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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 Andy Wingo <wingo@igalia.com>
;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2021 Andrew Tropin <andrew@trop.in>
;;; Copyright © 2022 Maxime Devos <maximedevos@telenet.be>
;;; Copyright © 2023 Bruno Victal <mirai@makinata.eu>
;;; Copyright © 2024 Herman Rimm <herman@rimm.ee>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu services configuration)
  #:use-module (guix packages)
  #:use-module (guix records)
  #:use-module (guix gexp)
  #:use-module ((guix utils) #:select (source-properties->location))
  #:use-module ((guix diagnostics)
                #:select (formatted-message location-file &error-location
                          warning))
  #:use-module ((guix modules) #:select (file-name->module-name))
  #:use-module (guix i18n)
  #:autoload   (texinfo) (texi-fragment->stexi)
  #:autoload   (texinfo serialize) (stexi->texi)
  #:use-module (ice-9 curried-definitions)
  #:use-module (ice-9 format)
  #:use-module (ice-9 match)
  #:use-module (srfi srfi-1)
  #:use-module (srfi srfi-26)
  #:use-module (srfi srfi-34)
  #:use-module (srfi srfi-35)
  #:use-module (srfi srfi-171)
  #:export (configuration-field
            configuration-field-name
            configuration-field-type
            configuration-missing-field
            configuration-field-error
            configuration-field-sanitizer
            configuration-field-serializer
            configuration-field-getter
            configuration-field-default-value-thunk
            configuration-field-documentation

            configuration-error?

            define-configuration
            define-configuration/no-serialization
            no-serialization

            empty-serializer?
            tfilter-maybe-value
            base-transducer

            serialize-configuration
            define-maybe
            define-maybe/no-serialization
            %unset-value
            maybe-value
            maybe-value-set?
            generate-documentation
            configuration->documentation
            empty-serializer
            serialize-package

            filter-configuration-fields

            interpose
            list-of

            list-of-packages?
            list-of-strings?
            list-of-symbols?
            alist?
            serialize-file-like
            text-config?
            serialize-text-config
            generic-serialize-alist-entry
            generic-serialize-alist))

;;; Commentary:
;;;
;;; Syntax for creating Scheme bindings to complex configuration files.
;;;
;;; Code:

(define-condition-type &configuration-error &error
  configuration-error?)

(define (configuration-error message)
  (raise (condition (&message (message message))
                    (&configuration-error))))
(define (configuration-field-error loc field value)
  (raise (apply
          make-compound-condition
          (formatted-message (G_ "invalid value ~s for field '~a'")
                             value field)
          (condition (&configuration-error))
          (if loc
              (list (condition
                     (&error-location (location loc))))
              '()))))

(define (configuration-missing-field kind field)
  (configuration-error
   (format #f "~a configuration missing required field ~a" kind field)))
(define (configuration-missing-default-value kind field)
  (configuration-error
   (format #f "The field `~a' of the `~a' configuration record \
does not have a default value" field kind)))

(define-record-type* <configuration-field>
  configuration-field make-configuration-field configuration-field?
  (name configuration-field-name)
  (type configuration-field-type)
  (getter configuration-field-getter)
  (predicate configuration-field-predicate)
  (sanitizer configuration-field-sanitizer)
  (serializer configuration-field-serializer)
  (default-value-thunk configuration-field-default-value-thunk)
  (documentation configuration-field-documentation))

(define (empty-serializer? field)
  "Predicate that checks whether FIELD is exempt from serialization."
  (eq? empty-serializer
       (configuration-field-serializer field)))

(define (tfilter-maybe-value config)
  "Return a transducer for CONFIG that removes all maybe-type fields whose
value is '%unset-marker."
  (tfilter (lambda (field)
             (let ((field-value ((configuration-field-getter field) config)))
               (maybe-value-set? field-value)))))

