputs + `(("guile" ,guile-2.2) + ,@(alist-delete "guile" (package-inputs guix)))) + (propagated-inputs + (fold alist-delete + (package-propagated-inputs guix) + '("guile-ssh")))))) (define (source-file? file stat) "Return true if FILE is likely a source file, false if it is a typical From a65177a657b0cb36d45f2e8db574ea9c10f89a1f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 6 Jan 2019 22:02:40 +0100 Subject: [PATCH 002/300] maint: Remove 'cond-expand' forms for Guile 2.0. Note: Leave 'cond-expand' forms used in the build-side modules that can run on %BOOTSTRAP-GUILE, which is currently Guile 2.0. * guix/build/compile.scm: Move 'use-modules' clause from 'cond-expand' to 'define-module' form. (%default-optimizations): Remove 'cond-expand'. * guix/build/download.scm (tls-wrap): Remove 'cond-expand'. * guix/build/syscalls.scm: Remove 'cond-expand' form around '%set-automatic-finalization-enabled?!' and 'without-automatic-finalization'. * guix/inferior.scm (port->inferior): Remove 'cond-expand'. * guix/scripts/pack.scm (wrapped-package)[build]: Remove 'cond-expand'. * guix/status.scm (build-event-output-port): Remove 'cond-expand'. * guix/store.scm (open-inet-socket): Remove 'cond-expand'. * guix/ui.scm (install-locale): Remove 'cond-expand'. * tests/status.scm ("current-build-output-port, UTF-8 + garbage"): Remove 'cond-expand'. * tests/store.scm ("current-build-output-port, UTF-8 + garbage"): Remove 'cond-expand'. --- guix/build/compile.scm | 18 +++++-------- guix/build/download.scm | 6 ++--- guix/build/syscalls.scm | 56 ++++++++++++++++++----------------------- guix/inferior.scm | 6 ++--- guix/scripts/pack.scm | 6 ++--- guix/status.scm | 6 ++--- guix/store.scm | 7 +----- guix/ui.scm | 5 ---- tests/status.scm | 6 ++--- tests/store.scm | 6 ++--- 10 files changed, 43 insertions(+), 79 deletions(-) diff --git a/guix/build/compile.scm b/guix/build/compile.scm index 5a1363556a..215489f136 100644 --- a/guix/build/compile.scm +++ b/guix/build/compile.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2013, 2014, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer ;;; ;;; This file is part of GNU Guix. @@ -26,28 +26,22 @@ #:use-module (system base message) #:use-module (guix modules) #:use-module (guix build utils) + #:use-module (language tree-il optimize) + #:use-module (language cps optimize) #:export (%default-optimizations %lightweight-optimizations compile-files)) ;;; Commentary: ;;; -;;; Support code to compile Guile code as efficiently as possible (both with -;;; Guile 2.0 and 2.2). +;;; Support code to compile Guile code as efficiently as possible (with 2.2). ;;; ;;; Code: -(cond-expand - (guile-2.2 (use-modules (language tree-il optimize) - (language cps optimize))) - (else #f)) - (define %default-optimizations ;; Default optimization options (equivalent to -O2 on Guile 2.2). - (cond-expand - (guile-2.2 (append (tree-il-default-optimization-options) - (cps-default-optimization-options))) - (else '()))) + (append (tree-il-default-optimization-options) + (cps-default-optimization-options))) (define %lightweight-optimizations ;; Lightweight optimizations (like -O0, but with partial evaluation). diff --git a/guix/build/download.scm b/guix/build/download.scm index 54163849a2..199702a679 100644 --- a/guix/build/download.scm +++ b/guix/build/download.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2017 Tobias Geerinckx-Rice ;;; @@ -314,9 +314,7 @@ host name without trailing dot." ;; Write HTTP requests line by line rather than byte by byte: ;; . This is possible with Guile >= 2.2. - (cond-expand - (guile-2.2 (setvbuf record 'line)) - (else #f)) + (setvbuf record 'line) record))) diff --git a/guix/build/syscalls.scm b/guix/build/syscalls.scm index 56a689f667..d75c11ada7 100644 --- a/guix/build/syscalls.scm +++ b/guix/build/syscalls.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2015 David Thompson ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2017 Mathieu Othacehe @@ -699,39 +699,31 @@ mounted at FILE." (define CLONE_NEWPID #x20000000) (define CLONE_NEWNET #x40000000) -(cond-expand - (guile-2.2 - (define %set-automatic-finalization-enabled?! - ;; When using a statically-linked Guile, for instance in the initrd, we - ;; cannot resolve this symbol, but most of the time we don't need it - ;; anyway. Thus, delay it. - (let ((proc (delay - (pointer->procedure int - (dynamic-func - "scm_set_automatic_finalization_enabled" - (dynamic-link)) - (list int))))) - (lambda (enabled?) - "Switch on or off automatic finalization in a separate thread. +(define %set-automatic-finalization-enabled?! + ;; When using a statically-linked Guile, for instance in the initrd, we + ;; cannot resolve this symbol, but most of the time we don't need it + ;; anyway. Thus, delay it. + (let ((proc (delay + (pointer->procedure int + (dynamic-func + "scm_set_automatic_finalization_enabled" + (dynamic-link)) + (list int))))) + (lambda (enabled?) + "Switch on or off automatic finalization in a separate thread. Turning finalization off shuts down the finalization thread as a side effect." - (->bool ((force proc) (if enabled? 1 0)))))) + (->bool ((force proc) (if enabled? 1 0)))))) - (define-syntax-rule (without-automatic-finalization exp) - "Turn off automatic finalization within the dynamic extent of EXP." - (let ((enabled? #t)) - (dynamic-wind - (lambda () - (set! enabled? (%set-automatic-finalization-enabled?! #f))) - (lambda () - exp) - (lambda () - (%set-automatic-finalization-enabled?! enabled?)))))) - - (else - (define-syntax-rule (without-automatic-finalization exp) - ;; Nothing to do here: Guile 2.0 does not have a separate finalization - ;; thread. - exp))) +(define-syntax-rule (without-automatic-finalization exp) + "Turn off automatic finalization within the dynamic extent of EXP." + (let ((enabled? #t)) + (dynamic-wind + (lambda () + (set! enabled? (%set-automatic-finalization-enabled?! #f))) + (lambda () + exp) + (lambda () + (%set-automatic-finalization-enabled?! enabled?))))) ;; The libc interface to sys_clone is not useful for Scheme programs, so the ;; low-level system call is wrapped instead. The 'syscall' function is diff --git a/guix/inferior.scm b/guix/inferior.scm index 973bd5264e..a6e6d2f16e 100644 --- a/guix/inferior.scm +++ b/guix/inferior.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2018 Ludovic Courtès +;;; Copyright © 2018, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -137,9 +137,7 @@ it's an old Guix." "Given PIPE, an input/output port, return an inferior that talks over PIPE. PIPE is closed with CLOSE when 'close-inferior' is called on the returned inferior." - (cond-expand - ((and guile-2 (not guile-2.2)) #t) - (else (setvbuf pipe 'line))) + (setvbuf pipe 'line) (match (read pipe) (('repl-version 0 rest ...) diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm index 98b06971bd..e137fb136a 100644 --- a/guix/scripts/pack.scm +++ b/guix/scripts/pack.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2017, 2018 Ludovic Courtès +;;; Copyright © 2015, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2017, 2018 Ricardo Wurmus ;;; Copyright © 2018 Konrad Hinsen ;;; Copyright © 2018 Chris Marusich @@ -553,9 +553,7 @@ please email '~a'~%") "run.c" "-o" result) (delete-file "run.c"))) - (setvbuf (current-output-port) - (cond-expand (guile-2.2 'line) - (else _IOLBF))) + (setvbuf (current-output-port) 'line) ;; Link the top-level files of PACKAGE so that search paths are ;; properly defined in PROFILE/etc/profile. diff --git a/guix/status.scm b/guix/status.scm index d4fc4ca16e..1a7cb313ea 100644 --- a/guix/status.scm +++ b/guix/status.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017, 2018 Ludovic Courtès +;;; Copyright © 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2018 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. @@ -636,9 +636,7 @@ The second return value is a thunk to retrieve the current state." ;; The build port actually receives Unicode strings. (set-port-encoding! port "UTF-8") - (cond-expand - ((and guile-2 (not guile-2.2)) #t) - (else (setvbuf port 'line))) + (setvbuf port 'line) (values port (lambda () %state))) (define (call-with-status-report on-event thunk) diff --git a/guix/store.scm b/guix/store.scm index 042dfab67f..1883829231 100644 --- a/guix/store.scm +++ b/guix/store.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2018 Jan Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. @@ -404,11 +404,6 @@ (define (open-inet-socket host port) "Connect to the Unix-domain socket at HOST:PORT and return it. Raise a '&nix-connection-error' upon error." - ;; Define 'TCP_NODELAY' on Guile 2.0. The value is the same on all GNU - ;; systems. - (cond-expand (guile-2.2 #t) - (else (define TCP_NODELAY 1))) - (let ((sock (with-fluids ((%default-port-encoding #f)) ;; This trick allows use of the `scm_c_read' optimization. (socket PF_UNIX SOCK_STREAM 0)))) diff --git a/guix/ui.scm b/guix/ui.scm index 4c31246920..f542cd3e3f 100644 --- a/guix/ui.scm +++ b/guix/ui.scm @@ -427,11 +427,6 @@ report them in a user-friendly way." (lambda _ (setlocale LC_ALL "")) (lambda args - (cond-expand - ;; Guile 2.2 already emits a warning, so let's not add a second one. - (guile-2.2 #t) - (else (warning (G_ "failed to install locale: ~a~%") - (strerror (system-error-errno args))))) (display-hint (G_ "Consider installing the @code{glibc-utf8-locales} or @code{glibc-locales} package and defining @code{GUIX_LOCPATH}, along these lines: diff --git a/tests/status.scm b/tests/status.scm index 99abb41c8b..08a3153218 100644 --- a/tests/status.scm +++ b/tests/status.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2018 Ludovic Courtès +;;; Copyright © 2018, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -125,9 +125,7 @@ (test-equal "current-build-output-port, UTF-8 + garbage" ;; What about a mixture of UTF-8 + garbage? - (let ((replacement (cond-expand - ((and guile-2 (not guile-2.2)) "?") - (else "�")))) + (let ((replacement "�")) `((build-log #f ,(string-append "garbage: " replacement "lambda: λ\n")))) (let-values (((port get-status) (build-event-output-port cons '()))) (display "garbage: " port) diff --git a/tests/store.scm b/tests/store.scm index 3ff526cdcf..5ff9308d7d 100644 --- a/tests/store.scm +++ b/tests/store.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -444,9 +444,7 @@ (package-derivation %store %bootstrap-guile)))) (guard (c ((nix-protocol-error? c) #t)) (build-derivations %store (list d)))))))) - (cond-expand - (guile-2.2 "garbage: �lambda: λ") - (else "garbage: ?lambda: λ")))) + "garbage: �lambda: λ")) (test-assert "log-file, derivation" (let* ((b (add-text-to-store %store "build" "echo $foo > $out" '())) From c3d9bca48a95a535a26eda38707dcd9798400ff3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 7 Jan 2019 10:42:26 +0100 Subject: [PATCH 003/300] download: Remove Guile 2.0 workaround. * guix/build/download.scm: Remove Guile 2.0 workaround. --- guix/build/download.scm | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/guix/build/download.scm b/guix/build/download.scm index 199702a679..24b5aa378f 100644 --- a/guix/build/download.scm +++ b/guix/build/download.scm @@ -504,18 +504,6 @@ port if PORT is a TLS session record port." (module-set! (resolve-module '(web http)) 'parse-rfc-822-date parse-rfc-822-date)) -;; XXX: Work around , present in Guile -;; up to 2.0.11. -(unless (or (> (string->number (major-version)) 2) - (> (string->number (minor-version)) 0) - (> (string->number (micro-version)) 11)) - (let ((var (module-variable (resolve-module '(web http)) - 'declare-relative-uri-header!))) - ;; If 'declare-relative-uri-header!' doesn't exist, forget it. - (when (and var (variable-bound? var)) - (let ((declare-relative-uri-header! (variable-ref var))) - (declare-relative-uri-header! "Location"))))) - ;; XXX: Work around broken proxy handling on Guile 2.2 <= 2.2.2, fixed in ;; Guile commits 7d0d9e2c25c1e872cfc7d14ab5139915f1813d56 and ;; 6ad28ae3bc6a6d9e95ab7d70510d12c97673a143. See bug report at From 76832d3420594c8b5feaf7682b84b5481a49a076 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 7 Jan 2019 10:57:18 +0100 Subject: [PATCH 004/300] Remove most uses of the _IO*F constants. These constants, for use with 'setvbuf', were deprecated in Guile 2.2 and disappeared in Guile 3.0. Here we keep these constants in build-side code where removing them is not feasible. * guix/build/download-nar.scm (download-nar): Adjust 'setvbuf' calls to the Guile 2.2+ API. * guix/build/download.scm (open-socket-for-uri): Likewise. (open-connection-for-uri, url-fetch): Likewise. * guix/build/make-bootstrap.scm (make-stripped-libc): Likewise. * guix/build/union.scm (setvbuf) [guile-2.0]: New conditional wrapper. (union-build): Adjust to new API. * guix/ftp-client.scm (ftp-open, ftp-list, ftp-retr): Likewise. * guix/http-client.scm (http-fetch): Likewise. * guix/inferior.scm (proxy): Likewise. * guix/scripts/substitute.scm (fetch, http-multiple-get): Likewise. * guix/self.scm (compiled-modules): Likewise. * guix/ssh.scm (remote-daemon-channel, store-import-channel) (store-export-channel): Likewise. * guix/ui.scm (initialize-guix): Likewise. * tests/publish.scm (http-get-port): Likewise. * guix/store.scm (%newlines): Adjust comment. --- guix/build/download-nar.scm | 6 +++--- guix/build/download.scm | 10 +++++----- guix/build/make-bootstrap.scm | 4 ++-- guix/build/union.scm | 21 +++++++++++++++++---- guix/ftp-client.scm | 8 ++++---- guix/http-client.scm | 2 +- guix/inferior.scm | 4 ++-- guix/scripts/substitute.scm | 6 +++--- guix/self.scm | 6 +++--- guix/ssh.scm | 12 ++++++------ guix/store.scm | 2 +- guix/ui.scm | 4 ++-- tests/publish.scm | 6 +++--- 13 files changed, 52 insertions(+), 39 deletions(-) diff --git a/guix/build/download-nar.scm b/guix/build/download-nar.scm index 13f01fb1e8..681f22238d 100644 --- a/guix/build/download-nar.scm +++ b/guix/build/download-nar.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017 Ludovic Courtès +;;; Copyright © 2017, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -93,8 +93,8 @@ ITEM." "Download and extract the normalized archive for ITEM. Return #t on success, #f otherwise." ;; Let progress reports go through. - (setvbuf (current-error-port) _IONBF) - (setvbuf (current-output-port) _IONBF) + (setvbuf (current-error-port) 'none) + (setvbuf (current-output-port) 'none) (let loop ((urls (urls-for-item item))) (match urls diff --git a/guix/build/download.scm b/guix/build/download.scm index 24b5aa378f..c08221b3b2 100644 --- a/guix/build/download.scm +++ b/guix/build/download.scm @@ -357,7 +357,7 @@ ETIMEDOUT error is raised." (connect* s (addrinfo:addr ai) timeout) ;; Buffer input and output on this port. - (setvbuf s _IOFBF) + (setvbuf s 'block) ;; If we're using a proxy, make a note of that. (when http-proxy (set-http-proxy-port?! s #t)) s) @@ -401,7 +401,7 @@ VERIFY-CERTIFICATE? is true, verify HTTPS server certificates." (with-https-proxy (let ((s (open-socket-for-uri uri #:timeout timeout))) ;; Buffer input and output on this port. - (setvbuf s _IOFBF %http-receive-buffer-size) + (setvbuf s 'block %http-receive-buffer-size) (if https? (tls-wrap s (uri-host uri) @@ -777,11 +777,11 @@ otherwise simply ignore them." hashes)) content-addressed-mirrors)) - ;; Make this unbuffered so 'progress-report/file' works as expected. _IOLBF + ;; Make this unbuffered so 'progress-report/file' works as expected. 'line ;; means '\n', not '\r', so it's not appropriate here. - (setvbuf (current-output-port) _IONBF) + (setvbuf (current-output-port) 'none) - (setvbuf (current-error-port) _IOLBF) + (setvbuf (current-error-port) 'line) (let try ((uri (append uri content-addressed-uris))) (match uri diff --git a/guix/build/make-bootstrap.scm b/guix/build/make-bootstrap.scm index 43b136248f..48799f7e90 100644 --- a/guix/build/make-bootstrap.scm +++ b/guix/build/make-bootstrap.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2017 Manolis Fragkiskos Ragkousis -;;; Copyright © 2015 Ludovic Courtès +;;; Copyright © 2015, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -67,7 +67,7 @@ when producing a bootstrap libc." util).*\\.so(\\..*)?|lib(machuser|hurduser).so.*|(libc(rt|)|libpthread)\ _nonshared\\.a)$") - (setvbuf (current-output-port) _IOLBF) + (setvbuf (current-output-port) 'line) (let* ((libdir (string-append output "/lib"))) (mkdir-p libdir) (for-each (lambda (file) diff --git a/guix/build/union.scm b/guix/build/union.scm index fff795c4d3..961ac3298b 100644 --- a/guix/build/union.scm +++ b/guix/build/union.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2012, 2013, 2014, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2014 Mark H Weaver ;;; Copyright © 2017 Huang Ying ;;; @@ -39,6 +39,19 @@ ;;; ;;; Code: +;; This code can be used with the bootstrap Guile, which is Guile 2.0, so +;; provide a compatibility layer. +(cond-expand + ((and guile-2 (not guile-2.2)) + (define (setvbuf port mode . rest) + (apply (@ (guile) setvbuf) port + (match mode + ('line _IOLBF) + ('block _IOFBF) + ('none _IONBF)) + rest))) + (else #f)) + (define (files-in-directory dirname) (let ((dir (opendir dirname))) (let loop ((files '())) @@ -179,10 +192,10 @@ returns #f, skip the faulty file altogether." (reverse dirs-with-file)))) table))) - (setvbuf (current-output-port) _IOLBF) - (setvbuf (current-error-port) _IOLBF) + (setvbuf (current-output-port) 'line) + (setvbuf (current-error-port) 'line) (when (file-port? log-port) - (setvbuf log-port _IOLBF)) + (setvbuf log-port 'line)) (union-of-directories output (delete-duplicates inputs))) diff --git a/guix/ftp-client.scm b/guix/ftp-client.scm index 0b8f61c276..8d5adcb8ed 100644 --- a/guix/ftp-client.scm +++ b/guix/ftp-client.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès +;;; Copyright © 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -154,7 +154,7 @@ TIMEOUT, an ETIMEDOUT error is raised." (catch 'system-error (lambda () (connect* s (addrinfo:addr ai) timeout) - (setvbuf s _IOLBF) + (setvbuf s 'line) (let-values (((code message) (%ftp-listen s))) (if (eqv? code 220) (begin @@ -237,7 +237,7 @@ TIMEOUT, an ETIMEDOUT error is raised." (s (socket (addrinfo:fam ai) (addrinfo:socktype ai) (addrinfo:protocol ai)))) (connect* s (address-with-port (addrinfo:addr ai) port) timeout) - (setvbuf s _IOLBF) + (setvbuf s 'line) (dynamic-wind (lambda () #t) @@ -293,7 +293,7 @@ must be closed before CONN can be used for other purposes." (throw 'ftp-error conn "LIST" code message)))) (connect* s (address-with-port (addrinfo:addr ai) port) timeout) - (setvbuf s _IOLBF) + (setvbuf s 'line) (%ftp-command (string-append "RETR " file) 150 (ftp-connection-socket conn)) diff --git a/guix/http-client.scm b/guix/http-client.scm index 07360e6108..067002a79a 100644 --- a/guix/http-client.scm +++ b/guix/http-client.scm @@ -97,7 +97,7 @@ Raise an '&http-get-error' condition if downloading fails." headers)) (_ headers)))) (unless (or buffered? (not (file-port? port))) - (setvbuf port _IONBF)) + (setvbuf port 'none)) (let*-values (((resp data) (http-get uri #:streaming? #t #:port port #:keep-alive? #t diff --git a/guix/inferior.scm b/guix/inferior.scm index a6e6d2f16e..ba8d00866b 100644 --- a/guix/inferior.scm +++ b/guix/inferior.scm @@ -389,8 +389,8 @@ input/output ports.)" ;; Use buffered ports so that 'get-bytevector-some' returns up to the ;; whole buffer like read(2) would--see . - (setvbuf client _IOFBF 65536) - (setvbuf backend _IOFBF 65536) + (setvbuf client 'block 65536) + (setvbuf backend 'block 65536) (let loop () (match (select* (list client backend) '() '()) diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm index 53b1777241..797a76db3f 100755 --- a/guix/scripts/substitute.scm +++ b/guix/scripts/substitute.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2014 Nikita Karetnikov ;;; Copyright © 2018 Kyle Meyer ;;; @@ -219,7 +219,7 @@ provide." (set! port (guix:open-connection-for-uri uri #:verify-certificate? #f)) (unless (or buffered? (not (file-port? port))) - (setvbuf port _IONBF))) + (setvbuf port 'none))) (http-fetch uri #:text? #f #:port port #:verify-certificate? #f)))))) (else @@ -567,7 +567,7 @@ initial connection on which HTTP requests are sent." verify-certificate?)))) ;; For HTTPS, P is not a file port and does not support 'setvbuf'. (when (file-port? p) - (setvbuf p _IOFBF (expt 2 16))) + (setvbuf p 'block (expt 2 16))) ;; Send REQUESTS, up to a certain number, in a row. ;; XXX: Do our own caching to work around inefficiencies when diff --git a/guix/self.scm b/guix/self.scm index e9a768bc90..a2ae441d42 100644 --- a/guix/self.scm +++ b/guix/self.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017, 2018 Ludovic Courtès +;;; Copyright © 2017, 2018, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -904,8 +904,8 @@ containing MODULE-FILES and possibly other files as well." #:report-load report-load #:report-compilation report-compilation))) - (setvbuf (current-output-port) _IONBF) - (setvbuf (current-error-port) _IONBF) + (setvbuf (current-output-port) 'none) + (setvbuf (current-error-port) 'none) (set! %load-path (cons #+module-tree %load-path)) (set! %load-path diff --git a/guix/ssh.scm b/guix/ssh.scm index 1ed8406633..d90cb77be0 100644 --- a/guix/ssh.scm +++ b/guix/ssh.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -140,12 +140,12 @@ right away." (match (select read write except) ((read write except) (select read write except 0)))))) - (setvbuf stdout _IONBF) + (setvbuf stdout 'none) ;; Use buffered ports so that 'get-bytevector-some' returns up to the ;; whole buffer like read(2) would--see . - (setvbuf stdin _IOFBF 65536) - (setvbuf sock _IOFBF 65536) + (setvbuf stdin 'block 65536) + (setvbuf sock 'block 65536) (connect sock AF_UNIX ,socket-name) @@ -218,7 +218,7 @@ can be written." (consume-input (current-input-port)) (list 'protocol-error (nix-protocol-error-message c)))) (with-store store - (setvbuf (current-input-port) _IONBF) + (setvbuf (current-input-port) 'none) (import-paths store (current-input-port)) '(success)))) (lambda args @@ -269,7 +269,7 @@ be read. When RECURSIVE? is true, the closure of FILES is exported." (write '(exporting)) ;we're ready (force-output) - (setvbuf (current-output-port) _IONBF) + (setvbuf (current-output-port) 'none) (export-paths store files (current-output-port) #:recursive? ,recursive?)))))) diff --git a/guix/store.scm b/guix/store.scm index 1883829231..1f88eb2b33 100644 --- a/guix/store.scm +++ b/guix/store.scm @@ -608,7 +608,7 @@ to OUT, using chunks of BUFFER-SIZE bytes." (define %newlines ;; Newline characters triggering a flush of 'current-build-output-port'. - ;; Unlike Guile's _IOLBF, we flush upon #\return so that progress reports + ;; Unlike Guile's 'line, we flush upon #\return so that progress reports ;; that use that trick are correctly displayed. (char-set #\newline #\return)) diff --git a/guix/ui.scm b/guix/ui.scm index f542cd3e3f..1e089753e1 100644 --- a/guix/ui.scm +++ b/guix/ui.scm @@ -454,8 +454,8 @@ See the \"Application Setup\" section in the manual, for more info.\n"))))) ;; notified via an EPIPE later. (sigaction SIGPIPE SIG_IGN) - (setvbuf (current-output-port) _IOLBF) - (setvbuf (current-error-port) _IOLBF)) + (setvbuf (current-output-port) 'line) + (setvbuf (current-error-port) 'line)) (define* (show-version-and-exit #:optional (command (car (command-line)))) "Display version information for COMMAND and `(exit 0)'." diff --git a/tests/publish.scm b/tests/publish.scm index 79a786e723..097ac036e0 100644 --- a/tests/publish.scm +++ b/tests/publish.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 David Thompson -;;; Copyright © 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -63,12 +63,12 @@ (let ((socket (open-socket-for-uri uri))) ;; Make sure to use an unbuffered port so that we can then peek at the ;; underlying file descriptor via 'call-with-gzip-input-port'. - (setvbuf socket _IONBF) + (setvbuf socket 'none) (call-with-values (lambda () (http-get uri #:port socket #:streaming? #t)) (lambda (response port) - ;; Don't (setvbuf port _IONBF) because of + ;; Don't (setvbuf port 'none) because of ;; (PORT might be a custom binary input port). port)))) From 6e54e488c6bbeca48f633b03333d856651f24077 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 7 Jan 2019 11:38:53 +0100 Subject: [PATCH 005/300] self: Drop support for Guix < 0.15 on Guile 2.0. * guix/self.scm (false-if-wrong-guile, package-for-guile): Remove. (specification->package): Remove "guile2.0-" variants. (compiled-guix): #:guile-for-build defaults to (default-guile). Use 'specification->package' instead of 'package-for-guile'. (guile-for-build): Remove. (guix-derivation): Use 'default-guile' instead of 'guile-for-build'. Check whether we're running on Guile 2.0 with PULL-VERSION < 1. --- guix/self.scm | 89 +++++++++++---------------------------------------- 1 file changed, 19 insertions(+), 70 deletions(-) diff --git a/guix/self.scm b/guix/self.scm index a2ae441d42..cf6110613c 100644 --- a/guix/self.scm +++ b/guix/self.scm @@ -31,6 +31,7 @@ #:use-module ((guix build compile) #:select (%lightweight-optimizations)) #:use-module (srfi srfi-1) #:use-module (srfi srfi-9) + #:use-module (srfi srfi-35) #:use-module (ice-9 match) #:export (make-config.scm whole-package ;for internal use in 'guix pull' @@ -43,35 +44,6 @@ ;;; Dependency handling. ;;; -(define* (false-if-wrong-guile package - #:optional (guile-version (effective-version))) - "Return #f if PACKAGE depends on the \"wrong\" major version of Guile (e.g., -2.0 instead of 2.2), otherwise return PACKAGE." - (let ((guile (any (match-lambda - ((label (? package? dep) _ ...) - (and (string=? (package-name dep) "guile") - dep))) - (package-direct-inputs package)))) - (and (or (not guile) - (string-prefix? guile-version - (package-version guile))) - package))) - -(define (package-for-guile guile-version . names) - "Return the package with one of the given NAMES that depends on -GUILE-VERSION (\"2.0\" or \"2.2\"), or #f if none of the packages matches." - (let loop ((names names)) - (match names - (() - #f) - ((name rest ...) - (match (specification->package name) - (#f - (loop rest)) - ((? package? package) - (or (false-if-wrong-guile package guile-version) - (loop rest)))))))) - (define specification->package ;; Use our own variant of that procedure because that of (gnu packages) ;; would traverse all the .scm files, which is wasteful. @@ -89,12 +61,7 @@ GUILE-VERSION (\"2.0\" or \"2.2\"), or #f if none of the packages matches." ("gzip" (ref '(gnu packages compression) 'gzip)) ("bzip2" (ref '(gnu packages compression) 'bzip2)) ("xz" (ref '(gnu packages compression) 'xz)) - ("guile2.0-json" (ref '(gnu packages guile) 'guile2.0-json)) - ("guile2.0-ssh" (ref '(gnu packages ssh) 'guile2.0-ssh)) - ("guile2.0-git" (ref '(gnu packages guile) 'guile2.0-git)) - ;; XXX: No "guile2.0-sqlite3". - ("guile2.0-gnutls" (ref '(gnu packages tls) 'gnutls/guile-2.0)) - (_ #f)))) ;no such package + (_ #f)))) ;no such package ;;; @@ -528,7 +495,7 @@ Info manual." (pull-version 1) (name (string-append "guix-" version)) (guile-version (effective-version)) - (guile-for-build (guile-for-build guile-version)) + (guile-for-build (default-guile)) (zlib (specification->package "zlib")) (gzip (specification->package "gzip")) (bzip2 (specification->package "bzip2")) @@ -536,32 +503,22 @@ Info manual." (guix (specification->package "guix"))) "Return a file-like object that contains a compiled Guix." (define guile-json - (package-for-guile guile-version - "guile-json" - "guile2.0-json")) + (specification->package "guile-json")) (define guile-ssh - (package-for-guile guile-version - "guile-ssh" - "guile2.0-ssh")) + (specification->package "guile-ssh")) (define guile-git - (package-for-guile guile-version - "guile-git" - "guile2.0-git")) + (specification->package "guile-git")) (define guile-sqlite3 - (package-for-guile guile-version - "guile-sqlite3" - "guile2.0-sqlite3")) + (specification->package "guile-sqlite3")) (define guile-gcrypt - (package-for-guile guile-version - "guile-gcrypt")) + (specification->package "guile-gcrypt")) (define gnutls - (package-for-guile guile-version - "gnutls" "guile2.0-gnutls")) + (specification->package "gnutls")) (define dependencies (match (append-map (lambda (package) @@ -950,21 +907,6 @@ containing MODULE-FILES and possibly other files as well." ;;; Building. ;;; -(define (guile-for-build version) - "Return a derivation for Guile 2.0 or 2.2, whichever matches the currently -running Guile." - (define canonical-package ;soft reference - (module-ref (resolve-interface '(gnu packages base)) - 'canonical-package)) - - (match version - ("2.2" - (canonical-package (module-ref (resolve-interface '(gnu packages guile)) - 'guile-2.2))) - ("2.0" - (module-ref (resolve-interface '(gnu packages guile)) - 'guile-2.0)))) - (define* (guix-derivation source version #:optional (guile-version (effective-version)) #:key (pull-version 0)) @@ -981,9 +923,16 @@ is not supported." (define guile ;; When PULL-VERSION >= 1, produce a self-contained Guix and use Guile 2.2 ;; unconditionally. - (guile-for-build (if (>= pull-version 1) - "2.2" - guile-version))) + (default-guile)) + + (when (and (< pull-version 1) + (not (string=? (package-version guile) guile-version))) + ;; Guix < 0.15.0 has PULL-VERSION = 0, where the host Guile is reused and + ;; can be any version. When that happens and Guile is not current (e.g., + ;; it's Guile 2.0), just bail out. + (raise (condition + (&message + (message "Guix is too old and cannot be upgraded"))))) (mbegin %store-monad (set-guile-for-build guile) From 804b9b18ac9188ffb6c6891cbb9241c6a80ed7c8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 9 Jan 2019 15:01:40 +0100 Subject: [PATCH 006/300] build-system/asdf: 'package-with-build-system' accesses inputs lazily. Fixes a bug whereby we would, at the top-level (while evaluation lisp.scm package definitions), attempt to access package inputs. Because of circular dependencies, this could lead to unbound variables as reported by Arun Isaac at . * guix/build-system/asdf.scm (package-with-build-system)[transform] (new-propagated-inputs): Turn into a procedure. Adjust user accordingly. --- guix/build-system/asdf.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/guix/build-system/asdf.scm b/guix/build-system/asdf.scm index 57e294d74d..af04084c86 100644 --- a/guix/build-system/asdf.scm +++ b/guix/build-system/asdf.scm @@ -172,7 +172,7 @@ set up using CL source package conventions." ;; Special considerations for source packages: CL inputs become ;; propagated, and un-handled arguments are removed. - (define new-propagated-inputs + (define (new-propagated-inputs) (if target-is-source? (map rewrite (append @@ -218,7 +218,7 @@ set up using CL source package conventions." (substitute-keyword-arguments base-arguments ((#:phases phases) (list phases-transformer phases)))) (inputs (new-inputs package-inputs)) - (propagated-inputs new-propagated-inputs) + (propagated-inputs (new-propagated-inputs)) (native-inputs (new-inputs package-native-inputs)) (outputs (if target-is-source? '("out") From 3088b3fc5b271c23face4cf82b0938f6aa872462 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 13:32:05 +0100 Subject: [PATCH 007/300] gnu: Add r-rspectra. * gnu/packages/cran.scm (r-rspectra): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 847e3ccacb..3e2e9298d6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8874,3 +8874,30 @@ Furthermore, functions are available for fast singular value decomposition, for computing the pseudoinverse, and for checking the rank and positive definiteness of a matrix.") (license license:gpl3+))) + +(define-public r-rspectra + (package + (name "r-rspectra") + (version "0.13-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "RSpectra" version)) + (sha256 + (base32 + "1sw80chwyyjzf5px278l6xmp94yhwrlj5xh8d3wlw3dnvdkycca7")))) + (properties `((upstream-name . "RSpectra"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (home-page "https://github.com/yixuan/RSpectra") + (synopsis "Solvers for large-scale Eigenvalue and SVD problems") + (description + "This package provides an R interface to the Spectra library for +large-scale eigenvalue and SVD problems. It is typically used to compute a +few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, +which is usually more efficient than @code{eigen()} if k << n.") + ;; MPL 2 or later. + (license license:mpl2.0))) From 5574cb812aec70dca7c99498487c3ef28318a828 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:03:03 +0100 Subject: [PATCH 008/300] gnu: Add r-rpostgresql. * gnu/packages/cran.scm (r-rpostgresql): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3e2e9298d6..87fd7d341a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2329,6 +2329,32 @@ is being phased out. A modern MySQL client based on Rcpp is available from the RMariaDB package.") (license license:gpl2))) +(define-public r-rpostgresql + (package + (name "r-rpostgresql") + (version "0.6-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "RPostgreSQL" version)) + (sha256 + (base32 + "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088")))) + (properties `((upstream-name . "RPostgreSQL"))) + (build-system r-build-system) + (inputs + `(("postgresql" ,postgresql))) + (propagated-inputs + `(("r-dbi" ,r-dbi))) + (home-page "https://github.com/tomoakin/RPostgreSQL") + (synopsis "R interface to the PostgreSQL database system") + (description + "This package provides a Database Interface (DBI) compliant driver for R +to access PostgreSQL database systems.") + ;; The whole package is released under GPL version 2. It includes code + ;; under the PostgreSQL license. + (license license:gpl2))) + (define-public r-geometry (package (name "r-geometry") From 029425cbcefe427bd4816110780acc5566ea9785 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:11:32 +0100 Subject: [PATCH 009/300] gnu: Add r-vbsr. * gnu/packages/cran.scm (r-vbsr): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 87fd7d341a..1839ead07c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8927,3 +8927,25 @@ few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than @code{eigen()} if k << n.") ;; MPL 2 or later. (license license:mpl2.0))) + +(define-public r-vbsr + (package + (name "r-vbsr") + (version "0.0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "vbsr" version)) + (sha256 + (base32 + "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/vbsr") + (synopsis "Variational Bayes spike regression regularized linear models") + (description + "This package provides an efficient algorithm for solving ultra-sparse +regularized regression models using a variational Bayes algorithm with a spike +prior. The algorithm is solved on a path, with coordinate updates, and is +capable of generating very sparse models. Very general model +diagnostics for controlling type-1 errors are also provided.") + (license license:gpl2))) From 3d62d98e694732fbeba3f17e7586f47e23c847bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:12:39 +0100 Subject: [PATCH 010/300] gnu: Add r-flare. * gnu/packages/cran.scm (r-flare): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1839ead07c..f73adb6bed 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -44,6 +44,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages gl) #:use-module (gnu packages gnome) + #:use-module (gnu packages graph) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell) #:use-module (gnu packages image) @@ -8949,3 +8950,28 @@ prior. The algorithm is solved on a path, with coordinate updates, and is capable of generating very sparse models. Very general model diagnostics for controlling type-1 errors are also provided.") (license license:gpl2))) + +(define-public r-flare + (package + (name "r-flare") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "flare" version)) + (sha256 + (base32 + "0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix))) + (home-page "https://cran.r-project.org/web/packages/flare") + (synopsis "Family of Lasso regression implementations") + (description + "This packages provides implementations of a family of Lasso variants +including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating +high dimensional sparse linear models.") + (license license:gpl2))) From 5f0fbfc0ad745fdc9e0f9cd6d36a23eec8bdf4fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:20:01 +0100 Subject: [PATCH 011/300] gnu: Add r-lassopv. * gnu/packages/cran.scm (r-lassopv): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f73adb6bed..8f2bd143a0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8975,3 +8975,25 @@ diagnostics for controlling type-1 errors are also provided.") including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear models.") (license license:gpl2))) + +(define-public r-lassopv + (package + (name "r-lassopv") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "lassopv" version)) + (sha256 + (base32 + "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) + (build-system r-build-system) + (propagated-inputs `(("r-lars" ,r-lars))) + (home-page "https://github.com/lingfeiwang/lassopv") + (synopsis "Non-parametric p-value estimation for predictors in Lasso") + (description + "This package enables you to estimate the p-values for predictors x +against target variable y in Lasso regression, using the regularization +strength when each predictor enters the active set of regularization path for +the first time as the statistic.") + (license license:gpl3))) From adcd0cc87e89ddcdb484493ca100a51fe9e491c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:23:50 +0100 Subject: [PATCH 012/300] gnu: Add r-splitstackshape. * gnu/packages/cran.scm (r-splitstackshape): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8f2bd143a0..aa9a063a76 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8997,3 +8997,30 @@ against target variable y in Lasso regression, using the regularization strength when each predictor enters the active set of regularization path for the first time as the statistic.") (license license:gpl3))) + +(define-public r-splitstackshape + (package + (name "r-splitstackshape") + (version "1.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "splitstackshape" version)) + (sha256 + (base32 + "03w6h64ga4zqilffdway4l38l5cbman4yrspkzhbigds12aqz25r")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table))) + (home-page "https://github.com/mrdwab/splitstackshape") + (synopsis "Stack and reshape datasets after splitting concatenated values") + (description + "Online data collection tools like Google Forms often export +multiple-response questions with data concatenated in cells. The +@code{concat.split} (cSplit) family of functions provided by this package +splits such data into separate cells. This package also includes functions to +stack groups of columns and to reshape wide data, even when the data are +\"unbalanced\"---something which @code{reshape} (from base R) does not handle, +and which @code{melt} and @code{dcast} from @code{reshape2} do not easily +handle.") + (license license:gpl3))) From b2e777b27cb677592f7a72fef491ec476d7ae65a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:37:36 +0100 Subject: [PATCH 013/300] gnu: Add r-tfmpvalue. * gnu/packages/cran.scm (r-tfmpvalue): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index aa9a063a76..16d576ecee 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9024,3 +9024,29 @@ stack groups of columns and to reshape wide data, even when the data are and which @code{melt} and @code{dcast} from @code{reshape2} do not easily handle.") (license license:gpl3))) + +(define-public r-tfmpvalue + (package + (name "r-tfmpvalue") + (version "0.0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "TFMPvalue" version)) + (sha256 + (base32 + "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) + (properties `((upstream-name . "TFMPvalue"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/ge11232002/TFMPvalue") + (synopsis "P-value computation for position weight matrices") + (description + "In putative @dfn{Transcription Factor Binding Sites} (TFBSs) +identification from sequence/alignments, we are interested in the significance +of certain match scores. TFMPvalue provides the accurate calculation of a +p-value with a score threshold for position weight matrices, or the score with +a given p-value. It is an interface to code originally made available by +Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. +Touzet and Varre (2007).") + (license license:gpl2))) From f79e63a57149bf1972aedfb088e7139b7af78ffd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:39:14 +0100 Subject: [PATCH 014/300] gnu: Add r-rnifti. * gnu/packages/cran.scm (r-rnifti): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 16d576ecee..a4b4897fd9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9050,3 +9050,26 @@ a given p-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).") (license license:gpl2))) + +(define-public r-rnifti + (package + (name "r-rnifti") + (version "0.10.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RNifti" version)) + (sha256 + (base32 + "07sfzps4yg5zdhbxh6i4rbjvbjvvf2d8i9jcf64ywbmi557sw1zv")))) + (properties `((upstream-name . "RNifti"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/jonclayden/RNifti") + (synopsis "Fast R and C++ access to NIfTI images") + (description + "This package provides very fast read and write access to images stored +in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between +compiled C and interpreted R code. It also provides a C/C++ API that can be +used by other packages.") + (license license:gpl2))) From 6e09f506130cc63b58bf7890d1a71b6f75c7610e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:40:31 +0100 Subject: [PATCH 015/300] gnu: Add r-shades. * gnu/packages/cran.scm (r-shades): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a4b4897fd9..da05dd4615 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9073,3 +9073,22 @@ in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between compiled C and interpreted R code. It also provides a C/C++ API that can be used by other packages.") (license license:gpl2))) + +(define-public r-shades + (package + (name "r-shades") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "shades" version)) + (sha256 + (base32 + "0qbg7b37ifgil7ka4vhk15wjf65rwha233yppqd9wlf3gys8784n")))) + (build-system r-build-system) + (home-page "https://github.com/jonclayden/shades") + (synopsis "Simple color manipulation") + (description + "This package provides functions for easily manipulating colors, +creating color scales and calculating color distances.") + (license license:bsd-3))) From cb03d6c6f39145c85350bd93d46941a2c178f4d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:42:39 +0100 Subject: [PATCH 016/300] gnu: Add r-ore. * gnu/packages/cran.scm (r-ore): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index da05dd4615..5fc0ee1a47 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9092,3 +9092,24 @@ used by other packages.") "This package provides functions for easily manipulating colors, creating color scales and calculating color distances.") (license license:bsd-3))) + +(define-public r-ore + (package + (name "r-ore") + (version "1.6.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ore" version)) + (sha256 + (base32 + "1l1ziljgm5gwjhvjq42wi5vcwbxlaj5dl9w8bhz0wh8vx4ajj07m")))) + (build-system r-build-system) + (home-page "https://github.com/jonclayden/ore") + (synopsis "R interface to the Onigmo regular expression library") + (description + "This package provides an alternative to R's built-in functionality for +handling regular expressions, based on the Onigmo library. It offers +first-class compiled regex objects, partial matching and function-based +substitutions, amongst other features.") + (license license:bsd-3))) From b98662c53ac4f92214b50668a8a1c1e0871af86b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:42:44 +0100 Subject: [PATCH 017/300] gnu: Add r-reportr. * gnu/packages/cran.scm (r-reportr): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5fc0ee1a47..96e7c9c915 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9113,3 +9113,26 @@ handling regular expressions, based on the Onigmo library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.") (license license:bsd-3))) + +(define-public r-reportr + (package + (name "r-reportr") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "reportr" version)) + (sha256 + (base32 + "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) + (build-system r-build-system) + (propagated-inputs `(("r-ore" ,r-ore))) + (home-page "https://github.com/jonclayden/reportr") + (synopsis "General message and error reporting system") + (description + "This package provides a system for reporting messages, which offers +certain useful features over the standard R system, such as the incorporation +of output consolidation, message filtering, assertions, expression +substitution, automatic generation of stack traces for debugging, and +conditional reporting based on the current \"output level\".") + (license license:gpl2))) From 7eec973e8154ff1d157e6a13db71a96e96dee828 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:44:58 +0100 Subject: [PATCH 018/300] gnu: Add r-tractor-base. * gnu/packages/cran.scm (r-tractor-base): New variable. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 96e7c9c915..6de82d344f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9136,3 +9136,31 @@ of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current \"output level\".") (license license:gpl2))) + +(define-public r-tractor-base + (package + (name "r-tractor-base") + (version "3.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tractor.base" version)) + (sha256 + (base32 + "0i62dwra0yh565ryz75byfgqv22bqwz7138zs48w46yj2h8q9hyj")))) + (properties `((upstream-name . "tractor.base"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ore" ,r-ore) + ("r-reportr" ,r-reportr) + ("r-rnifti" ,r-rnifti) + ("r-shades" ,r-shades))) + (home-page "http://www.tractor-mri.org.uk") + (synopsis "Read, manipulate and visualize magnetic resonance images") + (description + "This package provides functions for working with magnetic resonance +images. It supports reading and writing of popular file formats (DICOM, +Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive +visualization; flexible image manipulation; metadata and sparse image +handling.") + (license license:gpl2))) From d0eb09a13455ba767c54eaf577268326ebd6c61a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:45:36 +0100 Subject: [PATCH 019/300] gnu: Add r-grimport. * gnu/packages/cran.scm (r-grimport): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6de82d344f..54b0f4626e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -42,6 +42,7 @@ #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) + #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages gnome) #:use-module (gnu packages graph) @@ -9164,3 +9165,27 @@ Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualization; flexible image manipulation; metadata and sparse image handling.") (license license:gpl2))) + +(define-public r-grimport + (package + (name "r-grimport") + (version "0.9-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "grImport" version)) + (sha256 + (base32 + "1qhyw5wiyfqw1wcpvcgdwc1vgaz7j7dbc7qa5h85qgml7hb68mjv")))) + (properties `((upstream-name . "grImport"))) + (build-system r-build-system) + (inputs + `(("ghostscript" ,ghostscript))) + (propagated-inputs + `(("r-xml" ,r-xml))) + (home-page "https://cran.r-project.org/web/packages/grImport") + (synopsis "Convert, import, and draw PostScript pictures") + (description + "This package provides functions for converting, importing, and drawing +PostScript pictures in R plots.") + (license license:gpl2+))) From 2871b670a8075e876873296dfa7ac11628926fc9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:46:46 +0100 Subject: [PATCH 020/300] gnu: Add r-kohonen. * gnu/packages/cran.scm (r-kohonen): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 54b0f4626e..f768bcc5ba 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9189,3 +9189,27 @@ handling.") "This package provides functions for converting, importing, and drawing PostScript pictures in R plots.") (license license:gpl2+))) + +(define-public r-kohonen + (package + (name "r-kohonen") + (version "3.0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "kohonen" version)) + (sha256 + (base32 + "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/kohonen") + (synopsis "Supervised and unsupervised self-organising maps") + (description + "This package provides functions to train @dfn{self-organising +maps} (SOMs). Also interrogation of the maps and prediction using trained +maps are supported. The name of the package refers to Teuvo Kohonen, the +inventor of the SOM.") + (license license:gpl2+))) From 00436e2cacec4a70e6e86a7663af754e2921c1e9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:48:18 +0100 Subject: [PATCH 021/300] gnu: Add r-nnls. * gnu/packages/cran.scm (r-nnls): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f768bcc5ba..af8a4dae1d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9213,3 +9213,24 @@ maps} (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.") (license license:gpl2+))) + +(define-public r-nnls + (package + (name "r-nnls") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "nnls" version)) + (sha256 + (base32 + "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/nnls") + (synopsis "Lawson-Hanson algorithm for non-negative least squares") + (description + "This package provides an R interface to the Lawson-Hanson implementation +of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows +the combination of non-negative and non-positive constraints.") + (license license:gpl2+))) From 25861356edd07a2b2a00e1b05cb390187fdf16b1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:49:14 +0100 Subject: [PATCH 022/300] gnu: Add r-iso. * gnu/packages/cran.scm (r-iso): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index af8a4dae1d..b06c3505d5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9234,3 +9234,25 @@ inventor of the SOM.") of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows the combination of non-negative and non-positive constraints.") (license license:gpl2+))) + +(define-public r-iso + (package + (name "r-iso") + (version "0.0-17") + (source + (origin + (method url-fetch) + (uri (cran-uri "Iso" version)) + (sha256 + (base32 + "0lljc99sdzdqj6d56qbsggibr6pkdwkh821bj70ianikyvmdc1y0")))) + (properties `((upstream-name . "Iso"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://www.stat.auckland.ac.nz/~rolf/") + (synopsis "Functions to perform isotonic regression") + (description + "This package provides support for linear order and unimodal +order (univariate) isotonic regression and bivariate isotonic regression with +linear order on both variables.") + (license license:gpl2+))) From 9401f56b814d9ff68b280d0df853823e56865ab7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:51:08 +0100 Subject: [PATCH 023/300] gnu: Add r-chemometricswithr. * gnu/packages/cran.scm (r-chemometricswithr): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b06c3505d5..32f25956c5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9256,3 +9256,30 @@ the combination of non-negative and non-positive constraints.") order (univariate) isotonic regression and bivariate isotonic regression with linear order on both variables.") (license license:gpl2+))) + +(define-public r-chemometricswithr + (package + (name "r-chemometricswithr") + (version "0.1.11") + (source + (origin + (method url-fetch) + (uri (cran-uri "ChemometricsWithR" version)) + (sha256 + (base32 + "00z09bplm5qvd31y7m4b4knsrl0n27j9635m1gdak6lg4db4nxrd")))) + (properties + `((upstream-name . "ChemometricsWithR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-devtools" ,r-devtools) + ("r-kohonen" ,r-kohonen) + ("r-mass" ,r-mass) + ("r-pls" ,r-pls))) + (home-page "https://github.com/rwehrens/CWR") + (synopsis "Chemometrics with R") + (description + "This package provides functions and scripts used in the book +\"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and +Life Sciences\" by Ron Wehrens, Springer (2011).") + (license license:gpl2+))) From d28be7b76b58fd86cfc6fa5f0fa6ad95b1e633c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:53:07 +0100 Subject: [PATCH 024/300] gnu: Add r-als. * gnu/packages/cran.scm (r-als): New variable. --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 32f25956c5..44f79a5f3e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9283,3 +9283,34 @@ linear order on both variables.") \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences\" by Ron Wehrens, Springer (2011).") (license license:gpl2+))) + +(define-public r-als + (package + (name "r-als") + (version "0.0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ALS" version)) + (sha256 + (base32 + "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a")))) + (properties `((upstream-name . "ALS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-iso" ,r-iso) + ("r-nnls" ,r-nnls))) + (home-page "https://cran.r-project.org/web/packages/ALS") + (synopsis "Multivariate curve resolution alternating least squares") + (description + "Alternating least squares is often used to resolve components +contributing to data with a bilinear structure; the basic technique may be +extended to alternating constrained least squares. This package provides an +implementation of @dfn{multivariate curve resolution alternating least +squares} (MCR-ALS). + +Commonly applied constraints include unimodality, non-negativity, and +normalization of components. Several data matrices may be decomposed +simultaneously by assuming that one of the two matrices in the bilinear +decomposition is shared between datasets.") + (license license:gpl2+))) From 895efece3769a30d93badb20c0abfdfa86540fed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:55:43 +0100 Subject: [PATCH 025/300] gnu: Add r-strucchange. * gnu/packages/cran.scm (r-strucchange): New variable. --- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 44f79a5f3e..87edfafe20 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9314,3 +9314,33 @@ normalization of components. Several data matrices may be decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets.") (license license:gpl2+))) + +(define-public r-strucchange + (package + (name "r-strucchange") + (version "1.5-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "strucchange" version)) + (sha256 + (base32 + "0cdgvl6kphm2i59bmnppn1y3kv65ml111bk7yzpcx7vv8wh2w3kl")))) + (build-system r-build-system) + (propagated-inputs + `(("r-sandwich" ,r-sandwich) + ("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/strucchange") + (synopsis "Testing, monitoring, and dating structural changes") + (description + "This package provides tools for testing, monitoring and dating +structural changes in (linear) regression models. It features tests/methods +from the generalized fluctuation test framework as well as from the F +test (Chow test) framework. This includes methods to fit, plot and test +fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F +statistics, respectively. It is possible to monitor incoming data online +using fluctuation processes. Finally, the breakpoints in regression models +with structural changes can be estimated together with confidence intervals. +Emphasis is always given to methods for visualizing the data.") + ;; Either of these two GPL versions + (license (list license:gpl2 license:gpl3)))) From e7176ac5bd701524271856ae1948d82eebdf0cf4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:56:48 +0100 Subject: [PATCH 026/300] gnu: Add r-pixmap. * gnu/packages/cran.scm (r-pixmap): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 87edfafe20..4a85b237dd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9344,3 +9344,22 @@ with structural changes can be estimated together with confidence intervals. Emphasis is always given to methods for visualizing the data.") ;; Either of these two GPL versions (license (list license:gpl2 license:gpl3)))) + +(define-public r-pixmap + (package + (name "r-pixmap") + (version "0.4-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "pixmap" version)) + (sha256 + (base32 + "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/pixmap") + (synopsis "Tools for bitmap images") + (description + "This package provides functions for importing, exporting, plotting and +other manipulations of bitmapped images.") + (license license:gpl2))) From 9170eb7f1f62c2c79daa1d0059e285e2119db35c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:57:41 +0100 Subject: [PATCH 027/300] gnu: Add r-rapidjsonr. * gnu/packages/cran.scm (r-rapidjsonr): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4a85b237dd..c11202abf7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9363,3 +9363,22 @@ Emphasis is always given to methods for visualizing the data.") "This package provides functions for importing, exporting, plotting and other manipulations of bitmapped images.") (license license:gpl2))) + +(define-public r-rapidjsonr + (package + (name "r-rapidjsonr") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "rapidjsonr" version)) + (sha256 + (base32 + "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rapidjsonr") + (synopsis "JSON parser") + (description + "This package provides JSON parsing capability through the Rapidjson +library.") + (license license:expat))) From ad6fea1690c2a7ce3e1998e3ab402556be0973e5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 14:58:34 +0100 Subject: [PATCH 028/300] gnu: Add r-ontologyindex. * gnu/packages/cran.scm (r-ontologyindex): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c11202abf7..d3c22d2350 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9382,3 +9382,23 @@ other manipulations of bitmapped images.") "This package provides JSON parsing capability through the Rapidjson library.") (license license:expat))) + +(define-public r-ontologyindex + (package + (name "r-ontologyindex") + (version "2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "ontologyIndex" version)) + (sha256 + (base32 + "168m4jdwbzv8lpimx9063306691hnfdjmdhb5y8195d9vcq049jr")))) + (properties `((upstream-name . "ontologyIndex"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ontologyIndex") + (synopsis "Functions for processing ontologies in R") + (description + "This package provides functions for reading ontologies into R as lists +and manipulating sets of ontological terms.") + (license license:gpl2+))) From dfd09f7bad7c8c8803224900f7ce04ce4356471d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:00:24 +0100 Subject: [PATCH 029/300] gnu: Add r-bigrquery. * gnu/packages/cran.scm (r-bigrquery): New variable. --- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d3c22d2350..5766441827 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9402,3 +9402,33 @@ library.") "This package provides functions for reading ontologies into R as lists and manipulating sets of ontological terms.") (license license:gpl2+))) + +(define-public r-bigrquery + (package + (name "r-bigrquery") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "bigrquery" version)) + (sha256 + (base32 + "0z7wsqxla1pg2454l35kkfaz2s9hppwvpz1pds286ddldbbmyzis")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-curl" ,r-curl) + ("r-dbi" ,r-dbi) + ("r-glue" ,r-glue) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-prettyunits" ,r-prettyunits) + ("r-progress" ,r-progress) + ("r-rapidjsonr" ,r-rapidjsonr) + ("r-rcpp" ,r-rcpp) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/rstats-db/bigrquery") + (synopsis "R interface to Google's BigQuery API") + (description + "This package provides an R interface to Google's BigQuery database.") + (license license:gpl3))) From 1ab5160434fcdb7bfb8b56d5277c18c2cf44ef10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:27:21 +0100 Subject: [PATCH 030/300] gnu: Add r-gmp. * gnu/packages/cran.scm (r-gmp): New variable. