Re: Please help by becoming a maintainer for an Org Babel file

[Tyler Smith]

Bastien  writes:

we are looking for more maintainers of individual Org Babel 
files.




Hi,

I can volunteer to maintain ob-awk.el. I've signed my assignment 
form with FSF, and returned it to them this evening. I'll let you 
know when I'm official.


I have an account on code.orgmode.org already, but I think I only 
have access to worg.


I may also be able to maintain ob-shell.el. It is a bit more 
complex than ob-awk.el, so I'd like to hold off until I understand 
a bit better how ob works in general.


Is there any documentation for ob other than the source code?

Best,

Tyler

--
Tyler Smith
plantarum.ca

org-export-latex-packages-alist vs org-latex-packages-alist

[Tyler Smith]

Hello,

Can someone confirm if

 `org-export-latex-packages-alist` and 
 `org-export-latex-listings-langs`


are obsolete versions of

 `org-latex-packages-alist` and `org-listings-langs`?

I've had the former in my config for years, and today noticed that 
they no longer appear in the org source code. I failed to find any 
reference to this change in the documentation, so perhaps I've 
missed something? Can I just swap out the former and replace them 
with the latter?


I ran into some strange problems today that were due, in part, to 
some of my config not getting applied as I expected.


Best,

Tyler

--
Tyler Smith
plantarum.ca

running code with sessions on remote computers

[Tyler Smith]

Hi,

I am trying to run some code on a remote machine. This is R code, 
and uses the `:session` argument so that all blocks in the file 
use the same session. This works fine when I ssh into the machine 
and open Emacs running on that machine. However, when I use tramp 
from my local machine, everything works, except that the session 
argument is ignored. The top of my file looks like:


```

#+PROPERTY: header-args:R  :session *R-sdm*

* Current code
#+begin_src R setup :session *R-sdm*
 options(java.parameters = "-Xmx25g")
 library(raster)
 library(dismo)
#+end_src


```

I normally set the `:session` argument only in the file 
`#+PROPERTY:` line, but here I added it to the code block header 
as well, after it didn't work without it. It didn't make a 
difference though.


What I see when I evaluate the code in this block: I'm prompted 
for a directory to start in, and the new R process is started 
there, with the name `*R-2*`. If I evaluate another code block in 
the same file, I'm again prompted for the directory, and a new 
process is started there, with the name `*R-3*`. Note that there 
is no session named *R* running on the remote machine, although 
there is one running on my local machine.


What I expect is to have the R session names `*R-sdm*`, and to 
have the same session shared by all code blocks in this file.


My questions:
- is it possible to run code blocks in a session on a remote 
 machine?
- if it is, how can I approach sorting this out - is it an orgmode 
 problem, a tramp problem, or an ESS problem?


Thanks!

Tyler

--
Tyler Smith
plantarum.ca

Re: default units for graphics in R code blocks

[Tyler Smith]

Yes, org info is spread wide and thin, and it's hard to tell which
source is the most recent/accurate. I think it might be useful to
consolidate and delete as much as possible, but that's going to be a lot
of work.

The existence of a page called "Library of Babel",
https://orgmode.org/worg/library-of-babel.html that doesn't actually
refer to org-babel seems especially misleading!

In any case, I updated ob-doc-R with the correct info.

Best,

Tyler


John Hendy writes:

> Bummer, that does indeed read pretty straightforwardly about inches.
> Sorry about that.
>
> Thanks for your efforts. I find org documentation challenging at
> times, and am still not clear on worg vs. org. I believe I've asked on
> this list before why those pages exist, as this seems like it should
> be in the org official docs vs. in a sort of tutorial site. It makes
> it tough as you can't find certain header args in the org docs; you
> have to kind of know what you're looking for, or at least that the
> header arg is *only* for, say, R, and not for anything else.
>
> Anyway, thanks for contributing!
>
> Best,
> John
>
> On Mon, Mar 30, 2020 at 11:58 AM Tyler Smith  wrote:
>>
>> John Hendy writes:
>>
>> >
>> > Best to cite exactly which article you're referring to. Trying to look
>> > myself, for example, found me this as the only worg hit from googling
>> > "worg R plotting":
>> > - https://orgmode.org/worg/org-tutorials/org-R/org-R.html
>> > """
>> > Output options
>> > height:1000set height of graphical output in (pixels for png, jpeg,
>> > bmp, tiff; default 480) / (inches for pdf, ps; default 7)
>> > width:1000set width of graphical output in pixels (default 480 for png)
>> > """
>> >
>> The article I was referring to is:
>>
>> https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html
>>
>> The tutorial you found suggests the corrections needed in the one I
>> found; I can do that now!
>>
>> Tyler
>>
>>
>> > It seems that aligns with my recollection, but may very well differ
>> > from the article you found. Thanks for any edits/corrections you make!
>> >
>> > Best regards,
>> > John
>> >
>> >>
>> >> Best,
>> >>
>> >> Tyler
>> >>
>> >>
>> >>
>> >> --
>> >> Tyler Smith
>> >> http://plantarum.ca
>> >>
>>
>>
>> --
>> Tyler Smith
>> http://plantarum.ca


--
Tyler Smith
http://plantarum.ca

Re: default units for graphics in R code blocks

[Tyler Smith]

John Hendy writes:

>
> Best to cite exactly which article you're referring to. Trying to look
> myself, for example, found me this as the only worg hit from googling
> "worg R plotting":
> - https://orgmode.org/worg/org-tutorials/org-R/org-R.html
> """
> Output options
> height:1000set height of graphical output in (pixels for png, jpeg,
> bmp, tiff; default 480) / (inches for pdf, ps; default 7)
> width:1000set width of graphical output in pixels (default 480 for png)
> """
>
The article I was referring to is:

https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html

The tutorial you found suggests the corrections needed in the one I
found; I can do that now!

Tyler


> It seems that aligns with my recollection, but may very well differ
> from the article you found. Thanks for any edits/corrections you make!
>
> Best regards,
> John
>
>>
>> Best,
>>
>> Tyler
>>
>>
>>
>> --
>> Tyler Smith
>> http://plantarum.ca
>>


-- 
Tyler Smith
http://plantarum.ca

default units for graphics in R code blocks

[Tyler Smith]

Hi,

The worg documentation for R code indicates the default units for
graphics output is 'in', inches. However, when I try the following:

#+begin_src R :results file graphics :file ca.jpg :width 8 :height 11
  plot(1:10)
#+end_src

I get an error noting the margins are too large. If I change the width
and height arguments to 800, it works just fine, and the resulting image
is pretty small.

I can also get a working image by specifying units as in and res as 100.

I conclude from this that the default units are actually pixels? Is that
correct? If so I can update the docs.

Best,

Tyler



-- 
Tyler Smith
http://plantarum.ca

Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]

[Tyler Smith]

You're welcome! I think the examples could use refreshing/restructuring,  but 
I'm not sure when I'll have time to get to that.

Best,

Tyler 

-- 
plantarum.ca

On Mon, Feb 17, 2020, at 12:40 PM, Jack Kamm wrote:
> Hi Tyler,
> 
> >> The documentation for ob-R is now incorrect:
> >>
> >>   https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html
> >
> > Yes, also that page could use some other updates, e.g. there are some
> > dead links in there.
> 
> Just saw that you updated the docs a few days ago. Thanks for taking
> care of this!
> 
> Best,
> Jack
>

what happened to org-man?

