Commit Graph

158 Commits

Author SHA1 Message Date
Jeremie Juste 58db28db04
ob-R: Tidy up bits of the async implementation
* ob-R.el (ob-session-async-org-babel-R-evaluate-session): Use
defvaralias for `ess-eval-visibly-p' instead of modifying user-defined
variable.  Remove temporary declaration that silences the byte-compiler.

* ob-R.el (org-babel-R-evaluate,
ob-session-async-org-babel-R-evaluate-session, org-babel-R-evaluate):
Remove mentions of unused argument `result-params'.
2021-11-18 18:42:38 +08:00
Bastien 8b78d482a6 Fix email addresses in some *.el headers 2021-10-03 08:54:33 +02:00
Bastien 1344911585 lisp/ob-R.el: Fix compiler warnings 2021-09-29 14:16:47 +02:00
Bastien 806ac1b7f6 *el: Fix indentation 2021-09-29 09:22:47 +02:00
Jeremie Juste 72a48c306f ob-R.el: Patch async evaluation when :results output
* lisp/ob-R.el (ob-session-async-org-babel-R-evaluate-session):
Make sure that `ess-inject-source' is set to the default
'function-and-buffer before running `ess-eval-buffer'.  Return
`ess-inject-source' to its user-specified state afterwards.
2021-09-28 18:22:18 +02:00
Jeremie Juste 01557eef57 ob-R.el: Patch async evaluation when :results output
* lisp/ob-R.el (ob-session-async-org-babel-R-evaluate-session): Make
sure that `ess-eval-visibly' is nil before evaluating the temporary
buffer, but return ess-eval-visibly to it's original state afterwards.
2021-09-28 18:22:15 +02:00
Jeremie Juste 51a60cd53f lisp/ob-R: Async evaluation in R
* lisp/ob-R.el (ob-session-async-R-indicator): Add constant
representing a prefix R to identity session.
(ob-session-async-org-babel-R-evaluate-session): New function to
evaluate R src block asynchrously.
(ob-session-async-R-value-callback): New function that calls back
the result of the asynchronous evaluation.
(org-babel-R-evaluate): Add `async' parameter and call
`ob-session-async-org-babel-R-evaluate-session' if `async'
parameter is present.
(org-babel-execute:R): Call `org-babel-comint-use-async' to check
if async is among `params' and add async parameter to
`org-babel-R-evaluate'.

* testing/lisp/test-ob-R.el: Add 7 more tests for async
evaluations, also taken from the `ob-session-async' package.

This is almost a carbon copy of Jack Kamm's `ob-session-async'.
The original source code can be found
https://github.com/jackkamm/ob-session-async.

Please refer to the following thread to trace back the discussion
on async evaluation in R:

https://list.orgmode.org/87eed9g9p6.fsf@gmail.com/
2021-09-28 18:22:12 +02:00
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