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update of packages

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This commit is contained in:
Daniel Weschke
2023-11-04 19:26:41 +01:00
parent e162a12b58
commit 3b54a3236d
726 changed files with 297673 additions and 34585 deletions
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255
lisp/ess/ess-r-mode.el
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@@ -1,6 +1,6 @@
;;; ess-r-mode.el --- R customization -*- lexical-binding: t; -*-
;; Copyright (C) 1997-2020 Free Software Foundation, Inc.
;; Copyright (C) 1997-2022 Free Software Foundation, Inc.
;; Author: A.J. Rossini
;; Created: 12 Jun 1997
;; Maintainer: ESS-core <ESS-core@r-project.org>
@@ -442,7 +442,6 @@ To be used as part of `font-lock-defaults' keywords."
'((ess-local-customize-alist . 'ess-r-customize-alist)
(ess-dialect . "R")
(ess-suffix . "R")
(ess-format-command-alist . ess-r-format-command-alist)
(ess-traceback-command . ess-r-traceback-command)
(ess-call-stack-command . ess-r-call-stack-command)
(ess-mode-completion-syntax-table . ess-r-completion-syntax-table)
@@ -480,7 +479,7 @@ fill=TRUE); try(traceback(), silent=TRUE)})\n")
(defun ess-r-format-command (cmd &rest args)
(let ((sentinel (alist-get 'output-delimiter args)))
(format ".ess.command(local(%s), '%s')\n" cmd sentinel)))
(ess-r--format-call ".ess.command(local(%s), '%s')\n" cmd sentinel)))
(defvar ess-r-format-command-alist
'((fun . ess-r-format-command)
@@ -538,8 +537,18 @@ fill=TRUE); try(traceback(), silent=TRUE)})\n")
;;;*;;; Mode init
(define-obsolete-variable-alias 'ess-R-post-run-hook 'ess-r-post-run-hook "ESS 18.10.2")
;; We moved the set-wd instruction from `inferior-ess' to here to
;; avoid sending R code to gdb or lldb before we had a chance to
;; send "run". So this is no longer generic and inferior modes need
;; to call this manually. One way to fix this would be to make
;; `inferior-ess' a `cl-defgeneric'.
(defvar ess-r-post-run-hook nil
"Functions run in process buffer after the initialization of R process.")
"Functions run in process buffer after the initialization of R process.
Make sure to call blocking commands (e.g. based on `ess-command')
first. Streaming commands (e.g. based on `ess-send-string')
should come last, otherwise they will make R busy and the
blocking commands will throw an error.")
;;;###autoload
(defun run-ess-r (&optional start-args)
@@ -577,8 +586,8 @@ will be prompted to enter arguments interactively."
start-args)
((and start-args
(listp start-args)
(cl-every 'stringp start-args))
(mapconcat 'identity start-args " "))
(cl-every #'stringp start-args))
(mapconcat #'identity start-args " "))
(start-args
(read-string
(concat "Starting Args"
@@ -606,12 +615,8 @@ will be prompted to enter arguments interactively."
(ess-process-put 'callbacks '(inferior-ess-r--init-callback))
;; Trigger the callback
(process-send-string (get-buffer-process inf-buf) "r\n"))
(ess-wait-for-process)
(ess-r-initialize-on-start)
(comint-goto-process-mark))
(ess-write-to-dribble-buffer
(format "(R): inferior-ess-language-start=%s\n"
inferior-ess-language-start)))
(ess-r-initialize)
(comint-goto-process-mark)))
inf-buf)))
;;;###autoload
@@ -621,36 +626,73 @@ will be prompted to enter arguments interactively."
(set-buffer (run-ess-r start-args)))
(defun inferior-ess-r--init-callback (_proc _name)
(ess-r-initialize-on-start))
(ess-r-initialize))
(defmacro ess-r--without-format-command (&rest body)
(declare (indent 0)
(debug (&rest form)))
`(with-current-buffer (process-buffer (ess-command--get-proc nil nil))
(let ((old-alist ess-format-command-alist))
(unwind-protect
(progn
(setq ess-format-command-alist nil)
,@body)
(setq ess-format-command-alist old-alist)))))
(defvar ess-r--init-timeout 5
"Maximum time for R to become available on startup.
