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151 Commits

Author SHA1 Message Date
Jeremie Juste
ac8c009e00 lisp/ob-R.el: Fix session output with substrings matching prompts 
* lisp/ob-R.el (org-babel-R-evaluate-session): New implementation for session output
results, that concat "^" to comint-prompt-regexp to avoid prompt
confusion with R.

Patch suggested by Jack Kamm:
https://orgmode.org/list/87h7slgbi5.fsf@gmail.com/
 2021-05-03 00:15:09 +02:00
Kyle Meyer
e0fb2339f4 Merge branch 'km/from-emacs-master' 
Porting from Emacs's master to Org's maint branch has been on hold
leading up to the Emacs 27.2 release to avoid any required fixup syncs
carrying those commits into the emacs-27 branch.  This merge brings
those changes into master.  The km/from-emacs-master branch should be
merged to maint when Emacs 27.2 has been released (assuming Org 9.5
hasn't been released, in which case maint will be tracking 9.5.x and
already include these changes).
 2021-02-14 18:06:23 -05:00
Stefan Kangas
d904f9e5da Backport commit f88a7897a from Emacs 
* lisp/ob-R.el (org-babel-R-write-object-command):
* lisp/org-attach.el (org-attach-after-change-hook):
* lisp/org.el (org-stamp-time-of-day-regexp): Shorten doc strings to
not exceed 80-column limits.  (Bug#44858)

Shorten over-wide docstrings in variables
f88a7897a80ee9129bdc444cafff32d026c4b6d8
Stefan Kangas
Sat Dec 19 18:21:06 2020 +0100
 2021-02-14 17:38:07 -05:00
Jeremie Juste
0c6ab87d11 ob-R.el: For :results value return empty string instead of nil 2021-02-06 21:36:55 +01:00
Kyle Meyer
291993888d Merge branch 'maint' 2021-01-01 15:02:10 -05:00
Kyle Meyer
99eafe3787 Update copyright year to 2021 2021-01-01 14:59:01 -05:00
Bastien
36f4df8925 lisp/ob-R.el: Add Jeremie Juste as a maintainer 2020-10-26 10:52:12 +01:00
Bastien
d9fe6aeafe lisp/ob-R.el: Don't throw an error when result cannot be parsed 
* lisp/ob-R.el (org-babel-R-process-value-result): When the result
cannot be parsed, return an error as the output.