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5766441827..930a89245b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -54,6 +54,7 @@ #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) + #:use-module (gnu packages multiprecision) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -9432,3 +9433,30 @@ and manipulating sets of ontological terms.") (description "This package provides an R interface to Google's BigQuery database.") (license license:gpl3))) + +(define-public r-gmp + (package + (name "r-gmp") + (version "0.5-13.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "gmp" version)) + (sha256 + (base32 + "1xd6jjra4niqv1kps91y348lwgvy73p2faxaia4gfzdnrpw7wsxf")))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-CC + (lambda _ (setenv "CC" "gcc") #t))))) + (inputs `(("gmp" ,gmp))) + (home-page "https://cran.r-project.org/web/packages/gmp") + (synopsis "Multiple precision arithmetic") + (description + "This package supports multiple precision arithmetic (big integers and +rationals, prime number tests, matrix computation), \"arithmetic without +limitations\" using the GNU Multiple Precision library.") + ;; Any version of the GPL. + (license license:gpl3+))) From a536c7c9ad78ce95fb8dad61114c40c57b3c0be8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:27:27 +0100 Subject: [PATCH 031/300] gnu: Add r-rmpfr. * gnu/packages/cran.scm (r-rmpfr): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 930a89245b..f305f2be80 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9460,3 +9460,29 @@ rationals, prime number tests, matrix computation), \"arithmetic without limitations\" using the GNU Multiple Precision library.") ;; Any version of the GPL. (license license:gpl3+))) + +(define-public r-rmpfr + (package + (name "r-rmpfr") + (version "0.7-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rmpfr" version)) + (sha256 + (base32 + "0172px5ryi7i0gyyin9z2bzif8vnj292gk0s1w5p3c12g9hj2c4v")))) + (properties `((upstream-name . "Rmpfr"))) + (build-system r-build-system) + (inputs + `(("mpfr" ,mpfr))) + (propagated-inputs + `(("r-gmp" ,r-gmp))) + (home-page "http://rmpfr.r-forge.r-project.org/") + (synopsis "R bindings to the MPFR library") + (description + "This package supports arithmetic (via S4 classes and methods) for +arbitrary precision floating point numbers, including transcendental +functions. To this end, the package interfaces with the @dfn{Multiple +Precision Floating-Point Reliable} (MPFR) library.") + (license license:gpl2+))) From 8004bb2451d33d046dfa5db3894746deaf55a285 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:29:11 +0100 Subject: [PATCH 032/300] gnu: Add r-assertive-base. * gnu/packages/cran.scm (r-assertive-base): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f305f2be80..c449301abd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9486,3 +9486,25 @@ arbitrary precision floating point numbers, including transcendental functions. To this end, the package interfaces with the @dfn{Multiple Precision Floating-Point Reliable} (MPFR) library.") (license license:gpl2+))) + +(define-public r-assertive-base + (package + (name "r-assertive-base") + (version "0.0-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.base" version)) + (sha256 + (base32 + "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh")))) + (properties + `((upstream-name . "assertive.base"))) + (build-system r-build-system) + (home-page "https://bitbucket.org/richierocks/assertive.base") + (synopsis "Core of the assertive package") + (description + "This package provides a minimal set of predicates and assertions used by +the assertive package. This is mainly for use by other package developers who +want to include run-time testing features in their own packages.") + (license license:gpl3+))) From 4b2d17edaa0e296f197bc43adacefa2447d1e513 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:29:37 +0100 Subject: [PATCH 033/300] gnu: Add r-assertive-properties. * gnu/packages/cran.scm (r-assertive-properties): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c449301abd..28835bafd8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9508,3 +9508,28 @@ Precision Floating-Point Reliable} (MPFR) library.") the assertive package. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-properties + (package + (name "r-assertive-properties") + (version "0.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.properties" version)) + (sha256 + (base32 + "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw")))) + (properties + `((upstream-name . "assertive.properties"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.properties") + (synopsis "Assertions to check properties of variables") + (description + "This package provides a set of predicates and assertions for checking +the properties of variables, such as length, names and attributes. This is +mainly for use by other package developers who want to include run-time +testing features in their own packages.") + (license license:gpl3+))) From dac9c1f6048237ecc0eeaa959b3c7429adb2518a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:30:20 +0100 Subject: [PATCH 034/300] gnu: Add r-assertive-numbers. * gnu/packages/cran.scm (r-assertive-numbers): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 28835bafd8..270e402d40 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9533,3 +9533,27 @@ the properties of variables, such as length, names and attributes. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-numbers + (package + (name "r-assertive-numbers") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.numbers" version)) + (sha256 + (base32 + "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds")))) + (properties + `((upstream-name . "assertive.numbers"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.numbers") + (synopsis "Assertions to check properties of numbers") + (description + "This package provides a set of predicates and assertions for checking +the properties of numbers. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) From 2da2d2f60525ef87eb05753b093832f4ecd35f14 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:31:02 +0100 Subject: [PATCH 035/300] gnu: Add r-assertive-sets. * gnu/packages/cran.scm (r-assertive-sets): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 270e402d40..70d87c9f66 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9557,3 +9557,27 @@ testing features in their own packages.") the properties of numbers. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-sets + (package + (name "r-assertive-sets") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.sets" version)) + (sha256 + (base32 + "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7")))) + (properties + `((upstream-name . "assertive.sets"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.sets") + (synopsis "Assertions to check properties of sets") + (description + "This package provides a set of predicates and assertions for checking +the properties of sets. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) From 905aa46ae5dea7ab01a4e6e889ba56c7af4354f7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:32:07 +0100 Subject: [PATCH 036/300] gnu: Add r-assertive-matrices. * gnu/packages/cran.scm (r-assertive-matrices): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 70d87c9f66..beddefe683 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9581,3 +9581,28 @@ who want to include run-time testing features in their own packages.") the properties of sets. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-matrices + (package + (name "r-assertive-matrices") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.matrices" version)) + (sha256 + (base32 + "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil")))) + (properties + `((upstream-name . "assertive.matrices"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.matrices") + (synopsis "Assertions to check properties of matrices") + (description + "This package provides a set of predicates and assertions for checking +the properties of matrices. This is mainly for use by other package +developers who want to include run-time testing features in their own +packages.") + (license license:gpl3+))) From c358b5d418a89e1946f291c4be7d460acc36985e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:32:49 +0100 Subject: [PATCH 037/300] gnu: Add r-assertive-models. * gnu/packages/cran.scm (r-assertive-models): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index beddefe683..faecbf52fc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9606,3 +9606,27 @@ the properties of matrices. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-models + (package + (name "r-assertive-models") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.models" version)) + (sha256 + (base32 + "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr")))) + (properties + `((upstream-name . "assertive.models"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.models") + (synopsis "Assertions to check properties of models") + (description + "This package provides a set of predicates and assertions for checking +the properties of models. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) From dcafcfb4fd41016124edd0b24b96214fc3848622 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:33:30 +0100 Subject: [PATCH 038/300] gnu: Add r-assertive-reflection. * gnu/packages/cran.scm (r-assertive-reflection): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index faecbf52fc..a10d430b9e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9630,3 +9630,28 @@ packages.") the properties of models. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-reflection + (package + (name "r-assertive-reflection") + (version "0.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.reflection" version)) + (sha256 + (base32 + "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj")))) + (properties + `((upstream-name . "assertive.reflection"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.reflection") + (synopsis "Assertions for checking the state of R") + (description + "This package provides a set of predicates and assertions for checking +the state and capabilities of R, the operating system it is running on, and +the IDE being used. This is mainly for use by other package developers who +want to include run-time testing features in their own packages.") + (license license:gpl3+))) From 5e3bd355069649e37eb52d2194e486d8419c51c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:34:28 +0100 Subject: [PATCH 039/300] gnu: Add r-assertive-types. * gnu/packages/cran.scm (r-assertive-types): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a10d430b9e..b3f45f38f0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9655,3 +9655,29 @@ the state and capabilities of R, the operating system it is running on, and the IDE being used. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-types + (package + (name "r-assertive-types") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.types" version)) + (sha256 + (base32 + "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb")))) + (properties + `((upstream-name . "assertive.types"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-properties" ,r-assertive-properties) + ("r-codetools" ,r-codetools))) + (home-page "https://bitbucket.org/richierocks/assertive.types") + (synopsis "Assertions to check types of variables") + (description + "This package provides a set of predicates and assertions for checking +the types of variables. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) From 1f0a761a14373cfec2baf7b79671ab221ea79845 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:35:14 +0100 Subject: [PATCH 040/300] gnu: Add r-assertive-files. * gnu/packages/cran.scm (r-assertive-files): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b3f45f38f0..158ee16179 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9681,3 +9681,29 @@ want to include run-time testing features in their own packages.") the types of variables. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-files + (package + (name "r-assertive-files") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.files" version)) + (sha256 + (base32 + "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy")))) + (properties + `((upstream-name . "assertive.files"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-numbers" ,r-assertive-numbers))) + (home-page "https://bitbucket.org/richierocks/assertive.files") + (synopsis "Assertions to check properties of files") + (description + "This package provides a set of predicates and assertions for checking +the properties of files and connections. This is mainly for use by other +package developers who want to include run-time testing features in their own +packages.") + (license license:gpl3+))) From 50ce8b1e2c83d0a31bba6dfaff1d5035d3a94892 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:35:55 +0100 Subject: [PATCH 041/300] gnu: Add r-assertive-code. * gnu/packages/cran.scm (r-assertive-code): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 158ee16179..ee3852c99c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9707,3 +9707,29 @@ the properties of files and connections. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-code + (package + (name "r-assertive-code") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.code" version)) + (sha256 + (base32 + "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g")))) + (properties + `((upstream-name . "assertive.code"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-properties" ,r-assertive-properties) + ("r-assertive-types" ,r-assertive-types))) + (home-page "https://bitbucket.org/richierocks/assertive.code") + (synopsis "Assertions to check properties of code") + (description + "This package provides a set of predicates and assertions for checking +the properties of code. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) From 29d9a2affb7e876fbe620215da21e13d5d703927 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:36:52 +0100 Subject: [PATCH 042/300] gnu: Add r-assertive-datetimes. * gnu/packages/cran.scm (r-assertive-datetimes): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ee3852c99c..c8ad5edecc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9733,3 +9733,29 @@ packages.") the properties of code. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-datetimes + (package + (name "r-assertive-datetimes") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.datetimes" version)) + (sha256 + (base32 + "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78")))) + (properties + `((upstream-name . "assertive.datetimes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-types" ,r-assertive-types))) + (home-page "https://bitbucket.org/richierocks/assertive.datetimes") + (synopsis "Assertions to check properties of dates and times") + (description + "This package provides a set of predicates and assertions for checking +the properties of dates and times. This is mainly for use by other package +developers who want to include run-time testing features in their own +packages.") + (license license:gpl3+))) From 66d0a0a70657e0036cce20d6efd94dc179ca7636 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:37:33 +0100 Subject: [PATCH 043/300] gnu: Add r-assertive-strings. * gnu/packages/cran.scm (r-assertive-strings): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c8ad5edecc..16540f33fe 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9759,3 +9759,29 @@ the properties of dates and times. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-strings + (package + (name "r-assertive-strings") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.strings" version)) + (sha256 + (base32 + "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm")))) + (properties + `((upstream-name . "assertive.strings"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-types" ,r-assertive-types) + ("r-stringi" ,r-stringi))) + (home-page "https://bitbucket.org/richierocks/assertive.strings") + (synopsis "Assertions to check properties of strings") + (description + "This package provides a set of predicates and assertions for checking +the properties of strings. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) From 6d3702e5ced15dd7daacaad1b0754f2eeb7038ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:38:23 +0100 Subject: [PATCH 044/300] gnu: Add r-assertive-data-us. * gnu/packages/cran.scm (r-assertive-data-us): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 16540f33fe..8dfc303101 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9785,3 +9785,29 @@ packages.") the properties of strings. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-data-us + (package + (name "r-assertive-data-us") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.data.us" version)) + (sha256 + (base32 + "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq")))) + (properties + `((upstream-name . "assertive.data.us"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-strings" ,r-assertive-strings))) + (home-page "https://bitbucket.org/richierocks/assertive.data.us") + (synopsis "Assertions to check properties of strings") + (description + "This package provides a set of predicates and assertions for checking +the properties of US-specific complex data types. This is mainly for use by +other package developers who want to include run-time testing features in +their own packages.") + (license license:gpl3+))) From 39ef8e097b6f229bae17832835e5bc599d17576e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:38:54 +0100 Subject: [PATCH 045/300] gnu: Add r-assertive-data-uk. * gnu/packages/cran.scm (r-assertive-data-uk): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8dfc303101..28b266114a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9811,3 +9811,29 @@ the properties of US-specific complex data types. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-data-uk + (package + (name "r-assertive-data-uk") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.data.uk" version)) + (sha256 + (base32 + "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b")))) + (properties + `((upstream-name . "assertive.data.uk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-strings" ,r-assertive-strings))) + (home-page "https://bitbucket.org/richierocks/assertive.data.uk") + (synopsis "Assertions to check properties of strings") + (description + "This package provides a set of predicates and assertions for checking +the properties of UK-specific complex data types. This is mainly for use by +other package developers who want to include run-time testing features in +their own packages.") + (license license:gpl3+))) From 39231abf4d5cf71dc75ae4fc6907f3afbd2f91fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:39:31 +0100 Subject: [PATCH 046/300] gnu: Add r-assertive-data. * gnu/packages/cran.scm (r-assertive-data): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 28b266114a..dbce5a7815 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9837,3 +9837,29 @@ the properties of UK-specific complex data types. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive-data + (package + (name "r-assertive-data") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.data" version)) + (sha256 + (base32 + "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s")))) + (properties + `((upstream-name . "assertive.data"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-strings" ,r-assertive-strings))) + (home-page "https://bitbucket.org/richierocks/assertive.data") + (synopsis "Assertions to check properties of data") + (description + "This package provides a set of predicates and assertions for checking +the properties of (country independent) complex data types. This is mainly +for use by other package developers who want to include run-time testing +features in their own packages.") + (license license:gpl3+))) From 658b2b62cb62ebf8b55759d41e82dda4e54706bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 15:40:28 +0100 Subject: [PATCH 047/300] gnu: Add r-assertive. * gnu/packages/cran.scm (r-assertive): New variable. --- gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dbce5a7815..9001f07c74 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9863,3 +9863,40 @@ the properties of (country independent) complex data types. This is mainly for use by other package developers who want to include run-time testing features in their own packages.") (license license:gpl3+))) + +(define-public r-assertive + (package + (name "r-assertive") + (version "0.3-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive" version)) + (sha256 + (base32 + "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-code" ,r-assertive-code) + ("r-assertive-data" ,r-assertive-data) + ("r-assertive-data-uk" ,r-assertive-data-uk) + ("r-assertive-data-us" ,r-assertive-data-us) + ("r-assertive-datetimes" ,r-assertive-datetimes) + ("r-assertive-files" ,r-assertive-files) + ("r-assertive-matrices" ,r-assertive-matrices) + ("r-assertive-models" ,r-assertive-models) + ("r-assertive-numbers" ,r-assertive-numbers) + ("r-assertive-properties" ,r-assertive-properties) + ("r-assertive-reflection" ,r-assertive-reflection) + ("r-assertive-sets" ,r-assertive-sets) + ("r-assertive-strings" ,r-assertive-strings) + ("r-assertive-types" ,r-assertive-types) + ("r-knitr" ,r-knitr))) + (home-page "https://bitbucket.org/richierocks/assertive") + (synopsis "Readable check functions to ensure code integrity") + (description + "This package provides lots of predicates (@code{is_*} functions) to +check the state of your variables, and assertions (@code{assert_*} functions) +to throw errors if they aren't in the right form.") + (license license:gpl3+))) From f51dcc275e6c4de9b95e7a5d8584a307a259a0db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:28:19 +0100 Subject: [PATCH 048/300] gnu: Add r-dotcall64. * gnu/packages/cran.scm (r-dotcall64): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9001f07c74..4020ecdf9e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9900,3 +9900,27 @@ features in their own packages.") check the state of your variables, and assertions (@code{assert_*} functions) to throw errors if they aren't in the right form.") (license license:gpl3+))) + +(define-public r-dotcall64 + (package + (name "r-dotcall64") + (version "1.0-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "dotCall64" version)) + (sha256 + (base32 + "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9")))) + (properties `((upstream-name . "dotCall64"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") + (synopsis "Enhanced foreign function interface supporting long vectors") + (description + "This package provides @code{.C64()}, an enhanced version of @code{.C()} +and @code{.Fortran()} from the R foreign function interface. @code{.C64()} +supports long vectors, arguments of type 64-bit integer, and provides a +mechanism to avoid unnecessary copies of read-only and write-only arguments. +This makes it a convenient and fast interface to C/C++ and Fortran code.") + (license license:gpl2+))) From 90104ecd66526e708df0fca2cc6e93de89401883 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:31:33 +0100 Subject: [PATCH 049/300] gnu: Add r-spam. * gnu/packages/cran.scm (r-spam): New variable. --- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4020ecdf9e..e13fbc67cd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9924,3 +9924,33 @@ supports long vectors, arguments of type 64-bit integer, and provides a mechanism to avoid unnecessary copies of read-only and write-only arguments. This makes it a convenient and fast interface to C/C++ and Fortran code.") (license license:gpl2+))) + +(define-public r-spam + (package + (name "r-spam") + (version "2.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "spam" version)) + (sha256 + (base32 + "04bfwwna013hrbl4k6w1cdiz5bkc83jlasivriyn5l9gkj2qskr2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dotcall64" ,r-dotcall64))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://www.math.uzh.ch/pages/spam/") + (synopsis "Sparse matrix algebra") + (description + "This package provides a set of functions for sparse matrix algebra. +Differences with other sparse matrix packages are: + +@enumerate +@item it only supports (essentially) one sparse matrix format; +@item it is based on transparent and simple structure(s); +@item it is tailored for MCMC calculations within G(M)RF; +@item and it is fast and scalable (with the extension package @code{spam64}). +@end enumerate\n") + ;; Either of these licenses + (license (list license:bsd-3 license:lgpl2.0)))) From 32725458b744c46f0635ba9f73e1ba6c77477e4a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:32:59 +0100 Subject: [PATCH 050/300] gnu: Add r-fields. * gnu/packages/cran.scm (r-fields): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e13fbc67cd..70128d376c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9954,3 +9954,29 @@ Differences with other sparse matrix packages are: @end enumerate\n") ;; Either of these licenses (license (list license:bsd-3 license:lgpl2.0)))) + +(define-public r-fields + (package + (name "r-fields") + (version "9.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "fields" version)) + (sha256 + (base32 + "1v7z48a8jmdcil28rj8c3455k6rssr5v9qi6dyhhpbb193bj8121")))) + (build-system r-build-system) + (propagated-inputs + `(("r-maps" ,r-maps) + ("r-spam" ,r-spam))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://www.image.ucar.edu/fields") + (synopsis "Tools for spatial data") + (description + "This is a package for curve, surface and function fitting with an +emphasis on splines, spatial data and spatial statistics. The major methods +include cubic, and thin plate splines, Kriging, and compactly supported +covariance functions for large data sets.") + (license license:gpl2+))) From 99c164a5c7a4c17a7d8770a4ec86906cb67b61d6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:36:20 +0100 Subject: [PATCH 051/300] gnu: Add r-spatialextremes. * gnu/packages/cran.scm (r-spatialextremes): New variable. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 70128d376c..a3bc01ba0d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9980,3 +9980,31 @@ emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets.") (license license:gpl2+))) + +(define-public r-spatialextremes + (package + (name "r-spatialextremes") + (version "2.0-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "SpatialExtremes" version)) + (sha256 + (base32 + "1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050")))) + (properties + `((upstream-name . "SpatialExtremes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fields" ,r-fields) + ("r-maps" ,r-maps))) + (home-page "http://spatialextremes.r-forge.r-project.org/") + (synopsis "Modelling spatial extremes") + (description + "This package provides tools for the statistical modelling of spatial +extremes using max-stable processes, copula or Bayesian hierarchical models. +More precisely, this package allows (conditional) simulations from various +parametric max-stable models, analysis of the extremal spatial dependence, the +fitting of such processes using composite likelihoods or least square (simple +max-stable processes only), model checking and selection and prediction.") + (license license:gpl2+))) From c2d6e866ac8f480a98bcb27aa7c3cc5b8f588a23 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:38:11 +0100 Subject: [PATCH 052/300] gnu: Add r-drc. * gnu/packages/cran.scm (r-drc): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a3bc01ba0d..1b6196f4fd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10008,3 +10008,29 @@ parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction.") (license license:gpl2+))) + +(define-public r-drc + (package + (name "r-drc") + (version "3.0-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "drc" version)) + (sha256 + (base32 + "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y")))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-gtools" ,r-gtools) + ("r-mass" ,r-mass) + ("r-multcomp" ,r-multcomp) + ("r-plotrix" ,r-plotrix) + ("r-scales" ,r-scales))) + (home-page "https://cran.r-project.org/web/packages/drc") + (synopsis "Analysis of dose-response curves") + (description + "This package provides a suite of flexible and versatile model fitting +and after-fitting functions for the analysis of dose-response data.") + (license license:gpl2+))) From 4fcbd7eaf33bd597f8e982f4d230f3670bbd64cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:43:12 +0100 Subject: [PATCH 053/300] gnu: Add r-rmeta. * gnu/packages/cran.scm (r-rmeta): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1b6196f4fd..f2fb042112 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10034,3 +10034,24 @@ max-stable processes only), model checking and selection and prediction.") "This package provides a suite of flexible and versatile model fitting and after-fitting functions for the analysis of dose-response data.") (license license:gpl2+))) + +(define-public r-rmeta + (package + (name "r-rmeta") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rmeta" version)) + (sha256 + (base32 + "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rmeta") + (synopsis "Tools for meta-analysis") + (description + "This package provides functions for simple fixed and random effects +meta-analysis for two-sample comparisons and cumulative meta-analyses. It +draws standard summary plots, funnel plots, and computes summaries and tests +for association and heterogeneity.") + (license license:gpl2))) From afc0d8158b654381789b7e1c9dea9512cf63afbf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:44:13 +0100 Subject: [PATCH 054/300] gnu: Add r-bootstrap. * gnu/packages/cran.scm (r-bootstrap): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f2fb042112..00eab12c92 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10055,3 +10055,26 @@ meta-analysis for two-sample comparisons and cumulative meta-analyses. It draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.") (license license:gpl2))) + +(define-public r-bootstrap + (package + (name "r-bootstrap") + (version "2017.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "bootstrap" version)) + (sha256 + (base32 + "08lmsy7k8wsgv89yc904c6fidcymr1ma2ry4fl0p69p21v4iiwa4")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/bootstrap") + (synopsis "Functions for the book \"An Introduction to the Bootstrap\"") + (description + "This package provides software and data for the book \"An Introduction +to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. +This package is primarily provided for projects already based on it, and for +support of the book. New projects should preferentially use the recommended +package \"boot\".") + (license license:bsd-3))) From 1ea708af8cf89c15a508941d6af6ee36e401a3ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:45:08 +0100 Subject: [PATCH 055/300] gnu: Add r-survivalroc. * gnu/packages/cran.scm (r-survivalroc): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 00eab12c92..e2ad3ca03f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10078,3 +10078,24 @@ This package is primarily provided for projects already based on it, and for support of the book. New projects should preferentially use the recommended package \"boot\".") (license license:bsd-3))) + +(define-public r-survivalroc + (package + (name "r-survivalroc") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "survivalROC" version)) + (sha256 + (base32 + "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l")))) + (properties `((upstream-name . "survivalROC"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/survivalROC") + (synopsis "Time-dependent ROC curve estimation from censored survival data") + (description + "Compute time-dependent ROC curve from censored survival data using +Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, +Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") + (license license:gpl2+))) From 6a5bfe09ebfeff74b462e9260f5d902c86f88a61 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:45:58 +0100 Subject: [PATCH 056/300] gnu: Add r-longitudinal. * gnu/packages/cran.scm (r-longitudinal): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e2ad3ca03f..e420d2eb66 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10099,3 +10099,25 @@ package \"boot\".") Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") (license license:gpl2+))) + +(define-public r-longitudinal + (package + (name "r-longitudinal") + (version "1.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "longitudinal" version)) + (sha256 + (base32 + "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l")))) + (build-system r-build-system) + (propagated-inputs `(("r-corpcor" ,r-corpcor))) + (home-page "http://strimmerlab.org/software/longitudinal/") + (synopsis "Analysis of multiple time course data") + (description + "This package contains general data structures and functions for +longitudinal data with multiple variables, repeated measurements, and +irregularly spaced time points. It also implements a shrinkage estimator of +dynamical correlation and dynamical covariance.") + (license license:gpl3+))) From e50722c8e67994b5d24843c6920bb01b9e96bddb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:46:52 +0100 Subject: [PATCH 057/300] gnu: Add r-genenet. * gnu/packages/cran.scm (r-genenet): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e420d2eb66..dd924a1ca1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10121,3 +10121,30 @@ longitudinal data with multiple variables, repeated measurements, and irregularly spaced time points. It also implements a shrinkage estimator of dynamical correlation and dynamical covariance.") (license license:gpl3+))) + +(define-public r-genenet + (package + (name "r-genenet") + (version "1.2.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "GeneNet" version)) + (sha256 + (base32 + "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p")))) + (properties `((upstream-name . "GeneNet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-corpcor" ,r-corpcor) + ("r-fdrtool" ,r-fdrtool) + ("r-longitudinal" ,r-longitudinal))) + (home-page "http://strimmerlab.org/software/genenet/") + (synopsis "Modeling and inferring gene networks") + (description + "This package analyzes gene expression (time series) data with focus on +the inference of gene networks. In particular, GeneNet implements the methods +of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) +for learning large-scale gene association networks (including assignment of +putative directions).") + (license license:gpl3+))) From fe4e9f03492521f641e326cb21108367a44b1a63 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:47:51 +0100 Subject: [PATCH 058/300] gnu: Add r-rbamtools. * gnu/packages/cran.scm (r-rbamtools): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dd924a1ca1..e10465bb46 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10148,3 +10148,25 @@ of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).") (license license:gpl3+))) + +(define-public r-rbamtools + (package + (name "r-rbamtools") + (version "2.16.11.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rbamtools" version)) + (sha256 + (base32 + "0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj")))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-refgenome" ,r-refgenome))) + (home-page "https://cran.r-project.org/web/packages/rbamtools") + (synopsis "Read and write BAM (binary alignment) files") + (description + "This package provides an R interface to functions of the SAMtools +library.") + (license license:artistic2.0))) From e3c0e3e36033f9f46e7c8460c86b16cf9e8298ec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:54:39 +0100 Subject: [PATCH 059/300] gnu: Add r-protviz. * gnu/packages/cran.scm (r-protviz): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e10465bb46..5204677380 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10170,3 +10170,30 @@ putative directions).") "This package provides an R interface to functions of the SAMtools library.") (license license:artistic2.0))) + +(define-public r-protviz + (package + (name "r-protviz") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "protViz" version)) + (sha256 + (base32 + "1im3ajimycsc1zpzbihxlsibjk0462q0vldy7v5ypsqnjbi1ndxm")))) + (properties `((upstream-name . "protViz"))) + (build-system r-build-system) + (inputs + `(("perl" ,perl) + ("python-2" ,python-2))) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/protViz/protViz/") + (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") + (description + "This package helps with quality checks, visualizations and analysis of +mass spectrometry data, coming from proteomics experiments. The package is +developed, tested and used at the Functional Genomics Center Zurich, where it +is used mainly for prototyping, teaching, and having fun with proteomics data. +But it can also be used to do data analysis for small scale data sets.") + (license license:gpl3))) From 7aeec0cf374b9d911410ab87fd2fe985edad2430 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:56:10 +0100 Subject: [PATCH 060/300] gnu: Add r-cmprsk. * gnu/packages/cran.scm (r-cmprsk): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5204677380..f073124151 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10197,3 +10197,30 @@ developed, tested and used at the Functional Genomics Center Zurich, where it is used mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.") (license license:gpl3))) + +(define-public r-cmprsk + (package + (name "r-cmprsk") + (version "2.2-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "cmprsk" version)) + (sha256 + (base32 + "1imr3wpnj4g57n2x4ryahl4lk8lvq9y2r7319zv3k82mznha8bcm")))) + (build-system r-build-system) + (propagated-inputs + `(("r-survival" ,r-survival))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/cmprsk") + (synopsis "Subdistribution analysis of competing risks") + (description + "This package provides tool for estimation, testing and regression +modeling of subdistribution functions in competing risks, as described in +Gray (1988), A class of K-sample tests for comparing the cumulative incidence +of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999), +A proportional hazards model for the subdistribution of a competing risk, +JASA, 94:496-509.") + (license license:gpl2+))) From 728012dae8bbba2fd006300bfd046aa6b99846ae Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 16:57:43 +0100 Subject: [PATCH 061/300] gnu: Add r-etm. * gnu/packages/cran.scm (r-etm): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f073124151..481dcc1457 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10224,3 +10224,29 @@ of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999), A proportional hazards model for the subdistribution of a competing risk, JASA, 94:496-509.") (license license:gpl2+))) + +(define-public r-etm + (package + (name "r-etm") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "etm" version)) + (sha256 + (base32 + "0ws103b3pmli0z4xbyfxkly2wnnnxnnwc0r66qjjqjrlvm7pffl1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-lattice" ,r-lattice) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/etm") + (synopsis "Empirical transition matrix") + (description + "The @dfn{empirical transition matrix} (etm) package permits to estimate +the matrix of transition probabilities for any time-inhomogeneous multistate +model with finite state space using the Aalen-Johansen estimator.") + (license license:expat))) From 17932a0f63f54bb6ad37d773dfd9fad4e8c7146b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 17:07:19 +0100 Subject: [PATCH 062/300] gnu: Add r-epi. * gnu/packages/cran.scm (r-epi): New variable. --- gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 481dcc1457..8c0142d092 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10250,3 +10250,40 @@ JASA, 94:496-509.") the matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space using the Aalen-Johansen estimator.") (license license:expat))) + +(define-public r-epi + (package + (name "r-epi") + (version "2.32") + (source + (origin + (method url-fetch) + (uri (cran-uri "Epi" version)) + (sha256 + (base32 + "14n24xlm7pwdc54w2hlpjhfal1zpzm87rv3rjfckiz47d3w7dwqm")))) + (properties `((upstream-name . "Epi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cmprsk" ,r-cmprsk) + ("r-data-table" ,r-data-table) + ("r-etm" ,r-etm) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv) + ("r-numderiv" ,r-numderiv) + ("r-plyr" ,r-plyr) + ("r-survival" ,r-survival) + ("r-zoo" ,r-zoo))) + (home-page "http://BendixCarstensen.com/Epi/") + (synopsis "Statistical analysis in epidemiology") + (description + "This package provides functions for demographic and epidemiological +analysis in the Lexis diagram, i.e. register and cohort follow-up data, in +particular representation, manipulation and simulation of multistate data - +the Lexis suite of functions, which includes interfaces to the @code{mstate}, +@code{etm} and @code{cmprsk} packages. It also contains functions for +Age-Period-Cohort and Lee-Carter modeling and a function for interval censored +data and some useful functions for tabulation and plotting, as well as a +number of epidemiological data sets.") + (license license:gpl2))) From 879a15203b349d464a47b708a2ab37f09c3e36a3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 17:09:41 +0100 Subject: [PATCH 063/300] gnu: Add r-ppls. * gnu/packages/cran.scm (r-ppls): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8c0142d092..68e660a9a3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10287,3 +10287,25 @@ Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.") (license license:gpl2))) + +(define-public r-ppls + (package + (name "r-ppls") + (version "1.6-1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ppls" version)) + (sha256 + (base32 + "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx")))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ppls") + (synopsis "Penalized partial least squares") + (description + "This package contains linear and nonlinear regression methods based on +partial least squares and penalization techniques. Model parameters are +selected via cross-validation, and confidence intervals ans tests for the +regression coefficients can be conducted via jackknifing.") + (license license:gpl2+))) From 0af9616d9186874e3769f8b69f9a550b267ae767 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 17:10:29 +0100 Subject: [PATCH 064/300] gnu: Add r-huge. * gnu/packages/cran.scm (r-huge): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 68e660a9a3..40cb0b149d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10309,3 +10309,28 @@ partial least squares and penalization techniques. Model parameters are selected via cross-validation, and confidence intervals ans tests for the regression coefficients can be conducted via jackknifing.") (license license:gpl2+))) + +(define-public r-huge + (package + (name "r-huge") + (version "1.2.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "huge" version)) + (sha256 + (base32 + "134d951x42vy9dcmf155fbvik2934nh6qm2w5jlx3x2c6cf7faq4")))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix))) + (home-page "https://cran.r-project.org/web/packages/huge") + (synopsis "High-dimensional undirected graph estimation") + (description + "This package provides a general framework for high-dimensional +undirected graph estimation. It integrates data preprocessing, neighborhood +screening, graph estimation, and model selection techniques into a pipeline.") + (license license:gpl2))) From 39274ab4d956f6037bcd6ca814333bda5dddb650 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 17:11:08 +0100 Subject: [PATCH 065/300] gnu: Add r-parcor. * gnu/packages/cran.scm (r-parcor): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 40cb0b149d..9947ff3ab4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10334,3 +10334,30 @@ regression coefficients can be conducted via jackknifing.") undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline.") (license license:gpl2))) + +(define-public r-parcor + (package + (name "r-parcor") + (version "0.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "parcor" version)) + (sha256 + (base32 + "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-epi" ,r-epi) + ("r-genenet" ,r-genenet) + ("r-glmnet" ,r-glmnet) + ("r-mass" ,r-mass) + ("r-ppls" ,r-ppls))) + (home-page "https://cran.r-project.org/web/packages/parcor") + (synopsis "Regularized estimation of partial correlation matrices") + (description + "This package estimates the matrix of partial correlations based on +different regularized regression methods: lasso, adaptive lasso, PLS, and +Ridge Regression. In addition, the package provides model selection for +lasso, adaptive lasso and Ridge regression based on cross-validation.") + (license license:gpl2+))) From cba08f60a1c887569b13f6edac5cf92952d80fa3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Jan 2019 17:12:21 +0100 Subject: [PATCH 066/300] gnu: Add r-mcmc. * gnu/packages/cran.scm (r-mcmc): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9947ff3ab4..24d1ee85ed 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10361,3 +10361,27 @@ different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression. In addition, the package provides model selection for lasso, adaptive lasso and Ridge regression based on cross-validation.") (license license:gpl2+))) + +(define-public r-mcmc + (package + (name "r-mcmc") + (version "0.9-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "mcmc" version)) + (sha256 + (base32 + "1i3rahph8pbhi5dsyjnkazqklg4lhh3azlyvx4kvabx50q0awxn6")))) + (build-system r-build-system) + (home-page "http://www.stat.umn.edu/geyer/mcmc/") + (synopsis "Markov chain Monte Carlo") + (description + "This package simulates continuous distributions of random vectors using +@dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R +function that evaluates the log unnormalized density. Algorithms are random +walk Metropolis algorithm (function @code{metrop}), simulated +tempering (function @code{temper}), and morphometric random walk +Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity +by change of variable.") + (license license:expat))) From 25a0ffbf27e93b1745193f743b15cdcfc6b43aef Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Sat, 29 Dec 2018 21:38:13 -0600 Subject: [PATCH 067/300] gnu: emacs-md4rd: Update to c55512c. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs.scm (emacs-md4rd): Update to c55512c. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index bddc4891d4..f3f2440cc1 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -9328,11 +9328,11 @@ navigate and display hierarchy structures.") (license license:gpl3+)))) (define-public emacs-md4rd - (let ((commit "be0fc4951b2d1f5194ffa1fcaac706dbac560500") + (let ((commit "c55512c2f7680db2a1e73db6bdf93adecaf40fec") (revision "1")) (package (name "emacs-md4rd") - (version (string-append "0.0.1" "-" revision "." + (version (string-append "0.0.2" "-" revision "." (string-take commit 7))) (source (origin (method git-fetch) @@ -9342,7 +9342,7 @@ navigate and display hierarchy structures.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1i93shx5x192gd7cl2r6gvcvhhwyi1k08abi5w3izv1hn3pmksgq")))) + "0mvv1mvsrpkrmikcpfqf2zbawnzgq33j6zjdrlv48mcw57xb2ak9")))) (propagated-inputs `(("emacs-hierarchy" ,emacs-hierarchy) ("emacs-request" ,emacs-request) From 4287bd19c7706bc5f065192b4b9b7fee01d640d9 Mon Sep 17 00:00:00 2001 From: Vasile Dumitrascu Date: Sun, 30 Dec 2018 19:50:18 +0100 Subject: [PATCH 068/300] gnu: bind: Update to 9.12.3-P1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/dns.scm (bind): Update to 9.12.3-P1. Signed-off-by: Ludovic Courtès --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 2ebc3d8dad..09f0194bf7 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -106,7 +106,7 @@ and BOOTP/TFTP for network booting of diskless machines.") (define-public isc-bind (package (name "bind") - (version "9.12.2-P2") + (version "9.12.3-P1") (source (origin (method url-fetch) (uri (string-append @@ -114,7 +114,7 @@ and BOOTP/TFTP for network booting of diskless machines.") version ".tar.gz")) (sha256 (base32 - "0gk9vwqlbdmn10m21f2awvmiccfbadvcwi8zsgm91awbx4k7h0l7")))) + "0wzdbn6ig851354cjdys5q3gvqcvl2gmmih1gzr8ldl7sy4r7dvc")))) (build-system gnu-build-system) (outputs `("out" "utils")) (inputs From b2a5ef2e949986f98a2de28307bb44c7dd85adfc Mon Sep 17 00:00:00 2001 From: Vasile Dumitrascu Date: Sun, 30 Dec 2018 20:05:17 +0100 Subject: [PATCH 069/300] gnu: e2fsprogs: Update to 1.44.5. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (e2fsprogs): Update to 1.44.5. Signed-off-by: Ludovic Courtès --- gnu/packages/linux.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 4fb85f2f3c..ead45f7d42 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -31,6 +31,7 @@ ;;; Copyright © 2018 Brendan Tildesley ;;; Copyright © 2018 Manuel Graf ;;; Copyright © 2018 Pierre Langlois +;;; Copyright © 2018 Vasile Dumitrascu ;;; ;;; This file is part of GNU Guix. ;;; @@ -790,7 +791,7 @@ slabtop, and skill.") (define-public e2fsprogs (package (name "e2fsprogs") - (version "1.44.3") + (version "1.44.5") (source (origin (method url-fetch) (uri (string-append @@ -799,7 +800,7 @@ slabtop, and skill.") name "-" version ".tar.xz")) (sha256 (base32 - "1djb9qnid1j0vvna2bhq4jsz2ig1xckbx7h4d86cr0gl61yrz2ax")))) + "1ff56h6h1h17sj2zvlddv5c88nmbx46p1fcbh6b0s5k9kl3b6pms")))) (build-system gnu-build-system) (inputs `(("util-linux" ,util-linux))) (native-inputs `(("pkg-config" ,pkg-config) From ecf7e4ea432175f3556cde6956cfda889a470471 Mon Sep 17 00:00:00 2001 From: Tim Gesthuizen Date: Tue, 25 Dec 2018 11:22:19 +0100 Subject: [PATCH 070/300] gnu: emacs-ggtags: Don't require GNU Global in path MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit emacs-ggtags relies on the GNU Global tools (global and gtags) to be available in the path. This way it will grab some random executable if it will find executables at all. This is fixed by setting the prefix to GNU Global in the store. This way emacs-ggtags will use specific deterministic executables. * gnu/packages/emacs.scm (emacs-ggtags): [inputs]: Add GNU Global to the inputs [arguments]: Add a phase for substituting the right path to the executables Signed-off-by: Ludovic Courtès --- gnu/packages/emacs.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index f3f2440cc1..34b30862fb 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -1435,6 +1435,18 @@ environment set through Direnv.") (base32 "1qa7lcrcmf76sf6dy8sxbg4adq7rg59fm0n5848w3qxgsr0h45fg")))) (build-system emacs-build-system) + (inputs + `(("global" ,global))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'configure + (lambda* (#:key inputs #:allow-other-keys) + (chmod "ggtags.el" #o644) + (emacs-substitute-variables "ggtags.el" + ("ggtags-executable-directory" + (string-append (assoc-ref inputs "global") "/bin"))) + #t))))) (home-page "https://github.com/leoliu/ggtags") (synopsis "Frontend to the GNU Global source code tagging system") (description "@code{ggtags} provides a frontend to the GNU Global source From 037c3b0ea27ff4c428f4c54dc3d04f1d341a5a27 Mon Sep 17 00:00:00 2001 From: Tim Gesthuizen Date: Mon, 24 Dec 2018 14:46:27 +0100 Subject: [PATCH 071/300] gnu: emacs-irony-mode: Remove propagated input MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit emacs-irony-mode finds its server binary because its a propagated input and is in the path. We can substitute the variable `irony-server-install-prefix` to not propagate the input and keep the binary isolated from the user. * gnu/packages/emacs.scm (emacs-irony-mode): [propagated-inputs] Remove propagated inputs [inputs] Add emacs-irony-mode-server [arguments] Add phase substituting the variable of the server path Signed-off-by: Ludovic Courtès --- gnu/packages/emacs.scm | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 34b30862fb..b9d164a4cf 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -2840,9 +2840,16 @@ These are distributed in separate files and can be used individually.") "0nhjrnlmss535jbshjjd30vydbr8py21vkx4p294w6d8vg2rssf8")) (file-name (string-append name "-" version ".tar.gz")))) (build-system emacs-build-system) - (arguments '()) - (propagated-inputs - `(("emacs-irony-mode-server" ,emacs-irony-mode-server))) + (inputs `(("server" ,emacs-irony-mode-server))) + (arguments `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'configure + (lambda* (#:key inputs #:allow-other-keys) + (chmod "irony.el" #o644) + (emacs-substitute-variables "irony.el" + ("irony-server-install-prefix" + (assoc-ref inputs "server"))) + #t))))) (synopsis "C/C++/ObjC Code completion and syntax checks for Emacs") (description "Irony-mode provides Clang-assisted syntax checking and completion for C, C++, and ObjC in GNU Emacs. Using @code{libclang} it can @@ -2857,7 +2864,6 @@ described on the homepage.") (name "emacs-irony-mode-server") (inputs `(("clang" ,clang))) - (propagated-inputs '()) (arguments `(#:phases (modify-phases %standard-phases From 1b504b498ac3e70507ebe7cc3916688261be8103 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 9 Jan 2019 18:44:45 +0100 Subject: [PATCH 072/300] gnu: libgit2: Update to 0.27.7. * gnu/packages/version-control.scm (libgit2): Update to 0.27.7. --- gnu/packages/version-control.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 2eaf0c69f4..b62562902d 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -524,7 +524,7 @@ everything from small to very large projects with speed and efficiency.") (define-public libgit2 (package (name "libgit2") - (version "0.26.8") + (version "0.27.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/libgit2/libgit2/" @@ -532,7 +532,7 @@ everything from small to very large projects with speed and efficiency.