Re: [Orgmode] Creating files for a Kindle
Jeff, and Alan, Initial play around with has allowed me to find that: Firstly, the Kindle doesn't recognise the HTML extension and HTML files copied onto the Kindle simply don't appear as being available for viewing. If you change the extension to txt, the file appears and can be seen as an HTML files but includes some spuriois HTML code. The Orgmode to XHTML to SIGIL to ePub to Calibre to MOBI (for the Kindle) works extremely well, and for proper books looks good. But for quick updates Calibre wil read the HTML files directly and will convert to MOBI reasonably well, if its simple text and simple tables. This is stll better than Orgmode to PDF to Calibre to MOBI, as this route breaks even simple tables. Thanks for the help. Graham ___ 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
Re: [Orgmode] Creating files for a Kindle
Jeff, Ah, that's a bit disappointing. Do you have DX? My manual says that HTML is directly supported, with loads of other formats, so maybe it's a DX only feature? It's not the DX (I don't think the DX is available in the UK, it certainly isn't on the Amazon UK site) BUT on the US site it says that HTML is supported through conversion However, with the bigger screen PDFs might work OK, but they don't work very well on the smaller screen. The Orgmode to XHTML to SIGIL to ePub to Calibre to MOBI (for the Kindle) works extremely well, and for proper books looks good. Great! I'm really glad you found something that works! It certainly works well for proper documents, but a bit of a hassle for quick updates. Where in fact HTML files with the extension chnaged to txt might still be the best option. Graham ___ 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
Re: [Orgmode] Creating files for a Kindle
Mark, On 28 November 2010 18:08, marksc...@gmail.com wrote: One thing that works for me is this: export a file or subtree to html, then send to [myna...@kindle.free.com. Then, when my Kindle is connected to the internet, it will automatically download Amazon's conversion of my html file. This happens pretty quickly, in my experience, so it will almost certainly be faster than other methods described in this thread. I'm a little confused by this as it seems that if you are within Whispernet range the file is sent to your Kindle but will cost 99 cents per file (its per Megabyte, but rounded up to nearest Mb, and 15 cents if you are in the US) , but I agree costs apart this would seem the easiest solution. I'm not sure how this approach works with graphics. It's too expensive an approach for me. Graham ___ 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
Re: [Orgmode] Creating files for a Kindle
Mark The cost is nothing if you send it via email to your @free.kindle.com address. This is different from whispernet (which uses 3g, correct?). Perhaps you would need to turn off the 3g option? I don't know because I have the Kindle without 3g. It seems you are correct, I am still wading through the instructions. I haven't tried it with graphics at all, so I can't say. Perhaps someone has experimented? If there are no costs inolved this could still be a quick and easy way of keeping text only/tables up to date on the Kindle, even if it doesn't do graphics. A lot of what I want regularly updated will be text. Thanks, Graham ___ 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
Re: [Orgmode] Creating files for a Kindle
Just to follow this up, the kindle service to convert the HTML seems to work well, and I have now grasped how the free service works. Even if you have the 3g version of the Kindle, if you send it to the free email address for conversion it isn't delivered until you are connected to the Internet via a Wireless connection, and hence no charges are incurred. Sorry, this has gone somewhat off topic. I did start off looking for Orgmode tips, but it drifted off. Graham ___ 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] Creating files for a Kindle
Does anyone by chance use orgmode to create files for a Kindle? If you do I would appreciate some helpful hints or ideas on how you approach it. The Kindle file format is apparently modified HTML, but the guidance I have found seems to revolve around creating files in MSWord and then converting to Kindle by uploading to Amazon OR using Calibre to convert PDFs to Kindle. There is also a Mobi publisher that will convert files to Kindle, but its Windows only. The problem I have had, is that PDFs converted to Kindle lose a lot of formatting, including tables. The Kindle is a great bit of kit for reading documents (far better than a computer screen) and the free mobile phone connection makes it easy to check email etc, as well as browse the web at no cost. I'm much more impressed than I expected to be. I am slowly transferring a pile of paper documents/reference material onto it, but I am having problems producing documents that take full advantage of the Kindle features. You can upload PDFs directly but as native PDFs they aren't as user friendly as proper Kindle formatted flles. My guess is that orgmode files exported as HTML and then converted to Kindle may be the way to go, but, as I said, I would be interested if anyone has already established a work flow for this. Many thanks, Graham ___ 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
Re: [Orgmode] General question on dealing with Latex to word conversion
Tomas As an alternative to https://docq.com/ or http://a.nnotate.com/, you can have a look at OnDoc http://logand.com/sw/ondoc/index.html which I wrote to annotate PDF documents. Being an enthusiastic org-mode user, I would welcome any ideas that could make it worthwhile and easier to use OnDoc for people using org-mode. I will have a look at this, but you also have an email from me. Graham ___ 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
Re: [Orgmode] General question on dealing with Latex to word conversion
Marvin, Although, not exactly answering your question, I have just started using https://docq.com/ and http://a.nnotate.com/ You can compile as PDF from OrgMode and upload to either of these sites. Send a web link to the reviewer, who can then annotate and comment on your document. You still have to then manually add the comments back into OrgMode, but at least the reviewer sees the document as it is meant to look. Both are commercial sites, but have free options for low levels of use. Graham ___ 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
Re: [Orgmode] General question on dealing with Latex to word conversion
Marvin This looks very interesting, and would definitely save time - no more reading into word and reformatting. How much does docq cost ? I'm using the free version of docq, which has some limitations in terms of number of uploads etc. Paid versions are $7 and $13 depending on requirements https://docq.com/reg/pricing If I end up going the paying route, I will go with annotate as it is payg, and better suited to my occasional spurts of collaboration, with long periods of not needing to use it. This seems better than a monthly fee. Pricing for annotate is at http://a.nnotate.com/hosted-pricing.html Graham ___ 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
Re: [Orgmode] Re: *.org files showing up as exec files in Snow Leopard
Erik Do they have their executable bits set? Not sure how I tell, googling suggests that an x in the permissions says its an executable and it has rwx in the permissions (nothing else) but I see this is the same as other files that aren't labelled as exec. Indeed every file doc, excel etc is labelled with rwx in the permission. But an excel file I have just been sent has permissions -rw-r--r--(644) Compared with an existing excel file whis has -rwx---(700) It seems that all the files I brough back from the back up into the fresh install of Snow Leopard have had their attributes changed to rwx I think this is very much a Mac problem now, so I will move this to a mac forum. But thanks for your help. Graham ___ 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] *.org files showing up as exec files in Snow Leopard
I'm not sure how important this is, but having just upgraded to Snow Leopard, all my *.org files are now black with a green exec in the corner and trying to open them is giving a message that they is no application t view them and would I like to open a hex editor. More of a Mac problem than an Orgmode one, but has anyone come across this and know how to fix it? Many thanks, Graham ___ 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] [babel] babel creating corrupt pdf and png
PDFs created by Babel are giving a file corrupt message when trying to open them and a format not recognised message if I try pngs, Same files created directly from R are fine. This is with Ubuntu 10.04 and Org-mode version 6.36trans (release_7.01h.94.g25ac Example of code I am using is below. Can anyone suggest what I am doing wrong? Many thanks, Graham #+srcname:boxpip45byyear #+begin_src R :session bats :file boxpip45byyear.pdf :exports code boxplot(boxplot(allbats$count[allbats$species==p45]~allbats$year[allbats$species==p45]) #+end_src #+results: boxpip45byyear [[file:boxpip45byyear.pdf]] ___ 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
Re: [Orgmode] [babel] babel creating corrupt pdf and png
Eriic, Thanks, I'd suggest looking at the R session (bats in your case) to see what errors if any are being thrown by R during execution of the boxplot command. Will do, but sidetracked somewhere else now. Its strange because some are now being produced fine, and other not. They are all working fine if I copy the code into R. Not the code I posted, I hasten to add, as it was jibberish, I now realise, but that isn't the problem Graahm ___ 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
