Re: [O] Can't link to info nodes
Carsten Dominik writes: > I don't think this is needed, as this is in the default value for this > variable. So some way or another you have first *removed* this from > the variable. Maybe by setting it with `setq' in .emacs? You're right again, the module must have been added after I configured this variable it in my .emacs. Julien.
Re: [O] Can't link to info nodes
Carsten Dominik writes: > Take a look at the variable org-modules. Does it contain the symbol org-info? No it didn't. It's working now, thank you. Maybe there should be a mention of this dependency in the org manual ? Julien.
Re: [O] Is LaTeX pdf export that uses pgfSweave possible?
Mikhail Titov gmx.us> writes:
>
> Hello!
>
> First of all I’m not good at lisp as of now. I’d like to have an extra
> export option when I press C-c C-e that
> would create Rnw file instead of tex, pass it through pgfSweave
> in running R session.
Mikhail,
For vanilla Sweave, use the LaTeX style syntax (vs noweb style) to create an
Rtex file. Typing 'C-c C-e l' causes the following *.org to produce *.Rtex
which R CMD Sweave will turn to *.tex and R CMD pdflatex will turn into a
*.pdf.
Note this this will break ordinary R code export in latex, so be sure it
is not invoked when you want to go from *.org to *.pdf via 'C-c C-e d'
The trick is mainly to get the latex exporter to drop the verbatim wrapper.
---8<--->8
* Retooling org-babel to accept Rtex
Run this subtree once to start or put these blocks in your =~/.emacs=
Either way, run the elisp in this subtree once to start a session
** Nullify =\begin{verbatim}= ... =\end{verbatim}=
Under standard latex export, the code blocks get wrapped in verbatim
environments. To Sweave the resulting code as =*.Rtex= it is necessary
to unplug this behavior. 'Advising'
=org-export-format-source-code-or-example= like this has the desired
effect on =R= src blocks , but leaves others alone.
#+begin_src emacs-lisp :exports code
(defadvice
org-export-format-source-code-or-example
(around no-verbatim (lang code &optional opts indent caption))
"dont wrap R code in verbatim"
( let
(( old-verb-wrap org-export-latex-verbatim-wrap))
(if (equal lang "R") (setq org-export-latex-verbatim-wrap nil))
ad-do-it
(setq org-export-latex-verbatim-wrap old-verb-wrap)))
(ad-activate 'org-export-format-source-code-or-example)
#+end_src
#+results:
: org-export-format-source-code-or-example
** after processing convert =*.tex= to =*.Rtex=
Adding the commands to run Sweave and pdflatex to this hook function
is left as an exercise...
#+begin_src emacs-lisp :results silent
(add-hook
'org-export-latex-after-save-hook
(lambda ()
(rename-file (buffer-file-name)
(concat (file-name-sans-extension
(buffer-file-name)) ".Rtex") t )
))
#+end_src
* SRC BLOCKS
Two simple examples
** R graphics
A simple scatterplot. Here we want the verbatim omitted:
\begin{Scode}{fig=T}
#+begin_src R :eval never :exports code :results raw
plot(rnorm(10))
#+end_src
\end{Scode}
** shell script
Here we want to execute the shell script and pass it to the =*.Rtex= file
#+begin_src sh :eval t :results output verbatim :exports both
ls | wc
#+end_src
---8<--->8---
HTH,
Chuck
[rest deleted]
[O] vmin and probably vmax functions don't work
I'm getting identical numbers with vmean and vmode. I don't know if that information is correct but will check it with another system later this week. The same figures though also come up for vmin function and I know for a fact that isn't correct. That was after saving my org file and starting up emacs again to see if those figures would change and those figures did not change. The only functions from calc that may work are vmean and perhaps vsum but I've not tried vsum yet so won't make any more categorical statements about that yet. I modified the #+TBLFM: line with the original vmean formulas on it changing them first to vmode and later to vmin. And that's how I got these results. What I would have liked to have done would have been to calculate a mode and a min and max for each of the three figures I'm tracking then had that information show up at the bottom of the table. Something like: | stats: | systalic | diastalic | pulse | | mode | xxx | yyy | zzz | | min | xxx | yyy | zzz | | max | xxx | yyy | zzz | |- Though how to get a #+TBLFM: line to calculate for all of this and position correctly I'll have to figure out later. Jude "I love the Pope, I love seeing him in his Pope-Mobile, his three feet of bullet proof plexi-glass. That's faith in action folks! You know he's got God on his side." ~ Bill Hicks
