[BABEL,PATCH] ob-fortran

[BABEL,PATCH] ob-fortran

[Litvinov Sergey]

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Please consider an implementation of fortran support for
org-babel. The patch adds contrib/babel/langs/ob-fortran.el
(modification of lisp/ob-C.el) and
testing/examples/ob-fortran-test.org with tests.


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From 2ac9b86a6387cae1472e3ed288a3a133be72318c Mon Sep 17 00:00:00 2001
From: Litvinov Sergey <slitvinov@gmail.com>
Date: Mon, 18 Jul 2011 09:44:07 +0200
Subject: [PATCH] Add fortran to babel

---
 contrib/babel/langs/ob-fortran.el    |  191 ++++++++++++++++++++++++++++++++++
 testing/examples/ob-fortran-test.org |   76 ++++++++++++++
 2 files changed, 267 insertions(+), 0 deletions(-)
 create mode 100644 contrib/babel/langs/ob-fortran.el
 create mode 100644 testing/examples/ob-fortran-test.org

diff --git a/contrib/babel/langs/ob-fortran.el b/contrib/babel/langs/ob-fortran.el
new file mode 100644
index 0000000..6fdf416
--- /dev/null
+++ b/contrib/babel/langs/ob-fortran.el
@@ -0,0 +1,191 @@
+;;; ob-fortran.el --- org-babel functions for fortran
+;; Copyright (C) 2010  Free Software Foundation, Inc.
+
+;; Author: Sergey Litvinov (based on ob-C.el by Eric Schulte)
+;; Keywords: literate programming, reproducible research, fortran
+;; Homepage: http://orgmode.org
+;; Version: 7.6
+
+;; This file is part of GNU Emacs.
+
+;; GNU Emacs is free software: you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; GNU Emacs is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.
+
+;;; Commentary:
+
+;; Org-Babel support for evaluating fortran code.
+;;
+
+;;; Code:
+
+;; Org-Babel support for evaluating fortran code.
+;;
+
+(require 'ob)
+(require 'ob-eval)
+(require 'cc-mode)
+
+(declare-function org-entry-get "org"
+		  (pom property &optional inherit literal-nil))
+
+(defvar org-babel-tangle-lang-exts)
+(add-to-list 'org-babel-tangle-lang-exts '("fortran" . "F90"))
+
+(defvar org-babel-default-header-args:fortran '())
+
+(defvar org-babel-fortran-compiler "gfortran"
+  "fortran command used to compile a fortran source code file into an
+  executable.")
+
+(defun org-babel-execute:fortran (body params)
+  "Execute BODY according to PARAMS.  This function calls
+`org-babel-execute:fortran'."
+  (org-babel-execute:fortran body params))
+
+(defun org-babel-execute:fortran (body params)
+    "Execute a block of fortran code with org-babel.  This function is
+called by `org-babel-execute-src-block'."
+  (org-babel-fortran-execute body params))
+
+(defun org-babel-expand-body:fortran (body params)
+  "Expand a block of fortran code with org-babel according to it's
+header arguments (calls `org-babel-fortran-expand')."
+  (org-babel-fortran-expand body params))
+
+(defun org-babel-execute:fortran (body params)
+  "Execute a block of fortran code with org-babel.  This function is
+called by `org-babel-execute-src-block'."
+  (org-babel-fortran-execute body params))
+
+(defun org-babel-expand-body:fortran (body params)
+  "Expand a block of fortran code with org-babel according to it's
+header arguments (calls `org-babel-fortran-expand')."
+  (org-babel-fortran-expand body params))
+
+(defun org-babel-fortran-execute (body params)
+  "This function should only be called by `org-babel-execute:fortran'"
+  (let* ((tmp-src-file (org-babel-temp-file
+			"fortran-src-"
+			".F90"))
+         (tmp-bin-file (org-babel-temp-file "fortran-bin-"))
+         (cmdline (cdr (assoc :cmdline params)))
+         (flags (cdr (assoc :flags params)))
+         (full-body (org-babel-fortran-expand body params))
+         (compile
+	  (progn
+	    (with-temp-file tmp-src-file (insert full-body))
+	    (org-babel-eval
+	     (format "%s -o %s %s %s"
+		     org-babel-fortran-compiler
+		     (org-babel-process-file-name tmp-bin-file)
+		     (mapconcat 'identity
+				(if (listp flags) flags (list flags)) " ")
+		     (org-babel-process-file-name tmp-src-file)) ""))))
+    ((lambda (results)
+       (org-babel-reassemble-table
+	(if (member "vector" (cdr (assoc :result-params params)))
+	    (let ((tmp-file (org-babel-temp-file "f-")))
+	      (with-temp-file tmp-file (insert results))
+	      (org-babel-import-elisp-from-file tmp-file))
+	  (org-babel-read results))
+	(org-babel-pick-name
+	 (cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
+	(org-babel-pick-name
+	 (cdr (assoc :rowname-names params)) (cdr (assoc :rownames params)))))
+     (org-babel-trim
+       (org-babel-eval
+	(concat tmp-bin-file (if cmdline (concat " " cmdline) "")) "")))))
+
+(defun org-babel-fortran-expand (body params)
+  "Expand a block of fortran or fortran code with org-babel according to
+it's header arguments."
