* 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.
Eric Schulte
Carsten Dominik
Dan Davison
Bastien Guerry
Glenn Morris
Erik Iverson
Tom Dye