Re: [O] org-babel ruby 1.8 and 1.9
Hi Steve, You should be able to customize the value of the org-babel-ruby-command variable to control what external executable is called by ruby code blocks. The default value of that variable is simply "ruby" but presumably setting that variable to the name of the ruby 1.9 executable should work. Note that for code blocks which use a session (see the session header argument for more information) all execution is handled by inf-ruby, and the inf-ruby package controls which executable is used. Hope this helps Best -- Eric Steve Harman writes: > Hello, > > On my mac, I have rvm installed with ruby 1.9.2 being default. > On the terminal, if I execute ruby, it is always 1.9.2 version. > However, the ruby ran by org-babel is 1.8 version. > How can I make the ruby code blocks in my org files > executed by 1.9? > > Since I am new to Emacs, I would appreciate your help. > I found org-mode and org-babel extremely helpful in preparing > course notes. That's why, in fact, I switched to Emacs. > In an attempt to solve the above problem, I installed rvm.el > and put it in my init.el right before loading the org-babel languages. > > (add-to-list 'load-path "/Users/stvharman/.emacs.d/lisp/rvm") > (require 'rvm) > (rvm-use-default) ;; use rvm’s default ruby for the current Emacs session > > (org-babel-do-load-languages > 'org-babel-load-languages > '( >(R . t) >(ruby . t) > )) > > Thank you in advance. > > Have a nice weekend (and week ahead), > > Steve -- Eric Schulte http://cs.unm.edu/~eschulte/
[O] org-babel ruby 1.8 and 1.9
Hello, On my mac, I have rvm installed with ruby 1.9.2 being default. On the terminal, if I execute ruby, it is always 1.9.2 version. However, the ruby ran by org-babel is 1.8 version. How can I make the ruby code blocks in my org files executed by 1.9? Since I am new to Emacs, I would appreciate your help. I found org-mode and org-babel extremely helpful in preparing course notes. That's why, in fact, I switched to Emacs. In an attempt to solve the above problem, I installed rvm.el and put it in my init.el right before loading the org-babel languages. (add-to-list 'load-path "/Users/stvharman/.emacs.d/lisp/rvm") (require 'rvm) (rvm-use-default) ;; use rvm’s default ruby for the current Emacs session (org-babel-do-load-languages 'org-babel-load-languages '( (R . t) (ruby . t) )) Thank you in advance. Have a nice weekend (and week ahead), Steve
Re: [O] Overall organization/setup for org mode: Projects and Tasks
Max: This is an awesome, thought provoking "infodump." Full of ideas that I can use. Thank you, Alan On Sat, Sep 17, 2011 at 12:32 PM, Max Mikhanosha wrote: > Below is infodump on how I use org-mode personally.. You are welcome > to poach ideas. Generally I'm pretty happy with my setup, and do not > plan to do any radical changes to it. Wall of text warning. > > 1. Org file per project, with single top level heading.. Each file has > a #+TAGS cookie that assigns default tags. > > Such project files would have more then one level heading, usually > when project logically splits into sub-projects > > Example: Emacs.org, top level headings. This one has unusually large > amount of top level headings. > > - Emacs > - Org-Mode > - Paredit-Magic > - C-Paredit > - Cycle-buffer > > A few special org files which are not projects, one is called Assorted > Accounts for recording acc/pass/email info on various accounts, and > one is called Assorted Info for basically a knowledge base of anything > that is not a TODO. The way I access these are through C-c / search, > seems to work very well.. Another "special" project is Finances.org > and has everything to do with investments, encrypted entries for all > financial accounts, all recurring TODOS for bills, or portfolio > review, investment ideas, spreadsheets etc. > > Capture often. Write down just enough so you can re-construct idea > later.. If you often wondering "wtf did I meant by that, then you are > not writing down enough.. If possible write/assign yourself a shortcut > key to your window manager so you can capture a short sentence with 1 > key stroke even when in the other programs. > > If it takes less then 1 minute to do what you are capturing, > especially if it involves emacs customization, do it right there, and > mark it it done, or C-c C-k it.. I usually mark it done and C-c C-c > it. > > All captures go to Mind-Sweep.org, under top level heading.. Every few > days (once I have 10-20 items) in there, I go ahead and refile them to > appropriate projects, assigning priorities and efforts if these are > not there. > > Have two agenda keys to show agenda sorted by priority, and by effort > up..I use block agenda that shows day agenda first, then all NEXT > items, then all TODO items. > > Learn to use / key in agenda to quickly filter out stuff by tags.. For > me /e switches agenda to filter out be :emacs tag. > > Have areas of focus. The mind is like a process working set. If I had > been working on some emacs problem and have Emacs "booted up" in my > brain, it takes a while to switch reboot my brain into "Looking at my > investments mode". > > So as long as I'm working on lets say fixing something with paredit, > you can just as well knock out some other emacs things.. > > That is where agenda sorted by effort comes up. Since I'm hacking on > my emacs setup anyway, I bring up my effort-up agenda view, filter by > "emacs" and just knock out every item estimated at 10 minutes or > less. Sometimes knocking out up to 20 or so small TODO's in 2 hour > burst, taking care of everything that was annoying me with Emacs in > last 2 weeks. > > Assign priorities to prune aggressively. If you have that #A item > starting you for last 5 days, its not #A.. Demote it until it sits in > the #F pile way down in agenda. > > Temporary move projects out of agenda. Lets say you have a well > defined project and a bunch of nicely prioritized items, some of them > #A (which they are in the context of that project) but right now you > just don't feel like working on that project. > > Starting at these #A items on top of your agenda every day without > starting to work on them, may be demoralizing. Way I deal with it, is > that I have "hold" tag, which I put on top level headings of the > projects, and its excluded from my agenda by default... If you have > not touched a project for 2 weeks, it probably should be on > hold.. When you bored and looking for things to work on, they you can > use agenda view without filtering out the "hold" projects, and see if > you can get a start on some of them.. This way I have only 3-4 projects > that are "in focus" rather then 30.. > > Review low priority items once a week, if you remember reviewing that > item last few weeks, just delete it.. If you are type of person who > can't let go, move it to MAYBE state. > > If something computer related annoys you and interrupts your work flow > often, it should be #A item and needs to be fixed. Ie if you Emacs > session consists of 50% beeps, you need to fix something in your > setup.. If you dread doing something because its just too much effort, > you need to automate/rethink/change that process. > > Don't burn out.. The bodybuilders and athletes have it right, you have > to cycle. If you go 100% all the time, generating ideas and knocking > out TODO's like a robot, you'll burn out. Take it easy for 1 week each > month. Does not mean eat pizza and party every day, but ba
Re: [O] FYI: Org mode testing framework, Emacs 23 and 22
At Sat, 17 Sep 2011 14:56:09 -0600, Eric Schulte wrote: > > Hi David, > > > > > For Emacs22 the only thing we need from simple.el is the definition of > > special-mode; going to factor it out and trim it to Emacs22. > > > > Sounds great, thanks. > > > > > With HEAD at dbf0e6d5bcbe94c8ee57d68889d3c25bf9cdef55 and a fix for > > the check for featurep 'org (37db5deea5ef75186bb7413b196fa0c96e5bdfb9) > > I got: > > > > Thanks for compiling this information. > > > > > > > Selector: "\\(org\\|ob\\)" > > Passed: 99 > > Failed: 10 (10 unexpected) > > Total: 109/109 > > > > Started at: 2011-09-16 06:56:59+0200 > > Finished. > > Finished at: 2011-09-16 06:57:04+0200 > > > > ..FF...FF..F.F...FF.F..F. > > > > F ob-fortran/list-var > > Test real array input > > (void-function characterp) > > > > F ob-fortran/list-var-from-table > > Test real array from a table > > (void-function characterp) > > > > I've replaced the use of `characterp' in ob-fortran with integerp, which > should be backwards-compatible with emacs22. > > > > > F test-ob-exp/org-babel-exp-src-blocks/w-no-file > > Testing export from buffers which are not visiting any file. > > (wrong-type-argument stringp nil) > > > > F