[Tyler Smith]

Hi,

What happend to org-man? I think the file was deleted from org mode, but
I don't see any explanation in the news file. I think this qualifies as
an incompatible change, at least for those of us that used org-man?

Best,

Tyler

-- 
Tyler Smith
http://plantarum.ca

can't sign in to code.orgmode.org

[Tyler Smith]

Hello,

I am trying to set up an account with code.orgmode.org. I have already done 
this, but when I try to sign in, I get an error about incorrect username or 
password. I have clicked the link to send a password reset several times this 
morning, but no email has shown up in my account, or in my spam folder.

Is code.orgmode.org functioning properly, and if so, how do I log in?

Best,

Tyler

-- 
plantarum.ca

Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]

[Tyler Smith]

On Mon, Jan 27, 2020, at 12:29 PM, Jack Kamm wrote:
> 
> It should now be ":results graphics file". This behavior changed in Org
> 9.3, see https://orgmode.org/Changes.html (:file header argument no
> longer assume "file" :results).
>

That fixes it, thanks!

The documentation for ob-R is now incorrect:

  https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html

Is the rationale explained anywhere? After a bit of poking around, it looks 
like using the `:file` flag without a `file` argument to results doesn't do 
anything (no file is created), nor does the reverse. That is, unless you use 
both the `file` argument and the `:file` option, nothing happens. Is there a 
situation where you can use `:file` to do something that doesn't require a 
`file` argument to `:results`?

Best,

Tyler  

-- 
plantarum.ca

Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]

[Tyler Smith]

Hi Jeremie,

I tried with `:results output graphics`, and with the file as jpg, and also as 
pdf. In all cases I still get the same result : no link is inserted.

I first noticed this with the org version that was released at the end of 
December, and confirmed that the problem was still present in the latest 
version released today. I'm pretty confident that this worked prior to the 
December release.

Thanks,

Tyler

--
plantarum.ca



On Mon, Jan 27, 2020, at 11:27 AM, Jeremie wrote:
> Hello,
> 
> I don't have the lastest.version of org-mode so i can't confirm.
> 
> 
> But could you try with the option 
> 
> :results output graphics :file test.pdf
> 
> HTH,
> Jeremie
> 
> 
> On January 27, 2020 5:13:20 PM GMT+01:00, Tyler Smith  
> wrote:
>> To reproduce:
>> 
>> 1. Start from `emacs -Q`
>> 
>> 2. open the following org file:
>> 
>> ```
>> #+BEGIN_SRC elisp setup
>> (require 'package)
>> (setq package-load-list
>>   '((org-plus-contrib t)
>>  (ess t)
>>  (julia-mode t)))
>> (package-initialize)
>> (require 'org)
>> (require 'ess)
>> 
>> (org-babel-do-load-languages
>>  'org-babel-load-languages
>>  '((emacs-lisp . t)
>>(R . t)
>>(shell . t)))
>> #+END_SRC
>> 
>> #+RESULTS:
>> 
>> #+begin_src R :results graphics :file test.jpg
>> plot (1:10)
>> #+end_src
>> ```
>> 
>> 3. Evaluate the first code block (C-c C-c) to load ess and setup babel to 
>> evaluate R code blocks
>> 
>> 4.  Evaluate the second code block.
>> 
>> What I expect: 
>> 
>> A `#+RESULTS:` block is inserted, with a link to the file test.jpg;
>> 
>> What happens instead:
>> 
>> A message appears in the minibuffer:   'Code block produced no output'.
>> 
>> This worked previously. I'm not sure when it broke - sometime in the last 
>> two months I think, as I demoed this feature for colleagues in November.
>> 
>> Emacs state provided below.
>> 
>> Best,
>> 
>> Tyler
>> 
>> Emacs  : GNU Emacs 28.0.50 (build 2, x86_64-pc-linux-gnu, GTK+ Version 
>> 3.22.30)
>>  of 2020-01-02
>> Package: Org mode version 9.3 (release_9.3 @ 
>> /home/smithty/.emacs.d/elpa/org-plus-contrib-20200127/)
>> 
>> current state:(setq
>>  org-src-mode-hook '(org-src-babel-configure-edit-buffer 
>> org-src-mode-configure-edit-buffer)
>>  org-link-shell-confirm-function 'yes-or-no-p
>>  org-metadown-hook '(org-babel-pop-to-session-maybe)
>>  org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
>>  org-mode-hook '(org-eldoc-load
>>   #[0 "\300\301\302\303\304$\207"
>> [add-hook change-major-mode-hook org-show-all append local] 
>> 5]
>>   #[0 "\300\301\302\303\304$\207"
>> [add-hook change-major-mode-hook org-babel-show-result-all 
>> append local] 5]
>>   org-babel-result-hide-spec org-babel-hide-all-hashes)
>>  org-archive-hook '(org-attach-archive-delete-maybe)
>>  org-confirm-elisp-link-function 'yes-or-no-p
>>  org-agenda-before-write-hook '(org-agenda-add-entry-text)
>>  org-metaup-hook '(org-babel-load-in-session-maybe)
>>  org-bibtex-headline-format-function #[257 "\300
\236A\207" [:title] 3 
>> "\n\n(fn ENTRY)"]
>>  org-babel-pre-tangle-hook '(save-buffer)
>>  org-tab-first-hook '(org-babel-hide-result-toggle-maybe 
>> org-babel-header-arg-expand)
>>  org-babel-load-languages '((emacs-lisp . t) (R . t) (shell . t))
>>  org-src-lang-modes '(("redis" . redis) ("php" . php) ("arduino" . arduino) 
>> ("C" . c) ("C++" . c++)
>>("asymptote" . asy) ("bash" . sh) ("beamer" . latex) 
>> ("calc" . fundamental)
>>("cpp" . c++) ("ditaa" . artist) ("dot" . fundamental) 
>> ("elisp" . emacs-lisp)
>>("ocaml" . tuareg) ("screen" . shell-script) ("shell" . 
>> sh) ("sqlite" . sql))
>>  org-occur-hook '(org-first-headline-recenter)
>>  org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-show-empty-lines
>>org-optimize-window-after-visibility-change)
>>  org-speed-command-hook '(org-speed-command-activate 
>> org-babel-speed-command-activate)
>>  org-confirm-shell-link-function 'yes-or-no-p
>>  org-link-parameters '(("attachment" :follow org-attach-open-link :export 
>>

Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]

[Tyler Smith]

To reproduce:

1. Start from `emacs -Q`

2. open the following org file:

```
#+BEGIN_SRC elisp setup
(require 'package)
(setq package-load-list
  '((org-plus-contrib t)
(ess t)
(julia-mode t)))
(package-initialize)
(require 'org)
(require 'ess)

(org-babel-do-load-languages
 'org-babel-load-languages
 '((emacs-lisp . t)
   (R . t)
   (shell . t)))
#+END_SRC

#+RESULTS:

#+begin_src R :results graphics :file test.jpg
plot (1:10)
#+end_src
```

3. Evaluate the first code block (C-c C-c) to load ess and setup babel to 
evaluate R code blocks

4.  Evaluate the second code block.

What I expect: 

A `#+RESULTS:` block is inserted, with a link to the file test.jpg;

What happens instead:

A message appears in the minibuffer:   'Code block produced no output'.

This worked previously. I'm not sure when it broke - sometime in the last two 
months I think, as I demoed this feature for colleagues in November.