If the timeout is reached, an error is thrown advising the user
to run `ess-r-initialize' again.")
(define-obsolete-function-alias 'R-initialize-on-start 'ess-r-initialize-on-start "ESS 19.04")
(defun ess-r-initialize-on-start ()
(define-obsolete-function-alias 'R-initialize-on-start
#'ess-r-initialize "ESS 19.04")
(defun ess-r-initialize ()
"This function is run after the first R prompt.
Executed in process buffer."
(interactive)
(ess-r--without-format-command
(ess-command (format
"if (identical(getOption('pager'), file.path(R.home(), 'bin', 'pager')))
options(pager = '%s')\n"
inferior-ess-pager)))
(ess-r-load-ESSR)
(when inferior-ess-language-start
(ess-command (concat inferior-ess-language-start "\n")))
;; tracebug
(when ess-use-tracebug (ess-tracebug 1))
(add-hook 'ess-presend-filter-functions 'ess-R-scan-for-library-call nil 'local)
(run-hooks 'ess-r-post-run-hook))
(condition-case err
(progn
(unless (ess-wait-for-process nil nil nil nil ess-r--init-timeout)
(error "Process is busy"))
(ess-command (ess-r--init-options-command))
(ess-r-load-ESSR))
(error (ess-r--init-error-handler err))
(quit (ess-r--init-error-handler)))
(ess-process-put 'format-command-alist ess-r-format-command-alist)
(ess-process-put 'bg-eval-disabled nil)
(ess-execute-screen-options t)
(ess-set-working-directory default-directory)
(when ess-use-tracebug
(ess-tracebug 1))
(add-hook 'ess-presend-filter-functions #'ess-R-scan-for-library-call nil 'local)
;; Wait before running user hook so they can call blocking commands
(ess-wait-for-process)
(run-hooks 'ess-r-post-run-hook)
(ess-wait-for-process))
(defun ess-r--init-error-handler (&optional err)
(ess-write-to-dribble-buffer "Failed to start ESSR\n")
(when-let ((proc (and ess-local-process-name
(get-process ess-local-process-name))))
(process-put proc 'bg-eval-disabled t))
(let ((msgs `("ESSR failed to start, please call `ess-r-initialize' to recover"
,@(when err
(concat "Caused by error: " (error-message-string err))))))
(error (mapconcat 'identity msgs "\n"))))
;; FIXME: Should we stop setting `str.dendogram.last`? See:
;; https://emacs.stackexchange.com/questions/27673/ess-dendrograms-appearance-of-last-branch/27729#27729
;;
;; FIXME: We don't use `ess-r-pager`? It's nil by default and
;; documented that this should not normally be set
(defun ess-r--init-options-command ()
(let ((args (list (format "STERM = '%s'" ess-STERM)
"str.dendrogram.last = '\\''"
(format "editor = '%s'" ess-r-editor)
(ess-r--update-opt-if-eq "pager"
"file.path(R.home(), 'bin', 'pager')"
(format "'%s'" inferior-ess-pager))
"show.error.locations = TRUE")))
(format "options(%s)\n" (mapconcat 'identity args ", "))))
(defun ess-r--update-opt-if-eq (opt old new)
(let ((actual (format "getOption('%s')" opt)))
(format "%s = if (identical(%s, %s)) %s else %s"
opt
actual
old
new
actual)))
(defun ess-r--skip-function ()
;; Assumes the point is at function start
@@ -780,10 +822,10 @@ top level functions only."