+  (let ((vars (mapcar #'cdr (org-babel-get-header params :var)))
+        (main-p (not (string= (cdr (assoc :main params)) "no")))
+        (includes (or (cdr (assoc :includes params))
+                      (org-babel-read (org-entry-get nil "includes" t))))
+        (defines (org-babel-read
+                  (or (cdr (assoc :defines params))
+                      (org-babel-read (org-entry-get nil "defines" t))))))
+     (mapconcat 'identity
+		(list
+		 ;; includes
+		 (mapconcat
+		  (lambda (inc) (format "#include %s" inc))
+		  (if (listp includes) includes (list includes)) "\n")
+		 ;; defines
+		 (mapconcat
+		  (lambda (inc) (format "#define %s" inc))
+		  (if (listp defines) defines (list defines)) "\n")
+		 ;; body
+		 (if main-p
+		     (org-babel-fortran-ensure-main-wrap 
+		      (concat 
+		       ;; variables
+		       (mapconcat 'org-babel-fortran-var-to-fortran vars "\n") 
+		       body))
+		   body) "\n") "\n")))
+
+(defun org-babel-fortran-ensure-main-wrap (body)
+  "Wrap body in a \"program ... end program\" block if none exists."
+  (if (string-match "^[ \t]*program[ \t]*.*" (capitalize body))
+       (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
+	 (if vars (error "cannot use :vars if 'program' statment is present"))
+	 body)
+    (format "program main\n%s\nend program main\n" body)))
+
+(defun org-babel-prep-session:fortran (session params)
+  "This function does nothing as fortran is a compiled language with no
+support for sessions"
+  (error "fortran is a compiled languages -- no support for sessions"))
+
+(defun org-babel-load-session:fortran (session body params)
+  "This function does nothing as fortran is a compiled language with no
+support for sessions"
+  (error "fortran is a compiled languages -- no support for sessions"))
+
+;; helper functions
+
+(defun org-babel-fortran-var-to-fortran (pair)
+  "fortranonvert an elisp val into a string of fortran code specifying a var
+of the same value."
+  ;; TODO list support
+  (let ((var (car pair))
+        (val (cdr pair)))
+    (when (symbolp val)
+      (setq val (symbol-name val))
+      (when (= (length val) 1)
+        (setq val (string-to-char val))))
+    (cond
+     ((integerp val)
+      (format "integer, parameter  ::  %S = %S\n" var val))
+     ((floatp val)
+      (format "real, parameter ::  %S = %S\n" var val))
+     ((or (characterp val))
+      (format "character, parameter :: %S = '%S'\n" var val))
+     ((stringp val)
+      (format "character, parameter ::  %S(%d) = '%s'\n"
+              var (length val) val))
+     ((listp val)
+      (format "real, parameter :: %S(%d) = %s\n" var (length val) (ob-fortran-transform-list val)))
+     (t
+      (error (format "the type of parameter %s is not supported by ob-fortran" var))))))
+
+(defun ob-fortran-transform-list (val)
+  "Return a fortran representation of enclose syntactic lists."
+  (if (listp val)
+      (concat "(/" (mapconcat #'ob-fortran-transform-list val ", ") "/)")
+    (format "%S" val)))
+
+(provide 'ob-fortran)
+
+;;; ob-fortran.el ends here
diff --git a/testing/examples/ob-fortran-test.org b/testing/examples/ob-fortran-test.org
new file mode 100644
index 0000000..ade9f43
--- /dev/null
+++ b/testing/examples/ob-fortran-test.org
@@ -0,0 +1,76 @@
+* Test org fortran file
+#+begin_src fortran
+print *, 'Hello world'
+#+end_src
+
+#+begin_src fortran
+integer, parameter :: i = 10
+print *, 'i = ', i
+#+end_src
+
+#+begin_src fortran :var N = 10
+print *, 'N = ', N
+#+end_src
+
+Define for preprocessed fortran
+#+begin_src fortran :defines N 42
+implicit none
+print *, 'N = ', N
+#+end_src
+
+#+begin_src fortran :var s="word"
+print *, 's = ', s
+print *, 'size(s) = ', size(s)
+#+end_src
+
+#+begin_src fortran :var s=42.0
+print *, 's = ', s
+print *, 'kind(s) = ', kind(s)
+#+end_src
+
+#+begin_src fortran
+program ex
+print *, "output of ex program"
+end program ex
+#+end_src
+
+Should fail (TODO: add input variables for the case with explicit
+program statement)
+#+begin_src fortran :var s="word"
+program ex
+print *, "output of ex program"
+end program ex
+#+end_src
+
+Real array as input
+#+begin_src fortran :var s='(1.0 2.0 3.0)
+print *, s
+#+end_src
+
+#+tblname: test_tbl
+| 1.0 |
+| 2.0 |
+
+Real array as input
+#+begin_src fortran :var s=test_tbl
+print *, s
+#+end_src
+
+Fails to compile (TODO: error check in ob-fortran.el)
+#+begin_src fortran :var s='(1 ())
+print *, s
+#+end_src
+
+Should fail to compile with gfortran
+#+begin_src fortran :flags --std=f95 --pedantic-error
+program ex
+integer*8 :: i
+end program ex
+#+end_src
+
+Pass parameters to the program
+#+begin_src fortran :cmdline "23"
+character(len=255) :: cmd
+call get_command(cmd)
+write (*,*) trim(cmd)
+#+end_src
-- 
1.7.4.1