Thanks to Greg Minshall for reporting this.
 2020-05-24 16:08:52 +02:00
Bastien
6a1f6ee1f8 Tiny formatting fixes 
* lisp/ox.el (org-export-table-dimensions):
* lisp/ox-texinfo.el (org-texinfo-template):
* lisp/ox-md.el (org-md-link):
* lisp/ox-icalendar.el (org-icalendar-use-UTC-date-time-p):
* lisp/ox-ascii.el (org-ascii-fixed-width):
* lisp/org.el (org-context):
* lisp/org-table.el (org-table-eval-formula)
(org-table-export):
* lisp/org-refile.el:
* lisp/org-plot.el (org-plot/gnuplot-to-grid-data):
* lisp/org-num.el (org-num):
* lisp/org-mouse.el (org-mouse-popup-global-menu)
(org-mouse-context-menu):
* lisp/org-macro.el (org-macro):
* lisp/org-lint.el (org-lint):
* lisp/org-keys.el (org-keys):
* lisp/org-duration.el:
* lisp/org-clock.el (org-clock-get-last-clock-out-time)
(org-clock-update-mode-line, org-find-open-clocks):
* lisp/org-agenda.el (org-diary)
(org-agenda-check-for-timestamp-as-reason-to-ignore-todo-item)
(org-agenda-highlight-todo, org-cmp-alpha)
(org-agenda-filter-by-category):
* lisp/ol.el (org-link-expand-abbrev, ol):
* lisp/ol-docview.el (ol-docview):
* lisp/ol-bibtex.el (org-execute-file-search-in-bibtex)
(org-bibtex, org-bibtex-read):
* lisp/ol-bbdb.el (org-bbdb-anniversary-description):
* lisp/ob-tangle.el (org-babel-tangle-jump-to-org):
* lisp/ob-table.el (org-babel-table-truncate-at-newline):
* lisp/ob-stan.el:
* lisp/ob-sqlite.el (org-babel-sqlite-table-or-scalar):
* lisp/ob-sql.el:
* lisp/ob-shen.el:
* lisp/ob-shell.el (org-babel-prep-session:shell)
(org-babel-prep-session:shell):
* lisp/ob-sed.el (org-babel-execute:sed)
(org-babel-execute:sed):
* lisp/ob-screen.el:
* lisp/ob-sass.el:
* lisp/ob-ruby.el (org-babel-prep-session:ruby)
(org-babel-prep-session:ruby):
* lisp/ob-ref.el (org-babel-ref-resolve, ob-ref):
* lisp/ob-python.el (org-babel-prep-session:python)
(org-babel-prep-session:python):
* lisp/ob-plantuml.el:
* lisp/ob-picolisp.el:
* lisp/ob-perl.el:
* lisp/ob-org.el:
* lisp/ob-octave.el (org-babel-prep-session:octave)
(org-babel-prep-session:octave)
(org-babel-octave-evaluate-session):
* lisp/ob-ocaml.el:
* lisp/ob-mscgen.el (org-babel-execute:mscgen)
(org-babel-execute:mscgen):
* lisp/ob-maxima.el:
(ob-maxima):
* lisp/ob-matlab.el:
* lisp/ob-makefile.el:
* lisp/ob-lua.el (org-babel-prep-session:lua)
(org-babel-prep-session:lua):
* lisp/ob-lisp.el:
* lisp/ob-ledger.el:
* lisp/ob-latex.el (org-babel-expand-body:latex)
(org-babel-expand-body:latex, ob-latex):
* lisp/ob-js.el:
* lisp/ob-java.el:
* lisp/ob-io.el (org-babel-prep-session:io)
(org-babel-prep-session:io):
* lisp/ob-hledger.el:
* lisp/ob-haskell.el:
* lisp/ob-groovy.el (org-babel-groovy-wrapper-method)
(org-babel-groovy-evaluate):
* lisp/ob-gnuplot.el:
* lisp/ob-fortran.el (org-babel-expand-body:fortran)
(org-babel-expand-body:fortran):
* lisp/ob-forth.el (org-babel-forth-session-execute):
* lisp/ob-exp.el (ob-exp):
* lisp/ob-eval.el:
* lisp/ob-emacs-lisp.el:
* lisp/ob-ebnf.el:
* lisp/ob-dot.el:
* lisp/ob-ditaa.el:
* lisp/ob-css.el:
* lisp/ob-core.el (org-babel-put-rownames):
* lisp/ob-coq.el:
* lisp/ob-comint.el:
* lisp/ob-calc.el:
* lisp/ob-awk.el:
* lisp/ob-asymptote.el:
* lisp/ob-abc.el:
* lisp/ob-R.el (org-babel-prep-session:R): Formatting fixes.
 2020-02-18 22:57:37 +01:00
Kyle Meyer
ff5fc050d3 Update copyright year to 2020 2020-01-01 13:38:46 -05:00
Bastien
f584d37a67 Update copyright year 2019-01-01 11:50:56 +01:00
Tim Landscheidt
b289a65be7 Use https for links to orgmode.org 
TINYCHANGE
 2018-01-19 18:14:58 +01:00
Kyle Meyer
3e1641ef0a Update copyright years 2018-01-07 00:27:54 -05:00
Paul Eggert
ff0dcf52a5 Backport commit bc511a64f from Emacs 
Prefer HTTPS to FTP and HTTP in documentation
bc511a64f6da9ab51acc7c8865e80c4a4cb655c2
Paul Eggert
Wed Sep 13 15:54:37 2017 -0700
 2017-09-17 00:28:38 -04:00
Kyle Meyer
0d3683f2cd Merge branch 'maint' 2017-01-05 20:23:58 -05:00
Kyle Meyer
713f785017 Update copyright years 2017-01-05 20:19:37 -05:00
Charles Berry
ed0c8cb995 org-babel-execute:R fix :colnames yes' clash with :results graphics' 
* lisp/ob-R.el (org-babel-execute:R): The `:colnames' and `:rownames'
  header arguments are ignored if `:results graphics' is specified.

