* 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).
* 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.
* 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.
* 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.
* 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.
* 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.
* 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.
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
* lisp/ob-R.el (ess-local-process-name): This variable wasn't known to
be defined.
* lisp/ob-lisp.el (org-babel-lisp-dir-fmt): This defcustom now has a
group specified.
* lisp/ob-tangle.el (org-bracket-link-regexp): This variable wasn't
known to be defined.
(org-babel-tangle-combine-named-blocks): Roll my own version of a
forbidden common lisp function.
* lisp/ob.el (org-babel-sha1-hash): Using a non-deprecated version of
called-interactively.
Slight modification of patch by Christophe Rhodes
* lisp/ob-R.el (org-babel-R-write-object-command): Ensure that all
data is written to the results file before Emacs notices that the file
exists.
* lisp/ob-R.el (org-babel-edit-prep:R): Associate the appropriate R
process with the edit buffer when :session is specified.
* lisp/org-src.el (org-edit-src-code): Allow language-specific
edit-buffer preparation by calling the org-babel-edit-prep:lang
function when it is defined.
* lisp/ob-R.el (org-babel-R-write-object-command): Force evaluation of
user code prior to the R exception-handling, so that errors in user
code are unhandled.
":results graphics" is now required in addition to ":file filename" in
order for graphical output to be sent automatically to file. If :file
is supplied, but not ":results graphics", then the default behavior
obtains: i.e., either "value" or "output" results are written to file,
depending on which of those options is in effect.
* lisp/ob-R.el (org-babel-R-graphical-output-file): New function
returns the name of the output file iff R has been instructed to send
graphical output to file by means of the ":results graphics"
directive.
(org-babel-expand-body:R): Use `org-babel-R-graphical-output-file'
when constructing the R code to evaluate, which may be augmented with
code implementing the writing of graohical output to file.
(org-babel-execute:R): Use `org-babel-R-graphical-output-file' to
determine whether R is taking responsibility for writing output to
file; if so, this is signalled to ob.el by returning a nil result.
* lisp/ob-C.el (org-babel-C-execute): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-R.el (org-babel-execute:R): removing call to
org-babel-process-params which should no longer be called from
within a language file
(org-babel-R-variable-assignments): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-asymptote.el (org-babel-execute:asymptote): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-clojure.el (org-babel-execute:clojure): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-dot.el (org-babel-execute:dot): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-emacs-lisp.el (org-babel-expand-body:emacs-lisp): removing
call to org-babel-process-params which should no longer be called
from within a language file
(org-babel-execute:emacs-lisp): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-haskell.el (org-babel-execute:haskell): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-js.el (org-babel-execute:js): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-lisp.el (org-babel-execute:lisp): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-ocaml.el (org-babel-execute:ocaml): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-octave.el (org-babel-execute:octave): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-perl.el (org-babel-execute:perl): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-python.el (org-babel-execute:python): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-ruby.el (org-babel-execute:ruby): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-scheme.el (org-babel-execute:scheme): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-screen.el (org-babel-execute:screen): removing call to
org-babel-process-params which should no longer be called from
within a language file
(org-babel-prep-session:screen): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-sh.el (org-babel-execute:sh): removing call to
org-babel-process-params which should no longer be called from
within a language file
* lisp/ob-sql.el (org-babel-execute:sql): removing call to
org-babel-process-params which should no longer be called from
within a language file
* ob-haskell.el (org-babel-execute:haskell): Remove reference
to processed params
* ob-clojure.el (org-babel-execute:clojure): Remove reference
to processed params
* ob-R.el (org-babel-execute:R): Remove reference to processed
params
* ob-R.el (org-babel-expand-body:R): Use new function
`org-babel-variable-assignments:R'; don't trim body.
(org-babel-execute:R): Respond to changes in
`org-babel-expand-body:R'
(org-babel-prep-session:R): Called function is now named
`org-babel-variable-assignments:R'
(org-babel-variable-assignments:R): Receives processed-params
as new optional argument
* ob-R.el (org-babel-expand-body:R): Refactor: break variable
assignment part out into a separate function
(org-babel-R-variable-assignments): New function constructing
list of variable assignment statements
(org-babel-prep-session:R): Use new function
`org-babel-R-variable-assignments' instead of previous
(incorrect) variable assignment code.
* lisp/org-compat.el (org-number-sequence): New function.
* lisp/ob-R.el (org-babel-expand-body:R): Use `org-number-sequence'.
* lisp/ob.el (org-babel-where-is-src-block-result): Use `org-number-sequence'.
(org-babel-current-buffer-properties): Fix variable definition.
