[O] Configuring html footnote (or adding to end of body)
Sorry if this has been answered before, can’t seem to find a way to search for it… Is there a way to configure the default content of the footer produced during html formatted export? There is a javaScript that I would like to be the last bit of my html every time an org file is exported. Can’t seem to figure that one out. Thanks -- Marco Blanchette, Ph.D. Genomic Scientist Stowers Institute for Medical Research 1000 East 50th Street Kansas City MO 64110 www.stowers.org Tel: 816-926-4071 Cell: 816-726-8419 Fax: 816-926-2018
[Orgmode] Re: Problem whit with code evaluation
Hmm... Thanks Dan.
Do we have a different version of org-mode? I just pasted your code in emacs
and try to execute it with M-x org-babel-execute-buffer RET without success.
The emacs-lisp code works but the python and the R crashes with the
following errors taken from the *Org-Babel Error* Output buffer
Traceback (most recent call last):
File "", line 5, in
File "", line 3, in main
NameError: global name 'x' is not defined
Error in main() : object 'x' not found
Calls: write.table -> is.data.frame -> inherits -> main
Execution halted
The first 4 lines comes from the python script while the last 3 come from
the R script
Here is my .emacs org-mode configs in case you are wondering...
;;Load org-mode and set global keys
(require 'org-install)
(add-to-list 'auto-mode-alist '("\\.org$" . org-mode))
(add-hook 'org-mode-hook 'turn-on-font-lock) ; not needed when
global-font-lock-mode is on
(define-key global-map "\C-cl" 'org-store-link)
(define-key global-map "\C-ca" 'org-agenda)
(setq org-log-done t)
(setq org-startup-indented t)
;; active Babel languages
(org-babel-do-load-languages
'org-babel-load-languages
'(
(R . t)
(sh .t)
(python . t)
(emacs-lisp . t)
)
)
Thanks again
On 8/18/10 9:37 PM, "Dan Davison" wrote:
> * The python example
> #+source: square(x)
> #+begin_src python
> return x*x
> #+end_src
>
> #+call: square(x=6)
>
> #+results: square(x=6)
> : 36
>
> * The elisp example of the fibonacci series using a table as argument
>
> #+tblname: fibonacci-inputs
> | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
> | 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |
>
> #+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs)
> #+begin_src emacs-lisp
> (defun fibonacci (n)
> (if (or (= n 0) (= n 1))
> n
> (+ (fibonacci (- n 1)) (fibonacci (- n 2)
>
> (mapcar (lambda (row)
> (mapcar #'fibonacci row)) fib-inputs)
> #+end_src
>
> #+results: fibonacci-seq
> | 1 | 1 | 2 | 3 | 5 | 8 | 13 | 21 | 34 | 55 |
> | 1 | 3 | 8 | 21 | 55 | 144 | 377 | 987 | 2584 | 6765 |
>
> * Then my own trial in R
> #+srcname: test(x, y)
> #+begin_src R
>p <- x*y
> #+end_src
>
> #+call: test(x=4, y=9)
>
> #+results: test(x=4, y=9)
> : 36
>
> #+lob: test(x=3, y=8)
>
> #+results: test(x=3, y=8)
> : 24
--
Marco Blanchette, Ph.D.
Assistant Investigator
Stowers Institute for Medical Research
1000 East 50th St.
Kansas City, MO 64110
Tel: 816-926-4071
Cell: 816-726-8419
Fax: 816-926-2018
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[Orgmode] Problem whit with code evaluation
Sorry again if this is common knowledge, but the road to orgmode power user is seeded with challenges! I am trying to write an R function that would take 3 arguments, hopefully set up in an org table and have a function run every rows, taking every column as arguments to produce a set of report files... But I am going a bit ahead of myself as I am stuck quite early in the development... My problem is quite basic. For some reason, I can¹t seems to be able to execute the following lines in the org buffer using org-babel-execute-buffer or to export an html of the files. The code block just don't execute and return errors. * Examples take from [[http://orgmode.org/worg/org-contrib/babel/intro.php#sec-7]] * The python example #+source: square(x) #+begin_src python x*x #+end_src #+call: square(x=6) * The elisp example of the fibonacci series using a table as argument #+tblname: fibonacci-inputs | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | | 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 | #+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs) #+begin_src emacs-lisp (defun fibonacci (n) (if (or (= n 0) (= n 1)) n (+ (fibonacci (- n 1)) (fibonacci (- n 2) (mapcar (lambda (row) (mapcar #'fibonacci row)) fib-inputs) #+end_src * Then my own trial in R #+srcname: test(x y) #+begin_src R p <- x*y #+end_src #+call test(x=4 y=9) #+function test(x=3 y=8) Is there something I am missing? My current setup is: GNU Emacs 23.1.50.1 org-mode (v7.01g) R v2.11.1 XServer running Snow Leopard Server 10.6.4 Thanks for the help -- Marco Blanchette, Ph.D. Assistant Investigator Stowers Institute for Medical Research 1000 East 50th St. Kansas City, MO 64110 Tel: 816-926-4071 Cell: 816-726-8419 Fax: 816-926-2018 ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] R code not producing expected results
Dear all,
Sorry if this is something totally obvious but I am learning to use org-mode
for my everyday work with R. I just installed the latest stable release of
org-mode (v7.01g) on top of GNU Emacs 23.1.50.1 (x86_64-apple-darwin10.2.0, NS
apple-appkit-1038.25). I also installed the CRAN ascii package v0.7 on top of R
v2.11.1. I am currently working on a MacBook pro with Snow Leopard 10.6.4
Early on today, while reading the org-babel intro, I was able to run the
following example but somehow, later tonight, it started to break and I spent
the last few hours scratching my head to understand what change and why it now
suddenly break. Your help will be greatly appreciated as I am discovering that
org-mode in collaboration with org-babel have great potential to help us create
more readable report of our daily analysis, as long as I can get through these
early hurdles.
Here is the org buffer that now breaks:
* Two examples of R code that worked when I started the tutorial but suddenly
started to fail...
** some R code that should generate a nice table
#+BEGIN_SRC R
library(ascii)
options(asciiType="org")
d <- as.data.frame(replicate(4,rnorm(100)))
ascii(cor(d),include.rownames=T, include.colnames=T,header=T)
#+END_SRC
** Some code straight from
[[http://orgmode.org/worg/org-contrib/babel/languages/org-babel-doc-R.php][org-babel]]
#+BEGIN_SRC R
library(ascii)
options(asciiType="org")
ascii(summary(table(1:4, 1:4)))
#+END_SRC
With the following error recover from the *Org-Babel Error* buffer
Loading required package: proto
Error in as.data.frame.default(x[[i]], optional = TRUE) :
cannot coerce class 'c("ascii", "proto", "environment")' into a data.frame
Calls: write.table ... data.frame -> as.data.frame -> as.data.frame.default
Execution halted
Thanks for the helps.
--
Marco Blanchette, Ph.D.
Assistant Investigator
Stowers Institute for Medical Research
1000 East 50th St.
Kansas City, MO 64110
Tel: 816-926-4071
Cell: 816-726-8419
Fax: 816-926-2018
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