Commit Graph

96 Commits

Author SHA1 Message Date
Rainer M. Krug eaa3a761da Graphic: Catch errors and return error message
* lisp/ob-R.el (org-babel-expand-body:R): Added the opening of the
  tryCatch() wrapper

* lisp/ob-R.el (org-babel-R-construct-graphics-device-call): Added
  closing of the wrapper containing the error function.

Added tryCatch() wrapper around the execution of the source block so
that if an error occurs
- the R graphic device is closed even when an error occurs
- a graph containing the error message is created
- the error message is printed in the R session in the form
    ERROR : the error message

TINYCHANGE
2014-01-26 11:05:46 -07:00
Bastien Guerry f8e1745440 Merge branch 'maint'
Conflicts:
	contrib/lisp/org-favtable.el
2014-01-07 14:19:03 +01:00
Bastien Guerry 7d9a883b50 Update copyright years again.
Hint: copyright years are all updated in Emacs.
2014-01-07 14:18:17 +01:00
Bastien Guerry c41f5075ac Merge branch 'maint'
Conflicts:
	contrib/lisp/org-favtable.el
2014-01-05 06:36:11 +01:00
Bastien Guerry 0beda99171 Revert "Update copyright years."
This reverts commit 21105594fc.
2014-01-05 06:28:07 +01:00
Bastien Guerry 096ff7e078 Merge branch 'maint'
Conflicts:
	contrib/lisp/org-favtable.el
2014-01-04 18:58:12 +01:00
Bastien Guerry 21105594fc Update copyright years. 2014-01-04 18:56:11 +01:00
Achim Gratz 81815b7fb7 ob-R: declare org-every
* lisp/ob-R.el: Declare `org-every´ before first use.
2013-11-14 21:21:50 +01:00
Bastien Guerry 71884cc039 Merge branch 'maint'
Conflicts:
	lisp/ob-C.el
	lisp/ob-clojure.el
	lisp/ob-core.el
	lisp/ob-lisp.el
	lisp/org-clock.el
2013-11-12 21:00:49 +01:00
Bastien Guerry f95641c443 Backport changes from Emacs revs 115081 and 115082
2013-11-12  Stefan Monnier  <monnier@iro.umontreal.ca>

	Address some byte-compiler warnings.
	* ob-abc.el (org-babel-expand-body:abc): Use dolist.
	(org-babel-execute:abc): Fix regexp quoting.
	* ob-calc.el (org--var-syms): Rename from `var-syms'.
	* ob-lilypond.el (ly-compile-lilyfile): Remove redundant let-binding.
	* ob-table.el (sbe): Move debug declaration.
	* org-clock.el (org--msg-extra): Rename from `msg-extra'.
	* org.el (org-version): Avoid var name starting with _.
	(org-inhibit-startup, org-called-with-limited-levels)
	(org-link-search-inhibit-query, org-time-was-given)
	(org-end-time-was-given, org-def, org-defdecode, org-with-time):
	* org-colview.el (org-agenda-overriding-columns-format):
	* org-agenda.el (org-agenda-multi, org-depend-tag-blocked)
	(org-agenda-show-log-scoped):
	* ob-python.el (py-which-bufname, python-shell-buffer-name):
	* ob-haskell.el (org-export-copy-to-kill-ring):
	* ob-exp.el (org-link-search-inhibit-query):
	* ob-R.el (ess-eval-visibly-p):
	* ob-core.el (org-src-window-setup): Declare before use.
	(org-babel-expand-noweb-references): Remove unused `blocks-in-buffer'.
	* ox-odt.el (org-odt-hfy-face-to-css):
	* org-src.el (org-src-associate-babel-session, org-src-get-lang-mode):
	* org-bibtex.el (org-bibtex-get, org-bibtex-ask, org-bibtex)
	(org-bibtex-check):
	* ob-tangle.el (org-babel-tangle, org-babel-spec-to-string)
	(org-babel-tangle-single-block, org-babel-tangle-comment-links):
	* ob-table.el (sbe):
	* ob-sqlite.el (org-babel-sqlite-expand-vars):
	* ob-sql.el (org-babel-sql-expand-vars):
	* ob-shen.el (org-babel-execute:shen):
	* ob-sh.el (org-babel-execute:sh, org-babel-sh-evaluate):
	* ob-scala.el (org-babel-scala-evaluate):
	* ob-ruby.el (org-babel-ruby-table-or-string)
	(org-babel-ruby-evaluate):
	* ob-python.el (org-babel-python-table-or-string)
	(org-babel-python-evaluate-external-process)
	(org-babel-python-evaluate-session):
	* ob-picolisp.el (org-babel-execute:picolisp):
	* ob-perl.el (org-babel-perl-evaluate):
	* ob-maxima.el (org-babel-execute:maxima):
	* ob-lisp.el (org-babel-execute:lisp):
	* ob-java.el (org-babel-execute:java):
	* ob-io.el (org-babel-io-evaluate):
	* ob-haskell.el (org-babel-execute:haskell):
	* ob-fortran.el (org-babel-execute:fortran):
	* ob-exp.el (org-babel-exp-code):
	* ob-emacs-lisp.el (org-babel-execute:emacs-lisp):
	* ob-ditaa.el (org-babel-execute:ditaa):
	* ob-core.el (org-babel-execute-src-block, org-babel-sha1-hash)
	(org-babel-parse-header-arguments, org-babel-reassemble-table)
	(org-babel-goto-src-block-head, org-babel-mark-block)
	(org-babel-expand-noweb-references, org-babel-script-escape)
	(org-babel-process-file-name):
	* ob-clojure.el (org-babel-execute:clojure):
	* ob-calc.el (org-babel-execute:calc):
	* ob-awk.el (org-babel-execute:awk):
	* ob-abc.el (org-babel-execute:abc):
	* ob-R.el (org-babel-expand-body:R):
	* ob-C.el (org-babel-C-execute): Avoid deprecated ((lambda) ...).