Emacs state provided below.

Best,

Tyler

Emacs  : GNU Emacs 28.0.50 (build 2, x86_64-pc-linux-gnu, GTK+ Version 3.22.30)
 of 2020-01-02
Package: Org mode version 9.3 (release_9.3 @ 
/home/smithty/.emacs.d/elpa/org-plus-contrib-20200127/)

current state:
==
(setq
 org-src-mode-hook '(org-src-babel-configure-edit-buffer 
org-src-mode-configure-edit-buffer)
 org-link-shell-confirm-function 'yes-or-no-p
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-mode-hook '(org-eldoc-load
 #[0 "\300\301\302\303\304$\207"
   [add-hook change-major-mode-hook org-show-all append local] 
5]
 #[0 "\300\301\302\303\304$\207"
   [add-hook change-major-mode-hook org-babel-show-result-all 
append local] 5]
 org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-bibtex-headline-format-function #[257 "\300
\236A\207" [:title] 3 "\n\n(fn 
ENTRY)"]
 org-babel-pre-tangle-hook '(save-buffer)
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe 
org-babel-header-arg-expand)
 org-babel-load-languages '((emacs-lisp . t) (R . t) (shell . t))
 org-src-lang-modes '(("redis" . redis) ("php" . php) ("arduino" . arduino) 
("C" . c) ("C++" . c++)
  ("asymptote" . asy) ("bash" . sh) ("beamer" . latex) 
("calc" . fundamental)
  ("cpp" . c++) ("ditaa" . artist) ("dot" . fundamental) 
("elisp" . emacs-lisp)
  ("ocaml" . tuareg) ("screen" . shell-script) ("shell" . 
sh) ("sqlite" . sql))
 org-occur-hook '(org-first-headline-recenter)
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-show-empty-lines
  org-optimize-window-after-visibility-change)
 org-speed-command-hook '(org-speed-command-activate 
org-babel-speed-command-activate)
 org-confirm-shell-link-function 'yes-or-no-p
 org-link-parameters '(("attachment" :follow org-attach-open-link :export 
org-attach-export-link
:complete org-attach-complete-link)
   ("id" :follow org-id-open) ("eww" :follow eww :store 
org-eww-store-link)
   ("rmail" :follow org-rmail-open :store 
org-rmail-store-link)
   ("mhe" :follow org-mhe-open :store org-mhe-store-link)
   ("irc" :follow org-irc-visit :store org-irc-store-link 
:export org-irc-export)
   ("info" :follow org-info-open :export org-info-export 
:store
org-info-store-link)
   ("gnus" :follow org-gnus-open :store org-gnus-store-link)
   ("docview" :follow org-docview-open :export 
org-docview-export :store
org-docview-store-link)
   ("bibtex" :follow org-bibtex-open :store 
org-bibtex-store-link)
   ("bbdb" :follow org-bbdb-open :export org-bbdb-export 
:complete
org-bbdb-complete-link :store org-bbdb-store-link)
   ("w3m" :store org-w3m-store-link) ("file+sys") 
("file+emacs")
   ("shell" :follow org-link--open-shell)
   ("news" :follow
#[257 "\301\300\302Q!\207" ["news" browse-url ":"] 5 
"\n\n(fn URL)"])
   ("mailto" :follow
#[257 "\301\300\302Q!\207" ["mailto" browse-url ":"] 5 
"\n\n(fn URL)"])
   ("https" :follow
#[257 "\301\300\302Q!\207" ["https" browse-url ":"] 5 
"\n\n(fn URL)"])
   ("http" :follow
#[257 "\301\300\302Q!\207" ["http" browse-url ":"] 5 
"\n\n(fn URL)"])
   ("ftp" :follow
#[257 "\301\300\302Q!\207" ["ftp" browse-url ":"] 5 

Re: [O] default value for org-capture-templates

[Tyler Smith]

On Sat, Dec 29, 2018, at 8:41 AM, Nicolas Goaziou wrote:
> "Tyler Smith"  writes:
> 
> > I can put together a patch to do this if I haven't overlooked
> > a problem this would create.
> 
> I think you can go ahead. Thank you.
> 
> Have you signed FSF papers?
> 

Not yet. I just sent the request to ass...@gnu.org.

I'll put the patch together this week.

Best,

Tyler

[O] default value for org-capture-templates

[Tyler Smith]

Hi,

A question came up on StackOverflow asking about how to use the default capture 
template (`Task`) in combination with user-defined templates: 
https://emacs.stackexchange.com/questions/46794/where-is-default-org-mode-capture-template-for-tasks-located

The default Task template is actually stored in the function 
`org-capture-select-template`. This is a bit surprising, and requires the user 
to manually transfer it to the the variable `org-capture-templates` if they 
want to keep it as one of their options. 

Is there a reason not to set this built-in `Task` template as the default value 
of `org-capture-templates`? That would provide the user with a transparent way 
of keeping it as an option, modifying it, or removing it, as they prefer, 
through the usual customize interface.

I can put together a patch to do this if I haven't overlooked a problem this 
would create.

Best,

Tyler 

-- 
plantarum.ca

Re: [O] R output with session polluted with ascii color codes

[Tyler Smith]

On Fri, Mar 16, 2018, at 2:55 PM, William Denton wrote:
> On 16 March 2018, Tyler Smith wrote:
> 
> Anyway, I tried again, and there was still no problem in Emacs.  That made me 
> wonder if the difference was in R.  When I run "as_tibble(iris)" in the R 
> console in a terminal I don't get the ASCII colour codes, so maybe that's 
> where 
> the difference lies?  I'm running R 3.4.2, compiled from source, on Ubuntu 
> 17.10.

I've tried this as well, outside of Emacs. For me, it depends on which terminal 
emulator I use. xterm displays the colours, while gnome terminal does not. 
Which is odd, because I use ansi colour codes for my prompt and ls output 
(etc), and those do display as expected in both xterm and gnome terminal.

Weird!

Thanks,

Tyler

Re: [O] R output with session polluted with ascii color codes

[Tyler Smith]

On Fri, Mar 16, 2018, at 11:25 AM, William Denton wrote:
> 
> I tried the example in my configured setup and didn't get the ASCII codes.  I 
> don't know why and didn't dig into it, but I could; for now I figured I'd 
> just 
> mention this.
> 

Thanks for checking. I should have mentioned that I'm running 27.0.50 with org 
9.1.7 and ess 17.11. I see this problem with emacs -Q and regular emacs. If 
you're using the same versions and don't see this, then there should be 
something I can do in my config to fix it.

Best,

Tyler

[O] R output with session polluted with ascii color codes

[Tyler Smith]

Hi,

The printed output of some R functions includes ascii color codes (i.e., 
). This causes problems with R code blocks evaluated with the :session 
option. I've pasted a file below that demonstrates the problem. (should I 
attach it as a file? not sure what's preferable).

I can't find a way to disable this feature from R. However, I did find a way to 
filter out these codes from the babel side. The function of interest is 
~org-babel-R-evaluate-session` in ob-R.el. Adding a ~(replace-regexp-in-string 
ansi-color-control-seq-regexp "" ...)~ form around the output strips away the 
color codes so they don't mess up the output.  I've included that code in the 
example. If that makes sense I can put that together as a patch. If that 
doesn't make sense, please let me know how to fix this!

