Re: [O] org-odt: cannot find factory styles
On 3/2/2012 3:38 PM, Jambunathan K wrote: If the Org is meant for a global distribution (as opposed to personal installation), the distributor has to specifically ask the users to copy the styles file to<>/etc/org. C-h v data-directory In your case, the data-directory is c:/emacs-23.4/etc/org/. snipped Style files from the git repo is here: http://orgmode.org/w/?p=org-mode.git;a=tree;f=etc/styles;hb=HEAD Schema files form the git repo is here: http://orgmode.org/w/?p=org-mode.git;a=tree;f=contrib/odt/etc/schema;hb=HEAD Remember to download the raw files if you are downloading from git repo. dear K, Thanks very much for your response. Based on what you said above, I was able to get it working. I downloaded the Style and Schema files from the git repo, and put them in to the directories that emacs was searching, namely: Debug (org-odt): Using schema files under c:/emacs-23.4/site-lisp/contrib/odt/etc/schema/ Debug (org-odt): Using styles under c:/emacs-23.4/site-lisp/etc/styles/ In both cases, I had to create the directories. to put them in. I figured it was easier (for now) to put the files where this installation expected them, rather than fix the installation using ELPA etc. When I update, I'm sure I will use the other approaches you mentioned. Before I could get ODT success, I also had to install zip and unzip for my Windows machine, which I found at http://gnuwin32.sourceforge.net/packages.html Now it works great. thanks! M -- ~~~~~~ Matthew Landis, Ph.D. Research Scientist ISciences, LLC 61 Main St. Suite 200 Burlington VT 05401 802.864.2999 www.isciences.com ~~
Re: [O] Selectively export RESULTS
On 3/2/2012 2:33 PM, Eric Schulte wrote: The above line should be #+PROPERTY: singular. That explains why file-wide settings aren't working for you. THANK YOU. That makes it work, especially once I realized that the Property has to be set when the buffer is loaded. Now I have #+PROPERTY: eval no-export I would suggest either fixing the properties issue above, which will allow you to set eval to "no" before export when you are content with your current results, This is exactly what I did, and it does exactly what I want. org-babel totally rocks. -- ~~~~~~ Matthew Landis, Ph.D. Research Scientist ISciences, LLC 61 Main St. Suite 200 Burlington VT 05401 802.864.2999 www.isciences.com ~~
[O] org-odt: cannot find factory styles
Hello all, I've been googling this problem and searching the archives, but I can't seem to find a solution. When I try to export to ODT, I get Error (org-odt): Cannot find factory styles files. Aborting. Looking in my *Messages* buffer, I see at startup: Debug (org-odt): Searching for OpenDocument schema files... Debug (org-odt): Trying c:/c/Emacs-modified/tmpdir/emacs-23.4/etc/org/schema/... Debug (org-odt): Trying c:/emacs-23.4/site-lisp/contrib/odt/etc/schema/... Debug (org-odt): No OpenDocument schema files installed Debug (org-odt): Searching for OpenDocument styles files... Debug (org-odt): Trying c:/c/Emacs-modified/tmpdir/emacs-23.4/etc/org/styles/... Debug (org-odt): Trying c:/emacs-23.4/site-lisp/etc/styles/... Debug (org-odt): Trying c:/emacs-23.4/site-lisp/org/etc/styles/... Debug (org-odt): Trying c:/emacs-23.4/etc/org/... Problems while trying to load feature `org-odt' So you can see that i am using Windows (Win 7 64 bit). In fact, I am using Vincent Goulet's Windows installer (modified-2, FWIW), and I directed it to install into C:/emacs-23.4 instead of the default C:/Program Files (x86) directory. Looking in the site-lisp directories for the folders org-odt is searching, I don't see contrib, org, or etc directories. But I do see C:/emacs-23.4/etc/org/styles, which has OrgOdtStyles.xml, and C:/emacs-23.4/etc/schema, which doesn't obviously have any files to do with ODT. Is there a workaround or alternative installation to fix it? It would be really cool to export to ODT! M -- ~~~~~~ Matthew Landis, Ph.D. Research Scientist ISciences, LLC 61 Main St. Suite 200 Burlington VT 05401 802.864.2999 www.isciences.com ~~
Re: [O] Selectively export RESULTS
On 3/2/2012 12:59 PM, Christophe Pouzat wrote: Matthew, I think that you're wrongly expecting babel's cache header argument to behave like the argument of the same name in Sweave code chunks. Babel will cache, in your case, the value of your code block evaluation and there is none in your first code block, therefore nothing gets cached by babel, try that instead: #+name: my-random-vector #+begin_src R :session :cache yes rnorm(100) #+end_src #+headers: :var x=my-random-vector #+headers: :results graphics :exports results :file hist.png #+begin_src R :session :cache yes hist(x) #+end_src Does it work better? In that case you don't even need a session. Christophe Christophe - thanks for the suggestion. I haven't messed around much with variables passed between code blocks. When I try this, R tells me that 'x' must be numeric. When I query x in the R buffer, x is a data.frame. So the second code block reads x in as a data.frame instead of a numeric vector. For most purposes this would be OK (since a data.frame is the most usual outcome), but I'm reluctant to use this approach -- I'd like all of the variable passing to be in the R session. Intuitively this seems simpler, less error prone, and more conducive to tangling later. (Of course, I could be totally wrong - since I haven't really tried that approach). M -- ~~ Matthew Landis, Ph.D. Research Scientist ISciences, LLC 61 Main St. Suite 200 Burlington VT 05401 802.864.2999 www.isciences.com ~~
Re: [O] Selectively export RESULTS
Eric Schulte gmx.com> writes:
>
> Matthew Landis isciences.com> writes:
>
> Have you tried this? The cache header argument has special handling of
> code blocks with sessions to handle such cases.