(define (base-transducer config)
  "Return a transducer for CONFIG that calls the serializing procedures only
for fields marked for serialization and whose values are not '%unset-marker."
  (compose (tremove empty-serializer?)
           ;; Only serialize fields whose value isn't '%unset-marker%.
           (tfilter-maybe-value config)
           (tmap (lambda (field)
                   ((configuration-field-serializer field)
                    (configuration-field-name field)
                    ((configuration-field-getter field) config))))))

(define (serialize-configuration config fields)
  "Return a G-expression that contains the values corresponding to the
FIELDS of CONFIG, a record that has been generated by `define-configuration'.
The G-expression can then be serialized to disk by using something like
`mixed-text-file'."
  #~(string-append
     #$@(list-transduce (base-transducer config) rcons fields)))

(define-syntax-rule (id ctx parts ...)
  "Assemble PARTS into a raw (unhygienic) identifier."
  (datum->syntax ctx (symbol-append (syntax->datum parts) ...)))

(define (define-maybe-helper serialize? prefix syn)
  (syntax-case syn ()
    ((_ stem)
     (with-syntax
         ((stem?            (id #'stem #'stem #'?))
          (maybe-stem?      (id #'stem #'maybe- #'stem #'?))
          (serialize-stem   (if prefix
                                (id #'stem prefix #'serialize- #'stem)
                                (id #'stem #'serialize- #'stem)))
          (serialize-maybe-stem (if prefix
                                    (id #'stem prefix #'serialize-maybe- #'stem)
                                    (id #'stem #'serialize-maybe- #'stem))))
       #`(begin
           (define (maybe-stem? val)
             (or (not (maybe-value-set? val))
                 (stem? val)))
           #,@(if serialize?
                  (list #'(define (serialize-maybe-stem field-name val)
                            (if (stem? val)
                                (serialize-stem field-name val)
                                "")))
                  '()))))))

(define-syntax define-maybe
  (lambda (x)
    (syntax-case x (no-serialization prefix)
      ((_ stem (no-serialization))
       (define-maybe-helper #f #f #'(_ stem)))
      ((_ stem (prefix serializer-prefix))
       (define-maybe-helper #t #'serializer-prefix #'(_ stem)))
      ((_ stem)
       (define-maybe-helper #t #f #'(_ stem))))))

(define-syntax-rule (define-maybe/no-serialization stem)
  (define-maybe stem (no-serialization)))

(define (normalize-field-type+def s)
  (syntax-case s ()
    ((field-type def)
     (identifier? #'field-type)
     (values #'(field-type def)))
    ((field-type)
     (identifier? #'field-type)
     (values #'(field-type %unset-value)))
    (field-type
     (identifier? #'field-type)
     (values #'(field-type %unset-value)))))

(define (define-configuration-helper serialize? serializer-prefix syn)

  (define (normalize-extra-args s)
    "Extract and normalize arguments following @var{doc}."
    (let loop ((s s)
               (sanitizer* #f)
               (serializer* #f))
      (syntax-case s (sanitizer serializer empty-serializer)
        (((sanitizer proc) tail ...)
         (if sanitizer*
             (syntax-violation 'sanitizer
                               "duplicate entry" #'proc)
             (loop #'(tail ...) #'proc serializer*)))
        (((serializer proc) tail ...)
         (if serializer*
             (syntax-violation 'serializer
                               "duplicate or conflicting entry" #'proc)
             (loop #'(tail ...) sanitizer* #'proc)))
        ((empty-serializer tail ...)
         (if serializer*
             (syntax-violation 'empty-serializer
                               "duplicate or conflicting entry" #f)
             (loop #'(tail ...) sanitizer* #'empty-serializer)))
        (()  ; stop condition
         (values (list sanitizer* serializer*)))
        ((proc)  ; TODO: deprecated, to be removed.
         (not (or sanitizer* serializer*))
         (begin
           (warning #f (G_ "specifying serializers after documentation is \
deprecated, use (serializer ~a) instead~%") (syntax->datum #'proc))
           (values (list #f #'proc)))))))