Re: [BABEL,PATCH] ob-fortran

[Eric Schulte]

Hi Sergey,

Thank you for sharing ob-fortran.  After a quick scan it looks great,
and I would like to include it into the Org-mode core.

However a contribution of this size does require assignment of copyright
to the FSF.  See http://orgmode.org/worg/org-contribute.html#sec-2 for
information and instructions on the FSF assignment process.  Please let
me know if you will be able to assign copyright, I should be able to
include this into the core as soon as the process has begun.

Also, it is comforting to see a suite of test cases.  You may want to
consider wrapping these test cases up into ERT function so that they
could be folded into the remainder of the Org-mode test suite, I could
certainly help with this process.

Thanks! -- Eric

Litvinov Sergey <slitvinov@gmail.com> writes:

> Please consider an implementation of fortran support for
> org-babel. The patch adds contrib/babel/langs/ob-fortran.el
> (modification of lisp/ob-C.el) and
> testing/examples/ob-fortran-test.org with tests.
>
>
> From 2ac9b86a6387cae1472e3ed288a3a133be72318c Mon Sep 17 00:00:00 2001
> From: Litvinov Sergey <slitvinov@gmail.com>
> Date: Mon, 18 Jul 2011 09:44:07 +0200
> Subject: [PATCH] Add fortran to babel
>
> ---
>  contrib/babel/langs/ob-fortran.el    |  191 ++++++++++++++++++++++++++++++++++
>  testing/examples/ob-fortran-test.org |   76 ++++++++++++++
>  2 files changed, 267 insertions(+), 0 deletions(-)
>  create mode 100644 contrib/babel/langs/ob-fortran.el
>  create mode 100644 testing/examples/ob-fortran-test.org
>
> diff --git a/contrib/babel/langs/ob-fortran.el b/contrib/babel/langs/ob-fortran.el
> new file mode 100644
> index 0000000..6fdf416
> --- /dev/null
> +++ b/contrib/babel/langs/ob-fortran.el
> @@ -0,0 +1,191 @@
> +;;; ob-fortran.el --- org-babel functions for fortran
> +;; Copyright (C) 2010  Free Software Foundation, Inc.
> +
> +;; Author: Sergey Litvinov (based on ob-C.el by Eric Schulte)
> +;; Keywords: literate programming, reproducible research, fortran
> +;; Homepage: http://orgmode.org
> +;; Version: 7.6
> +
> +;; This file is part of GNU Emacs.
> +
> +;; GNU Emacs is free software: you can redistribute it and/or modify
> +;; it under the terms of the GNU General Public License as published by
> +;; the Free Software Foundation, either version 3 of the License, or
> +;; (at your option) any later version.
> +
> +;; GNU Emacs is distributed in the hope that it will be useful,
> +;; but WITHOUT ANY WARRANTY; without even the implied warranty of
> +;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
> +;; GNU General Public License for more details.
> +
> +;; You should have received a copy of the GNU General Public License
> +;; along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.
> +
> +;;; Commentary:
> +
> +;; Org-Babel support for evaluating fortran code.
> +;;
> +
> +;;; Code:
> +
> +;; Org-Babel support for evaluating fortran code.
> +;;
> +
> +(require 'ob)
> +(require 'ob-eval)
> +(require 'cc-mode)
> +
> +(declare-function org-entry-get "org"
> +		  (pom property &optional inherit literal-nil))
> +
> +(defvar org-babel-tangle-lang-exts)
> +(add-to-list 'org-babel-tangle-lang-exts '("fortran" . "F90"))
> +
> +(defvar org-babel-default-header-args:fortran '())
> +
> +(defvar org-babel-fortran-compiler "gfortran"
> +  "fortran command used to compile a fortran source code file into an
> +  executable.")
> +
> +(defun org-babel-execute:fortran (body params)
> +  "Execute BODY according to PARAMS.  This function calls
> +`org-babel-execute:fortran'."
> +  (org-babel-execute:fortran body params))
> +
> +(defun org-babel-execute:fortran (body params)
> +    "Execute a block of fortran code with org-babel.  This function is