Best,

Tyler

* Reproducible Example

Start with ~emacs -Q~, then evaluate each of the following code blocks
in turn.

#+BEGIN_SRC elisp setup
(require 'package)
(setq package-load-list
  '((org-plus-contrib t)
(ess t)
(julia-mode t)))
(package-initialize)
(require 'org)
(require 'ess)

(org-babel-do-load-languages
 'org-babel-load-languages
 '((emacs-lisp . t)
   (R . t)
   (shell . t)))
#+END_SRC

#+RESULTS:

If you don't already have ~tidyr~ and ~dplyr~ installed, you need to
do that before running the following:

#+BEGIN_SRC R :results output
library(tidyr)
library(dplyr)
as_tibble(iris)
#+END_SRC

#+RESULTS:
#+begin_example
# A tibble: 150 x 5
   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
   
 1 5.103.50 1.40   0.200 setosa 
 2 4.903.00 1.40   0.200 setosa 
 3 4.703.20 1.30   0.200 setosa 
 4 4.603.10 1.50   0.200 setosa 
 5 5.003.60 1.40   0.200 setosa 
 6 5.403.90 1.70   0.400 setosa 
 7 4.603.40 1.40   0.300 setosa 
 8 5.003.40 1.50   0.200 setosa 
 9 4.402.90 1.40   0.200 setosa 
10 4.903.10 1.50   0.100 setosa 
# ... with 140 more rows
#+end_example

#+BEGIN_SRC R :results output :session RSESSION
library(tidyr)
library(dplyr)
as_tibble(iris)
#+END_SRC

#+RESULTS:
#+begin_example

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union
# A tibble: 150 x 5
   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
     
    
  
 1 5.103.50 1.40   
0.200 setosa 
 2 4.903.00 1.40   
0.200 setosa 
 3 4.703.20 1.30   
0.200 setosa 
 4 4.603.10 1.50   
0.200 setosa 
 5 5.003.60 1.40   
0.200 setosa 
 6 5.403.90 1.70   
0.400 setosa 
 7 4.603.40 1.40   
0.300 setosa 
 8 5.003.40 1.50   
0.200 setosa 
 9 4.402.90 1.40   
0.200 setosa 
10 4.903.10 1.50   
0.100 setosa 
# ... with 140 more rows
#+end_example

* Proposed Fix

Evaluating the following replaces the built-in function with my fix:

#+BEGIN_SRC elisp fix
(defun org-babel-R-evaluate-session
(session body result-type result-params column-names-p row-names-p)
  "Evaluate BODY in SESSION.
If RESULT-TYPE equals `output' then return standard output as a
string.  If RESULT-TYPE equals `value' then return the value of the
last statement in BODY, as elisp."
  (cl-case result-type
(value
 (with-temp-buffer
   (insert (org-babel-chomp body))
   (let ((ess-local-process-name
  (process-name (get-buffer-process session)))
 (ess-eval-visibly-p nil))
 (ess-eval-buffer nil)))
 (let ((tmp-file (org-babel-temp-file "R-")))
   (org-babel-comint-eval-invisibly-and-wait-for-file
session tmp-file
(format org-babel-R-write-object-command
(if row-names-p "TRUE" "FALSE")
(if column-names-p
(if row-names-p "NA" "TRUE")
  "FALSE")
".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
   (org-babel-R-process-value-result
(org-babel-result-cond result-params
  (with-temp-buffer

Re: [O] org alters output of bash code blocks when run with :session

[Tyler Smith]

On Mon, Feb 26, 2018, at 6:27 AM, Nicolas Goaziou wrote:
> Tyler Smith <ty...@plantarum.ca> writes:
> >
> > How do I force the babel session to leave the output alone, and print
> > it verbatim into the org file?
> 
> It may be related to other problems related to prompt in shell sessions.
> See for example
> <http://lists.gnu.org/r/emacs-orgmode/2018-02/msg00081.html>,
> <http://lists.gnu.org/r/emacs-orgmode/2018-01/msg00415.html>, and for
> step forward a solution
> <http://lists.gnu.org/archive/html/emacs-orgmode/2017-04/msg00147.html>.
> 
> Patches welcome!

It looks like ob-shell sets up sessions just by calling `shell`, which means 
all the user's customizations for shell-mode are automatically applied. This 
includes setting the prompt (e.g., from .emacs.d/init_bash.sh), as well as the 
value of `comint-prompt-regexp`.

I can't see any straightforward way to modify ob-shell sessions without also 
changing regular shell-mode. So I wonder if the easiest way to address this 
would be to create a new mode derived from shell-mode, ('ob-shell-mode')? That 
would give us a way to modify the prompt code inside babel without interfering 
with shell-mode.

If that sounds sensible I can put together a patch for ob-shell.el. Let me know 
what you think.

Best,

Tyler

[O] org alters output of bash code blocks when run with :session

[Tyler Smith]

Hi,

(originally posted to emacs.stackexchange[1] with no answers, )

I am running a short bash command from an org mode code block, using the 
program `fold` to wrap it at 60 characters. If I run the code without a session 
argument, the results display as expected. However, when I set the session 
argument (which I have to do in the context of the long literate analysis I'm 
doing), some of the output characters don't appear.

Steps to reproduce:

emacs -Q

Open the following file and execute each code block in turn:

+
#+BEGIN_SRC elisp setup
(org-babel-do-load-languages
 'org-babel-load-languages
 '((shell . t)))
#+END_SRC

#+RESULTS:

#+BEGIN_SRC bash no session :results replace verbatim
 echo 
'8,,CEFGDF,,,CC,CF:,,C8CFGFCF@G+FF:B3CDFGGGFGGCFDGGGFCF:,FF9>FEC,FFDGGDGFDFFEEFGEGC5>5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGGFEC,FFDGGDGFDFFEEFGE
: GC5>5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGGFEC,FFDGGDGFDFFEEFGEGC5>5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGGFDGGDGFDFFEEFGE
: 5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGG` from the beginning of the third line 
- `GC5>` from the beginning of the fourth line

The fact that the deleted strings both start at the beginning of a line and end 
with a `>` suggests that the session thinks they should be redirected somehow, 
and in the process is dropping them completely. However, when I look at the 
session buffer, the output appears as expected, with no missing characters.

How do I force the babel session to leave the output alone, and print it 
verbatim into the org file?


Thanks!

Tyler

GNU Emacs 26.0.90
Org mode version 9.1.4

[1] 
https://emacs.stackexchange.com/questions/38964/org-alters-output-of-bash-code-blocks-when-run-with-session

-- 
plantarum.ca

[O] org-clock-report overrides default :scope argument

[Tyler Smith]

Hi,

I have set org-clock-clocktable-default-properties to:

(:scope agenda :stepskip0 t :fileskip0 t :compact t :block today)

However, if I'm in a subtree and I try to insert a new clock table via ~C-c C-x 
C-r~ / ~org-clock-report~, org sets the options to ~:scope subtree~, ignoring 
my customiztion.  

This appears to be by design. However, it's unexpected, as there's nothing in 
the org manual to indicate that the ~:scope~ option is treated differently than 
the others with respect to customization. It might be nicer to users to give 
their preferred options a higher priority than the automatically generated 
ones, i.e., change

(org-create-dblock
   (org-combine-plists org-clock-clocktable-default-properties props))

to

(org-create-dblock
   (org-combine-plists props org-clock-clocktable-default-properties))

In the body of ~org-clock-report~. Alternatively, perhaps the org-info manual 
and/or the documentation for ~org-clock-clocktable-default-properties~ could be 
updated to indicate that a custom ~:scope~ setting will be ignored when invoked 
from a subtree?