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "15kp4sq72kh762bm7dgspyrk0a6siarvll3k7nrhs0xy77idf80g")) + "0c95pbv7hwclwmn51nqnh1lb0cajpcdb24pbdzcir6vmhfj3am0s")) (patches (search-patches "libgit2-mtime-0.patch" "libgit2-oom-test.patch")) From ab7aa06cac4f0695d08ac84eb715b98962c49fa9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 9 Jan 2019 20:25:39 +0200 Subject: [PATCH 073/300] gnu: python-pygit2: Update to 0.27.3. * gnu/packages/python.scm (python-pygit2): Update to 0.27.3. [arguments]: Add custom phase to compile with cffi support. Add custom phase to not require specific versions of python-cffi. [native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 5a32681643..507cdd3db4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3344,20 +3344,38 @@ color scales, and color space conversion easy. It has support for: (define-public python-pygit2 (package (name "python-pygit2") - (version "0.26.4") + (version "0.27.3") (source (origin (method url-fetch) (uri (pypi-uri "pygit2" version)) (sha256 (base32 - "145k3fsd21274swia7mcc7n3kzlbd47xmg55mxsjdb5d9b7fr858")))) + "046ahvsb7a20sgvscqfm3cb32sp3sii4gim9vz7zzrkf7yz16xlv")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + ;; Remove after the next update. See: + ;; https://github.com/libgit2/pygit2/pull/851 + (add-after 'unpack 'compile-with-cffi + (lambda _ + (substitute* "setup.py" + (("install_requires") + "setup_requires=['cffi'],\n install_requires")) + #t)) + (add-after 'unpack 'fix-dependency-versioning + (lambda _ + (substitute* "setup.py" + (("<") "<=")) + #t))))) (propagated-inputs `(("python-six" ,python-six) ("python-cffi" ,python-cffi) ("libgit2" ,libgit2) ("python-tox" ,python-tox))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/libgit2/pygit2") (synopsis "Python bindings for libgit2") (description "Pygit2 is a set of Python bindings to the libgit2 shared From 1bde3d2cbf311f6d6c733339a000b7395cb2f945 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 9 Jan 2019 19:28:02 +0100 Subject: [PATCH 074/300] gnu: Add dev86. * gnu/packages/assembly.scm (dev86): New variable. --- gnu/packages/assembly.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm index 813eea466f..d7a5e2c4bf 100644 --- a/gnu/packages/assembly.scm +++ b/gnu/packages/assembly.scm @@ -168,3 +168,40 @@ It does multiple passes to optimize machine code.It have macro abilities and focus on operating system portability.") (home-page "https://flatassembler.net/") (license license:bsd-2))) + +(define-public dev86 + (package + (name "dev86") + (version "0.16.21") + (source (origin + (method url-fetch) + (uri (string-append "http://v3.sk/~lkundrak/dev86/Dev86src-" + version ".tar.gz")) + (sha256 + (base32 + "154dyr2ph4n0kwi8yx0n78j128kw29rk9r9f7s2gddzrdl712jr3")))) + (build-system gnu-build-system) + (arguments + `(#:parallel-build? #f ; They use submakes wrong + #:make-flags (list "CC=gcc" + (string-append "PREFIX=" + (assoc-ref %outputs "out"))) + #:system "i686-linux" ; Standalone ld86 had problems otherwise + #:tests? #f ; No tests exist + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'install 'mkdir + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (mkdir-p (string-append out "/bin")) + (mkdir-p (string-append out "/man/man1")) + #t)))))) + (synopsis "Intel 8086 (primarily 16-bit) assembler, C compiler and +linker") + (description "This package provides a Intel 8086 (primarily 16-bit) +assembler, a C compiler and a linker. The assembler uses Intel syntax +(also Intel order of operands).") + (home-page "https://github.com/jbruchon/dev86") + (supported-systems '("i686-linux" "x86_64-linux")) + (license license:gpl2+))) From cb95e79f14716b5db94d18e16a8f84243132dac3 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 9 Jan 2019 19:30:21 +0100 Subject: [PATCH 075/300] gnu: fasm: Fix grammatical errors in description. * gnu/packages/assembly.scm (fasm)[description]: Modify. --- gnu/packages/assembly.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm index d7a5e2c4bf..ef5c9f6f1d 100644 --- a/gnu/packages/assembly.scm +++ b/gnu/packages/assembly.scm @@ -163,9 +163,9 @@ to the clients.") (supported-systems '("x86_64-linux" "i686-linux")) (synopsis "Assembler for x86 processors") (description - "FASM is a assembler that supports x86, and IA-64 Intel architectures. -It does multiple passes to optimize machine code.It have macro abilities and -focus on operating system portability.") + "FASM is an assembler that supports x86 and IA-64 Intel architectures. +It does multiple passes to optimize machine code. It has macro abilities and +focuses on operating system portability.") (home-page "https://flatassembler.net/") (license license:bsd-2))) From f73b7bf6e20be3429570822036a38b3f00239fa5 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 9 Jan 2019 19:32:03 +0100 Subject: [PATCH 076/300] gnu: fasm: Update comments. * gnu/packages/assembly.scm (fasm): Update comments. --- gnu/packages/assembly.scm | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm index ef5c9f6f1d..dd9e6d0dc4 100644 --- a/gnu/packages/assembly.scm +++ b/gnu/packages/assembly.scm @@ -140,18 +140,17 @@ to the clients.") "02wqkqxpn3p0iwcagsm92qd9cdfcnbx8a09qg03b3pjppp30hmp6")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ;;no tests - #:strip-binaries? #f ;; fasm has no sections + `(#:tests? #f ; No tests exist + #:strip-binaries? #f ; fasm has no sections #:phases (modify-phases %standard-phases - (delete 'configure) ;;no configure script used + (delete 'configure) ; no "configure" script exists (replace 'build (lambda _ - ;;source code are in this directory (chdir "source/Linux/") (if (string=? ,(%current-system) "x86_64-linux") - ;;use pre-compiled binaries in top-level directory to build - ;;itself + ;; Use pre-compiled binaries in top-level directory to build + ;; fasm. (invoke "../../fasm.x64" "fasm.asm") (invoke "../../fasm" "fasm.asm")))) (replace 'install @@ -159,7 +158,6 @@ to the clients.") (let ((out (assoc-ref %outputs "out"))) (install-file "fasm" (string-append out "/bin"))) #t))))) - ;;support only intel x86 family processors (supported-systems '("x86_64-linux" "i686-linux")) (synopsis "Assembler for x86 processors") (description From 45ee3fde877ef39dca8382efbbb320c4062637c2 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 30 Dec 2018 14:06:13 -0500 Subject: [PATCH 077/300] gnu: hashcat: Update to 5.1.0. * gnu/packages/password-utils.scm (hashcat): Update to 5.1.0. --- gnu/packages/password-utils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 357ef86d56..3962034076 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -705,7 +705,7 @@ your online accounts makes it necessary.") (define-public hashcat (package (name "hashcat") - (version "4.1.0") + (version "5.1.0") (source (origin (method url-fetch) @@ -713,7 +713,7 @@ your online accounts makes it necessary.") version ".tar.gz")) (sha256 (base32 - "170i2y32ykgzb1qf1wz3klwn31c09bviz4x3bnrwia65adqrj8xx")))) + "0f73y4cg8c7a6q7x34qvpfi4g3lw6j9bnn0a13g43aqyiskflfr8")))) (native-inputs `(("opencl-headers" ,opencl-headers))) (build-system gnu-build-system) From e82c98abe93c749296c831691c7c67c736f0807f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 9 Jan 2019 15:37:44 -0500 Subject: [PATCH 078/300] gnu: aria2: Fix CVE-2019-3500. * gnu/packages/patches/aria2-CVE-2019-3500.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/bittorrent.scm (aria2)[source]: Use it. --- gnu/local.mk | 1 + gnu/packages/bittorrent.scm | 1 + .../patches/aria2-CVE-2019-3500.patch | 55 +++++++++++++++++++ 3 files changed, 57 insertions(+) create mode 100644 gnu/packages/patches/aria2-CVE-2019-3500.patch diff --git a/gnu/local.mk b/gnu/local.mk index bc54b61c21..6344144f08 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -586,6 +586,7 @@ dist_patch_DATA = \ %D%/packages/patches/antlr3-3_3-fix-java8-compilation.patch \ %D%/packages/patches/ao-cad-aarch64-support.patch \ %D%/packages/patches/apr-skip-getservbyname-test.patch \ + %D%/packages/patches/aria2-CVE-2019-3500.patch \ %D%/packages/patches/aspell-default-dict-dir.patch \ %D%/packages/patches/ath9k-htc-firmware-binutils.patch \ %D%/packages/patches/ath9k-htc-firmware-gcc.patch \ diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm index e834ba3d2a..ee094a4814 100644 --- a/gnu/packages/bittorrent.scm +++ b/gnu/packages/bittorrent.scm @@ -264,6 +264,7 @@ maintained upstream.") (uri (string-append "https://github.com/tatsuhiro-t/aria2/" "releases/download/release-" version "/" name "-" version ".tar.xz")) + (patches (search-patches "aria2-CVE-2019-3500.patch")) (sha256 (base32 "18vpgr430vxlwbcc3598rr1srfmwypls6wp1m4wf21hncc1ahi1s")))) diff --git a/gnu/packages/patches/aria2-CVE-2019-3500.patch b/gnu/packages/patches/aria2-CVE-2019-3500.patch new file mode 100644 index 0000000000..891c9047ba --- /dev/null +++ b/gnu/packages/patches/aria2-CVE-2019-3500.patch @@ -0,0 +1,55 @@ +Fix CVE-2019-3500: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2019-3500 +https://github.com/aria2/aria2/issues/1329 + +Patch copied from upstream source repository: + +https://github.com/aria2/aria2/commit/37368130ca7de5491a75fd18a20c5c5cc641824a + +From 37368130ca7de5491a75fd18a20c5c5cc641824a Mon Sep 17 00:00:00 2001 +From: Tatsuhiro Tsujikawa +Date: Sat, 5 Jan 2019 09:32:40 +0900 +Subject: [PATCH] Mask headers + +--- + src/HttpConnection.cc | 18 ++++++++++++------ + 1 file changed, 12 insertions(+), 6 deletions(-) + +diff --git a/src/HttpConnection.cc b/src/HttpConnection.cc +index 77cb9d27a..be5b97723 100644 +--- a/src/HttpConnection.cc ++++ b/src/HttpConnection.cc +@@ -102,11 +102,17 @@ std::string HttpConnection::eraseConfidentialInfo(const std::string& request) + std::string result; + std::string line; + while (getline(istr, line)) { +- if (util::startsWith(line, "Authorization: Basic")) { +- result += "Authorization: Basic ********\n"; ++ if (util::istartsWith(line, "Authorization: ")) { ++ result += "Authorization: \n"; + } +- else if (util::startsWith(line, "Proxy-Authorization: Basic")) { +- result += "Proxy-Authorization: Basic ********\n"; ++ else if (util::istartsWith(line, "Proxy-Authorization: ")) { ++ result += "Proxy-Authorization: \n"; ++ } ++ else if (util::istartsWith(line, "Cookie: ")) { ++ result += "Cookie: \n"; ++ } ++ else if (util::istartsWith(line, "Set-Cookie: ")) { ++ result += "Set-Cookie: \n"; + } + else { + result += line; +@@ -154,8 +160,8 @@ std::unique_ptr HttpConnection::receiveResponse() + const auto& proc = outstandingHttpRequests_.front()->getHttpHeaderProcessor(); + if (proc->parse(socketRecvBuffer_->getBuffer(), + socketRecvBuffer_->getBufferLength())) { +- A2_LOG_INFO( +- fmt(MSG_RECEIVE_RESPONSE, cuid_, proc->getHeaderString().c_str())); ++ A2_LOG_INFO(fmt(MSG_RECEIVE_RESPONSE, cuid_, ++ eraseConfidentialInfo(proc->getHeaderString()).c_str())); + auto result = proc->getResult(); + if (result->getStatusCode() / 100 == 1) { + socketRecvBuffer_->drain(proc->getLastBytesProcessed()); From 817e09c1745e2ec1454e486ae0d14a959e2e1b6f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 9 Jan 2019 15:43:36 -0500 Subject: [PATCH 079/300] gnu: Django: Update to 1.11.18 [fixes CVE-2019-3498]. * gnu/packages/django.scm (python-django, python2-django): Update to 1.11.18. --- gnu/packages/django.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index ea2e65a588..63570bfd48 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -37,13 +37,13 @@ (define-public python-django (package (name "python-django") - (version "1.11.17") + (version "1.11.18") (source (origin (method url-fetch) (uri (pypi-uri "Django" version)) (sha256 (base32 - "10xlpm21ll8mgz5py41sz9vrd603qv7an736agbqxkxlyikfx1x7")))) + "19b6f020als9hr4q1im5282yn2b1hzf586n9kjrlkrslq7da3k3k")))) (build-system python-build-system) (arguments '(#:modules ((srfi srfi-1) From d4e915f9b5bf817c0e8f3832b8013a7be198a604 Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Sat, 29 Dec 2018 14:38:06 +0100 Subject: [PATCH 080/300] gnu: emacs-closql: Update to 1.0.0. * gnu/packages/emacs.scm (emacs-closql): Update to 1.0.0. [source]: Use 'git-fetch'. --- gnu/packages/emacs.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index b9d164a4cf..b004345717 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -8856,16 +8856,17 @@ object @code{nil} corresponds 1:1 with @code{NULL} in the database.") (define-public emacs-closql (package (name "emacs-closql") - (version "0.5.1") + (version "1.0.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/emacscollective/closql/archive/" - "v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacscollective/closql.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0wa6r0kgbb7f19039p5f3di4dvrvxfgpd8bkam94fca7jvzj536c")))) + "0cy44d1fxkvah6fhjkn3mp6gzzrjmws1c4c20ayrma74y9xich3v")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-emacsql" ,emacs-emacsql))) From 56c50c71b57b03251474f9ece4d1f2a6359d33f4 Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Sat, 29 Dec 2018 14:38:35 +0100 Subject: [PATCH 081/300] gnu: emacs-emacsql: Update to 3.0.0. * gnu/packages/emacs.scm (emacs-emacsql): Update to 3.0.0. [source]: Use 'git-fetch'. [arguments]: Remove unnecessary fix. --- gnu/packages/emacs.scm | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index b004345717..32919d810d 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -8775,16 +8775,16 @@ object has been freed.") (define-public emacs-emacsql (package (name "emacs-emacsql") - (version "2.0.3") - (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/skeeto/emacsql/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "04hfjdgl1zc7jysgjc7d7d3xqpr7q1q9gsmzffjd91ii3hpqjgx6")))) + (version "3.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/skeeto/emacsql.git") + (commit (string-append version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1c84gxr1majqj4b59wgdy3lzm3ap66w9qsrnkx8hdbk9895ak81g")))) (build-system emacs-build-system) (arguments `(#:modules ((guix build emacs-build-system) @@ -8819,8 +8819,6 @@ object has been freed.") (let ((file "emacsql-sqlite.el")) (chmod file #o644) (emacs-substitute-sexps file - ;; Avoid interactive prompts. - ("(defvar emacsql-sqlite-user-prompted" 't) ;; Make sure Emacs looks for ‘GCC’ binary in the right place. ("(executable-find" (which "gcc")) ;; Make sure Emacs looks for ‘emacsql-sqlite’ binary From abb8dff054a9e27fcb2b1f4d2d08c2fb66917f84 Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Sat, 29 Dec 2018 14:39:40 +0100 Subject: [PATCH 082/300] gnu: Add emacs-treepy. * gnu/packages/emacs.scm (emacs-treepy): New variable. --- gnu/packages/emacs.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 32919d810d..926e118033 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -622,6 +622,28 @@ these arguments. The prototypical use is for the command to call an external process, passing on the arguments as command line arguments.") (license license:gpl3+))) +(define-public emacs-treepy + (package + (name "emacs-treepy") + (version "0.1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/volrath/treepy.el.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "04zwm6gx9pxfvgfkizx6pvb1ql8pqxjyzqp8flz0432x0gq5nlxk")))) + (build-system emacs-build-system) + (home-page + "https://github.com/volrath/treepy.el") + (synopsis "Tree traversal tools") + (description + "Generic tools for recursive and iterative tree traversal based on +clojure.walk and clojure.zip respectively.") + (license license:gpl3+))) + (define-public emacs-ghub (package (name "emacs-ghub") From 5b07f06804cc6089226b9fa7a66dafaec03fc263 Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Sat, 29 Dec 2018 14:42:50 +0100 Subject: [PATCH 083/300] gnu: Add emacs-graphql. * gnu/packages/emacs.scm (emacs-graphql): New variable. --- gnu/packages/emacs.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 926e118033..8748146131 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -644,6 +644,36 @@ process, passing on the arguments as command line arguments.") clojure.walk and clojure.zip respectively.") (license license:gpl3+))) +(define-public emacs-graphql + (package + (name "emacs-graphql") + (version "0.1.1") + (source (origin + (modules '((guix build utils))) + ;; Remove examples file with references to external packages as + ;; they do not exist at compilation time. + (snippet + '(begin (delete-file "examples.el") + #t)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/vermiculus/graphql.el.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0sp0skc1rnhi39szfbq1i99pdgd3bhn4c15cff05iqhjy2d4hniw")))) + (build-system emacs-build-system) + (home-page + "https://github.com/vermiculus/graphql.el") + (synopsis "GraphQL utilities") + (description + "GraphQL.el provides a generally-applicable domain-specific language for +creating and executing GraphQL queries against your favorite web services. +GraphQL is a data query language and runtime designed and used to request and +deliver data to mobile and web apps.") + (license license:gpl3+))) + (define-public emacs-ghub (package (name "emacs-ghub") From 8d59ef68cb03292e8134524a58f07fca98edef1d Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Sat, 29 Dec 2018 14:43:23 +0100 Subject: [PATCH 084/300] gnu: emacs-with-editor: Update to 2.8.0. * gnu/packages/emacs.scm (emacs-with-editor): Update to 2.8.0. [source]: Use 'git-fetch'. --- gnu/packages/emacs.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 8748146131..ab5b66323f 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -428,16 +428,16 @@ configuration files, such as .gitattributes, .gitignore, and .git/config.") (define-public emacs-with-editor (package (name "emacs-with-editor") - (version "2.7.3") + (version "2.8.0") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/magit/with-editor/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/magit/with-editor.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1ln2s0kckzkv50qmr6x1kb2j30cfjii0vs6lpghg7ff4lav8jqgh")))) + "1bbzvxnjpxqyvi808isld025b3pcidn4r2xf8hnk9bmzcfdvdr6q")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash))) From 9bc7dd62b492725df5b9541da468dea0038e172f Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Sat, 29 Dec 2018 14:43:54 +0100 Subject: [PATCH 085/300] gnu: emacs-magit-popup: Update to 2.12.5. * gnu/packages/emacs.scm (emacs-magit-popup): Update to 2.12.5. --- gnu/packages/emacs.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index ab5b66323f..a9f91d6c2f 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -592,7 +592,7 @@ support for Git-SVN.") (define-public emacs-magit-popup (package (name "emacs-magit-popup") - (version "2.12.4") + (version "2.12.5") (source (origin (method git-fetch) (uri (git-reference @@ -601,7 +601,7 @@ support for Git-SVN.") (file-name (git-file-name name version)) (sha256 (base32 - "08952nzn0cb6gxscqyiljk4fq2zxjvr3ism0lvgw0gs9hl5phiwx")))) + "13riknyqr6vxqll80sfhvz165flvdz367rbd0pr5slb01bnfsi2i")))) (build-system emacs-build-system) (arguments `(#:phases From b96f0e6ff9f8f36d250b5ae94a908272babb35cf Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Sat, 29 Dec 2018 14:55:19 +0100 Subject: [PATCH 086/300] gnu: emacs-ghub: Update to 3.2.0. * gnu/packages/emacs.scm (emacs-ghub): Update to 3.2.0. [source]: Use 'git-fetch'. [propagated-inputs]: Add emacs-dash, emacs-graphql, emacs-let-alist, emacs-treepy. --- gnu/packages/emacs.scm | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index a9f91d6c2f..6a0429aabc 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -677,16 +677,16 @@ deliver data to mobile and web apps.") (define-public emacs-ghub (package (name "emacs-ghub") - (version "2.0.1") + (version "3.2.0") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/magit/ghub/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/magit/ghub.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0d0qj5r1bm2aidi61rigrdaycxnyb7y1ivb3h8rpvvapsf8sk7z0")))) + "0lp52qygyavddl1lrgsyb6mq7hcf9h89dy2pzya3mb2va49f0vvl")))) (build-system emacs-build-system) (arguments `(#:phases @@ -694,6 +694,11 @@ deliver data to mobile and web apps.") (add-before 'install 'make-info (lambda _ (invoke "make" "info")))))) + (propagated-inputs + `(("emacs-dash" ,emacs-dash) + ("emacs-graphql" ,emacs-graphql) + ("emacs-let-alist" ,emacs-let-alist) + ("emacs-treepy" ,emacs-treepy))) (native-inputs `(("texinfo" ,texinfo))) (home-page "https://github.com/magit/ghub") From fc51c28ae8172c9f4370772bd76601f89b9498e6 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 25 Dec 2018 01:58:35 -0500 Subject: [PATCH 087/300] gnu: Blender: Update to a beta release of 2.80. Fixes and . * gnu/packages/graphics.scm (blender): Update to 2.80-beta-0.3c3d80e. [source]: Fetch from the Git repository. [inputs]: Use OpenJPEG 2. Add Numpy. [arguments]: Specify the location of Numpy. Remove some configure flags that are no longer used. Comment out the 'fix-broken-import' phase because the file it patches doesn't exist in the Git sources. [description]: Add a warning about the beta status. --- gnu/packages/graphics.scm | 46 +++++++++++++++++++++++---------------- 1 file changed, 27 insertions(+), 19 deletions(-) diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 6e184d3334..73620bb2d4 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -76,17 +76,20 @@ #:use-module (guix utils)) (define-public blender + (let ((revision "0") + (commit "3c3d80ea22af15e13237f978181a881b90c41e7c")) (package (name "blender") - (version "2.79b") + (version (git-version "2.80-beta" revision commit)) (source (origin - (method url-fetch) - (uri (string-append "https://download.blender.org/source/" - "blender-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://git.blender.org/blender.git") + (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 - "1g4kcdqmf67srzhi3hkdnr4z1ph4h9sza1pahz38mrj998q4r52c")) - (patches (search-patches "blender-newer-ffmpeg.patch")))) + "1hhn8pf3a5556mxyrb2ggsiy6q0h75hnkdpcgq9b6vg284jl2l4q")))) (build-system cmake-build-system) (arguments (let ((python-version (version-major+minor (package-version python)))) @@ -98,29 +101,30 @@ "-DWITH_CYCLES=ON" "-DWITH_DOC_MANPAGE=ON" "-DWITH_FFTW3=ON" - "-DWITH_GAMEENGINE=ON" "-DWITH_IMAGE_OPENJPEG=ON" "-DWITH_INPUT_NDOF=ON" "-DWITH_INSTALL_PORTABLE=OFF" "-DWITH_JACK=ON" "-DWITH_MOD_OCEANSIM=ON" - "-DWITH_PLAYER=ON" "-DWITH_PYTHON_INSTALL=OFF" - "-DWITH_PYTHON_INSTALL=OFF" - "-DWITH_SYSTEM_OPENJPEG=ON" (string-append "-DPYTHON_LIBRARY=python" ,python-version "m") (string-append "-DPYTHON_LIBPATH=" (assoc-ref %build-inputs "python") "/lib") (string-append "-DPYTHON_INCLUDE_DIR=" (assoc-ref %build-inputs "python") "/include/python" ,python-version "m") - (string-append "-DPYTHON_VERSION=" ,python-version)) + (string-append "-DPYTHON_VERSION=" ,python-version) + (string-append "-DPYTHON_NUMPY_PATH=" + (assoc-ref %build-inputs "python-numpy") + "/lib/python" ,python-version "/site-packages/")) #:phases (modify-phases %standard-phases - (add-after 'unpack 'fix-broken-import - (lambda _ - (substitute* "release/scripts/addons/io_scene_fbx/json2fbx.py" - (("import encode_bin") "from . import encode_bin")) - #t)) + ;; XXX This file doesn't exist in the Git sources but will probably + ;; exist in the eventual 2.80 source tarball. +; (add-after 'unpack 'fix-broken-import +; (lambda _ +; (substitute* "release/scripts/addons/io_scene_fbx/json2fbx.py" +; (("import encode_bin") "from . import encode_bin")) +; #t)) (add-after 'set-paths 'add-ilmbase-include-path (lambda* (#:key inputs #:allow-other-keys) ;; OpenEXR propagates ilmbase, but its include files do not appear @@ -138,7 +142,7 @@ ("openimageio" ,openimageio) ("openexr" ,openexr) ("ilmbase" ,ilmbase) - ("openjpeg" ,openjpeg-1) + ("openjpeg" ,openjpeg) ("libjpeg" ,libjpeg) ("libpng" ,libpng) ("libtiff" ,libtiff) @@ -150,6 +154,7 @@ ("glew" ,glew) ("openal" ,openal) ("python" ,python) + ("python-numpy" ,python-numpy) ("zlib" ,zlib))) (home-page "https://blender.org/") (synopsis "3D graphics creation suite") @@ -157,8 +162,11 @@ "Blender is a 3D graphics creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. The -application can be customized via its API for Python scripting.") - (license license:gpl2+))) +application can be customized via its API for Python scripting. + +WARNING: This package offers a beta build of Blender, because the stable release +no longer works in Guix. See @uref{https://issues.guix.info/issue/33882}.") + (license license:gpl2+)))) (define-public assimp (package From f87ea24a821c1cee8f9a8f0d38d7f02fa43d8383 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Mon, 7 Jan 2019 20:01:34 +0100 Subject: [PATCH 088/300] gnu: Add docker. * gnu/packages/docker.scm (docker): New variable. * gnu/packages/patches/docker-engine-test-noinstall.patch: New file. * gnu/packages/patches/docker-fix-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add them. --- gnu/local.mk | 2 + gnu/packages/docker.scm | 178 ++++++++++++++++++ .../docker-engine-test-noinstall.patch | 23 +++ gnu/packages/patches/docker-fix-tests.patch | 28 +++ 4 files changed, 231 insertions(+) create mode 100644 gnu/packages/patches/docker-engine-test-noinstall.patch create mode 100644 gnu/packages/patches/docker-fix-tests.patch diff --git a/gnu/local.mk b/gnu/local.mk index 6344144f08..25363869dd 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -663,6 +663,8 @@ dist_patch_DATA = \ %D%/packages/patches/docbook-xsl-nonrecursive-string-subst.patch \ %D%/packages/patches/doc++-include-directives.patch \ %D%/packages/patches/doc++-segfault-fix.patch \ + %D%/packages/patches/docker-engine-test-noinstall.patch \ + %D%/packages/patches/docker-fix-tests.patch \ %D%/packages/patches/dovecot-trees-support-dovecot-2.3.patch \ %D%/packages/patches/doxygen-test.patch \ %D%/packages/patches/dropbear-CVE-2018-15599.patch \ diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index d928c4e61e..31bb34b4a6 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -23,10 +23,12 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix build-system gnu) #:use-module (guix build-system go) #:use-module (guix build-system python) #:use-module (guix utils) #:use-module (gnu packages check) + #:use-module (gnu packages compression) #:use-module (gnu packages golang) #:use-module (gnu packages linux) #:use-module (gnu packages pkg-config) @@ -34,6 +36,8 @@ #:use-module (gnu packages python-web) #:use-module (gnu packages virtualization)) +(define %docker-version "18.09.0") + (define-public python-docker-py (package (name "python-docker-py") @@ -210,3 +214,177 @@ It includes image transfer and storage, container execution and supervision, network attachments.") (home-page "http://containerd.io/") (license license:asl2.0))) + +(define-public docker + (package + (name "docker") + (version %docker-version) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/docker/engine.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1liqbx58grqih6m8hz9y20y5waflv19pv15l3wl64skap2bsn21c")) + (patches + (search-patches "docker-engine-test-noinstall.patch" + "docker-fix-tests.patch")))) + (build-system gnu-build-system) + (arguments + `(#:modules + ((guix build gnu-build-system) + ((guix build go-build-system) #:prefix go:) + (guix build utils)) + #:imported-modules + (,@%gnu-build-system-modules + (guix build go-build-system)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "builder/builder-next/executor_unix.go" + (("CommandCandidates:.*runc.*") + (string-append "CommandCandidates: []string{\"" + (assoc-ref inputs "runc") + "/sbin/runc\"},\n"))) + (substitute* "vendor/github.com/containerd/go-runc/runc.go" + (("DefaultCommand = .*") + (string-append "DefaultCommand = \"" + (assoc-ref inputs "runc") + "/sbin/runc\"\n"))) + (substitute* "vendor/github.com/containerd/containerd/runtime/v1/linux/runtime.go" + (("defaultRuntime[ \t]*=.*") + (string-append "defaultRuntime = \"" + (assoc-ref inputs "runc") + "/sbin/runc\"\n")) + (("defaultShim[ \t]*=.*") + (string-append "defaultShim = \"" + (assoc-ref inputs "containerd") + "/bin/containerd-shim\"\n"))) + (substitute* "daemon/daemon_unix.go" + (("DefaultShimBinary = .*") + (string-append "DefaultShimBinary = \"" + (assoc-ref inputs "containerd") + "/bin/containerd-shim\"\n")) + (("DefaultRuntimeBinary = .*") + (string-append "DefaultRuntimeBinary = \"" + (assoc-ref inputs "runc") + "/sbin/runc\"\n")) + (("DefaultRuntimeName = .*") + (string-append "DefaultRuntimeName = \"" + (assoc-ref inputs "runc") + "/sbin/runc\"\n"))) + (substitute* "daemon/config/config.go" + (("StockRuntimeName = .*") + (string-append "StockRuntimeName = \"" + (assoc-ref inputs "runc") + "/sbin/runc\"\n"))) + (substitute* "vendor/github.com/moby/buildkit/executor/runcexecutor/executor.go" + (("var defaultCommandCandidates = .*") + (string-append "var defaultCommandCandidates = []string{\"" + (assoc-ref inputs "runc") "/sbin/runc\"}"))) + (let ((source-files (filter (lambda (name) + (not (string-contains name "test"))) + (find-files "." "\\.go$")))) + (let-syntax ((substitute-LookPath + (lambda (x) + (syntax-case x () + ((substitute-LookPath source-text package + relative-path) + #`(substitute* source-files + ((#,(string-append "exec\\.LookPath\\(\"" + (syntax->datum + #'source-text) + "\")")) + (string-append "\"" + (assoc-ref inputs package) + relative-path + "\", error(nil)")))))))) + (substitute-LookPath "ps" "procps" "/bin/ps") + (substitute-LookPath "mkfs.xfs" "xfsprogs" "/bin/mkfs.xfs") + (substitute-LookPath "lvmdiskscan" "lvm2" "/sbin/lvmdiskscan") + (substitute-LookPath "pvdisplay" "lvm2" "/sbin/pvdisplay") + (substitute-LookPath "blkid" "util-linux" "/sbin/blkid") + (substitute-LookPath "unpigz" "pigz" "/bin/unpigz") + (substitute-LookPath "iptables" "iptables" "/sbin/iptables") + (substitute-LookPath "ip" "iproute2" "/sbin/ip"))) + #t)) + (add-after 'patch-paths 'delete-failing-tests + (lambda _ + ;; Needs internet access. + (delete-file "builder/remotecontext/git/gitutils_test.go") + ;; Permission denied. + (delete-file "daemon/graphdriver/devmapper/devmapper_test.go") + ;; Operation not permitted (idtools.MkdirAllAndChown). + (delete-file "daemon/graphdriver/vfs/vfs_test.go") + ;; Timeouts after 5 min. + (delete-file "plugin/manager_linux_test.go") + #t)) + (replace 'configure + (lambda _ + (setenv "DOCKER_GITCOMMIT" (string-append "v" ,%docker-version)) + ;; Automatically use bundled dependencies. + ;; TODO: Unbundle - see file "vendor.conf". + (setenv "AUTO_GOPATH" "1") + ;; Respectively, strip the symbol table and debug + ;; information, and the DWARF symbol table. + (setenv "LDFLAGS" "-s -w") + ;; Make build faster + (setenv "GOCACHE" "/tmp") + #t)) + (add-before 'build 'setup-environment + (assoc-ref go:%standard-phases 'setup-environment)) + (replace 'build + (lambda _ + ;; Our LD doesn't like the statically linked relocatable things + ;; that go produces, so install the dynamic version of + ;; dockerd instead. + (invoke "hack/make.sh" "dynbinary"))) + (replace 'check + (lambda _ + ;; The build process generated a file because the environment + ;; variable "AUTO_GOPATH" was set. Use it. + (setenv "GOPATH" (string-append (getcwd) "/.gopath")) + ;; ".gopath/src/github.com/docker/docker" is a link to the current + ;; directory and chdir would canonicalize to that. + ;; But go needs to have the uncanonicalized directory name, so + ;; store that. + (setenv "PWD" (string-append (getcwd) + "/.gopath/src/github.com/docker/docker")) + (with-directory-excursion ".gopath/src/github.com/docker/docker" + (invoke "hack/test/unit")) + (setenv "PWD" #f) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (out-bin (string-append out "/bin"))) + (install-file "bundles/dynbinary-daemon/dockerd" out-bin) + (install-file "bundles/dynbinary-daemon/dockerd-dev" out-bin) + #t)))))) + (inputs + `(("btrfs-progs" ,btrfs-progs) + ("containerd" ,containerd) ; for containerd-shim + ("runc" ,runc) + ("iproute2" ,iproute) + ("iptables" ,iptables) + ("libseccomp" ,libseccomp) + ("pigz" ,pigz) + ("procps" ,procps) + ("util-linux" ,util-linux) + ("lvm2" ,lvm2) + ("xfsprogs" ,xfsprogs))) + (native-inputs + `(("eudev" ,eudev) ; TODO: Should be propagated by lvm2 (.pc -> .pc) + ("go" ,go) + ("pkg-config" ,pkg-config))) + (synopsis "Docker container component library, and daemon") + (description "This package provides a framework to assemble specialized +container systems. It includes components for orchestration, image +management, secret management, configuration management, networking, +provisioning etc.") + (home-page "https://mobyproject.org/") + (license license:asl2.0))) diff --git a/gnu/packages/patches/docker-engine-test-noinstall.patch b/gnu/packages/patches/docker-engine-test-noinstall.patch new file mode 100644 index 0000000000..85d56a3465 --- /dev/null +++ b/gnu/packages/patches/docker-engine-test-noinstall.patch @@ -0,0 +1,23 @@ +Last-Update: 2018-06-18 +Forwarded: not-needed +Author: Dmitry Smirnov +Description: prevents test-time installation that causes FTBFS. +~~~~ + go test net: open /usr/lib/go-1.10/pkg/linux_amd64/net.a: permission denied +~~~~ + +--- a/hack/test/unit ++++ b/hack/test/unit +@@ -18,12 +18,8 @@ + + exclude_paths="/vendor/|/integration" + pkg_list=$(go list $TESTDIRS | grep -vE "($exclude_paths)") + +-# install test dependencies once before running tests for each package. This +-# significantly reduces the runtime. +-go test -i "${BUILDFLAGS[@]}" $pkg_list +- + for pkg in $pkg_list; do + go test "${BUILDFLAGS[@]}" \ + -cover \ + -coverprofile=profile.out \ diff --git a/gnu/packages/patches/docker-fix-tests.patch b/gnu/packages/patches/docker-fix-tests.patch new file mode 100644 index 0000000000..3e3e318e25 --- /dev/null +++ b/gnu/packages/patches/docker-fix-tests.patch @@ -0,0 +1,28 @@ +Author: Danny Milosavljevic +The socket name ended up too long inside the container. +Use a shorter one. +--- a/pkg/authorization/authz_unix_test.go 2019-01-10 01:55:02.997985947 +0100 ++++ b/pkg/authorization/authz_unix_test.go 2019-01-10 02:03:21.177439757 +0100 +@@ -24,7 +24,7 @@ + ) + + const ( +- pluginAddress = "authz-test-plugin.sock" ++ pluginAddress = "/tmp/authz-test-plugin.sock" + ) + + func TestAuthZRequestPluginError(t *testing.T) { +@@ -263,12 +263,7 @@ + + // createTestPlugin creates a new sample authorization plugin + func createTestPlugin(t *testing.T) *authorizationPlugin { +- pwd, err := os.Getwd() +- if err != nil { +- t.Fatal(err) +- } +- +- client, err := plugins.NewClient("unix:///"+path.Join(pwd, pluginAddress), &tlsconfig.Options{InsecureSkipVerify: true}) ++ client, err := plugins.NewClient("unix:///"+path.Join("/", pluginAddress), &tlsconfig.Options{InsecureSkipVerify: true}) + if err != nil { + t.Fatalf("Failed to create client %v", err) + } From 8af4c335e32fbed7556a4cd7f26f93bc66afaace Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Mon, 31 Dec 2018 00:39:02 +0100 Subject: [PATCH 089/300] services: Add docker. * gnu/services/docker.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * doc/guix.texi (Miscellaneous Services): Document the service. --- doc/guix.texi | 27 ++++++++++++ gnu/local.mk | 1 + gnu/services/docker.scm | 94 +++++++++++++++++++++++++++++++++++++++++ 3 files changed, 122 insertions(+) create mode 100644 gnu/services/docker.scm diff --git a/doc/guix.texi b/doc/guix.texi index 7c6a714830..c0cc8d4169 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -22118,6 +22118,33 @@ The following is an example @code{dicod-service} configuration. %dicod-database:gcide)))) @end example +@cindex Docker +@subsubheading Docker Service + +The @code{(gnu services docker)} module provides the following service. + +@defvr {Scheme Variable} docker-service-type + +This is the type of the service that runs @url{http://www.docker.com,Docker}, +a daemon that can execute application bundles (sometimes referred to as +``containers'') in isolated environments. + +@end defvr + +@deftp {Data Type} docker-configuration +This is the data type representing the configuration of Docker and Containerd. + +@table @asis + +@item @code{package} (default: @code{docker}) +The Docker package to use. + +@item @code{containerd} (default: @var{containerd}) +The Containerd package to use. + +@end table +@end deftp + @node Setuid Programs @subsection Setuid Programs diff --git a/gnu/local.mk b/gnu/local.mk index 25363869dd..7c319b727f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -483,6 +483,7 @@ GNU_SYSTEM_MODULES = \ %D%/services/desktop.scm \ %D%/services/dict.scm \ %D%/services/dns.scm \ + %D%/services/docker.scm \ %D%/services/authentication.scm \ %D%/services/games.scm \ %D%/services/kerberos.scm \ diff --git a/gnu/services/docker.scm b/gnu/services/docker.scm new file mode 100644 index 0000000000..6d270831b3 --- /dev/null +++ b/gnu/services/docker.scm @@ -0,0 +1,94 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2018 Danny Milosavljevic +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu services docker) + #:use-module (gnu services) + #:use-module (gnu services configuration) + #:use-module (gnu services base) + #:use-module (gnu services dbus) + #:use-module (gnu services shepherd) + #:use-module (gnu system shadow) + #:use-module (gnu packages docker) + #:use-module (guix records) + #:use-module (guix gexp) + #:use-module (guix packages) + + #:export (docker-configuration + docker-service-type)) + +(define-configuration docker-configuration + (docker + (package docker) + "Docker daemon package.") + (containerd + (package containerd) + "containerd package.")) + +(define %docker-accounts + (list (user-group (name "docker") (system? #t)))) + +(define (%containerd-activation config) + (let ((state-dir "/var/lib/containerd")) + #~(begin + (use-modules (guix build utils)) + (mkdir-p #$state-dir)))) + +(define (%docker-activation config) + (%containerd-activation config) + (let ((state-dir "/var/lib/docker")) + #~(begin + (use-modules (guix build utils)) + (mkdir-p #$state-dir)))) + +(define (containerd-shepherd-service config) + (let* ((package (docker-configuration-containerd config))) + (shepherd-service + (documentation "containerd daemon.") + (provision '(containerd)) + (start #~(make-forkexec-constructor + (list (string-append #$package "/bin/containerd")))) + (stop #~(make-kill-destructor))))) + +(define (docker-shepherd-service config) + (let* ((docker (docker-configuration-docker config))) + (shepherd-service + (documentation "Docker daemon.") + (provision '(dockerd)) + (requirement '(containerd)) + (start #~(make-forkexec-constructor + (list (string-append #$docker "/bin/dockerd") + "-p" "/var/run/docker.pid") + #:pid-file "/var/run/docker.pid" + #:log-file "/var/log/docker.log")) + (stop #~(make-kill-destructor))))) + +(define docker-service-type + (service-type (name 'docker) + (description "Provide capability to run Docker application +bundles in Docker containers.") + (extensions + (list + (service-extension activation-service-type + %docker-activation) + (service-extension shepherd-root-service-type + (lambda args + (list (apply containerd-shepherd-service args) + (apply docker-shepherd-service args)))) + (service-extension account-service-type + (const %docker-accounts)))) + (default-value (docker-configuration)))) From e9b316453eeb9187c6c5bb538552a1927e077e64 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Mon, 31 Dec 2018 00:39:03 +0100 Subject: [PATCH 090/300] gnu: Add docker-cli. * gnu/packages/docker.scm (docker-cli): New variable. --- gnu/packages/docker.scm | 63 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index 31bb34b4a6..d06a894c0b 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -27,6 +27,7 @@ #:use-module (guix build-system go) #:use-module (guix build-system python) #:use-module (guix utils) + #:use-module (gnu packages autotools) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages golang) @@ -388,3 +389,65 @@ management, secret management, configuration management, networking, provisioning etc.") (home-page "https://mobyproject.org/") (license license:asl2.0))) + +(define-public docker-cli + (package + (name "docker-cli") + (version %docker-version) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/docker/cli.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ivisys20kphvbqlazc3bsg7pk0ykj9gjx5d4yg439x4n13jxwvb")))) + (build-system go-build-system) + (arguments + `(#:import-path "github.com/docker/cli" + ;; TODO: Tests require a running Docker daemon. + #:tests? #f + #:phases + (modify-phases %standard-phases + (add-before 'build 'setup-environment-2 + (lambda _ + ;; Respectively, strip the symbol table and debug + ;; information, and the DWARF symbol table. + (setenv "LDFLAGS" "-s -w") + + ;; Make build reproducible. + (setenv "BUILDTIME" "1970-01-01 00:00:01.000000000+00:00") + (symlink "src/github.com/docker/cli/scripts" "./scripts") + (symlink "src/github.com/docker/cli/docker.Makefile" "./docker.Makefile") + #t)) + (replace 'build + (lambda _ + (invoke "./scripts/build/dynbinary"))) + (replace 'check + (lambda* (#:key make-flags tests? #:allow-other-keys) + (setenv "PATH" (string-append (getcwd) "/build:" (getenv "PATH"))) + (if tests? + ;; Use the newly-built docker client for the tests. + (with-directory-excursion "src/github.com/docker/cli" + ;; TODO: Run test-e2e as well? + (apply invoke "make" "-f" "docker.Makefile" "test-unit" + (or make-flags '()))) + #t))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (out-bin (string-append out "/bin"))) + (chdir "build") + (install-file (readlink "docker") out-bin) + (install-file "docker" out-bin) + #t)))))) + (native-inputs + `(("go" ,go) + ("libltdl" ,libltdl) + ("pkg-config" ,pkg-config))) + (synopsis "Command line interface to Docker") + (description "This package provides a command line interface to Docker.") + (home-page "http://www.docker.com/") + (license license:asl2.0))) From 65a7e35cb530c9da434ebab06d59aa97b9e66f63 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 03:12:32 +0100 Subject: [PATCH 091/300] gnu: docker: Substitute LookPath of literals generally. * gnu/packages/docker.scm (docker)[arguments]<#:phases>[patch-paths]: Substitute LookPath of literals generally. --- gnu/packages/docker.scm | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index d06a894c0b..472da0ef08 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -311,7 +311,14 @@ network attachments.") (substitute-LookPath "blkid" "util-linux" "/sbin/blkid") (substitute-LookPath "unpigz" "pigz" "/bin/unpigz") (substitute-LookPath "iptables" "iptables" "/sbin/iptables") - (substitute-LookPath "ip" "iproute2" "/sbin/ip"))) + (substitute-LookPath "ip" "iproute2" "/sbin/ip")) + ;; Make compilation fail when, in future versions, Docker + ;; invokes other programs we don't know about and thus don't + ;; substitute. + (substitute* source-files + (("LookPath\\(\"zfs\"\\)") "LooxPath(\"zfs\")") + (("LookPath\\(\"") "Guix_doesnt_want_LookPath\\(\"") + (("LooxPath") "LookPath"))) #t)) (add-after 'patch-paths 'delete-failing-tests (lambda _ From 7d8a4eeacc534c8742e0b22d855aa73e5ab66b7f Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 03:44:20 +0100 Subject: [PATCH 092/300] tests: Add Docker system test. * gnu/tests/docker.scm: New file. --- gnu/tests/docker.scm | 95 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 95 insertions(+) create mode 100644 gnu/tests/docker.scm diff --git a/gnu/tests/docker.scm b/gnu/tests/docker.scm new file mode 100644 index 0000000000..4d21324294 --- /dev/null +++ b/gnu/tests/docker.scm @@ -0,0 +1,95 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2017 Christopher Baines +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu tests docker) + #:use-module (gnu tests) + #:use-module (gnu system) + #:use-module (gnu system file-systems) + #:use-module (gnu system vm) + #:use-module (gnu services) + #:use-module (gnu services dbus) + #:use-module (gnu services networking) + #:use-module (gnu services docker) + #:use-module (gnu packages docker) + #:use-module (guix gexp) + #:use-module (guix store) + #:export (%test-docker)) + +(define %docker-os + (simple-operating-system + (service dhcp-client-service-type) + (dbus-service) + (polkit-service) + (service docker-service-type))) + +(define (run-docker-test) + "Run tests in %DOCKER-OS." + (define os + (marionette-operating-system + %docker-os + #:imported-modules '((gnu services herd) + (guix combinators)))) + + (define vm + (virtual-machine + (operating-system os) + (port-forwardings '()))) + + (define test + (with-imported-modules '((gnu build marionette)) + #~(begin + (use-modules (srfi srfi-11) (srfi srfi-64) + (gnu build marionette)) + + (define marionette + (make-marionette (list #$vm))) + + (mkdir #$output) + (chdir #$output) + + (test-begin "docker") + + (test-assert "service running" + (marionette-eval + '(begin + (use-modules (gnu services herd)) + (match (start-service 'dockerd) + (#f #f) + (('service response-parts ...) + (match (assq-ref response-parts 'running) + ((pid) (number? pid)))))) + marionette)) + + (test-eq "fetch version" + 0 + (marionette-eval + `(begin + (system* ,(string-append #$docker-cli "/bin/docker") + "version")) + marionette)) + + (test-end) + (exit (= (test-runner-fail-count (test-runner-current)) 0))))) + + (gexp->derivation "docker-test" test)) + +(define %test-docker + (system-test + (name "docker") + (description "Connect to the running Docker service.") + (value (run-docker-test)))) From f0bfd0fc217a9af44b122f4e3cdf389a74594096 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 03:54:28 +0100 Subject: [PATCH 093/300] services: docker: Specify log file for containerd. * gnu/services/docker.scm (containerd-shepherd-service): Specify log file for containerd. --- gnu/services/docker.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/services/docker.scm b/gnu/services/docker.scm index 6d270831b3..c88fc342e8 100644 --- a/gnu/services/docker.scm +++ b/gnu/services/docker.scm @@ -61,7 +61,8 @@ (documentation "containerd daemon.") (provision '(containerd)) (start #~(make-forkexec-constructor - (list (string-append #$package "/bin/containerd")))) + (list (string-append #$package "/bin/containerd")) + #:log-file "/var/log/containerd.log")) (stop #~(make-kill-destructor))))) (define (docker-shepherd-service config) From 58adcaa19f152c5c0554103c0ad13e4faf451f68 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 04:31:34 +0100 Subject: [PATCH 094/300] gnu: docker: Fix more paths. * gnu/packages/docker.scm (docker)[inputs]: Add util-linux. [arguments]<#:phases>[patch-paths]: Fix more paths. --- gnu/packages/docker.scm | 50 +++++++++++++++++++++++++++++++++++++---- 1 file changed, 46 insertions(+), 4 deletions(-) diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index 472da0ef08..9ff1361954 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -28,6 +28,7 @@ #:use-module (guix build-system python) #:use-module (guix utils) #:use-module (gnu packages autotools) + #:use-module (gnu packages base) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages golang) @@ -303,7 +304,21 @@ network attachments.") (string-append "\"" (assoc-ref inputs package) relative-path - "\", error(nil)")))))))) + "\", error(nil)"))))))) + (substitute-Command + (lambda (x) + (syntax-case x () + ((substitute-LookPath source-text package + relative-path) + #`(substitute* source-files + ((#,(string-append "exec\\.Command\\(\"" + (syntax->datum + #'source-text) + "\"")) ; ) + (string-append "exec.Command(\"" + (assoc-ref inputs package) + relative-path + "\"")))))))) ; ) (substitute-LookPath "ps" "procps" "/bin/ps") (substitute-LookPath "mkfs.xfs" "xfsprogs" "/bin/mkfs.xfs") (substitute-LookPath "lvmdiskscan" "lvm2" "/sbin/lvmdiskscan") @@ -311,13 +326,37 @@ network attachments.") (substitute-LookPath "blkid" "util-linux" "/sbin/blkid") (substitute-LookPath "unpigz" "pigz" "/bin/unpigz") (substitute-LookPath "iptables" "iptables" "/sbin/iptables") - (substitute-LookPath "ip" "iproute2" "/sbin/ip")) + (substitute-LookPath "ip" "iproute2" "/sbin/ip") + (substitute-Command "modprobe" "kmod" "/bin/modprobe") + (substitute-Command "pvcreate" "lvm2" "/sbin/pvcreate") + (substitute-Command "vgcreate" "lvm2" "/sbin/vgcreate") + (substitute-Command "lvcreate" "lvm2" "/sbin/lvcreate") + (substitute-Command "lvconvert" "lvm2" "/sbin/lvconvert") + (substitute-Command "lvchange" "lvm2" "/sbin/lvchange") + (substitute-Command "mkfs.xfs" "xfsprogs" "/sbin/mkfs.xfs") + (substitute-Command "xfs_growfs" "xfsprogs" "/sbin/xfs_growfs") + (substitute-Command "mkfs.ext4" "e2fsprogs" "/sbin/mkfs.ext4") + (substitute-Command "tune2fs" "e2fsprogs" "/sbin/tune2fs") + (substitute-Command "blkid" "util-linux" "/sbin/blkid") + (substitute-Command "resize2fs" "e2fsprogs" "/sbin/resize2fs") +; docker-mountfrom ?? +; docker +; docker-untar +; docker-applyLayer +; uname +; /usr/bin/uname +; dbus-launch +; grep +; apparmor_parser + (substitute-Command "ps" "procps" "/bin/ps") + (substitute-Command "losetup" "util-linux" "/sbin/losetup") + (substitute-Command "uname" "coreutils" "/bin/uname")) ;; Make compilation fail when, in future versions, Docker ;; invokes other programs we don't know about and thus don't ;; substitute. (substitute* source-files (("LookPath\\(\"zfs\"\\)") "LooxPath(\"zfs\")") - (("LookPath\\(\"") "Guix_doesnt_want_LookPath\\(\"") + (("LookPath\\(\"") "Guix_doesnt_want_LookPath\\(\"") ; )) (("LooxPath") "LookPath"))) #t)) (add-after 'patch-paths 'delete-failing-tests @@ -376,12 +415,15 @@ network attachments.") (inputs `(("btrfs-progs" ,btrfs-progs) ("containerd" ,containerd) ; for containerd-shim - ("runc" ,runc) + ("coreutils" ,coreutils) + ("e2fsprogs" ,e2fsprogs) ("iproute2" ,iproute) ("iptables" ,iptables) + ("kmod" ,kmod) ("libseccomp" ,libseccomp) ("pigz" ,pigz) ("procps" ,procps) + ("runc" ,runc) ("util-linux" ,util-linux) ("lvm2" ,lvm2) ("xfsprogs" ,xfsprogs))) From 8b487bf84f3e93883821910148bec6d3dfa80477 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 04:34:57 +0100 Subject: [PATCH 095/300] gnu: containerd: Fix more paths. * gnu/packages/docker.scm (containerd)[inputs]: Add util-linux. [arguments]<#:phases>[patch-paths]: Fix more paths. --- gnu/packages/docker.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index 9ff1361954..5aadfe475f 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -194,6 +194,11 @@ Python without keeping their credentials in a Docker configuration file.") (string-append "DefaultCommand = \"" (assoc-ref inputs "runc") "/sbin/runc\"\n"))) + (substitute* "vendor/github.com/containerd/continuity/testutil/loopback/loopback_linux.go" + (("exec\\.Command\\(\"losetup\"") ; ) + (string-append "exec.Command(\"" + (assoc-ref inputs "util-linux") + "/sbin/losetup\""))) ;) #t)) (replace 'build (lambda* (#:key (make-flags '()) #:allow-other-keys) @@ -206,7 +211,8 @@ Python without keeping their credentials in a Docker configuration file.") (inputs `(("btrfs-progs" ,btrfs-progs) ("libseccomp" ,libseccomp) - ("runc" ,runc))) + ("runc" ,runc) + ("util-linux" ,util-linux))) (native-inputs `(("go" ,go) ("pkg-config" ,pkg-config))) From 8cd958608c3b08252fcdc7996e9b490ef9f3cdd9 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 04:40:58 +0100 Subject: [PATCH 096/300] gnu: docker: Disable tests requiring elevated permissions. * gnu/packages/docker.scm (docker)[arguments]<#:phases>[delete-failing-tests]: Disable tests requiring elevated permissions. --- gnu/packages/docker.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index 5aadfe475f..b06d48d101 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -375,6 +375,9 @@ network attachments.") (delete-file "daemon/graphdriver/vfs/vfs_test.go") ;; Timeouts after 5 min. (delete-file "plugin/manager_linux_test.go") + ;; Operation not permitted. + (delete-file "daemon/graphdriver/overlay/overlay_test.go") + (delete-file "daemon/graphdriver/overlay2/overlay_test.go") #t)) (replace 'configure (lambda _ From 28f6b275437dbac03c6754f32483799dd5049f7f Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 9 Jan 2019 22:50:17 -0500 Subject: [PATCH 097/300] gnu: linux-libre: Enable pressure stall information. * gnu/packages/aux-files/linux-libre/4.20-arm.conf, gnu/packages/aux-files/linux-libre/4.20-arm64.conf, gnu/packages/aux-files/linux-libre/4.20-i686.conf, gnu/packages/aux-files/linux-libre/4.20-x86_64.conf: Enable CONFIG_PSI. --- gnu/packages/aux-files/linux-libre/4.20-arm.conf | 3 ++- gnu/packages/aux-files/linux-libre/4.20-arm64.conf | 3 ++- gnu/packages/aux-files/linux-libre/4.20-i686.conf | 3 ++- gnu/packages/aux-files/linux-libre/4.20-x86_64.conf | 3 ++- 4 files changed, 8 insertions(+), 4 deletions(-) diff --git a/gnu/packages/aux-files/linux-libre/4.20-arm.conf b/gnu/packages/aux-files/linux-libre/4.20-arm.conf index 309e832844..514a6d4748 100644 --- a/gnu/packages/aux-files/linux-libre/4.20-arm.conf +++ b/gnu/packages/aux-files/linux-libre/4.20-arm.conf @@ -94,7 +94,8 @@ CONFIG_TASKSTATS=y CONFIG_TASK_DELAY_ACCT=y CONFIG_TASK_XACCT=y CONFIG_TASK_IO_ACCOUNTING=y -# CONFIG_PSI is not set +CONFIG_PSI=y +# CONFIG_PSI_DEFAULT_DISABLED is not set CONFIG_CPU_ISOLATION=y # diff --git a/gnu/packages/aux-files/linux-libre/4.20-arm64.conf b/gnu/packages/aux-files/linux-libre/4.20-arm64.conf index 9a756c16e5..9e71cadf0c 100644 --- a/gnu/packages/aux-files/linux-libre/4.20-arm64.conf +++ b/gnu/packages/aux-files/linux-libre/4.20-arm64.conf @@ -86,7 +86,8 @@ CONFIG_TASKSTATS=y CONFIG_TASK_DELAY_ACCT=y CONFIG_TASK_XACCT=y CONFIG_TASK_IO_ACCOUNTING=y -# CONFIG_PSI is not set +CONFIG_PSI=y +# CONFIG_PSI_DEFAULT_DISABLED is not set CONFIG_CPU_ISOLATION=y # diff --git a/gnu/packages/aux-files/linux-libre/4.20-i686.conf b/gnu/packages/aux-files/linux-libre/4.20-i686.conf index 930ea6ddd7..c3ed028442 100644 --- a/gnu/packages/aux-files/linux-libre/4.20-i686.conf +++ b/gnu/packages/aux-files/linux-libre/4.20-i686.conf @@ -99,7 +99,8 @@ CONFIG_TASKSTATS=y CONFIG_TASK_DELAY_ACCT=y CONFIG_TASK_XACCT=y CONFIG_TASK_IO_ACCOUNTING=y -# CONFIG_PSI is not set +CONFIG_PSI=y +# CONFIG_PSI_DEFAULT_DISABLED is not set CONFIG_CPU_ISOLATION=y # diff --git a/gnu/packages/aux-files/linux-libre/4.20-x86_64.conf b/gnu/packages/aux-files/linux-libre/4.20-x86_64.conf index d9ea8ebb59..4918e6bdf2 100644 --- a/gnu/packages/aux-files/linux-libre/4.20-x86_64.conf +++ b/gnu/packages/aux-files/linux-libre/4.20-x86_64.conf @@ -101,7 +101,8 @@ CONFIG_TASKSTATS=y CONFIG_TASK_DELAY_ACCT=y CONFIG_TASK_XACCT=y CONFIG_TASK_IO_ACCOUNTING=y -# CONFIG_PSI is not set +CONFIG_PSI=y +# CONFIG_PSI_DEFAULT_DISABLED is not set CONFIG_CPU_ISOLATION=y # From c37f52e3bea44d53f5e23928a413a7637f2a44b9 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 9 Jan 2019 22:54:08 -0500 Subject: [PATCH 098/300] gnu: linux-libre@4.9: Update to 4.9.149. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.149. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index ead45f7d42..5632687301 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -451,8 +451,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.148" - "0yrjgvdzbcp750j4fhlxi4ia1v0fqh0y3p99wnbpfvg17j01lbjl" + (make-linux-libre "4.9.149" + "1qw1hahqiai8xbv769pdfnx3yan3rl2zh00fmi1nx0khan6i5as3" '("x86_64-linux" "i686-linux") #:configuration-file kernel-config)) From 166c6ad39c550990ff5905485082b4e6347ed372 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 9 Jan 2019 22:56:48 -0500 Subject: [PATCH 099/300] gnu: linux-libre@4.14: Update to 4.14.92. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.92. (%linux-libre-4.14-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 5632687301..18bf50981e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -441,8 +441,8 @@ It has been modified to remove all non-free binary blobs.") #:patches %linux-libre-4.19-patches #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.91") -(define %linux-libre-4.14-hash "1xr4q6hqjg4fjcd1w8qi2x9a11ms9wvascy9b1p6czblg9j9dd6a") +(define %linux-libre-4.14-version "4.14.92") +(define %linux-libre-4.14-hash "09s479krcjzgp53s5i6h7ld1mdagjci6lqvkv8mc1nj0ja8niiq3") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version From f7ed0b1db5f6823e511c6c6f88be794c7725ff05 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 9 Jan 2019 22:57:30 -0500 Subject: [PATCH 100/300] gnu: linux-libre@4.19: Update to 4.19.14. * gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.14. (%linux-libre-4.19-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 18bf50981e..d802472c70 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -427,8 +427,8 @@ It has been modified to remove all non-free binary blobs.") #:patches %linux-libre-4.20-patches #:configuration-file kernel-config)) -(define %linux-libre-4.19-version "4.19.13") -(define %linux-libre-4.19-hash "0ac0ywy542fiwdiab2z12rbjn9zw8vjbzkbpmpk9nfic2mcyrg8r") +(define %linux-libre-4.19-version "4.19.14") +(define %linux-libre-4.19-hash "12ihsp3k8gznc1hjvlpy8jdb27ijr3zsvn8wcgr5za18pg5ncjl9") (define %linux-libre-4.19-patches (list %boot-logo-patch From 60893e5c846f3d85f12ef0265d694abcb5d549a0 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 9 Jan 2019 22:58:13 -0500 Subject: [PATCH 101/300] gnu: linux-libre: Update to 4.20.1. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.20.1. (%linux-libre-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index d802472c70..d8f37e705f 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -413,8 +413,8 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." It has been modified to remove all non-free binary blobs.") (license license:gpl2))) -(define %linux-libre-version "4.20") -(define %linux-libre-hash "07ss8nx95f4pqzzjy382fy5hk7anjm3hpbb3mzl1x8fzfq05q3dq") +(define %linux-libre-version "4.20.1") +(define %linux-libre-hash "10b1cgx7246lxwml66bzzc57sk5bbh7mjxc9zv6qncwh0xhsjv5n") (define %linux-libre-4.20-patches (list %boot-logo-patch From dc4b4a38fa2577d4dd01f80b4bc8c9255304e576 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 05:10:03 +0100 Subject: [PATCH 102/300] tests: docker: Fix test. * gnu/tests/docker.scm (run-docker-test): Set memory and disk size. (%docker-os): Add elogind service. --- gnu/tests/docker.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/tests/docker.scm b/gnu/tests/docker.scm index 4d21324294..973a84c558 100644 --- a/gnu/tests/docker.scm +++ b/gnu/tests/docker.scm @@ -25,6 +25,7 @@ #:use-module (gnu services dbus) #:use-module (gnu services networking) #:use-module (gnu services docker) + #:use-module (gnu services desktop) #:use-module (gnu packages docker) #:use-module (guix gexp) #:use-module (guix store) @@ -35,6 +36,7 @@ (service dhcp-client-service-type) (dbus-service) (polkit-service) + (service elogind-service-type) (service docker-service-type))) (define (run-docker-test) @@ -48,6 +50,8 @@ (define vm (virtual-machine (operating-system os) + (memory-size 500) + (disk-image-size (* 250 (expt 2 20))) (port-forwardings '()))) (define test From f946a370edbf65baab41e8373e25157da5029a88 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 05:14:43 +0100 Subject: [PATCH 103/300] services: docker: Depend on elogind. * gnu/services/docker.scm (docker-shepherd-service)[requirement]: Add elogind. --- gnu/services/docker.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/services/docker.scm b/gnu/services/docker.scm index c88fc342e8..9e24bcd950 100644 --- a/gnu/services/docker.scm +++ b/gnu/services/docker.scm @@ -70,7 +70,8 @@ (shepherd-service (documentation "Docker daemon.") (provision '(dockerd)) - (requirement '(containerd)) + ;; Note: elogind is required because it's mounting the cgroups. + (requirement '(containerd elogind)) (start #~(make-forkexec-constructor (list (string-append #$docker "/bin/dockerd") "-p" "/var/run/docker.pid") From 6b6a25d4d2596bb75bc185c82fbaa45c8880da0c Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 05:32:35 +0100 Subject: [PATCH 104/300] gnu: docker: Fix more paths. * gnu/packages/docker.scm (docker)[inputs]: Add dbus, git. [arguments]<#:phases>[patch-paths]: Use them. --- gnu/packages/docker.scm | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index b06d48d101..ab1a575393 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -31,11 +31,13 @@ #:use-module (gnu packages base) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages glib) #:use-module (gnu packages golang) #:use-module (gnu packages linux) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-web) + #:use-module (gnu packages version-control) #:use-module (gnu packages virtualization)) (define %docker-version "18.09.0") @@ -347,16 +349,16 @@ network attachments.") (substitute-Command "resize2fs" "e2fsprogs" "/sbin/resize2fs") ; docker-mountfrom ?? ; docker -; docker-untar -; docker-applyLayer -; uname +; docker-untar ?? +; docker-applyLayer ?? ; /usr/bin/uname -; dbus-launch ; grep ; apparmor_parser (substitute-Command "ps" "procps" "/bin/ps") (substitute-Command "losetup" "util-linux" "/sbin/losetup") - (substitute-Command "uname" "coreutils" "/bin/uname")) + (substitute-Command "uname" "coreutils" "/bin/uname") + (substitute-Command "dbus-launch" "dbus" "/bin/dbus-launch") + (substitute-Command "git" "git" "/bin/git")) ;; Make compilation fail when, in future versions, Docker ;; invokes other programs we don't know about and thus don't ;; substitute. @@ -425,7 +427,9 @@ network attachments.") `(("btrfs-progs" ,btrfs-progs) ("containerd" ,containerd) ; for containerd-shim ("coreutils" ,coreutils) + ("dbus" ,dbus) ("e2fsprogs" ,e2fsprogs) + ("git" ,git) ("iproute2" ,iproute) ("iptables" ,iptables) ("kmod" ,kmod) From 1f61cc102e205dc1cda8f1ea4bc10dd82b1864e9 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Fri, 28 Dec 2018 20:15:22 +0100 Subject: [PATCH 105/300] gnu: ffmpeg: Add libdrm support. * gnu/packages/video.scm (ffmpeg): Add libdrm support. --- gnu/packages/video.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 52facebe42..15e28d89f3 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -704,6 +704,7 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).") ("libbluray" ,libbluray) ("libcaca" ,libcaca) ("libcdio-paranoia" ,libcdio-paranoia) + ("libdrm" ,libdrm) ("libtheora" ,libtheora) ("libva" ,libva) ("libvdpau" ,libvdpau) @@ -805,6 +806,7 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).") "--enable-libx265" "--enable-openal" "--enable-opengl" + "--enable-libdrm" "--enable-runtime-cpudetect" From 20b4aa6babde823b577f58546fae5ba5297d3ea4 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Thu, 10 Jan 2019 08:38:32 +0100 Subject: [PATCH 106/300] gnu: Add wlstream. * gnu/packages/video.scm (wlstream): New variable. --- gnu/packages/video.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 15e28d89f3..cddb714024 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -3269,3 +3269,32 @@ transitions, and effects and then export your film to many common formats.") (description "dav1d is a new AV1 cross-platform decoder, and focused on speed and correctness.") (license license:bsd-2))) + +(define-public wlstream + (let ((commit "182076a94562b128c3a97ecc53cc68905ea86838") + (revision "1")) + (package + (name "wlstream") + (version (git-version "0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/atomnuker/wlstream.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "01qbcgfl3g9kfwn1jf1z9pdj3bvf5lmg71d1vwkcllc2az24bjqp")))) + (build-system meson-build-system) + (native-inputs `(("libdrm" ,libdrm) + ("pkg-config" ,pkg-config))) + (inputs `(("ffmpeg" ,ffmpeg) + ("pulseaudio" ,pulseaudio) + ("wayland" ,wayland) + ("wayland-protocols" ,wayland-protocols))) + (home-page "https://github.com/atomnuker/wlstream") + (synopsis "Screen capture tool for Wayland sessions") + (description "Wlstream is a screen capture tool for recording audio and +video from a Wayland session.") + (license license:lgpl2.1+)))) From 1d591432c75170a03b73b8a6c732b604fdb3fcfd Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Thu, 10 Jan 2019 08:52:42 +0100 Subject: [PATCH 107/300] gnu: wlstream: Fix indentation. * gnu/packages/video.scm (wlstream): Fix indentation. --- gnu/packages/video.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index cddb714024..7c18c4dbb3 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -3277,15 +3277,15 @@ speed and correctness.") (name "wlstream") (version (git-version "0.0" revision commit)) (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/atomnuker/wlstream.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "01qbcgfl3g9kfwn1jf1z9pdj3bvf5lmg71d1vwkcllc2az24bjqp")))) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/atomnuker/wlstream.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "01qbcgfl3g9kfwn1jf1z9pdj3bvf5lmg71d1vwkcllc2az24bjqp")))) (build-system meson-build-system) (native-inputs `(("libdrm" ,libdrm) ("pkg-config" ,pkg-config))) From 394207c1ee05c4bb148896852f5dd90cdbff4bb5 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Thu, 10 Jan 2019 08:58:36 +0100 Subject: [PATCH 108/300] gnu: Add missing copyright line. * gnu/packages/video.scm: Add missing copyright line for commit 20b4aa6. --- gnu/packages/video.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 7c18c4dbb3..a040031015 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -21,7 +21,7 @@ ;;; Copyright © 2017 Ethan R. Jones ;;; Copyright © 2017, 2018 Clément Lassieur ;;; Copyright © 2017 Gregor Giesen -;;; Copyright © 2017, 2018 Rutger Helling +;;; Copyright © 2017, 2018, 2019 Rutger Helling ;;; Copyright © 2018 Roel Janssen ;;; Copyright © 2018 Marius Bakke ;;; Copyright © 2018 Pierre Neidhardt From 40fa21c22e1d11b741515fd38f5204a5fa57fbaa Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 7 Jan 2019 23:11:58 +0530 Subject: [PATCH 109/300] guix: lint: Warn only if GitHub URI is not same as the package URI. * guix/scripts/lint.scm (check-github-url): Warn only if the GitHub URI obtained after following redirects is not same as the original URI. * tests/lint.scm ("github-url: already the correct github url"): New test. --- guix/scripts/lint.scm | 11 ++++++----- tests/lint.scm | 13 +++++++++++-- 2 files changed, 17 insertions(+), 7 deletions(-) diff --git a/guix/scripts/lint.scm b/guix/scripts/lint.scm index 9acec48577..0f315a9352 100644 --- a/guix/scripts/lint.scm +++ b/guix/scripts/lint.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2017 Alex Kost ;;; Copyright © 2017 Tobias Geerinckx-Rice ;;; Copyright © 2017, 2018 Efraim Flashner -;;; Copyright © 2018 Arun Isaac +;;; Copyright © 2018, 2019 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -820,10 +820,11 @@ descriptions maintained upstream." (lambda (uri) (and=> (follow-redirects-to-github uri) (lambda (github-uri) - (emit-warning - package - (format #f (G_ "URL should be '~a'") github-uri) - 'source)))) + (unless (string=? github-uri uri) + (emit-warning + package + (format #f (G_ "URL should be '~a'") github-uri) + 'source))))) (origin-uris origin))))) (define (check-derivation package) diff --git a/tests/lint.scm b/tests/lint.scm index fe12bebd88..912a78d111 100644 --- a/tests/lint.scm +++ b/tests/lint.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016 Hartmut Goebel ;;; Copyright © 2017 Alex Kost ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2018 Arun Isaac +;;; Copyright © 2018, 2019 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -775,7 +775,16 @@ (method url-fetch) (uri (%local-url)) (sha256 %null-sha256)))))))))) - github-url))) + github-url)) + (test-assert "github-url: already the correct github url" + (string-null? + (with-warnings + (check-github-url + (dummy-package "x" (source + (origin + (method url-fetch) + (uri github-url) + (sha256 %null-sha256))))))))) (test-assert "cve" (mock ((guix scripts lint) package-vulnerabilities (const '())) From 01b3625df6721d27c0b224ee9e58d8edf2cbc4ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 9 Jan 2019 22:52:16 +0100 Subject: [PATCH 110/300] services: gdm: Add default value. * gnu/services/xorg.scm ()[x-server]: Add default value. (gdm-service-type)[default-value, description]: New fields. (gdm-service): Mark as deprecated. --- gnu/services/xorg.scm | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/gnu/services/xorg.scm b/gnu/services/xorg.scm index b3c24746d1..4d1674f063 100644 --- a/gnu/services/xorg.scm +++ b/gnu/services/xorg.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 Andy Wingo -;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2019 Ludovic Courtès ;;; Copyright © 2015 Sou Bunnbu ;;; Copyright © 2018 Timothy Sample ;;; @@ -628,7 +628,8 @@ makes the good ol' XlockMore usable." (allow-empty-passwords? gdm-configuration-allow-empty-passwords? (default #t)) (auto-login? gdm-configuration-auto-login? (default #f)) (default-user gdm-configuration-default-user (default #f)) - (x-server gdm-configuration-x-server)) + (x-server gdm-configuration-x-server + (default (xorg-wrapper)))) (define (gdm-etc-service config) (define gdm-configuration-file @@ -719,12 +720,17 @@ makes the good ol' XlockMore usable." (service-extension etc-service-type gdm-etc-service) (service-extension dbus-root-service-type - (compose list gdm-configuration-gdm)))))) + (compose list + gdm-configuration-gdm)))) + (default-value (gdm-configuration)) + (description + "Run the GNOME Desktop Manager (GDM), a program that allows +you to log in in a graphical session, whether or not you use GNOME."))) ;; This service isn't working yet; it gets as far as starting to run the ;; greeter from gnome-shell but doesn't get any further. It is here because ;; it doesn't hurt anyone and perhaps it inspires someone to fix it :) -(define* (gdm-service #:key (gdm gdm) +(define* (gdm-service #:key (gdm gdm) ;deprecated (allow-empty-passwords? #t) (x-server (xorg-wrapper))) "Return a service that spawns the GDM graphical login manager, which in turn From 7d4b3e1e2b936b986a474cf038788304edb2ae7d Mon Sep 17 00:00:00 2001 From: Tim Gesthuizen Date: Sat, 29 Dec 2018 23:21:58 +0100 Subject: [PATCH 111/300] gnu: Add pwsafe MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/password-utils.scm (pwsafe): New variable Signed-off-by: Ludovic Courtès --- gnu/packages/password-utils.scm | 58 +++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 3962034076..f10fc76e9d 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2018 Arun Isaac ;;; Copyright © 2018 Pierre Neidhardt ;;; Copyright © 2018 Amirouche Boubekki +;;; Copyright © 2018 Tim Gesthuizen ;;; ;;; This file is part of GNU Guix. ;;; @@ -42,6 +43,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix packages) #:use-module (gnu packages) #:use-module (gnu packages admin) @@ -51,7 +53,9 @@ #:use-module (gnu packages compression) #:use-module (gnu packages crypto) #:use-module (gnu packages curl) + #:use-module (gnu packages file) #:use-module (gnu packages freedesktop) + #:use-module (gnu packages gettext) #:use-module (gnu packages glib) #:use-module (gnu packages gnupg) #:use-module (gnu packages gnuzilla) @@ -72,6 +76,7 @@ #:use-module (gnu packages tls) #:use-module (gnu packages qt) #:use-module (gnu packages version-control) + #:use-module (gnu packages wxwidgets) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg) #:use-module (gnu packages xml) @@ -168,6 +173,59 @@ algorithms AES or Twofish.") (license license:gpl3) (properties `((superseded . ,keepassxc))))) +(define-public pwsafe + (package + (name "pwsafe") + (version "3.48.0") + (home-page "https://www.pwsafe.org/" ) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pwsafe/pwsafe.git") + (commit version))) + (sha256 (base32 "0hxv23yh76liggxbjn4m132z15sklra8ms341xgzl4n5vjx30ihi")) + (file-name (string-append name "-" version "-checkout")))) + (build-system cmake-build-system) + (native-inputs `(("gettext" ,gettext-minimal) + ("perl" ,perl) + ("zip" ,zip))) + (inputs `(("curl" ,curl) + ("file" ,file) + ("gtest" ,googletest) + ("libuuid" ,util-linux) + ("libxt" ,libxt) + ("libxtst" ,libxtst) + ("openssl" ,openssl) + ("qrencode" ,qrencode) + ("wxwidgets" ,wxwidgets) + ("xerces-c" ,xerces-c))) + (arguments '(#:configure-flags (list "-DNO_GTEST=YES") + #:phases (modify-phases %standard-phases + (add-after 'unpack 'add-gtest + (lambda* (#:key inputs #:allow-other-keys) + (chmod "CMakeLists.txt" #o644) + (let ((cmake-port (open-file "CMakeLists.txt" + "a"))) + (display "find_package(GTest) +add_subdirectory(src/test)\n" cmake-port) + (close cmake-port) + #t))) + (add-after 'add-gtest 'patch-executables + (lambda* (#:key inputs #:allow-other-keys) + (chmod "src/test/OSTest.cpp" #o644) + (substitute* "src/os/unix/media.cpp" + (("/usr/bin/file") + (string-append (assoc-ref inputs "file") + "/bin/file"))) + #t))))) + (synopsis "Password safe with automatic input and key generation") + (description "pwsafe is a password manager originally designed by Bruce +Schneier. It offers a simple UI to manage passwords for different services. +There are other programs that support the file format on different +platforms.") + (license license:artistic2.0))) + (define-public shroud (package (name "shroud") From 787da810a03b8113448dc5d9032a71dee51cb0bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 10 Jan 2019 14:45:12 +0100 Subject: [PATCH 112/300] Add (guix deprecation). * guix/deprecation.scm: New file. * Makefile.am (MODULES): Add it. * po/guix/POTFILES.in: Add it. --- Makefile.am | 1 + guix/deprecation.scm | 89 ++++++++++++++++++++++++++++++++++++++++++++ po/guix/POTFILES.in | 1 + 3 files changed, 91 insertions(+) create mode 100644 guix/deprecation.scm diff --git a/Makefile.am b/Makefile.am index 9f30d5b2b0..0590c51519 100644 --- a/Makefile.am +++ b/Makefile.am @@ -64,6 +64,7 @@ MODULES = \ guix/base64.scm \ guix/ci.scm \ guix/cpio.scm \ + guix/deprecation.scm \ guix/docker.scm \ guix/records.scm \ guix/pki.scm \ diff --git a/guix/deprecation.scm b/guix/deprecation.scm new file mode 100644 index 0000000000..453aad7106 --- /dev/null +++ b/guix/deprecation.scm @@ -0,0 +1,89 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2019 Ludovic Courtès +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (guix deprecation) + #:use-module (guix i18n) + #:use-module (ice-9 format) + #:export (define-deprecated + without-deprecation-warnings + deprecation-warning-port)) + +;;; Commentary: +;;; +;;; Provide a mechanism to mark bindings as deprecated. +;;; +;;; We don't reuse (guix ui) mostly to avoid pulling in too many things. +;;; +;;; Code: + +(define deprecation-warning-port + ;; Port where deprecation warnings go. + (make-parameter (current-warning-port))) + +(define (source-properties->location-string properties) + "Return a human-friendly, GNU-standard representation of PROPERTIES, a +source property alist." + (let ((file (assq-ref properties 'filename)) + (line (assq-ref properties 'line)) + (column (assq-ref properties 'column))) + (if (and file line column) + (format #f "~a:~a:~a" file (+ 1 line) column) + (G_ "")))) + +(define* (warn-about-deprecation variable properties + #:key replacement) + (format (deprecation-warning-port) + (G_ "~a: warning: '~a' is deprecated~@[, use '~a' instead~]~%") + (source-properties->location-string properties) + variable replacement)) + +(define-syntax define-deprecated + (lambda (s) + "Define a deprecated variable or procedure, along these lines: + + (define-deprecated foo bar 42) + (define-deprecated (baz x y) qux (qux y x)) + +This will write a deprecation warning to DEPRECATION-WARNING-PORT." + (syntax-case s () + ((_ (proc formals ...) replacement body ...) + #'(define-deprecated proc replacement + (lambda* (formals ...) body ...))) + ((_ variable replacement exp) + (identifier? #'variable) + (with-syntax ((real (datum->syntax + #'variable + (symbol-append '% + (syntax->datum #'variable) + '/deprecated)))) + #`(begin + (define real + (begin + (lambda () replacement) ;just to ensure it's bound + exp)) + + (define-syntax variable + (lambda (s) + (warn-about-deprecation 'variable (syntax-source s) + #:replacement 'replacement) + (syntax-case s () + ((_ args (... ...)) + #'(real args (... ...))) + (id + (identifier? #'id) + #'real)))))))))) diff --git a/po/guix/POTFILES.in b/po/guix/POTFILES.in index c432973f9e..f7360489c6 100644 --- a/po/guix/POTFILES.in +++ b/po/guix/POTFILES.in @@ -45,4 +45,5 @@ guix/nar.scm guix/channels.scm guix/profiles.scm guix/git.scm +guix/deprecation.scm nix/nix-daemon/guix-daemon.cc From 65a67bf711b14bc7200f6730c0f173375ca12974 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 10 Jan 2019 14:50:09 +0100 Subject: [PATCH 113/300] services: Use 'define-deprecated' for service procedures. * gnu/services/base.scm (urandom-seed-service, gpm-service): Define using 'define-deprecated'. * gnu/services/messaging.scm (bitlbee-service): Likewise. * gnu/services/networking.scm (dhcp-client-service): Likewise. (ntp-service): Likewise. * gnu/services/xorg.scm (slim-service): Likewise. (gdm-service): Likewise. --- gnu/services/base.scm | 13 ++++++++----- gnu/services/messaging.scm | 10 ++++++---- gnu/services/networking.scm | 13 ++++++++----- gnu/services/xorg.scm | 25 ++++++++++++++----------- 4 files changed, 36 insertions(+), 25 deletions(-) diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 67bdaef18c..6e99cbfec4 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2015, 2016 Alex Kost ;;; Copyright © 2015, 2016 Mark H Weaver ;;; Copyright © 2015 Sou Bunnbu @@ -25,6 +25,7 @@ (define-module (gnu services base) #:use-module (guix store) + #:use-module (guix deprecation) #:use-module (gnu services) #:use-module (gnu services shepherd) #:use-module (gnu system pam) @@ -614,8 +615,9 @@ file systems, as well as corresponding @file{/etc/fstab} entries."))) generator (RNG) with the value recorded when the system was last shut down."))) -(define (urandom-seed-service) ;deprecated - (service urandom-seed-service-type #f)) +(define-deprecated (urandom-seed-service) + urandom-seed-service-type + (service urandom-seed-service-type)) ;;; @@ -2078,8 +2080,9 @@ command-line options. GPM allows users to use the mouse in the console, notably to select, copy, and paste text. The default options use the @code{ps2} protocol, which works for both USB and PS/2 mice."))) -(define* (gpm-service #:key (gpm gpm) ;deprecated - (options %default-gpm-options)) +(define-deprecated (gpm-service #:key (gpm gpm) + (options %default-gpm-options)) + gpm-service-type "Run @var{gpm}, the general-purpose mouse daemon, with the given command-line @var{options}. GPM allows users to use the mouse in the console, notably to select, copy, and paste text. The default value of @var{options} diff --git a/gnu/services/messaging.scm b/gnu/services/messaging.scm index 92f86a1b83..e70f1b70ef 100644 --- a/gnu/services/messaging.scm +++ b/gnu/services/messaging.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017, 2018 Clément Lassieur ;;; Copyright © 2017 Mathieu Othacehe -;;; Copyright © 2015, 2017, 2018 Ludovic Courtès +;;; Copyright © 2015, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2018 Pierre-Antoine Rouby ;;; ;;; This file is part of GNU Guix. @@ -32,6 +32,7 @@ #:use-module (guix modules) #:use-module (guix records) #:use-module (guix packages) + #:use-module (guix deprecation) #:use-module (srfi srfi-1) #:use-module (srfi srfi-35) #:use-module (ice-9 match) @@ -882,9 +883,10 @@ string, you could instantiate a prosody service like this: "Run @url{http://bitlbee.org,BitlBee}, a daemon that acts as a gateway between IRC and chat networks."))) -(define* (bitlbee-service #:key (bitlbee bitlbee) ;deprecated - (interface "127.0.0.1") (port 6667) - (extra-settings "")) +(define-deprecated (bitlbee-service #:key (bitlbee bitlbee) + (interface "127.0.0.1") (port 6667) + (extra-settings "")) + bitlbee-service-type "Return a service that runs @url{http://bitlbee.org,BitlBee}, a daemon that acts as a gateway between IRC and chat networks. diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index bfa6e297e6..2f49bf28dd 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2016, 2018 Efraim Flashner ;;; Copyright © 2016 John Darrington @@ -45,6 +45,7 @@ #:use-module (guix gexp) #:use-module (guix records) #:use-module (guix modules) + #:use-module (guix deprecation) #:use-module (srfi srfi-1) #:use-module (srfi srfi-9) #:use-module (srfi srfi-26) @@ -206,7 +207,8 @@ fe80::1%lo0 apps.facebook.com\n") (stop #~(make-kill-destructor)))) isc-dhcp)) -(define* (dhcp-client-service #:key (dhcp isc-dhcp)) ;deprecated +(define-deprecated (dhcp-client-service #:key (dhcp isc-dhcp)) + dhcp-client-service-type "Return a service that runs @var{dhcp}, a Dynamic Host Configuration Protocol (DHCP) client, on all the non-loopback network interfaces." (service dhcp-client-service-type dhcp)) @@ -374,9 +376,10 @@ daemon of the @uref{http://www.ntp.org, Network Time Foundation}. The daemon will keep the system clock synchronized with that of the given servers.") (default-value (ntp-configuration)))) -(define* (ntp-service #:key (ntp ntp) ;deprecated - (servers %ntp-servers) - allow-large-adjustment?) +(define-deprecated (ntp-service #:key (ntp ntp) + (servers %ntp-servers) + allow-large-adjustment?) + ntp-service-type "Return a service that runs the daemon from @var{ntp}, the @uref{http://www.ntp.org, Network Time Protocol package}. The daemon will keep the system clock synchronized with that of @var{servers}. diff --git a/gnu/services/xorg.scm b/gnu/services/xorg.scm index 4d1674f063..2f91619219 100644 --- a/gnu/services/xorg.scm +++ b/gnu/services/xorg.scm @@ -40,6 +40,7 @@ #:use-module (guix packages) #:use-module (guix derivations) #:use-module (guix records) + #:use-module (guix deprecation) #:use-module (srfi srfi-1) #:use-module (srfi srfi-9) #:use-module (srfi srfi-26) @@ -521,14 +522,15 @@ reboot_cmd " shepherd "/sbin/reboot\n" (const (list xterm))))) (default-value (slim-configuration)))) -(define* (slim-service #:key (slim slim) ;deprecated - (allow-empty-passwords? #t) auto-login? - (default-user "") - (theme %default-slim-theme) - (theme-name %default-slim-theme-name) - (xauth xauth) (shepherd shepherd) - (auto-login-session #f) - (startx (xorg-start-command))) +(define-deprecated (slim-service #:key (slim slim) + (allow-empty-passwords? #t) auto-login? + (default-user "") + (theme %default-slim-theme) + (theme-name %default-slim-theme-name) + (xauth xauth) (shepherd shepherd) + (auto-login-session #f) + (startx (xorg-start-command))) + slim-service-type "Return a service that spawns the SLiM graphical login manager, which in turn starts the X display server with @var{startx}, a command as returned by @code{xorg-start-command}. @@ -730,9 +732,10 @@ you to log in in a graphical session, whether or not you use GNOME."))) ;; This service isn't working yet; it gets as far as starting to run the ;; greeter from gnome-shell but doesn't get any further. It is here because ;; it doesn't hurt anyone and perhaps it inspires someone to fix it :) -(define* (gdm-service #:key (gdm gdm) ;deprecated - (allow-empty-passwords? #t) - (x-server (xorg-wrapper))) +(define-deprecated (gdm-service #:key (gdm gdm) + (allow-empty-passwords? #t) + (x-server (xorg-wrapper))) + gdm-service-type "Return a service that spawns the GDM graphical login manager, which in turn starts the X display server with @var{X}, a command as returned by @code{xorg-wrapper}. From dbd346ae88b21dd138a83e2a742f050cf70e099c Mon Sep 17 00:00:00 2001 From: Nam Nguyen Date: Sun, 6 Jan 2019 20:56:22 -0800 Subject: [PATCH 114/300] gnu: sct: Correct license. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/xdisorg.scm (sct)[license]: Change to non-copyleft. Signed-off-by: Ludovic Courtès --- gnu/packages/xdisorg.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 7c119def4d..fdfa1511d8 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -1613,7 +1613,7 @@ colors on all monitors attached to an XRandR-capable X11 display server.") (synopsis "Set the color temperature of the screen") (description "@code{sct} is a lightweight utility to set the color temperature of the screen.") - (license license:bsd-3))) + (license (license:non-copyleft "file://sct.c")))) ; "OpenBSD" license (define-public wl-clipboard (package From d3a0e74d6a303cd46b0761b5a84c8e8b290e3797 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 14:50:47 +0100 Subject: [PATCH 115/300] services: docker: Clarify service-extension shepherd-root-service-type. * gnu/services/docker.scm (docker-service-type)[extensions]: Clarify service-extension shepherd-root-service-type. --- gnu/services/docker.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/services/docker.scm b/gnu/services/docker.scm index 9e24bcd950..87931f83f5 100644 --- a/gnu/services/docker.scm +++ b/gnu/services/docker.scm @@ -88,9 +88,9 @@ bundles in Docker containers.") (service-extension activation-service-type %docker-activation) (service-extension shepherd-root-service-type - (lambda args - (list (apply containerd-shepherd-service args) - (apply docker-shepherd-service args)))) + (lambda (config) + (list (containerd-shepherd-service config) + (docker-shepherd-service config)))) (service-extension account-service-type (const %docker-accounts)))) (default-value (docker-configuration)))) From 8b0c1744154f0e9a008c4e4586bfdb0876749139 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 19:16:06 +0100 Subject: [PATCH 116/300] services: docker: Use more minimal service requrements. * gnu/services/docker.scm (docker-service-type)[requirement]: Add file-system-/sys/fs/cgroup/blkio, file-system-/sys/fs/cgroup/cpu, file-system-/sys/fs/cgroup/cpuset, file-system-/sys/fs/cgroup/devices, file-system-/sys/fs/cgroup/memory. Remove elogind. --- gnu/services/docker.scm | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/gnu/services/docker.scm b/gnu/services/docker.scm index 87931f83f5..c84c887612 100644 --- a/gnu/services/docker.scm +++ b/gnu/services/docker.scm @@ -71,7 +71,14 @@ (documentation "Docker daemon.") (provision '(dockerd)) ;; Note: elogind is required because it's mounting the cgroups. - (requirement '(containerd elogind)) + (requirement '(containerd + file-system-/sys/fs/cgroup/blkio + file-system-/sys/fs/cgroup/cpu + file-system-/sys/fs/cgroup/cpuset + file-system-/sys/fs/cgroup/devices + file-system-/sys/fs/cgroup/memory + ; TODO: file-system-/sys/fs/cgroup/pids + )) (start #~(make-forkexec-constructor (list (string-append #$docker "/bin/dockerd") "-p" "/var/run/docker.pid") From 35ac66eec1bddbe5a2244b1964ec64d93227766c Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Wed, 9 Jan 2019 21:11:41 +0100 Subject: [PATCH 117/300] gnu: crypto++: Update to 8.0.0. * gnu/packages/crypto.scm (crypto++): Update to 8.0.0. [arguments]: Build shared library. [arguments]: Generate .pc file. --- gnu/packages/crypto.scm | 32 ++++++++++++++++++++++++++++---- 1 file changed, 28 insertions(+), 4 deletions(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index e8062f0e1f..082d6ecde1 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -632,7 +632,7 @@ data on your platform, so the seed itself will be as random as possible. (define-public crypto++ (package (name "crypto++") - (version "6.0.0") + (version "8.0.0") (source (origin (method url-fetch/zipbomb) (uri (string-append "https://cryptopp.com/cryptopp" @@ -640,11 +640,14 @@ data on your platform, so the seed itself will be as random as possible. ".zip")) (sha256 (base32 - "1nidm6xbdza5cbgf5md2zznmaq692rfyjasycwipl6rzdfwjvb34")))) + "0b5qrsm4jhy4nzxgrm13nixhvbswr242plx1jw6r4sw492rqkzdv")))) (build-system gnu-build-system) (arguments `(#:make-flags - (list (string-append "PREFIX=" (assoc-ref %outputs "out"))) + (list (string-append "PREFIX=" (assoc-ref %outputs "out")) + ;; Override "/sbin/ldconfig" with simply "echo" since + ;; we don't need ldconfig(8). + "LDCONF=echo") #:phases (modify-phases %standard-phases (add-after 'unpack 'disable-native-optimisation @@ -654,7 +657,28 @@ data on your platform, so the seed itself will be as random as possible. (substitute* "GNUmakefile" ((" -march=native") "")) #t)) - (delete 'configure)))) + (delete 'configure) + (add-after 'build 'build-shared + (lambda _ + ;; By default, only the static library is built. + (invoke "make" "shared"))) + (add-after 'install 'install-pkg-config + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (pkg-dir (string-append out "/lib/pkgconfig"))) + (mkdir-p pkg-dir) + (with-output-to-file (string-append pkg-dir "/libcrypto++.pc") + (lambda _ + (display + (string-append + "prefix=" out "\n" + "libdir=" out "/lib\n" + "includedir=" out "/include\n\n" + "Name: libcrypto++-" ,version "\n" + "Description: Class library of cryptographic schemes" + "Version: " ,version "\n" + "Libs: -L${libdir} -lcryptopp\n" + "Cflags: -I${includedir}\n")))))))))) (native-inputs `(("unzip" ,unzip))) (home-page "https://cryptopp.com/") From 6fe6840dab54c10ce898cb37ffcc455e6c576465 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Wed, 9 Jan 2019 21:12:29 +0100 Subject: [PATCH 118/300] gnu: Add libsecp256k1. * gnu/packages/crypto.scm (libsecp256k1): New variable. --- gnu/packages/crypto.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 082d6ecde1..84b00e0d8c 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -905,3 +905,44 @@ GnuPG or encrypted filesystems. Enchive has no external dependencies and is trivial to build for local use. Portability is emphasized over performance.") (home-page "https://github.com/skeeto/enchive") (license license:unlicense))) + +(define-public libsecp256k1 + (let ((commit "e34ceb333b1c0e6f4115ecbb80c632ac1042fa49")) + (package + (name "libsecp256k1") + (version (git-version "20181126" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bitcoin-core/secp256k1") + (commit commit))) + (sha256 + (base32 + "0as78s179hcr3ysk3fw98k5wzabgnwri7vkkc17wg31lyz6ids6c")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + ;; WARNING: This package might need additional configure flags to run properly. + ;; See https://git.archlinux.org/svntogit/community.git/tree/trunk/PKGBUILD?h=packages/libsecp256k1. + (synopsis "C library for EC operations on curve secp256k1") + (description + "Optimized C library for EC operations on curve secp256k1. + +This library is a work in progress and is being used to research best +practices. Use at your own risk. + +Features: + +@itemize +@item secp256k1 ECDSA signing/verification and key generation. +@item Adding/multiplying private/public keys. +@item Serialization/parsing of private keys, public keys, signatures. +@item Constant time, constant memory access signing and pubkey generation. +@item Derandomized DSA (via RFC6979 or with a caller provided function.) +@item Very efficient implementation. +@end itemize\n") + (home-page "https://github.com/bitcoin-core/secp256k1") + (license license:unlicense)))) From 6a6e5d84dacb4b127120ec150c52549a2bc111d6 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Wed, 9 Jan 2019 21:12:44 +0100 Subject: [PATCH 119/300] gnu: opendht: Update to 1.8.1. * gnu/packages/crypto.scm (opendht): Update to 1.8.1. [source]: Remove snippet that deletes argon2, which is no longer bundled. [arguments]: Add "--with-argon2" to use system argon2. [license]: Update to GPLv3+ following the README and source headers. --- gnu/packages/crypto.scm | 24 ++++++++---------------- 1 file changed, 8 insertions(+), 16 deletions(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 84b00e0d8c..56f909ed2f 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -11,6 +11,8 @@ ;;; Copyright © 2018 Arun Isaac ;;; Copyright © 2018 Nicolas Goaziou ;;; Copyright © 2018 Nicolò Balzarotti +;;; Copyright © 2018 Tim Gesthuizen +;;; Copyright © 2019 Pierre Neidhardt ;;; ;;; This file is part of GNU Guix. ;;; @@ -167,28 +169,16 @@ OpenBSD tool of the same name.") (define-public opendht (package (name "opendht") - (version "0.6.1") + (version "1.8.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/savoirfairelinux/opendht.git") (commit version))) (file-name (git-file-name name version)) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file-recursively "src/argon2") - (substitute* "src/Makefile.am" - (("./argon2/libargon2.la") "") - (("SUBDIRS = argon2") "")) - (substitute* "src/crypto.cpp" - (("argon2/argon2.h") "argon2.h")) - (substitute* "configure.ac" - (("src/argon2/Makefile") "")) - #t)) (sha256 (base32 - "1akk613f18rc8kqs0cxdm34iq7wwc9kffhgp5rng09arwlw8gw3w")))) + "0vninb5mak27wigajslyvr05vq7wbrwqhbr4wzl2nmqcb20wmlq2")))) (build-system gnu-build-system) (inputs `(("gnutls" ,gnutls) @@ -203,13 +193,15 @@ OpenBSD tool of the same name.") ("automake" ,automake) ("libtool" ,libtool))) (arguments - `(#:configure-flags '("--disable-tools" "--disable-python"))) + `(#:configure-flags '("--disable-tools" + "--disable-python" + "--with-argon2"))) (home-page "https://github.com/savoirfairelinux/opendht/") (synopsis "Distributed Hash Table (DHT) library") (description "OpenDHT is a Distributed Hash Table (DHT) library. It may be used to manage peer-to-peer network connections as needed for real time communication.") - (license license:gpl3))) + (license license:gpl3+))) (define-public encfs (package From ffcd282702fedf90c80b5b2a05a5e2f473cf4c9c Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 10 Jan 2019 20:17:34 +0100 Subject: [PATCH 120/300] gnu: docker: Booby-trap "Command" and "LookPath" calls. * gnu/packages/docker.scm (docker)[arguments]<#:phases>[patch-paths]: Booby-trap "Command" and "LookPath" calls. --- gnu/packages/docker.scm | 21 ++++++++++++++++++--- 1 file changed, 18 insertions(+), 3 deletions(-) diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index ab1a575393..23695a0c06 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -363,9 +363,24 @@ network attachments.") ;; invokes other programs we don't know about and thus don't ;; substitute. (substitute* source-files - (("LookPath\\(\"zfs\"\\)") "LooxPath(\"zfs\")") - (("LookPath\\(\"") "Guix_doesnt_want_LookPath\\(\"") ; )) - (("LooxPath") "LookPath"))) + ;; Search for Java in PATH. + (("\\ Date: Thu, 10 Jan 2019 12:56:04 -0500 Subject: [PATCH 121/300] gnu: irssi: Update to 1.1.2 [fixes CVE-2019-5882]. * gnu/packages/irc.scm (irssi): Update to 1.1.2. --- gnu/packages/irc.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index ba31d36b9e..ec1c4aae9f 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -126,15 +126,15 @@ irssi, but graphical.") (define-public irssi (package (name "irssi") - (version "1.1.1") + (version "1.1.2") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/irssi/irssi/" - "releases/download/" version "/irssi-" - version ".tar.xz")) - (sha256 - (base32 - "1gx1flfh4a09nb3b5pvf0ygnbl7rry3l4gph8wij29dsl7khfj3q")))) + (method url-fetch) + (uri (string-append "https://github.com/irssi/irssi/" + "releases/download/" version "/irssi-" + version ".tar.xz")) + (sha256 + (base32 + "0clppwqhllrmqjg1dd47v9v1qiqx7cf9afm81bm1pscllf4jpk2w")))) (build-system gnu-build-system) (arguments `(#:phases From d4d9a1ece0dbf0bc65cc98e971e88a1406bb9c27 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 10 Jan 2019 22:30:54 +0100 Subject: [PATCH 122/300] gnu: Update texlive packages. * guix/build-system/texlive.scm (%texlive-tag, %texlive-revision): Update to texlive-2018.2, revision 49435. * gnu/packages/tex.scm (texlive-dvips, texlive-generic-unicode-data, texlive-generic-dehyph-exptl, texlive-generic-hyph-utf8, texlive-fontname, texlive-fonts-cm, texlive-tex-plain, texlive-latex-base, texlive-latex-graphics, texlive-latex-graphics, texlive-latex-oberdiek, texlive-latex-tools, texlive-latex-l3kernel, texlive-latex-l3packages, texlive-latex-fontspec, texlive-latex-amsmath, texlive-latex-amscls, texlive-latex-babel, texlive-latex-cyrillic, texlive-latex-eqparbox, texlive-latex-ifplatform, texlive-latex-etoolbox, texlive-latex-galois, texlive-latex-polyglossia, texlive-tex-texinfo, texlive-latex-changebar, texlive-latex-fancyhdr, texlive-latex-overpic, texlive-latex-parskip, texlive-metapost, texlive-latex-ucs, texlive-generic-pdftex, texlive-latex-media9, texlive-latex-ocgx2, texlive-latex-koma-script, texlive-generic-listofitems, texlive-bibtex, texlive-context-base): Update hashes. (texlive-latex-fontspec)[arguments]: Remove custom build target. (texlive-latex-dinbrief)[arguments]: Add build phase "fix-encoding-error". (texlive-latex-xkeyval): New variable. (texlive-latex-pstool)[source]: Fetch from new location. [build-system]: Use trivial-build-system. [arguments]: Write simple builder. [propagated-inputs]: Add texlive-latex-l3kernel, texlive-latex-tools, and texlive-latex-xkeyval. [synopsis]: Fix typo. --- gnu/packages/tex.scm | 150 ++++++++++++++++++++++------------ guix/build-system/texlive.scm | 7 +- 2 files changed, 100 insertions(+), 57 deletions(-) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 3bfde1d714..7aa83e4404 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -255,7 +255,7 @@ This package contains the binaries.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0fcy2hpapbj01ncpjj3v39yhr0jjxb6rm13qaxjjw66s3vydxls1")))) + "1ky6wc173jhf0b33lhyb4r3bx1d4bmiqkn6y1hxn92kwjdzl42p7")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -286,7 +286,7 @@ This package contains the binaries.") (file-name (string-append "dvips-font-maps-" version "-checkout")) (sha256 (base32 - "09hply3nmy24ilnc6cl8q70jcqxvq6bwri572kms008ini3h9vqh")))) + "0nxvfbb5vsvakiw0iviicghdc2sxk05cj056ilqnpa62fffc36a6")))) ("dvips-base-enc" ,(origin (method svn-fetch) @@ -322,7 +322,7 @@ to PostScript.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0ivrhp6jz31pl4z841g4ws41lmvdiwz4sslmhf02inlib79gz6r2")))) + "0r1v16jyfpz6dwqsgm6b9jcj4kf2pkzc9hg07s6fx9g8ba8qglih")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -361,7 +361,7 @@ out to date by @code{unicode-letters.tex}. ") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1l9wgv99qq0ysvlxqpj4g8bl0dywbzra4g8m2kmpg2fb0i0hczap")))) + "03yj1di9py92drp6gpfva6q69vk2iixr79r7cp7ja570s3pr0m33")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -432,7 +432,7 @@ to adapt the plain e-TeX source file to work with XeTeX and LuaTeX.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0ghizcz7ps16dzfqf66wwg5i181assc6qsm0g7g5dbmp909931vi")))) + "1alnn9cd60m2c12vym9f9q22ap1ngywxpkjl9dk472why44g1dmy")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -541,7 +541,7 @@ build fonts using the Metafont system.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0cssbzcx15221dynp5sii72qh4l18mwkr14n8w1xb19j8pbaqasz")))) + "05rbn7z30xawd3n6w7c3ijp2yc67ga220jgqmkla9pd9wx185rzq")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -575,7 +575,7 @@ documents.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "045k5b9rdmbxpy1a3006l1x96z1rd18vg3cwrvnld9bqybw5qz44")))) + "0vfjhidr9pha613h8mfhnpcpvld6ahdfb449918fpsfs93cppkyj")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) @@ -916,7 +916,7 @@ individual symbols defined in @code{amssymb.sty}.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0mjgl3gscn3ps29yjambz1j9fg81ynnncb96vpprwx4xsijhsns0")))) + "1xknlb3gcw6jjqh97bhghxi594bzpj1zfzzfsrr9pvr9s1bx7dnf")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -961,7 +961,7 @@ book).") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1h9pir2hz6i9avc4lrl733p3zf4rpkg8537x1zdbhs91hvhikw9k")))) + "17bqrzzjz16k52sc7ydl4vw7ddy2z3g0p1xsk2c35h1ynq9h3wwm")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) @@ -1082,7 +1082,7 @@ book).") "1cfwdg2rhbayl3w0x1xqd36d45zbc96f029myp13s7cb6kbmbppv")) ("texlive-generic-config" ,(texlive-dir "tex/generic/config/" - "19vj088p4kkp6xll0141m4kl6ssgdzhs3g10i232khb07aqiag8s")) + "1v90iihy112q93zdpblpdk8zv8rf99fgslsg06s1sxm27zjm9nap")) ("texlive-latex-base-support-files" ,(origin (method svn-fetch) @@ -1094,7 +1094,7 @@ book).") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "16bs9pi3nq407xhg59glklqv43v102cg3yim6k3zcri5d9nkbv3a")))) + "18wy8dlcw8adl6jzqwbg54pdwlhs8hilnfvqbw6ikj6y3zhqkj7q")))) ("texlive-tex-plain" ,texlive-tex-plain) ("texlive-fonts-cm" ,texlive-fonts-cm) ("texlive-fonts-latex" ,texlive-fonts-latex) @@ -1233,7 +1233,7 @@ verbatim source).") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "07azyn0b1s49vbdlr6dmygrminxp72ndl24j1091hiiccvrjq3xc")))) + "0nlfhn55ax89rcvpkrl9570671b62kcr4c9l5ch3w5zw9vmi00dz")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/graphics" @@ -1282,7 +1282,7 @@ verbatim source).") "-checkout")) (sha256 (base32 - "0gi4qv6378nl84s8n1yx3hjqvv7r4lza7hpbymbl5rzwgw8qrnyb")))))) + "17zpcgrfsr29g1dkz9np1qi63kjv7gb12rg979c6dai6qksbr3vq")))))) (home-page "https://www.ctan.org/pkg/latex-graphics") (synopsis "LaTeX standard graphics bundle") (description @@ -1358,7 +1358,7 @@ pdf and HTML backends. The package is distributed with the @code{backref} and (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0aswvsxgsn709xmvpcg50d2xl7vcy1ckdxb9c1cligqqfjjvviqf")))) + "1m9fg8ddhpsl1212igr9a9fmj012lv780aghjn6fpidg2wqrffmn")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/oberdiek" @@ -1389,7 +1389,7 @@ arrows; record information about document class(es) used; and many more.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "052a0pch2k5zls5jlay9xxcf93rw3i60a2x28y3ip3rhbsv3xgiz")))) + "0vj7h1fgf1396h4qjdc2m07y08i54gbbfrxl8y327cn3r1n093s6")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/tools" @@ -1455,7 +1455,7 @@ of file names.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0r0wfk594j8wkdqhh21haimwsfq8x5jch4ldm21hkzk5dnmvpbg6")))) + "0p3fsxap1ilwjz356aq4s5ygwvdscis8bh93g8klf8mhrd8cr2jy")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/l3kernel")) @@ -1479,7 +1479,7 @@ that the LaTeX3 conventions can be used with regular LaTeX 2e packages.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "16jplkvzdysfssijq9l051nsks65c2nrarsl17k8gjhc28yznj8y")))) + "0pyx0hffiyss363vv7fkrcdiaf7p099xnq0mngzqc7v8v9q849hs")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/l3packages" @@ -1534,11 +1534,10 @@ programming tools and kernel sup­port. Packages provided in this release are: (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1rx43y5xmjqvc27pjdnmqwp4pcw3czcfd6nfpmzc1gnqfl1hlc0q")))) + "1p0mkn6iywl0k4m9cx3hnhylpi499inisff3f72pcf349baqsnvq")))) (build-system texlive-build-system) (arguments - '(#:tex-directory "latex/fontspec" - #:build-targets '("fontspec.dtx"))) + '(#:tex-directory "latex/fontspec")) (inputs `(("texlive-latex-l3kernel" ,texlive-latex-l3kernel))) (home-page "https://www.ctan.org/pkg/fontspec") @@ -1598,7 +1597,7 @@ this bundle for use independent of ConTeXt.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "178ywjpdlv78qmfzqdyn6gy14620zjsn2q9wap76fbr9s4hw6dba")))) + "0arvk7gn32mshnfdad5qkgf3i1arxq77k3vq7wnpm4nwnrzclxal")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/amsmath")) (home-page "https://www.ctan.org/pkg/amsmath") @@ -1627,7 +1626,7 @@ definitions.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0jmcr37mcdi7drczppvr6lmz5d5yd9m67ii79gp2nglg1xpw934j")))) + "0c2j9xh4qpi0x1vvcxdjxq6say0zhyr569fryi5cmhp8bclh4kca")))) (build-system texlive-build-system) (arguments `(#:tex-directory "latex/amscls")) @@ -1651,7 +1650,7 @@ distribution.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1n3i5adsyy7jw0imnzrm2i8wkf73i3mjk9h3ic8cb9cd19i4r9r3")))) + "0yhlfiz3fjc8jd46f1zrjj4jig48l8rrzh8cmd8ammml8z9a01z6")))) (build-system texlive-build-system) (arguments '(#:tex-directory "generic/babel" @@ -1708,7 +1707,7 @@ for Canadian and USA text.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1mdhl35hwas68ki56qqngzar37dwv4mm64l2canihr255bz34lbv")))) + "083xbwg7hrnlv47fkwvz8yjb830bhxx7y0mq7z7nz2f96y2ldr6b")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/cyrillic")) @@ -1942,6 +1941,13 @@ ipsum\" text, see the @code{lipsum} package).") (add-after 'unpack 'remove-generated-file (lambda _ (delete-file "dinbrief.drv") + #t)) + (add-after 'unpack 'fix-encoding-error + (lambda _ + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* "dinbrief.dtx" + (("zur Verf.+ung. In der Pr\"aambel") + "zur Verf\"ung. In der Pr\"aambel"))) #t))))) (home-page "https://www.ctan.org/pkg/dinbrief") (synopsis "German letter DIN style") @@ -2012,7 +2018,7 @@ define a new author interface to creating new environments.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0pvmhsd4xmpil0m3c7qcgwilbk266mlkzv03g0jr8r3zd8jxlyzq")))) + "1ib5xdwcj5wk23wgk41m2hdcjr1dzrs4l3wwnpink9mlapz12wjs")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/eqparbox")) (home-page "https://www.ctan.org/pkg/eqparbox") @@ -2110,7 +2116,7 @@ but non-expandable ones.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "11gvvjvmdfs9b7mm19yf80zwkx49jqcbq6g8qb9y5ns1r1qvnixp")))) + "157pplavvm2z97b3jl4x41w11k6q9wgy074mfg0dwmsx5lm328jy")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/ifplatform")) (home-page "https://www.ctan.org/pkg/ifplatform") @@ -2174,34 +2180,70 @@ with a user specified LaTeX construction, properly aligned, scaled, and/or rotated.") (license (license:fsf-free "file://psfrag.dtx")))) +(define-public texlive-latex-xkeyval + (package + (name "texlive-latex-xkeyval") + (version (number->string %texlive-revision)) + (source (origin + (method svn-fetch) + (uri (texlive-ref "latex" "xkeyval")) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0wancavix39j240pd8m9cgmwsijwx6jd6n54v8wg0x2rk5m44myp")))) + (build-system texlive-build-system) + (arguments '(#:tex-directory "latex/xkeyval")) + (home-page "https://www.ctan.org/pkg/xkeyval") + (synopsis "Macros for defining and setting keys") + (description + "This package is an extension of the @code{keyval} package and offers +more flexible macros for defining and setting keys. The package provides a +pointer and a preset system. Furthermore, it supplies macros to allow class +and package options to contain options of the @code{key=value} form. A LaTeX +kernel patch is provided to avoid premature expansions of macros in class or +package options. A specialized system for setting @code{PSTricks} keys is +provided by the @code{pst-xkey} package.") + (license license:lppl1.3+))) + (define-public texlive-latex-pstool (package (name "texlive-latex-pstool") (version (number->string %texlive-revision)) (source (origin (method svn-fetch) - (uri (texlive-ref "latex" "pstool")) + (uri (svn-reference + (url (string-append "svn://www.tug.org/texlive/tags/" + %texlive-tag "/Master/texmf-dist/" + "/tex/latex/pstool")) + (revision %texlive-revision))) (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1kwlk1x67lad4xb7gpkxqgdlxwpi6nvq1r9wika7m92abmyf18h3")))) - (build-system texlive-build-system) + "1h816jain8c9nky75kk8pmmwj5b4yf9dpqvdvi2l6jhfj5iqkzr8")))) + (build-system trivial-build-system) (arguments - '(#:tex-directory "latex/pstool" - #:tex-format "latex")) - (inputs - `(("texlive-fonts-cm" ,texlive-fonts-cm) - ("texlive-latex-filecontents" ,texlive-latex-filecontents))) + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/tex/latex/pstool"))) + (mkdir-p target) + (copy-recursively (assoc-ref %build-inputs "source") target) + #t)))) (propagated-inputs - `(("texlive-latex-bigfoot" ,texlive-latex-bigfoot) + `(("texlive-latex-bigfoot" ,texlive-latex-bigfoot) ; for suffix ("texlive-latex-filemod" ,texlive-latex-filemod) ("texlive-latex-graphics" ,texlive-latex-graphics) ("texlive-latex-ifplatform" ,texlive-latex-ifplatform) + ("texlive-latex-l3kernel" ,texlive-latex-l3kernel) ; for expl3 ("texlive-latex-oberdiek" ,texlive-latex-oberdiek) ("texlive-latex-psfrag" ,texlive-latex-psfrag) - ("texlive-latex-trimspaces" ,texlive-latex-trimspaces))) + ("texlive-latex-tools" ,texlive-latex-tools) ; for shellesc + ("texlive-latex-trimspaces" ,texlive-latex-trimspaces) + ("texlive-latex-xkeyval" ,texlive-latex-xkeyval))) (home-page "https://www.ctan.org/pkg/pstool") - (synopsis "Process PostScript graphisc within pdfLaTeX documents") + (synopsis "Process PostScript graphics within pdfLaTeX documents") (description "This is a package for processing PostScript graphics with @code{psfrag} labels within pdfLaTeX documents. Every graphic is compiled individually, @@ -2356,7 +2398,7 @@ hyperlink to the target of the DOI.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0016bscnpima9krrg2569mva78xzwnygzlvg87dznsm6gf8g589v")))) + "1agmq6bf8wzcd77n20ng8bl4kh69cg5f6sjniii7bcw4llhd3nc8")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -2538,7 +2580,7 @@ BibLaTeX, and is considered experimental.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1r2kfcwclg33yk5z8mvlagwxj7nr1mc3w4bdpmhrwv6dn8mrbvw8")))) + "0yw6bjfgsli3s1dldsgb7mkr7lnk329cgdjbgs8z2xn59pmmdsn4")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/geometry")) (home-page "https://www.ctan.org/pkg/geometry") @@ -2587,7 +2629,7 @@ array environments; verbatim handling; and syntax diagrams.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "09mvszd5qgqg4cfglpj5qxyzjz190ppb9p8gnsnjydwp1akvhayf")))) + "03ma58z3ypsbp7zgkzb1ylpn2ygr27cxzkf042ns0rif4g8s491f")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/polyglossia")) (home-page "https://www.ctan.org/pkg/polyglossia") @@ -2633,7 +2675,7 @@ situations where longtable has problems.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "09zj2w3lx0y6i2syfjjgizahf86z301dw8p37ln6syfhqhzqdz46")))) + "06cf821y1j7jdg93pb41ayigrfwgn0y49d7w1025zlijjxi6bvjp")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -2750,7 +2792,7 @@ command.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1ik4m8pzfsn1grlda6fniqqfwmgj7rfxwg63jdw0p0qv002vc7ik")))) + "05x15ilynqrl448h8l6qiraygamdldlngz89a2bw7kg74fym14ch")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/changebar")) (home-page "https://www.ctan.org/pkg/changebar") @@ -2866,7 +2908,7 @@ floats, center, flushleft, and flushright, lists, and pages.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "04h430agf8aj7ziwyb46xpk95c605rjk1wzhr63m6ylipihidlgw")))) + "1xsnzx7vgdfh9zh2m7bjz6bgdpxsgb1kyc19p50vhs34x5nbgsnr")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -3284,7 +3326,7 @@ entry at the \"natural\" width of its text.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0m29q9qdb00558b7g2i7iw6w62n5s46yx81j8m99qkv77magk4fm")))) + "1rpx4ibjncj5416rg19v0xjbj3z9avhfdfn2gzp8r8sz9vz25c6g")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -3350,7 +3392,7 @@ designed class) helps alleviate this untidiness.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "06p5smfq66559ppdnmkl3hp8534x84ywbscimsiir4gllpya3i9h")))) + "0s4izcah7im67889qz4d26pcfpasmm35sj1rw4ragkkdk3rlbbbd")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/pdfpages")) (home-page "https://www.ctan.org/pkg/pdfpages") @@ -3764,7 +3806,7 @@ OT2 encoded fonts, CM bright shaped fonts and Concrete shaped fonts.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "03nvjddffiz796wll6axzmgfvynyciy2mqamv20qx252w71vwkwd")))) + "0sf18pc6chgy26p9bxxn44xcqhzjrfb53jxjr2y7l3jb6xllhblq")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -3944,7 +3986,7 @@ package of that name now exists.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0j6fff6q0ca96nwfdgay2jm55792z4q9aa0rczmiw2qccyg5n2dv")))) + "1hpsk4yp08qvbl43kqiv0hhwxv3gcqqxcpahyv6ch2b38pbj4bh6")))) (build-system texlive-build-system) (arguments '(#:tex-directory "latex/preview" @@ -4031,7 +4073,7 @@ e-TeX.") (file-name (string-append name "-map-" version "-checkout")) (sha256 (base32 - "197z9kx3bpnz58f5xrn5szyvmb3fxqq12y5sc4dw4jnm3xll8ji2")))))) + "18jvcm0vwpg6wwzijvnb92xx78la45kkh71k6l44425krp2vnwm0")))))) (home-page "https://www.ctan.org/pkg/pdftex") (synopsis "TeX extension for direct creation of PDF") (description @@ -4511,7 +4553,7 @@ required: automatic sectioning and pagination, spell checking and so forth.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "01ysky8h8s6q12dxfahkzwhbkc9j5wl50xzcczy0cbjx9f6aj9kv")))) + "0lhb2h5hxjq9alpk4r3gvg21pwyifs4ah6hqzp92k55mkp1xv73j")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -4551,7 +4593,7 @@ specification. It replaces the now obsolete @code{movie15} package.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "12kkl7n534j0p4frwyrlw22dc3ik50kxv97cxp4xpmji13m0hxpf")))) + "0zp00jg058djx8xp0xqwas92y3j97clkyd8z6pqr890yqy06myqb")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -4781,7 +4823,7 @@ produce either PostScript or PDF output.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1g8qg796hc6s092islnybaxs115ldsqwp2vxkk3gpy6vh7wc9r50")))) + "0nqwf0sr4mf3v9gqa6apv6ml2xhcdwax0vgyf12a672g7rpdyvgm")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils) @@ -4841,7 +4883,7 @@ typearea (which are the main parts of the bundle).") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1k50z6ixgwwzy84mi0dr5vcjah5p7wvgq66y45bilm91a4m8sgla")))) + "0hs28fc0v2l92ad9las9b8xcckyrdrwmyhcx1yzmbr6s7s6nvsx8")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -5107,7 +5149,7 @@ TeX).") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1gk9q22fcb2fa1ql6cf9yw505x6a6axdzzfxbsya7nkrph860af8")))) + "0hnbs0s1znbn32hfcsyijl39z81sdb00jf092a4blqz421qs2mbv")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -5211,7 +5253,7 @@ for use with LaTeX is available in @code{freenfss}, part of (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0zwl0cg6pka13i26dpqh137391f3j9sk69cpvwrm4ivsa0rqnw6g")))) + "0rlx4qqijms1n64gjx475kvip8l322fh7v17zkmwp1l1g0w3vlyz")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) diff --git a/guix/build-system/texlive.scm b/guix/build-system/texlive.scm index 80882b144b..b6a86a1c62 100644 --- a/guix/build-system/texlive.scm +++ b/guix/build-system/texlive.scm @@ -39,9 +39,10 @@ ;; ;; Code: -;; These variables specify the SVN tag and the matching SVN revision. -(define %texlive-tag "texlive-2017.1") -(define %texlive-revision 44591) +;; These variables specify the SVN tag and the matching SVN revision. They +;; are taken from https://www.tug.org/svn/texlive/tags/ +(define %texlive-tag "texlive-2018.2") +(define %texlive-revision 49435) (define (texlive-ref component id) "Return a object for the package ID, which is part of the From ac5c9f6ba6e80f9e7255442a4e0f0f3aeb2960d5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 10 Jan 2019 22:41:23 +0100 Subject: [PATCH 123/300] build-system: texlive: Do not truncate lines. * guix/build/texlive-build-system.scm (configure): Set environment variables to prevent build output lines from being truncated. --- guix/build/texlive-build-system.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/guix/build/texlive-build-system.scm b/guix/build/texlive-build-system.scm index 1c393ecd9d..a7cb8dd1ad 100644 --- a/guix/build/texlive-build-system.scm +++ b/guix/build/texlive-build-system.scm @@ -60,7 +60,12 @@ (("^TEXMF = .