Reported by: Kodi Arfer <kodi@arfer.net>
Archived-At: <http://permalink.gmane.org/gmane.emacs.orgmode/111072>
 2016-12-28 18:35:59 -08:00
Aaron Ecay
79650ffbbd Use assq instead of assoc for :keywords 
* lisp/ob-C.el (org-babel-C-execute):
* lisp/ob-J.el (org-babel-execute:J):
* lisp/ob-R.el (org-babel-edit-prep:R):
(org-babel-expand-body:R):
(org-babel-execute:R):
(org-babel-variable-assignments:R):
(org-babel-R-initiate-session):
* lisp/ob-abc.el (org-babel-execute:abc):
* lisp/ob-asymptote.el (org-babel-execute:asymptote):
* lisp/ob-awk.el (org-babel-execute:awk):
* lisp/ob-clojure.el (org-babel-expand-body:clojure):
(org-babel-execute:clojure):
* lisp/ob-core.el (org-babel-expand-body:generic):
(org-babel-load-in-session):
(org-babel-initiate-session):
(org-babel-open-src-block-result):
(org-babel-process-params):
(org-babel-insert-result):
(org-babel-expand-noweb-references):
* lisp/ob-ditaa.el (org-babel-execute:ditaa):
* lisp/ob-dot.el (org-babel-execute:dot):
* lisp/ob-ebnf.el (org-babel-execute:ebnf):
* lisp/ob-emacs-lisp.el (org-babel-expand-body:emacs-lisp):
(org-babel-execute:emacs-lisp):
* lisp/ob-exp.el (org-babel-exp-process-buffer):
(org-babel-exp-do-export):
(org-babel-exp-code):
* lisp/ob-forth.el (org-babel-execute:forth):
* lisp/ob-fortran.el (org-babel-execute:fortran):
* lisp/ob-gnuplot.el (org-babel-gnuplot-process-vars):
(org-babel-expand-body:gnuplot):
(org-babel-execute:gnuplot):
* lisp/ob-groovy.el (org-babel-execute:groovy):
* lisp/ob-haskell.el (org-babel-execute:haskell):
* lisp/ob-io.el (org-babel-execute:io):
* lisp/ob-java.el (org-babel-execute:java):
* lisp/ob-js.el (org-babel-execute:js):
* lisp/ob-latex.el (org-babel-execute:latex):
* lisp/ob-ledger.el (org-babel-execute:ledger):
* lisp/ob-lilypond.el (org-babel-lilypond-process-basic):
* lisp/ob-lisp.el (org-babel-expand-body:lisp):
(org-babel-execute:lisp):
* lisp/ob-lua.el (org-babel-execute:lua):
* lisp/ob-maxima.el (org-babel-execute:maxima):
* lisp/ob-mscgen.el (org-babel-execute:mscgen):
* lisp/ob-ocaml.el (org-babel-execute:ocaml):
* lisp/ob-octave.el (org-babel-execute:octave):
* lisp/ob-org.el (org-babel-execute:org):
* lisp/ob-perl.el (org-babel-execute:perl):
* lisp/ob-picolisp.el (org-babel-execute:picolisp):
* lisp/ob-plantuml.el (org-babel-execute:plantuml):
* lisp/ob-python.el (org-babel-execute:python):
* lisp/ob-ruby.el (org-babel-execute:ruby):
* lisp/ob-sass.el (org-babel-execute:sass):
* lisp/ob-scala.el (org-babel-execute:scala):
* lisp/ob-scheme.el (org-babel-execute:scheme):
* lisp/ob-screen.el (org-babel-execute:screen):
(org-babel-prep-session:screen):
* lisp/ob-shell.el (org-babel-execute:shell):
(org-babel-variable-assignments:shell):
(org-babel-sh-evaluate):
* lisp/ob-shen.el (org-babel-execute:shen):
* lisp/ob-sql.el (org-babel-execute:sql):
* lisp/ob-sqlite.el (org-babel-execute:sqlite):
* lisp/ob-tangle.el (org-babel-tangle):
(org-babel-tangle-single-block):
* lisp/org-src.el (org-src-associate-babel-session):
* lisp/org.el (org-next-link):
Use `assq' instead of `assoc' with :keyword keys.
 2016-09-23 11:20:09 +01:00
Aaron Ecay
ab21e2b72d Use file-name-extension where appropriate 
* lisp/ob-R.el (org-babel-R-construct-graphics-device-call):
* lisp/ob-asymptote.el (org-babel-execute:asymptote):
* lisp/ob-latex.el (org-babel-execute:latex):
* lisp/org-agenda.el (org-agenda-write):
* lisp/ox-odt.el (org-odt--copy-formula-file): Use `file-name-extension'
instead of string munging.
 2016-09-01 18:46:48 +01:00
Aaron Ecay
6b52bc6a21 Clean up string handling. 
* lisp/org-compat.el (string-prefix-p, string-suffix-p):
Add compatibility definitions for 24.3.