Best,

Tyler 

Org mode version 9.1.6 (9.1.6-44-ge6f891-elpaplus
GNU Emacs 26.0.90 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.22.24) of 
2017-12-21



-- 
plantarum.ca

Re: [O] Insert timestamp other than DEADLINE: or SCHEDULED: for heading

[Tyler Smith]

Ok, thanks for the info.


On Tue, Feb 6, 2018, at 8:55 PM, Samuel Wales wrote:
> regular tses can be anywhere.  there is no command to put it after the
> maiin org thingies.  there was discussion a while back about adding
> EVENT: but it has not been implemented yet.
> 

[O] Insert timestamp other than DEADLINE: or SCHEDULED: for heading

[Tyler Smith]

Hi,

I'm trying to take full advantage of scheduling, deadlines and timestamps for 
my TODO lists.  It's easy to add deadlines and schedule times via `C-c C-s` and 
`C-c C-d`. However,  if I want to set a time for a meeting, I should be using a 
regular timestamp, rather than a SCHEDULE: property. There doesn't seem to be a 
way to do this automatically.

I know I can enter a timestamp with `C-c .`, but that just inserts it at point, 
regardless of where point is with respect to the headline, logbook, property 
drawers etc. Is there a function I could use to do the equivalent of `C-c C-s`, 
i.e., jump back to the headline, move past any property drawers, and insert a 
timestamp at the beginning of a line, and then return me to where I started?

I looked at `org--deadline-or-schedule`, but there's a lot going on in there,  
and my naive hacking quickly broke it.

Best,

Tyler

-- 
plantarum.ca

Re: [O] org-capture quitting and make-capture-frame

[Tyler Smith]

On Mon, Oct 23, 2017, at 04:03 PM, Nicolas Goaziou wrote:
> 
> Wouldn't it make more sense to turn it into 
> 
>  (message "Abort")
> 
> ? After all, it is not an error. It also allow to call other functions,
> e.g., `delete-frame' after exiting capture.
> 
> WDYT?
> 

I did think it was odd that this called an error, as it isn't an error
at all. 

I'm not sure how calling `(message ...)` at that point would enable
calling `delete-frame` after exiting capture? At the moment I'm calling
`delete` frame it by advising org-capture-destroy and
org-capture-finalize. I don't think either are called when you quit out
of the template selection dialog. Quitting needs to do something that
you can respond to, either with a hook, an advised function or something
else?

My proposal was just the first thing that I thought of, I'm sure there
are better solutions. That could be (message ...), but I'm missing
something in that case.

Best,

Tyler

[O] org-capture quitting and make-capture-frame

[Tyler Smith]

Hi,

I use org-capture with a new frame, so I can call it quickly when from
the OS (see
http://www.windley.com/archives/2010/12/capture_mode_and_emacs.shtml).

This works well, except that if I quit a capture, the frame is left
hanging. I looked through the code, and this is due to org-capture
calling `(user-error "Abort")` in response to my entering 'q' to
indicate I want to cancel my capture. 

It would be nice to allow for some configuration here. In my case, I
have replaced this line:

((equal entry "q")
(user-error "Abort"))

(source:
http://orgmode.org/cgit.cgi/org-mode.git/tree/lisp/org-capture.el?h=emacs-sync#n632
)

with

((equal entry "q")
   (if (equal "capture" (frame-parameter nil 'name))  
   (delete-frame))

That will work for my use case, until org-mode is updated at least.
Would it be possible to do something like this instead:

((equal entry "q")
  (funcall org-capture-quite-function))

That would allow you to provide a sensible default, such as '(user-error
"Abort")', while allowing users to tweak this behaviour, as needed for
cleaning up capture frames.

I've pasted the additional functions I'm using below, FYI.

Best,

Tyler

(defun make-capture-frame ()  
  "Create a new frame and run org-capture."  
  (interactive)  
  (select-frame-set-input-focus
   (make-frame '((name . "capture") 
 (width . 120) 
 (height . 15  
  (setq word-wrap 1)
  (setq truncate-lines nil)
  (org-capture))

(defadvice org-switch-to-buffer-other-window 
  (after supress-window-splitting activate)  
  "Delete the extra window if we're in a capture frame"  
  (if (equal "capture" (frame-parameter nil 'name))  
  (delete-other-windows)))

(defadvice org-capture-destroy 
(after delete-capture-frame activate)  
  "Advise capture-destroy to close the frame"  
  (if (equal "capture" (frame-parameter nil 'name))  
  (delete-frame)))

(defadvice org-capture-finalize 
(after delete-capture-frame activate)  
  "Advise capture-finalize to close the frame"  
  (if (equal "capture" (frame-parameter nil 'name))  
  (delete-frame)))
 

-- 
plantarum.ca

Re: [O] run bash sessions without config files

[Tyler Smith]

On Wed, Aug 2, 2017, at 11:53 AM, Tyler Smith wrote:
> 
> Is it possible to configure org-babel to ignore any customization files,
> such as .emacs.d/init_bash.el and .bashrc?
> 

After some digging around, it looks like this isn't possible.
~org-babel~ starts shell sessions via the standard function ~(shell)~.
Loading ~init_bash.el~ is hard-coded into this function, so there's no
user-visible way to direct Emacs not to read it for org-mode code
blocks, while still using it in other contexts. 

Best,

Tyler

[O] run bash sessions without config files

[Tyler Smith]

Hi,

I use shell-mode a lot, and have a very complex prompt, coloured with
escape codes and lots of bells and whistles. This appears to confuse
org-babel when I'm running code blocks in a session, similar to what's
described here:

https://emacs.stackexchange.com/questions/19735/emacs-freezes-with-any-org-babel-snippet-using-session

Is it possible to configure org-babel to ignore any customization files,
such as .emacs.d/init_bash.el and .bashrc?

As a workaround, I redefine PS1 and PS2 at the top of my org buffer,
which fixes the problem temporarily. I'd like a permanent fix if
possible.

Best,

Tyler

-- 
plantarum.ca

Re: [O] exporting inline source code with listings broken by color commands

[Tyler Smith]

Nicolas Goaziou writes:

> Hello,
>
> Tyler Smith <ty...@plantarum.ca> writes:
>
>> (setq org-latex-listings t
>>   org-latex-listings-options
>>   '(("backgroundcolor" "\\color[gray]{0.95}")
>
> This is incorrect. Per "listings" manual, a commend with an optional
> argument needs to be included within curly braces:
>
>   ("backgroundcolor" "{\\color[gray]{0.95}}")

Aha! That was my mistake. The fact that that syntax worked for
lstlistings, or at least appeared to be less obviously broken, and not
in lstinline confused me.

>>
>> What I expect to happen is that the last line is rendered as "Inline
>> code: 2".
>
> This is not going to happen. Since you set `org-export-babel-evaluate'
> to nil, you have a somewhat WYSIWYG behaviour; the "1 + 1" is not going
> to disapper.

Echoing the source code wasn't my concern here; rather it was the
display of several lines of broken LaTeX code. The correction above
fixes this, so now I can tweak the evaluation and export settings with a
reasonable chance of success.

Thanks for your help!