Fair enough! I hadn't tried it. But I did just try this example:
-
#+TITLE: Super simple example using cache header arguments
#+PROPERTIES: eval no
Here is a really simple example.
#+begin_src R :session :results silent :exports code :cache yes
x <- rnorm(100)
cat('ran this code block')
#+end_src
here is code block two.
#+begin_src R :session :results graphics :exports both :file hist.png :cache yes
hist(x, main = 'A new title' )
#+end_src
#+results[1987d49b46ffd8b7263dc04e7c7b5d25f90342aa]:
[[file:hist.png]]
-
RESULTS:
On 1st export to html, both code blocks are run, and #+results block is *not*
created.
On 2nd export, both code blocks are run again, counter to my desires.
IF I run the code blocks interactively first using C-c C-c, the #+results block
is created for the code block 2. After that, subsequent exports run code block
1 but not code block 2. Again, this is counter to my desires because I want
code block 1 to be ignored as well. I understand why code block 1 is rerun,
because I have :results silent, but I'd rather not have to change that.
Generally, code block 1 is producing large R data.frames which don't need to be
viewed anywhere.
> Are you requesting a new option to :cache, such that even if the code
> block has changes the old results are used anyway?
Sort of. I think I'm asking for a file wide option to decide whether to run
any
code blocks, or just do the export based on whatever is currently existing in
the #+results blocks.
As in this example, I tried #+PROPERTIES: eval no but it is ignored. It would
be great if I could set an eval argument at the top of the file to be either
'no' (don't run any code blocks) 'yes' (run all code blocks) or 'block' respect
block level eval settings
Maybe such functionality exists in some other way - I claim only beginners
knowledge of org-babel.
Re: [O] org-export-blocks-preprocess: Marker does not point anywhere
Nick Dokos hp.com> writes: > > Matthew Landis isciences.com> wrote: > > I can't reproduce it either with latest (more or less) or with 7.8.03. > The html export succeeds and the code is exported, pdf export (with > minted) succeeds except that the code block is not processed, because > there is no minted lexer for R (at least in my setup). But I get no > error. > > Nick Well, thanks for trying. In my current work flow, I tend to have an R session running before I try to export, so I'm not troubled by this anymore. I guess I'll just wait until it's a problem. M
Re: [O] Selectively export RESULTS
tajo.ucsd.edu> writes: > > Eric Schulte gmx.com> writes: > > >>> Does this do what you want? > > > > Have you looked at the :cache header argument [1], from my understanding > > of your use case it should be exactly what you are after. > > > > Its a step in the right direction. > > It seems I have to set :cache yes on every block I use before I invoke > it. My attempt to use a buffer-wide PROPERTY setting for cache did not > pan out. > I'd like to put in a vote for the kind of functionality that cberry is describing. I have a very similar situation - a large org file that uses R to do a lot of time consuming data manipulation and model fitting, resulting in statistical tables and graphs. I run a lot of the code blocks as I'm writing it, resulting in :results in the org file. In the end, I'd like to export the org file to html or ODT, but I'd like to be able to choose buffer-wide whether to rerun all of the code blocks or just use the results that are already in the buffer. I tried setting #+PROPERTY: eval no at the top of the buffer in the hopes that on export, it would ignore all my code blocks and just incorporate the :results, but this was ignored and my code blocks were rerun. The cache argument only partially deals with the problem, as this example illustrates: #+begin_src R :session :cache yes x <- rnorm(100) #+end_src #+begin_src R :session :results graphics :exports results :file hist.png :cache yes hist(x) #+end_src Now after the first export, I change code block 2, but not code block 1. If I understand how cache works correctly, code block 2 will be rerun, but it will fail because code block 1 is not rerun, so x doesn't exist in the R session. For this reason, I'd prefer to be able to decide whether to re-run on a file- wide basis. Many thanks to all of you who have created such an amazing system. M
Re: [O] org-export-blocks-preprocess: Marker does not point anywhere