> +called by `org-babel-execute-src-block'."
> +  (org-babel-fortran-execute body params))
> +
> +(defun org-babel-expand-body:fortran (body params)
> +  "Expand a block of fortran code with org-babel according to it's
> +header arguments (calls `org-babel-fortran-expand')."
> +  (org-babel-fortran-expand body params))
> +
> +(defun org-babel-execute:fortran (body params)
> +  "Execute a block of fortran code with org-babel.  This function is
> +called by `org-babel-execute-src-block'."
> +  (org-babel-fortran-execute body params))
> +
> +(defun org-babel-expand-body:fortran (body params)
> +  "Expand a block of fortran code with org-babel according to it's
> +header arguments (calls `org-babel-fortran-expand')."
> +  (org-babel-fortran-expand body params))
> +
> +(defun org-babel-fortran-execute (body params)
> +  "This function should only be called by `org-babel-execute:fortran'"
> +  (let* ((tmp-src-file (org-babel-temp-file
> +			"fortran-src-"
> +			".F90"))
> +         (tmp-bin-file (org-babel-temp-file "fortran-bin-"))
> +         (cmdline (cdr (assoc :cmdline params)))
> +         (flags (cdr (assoc :flags params)))
> +         (full-body (org-babel-fortran-expand body params))
> +         (compile
> +	  (progn
> +	    (with-temp-file tmp-src-file (insert full-body))
> +	    (org-babel-eval
> +	     (format "%s -o %s %s %s"
> +		     org-babel-fortran-compiler
> +		     (org-babel-process-file-name tmp-bin-file)
> +		     (mapconcat 'identity
> +				(if (listp flags) flags (list flags)) " ")
> +		     (org-babel-process-file-name tmp-src-file)) ""))))
> +    ((lambda (results)
> +       (org-babel-reassemble-table
> +	(if (member "vector" (cdr (assoc :result-params params)))
> +	    (let ((tmp-file (org-babel-temp-file "f-")))
> +	      (with-temp-file tmp-file (insert results))
> +	      (org-babel-import-elisp-from-file tmp-file))
> +	  (org-babel-read results))
> +	(org-babel-pick-name
> +	 (cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
> +	(org-babel-pick-name
> +	 (cdr (assoc :rowname-names params)) (cdr (assoc :rownames params)))))
> +     (org-babel-trim
> +       (org-babel-eval
> +	(concat tmp-bin-file (if cmdline (concat " " cmdline) "")) "")))))
> +
> +(defun org-babel-fortran-expand (body params)
> +  "Expand a block of fortran or fortran code with org-babel according to
> +it's header arguments."
> +  (let ((vars (mapcar #'cdr (org-babel-get-header params :var)))
> +        (main-p (not (string= (cdr (assoc :main params)) "no")))
> +        (includes (or (cdr (assoc :includes params))
> +                      (org-babel-read (org-entry-get nil "includes" t))))
> +        (defines (org-babel-read
> +                  (or (cdr (assoc :defines params))
> +                      (org-babel-read (org-entry-get nil "defines" t))))))
> +     (mapconcat 'identity
> +		(list
> +		 ;; includes
> +		 (mapconcat
> +		  (lambda (inc) (format "#include %s" inc))
> +		  (if (listp includes) includes (list includes)) "\n")
> +		 ;; defines
> +		 (mapconcat
> +		  (lambda (inc) (format "#define %s" inc))
> +		  (if (listp defines) defines (list defines)) "\n")
> +		 ;; body
> +		 (if main-p
> +		     (org-babel-fortran-ensure-main-wrap 
> +		      (concat 
> +		       ;; variables
> +		       (mapconcat 'org-babel-fortran-var-to-fortran vars "\n") 
> +		       body))
> +		   body) "\n") "\n")))
> +
> +(defun org-babel-fortran-ensure-main-wrap (body)
> +  "Wrap body in a \"program ... end program\" block if none exists."
> +  (if (string-match "^[ \t]*program[ \t]*.*" (capitalize body))
> +       (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
> +	 (if vars (error "cannot use :vars if 'program' statment is present"))