Re: [Orgmode] [babel] No org-babel-execute function for R! after update
Erik You need to setup the variable org-babel-do-load-languages as in the following: http://orgmode.org/org.html#Languages So I see, this has obviously changed as it was working without this before. BUT all working now, so thanks. Graham ___ 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
Re: [Orgmode] [babel] No org-babel-execute function for R! after update
Erik, Great, see http://eschulte.github.com/babel-dev/DONE-document-configuration-changes-for-Babel-integration.html for a description of why/when this done. Thanks, very useful. Graham ___ 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
Re: [Orgmode] Org babel R Help
Joseph/Dan 2) Width/Height exports for R graphics output. Do they work? I've tried a lot of combinations of :width and :height as exports, and they don't seem to work at all. I've tried small numbers (1-10), large numbers (100-2000) and numbers prefixed by cm with no luck. Hmm, I'm not seeing a problem here. It works for me with both png and pdf output. E.g. #+begin_src R :file z.pdf :width 20 :height 40 :exports both plot(1:10) #+end_src What image format (i.e. R graphics device) are you using? Can you post an example block that is not working? The values for :width and :height will be passed straight on to the graphics device, so their meaning depends on which graphics device is being used in R. I'm trying the code you posted with the latest org-mode from ubuntu and getting nothing in my results if I use png. If I use pdf, I get a really tiny chart which is incomprehensible. Width and height seem to work randomly, as using 20:40 work with pdf (although tiny), but 100,100 do not work at all. It only works correctly if I use the #+attr_latex: width=Xcm and omit the width and height. Based on what is happening here with me on Ubuntu 9.10, R 2.10 and orgmode 6.34. The :file z.pdf :width 20 :height 40 :exports both is affecting the size of the graphic that R produces. If you open x.pdf directly you will find that it changes size as expected. BUT regardless of the size of the z.pdf, Latex defaults to a fixed, and tiny, standard size. Unless you give an explicit latex command #+attr_latex: width=Xcm Using babel. For some reason my R graphics embedded within my pdf's don't seem to be as nice as viewing them from within R, i.e. slightly fuzzy edges. It's like the antialiasing has failed or something. The text labels on the axes are definitely not up to latex standard. Are you just viewing them or printing them. I find with Ubuntu that the default viewer seems to arbitrarily change between programs and the quality of graphics on the screen varies, but the quality of printed output stays the same. Try opening the final PDF in an alternative viewer and see if things still appear the same. Graham ___ 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
Re: [Orgmode] Org babel R Help
Dan So I believe we do understand the situation. The question is how do we improve it. First the facts: As for improvements, it is tempting to think that 1. org-babel should automatically insert the ATTR_LaTeX line in accordance with :width and :height when creating latex output. 2. org-babel should keep existing ATTR_LaTeX lines attached to their respective figures (contra Graham's thread linked above) I've had a brief look and doubtless all this is possible. It brings up issues of what units :width and :height are assumed to be in (e.g. just because R uses inches for pdf() doesn't mean that anyone else thinks that's a sensible decision). And we have to be a careful because it means altering what org-babel considers to be part of its results. Now that I know what is happening I am reasonably content with it as it is. However, it would seem to make sense that :width and :height commands should relate to the image size in the compiled pdf. And it would also make sense that these should be consistently in mm, regardless of file format. Graham ___ 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] [babel] multiple result outputs from function
Below is a function that I am trying to run in orgmode/babel.
It seems to run OK, but instead of printing out three values, its only
printing the final result.
Once again, i would appreciate some help with what I am missing.
Thanks,
Graham
#+srcname: CI_function
#+begin_src R :session daf
summary.ci-function(x){
xbar-mean(x)
sigma-sd(x)
n-length(x)
sem-sigma/sqrt(n)
lower.ci-xbar+sem*qnorm(0.025)
upper.ci-xbar+sem*qnorm(0.975)
print (xbar)
print (lower.ci)
print (upper.ci)
}
#+end_src
#+srcname: SumFlowering2005
#+begin_src R :session daf
summary.ci(daf$Flower[daf$YEAR==2005])
#+end_src
#+results: SumFlowering2005
: 1.97860201016947
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Re: [Orgmode] [babel] multiple result outputs from function
Dan Use ':results output' to get the printed output. The default mode is ':results value' which returns the value of the last expression in the block. Thanks, that's great. At least I managed to sort out my other two problems today on my own !! Graham ___ 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
Re: [Orgmode] [babel] multiple result outputs from function
Erik So, add :results output to your source header block. Dan beat you to it, but.. list(xbar, lower.ci, upper.ci) This is useful, but the output isn't exactly as I expected #+results: SumFlowering2005 : [[1]] : [1] 1.51 : : [[2]] : [1] 1.048065 : : [[3]] : [1] 1.978602 is there a way of replacing the [1] [2] and [3] with the object names (I know this is really an R question) Thanks, Graham ___ 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
Re: [Orgmode] [babel] multiple result outputs from function
Dan, is there a way of replacing the [1] [2] and [3] with the object names I think you meant replacing the [[1]], [[2]], [[3]]. That would be list(myname1=xbar, myname2=lower.ci, myname3=upper.ci) (I know this is really an R question) Thanks again :-) Graham ___ 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
Re: [Orgmode] Re: [babel] captions and figure size on export
Dan As a workaround, is it necessary for you to execute the block on export? Or could you instead use :exports code? I.e. before export, execute the block manually and ensure that the #+ATTR_LaTeX and #+results lines are arranged in the correct way. Many thanks for this, I'm glad it can be explained and the :exports code option works perfectly. I have executed the code manually anyway and I can't remember why I ended up withe the :exports both option. Graham ___ 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
Re: [Orgmode] Re: [babel] captions and figure size on export
Mmmm, this seems to be something to do with the placement of the code in orgmode as I now realise that although fig 1 isn't resized or captioned, the fig 1 caption iand size commands are attached to fig 2. and the fig2 commands attached to fig 3 etc. I will try and re-arrange these until they work, but hopefully someone will still be able to instantly see what I am doing wrong from the sample I gave in the original post ___ 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
Re: [Orgmode] Re: [babel] captions and figure size on export
This is driving me mad here: I have removed all the fig and size code and replaced it with onky one line that should be resizing the first graph(FloweringBoxplot.pdf). However, its resizing the second graph (NonFloweringBoxplot/pdf) and not affecting the first graph. This works on other files, so I am really at a loss here. #+srcname:BoxplotFlowering #+begin_src R :session daf :file FloweringBoxplot.pdf :exports both boxplot(daf$Flower~daf $YEAR) #+end_src #+ATTR_LaTeX: width=10cm #+results: BoxplotFlowering [[file:FloweringBoxplot.pdf]] #+srcname:BoxplotNonFlowering #+begin_src R :session daf :file NonFloweringBoxplot.pdf :exports both boxplot(daf$No.Flower~daf$YEAR) #+end_src #+results: BoxplotNonFlowering [[file:NonFloweringBoxplot.pdf]] Graham ___ 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] [babel] cannot code to execute since changing to emacs starter kit
I guess I am being stupid here, but I have changed my set up to using Eric's (Schulte) start up kit for emacs and now when I try to use C-c C-c to execute a code block I get an error C-c C-c can do nothing useful at this location As far as I can see form the files that came with the start up kit, babel should be initiated. Here is my bit of code; ** Tarsus data #+srcname:Tarsus #+begin_src R :session BirdData Tarsus-c(22.3,19.7,20.8,20.3,20.8,21.5,20.6,21.5) #+end_src Which was working during my try out of babel a few months ago. Once again I am stuck and would appreciate some help. This is emacs 23.1.1, and orgmode 6.34c.73.gb3e9, on Ubuntu 9.10 Many thanks, Graham ___ 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
Re: [Orgmode] [babel] cannot code to execute since changing to emacs starter kit
Tom Your example is R code. I have this is in my starter-kit: *** ON Org-babel R setup #+begin_src emacs-lisp :tangle yes (require 'org-babel-R) ;; requires R and ess-mode (add-to-list 'org-babel-noweb-error-langs R) #+end_src Perhaps when you changed the setup you got rid of these by mistake? Thanks for this, no I didn't get rid of these by mistake, but mistakenly thought that the set up I had in my .emacs file for orgmode babel was built into the starter kit and I didn't need to explicitly add these commands. I have now added the lines you have suggested and all seems to be working. Graham ___ 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] selective export