(ess--setup-company ess-r-company-backends)
(setq-local prettify-symbols-alist ess-r-prettify-symbols)
(setq font-lock-defaults '(ess-build-font-lock-keywords nil nil ((?\. . "w") (?\_ . "w"))))
(remove-hook 'completion-at-point-functions 'ess-filename-completion 'local) ;; should be first
(add-hook 'completion-at-point-functions 'ess-r-object-completion nil 'local)
(remove-hook 'completion-at-point-functions #'ess-filename-completion 'local) ;; should be first
(add-hook 'completion-at-point-functions #'ess-r-object-completion nil 'local)
(add-hook 'completion-at-point-functions #'ess-r-package-completion nil 'local)
(add-hook 'completion-at-point-functions 'ess-filename-completion nil 'local)
(add-hook 'completion-at-point-functions #'ess-filename-completion nil 'local)
(add-hook 'xref-backend-functions #'ess-r-xref-backend nil 'local)
(add-hook 'project-find-functions #'ess-r-project nil 'local)
@@ -796,9 +838,9 @@ top level functions only."
(setq-local end-of-defun-function #'ess-r-end-of-defun)
(ess-roxy-mode))
;;;###autoload
(defalias 'R-mode 'ess-r-mode)
(defalias 'R-mode #'ess-r-mode)
;;;###autoload
(defalias 'r-mode 'ess-r-mode)
(defalias 'r-mode #'ess-r-mode)
;;;###autoload
@@ -959,7 +1001,7 @@ Set SYM to VAL and call `ess-r-redefine-runners'."
(ess-r-redefine-runners))
(define-obsolete-function-alias
'ess-r-versions-create 'ess-r-define-runners "ESS 18.10")
'ess-r-versions-create #'ess-r-define-runners "ESS 18.10")
(defvar ess-newest-R nil
"Stores the newest version of R that has been found.
@@ -1044,7 +1086,8 @@ returned."
(defun ess-current-R-version ()
"Get the version of R currently running in the ESS buffer as a string."
(ess-make-buffer-current)
(car (ess-get-words-from-vector "as.character(.ess.Rversion)\n")))
(car (ess-get-words-from-vector (format "base::as.character(%s)\n"
(ess-r--format-call ".ess.Rversion")))))
(defun ess-current-R-at-least (version)
"Is the version of R (in the ESS buffer) at least (\">=\") VERSION ?
@@ -1053,7 +1096,9 @@ Examples: (ess-current-R-at-least '2.7.0)
(ess-make-buffer-current)
(string= "TRUE"
(car (ess-get-words-from-vector
(format "as.character(.ess.Rversion >= \"%s\")\n" version)))))
(format "base::as.character(%s >= \"%s\")\n"
(ess-r--format-call ".ess.Rversion")
version)))))
(defun ess-find-newest-date (rvers)
"Find the newest version of R given in the a-list RVERS.
Each element of RVERS is a dotted pair (date . R-version), where
@@ -1128,7 +1173,7 @@ use \"bin/Rterm.exe\"."
(setq font-lock-defaults '(ess-build-font-lock-keywords
nil nil ((?\. . "w") (?\_ . "w") (?' . ".")))))
(fset 'r-transcript-mode 'ess-r-transcript-mode)
(defalias 'r-transcript-mode #'ess-r-transcript-mode)
;;;###autoload
(add-to-list 'auto-mode-alist '("\\.[Rr]out\\'" . ess-r-transcript-mode))
@@ -1150,7 +1195,7 @@ not issue messages."
(goto-char from)
(ess-rep-regexp "\\(\\([][=,()]\\|<-\\) *\\)F\\>" "\\1FALSE"
'fixcase nil (not quietly))))
(define-obsolete-function-alias 'R-fix-T-F 'ess-r-fix-T-F
(define-obsolete-function-alias 'R-fix-T-F #'ess-r-fix-T-F
"ESS 18.10")
(defvar ess--packages-cache nil
@@ -1200,7 +1245,7 @@ With argument UPDATE, update cached packages list."
(match-string 2 url)))
(ess-command (format mirror-cmd ess--CRAN-mirror)))))
(message "CRAN mirror: %s" (car (ess-get-words-from-vector "getOption('repos')[['CRAN']]\n"))))
(define-obsolete-function-alias 'ess-setCRANMiror 'ess-set-CRAN-mirror "ESS 18.10")
(define-obsolete-function-alias 'ess-setCRANMiror #'ess-set-CRAN-mirror "ESS 18.10")
(defun ess-r-check-install-package (pkg)
"Check if package PKG is installed and offer to install if not."
@@ -1231,7 +1276,7 @@ Placed into `ess-presend-filter-functions' for R dialects."
