[ESS] remote R execution via tramp hangs
Chris Wallace
chris.wallace at cimr.cam.ac.uk
Fri Sep 26 13:54:48 CEST 2014
Jannis,
I'm afraid I can't help directly with your problem, but I recall similar
hangs. I wonder have you tried any alternate way to start the remote
R? I typically run R over multi-hop ssh, and the reliable method I've
now adopted is to set ess-directory to "/ssh:user at crazyhophost:~/" via
the customize-variable, and ess-ask-for-ess-directory to t via the same
method, so I can easily edit where I want ess to start. Then every time
I start R it is on the remote host, but I can edit the location if needed.
I start every R script with a setwd() so I can always know in which
directory it should be run.
Does this help at all?
Chris
On 26/09/14 12:42, Jannis wrote:
> Thanks for your reply. No Buffer is created. I only see some messages
> in the "message buffer" on the bottom left and it freezes after the
> "opening connection ..." message. C- g seems to stop process of
> starting R (i.e. the message disappears and emacs is responsive
> again). This is not getting R started, however. Is there any way (i.e.
> logs) to find out what causes this error?
>
> Jannis
>
> On 25.09.2014 19:31, Vitalie Spinu wrote:
>> Does C-g help? Do you see an *R* buffer created?
>>
>> Vitalie
>>
>> >>> Jannis on Thu, 25 Sep 2014 17:17:08 +0200 wrote:
>>
>> > Dear ESS users,
>>
>> > after updating to ubuntu 14.04 I have problems to remotely run R
>> on another
>> > machine via ess and tramp. I start tramp via Ctr - x Ctr -f and
>> then point emacs
>> > to a file on the remote machine (.i.e
>> > /machine_name/path_to_file/file_name.R). When I then hit Alt -x R
>> (as I used to
>> > do before the update), emacs hangs after the message
>>
>> > "Tramp: Opening connection for machine_name using ssh...done"
>>
>> > and is not responsive anymore. The exact same mechanism worked
>> before. I can
>> > also connect directly to the machine via ssa (i.e. via Alt -x
>> ssh) without any
>> > problems. Does anybody have an idea on how to narrow down on the
>> cause of the
>> > error?
>>
>> > Cheers
>> > Jannis
>>
>> > This is my .emacs file:
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;; general and startup
>> ;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> > ;; Tell emacs where is your personal elisp lib dir
>> > ;; this is the dir you place all your extra packages
>> > (add-to-list 'load-path "~/.emacs.d/")
>>
>> > ;;disable startup messages
>> > (setq inhibit-startup-message t)
>>
>> > ;; want two windows at startup
>> > (split-window-horizontally)
>>
>> > ;;fullscreen mode
>> > (defun toggle-fullscreen ()
>> > (interactive)
>> > (x-send-client-message nil 0 nil "_NET_WM_STATE" 32
>> > '(2 "_NET_WM_STATE_MAXIMIZED_VERT" 0))
>> > (x-send-client-message nil 0 nil "_NET_WM_STATE" 32
>> > '(2 "_NET_WM_STATE_MAXIMIZED_HORZ" 0)))
>> > (toggle-fullscreen)
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; misc tools
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> > ;; show tabs
>> > (require 'tabbar)
>> > (tabbar-mode)
>>
>> > ;; ido stuff
>> > (require 'ido)
>> > (ido-mode t)
>> > (setq ido-enable-flex-matching t)
>> > (setq ido-create-new-buffer 'always)
>>
>> > ;; open recent files
>> > (require 'recentf)
>> > (setq recentf-auto-cleanup 'never) ;; disable before we start
>> recentf!
>> > (recentf-mode 1)
>>
>> > ;;regex tool
>> > (load "regex-tool" t)
>>
>> > ;; bind recent files
>> > (global-set-key "\C-x\C-r" 'recentf-open-files)
>>
>> > ;; clipboard
>> > (setq x-select-enable-clipboard t)
>>
>> > ;; global
>> > (require 'smartparens-config)
>> > (require 'smartparens-latex)
>> > (smartparens-global-mode t)
>> > (add-hook 'post-command-hook 'sp--post-command-hook-handler)
>>
>> > ;; highlights matching pairs
>> > (show-smartparens-global-mode t)
>>
>> > ;;(add-hook 'inferior-ess-mode-hook (lambda () (smartparens-mode
>> 1)))
>>
>> > ;;(add-hook 'ess-R-post-run-hook 'smartparens-mode)
>> > ;; (add-hook 'ess-post-run-hook 'smartparens-mode)
>>
>> > ;;(require 'smart-operator)
>> > ;;(add-hook 'ess-mode-hook 'smart-operator-mode)
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> > (require 'fixme-mode)
>> > (require 'fic-mode)
>> > ;(require 'fic-mode)
>> > ;(add-hook 'ess-mode-hook 'turn-on-fic-mode)
>> > ;(add-hook 'latex-mode-hook 'turn-on-fic-mode)
>> > ;(add-hook 'LaTeX-mode-hook 'turn-on-fic-mode)
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;; autosave
>> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> > (require 'backup-each-save)
>> > (add-hook 'after-save-hook 'backup-each-save)
>>
>> > ;; Put autosave files (ie #foo#) and backup files (ie foo~) in
>> ~/.emacs.d/.