Using babel I have the data used for the analysis (in R) under a top level heading just called data. I want to keep this in the org file but not in the compiled pdf. I have had a look at the selective export in the manual, but could do with a bit more step by step instructions on how to exclude this bit of the outline. Could someone give me a bit of hand holding on how to do this. Many thanks, Graha, ___ 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] [babel] captions and figure size on export
I have the following code beside each other in an orgmode/babel file creating two boxplots. When exported the first boxplot remains the default size and has no caption or figure number, while the second is 10cm across, and has a caption and figuer number(Fig1). Could someone have a look at my code and see where my error is. They look identical to me. Thanks, Graham #+srcname:BoxplotFlowering #+begin_src R :session daf :file FloweringBoxplot.pdf :exports both boxplot(daf$Flower~daf$YEAR) #+end_src #+CAPTION:Boxplot comparing number of flowering daffodils between 2005 and 2006 #+LABEL: fig:BoxplotFlowering #+ATTR_LaTeX: width=10cm #+results: BoxplotFlowering [[file:FloweringBoxplot.pdf]] #+srcname:BoxplotNonFlowering #+begin_src R :session daf :file NonFloweringBoxplot.pdf :exports both boxplot(daf$No.Flower~daf$YEAR) #+end_src #+CAPTION:Boxplot comparing number of non flowering daffodils between 2005 and 2006 #+LABEL: fig:BoxplotNonFlowering #+ATTR_LaTeX: width=10cm #+results: BoxplotNonFlowering [[file:NonFloweringBoxplot.pdf]] ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] selective export
Thanks to you both, so easy when you know how. The manual makes sense as well now. Graham ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Re: [babel] captions and figure size on export
Graham Smith myotisone at gmail.com writes:
To follow this up, it seems that looking at the tex file that none of the latex
code is being exported
\subsection{Boxplots}
\label{sec-2.1}
\begin{verbatim}
boxplot(daf$Flower~daf$YEAR)
\end{verbatim}
\includegraphics[width=10em]{FloweringBoxplot.pdf}
\begin{verbatim}
boxplot(daf$No.Flower~daf$YEAR)
\end{verbatim}
\begin{figure}[htb]
\centering
\includegraphics[width=10cm]{NonFloweringBoxplot.pdf}
\caption{\label{fig:BoxplotFlowering}Boxplot comparing number of flowering
daffodils between 2005 and 2006}
\end{figure}
Graham
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Re: [Orgmode] Which Emacs on Ubuntu
Ian, I use the emacs-snapshot ppa from https://launchpad.net/~ubuntu-elisp/+archive/ppa. I had some problems with the Ubuntu Emacs 23 package (menu drawing, etc). However, these have probably been fixed by now. The snapshot is a bleeding edge version of Emacs, so you can expect bug fixes and new bugs - best of both worlds! Having said that I haven't encountered any bugs that affected me. Given my limited experience with Ubuntu I am always a bit nervous with bleeding edge but equally there is some confusion in Synaptic with versions. However, this confusion is well and truly a Ubuntu issues and well off topic. Graham ___ 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
Re: [Orgmode] Re: Which Emacs on Ubuntu
Ben, Right. So, people who installed ‘emacs’ several years ago would have Emacs 22, and then later, without changing their selection, the same people got Emacs 23 when the Ubuntu package maintainers decided it was ready. Thanks In fact 'emacs' says its 23 but it actually installs 22. I was pointed to this https://bugs.launchpad.net/ubuntu/+source/emacs22/+bug/462936 However, this confusion seems to 100% a Ubuntu issue and now well off topic as it seems the consensus as regards Orgmode is Emacs 23. Graham ___ 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] Which Emacs on Ubuntu
I have had to do a fresh install of Ubuntu 9.10, and on going to re-install Emacs, I see lots of choices. As I primarily use Emacs to run Orgmode and I find the list of Emacs options rather confusing, can anyone here suggest which is the best option to install. The key choices seem to be Emacs 22 or 23 with or without GTK. But there is also just an emacs option which is described as an Emacs 23 meta package. I realise this may well be an Ubuntu or Emacs question, but as I said my main use for Emacs is Orgmode, so I think some advice from here may be useful. So any help would be appreciated. Many thanks, Graham ___ 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
Re: [Orgmode] Which Emacs on Ubuntu
Eric, Emacs 23 without a doubt! I cannot see any reason for using version 22 unless you have to. Thanks, I was tempted to go for 23, but wasn't sure. Graham ___ 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
Re: [Orgmode] [babel] changing size of R graphics in pdf output
Dan, Before running the export, do you have a link to the image *already* in your org buffer? If no, then you should just get one copy of the image. If yes, then, if the link is positioned in such a way that it will get replaced by the output (no intervening lines between end of source block and results) then you should get one copy. I would almost certainly already have the link as I have been making minor changes and recompiling , what seems like hundreds of times trying to sort out how to fix it #+options toc:nil #+title: R latex graphics Text before figure. #+CAPTION: Trial boxplots with babel #+LABEL: fig:trial boxplots #+ATTR_LaTeX: width=5cm #+srcname:Boxplots Summary #+begin_src R :session BirdData :file BoxplotSummary.pdf :exports both Wingcrd - rnorm(100, 20) ; Tarsus - rnorm(100, 5) ; Head - rnorm(100, 3) ; Wt - rnorm(100, 40) boxplot(Wingcrd,Tarsus,Head,Wt,names=c(Wingcrd,Tarsus,Head,Wt)) #+end_src #+results: Boxplots [[file:BoxplotSummary.pdf]] Text after figure. Thanks for this. It has to be said I am really excited about this babel and R combination. I often do a few pages of R explanation on a specific topic for students where I need to combine text and R output, and this is a brilliant solution for this. Graham ___ 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
Re: [Orgmode] [babel] changing size of R graphics in pdf output
IGNORE everything in my last email.
The only relevant bit is
\includegraphics[width=10em]{BoxplotSummary.pdf}
\includegraphics[width=10em]{z.pdf}
So it seems to be ignoring the change in height and width commands for
z.pdf, and defaulting to 10em.
If I then edit the [width=10em] bit in the tex file I can change the
size easily.
It just seems that babel isn't passing the changes made in the org
file onto the tex file.
Graham
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Re: [Orgmode] [babel] changing size of R graphics in pdf output
A little progress here #+srcname:Boxplots Summary #+begin_src R :session BirdData :file BoxplotSummary.pdf :exports both boxplot(Wingcrd,Tarsus,Head,Wt,names=c(Wingcrd,Tarsus,Head,Wt)) #+end_src #+resname: Boxplots #+ATTR_LaTeX: width=10cm [[file:BoxplotSummary.pdf]] This gives me a plot 10cm wide, but in addition to the small plot. Not sure I understand why I am getting two plots. Graham ___ 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
Re: [Orgmode] [babel] changing size of R graphics in pdf output
This works #+srcname:Boxplots Summary #+begin_src R :session BirdData :file BoxplotSummary.pdf :exports none boxplot(Wingcrd,Tarsus,Head,Wt,names=c(Wingcrd,Tarsus,Head,Wt)) #+end_src #+resname: Boxplots #+CAPTION:Trial boxplots with babel #+LABEL: fig:trial boxplots #+ATTR_LaTeX: width=10cm [[file:BoxplotSummary.pdf]] However, it needs :exports none I actually want the code to still be present, but if I use :exports code I get the both boxplots again :-( I assume this is becasue the graphics are treated differently from numerical code output. Graham ___ 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
Re: [Orgmode] [babel] changing size of R graphics in pdf output
OK, This was all to do with the ordering of the latex code Below works, includes the R code, but only one plot of the expected size. #+srcname:Boxplots Summary #+begin_src R :session BirdData :file BoxplotSummary.pdf :exports both boxplot(Wingcrd,Tarsus,Head,Wt,names=c(Wingcrd,Tarsus,Head,Wt)) #+end_src #+CAPTION:Trial boxplots with babel #+LABEL: fig:trial boxplots #+ATTR_LaTeX: width=10cm #+resname: Boxplots [[file:BoxplotSummary.pdf]] I await for someone to tell me how it should be done :-) Graham ___ 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] [babel] changing size of R graphics in pdf output
I don't seem able to change the size of graphics in the PDF output. #+begin_src R :file z.pdf :width 20 :height 20 :R-dev-args bg=olivedrab, fg=hotpink plot(matrix(rnorm(100), ncol=2), type=l) #+end_src Using this example from an earlier post, regardless of how I change the width and height settings the image in the PDF stays the same. With this next example: #+srcname:Boxplots Summary #+begin_src R :session BirdData :file BoxplotSummary.pdf :exports both boxplot(Wingcrd,Tarsus,Head,Wt,names=c(Wingcrd,Tarsus,Head,Wt)) #+end_src If I add height and width arguments the image stays the same size regardless of settings, but the labels for the boxplots become tiny. Am I missing some code somewhere that allows the graphs to be modified. Thanks, Graham ___ 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
Re: [Orgmode] [babel] changing size of R graphics in pdf output
Dan/Torsten
Thanks, It seems to be a orgemode/babel/Latex issue.
