With emacs -Q, and this org file:

#+BEGIN_SRC emacs-lisp

(org-babel-do-load-languages

 'org-babel-load-languages

 '((emacs-lisp . t)

   (python . t)))

#+END_SRC

#+RESULTS:

#+BEGIN_SRC python :session with_matplotlib :results file :exports both

import matplotlib

matplotlib.use('Agg')

import matplotlib.pyplot as plt

fig=plt.figure(figsize=(3,2))

plt.plot([1,3,2])

plt.savefig('myfig.png')

'myfig.png'

#+END_SRC

#+RESULTS:

[[file:myfig.png]]

I get what you expect to happen. In my customized emacs, I get something else that is more like you see.

John

-----------------------------------
Professor John Kitchin 
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803

@johnkitchin
http://kitchingroup.cheme.cmu.edu

On Mon, May 25, 2015 at 2:22 PM, Dror Atariah <drorata@gmail.com> wrote:

On Mon, May 25, 2015 at 7:29 PM, Ken Mankoff <mankoff@gmail.com> wrote:

On 2015-05-25 at 13:25, Dror Atariah <drorata@gmail.com> wrote:
> I am sorry for reposting, but I'm still in the dark. Am I the only one who
> experience this kind of issue?

Don't know.

> Did someone managed to reproduce the problem?

I could not reproduce it.

> Does anyone see this message? :)

Yes.

Thanks for your reply!!!! :)

 

I'm on Mac too, which is where your problem is. Are you starting with "emacs -Q"? I haven't seen you post a full MWE with both =init.el= and =test.org=. You did provide a test Org file but it wasn't clear to me if that was being used with emacs -Q.

I tried to evaluate the problematic file using =emacs -Q= and the problem is the same.

Following is the section of my =init.el= that deals with org-mode (if you need more, let me know):

------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; Org Mode related

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(setq org-directory "~/Dropbox/org")

;; Set a location for the list of agena files

(setq org-agenda-files "~/.emacs.d/agenda_files")

;; Assigns org-mode to .org files

(add-to-list 'auto-mode-alist '("\\.org$" . org-mode))

(define-key global-map "\C-cl" 'org-store-link)

(define-key global-map "\C-ca" 'org-agenda)

(setq org-log-done t)

(when window-system (require 'org-mouse))

;; Auto enable flyspell-mode

(add-hook 'org-mode-hook 'turn-on-flyspell)

;; Auto fill minor mode in org files

(add-hook 'org-mode-hook 'turn-on-auto-fill)

;; Enable org-indent-mode for org buffers

(add-hook 'org-mode-hook

          (lambda ()(org-indent-mode t)) t)

;; Use text-mode abbrev table in org-mode

(add-hook 'org-mode-hook '(lambda () (setq local-abbrev-table text-mode-abbrev-table)))

;; Enables selection using SHIFT, while maintaining useful actions

;; related to SHITF in org

(setq org-support-shift-select 't)

;; Enable smart qoutes (http://stackoverflow.com/q/15097114/671013)

(setq org-export-with-smart-quotes t)

;; Customize the TODO-like keywords

(setq org-use-fast-todo-selection t)

(setq org-todo-keywords

      '((sequence "TODO(t)" "PROCESS(p@/!)" "|" "DONE(d!)" "CANCELED(c@/!)")))

(setq org-todo-keyword-faces

      (quote (("TODO" :foreground "red" :weight bold)

              ("PROCESS" :foreground "blue" :weight bold)

              ("DONE" :foreground "forest green" :weight bold)

              ("CANCELLED" :foreground "forest green" :weight bold))))

(setq org-log-into-drawer t)

;; Capture-org

(setq org-default-notes-file (concat org-directory "/notes.org"))

(define-key global-map "\C-cc" 'org-capture)

(setq org-capture-templates

      (quote (("t" "todo" entry (file (concat org-directory "/gtd.org"))

               "* TODO %?\n%U\n%a\n" :clock-in t :clock-resume t)

              ("n" "note" entry (file (concat org-directory "/gtd.org"))

               "* %? :NOTE:\n%U\n%a\n" :clock-in t :clock-resume t)