  (syntax-case syn ()
    ((_ stem (field field-type+def doc extra-args ...) ...)
     (with-syntax
         ((((field-type def) ...)
           (map normalize-field-type+def #'(field-type+def ...)))
          (((sanitizer* serializer*) ...)
           (map normalize-extra-args #'((extra-args ...) ...))))
       (with-syntax
           (((field-getter ...)
             (map (lambda (field)
                    (id #'stem #'stem #'- field))
                  #'(field ...)))
            ((field-predicate ...)
             (map (lambda (type)
                    (id #'stem type #'?))
                  #'(field-type ...)))
            ((field-default ...)
             (map (match-lambda
                    ((field-type default-value)
                     default-value))
                  #'((field-type def) ...)))
            ((field-sanitizer ...)
             #'(sanitizer* ...))
            ((field-serializer ...)
             (map (lambda (type proc)
                    (and serialize?
                         (or proc
                             (if serializer-prefix
                                 (id #'stem serializer-prefix #'serialize- type)
                                 (id #'stem #'serialize- type)))))
                  #'(field-type ...)
                  #'(serializer* ...))))
         (define (default-field-sanitizer name pred)
           ;; Define a macro for use as a record field sanitizer, where NAME
           ;; is the name of the field and PRED is the predicate that tells
           ;; whether a value is valid for this field.
           #`(define-syntax #,(id #'stem #'validate- #'stem #'- name)
               (lambda (s)
                 ;; Make sure the given VALUE, for field NAME, passes PRED.
                 (syntax-case s ()
                   ((_ value)
                    (with-syntax ((name #'#,name)
                                  (pred #'#,pred)
                                  (loc (datum->syntax #'value
                                                      (syntax-source #'value))))
                      #'(if (pred value)
                            value
                            (configuration-field-error
                             (and=> 'loc source-properties->location)
                             'name value))))))))

         #`(begin
             ;; Define field validation macros.
             #,@(filter-map (lambda (name pred sanitizer)
                              (if sanitizer
                                  #f
                                  (default-field-sanitizer name pred)))
                            #'(field ...)
                            #'(field-predicate ...)
                            #'(field-sanitizer ...))

             (define-record-type* #,(id #'stem #'< #'stem #'>)
               stem
               #,(id #'stem #'make- #'stem)
               #,(id #'stem #'stem #'?)
               #,@(map (lambda (name getter def sanitizer)
                         #`(#,name #,getter
                                   (default #,def)
                                   (sanitize
                                    #,(or sanitizer
                                          (id #'stem
                                              #'validate- #'stem #'- name)))))
                       #'(field ...)
                       #'(field-getter ...)
                       #'(field-default ...)
                       #'(field-sanitizer ...))
               (%location #,(id #'stem #'stem #'-source-location)
                          (default (and=> (current-source-location)
                                          source-properties->location))
                          (innate)))

             (define #,(id #'stem #'stem #'-fields)
               (list (configuration-field
                      (name 'field)
                      (type 'field-type)
                      (getter field-getter)
                      (predicate field-predicate)
                      (sanitizer
                       (or field-sanitizer
                           (id #'stem #'validate- #'stem #'- #'field)))
                      (serializer field-serializer)
                      (default-value-thunk
                        (lambda ()
                          (if (maybe-value-set? (syntax->datum field-default))
                              field-default
                              (configuration-missing-default-value
                               '#,(id #'stem #'% #'stem) 'field))))
                      (documentation doc))
                     ...))))))))

(define no-serialization         ;syntactic keyword for 'define-configuration'
  '(no serialization))

(define-syntax define-configuration
  (lambda (s)
    (syntax-case s (no-serialization prefix)
      ((_ stem (field field-type+def doc custom-serializer ...) ...
          (no-serialization))
       (define-configuration-helper
         #f #f #'(_ stem (field field-type+def doc custom-serializer ...)
                 ...)))
      ((_ stem  (field field-type+def doc custom-serializer ...) ...
          (prefix serializer-prefix))
       (define-configuration-helper
         #t #'serializer-prefix #'(_ stem (field field-type+def
                                                 doc custom-serializer ...)
                 ...)))
      ((_ stem (field field-type+def doc custom-serializer ...) ...)
       (define-configuration-helper
         #t #f #'(_ stem (field field-type+def doc custom-serializer ...)
                 ...))))))