If I view the pdf from within Emacs by double clicking on the link,
the size changes as expected, but if I compile the whole document as a
pdf the plots appear as small.
The error in the log is
! LaTeX Error: Cannot determine size of graphic in z.pdf (no BoundingBox).
See the LaTeX manual or LaTeX Companion for explanation.
Type H return for immediate help.
...
l.283 \includegraphics[width=10em]{z.pdf}
The actual TEX file has
\includegraphics[width=10em]{BoxplotSummary.pdf}
\includegraphics[width=10em]{z.pdf}
So it seems to be ignoring the change in height and width commands for
z.pdf, and defaulting to 10em.
Graham
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Re: [Orgmode] Re: [babel] R - variable names in summary
Austin This is help from the R side, not from the org-babel side. If these suggestions don't work, one of the babelers will have to step in. Many functions that print output to the interactive buffer will not produce that output when called outside of the interactive buffer. For these functions, if you wrap them in print() you can usually get the Thanks, yes, I have that problem with lattice plots and sweave, didn't think about it for this problem, However, some examples that Tom gave me use str unwrapped so I assume it should work. But I will bear that in mind. Graham ___ 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
Re: [Orgmode] [babel] R - variable names in summary
Dan, The colnames t works as expected, but how do I then see the variable names when using the summary command, Just use :colnames t again for that. Thanks again, I almost had this solved but in #+begin_src R :session babeltest :colnames t I hadn't left a space between the end of babeltest and the : But I would never have figured out the :results output method, however. Next question is is to do with output with things like summary. In R if you have lots of variables,the output wraps so it fits on the screen. With babel it runs off the edge of the page. is there a quick way of getting the output to fit an anticipated a4 pdf output. I appreciate this may be more an Emacs/orgmode question than a babel one. Graham ___ 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
Re: [Orgmode] [babel] R - variable names in summary
Dan, That's great, I am beginning to grasp how this works But I would never have figured out the :results output method, however. OK, it would be really helpful if you could let us know how we should improve the documentation of it. I'm not sure if I'm the one to ask about the documentation, as I struggled with most of it, but that is my problem and probably not typical. I'm also still very much trying to get to grips with Emacs and orgmode. Not being a programmer, I find the terminology and phrasing of these sorts of things difficult to follow, and need examples to copy , and then try and extract from the documentation and other examples, how things work. My problem was therefore the lack of examples specific to R. My guess is that the majority of emacs/orgmode users won't have the same problems. Graham ___ 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
Re: [Orgmode] [babel] R - variable names in summary
Dan Not being a programmer, I find the terminology and phrasing of these I wouldn't classify someone who analyses their data with R as a non-programmer. Mmmm, I can see why you would say this, but I don't really program in R, but have collected a library of R code over the years which I know how to use and tweak. My problem was therefore the lack of examples specific to R. Yes, I can see that. I can imagine that if shell/python/ruby code looks alien then the examples using those languages are not very inviting. Thanks for pointing that out. Tom Dye and Eric and I are working on documentation, including a Worg page specifically for R with org-babel. Currently it doesn't contain anything you don't know but we'll let you know when the first version goes up on Worg. I look forward to it. Thanks again, Graham ___ 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
Re: [Orgmode] [babel] R - variable names in summary
Tom, Thanks for your comments. When you find an example that fills a gap you perceive in the documentation, please pass that along, too. The more examples the better. Now that I have basics working, I will try and use it for something specific over the next few weeks and certainly feedback anything I think might be helpful. Graham ___ 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
Re: [Orgmode] Re: [babel] R - variable names in summary
Austin I don't know whether this will end up fitting into your setup, but there's an emacs function `ess-execute-screen-options' that does what Dan just suggested on a per-session basis taking the width of the current buffer into account. Even if it doesn't help with org-bable, it makes life in ESS much pleasanter. Wasn't aware of this, but will have a look You can also look at the latex() function in the R package Hmisc and the function xtable() from the R package xtable. For data frames, matrices, and some common summary functions, these functions will create a latex table out of your R object. Maybe Dan can suggest how latex code generated in R could be properly included and typeset in org-babel. I have played with xtable() in the past, but I am now rethinking things now that babel looks so promising. Thanks for the pointers. Graham ___ 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] Babel - importing a data file- missing header row
I need a bit of help importing a data file into orgmode/babel. The import doesn't seem to know about having a header row #+srcname:woodland #+begin_src R read.table(/home/graham/Dropbox/College/BY4001/WoodlandData/BY4001WoodlandDataFinal.txt,header=TRUE) #+end_src #+resname: woodland | V1.1 | v | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 10 | 0 | 0 | 0 | 100 | 0 | 3 | B But strangely if I change the command and run the names(woodland) after the import, I get a table of variable names but no data. I'm not sure if the data is there but hidden as I can't get any commands to work on the woodland object. * Woodland Data #+srcname:woodland #+begin_src R woodland-read.table(/home/graham/Dropbox/College/BY4001/WoodlandData/BY4001WoodlandDataFinal.txt,header=TRUE) names(woodland) #+end_src #+resname: woodland | ID | | wood | | Ajug.Rept| | Ange.sylv| | Brac.sylv| | Brom.ramo| | Care.pend| | Care.remo| | Care.sylv| | Cirs.palu| | Cory.avel| | Desc.caes| | Dryo.fili| | Endy.non | | Euph.amyg| So it seems I already need some more help. Graham ___ 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
Re: [babel] [Orgmode] Babel - importing a data file- missing header row
Dan, Using session gets everything working as I expect it to, at least so far it does. I will work through the other aspects you suggest but for now its looking good. Could you post the first few lines of your data file, or a small example with the same format, as I don't completely understand the output you are getting. The difficulty in understanding the output I posted was probably because while it looked OK when I posted it, the version that appeared wrapped twice. But its working now. p.s. Please include the string [babel] in the subject line! Ah yes, I misunderstood your first request and just thought you meant to make sure babel was in the subject line,which I did, but you mean [babel] not just babel. Many thanks again, Graham ___ 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] [babel] R - variable names in summary