On 3/1/2012 12:47 AM, Nick Dokos wrote: Matthew Landis wrote: Hello orgmode fans, Another issue with org and R giving me headaches tonight. In the example below, using the :session header argument seems to cause problems with export to html. On export, the *R* buffer is opened up, but no file is created. in the *Messages* buffer, I see org-export-blocks-preprocess: Marker does not point anywhere however, if I try to export again, with the *R* buffer already open, then things work fine. This is an OK work around I guess, but I thought someone ought to know about it. Session info: Windows 7, 64 bit. Emacs version: GNU Emacs 23.4.1 (i386-mingw-nt6.1.7601) of 2012-02-04 on MARVIN Org mode version 7.8.03 ESS version 5.14 R version 2.14.1 Example now included! (Thanks Nick, for pointing that out...) #+begin_src R :session :exports code :results silent x <- runif(n = 100, min = 0, max = 20) y <- 4*x^2 + 0.3*x + 3 + rnorm(100, sd = 200) #+end_src
[O] org-export-blocks-preprocess: Marker does not point anywhere
Hello orgmode fans, Another issue with org and R giving me headaches tonight. In the example below, using the :session header argument seems to cause problems with export to html. On export, the *R* buffer is opened up, but no file is created. in the *Messages* buffer, I see org-export-blocks-preprocess: Marker does not point anywhere however, if I try to export again, with the *R* buffer already open, then things work fine. This is an OK work around I guess, but I thought someone ought to know about it. Session info: Windows 7, 64 bit. Emacs version: GNU Emacs 23.4.1 (i386-mingw-nt6.1.7601) of 2012-02-04 on MARVIN Org mode version 7.8.03 ESS version 5.14 R version 2.14.1 M -- ~~ Matthew Landis, Ph.D. Research Scientist ISciences, LLC 61 Main St. Suite 200 Burlington VT 05401 802.864.2999 www.isciences.com ~~
Re: [O] problems with R graphics
Matthew Landis isciences.com> writes: > > Hello all, ... > Unfortunately, I can't seem to get graphics > to insert themselves properly on export. > org example > ... > * A stand-alone code block > > First, create some data, perform a regression, and plot it. This > works great. > #+begin_src R :results graphics :file regress.png :exports both > > x <- runif(n = 100, min = 0, max = 20) > y <- 5*x^2 + 0.3*x + 3 + rnorm(100, sd = 200) > > f <- lm(y ~ x) > > plot(x, y, bty = 'n') > abline(f, lty = 'dashed') > > #+end_src > Success. ... > #+begin_src R :session :results graphics :file regress_session.png :exports both > > plot(x, y, bty = 'n') > abline(f, lty = 'dashed') > > #+end_src > This code block doesn't work. No error, but no file is created. ... I actually figured this one out just now. If creating a file in a 'stand alone' code block, the default directory is the directory that the org file itself is in. However, in a 'session' code block, the default directory is something else (R's default?). If I specify the full path to the file in the 'session' code block, things work better. Sorry for the noise! M
[O] problems with R graphics
Hello all, I believe this is my first post on this list, and I'm very new to org-babel, so forgive me if I am posting nonsense. However, I'm really enthused about the possibilities org-babel presents. Unfortunately, I can't seem to get graphics to insert themselves properly on export. I've included an example that reproduces my problem below. For what it's worth, I am using Windows 7 with a freshly downloaded issue of Vincent Goulet's package. Session info: Emacs version: GNU Emacs 23.4.1 (i386-mingw-nt6.1.7601) of 2012-02-04 on MARVIN Org mode version 7.8.03 ESS version 5.14 R version 2.14.1 Many thanks for any thoughts or requests for more info. Matt org example #+TITLE: An attempt to make org-mode work with R In this example, I want to fit a regression and plot it. I'm following the examples at the [[http://orgmode.org/worg/org- contrib/babel/languages/ob-doc-R.html][org manual]] and Erik Iverson's [[https://github.com/erikriverson/org-mode-R-tutorial][tutorial]]. * A stand-alone code block First, create some data, perform a regression, and plot it. This works great. #+begin_src R :results graphics :file regress.png :exports both x <- runif(n = 100, min = 0, max = 20) y <- 5*x^2 + 0.3*x + 3 + rnorm(100, sd = 200) f <- lm(y ~ x) plot(x, y, bty = 'n') abline(f, lty = 'dashed') #+end_src Success. * In code blocks using ":session" Now do the same thing, but across an unnamed session #+begin_src R :session :exports code :results silent x <- runif(n = 100, min = 0, max = 20) y <- 5*x^2 + 0.3*x + 3 + rnorm(100, sd = 200) #+end_src Now, I would like to display the results of the regression as R output. #+begin_src R :session :results output :exports both f <- lm(y ~ x) summary(f) #+end_src Again, success! This is really going to come in handy. #+begin_src R :session :results graphics :file regress_session.png :exports both plot(x, y, bty = 'n') abline(f, lty = 'dashed') #+end_src This code block doesn't work. No error, but no file is created. Also, if I press C-c C-c in the code block, in the org file I get #+begin_example #+results: [[file:regress_session.png]] #+end_example But no file is actually created. What could be going wrong?