2013-11-12  Glenn Morris  <rgm@gnu.org>

	* ox-html.el (org-html-scripts): Add 2013 to copyright years.
	(org-html-infojs-template): Copyright holder to FSF.
2013-11-12 20:57:31 +01:00
Aaron Ecay 49bee6052c mark o-b-default-header-args:R as a safe local under proper conditions
* lisp/ob-R.el (org-babel-default-header-args:R): mark as a safe local
variable
2013-10-30 11:23:38 -06:00
Eric Schulte bec8839cd6 prologue and epilogue for R blocks 2013-07-04 08:37:02 -06:00
Aaron Ecay 4be6832fdf ob-R.el: allow use of alternative graphics devices
* lisp/ob-R.el (org-babel-R-graphics-devices): New defvar.
(org-babel-R-construct-graphics-device-call): Use it instead of a
hard-coded list of graphics devices.

The `org-babel-R-graphics-devices' variable now holds the association
between graphics file types and R functions.  This allows users by
modifying this alist to choose to use e.g. the Cairo* functions from the
R package “Cairo” or one of several alternative devices for SVG
output (SVGAnnotation, RSVGTipsDevice).
2013-04-21 23:28:26 -04:00
Eric Schulte cd9d3d948e remove save-excursion inside save-window-excursion
it is not necessary

* lisp/ob-R.el (org-babel-R-initiate-session): Remove unnecessary
  save-excursion nested inside a save-window-excursion.
2013-04-03 09:17:12 -06:00
Aaron Ecay fe98647f14 Fix org-babel-R-initiate-session
* lisp/ob-R.el (org-babel-R-initiate-session): handle case where the
  session buffer exists, but does not have a live process

If the session buffer exists, but the user has exited the R process
manually, then the (R) command will create a new buffer, then try to
rename it over the old buffer, causing an error.  The right thing to do
is to start R within the existing buffer.
2013-04-03 09:17:06 -06:00
Aaron Ecay 42576eaac1 ox-latex: Support tikz images, :width, and :height
* ox-latex.el:
(org-latex-image-default-option): Change default value to ""
(org-latex-image-default-width)
(org-latex-image-default-height): Add variables
(org-latex-inline-image-rules): Make .tikz files as exportable with
latex
(org-latex--inline-image): Support tikz images.  Also support separate
:width and :height parameters for images.

* ob-R.el (org-babel-R-construct-graphics-device-call): Change file
extension of tikz graphics files to .tikz

Tikz graphics should be exported to LaTeX by \include, not as a link.
This commit changes the file extension used for tikz graphics from .tex
to .tikz, and inserts code for including such images.  The :options for
tikz graphics are passed as an optional argument to a tikzpicture
environment.

Also provide :width and :height ATTR_LATEX entries for images.  For tikz
graphics, these are implemented with \resizebox; for other image types
they are inserted in the optional arguments to \includegraphics.
2013-03-06 09:29:37 +01:00
Bastien Guerry 5fc740a230 Merge branch 'maint' 2013-01-08 15:04:40 +01:00
Bastien Guerry 72bc144c15 Update Copyright lines to match Emacs format. 2013-01-08 15:04:32 +01:00
Bastien Guerry 60b23bdeac Merge branch 'maint'
Conflicts:
	contrib/lisp/htmlize.el
	etc/schema/od-manifest-schema-v1.2-os.rnc
	etc/schema/od-schema-v1.2-os.rnc
	lisp/org-exp-blocks.el
2013-01-01 16:06:17 +01:00
Bastien Guerry 98cd4687a2 Update copyright years.
Happy new year!
2013-01-01 16:04:24 +01:00
Eric Schulte ff0081847c requiring ob now pulls in all of Babel 2012-12-12 10:48:56 -07:00
Eric Schulte 78cdf14939 org-babel-result-cond - unified handling of results
* lisp/ob.el (org-babel-result-cond): This function should now be used
  by all language backends to handle the processing of raw code block
  output into scalar results, table results, or ignored results
  depending on the value of result-params.