Dan I have started a new thread so it has a propel babel string. I have also created a small file for testing. The colnames t works as expected, but how do I then see the variable names when using the summary command, and str doesn't work at all (source block produced no output) . They appear OK in the R buffer. Orgmode+babel output below Graham #+srcname:babeltest #+begin_src R :colnames t babeltest-read.csv(/home/graham/Dropbox/myotis/Learn/learn/babeltest.csv,header=TRUE) #+end_src #+resname: babeltest | ID | var1 | var2 | var3 | |--+++| |1 | 34 | 1 |400 | |2 | 56 | 4 |499 | |3 | 78 | 3 |500 | |4 | 34 | 5 |600 | |5 | 56 | 6 |500 | |6 | 23 | 7 |300 | |7 | 45 | 5 |200 | |8 | 23 | 6 |340 | |9 | 89 | 7 |400 | | 10 | 46 | 4 |450 | #+begin_src R :session babeltest summary(babeltest) #+end_src #+resname: | Min. : 1.00 | Min. :23.0 | Min. :1.0 | Min. :200.0 | | 1st Qu.: 3.25 | 1st Qu.:34.0 | 1st Qu.:4.0 | 1st Qu.:355.0 | | Median : 5.50 | Median :45.5 | Median :5.0 | Median :425.0 | | Mean : 5.50 | Mean :48.4 | Mean :4.8 | Mean :418.9 | | 3rd Qu.: 7.75 | 3rd Qu.:56.0 | 3rd Qu.:6.0 | 3rd Qu.:499.8 | | Max. :10.00 | Max. :89.0 | Max. :7.0 | Max. :600.0 | #+begin_src R :session babeltest str(babeltest) #+end_src #+resname: ID,var1,var2,var3 1,34,1,400 2,56,4,499 3,78,3,500 4,34,5,600 5,56,6,500 6,23,7,300 7,45,5,200 8,23,6,340 9,89,7,400 10,46,4,450 ___ 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
Re: [Orgmode] Re: Babel - simple getting started problem
Seb You must pass somehow the variable you want to work with. See http://eschulte.github.com/org-babel/org-babel.org.html and its example 1. Thanks, I will look at the link, I thought I had done this by assigning a name to the output #+srcname:trial and then trying to run the command on the output mean(trial) But obviously this isn't how it works. Graham ___ 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
Re: [Orgmode] Re: Babel - simple getting started problem
Seb, I am obviously not following this at all. I am assuming you need to keep all the code under the same heading so OrgMode knows which table is being referred to. But if I put the cursor in the table and use C-u C-c C-c I get a message in the mini buffer, that the formulas are being re-applied, but an error in the table. Graham * Example 1: data summaries using R #+srcname: tbl-example-data() #+begin_src R runif(n=5, min=0, max=1) #+end_src #+resname: tbl-example-data | 0.142434993525967 | | 0.636120659532025 | | 0.16730977254 | | 0.96337740519084 | | 0.276034632697701 | #+srcname: R-mean(x) #+begin_src R mean(x) #+end_src #+tblname: summaries | mean | || | #ERROR | #+TBLFM: @2$1='(sbe R-mean (x generate-data())) ___ 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
Re: [Orgmode] Babel - simple getting started problem
Dan Here's a version of your example that works. Thanks, this all works for me now. In addition to the tutorial on the worg, is there a manual somewhere, because the var option isn't mentioned in the tutorial. And judging by the trouble I am having, I'm going to need a lot more help to get this working for me. But it looks very promising. Graham ___ 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
Re: [Orgmode] Babel - simple getting started problem
Dan The Worg pages is the current documentation, but please just ask when you have any problems -- include the string [babel] in the subject line so people can filter it out. One suggestion: are you looking at the HTML version of the tutorial? If so, how about getting hold of the source org file, and working through that? Thanks, Seb sent me a link to the original version of the tutorial so I could see the underlying code. I've now tried out a few things and seem to have sorted out my immediate problems. I think I will now try and use it for real, and see how I get on. This is probably the best way of leaning. And yes, I will ask for help as I go along. Graham ___ 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] Babel - simple getting started problem
I know I must be missing the obvious here, but why can't I get babel+R to calculate a mean. See below Many thanks, Graham * test #+srcname:trial #+begin_src R x-c(4,5,6,7,8,9) #+end_src #+resname: trial | 4 | | 5 | | 6 | | 7 | | 8 | | 9 | * meantest #+begin_src R mean(trial) #+end_src #+resname: error in buffer source block produced no output * meantest2 #+begin_src R mean(x) #+end_src #+resname: error in buffer source block produced no output ___ 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] Latex export to A4
As I understand it, orgmode defaults to A4, but I seem to be exporting to PDF via Latex in letter. And I have never had a problem before, but I am now exporting to PDF and when viewed the bottom of the page is cut off. Its strange because usually the viewer adjusts to the page size, but Acrobat is identifying the page as being letter size but only showing an A4 window of the text. The last line is listed in the hyperlinks, but not viewable. A4 is my normal default for everything Any one any idea what is going on here, I have the same problem with other viewers (Okular) Its 6.31a on Ubuntu 9.04 Thanks, Graham ___ 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] text ignoring page breaks (was Latex export to A4)
Well this seems to be nothing to do with the page size as other files are working fine. I have now opened a new file and typed everything in from scratch and still getting the same problem. I have looked at the tex file and can't see anything obvious, but as a PDF the text runs over the page number and off the bottom of the page. I have attached the file in the hope someone can tell me what I am doing wrong. For now I have transferred it to Open Office to finish it, but really need to sort this out. I have upgraded to OrgMode 6.33f, still Ubuntu 9.04 Many thanks, Graham LatexTest.org Description: Binary data ___ 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
Re: [Orgmode] text ignoring page breaks (was Latex export to A4)
Ed, I think the problem is that you have no paragraphs, just headers. I hacked your file to have some random junk in a few of the sections and it turned out a lot better. Indeed, I have just done the same, added a bit of text and it is working fine. I guess I haven't had a file of all headings before. Many thanks. That was a big help. Graham ___ 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
Re: [Orgmode] how to draw picture in org-mode ? Does it support tikz/pgf ?
Something I, as a comparative beginner can answer :-) how to draw picture in org-mode ? Does it support tikz/pgf ? Yes, I found it worked fine for me. I had a silly problem with page margins (searchng the forum for tikz/pgf will find my recent posts), that was my fault but other than that the flow charts and mindmaps I have done work well. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: Positioning Latex diagram on PDF output
leo
2009/8/9 Leo sdl@gmail.com:
On 2009-08-09 08:33 +0100, Graham Smith wrote:
Leo,
Thanks again, it seems the answer lies in Latex, rather than OrgMode,
so I will work away at that.
having said that, the commands you gave me are extremely useful for
making a stand alone diagram to insert as a graphic into some other
document. So well worth knowing.
You're welcome, Graham.
Leo
Just for completeness, and should anyone search the forum with a
similar problem,the answer lay in the wide margins used by default in
the article class, so new headers are:
#+LATEX_HEADER: \usepackage{tikz}
#+LATEX_HEADER: \usetikzlibrary{mindmap,trees}
#+LATEX_HEADER: \usepackage[a4paper, left=3cm,right=2cm]{geometry}
Plus you can scale the tikz drawing using
\begin{tikzpicture}[scale=0.85]
However, it doesn't scale very well and the different elements do not
scale proportionally, so while it works fine for a small tweak, it is
useless for the large changes.
Graham
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Re: [Orgmode] Re: Positioning Latex diagram on PDF output
Leo,
Thanks again, it seems the answer lies in Latex, rather than OrgMode,
so I will work away at that.
having said that, the commands you gave me are extremely useful for
making a stand alone diagram to insert as a graphic into some other
document. So well worth knowing.
Graham
2009/8/8 Leo sdl@gmail.com:
On 2009-08-08 22:14 +0100, Graham Smith wrote:
Based on this I have altered the headers in orgmode to
#+LATEX_HEADER: \usepackage{tikz}
#+LATEX_HEADER: \usetikzlibrary{mindmap,trees}
#+LATEX_HEADER: \usepackage[active,tightpage]{preview}
#+LATEX_HEADER: \PreviewEnvironment{tikzpicture}
#+LATEX_HEADER: \setlength\PreviewBorder{20pt}
This has certainly solved the mindmap position problem, but now the
resultant pdf loses all the text from the original orgmode file. :-(
I assume I don't need to add the document class line?
In that case, you can use geometry package or scale your tikz picture so
that it fits into the textwidth.