Tyler

[O] exporting inline source code with listings broken by color commands

[Tyler Smith]

When exporting an org file to pdf via latex, and using the listings
package to markup source code, my inline code is not processed properly.

To reproduce:
 
emacs -Q -l minimal.el

where minimal.el contains the following:

;;; Minimal setup to load latest 'org-mode'

;; activate debugging
(setq debug-on-error t
  debug-on-signal nil
  debug-on-quit nil)
 
;; add latest org-mode to load path
(add-to-list 'load-path (expand-file-name
"/home/tws/.emacs.d/elpa/org-plus-contrib-20170606"))

(setq org-latex-listings t
  org-latex-listings-options
  '(("backgroundcolor" "\\color[gray]{0.95}")
   ("keywordstyle" "\\color{blue}")
   ("commentstyle" "\\color{BrickRed}")
   ("stringstyle" "\\color{Red}")
   ("keepspaces" "true")
   ("deletekeywords" "{ps,scan}"))
  org-latex-packages-alist
  '(("usenames,dvipsnames" "color" nil)
("" "listings" nil)))

(org-babel-do-load-languages
 'org-babel-load-languages
 '((emacs-lisp . t)
   (R . t)
   (shell . t)))


Then open tmp.org, which contains the following:

# -*- org-export-babel-evaluate: nil -*-
#+PROPERTY: header-args:sh :session *bp*

* Init
  Set working directory, set path to taxonomy tree and database.
  
  #+BEGIN_SRC sh :results silent 
cd /home/tws/research

## do other shell stuff here

  #+END_SRC

  #+BEGIN_SRC R :session tmp
1 + 1   
  #+END_SRC

  #+RESULTS:
  : 2

  Inline code: src_R{1 + 1} {{{results(=2=)}}}


Export to pdf via C-c C-e l o

What I expect to happen is that the last line is rendered as "Inline
code: 2". What I see instead is: 

Inline code:
0.95,keywordstyle=,commentstyle=,stringstyle=,keepspaces=true,deletekeywords=ps,sc
+1 2

I think this may be due to the latex listings package being able to
accommodate color macros in code blocks (\lstlisting), but in inline
code (\lstinline). I can eliminate the problem by removing the color
commands. However, it would be better to provide an option to pass
separate arguments to lstlisting and lstinline, so that we can still use
colors where they are supported.

Additional details below.

Best,

Tyler


Emacs  : GNU Emacs 26.0.50 (build 2, x86_64-pc-linux-gnu, GTK+ Version
3.22.11)
 of 2017-06-18
Package: Org mode version 9.0.8 (9.0.8-elpaplus @
/home/tws/.emacs.d/elpa/org-plus-contrib-20170606/)

current state:
==
(setq
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
 org-src-mode-configure-edit-buffer)
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-latex-listings t
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-html-format-inlinetask-function
 'org-html-format-inlinetask-default-function
 org-odt-format-headline-function
 'org-odt-format-headline-default-function
 org-ascii-format-inlinetask-function
 'org-ascii-format-inlinetask-default
 org-mode-hook '(#[0 "\300\301\302\303\304$\207"
   [add-hook change-major-mode-hook
org-show-block-all append local]
   5]
 #[0 "\300\301\302\303\304$\207"
   [add-hook change-major-mode-hook
org-babel-show-result-all append local]
   5]
 org-babel-result-hide-spec
 org-babel-hide-all-hashes org-eldoc-load)
 org-odt-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME
 CONTENTS)"]
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-latex-format-drawer-function #[514 "\207" [] 3 "\n\n(fn _
 CONTENTS)"]
 org-babel-pre-tangle-hook '(save-buffer)
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe
  org-babel-header-arg-expand)
 org-babel-load-languages '((emacs-lisp . t) (R . t) (shell . t))
 org-ascii-format-drawer-function #[771 "
\207" [] 4 "\n\n(fn NAME
 CONTENTS WIDTH)"]
 org-occur-hook '(org-first-headline-recenter)
 org-cycle-hook '(org-cycle-hide-archived-subtrees
  org-cycle-hide-drawers
  org-cycle-show-empty-lines
  org-optimize-window-after-visibility-change)
 org-speed-command-hook '(org-speed-command-default-hook
  org-babel-speed-command-hook)
 org-odt-format-inlinetask-function
 'org-odt-format-inlinetask-default-function
 org-confirm-shell-link-function 'yes-or-no-p
 org-link-parameters '(("id" :follow org-id-open)
   ("rmail" :follow org-rmail-open :store
org-rmail-store-link)
   ("mhe" :follow org-mhe-open :store
org-mhe-store-link)
   ("irc" :follow org-irc-visit :store
org-irc-store-link)
   ("info" :follow org-info-open :export

Re: [O] [PATCH] protocol: allow users to disable warning about old style links

[Tyler Smith]

On Wed, Jun 21, 2017, at 12:51 PM, Mario Martelli wrote:
> 
>>  it would make sense to suggest the
>> new style syntax as the default for use by us newbies.
> 
> yeah, thought about that too. At the moment it’s still a copy of the old doc. 
> 
> Got no feedback so far wether my approach would be acceptable or not. 
> Therefore I did not put much effort into it. 
> 
> But you’re right. The examples should be new style URIs and the infobox 
> should reference the old style URIs.

One last question/suggestion:

The default capture template didn't work for me:

(*"w"*
 *"Default template"*
 entry
 (file+headline *"~/org/capture.org"* *"Notes"*)
 *"* %^{Title}\n\n  Source: %u, %c\n\n  %i"*
 *:empty-lines* 1)

The %u and %c bits got replaced by the actual link code (i.e.,
javascript:...). The following works as I wanted:

("w" "Default capture " entry
  (file "~/org/notes.org")
  "* %^{Title}
Source: [[%:link][%:description]]
%:initial" :empty-lines 1)

At this point I'm still a little confused, so perhaps I borked something
else up and the problem is local to my setup.

Best,

Tyler

Re: [O] [PATCH] protocol: allow users to disable warning about old style links

[Tyler Smith]

On Wed, Jun 21, 2017, at 12:24 PM, Tyler Smith wrote:
> 
> whereas the new-style key-value links would be:
> 
> javascript:location.href='org-protocol://sub-protocol?url='+
>   encodeURIComponent(location.href)+'='+
>   encodeURIComponent(document.title)+'='+
>   encodeURIComponent(window.getSelection())
> 

Aha! The new-style links are documented in the function docs. E.g., for
`org-protocol-capture`:

  javascript:location.href = 'org-protocol://capture?url='+ 
encodeURIComponent(location.href) + '=' 
encodeURIComponent(document.title) + '=' + 
encodeURIComponent(window.getSelection())

It would be very helpful to have that visible in the new documentation.

Thanks,

Tyler

Re: [O] [PATCH] protocol: allow users to disable warning about old style links

[Tyler Smith]

On Wed, Jun 21, 2017, at 12:01 PM, Mario Martelli wrote:
> 
> I have shared a proposal to move org-protocol documentation to core 
> documentation.
> It’s mainly copied together from the old one and 9.0 NEWS.
> 
> The important part regarding the new syntax could be found here:
> 
> https://github.com/mgmart/org-mode/blob/documentation/org-protocol/contrib/orgmanual.org#L7347-L7364
> 
> Would that help or is there still something to add?

Thanks, Mario.