"Load an R package."
(ess-eval-linewise (format "library('%s')\n" pack)))
(define-obsolete-function-alias 'ess-library 'ess-load-library "ESS[12.09-1]")
(define-obsolete-function-alias 'ess-library #'ess-load-library "ESS[12.09-1]")
;;; smart-comma was a bad idea
(eval-after-load "eldoc"
@@ -1257,13 +1302,19 @@ Placed into `ess-presend-filter-functions' for R dialects."
(ess-r-arg "verbose" "TRUE"))))
(concat visibly output pkg verbose)))
(defun ess-r--format-call (cmd &rest objects)
"Prefix an ESSR command with a namespace qualifier.
CMD is formatted with OBJECTS using `format'."
(concat "base::as.environment('ESSR')$"
(apply #'format cmd objects)))
(cl-defmethod ess-build-eval-command--override (string &context (ess-dialect "R")
&optional visibly output file &rest args)
"R method to build eval command."
(let* ((namespace (caar args))
(namespace (unless ess-debug-minor-mode
(or namespace (ess-r-get-evaluation-env))))
(cmd (if namespace ".ess.ns_eval" ".ess.eval"))
(cmd (ess-r--format-call (if namespace ".ess.ns_eval" ".ess.eval")))
(file (when file (ess-r-arg "file" file t)))
(rargs (ess-r-build-args visibly output namespace)))
(concat cmd "(\"" string "\"" rargs file ")\n")))
@@ -1271,7 +1322,7 @@ Placed into `ess-presend-filter-functions' for R dialects."
(cl-defmethod ess-build-load-command (string &context (ess-dialect "R")
&optional visibly output file &rest _args)
(let* ((namespace (or file (ess-r-get-evaluation-env)))
(cmd (if namespace ".ess.ns_source" ".ess.source"))
(cmd (ess-r--format-call (if namespace ".ess.ns_source" ".ess.source")))
(rargs (ess-r-build-args visibly output namespace)))
(concat cmd "('" string "'" rargs ")\n")))
@@ -1394,7 +1445,7 @@ selected (see `ess-r-set-evaluation-env')."
(setq ess-r-help--local-object obj)
(let ((obj-arg (concat "'" obj "'"))
(pkg-arg (ess-r-arg "package" pkg t)))
(concat ".ess.help(" obj-arg pkg-arg ")\n")))
(ess-r--format-call ".ess.help(%s%s)\n" obj-arg pkg-arg)))
(defun ess-r-help--build-help-command--unqualified (obj)
(if (eq ess-help-type 'index)
@@ -1500,21 +1551,20 @@ process."
;; `.ess.command()` is not defined until ESSR is loaded so disable
;; it temporarily. Would be helpful to implement an `inferior-ess-let'
;; macro .
(ess-r--without-format-command
(cond
((file-remote-p (ess-get-process-variable 'default-directory))
(if (eq ess-r-fetch-ESSR-on-remotes t)
(or (ess-r--fetch-ESSR-remote)
(ess-r--load-ESSR-remote))
(ess-r--load-ESSR-remote)))
((and (bound-and-true-p ess-remote))
;; NB: With ess-remote we send by chunks because sending large sources is
;; fragile
(if ess-r-fetch-ESSR-on-remotes
(or (ess-r--fetch-ESSR-remote)
(ess-r--load-ESSR-remote t))
(ess-r--load-ESSR-remote t)))
(t (ess-r--load-ESSR-local)))))
(cond
((file-remote-p (ess-get-process-variable 'default-directory))
(if (eq ess-r-fetch-ESSR-on-remotes t)
(or (ess-r--fetch-ESSR-remote)
(ess-r--load-ESSR-remote))
(ess-r--load-ESSR-remote)))
((and (bound-and-true-p ess-remote))
;; NB: With ess-remote we send by chunks because sending large sources is
;; fragile
(if ess-r-fetch-ESSR-on-remotes
(or (ess-r--fetch-ESSR-remote)
(ess-r--load-ESSR-remote t))
(ess-r--load-ESSR-remote t)))
(t (ess-r--load-ESSR-local))))
(defun ess-r--load-ESSR-local ()
"Load ESSR into a local process.