--
Emacs uptime: 1 day, 5 hours, 57 minutes, 35 seconds
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[Orgmode] Positioning Latex diagram on PDF output
I am experimenting with a TiKZ/pgf mindmap in orgmode. Although it
looks as if it should fit on the (A4) PDF page, it is offset to the
right and cut off, even though there seems to plenty of room on the
page to left of the diagram.
The code is just the example from the manual, which I have modified a
bit, and is shown below.
Is there some way of moving it across to the left a bit, so it will
fit on the page?
Many thanks,
Graham
\begin{tikzpicture}
\path[mindmap,concept color=black,text=white]
node[concept] {Ecological Impact Assessment}
[clockwise from=0]
child[concept color=green!50!black] {
node[concept] {Ecology}
[clockwise from=90]
child { node[concept] {theory} }
child { node[concept] {field skills} }
child { node[concept] {methods} }
child { node[concept] {software engineer\-ing} }
}
child[concept color=blue] {
node[concept] {Legislation}
[clockwise from=-30]
child { node[concept] {EIA} }
child { node[concept] {Policy and Planning} }
}
child[concept color=red] {
node[concept] {Data Analysis}
[clockwise from=-30]
child{node[concept]{Statistics}}
child{node[concept]{GIS}}
child{node[concept]{Decision Science}}
}
child[concept color=orange] {
node[concept] {Professional Practice}
[clockwise from=-75]
child{node[concept]{Business skills}}
child{node[concept]{Presentation skills}}
child{node[concept]{EcIA best practice}}
};
\end{tikzpicture}
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Re: [Orgmode] Re: Positioning Latex diagram on PDF output
leo
Thanks, this was useful, but...
%%
\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{mindmap}
\usepackage[active,tightpage]{preview}
\PreviewEnvironment{tikzpicture}
\setlength\PreviewBorder{1pt}
Based on this I have altered the headers in orgmode to
#+LATEX_HEADER: \usepackage{tikz}
#+LATEX_HEADER: \usetikzlibrary{mindmap,trees}
#+LATEX_HEADER: \usepackage[active,tightpage]{preview}
#+LATEX_HEADER: \PreviewEnvironment{tikzpicture}
#+LATEX_HEADER: \setlength\PreviewBorder{20pt}
This has certainly solved the mindmap position problem, but now the
resultant pdf loses all the text from the original orgmode file. :-(
I assume I don't need to add the document class line?
Graham
P.S. I'm not working on a Mindmap exporter just trying some pgf graphics.
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Re: [Orgmode] Orgmode for research information management
Shrutarshi 2009/6/24 Shrutarshi Basu s...@basushr.net: I just started using orgmode today to organize the papers that I'm collecting for my own research. The way I work is a bit complicated, but I like it. I have all my PDFs in a single directory and my notes in a separate directory. That sounds really interesting, thanks. And yes I would like to have a look at the python script, but I may need to come back and ask for help in using it. None the less, this is the sort of set up I would like to try and get working. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Orgmode for research information management
I have used several information management tools over the years, but I am trying to use Emacs/orgmode more. There are many examples of people using Orgmode for time management type tasks, but not a lot on information management. I would be interested in any insights into how people use orgmode for information management eg. gathering information for scientific paper. Many thanks, Graahm ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: Orgmode for research information management
Chris, Thanks, but I have a couple of more questions if that's OK For me, it works great because it is so easy to use as an outliner. Do you use tags for particular linked topics or do you just rely on the outline and drop related information into the same level of the outline However, I still keep all my references in a separate database (I use the Zotero plugin for Firefox, which I export to bibtex). Do you keep notes specific to a paper in Zotero, or keep them in Orgmode. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: Orgmode for research information management
Eric It's this flexibility that encourages one to simply jump in and use it and the benefits then quickly make you wonder how you got along without it! Strangely, when you are used to a more structured approach this makes it difficult to start. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] In response to: .emacs works on Mac but not on Ubuntu
Thanks everyone picked up and not your latest version. To check that, type dpkg --list | grep org and see if org mode was installed by the package manager. If so, just do a normal remove and see if that doesn't take care of it. Jere may be right: I recall previous discussions on the list that indicated this kind of problem. You might want to check for the existence of /etc/emacsXXX/site-start.d/50org-mode.el. Tries both these thngs and can't find any installed org-mode or that 50org-mode/.el file. I will try a few more commentin outs and retyping things, but I still find it strange that it wa working fine in Ubuntu 8.01 and not now., but I then find Linux a bit like that. Should anyone have any othe suggestions, I would still appreciate them. Many thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] In response to: .emacs works on Mac but not on Ubuntu
Ian Thanks, it just worked with 8.01 which is why I am struggling now. I am using Ubuntu Jaunty with a setup almost identical to yours and mine Just works. Are you certain that: (setq load-path (cons ~/EmacsAddins/OrgMode/lisp load-path)) (setq load-path (cons ~/EmacsAddins/OrgMode/contrib/lisp load-path)) Points to the correct version of org? Some things to try: It was the directory copied from the Mac, so it was 6.xx, but I have just updated to latest version of web site. Remove the compiled lisp files (*.elc). I have none to remove that I can find. Edit org-install.el and type in some garbage. If emacs is trying to load this library it should blow up with an error. I haven't tried this, but the error message I get suggests an error trying to load org.install, which I assume is because it can't find it. The error message is Loading /home/graham/.recentf...done Cleaning up the recentf list...done (0 removed) An error has occurred while loading `/home/graham/.emacs': File error: Cannot open load file, org-install My default ubuntu emacs22 doesn't have any org packages loaded by default. Try doing an apt-cache purge org-mode, which should completely remove the Ubuntu version if it's installed. I have run this and get an error gra...@t42-laptop:~$ sudo apt-cache purge org-mode [sudo] password for graham: E: Invalid operation purge I have also tried this: gra...@t42-laptop:~$ emacs --debug-init but get Loading /home/graham/.recentf...done Cleaning up the recentf list...done (0 removed) require: Cannot open load file: debug Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] In response to: .emacs works on Mac but not on Ubuntu
I really don't understand why, but I have written out the paths in full and it seems to work now (setq load-path (cons /home/graham/EmacsAddIns/OrgMode/lisp load-path)) (setq load-path (cons /home/graham/EmacsAddIns/OrgMode/contrib/lisp load-path)) Can anyone see any obvious differences between what I posted earlier and what I have now. Below is what wouldn't work (setq load-path (cons ~/EmacsAddins/OrgMode/lisp load-path)) (setq load-path (cons ~/EmacsAddins/OrgMode/contrib/lisp load-path)) Thanks for everyones help. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] In response to: .emacs works on Mac but not on Ubuntu
Ian, Doh, finger/brain communication mismatch. I get that as well :-) It should be: sudo apt-get purge org-mode As you will have seen now, its working, but I'm still puzzled as to why. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] .emacs works on Mac but not on Ubuntu
I have gone back to using Ubuntu and in the past I used to copy any updates of the .emacs file from Ubuntu to the Mac. So I expected to be able to copy the .emacs from the Mac to the newly installed Ubuntu. But it isn't loading the current version of Org-mode, I am getting 4.67 where I should be getting 6.xx. The EmacsAddins folder has been copied from my Mac home directory into my Ubuntu home directory. Has anyone any idea where the errors might be. Many thanks, Graham The lines in my emacs are (setq load-path (cons ~/EmacsAddins/OrgMode/lisp load-path)) (setq load-path (cons ~/EmacsAddins/OrgMode/contrib/lisp load-path)) (setq org-hide-leading-stars t) (require 'org-install) (require 'org-mouse) (load org-R) ;; The following lines are always needed. Choose your own keys. (add-to-list 'auto-mode-alist '(\\.org\\' . org-mode)) (global-set-key \C-cl 'org-store-link) (global-set-key \C-ca 'org-agenda) (global-set-key \C-cb 'org-iswitchb) (global-font-lock-mode 1); for all buffers ;;(add-hook 'org-mode-hook 'turn-on-font-lock) ; Org buffers only ;Basic Remember;; (add-to-list 'load-path ~/EmacsAddins/remember) ;;Remember plus Org-Mode;;; (org-remember-insinuate) ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] In response to: .emacs works on Mac but not on Ubuntu