test-ob-exp/org-babel-exp-src-blocks/w-no-headers > > Testing export without any headlines in the org-mode file. > > (wrong-type-argument stringp nil) > > > > F test-ob-lob/export-lob-lines > > Test the export of a variety of library babel call lines. > > (wrong-type-argument stringp nil) > > > > I have no idea what could be going wrong with these executions, would it > be difficult to generate backtraces for these failures? > > > > > F test-ob-sh/dont-error-on-empty-results > > Was throwing an elisp error when shell blocks threw errors and > > (void-function org-babel-execute:sh) > > > > F test-org-babel/inline-src-blocks > > (error "No org-babel-execute function for sh!") > > > > F test-org-babel/inline-src_blk-default-results-replace-line-1 > > (error "No org-babel-execute function for sh!") > > > > It looks like you need to load ob-sh.el. > > > > > F test-org-exp/stripping-commas > > Test the stripping of commas from within blocks during export. > > (wrong-type-argument stringp nil) > > > > F test-org/org-link-unescape-ascii-extended-char > > Unescape old style percent escaped character. > > (ert-test-failed > > ((should > >(string= "àâçèéêîôùû" > > (org-link-unescape "%E0%E2%E7%E8%E9%EA%EE%F4%F9%FB"))) > > :form > > (string= "àâçèéêîôùû" "\340\342\347\350\351\352\356\364\371\373") > > :value nil)) > > > > Hmm, I don't know anything about possible differences in string handling > between Emacs22 and more modern Emacsen, but I wouldn't be surprised if > support for accented characters was less complete in Emacs22. Perhaps > we should just skip this test on Emacs22. Nope, this test is fixed. Had to explicitely tell Emacs that the expected output string is latin-1; i.e. the input is extended ASCII which is covered by latin-1 encoding. The test failed because org-link-unescape returned the raw byte sequence. I am aware that there might be a problem with opening links that contain extended ASCII characters (=Org's old escaping choice) and I'm going to test this next. The test is fine, though. The expected output is a latin-1 encoded string. Best, -- David -- OpenPGP... 0x99ADB83B5A4478E6 Jabber dmj...@jabber.org Email. dm...@ictsoc.de pgpNWtYccCf5Q.pgp Description: PGP signature
Re: [O] Can't link to info nodes
On 18.9.2011, at 15:52, Julien Cubizolles wrote: > Carsten Dominik writes: >> Take a look at the variable org-modules. Does it contain the symbol >> org-info? > No it didn't. It's working now, thank you. Maybe there should be a > mention of this dependency in the org manual ? I don't think this is needed, as this is in the default value for this variable. So some way or another you have first *removed* this from the variable. Maybe by setting it with `setq' in .emacs? - Carsten
Re: [O] Exporting subtree to LaTeX?
Thanks! That was what I was looking for. Best regards, Johan On Sun, Sep 18, 2011 at 1:28 PM, Bernt Hansen wrote: > Johan Ekh writes: > > > Hi all, > > is it possible to export a subtree to LaTeX, i.e. not the entire > > org-file? > > I just want a latex file that I later include manually in an existing > > LaTeX document. > > > > Best regards, > > Johan > > Select the subtree first with C-c @ and then export normally. > > Regards, > Bernt >
Re: [O] Exporting subtree to LaTeX?
Johan Ekh writes: > Hi all, > is it possible to export a subtree to LaTeX, i.e. not the entire > org-file? > I just want a latex file that I later include manually in an existing > LaTeX document. > > Best regards, > Johan Select the subtree first with C-c @ and then export normally. Regards, Bernt
Re: [O] Can't link to info nodes
On 18.9.2011, at 13:04, Julien Cubizolles wrote: > > I cannot link to info nodes. > > * If I type a link like : > > info:org.info#External%20links, I get "No match- Create this as a new > heading" > > * If I do C-c l while visiting a info buffer, I get > "Cannot link to a buffer that is not visiting a file" > > What am I doing wrong ? This works without any problems for me. Take a look at the variable org-modules. Does it contain the symbol org-info? If not, customize the variable and make sure to tick this module on. - Carsten > > Julien. > >
[O] Can't link to info nodes
I cannot link to info nodes. * If I type a link like : info:org.info#External%20links, I get "No match- Create this as a new heading" * If I do C-c l while visiting a info buffer, I get "Cannot link to a buffer that is not visiting a file" What am I doing wrong ? Julien.