@@ -1523,16 +1573,26 @@ Source the etc/ESSR/.load.R file into the R process. The
etc/ESSR/R directory into the ESSR environment and attaches the
environment to the search path."
(let* ((src-dir (expand-file-name "ESSR/R" ess-etc-directory))
(cmd (format "local({
source('%s/.load.R', local=TRUE) #define load.ESSR
.ess.ESSR.load('%s')
})\n"
src-dir src-dir)))
(with-current-buffer (ess-command cmd)
(buf (ess-command (ess-r--load-ESSR-command src-dir))))
(with-current-buffer buf
(let ((msg (buffer-string)))
(when (> (length msg) 1)
(message (format "Messages while loading ESSR: %s" msg)))))))
(defun ess-r--load-ESSR-command (src-dir)
(format "base::tryCatch(
base::local({
base::source('%s/.load.R', local=TRUE) #define load.ESSR
.ess.ESSR.load('%s')
}),
error = function(cnd) {
msg <- paste0('ESSR::ERROR \"', conditionMessage(cnd), '\"')
writeLines(msg)
}
)\n"
src-dir
src-dir))
(defun ess-r--load-ESSR-remote (&optional chunked)
"Load ESSR into a remote process through the process connection.
Send the contents of the etc/ESSR/R directory to the remote
@@ -1642,7 +1702,8 @@ Return the amount the indentation changed by."
(indent-region start (point)))))
(defun ess-offset (offset)
(setq offset (eval (intern (concat "ess-offset-" (symbol-name offset)))))
(setq offset
(symbol-value (intern (concat "ess-offset-" (symbol-name offset)))))
(when (and (not (eq offset nil))
(listp offset)
(or (numberp (cadr offset))
@@ -1657,7 +1718,8 @@ Return the amount the indentation changed by."
ess-indent-offset)))
(defun ess-offset-type (offset)
(setq offset (eval (intern (concat "ess-offset-" (symbol-name offset)))))
(setq offset
(symbol-value (intern (concat "ess-offset-" (symbol-name offset)))))
(if (listp offset)
(car offset)
offset))
@@ -1788,7 +1850,7 @@ Returns nil if line starts inside a string, t if in a comment."
(when (ess-at-containing-sexp
(looking-at "{"))
(ess-escape-prefixed-block))))
(cl-some 'looking-at
(cl-some #'looking-at
(ess-overridden-blocks)))
(+ (current-column) offset))))))
@@ -1920,7 +1982,7 @@ Returns nil if line starts inside a string, t if in a comment."
(override (and ess-align-arguments-in-calls
(save-excursion
(ess-climb-object)
(cl-some 'looking-at
(cl-some #'looking-at
ess-align-arguments-in-calls))))
(type-sym (cond (block 'block)
((looking-at "[[:blank:]]*[([][[:blank:]]*\\($\\|#\\)")
@@ -2149,7 +2211,7 @@ Returns nil if line starts inside a string, t if in a comment."
(defun ess-calculate-indent--nested-calls ()
(when ess-align-nested-calls
(let ((calls (mapconcat 'identity ess-align-nested-calls "\\|"))
(let ((calls (mapconcat #'identity ess-align-nested-calls "\\|"))
match)
(save-excursion
(and containing-sexp
@@ -2455,9 +2517,9 @@ state.")
(setq-local comint-prompt-regexp inferior-S-prompt)
(setq-local syntax-propertize-function ess-r--syntax-propertize-function)
(setq comint-input-sender 'inferior-ess-r-input-sender)
(remove-hook 'completion-at-point-functions 'ess-filename-completion 'local) ;; should be first
(add-hook 'completion-at-point-functions 'ess-r-object-completion nil 'local)
(add-hook 'completion-at-point-functions 'ess-filename-completion nil 'local)
(remove-hook 'completion-at-point-functions #'ess-filename-completion 'local) ;; should be first
(add-hook 'completion-at-point-functions #'ess-r-object-completion nil 'local)
(add-hook 'completion-at-point-functions #'ess-filename-completion nil 'local)
(add-hook 'xref-backend-functions #'ess-r-xref-backend nil 'local)
(add-hook 'project-find-functions #'ess-r-project nil 'local)
;; eldoc
@@ -2467,7 +2529,7 @@ state.")