Jere, What may be happening is that Ubuntu has a default version of org-mode pre-installed in the primary load path directories, so that is what is being picked up and not your latest version. To check that, type dpkg --list | grep org and see if org mode was installed by the package manager. If so, just do a normal remove and see if that doesn't take care of it. I can't check this just now (as I don't have access to my ubuntu machine at the moment) but as I understand it Org-mode is distributed with Emacs now, but the commands in the .emacs file over ride the built in version and use the version in the path set up in .emacs. That is what happens on the Mac, unless I have misunderstood. Thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] org-R tutorial on Worg
Dan, I'm working through the tutorial and not got very far :-( #+TBLNAME:continuous-data | | |---| | -4.76347066844695 | | -1.83010300550287 | | -3.62646358009839 | | -3.06483847781371 | | -3.29886543850004 | | -3.33136718271076 | | -2.92393768071614 | | -1.81447109443947 | | -2.77876256693823 | | -3.04428187935138 | | 2.68011061127436 | | 3.8462031281076 | | 3.26010701204355 | | 3.13388406902156 | | 2.64108043612206 | | 2.79307900174277 | | 2.63510171209823 | | 0.382633073598201 | | 1.36106585545773 | | 3.15710034712042 | #+RR: x-c(rnorm(10, mean=-3, sd=1), rnorm(10, mean=3, sd=1)) #+R: title:continuous-data output-to-buffer:t [[file:tmp.png][histogram example]] #+R: action:hist columns:1 colour:hotpink #+R: intable:continuous-data outfile:png title:histogram example This is cut and pasted from Emacs and when I run org-R I get and error: before first headline at position 975 in buffer RorgTest.org Have you any suggestions ? Thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: Beginners guide to Org customization
Carsten, Wearing my beginner to Emacs and Orgmode, this looks really useful. Graham 2009/2/5 Carsten Dominik domi...@science.uva.nl: I have my home^h^h^h^h trainwork up as a new attempt for the Beginners Guide. A lot more appropriate now, I think. Bernt? - Carsten http://orgmode.org/worg/org-customization-guide.php On Feb 5, 2009, at 3:21 PM, Bernt Hansen wrote: Carsten Dominik domi...@science.uva.nl writes: I have made a structured list of 43 (which one can we remove, please) Variables that came in as frequently customized variables in the customization survey. It is not exactly the top 43, I have used some additional judgement. I think a lot of these variables are things you play with _after_ using org-mode for awhile. Maybe the following variables should be introduced later? - org-archive-location the default works, and you don't archive anytime soon after starting to use org-mode. - org-startup-folded start with #STARTUP first? - org-odd-levels-only Talk about the conversion functions too (org-convert-to-odd-levels and org-convert-to-oddeven-levels.) I switched my files back and forth a few times but ended up with oddeven levels due to the depth of some of my tasks. - org-special-ctrl-a/e - org-special-ctrl-k I should maybe try these one day :) I've used org-mode for a few years now and I don't currently use these variables. They're great to have but not essential to getting started. The default values for the variables work in most cases. I think the ones that should be listed first are the ones you really have to customize to get org-mode to work for you. Beginners will not want nor need this amount of detail to be productive with org-mode. Having too many variables to set up or play with up front may just scare people away. Maybe we just need to stress that customizations are optional and you can completely ignore entire sections that don't apply to you (clocking, exporting, etc.) until you feel you need these additional features. HTH, Bernt ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] org-R tutorial on Worg
Nick (load-library org-R) Thanks, this sorted out the error messages, I'm now getting new ones but these seem to be R generated so I will now have a look at that next. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] org-R tutorial on Worg
Dan If you have added it to the contrib/lisp directory, then you could do (add-to-list 'load-path path\to\contrib\lisp load-path) (load org-R) (load-library org-R) as suggested by Nick worked I already had the load path line in my .emacs But perhaps what I should do is add (provide 'org-R) It seems it might make things easier for people like me :-) at the end of my code. I'm pretty new to elisp so not sure but I've added that now. I'm sure someone will tell us if it's wrong. That may be, but this is a great idea of pulling R into org-mode, and I for one will find it very useful. Many thanks for the help and for org-R. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Thanks for the Org-R tutorial
Just wanted to say a quick thanks for a very useful tutorial - org-R: Computing and data visualisation in Org-mode using R. Just to add a thanks from me as well, this looks really useful. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: [OT] basic emacs tips you will need someday (was: Footnotes and R output when exporting to HTML or Latex)
Manish, I will have a look at this. Thansk fro the pointer. Graham 2009/1/22 Manish Sharma mailtomanish.sha...@gmail.com: Paul R paul.r...@gmail.com writes: Graham, Graham Thanks, but I would appreciate a bit more hand holding on this. Graham I don't actually know how to check org-footnote-re and Graham org-footnote-definition-re I think the best help I can do is to describe the first steps to find your way in the emacs jungle. [snip: nice helpful introduction to Emacs help (206 lines)] I hope this does not sounds too much like a stupid RTFM. This was a RTFM, indeed, but a nice one I hope :) One of the best introductory materials to Emacs I have come across is a series of tutorials on IBM DeveloperWorks website at http://www.ibm.com/developerworks/views/aix/libraryview.jsp?search_by=emacs+editing+environment Hope someone finds it useful. -- Manish Life is beautiful.* * Conditions apply. ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] org tables and R
Carsten should we include Dan's code as a contributed package or even merge it into org-plot? I would like to see it included some how, as, for me, the more integration between org-mode and R the better. As to how it should be included, I must leave to other who more about Org-mode, Emacs, ESS and R than I do. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Footnotes and R output when exporting to HTML or Latex
Mmmm, so busy concerened about the graphics I didn't realise I had such a major issue with footnotes. I am pasting R output into an org file which comes in like: names(gq3hazard) [1] H1aH1bH1cH2aH2bH2cH3aH3b [9] H3cH3dH4aH4bH4cH5aH5bH5c [17] Htotal I suspect some of you are ahead of me, becasue the Org mode export takes these to be footnotes so in the PDF I get names(gq3hazard) 1 H1a H1b H1c H2a H2b H2c H3a H3b $ˆ9$ H3c H3d H4a H4b H4c H5a H5b H5c $ˆ17$ Htotal with a footnote 1 5 3 7 library(boot) medianCI(na.omit(H1b)) I have no idea where the medianCI bit has come from but looking through the file, the spurious footnotes seems to be causing havoc with the layout. Is it possible to disable the footnote feature and then explicityly tell orgmode that a specific instance of square brackets should be interpreted as a footnote. Thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Re: Footnotes and R output when exporting to HTML or Latex
Paul, Check org-footnote-re and org-footnote-definition-re Thanks, but I would appreciate a bit more hand holding on this. I don't actually know how to check org-footnote-re and org-footnote-definition-re sorry Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Re: [OT] basic emacs tips you will need someday (was: Footnotes and R output when exporting to HTML or Latex)
Paul, This looks really useful, the problem with the Friendly manual (and I have the O'Reilly book and the SAMS book) is that its difficult to know where to start and this very focussed help I am sure will give me a kick start. I have now printed it out and will work through it. Many thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: Footnotes and R output when exporting to HTML or Latex
Nick But I suspect that you are going to run into a much harder wall after you've done this. The description reads as follows: --- org-footnote-re is a variable defined in `/home/nick/src/emacs/org/git/org-mode/lisp/org-footnote.elc'. Its value is [^][\n]\\[\\(?:\\([0-9]+\\)\\|\\(fn:\\([-_[:word:]]+?\\)?\\)\\(?::\\([^]]*?\\)\\)?\\)\\] Documentation: Regular expression for matching footnotes. --- Errm yes, my knowledge of reglar expressions is zero, but thanks :-) Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Problems downloading 6.18?