> +	 body)
> +    (format "program main\n%s\nend program main\n" body)))
> +
> +(defun org-babel-prep-session:fortran (session params)
> +  "This function does nothing as fortran is a compiled language with no
> +support for sessions"
> +  (error "fortran is a compiled languages -- no support for sessions"))
> +
> +(defun org-babel-load-session:fortran (session body params)
> +  "This function does nothing as fortran is a compiled language with no
> +support for sessions"
> +  (error "fortran is a compiled languages -- no support for sessions"))
> +
> +;; helper functions
> +
> +(defun org-babel-fortran-var-to-fortran (pair)
> +  "fortranonvert an elisp val into a string of fortran code specifying a var
> +of the same value."
> +  ;; TODO list support
> +  (let ((var (car pair))
> +        (val (cdr pair)))
> +    (when (symbolp val)
> +      (setq val (symbol-name val))
> +      (when (= (length val) 1)
> +        (setq val (string-to-char val))))
> +    (cond
> +     ((integerp val)
> +      (format "integer, parameter  ::  %S = %S\n" var val))
> +     ((floatp val)
> +      (format "real, parameter ::  %S = %S\n" var val))
> +     ((or (characterp val))
> +      (format "character, parameter :: %S = '%S'\n" var val))
> +     ((stringp val)
> +      (format "character, parameter ::  %S(%d) = '%s'\n"
> +              var (length val) val))
> +     ((listp val)
> +      (format "real, parameter :: %S(%d) = %s\n" var (length val) (ob-fortran-transform-list val)))
> +     (t
> +      (error (format "the type of parameter %s is not supported by ob-fortran" var))))))
> +
> +(defun ob-fortran-transform-list (val)
> +  "Return a fortran representation of enclose syntactic lists."
> +  (if (listp val)
> +      (concat "(/" (mapconcat #'ob-fortran-transform-list val ", ") "/)")
> +    (format "%S" val)))
> +
> +(provide 'ob-fortran)
> +
> +;;; ob-fortran.el ends here
> diff --git a/testing/examples/ob-fortran-test.org b/testing/examples/ob-fortran-test.org
> new file mode 100644
> index 0000000..ade9f43
> --- /dev/null
> +++ b/testing/examples/ob-fortran-test.org
> @@ -0,0 +1,76 @@
> +* Test org fortran file
> +#+begin_src fortran
> +print *, 'Hello world'
> +#+end_src
> +
> +#+begin_src fortran
> +integer, parameter :: i = 10
> +print *, 'i = ', i
> +#+end_src
> +
> +#+begin_src fortran :var N = 10
> +print *, 'N = ', N
> +#+end_src
> +
> +Define for preprocessed fortran
> +#+begin_src fortran :defines N 42
> +implicit none
> +print *, 'N = ', N
> +#+end_src
> +
> +#+begin_src fortran :var s="word"
> +print *, 's = ', s
> +print *, 'size(s) = ', size(s)
> +#+end_src
> +
> +#+begin_src fortran :var s=42.0
> +print *, 's = ', s
> +print *, 'kind(s) = ', kind(s)
> +#+end_src
> +
> +#+begin_src fortran
> +program ex
> +print *, "output of ex program"
> +end program ex
> +#+end_src
> +
> +Should fail (TODO: add input variables for the case with explicit
> +program statement)
> +#+begin_src fortran :var s="word"
> +program ex
> +print *, "output of ex program"
> +end program ex
> +#+end_src
> +
> +Real array as input
> +#+begin_src fortran :var s='(1.0 2.0 3.0)
> +print *, s
> +#+end_src
> +
> +#+tblname: test_tbl
> +| 1.0 |
> +| 2.0 |
> +
> +Real array as input
> +#+begin_src fortran :var s=test_tbl
> +print *, s
> +#+end_src
> +
> +Fails to compile (TODO: error check in ob-fortran.el)
> +#+begin_src fortran :var s='(1 ())
> +print *, s
> +#+end_src
> +
> +Should fail to compile with gfortran
> +#+begin_src fortran :flags --std=f95 --pedantic-error
> +program ex
> +integer*8 :: i
> +end program ex
> +#+end_src
> +
> +Pass parameters to the program
> +#+begin_src fortran :cmdline "23"
> +character(len=255) :: cmd
> +call get_command(cmd)
> +write (*,*) trim(cmd)
> +#+end_src