* lisp/ob-R.el (org-babel-edit-prep:R):
* lisp/ob-core.el (org-babel-demarcate-block):
* lisp/ob-js.el (org-babel-js-read):
* lisp/ob-latex.el (org-babel-execute:latex):
* lisp/ob-ref.el (org-babel-ref-parse):
* lisp/ob-shell.el (org-babel-variable-assignments:shell):
* lisp/org-protocol.el (org-protocol-create):
* lisp/org-table.el (org-table-field-info):
* lisp/org.el (org-get-buffer-for-internal-link):
* lisp/ox-publish.el (org-publish-compare-directory-files):
* lisp/ox-texinfo.el (org-texinfo-template):
Use `string-{suffix,prefix}-p' instead of `string-match(-p)'.

* lisp/ob-python.el (org-babel-python-read-string):
Ditto, also use `substring' rather than `match-string'.

* lisp/org-table.el (org-table-copy-down):
(org-table-insert-hline, org-table-current-field-formula):
(org-table-get-formula): Use `string-match-p' instead of
`string-match'.
 2016-08-24 16:05:54 +01:00
Nicolas Goaziou
31b30e5aee ob-R: Silence byte-compiler 
* lisp/ob-R.el (org-babel-R-evaluate-external-process):
(org-babel-R-evaluate-session): Silence byte-compiler.
 2016-07-25 16:24:14 +02:00
Nicolas Goaziou
d13b0745dc Mark a few functions as obsolete 
* lisp/ob-R.el (org-babel-variable-assignments:R):
* lisp/ob-ref.el (org-babel-ref-goto-headline-id):
* lisp/org-agenda.el (org-agenda-prepare-window):
(org-agenda-switch-to):
* lisp/org-capture.el (org-capture-goto-target):
* lisp/org-clock.el (org-clock-goto):
(org-clock-special-range):
* lisp/org-ctags.el (org-ctags-visit-buffer-or-file):
* lisp/org-eshell.el (org-eshell-open):
* lisp/org-feed.el (org-feed-show-raw-feed):
* lisp/org-id.el (org-id-goto):
* lisp/org-irc.el (org-irc-visit-erc):
* lisp/org-macs.el (org-string-nw-p):
* lisp/org-mobile.el (org-mobile-apply):
* lisp/org-src.el (org-src-switch-to-buffer):
* lisp/org.el (org-get-location):
(org-tree-to-indirect-buffer):
(org-mark-ring-goto):
(org-refile):
(org-add-log-note):
(org-revert-all-org-buffers):
(org-switchb):
(org-cycle-agenda-files):
(org-submit-bug-report):
(org-goto-marker-or-bmk):
* lisp/ox-html.el (org-html-htmlize-generate-css): Silence byte
  compiler.

The following functions are marked as obsolete:
- `org-string-match-p'
- `org-number-sequence'
- `org-floor*'
- `org-pop-to-buffer-same-window'
- `org-delete-directory'
- `org-buffer-narrowed-p'
 2016-06-23 10:00:00 +02:00
Kyle Meyer
4925d5be7b Merge branch 'maint' 2016-05-15 19:00:30 -04:00
Kyle Meyer
19cf68da90 Fix remaining declare-function issues 
* lisp/ob-shell.el (org-babel-comint-in-buffer):
(org-babel-comint-with-output):
* lisp/org-table.el (org-export-create-backend):
* lisp/org.el (org-babel-do-in-edit-buffer): Indicate that FN is not a
defun.
* lisp/ob-tangle.el (org-string-nw-p):
* lisp/org-table.el (org-export-create-backend):
(org-export-data-with-backend):
(org-export-filter-apply-functions):
(org-export-first-sibling-p):
(org-export-get-backend):
(org-export-get-environment):
(org-export-install-filters):
(org-export-table-has-special-column-p):
(org-export-table-row-is-special-p): Correct source file name.
* lisp/ob-R.el (ess-wait-for-process):
* lisp/org-clock.el (calendar-iso-to-absolute):
* lisp/org-list.el (org-previous-line-empty-p):
* lisp/org-pcomplete.el (org-entry-properties):
* lisp/org-table.el (org-export-data-with-backend):
(org-export-get-environment):
* lisp/org.el (org-element-interpret-data): Correct argument list.
 2016-05-15 18:59:20 -04:00
Nicolas Goaziou
7213aa0f76 ob-R: Silence byte-compiler 
* lisp/ob-R.el (org-babel-expand-body:R): Silence byte-compiler.
 2016-02-02 18:02:08 +01:00
Charles Berry
4d02140130 lisp/ob-R.el: Rename graphics-file arg of org-babel-expand-body:R. 
* lisp/ob-R.el: (org-babel-expand-body:R) The third arg is now
  `graphics-file' with no `&' prefix, so edebug can instrument it.
 2016-02-01 19:48:49 -08:00
Charles Berry
3142d139fa ob-R.el: Trim extraneous newline from results 
* lisp/ob-R.el: org-babel-R-evaluate-external-process and
  org-babel-R-evaluate-session trim the extraneous newlines from the
  end of R output.