Maybe this in hand, but when I try to download 6.18 I get switched to the 6.17c page and 6.17c is the only version available. Or is it just me :-( Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Re: Problems downloading 6.18?
Bernt, Thanks, I will do as yuo suggest. Graham 2009/1/20 Bernt Hansen be...@norang.ca: Graham Smith myotis...@gmail.com writes: Maybe this in hand, but when I try to download 6.18 I get switched to the 6.17c page and 6.17c is the only version available. Or is it just me :-( It's not just you. It looks like the org-mode page has not been updated yet but the 6.18 version is available. You can just change the link manually like this: http://orgmode.org/org-6.18.zip HTH, Bernt ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: Inline images in exported HTML
Carsten, Just to say many thanks for version 6.18 as this solves this problem of a quick preview with inline PDFs via Latex. Graham 2009/1/14 Carsten Dominik domi...@science.uva.nl: On Jan 12, 2009, at 9:14 PM, Bernt Hansen wrote: Graham Smith myotis...@gmail.com writes: I am exporting to HTML with a lnk to a pdf with instant opening in Firefox on a Mac. Originally, I had a description on the link, and as the manual says, in the browser, I get the description in the browser which opens the pdf when I click on it. But I want the image to appear without clicking on it, so I can print out the file with the images visible After reading the manual, I have edited the link to remove the description, but it still needs me to click on the link in the browser to open the pdf. I have now added file: to the front of the link and I still need to click on it to see the pdf in the browser. The link is now: [[file:/Users/graham/Dropbox/Jacobs/GQ3/Analysis/Graphics/Hazard1aBootsrappedMedianProbabilityPlot.pdf]] Which still works fine when I click on it, but doesn't automatically open. Can someone tell me what I am doing wrong. Many thanks, I was under the impression that only graphic files (PNG/JPG, etc) were inlined - I didn't think inlining a PDF was possible. Unfortunately, the right thing to do here depends on the LaTeX processor you use. If you use latex and then something like dvips to process to postscript, only .ps and .eps files can be inlined in LaTeX output. On the other hand, if you use pdflatex to process the files, only .jpg and .pdf files cab be included. I am not sure if HTML allows to *inline* pdf, probably not. Hmm, I welcome suggestions on a strategy for this. - Carsten -Bernt ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Announcing a new tutorial about org-mode, GTD using effort, column view and custom agenda commands
Charles, This looks really useful, thanks for posting it. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: Inline images in exported HTML
Carsten, 2009/1/14 Carsten Dominik domi...@science.uva.nl: On Jan 12, 2009, at 9:14 PM, Bernt Hansen wrote: Graham Smith myotis...@gmail.com writes: I am exporting to HTML with a lnk to a pdf with instant opening in Firefox on a Mac. Originally, I had a description on the link, and as the manual says, in the browser, I get the description in the browser which opens the pdf when I click on it. But I want the image to appear without clicking on it, so I can print out the file with the images visible After reading the manual, I have edited the link to remove the description, but it still needs me to click on the link in the browser to open the pdf. I have now added file: to the front of the link and I still need to click on it to see the pdf in the browser. The link is now: [[file:/Users/graham/Dropbox/Jacobs/GQ3/Analysis/Graphics/Hazard1aBootsrappedMedianProbabilityPlot.pdf]] Which still works fine when I click on it, but doesn't automatically open. Can someone tell me what I am doing wrong. Many thanks, I was under the impression that only graphic files (PNG/JPG, etc) were inlined - I didn't think inlining a PDF was possible. Unfortunately, the right thing to do here depends on the LaTeX processor you use. If you use latex and then something like dvips to process to postscript, only .ps and .eps files can be inlined in LaTeX output. On the other hand, if you use pdflatex to process the files, only .jpg and .pdf files cab be included. I am not sure if HTML allows to *inline* pdf, probably not. Hmm, I welcome suggestions on a strategy for this. It does seem that HTML doesn't allow inline PDFs. I think it worth while mentioning that I am looking for a quick preview of my document, that also shows the images. These are natively produced by R on the Mac as PDFs. I want to keep them in vector format for the final report, so a) don't really want to change the output from R, Or b) convert them to PNGs just to allow me a quick Preview, which would no longer be quick So the strategy is likely to be different depending on the needs of the final graphic to be part of finished document (eg a web page) or a workaround to give a quick preview. It has to be said that I can't get it to work via Latex either as the graphic component throws up errors during compile, If you ignore the errors and still preview the output, the text is all there, but no graphics. I haven't spent any time trying to sort out the errors yet. Graham Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: Inline images in exported HTML
Manish Saw this wonder a while ago http://tsdh.wordpress.com/2007/08/22/view-documents-pdfpostscriptdvi-inside-emacs/ Who knows someday doc-view.el's facilities can be called by Orgmode to achieve this. I don't know enough about emacs/Org-mode to comment but it says it is already part of Emacs. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: Inline images in exported HTML
Emacs23, I think. And I recall watching a video demonstration of it... it was quite slow. It converts the PDF pages into images for display. I see, thanks. Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: Inline images in exported HTML
Austin As another option, you might consider svg() from the RSvgDevice package. SVG images display in some modern web browsers. I didn't know about the SVG device, but it hasn't helped, unless its a firefox setting (which I can't find) PNGs appear inlne as they should, but not SVG (which from my gogling Firefox has supported since 2006). Thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Inline images in exported HTML
I am exporting to HTML with a lnk to a pdf with instant opening in Firefox on a Mac. Originally, I had a description on the link, and as the manual says, in the browser, I get the description in the browser which opens the pdf when I click on it. But I want the image to appear without clicking on it, so I can print out the file with the images visible After reading the manual, I have edited the link to remove the description, but it still needs me to click on the link in the browser to open the pdf. I have now added file: to the front of the link and I still need to click on it to see the pdf in the browser. The link is now: [[file:/Users/graham/Dropbox/Jacobs/GQ3/Analysis/Graphics/Hazard1aBootsrappedMedianProbabilityPlot.pdf]] Which still works fine when I click on it, but doesn't automatically open. Can someone tell me what I am doing wrong. Many thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Re: Inline images in exported HTML
Bernt, I was under the impression that only graphic files (PNG/JPG, etc) were inlined - I didn't think inlining a PDF was possible. Ah that would explain it then, maybe I need to go the Latex route, but I was looking for a quick route to get a printed output. Thank, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Clearing highlighting after a tag search
If I use C+c \ to search for a tag, it highlights the todo entries which have that tag. BUT how do I then clear the highlighting. Maybe its some generic Emacs command, becausue I can't find it in the org manual, so would appreciate some help. Thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Re: Clearing highlighting after a tag search
That was quick !! C-c C-c clears it. Many thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Writing in Org Mode - line wrap and tables
I am really enjoying Org Mode / Emacs but find the line wrap issue a bit irritating and wondering if I am missing an obvious solution. When I am just writing I use longlines mode, which is fine, but I also use a lot of tables, and the tables feature is great, but tables wrap unusably when longlines mode is enabled, which is OK when I don't need to refer to them, but difficult when I do. So, at the moment, I am toggling longlines mode off and on every few seconds/minutes to let me write. Is there a better way of dealing with this? Many thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Writing in Org Mode - line wrap and tables
Eric Have you tried `auto-fill-mode'? I have now :-) Thanks this seems to do the job Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] Re: Org-mode and ESS
Austin In my local git repo of the org sources I have a pretty nice setup for using R or S inside org-mode. I did see the original posts on this, and was interested in what you were doing, but its a bit beyond me at the moment while I am still trying to grasp how Emacs/org works. At the moment, as you surmised I am just looking to add a bit of structure to the notes I make while working on an analysis. But I may well come back to what you are doing, as I become more comfortable with Emacs. Thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
[Orgmode] Org-mode and ESS
Is any one using Org-mode with ESS. ESS seems to need a file with a *.R name to work, but it would be really useful to use Org-mode features to keep notes of comments and code, before sending to R, and of course to copy results back into an Org-Mode file from R. As a search here and a google hasn't thrown up anything obvious, I assume not, but I thought I would ask. Thanks, Graham ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
