[ESS] remote R execution via tramp hangs
Vitalie Spinu
spinuvit at gmail.com
Mon Sep 29 12:05:12 CEST 2014
Ok. so it's not even getting to R. It's your most likely your tramp. See
the *tramp/ssh* buffer. You might see some clues there.
Also try running something else on remote, M-x shell, M-x run-python
etc.
Vitalie
>>> Jannis on Mon, 29 Sep 2014 11:24:40 +0200 wrote:
> I get this in *messages*:
> Tramp: Waiting for prompts from remote shell
> Tramp: Sending command `exec ssh -q -e none PC028'
> Tramp: Found remote shell prompt on `PC028'
> Tramp: Opening connection for PC028 using ssh...done
> Then everything freezes.
> Any further ideas?
> Thanks
> Jannis
> On 26.09.2014 19:26, Vitalie Spinu wrote:
>> Then it's probably not ess related. Look into your *tramp/ssh XXX*
>> buffer. Tramp is probably waiting for shell prompt.
>>
>> Vitalie
>>
>> You should see in *messages* something along the following lines:
>>
>> Tramp: Inserting `/ssh:vspinu2:/home/vspinu/.Rhistory'...
>> Tramp: Encoding remote file `/ssh:vspinu2:/home/vspinu/.Rhistory' with `base64 <%s'...done
>> Tramp: Decoding local file `/tmp/tramp.5255SVj' with `base64-decode-region'...done
>> Tramp: Inserting `/ssh:vspinu2:/home/vspinu/.Rhistory'...done
>> Tramp: Opening connection for vspinu2 using ssh...
>> Tramp: Sending command `exec ssh -q -o ControlPersist=no -e none vspinu2'
>> Tramp: Waiting for prompts from remote shell...done
>> Tramp: Found remote shell prompt on `vspinu2'
>> Tramp: Opening connection for vspinu2 using ssh...done
>> ess-tracebug mode enabled
>> Tramp: Encoding local file `/tmp/tramp.5255ffp' using `base64-encode-region'...done
>> Tramp: Decoding remote file `/ssh:vspinu2:/home/vspinu/.Rhistory' using `base64 -d -i >%s'...done
>>
>>
>> >>> Jannis on Fri, 26 Sep 2014 13:42:43 +0200 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
>> >> > ;; cusTramp: Waiting for prompts from remote shell
>> Tramp: Sending command `exec ssh -q -e none PC028'
>> Tramp: Found remote shell prompt on `PC028'
>> Tramp: Opening connection for PC028 using ssh...donetom-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>>
>>
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