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: [BABEL,PATCH] ob-fortran

[Bastien]

Hi Sergey,

Litvinov Sergey <slitvinov@gmail.com> writes:

> Please consider an implementation of fortran support for
> org-babel. The patch adds contrib/babel/langs/ob-fortran.el
> (modification of lisp/ob-C.el) and
> testing/examples/ob-fortran-test.org with tests.

Great -- thanks a lot for this!

I let Eric (cc'ed) decide about integrating this in the contrib/ dir.

> diff --git a/contrib/babel/langs/ob-fortran.el b/contrib/babel/langs/ob-fortran.el
> new file mode 100644
> index 0000000..6fdf416
> --- /dev/null
> +++ b/contrib/babel/langs/ob-fortran.el
> @@ -0,0 +1,191 @@
> +;;; ob-fortran.el --- org-babel functions for fortran
> +;; Copyright (C) 2010  Free Software Foundation, Inc.
> +
> +;; Author: Sergey Litvinov (based on ob-C.el by Eric Schulte)
> +;; Keywords: literate programming, reproducible research, fortran
> +;; Homepage: http://orgmode.org
> +;; Version: 7.6
> +
> +;; This file is part of GNU Emacs.

(Nitpicking: files in Org's contrib/ directory are *not* part of GNU
Emacs, only those in lisp/.)

Best,

-- 
 Bastien