>> > (custom-set-variables
>> > ;; custom-set-variables was added by Custom.
>> > ;; If you edit it by hand, you could mess it up, so be careful.
>> > ;; Your init file should contain only one such instance.
>> > ;; If there is more than one, they won't work right.
>> > '(LaTeX-command "latex -synctex=1")
>> > '(auto-save-file-name-transforms (quote ((".*"
>> "~/.emacs.d/autosaves/\\1" t))))
>> > '(backup-directory-alist (quote ((".*" .
>> "~/.emacs.d/autosaves/"))))
>> > '(comint-move-point-for-output (quote others))
>> > '(csv-separators (quote ("" ",")))
>> > '(delete-old-versions t)
>> > '(kept-new-versions 100)
>> > '(kept-old-versions 100)
>> > '(make-directory "~/.emacs.d/autosaves/" t)
>> > '(version-control t))
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ess stuff
>> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> > ;; r profile
>> > (setenv "R_PROFILE_USER" "/home/my_name/.R/.RProfile")
>>
>> > ;; path of R program
>> > (setq inferior-R-program-name "/usr/lib/R/bin/R")
>>
>> > ;; define startup options
>> > (setq inferior-R-args "--no-save --no-restore --silent")
>>
>> > ;; ess stuff
>> > (require 'ess-site)
>>
>> > ;; turn off echoing of commands
>> > (setq ess-eval-visibly-p nil)
>>
>> > ;; save history to one specific file
>> > (setq ess-history-directory "~/.R/")
>>
>> > ;; Enable function argument hint for ESS
>> > (require 'ess-eldoc)
>>
>> > ;;start tracebug
>> > (require 'ess-tracebug)
>> > (add-hook 'ess-post-run-hook 'ess-tracebug t)
>>
>> > (ess-toggle-underscore nil)
>> > (server-start)
>>
>> > ;; Code folding in ess mode
>> > (add-hook 'ess-mode-hook
>> > (lambda()
>> > (local-set-key (kbd "C-c <right>") 'hs-show-block)
>> > (local-set-key (kbd "C-c <left>") 'hs-hide-block)
>> > (local-set-key (kbd "C-c <up>") 'hs-hide-all)
>> > (local-set-key (kbd "C-c <down>") 'hs-show-all)
>> > (hs-minor-mode t)))
>>
>> > (autoload 'ess-rdired "ess-rdired"
>> > "View *R* objects in a dired-like buffer." t)
>>
>> > ;;speed up emacs by removing echoing
>> > (setq ess-eval-visibly-p nil)
>>
>> > (define-key comint-mode-map [C-up]
>> 'comint-previous-matching-input-from-input)
>> > (define-key comint-mode-map [C-down]
>> 'comint-next-matching-input-from-input)
>>
>> > ;;'(ess-auto-newline t)
>>
>> > (add-hook 'inferior-ess-mode-hook
>> > (lambda()
>> > ; ess-S-mouse-me-menu-commands
>> > ; turn-on-font-lock
>> > (smartparens-mode 1)))
>>
>> > ; no wuatsion for startup directory
>> > (setq ess-ask-for-ess-directory nil)
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ssh stuff
>> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> > ;;set up ssh tunelling
>> > (load "~/.emacs.d/ssh.el")
>> > (setq ssh-program "ssh")
>>
>> > ;; turn off shell command echo
>> > (defun my-comint-init ()
>> > (setq comint-process-echoes t))
>> > (add-hook 'comint-mode-hook 'my-comint-init)
>>
>> > ;; allow interaction with screen
>> > ;; used to send screen keybindings to shell in emacs
>> > (define-key shell-mode-map (kbd "C-l") (lambda (seq) (interactive
>> "k")
>> > (process-send-string nil seq)))
>> > (define-key inferior-ess-mode-map (kbd "C-l") (lambda (seq)
>> (interactive "k")
>> > (process-send-string nil seq)))
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; Tex stuff
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> > (setq TeX-auto-save t)
>> > (setq TeX-parse-self t)
>> > (setq TeX-save-query nil)
>> > (setq TeX-PDF-mode t)
>> > (setq-default TeX-master nil)
>>
>> > ;; (setq TeX-view-program-list '(("Okular" "okular --unique %u")))
>>
>> > ;; (add-hook 'LaTeX-mode-hook '(lambda ()
>> > ;; (add-to-list 'TeX-expand-list
>> > ;; '("%u" Okular-make-url))))
>>
>> > ;; (defun Okular-make-url () (concat
>> > ;; "file://"
>> > ;; (expand-file-name (funcall file
>> (TeX-output-extension) t)
>> > ;; (file-name-directory (TeX-master-file)))
>> > ;; "#src:"
>> > ;; (TeX-current-line)
>> > ;; (expand-file-name (TeX-master-directory))
>> > ;; "./"
>> > ;; (TeX-current-file-name-master-relative)))
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>> > ;; Enable synctex correlation
>> > (setq TeX-source-correlate-method 'synctex)
>> > ;; Enable synctex generation. Even though the command shows
>> > ;; as "latex" pdflatex is actually called
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>> > ;; Use Okular as the pdf viewer. Build okular
>> > ;; command, so that Okular jumps to the current line
>> > ;; in the viewer.
