[ESS] remote R execution via tramp hangs
Jannis
bt_jannis at yahoo.de
Mon Sep 29 16:19:19 CEST 2014
M-x shell, M-x run-python works. the buffer called *tramp/ssh remotecomputer* does not show anything. I can not find any buffer called *tramp/ssh*
. Am I looking at the correct buffer?
Thanks
Jannis
On 29.09.2014 12:05, Vitalie Spinu wrote:
> 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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