              ("j" "Journal" entry (file+datetree (concat org-directory "/diary.org"))

               "* %?\n%U\n" :clock-in t :clock-resume t)

              ("v" "Vocabulary" entry

               (file+headline (concat org-directory "/vocab.org")

                              "Vocabulary")

               "* %^{The word} :drill:\n:PROPERTIES:\n:Part-of-speech: %^{Part of speech|verb|noun|adj|adv}\n:END:\n %t\n %^{Extended word (may be empty)} \n** Answer \n%^{The definition}")

              )))

;; Make use of refTeX in org-mode

(defun org-mode-reftex-setup ()

  "Setups RefTeX to be used with a org file. Code is based on http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers/.

Once you run this, you will be asked to set a master file of the org."

  (interactive)

  (load-library "reftex")

  (and (buffer-file-name)

       (file-exists-p (buffer-file-name))

       (reftex-parse-all))

  (define-key org-mode-map (kbd "C-c )") 'reftex-citation)

  )

;; Open indirect buffer in new frame

(setq org-indirect-buffer-display 'new-frame)

;; Set common TAGS

;; Check: http://sachachua.com/blog/2008/01/tagging-in-org-plus-bonus-code-for-timeclocks-and-tags/

(setq org-tag-alist '(

                      ("PRIVATE" . ?p)

                      (:startgroup . nil)

                      ("WORK" .?w)

                      (:grouptags . nil)

                      ("WORK@mittagseminar" . ?m)

                      ("WORK@open_questions" . ?i)

                      ("WORK@diss" . ?d)

                      ("WORK@CV" . nil)

                      (:endgroup . nil)

                      (:startgroup . nil)

                      ("IT" . ?I)

                      (:grouptags . nil)

                      ("IT@emacs" . nil)

                      ("IT@git" . nil)

                      ("IT@TeX" . nil)

                      (:endgroup . nil)

                      (:startgroup . nil)

                      ("PROG" . ?p)

                      (:grouptags . nil)

                      ("PROG@mathematica" . nil)

                      ("PROG@cgal" . nil)

                      (:endgroup . nil)

                      (:endgroup . nil)

                      ("4freeTime" . ?4)

                      ))

;; Targets include this file and any file contributing to the agenda - up to 9 levels deep

(setq org-refile-targets (quote ((nil :maxlevel . 9)

                                 (org-agenda-files :maxlevel . 9))))

;; Add time stamp of refiling

(setq org-log-refile 'time)

;; Use full outline paths for refile targets - we file directly with IDO

(setq org-refile-use-outline-path t)

;; Targets complete directly with IDO

(setq org-outline-path-complete-in-steps nil)

;; Allow refile to create parent tasks with confirmation

(setq org-refile-allow-creating-parent-nodes (quote confirm))

;; Use IDO for both buffer and file completion and ido-everywhere to t

(setq org-completion-use-ido t)

(setq ido-everywhere t)

(setq ido-max-directory-size 100000)

(ido-mode (quote both))

;; set latexmk the default LaTeX compiler for org-mode and in general

(setq org-latex-to-pdf-process (list "latexmk -f -pdf %f"))

;; Enable clocking across sessions

(setq org-clock-persist 'history)

(org-clock-persistence-insinuate)

;; Set the number of clock items before wrapping them in a LOGBOOK drawer

(setq org-clock-into-drawer '2)

;; Set the number of clock items before wrapping them in a LOGBOOK drawer

(setq org-clock-into-drawer '2)

;; MobileOrg

(load "mobileorg-setup")

;; Org drill

(require 'org-drill)

(setq org-drill-save-buffers-after-drill-sessions-p nil)

(setq org-drill-scope 'file-no-restriction)

;; org2blog

(require 'metaweblog)

(require 'org2blog-autoloads)

;; Babel

(setq org-src-preserve-indentation t) ;; http://stackoverflow.com/a/20903001/671013

(setq org-src-fontify-natively t)

(setq org-confirm-babel-evaluate nil)

(org-babel-do-load-languages

 'org-babel-load-languages

 '((elasticsearch . t)

   (emacs-lisp . t)

   (python . t)

   (R . t)))

------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------

Best,

Dror