Your documentation refers to the new-style links, but the examples still
use the old style I think? My javascript is very basic, but from some
experimenting here, I think the old style links are what you've used:

javascript:location.href='org-protocol://sub-protocol://'+
  encodeURIComponent(location.href)+'/'+
  encodeURIComponent(document.title)+'/'+
  encodeURIComponent(window.getSelection())

whereas the new-style key-value links would be:

javascript:location.href='org-protocol://sub-protocol?url='+
  encodeURIComponent(location.href)+'='+
  encodeURIComponent(document.title)+'='+
  encodeURIComponent(window.getSelection())

(I'm not actually sure what the name corresponding to `getSelection()`
is)

This is based on the following link style for store-link, which works
for me with Firefox 45.9 and Org 9.0 on Emacs 26.0.50:

    
javascript:location.href='org-protocol://store-link?url='+encodeURIComponent(location.href)+'='+encodeURIComponent(document.title)

Also, I think your example for store-link should include the
document.title element?


javascript:location.href='org-protocol://store-link://'+encodeURIComponent(location.href)

It's true that old style links are still supported, but if they produce
a warning error when you use them, it would make sense to suggest the
new style syntax as the default for use by us newbies.

Best,

Tyler

--
plantarum.ca

Re: [O] [PATCH] protocol: allow users to disable warning about old style links

[Tyler Smith]

On Fri, Jun 16, 2017, at 02:13 AM, Nicolas Goaziou wrote:
> 
> Wouldn't it be better to report it upstream as a bug? I don't think
> there are many Org protocols applications out there and the conversion
> to the new syntax is easy.

I'm just starting to use org-protocol, and I'm confused by this warning.
I can't find any description of the differences between the old and new
link styles in the documentation, or any pointers as to how and what I
should change to adopt the new syntax. The org manual links to
http://orgmode.org/worg/org-contrib/org-protocol.html, which seems to be
a year or more out of date.

I'm not sure who is 'upstream' in this context, and what, if anything, I
can do as an end-user to use the new style. Any suggestions?

Thanks,

Tyler

 

[O] tangling inline source code

[Tyler Smith]

Hello,

A question came up on Stack Exchange asking about less-verbose ways to
indicate code blocks:
http://emacs.stackexchange.com/questions/26163/one-liner-org-source-tangle

I suggested using the inline format, e.g., 'src_perl{set $variable =
1;}'. However, this is ignored when tangling the org file into a source
file.

The manual indicates that blocks and inline code are treated the same:
http://orgmode.org/manual/Structure-of-code-blocks.html

Is this a bug in the documentation? From the documentation, I expect
inline code to be tangled the same as a code block, at least when
appropriate `tangle` options are set in the header.

Here's a short example file illustrating the problem:

+
* Taking notes
:PROPERTIES:
:tangle: whatever.R
:comments: org
:END:

R commands
#+BEGIN_SRC R
var1 <- 1
#+END_SRC

And here's an inline command: src_R{var2 <- 2}.

Perl unset command (just making it up... :P)
#+BEGIN_SRC R
rm(list = c("var1", "var2"))
#+END_SRC

And some more text.
+

Tangling this will insert the two code blocks into the tangled file, but
the inline code gets treated as regular text, and is converted into a
comment.

Am I doing something wrong, or could the documentation be clarified on
this point?

Best,

Tyler

-- 
plantarum.ca

[O] clock tables and archived trees

[Tyler Smith]

Hi,

I've been using clock tables to track my work, and it works pretty well.
I have a journal.org file, with a different heading for each month.
Under that heading is a clocktable with the :block property set to that
month, and :step day. This gives me a daily summary for the month.

However, if I complete a task early in the month, and then archive its
heading, any further updates to the clocktable will not reflect the time
spent on that item - the effort is no longer included in the clock
table.

Is there a way to cope with this? Perhaps a setting to keep the times
for archived items, or a different workflow that will allow for dynamic
work time-tracking that is compatible with archiving completed tasks?

Thanks for any suggestions,

Tyler 

-- 
plantarum.ca

[O] habits not working

[Tyler Smith]

Hi,

Habits don't seem to be working for me anymore, and I'm not sure why.

Steps to reproduce:

emacs -Q

load org mode with minimal config for habits:

;; test-org.el
(require 'package)
(setq package-load-list
  '((org-plus-contrib t)))
(package-initialize)

(setq org-agenda-files '("~/scratch/orghabits.org"))

(setq org-modules '(org-habit))

With one habit defined in ~/scratch/orghabits.org:

* Habits
** TODO Exercise
   SCHEDULED: <2016-01-04 Mon .+1d>
   :LOGBOOK:  
   - State "DONE"   from "TODO"   [2016-01-03 Sun 22:32]
   - State "DONE"   from "TODO"   [2016-01-02 Sat 17:07]
   - State "DONE"   from "TODO"   [2016-01-01 Fri 23:03]
   - State "DONE"   from "TODO"   [2015-12-31 Thu 16:24]
   - State "DONE"   from "TODO"   [2015-12-30 Wed 20:53]
   :END:  
   :PROPERTIES:
   :STYLE: habit
   :LAST_REPEAT: [2016-01-03 Sun 22:32]
   :END:  

My agenda looks like:

Week-agenda (W01):
Monday  4 January 2016 W01
  orghabits:  Scheduled:  TODO Exercise
Tuesday 5 January 2016
  orghabits:  Scheduled:  TODO Exercise
Wednesday   6 January 2016
  orghabits:  Scheduled:  TODO Exercise
Thursday7 January 2016
  orghabits:  Scheduled:  TODO Exercise
Friday  8 January 2016
  orghabits:  Scheduled:  TODO Exercise
Saturday9 January 2016
  orghabits:  Scheduled:  TODO Exercise
Sunday 10 January 2016
  orghabits:  Scheduled:  TODO Exercise

When I looked at this yesterday only the next habit was listed, and was
displayed along with its consistency graph, which is what I expect to
happen.

"Habit" is listed in the modeline, and pressing 'K' brings up a message
that habits have been turned off, but no other change. Pressing 'K'
repeatedly turns habits on and off, but the agenda itself doesn't
change. 

How did I break this?

Emacs version:
GNU Emacs 25.0.50.2 (x86_64-pc-linux-gnu, GTK+ Version 3.18.5) of
2015-12-24

Org mode version:
Org-mode version 8.3.2 (8.3.2-59-g3d4c46-elpaplus @
/home/tws/.emacs.d/elpa/org-plus-contrib-20160104/)

Best,

Tyler
-- 
plantarum.ca

Re: [O] habits not working

[Tyler Smith]

On Mon, Jan 4, 2016, at 09:59 AM, Dave Marquardt wrote:
> Tyler Smith <ty...@plantarum.ca> writes:
> 
> > Habits don't seem to be working for me anymore, and I'm not sure why.
> 
> > How did I break this?
> >
> > Emacs version:
> > GNU Emacs 25.0.50.2 (x86_64-pc-linux-gnu, GTK+ Version 3.18.5) of
> > 2015-12-24
> >
> > Org mode version:
> > Org-mode version 8.3.2 (8.3.2-59-g3d4c46-elpaplus @
> > /home/tws/.emacs.d/elpa/org-plus-contrib-20160104/)
> 
> Did you happen to update org-mode recently? There was a change around
> the 8.3 timeframe about where you could put properties. See
> http://orgmode.org/Changes.html
> 

That was it, thanks. Following the change, the format must be:

* TODO Headline
  SCHEDULED: 
  :PROPERTIES:
  :style: habit:
  ...
  :END:
  :LOGBOOK:
  ...