(define-syntax-rule (define-configuration/no-serialization
                      stem (field field-type+def
                                  doc custom-serializer ...) ...)
  (define-configuration stem (field field-type+def
                                    doc custom-serializer ...) ...
    (no-serialization)))

(define (empty-serializer field-name val) "")
(define serialize-package empty-serializer)

;; Ideally this should be an implementation detail, but we export it
;; to provide a simpler API that enables unsetting a configuration
;; field that has a maybe type, but also a default value.  We give it
;; a value that sticks out to the reader when something goes wrong.
;;
;; An example use-case would be something like a network application
;; that uses a default port, but the field can explicitly be unset to
;; request a random port at startup.
(define %unset-value '%unset-marker%)

(define (maybe-value-set? value)
  "Predicate to check whether a 'maybe' value was explicitly provided."
  (not (eq? %unset-value value)))

;; Ideally there should be a compiler macro for this predicate, that expands
;; to a conditional that only instantiates the default value when needed.
(define* (maybe-value value #:optional (default #f))
  "Returns VALUE, unless it is the unset value, in which case it returns
DEFAULT."
  (if (maybe-value-set? value)
      value
      default))

;; A little helper to make it easier to document all those fields.
(define (generate-documentation documentation documentation-name)
  (define (str x) (object->string x))

  (define (package->symbol package)
    "Return the first symbol name of a package that matches PACKAGE, else #f."
    (let* ((module (file-name->module-name
                    (location-file (package-location package))))
           (symbols (filter-map
                     identity
                     (module-map (lambda (symbol var)
                                   (and (equal? package (variable-ref var))
                                        symbol))
                                 (resolve-module module)))))
      (if (null? symbols)
          #f
          (first symbols))))

  (define (generate configuration-name)
    (match (assq-ref documentation configuration-name)
      ((fields . sub-documentation)
       `((deftp (% (category "Data Type") (name ,(str configuration-name)))
           (para "Available " (code ,(str configuration-name)) " fields are:")
           (table
            (% (formatter (asis)))
            ,@(map
               (lambda (f)
                 (let ((field-name (configuration-field-name f))
                       (field-type (configuration-field-type f))
                       (field-docs (cdr (texi-fragment->stexi
                                         (configuration-field-documentation f))))
                       (default (catch #t
                                  (configuration-field-default-value-thunk f)
                                  (lambda _ '%invalid))))
                   (define (show-default? val)
                     (or (string? val) (number? val) (boolean? val)
                         (package? val)
                         (and (symbol? val) (not (eq? val '%invalid)))
                         (and (list? val) (and-map show-default? val))))

                   (define (show-default val)
                     (cond
                      ((package? val)
                       (symbol->string (package->symbol val)))
                      (((list-of package?) val)
                       (format #f "(~{~a~^ ~})" (map package->symbol val)))
                      (else (str val))))

                   `(entry (% (heading
                               (code ,(str field-name))
                               ,@(if (show-default? default)
                                     `(" (default: "
                                       (code ,(show-default default)) ")")
                                     '())
                               " (type: " ,(str field-type) ")"))
                           (para ,@field-docs)
                           ,@(append-map
                              generate
                              (filter-map
                                (match-lambda
                                  ((name config)
                                   (and (eq? name field-name)
                                        config)))
                                sub-documentation)))))
               fields)))))))
  (stexi->texi `(*fragment* . ,(generate documentation-name))))

(define (configuration->documentation configuration-symbol)
  "Take CONFIGURATION-SYMBOL, the symbol corresponding to the name used when
defining a configuration record with DEFINE-CONFIGURATION, and output the
Texinfo documentation of its fields."
  ;; This is helper for a simple, straight-forward application of
  ;; GENERATE-DOCUMENTATION.
  (let ((fields-getter (module-ref (current-module)
                                   (symbol-append configuration-symbol
                                                  '-fields))))
    (display (generate-documentation `((,configuration-symbol ,fields-getter))
                                     configuration-symbol))))