>> > (setq TeX-view-program-selection
>> > '((output-pdf "PDF Viewer")))
>> > (setq TeX-view-program-list
>> > '(("PDF Viewer" "okular --unique %o#src:%n%b")))
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> > (load "preview-latex.el" nil t t)
>>
>> > (setq ispell-program-name "aspell") ; could be ispell as well,
>> depending on your
>> > preferences
>> > (setq ispell-dictionary "english") ; this can obviously be set to
>> any language
>> > your spell-checking program supports
>>
>> > (dolist (hook '(lisp-mode-hook
>> > emacs-lisp-mode-hook
>> > shell-mode-hook
>> > ess-mode-hook))
>> > (add-hook hook 'flyspell-prog-mode))
>>
>> > (require 'tex-site)
>> > (autoload 'reftex-mode "reftex" "RefTeX Minor Mode" t)
>> > (autoload 'turn-on-reftex "reftex" "RefTeX Minor Mode" nil)
>> > (autoload 'reftex-citation "reftex-cite" "Make citation" nil)
>> > (autoload 'reftex-index-phrase-mode "reftex-index" "Phrase Mode" t)
>> > ;(add-hook 'latex-mode-hook 'turn-on-reftex) ; with Emacs latex mode
>> > ;(add-hook 'plain-tex-mode-hook 'turn-on-reftex) ; with Emacs
>> latex mode
>>
>> > ;; (add-hook 'reftex-load-hook 'imenu-add-menubar-index)
>> > (add-hook 'LaTeX-mode-hook 'turn-on-reftex)
>>
>> > (add-hook 'LaTeX-mode-hook 'turn-on-auto-fill)
>> > ;(add-hook 'latex-mode-hook 'turn-on-auto-fill)
>> > (add-hook 'text-mode-hook 'turn-on-auto-fill)
>> > (setq-default fill-column 80)
>>
>> > (dolist (hook '(LaTeX-mode-hook))
>> > (add-hook hook (lambda () (flyspell-mode 1))))
>> > ;(dolist (hook '(latex-mode-hook))
>> > ; (add-hook hook (lambda () (flyspell-mode 1))))
>>
>> > (setq TeX-parse-self t) ; Enable parse on load.
>> > (setq TeX-auto-save t) ; Enable parse on save.
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; layout stuff
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> > ;; show changes since last save
>> > (global-highlight-changes-mode t)
>> > (global-set-key (kbd "<M-down>") 'highlight-changes-next-change)
>> > (global-set-key (kbd "<M-up>") 'highlight-changes-previous-change)
>> > (set-face-foreground 'highlight-changes nil)
>> > (set-face-background 'highlight-changes "#6495ed")
>> > (set-face-foreground 'highlight-changes-delete nil)
>> > (set-face-background 'highlight-changes-delete "#ff8c00")
>> > (global-set-key (kbd "<f6>") 'highlight-changes-visible-mode) ;;
>> changes
>> > (add-hook 'text-mode-hook
>> > (defun highlight-changes-remove-after-save ()
>> > "Remove previous changes after save."
>> > (make-local-variable 'after-save-hook)
>> > (add-hook 'after-save-hook
>> > (lambda ()
>> > (highlight-changes-remove-highlight (point-min)
>> (point-max))))))
>>
>> > (add-hook 'ess-mode-hook
>> > (defun highlight-changes-remove-after-save ()
>> > "Remove previous changes after save."