* lisp/ob-C.el (org-babel-C-execute): Use org-babel-result-cond.
* lisp/ob-R.el (org-babel-R-evaluate-external-process): Use
  org-babel-result-cond.
  (org-babel-R-evaluate-session): Use org-babel-result-cond.
* lisp/ob-awk.el (org-babel-execute:awk): Use org-babel-result-cond.
* lisp/ob-clojure.el (org-babel-execute:clojure): Use
  org-babel-result-cond.
* lisp/ob-emacs-lisp.el (org-babel-execute:emacs-lisp): Use
  org-babel-result-cond.
* lisp/ob-fortran.el (org-babel-execute:fortran): Use
  org-babel-result-cond.
* lisp/ob-io.el (org-babel-io-evaluate): Use org-babel-result-cond.
* lisp/ob-java.el (org-babel-execute:java): Use org-babel-result-cond.
* lisp/ob-lisp.el (org-babel-execute:lisp): Use org-babel-result-cond.
* lisp/ob-maxima.el (org-babel-execute:maxima): Use
  org-babel-result-cond.
* lisp/ob-picolisp.el (org-babel-execute:picolisp): Use
  org-babel-result-cond.
* lisp/ob-python.el (org-babel-python-evaluate-external-process): Use
  org-babel-result-cond.
  (org-babel-python-evaluate-session): Use org-babel-result-cond.
* lisp/ob-scala.el (org-babel-scala-evaluate): Use org-babel-result-cond.
* lisp/ob-sh.el (org-babel-sh-evaluate): Use org-babel-result-cond.
* lisp/ob-shen.el (org-babel-execute:shen): Use org-babel-result-cond.
* lisp/ob-sql.el (org-babel-execute:sql): Use org-babel-result-cond.
* lisp/ob-sqlite.el (org-babel-execute:sqlite): Use
  org-babel-result-cond.
2012-11-18 21:58:38 -07:00
Achim Gratz b20ef32b9a do not set variables belonging to ESS
* lisp/ob-R.el (org-babel-R-initiate-session): Protect against use of
  unbound variable `ess-ask-for-ess-directory´. The default for this
  variable is true, so act accordingly if it is found unbound.

* lisp/ob-R.el: Remove initialization with `nil´ from
 `ess-ask-for-ess-directory´ and `ess-local-process-name´.  Remove
 second declaration for `ess-local-process-name´.

* testing/lisp/test-ob-R.el (test-ob-R/simple-session): Bind
  `ess-ask-for-ess-directory´ to nil to facilitate batch testing.
2012-09-23 11:07:18 +02:00
Bastien Guerry b57a91f8dd ob-R.el (org-babel-edit-prep:R): Don't set the session
* ob-R.el (org-babel-edit-prep:R): Don't set the session.

See the discussion for this issue here:
http://article.gmane.org/gmane.emacs.orgmode/58600