* testing/lisp/test-ob-R.el: test-ob-R/results-file tests that
  `:results file' yields one line enclosed in square brackets for a
  result like "abc/def.ghi".

Fixes issue noted by Andreas Leha
Subject: [babel] return file from R
Archived-At: <http://permalink.gmane.org/gmane.emacs.orgmode/103658>
 2016-01-19 20:10:43 -08:00
Kyle Meyer
6345de2d05 Merge branch 'maint' 2016-01-09 17:43:27 -05:00
Kyle Meyer
6bc48c5f41 Update copyright years 2016-01-09 17:12:03 -05:00
Charles Berry
27aa7b3f1e ob-R.el: org-babel-R-evaluate-session finds prompts more reliably 
* lisp/ob-R.el (org-babel-R-evaluate-session) should find prompts more
  reliably.  First, the regular expression used requires spacing
  between and after instances of `[>+.]'.  Also, the search terminates
  at the first `\n', so complicated results with prompt like strings
  in them are not deleted.

Prompt finding is necessarily heuristic. It may be necessary to render
the regular expression with a defcustom as is done in ess-mode.
 2015-11-07 13:26:11 -08:00
Aaron Ecay
e4cd3dd22b Remove some home-grown copies of cl-lib functions. 
* lisp/org.el (org-count, org-remove-if, org-remove-if-not):
(org-reduce, org-every, org-some): Obsolete, use cl-lib versions
everywhere.
(org-sublist): Reimplement in terms of `cl-subseq'; make obsolete.
 2015-11-06 12:50:40 +00:00
Aaron Ecay
0d000f5680 babel: small change in API. 
* lisp/ob-core.el (org-babel--get-vars): New function.
(org-babel-get-header): Delete.
* lisp/ob-C.el (org-babel-C-expand-C):
(org-babel-C-expand-D):
* lisp/ob-R.el (org-babel-variable-assignments:R):
* lisp/ob-abc.el (org-babel-expand-body:abc):
* lisp/ob-asymptote.el (org-babel-variable-assignments:asymptote):
* lisp/ob-awk.el (org-babel-execute:awk):
* lisp/ob-calc.el (org-babel-execute:calc):
* lisp/ob-clojure.el (org-babel-expand-body:clojure):
* lisp/ob-dot.el (org-babel-expand-body:dot):
* lisp/ob-emacs-lisp.el (org-babel-expand-body:emacs-lisp):
* lisp/ob-fortran.el (org-babel-expand-body:fortran):
(org-babel-fortran-ensure-main-wrap):
* lisp/ob-gnuplot.el (org-babel-gnuplot-process-vars):
* lisp/ob-haskell.el (org-babel-variable-assignments:haskell):
* lisp/ob-js.el (org-babel-variable-assignments:js):
* lisp/ob-latex.el (org-babel-expand-body:latex):
* lisp/ob-lilypond.el (org-babel-expand-body:lilypond):
* lisp/ob-lisp.el (org-babel-expand-body:lisp):
* lisp/ob-maxima.el (org-babel-maxima-expand):
* lisp/ob-ocaml.el (org-babel-variable-assignments:ocaml):
* lisp/ob-octave.el (org-babel-variable-assignments:octave):
* lisp/ob-org.el (org-babel-expand-body:org):
* lisp/ob-perl.el (org-babel-variable-assignments:perl):
* lisp/ob-picolisp.el (org-babel-expand-body:picolisp):
* lisp/ob-processing.el (org-babel-variable-assignments:processing):
* lisp/ob-python.el (org-babel-variable-assignments:python):
* lisp/ob-ruby.el (org-babel-variable-assignments:ruby):
* lisp/ob-scheme.el (org-babel-expand-body:scheme):
* lisp/ob-shell.el (org-babel-variable-assignments:shell):
* lisp/ob-shen.el (org-babel-expand-body:shen):
* lisp/ob-sql.el (org-babel-expand-body:sql):
* lisp/ob-sqlite.el (org-babel-expand-body:sqlite): Adapt to change.
* etc/ORG-NEWS: Document change.
 2015-10-29 19:26:11 +00:00
Nicolas Goaziou
f0bf77e82a Activate lexical binding in some libraries 
* lisp/ob-C.el (org-babel-prep-session:C):
(org-babel-load-session:C):
* lisp/ob-J.el:
(org-babel-expand-body:J):
(org-babel-execute:J):
* lisp/ob-R.el:
(org-babel-expand-body:R):
* lisp/ob-abc.el:
(org-babel-execute:abc):
(org-babel-prep-session:abc):
* lisp/ob-asymptote.el:
(org-babel-execute:asymptote):
(org-babel-prep-session:asymptote):
* lisp/ob-awk.el:
(org-babel-expand-body:awk):
* lisp/ob-calc.el:
(org-babel-expand-body:calc):
* lisp/ob-clojure.el:
* lisp/ob-comint.el:
(org-babel-comint-in-buffer):
(org-babel-comint-with-output):
(org-babel-comint-eval-invisibly-and-wait-for-file):
* lisp/ob-coq.el:
* lisp/ob-css.el:
(org-babel-execute:css):
(org-babel-prep-session:css):
* lisp/ob-ditaa.el:
(org-babel-execute:ditaa):
(org-babel-prep-session:ditaa):
* lisp/ob-dot.el:
(org-babel-execute:dot):
(org-babel-prep-session:dot):
* lisp/ob-ebnf.el:
* lisp/ob-emacs-lisp.el:
