This deals with external process :results value mode for R, ruby,
python, perl and clojure: if the shell process has a non-zero exit
code, a buffer containing stderr is displayed.
At this commit, org-babel-shell-command-on-region is a direct copy of
shell-command-on-region. In addition to switching to use the org-babel
version, we change the argument passed so that they agree with the
docstring of s-c-o-r.
Despite the change in arguments, the same behaviour results because
s-c-o-r does not behave as documented in emacs23. Future commits will
be able to fix these bugs in the org-babel version, as necessary.
When using ':results value' in certain situations, results are written
to file by the foreign language process and subsequently read from
file by emacs into an elisp table structure. If the foreign language
process is running remotely, then the results are written
remotely. These changes ensure that in that case, an appropriate
remote file name is constructed to read the remote data.
This introduces a new header argument :dir. For the duration of source
block execution, default-directory is set to the value of this header
argument. Consequences include:
- external interpreter processes run in that directory
- new session processes run in that directory (but existing ones are unaffected)
- relative paths for file output are relative to that directory
The name of a directory on a remote machine may be specified with
tramp syntax (/user@host:path), in which case the interpreter
executable will be sought in tramp-remote-path, and if found will
execute on the remote machine in the specified remote directory.
Use shell-command-on-region, bringing R into line with ruby, python,
clojure, shell. In addition to consistency (and perhaps efficiency),
this will also be preferable in the case of a remote R process because
it means that transfer of the input to the remote process is dealt
with automatically by tramp.
Before this change we have
#+begin_src ruby :results value :session
["1", "3"]
#+end_src
#+results:
: 1", "3
After, we have
#+begin_src ruby :results value :session
["1", "3"]
#+end_src
#+results:
| 1 | 3 |
Variable names in gnuplot source code preceded by the '$' character
will be expanded to their value before the code is executed. For
example the following will results in the evaluation of 'plot
sin(x)' by gnuplot.
"sin(x)"
plot $fun
With this change, if :file <filepath> is specified, ruby and python
blindly output a link to <filepath>. Responsibility for creating the
contents in <filepath> lies with the python/ruby code.
One half of this patch is a revert of c167a4ac32.
These changes are necessary so that :results output works correctly
with #+lob calls. For example the following example did not work:
--------------------------------------------------
3. :results output org -> doesn't work with #+lob:
--------------------------------------------------
\#+srcname: randthree(n,max)
\#+begin_src ruby
number = n
maximum = max
puts "* Random numbers\n" +
"Here are some random numbers: " +
(1..number).collect {|x| (rand * maximum).ceil }.join(", ") +
"."
\#+end_src
\#+lob: randthree(n=3,max=10) :results output org
When evaluating R code in a persistent session, lines of output
typically start with a single prompt character. However, under certain
circumstances, lines start with a concatenation of (primary and
secondary) prompt characters separated by spaces. This seems to be
related to having blank lines in the input. This fix ensures that all
such prompt characters are removed from the output.
If a [:file filename.ext] header arg is provided, then all graphical
output from the source block is captured on disk, and output of the
source block is a link to the resulting file, as with the
graphics-only languages such as gnuplot, ditaa, dot, asymptote. An
attempt is made to find a graphics device corresponding to the file
extension (currently .png, .jpg, .jpeg, .tiff, .bmp, .pdf, .ps,
.postscript are recognised); if that fails, png format output is
created.
Additionally, values for several arguments to the R graphics
device can be passed using header args:
:width :height :bg :units :pointsize
:antialias :quality :compression :res :type
:family :title :fonts :version :paper :encoding
:pagecentre :colormodel :useDingbats :horizontal
Arguments to the R graphics device that are not supported as header
args can be passed as a string in R argument syntax, using the header
arg :R-dev-args
An example block is (although both bg and fg can be passed directly as
header args)
\#+begin_src R :file z.pdf :width 8 :height 8 :R-dev-args bg="olivedrab", fg="hotpink"
plot(matrix(rnorm(100), ncol=2), type="l")
\#+end_src
This includes the required changes to org-babel.el and a
language-specific implementation for emacs-lisp. The emacs-lisp
changes are from a patch by Benny Andresen.