;; company
(ess--setup-company ess-r-company-backends t)
(setq comint-get-old-input #'inferior-ess-get-old-input)
(add-hook 'comint-input-filter-functions 'ess-search-path-tracker nil 'local))
(add-hook 'comint-input-filter-functions #'ess-search-path-tracker nil 'local))
@@ -2517,9 +2579,10 @@ state.")
"Add links to the help buffer."
(let ((links (when (ess-process-live-p)
(ess-get-words-from-vector
(format ".ess.helpLinks('%s' %s)\n"
ess-r-help--local-object
(ess-r-arg "package" ess-r-help--local-package t)))))
(ess-r--format-call
".ess.helpLinks('%s' %s)\n"
ess-r-help--local-object
(ess-r-arg "package" ess-r-help--local-package t)))))
(inhibit-read-only t))
(save-excursion
;; Search for fancy quotes only. If users have
@@ -2549,7 +2612,7 @@ from all installed packages, which can be very slow."
(goto-char (point-min))
(when (re-search-forward "(list" nil t)
(goto-char (match-beginning 0))
(ignore-errors (eval (read (current-buffer)))))))
(ignore-errors (eval (read (current-buffer)) t)))))
(proc-name ess-current-process-name)
(alist ess-local-customize-alist)
(remote (file-remote-p default-directory))
@@ -2559,7 +2622,7 @@ from all installed packages, which can be very slow."
(with-current-buffer buff
(setq buffer-read-only nil)
(delete-region (point-min) (point-max))
(ess-setq-vars-local (eval alist))
(ess-setq-vars-local (eval alist t))
(setq ess-local-process-name proc-name)
(ess--help-major-mode)
(setq ess-help-sec-regex "^\\w+:$"
@@ -2682,13 +2745,13 @@ from all installed packages, which can be very slow."
des-col-beginning des-col-end entries)
(with-current-buffer (ess-command cmd (get-buffer-create " *ess-rutils-pkgs*"))
(goto-char (point-min))
(delete-region (point) (1+ (point-at-eol)))
(delete-region (point) (1+ (line-end-position)))
;; Now we have a buffer with package name, description, and
;; version. description and version are surrounded by quotes,
;; description is separated by whitespace.
(re-search-forward "\\>[[:space:]]+")
(setq des-col-beginning (current-column))
(goto-char (point-at-eol))
(goto-char (line-end-position))
;; Unless someone has a quote character in their package version,
;; two quotes back will be the end of the package description.
(dotimes (_ 2) (search-backward "\""))
@@ -2861,7 +2924,8 @@ given field. Options should be separated by value of
(interactive "sSearch string: ")
(let ((site "https://search.r-project.org/cgi-bin/namazu.cgi?query=")
(okstring (replace-regexp-in-string " +" "+" string)))
(if current-prefix-arg
(browse-url
(if current-prefix-arg
(let ((mpp (concat
"&max="
(completing-read
@@ -2885,16 +2949,17 @@ given field. Options should be separated by value of
(restrict (concat
"&idxname="
(mapconcat
'identity
#'identity
(completing-read-multiple
"Limit search to: "
'(("Rhelp02a" 1) ("functions" 2)
("docs" 3) ("Rhelp01" 4))
nil t "Rhelp02a,functions,docs" nil
"Rhelp02a,functions,docs") "&idxname="))))
(browse-url (concat site okstring mpp format sortby restrict)))
(browse-url (concat site okstring "&max=20&result=normal&sort=score"
"&idxname=Rhelp02a&idxname=functions&idxname=docs")))))
"Rhelp02a,functions,docs")
"&idxname="))))
(concat site okstring mpp format sortby restrict))
(concat site okstring "&max=20&result=normal&sort=score"
"&idxname=Rhelp02a&idxname=functions&idxname=docs")))))
(defun ess-rutils-help-search (string)
"Search for STRING using help.search()."