* lisp/ob-eval.el:
* lisp/ob-forth.el:
* lisp/ob-fortran.el:
(org-babel-execute:fortran):
(org-babel-prep-session:fortran):
(org-babel-load-session:fortran):
* lisp/ob-gnuplot.el:
(org-babel-expand-body:gnuplot):
(org-babel-prep-session:gnuplot):
(org-babel-gnuplot-initiate-session):
* lisp/ob-groovy.el:
(org-babel-prep-session:groovy):
(org-babel-groovy-initiate-session):
* lisp/ob-haskell.el:
(org-babel-haskell-initiate-session):
* lisp/ob-io.el:
(org-babel-prep-session:io):
(org-babel-io-initiate-session):
* lisp/ob-java.el:
(org-babel-execute:java):
* lisp/ob-js.el:
* lisp/ob-keys.el:
* lisp/ob-latex.el:
(org-babel-prep-session:latex):
* lisp/ob-ledger.el:
(org-babel-execute:ledger):
(org-babel-prep-session:ledger):
* lisp/ob-lilypond.el:
(org-babel-lilypond-commands):
(org-babel-lilypond-process-basic):
(org-babel-prep-session:lilypond):
(org-babel-lilypond-parse-line-num):
* lisp/ob-lisp.el:
* lisp/ob-makefile.el:
(org-babel-execute:makefile):
(org-babel-prep-session:makefile):
* lisp/ob-matlab.el:
* lisp/ob-maxima.el:
(org-babel-prep-session:maxima):
* lisp/ob-mscgen.el:
(org-babel-prep-session:mscgen):
* lisp/ob-ocaml.el:
(org-babel-execute:ocaml):
(org-babel-prep-session:ocaml):
* lisp/ob-octave.el:
(org-babel-execute:octave):
(org-babel-octave-initiate-session):
* lisp/ob-org.el:
(org-babel-prep-session:org):
* lisp/ob-perl.el:
(org-babel-prep-session:perl):
(org-babel-perl--var-to-perl):
(org-babel-perl-initiate-session):
* lisp/ob-picolisp.el:
(org-babel-expand-body:picolisp):
(org-babel-execute:picolisp):
* lisp/ob-plantuml.el:
(org-babel-execute:plantuml):
(org-babel-prep-session:plantuml):
* lisp/ob-processing.el:
(org-babel-prep-session:processing):
* lisp/ob-python.el:
(org-babel-python-initiate-session):
* lisp/ob-ref.el:
(org-babel-ref-resolve):
* lisp/ob-ruby.el:
(org-babel-ruby-initiate-session):
* lisp/ob-sass.el:
(org-babel-execute:sass):
(org-babel-prep-session:sass):
* lisp/ob-scala.el:
(org-babel-execute:scala):
(org-babel-prep-session:scala):
(org-babel-scala-initiate-session):
* lisp/ob-scheme.el:
* lisp/ob-screen.el:
(org-babel-prep-session:screen):
(org-babel-screen-session-write-temp-file):
(org-babel-screen-test):
* lisp/ob.el:
* lisp/org-colview.el:
(org-columns-todo):
(org-columns-set-tags-or-toggle):
(org-columns-new):
(org-columns-uncompile-format):
(org-agenda-colview-summarize):
* lisp/org-footnote.el:
(electric-indent-mode):
* lisp/org-indent.el:
(org-indent-refresh-maybe):
* lisp/org-list.el:
* lisp/org-macro.el:
(org-macro--collect-macros):
* lisp/org-src.el:
* lisp/org-table.el:
(sort-fold-case):
(org-table-create):
(org-table-field-info):
(org-table-transpose-table-at-point):
(org-table-remove-rectangle-highlight):
(orgtbl-create-or-convert-from-region):
(org-define-lookup-function):
* lisp/ox-ascii.el:
(org-ascii-format-drawer-function):
(org-ascii--has-caption-p):
(org-ascii-bold):
(org-ascii-center-block):
(org-ascii-clock):
(org-ascii-code):
(org-ascii-dynamic-block):
(org-ascii-entity):
(org-ascii-example-block):
(org-ascii-export-snippet):
(org-ascii-export-block):
(org-ascii-fixed-width):
(org-ascii-footnote-reference):
(org-ascii-horizontal-rule):
(org-ascii-inline-src-block):
(org-ascii-format-inlinetask-default):
(org-ascii-italic):
(org-ascii-keyword):
(org-ascii-latex-environment):
(org-ascii-latex-fragment):
(org-ascii-line-break):
(org-ascii-node-property):
(org-ascii-planning):
(org-ascii-quote-block):
(org-ascii-radio-target):
(org-ascii-special-block):
(org-ascii-src-block):
(org-ascii-statistics-cookie):
(org-ascii-subscript):
(org-ascii-superscript):
(org-ascii-strike-through):
(org-ascii-timestamp):
(org-ascii-underline):
(org-ascii-verbatim):
(org-ascii-verse-block):
(org-ascii-filter-headline-blank-lines):
(org-ascii-filter-paragraph-spacing):
(org-ascii-filter-comment-spacing): Use lexical binding.
 2015-10-26 01:56:00 +01:00
Kyle Meyer
0839dc4322 Protect remaining apostrophes in docstrings 
Protect apostrophes not covered by the last backport.  Convert
expressions like '(...)  to \\='(...)  and symbols written as 'name to
`name'.  (In addition to ensuring the correct display, the latter also
improves consistency with many Org docstrings.)