* lisp/ob-ref.el (org-babel-ref-index-list): Use `org-number-sequence'.
* lisp/ob-latex.el (org-babel-latex-tex-to-pdf): Use the 2-argument version
of `shell-command'.
* lisp/org-latex.el (org-export-as-pdf): Use the 2-argument version
of `shell-command'.
* ob.el (org-babel-process-file-name): New function
(org-babel-maybe-remote-file): Delete function
* ob-sql.el (org-babel-execute:sql):
Use org-babel-process-file-name
* ob-scheme.el (org-babel-execute:scheme):
Use org-babel-process-file-name
* ob-sass.el (org-babel-execute:sass):
Use org-babel-process-file-name
* ob-ruby.el (org-babel-ruby-evaluate):
Use org-babel-process-file-name
* ob-python.el (org-babel-python-evaluate-external-process):
Use org-babel-process-file-name
(org-babel-python-evaluate-session):
Use org-babel-process-file-name
* ob-plantuml.el (org-babel-execute:plantuml):
Use org-babel-process-file-name
* ob-perl.el (org-babel-perl-evaluate):
Use org-babel-process-file-name
* ob-octave.el (org-babel-octave-evaluate-external-process):
Use org-babel-process-file-name
(org-babel-octave-evaluate-session):
Use org-babel-process-file-name,
don't use org-babel-maybe-remote-file
* ob-lisp.el (org-babel-execute:lisp):
Use org-babel-process-file-name
* ob-ledger.el (org-babel-execute:ledger):
Use org-babel-process-file-name
* ob-js.el (org-babel-execute:js):
Use org-babel-process-file-name
* ob-haskell.el (org-babel-haskell-export-to-lhs):
Use org-babel-process-file-name
* ob-gnuplot.el (org-babel-execute:gnuplot):
Use org-babel-process-file-name
* ob-eval.el (org-babel-eval-read-file): Don't use
org-babel-maybe-remote-file
* ob-dot.el (org-babel-execute:dot):
Use org-babel-process-file-name
* ob-ditaa.el (org-babel-execute:ditaa):
Use org-babel-process-file-name
* ob-clojure.el (org-babel-clojure-evaluate-external-process):
Use org-babel-process-file-name
* ob-asymptote.el (org-babel-execute:asymptote):
Use org-babel-process-file-name
* ob-R.el (org-babel-R-assign-elisp): Don't use
org-babel-maybe-remote-file, use org-babel-process-file-name
(org-babel-R-evaluate-external-process):
Use org-babel-process-file-name
(org-babel-R-evaluate-session):
Use org-babel-process-file-name
* ob-C.el (org-babel-C-execute):
Use org-babel-process-file-name
In addition to passing the file path through `expand-file-name',
tramp-style remote file names are converted to conventional (local)
file paths. The reason is that, if a tramp file name was in use in
emacs, then the shell command will be executing on the remote machine
in question. Further, by default the file name is passed through
`shell-quote-argument'.
* ob.el (org-babel-temp-file): Don't use babel temporary
directory in remote case; use make-temp-file with remote file
name so that temp file is guaranteed not to exist previously
on remote machine.
(org-babel-tramp-localname): New function to return local name
portion of possibly remote file specification
* ob-R.el (org-babel-R-evaluate-external-process): Respond to
changes in `org-babel-temp-file'; pass local file name to
remote R process.
(org-babel-R-evaluate-session) Respond to
changes in `org-babel-temp-file'; pass local file name to
remote R process.
* ob-R.el (org-babel-R-write-object-command): New unified R
command for writing results to file
(org-babel-R-wrapper-method): Remove variable
(org-babel-R-wrapper-lastvar): Remove variable
(org-babel-R-evaluate-external-process): Use new R command
(org-babel-R-evaluate-session): Use new R command
* ob-comint.el (org-babel-comint-eval-invisibly-and-wait-for-file): New
function to evaluate code invisibly and block until output file exists.
* ob-R.el (org-babel-R-evaluate-session): Use
`ess-eval-buffer' to evaluate R code in session for :results
value. Write result to file invisibly using new function
`org-babel-comint-eval-invisibly-and-wait-for-file'.
These changes move to using standard ESS code evaluation in R sessions
in the :results value case, which avoids unnecessary output to the
comint buffer. In addition, the R command responsible for writing the
result to file is hidden from the user.