*") "TEXMF = $TEXMFROOT/share/texmf-dist\n")) (setenv "TEXMFCNF" (dirname texmf.cnf)) - (setenv "TEXMF" (string-append out "/share/texmf-dist"))) + (setenv "TEXMF" (string-append out "/share/texmf-dist")) + + ;; Don't truncate lines. + (setenv "error_line" "254") ; must be less than 255 + (setenv "half_error_line" "238") ; must be less than error_line - 15 + (setenv "max_print_line" "1000")) (mkdir "build") #t) From bf6fb59a3372a23244f84298e8432195cb8f729b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 10 Jan 2019 22:42:17 +0100 Subject: [PATCH 124/300] build-system: texlive: Do not hide build output. * guix/build/texlive-build-system.scm (compile-with-latex): Use "nonstopmode" instead of "batchmode". --- guix/build/texlive-build-system.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/build/texlive-build-system.scm b/guix/build/texlive-build-system.scm index a7cb8dd1ad..841c631dae 100644 --- a/guix/build/texlive-build-system.scm +++ b/guix/build/texlive-build-system.scm @@ -35,7 +35,7 @@ (define (compile-with-latex format file) (invoke format - "-interaction=batchmode" + "-interaction=nonstopmode" "-output-directory=build" (string-append "&" format) file)) From adf0b482ebe56e763a8dfed8a60d9451c8475bb7 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 10 Jan 2019 16:21:44 -0500 Subject: [PATCH 125/300] gnu: gexiv2: Update to 0.10.10. * gnu/packages/gnome.scm (gexiv2): Update to 0.10.10. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 12a0abdc56..ffd84cd78d 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4433,7 +4433,7 @@ classes for commonly used data structures.") (define-public gexiv2 (package (name "gexiv2") - (version "0.10.8") + (version "0.10.10") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -4441,7 +4441,7 @@ classes for commonly used data structures.") name "-" version ".tar.xz")) (sha256 (base32 - "0088m7p044n741ly1m6i7w25z513h9wpgyw0rmx5f0sy3vyjiic1")))) + "1qbcwq89g4r67k1dj4laqj441pj4195c8hzhxn8vc6mmg8adg6kx")))) (build-system meson-build-system) (native-inputs `(("glib" ,glib "bin") From 9757b57f4efd13b2fcf5277145231288770d46d0 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 11 Jan 2019 02:53:28 +0100 Subject: [PATCH 126/300] services: docker: Update comment. * gnu/services/docker.scm (docker-shepherd-service): Update comment. --- gnu/services/docker.scm | 1 - 1 file changed, 1 deletion(-) diff --git a/gnu/services/docker.scm b/gnu/services/docker.scm index c84c887612..09fe3cc1c3 100644 --- a/gnu/services/docker.scm +++ b/gnu/services/docker.scm @@ -70,7 +70,6 @@ (shepherd-service (documentation "Docker daemon.") (provision '(dockerd)) - ;; Note: elogind is required because it's mounting the cgroups. (requirement '(containerd file-system-/sys/fs/cgroup/blkio file-system-/sys/fs/cgroup/cpu From e7c6bc45ed440fd895b03b60878cb75ca8dea2f2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 11 Jan 2019 06:08:00 +0100 Subject: [PATCH 127/300] gnu: jamm: Remove broken "build" phase. * gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase. --- gnu/packages/bioinformatics.scm | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 58ba2f05d6..433d322b08 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14217,12 +14217,7 @@ absolute GSEA.") #:phases (modify-phases %standard-phases (delete 'configure) - (replace 'build - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* "JAMM.sh" - (("^sPath=.*") - (string-append ""))) - #t)) + (delete 'build) (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) From cb2ad4f5083d098ec92536643d1ec23ceca8a2ab Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Fri, 11 Jan 2019 10:59:01 +0100 Subject: [PATCH 128/300] gnu: wine-staging: Hard-code vulkan loader. * gnu/packages/wine.scm (wine-staging-patchset-data): Fix indentation. * gnu/packages/wine.scm (wine-staging)[arguments]: Add 'wrap-executable phase. * gnu/packages/wine.scm (wine64-staging)[arguments]: Add 'wrap-executable phase. Copy the real wine-preloader instead of the wrapped version. --- gnu/packages/wine.scm | 138 +++++++++++++++++++++++++++++------------- 1 file changed, 95 insertions(+), 43 deletions(-) diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm index 17e0b853e0..b0cba94c00 100644 --- a/gnu/packages/wine.scm +++ b/gnu/packages/wine.scm @@ -224,48 +224,48 @@ integrate Windows applications into your desktop.") (define-public wine-staging-patchset-data (package - (name "wine-staging-patchset-data") - (version "4.0-rc5") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/wine-staging/wine-staging") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0smp6ngs77vk1yg0saavhhn7kmi9ri8y8gc3vcgg837ycwg5i5qb")))) - (build-system trivial-build-system) - (native-inputs - `(("bash" ,bash) - ("coreutils" ,coreutils))) - (arguments - `(#:modules ((guix build utils)) - #:builder - (begin - (use-modules (guix build utils)) - (let* ((build-directory ,(string-append name "-" version)) - (source (assoc-ref %build-inputs "source")) - (bash (assoc-ref %build-inputs "bash")) - (coreutils (assoc-ref %build-inputs "coreutils")) - (out (assoc-ref %outputs "out")) - (wine-staging (string-append out "/share/wine-staging"))) - (copy-recursively source build-directory) - (with-directory-excursion build-directory - (substitute* "patches/patchinstall.sh" - (("/bin/sh") - (string-append bash "/bin/sh"))) - (substitute* "patches/gitapply.sh" - (("/usr/bin/env") - (string-append coreutils "/bin/env")))) - (copy-recursively build-directory wine-staging) - #t)))) - (home-page "https://github.com/wine-staging") - (synopsis "Patchset for Wine") - (description - "wine-staging-patchset-data contains the patchset to build Wine-Staging.") - (license license:lgpl2.1+))) + (name "wine-staging-patchset-data") + (version "4.0-rc5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wine-staging/wine-staging") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0smp6ngs77vk1yg0saavhhn7kmi9ri8y8gc3vcgg837ycwg5i5qb")))) + (build-system trivial-build-system) + (native-inputs + `(("bash" ,bash) + ("coreutils" ,coreutils))) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((build-directory ,(string-append name "-" version)) + (source (assoc-ref %build-inputs "source")) + (bash (assoc-ref %build-inputs "bash")) + (coreutils (assoc-ref %build-inputs "coreutils")) + (out (assoc-ref %outputs "out")) + (wine-staging (string-append out "/share/wine-staging"))) + (copy-recursively source build-directory) + (with-directory-excursion build-directory + (substitute* "patches/patchinstall.sh" + (("/bin/sh") + (string-append bash "/bin/sh"))) + (substitute* "patches/gitapply.sh" + (("/usr/bin/env") + (string-append coreutils "/bin/env")))) + (copy-recursively build-directory wine-staging) + #t)))) + (home-page "https://github.com/wine-staging") + (synopsis "Patchset for Wine") + (description + "wine-staging-patchset-data contains the patchset to build Wine-Staging.") + (license license:lgpl2.1+))) (define-public wine-staging (package @@ -286,6 +286,7 @@ integrate Windows applications into your desktop.") ("ffmpeg" ,ffmpeg) ("gtk+" ,gtk+) ("libva" ,libva) + ("mesa" ,mesa) ("python" ,python) ("sdl2" ,sdl2) ("util-linux" ,util-linux) ; for hexdump @@ -296,6 +297,27 @@ integrate Windows applications into your desktop.") (arguments `(#:phases (modify-phases %standard-phases + ;; Explicitely set the 32-bit version of vulkan-loader when installing + ;; to i686-linux or x86_64-linux. + ;; TODO: Add more JSON files as they become available in Mesa. + ,@(match (%current-system) + ((or "i686-linux" "x86_64-linux") + `((add-after 'install 'wrap-executable + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (icd (string-append out "/share/vulkan/icd.d"))) + (mkdir-p icd) + (copy-file (string-append (assoc-ref inputs "mesa") + "/share/vulkan/icd.d/radeon_icd.i686.json") + (string-append icd "/radeon_icd.i686.json")) + (wrap-program (string-append out "/bin/wine-preloader") + `("VK_ICD_FILENAMES" ":" = + (,(string-append icd + "/radeon_icd.i686.json")))) + #t))))) + (_ + `()) + ) (add-before 'configure 'patch-source-wine-staging (lambda* (#:key outputs #:allow-other-keys) (let* ((source (assoc-ref %build-inputs "source")) @@ -344,6 +366,34 @@ integrated into the main branch.") (string-append "libdir=" %output "/lib/wine64")) #:phases (modify-phases %standard-phases + ;; Explicitely set both the 64-bit and 32-bit versions of vulkan-loader + ;; when installing to x86_64-linux so both are available. + ;; TODO: Add more JSON files as they become available in Mesa. + ,@(match (%current-system) + ((or "x86_64-linux") + `((add-after 'copy-wine32-binaries 'wrap-executable + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/wine-preloader") + `("VK_ICD_FILENAMES" ":" = + (,(string-append (assoc-ref inputs "mesa") + "/share/vulkan/icd.d/radeon_icd.x86_64.json" ":" + (assoc-ref inputs "mesa") + "/share/vulkan/icd.d/intel_icd.x86_64.json" ":" + (assoc-ref inputs "wine-staging") + "/share/vulkan/icd.d/radeon_icd.i686.json")))) + (wrap-program (string-append out "/bin/wine64-preloader") + `("VK_ICD_FILENAMES" ":" = + (,(string-append (assoc-ref inputs "mesa") + "/share/vulkan/icd.d/radeon_icd.x86_64.json" + ":" (assoc-ref inputs "mesa") + "/share/vulkan/icd.d/intel_icd.x86_64.json" + ":" (assoc-ref inputs "wine-staging") + "/share/vulkan/icd.d/radeon_icd.i686.json")))) + #t))))) + (_ + `()) + ) (add-before 'configure 'patch-source-wine-staging (lambda* (#:key outputs #:allow-other-keys) (let* ((source (assoc-ref %build-inputs "source")) @@ -359,7 +409,9 @@ integrated into the main branch.") ;; Copy the 32-bit binaries needed for WoW64. (copy-file (string-append wine32 "/bin/wine") (string-append out "/bin/wine")) - (copy-file (string-append wine32 "/bin/wine-preloader") + ;; Copy the real 32-bit wine-preloader instead of the wrapped + ;; version. + (copy-file (string-append wine32 "/bin/.wine-preloader-real") (string-append out "/bin/wine-preloader")) #t))) (add-after 'compress-documentation 'copy-wine32-manpage From babfd9447df08a809622238b4830eb046dab2ba6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 10 Jan 2019 23:30:43 +0100 Subject: [PATCH 129/300] tests: Nitpick on Docker test. This is a followup to 7d8a4eeacc534c8742e0b22d855aa73e5ab66b7f. * gnu/local.mk (GNU_SYSTEM_MODULES): Add gnu/tests/docker.scm. * gnu/tests/docker.scm: Update copyright line. --- gnu/local.mk | 3 ++- gnu/tests/docker.scm | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/local.mk b/gnu/local.mk index 7c319b727f..306cfa3a62 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1,5 +1,5 @@ # GNU Guix --- Functional package management for GNU -# Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +# Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès # Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Andreas Enge # Copyright © 2016 Mathieu Lirzin # Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Mark H Weaver @@ -542,6 +542,7 @@ GNU_SYSTEM_MODULES = \ %D%/tests/databases.scm \ %D%/tests/desktop.scm \ %D%/tests/dict.scm \ + %D%/tests/docker.scm \ %D%/tests/monitoring.scm \ %D%/tests/nfs.scm \ %D%/tests/install.scm \ diff --git a/gnu/tests/docker.scm b/gnu/tests/docker.scm index 973a84c558..453ed4893d 100644 --- a/gnu/tests/docker.scm +++ b/gnu/tests/docker.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017 Christopher Baines +;;; Copyright © 2019 Danny Milosavljevic ;;; ;;; This file is part of GNU Guix. ;;; From 84a2de36a10dc2ab80f86e16721cbd228c85279e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 10 Jan 2019 23:33:36 +0100 Subject: [PATCH 130/300] services: Deprecate a few more service procedures. These procedures were already either undocumented (and de facto deprecated) or documented as deprecated or redundant. * gnu/services/base.scm (guix-service, guix-publish-service): Mark as deprecated. * gnu/services/mcron.scm (mcron-service): Likewise. * gnu/services/networking.scm (tor-service): Likewise. * doc/guix.texi (Scheduled Job Execution): Remove 'mcron-service' and adjust example. (Networking Services): Remove 'tor-service'. * gnu/tests/base.scm (%mcron-os): Use 'mcron-service-type' instead of 'mcron-service'. * gnu/tests/networking.scm (%tor-os): Use 'tor-service-type' instead of 'tor-service'. * tests/guix-system.sh: Likewise. --- doc/guix.texi | 25 +++++-------------------- gnu/services/base.scm | 8 ++++++-- gnu/services/mcron.scm | 6 ++++-- gnu/services/networking.scm | 7 ++++--- gnu/system/install.scm | 3 ++- gnu/tests/base.scm | 5 +++-- gnu/tests/networking.scm | 2 +- tests/guix-system.sh | 6 ++++-- 8 files changed, 29 insertions(+), 33 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index c0cc8d4169..ed7723c00b 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -11684,9 +11684,11 @@ gexps to introduce job definitions that are passed to mcron (operating-system ;; @dots{} - (services (cons (mcron-service (list garbage-collector-job - updatedb-job - idutils-job)) + (services (cons (service mcron-service-type + (mcron-configuration + (jobs (list garbage-collector-job + updatedb-job + idutils-job)))) %base-services))) @end lisp @@ -11709,17 +11711,6 @@ also specify the number of tasks to display: # herd schedule mcron 10 @end example -@deffn {Scheme Procedure} mcron-service @var{jobs} [#:mcron @var{mcron}] -Return an mcron service running @var{mcron} that schedules @var{jobs}, a -list of gexps denoting mcron job specifications. - -This is a shorthand for: -@example -(service mcron-service-type - (mcron-configuration (mcron mcron) (jobs jobs))) -@end example -@end deffn - @defvr {Scheme Variable} mcron-service-type This is the type of the @code{mcron} service, whose value is an @code{mcron-configuration} object. @@ -12313,12 +12304,6 @@ Tor} anonymous networking daemon. The service is configured using a @end defvr -@deffn {Scheme Procedure} tor-service [@var{config-file}] [#:tor @var{tor}] -This procedure is deprecated and will be removed in a future release. Return -a service of the @code{tor-service-type} type. @var{config-file} and -@var{tor} have the same meaning as in @code{}. -@end deffn - @deftp {Data Type} tor-configuration @table @asis @item @code{tor} (default: @code{tor}) diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 6e99cbfec4..8395a856fc 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -1688,7 +1688,9 @@ failed to register public key '~a': ~a~%" key status))))))) (description "Run the build daemon of GNU@tie{}Guix, aka. @command{guix-daemon}."))) -(define* (guix-service #:optional (config %default-guix-configuration)) +(define-deprecated (guix-service #:optional + (config %default-guix-configuration)) + guix-service-type "Return a service that runs the Guix build daemon according to @var{config}." (service guix-service-type config)) @@ -1789,7 +1791,9 @@ failed to register public key '~a': ~a~%" key status))))))) "Add a Shepherd service running @command{guix publish}, a command that allows you to share pre-built binaries with others over HTTP."))) -(define* (guix-publish-service #:key (guix guix) (port 80) (host "localhost")) +(define-deprecated (guix-publish-service #:key (guix guix) + (port 80) (host "localhost")) + guix-publish-service-type "Return a service that runs @command{guix publish} listening on @var{host} and @var{port} (@pxref{Invoking guix publish}). diff --git a/gnu/services/mcron.scm b/gnu/services/mcron.scm index 120b663e3e..e4b652b3d4 100644 --- a/gnu/services/mcron.scm +++ b/gnu/services/mcron.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -21,6 +21,7 @@ #:use-module (gnu services base) #:use-module (gnu services shepherd) #:autoload (gnu packages guile) (mcron) + #:use-module (guix deprecation) #:use-module (guix records) #:use-module (guix gexp) #:use-module (srfi srfi-1) @@ -142,7 +143,8 @@ files." jobs))))) (default-value (mcron-configuration)))) ;empty job list -(define* (mcron-service jobs #:optional (mcron mcron)) +(define-deprecated (mcron-service jobs #:optional (mcron mcron)) + mcron-service-type "Return an mcron service running @var{mcron} that schedules @var{jobs}, a list of gexps denoting mcron job specifications. diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index 2f49bf28dd..cab129e0c3 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -755,9 +755,10 @@ HiddenServicePort ~a ~a~%" "Run the @uref{https://torproject.org, Tor} anonymous networking daemon."))) -(define* (tor-service #:optional - (config-file (plain-file "empty" "")) - #:key (tor tor)) +(define-deprecated (tor-service #:optional + (config-file (plain-file "empty" "")) + #:key (tor tor)) + tor-service-type "Return a service to run the @uref{https://torproject.org, Tor} anonymous networking daemon. diff --git a/gnu/system/install.scm b/gnu/system/install.scm index c345ba0626..19a6f6a038 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -253,7 +253,8 @@ You have been warned. Thanks for being so brave.\x1b[0m ;; The build daemon. Register the official server keys as trusted. ;; This allows the installation process to use substitutes by ;; default. - (guix-service (guix-configuration (authorize-key? #t))) + (service guix-service-type + (guix-configuration (authorize-key? #t))) ;; Start udev so that useful device nodes are available. ;; Use device-mapper rules for cryptsetup & co; enable the CRDA for diff --git a/gnu/tests/base.scm b/gnu/tests/base.scm index 8d4e218a8f..2b20aac1dc 100644 --- a/gnu/tests/base.scm +++ b/gnu/tests/base.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2018 Clément Lassieur ;;; ;;; This file is part of GNU Guix. @@ -627,7 +627,8 @@ non-ASCII names from /tmp.") (job3 #~(job next-second-from ;to test $PATH "touch witness-touch"))) (simple-operating-system - (mcron-service (list job1 job2 job3))))) + (service mcron-service-type + (mcron-configuration (jobs (list job1 job2 job3))))))) (define (run-mcron-test name) (define os diff --git a/gnu/tests/networking.scm b/gnu/tests/networking.scm index 9f12a4ae8d..a97b29bc4b 100644 --- a/gnu/tests/networking.scm +++ b/gnu/tests/networking.scm @@ -351,7 +351,7 @@ subnet 192.168.1.0 netmask 255.255.255.0 { (define %tor-os (simple-operating-system - (tor-service))) + (service tor-service-type))) (define %tor-os/unix-socks-socket (simple-operating-system diff --git a/tests/guix-system.sh b/tests/guix-system.sh index 23d2da4903..adb623d244 100644 --- a/tests/guix-system.sh +++ b/tests/guix-system.sh @@ -1,5 +1,5 @@ # GNU Guix --- Functional package management for GNU -# Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +# Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès # Copyright © 2017 Tobias Geerinckx-Rice # Copyright © 2018 Chris Marusich # @@ -258,7 +258,9 @@ cat > "$tmpdir/config.scm"< Date: Sun, 6 Jan 2019 10:41:09 +0100 Subject: [PATCH 131/300] gnu: Add emacs-general. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit [[PGP Signed Part:Good signature from 31BC8105F659D425 Gabriel Hondet (trust undefined) created at 2019-01-06T10:42:43+0100 using RSA]] * gnu/packages/emacs.scm (emacs-general): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 6a0429aabc..3978d9ab6d 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -12907,3 +12907,34 @@ other frame parameters.") (description "Emacs major mode for editing Arduino sketches.") (home-page "https://github.com/bookest/arduino-mode") (license license:gpl3+)))) + +(define-public emacs-general + (let ((commit "675050199b5a30d54a24b58a367db32c0bdc47f5")) + (package + (name "emacs-general") + (version (git-version "0" "0" commit)) + (home-page "https://github.com/noctuid/general.el") + (source (origin + (method git-fetch) + (uri (git-reference + (url (string-append home-page ".git")) + (commit commit))) + (sha256 + (base32 + "175yyhzk57yk1sskxh3d2jzhrh2waiibbcfsll167qxr117yji5h")) + (file-name (git-file-name name version)))) + (build-system emacs-build-system) + (synopsis "More convenient key definitions in emacs") + (description "@code{general.el} provides a more convenient method for +binding keys in emacs (for both evil and non-evil users). Like +@code{use-package}, which provides a convenient, unified interface for +managing packages, @code{general.el} is intended to provide a convenient, +unified interface for key definitions. While this package does implement some +completely new functionality (such as the ability to make vim-style +keybindings under non-prefix keys with an optional timeout), its primary +purpose is to build on existing functionality to make key definition more +clear and concise. @code{general-define-key} is user-extensible and supports +defining multiple keys in multiple keymaps at once, implicitly wrapping key +strings with (@code{kbd ...}), using named prefix key sequences (like the +leader key in vim), and much more.") + (license license:gpl3+)))) From fca43e14f70c0536668981eb1aed9e46a42de935 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 11 Jan 2019 11:44:26 +0100 Subject: [PATCH 132/300] refresh: Refactor option handling and '--recursive'. This allows us to combine '--recursive' with other options (-u, -m, etc.), turns off warnings when '--recursive' is used, and avoids the hazards of I/O in the presence of multithreading. * guix/scripts/refresh.scm (options->packages): New procedure, with code formerly in 'guix-refresh'. (refresh-recursive): Remove. (guix-refresh)[keep-newest, core-package?, args-packages, packages]: Remove. [warn?]: Set to #f when RECURSIVE? is true. Call 'options->packages' in monadic context. --- guix/scripts/refresh.scm | 211 +++++++++++++++++++-------------------- 1 file changed, 104 insertions(+), 107 deletions(-) diff --git a/guix/scripts/refresh.scm b/guix/scripts/refresh.scm index 003c915da3..64019b6eb3 100644 --- a/guix/scripts/refresh.scm +++ b/guix/scripts/refresh.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2013 Nikita Karetnikov ;;; Copyright © 2014 Eric Bavier ;;; Copyright © 2015 Alex Kost @@ -41,7 +41,6 @@ #:use-module (ice-9 regex) #:use-module (ice-9 vlist) #:use-module (ice-9 format) - #:use-module (ice-9 threads) ; par-for-each #:use-module (srfi srfi-1) #:use-module (srfi srfi-11) #:use-module (srfi srfi-26) @@ -172,6 +171,79 @@ specified with `--select'.\n")) (newline) (show-bug-report-information)) +(define (options->packages opts) + "Return the list of packages requested by OPTS, honoring options like +'--recursive'." + (define core-package? + (let* ((input->package (match-lambda + ((name (? package? package) _ ...) package) + (_ #f))) + (final-inputs (map input->package %final-inputs)) + (core (append final-inputs + (append-map (compose (cut filter-map input->package <>) + package-transitive-inputs) + final-inputs))) + (names (delete-duplicates (map package-name core)))) + (lambda (package) + "Return true if PACKAGE is likely a \"core package\"---i.e., one whose +update would trigger a complete rebuild." + ;; Compare by name because packages in base.scm basically inherit + ;; other packages. So, even if those packages are not core packages + ;; themselves, updating them would also update those who inherit from + ;; them. + ;; XXX: Fails to catch MPFR/MPC, whose *source* is used as input. + (member (package-name package) names)))) + + (define (keep-newest package lst) + ;; If a newer version of PACKAGE is already in LST, return LST; otherwise + ;; return LST minus the other version of PACKAGE in it, plus PACKAGE. + (let ((name (package-name package))) + (match (find (lambda (p) + (string=? (package-name p) name)) + lst) + ((? package? other) + (if (version>? (package-version other) (package-version package)) + lst + (cons package (delq other lst)))) + (_ + (cons package lst))))) + + (define args-packages + ;; Packages explicitly passed as command-line arguments. + (match (filter-map (match-lambda + (('argument . spec) + ;; Take either the specified version or the + ;; latest one. + (specification->package spec)) + (('expression . exp) + (read/eval-package-expression exp)) + (_ #f)) + opts) + (() ;default to all packages + (let ((select? (match (assoc-ref opts 'select) + ('core core-package?) + ('non-core (negate core-package?)) + (_ (const #t))))) + (fold-packages (lambda (package result) + (if (select? package) + (keep-newest package result) + result)) + '()))) + (some ;user-specified packages + some))) + + (define packages + (match (assoc-ref opts 'manifest) + (#f args-packages) + ((? string? file) (packages-from-manifest file)))) + + (if (assoc-ref opts 'recursive?) + (mlet %store-monad ((edges (node-edges %bag-node-type + (all-packages)))) + (return (node-transitive-edges packages edges))) + (with-monad %store-monad + (return packages)))) + ;;; ;;; Updates. @@ -335,19 +407,6 @@ dependent packages are rebuilt: ~{~a~^ ~}~%" (map full-name covering)))) (return #t)))) -(define (refresh-recursive packages) - "Check all of the package inputs of PACKAGES for newer upstream versions." - (mlet %store-monad ((edges (node-edges %bag-node-type - ;; Here we don't want the -boot0 packages. - (fold-packages cons '())))) - (let ((dependent (node-transitive-edges packages edges))) - ;; par-for-each has an undefined return value, so packages which cause - ;; errors can be ignored. - (par-for-each (lambda (package) - (guix-refresh package)) - (map package-name dependent))) - (return #t))) - (define (list-transitive packages) "List all the packages that would cause PACKAGES to be rebuilt if they are changed." ;; Using %BAG-NODE-TYPE is more accurate than using %PACKAGE-NODE-TYPE @@ -414,40 +473,6 @@ all are dependent packages: ~{~a~^ ~}~%") (lists (concatenate lists)))) - (define (keep-newest package lst) - ;; If a newer version of PACKAGE is already in LST, return LST; otherwise - ;; return LST minus the other version of PACKAGE in it, plus PACKAGE. - (let ((name (package-name package))) - (match (find (lambda (p) - (string=? (package-name p) name)) - lst) - ((? package? other) - (if (version>? (package-version other) (package-version package)) - lst - (cons package (delq other lst)))) - (_ - (cons package lst))))) - - (define core-package? - (let* ((input->package (match-lambda - ((name (? package? package) _ ...) package) - (_ #f))) - (final-inputs (map input->package %final-inputs)) - (core (append final-inputs - (append-map (compose (cut filter-map input->package <>) - package-transitive-inputs) - final-inputs))) - (names (delete-duplicates (map package-name core)))) - (lambda (package) - "Return true if PACKAGE is likely a \"core package\"---i.e., one whose -update would trigger a complete rebuild." - ;; Compare by name because packages in base.scm basically inherit - ;; other packages. So, even if those packages are not core packages - ;; themselves, updating them would also update those who inherit from - ;; them. - ;; XXX: Fails to catch MPFR/MPC, whose *source* is used as input. - (member (package-name package) names)))) - (let* ((opts (parse-options)) (update? (assoc-ref opts 'update?)) (updaters (options->updaters opts)) @@ -458,65 +483,37 @@ update would trigger a complete rebuild." ;; Warn about missing updaters when a package is explicitly given on ;; the command line. - (warn? (or (assoc-ref opts 'argument) - (assoc-ref opts 'expression))) - (args-packages - (match (filter-map (match-lambda - (('argument . spec) - ;; Take either the specified version or the - ;; latest one. - (specification->package spec)) - (('expression . exp) - (read/eval-package-expression exp)) - (_ #f)) - opts) - (() ; default to all packages - (let ((select? (match (assoc-ref opts 'select) - ('core core-package?) - ('non-core (negate core-package?)) - (_ (const #t))))) - (fold-packages (lambda (package result) - (if (select? package) - (keep-newest package result) - result)) - '()))) - (some ; user-specified packages - some))) - (packages - (match (assoc-ref opts 'manifest) - (#f args-packages) - ((? string? file) (packages-from-manifest file))))) + (warn? (and (or (assoc-ref opts 'argument) + (assoc-ref opts 'expression)) + (not recursive?)))) (with-error-handling (with-store store (run-with-store store - (cond - (list-dependent? - (list-dependents packages)) - (list-transitive? - (list-transitive packages)) - (recursive? - (refresh-recursive packages)) - (update? - (parameterize ((%openpgp-key-server - (or (assoc-ref opts 'key-server) - (%openpgp-key-server))) - (%gpg-command - (or (assoc-ref opts 'gpg-command) - (%gpg-command))) - (current-keyring - (or (assoc-ref opts 'keyring) - (string-append (config-directory) - "/upstream/trustedkeys.kbx")))) - (for-each - (cut update-package store <> updaters - #:key-download key-download - #:warn? warn?) - packages) - (with-monad %store-monad - (return #t)))) - (else - (for-each (cut check-for-package-update <> updaters - #:warn? warn?) - packages) - (with-monad %store-monad + (mlet %store-monad ((packages (options->packages opts))) + (cond + (list-dependent? + (list-dependents packages)) + (list-transitive? + (list-transitive packages)) + (update? + (parameterize ((%openpgp-key-server + (or (assoc-ref opts 'key-server) + (%openpgp-key-server))) + (%gpg-command + (or (assoc-ref opts 'gpg-command) + (%gpg-command))) + (current-keyring + (or (assoc-ref opts 'keyring) + (string-append (config-directory) + "/upstream/trustedkeys.kbx")))) + (for-each + (cut update-package store <> updaters + #:key-download key-download + #:warn? warn?) + packages) + (return #t))) + (else + (for-each (cut check-for-package-update <> updaters + #:warn? warn?) + packages) (return #t))))))))) From 7489207ff788d6f4a9c2b9aec87c9835753dfd2f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 11 Jan 2019 11:49:03 +0100 Subject: [PATCH 133/300] refresh: Turn on warnings when '--manifest' is used. * guix/scripts/refresh.scm (guix-refresh): Set WARN? when '-m' is used. --- guix/scripts/refresh.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/guix/scripts/refresh.scm b/guix/scripts/refresh.scm index 64019b6eb3..516e09b4ce 100644 --- a/guix/scripts/refresh.scm +++ b/guix/scripts/refresh.scm @@ -484,7 +484,8 @@ all are dependent packages: ~{~a~^ ~}~%") ;; Warn about missing updaters when a package is explicitly given on ;; the command line. (warn? (and (or (assoc-ref opts 'argument) - (assoc-ref opts 'expression)) + (assoc-ref opts 'expression) + (assoc-ref opts 'manifest)) (not recursive?)))) (with-error-handling (with-store store From 7804c45b9ce5a8edd06452d828249e588ae26263 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 9 Jan 2019 11:25:11 +0100 Subject: [PATCH 134/300] status: Add 'with-status-verbosity'. * guix/status.scm (logger-for-level, call-with-status-verbosity): New procedures. (with-status-verbosity): New macro. * guix/scripts/environment.scm (guix-environment): Use 'with-status-verbosity' instead of 'with-status-report'. * guix/scripts/pack.scm (guix-pack): Likewise. * guix/scripts/package.scm (guix-package): Likewise. * guix/scripts/pull.scm (guix-pull): Likewise. * guix/scripts/system.scm (guix-system): Likewise. * build-aux/run-system-tests.scm (run-system-tests): Likewise. --- .dir-locals.el | 1 + build-aux/run-system-tests.scm | 4 ++-- guix/scripts/environment.scm | 4 ++-- guix/scripts/pack.scm | 2 +- guix/scripts/package.scm | 4 ++-- guix/scripts/pull.scm | 2 +- guix/scripts/system.scm | 7 +++---- guix/status.scm | 17 ++++++++++++++++- 8 files changed, 28 insertions(+), 13 deletions(-) diff --git a/.dir-locals.el b/.dir-locals.el index 1a3a05f100..593c767d2b 100644 --- a/.dir-locals.el +++ b/.dir-locals.el @@ -61,6 +61,7 @@ (eval . (put 'with-derivation-narinfo 'scheme-indent-function 1)) (eval . (put 'with-derivation-substitute 'scheme-indent-function 2)) (eval . (put 'with-status-report 'scheme-indent-function 1)) + (eval . (put 'with-status-verbosity 'scheme-indent-function 1)) (eval . (put 'mlambda 'scheme-indent-function 1)) (eval . (put 'mlambdaq 'scheme-indent-function 1)) diff --git a/build-aux/run-system-tests.scm b/build-aux/run-system-tests.scm index 953ba3e221..bcd7547704 100644 --- a/build-aux/run-system-tests.scm +++ b/build-aux/run-system-tests.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2018 Ludovic Courtès +;;; Copyright © 2016, 2018, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -64,7 +64,7 @@ (length tests)) (with-store store - (with-status-report print-build-event + (with-status-verbosity 2 (run-with-store store (mlet* %store-monad ((drv (mapm %store-monad system-test-value tests)) (out -> (map derivation->output-path drv))) diff --git a/guix/scripts/environment.scm b/guix/scripts/environment.scm index 86e1eb115f..9461d04976 100644 --- a/guix/scripts/environment.scm +++ b/guix/scripts/environment.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2018 David Thompson -;;; Copyright © 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2018 Mike Gerwitz ;;; ;;; This file is part of GNU Guix. @@ -674,7 +674,7 @@ message if any test fails." (leave (G_ "'--user' cannot be used without '--container'~%"))) (with-store store - (with-status-report print-build-event + (with-status-verbosity 1 (define manifest (options/resolve-packages store opts)) diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm index e137fb136a..d9e0050159 100644 --- a/guix/scripts/pack.scm +++ b/guix/scripts/pack.scm @@ -772,7 +772,7 @@ Create a bundle of PACKAGE.\n")) (with-error-handling (with-store store - (with-status-report print-build-event + (with-status-verbosity 2 ;; Set the build options before we do anything else. (set-build-options-from-command-line store opts) diff --git a/guix/scripts/package.scm b/guix/scripts/package.scm index 5743816324..876787fbe2 100644 --- a/guix/scripts/package.scm +++ b/guix/scripts/package.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2013 Nikita Karetnikov ;;; Copyright © 2013, 2015 Mark H Weaver ;;; Copyright © 2014, 2016 Alex Kost @@ -914,7 +914,7 @@ processed, #f otherwise." (or (process-query opts) (parameterize ((%store (open-connection)) (%graft? (assoc-ref opts 'graft?))) - (with-status-report print-build-event/quiet + (with-status-verbosity 1 (set-build-options-from-command-line (%store) opts) (parameterize ((%guile-for-build (package-derivation diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm index e7ff44c0d5..6389d5ec09 100644 --- a/guix/scripts/pull.scm +++ b/guix/scripts/pull.scm @@ -510,7 +510,7 @@ Use '~/.config/guix/channels.scm' instead.")) (process-query opts profile)) (else (with-store store - (with-status-report print-build-event + (with-status-verbosity 2 (parameterize ((%current-system (assoc-ref opts 'system)) (%graft? (assoc-ref opts 'graft?)) (%repository-cache-directory cache)) diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm index 6cda3ccbd6..9e31baaddb 100644 --- a/guix/scripts/system.scm +++ b/guix/scripts/system.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès +;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2016 Alex Kost ;;; Copyright © 2016, 2017, 2018 Chris Marusich ;;; Copyright © 2017 Mathieu Othacehe @@ -1267,9 +1267,8 @@ argument list and OPTS is the option alist." (args (option-arguments opts)) (command (assoc-ref opts 'action))) (parameterize ((%graft? (assoc-ref opts 'graft?))) - (with-status-report (if (memq command '(init reconfigure)) - print-build-event/quiet - print-build-event) + (with-status-verbosity (if (memq command '(init reconfigure)) + 1 2) (process-command command args opts)))))) ;;; Local Variables: diff --git a/guix/status.scm b/guix/status.scm index 1a7cb313ea..2928733257 100644 --- a/guix/status.scm +++ b/guix/status.scm @@ -63,7 +63,8 @@ print-build-event/quiet print-build-status - with-status-report)) + with-status-report + with-status-verbosity)) ;;; Commentary: ;;; @@ -649,3 +650,17 @@ The second return value is a thunk to retrieve the current state." "Set up build status reporting to the user using the ON-EVENT procedure; evaluate EXP... in that context." (call-with-status-report on-event (lambda () exp ...))) + +(define (logger-for-level level) + "Return the logging procedure that corresponds to LEVEL." + (cond ((<= level 0) (const #t)) + ((= level 1) print-build-event/quiet) + (else print-build-event))) + +(define (call-with-status-verbosity level thunk) + (call-with-status-report (logger-for-level level) thunk)) + +(define-syntax-rule (with-status-verbosity level exp ...) + "Set up build status reporting to the user at the given LEVEL: 0 means +silent, 1 means quiet, 2 means verbose. Evaluate EXP... in that context." + (call-with-status-verbosity level (lambda () exp ...))) From f1de676ea82c2bed9a435fce37ade0186296bfc9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 9 Jan 2019 14:17:19 +0100 Subject: [PATCH 135/300] guix build: Re-purpose '--verbosity' and add '--debug'. The previous '--verbosity' option was misleading and rarely what users were looking for. The new option provides a consistent way to choose whether or not to display the build log. * guix/scripts/build.scm (show-build-options-help): Remove "--verbosity" and add "--debug". (set-build-options-from-command-line): Use the 'debug key of OPTS for #:verbosity. (%standard-build-options): Change "verbosity" to "debug". Use 'string->number*' instead of 'string->number'. (%default-options): Change 'verbosity to 'debug and add a 'verbosity key. (show-help): Add '--verbosity'. (%options): Likewise, and change '--quiet' to set the 'verbosity key of RESULT. (guix-build): Use 'with-status-verbosity' instead of parameterizing CURRENT-BUILD-OUTPUT-PORT, honor the 'verbosity key of OPTS, and remove 'quiet?'. * guix/scripts/environment.scm (show-help, %options): Add '--verbosity'. (%default-options): Add 'debug'. (guix-environment): Honor the 'verbosity key of OPTS. * guix/scripts/pack.scm (%default-options): Add 'debug. (%options, show-help): Add '--verbosity'. (guix-pack): Honor the 'verbosity key of OPTS. * guix/scripts/package.scm (%default-options): Add 'debug. (show-help, %options): Add '--verbosity'. Mark '--verbose' as deprecated and change it to set 'verbosity. (guix-package): Honor the 'verbosity key of OPTS and remove 'verbose?'. * guix/scripts/pull.scm (%default-options): Add 'debug. (show-help, %options): Add '--verbosity'. (guix-pull): Honor the 'verbosity key of OPTS. * guix/scripts/system.scm (show-help, %options): Add '--verbosity'. (%default-options): Add 'debug. (guix-system): Honor the 'verbosity key of OPTS. * guix/scripts/archive.scm (%default-options): Add 'debug, 'print-build-trace?, 'print-extended-build-trace?, and 'multiplexed-build-output?. (show-help, %options): Add '--verbosity'. (export-from-store): Remove call to 'set-build-options-from-command-line'. (guix-archive): Wrap body in 'with-status-verbosity'. Add call to 'set-build-options-from-command-line. * doc/guix.texi (Common Build Options): Document '--verbosity' and '--debug'. (Additional Build Options): Adjust description of '--quiet'. --- doc/guix.texi | 28 +++++--- guix/scripts/archive.scm | 55 ++++++++------ guix/scripts/build.scm | 134 ++++++++++++++++++----------------- guix/scripts/environment.scm | 12 +++- guix/scripts/pack.scm | 12 +++- guix/scripts/package.scm | 21 ++++-- guix/scripts/pull.scm | 12 +++- guix/scripts/system.scm | 15 +++- 8 files changed, 175 insertions(+), 114 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index ed7723c00b..2039ff67cf 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -2101,10 +2101,6 @@ By default, @command{guix package} reports as an error @dfn{collisions} in the profile. Collisions happen when two or more different versions or variants of a given package end up in the profile. -@item --verbose -Produce verbose output. In particular, emit the build log of the -environment on the standard error port. - @item --bootstrap Use the bootstrap Guile to build the profile. This option is only useful to distribution developers. @@ -6363,10 +6359,15 @@ Likewise, when the build or substitution process lasts for more than By default, the daemon's setting is honored (@pxref{Invoking guix-daemon, @code{--timeout}}). -@item --verbosity=@var{level} -Use the given verbosity level. @var{level} must be an integer between 0 -and 5; higher means more verbose output. Setting a level of 4 or more -may be helpful when debugging setup issues with the build daemon. +@c Note: This option is actually not part of %standard-build-options but +@c most programs honor it. +@cindex verbosity, of the command-line tools +@cindex build logs, verbosity +@item -v @var{level} +@itemx --verbosity=@var{level} +Use the given verbosity @var{level}, an integer. Choosing 0 means that no +output is produced, 1 is for quiet output, and 2 shows all the build log +output on standard error. @item --cores=@var{n} @itemx -c @var{n} @@ -6379,6 +6380,11 @@ Allow at most @var{n} build jobs in parallel. @xref{Invoking guix-daemon, @code{--max-jobs}}, for details about this option and the equivalent @command{guix-daemon} option. +@item --debug=@var{level} +Produce debugging output coming from the build daemon. @var{level} must be an +integer between 0 and 5; higher means more verbose output. Setting a level of +4 or more may be helpful when debugging setup issues with the build daemon. + @end table Behind the scenes, @command{guix build} is essentially an interface to @@ -6547,9 +6553,9 @@ build}. @item --quiet @itemx -q -Build quietly, without displaying the build log. Upon completion, the -build log is kept in @file{/var} (or similar) and can always be -retrieved using the @option{--log-file} option. +Build quietly, without displaying the build log; this is equivalent to +@code{--verbosity=0}. Upon completion, the build log is kept in @file{/var} +(or similar) and can always be retrieved using the @option{--log-file} option. @item --file=@var{file} @itemx -f @var{file} diff --git a/guix/scripts/archive.scm b/guix/scripts/archive.scm index fb2f61ce30..950f0f41d8 100644 --- a/guix/scripts/archive.scm +++ b/guix/scripts/archive.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, 2019 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,6 +23,7 @@ #:use-module ((guix build utils) #:select (mkdir-p)) #:use-module ((guix serialization) #:select (restore-file)) #:use-module (guix store) + #:use-module (guix status) #:use-module (guix grafts) #:use-module (guix packages) #:use-module (guix derivations) @@ -55,7 +56,11 @@ (substitutes? . #t) (build-hook? . #t) (graft? . #t) - (verbosity . 0))) + (print-build-trace? . #t) + (print-extended-build-trace? . #t) + (multiplexed-build-output? . #t) + (verbosity . 2) + (debug . 0))) (define (show-help) (display (G_ "Usage: guix archive [OPTION]... PACKAGE... @@ -85,6 +90,8 @@ Export/import one or more packages from/to the store.\n")) -s, --system=SYSTEM attempt to build for SYSTEM--e.g., \"i686-linux\"")) (display (G_ " --target=TRIPLET cross-build for TRIPLET--e.g., \"armel-linux-gnu\"")) + (display (G_ " + -v, --verbosity=LEVEL use the given verbosity LEVEL")) (newline) (show-build-options-help) @@ -161,6 +168,11 @@ Export/import one or more packages from/to the store.\n")) (option '(#\e "expression") #t #f (lambda (opt name arg result) (alist-cons 'expression arg result))) + (option '(#\v "verbosity") #t #f + (lambda (opt name arg result) + (let ((level (string->number* arg))) + (alist-cons 'verbosity level + (alist-delete 'verbosity result))))) (option '(#\n "dry-run") #f #f (lambda (opt name arg result) (alist-cons 'dry-run? #t (alist-cons 'graft? #f result)))) @@ -239,7 +251,6 @@ build and a list of store files to transfer." resulting archive to the standard output port." (let-values (((drv files) (options->derivations+files store opts))) - (set-build-options-from-command-line store opts) (show-what-to-build store drv #:use-substitutes? (assoc-ref opts 'substitutes?) #:dry-run? (assoc-ref opts 'dry-run?)) @@ -329,21 +340,23 @@ the input port." ((assoc-ref opts 'authorize) (authorize-key)) (else - (with-store store - (cond ((assoc-ref opts 'export) - (export-from-store store opts)) - ((assoc-ref opts 'import) - (import-paths store (current-input-port))) - ((assoc-ref opts 'missing) - (let* ((files (lines (current-input-port))) - (missing (remove (cut valid-path? store <>) - files))) - (format #t "~{~a~%~}" missing))) - ((assoc-ref opts 'extract) - => - (lambda (target) - (restore-file (current-input-port) target))) - (else - (leave - (G_ "either '--export' or '--import' \ -must be specified~%")))))))))))) + (with-status-verbosity (assoc-ref opts 'verbosity) + (with-store store + (set-build-options-from-command-line store opts) + (cond ((assoc-ref opts 'export) + (export-from-store store opts)) + ((assoc-ref opts 'import) + (import-paths store (current-input-port))) + ((assoc-ref opts 'missing) + (let* ((files (lines (current-input-port))) + (missing (remove (cut valid-path? store <>) + files))) + (format #t "~{~a~%~}" missing))) + ((assoc-ref opts 'extract) + => + (lambda (target) + (restore-file (current-input-port) target))) + (else + (leave + (G_ "either '--export' or '--import' \ +must be specified~%"))))))))))))) diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm index 564bdf0ced..5a158799ae 100644 --- a/guix/scripts/build.scm +++ b/guix/scripts/build.scm @@ -449,14 +449,14 @@ options handled by 'set-build-options-from-command-line', and listed in mark the build as failed after SECONDS of silence")) (display (G_ " --timeout=SECONDS mark the build as failed after SECONDS of activity")) - (display (G_ " - --verbosity=LEVEL use the given verbosity LEVEL")) (display (G_ " --rounds=N build N times in a row to detect non-determinism")) (display (G_ " -c, --cores=N allow the use of up to N CPU cores for the build")) (display (G_ " - -M, --max-jobs=N allow at most N build jobs"))) + -M, --max-jobs=N allow at most N build jobs")) + (display (G_ " + --debug=LEVEL produce debugging output at LEVEL"))) (define (set-build-options-from-command-line store opts) "Given OPTS, an alist as returned by 'args-fold' given @@ -479,7 +479,7 @@ options handled by 'set-build-options-from-command-line', and listed in (assoc-ref opts 'print-extended-build-trace?) #:multiplexed-build-output? (assoc-ref opts 'multiplexed-build-output?) - #:verbosity (assoc-ref opts 'verbosity))) + #:verbosity (assoc-ref opts 'debug))) (define set-build-options-from-command-line* (store-lift set-build-options-from-command-line)) @@ -553,12 +553,12 @@ options handled by 'set-build-options-from-command-line', and listed in (apply values (alist-cons 'timeout (string->number* arg) result) rest))) - (option '("verbosity") #t #f + (option '("debug") #t #f (lambda (opt name arg result . rest) - (let ((level (string->number arg))) + (let ((level (string->number* arg))) (apply values - (alist-cons 'verbosity level - (alist-delete 'verbosity result)) + (alist-cons 'debug level + (alist-delete 'debug result)) rest)))) (option '(#\c "cores") #t #f (lambda (opt name arg result . rest) @@ -590,7 +590,8 @@ options handled by 'set-build-options-from-command-line', and listed in (print-build-trace? . #t) (print-extended-build-trace? . #t) (multiplexed-build-output? . #t) - (verbosity . 0))) + (verbosity . 2) + (debug . 0))) (define (show-help) (display (G_ "Usage: guix build [OPTION]... PACKAGE-OR-DERIVATION... @@ -619,6 +620,8 @@ Build the given PACKAGE-OR-DERIVATION and return their output paths.\n")) -r, --root=FILE make FILE a symlink to the result, and register it as a garbage collector root")) (display (G_ " + -v, --verbosity=LEVEL use the given verbosity LEVEL")) + (display (G_ " -q, --quiet do not show the build log")) (display (G_ " --log-file return the log file names for the given derivations")) @@ -694,9 +697,15 @@ must be one of 'package', 'all', or 'transitive'~%") (option '(#\r "root") #t #f (lambda (opt name arg result) (alist-cons 'gc-root arg result))) + (option '(#\v "verbosity") #t #f + (lambda (opt name arg result) + (let ((level (string->number* arg))) + (alist-cons 'verbosity level + (alist-delete 'verbosity result))))) (option '(#\q "quiet") #f #f (lambda (opt name arg result) - (alist-cons 'quiet? #t result))) + (alist-cons 'verbosity 0 + (alist-delete 'verbosity result)))) (option '("log-file") #f #f (lambda (opt name arg result) (alist-cons 'log-file? #t result))) @@ -819,66 +828,59 @@ needed." (parse-command-line args %options (list %default-options))) - (define quiet? - (assoc-ref opts 'quiet?)) - (with-error-handling ;; Ask for absolute file names so that .drv file names passed from the ;; user to 'read-derivation' are absolute when it returns. (with-fluids ((%file-port-name-canonicalization 'absolute)) - (with-store store - ;; Set the build options before we do anything else. - (set-build-options-from-command-line store opts) + (with-status-verbosity (assoc-ref opts 'verbosity) + (with-store store + ;; Set the build options before we do anything else. + (set-build-options-from-command-line store opts) - (parameterize ((current-terminal-columns (terminal-columns)) - (current-build-output-port - (if quiet? - (%make-void-port "w") - (build-event-output-port - (build-status-updater print-build-event))))) - (let* ((mode (assoc-ref opts 'build-mode)) - (drv (options->derivations store opts)) - (urls (map (cut string-append <> "/log") - (if (assoc-ref opts 'substitutes?) - (or (assoc-ref opts 'substitute-urls) - ;; XXX: This does not necessarily match the - ;; daemon's substitute URLs. - %default-substitute-urls) - '()))) - (items (filter-map (match-lambda - (('argument . (? store-path? file)) - file) - (_ #f)) - opts)) - (roots (filter-map (match-lambda - (('gc-root . root) root) - (_ #f)) - opts))) + (parameterize ((current-terminal-columns (terminal-columns))) + (let* ((mode (assoc-ref opts 'build-mode)) + (drv (options->derivations store opts)) + (urls (map (cut string-append <> "/log") + (if (assoc-ref opts 'substitutes?) + (or (assoc-ref opts 'substitute-urls) + ;; XXX: This does not necessarily match the + ;; daemon's substitute URLs. + %default-substitute-urls) + '()))) + (items (filter-map (match-lambda + (('argument . (? store-path? file)) + file) + (_ #f)) + opts)) + (roots (filter-map (match-lambda + (('gc-root . root) root) + (_ #f)) + opts))) - (unless (or (assoc-ref opts 'log-file?) - (assoc-ref opts 'derivations-only?)) - (show-what-to-build store drv - #:use-substitutes? - (assoc-ref opts 'substitutes?) - #:dry-run? (assoc-ref opts 'dry-run?) - #:mode mode)) + (unless (or (assoc-ref opts 'log-file?) + (assoc-ref opts 'derivations-only?)) + (show-what-to-build store drv + #:use-substitutes? + (assoc-ref opts 'substitutes?) + #:dry-run? (assoc-ref opts 'dry-run?) + #:mode mode)) - (cond ((assoc-ref opts 'log-file?) - (for-each (cut show-build-log store <> urls) - (delete-duplicates - (append (map derivation-file-name drv) - items)))) - ((assoc-ref opts 'derivations-only?) - (format #t "~{~a~%~}" (map derivation-file-name drv)) - (for-each (cut register-root store <> <>) - (map (compose list derivation-file-name) drv) - roots)) - ((not (assoc-ref opts 'dry-run?)) - (and (build-derivations store drv mode) - (for-each show-derivation-outputs drv) - (for-each (cut register-root store <> <>) - (map (lambda (drv) - (map cdr - (derivation->output-paths drv))) - drv) - roots)))))))))) + (cond ((assoc-ref opts 'log-file?) + (for-each (cut show-build-log store <> urls) + (delete-duplicates + (append (map derivation-file-name drv) + items)))) + ((assoc-ref opts 'derivations-only?) + (format #t "~{~a~%~}" (map derivation-file-name drv)) + (for-each (cut register-root store <> <>) + (map (compose list derivation-file-name) drv) + roots)) + ((not (assoc-ref opts 'dry-run?)) + (and (build-derivations store drv mode) + (for-each show-derivation-outputs drv) + (for-each (cut register-root store <> <>) + (map (lambda (drv) + (map cdr + (derivation->output-paths drv))) + drv) + roots))))))))))) diff --git a/guix/scripts/environment.scm b/guix/scripts/environment.scm index 9461d04976..116b8dcbce 100644 --- a/guix/scripts/environment.scm +++ b/guix/scripts/environment.scm @@ -157,6 +157,8 @@ COMMAND or an interactive shell in that environment.\n")) (display (G_ " --expose=SPEC for containers, expose read-only host file system according to SPEC")) + (display (G_ " + -v, --verbosity=LEVEL use the given verbosity LEVEL")) (display (G_ " --bootstrap use bootstrap binaries to build the environment")) (newline) @@ -179,7 +181,8 @@ COMMAND or an interactive shell in that environment.\n")) (print-build-trace? . #t) (print-extended-build-trace? . #t) (multiplexed-build-output? . #t) - (verbosity . 0))) + (debug . 0) + (verbosity . 2))) (define (tag-package-arg opts arg) "Return a two-element list with the form (TAG ARG) that tags ARG with either @@ -260,6 +263,11 @@ COMMAND or an interactive shell in that environment.\n")) (option '(#\r "root") #t #f (lambda (opt name arg result) (alist-cons 'gc-root arg result))) + (option '(#\v "verbosity") #t #f + (lambda (opt name arg result) + (let ((level (string->number* arg))) + (alist-cons 'verbosity level + (alist-delete 'verbosity result))))) (option '("bootstrap") #f #f (lambda (opt name arg result) (alist-cons 'bootstrap? #t result))) @@ -674,7 +682,7 @@ message if any test fails." (leave (G_ "'--user' cannot be used without '--container'~%"))) (with-store store - (with-status-verbosity 1 + (with-status-verbosity (assoc-ref opts 'verbosity) (define manifest (options/resolve-packages store opts)) diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm index d9e0050159..b19a4ae1b1 100644 --- a/guix/scripts/pack.scm +++ b/guix/scripts/pack.scm @@ -598,7 +598,8 @@ please email '~a'~%") (print-build-trace? . #t) (print-extended-build-trace? . #t) (multiplexed-build-output? . #t) - (verbosity . 0) + (debug . 0) + (verbosity . 2) (symlinks . ()) (compressor . ,(first %compressors)))) @@ -685,6 +686,11 @@ please email '~a'~%") (alist-cons 'profile-name arg result)) (_ (leave (G_ "~a: unsupported profile name~%") arg))))) + (option '(#\v "verbosity") #t #f + (lambda (opt name arg result) + (let ((level (string->number* arg))) + (alist-cons 'verbosity level + (alist-delete 'verbosity result))))) (option '("bootstrap") #f #f (lambda (opt name arg result) (alist-cons 'bootstrap? #t result))) @@ -722,6 +728,8 @@ Create a bundle of PACKAGE.\n")) (display (G_ " --profile-name=NAME populate /var/guix/profiles/.../NAME")) + (display (G_ " + -v, --verbosity=LEVEL use the given verbosity LEVEL")) (display (G_ " --bootstrap use the bootstrap binaries to build the pack")) (newline) @@ -772,7 +780,7 @@ Create a bundle of PACKAGE.\n")) (with-error-handling (with-store store - (with-status-verbosity 2 + (with-status-verbosity (assoc-ref opts 'verbosity) ;; Set the build options before we do anything else. (set-build-options-from-command-line store opts) diff --git a/guix/scripts/package.scm b/guix/scripts/package.scm index 876787fbe2..7ff6bfd6d8 100644 --- a/guix/scripts/package.scm +++ b/guix/scripts/package.scm @@ -293,7 +293,8 @@ ENTRIES, a list of manifest entries, in the context of PROFILE." (define %default-options ;; Alist of default option values. - `((verbosity . 0) + `((verbosity . 1) + (debug . 0) (graft? . #t) (substitutes? . #t) (build-hook? . #t) @@ -346,7 +347,7 @@ Install, remove, or upgrade packages in a single transaction.\n")) (display (G_ " --bootstrap use the bootstrap Guile to build the profile")) (display (G_ " - --verbose produce verbose output")) + -v, --verbosity=LEVEL use the given verbosity LEVEL")) (newline) (display (G_ " -s, --search=REGEXP search in synopsis and description using REGEXP")) @@ -472,13 +473,21 @@ kind of search path~%") (values (alist-cons 'dry-run? #t (alist-cons 'graft? #f result)) #f))) + (option '(#\v "verbosity") #t #f + (lambda (opt name arg result arg-handler) + (let ((level (string->number* arg))) + (values (alist-cons 'verbosity level + (alist-delete 'verbosity result)) + #f)))) (option '("bootstrap") #f #f (lambda (opt name arg result arg-handler) (values (alist-cons 'bootstrap? #t result) #f))) - (option '("verbose") #f #f + (option '("verbose") #f #f ;deprecated (lambda (opt name arg result arg-handler) - (values (alist-cons 'verbose? #t result) + (values (alist-cons 'verbosity 2 + (alist-delete 'verbosity + result)) #f))) (option '("allow-collisions") #f #f (lambda (opt name arg result arg-handler) @@ -907,14 +916,12 @@ processed, #f otherwise." (define opts (parse-command-line args %options (list %default-options #f) #:argument-handler handle-argument)) - (define verbose? - (assoc-ref opts 'verbose?)) (with-error-handling (or (process-query opts) (parameterize ((%store (open-connection)) (%graft? (assoc-ref opts 'graft?))) - (with-status-verbosity 1 + (with-status-verbosity (assoc-ref opts 'verbosity) (set-build-options-from-command-line (%store) opts) (parameterize ((%guile-for-build (package-derivation diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm index 6389d5ec09..6d1914f7c2 100644 --- a/guix/scripts/pull.scm +++ b/guix/scripts/pull.scm @@ -66,7 +66,8 @@ (print-extended-build-trace? . #t) (multiplexed-build-output? . #t) (graft? . #t) - (verbosity . 0))) + (debug . 0) + (verbosity . 2))) (define (show-help) (display (G_ "Usage: guix pull [OPTION]... @@ -89,6 +90,8 @@ Download and deploy the latest version of Guix.