If these aren't protected, Emacs 25 may display them as curved quotes in
the help buffer, depending on the value of text-quoting-style.
 2015-09-21 18:38:39 -04:00
Nicolas Goaziou
c8bfd52f5f ob-R: Allow more :results values 
* lisp/ob-R.el (org-babel-header-args:R): Allow "drawer" and "none",
  since they are supported in `org-babel-common-header-args-w-values'.

Reported-by: Andreas Leha <andreas.leha@med.uni-goettingen.de>
<http://permalink.gmane.org/gmane.emacs.orgmode/97683>
 2015-05-19 23:22:11 +02:00
Nicolas Goaziou
0d24086657 Update some copyright years 2015-02-16 01:40:07 +01:00
Aaron Ecay
3996de60da ob-R: Convert some defvars to defconsts. 
* lisp/ob-R.el (org-babel-R-eoe-indicator):
(org-babel-R-eoe-output): Convert from defvar to defconst.
(org-babel-R-write-object-command): Convert from defvar to defconst.
Add line breaks and indentation.
 2015-01-23 14:39:30 -05:00
Aaron Ecay
fcce67cdeb ob-R: fix interaction with ESS for new sessions 
* lisp/ob-R.el (org-babel-R-initiate-session): Properly wait on a new
ESS process.
 2014-10-10 12:35:57 -04:00
Rainer M. Krug
780db69cdf ob-R.el: Add package name to read.table call 
* lisp/ob-R.el: (ob-R-transfer-variable-table-with-header)
(ob-R-transfer-variable-table-without-header): Add package name to
call of R function `read.table'.