* lisp/ob.el (org-babel-temporary-directory): variable to hold the
value of the Babel temporary directory
(org-babel-temp-file): replacement for make-temp-file with cleanup
on exit of Emacs
(org-babel-remove-temporary-directory): cleanup function run on exit
of Emacs
(kill-emacs-hook): now includes babel cleanup function
* lisp/ob-C.el (org-babel-C-execute): using org-babel-temp-file
instead of make-temp-file
* lisp/ob-R.el (org-babel-R-assign-elisp): using `org-babel-temp-file'
instead of `make-temp-file'
(org-babel-R-evaluate-external-process): using `org-babel-temp-file'
instead of `make-temp-file'
(org-babel-R-evaluate-session): using `org-babel-temp-file' instead of
`make-temp-file'
* lisp/ob-asymptote.el (org-babel-execute:asymptote): using
`org-babel-temp-file' instead of `make-temp-file'
* lisp/ob-clojure.el (org-babel-clojure-evaluate-external-process):
using `org-babel-temp-file' instead of `make-temp-file'
* lisp/ob-ditaa.el (org-babel-execute:ditaa): using
`org-babel-temp-file' instead of `make-temp-file'
* lisp/ob-dot.el (org-babel-execute:dot): using `org-babel-temp-file'
instead of `make-temp-file'
* lisp/ob-gnuplot.el (org-babel-gnuplot-process-vars): using
`org-babel-temp-file' instead of `make-temp-file'
(org-babel-execute:gnuplot): using `org-babel-temp-file' instead of
`make-temp-file'
* lisp/ob-haskell.el (org-babel-load-session:haskell): using
`org-babel-temp-file' instead of `make-temp-file'
(org-babel-haskell-export-to-lhs): using `org-babel-temp-file' instead
of `make-temp-file'
* lisp/ob-latex.el (org-babel-execute:latex): using
`org-babel-temp-file' instead of `make-temp-file'
* lisp/ob-ledger.el (org-babel-execute:ledger): using
`org-babel-temp-file' instead of `make-temp-file'
* lisp/ob-lisp.el (org-babel-execute:lisp): using
`org-babel-temp-file' instead of `make-temp-file'
* lisp/ob-octave.el (org-babel-octave-evaluate-external-process):
using `org-babel-temp-file' instead of `make-temp-file'
(org-babel-octave-evaluate-session): using `org-babel-temp-file'
instead of `make-temp-file'
(org-babel-octave-import-elisp-from-file): using `org-babel-temp-file'
instead of `make-temp-file'
* lisp/ob-perl.el (org-babel-perl-evaluate): using
`org-babel-temp-file' instead of `make-temp-file'
* lisp/ob-python.el (org-babel-python-evaluate): using
`org-babel-temp-file' instead of `make-temp-file'
using `org-babel-temp-file' instead of `make-temp-file'
* lisp/ob-ruby.el (org-babel-ruby-evaluate): using
`org-babel-temp-file' instead of `make-temp-file'
using `org-babel-temp-file' instead of `make-temp-file'
* lisp/ob-sass.el (org-babel-execute:sass): using
`org-babel-temp-file' instead of `make-temp-file'
* lisp/ob-sh.el (org-babel-sh-evaluate): using `org-babel-temp-file'
instead of `make-temp-file'
* lisp/ob-sql.el (org-babel-execute:sql): using `org-babel-temp-file'
instead of `make-temp-file'
* lisp/ob-sqlite.el (org-babel-execute:sqlite): using
`org-babel-temp-file' instead of `make-temp-file'
(org-babel-sqlite-expand-vars): using `org-babel-temp-file' instead of
`make-temp-file'
* ob-R.el (org-babel-R-evaluate): Break the two branches into
two separate functions
(org-babel-R-evaluate-external-process): New function to
handle external process evaluation
(org-babel-R-evaluate-session): New function to handle session
evaluation
2010-08-03 Dan Davison <davison@stats.ox.ac.uk>
* ob-R.el (org-babel-R-evaluate): Specify that tabular data is
tab-delimited
Prior to this we had
#+begin_src R
c("some words", "with spaces")
#+end_src
#+results:
| some | words |
| with | spaces |
For some reason ob-R refuses to compile when it requires ob-comint.
When (require 'ob-comint) is not included in ob-R.el everything
compiles without error, but warnings are thrown because the
arguments to a macro defined in ob-comint are mis-interpreted as
functions.
When (require 'ob-comint) is added to ob-R.el then it throws errors
complaining that the last argument to a function is nil and should
be a string. I don't understand this error at all and can't fix it.
Bastien Guerry
Achim Gratz
Aaron Ecay
Eric Schulte
Eric Schulte
Thomas Dye
Thomas Dye
Vitalie Spinu
Thomas Dye
emacs
Dan Davison
Carsten Dominik
Dan Davison
Glenn Morris
Erik Iverson