\n")) (display (G_ " -n, --dry-run show what would be pulled and built")) (display (G_ " + -v, --verbosity=LEVEL use the given verbosity LEVEL")) + (display (G_ " -s, --system=SYSTEM attempt to build for SYSTEM--e.g., \"i686-linux\"")) (display (G_ " --bootstrap use the bootstrap Guile to build the new Guix")) @@ -135,6 +138,11 @@ Download and deploy the latest version of Guix.\n")) (option '(#\n "dry-run") #f #f (lambda (opt name arg result) (alist-cons 'dry-run? #t (alist-cons 'graft? #f result)))) + (option '(#\v "verbosity") #t #f + (lambda (opt name arg result) + (let ((level (string->number* arg))) + (alist-cons 'verbosity level + (alist-delete 'verbosity result))))) (option '("bootstrap") #f #f (lambda (opt name arg result) (alist-cons 'bootstrap? #t result))) @@ -510,7 +518,7 @@ Use '~/.config/guix/channels.scm' instead.")) (process-query opts profile)) (else (with-store store - (with-status-verbosity 2 + (with-status-verbosity (assoc-ref opts 'verbosity) (parameterize ((%current-system (assoc-ref opts 'system)) (%graft? (assoc-ref opts 'graft?)) (%repository-cache-directory cache)) diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm index 9e31baaddb..569b826acd 100644 --- a/guix/scripts/system.scm +++ b/guix/scripts/system.scm @@ -1015,6 +1015,8 @@ Some ACTIONS support additional ARGS.\n")) --full-boot for 'vm', make a full boot sequence")) (display (G_ " --skip-checks skip file system and initrd module safety checks")) + (display (G_ " + -v, --verbosity=LEVEL use the given verbosity LEVEL")) (newline) (display (G_ " -h, --help display this help and exit")) @@ -1074,6 +1076,11 @@ Some ACTIONS support additional ARGS.\n")) (option '(#\n "dry-run") #f #f (lambda (opt name arg result) (alist-cons 'dry-run? #t (alist-cons 'graft? #f result)))) + (option '(#\v "verbosity") #t #f + (lambda (opt name arg result) + (let ((level (string->number* arg))) + (alist-cons 'verbosity level + (alist-delete 'verbosity result))))) (option '(#\s "system") #t #f (lambda (opt name arg result) (alist-cons 'system arg @@ -1092,7 +1099,8 @@ Some ACTIONS support additional ARGS.\n")) (print-extended-build-trace? . #t) (multiplexed-build-output? . #t) (graft? . #t) - (verbosity . 0) + (debug . 0) + (verbosity . #f) ;default (file-system-type . "ext4") (image-size . guess) (install-bootloader? . #t))) @@ -1267,8 +1275,9 @@ argument list and OPTS is the option alist." (args (option-arguments opts)) (command (assoc-ref opts 'action))) (parameterize ((%graft? (assoc-ref opts 'graft?))) - (with-status-verbosity (if (memq command '(init reconfigure)) - 1 2) + (with-status-verbosity (or (assoc-ref opts 'verbosity) + (if (memq command '(init reconfigure)) + 1 2)) (process-command command args opts)))))) ;;; Local Variables: From 5a26f879c3f2f417f594171d909acc3f8227a99c Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Fri, 11 Jan 2019 13:31:47 +0100 Subject: [PATCH 136/300] Revert "gnu: emacs-ghub: Update to 3.2.0." This change should be applied once we update our magit package. This reverts commit b96f0e6ff9f8f36d250b5ae94a908272babb35cf. --- gnu/packages/emacs.scm | 19 +++++++------------ 1 file changed, 7 insertions(+), 12 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 3978d9ab6d..885bb7d5d2 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -677,16 +677,16 @@ deliver data to mobile and web apps.") (define-public emacs-ghub (package (name "emacs-ghub") - (version "3.2.0") + (version "2.0.1") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/magit/ghub.git") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) + (method url-fetch) + (uri (string-append + "https://github.com/magit/ghub/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0lp52qygyavddl1lrgsyb6mq7hcf9h89dy2pzya3mb2va49f0vvl")))) + "0d0qj5r1bm2aidi61rigrdaycxnyb7y1ivb3h8rpvvapsf8sk7z0")))) (build-system emacs-build-system) (arguments `(#:phases @@ -694,11 +694,6 @@ deliver data to mobile and web apps.") (add-before 'install 'make-info (lambda _ (invoke "make" "info")))))) - (propagated-inputs - `(("emacs-dash" ,emacs-dash) - ("emacs-graphql" ,emacs-graphql) - ("emacs-let-alist" ,emacs-let-alist) - ("emacs-treepy" ,emacs-treepy))) (native-inputs `(("texinfo" ,texinfo))) (home-page "https://github.com/magit/ghub") From 46b082f97f73cd79b40bde15cfe3e4ddb28ba209 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Wed, 9 Jan 2019 15:54:55 +0100 Subject: [PATCH 137/300] gnu: kinit: Use KDEINIT5_LIBRARY_PATH to search for dynlibs. Using LIBRARY_PATH was introduced in 16b8aff85bcdb9799496c4a27257210cd45158e5, but is wrong since this variable is used by the compiler (gcc) at link time. * gnu/packages/patches/kinit-kdeinit-libpath.patch: Change LIBRARY_PATH to KDEINIT5_LIBRARY_PATH. * gnu/packages/kde-frameworks.scm (kinit)[native-search-paths]: New field. --- gnu/packages/kde-frameworks.scm | 4 ++++ gnu/packages/patches/kinit-kdeinit-libpath.patch | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 0d14c8f887..fff98bd16d 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -2556,6 +2556,10 @@ in applications using the KDE Frameworks.") (("GUIX_PKGS_KF5_PARTS") (assoc-ref inputs "kparts")) (("GUIX_PKGS_KF5_PLASMA") (assoc-ref inputs "plasma-framework"))) #t))))) + (native-search-paths + (list (search-path-specification + (variable "KDEINIT5_LIBRARY_PATH") + (files '("lib/"))))) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) ("pkg-config" ,pkg-config))) diff --git a/gnu/packages/patches/kinit-kdeinit-libpath.patch b/gnu/packages/patches/kinit-kdeinit-libpath.patch index 89cf1a941d..6382e8804b 100644 --- a/gnu/packages/patches/kinit-kdeinit-libpath.patch +++ b/gnu/packages/patches/kinit-kdeinit-libpath.patch @@ -23,7 +23,7 @@ pkgs/development/libraries/kde-frameworks/kinit/kinit-libpath.patch - l.load(); - } + // Try to load the library relative to the active profiles. -+ QByteArrayList profiles = qgetenv("LIBRARY_PATH").split(':'); ++ QByteArrayList profiles = qgetenv("KDEINIT5_LIBRARY_PATH").split(':'); + for (const QByteArray &profile: profiles) { + if (!profile.isEmpty()) { + l.setFileName(QFile::decodeName(profile) + QStringLiteral("/") + libpath); From 50e1843b3a01eb83e83e33f96b9e50dfb10a1935 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Fri, 11 Jan 2019 11:58:03 +0100 Subject: [PATCH 138/300] gnu: libupnp: Update to 1.6.25. * gnu/packages/upnp.scm (libupnp): Update to 1.6.25. --- gnu/packages/upnp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/upnp.scm b/gnu/packages/upnp.scm index 24b17111e9..e7da5b30c0 100644 --- a/gnu/packages/upnp.scm +++ b/gnu/packages/upnp.scm @@ -125,7 +125,7 @@ over IRC, instant messaging, network games, and most server software.") (define-public libupnp (package (name "libupnp") - (version "1.6.24") + (version "1.6.25") (source (origin (method url-fetch) @@ -133,7 +133,7 @@ over IRC, instant messaging, network games, and most server software.") version "/" name "-" version ".tar.bz2")) (sha256 (base32 - "15ngi1i7cvsv7g15fb9bkswvi99d1plz52x5qgjn4h5vyfddg0vx")))) + "0hzsd7rvfa87b4hxg9yj4xhdfxx9sp09r9sqdl3mqhvmcyw018y5")))) (build-system gnu-build-system) (arguments ;; The tests require a network device capable of multicasting which is From 362fba83ddefd706641924f5e4c7b5681eb8e216 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Fri, 11 Jan 2019 19:44:51 +0100 Subject: [PATCH 139/300] gnu: Add restbed. * gnu/packages/networking.scm (restbed): New variable. --- gnu/packages/networking.scm | 53 +++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 3b0714865d..4647f02878 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2271,3 +2271,56 @@ allow all other machines, without direct access to that network, to be relayed through the machine the Dante server is running on. The external network will never see any machines other than the one Dante is running on.") (license (license:non-copyleft "file://LICENSE")))) + +(define-public restbed + (let ((commit "6eb385fa9051203f28bf96cc1844bbb5a9a6481f")) + (package + (name "restbed") + (version (git-version "4.6" "1" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Corvusoft/restbed/") + (commit commit))) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0k60i5drklqqrb4khb25fzkgz9y0sncxf1sp6lh2bm1m0gh0661n")))) + (build-system cmake-build-system) + (inputs + `(("asio" ,asio) + ("catch" ,catch-framework) + ("openssl" ,openssl))) + (arguments + `(#:tests? #f + #:configure-flags + '("-DBUILD_TESTS=NO" + "-DBUILD_EXAMPLES=NO" + "-DBUILD_SSL=NO" + "-DBUILD_SHARED=NO") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'apply-patches-and-fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (let ((asio (assoc-ref inputs "asio")) + (catch (assoc-ref inputs "catch")) + (openssl (assoc-ref inputs "openssl"))) + (substitute* "cmake/Findasio.cmake" + (("(find_path\\( asio_INCLUDE asio\\.hpp HINTS ).*$" all begin) + (string-append begin " \"" asio "/include\" )"))) + (substitute* "cmake/Findcatch.cmake" + (("(find_path\\( catch_INCLUDE catch\\.hpp HINTS ).*$" all begin) + (string-append begin " \"" catch "/include\" )"))) + (substitute* "cmake/Findopenssl.cmake" + (("(find_library\\( ssl_LIBRARY ssl ssleay32 HINTS ).*$" all begin) + (string-append begin " \"" openssl "/lib\" )")) + (("(find_library\\( crypto_LIBRARY crypto libeay32 HINTS ).*$" all begin) + (string-append begin " \"" openssl "/lib\" )")) + (("(find_path\\( ssl_INCLUDE openssl/ssl\\.h HINTS ).*$" all begin) + (string-append begin " \"" openssl "/include\" )"))))))))) + (synopsis "Asynchronous RESTful functionality to C++11 applications") + (description "Restbed is a comprehensive and consistent programming +model for building applications that require seamless and secure +communication over HTTP.") + (home-page "https://github.com/Corvusoft/restbed") + (license license:agpl3+)))) From e0fa641380cf276eee199a17904c63a7e8e5ea04 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Fri, 11 Jan 2019 12:33:41 +0100 Subject: [PATCH 140/300] gnu: opendht: Use jsoncpp and restbed. * gnu/packages/crypto.scm (opendht): Move definition to networking.scm. * gnu/packages/networking.scm (opendht)[inputs]: Add jsoncpp and restbed. --- gnu/packages/crypto.scm | 37 -------------------------------- gnu/packages/networking.scm | 42 +++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+), 37 deletions(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 56f909ed2f..d72162d6a8 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -166,43 +166,6 @@ OpenBSD tool of the same name.") "See base64.c in the distribution for the license from IBM."))))) -(define-public opendht - (package - (name "opendht") - (version "1.8.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/savoirfairelinux/opendht.git") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0vninb5mak27wigajslyvr05vq7wbrwqhbr4wzl2nmqcb20wmlq2")))) - (build-system gnu-build-system) - (inputs - `(("gnutls" ,gnutls) - ("nettle" ,nettle) - ("readline" ,readline) - ("argon2" ,argon2))) - (propagated-inputs - `(("msgpack" ,msgpack))) ;included in several installed headers - (native-inputs - `(("autoconf" ,autoconf) - ("pkg-config" ,pkg-config) - ("automake" ,automake) - ("libtool" ,libtool))) - (arguments - `(#:configure-flags '("--disable-tools" - "--disable-python" - "--with-argon2"))) - (home-page "https://github.com/savoirfairelinux/opendht/") - (synopsis "Distributed Hash Table (DHT) library") - (description "OpenDHT is a Distributed Hash Table (DHT) library. It may -be used to manage peer-to-peer network connections as needed for real time -communication.") - (license license:gpl3+))) - (define-public encfs (package (name "encfs") diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 4647f02878..ad478ca2ae 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -82,6 +82,8 @@ #:use-module (gnu packages multiprecision) #:use-module (gnu packages kerberos) #:use-module (gnu packages ncurses) + #:use-module (gnu packages nettle) + #:use-module (gnu packages password-utils) #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages perl-check) @@ -90,6 +92,7 @@ #:use-module (gnu packages python-web) #:use-module (gnu packages qt) #:use-module (gnu packages readline) + #:use-module (gnu packages serialization) #:use-module (gnu packages ssh) #:use-module (gnu packages textutils) #:use-module (gnu packages tls) @@ -2324,3 +2327,42 @@ model for building applications that require seamless and secure communication over HTTP.") (home-page "https://github.com/Corvusoft/restbed") (license license:agpl3+)))) + +(define-public opendht + (package + (name "opendht") + (version "1.8.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/savoirfairelinux/opendht.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0vninb5mak27wigajslyvr05vq7wbrwqhbr4wzl2nmqcb20wmlq2")))) + (build-system gnu-build-system) + (inputs + `(("gnutls" ,gnutls) + ("nettle" ,nettle) + ("readline" ,readline) + ("argon2" ,argon2) + ("jsoncpp" ,jsoncpp) + ("restbed" ,restbed))) + (propagated-inputs + `(("msgpack" ,msgpack))) ;included in several installed headers + (native-inputs + `(("autoconf" ,autoconf) + ("pkg-config" ,pkg-config) + ("automake" ,automake) + ("libtool" ,libtool))) + (arguments + `(#:configure-flags '("--disable-tools" + "--disable-python" + "--with-argon2"))) + (home-page "https://github.com/savoirfairelinux/opendht/") + (synopsis "Distributed Hash Table (DHT) library") + (description "OpenDHT is a Distributed Hash Table (DHT) library. It may +be used to manage peer-to-peer network connections as needed for real time +communication.") + (license license:gpl3+))) From 1ac0c1b8990317c0675df2d84b68ce4c85b18104 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Fri, 11 Jan 2019 18:46:22 +0100 Subject: [PATCH 141/300] gnu: opendht: Make argon2 a propagated input so that its .pc is found. * gnu/packages/networking.scm (opendht)[inputs]: Remove argon2. [propagated-inputs]: Add it here. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index ad478ca2ae..65148bb000 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2346,11 +2346,11 @@ communication over HTTP.") `(("gnutls" ,gnutls) ("nettle" ,nettle) ("readline" ,readline) - ("argon2" ,argon2) ("jsoncpp" ,jsoncpp) ("restbed" ,restbed))) (propagated-inputs - `(("msgpack" ,msgpack))) ;included in several installed headers + `(("argon2" ,argon2) ; TODO: Needed for the pkg-config .pc file to work? + ("msgpack" ,msgpack))) ;included in several installed headers (native-inputs `(("autoconf" ,autoconf) ("pkg-config" ,pkg-config) From 81c64748bad51c7449eea8bab4953ecb89d02fa2 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 10 Jan 2019 19:29:33 -0500 Subject: [PATCH 142/300] gnu: Stellarium: Update to 0.18.3. * gnu/packages/astronomy.scm (stellarium): Update to 0.18.3. [arguments]: Skip a broken test. --- gnu/packages/astronomy.scm | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 7e6a56c545..2813062e95 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -131,7 +131,7 @@ programs for the manipulation and analysis of astronomical data.") (define-public stellarium (package (name "stellarium") - (version "0.18.1") + (version "0.18.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/Stellarium/" name @@ -139,7 +139,7 @@ programs for the manipulation and analysis of astronomical data.") "/" name "-" version ".tar.gz")) (sha256 (base32 - "0vjkwrjy22b4wdjkafm63pmb0fck14ffnylpq8xr91ywycw4blrq")))) + "1mm8rjcb8j56m3kfigpix5vxviw1616kvl9ws2s3s5gdyngljrc3")))) (build-system cmake-build-system) (inputs `(("qtbase" ,qtbase) @@ -161,6 +161,13 @@ programs for the manipulation and analysis of astronomical data.") (assoc-ref %build-inputs "qtserialport") "/include/qt5")) #:phases (modify-phases %standard-phases + ;; Skip a test that assumes Stellarium is "installed": + ;; https://bugs.gentoo.org/674472 + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "src/tests/testEphemeris.cpp" + (("ifndef Q_OS_WIN") "if 0")) + #t)) (add-before 'check 'set-offscreen-display (lambda _ ;; make Qt render "offscreen", required for tests From 170436771968dfa272225ea45b63689b900fd317 Mon Sep 17 00:00:00 2001 From: guy fleury iteriteka Date: Thu, 10 Jan 2019 17:33:30 +0100 Subject: [PATCH 143/300] gnu: Add Bochs. * gnu/packages/virtualization.scm (bochs): New variable. Signed-off-by: Leo Famulari --- gnu/packages/virtualization.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 57c5c34da1..9b82535aa7 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2018 Danny Milosavljevic ;;; Copyright © 2018 Sou Bunnbu ;;; Copyright © 2018 Julien Lepiller +;;; Copyright © 2019 Guy Fleury Iteriteka ;;; ;;; This file is part of GNU Guix. ;;; @@ -1074,3 +1075,30 @@ and the user can specify exactly what parts of the filesystem should be visible in the sandbox. Any such directories specified is mounted nodev by default, and can be made readonly.") (license license:lgpl2.0+))) + +(define-public bochs + (package + (name "bochs") + (version "2.6.9") + (source + (origin + (method url-fetch) + (uri (string-append "https://sourceforge.net/projects/bochs/files/bochs/" + version "/bochs-" version ".tar.gz")) + (sha256 + (base32 + "1379cq4cnfprhw8mgh60i0q9j8fz8d7n3d5fnn2g9fdiv5znfnzf")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f)) ; No tests exist + (inputs + `(("libxrandr" ,libxrandr))) + (home-page "http://bochs.sourceforge.net/") + (synopsis "Emulator for x86 PC") + (description + "Bochs is an emulator which can emulate Intel x86 CPU, common I/O +devices, and a custom BIOS. It can also be compiled to emulate many different +x86 CPUs, from early 386 to the most recent x86-64 Intel and AMD processors. +Bochs can run most Operating Systems inside the emulation including Linux, +DOS or Microsoft Windows.") + (license license:lgpl2.0+))) From 24155bf40db2dfd25c167f41452ea0227a712654 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 10 Jan 2019 14:55:50 +0100 Subject: [PATCH 144/300] gnu: Move Java compression packages to new module. * gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable. (java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz): Move these variables from here... * gnu/packages/java-compression.scm: ...to this new file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module references. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 1 + gnu/packages/compression.scm | 280 +-------------------------- gnu/packages/java-compression.scm | 308 ++++++++++++++++++++++++++++++ gnu/packages/java.scm | 1 + 5 files changed, 312 insertions(+), 279 deletions(-) create mode 100644 gnu/packages/java-compression.scm diff --git a/gnu/local.mk b/gnu/local.mk index 306cfa3a62..7eb4366af2 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -241,6 +241,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/irc.scm \ %D%/packages/iso-codes.scm \ %D%/packages/java.scm \ + %D%/packages/java-compression.scm \ %D%/packages/javascript.scm \ %D%/packages/jemalloc.scm \ %D%/packages/jrnl.scm \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 433d322b08..2ecc782324 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -78,6 +78,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) + #:use-module (gnu packages java-compression) #:use-module (gnu packages jemalloc) #:use-module (gnu packages dlang) #:use-module (gnu packages linux) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index b2b4488683..029d11ef21 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -45,7 +45,6 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) - #:use-module (guix build-system ant) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system perl) @@ -59,7 +58,6 @@ #:use-module (gnu packages check) #:use-module (gnu packages curl) #:use-module (gnu packages file) - #:use-module (gnu packages java) #:use-module (gnu packages maths) #:use-module (gnu packages perl) #:use-module (gnu packages perl-check) @@ -1265,7 +1263,7 @@ for most inputs, but the resulting compressed files are anywhere from 20% to 100% bigger.") (license license:asl2.0))) -(define bitshuffle-for-snappy +(define-public bitshuffle-for-snappy (package (inherit bitshuffle) (name "bitshuffle-for-snappy") @@ -1302,245 +1300,6 @@ install: libbitshuffle.so (inputs '()) (native-inputs '()))) -(define-public java-snappy - (package - (name "java-snappy") - (version "1.1.7.2") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/xerial/snappy-java/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1p557vdv006ysgxbpp83krmq0066k46108vyiyka69w8i4i8rbbm")))) - (build-system ant-build-system) - (arguments - `(#:jar-name "snappy.jar" - #:source-dir "src/main/java" - #:phases - (modify-phases %standard-phases - (add-before 'build 'remove-binaries - (lambda _ - (delete-file "lib/org/xerial/snappy/OSInfo.class") - (delete-file-recursively "src/main/resources/org/xerial/snappy/native") - #t)) - (add-before 'build 'build-jni - (lambda _ - ;; Rebuild one of the binaries we removed earlier - (invoke "javac" "src/main/java/org/xerial/snappy/OSInfo.java" - "-d" "lib") - ;; Link to the dynamic bitshuffle and snappy, not the static ones - (substitute* "Makefile.common" - (("-shared") - "-shared -lbitshuffle -lsnappy")) - (substitute* "Makefile" - ;; Don't try to use git, don't download bitshuffle source - ;; and don't build it. - (("\\$\\(SNAPPY_GIT_UNPACKED\\) ") - "") - ((": \\$\\(SNAPPY_GIT_UNPACKED\\)") - ":") - (("\\$\\(BITSHUFFLE_UNPACKED\\) ") - "") - ((": \\$\\(SNAPPY_SOURCE_CONFIGURED\\)") ":") - ;; What we actually want to build - (("SNAPPY_OBJ:=.*") - "SNAPPY_OBJ:=$(addprefix $(SNAPPY_OUT)/, \ - SnappyNative.o BitShuffleNative.o)\n") - ;; Since we removed the directory structure in "native" during - ;; the previous phase, we need to recreate it. - (("NAME\\): \\$\\(SNAPPY_OBJ\\)") - "NAME): $(SNAPPY_OBJ)\n\t@mkdir -p $(@D)")) - ;; Finally we can run the Makefile to build the dynamic library. - ;; Use the -nocmake target to avoid a dependency on cmake, - ;; which in turn requires the "git_unpacked" directory. - (invoke "make" "native-nocmake"))) - ;; Once we have built the shared library, we need to place it in the - ;; "build" directory so it can be added to the jar file. - (add-after 'build-jni 'copy-jni - (lambda _ - (copy-recursively "src/main/resources/org/xerial/snappy/native" - "build/classes/org/xerial/snappy/native") - #t)) - (add-before 'check 'fix-failing - (lambda _ - (with-directory-excursion "src/test/java/org/xerial/snappy" - ;; This package assumes maven build, which puts results in "target". - ;; We put them in "build" instead, so fix that. - (substitute* "SnappyLoaderTest.java" - (("target/classes") "build/classes")) - ;; This requires Hadoop, which is not in Guix yet. - (delete-file "SnappyHadoopCompatibleOutputStreamTest.java")) - #t))))) - (inputs - `(("osgi-framework" ,java-osgi-framework))) - (propagated-inputs - `(("bitshuffle" ,bitshuffle-for-snappy) - ("snappy" ,snappy))) - (native-inputs - `(("junit" ,java-junit) - ("hamcrest" ,java-hamcrest-core) - ("xerial-core" ,java-xerial-core) - ("classworlds" ,java-plexus-classworlds) - ("commons-lang" ,java-commons-lang) - ("commons-io" ,java-commons-io) - ("perl" ,perl))) - (home-page "https://github.com/xerial/snappy-java") - (synopsis "Compression/decompression algorithm in Java") - (description "Snappy-java is a Java port of snappy, a fast C++ -compressor/decompressor.") - (license license:asl2.0))) - -(define-public java-snappy-1 - (package - (inherit java-snappy) - (version "1.0.3-rc3") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/xerial/snappy-java/archive/" - "snappy-java-" version ".tar.gz")) - (sha256 - (base32 - "08hsxlqidiqck0q57fshwyv3ynyxy18vmhrai9fyc8mz17m7gsa3")))) - (arguments - `(#:jar-name "snappy.jar" - #:source-dir "src/main/java" - #:phases - (modify-phases %standard-phases - (add-before 'build 'remove-binaries - (lambda _ - (delete-file "lib/org/xerial/snappy/OSInfo.class") - (delete-file-recursively "src/main/resources/org/xerial/snappy/native") - #t)) - (add-before 'build 'build-jni - (lambda _ - ;; Rebuild one of the binaries we removed earlier - (invoke "javac" "src/main/java/org/xerial/snappy/OSInfo.java" - "-d" "lib") - ;; Link to the dynamic snappy, not the static ones - (substitute* "Makefile.common" - (("-shared") "-shared -lsnappy")) - (substitute* "Makefile" - ;; Don't download the sources here. - (("\\$\\(SNAPPY_UNPACKED\\) ") "") - ((": \\$\\(SNAPPY_UNPACKED\\) ") ":") - ;; What we actually want to build - (("SNAPPY_OBJ:=.*") - "SNAPPY_OBJ:=$(addprefix $(SNAPPY_OUT)/, SnappyNative.o)\n") - ;; Since we removed the directory structure in "native" during - ;; the previous phase, we need to recreate it. - (("NAME\\): \\$\\(SNAPPY_OBJ\\)") - "NAME): $(SNAPPY_OBJ)\n\t@mkdir -p $(@D)")) - ;; Finally we can run the Makefile to build the dynamic library. - (invoke "make" "native"))) - ;; Once we have built the shared library, we need to place it in the - ;; "build" directory so it can be added to the jar file. - (add-after 'build-jni 'copy-jni - (lambda _ - (copy-recursively "src/main/resources/org/xerial/snappy/native" - "build/classes/org/xerial/snappy/native") - #t)) - (add-before 'check 'fix-tests - (lambda _ - (mkdir-p "src/test/resources/org/xerial/snappy/") - (copy-recursively "src/test/java/org/xerial/snappy/testdata" - "src/test/resources/org/xerial/snappy/testdata") - (install-file "src/test/java/org/xerial/snappy/alice29.txt" - "src/test/resources/org/xerial/snappy/") - #t))))))) - -(define-public java-iq80-snappy - (package - (name "java-iq80-snappy") - (version "0.4") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/dain/snappy/archive/snappy-" - version ".tar.gz")) - (sha256 - (base32 - "0rb3zhci7w9wzd65lfnk7p3ip0n6gb58a9qpx8n7r0231gahyamf")))) - (build-system ant-build-system) - (arguments - `(#:jar-name "iq80-snappy.jar" - #:source-dir "src/main/java" - #:test-dir "src/test" - #:jdk ,icedtea-8 - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (define (test class) - (invoke "java" "-cp" (string-append (getenv "CLASSPATH") - ":build/classes" - ":build/test-classes") - "-Dtest.resources.dir=src/test/resources" - "org.testng.TestNG" "-testclass" - class)) - (invoke "ant" "compile-tests") - (test "org.iq80.snappy.SnappyFramedStreamTest") - (test "org.iq80.snappy.SnappyStreamTest") - #t)) - (add-before 'build 'remove-hadoop-dependency - (lambda _ - ;; We don't have hadoop - (delete-file "src/main/java/org/iq80/snappy/HadoopSnappyCodec.java") - (delete-file "src/test/java/org/iq80/snappy/TestHadoopSnappyCodec.java") - #t))))) - (home-page "https://github.com/dain/snappy") - (native-inputs - `(("guava" ,java-guava) - ("java-snappy" ,java-snappy) - ("hamcrest" ,java-hamcrest-core) - ("testng" ,java-testng))) - (synopsis "Java port of the Snappy (de)compressor") - (description - "Iq80-snappy is a port of the Snappy compressor and decompressor rewritten -in pure Java. This compression code produces a byte-for-byte exact copy of the -output created by the original C++ code, and is extremely fast.") - (license license:asl2.0))) - -(define-public java-jbzip2 - (package - (name "java-jbzip2") - (version "0.9.1") - (source (origin - (method url-fetch) - (uri (string-append "https://storage.googleapis.com/" - "google-code-archive-source/v2/" - "code.google.com/jbzip2/" - "source-archive.zip")) - (file-name (string-append name "-" version ".zip")) - (sha256 - (base32 - "0ncmhlqmrfmj96nqf6p77b9ws35lcfsvpfxzwxi2asissc83z1l3")))) - (build-system ant-build-system) - (native-inputs - `(("unzip" ,unzip) - ("java-junit" ,java-junit))) - (arguments - `(#:tests? #f ; no tests - #:jar-name "jbzip2.jar" - #:source-dir "tags/release-0.9.1/src" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-encoding-problems - (lambda _ - ;; Some of the files we're patching are - ;; ISO-8859-1-encoded, so choose it as the default - ;; encoding so the byte encoding is preserved. - (with-fluids ((%default-port-encoding #f)) - (substitute* "tags/release-0.9.1/src/org/itadaki/bzip2/HuffmanAllocator.java" - (("Milidi.") "Milidiu"))) - #t))))) - (home-page "https://code.google.com/archive/p/jbzip2/") - (synopsis "Java bzip2 compression/decompression library") - (description "Jbzip2 is a Java bzip2 compression/decompression library. -It can be used as a replacement for the Apache @code{CBZip2InputStream} / -@code{CBZip2OutputStream} classes.") - (license license:expat))) - (define-public p7zip (package (name "p7zip") @@ -2099,43 +1858,6 @@ without having to worry how it does so, or use different interfaces for each type by using either Perl modules, or command-line tools on your system.") (license license:perl-license))) -(define-public java-tukaani-xz - (package - (name "java-tukaani-xz") - (version "1.6") - (source (origin - (method url-fetch) - (uri (string-append "https://tukaani.org/xz/xz-java-" version ".zip")) - (sha256 - (base32 - "1z3p1ri1gvl07inxn0agx44ck8n7wrzfmvkz8nbq3njn8r9wba8x")))) - (build-system ant-build-system) - (arguments - `(#:tests? #f; no tests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'chdir - (lambda _ - ;; Our build system enters the first directory in the archive, but - ;; the package is not contained in a subdirectory - (chdir "..") - #t)) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - ;; Do we want to install *Demo.jar? - (install-file "build/jar/xz.jar" - (string-append - (assoc-ref outputs "out") - "/share/java/xz.jar")) - #t))))) - (native-inputs - `(("unzip" ,unzip))) - (home-page "https://tukaani.org") - (synopsis "XZ in Java") - (description "Tukaani-xz is an implementation of xz compression/decompression -algorithms in Java.") - (license license:public-domain))) - (define-public lunzip (package (name "lunzip") diff --git a/gnu/packages/java-compression.scm b/gnu/packages/java-compression.scm new file mode 100644 index 0000000000..8cebfc65a5 --- /dev/null +++ b/gnu/packages/java-compression.scm @@ -0,0 +1,308 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2017, 2019 Ricardo Wurmus +;;; Copyright © 2017, 2018 Julien Lepiller +;;; Copyright © 2018 Marius Bakke +;;; Copyright © 2018 Mark H Weaver +;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages java-compression) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix utils) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix build-system ant) + #:use-module (gnu packages) + #:use-module (gnu packages compression) + #:use-module (gnu packages java) + #:use-module (gnu packages perl)) + +(define-public java-snappy + (package + (name "java-snappy") + (version "1.1.7.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/xerial/snappy-java/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1p557vdv006ysgxbpp83krmq0066k46108vyiyka69w8i4i8rbbm")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "snappy.jar" + #:source-dir "src/main/java" + #:phases + (modify-phases %standard-phases + (add-before 'build 'remove-binaries + (lambda _ + (delete-file "lib/org/xerial/snappy/OSInfo.class") + (delete-file-recursively "src/main/resources/org/xerial/snappy/native") + #t)) + (add-before 'build 'build-jni + (lambda _ + ;; Rebuild one of the binaries we removed earlier + (invoke "javac" "src/main/java/org/xerial/snappy/OSInfo.java" + "-d" "lib") + ;; Link to the dynamic bitshuffle and snappy, not the static ones + (substitute* "Makefile.common" + (("-shared") + "-shared -lbitshuffle -lsnappy")) + (substitute* "Makefile" + ;; Don't try to use git, don't download bitshuffle source + ;; and don't build it. + (("\\$\\(SNAPPY_GIT_UNPACKED\\) ") + "") + ((": \\$\\(SNAPPY_GIT_UNPACKED\\)") + ":") + (("\\$\\(BITSHUFFLE_UNPACKED\\) ") + "") + ((": \\$\\(SNAPPY_SOURCE_CONFIGURED\\)") ":") + ;; What we actually want to build + (("SNAPPY_OBJ:=.*") + "SNAPPY_OBJ:=$(addprefix $(SNAPPY_OUT)/, \ + SnappyNative.o BitShuffleNative.o)\n") + ;; Since we removed the directory structure in "native" during + ;; the previous phase, we need to recreate it. + (("NAME\\): \\$\\(SNAPPY_OBJ\\)") + "NAME): $(SNAPPY_OBJ)\n\t@mkdir -p $(@D)")) + ;; Finally we can run the Makefile to build the dynamic library. + ;; Use the -nocmake target to avoid a dependency on cmake, + ;; which in turn requires the "git_unpacked" directory. + (invoke "make" "native-nocmake"))) + ;; Once we have built the shared library, we need to place it in the + ;; "build" directory so it can be added to the jar file. + (add-after 'build-jni 'copy-jni + (lambda _ + (copy-recursively "src/main/resources/org/xerial/snappy/native" + "build/classes/org/xerial/snappy/native") + #t)) + (add-before 'check 'fix-failing + (lambda _ + (with-directory-excursion "src/test/java/org/xerial/snappy" + ;; This package assumes maven build, which puts results in "target". + ;; We put them in "build" instead, so fix that. + (substitute* "SnappyLoaderTest.java" + (("target/classes") "build/classes")) + ;; This requires Hadoop, which is not in Guix yet. + (delete-file "SnappyHadoopCompatibleOutputStreamTest.java")) + #t))))) + (inputs + `(("osgi-framework" ,java-osgi-framework))) + (propagated-inputs + `(("bitshuffle" ,bitshuffle-for-snappy) + ("snappy" ,snappy))) + (native-inputs + `(("junit" ,java-junit) + ("hamcrest" ,java-hamcrest-core) + ("xerial-core" ,java-xerial-core) + ("classworlds" ,java-plexus-classworlds) + ("commons-lang" ,java-commons-lang) + ("commons-io" ,java-commons-io) + ("perl" ,perl))) + (home-page "https://github.com/xerial/snappy-java") + (synopsis "Compression/decompression algorithm in Java") + (description "Snappy-java is a Java port of snappy, a fast C++ +compressor/decompressor.") + (license license:asl2.0))) + +(define-public java-snappy-1 + (package + (inherit java-snappy) + (version "1.0.3-rc3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/xerial/snappy-java/archive/" + "snappy-java-" version ".tar.gz")) + (sha256 + (base32 + "08hsxlqidiqck0q57fshwyv3ynyxy18vmhrai9fyc8mz17m7gsa3")))) + (arguments + `(#:jar-name "snappy.jar" + #:source-dir "src/main/java" + #:phases + (modify-phases %standard-phases + (add-before 'build 'remove-binaries + (lambda _ + (delete-file "lib/org/xerial/snappy/OSInfo.class") + (delete-file-recursively "src/main/resources/org/xerial/snappy/native") + #t)) + (add-before 'build 'build-jni + (lambda _ + ;; Rebuild one of the binaries we removed earlier + (invoke "javac" "src/main/java/org/xerial/snappy/OSInfo.java" + "-d" "lib") + ;; Link to the dynamic snappy, not the static ones + (substitute* "Makefile.common" + (("-shared") "-shared -lsnappy")) + (substitute* "Makefile" + ;; Don't download the sources here. + (("\\$\\(SNAPPY_UNPACKED\\) ") "") + ((": \\$\\(SNAPPY_UNPACKED\\) ") ":") + ;; What we actually want to build + (("SNAPPY_OBJ:=.*") + "SNAPPY_OBJ:=$(addprefix $(SNAPPY_OUT)/, SnappyNative.o)\n") + ;; Since we removed the directory structure in "native" during + ;; the previous phase, we need to recreate it. + (("NAME\\): \\$\\(SNAPPY_OBJ\\)") + "NAME): $(SNAPPY_OBJ)\n\t@mkdir -p $(@D)")) + ;; Finally we can run the Makefile to build the dynamic library. + (invoke "make" "native"))) + ;; Once we have built the shared library, we need to place it in the + ;; "build" directory so it can be added to the jar file. + (add-after 'build-jni 'copy-jni + (lambda _ + (copy-recursively "src/main/resources/org/xerial/snappy/native" + "build/classes/org/xerial/snappy/native") + #t)) + (add-before 'check 'fix-tests + (lambda _ + (mkdir-p "src/test/resources/org/xerial/snappy/") + (copy-recursively "src/test/java/org/xerial/snappy/testdata" + "src/test/resources/org/xerial/snappy/testdata") + (install-file "src/test/java/org/xerial/snappy/alice29.txt" + "src/test/resources/org/xerial/snappy/") + #t))))))) + +(define-public java-iq80-snappy + (package + (name "java-iq80-snappy") + (version "0.4") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/dain/snappy/archive/snappy-" + version ".tar.gz")) + (sha256 + (base32 + "0rb3zhci7w9wzd65lfnk7p3ip0n6gb58a9qpx8n7r0231gahyamf")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "iq80-snappy.jar" + #:source-dir "src/main/java" + #:test-dir "src/test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (define (test class) + (invoke "java" "-cp" (string-append (getenv "CLASSPATH") + ":build/classes" + ":build/test-classes") + "-Dtest.resources.dir=src/test/resources" + "org.testng.TestNG" "-testclass" + class)) + (invoke "ant" "compile-tests") + (test "org.iq80.snappy.SnappyFramedStreamTest") + (test "org.iq80.snappy.SnappyStreamTest") + #t)) + (add-before 'build 'remove-hadoop-dependency + (lambda _ + ;; We don't have hadoop + (delete-file "src/main/java/org/iq80/snappy/HadoopSnappyCodec.java") + (delete-file "src/test/java/org/iq80/snappy/TestHadoopSnappyCodec.java") + #t))))) + (home-page "https://github.com/dain/snappy") + (native-inputs + `(("guava" ,java-guava) + ("java-snappy" ,java-snappy) + ("hamcrest" ,java-hamcrest-core) + ("testng" ,java-testng))) + (synopsis "Java port of the Snappy (de)compressor") + (description + "Iq80-snappy is a port of the Snappy compressor and decompressor rewritten +in pure Java. This compression code produces a byte-for-byte exact copy of the +output created by the original C++ code, and is extremely fast.") + (license license:asl2.0))) + +(define-public java-jbzip2 + (package + (name "java-jbzip2") + (version "0.9.1") + (source (origin + (method url-fetch) + (uri (string-append "https://storage.googleapis.com/" + "google-code-archive-source/v2/" + "code.google.com/jbzip2/" + "source-archive.zip")) + (file-name (string-append name "-" version ".zip")) + (sha256 + (base32 + "0ncmhlqmrfmj96nqf6p77b9ws35lcfsvpfxzwxi2asissc83z1l3")))) + (build-system ant-build-system) + (native-inputs + `(("unzip" ,unzip) + ("java-junit" ,java-junit))) + (arguments + `(#:tests? #f ; no tests + #:jar-name "jbzip2.jar" + #:source-dir "tags/release-0.9.1/src" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-encoding-problems + (lambda _ + ;; Some of the files we're patching are + ;; ISO-8859-1-encoded, so choose it as the default + ;; encoding so the byte encoding is preserved. + (with-fluids ((%default-port-encoding #f)) + (substitute* "tags/release-0.9.1/src/org/itadaki/bzip2/HuffmanAllocator.java" + (("Milidi.") "Milidiu"))) + #t))))) + (home-page "https://code.google.com/archive/p/jbzip2/") + (synopsis "Java bzip2 compression/decompression library") + (description "Jbzip2 is a Java bzip2 compression/decompression library. +It can be used as a replacement for the Apache @code{CBZip2InputStream} / +@code{CBZip2OutputStream} classes.") + (license license:expat))) + +(define-public java-tukaani-xz + (package + (name "java-tukaani-xz") + (version "1.6") + (source (origin + (method url-fetch) + (uri (string-append "https://tukaani.org/xz/xz-java-" version ".zip")) + (sha256 + (base32 + "1z3p1ri1gvl07inxn0agx44ck8n7wrzfmvkz8nbq3njn8r9wba8x")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f; no tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + ;; Our build system enters the first directory in the archive, but + ;; the package is not contained in a subdirectory + (chdir "..") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + ;; Do we want to install *Demo.jar? + (install-file "build/jar/xz.jar" + (string-append + (assoc-ref outputs "out") + "/share/java/xz.jar")) + #t))))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "https://tukaani.org") + (synopsis "XZ in Java") + (description "Tukaani-xz is an implementation of xz compression/decompression +algorithms in Java.") + (license license:public-domain))) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index c607cbbcc5..163c296278 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -60,6 +60,7 @@ #:use-module (gnu packages guile) #:use-module (gnu packages icu4c) #:use-module (gnu packages image) + #:use-module (gnu packages java-compression) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) ;alsa #:use-module (gnu packages maths) From 7d8baff97be6654fe2910ea54544cb273d9fc560 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 10 Jan 2019 15:07:10 +0100 Subject: [PATCH 145/300] gnu: impressive: Update to 0.12.0. * gnu/packages/pdf.scm (impressive): Update to 0.12.0. --- gnu/packages/pdf.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index a881fe34e1..454712f923 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -785,7 +785,7 @@ vector formats.") (define-public impressive (package (name "impressive") - (version "0.11.1") + (version "0.12.0") (source (origin (method url-fetch) (uri (string-append @@ -793,7 +793,7 @@ vector formats.") version "/Impressive-" version ".tar.gz")) (sha256 (base32 - "0b3rmy6acp2vmf5nill3aknxvr9a5aawk1vnphkah61anxp62gsr")))) + "0zaqq3yvd296mfr5bxpj2hqlk7vrb0rsbgd4dc1l5ag46giqvivx")))) (build-system python-build-system) ;; TODO: Add dependency on pdftk. From 146c6b62bf72abbe710ce29972a8db17c6285b54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 10 Jan 2019 15:10:07 +0100 Subject: [PATCH 146/300] gnu: Sort package modules in (gnu packages guile). * gnu/packages/guile.scm: Sort list of gnu/packages modules. --- gnu/packages/guile.scm | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 07b568ee7c..e14c23a1d2 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -40,39 +40,39 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages aspell) + #:use-module (gnu packages autotools) + #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bdw-gc) #:use-module (gnu packages compression) + #:use-module (gnu packages databases) + #:use-module (gnu packages ed) + #:use-module (gnu packages flex) #:use-module (gnu packages gawk) + #:use-module (gnu packages gettext) + #:use-module (gnu packages gl) #:use-module (gnu packages gperf) #:use-module (gnu packages hurd) + #:use-module (gnu packages image) #:use-module (gnu packages libffi) - #:use-module (gnu packages autotools) - #:use-module (gnu packages flex) #:use-module (gnu packages libunistring) #:use-module (gnu packages linux) #:use-module (gnu packages m4) - #:use-module (gnu packages multiprecision) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages readline) - #:use-module (gnu packages ncurses) - #:use-module (gnu packages ed) - #:use-module (gnu packages base) - #:use-module (gnu packages texinfo) #:use-module (gnu packages man) - #:use-module (gnu packages gettext) - #:use-module (gnu packages databases) - #:use-module (gnu packages python) - #:use-module (gnu packages tls) - #:use-module (gnu packages gl) - #:use-module (gnu packages sdl) #:use-module (gnu packages maths) - #:use-module (gnu packages image) - #:use-module (gnu packages version-control) + #:use-module (gnu packages multiprecision) + #:use-module (gnu packages ncurses) + #:use-module (gnu packages networking) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) + #:use-module (gnu packages readline) + #:use-module (gnu packages sdl) #:use-module (gnu packages slang) + #:use-module (gnu packages texinfo) + #:use-module (gnu packages tls) + #:use-module (gnu packages version-control) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg) - #:use-module (gnu packages networking) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) From acbf312573be8a1f211986169710dd77d460f189 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Sun, 6 Jan 2019 00:50:55 -0500 Subject: [PATCH 147/300] gnu: python-pillow: Update to 5.4.0 * gnu/packages/python.scm (python-pillow): Update to 5.4.0. [arguments]: Add 'patch-ldconfig' phase. --- gnu/packages/python.scm | 33 ++++++++++++++++++--------------- 1 file changed, 18 insertions(+), 15 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 507cdd3db4..d412ee5077 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4075,17 +4075,17 @@ the OleFileIO module from PIL, the Python Image Library.") (define-public python-pillow (package (name "python-pillow") - (version "5.2.0") + (version "5.4.0") (source (origin (method url-fetch) (uri (pypi-uri "Pillow" version)) (sha256 (base32 - "1ary9mj2ddllq3lkxgn6aac7qxqiwbcg2pacrl94py58ql9x9czq")))) + "0qrkcjszym7ixffg5zphhp8a07w8w11yyc2ylcbdrhwm771z316m")))) (build-system python-build-system) (native-inputs - `(("python-pytest" ,python-pytest))) + `(("python-pytest" ,python-pytest))) (inputs `(("freetype" ,freetype) ("lcms" ,lcms) @@ -4097,18 +4097,21 @@ the OleFileIO module from PIL, the Python Image Library.") (propagated-inputs `(("python-olefile" ,python-olefile))) (arguments - `(#:phases (modify-phases %standard-phases - (add-after - 'install 'check-installed - (lambda* (#:key outputs inputs #:allow-other-keys) - (begin - (setenv "HOME" (getcwd)) - ;; Make installed package available for running the - ;; tests - (add-installed-pythonpath inputs outputs) - (invoke "python" "selftest.py" "--installed") - (invoke "python" "-m" "pytest" "-vv")))) - (delete 'check)))) + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-ldconfig + (lambda _ + (substitute* "setup.py" + (("\\['/sbin/ldconfig', '-p'\\]") "['true']")))) + (delete 'check) ; We must run checks after python-pillow is installed. + (add-after 'install 'check-installed + (lambda* (#:key outputs inputs #:allow-other-keys) + (begin + (setenv "HOME" (getcwd)) + ;; Make installed package available for running the tests. + (add-installed-pythonpath inputs outputs) + (invoke "python" "selftest.py" "--installed") + (invoke "python" "-m" "pytest" "-vv"))))))) (home-page "https://pypi.python.org/pypi/Pillow") (synopsis "Fork of the Python Imaging Library") (description From ea600ff709f6688589435b8bd617341ee03def78 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Sat, 12 Jan 2019 16:39:26 -0500 Subject: [PATCH 148/300] gnu: python-pillow: Update homepage. * gnu/packages/python.scm (python-pillow)[homepage]: Update URL. --- gnu/packages/python.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index d412ee5077..86ff4f2044 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4112,7 +4112,7 @@ the OleFileIO module from PIL, the Python Image Library.") (add-installed-pythonpath inputs outputs) (invoke "python" "selftest.py" "--installed") (invoke "python" "-m" "pytest" "-vv"))))))) - (home-page "https://pypi.python.org/pypi/Pillow") + (home-page "https://python-pillow.org") (synopsis "Fork of the Python Imaging Library") (description "The Python Imaging Library adds image processing capabilities to your From 7e634c2f530767c63d0c5773b5aad2351034ede4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 11 Jan 2019 09:26:44 +0100 Subject: [PATCH 149/300] refresh: Suggest input changes when updating. * guix/upstream.scm ()[input-changes]: New field. (): New record. (upstream-input-change?, upstream-input-change-name, upstream-input-change-type, upstream-input-change-action, changed-inputs): New procedures. (package-update): Pass along input changes. * guix/script/refresh.scm (update-package): Process input changes. --- guix/scripts/refresh.scm | 23 +++++++++- guix/upstream.scm | 90 ++++++++++++++++++++++++++++++++++++---- 2 files changed, 104 insertions(+), 9 deletions(-) diff --git a/guix/scripts/refresh.scm b/guix/scripts/refresh.scm index 516e09b4ce..a0de9f6c10 100644 --- a/guix/scripts/refresh.scm +++ b/guix/scripts/refresh.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Mathieu Othacehe ;;; Copyright © 2018 Efraim Flashner +;;; Copyright © 2019 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -296,7 +297,7 @@ KEY-DOWNLOAD specifies a download policy for missing OpenPGP keys; allowed values: 'interactive' (default), 'always', and 'never'. When WARN? is true, warn about packages that have no matching updater." (if (lookup-updater package updaters) - (let-values (((version tarball) + (let-values (((version tarball changes) (package-update store package updaters #:key-download key-download)) ((loc) @@ -310,6 +311,26 @@ warn about packages that have no matching updater." (location->string loc) (package-name package) (package-version package) version) + (for-each + (lambda (change) + (format (current-error-port) + (match (list (upstream-input-change-action change) + (upstream-input-change-type change)) + (('add 'regular) + (G_ "~a: consider adding this input: ~a~%")) + (('add 'native) + (G_ "~a: consider adding this native input: ~a~%")) + (('add 'propagated) + (G_ "~a: consider adding this propagated input: ~a~%")) + (('remove 'regular) + (G_ "~a: consider removing this input: ~a~%")) + (('remove 'native) + (G_ "~a: consider removing this native input: ~a~%")) + (('remove 'propagated) + (G_ "~a: consider removing this propagated input: ~a~%"))) + (package-name package) + (upstream-input-change-name change))) + (changes)) (let ((hash (call-with-input-file tarball port-sha256))) (update-package-source package version hash))) diff --git a/guix/upstream.scm b/guix/upstream.scm index 9e1056f7a7..9163478099 100644 --- a/guix/upstream.scm +++ b/guix/upstream.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2015 Alex Kost +;;; Copyright © 2019 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -45,6 +46,7 @@ upstream-source-urls upstream-source-signature-urls upstream-source-archive-types + upstream-source-input-changes url-prefix-predicate coalesce-sources @@ -56,6 +58,12 @@ upstream-updater-predicate upstream-updater-latest + upstream-input-change? + upstream-input-change-name + upstream-input-change-type + upstream-input-change-action + changed-inputs + %updaters lookup-updater @@ -82,7 +90,73 @@ (version upstream-source-version) ;string (urls upstream-source-urls) ;list of strings (signature-urls upstream-source-signature-urls ;#f | list of strings - (default #f))) + (default #f)) + (input-changes upstream-source-input-changes + (default '()) (thunked))) + +;; Representation of an upstream input change. +(define-record-type* + upstream-input-change make-upstream-input-change + upstream-input-change? + (name upstream-input-change-name) ;string + (type upstream-input-change-type) ;symbol: regular | native | propagated + (action upstream-input-change-action)) ;symbol: add | remove + +(define (changed-inputs package package-sexp) + "Return a list of input changes for PACKAGE based on the newly imported +S-expression PACKAGE-SEXP." + (match package-sexp + ((and expr ('package fields ...)) + (let* ((input->name (match-lambda ((name pkg . out) name))) + (new-regular + (match expr + ((path *** ('inputs + ('quasiquote ((label ('unquote sym)) ...)))) label) + (_ '()))) + (new-native + (match expr + ((path *** ('native-inputs + ('quasiquote ((label ('unquote sym)) ...)))) label) + (_ '()))) + (new-propagated + (match expr + ((path *** ('propagated-inputs + ('quasiquote ((label ('unquote sym)) ...)))) label) + (_ '()))) + (current-regular + (map input->name (package-inputs package))) + (current-native + (map input->name (package-native-inputs package))) + (current-propagated + (map input->name (package-propagated-inputs package)))) + (append-map + (match-lambda + ((action type names) + (map (lambda (name) + (upstream-input-change + (name name) + (type type) + (action action))) + names))) + `((add regular + ,(lset-difference equal? + new-regular current-regular)) + (remove regular + ,(lset-difference equal? + current-regular new-regular)) + (add native + ,(lset-difference equal? + new-native current-native)) + (remove native + ,(lset-difference equal? + current-native new-native)) + (add propagated + ,(lset-difference equal? + new-propagated current-propagated)) + (remove propagated + ,(lset-difference equal? + current-propagated new-propagated)))))) + (_ '()))) (define (url-prefix-predicate prefix) "Return a predicate that returns true when passed a package where one of its @@ -268,12 +342,12 @@ values: the item from LST1 and the item from LST2 that match PRED." (define* (package-update store package updaters #:key (key-download 'interactive)) - "Return the new version and the file name of the new version tarball for -PACKAGE, or #f and #f when PACKAGE is up-to-date. KEY-DOWNLOAD specifies a -download policy for missing OpenPGP keys; allowed values: 'always', 'never', -and 'interactive' (default)." + "Return the new version, the file name of the new version tarball, and input +changes for PACKAGE; return #f (three values) when PACKAGE is up-to-date. +KEY-DOWNLOAD specifies a download policy for missing OpenPGP keys; allowed +values: 'always', 'never', and 'interactive' (default)." (match (package-latest-release* package updaters) - (($ _ version urls signature-urls) + (($ _ version urls signature-urls changes) (let*-values (((name) (package-name package)) ((archive-type) @@ -299,9 +373,9 @@ and 'interactive' (default)." (or signature-urls (circular-list #f))))) (let ((tarball (download-tarball store url signature-url #:key-download key-download))) - (values version tarball)))) + (values version tarball changes)))) (#f - (values #f #f)))) + (values #f #f #f)))) (define (update-package-source package version hash) "Modify the source file that defines PACKAGE to refer to VERSION, From 91e05559bdf21b49686cc2629c44a6d0a6db0a61 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 11 Jan 2019 09:27:21 +0100 Subject: [PATCH 150/300] import: cran: Suggest input changes. * guix/import/cran.scm (latest-cran-release, latest-bioconductor-release): Return input-changes. --- guix/import/cran.scm | 29 ++++++++++++++++++----------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 15163bd165..b287be6941 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2015, 2016, 2017 Ludovic Courtès ;;; Copyright © 2017 Mathieu Othacehe ;;; @@ -390,11 +390,11 @@ s-expression corresponding to that package, or #f on failure." (_ #f))) (_ #f))))) -(define (latest-cran-release package) - "Return an for the latest release of PACKAGE." +(define (latest-cran-release pkg) + "Return an for the latest release of the package PKG." (define upstream-name - (package->upstream-name package)) + (package->upstream-name pkg)) (define meta (fetch-description 'cran upstream-name)) @@ -403,15 +403,18 @@ s-expression corresponding to that package, or #f on failure." (let ((version (assoc-ref meta "Version"))) ;; CRAN does not provide signatures. (upstream-source - (package (package-name package)) + (package (package-name pkg)) (version version) - (urls (cran-uri upstream-name version)))))) + (urls (cran-uri upstream-name version)) + (input-changes + (changed-inputs pkg + (description->package 'cran meta))))))) -(define (latest-bioconductor-release package) - "Return an for the latest release of PACKAGE." +(define (latest-bioconductor-release pkg) + "Return an for the latest release of the package PKG." (define upstream-name - (package->upstream-name package)) + (package->upstream-name pkg)) (define version (latest-bioconductor-package-version upstream-name)) @@ -419,9 +422,13 @@ s-expression corresponding to that package, or #f on failure." (and version ;; Bioconductor does not provide signatures. (upstream-source - (package (package-name package)) + (package (package-name pkg)) (version version) - (urls (bioconductor-uri upstream-name version))))) + (urls (bioconductor-uri upstream-name version)) + (input-changes + (changed-inputs + pkg + (cran->guix-package upstream-name 'bioconductor)))))) (define (cran-package? package) "Return true if PACKAGE is an R package from CRAN." From a2315c670281457fe432f804c563919ce8e49af8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 13:59:22 +0100 Subject: [PATCH 151/300] gnu: r-jsonlite: Update to 1.6. * gnu/packages/cran.scm (r-jsonlite): Update to 1.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 24d1ee85ed..e638c81fe8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -320,13 +320,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.5") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "00lfg464jhf7k01bal9pcjvbdf5cxk6xi2h46hccp1x3h883g434")))) + "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8")))) (build-system r-build-system) (home-page "http://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") From 04a18a81ae85b88ed8858cd4591636494d2ea85e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:00:17 +0100 Subject: [PATCH 152/300] gnu: r-writexl: Update to 1.1. * gnu/packages/cran.scm (r-writexl): Update to 1.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e638c81fe8..550b815225 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5819,14 +5819,14 @@ documents.") (define-public r-writexl (package (name "r-writexl") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "writexl" version)) (sha256 (base32 - "0r2v12dc4zqmr1agp6vbw0fc48i278018684x84psjjqfmnv14cf")))) + "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/ropensci/writexl") From 48102ce12326e05801d0d3c1bbbb171605eadda4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:09:49 +0100 Subject: [PATCH 153/300] gnu: r-mvabund: Update to 4.0.1. * gnu/packages/cran.scm (r-mvabund): Update to 4.0.