Re: [O] FYI: Org mode testing framework, Emacs 23 and 22
At Sat, 17 Sep 2011 14:56:09 -0600, Eric Schulte wrote: > > Hi David, > > > > > For Emacs22 the only thing we need from simple.el is the definition of > > special-mode; going to factor it out and trim it to Emacs22. > > > > Sounds great, thanks. > > > > > With HEAD at dbf0e6d5bcbe94c8ee57d68889d3c25bf9cdef55 and a fix for > > the check for featurep 'org (37db5deea5ef75186bb7413b196fa0c96e5bdfb9) > > I got: > > > > Thanks for compiling this information. > > > > > > > Selector: "\\(org\\|ob\\)" > > Passed: 99 > > Failed: 10 (10 unexpected) > > Total: 109/109 > > > > Started at: 2011-09-16 06:56:59+0200 > > Finished. > > Finished at: 2011-09-16 06:57:04+0200 > > > > ..FF...FF..F.F...FF.F..F. > > > > F ob-fortran/list-var > > Test real array input > > (void-function characterp) > > > > F ob-fortran/list-var-from-table > > Test real array from a table > > (void-function characterp) > > > > I've replaced the use of `characterp' in ob-fortran with integerp, which > should be backwards-compatible with emacs22. > > > > > F test-ob-exp/org-babel-exp-src-blocks/w-no-file > > Testing export from buffers which are not visiting any file. > > (wrong-type-argument stringp nil) > > > > F test-ob-exp/org-babel-exp-src-blocks/w-no-headers > > Testing export without any headlines in the org-mode file. > > (wrong-type-argument stringp nil) > > > > F test-ob-lob/export-lob-lines > > Test the export of a variety of library babel call lines. > > (wrong-type-argument stringp nil) > > > > I have no idea what could be going wrong with these executions, would it > be difficult to generate backtraces for these failures? > > > > > F test-ob-sh/dont-error-on-empty-results > > Was throwing an elisp error when shell blocks threw errors and > > (void-function org-babel-execute:sh) > > > > F test-org-babel/inline-src-blocks > > (error "No org-babel-execute function for sh!") > > > > F test-org-babel/inline-src_blk-default-results-replace-line-1 > > (error "No org-babel-execute function for sh!") > > > > It looks like you need to load ob-sh.el. > > > > > F test-org-exp/stripping-commas > > Test the stripping of commas from within blocks during export. > > (wrong-type-argument stringp nil) And last not least: In this case it is `org-todo-line-regexp' bound to nil, too. > > > > F test-org/org-link-unescape-ascii-extended-char > > Unescape old style percent escaped character. > > (ert-test-failed > > ((should > >(string= "àâçèéêîôùû" > > (org-link-unescape "%E0%E2%E7%E8%E9%EA%EE%F4%F9%FB"))) > > :form > > (string= "àâçèéêîôùû" "\340\342\347\350\351\352\356\364\371\373") > > :value nil)) > > > > Hmm, I don't know anything about possible differences in string handling > between Emacs22 and more modern Emacsen, but I wouldn't be surprised if > support for accented characters was less complete in Emacs22. Perhaps > we should just skip this test on Emacs22. I'll dig into the link escaping failure. Best, -- David -- OpenPGP... 0x99ADB83B5A4478E6 Jabber dmj...@jabber.org Email. dm...@ictsoc.de pgp068gV55Vhj.pgp Description: PGP signature
Re: [O] FYI: Org mode testing framework, Emacs 23 and 22
At Sat, 17 Sep 2011 14:56:09 -0600, Eric Schulte wrote: > > > > > F test-ob-sh/dont-error-on-empty-results > > Was throwing an elisp error when shell blocks threw errors and > > (void-function org-babel-execute:sh) > > > > F test-org-babel/inline-src-blocks > > (error "No org-babel-execute function for sh!") > > > > F test-org-babel/inline-src_blk-default-results-replace-line-1 > > (error "No org-babel-execute function for sh!") > > > > It looks like you need to load ob-sh.el. Yes, (require 'ob-sh) is sufficient to remove these three from the list of failing tests. Best, -- David -- OpenPGP... 0x99ADB83B5A4478E6 Jabber dmj...@jabber.org Email. dm...@ictsoc.de pgpGa49QTgzBi.pgp Description: PGP signature
Re: [O] Exporting subtree to LaTeX?
Johan Ekh writes: > Hi all, > is it possible to export a subtree to LaTeX, i.e. not the entire > org-file? > I just want a latex file that I later include manually in an existing > LaTeX document. Hint: Just hit C-c C-e and see what is on offer. > Best regards, > Johan > > --
[O] Exporting subtree to LaTeX?
Hi all, is it possible to export a subtree to LaTeX, i.e. not the entire org-file? I just want a latex file that I later include manually in an existing LaTeX document. Best regards, Johan