(define* (filter-configuration-fields configuration-fields fields
                                      #:optional negate?)
  "Retrieve the fields listed in FIELDS from CONFIGURATION-FIELDS.
If NEGATE? is @code{#t}, retrieve all fields except FIELDS."
  (filter (lambda (field)
            (let ((member? (member (configuration-field-name field) fields)))
              (if (not negate?) member? (not member?))))
          configuration-fields))


(define* (interpose ls  #:optional (delimiter "\n") (grammar 'infix))
  "Same as @code{string-join}, but without join and string, returns a
DELIMITER interposed LS.  Support 'infix and 'suffix GRAMMAR values."
  (when (not (member grammar '(infix suffix)))
    (raise
     (formatted-message
      (G_ "The GRAMMAR value must be 'infix or 'suffix, but ~a provided.")
      grammar)))
  (fold-right (lambda (e acc)
                (cons e
                      (if (and (null? acc) (eq? grammar 'infix))
                          acc
                          (cons delimiter acc))))
              '() ls))


;;;
;;; Commonly used predicates
;;;

(define (list-of pred?)
  "Return a procedure that takes a list and check if all the elements of
the list result in @code{#t} when applying PRED? on them."
    (lambda (x)
      (if (list? x)
          (every pred? x)
          #f)))

(define list-of-packages?
  (list-of package?))

(define list-of-strings?
  (list-of string?))

(define list-of-symbols?
  (list-of symbol?))


;;;
;;; Special serializers
;;;

(define alist?
  (list-of pair?))

(define serialize-file-like empty-serializer)

(define (text-config? config)
  (list-of file-like?))

(define (serialize-text-config field-name val)
  #~(string-append
     #$@(interpose
         (map
          (lambda (e)
            #~(begin
                (use-modules (ice-9 rdelim))
                (with-fluids ((%default-port-encoding "UTF-8"))
                  (with-input-from-file #$e read-string))))
          val)
         "\n" 'suffix)))

(define ((generic-serialize-alist-entry serialize-field) entry)
  "Apply the SERIALIZE-FIELD procedure on the field and value of ENTRY."
  (match entry
    ((field . val) (serialize-field field val))))

(define (generic-serialize-alist combine serialize-field fields)
  "Generate a configuration from an association list FIELDS.

SERIALIZE-FIELD is a procedure that takes two arguments, it will be
applied on the fields and values of FIELDS using the
@code{generic-serialize-alist-entry} procedure.