Thanks to Mikhail Titov and to Andrew Young for exploring it.
2012-08-14 23:57:24 +02:00
Bastien Guerry 70dd1196d2 Massive code clean-up.
Delete trailing whitespaces.
Indent all sexps correctly.
Sentences end with double spaces.
2012-08-11 19:10:44 +02:00
Bastien Guerry 8eb584331a Add punctuation at the end of the first line of docstrings. Code cleanup. 2012-07-30 10:08:15 +02:00
Eric Schulte 35caf8b35a org-babel-R-command is now customizable
* lisp/ob-R.el (org-babel-R-command): From a defvar to a defcustom.
2012-06-30 07:13:27 -06:00
Eric Schulte d3ee6f8a98 Revert "* lisp/ob-R.el: Removed reduntant list of header arguments"
This reverts commit 829af89f48.
2012-06-19 15:31:54 -06:00
Thomas Dye 829af89f48 * lisp/ob-R.el: Removed reduntant list of header arguments 2012-06-19 07:25:05 -06:00
Thomas Dye bc9dc31465 * lisp/ob-R.el: Handle quoted string values to device header arguments 2012-06-19 07:24:40 -06:00
Bastien Guerry d34c0b3496 ob-R.el: Fix compiler warning about `org-remove-if-not'. 2012-05-16 16:40:18 +02:00
Eric Schulte eabc823bee Can't assume every entry in a table is a sequence
* lisp/ob-R.el (org-babel-R-assign-elisp): Can't assume every entry in
  a table is a sequence.
2012-05-11 16:50:34 -04:00
Eric Schulte fb7ebd2dae clean up the code implementing reads of irregular data into R
* lisp/ob-R.el (org-babel-R-assign-elisp): Clean up the code
  implementing reads of irregular data into R.
2012-04-25 15:40:13 -04:00
Thomas Dye 870b4e3c9d R-based solution to variable-row-length tables 2012-04-25 15:40:13 -04:00
Eric Schulte 5e4cffbb06 code-block languages may specify their own headers and values
* lisp/ob-R.el (org-babel-header-args:R): Adding values.
* lisp/ob-clojure.el (org-babel-header-args:clojure): Adding values.
* lisp/ob-lisp.el (org-babel-header-args:lisp): Adding values.
* lisp/ob-sql.el (org-babel-header-args:sql): Adding values.
* lisp/ob-sqlite.el (org-babel-header-args:sqlite): Adding values.
* lisp/ob.el (org-babel-combine-header-arg-lists): Combine lists of
  arguments and values.
  (org-babel-insert-header-arg): Use new combined header argument
  lists.
  (org-babel-header-arg-expand): Add support for completing-read
  insertion of header arguments after ":"
  (org-babel-enter-header-arg-w-completion): Completing read insertion
  of header arguments
  (org-tab-first-hook): Adding header argument completion.
  (org-babel-params-from-properties): Combining header argument lists.
* testing/lisp/test-ob.el (ob-test/org-babel-combine-header-arg-lists):
  Test the new header argument combination functionality.
2012-04-13 08:43:16 -04:00
Eric Schulte c90ea7a979 Merge branch 'origin-maint' 2012-01-30 18:36:31 -07:00
Eric Schulte 900b988742 fix bug introduced by 794319dfd9 2012-01-30 18:35:49 -07:00
Vitalie Spinu ae87b6e5f2 inhibit R evaluation visibility regardless of local user customization
* lisp/ob-R.el (org-babel-R-evaluate-session): Inhibit R evaluation
  visibility regardless of local user customization.
2012-01-30 09:32:56 -07:00
Vitalie Spinu 794319dfd9 inhibit R evaluation visibility regardless of local user customization
* lisp/ob-R.el (org-babel-R-evaluate-session): Inhibit R evaluation
  visibility regardless of local user customization.
2012-01-30 09:31:40 -07:00
Bastien Guerry e44d2975ff Fix copyright (to 2012) year and Org version (to 7.8.03). 2012-01-03 18:47:01 +01:00
Thomas Dye 811f9160de * lisp/ob-R.el: Added tikzDevice support. 2011-11-28 00:07:46 -07:00
Eric Schulte ad21eeff85 fix bug in R session evaluation
* lisp/ob-R.el (org-babel-R-evaluate): Fix bug in R session
  evaluation.
2011-09-21 09:10:21 -06:00
Eric Schulte 65d05b00b0 ob-R: don't process output when "scalar" or "verbatim"
* lisp/ob-R.el (org-babel-execute:R): Collect and pass along the
  result-params.
  (org-babel-R-evaluate): Accept result-params and if "scalar" or
  "verbatim" don't process output.
  (org-babel-R-evaluate-session): Accept result-params and if "scalar"
  or "verbatim" don't process output.
2011-09-15 15:43:35 -06:00
Eric Schulte a611170b57 ob-R: improve prompt detection regexp. Thanks to the users of ess-tracebug for this new regexp
* lisp/ob-R.el (org-babel-R-evaluate-session): Improve prompt
  detection regexp.
2011-09-01 12:03:43 -06:00
Achim Gratz ccc99317de backport copyright and license headers from Emacs trunk 2011-08-24 22:32:38 +02:00
Bastien Guerry 58f1dbccf8 Remove the "Version" header in Org libraries (leave it in org.el).
Also remove blank lines before the ";;; org*el ends here" declarations.

Having a "Version" header forced us to update every file when releasing a
new version of Org; it also forced us to update every file when merging Org
with Emacs trunk, thus cluttering the diffs between the previously merged
version and the new one with useless information.

Glenn Morris suggested this in emacs-devel:
http://lists.gnu.org/archive/html/emacs-devel/2011-08/msg00322.html
2011-08-17 14:42:34 +02:00
Bastien Guerry 7a18799e25 Remove arch-tag at the bottom of files. 2011-08-15 20:04:38 +02:00
Bastien Guerry 904ed18bc2 Fix copyright years for elisp files in core and contrib.
Also add "This file is not part of GNU Emacs." when this is the case.
2011-08-15 15:23:11 +02:00
emacs 7340cee33a Update website to show 7.7 as current release 2011-07-28 10:33:35 +00:00
Bastien Guerry 9c05a7c781 Bump to version 7.6 2011-07-06 21:06:03 +02:00