>> > (make-local-variable 'after-save-hook)
>> > (add-hook 'after-save-hook
>> > (lambda ()
>> > (highlight-changes-remove-highlight (point-min)
>> (point-max))))))
>>
>> > ;; In every buffer, the line which contains the cursor will be fully
>> > ;; highlighted
>> > (global-hl-line-mode 1)
>>
>> > ;; ;; autocomplete stuff
>> > ;; (add-to-list 'load-path "~/.emacs.d/autocomplete/")
>> > ;; (require 'auto-complete-config)
>> > ;; (add-to-list 'ac-dictionary-directories
>> "~/.emacs.d/autocomplete//ac-dict")
>> > ;; (ac-config-default)
>> > ;; (define-key ac-completing-map "\r" nil)
>> > ;; (setq
>> > ;; ;; ac-auto-show-menu 1
>> > ;; ;; ac-candidate-limit nil
>> > ;; ;; ac-delay 0.1
>> > ;; ;; ac-disable-fafluxes_clean[ siteT, 'NEE_f', idx_extreme]ces
>> (quote (font-lock-comment-face font-lock-doc-face))
>> > ;; ac-ignore-case 'smart
>> > ;; ;;ac-menu-height 20
>> > ;; ac-quick-help-delay 3
>> > ;; ;; ac-quick-help-prefer-pos-tip t
>> > ;; ;; ac-use-quick-help nil
>> > ;; ac-fuzzy-enable t
>> > ;; )
>> > (add-to-list 'load-path "~/.emacs.d/")
>> > (require 'auto-complete-config)
>> > (add-to-list 'ac-dictionary-directories "~/.emacs.d//ac-dict")
>> > (ac-config-default)
>>
>> > ;; align equal signs
>> > ;; Align with spaces only
>> > (defadvice align-regexp (around align-regexp-with-spaces)
>> > "Never use tabs for alignment."
>> > (let ((indent-tabs-mode nil))
>> > ad-do-it))
>> > (ad-activate 'align-regexp)
>>
>> > ;; activate parenthesis matching
>> > (show-paren-mode t)
>>
>> > ;; no line wrap
>> > (setq default-truncate-lines t)
>>
>> > (require 'fill-column-indicator)
>> > (add-hook 'ess-mode-hook 'fci-mode)
>>
>> > ;;highlight FIXMES
>>
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>> > (add-hook 'text-mode-hook
>> > (lambda()
>> > (font-lock-add-keywords nil
>> > '(("\\<\\(FIXME\\|TODO\\|XXX+\\|BUG\\):"
>> > 1 font-lock-warning-face prepend)))))
>>
>> > (add-hook 'ess-mode-hook
>> > (lambda()
>> > (font-lock-add-keywords nil
>> > '(("\\<\\(FIXME\\|TODO\\|XXX+\\|BUG\\):"
>> > 1 font-lock-warning-face prepend)))))
>>
>> > (add-hook 'LaTeX-mode-hook
>> > (lambda ()
>> > (font-lock-add-keywords nil
>> > '(("\\<\\(FIXME\\|TODO\\|BUG\\):" 1
>> font-lock-warning-face
>> > t)))))
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; behaviur
>> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> > ;; ===== Set standard indent to 2 rather that 4 ====
>> > (setq standard-indent 2)
>>
>> > ;; scroll only one line
>> > (setq scroll-step 1)
>>
>> > ;; ========== Support Wheel Mouse Scrolling ==========
>> > (mouse-wheel-mode t)
>>
>> > (global-set-key (kbd "C-l") 'highlight-regexp)
>>
>> > (defun sort-words (reverse beg end))
>>
>> > (global-set-key "\C-x\C-b" 'buffer-menu)
>>
>> > (setq tramp-default-method "ssh")
>> > ;(getenv "R_PROFILE_USER")
>>
>> > (custom-set-faces
>> > ;; custom-set-faces was added by Custom.
>> > ;; If you edit it by hand, you could mess it up, so be careful.
>> > ;; Your init file should contain only one such instance.
>> > ;; If there is more than one, they won't work right.
>> > )
>>
>> > ______________________________________________
>> > ESS-help at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/ess-help
>>
>
> ______________________________________________
> ESS-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/ess-help
--
JDRF/WT Diabetes & Inflammation Laboratory (DIL),
NIHR Cambridge Biomedical Research Centre,
Cambridge Institute for Medical Research,
University of Cambridge
Website: http://www-gene.cimr.cam.ac.uk/staff/wallace
DIL Website: http://www-gene.cimr.cam.ac.uk
More information about the ESS-help
mailing list