COMBINE is a procedure that takes one or more arguments and combines
all the alist entries into one value, @code{string-append} or
@code{append} are usually good candidates for this."
  (apply combine
         (map (generic-serialize-alist-entry serialize-field) fields)))
ri "vctrs" version)) (sha256 (base32 - "03hyxk3x635xfdn2x707gygdb2xk0cayl1nl44zib9bwqyyb7nas")))) + "1c8v5lmap6iq4jpi7p3w05hsv2dq7rjg057pvnfyc5d1xmsqnkkz")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) -- cgit v1.2.3 From f65d223eecc13630317d5a13dd2a9582eee9d045 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:06 +0200 Subject: gnu: r-pillar: Update to 1.6.0. * gnu/packages/cran.scm (r-pillar): Update to 1.6.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 621b40f736..c8d8ca6d2f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5507,14 +5507,14 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.5.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "0wp68cg95895aybi7yjqy0sidvc68lmfqndinpd63dysci9x3r8c")))) + "1pfa6q63ji6mqsvkbpjvvlaivw66nyinwbk82jh0a0c6dy41w47i")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) -- cgit v1.2.3 From 22778956e822ae2994f64a13b222bbb6e732469f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:07 +0200 Subject: gnu: r-parsedate: Update to 1.2.1. * gnu/packages/cran.scm (r-parsedate): Update to 1.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c8d8ca6d2f..1782221719 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6874,14 +6874,14 @@ and Eclat.") (define-public r-parsedate (package (name "r-parsedate") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "parsedate" version)) (sha256 (base32 - "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr")))) + "05l6f1n3dsm383w7jfg3j38klvmzzfvc7qi9zr5ij13rljj8s1vb")))) (build-system r-build-system) (propagated-inputs `(("r-rematch2" ,r-rematch2))) -- cgit v1.2.3 From 0161d0bcf0b0bc465159af9c0a04a1a171a47f43 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:07 +0200 Subject: gnu: r-later: Update to 1.2.0. * gnu/packages/cran.scm (r-later): Update to 1.2.0. [propagated-inputs]: Remove r-bh. --- gnu/packages/cran.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1782221719..a4a0cdf556 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7060,18 +7060,17 @@ exchanging spatial objects with other R packages.") (define-public r-later (package (name "r-later") - (version "1.1.0.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 - "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki")))) + "00f4n1b2ykrs2cd61pypa4d00ydx9hqq2c1a1p8psa2yym6979bm")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp) + `(("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang))) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit v1.2.3 From c2cc32c88ae237ff2854ff65a153af05b2a79a9d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:07 +0200 Subject: gnu: r-rastervis: Update to 0.50.2. * gnu/packages/cran.scm (r-rastervis): Update to 0.50.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a4a0cdf556..7060b43558 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7410,14 +7410,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-rastervis (package (name "r-rastervis") - (version "0.50.1") + (version "0.50.2") (source (origin (method url-fetch) (uri (cran-uri "rasterVis" version)) (sha256 (base32 - "1fkmyllydnmk3j2cmgf86r91wyxf2kh573x8bkck7wgkfniw4h7w")))) + "0fl766wx5jz8ylpd28czkvl32pk1s57nbfsn8kxrwfvx5cfnfkxr")))) (properties `((upstream-name . "rasterVis"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 58327ba184099ced60b15053cdde7d048af415ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:07 +0200 Subject: gnu: r-reticulate: Update to 1.20. * gnu/packages/cran.scm (r-reticulate): Update to 1.20. [propagated-inputs]: Add r-png and r-withr. --- gnu/packages/cran.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7060b43558..ef71c15f4b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7564,21 +7564,23 @@ obtain a better initial configuration in non-metric MDS.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.18") + (version "1.20") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk")))) + "0ay8cb0d3lj702aw338lkc7sxj9j05izji3waww1z0lph16406bh")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs `(("r-rappdirs" ,r-rappdirs) ("r-jsonlite" ,r-jsonlite) ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + ("r-png" ,r-png) + ("r-rcpp" ,r-rcpp) + ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rstudio/reticulate") -- cgit v1.2.3 From d11b3f575f177f8ddadc136fa0c49989ba7f2182 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:07 +0200 Subject: gnu: r-rbibutils: Update to 2.1.1. * gnu/packages/cran.scm (r-rbibutils): Update to 2.1.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ef71c15f4b..778bab1419 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8042,14 +8042,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.1") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "13phw0dk3p3s1z45ff7dbqnn27zws1209mp3d4763zh7xnsdsl44")))) + "0vk8pc9nsf28jxlb2vv1kydqfnvlh7q4kd2wyva4mwhl51s36bpl")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") -- cgit v1.2.3 From 070b76612732c927eb6f3403fb4c814a0c1e6a67 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:07 +0200 Subject: gnu: r-brglm: Update to 0.7.2. * gnu/packages/cran.scm (r-brglm): Update to 0.7.