Thus, it now reads `utils::read.table'.  This clarifies the call as
well as avoids "could not find function" error in R with the devtools
package.  See
<https://github.com/hadley/devtools/issues/336#issuecomment-23517837>.
 2014-10-10 00:16:31 -04:00
Achim Gratz
37e1a11b9e ob-R: declare ess-current-process-name 
* lisp/ob-R.el: Forward declare `ess-current-process-name'.
 2014-09-19 12:03:43 +02:00
Achim Gratz
e5f61642a3 ob-R: make it work with older ESS versions 
* lisp/ob-R.el (org-babel-R-initiate-session): The PROC argument is
  mandatory for older ESS versions.
 2014-09-18 21:56:53 +02:00
chasberry
0fd29a5ee7 lisp/ob-R.el: use `ess-wait-for-process' to assure clean session startup 
* lisp/ob-R.el (org-babel-R-initiate-session): Make sure that (R) has
finished before `rename-buffer' is run.

TINYCHANGE
 2014-09-17 21:10:40 -04:00
Aaron Ecay
2cbaa47fcc ob-R: Fix redundant code. 
* lisp/ob-R.el (org-babel-R-check-evaluate-package): Fix redundant
code.
 2014-08-16 00:48:10 -04:00
Aaron Ecay
59cd25cd75 Revert "ob-R.el: Improve the capturing of output-type results in sessions." 
This reverts commit b51746332d.
 2014-08-07 14:00:01 -04:00
Aaron Ecay
b51746332d ob-R.el: Improve the capturing of output-type results in sessions. 
* lisp/ob-R.el (org-babel-R-evaluate-session): Improve the capturing
of R output.

This uses a built-in facility of R to write the output to a file,
rather than trying to capture it in an emacs buffer using ESS (a
process by which the output can get mixed with other irrelevant text,
such as R command prompts).
 2014-08-07 01:54:23 -04:00
Aaron Ecay
d035c14765 ob-R.el: fix a bug when a :var is propertized text 
* lisp/ob-R.el (org-babel-R-assign-elisp): Strip text properties from
strings.

Before this change, babel would try to format propertized strings
using elisp read syntax.  The upshot is that evaluating the following
code block would give an error (in R, not emacs), since the “bar” in
foo-ex gets text properties via font lock:

| #+name: foo-ex
| #+begin_example
| bar
| #+end_example
|
| #+name: foo
| #+begin_src R :var foo=foo-ex
|   foo
| #+end_src
 2014-08-07 01:54:23 -04:00
Bastien Guerry
8f3a1f3d22 Fix trailing whitespace in previous commit 2014-07-28 00:01:23 +02:00
Rainer M. Krug
4c415f38a5 Make transfer of values from R type aware 
* lisp/ob-R.el (org-babel-R-assign-elisp): Add different cases for
transfering integer, float, string and other variables to R so that
integer values are transferred as integers (L) and stored in R as
such.  This change is backward compatible as integer values are
numerical values in R.

Moved definition of R functions for transfer of tables into defconst
ob-R-transfer-variable-table-with-header and
ob-R-transfer-variable-table-without-header.
 2014-07-28 00:01:00 +02:00
Rainer M. Krug
fdfb59454a lisp/ob-R.el: Fix tangling with tables 
* lisp/ob-R.el (org-babel-R-assign-elisp): Fix variable transfer of
tables by using text connections in R instead of files.  Variable
transfer of tables does not depend on files anymore, i.e. works also
when tangling.
 2014-07-28 00:00:52 +02:00
Bastien Guerry
a5686d8778 ob-R.el: minor code cleanup 
* ob-R.el (org-babel-expand-body:R, org-babel-execute:R)
(org-babel-variable-assignments:R)
(org-babel-R-evaluate-session): Don't use "#'" forms.
 2014-05-21 04:22:30 +02:00