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 550b815225..5c9b8b34bc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8007,14 +8007,14 @@ the interfaces between R and C++.") (define-public r-mvabund (package (name "r-mvabund") - (version "3.13.1") + (version "4.0.1") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 - "1z8bj9zbc8h7w1xki9sc2p2rq6lv8gbcmiy9819z54d7lx1i9cnj")))) + "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) From ef91530362de7b3ddba714893c63d9e3d459b632 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:34:57 +0100 Subject: [PATCH 154/300] gnu: r-readr: Update to 1.3.1. * gnu/packages/statistics.scm (r-readr): Update to 1.3.1. [propagated-inputs]: Add r-clipr and r-crayon. --- gnu/packages/statistics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index e78e8d199d..0952f08d25 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2467,16 +2467,18 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "1.1.1") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "1cvw5wdcqk88cp5fyv678mnmp66l3whcd2yh33p2qvx0168bja8s")))) + "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) + `(("r-clipr" ,r-clipr) + ("r-crayon" ,r-crayon) + ("r-rcpp" ,r-rcpp) ("r-hms" ,r-hms) ("r-tibble" ,r-tibble) ("r-r6" ,r-r6) From 646e1ef059933128bb63be684a56a17ebbab4e79 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:40:35 +0100 Subject: [PATCH 155/300] gnu: r-curl: Update to 3.3. * gnu/packages/cran.scm (r-curl): Update to 3.3. [inputs]: Add zlib. [native-inputs]: Add pkg-config. --- gnu/packages/cran.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5c9b8b34bc..31fab14540 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -458,13 +458,13 @@ LaTeX.") (define-public r-curl (package (name "r-curl") - (version "3.2") + (version "3.3") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "15hmy71310hnf9yqvz0icx4cq939gv6iqaifzlfdh2ia8akawdhn")))) + "1gd5i25anzi28lg1f8p7g63z9d46xi0qaw4lxpml5p0f52lvkc0c")))) (build-system r-build-system) (arguments `(#:phases @@ -481,7 +481,10 @@ LaTeX.") (("#ifdef _WIN32") "#if 1")) #t))))) (inputs - `(("libcurl" ,curl))) + `(("libcurl" ,curl) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "https://github.com/jeroenooms/curl") (synopsis "HTTP client for R") (description From 25c67ecfc69bb5d4985e130c3d31c2caee909e6f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:43:32 +0100 Subject: [PATCH 156/300] gnu: Add r-generics. * gnu/packages/cran.scm (r-generics): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 31fab14540..b47df16df6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2532,6 +2532,26 @@ displays of path diagrams, factor analysis and structural equation models are created using basic graphics.") (license license:gpl2+))) +(define-public r-generics + (package + (name "r-generics") + (version "0.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "generics" version)) + (sha256 + (base32 + "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi")))) + (build-system r-build-system) + (home-page "https://github.com/r-lib/generics") + (synopsis "Common S3 generics not provided by base R methods") + (description + "In order to reduce potential package dependencies and conflicts, +generics provides a number of commonly used S3 generics that are not provided +by base R methods related to model fitting.") + (license license:gpl2))) + (define-public r-broom (package (name "r-broom") From 813d9c51e359d1971bb30624e03963b2109156b5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:43:41 +0100 Subject: [PATCH 157/300] gnu: r-broom: Update to 0.5.1. * gnu/packages/cran.scm (r-broom): Update to 0.5.1. [propagated-inputs]: Add r-generics. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b47df16df6..610282569f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2555,18 +2555,19 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1r3831vq0fd5sh5841xr844sghg88z7ws91hg4jgnzbbkxfjp4ag")))) + "0bmf38yvwalqf5j5yrr48nsk5k3n75s0gwcw621hp5lgrgvnp7ns")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) ("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) ("r-nlme" ,r-nlme) ("r-purrr" ,r-purrr) ("r-reshape2" ,r-reshape2) From 2766d3436ab6690a767bbe2db66aa91f2d988940 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:44:25 +0100 Subject: [PATCH 158/300] gnu: r-sjlabelled: Update to 1.0.16. * gnu/packages/cran.scm (r-sjlabelled): Update to 1.0.16. [propagated-inputs]: Remove r-tibble and r-tidyselect. --- gnu/packages/cran.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 610282569f..e431ee9d08 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5697,14 +5697,14 @@ other add-on packages.") (define-public r-sjlabelled (package (name "r-sjlabelled") - (version "1.0.14") + (version "1.0.16") (source (origin (method url-fetch) (uri (cran-uri "sjlabelled" version)) (sha256 (base32 - "0ayfzhm9bwjfaarq5z0gvn9kapjwj3532azgin97nr5fnjdhvgaw")))) + "1zi1ncna16zl9hcy7mzara4kjxqkgwcw9ncp388ss353wwc9y2nc")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -5714,9 +5714,7 @@ other add-on packages.") ("r-prediction" ,r-prediction) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) - ("r-snakecase" ,r-snakecase) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect))) + ("r-snakecase" ,r-snakecase))) (home-page "https://github.com/strengejacke/sjlabelled") (synopsis "Labelled data utility functions") (description From 0e87bf017747adfc8ce6375aa5d94f3b75cea79d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:45:54 +0100 Subject: [PATCH 159/300] gnu: r-processx: Update to 3.2.1. * gnu/packages/cran.scm (r-processx): Update to 3.2.1. [propagated-inputs]: Remove r-assertthat, r-crayon, and r-testthat. --- gnu/packages/cran.scm | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e431ee9d08..da899ae52d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3348,21 +3348,18 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.2.0") + (version "3.2.1") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 - "1pzx4ap4xa07gf9zkd6hacdsnb9sp3kb60a7v7ljl0ywrcpn1fn4")))) + "1skjyi767avc3safajlj3ikk9lf11zzyjybdcmx8m9y59rf319ql")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-crayon" ,r-crayon) - ("r-ps" ,r-ps) - ("r-r6" ,r-r6) - ("r-testthat" ,r-testthat))) + `(("r-ps" ,r-ps) + ("r-r6" ,r-r6))) (home-page "https://github.com/r-lib/processx3") (synopsis "Execute and control system processes") (description From 44c69a536ef84a1aac3cf71eee4e65b07941aeb1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:50:30 +0100 Subject: [PATCH 160/300] gnu: r-rcpparmadillo: Update to 0.9.200.5.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.5.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0952f08d25..f831033f5d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2552,13 +2552,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.9.200.4.0") + (version "0.9.200.5.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1ayvpyi4hgaqrhx1kqi640iillc2byj4kam7vydlgqmdrzpgrfvz")))) + "09041jnalh7352kj6lv4d0xr9c0mvf8p860q5c8m13mp214x5x7k")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (native-inputs From 0aad198e2b9fe5f9376fd9d67c1b33028c59f139 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:51:59 +0100 Subject: [PATCH 161/300] gnu: r-pracma: Update to 2.2.2. * gnu/packages/maths.scm (r-pracma): Update to 2.2.2. --- gnu/packages/maths.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 4138c7a3bd..d4ead475b0 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier ;;; Copyright © 2014 Federico Beffa ;;; Copyright © 2014 Mathieu Lirzin -;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2015 Sou Bunnbu ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner @@ -2179,12 +2179,12 @@ programming problems.") (define-public r-pracma (package (name "r-pracma") - (version "2.1.8") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "0m8ladhrfyxwybblkcdgg4xv1mk5kibmwarpj2k0c2y34zzcix4z")))) + (base32 "18zhni05gwnxbphl6bmjjxmsgg5wwnnkwlb4g971cqyw3dsd83ki")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") From b140569e18b7352a8d6021b519dd8f680276a4d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:53:49 +0100 Subject: [PATCH 162/300] gnu: r-readxl: Update to 1.2.0. * gnu/packages/cran.scm (r-readxl): Update to 1.2.0. [propagated-inputs]: Add r-progress. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index da899ae52d..b6cc44c9b2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -237,17 +237,18 @@ that.") (define-public r-readxl (package (name "r-readxl") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "readxl" version)) (sha256 (base32 - "05ii8knrg4jji6h7bv6bfpn279b6x52yrskdx5rv7b0hcpy22gdn")))) + "1mwm389skl4ahcwsmhvx31pjkrn6y9igpnhsczwg6yza886q7j19")))) (build-system r-build-system) (propagated-inputs `(("r-cellranger" ,r-cellranger) + ("r-progress" ,r-progress) ("r-rcpp" ,r-rcpp) ("r-tibble" ,r-tibble))) (home-page "https://readxl.tidyverse.org") From 527c6055989019231e1ab5288ffd5a051d8a8bc2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:54:48 +0100 Subject: [PATCH 163/300] gnu: r-callr: Update to 3.1.1. * gnu/packages/cran.scm (r-callr): Update to 3.1.1. [propagated-inputs]: Remove r-base64enc. --- gnu/packages/cran.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b6cc44c9b2..19930173ac 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -213,18 +213,17 @@ such as copy/paste from an R session.") (define-public r-callr (package (name "r-callr") - (version "3.0.0") + (version "3.1.1") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "1rxbxy6kn7dj90z9hpppr9cnpvnxzknba2dwrdp0lrk5dh462qz3")))) + "15l1qfa3aigba2ghgr2gwcjjy7anagrwg8khsd36fymwkmqj5g69")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-r6" ,r-r6) + `(("r-r6" ,r-r6) ("r-processx" ,r-processx))) (home-page "https://github.com/r-lib/callr#readme") (synopsis "Call R from R") From 11a36548d9dcefd45348809460899d3405292616 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 14:56:43 +0100 Subject: [PATCH 164/300] gnu: r-argparse: Update to 2.0.0. * gnu/packages/cran.scm (r-argparse): Update to 2.0.0. [propagated-inputs]: Add r-r6; remove r-proto. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 19930173ac..35cdef00bc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5955,21 +5955,21 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "1.1.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "0fzrbj87b274vf96azdnsjxk2nf45d5wy58vzmlah4b4h7q4j524")))) + "1qrp7hc8sm6ryw0zws76al865ansig1xbx8ljxz4wabh60msrz3i")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs `(("r-findpython" ,r-findpython) ("r-getopt" ,r-getopt) ("r-jsonlite" ,r-jsonlite) - ("r-proto" ,r-proto))) + ("r-r6" ,r-r6))) (home-page "https://github.com/trevorld/argparse") (synopsis "Command line optional and positional argument parser") (description From 35cf4874ccf9c7ef06325e695e592add2dbbf94a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:17:24 +0100 Subject: [PATCH 165/300] gnu: r-survival: Update to 2.43-3. * gnu/packages/statistics.scm (r-survival): Update to 2.43-3. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f831033f5d..a6302db0b6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2015 Vicente Vera Parra ;;; Copyright © 2016 Andreas Enge ;;; Copyright © 2016, 2017 Efraim Flashner @@ -652,14 +652,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "2.43-1") + (version "2.43-3") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "0220fjsq4ycx1n5zc5h39wdbj5j6xr8rzqbcixx2p25akzdn7kqk")))) + "0ldrjja1dj4n1ic0lbggm7jvk52sl5h85i8m23nrgndi60acsv4r")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) From 3dbd87f504394a51952a01babde7671e81c8713c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:39:52 +0100 Subject: [PATCH 166/300] gnu: r-class: Update to 7.3-15. * gnu/packages/statistics.scm (r-class): Update to 7.3-15. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a6302db0b6..ead3509ee1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -398,14 +398,14 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") (define-public r-class (package (name "r-class") - (version "7.3-14") + (version "7.3-15") (source (origin (method url-fetch) (uri (cran-uri "class" version)) (sha256 (base32 - "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q")))) + "1x1hqz8xyhbpq4krsh02glqnlzcch25agkmn4a3da9n723b37gzn")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) From 60f1bce09f3aed47dbac61dd70450a0e77a31810 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:40:07 +0100 Subject: [PATCH 167/300] gnu: r-codetools: Update to 0.2-16. * gnu/packages/statistics.scm (r-codetools): Update to 0.2-16. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ead3509ee1..bead2d4e06 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -442,14 +442,14 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") (define-public r-codetools (package (name "r-codetools") - (version "0.2-15") + (version "0.2-16") (source (origin (method url-fetch) (uri (cran-uri "codetools" version)) (sha256 (base32 - "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf")))) + "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/codetools") (synopsis "Code analysis tools for R") From ca2bc7e0377fb69349498779bf03fcd4a1bd5142 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:40:17 +0100 Subject: [PATCH 168/300] gnu: r-mgcv: Update to 1.8-26. * gnu/packages/statistics.scm (r-mgcv): Update to 1.8-26. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index bead2d4e06..f7bbc042d3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -570,14 +570,14 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-25") + (version "1.8-26") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 (base32 - "1y2rq6v45pr2wcxihhgmingcdvcsilim2cvskrlb7k2n00qg6v2q")))) + "02bsz455fr5hyhpmgcrd266qafs2wbz3ygdipxg9gfazbdvq2v4q")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) From b6e27673e652fdc628948cdd669efa8857a4e755 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:40:26 +0100 Subject: [PATCH 169/300] gnu: r-pheatmap: Update to 1.0.12. * gnu/packages/statistics.scm (r-pheatmap): Update to 1.0.12. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f7bbc042d3..ec9aaee9e7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -811,14 +811,14 @@ non-estimable cases correctly.") (define-public r-pheatmap (package (name "r-pheatmap") - (version "1.0.10") + (version "1.0.12") (source (origin (method url-fetch) (uri (cran-uri "pheatmap" version)) (sha256 (base32 - "1jzxs5hwbz3r0z2pp09i7fd14sndxnrbm3zibaac3kny4nzydzf7")))) + "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap")))) (build-system r-build-system) (propagated-inputs `(("r-gtable" ,r-gtable) From eae93bd3f283c1046a97ee5b7ac8d71e738ef49e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:40:35 +0100 Subject: [PATCH 170/300] gnu: r-bh: Update to 1.69.0-1. * gnu/packages/statistics.scm (r-bh): Update to 1.69.0-1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ec9aaee9e7..62420231e8 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1269,13 +1269,13 @@ R/DBMS implementations.") (define-public r-bh (package (name "r-bh") - (version "1.66.0-1") + (version "1.69.0-1") (source (origin (method url-fetch) (uri (cran-uri "BH" version)) (sha256 (base32 - "14kab6wp0c27d8x4jqyf065p4bj210s9b67c0bfsfjnp29aypn8p")))) + "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0")))) (build-system r-build-system) (home-page "https://github.com/eddelbuettel/bh") (synopsis "R package providing subset of Boost headers") From bf3aded0cf223e572ddff88878c28f7766ef7f27 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:40:46 +0100 Subject: [PATCH 171/300] gnu: r-markdown: Update to 0.9. * gnu/packages/statistics.scm (r-markdown): Update to 0.9. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 62420231e8..56a49db417 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1364,13 +1364,13 @@ data derived from /etc/mime.types in UNIX-type systems.") (define-public r-markdown (package (name "r-markdown") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "markdown" version)) (sha256 (base32 - "1vcgsh2m2f5kfgappgg71nbf04ff0j1sbk668krjs3r2n89dk3sk")))) + "08xzs4bcf12jxp0276m6xqvq8kcgg5qp6fxrvsz6r9x73jjccs1h")))) (build-system r-build-system) ;; Skip check phase because the tests require the r-knitr package to be ;; installed. This prevents installation failures. Knitr normally From 495866a9d787f353a592f5949d5950c942d6e49f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:40:56 +0100 Subject: [PATCH 172/300] gnu: r-knitr: Update to 1.21. * gnu/packages/statistics.scm (r-knitr): Update to 1.21. [propagated-inputs]: Add r-xfun. --- gnu/packages/statistics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 56a49db417..96018c387d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1408,19 +1408,20 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.20") + (version "1.21") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "1408dm25cxahk2clff8hlajaqdj5v1gs40nm3q6rf0ghd82hj93v")))) + "0xzymi4gkilqaa5b2ay9zk1advavzkwxf7mb064bqfb09y8rak0j")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) ("r-highr" ,r-highr) ("r-markdown" ,r-markdown) ("r-stringr" ,r-stringr) + ("r-xfun" ,r-xfun) ("r-yaml" ,r-yaml))) (home-page "http://yihui.name/knitr/") (synopsis "General-purpose package for dynamic report generation in R") From c668a958610b84100368e17504a74dcbc2ad9b7d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:41:11 +0100 Subject: [PATCH 173/300] gnu: r-rlang: Update to 0.3.1. * gnu/packages/statistics.scm (r-rlang): Update to 0.3.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 96018c387d..cf59d014cd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1612,13 +1612,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.3.0.1") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "0j7kp6h25wbkvpzr7dpc0zgdpjiwsjjlgprj3mv7bgfalfq1si99")))) + "0lbi66bavca866k26dnpkxj3l106xr4a6khcsfn8i3i8w8mpnhih")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") From f12ed3664da23bb042ad3fa3ecf384e1bbd23979 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:41:26 +0100 Subject: [PATCH 174/300] gnu: r-tibble: Update to 2.0.0. * gnu/packages/statistics.scm (r-tibble): Update to 2.0.0. [propagated-inputs]: Add r-fansi and r-pkgconfig. --- gnu/packages/statistics.scm | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index cf59d014cd..9dc2ae8f2d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1630,20 +1630,22 @@ like tidy evaluation.") (define-public r-tibble (package (name "r-tibble") - (version "1.4.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "05svbjkm1xqv56ybjgsqqg2pp8nn6hams1yxcr8aanbhzx9h6rqi")))) + "1flrvmgc77c8s0brgyha6cdz2883h6bcb2mvqi49b429x5i2vb85")))) (build-system r-build-system) (propagated-inputs - `(("r-rlang" ,r-rlang) - ("r-cli" ,r-cli) + `(("r-cli" ,r-cli) ("r-crayon" ,r-crayon) - ("r-pillar" ,r-pillar))) + ("r-fansi" ,r-fansi) + ("r-pkgconfig" ,r-pkgconfig) + ("r-pillar" ,r-pillar) + ("r-rlang" ,r-rlang))) (home-page "https://github.com/hadley/tibble") (synopsis "Simple data frames") (description From 23347dc35396227ccc6b33e957b719d688b2d7c1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:42:04 +0100 Subject: [PATCH 175/300] gnu: r-dbplyr: Update to 1.3.0. * gnu/packages/statistics.scm (r-dbplyr): Update to 1.3.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9dc2ae8f2d..3fe20d5523 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1693,14 +1693,14 @@ database.") (define-public r-dbplyr (package (name "r-dbplyr") - (version "1.2.2") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "dbplyr" version)) (sha256 (base32 - "0j5w6a1qim972kv4vmvinp3j50yr4idmm9cd3w7y3zsz0nq0nhcx")))) + "07p23vyvi7s4abldhkyir05kcf7xnfc18igfryq12j67xd0jql0m")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) From ca4861c602f7b67a9f8057b528cd90af5f712518 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:42:16 +0100 Subject: [PATCH 176/300] gnu: r-backports: Update to 1.1.3. * gnu/packages/statistics.scm (r-backports): Update to 1.1.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3fe20d5523..02e65ffe34 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2075,14 +2075,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "0mml9h3xagi7144pyb3jj9zbh9qzns7izkhdg7df20v7bikr6nz8")))) + "1hac46xaawnqajlsfb5k7pfkc2ya9h76s5qv9ycj3jafh93d26z4")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") From fe8c44502b2a5a975166207d99a164763861f2e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:42:27 +0100 Subject: [PATCH 177/300] gnu: r-checkmate: Update to 1.9.0. * gnu/packages/statistics.scm (r-checkmate): Update to 1.9.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 02e65ffe34..eaaff2363d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2098,14 +2098,14 @@ R version.") (define-public r-checkmate (package (name "r-checkmate") - (version "1.8.5") + (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "checkmate" version)) (sha256 (base32 - "1q6igk50lq4fp5d3imgcn1j063h3gsp214ra4nlf534hf4wjlkg9")))) + "00bjlc910y4paddvpz68pl3qyvjxlwqgyh39wpfkq43p99gvnj37")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports))) From 02c89c58121f9a06471c5b6f84a6c730cd2c011d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:42:39 +0100 Subject: [PATCH 178/300] gnu: r-commonmark: Update to 1.7. * gnu/packages/statistics.scm (r-commonmark): Update to 1.7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index eaaff2363d..8eb6d76d81 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2240,14 +2240,14 @@ other packages.") (define-public r-commonmark (package (name "r-commonmark") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) (uri (cran-uri "commonmark" version)) (sha256 (base32 - "1xymqncf8byqxzpx64zlp6vbx7gry572jkr2ax0zlavr8bli861x")))) + "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/commonmark") (synopsis "CommonMark and Github Markdown Rendering in R") From c12e429348f31c82996ffc242ae887bf98bdbb37 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:42:48 +0100 Subject: [PATCH 179/300] gnu: r-httr: Update to 1.4.0. * gnu/packages/statistics.scm (r-httr): Update to 1.4.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8eb6d76d81..7613ec8827 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2324,13 +2324,13 @@ integers.") (define-public r-httr (package (name "r-httr") - (version "1.3.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "httr" version)) (sha256 (base32 - "0n7jz2digbgv48rbr9vmzv4vmf4rahl9jjy31izs7sxj4rs4s4r2")))) + "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) From 8f49d99a84032416b5071526323bd266bcfebdf7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:42:59 +0100 Subject: [PATCH 180/300] gnu: r-git2r: Update to 0.24.0. * gnu/packages/statistics.scm (r-git2r): Update to 0.24.0. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7613ec8827..42e4efed55 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2350,19 +2350,19 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.23.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "01250jz255fnyy2ap90nskvzhd8nhlmbhwgpvb43mk1fax077lrz")))) + "0vfc25z4j53pc49cnp3zjwzjb72kvc0aq96wgyg10xpgvhl3z0gg")))) (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 ;; not among the inputs of this package. (inputs - `(("libssh2" ,libssh2) + `(("libssh2" ,libssh2) ; for SSH transport ("openssl" ,openssl) ("zlib" ,zlib))) (native-inputs From fb4593420238d5d0349c4e322b05e1f627f91b01 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:43:11 +0100 Subject: [PATCH 181/300] gnu: r-rstudioapi: Update to 0.9.0. * gnu/packages/statistics.scm (r-rstudioapi): Update to 0.9.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 42e4efed55..589a2c0d51 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2378,13 +2378,13 @@ pure C implementation of the Git core methods.") (define-public r-rstudioapi (package (name "r-rstudioapi") - (version "0.8") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "rstudioapi" version)) (sha256 (base32 - "0d6r0in13k0rcyr6asanwy0a9dv4lizq6l2w913rr222pq6vrrck")))) + "0gn1pvaxfh2gh2ikvxcr8f6k97ygcfr68iz6dhwlq4z71a1s4jai")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rstudioapi") (synopsis "Safely access the RStudio API") From 54ebdf6f749a94848e8de2288b7af843431f0142 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:43:26 +0100 Subject: [PATCH 182/300] gnu: r-rmarkdown: Update to 1.11. * gnu/packages/statistics.scm (r-rmarkdown): Update to 1.11. [propagated-inputs]: Remove r-rprojroot. --- gnu/packages/statistics.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 589a2c0d51..c061cb851f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2649,14 +2649,14 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.10") + (version "1.11") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "0mh2f3k98w7pgz0ri34149s4kx5y0kfm27nwq64k0qwxd16hwd9r")))) + "0yyjbh891mdqzpjkblz8510ng71i7mxmyiqr69x3rwlwk2vakk79")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2666,7 +2666,6 @@ certain criterion, e.g., it contains a certain regular file.") ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-mime" ,r-mime) - ("r-rprojroot" ,r-rprojroot) ("r-stringr" ,r-stringr) ("r-tinytex" ,r-tinytex) ("r-yaml" ,r-yaml) From 2c8594d96317663d89579e8b225a889c2c0744cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:43:43 +0100 Subject: [PATCH 183/300] gnu: r-sfsmisc: Update to 1.1-3. * gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c061cb851f..314719fda1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4109,14 +4109,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-2") + (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "0cgq2h11ngkzd6p34k6mqjnvlvc5vj4lnqrl64k05lb391j391w0")))) + "1y25nnw09qfm66523w1z4q766lv15a6ykvsq30r154n7m7aggvsq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") From 7213ef07c6773c7dadb3712e08b4531f38a016cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:43:54 +0100 Subject: [PATCH 184/300] gnu: r-rann: Update to 2.6.1. * gnu/packages/statistics.scm (r-rann): Update to 2.6.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 314719fda1..8cbec537a4 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4450,13 +4450,13 @@ dispersion modeling and Tweedie power-law families.") (define-public r-rann (package (name "r-rann") - (version "2.6") + (version "2.6.1") (source (origin (method url-fetch) (uri (cran-uri "RANN" version)) (sha256 (base32 - "1r6rivh9ba4gwnzryip0aiwsbm46zma7nvd9z5y456p2dgzp9lii")))) + "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj")))) (properties `((upstream-name . "RANN"))) (build-system r-build-system) From 70ee5ab13755816a953509a09705ad82457e7207 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:44:03 +0100 Subject: [PATCH 185/300] gnu: r-cowplot: Update to 0.9.4. * gnu/packages/statistics.scm (r-cowplot): Update to 0.9.4. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8cbec537a4..88f263938f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4519,14 +4519,14 @@ Farebrother's algorithm or Liu et al.'s algorithm.") (define-public r-cowplot (package (name "r-cowplot") - (version "0.9.3") + (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "cowplot" version)) (sha256 (base32 - "1jrx1h0blkk577y4cvnjk7xccn7qmjiv2bnpgqlsjvjhsxglf41y")))) + "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) From bcc17f7f11d93d181351ab0034b7f696bc626cf3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:44:13 +0100 Subject: [PATCH 186/300] gnu: r-rrcov: Update to 1.4-7. * gnu/packages/statistics.scm (r-rrcov): Update to 1.4-7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 88f263938f..7efd5a6c97 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4817,14 +4817,14 @@ analysis} (PCA) by projection pursuit.") (define-public r-rrcov (package (name "r-rrcov") - (version "1.4-4") + (version "1.4-7") (source (origin (method url-fetch) (uri (cran-uri "rrcov" version)) (sha256 (base32 - "0wn5h8vi0zyk5ah898m37ysz4kiih6y792nb9zdvhvd8r07f0sc5")))) + "14zjyqcdiqx6js99nx5s8hmyx564ixy2d8s6i7wa50xmx368rl6b")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) From 9b7df80b9bc8754f356200694a217e6cb59b0796 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:44:24 +0100 Subject: [PATCH 187/300] gnu: r-rcppeigen: Update to 0.3.3.5.0. * gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.3.5.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7efd5a6c97..0c072d6a8c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5023,14 +5023,14 @@ based on an interface to Fortran implementations by M. J. D. Powell.") (define-public r-rcppeigen (package (name "r-rcppeigen") - (version "0.3.3.4.0") + (version "0.3.3.5.0") (source (origin (method url-fetch) (uri (cran-uri "RcppEigen" version)) (sha256 (base32 - "1m6ssq6lvi36ggf26y4hhq996583pxxdb978jnn1x6r9gdb0q0hi")))) + "01bz41c29591ybzqn4z88ss036ai3anh9figryvmfpqcfwbszip5")))) (properties `((upstream-name . "RcppEigen"))) (build-system r-build-system) (propagated-inputs From aa72d7f7f57145038ff182571795cd189add0069 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:44:37 +0100 Subject: [PATCH 188/300] gnu: r-quantreg: Update to 5.38. * gnu/packages/statistics.scm (r-quantreg): Update to 5.38. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0c072d6a8c..c5b5f69df7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5093,14 +5093,14 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.36") + (version "5.38") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 (base32 - "023gdzahxp582rpabilpxbl3wyjrgjjnnrhcv9xhrqdfiq5l2yza")))) + "1vvvnk291f0dccg04l3nsnk585gq75sk0b2vdbrqv3lczvv18nw1")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) From 2e4fc4ac626ae88525cecab6057176b604866949 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 15:44:47 +0100 Subject: [PATCH 189/300] gnu: r-caret: Update to 6.0-81. * gnu/packages/statistics.scm (r-caret): Update to 6.0-81. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c5b5f69df7..23ac6832fe 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5255,14 +5255,14 @@ to Applied regression, Second Edition, Sage, 2011.") (define-public r-caret (package (name "r-caret") - (version "6.0-80") + (version "6.0-81") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 - "0xhdhazzfh0hiqv2hgxglj9ffd2p4ls8acqn2sjn0ndx6158f187")))) + "1fibrskjzq2f06b8gbrfp3263svfc5s5apsjwaqdg9qzs7sy7fpc")))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,r-foreach) From 0c025a7f794b4cd75b9c713b00a86df23e1f8d30 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:33:05 +0100 Subject: [PATCH 190/300] gnu: r-clipr: Update to 0.5.0. * gnu/packages/cran.scm (r-clipr): Update to 0.5.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 35cdef00bc..32547715d7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -66,14 +66,14 @@ (define-public r-clipr (package (name "r-clipr") - (version "0.4.1") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "clipr" version)) (sha256 (base32 - "061x84ildc7g1p91yw5iyj8lpqdf4hqv36as85lw8c6qv9ywbsqv")))) + "1grx0lyww1cxmdvsr44wmbhz9i6zmiwxbchb97gxrfi9gy5kyc7x")))) (build-system r-build-system) (home-page "https://github.com/mdlincoln/clipr") (synopsis "Read and write from the system clipboard") From 37349c717ee1f9609fcea38f277590e621c8028a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:33:27 +0100 Subject: [PATCH 191/300] gnu: r-httpuv: Update to 1.4.5.1. * gnu/packages/cran.scm (r-httpuv): Update to 1.4.5.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 32547715d7..36d9e490e4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -290,13 +290,13 @@ into a pipeline of data manipulation and visualisation.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.4.5") + (version "1.4.5.1") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "1ddpcarzf694h0gy5pdz7l5glqfv4hr9dmxb4vw7yqd0bga174gi")))) + "0mqd40jckdpkjw1jjd860cdwkb03l6dkh931maijfdaqr1w9hwvn")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp) From 1add168ab5139baca83148df984a9278e4ce1a47 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:33:39 +0100 Subject: [PATCH 192/300] gnu: r-htmltable: Update to 1.13.1. * gnu/packages/cran.scm (r-htmltable): Update to 1.13.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 36d9e490e4..ac1f8866dd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -425,14 +425,14 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "1.12") + (version "1.13.1") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 (base32 - "1n5136vb7mi4rxl5jgwdmdhn4mwv2pcqyw2mrj406ih4hy6hpxa2")))) + "1l44b33xgj2698k6nz17r8fl0ink14ryzng803apm9d6bnv357v8")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs From 69aad34ae0f369b36a37d9c54c8e4265b25fd657 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:33:49 +0100 Subject: [PATCH 193/300] gnu: r-feather: Update to 0.3.2. * gnu/packages/cran.scm (r-feather): Update to 0.3.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ac1f8866dd..f9be88392e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -788,14 +788,14 @@ work well on small screens.") (define-public r-feather (package (name "r-feather") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "feather" version)) (sha256 (base32 - "1q6dbkfnkpnabq8lb6bm9ma44cfcghx2lm23pyk3vg7943wrn1pi")))) + "138vnlwhkwayyim4rbx6rnf91kzhfij6v2f91ppx2174ky5611h6")))) (build-system r-build-system) (propagated-inputs `(("r-hms" ,r-hms) From dcf89cc0cf21dabeac59e33e91e7dd8e168647aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:33:57 +0100 Subject: [PATCH 194/300] gnu: r-haven: Update to 2.0.0. * gnu/packages/cran.scm (r-haven): Update to 2.0.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f9be88392e..4de60d3543 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -929,14 +929,14 @@ including functions for geolocation and routing.") (define-public r-haven (package (name "r-haven") - (version "1.1.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 - "0pp8xjf5lzqg1wr8cwxj4njx99vxwlflwjrd7jvyzwlfpwh7n1qa")))) + "12qh8nba1dxlsmcihrx126wmjyj8n511k17vqj10lfgvpwq2sydy")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) From 422dea177463ed022951c35b1262240bef76708b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:34:05 +0100 Subject: [PATCH 195/300] gnu: r-ps: Update to 1.3.0. * gnu/packages/cran.scm (r-ps): Update to 1.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4de60d3543..d9b660938e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1147,13 +1147,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "1zxylcb0nr4qb5v6j199mc2pfgf2bpf00jrw47jajmv59qb0fwmx")))) + (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498")))) (build-system r-build-system) (home-page "http://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") From 72c498750677eb07e61fc843e5d40fa60cac93af Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:34:13 +0100 Subject: [PATCH 196/300] gnu: r-circlize: Update to 0.4.5. * gnu/packages/cran.scm (r-circlize): Update to 0.4.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d9b660938e..7fa5f2a1b2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1373,14 +1373,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.4") + (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "1l28maiqi549z191srncxgabx5fnvf0lld7smzwfd3vr5cx8nqww")))) + "0qhn9jzw7gd0jp9rmqrlbmy5ql6hjsa68pkp0acfz1h215dl8ah9")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) From 397dba01c6cc2ade6f9eddfe5f086612bc9c0f83 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:34:25 +0100 Subject: [PATCH 197/300] gnu: r-powerlaw: Update to 0.70.2. * gnu/packages/cran.scm (r-powerlaw): Update to 0.70.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7fa5f2a1b2..b887aed510 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1403,14 +1403,14 @@ multi-dimensional data.") (define-public r-powerlaw (package (name "r-powerlaw") - (version "0.70.1") + (version "0.70.2") (source (origin (method url-fetch) (uri (cran-uri "poweRlaw" version)) (sha256 (base32 - "04sr0nhdd1v915m0zf5gasznzgi08ykcy20kkwdw0l5mvvdbic8m")))) + "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4")))) (properties `((upstream-name . "poweRlaw"))) (build-system r-build-system) (propagated-inputs From 8f88701491573021ccedf18227e7dce545ec4af2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:34:43 +0100 Subject: [PATCH 198/300] gnu: r-lava: Update to 1.6.4. * gnu/packages/cran.scm (r-lava): Update to 1.6.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b887aed510..eeb55d84dc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2171,14 +2171,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6.3") + (version "1.6.4") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "0cayjspry3r2lcbvl77v5v52b2zarri3b8xsf87pw5a3jn9anxcf")))) + "0627cjlg55kzbzcy82w6wykmw2i57qhgfcabn2zy3ydfdswyxij1")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) From 77f97229c93ef0524a3bb74741ce9401884f633e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:35:07 +0100 Subject: [PATCH 199/300] gnu: r-dimred: Add missing input. * gnu/packages/cran.scm (r-dimred)[propagated-inputs]: Add r-magrittr. --- gnu/packages/cran.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index eeb55d84dc..0a6a0c55f9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2253,7 +2253,9 @@ the Kaplan-Meier and Aalen-Johansen methods.") "0ssy2qriiy6zdawriqcbl67qiq68ipml3frq7aqlq70r2fqyyw48")))) (properties `((upstream-name . "dimRed"))) (build-system r-build-system) - (propagated-inputs `(("r-drr" ,r-drr))) + (propagated-inputs + `(("r-drr" ,r-drr) + ("r-magrittr" ,r-magrittr))) (home-page "https://github.com/gdkrmr/dimRed") (synopsis "Framework for dimensionality reduction") (description From 570399184179bbe2b6c687fc6443c4915494e8df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:35:38 +0100 Subject: [PATCH 200/300] gnu: r-recipes: Add missing input. * gnu/packages/cran.scm (r-recipes)[propagated-inputs]: Add r-withr. --- gnu/packages/cran.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0a6a0c55f9..dc2d064307 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2617,7 +2617,8 @@ provides a one-row summary of model-level statistics.") ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyselect" ,r-tidyselect) - ("r-timedate" ,r-timedate))) + ("r-timedate" ,r-timedate) + ("r-withr" ,r-withr))) (home-page "https://github.com/topepo/recipes") (synopsis "Preprocessing tools to create design matrices") (description From 1c6d199ee88b2794b6d9acce1b8170c26f5e7dd9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:35:59 +0100 Subject: [PATCH 201/300] gnu: r-mitml: Update to 0.3-7. * gnu/packages/cran.scm (r-mitml): Update to 0.3-7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dc2d064307..f3ed43eba9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2826,14 +2826,14 @@ clustered data.") (define-public r-mitml (package (name "r-mitml") - (version "0.3-6") + (version "0.3-7") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 - "1pkqv4qazih3byws5z6629pp232n8ra56lip7502727b0b4bsndw")))) + "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6")))) (build-system r-build-system) (propagated-inputs `(("r-haven" ,r-haven) From 221b3b164d56771cddf95395d2a877765650657b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:45:42 +0100 Subject: [PATCH 202/300] gnu: r-rmysql: Update to 0.10.16. * gnu/packages/cran.scm (r-rmysql): Update to 0.10.16. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f3ed43eba9..16f8236101 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2311,14 +2311,14 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.15") + (version "0.10.16") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "0bmc7w5fnkjaf333sgc0hskiy332m9gmfaxg0yzkjxscpizdw43n")))) + "1gh4b730g2v78jg5iln8fkz808ri2vhnhnw43wzkkjpy53jh48sp")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (native-inputs From fc74de42da6f078743f8f2ff88fed4bad7c99586 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:45:58 +0100 Subject: [PATCH 203/300] gnu: r-ddalpha: Update to 1.3.8. * gnu/packages/cran.scm (r-ddalpha): Update to 1.3.8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 16f8236101..777180235a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2396,14 +2396,14 @@ Delaunay triangulation and convex hull computation.") (define-public r-ddalpha (package (name "r-ddalpha") - (version "1.3.4") + (version "1.3.8") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 - "16cn0bhbaz9l9k4y79sv2d4f7pvs7dyka273y89igs5jvr99kfj1")))) + "0gi0hl14ghgf65zxsvgzh9z6xx1nyi49cpx192lmwrwqn3dy7ba0")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) From ed46a05c7534385e8d4d1f99f1bfb055a1191963 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:48:36 +0100 Subject: [PATCH 204/300] gnu: r-laeken: Update to 0.5.0. * gnu/packages/cran.scm (r-laeken): Update to 0.5.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 777180235a..e608df0348 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3108,14 +3108,14 @@ where possible.") (define-public r-laeken (package (name "r-laeken") - (version "0.4.6") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "laeken" version)) (sha256 (base32 - "1rhkv1kk508pwln1d325iq4fink2ncssps0ypxi52j9d7wk78la6")))) + "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) From 111516f9d69f60bc7e446d09d903f3238438dbc7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:49:01 +0100 Subject: [PATCH 205/300] gnu: r-gclus: Update to 1.3.2. * gnu/packages/cran.scm (r-gclus): Update to 1.3.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e608df0348..0e31b98006 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3419,14 +3419,14 @@ available.") (define-public r-gclus (package (name "r-gclus") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "gclus" version)) (sha256 (base32 - "02ba6zj9bjwrzykamjp40ajynx9xjx9h2i85n0ym0r5lcki4x6fn")))) + "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster))) (home-page "https://cran.r-project.org/web/packages/gclus/") From fc00a1f0fcc9aba68dc9eb48c0c734ef29e5ecc9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:49:18 +0100 Subject: [PATCH 206/300] gnu: r-pillar: Update to 1.3.1. * gnu/packages/cran.scm (r-pillar): Update to 1.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0e31b98006..eaf2fdd768 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3538,14 +3538,14 @@ display.") (define-public r-pillar (package (name "r-pillar") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1q6arybmfqxhp5zqj1fri5pb8v7ywcv7bmgf81rrmgl892p4bn5f")))) + "1xnbb9sr5wn9dmp6m7cr4z7i6pmjvyabnfcx6x7i7mvdjmgvaf5k")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) From 7e9e9c9c46d0fb92eb983de44cb7069b0a02fb15 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:49:32 +0100 Subject: [PATCH 207/300] gnu: r-tinytex: Update to 0.10. * gnu/packages/cran.scm (r-tinytex): Update to 0.10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index eaf2fdd768..4f6a4dbc06 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3583,14 +3583,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.9") + (version "0.10") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "08w5hyq3ysh631d5whgcfv1bb007cdc0bjhb83vwmhazs6rgvyjy")))) + "02bz8zaka5j51zin976n5nmk19a0390d0gwgj4zrbh48hl313rqm")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) From 9d8313275765bb19dcd4cad0fb6419ee3a1398e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:49:49 +0100 Subject: [PATCH 208/300] gnu: r-statnet-common: Update to 4.2.0. * gnu/packages/cran.scm (r-statnet-common): Update to 4.2.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4f6a4dbc06..4edb701d11 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3652,14 +3652,14 @@ supports arbitrary vertex/edge/graph attributes.") (define-public r-statnet-common (package (name "r-statnet-common") - (version "4.1.4") + (version "4.2.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 - "14dydm4c4dzc4v6ldxpn04q551nczzfablwibrd8lzgja8x9ksic")))) + "0q942g6kqmqxfss1cxb3yg8y5r1k1h5cyy99s1cfisrn6hqc6xhi")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) From 7abb15f2bbe382187a958d21d9dae911c4c6c030 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:50:05 +0100 Subject: [PATCH 209/300] gnu: r-tseries: Update to 0.10-46. * gnu/packages/cran.scm (r-tseries): Update to 0.10-46. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4edb701d11..5d7a355dc8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3852,14 +3852,14 @@ financial trading strategies.") (define-public r-tseries (package (name "r-tseries") - (version "0.10-45") + (version "0.10-46") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 - "14s1glh5zzdvdl05a2z7ymhgf962svxf8xircghg5sc649lb33n0")))) + "08kjw0bfj5gfcrxpblwqxwna8a5g9gnr7ya61qb02r263pyhm50j")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog) From 5f1f11049f04c35ae9de07def63fc8cff3088701 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:50:22 +0100 Subject: [PATCH 210/300] gnu: r-cubature: Update to 2.0.3. * gnu/packages/cran.scm (r-cubature): Update to 2.0.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5d7a355dc8..107bf464f6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3996,14 +3996,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "1.4-1") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "10jl5l3xnigiq95829ssq69xbim97k851187dghc30awszcx4clh")))) + "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) From f0fe1a5a45b7398fc5b96f5e08b6468d4715688f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:50:49 +0100 Subject: [PATCH 211/300] gnu: r-shinyace: Update to 0.3.3. * gnu/packages/cran.scm (r-shinyace): Update to 0.3.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 107bf464f6..bb3faeab6a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4286,14 +4286,14 @@ files.") (define-public r-shinyace (package (name "r-shinyace") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 - "1fbk5i6w6cpam8s3acf4bgdp8hajn4digjjix3i6i4q3p2rvn6zx")))) + "02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs From f2fc34f241247a1fc52923df10780ca6665bcf6c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:51:07 +0100 Subject: [PATCH 212/300] gnu: r-fnn: Update to 1.1.2.2. * gnu/packages/cran.scm (r-fnn): Update to 1.1.2.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bb3faeab6a..7f3259039e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4555,14 +4555,14 @@ multivariate plot methods.") (define-public r-fnn (package (name "r-fnn") - (version "1.1.2.1") + (version "1.1.2.2") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 - "1n61jrcmakqif8f827x4qnlhm2jqpj5fgjj65c4p0kdd8lzw8pqp")))) + "09k3k0h9ikbwq6225l7gd0nhimbji722680cr66c8n7zpvxn06mm")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") From 962304c31cc5e460ade36d5467fe79a02e915aca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:52:24 +0100 Subject: [PATCH 213/300] gnu: r-arules: Update to 1.6-2. * gnu/packages/cran.scm (r-arules): Update to 1.6-2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7f3259039e..41ebe42a94 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4673,14 +4673,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).") (define-public r-arules (package (name "r-arules") - (version "1.6-1") + (version "1.6-2") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 - "0glfqgxr87900kigmkby2ff7qrjvd6aq595q85y056i5ckjcp615")))) + "0vnss6akk3564kbci3h5rq8ylpckz77cgmflly3gn6fki66f7g96")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) From 1417d5f1d5abb8a368790e31929e35bc1b5813d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:52:40 +0100 Subject: [PATCH 214/300] gnu: r-rio: Update to 0.5.16. * gnu/packages/cran.scm (r-rio): Update to 0.5.16. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 41ebe42a94..4b9a17eff1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4813,14 +4813,14 @@ dependency on Java.") (define-public r-rio (package (name "r-rio") - (version "0.5.10") + (version "0.5.16") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 - "158xg3vj0glk3fslwi6fywwmfym2b6kn3fdmjligdfy5lf68khix")))) + "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) From 1afe56444e19816477e98bdce38a1c3d3fd2ac1e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 16:53:11 +0100 Subject: [PATCH 215/300] gnu: r-glmmtmb: Update to 0.2.3. * gnu/packages/cran.scm (r-glmmtmb): Update to 0.2.3. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4b9a17eff1..548c557d09 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7495,14 +7495,14 @@ models.") (define-public r-glmmtmb (package (name "r-glmmtmb") - (version "0.2.2.0") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 - "1clpkjlmsjmn3m1z5jqv8cgw6bvpqsy4nx6k947r0jya017ny5y5")))) + "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs @@ -7512,7 +7512,7 @@ models.") ("r-rcppeigen" ,r-rcppeigen) ("r-tmb" ,r-tmb))) (native-inputs - `(("r-knitr" ,r-knitr))) + `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/glmmTMB") (synopsis "Generalized linear mixed models") (description From 9df469a1d491a669f8d939ae488550b3eebd129b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 18:42:34 +0100 Subject: [PATCH 216/300] gnu: r-emmeans: Update to 1.3.1. * gnu/packages/cran.scm (r-emmeans): Update to 1.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 548c557d09..def3bab57c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7317,14 +7317,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "0kdyy4qp332c4yyvp1cnh48h6ks6ffir5rjcv0py0vm3m8c3hh61")))) + "1sf7gmdb7aqhdpx489vg693ivc5677n4yjx27ixv8v7pjh8mlwwx")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) From 1b1444012b07e4a1929e7fe5427fce2f4215223f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 18:42:59 +0100 Subject: [PATCH 217/300] gnu: r-sjstats: Update to 0.17.3. * gnu/packages/cran.scm (r-sjstats): Update to 0.17.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index def3bab57c..b138c58b51 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7449,14 +7449,14 @@ detection, parallelism through BLAS and parallel user templates.") (define-public r-sjstats (package (name "r-sjstats") - (version "0.17.2") + (version "0.17.3") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 (base32 - "0c7g35vn7r9rylhp0gj1yfslg7jybwrhpqpp7vdcd90xfccih24r")))) + "02na2pzxp88yp52h7vs959fgydiddmns39m9x4i0vz8fp016bdf8")))) (build-system r-build-system) (propagated-inputs `(("r-bayesplot" ,r-bayesplot) From fbd263cd4a679efe5797bc14295accbac325cf6e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:31:02 +0100 Subject: [PATCH 218/300] gnu: r-abn: Update to 1.3. * gnu/packages/cran.scm (r-abn): Update to 1.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b138c58b51..c768a3748b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5545,14 +5545,14 @@ to help insert or delete content at a specific location in the document.") (define-public r-abn (package (name "r-abn") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "00k0razgdb5y5f62622fm7rxkcxrxg470nyyb02dvpfp60254kvs")))) + "1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) From 12502bf4e87c1d2fc10373a2a92f270e6b72dcc5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:33:54 +0100 Subject: [PATCH 219/300] gnu: r-prediction: Update to 0.3.6.1. * gnu/packages/cran.scm (r-prediction): Update to 0.3.6.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c768a3748b..ab55365841 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5673,14 +5673,14 @@ parse and convert strings into cases like snake or camel among others.") (define-public r-prediction (package (name "r-prediction") - (version "0.3.6") + (version "0.3.6.1") (source (origin (method url-fetch) (uri (cran-uri "prediction" version)) (sha256 (base32 - "19d7312f5lkqfglfvlgssnvyw7gl161s0xradcry44r1i6qp05j1")))) + "1znxpacd79fjkf84w3493p1vmafanqfxsspwpwpkmda323bsxj0n")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table))) From f0867a0e8beca0fc285274b5054a2799f55da848 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:34:33 +0100 Subject: [PATCH 220/300] gnu: r-findpython: Update to 1.0.4. * gnu/packages/cran.scm (r-findpython): Update to 1.0.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ab55365841..2c87dfec42 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5938,14 +5938,14 @@ support for default values, positional argument support, etc.") (define-public r-findpython (package (name "r-findpython") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "findpython" version)) (sha256 (base32 - "1y08jk2ffmkf9zpwiz2xymjhfwqvls9vzsnq62v278ghw9d571jl")))) + "1zfcdcp4d48d2pzf5n59kqrfk2z9nnyzkx5j00gfmgfkadnv93x5")))) (build-system r-build-system) (home-page "https://github.com/trevorld/findpython") (synopsis "Functions to find an acceptable Python binary") From 2652e2534fb1f0cfc1d8b30b15bdcec31fc11002 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:37:18 +0100 Subject: [PATCH 221/300] gnu: r-refgenome: Update to 1.7.3.1. * gnu/packages/cran.scm (r-refgenome): Update to 1.7.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2c87dfec42..9987ad4145 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6063,14 +6063,14 @@ Group (Non-)Overlap considerations.") (define-public r-refgenome (package (name "r-refgenome") - (version "1.7.3") + (version "1.7.3.1") (source (origin (method url-fetch) (uri (cran-uri "refGenome" version)) (sha256 (base32 - "15p0ra2p1pwhy5ixbhsz1g79c5sc2aap4i4c8kil0m2syg9y45sn")))) + "1s4lxv5pqk6d0f0a9iclgv88yl346fwvzgraxh0gwpbym1yhh787")))) (properties `((upstream-name . "refGenome"))) (build-system r-build-system) (propagated-inputs From de7631b27896d5abbaa064dd334d1afe84bbe68b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:37:58 +0100 Subject: [PATCH 222/300] gnu: r-slam: Update to 0.1-44. * gnu/packages/cran.scm (r-slam): Update to 0.1-44. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9987ad4145..17a06a9b3e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6219,13 +6219,13 @@ the analyzed items.") (define-public r-slam (package (name "r-slam") - (version "0.1-43") + (version "0.1-44") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 - (base32 "0hy4qzngcgafxxr6ld7n9a9wy979ji998gpcc32vidwyab66dj5h")))) + (base32 "11n956kid70931z0qyiql3v7nac1cfkamq44kzf9wl670pf8b033")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") From 6eab52e0dd1229bef0752e53f4fc11f4fe9499aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:38:17 +0100 Subject: [PATCH 223/300] gnu: r-ggeffects: Update to 0.8.0. * gnu/packages/cran.scm (r-ggeffects): Update to 0.8.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 17a06a9b3e..7ccbd5a531 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7527,14 +7527,14 @@ differentiation.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "070c3fxmzajq2fy816s5pfqdyjlnzkabj97z7fcsva4h5rnqi9d6")))) + "152xyadj5m171z7dlzzy40y1fp2l9v46525dlw2al3qr0b7zpm61")))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon) From 16d296bbd185663c573710495a87ca4bc99d0b45 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:38:50 +0100 Subject: [PATCH 224/300] gnu: r-shades: Update to 1.3.1. * gnu/packages/cran.scm (r-shades): Update to 1.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7ccbd5a531..b66fc783cc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9101,14 +9101,14 @@ used by other packages.") (define-public r-shades (package (name "r-shades") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "shades" version)) (sha256 (base32 - "0qbg7b37ifgil7ka4vhk15wjf65rwha233yppqd9wlf3gys8784n")))) + "0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/shades") (synopsis "Simple color manipulation") From 9ad5f4ba1978e4122fd4237aa52ae22d2b4f0b58 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:39:19 +0100 Subject: [PATCH 225/300] gnu: r-grimport: Update to 0.9-1.1. * gnu/packages/cran.scm (r-grimport): Update to 0.9-1.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b66fc783cc..e445d119ed 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9192,14 +9192,14 @@ handling.") (define-public r-grimport (package (name "r-grimport") - (version "0.9-1") + (version "0.9-1.1") (source (origin (method url-fetch) (uri (cran-uri "grImport" version)) (sha256 (base32 - "1qhyw5wiyfqw1wcpvcgdwc1vgaz7j7dbc7qa5h85qgml7hb68mjv")))) + "19d05ygpiv47lfzhfih35pdfll0axbrgd6p86l59mmg2d0j0s8bd")))) (properties `((upstream-name . "grImport"))) (build-system r-build-system) (inputs From e041740289c35bdf65e0636184ec532d5d97c698 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:39:52 +0100 Subject: [PATCH 226/300] gnu: r-chemometricswithr: Update to 0.1.13. * gnu/packages/cran.scm (r-chemometricswithr): Update to 0.1.13. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e445d119ed..035ea3aa93 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9283,14 +9283,14 @@ linear order on both variables.") (define-public r-chemometricswithr (package (name "r-chemometricswithr") - (version "0.1.11") + (version "0.1.13") (source (origin (method url-fetch) (uri (cran-uri "ChemometricsWithR" version)) (sha256 (base32 - "00z09bplm5qvd31y7m4b4knsrl0n27j9635m1gdak6lg4db4nxrd")))) + "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq")))) (properties `((upstream-name . "ChemometricsWithR"))) (build-system r-build-system) From 209e504bb1785f75a547083844ef9d604b13375c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:40:31 +0100 Subject: [PATCH 227/300] gnu: r-ontologyindex: Update to 2.5. * gnu/packages/cran.scm (r-ontologyindex): Update to 2.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 035ea3aa93..9af8744706 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9409,14 +9409,14 @@ library.") (define-public r-ontologyindex (package (name "r-ontologyindex") - (version "2.4") + (version "2.5") (source (origin (method url-fetch) (uri (cran-uri "ontologyIndex" version)) (sha256 (base32 - "168m4jdwbzv8lpimx9063306691hnfdjmdhb5y8195d9vcq049jr")))) + "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry")))) (properties `((upstream-name . "ontologyIndex"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ontologyIndex") From c3e5b456befacfc9734cb8d551a46b3109c4b749 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:41:31 +0100 Subject: [PATCH 228/300] gnu: r-protviz: Update to 0.4.0. * gnu/packages/cran.scm (r-protviz): Update to 0.