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 778bab1419..eca9a7a466 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8145,14 +8145,14 @@ on the methods that are implemented can be found in Kosmidis (2008) (define-public r-brglm (package (name "r-brglm") - (version "0.7.1") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "brglm" version)) (sha256 (base32 - "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa")))) + "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an")))) (properties `((upstream-name . "brglm"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8067bcdf53d7cdfbc5aae6c99435ff566550cec5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:08 +0200 Subject: gnu: r-entropy: Update to 1.3.0. * gnu/packages/cran.scm (r-entropy): Update to 1.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index eca9a7a466..1f6fad64d5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8176,14 +8176,14 @@ reduced-bias estimates.") (define-public r-entropy (package (name "r-entropy") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "entropy" version)) (sha256 (base32 - "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd")))) + "0fhhsy8ci9c73xwr2b167dfix0b7kqsk6kf46qqv1lmvbv11vxqa")))) (properties `((upstream-name . "entropy"))) (build-system r-build-system) (home-page "https://www.strimmerlab.org/software/entropy/") -- cgit v1.2.3 From 2f88711ce392b42c2fbe9c08940e66cae0fd2f5c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:08 +0200 Subject: gnu: r-flextable: Update to 0.6.5. * gnu/packages/cran.scm (r-flextable): Update to 0.6.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1f6fad64d5..705d95ba21 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8452,14 +8452,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.6.4") + (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "1ykjfnqhn8nd9f3l4jj8hf1bbjjckkna3p7fdsg0a73c05a17yma")))) + "1njk4kc19r2n2awxjfz4svf1pivxhn12r9dqsdvbdpbfl5wmvxzl")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) -- cgit v1.2.3 From b30b025c6f2d34ed32547a1f93cf36c2ed20af00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:08 +0200 Subject: gnu: r-writexl: Update to 1.4.0. * gnu/packages/cran.scm (r-writexl): Update to 1.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 705d95ba21..58d51bf48f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8487,14 +8487,14 @@ documents.") (define-public r-writexl (package (name "r-writexl") - (version "1.3.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "writexl" version)) (sha256 (base32 - "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb")))) + "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/ropensci/writexl") -- cgit v1.2.3 From ea359fb92f86e3590bbe80d1d803db143953e866 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:08 +0200 Subject: gnu: r-doby: Update to 4.6.10. * gnu/packages/cran.scm (r-doby): Update to 4.6.10. [propagated-inputs]: Add r-curry and r-microbenchmark. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 58d51bf48f..656c564c95 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8700,24 +8700,26 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.9") + (version "4.6.10") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "02f545md5yhbpp3wb3q2c8zabqwgf02555r5c6g7znab5zjbyr00")))) + "0vqmmxhr3mx8yyl38abvy0zqswfgn7jqgwvc5gdchdiq6v8flnfr")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) + ("r-curry" ,r-curry) ("r-deriv" ,r-deriv) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) + ("r-microbenchmark" ,r-microbenchmark) ("r-pbkrtest" ,r-pbkrtest) ("r-tibble" ,r-tibble))) (native-inputs -- cgit v1.2.3 From 0ef00dd7f676ff388d63463695f04a4374628974 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:08 +0200 Subject: gnu: r-raster: Update to 3.4-10. * gnu/packages/cran.scm (r-raster): Update to 3.4-10. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 656c564c95..1213777d13 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9220,14 +9220,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.4-5") + (version "3.4-10") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6")))) + "1x9d364r6wsm261a0s303mfalk79d4h0lwqlvbwzg7khmz991rlr")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) -- cgit v1.2.3 From c4300dc2984038b8f9aea39a335365dd9d41d232 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:09 +0200 Subject: gnu: r-svgui: Update to 1.0.1. * gnu/packages/cran.scm (r-svgui): Update to 1.0.1. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1213777d13..8b91f9eecb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9307,15 +9307,17 @@ biological data by Michael Whitlock and Dolph Schluter.") (define-public r-svgui (package (name "r-svgui") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "svGUI" version)) (sha256 - (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc")))) + (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979")))) (properties `((upstream-name . "svGUI"))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/SciViews/svGUI/") (synopsis "Functions for managing GUI clients in R") (description -- cgit v1.2.3 From 799e6b1b20bb3f3d3e529d73ea1497dc600a7c4e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:09 +0200 Subject: gnu: r-svdialogs: Update to 1.0.3. * gnu/packages/cran.scm (r-svdialogs): Update to 1.0.3. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8b91f9eecb..bcfce1347b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9330,13 +9330,13 @@ calls to the particular toolkits in use in function of the context.") (define-public r-svdialogs (package (name "r-svdialogs") - (version "1.0.0") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "svDialogs" version)) (sha256 - (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97")))) + (base32 "0j00xjvkwv992ir48czhvyj29rb9vpd243vbyyj2binn0q0qa431")))) (properties `((upstream-name . "svDialogs"))) (build-system r-build-system) (inputs @@ -9345,6 +9345,8 @@ calls to the particular toolkits in use in function of the context.") (propagated-inputs `(("r-rstudioapi" ,r-rstudioapi) ("r-svgui" ,r-svgui))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/SciViews/svDialogs/") (synopsis "Portable dialog boxes") (description -- cgit v1.2.3 From 94080fc0aa9d7bd2b3513144515ba84023ef6bd1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:09 +0200 Subject: gnu: r-magick: Update to 2.7.2. * gnu/packages/cran.scm (r-magick): Update to 2.7.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bcfce1347b..3135ceacce 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9819,14 +9819,14 @@ samples is large and the number of mixture components is not too large.") (define-public r-magick (package (name "r-magick") - (version "2.7.1") + (version "2.7.2") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "16svy84dq25g69axqgympsrh8dzssa1w3zz08zc8m6nprr3jqwqf")))) + "1ckp85wk9lj6jjm92ww4mg1r4h4zm2cm68y6fyb1hz4mr3nihmji")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) -- cgit v1.2.3 From 795516ff571dcbafb746e1ae5994867ccbf3ae57 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:09 +0200 Subject: gnu: r-multcomp: Update to 1.4-17. * gnu/packages/cran.scm (r-multcomp): Update to 1.4-17. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3135ceacce..72fee5c03c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10233,14 +10233,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-16") + (version "1.4-17") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s")))) + "02zv739mbmx672yrqqx8am229h7ps476wphig7jrrbfgay29sl21")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) -- cgit v1.2.3 From 3e4baacd9186308f4481d14f18c6a2978305e288 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:09 +0200 Subject: gnu: r-emmeans: Update to 1.6.0. * gnu/packages/cran.scm (r-emmeans): Update to 1.6.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 72fee5c03c..1fd4958a9f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10261,14 +10261,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.5.5-1") + (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "0l5dd71ihhs7zy6ygniy07iisgy7a1ai1w41hqf84swb0j3cl6iz")))) + "07iw3faprf98mncymbjbmfm2yi294yiwdg30xlql5sfx12qbf6r0")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) -- cgit v1.2.3 From da20f1f0b271cd672c7d2d93086f166758e69f82 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:09 +0200 Subject: gnu: r-tmb: Update to 1.7.20. * gnu/packages/cran.scm (r-tmb): Update to 1.7.20. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1fd4958a9f..242614e67c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10394,14 +10394,14 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.7.19") + (version "1.7.20") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s")))) + "14wapc8bicr4j7mmrv1hrsw407lsbr7l4cfvy3j9sfjdbrq31a37")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 787a0b26e184e97e2251fca9ad4425da3ec41780 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:10 +0200 Subject: gnu: r-bayestestr: Update to 0.9.0. * gnu/packages/cran.scm (r-bayestestr): Update to 0.9.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 242614e67c..c5c7fb8dbd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10497,14 +10497,14 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.8.2") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4")))) + "0msr24ymnazpaz8s9qs5v3xn1i9984p98lr9x4qq9cxgx34rm9h0")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 363a6692765bdc0b6a15ebeca2c53ba16b64c953 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:10 +0200 Subject: gnu: r-performance: Update to 0.7.1. * gnu/packages/cran.scm (r-performance): Update to 0.7.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c5c7fb8dbd..db52cd55ee 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10524,14 +10524,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.7.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj")))) + "1kf8z7lrjv1bg8mqb7sq4651k2xg3d02azq7gr0jc4c52cr2yaqm")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) -- cgit v1.2.3 From 47a15ac7d009b70eef191557f8f2d6934e20ea4d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:13:10 +0200 Subject: gnu: r-ggeff