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9af8744706..f01128b67f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10196,14 +10196,14 @@ library.") (define-public r-protviz (package (name "r-protviz") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "protViz" version)) (sha256 (base32 - "1im3ajimycsc1zpzbihxlsibjk0462q0vldy7v5ypsqnjbi1ndxm")))) + "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) (inputs From 3bc0667f3c5552d3574823025e7ebf011ab21060 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:41:56 +0100 Subject: [PATCH 229/300] gnu: r-bookdown: Update to 0.9. * gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2ecc782324..98c4be3354 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7161,13 +7161,13 @@ also known as views, in a controlled vocabulary.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.7") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "1b3fw1f41zph5yw3kynb47aijq53vhaa6mnnvxly72zamyzdf95q")))) + "0vg1s1w0l9pm95asqb21yf39mfk1nc9rdhmlys9xwr7p7i7rsz32")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) From 80c4e75b87ee1060af20f609a415eea5ba8f05bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:42:19 +0100 Subject: [PATCH 230/300] gnu: r-seqminer: Update to 7.1. * gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 98c4be3354..1afff237e0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9477,14 +9477,14 @@ unmodeled, or latent sources of noise.") (define-public r-seqminer (package (name "r-seqminer") - (version "6.1") + (version "7.1") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "15yhg4vfc7jg1jnqb3371j00pgbmbyc9l1xx63hq1l3p34lazq2l")))) + "1jydcpkw4rwfp983j83kipvsvr10as9pb49zzn3c2v09k1gh3ymy")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) From 5e8282a4a092c4e302ae3572f3c546797a3a4cdb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:42:37 +0100 Subject: [PATCH 231/300] gnu: r-rmpi: Update to 0.6-9. * gnu/packages/cran.scm (r-rmpi): Update to 0.6-9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f01128b67f..8844d9541a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1740,13 +1740,13 @@ matrices.") (define-public r-rmpi (package (name "r-rmpi") - (version "0.6-7") + (version "0.6-9") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 - "1b62gs7w1xqadqd7ir41jnxlcf14gcqfxd0915kn9ckdlsdrh0sw")))) + "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj")))) (properties `((upstream-name . "Rmpi"))) (build-system r-build-system) (arguments From e45f4a4dab175868bf335e4a9dc3432a16aeac22 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:43:08 +0100 Subject: [PATCH 232/300] gnu: r-sjmisc: Update to 2.7.7. * gnu/packages/cran.scm (r-sjmisc): Update to 2.7.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8844d9541a..12d0f52b07 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5728,14 +5728,14 @@ vice versa), or to deal with multiple declared missing values.") (define-public r-sjmisc (package (name "r-sjmisc") - (version "2.7.6") + (version "2.7.7") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 - "1jhrigikjpkdar3jxvi7qhqsg6lgjkjqhqll9vaay98b88rfc2im")))) + "0xm9pmq17maivmjsygwx3bdjd71hf829qbx735hyxa69z9dhp24q")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) From fd7301676e66422f8ebe27e40ed5f86ecac73984 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 21:43:39 +0100 Subject: [PATCH 233/300] gnu: r-sjplot: Update to 2.6.2. * gnu/packages/cran.scm (r-sjplot): Update to 2.6.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 12d0f52b07..09cb2a1d02 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7566,14 +7566,14 @@ results using @code{ggplot2}.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.6.1") + (version "2.6.2") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 (base32 - "13qvw2s3r96qfi8kfsn76m050ccnmckl31a9qv94xws8da99v2fk")))) + "0x9pbchmz4qf4c9bi52dhhgv1phfj03q1hnxic8vndl6xwib63cy")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs From feb561f721beee8798ae2a6610a6d099df0852b0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 22:59:36 +0100 Subject: [PATCH 234/300] gnu: r-scran: Update to 1.10.2. * gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1afff237e0..13e7323e69 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11041,14 +11041,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1viyzrwfm9vccsf54c6g7k1dn7skkfx4ml1jy12q67wa20sx8l03")))) + "07mgilr3gq3lnrm1fjm9zhz4w7970bjhsykln1drqy9gkzj5sn7g")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) From f7e95c50b8fa93d4ff6a58d12a73143384c43c6d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:00:01 +0100 Subject: [PATCH 235/300] gnu: r-deseq2: Update to 1.22.2. * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 13e7323e69..dc418222e6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6473,14 +6473,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.22.1") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1b2bmvcsfzvks47d7w46zplcwz0kgcdhx5xmx3x9lp2gvx2p84r5")))) + "0n5ah84mxn87p45drzy0wh2yknmzj1q5i6gv0v9vgg1lj7awb91r")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs From ffe16ef33cf14242f8b683b01a79a5ca16f59aab Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:00:10 +0100 Subject: [PATCH 236/300] gnu: r-dexseq: Update to 1.28.1. * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dc418222e6..719a502eb8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6510,14 +6510,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0jh1640cnzpk8x3155cqc8dvrs1rciw3d6nv2k70baw96bhrynp8")))) + "0g5w9bn2nb3m670hkcsnhfvvkza2318z9irlhhwhb3n8rdzlsdym")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs From 3b8c88428563709780b17af5f0199321234a5235 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:00:20 +0100 Subject: [PATCH 237/300] gnu: r-rbgl: Update to 1.58.1. * gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 719a502eb8..9114b2778c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6583,14 +6583,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.58.0") + (version "1.58.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0jy95m38c4qp0a12097hhm2gg63k96k6ydhb11dy379h3ziapcar")))) + "1l5x2icv9di1lr3gqfi0vjnyd9xc3l77yc42ippqd4cadj3d1pzf")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph))) From 9c1b2b2ae0de79b8fbc0f4c2a89c7e98eb8e6d7d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:00:37 +0100 Subject: [PATCH 238/300] gnu: r-systempiper: Update to 1.16.1. * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9114b2778c..5e157c05d2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6735,14 +6735,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "0l26q8zjdmzg84g7f25gv9z60sykybahlpg5bg9bmpbg5lzcsx04")))) + "0qzydz87rld2nhwzbfgrw5jfgh8maa9y54mjx9c4285m11qj2shq")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs From 00f105fe20f53376889a76aee452ba4ac422a67f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:00:47 +0100 Subject: [PATCH 239/300] gnu: r-biocviews: Update to 1.50.10. * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5e157c05d2..f51dfad073 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7134,13 +7134,13 @@ Bioconductor, CRAN, and Github.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.50.5") + (version "1.50.10") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz")))) + "06ms82pyc5rxbd9crfvqjxcwpafv0c627i83v80d12925mrc51h8")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) From a619850930269f6ca0788488890d526ffeff21d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:00:58 +0100 Subject: [PATCH 240/300] gnu: r-edger: Update to 3.24.3. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f51dfad073..542d91dcce 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7435,13 +7435,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.24.0") + (version "3.24.3") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0ihihgzrgb4q3xc8xkzp1v76ndgihrj4gas00fa25vggfs1v6hvg")))) + "15yimsbsxmxhlsfmgw5j7fd8qn08zz4xqxrir1c6n2dc103y22xg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs From 3fd48846ebe42c49f5f07fa717e685006791a324 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:01:07 +0100 Subject: [PATCH 241/300] gnu: r-variantannotation: Update to 1.28.8. * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 542d91dcce..00e84c7fc1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7463,13 +7463,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.28.1") + (version "1.28.8") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "0gvah258mkaafhbna81zwknx8qr3lidbcx5qvwk39q3yswr9mi49")))) + "0gf36lr9xy3zmcc4rxs5bi2ccrrc7b6wqp6p3cvnclgif4i0l66k")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs From 52c977a05b4c23795867448853cb8731e1b8ebcc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:01:19 +0100 Subject: [PATCH 242/300] gnu: r-limma: Update to 3.38.3. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 00e84c7fc1..425bc5fc20 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7501,13 +7501,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.38.2") + (version "3.38.3") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1wkh362rmn24q7bkinb6nx62a31wl3r3myg5l326gx65wpwdnx97")))) + "08va8jggmv61wym955mnb1n31mgikrmjys7dl1kp5hp3yia8jg7l")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") From d4fc834cf71075c73919af334704fa9601996df7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:01:29 +0100 Subject: [PATCH 243/300] gnu: r-biocparallel: Update to 1.16.5. * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 425bc5fc20..5488bde226 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7667,13 +7667,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.16.0") + (version "1.16.5") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0g16cy0vjapqkb188z63r1b6y96m9g8vx0a3v2qavzxc177k0cja")))) + "1164dk0fajb2vrkfpcjs11055qf1cs4vvbnq0aqdaaf2p4lyx41l")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) From 1fa12b2f06a9583cc31d8d8696f274810b23c32f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:01:39 +0100 Subject: [PATCH 244/300] gnu: r-biostrings: Update to 2.50.2. * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5488bde226..2d870177b5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7692,13 +7692,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.50.1") + (version "2.50.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8")))) + "16cqqc8i6gb0jcz0lizfqqxsq7g0yb0ll2s9qzmb45brp07dg8f7")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) From 4bfde5217801992dcd7b27e73e047b3094cf6d69 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:01:49 +0100 Subject: [PATCH 245/300] gnu: r-genomicalignments: Update to 1.18.1. * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2d870177b5..a1c9fd4730 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7824,13 +7824,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0a3zhwripfw2508fvgx3wzqa8nq8vnslg97a911znpwvxh53jl24")))) + "1maslav2r34wjyzh2nlwa862in1ir7i5xk57nw2nlfh5gqy112jd")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) From 4c7b9222dd56ff41e3e934a1c052f8bf539d6841 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:02:03 +0100 Subject: [PATCH 246/300] gnu: r-tximport: Update to 1.10.1. * gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a1c9fd4730..eeb24dd797 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8954,13 +8954,13 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (define-public r-tximport (package (name "r-tximport") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0za2js8hqjgz8ria09cglynffj4w9vrzg85nmn1xgpvmc1xk813h")))) + "16wp09dm0cpb4mc00nmglfb8ica7qb4a55vm8ajgzyagbpfdd44l")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") From 86162c767ef15399333c98b12fefefb3a044b0ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:02:13 +0100 Subject: [PATCH 247/300] gnu: r-rhdf5: Update to 2.26.2. * gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eeb24dd797..f383a39179 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8976,13 +8976,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.26.0") + (version "2.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "0xmpkfdsmgl79ffffj7cf9fx3zxki2rk0xn25k778kr3s0sbmhis")))) + "10zkw3k13wmvyif417gplyf6rwp2gpkjasw97lhwv2f9i32rry9l")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) From 5c72ebafeb425e9c41c002bcc65ca3d581853f59 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:02:23 +0100 Subject: [PATCH 248/300] gnu: r-copywriter: Update to 2.14.1. * gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f383a39179..a6d10875fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9361,14 +9361,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.14.0") + (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0aamxafdk98n7s92jyqs65d6ljpnc2463vanvsw80p44qn6l6awn")))) + "1hbiw0m9hmx4na9v502pxf8y5wvxzr68r4d3fqr2755gxx86qck6")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs From c20426ec5cdb846f1f1416942a055651a2a3cb65 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:02:34 +0100 Subject: [PATCH 249/300] gnu: r-methylkit: Update to 1.8.1. * gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a6d10875fd..62ac6fcd6b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9401,13 +9401,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "0mz6lil1wax931incnw5byx0v9i8ryhwq9mv0nv8s48ai33ch3x6")))) + "1zcfwy7i10aqgnf7r0c41hakb5aai3s3n9y8pc6a98vimz51ly2z")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs From 46508c3a92560b7d92e54dc8d42011620188a581 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:02:45 +0100 Subject: [PATCH 250/300] gnu: r-sva: Update to 3.30.1. * gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 62ac6fcd6b..2158d345b6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9447,14 +9447,14 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.30.0") + (version "3.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "1xf0hlrqjxl0y3x13mrkxghiv39fd9v2g8gq3qzbf1wj7il6bph3")))) + "0czja4c5jxa0g3fspi90nyajqmvzb29my4ykv2wi66h43f5dlwhq")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) From a4f038dc97cbbd4c314fa563fb6af6584aed5d72 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:02:54 +0100 Subject: [PATCH 251/300] gnu: r-mzr: Update to 2.16.1. * gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2158d345b6..cc68c9a569 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9577,14 +9577,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.16.0") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "0li1y6p95ljiva4lvfmql9sipn4dq42sknbh60b36ycjppnf8lj5")) + "0mlwg646k49klxrznckzfv54a9mz6irj42fqpaaa0xjm6cw2lwaa")) (modules '((guix build utils))) (snippet '(begin From 6451af78e1a0bb6ed4f4f2fa1911a06240133c1f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:03:04 +0100 Subject: [PATCH 252/300] gnu: r-mzid: Update to 1.20.1. * gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cc68c9a569..9191b1f464 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9715,14 +9715,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "08jbq223viwknsmsi30hyxyxslvmb0l4wx3vmqlkl6qk4vfmxzjz")))) + "15yd4bdxprw3kg7zj2k652y3yr3si781iw28jqvnkm0gsc23rd0c")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs From 880ed11e9f67afb0f14ac7a9cf1e94814ff8fe83 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:03:12 +0100 Subject: [PATCH 253/300] gnu: r-msnbase: Update to 2.8.3. * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9191b1f464..bb10dc8ff9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9775,14 +9775,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.8.1") + (version "2.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0y658anh06vnvbkfs7r8q40gqgyqr2r8kj7jlpnp33fy1lvp1nv7")))) + "1kl1d7byphnfpmbl5fzbgs68dxskhpsdyx7ka51bpfn0nv3pp492")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs From 9abf344f8b76789010b7a61265e8c9c50c51ddc0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:03:24 +0100 Subject: [PATCH 254/300] gnu: r-msnid: Update to 1.16.1. * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bb10dc8ff9..6a677a724a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9818,14 +9818,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0hgq4argllhh5hvxqi8vkf1blc3nibsslhx4zsv2mcv4yj75bv4n")))) + "077n6ljcnnl7q4w0qj8v46vm4sjk9vzzfqf7wsc6lz0wmyzqdng3")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs From 3bdc41b352efb2bb8dcb4077c25c897ccfcabf27 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:03:34 +0100 Subject: [PATCH 255/300] gnu: r-deseq: Update to 1.34.1. * gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6a677a724a..49aea69223 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9947,14 +9947,14 @@ classes.") (define-public r-deseq (package (name "r-deseq") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "1klv1xrh3173srywr6dnq6i7m9djn4gc9aflr1p3a6yjlqcq6fya")))) + "0bpiixczbhlyaiinpbl6xrpmv72k2bq76bxnw06gl35m4pgs94p2")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs From ab4a862ab822c2848410a73d362c00af5c3cfb3a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:03:53 +0100 Subject: [PATCH 256/300] gnu: r-edaseq: Update to 2.16.3. * gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3. [propagated-inputs]: Add r-biocmanager. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 49aea69223..6a7009705f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9978,14 +9978,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.16.0") + (version "2.16.3") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "1gjqzn1kg9qwyz2gwjyy9xzzr1lnc7xd5zwdyvzkadz97gckzxwf")))) + "0559ph606ps2g9bwbl0a2knkcs5w581n9igngpjxvk5p56k24gb5")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -9993,6 +9993,7 @@ distribution.") ("r-aroma-light" ,r-aroma-light) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) ("r-biomart" ,r-biomart) ("r-biostrings" ,r-biostrings) ("r-deseq" ,r-deseq) From 4615cf9f1a984cb52579775f65dee1cb226aa176 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:04:14 +0100 Subject: [PATCH 257/300] gnu: r-annotationhub: Update to 2.14.2. * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6a7009705f..db5acb2584 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10041,14 +10041,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.14.1") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "00288x3na0izpmbcvsqac1br1qwry86vwc2slj1l47crdfb7za6c")))) + "17fgrvcnbii9siv5rq5j09bxhqffx47f6jf10418qvr7hh61ic1g")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs From 15d89fe9f8ba957df4e51383968476d5a22184e8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:04:25 +0100 Subject: [PATCH 258/300] gnu: r-gage: Update to 2.32.1. * gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index db5acb2584..a718d783a3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10130,14 +10130,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.32.0") + (version "2.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "07b098wvryxf0zd423nk6h52s3gyngwjcx2vplqybpbpgl8h2931")))) + "02g796sb1800ff0f1mq9f2m5wwzpf8pnfzajs49i68dhq2hm01a8")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) From 43931ff72fcf1675b8b16fa9b8922b187e2123d6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:04:43 +0100 Subject: [PATCH 259/300] gnu: r-dirichletmultinomial: Update to 1.24.1. * gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a718d783a3..28da8285b9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10222,14 +10222,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "19bzn0a5jal1xv0ad6wikxc7wrk582hczqamlln0vb2ffwkj1z3f")))) + "0vazfjzqy78p5g7dnv30lbqbj4bhq4zafd2wh6gdwy2il1fd78xa")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) From 27194effd74344df2ae8131edf67e88083745610 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:04:53 +0100 Subject: [PATCH 260/300] gnu: r-ensembldb: Update to 2.6.3. * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 28da8285b9..89d5971da4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10251,14 +10251,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.6.2") + (version "2.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "0hdz1f34v7sas2v4225icwl3wd4sf17ykpd5dkbx1hc7wcy4w3np")))) + "0kzdsfk6mdwlp57sw4j2cf7lx5nc67v5j0xr3iag9kzmgikaq1lb")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) From c80595935df696d4bf0484a57aaa0846c06143a2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:05:14 +0100 Subject: [PATCH 261/300] gnu: r-biovizbase: Update to 1.30.1. * gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 89d5971da4..62c6f37721 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10326,14 +10326,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.30.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "0v54mcn3rnnfx8dmcrms5z3rgq19n3hp4r23azlgzwq6hjw7cccx")))) + "0v5gvcx180qn5487i1dph9abadw3ggqwp5yzy41jswzbdc8q6sbm")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs From 19cacb5a2d009bbe3d4fb7f37e16e08c12e43e90 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:05:23 +0100 Subject: [PATCH 262/300] gnu: r-gviz: Update to 1.26.4. * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 62c6f37721..b8a637948c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10663,14 +10663,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.26.0") + (version "1.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "05zk9hf30afg6rjg97lzn5v8xij90v8zm09y9vcz0asmc3c8xs0a")))) + "0jvcivgw0ahv2rjadxmrww76xambhf7silczmh38nn4yn4qw6w9y")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs From ad10b3979dc0e41c50cc6f628edd5bb5524b76f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:05:33 +0100 Subject: [PATCH 263/300] gnu: r-qvalue: Update to 2.14.1. * gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b8a637948c..769a2e039f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10824,14 +10824,14 @@ provided.") (define-public r-qvalue (package (name "r-qvalue") - (version "2.14.0") + (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "03qxshqwwq1rj23p6pjrz08jm3ziikvy9badi4mz2rcwy2nz783a")))) + "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) From 40561d024947fb5d5fd553921afd11d8f56562bf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:05:43 +0100 Subject: [PATCH 264/300] gnu: r-hdf5array: Update to 1.10.1. * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 769a2e039f..fbb764fd60 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10853,14 +10853,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1w7ad8cfsbh5xx82m3l4lc0vbmj9lcsqxxpiy3ana2ycgn1bqv3g")))) + "1qwdsygcadl58qj598hfyvs8hp0hqcl9ghnhknahrlhmb7k2bd2d")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (propagated-inputs From a0224bd4f642bbb1633b9731ef6993502db9ea50 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:05:57 +0100 Subject: [PATCH 265/300] gnu: r-rhdf5lib: Update to 1.4.2. * gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fbb764fd60..94bae01ed9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10879,14 +10879,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "01gpz780g850ql20b2ql6pvr678ydk4nq4sn5iiih94a4crb9lz1")) + "06bxd3wz8lrvh2hzvmjpdv4lvzj5lz9353bw5b3zb98cb8w9r2j5")) (modules '((guix build utils))) (snippet '(begin From 0f268bb2757f410a4d71db64910469b189085df4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:06:08 +0100 Subject: [PATCH 266/300] gnu: r-singlecellexperiment: Update to 1.4.1. * gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 94bae01ed9..79783b4a30 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10979,14 +10979,14 @@ matrices.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "19r4r7djrn46qlijkj1g926vcklxzcrxjlxv6cg43m9j9jgfs3dj")))) + "12139kk9cqgzpm6f3cwdsq31gj5lxamz2q939dy9fa0fa54gdaq4")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) From 1e107b0960b10d61166637b0ec1461bbbc5bb10a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:06:18 +0100 Subject: [PATCH 267/300] gnu: r-scater: Update to 1.10.1. * gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 79783b4a30..652bd5f831 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11006,13 +11006,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "1kwa9n70c5j0xcj6nkmlkzjr63cnj78mp8nhg58n07fq1ijm4ns3")))) + "0rijhy7g5qmcn927y1wyd63la1fhyar9fv1hccsqd23jd98yc55a")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) From c476edc2cdb67087347060f03be1cb52c125e5d5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:06:31 +0100 Subject: [PATCH 268/300] gnu: r-rtracklayer: Update to 1.42.1. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 652bd5f831..42f5c3b80d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7857,13 +7857,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.42.0") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0a4mhd926w9slkfil5xgngjsfdj024a4w57w2bm3d4r0pj8y5da7")))) + "1ycmcxvgvszvjv75hlmg0i6pq8i7r8720vgmfayb905s9l6j82x6")))) (build-system r-build-system) (arguments `(#:phases From add2b195611849c4122a0b2a9c41a3b0949fb3db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:06:52 +0100 Subject: [PATCH 269/300] gnu: r-chippeakanno: Update to 3.16.1. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.16.1. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7f11dead3..8adac8cc16 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2018 Ricardo Wurmus +;;; Copyright © 2018, 2019 Ricardo Wurmus ;;; Copyright © 2018 Roel Janssen ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; @@ -411,14 +411,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.16.0") + (version "3.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3")))) + "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs From 7f2b1c4af0d24f8ce36b1a546d6d853126929551 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:07:01 +0100 Subject: [PATCH 270/300] gnu: r-goseq: Update to 1.34.1. * gnu/packages/bioconductor.scm (r-goseq): Update to 1.34.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8adac8cc16..a28b45fabf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -778,14 +778,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "1401x0jn5f8hqc12r3gd1wammp1nxir3is1k5ldd03ln97x00i7a")))) + "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) From 0b469ee225b9a043a68302e6d78f2ddac1b84c6f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:07:10 +0100 Subject: [PATCH 271/300] gnu: r-glimma: Update to 1.10.1. * gnu/packages/bioconductor.scm (r-glimma): Update to 1.10.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a28b45fabf..fdca41bbab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -804,14 +804,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0cbsi6g8k1whkh21jxfn22sj7wry2g3rshiracf5nyvrl2fnl947")))) + "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs From 45dcd7dcfd1dcfa7cacd0e7d996bc5fa04891fed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:07:18 +0100 Subject: [PATCH 272/300] gnu: r-rots: Update to 1.10.1. * gnu/packages/bioconductor.scm (r-rots): Update to 1.10.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fdca41bbab..06dc258005 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -831,14 +831,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5")))) + "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs From cad6fb2dec67e41498ee4cf9026ea5d12d8050e6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:07:29 +0100 Subject: [PATCH 273/300] gnu: Add r-plgem. * gnu/packages/bioconductor.scm (r-plgem): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 06dc258005..0ded2a7b67 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -852,6 +852,31 @@ information.") in omics data.") (license license:gpl2+))) +(define-public r-plgem + (package + (name "r-plgem") + (version "1.54.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "plgem" version)) + (sha256 + (base32 + "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-mass" ,r-mass))) + (home-page "http://www.genopolis.it") + (synopsis "Detect differential expression in microarray and proteomics datasets") + (description + "The Power Law Global Error Model (PLGEM) has been shown to faithfully +model the variance-versus-mean dependence that exists in a variety of +genome-wide datasets, including microarray and proteomics data. The use of +PLGEM has been shown to improve the detection of differentially expressed +genes or proteins in these datasets.") + (license license:gpl2))) + (define-public r-inspect (package (name "r-inspect") From d220babf34d4e968159a6fd8165d0deeaa49905c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:23:20 +0100 Subject: [PATCH 274/300] gnu: Add r-txdb-mmusculus-ucsc-mm9-knowngene. * gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm9-knowngene): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0ded2a7b67..32391d6d4b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -197,6 +197,36 @@ default." ) genomes and gene ID formats, largely based on the UCSC table browser.") (license license:lgpl2.0+))) +(define-public r-txdb-mmusculus-ucsc-mm9-knowngene + (package + (name "r-txdb-mmusculus-ucsc-mm9-knowngene") + (version "3.2.2") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "https://bioconductor.org/packages/" + "release/data/annotation/src/contrib" + "/TxDb.Mmusculus.UCSC.mm9.knownGene_" + version ".tar.gz")) + (sha256 + (base32 + "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) + (properties + `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicfeatures" ,r-genomicfeatures) + ("r-annotationdbi" ,r-annotationdbi))) + (home-page + "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") + (synopsis "Annotation package for mouse genome in TxDb format") + (description + "This package provides an annotation database of Mouse genome data. It +is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The +database is exposed as a @code{TxDb} object.") + (license license:artistic2.0))) + (define-public r-hpar (package From c86fc969878483d9aab6c0fe7e533650104da44a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:07:38 +0100 Subject: [PATCH 275/300] gnu: r-inspect: Update to 1.12.1. * gnu/packages/bioconductor.scm (r-inspect): Update to 1.12.1. [propagated-inputs]: Add r-deseq2, r-plgem, r-shiny, r-summarizedexperiment, and r-txdb-mmusculus-ucsc-mm9-knowngene. --- gnu/packages/bioconductor.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 32391d6d4b..258185316b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -910,30 +910,36 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0b671x5v2wyq5np2flq2m1fnjz32f303yjlw64a1inwc9k2w2pz2")))) + "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) + ("r-deseq2" ,r-deseq2) ("r-desolve" ,r-desolve) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-plgem" ,r-plgem) ("r-preprocesscore" ,r-preprocesscore) ("r-proc" ,r-proc) ("r-rootsolve" ,r-rootsolve) ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-txdb-mmusculus-ucsc-mm9-knowngene" + ,r-txdb-mmusculus-ucsc-mm9-knowngene))) (home-page "https://bioconductor.org/packages/INSPEcT") (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") (description From c6e9b494e8b2ce3bbfa555610fe9511d788d5f19 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 12 Jan 2019 23:08:15 +0100 Subject: [PATCH 276/300] gnu: r-ruvseq: Update to 1.16.1. * gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.16.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 258185316b..37ac94128b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -979,14 +979,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m")))) + "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs From 5b9c2690afae77740ac9136e45ad73de52ff64fb Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Sat, 12 Jan 2019 18:37:38 -0500 Subject: [PATCH 277/300] gnu: tintin++: Update to 2.01.5. * gnu/packages/games.scm (tintin++): Update to 2.01.5. --- gnu/packages/games.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 80d48dbe56..852de8b435 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -3463,7 +3463,7 @@ the GNU GPL.") (define-public tintin++ (package (name "tintin++") - (version "2.01.4") + (version "2.01.5") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/tintin" @@ -3471,7 +3471,7 @@ the GNU GPL.") "/tintin" "-" version ".tar.gz")) (sha256 (base32 - "1g7bh8xs1ml0iyraps3a3dzaycci922y7fk5j0wyr4ssyjzsy8nx")))) + "0pnnbcm96xbj69358568rpvp164rjmcvhnnzs7nvj062pi2hqcxx")))) (inputs `(("gnutls" ,gnutls) ("pcre" ,pcre) @@ -3490,10 +3490,10 @@ the GNU GPL.") (home-page "http://tintin.sourceforge.net/") (synopsis "MUD client") (description - "TinTin++ is a MUD client which supports MCCP (Mud Client Compression Protocol), -MMCP (Mud Master Chat Protocol), xterm 256 colors, most TELNET options used by MUDs, -as well as those required to login via telnet on Linux / Mac OS X servers, and an -auto mapper with a VT100 map display.") + "TinTin++ is a MUD client which supports MCCP (Mud Client Compression +Protocol), MMCP (Mud Master Chat Protocol), xterm 256 colors, most TELNET +options used by MUDs, as well as those required to login via telnet on +Linux / Mac OS X servers, and an auto mapper with a VT100 map display.") (license license:gpl2+))) (define-public laby From b1d2e0b4e0a22c1cdda376b1c9950f14ca99230e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 2 Jan 2019 23:11:36 +0100 Subject: [PATCH 278/300] gnu: libcdr: Update to 0.1.5. * gnu/packages/libreoffice.scm (libcdr): Update to 0.1.5. [source](uri): Download over HTTPS. [arguments]: Remove. --- gnu/packages/libreoffice.scm | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 7e179ebfb9..631c1722d0 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2017 Andy Wingo ;;; Copyright © 2017, 2018 Ludovic Courtès -;;; Copyright © 2017, 2018 Marius Bakke +;;; Copyright © 2017, 2018, 2019 Marius Bakke ;;; Copyright © 2017 Rutger Helling ;;; Copyright © 2018 Ricardo Wurmus ;;; Copyright © 2018 Jonathan Brielmaier @@ -370,14 +370,14 @@ AbiWord documents.") (define-public libcdr (package (name "libcdr") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) - (uri (string-append "http://dev-www.libreoffice.org/src/" name "/" + (uri (string-append "https://dev-www.libreoffice.org/src/" name "/" name "-" version ".tar.xz")) (sha256 (base32 - "0vd6likgk51j46llybkx4wq3674xzrhp0k82220pkx9x1aqfi9z7")))) + "0j1skr11jwvafn0l6p37v3i4lqc8wcn489g8f7c4mqwbk94mrkka")))) (build-system gnu-build-system) (native-inputs `(("cppunit" ,cppunit) @@ -390,9 +390,6 @@ AbiWord documents.") ("zlib" ,zlib))) (inputs `(("boost" ,boost))) - (arguments - ;; avoid triggering a build failure due to warnings - `(#:configure-flags '("--disable-werror"))) (home-page "https://wiki.documentfoundation.org/DLP/Libraries/libcdr") (synopsis "Library for parsing the CorelDRAW format") (description "Libcdr is a library that parses the file format of From 7c3acfcb69c00bc59b5c8cb51540560042045043 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 2 Jan 2019 23:12:16 +0100 Subject: [PATCH 279/300] gnu: libetonyek: Update to 0.1.9. * gnu/packages/libreoffice.scm (libetonyek): Update to 0.1.9. [arguments]: Remove #:phases. --- gnu/packages/libreoffice.scm | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 631c1722d0..cd300b05f4 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -399,26 +399,17 @@ CorelDRAW documents of all versions.") (define-public libetonyek (package (name "libetonyek") - (version "0.1.8") + (version "0.1.9") (source (origin (method url-fetch) (uri (string-append "http://dev-www.libreoffice.org/src/" name "/" name "-" version ".tar.xz")) (sha256 (base32 - "0bfq9rwm040xhh7b3v0gsdavwvnrz4hkwnhpggarxk70mr3j7jcx")))) + "0jhsbdimiyijdqriy0zzkjjgc4wi6fjimhdg4mdybrlwg7l7f5p6")))) (build-system gnu-build-system) (arguments - `(#:configure-flags '("--with-mdds=1.4") - #:phases (modify-phases %standard-phases - (add-before 'configure 'support-mdds-1.4 - (lambda _ - ;; This package already works fine with mdds 1.4, but the - ;; configure check is too strict. Taken from upstream. - (substitute* "configure" - (("mdds=1\\.2") "mdds=1.4") - (("mdds=\"1\\.2\"") "mdds=\"1.4\"")) - #t))))) + `(#:configure-flags '("--with-mdds=1.4"))) (native-inputs `(("cppunit" ,cppunit) ("doxygen" ,doxygen) From 9c2094785d5077d82b8f238e4d7aaf372e61fd06 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 2 Jan 2019 23:22:58 +0100 Subject: [PATCH 280/300] gnu: libetonyek: Adjust inputs. * gnu/packages/libreoffice.scm (libetonyek)[native-inputs]: Remove LIBLANGTAG. Move GLM and MDDS to ... [inputs]: ... here. [propagated-inputs]: Add LIBLANGTAG and ZLIB. --- gnu/packages/libreoffice.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index cd300b05f4..2cbb0ca2e5 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -413,16 +413,17 @@ CorelDRAW documents of all versions.") (native-inputs `(("cppunit" ,cppunit) ("doxygen" ,doxygen) - ("glm" ,glm) ("gperf" ,gperf) - ("liblangtag" ,liblangtag) - ("mdds" ,mdds) ("pkg-config" ,pkg-config))) (propagated-inputs ; in Requires or Requires.private field of .pkg - `(("librevenge" ,librevenge) - ("libxml2" ,libxml2))) + `(("liblangtag" ,liblangtag) + ("librevenge" ,librevenge) + ("libxml2" ,libxml2) + ("zlib" ,zlib))) (inputs - `(("boost" ,boost))) + `(("boost" ,boost) + ("glm" ,glm) + ("mdds" ,mdds))) (home-page "https://wiki.documentfoundation.org/DLP/Libraries/libetonyek") (synopsis "Library for parsing the Apple Keynote format") (description "Libetonyek is a library that parses the file format of From 304db09257b353a677440e3b3c94f08446015ed2 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 2 Jan 2019 23:33:12 +0100 Subject: [PATCH 281/300] gnu: http-parser: Download from git. * gnu/packages/web.scm (http-parser)[source]: Change to GIT-FETCH. --- gnu/packages/web.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index d1713c7a0d..52da99ce2b 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -5075,14 +5075,15 @@ into your tests. It automatically starts up a HTTP server in a separate thread (package (name "http-parser") (version "2.8.1") + (home-page "https://github.com/nodejs/http-parser") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/nodejs/http-parser/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "15ids8k2f0xhnnxh4m85w2f78pg5ndiwrpl24kyssznnp1l5yqai")))) + "0d2ni77pdw51n6qf0pq2gkc78i6yvnaw3nds6ldgmqqndzp2yv31")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -5093,7 +5094,6 @@ into your tests. It automatically starts up a HTTP server in a separate thread #:phases (modify-phases %standard-phases (delete 'configure)))) - (home-page "https://github.com/nodejs/http-parser") (synopsis "HTTP request/response parser for C") (description "This is a parser for HTTP messages written in C. It parses both requests and responses. The parser is designed to be used in From 48a51af9d2c14e46ee073c6925e0d1b68e3292c9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 2 Jan 2019 23:34:06 +0100 Subject: [PATCH 282/300] gnu: http-parser: Update to 2.9.0. * gnu/packages/web.scm (http-parser): Update to 2.9.0. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 52da99ce2b..1ea4333a90 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -5074,7 +5074,7 @@ into your tests. It automatically starts up a HTTP server in a separate thread (define-public http-parser (package (name "http-parser") - (version "2.8.1") + (version "2.9.0") (home-page "https://github.com/nodejs/http-parser") (source (origin (method git-fetch) @@ -5083,7 +5083,7 @@ into your tests. It automatically starts up a HTTP server in a separate thread (file-name (git-file-name name version)) (sha256 (base32 - "0d2ni77pdw51n6qf0pq2gkc78i6yvnaw3nds6ldgmqqndzp2yv31")))) + "1qa3rh9x4as2fc2p0y2hah83iqs7jr5106a8anv317359dgf3ssj")))) (build-system gnu-build-system) (arguments `(#:test-target "test" From 0c4cee13b26a953e54f47da081e1f461b46c1976 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 3 Jan 2019 00:38:28 +0100 Subject: [PATCH 283/300] gnu: libcmis: Update to 0.5.2. * gnu/packages/libreoffice.scm (libcmis): Update to 0.5.2. [source](uri): Use XZ-compressed tarball. [arguments]: Remove #:phases. Don't pass "--disable-werror" in #:configure-flags. --- gnu/packages/libreoffice.scm | 20 ++++---------------- 1 file changed, 4 insertions(+), 16 deletions(-) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 2cbb0ca2e5..ccef2c2e9b 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -287,15 +287,15 @@ working with graphics in the WPG (WordPerfect Graphics) format.") (define-public libcmis (package (name "libcmis") - (version "0.5.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/tdf/libcmis/releases/download/v" - version "/libcmis-" version ".tar.gz")) + version "/libcmis-" version ".tar.xz")) (sha256 (base32 - "03kvl8ywsv5qrxblf0m6955mmvl5q2zpb6vj51vs7ayvxhidzjva")))) + "18h0a2gsfxvlv03nlcfvw9bzsflq5sin9agq6za103hr0ab8vcfp")))) (build-system gnu-build-system) (native-inputs `(("cppunit" ,cppunit) @@ -313,22 +313,10 @@ working with graphics in the WPG (WordPerfect Graphics) format.") ;; FIXME: Man pages generation requires docbook-to-man; reenable ;; it once this is available. "--without-man" - ;; avoid triggering configure errors by simple inclusion of - ;; boost headers - "--disable-werror" ;; During configure, the boost headers are found, but linking ;; fails without the following flag. (string-append "--with-boost=" - (assoc-ref %build-inputs "boost"))) - #:phases (modify-phases %standard-phases - (add-before 'build 'fix-boost-include - (lambda _ - ;; This library moved in Boost and the compatibility - ;; redirect is no longer available since version 1.68.0. - (substitute* "src/libcmis/xml-utils.cxx" - (("boost/uuid/sha1.hpp") - "boost/uuid/detail/sha1.hpp")) - #t))))) + (assoc-ref %build-inputs "boost"))))) (home-page "https://github.com/tdf/libcmis") (synopsis "CMIS client library") (description "LibCMIS is a C++ client library for the CMIS interface. It From 2bb187c4844c248c66472eacef0570bc7c92e1fe Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 3 Jan 2019 00:43:04 +0100 Subject: [PATCH 284/300] gnu: xscreensaver: Update to 5.42. * gnu/packages/xdisorg.scm (xscreensaver): Update to 5.42. [arguments]: Add "CFLAGS=-std=c99" to #:make-flags. --- gnu/packages/xdisorg.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index fdfa1511d8..b64094ed18 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -992,7 +992,7 @@ color temperature should be set to match the lamps in your room.") (define-public xscreensaver (package (name "xscreensaver") - (version "5.40") + (version "5.42") (source (origin (method url-fetch) @@ -1001,7 +1001,7 @@ color temperature should be set to match the lamps in your room.") version ".tar.gz")) (sha256 (base32 - "1q2sr7h6ps6d3hk8895g12rrcqiihjl7py1ly077ikv4866r181h")))) + "1qfbsnj7201d03vf0b2lzxmlcq4kvkvzp48r5gcgsjr17c1sl7a4")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no check target @@ -1015,7 +1015,9 @@ color temperature should be set to match the lamps in your room.") #t))) #:configure-flags '("--with-pam" "--with-proc-interrupts" "--without-readdisplay") - #:make-flags (list (string-append "AD_DIR=" + ;; FIXME: Remove CFLAGS once our default compiler is GCC6 or later. + #:make-flags (list "CFLAGS=-std=c99" + (string-append "AD_DIR=" (assoc-ref %outputs "out") "/usr/lib/X11/app-defaults")))) (native-inputs From bf135622bd1322e284e77d01d3ca2d1a82e0f2a6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 3 Jan 2019 00:47:28 +0100 Subject: [PATCH 285/300] gnu: rofi: Update to 1.5.2. * gnu/packages/xdisorg.scm (rofi): Update to 1.5.2. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index b64094ed18..ea16db7af0 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -1109,7 +1109,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.") (define-public rofi (package (name "rofi") - (version "1.5.1") + (version "1.5.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/DaveDavenport/rofi/" @@ -1117,7 +1117,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.") version "/rofi-" version ".tar.xz")) (sha256 (base32 - "0wx118banbwfqdwc5y44fkp3hxg97gj3vma16528slhy408hkg7i")))) + "17faa0rj8vqidrijwx9jrq0c29003n8v3izvc66yssfljgb8kcpj")))) (build-system gnu-build-system) (inputs `(("pango" ,pango) From 48d5818a0e9cf9ceec4e1b76ee4309e048e5f57e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 3 Jan 2019 00:51:34 +0100 Subject: [PATCH 286/300] gnu: fluidsynth: Update to 2.0.3. * gnu/packages/audio.scm (fluidsynth): Update to 2.0.3. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index d47dd90f56..fe7820502d 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1152,7 +1152,7 @@ follower.") (define-public fluidsynth (package (name "fluidsynth") - (version "2.0.2") + (version "2.0.3") (source (origin (method git-fetch) (uri (git-reference @@ -1161,7 +1161,7 @@ follower.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "02vs5sfsyh1dl7wlcvgs4w3x0qcmsl7vi000qgp99ynwh3wjb274")))) + "00f6bhw4ddrinb5flvg5y53rcvnf4km23a6nbvnswmpq13568v78")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no check target From c06ef010e3fbffcb80f2560a4946b182b132b539 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 3 Jan 2019 00:54:35 +0100 Subject: [PATCH 287/300] gnu: libsecret: Update to 0.18.7. * gnu/packages/gnome.scm (libsecret): Update to 0.18.7. [native-inputs]: Remove INTLTOOL. Add GETTEXT-MINIMAL. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index ffd84cd78d..f4d4dfd922 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -2634,9 +2634,9 @@ and the GLib main loop, to integrate well with GNOME applications.") (assoc-ref %outputs "doc") "/share/gtk-doc/html")))) (native-inputs - `(("glib:bin" ,glib "bin") ; for gdbus-codegen, etc. + `(("gettext" ,gettext-minimal) + ("glib:bin" ,glib "bin") ; for gdbus-codegen, etc. ("gobject-introspection" ,gobject-introspection) - ("intltool" ,intltool) ("pkg-config" ,pkg-config) ("vala" ,vala) ("xsltproc" ,libxslt))) From ef61969c52f3180cd79dcbac2765814fa698b395 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 3 Jan 2019 00:57:52 +0100 Subject: [PATCH 288/300] gnu: re2: Update to 2019-01-01. * gnu/packages/regex.scm (re2): Update to 2019-01-01. --- gnu/packages/regex.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/regex.scm b/gnu/packages/regex.scm index 08501aef6f..f526d1c237 100644 --- a/gnu/packages/regex.scm +++ b/gnu/packages/regex.scm @@ -30,7 +30,7 @@ (define-public re2 (package (name "re2") - (version "2018-12-01") + (version "2019-01-01") (home-page "https://github.com/google/re2") (source (origin (method git-fetch) @@ -38,7 +38,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "181fq0idwzgfmmpyhmqdxi37rbynzgf1b8s99aaka9kqs9ffwj22")))) + "0wys8bbhj8ppgmgp3842qjmnvkynnzxrm8d7c3a3qyq3p6grqa29")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) From 9f1448b74ac3eaeb493645e8c3cc3b51246571da Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 3 Jan 2019 01:00:10 +0100 Subject: [PATCH 289/300] gnu: libgphoto2: Update to 2.5.22. * gnu/packages/photo.scm (libgphoto2): Update to 2.5.22. --- gnu/packages/photo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index 07047f4cf3..5b6114e051 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -131,14 +131,14 @@ data as produced by digital cameras.") (define-public libgphoto2 (package (name "libgphoto2") - (version "2.5.21") + (version "2.5.22") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gphoto/libgphoto/" version "/libgphoto2-" version ".tar.bz2")) (sha256 (base32 - "1ccb8idjkv19p9zxg6hh8y6vbgs8flpnh550lq6a8cmga8d2nmy5")))) + "0n6f6nagys775ib483nka1sbclhkm1dz3n5z3lgaz1m9m5x35mqm")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) (inputs From 80459f5a217fc169937bd28b84f7ecf3dcfb30e1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 3 Jan 2019 02:16:42 +0100 Subject: [PATCH 290/300] gnu: nasm: Update home page. * gnu/packages/assembly.scm (nasm)[home-page]: Use HTTPS. --- gnu/packages/assembly.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm index dd9e6d0dc4..1891cec452 100644 --- a/gnu/packages/assembly.scm +++ b/gnu/packages/assembly.scm @@ -64,7 +64,7 @@ (add-after 'install 'install-info (lambda _ (invoke "make" "install_doc")))))) - (home-page "http://www.nasm.us/") + (home-page "https://www.nasm.us/") (synopsis "80x86 and x86-64 assembler") (description "NASM, the Netwide Assembler, is an 80x86 and x86-64 assembler designed From 1d7fbe09473fb4bf1c3186b79a0db5ae001f3b9e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 3 Jan 2019 02:17:39 +0100 Subject: [PATCH 291/300] gnu: nasm: Update license. * gnu/packages/assembly.scm (nasm)[license]: Change to BSD-2. --- gnu/packages/assembly.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm index 1891cec452..9b8ef562d3 100644 --- a/gnu/packages/assembly.scm +++ b/gnu/packages/assembly.scm @@ -74,7 +74,7 @@ Windows32 and Windows64. It will also output plain binary files. Its syntax is designed to be simple and easy to understand, similar to Intel's but less complex. It supports all currently known x86 architectural extensions, and has strong support for macros.") - (license license:bsd-3))) + (license license:bsd-2))) (define-public yasm (package From b2e765de4c3d66d96d89cd0b7698f9d23a91de19 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Jan 2019 20:33:52 +0100 Subject: [PATCH 292/300] gnu: httpd: Update to 2.4.37. * gnu/packages/web.scm (httpd): Update to 2.4.37. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 1ea4333a90..37f0adfb56 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -121,14 +121,14 @@ (define-public httpd (package (name "httpd") - (version "2.4.35") + (version "2.4.37") (source (origin (method url-fetch) (uri (string-append "mirror://apache/httpd/httpd-" version ".tar.bz2")) (sha256 (base32 - "0mlvwsm7hmpc7db6lfc2nx3v4cll3qljjxhjhgsw6aniskywc1r6")))) + "09npb7vlz5sizgj0nvl0bqxj9zig29ipkp07fgmw5ykjcxfdr61l")))) (build-system gnu-build-system) (native-inputs `(("pcre" ,pcre "bin"))) ;for 'pcre-config' (inputs `(("apr" ,apr) From 00262db23adb2666fa6d00d40e53f2145be26026 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Jan 2019 21:03:47 +0100 Subject: [PATCH 293/300] gnu: seabios: Update to 1.12.0. * gnu/packages/firmware.scm (seabios): Update to 1.12.0. --- gnu/packages/firmware.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 0f2d32bbd9..0f3e1009ac 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -186,14 +186,14 @@ by the b43-open driver of Linux-libre.") (define-public seabios (package (name "seabios") - (version "1.11.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (string-append "https://www.seabios.org/downloads/" "seabios-" version ".tar.gz")) (sha256 (base32 - "1xwvp77djxbxbxg82hzj26pv6zka3556vkdcp09hnfwapcp46av2")))) + "0jx7pnsc2s4a7wbvvwqig6x8wmkw7f2sz0pbgj4jfp77cpjvh5yz")))) (build-system gnu-build-system) (native-inputs `(("python-2" ,python-2))) From 0b014776c9966d64f710f67f245195b5780a0d44 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Jan 2019 21:04:19 +0100 Subject: [PATCH 294/300] gnu: exempi: Update to 2.5.0. * gnu/packages/freedesktop.scm (exempi): Update to 2.5.0. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 8982c0ec35..039188d13b 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -530,7 +530,7 @@ multiplexer to the KMS/DRM Linux kernel devices.") (define-public exempi (package (name "exempi") - (version "2.4.5") + (version "2.5.0") (source (origin (method url-fetch) (uri (string-append @@ -538,7 +538,7 @@ multiplexer to the KMS/DRM Linux kernel devices.") name "-" version ".tar.bz2")) (sha256 (base32 - "07i29xmg8bqriviaf4vi1mwha4lrw85kfla29cfym14fp3z8aqa0")))) + "06vi7dc2gappwqm3xpfyy5ihxq14bmvj3bd47yk482jlq0jgr0nw")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list (string-append "--with-boost=" From 8bcae1e60c2c1d54362739ab913f762528ff3227 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Jan 2019 21:56:48 +0100 Subject: [PATCH 295/300] gnu: libsodium: Update to 1.0.17. * gnu/packages/crypto.scm (libsodium): Update to 1.0.17. --- gnu/packages/crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index d72162d6a8..0a507aead6 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -73,7 +73,7 @@ (define-public libsodium (package (name "libsodium") - (version "1.0.16") + (version "1.0.17") (source (origin (method url-fetch) (uri (list (string-append @@ -84,7 +84,7 @@ "releases/old/libsodium-" version ".tar.gz"))) (sha256 (base32 - "0cq5pn7qcib7q70mm1lgjwj75xdxix27v0xl1xl0kvxww7hwgbgf")))) + "1cf2d9v1gylz1qcy2zappbf526qfmph6gd6fnn3w2b347vixmhqc")))) (build-system gnu-build-system) (synopsis "Portable NaCl-based crypto library") (description From de261ace27d5fb349cc614e0370bf07ca390becd Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Jan 2019 21:57:16 +0100 Subject: [PATCH 296/300] gnu: libmbim: Update to 1.18.0. * gnu/packages/freedesktop.scm (libmbim): Update to 1.18.0. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 039188d13b..7adeae7bb0 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -732,7 +732,7 @@ interfaces, based on the useradd, usermod and userdel commands.") (define-public libmbim (package (name "libmbim") - (version "1.16.2") + (version "1.18.0") (source (origin (method url-fetch) (uri (string-append @@ -740,7 +740,7 @@ interfaces, based on the useradd, usermod and userdel commands.") name "-" version ".tar.xz")) (sha256 (base32 - "0qmjvjbgs9m8qsaiq5arikzglgaas9hh1968bi7sy3905kp4yjgb")))) + "10mjjy860aakfd3h1yaj9l1jw816amrpwmyqlx37j21xv0l03x3c")))) (build-system gnu-build-system) (native-inputs `(("glib:bin" ,glib "bin") ; for glib-mkenums From ad55c19211e6aba4ac8b3cdc7aec8551e6e2349a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Jan 2019 21:57:45 +0100 Subject: [PATCH 297/300] gnu: libqmi: Update to 1.22.0. * gnu/packages/freedesktop.scm (libqmi): Update to 1.22.0. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 7adeae7bb0..4801f7e616 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -763,7 +763,7 @@ which speak the Mobile Interface Broadband Model (MBIM) protocol.") (define-public libqmi (package (name "libqmi") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (string-append @@ -771,7 +771,7 @@ which speak the Mobile Interface Broadband Model (MBIM) protocol.") name "-" version ".tar.xz")) (sha256 (base32 - "1d3fca477sdwbv4bsq1cl98qc8sixrzp0gqjcmjj8mlwfk9qqhi1")))) + "05xamy608mhvmw9zbnv9n8w3xpk96n10v5mixnvpnqgih6s9ih91")))) (build-system gnu-build-system) (inputs `(("libgudev" ,libgudev))) From 66470a5ad0d0967c52af83becd997af90fe4b292 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Jan 2019 21:58:20 +0100 Subject: [PATCH 298/300] gnu: libgxps: Update to 0.3.1. * gnu/packages/gnome.scm (libgxps): Update to 0.3.1. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index f4d4dfd922..1ffdc25010 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -402,7 +402,7 @@ access the common Google services, and has full asynchronous support.") (define-public libgxps (package (name "libgxps") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -410,7 +410,7 @@ access the common Google services, and has full asynchronous support.") name "-" version ".tar.xz")) (sha256 (base32 - "1bhgrpb6ndlp11qwr95g9piklmjcsca7bi04f8gy9ziipm1i6as1")))) + "157s4c9gjjss6yd7qp7n4q6s72gz1k4ilsx4xjvp357azk49z4qs")))) (build-system meson-build-system) (native-inputs `(("gobject-introspection" ,gobject-introspection) From cb3e055f8627f59f2b08d7192b2d6d64862045ac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Jan 2019 21:58:40 +0100 Subject: [PATCH 299/300] gnu: libassuan: Update to 2.5.2. * gnu/packages/gnupg.scm (libassuan): Update to 2.5.2. --- gnu/packages/gnupg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 4eec697a90..d905de2a0c 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -137,7 +137,7 @@ generation.") (define-public libassuan (package (name "libassuan") - (version "2.5.1") + (version "2.5.2") (source (origin (method url-fetch) @@ -145,7 +145,7 @@ generation.") version ".tar.bz2")) (sha256 (base32 - "0jb4nb4nrjr949gd3lw8lh4v5d6qigxaq6xwy24w5apjnhvnrya7")))) + "1rw8nw6fx6ppxga6m4cqcp898lnlzf7vn3s5c2lzfxg3fzr1nswq")))) (build-system gnu-build-system) (propagated-inputs `(("libgpg-error" ,libgpg-error) From 1710ffa4c79c79079ebd4e523eef8883eb2d3953 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 12 Jan 2019 22:22:26 +0100 Subject: [PATCH 300/300] gnu: sudo: Update to 1.8.27. * gnu/packages/admin.scm (sudo): Update to 1.8.27. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index fa5fa3ab86..5ad3f6d873 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -986,7 +986,7 @@ system administrator.") (define-public sudo (package (name "sudo") - (version "1.8.26") + (version "1.8.27") (source (origin (method url-fetch) (uri @@ -996,7 +996,7 @@ system administrator.") version ".tar.gz"))) (sha256 (base32 - "1qpyyfga8rs02p3186sns8qvh2bzwa48ka845nrcqh83dyd23nj0")) + "1h1f7v9pv0rzp14cxzv8kaa8mdd717fbqv83l7c5dvvi8jwnisvv")) (modules '((guix build utils))) (snippet '(begin