I got thrown off because I store my past 'completions' in a :LOGBOOK:
drawer which was placed before the :PROPERTIES: drawer, which used to be
ok.

Best,

Tyler

Re: [O] org files and projects nested git repositories

[Tyler Smith]

Kyle Meyer  writes:
>
> In addition to what Ken suggested, another option is to use links to
> populate the agenda directory.  Have a git repo for your Org notes and
> agenda file (your "org" directory above), and add this directory (or one
> of its subdirectories) to org-agenda-files so that all the Org files in
> that directory are considered agenda files.
>
> Keep project-related Org files in the given project directory (as you do
> above), and create a symbolic link for the Org file in the agenda
> directory.  The project directory will then track the content of the Org
> file, and the agenda repo will just track the presence of the link.
>

Thanks Kyle.

I have tried links, but in all my attempts the links break whenever the
source or the target is committed to version control. My understanding
that each new commit to a file effectively changes the inode, breaking
the link. In your use, are the targets and their links both under
version control? If so, obviously they aren't breaking, so I must be
doing something wrong when I try the same thing.

Best,

Tyler

-- 
http://plantarum.ca

Re: [O] org files and projects nested git repositories

[Tyler Smith]

Brenda Butler  writes:

>  I have tried links, but in all my attempts the links break whenever the
>  source or the target is committed to version control. My understanding
>  that each new commit to a file effectively changes the inode, breaking
>  the link
>
> Sounds like you might be using hard links instead of symbolic links ... 
> but first, are you using a unix-like system or another system? The symbolic 
> link is a unix-like thing.
>

I'm on Debian, so links are available. I recall having to fix an issue
with Emacs' backup-files taking over the inodes. That was easily fixed
once I knew it was an issue. I don't recall the details, but it seemed
that the links still got garbled on commit. I'll take another look,
now that I know it should work.

Tyler

-- 
http://plantarum.ca

Re: [O] org files and projects nested git repositories

[Tyler Smith]

Ken Mankoff  writes:
>
> In my version of this, I have each project as its own git repository,
> where git contains the Org file, other code, the manuscript, etc. I
> add any Org files to my global agenda with =M-x
> org-agenda-file-to-front= and remove with = M-x org-remove-file=.
>
>>  most tutorials assume that all your planning files are found in one
>>  directory (e.g., ~/org).
>
> That is only because it is easier to show that setup in the tutorial. You
> can have Org files all over the place, and each can be added to the Agenda
> or not, as you wish.

Thanks Ken. Perhaps I've been trying to hard to force everything into
one directory. I did find a post on Reddit that describes a convenient
way to create org files for projects anywhere in the directory tree in a
shared global location:

https://www.reddit.com/r/emacs/comments/2qwh8q/org_mode_one_massive_file_or_tons_of_small_ones/cnacdpl

This has the benefit of keeping all my planning (.org) files in one
repo, but the disadvantage of separating the planning files from the
project they relate to. Something your approach deals with nicely. I'll
try that out.

Best,

Tyler

-- 
http://plantarum.ca

[O] adding file to agenda removes directories

[Tyler Smith]

Hi again,

Continuing to play around with getting org files into my agenda, I run
into this:

I set up org-agenda-files to contain ~/org/, such that all files in that
directory are in my agenda. I then add an individual file from
elsewhere, via org-agenda-file-to-front. In the process, the entry for
the ~/org/ directory is removed, and replaced with explicit entries for
every org file in that directory. This leads to surprising behaviour,
where new org files in ~/org/ aren't detected by the agenda.

The help suggests that org-agenda-files can be a list of 'files and
directories', but this behaviour seems to suggest that it can be a list
of files, *or* a directory. Am I doing something wrong, or can I not
combine files and directories in org-agenda-files?

Thanks,

Tyler

-- 
http://plantarum.ca

[O] org files and projects nested git repositories

[Tyler Smith]

Hello list,

I'm struggling to incorporate project-specific org files into my global
org system. My file system looks something like this:

~
├── org
│   ├── todo.org
│   ├── reading.org
│   └── personal.org
└── research
├── project1
│   ├── project1.org
│   └── project1_reference.pdf
└── project2
├── project2.org
├── data2
│   ├── data2A.csv
│   └── data2B.csv
└── project2_reference.pdf

When I open a new project, it gets its own folder, containing supporting
documents, code, data, as well as an org file to manage todos and
timelines. This doesn't seem to work well with org: most tutorials
assume that all your planning files are found in one directory (e.g.,
~/org).

I wonder if it would be possible to maintain a global git repository
containing my entire directory tree, but only the org files; and have
all of these org files incorporated into (and new ones automatically
detected by) the agenda. At the same time, I need to maintain individual
git repositories for each project directory.

Does anyone here have experience with such a system? Or other advice on
how to keep many scattered org files in a single git repo and also
captured in the org agenda?

Thanks for your patience,

Tyler

-- 
http://plantarum.ca

[O] customizing Agenda mode line

[Tyler Smith]

Hi,

The major mode name displayed in the mode line for my agenda buffer is
so long that it is pushing other info off the screen. Is there a cleaner
way to customize this than directly editing the definition of
org-agenda-set-mode-name?

Thanks,

Tyler
-- 

Re: [O] org-insert-drawer completion targets

[Tyler Smith]

On Wed, Oct 29, 2014, at 02:10 PM, Eric Abrahamsen wrote:

 If you've got org-log-into-drawer set to a non-nil value, the drawer
 should be created automatically for you the first time you take a note
 on the heading (org-add-note), or switch TODO states in such a way that
 records a state-change note. Those are the two purposes of the LOGBOOK
 drawer, so you might as well use one or the other to create the drawer.
 

Thanks. I guess I was re-inventing the notes feature without
understanding how the existing setup worked. It makes sense now.

Best,


Tyler

[O] org-insert-drawer completion targets

[Tyler Smith]

Hello,

I'm trying to figure out how drawers work. I see that `C-c C-x d`
provides automatic drawer insertion, and wraps around the region if
active. However, `LOGBOOK` is explicitly excluded from the completion
targets. However, I don't see another way to add a LOGBOOK without
typing the word out manually. This seems strange - is there another
shortcut for adding LOGBOOK drawers? If not, why isn't it allowed as a
completion target?

I'm not complaining, just confused about the preferred workflow for
LOGBOOK drawers.

Best,

Tyler

Org-mode version 8.2.8 (8.2.8-elpaplus @
/home/tws/.emacs.d/elpa/org-plus-contrib-20141006/)

Re: [O] [ESS] Keyboard shortcut - is there a principle behind them?

[Tyler Smith]

Rainer M Krug rai...@krugs.de wrote:
On 12/06/13, 10:49 , Oleh wrote:

 Now only few shortcuts are reserved for user space and plugins, the
 most notable of which is the `C-c` prefix. That's why most custom
 modes such as org-mode and ESS bind to shortcuts with `C-c` prefix:
 there's a convention that Emacs core will not use `C-c`.

To be clear, C-c followed by another modified key (C-x, for example) is 
reserved for major modes. C-c followed by a regular letter (e.g. C-c x) is 
reserved for use by the user, and should not be used by major modes.

Tyler

Re: [O] Can't export two figures in one document to odt

[Tyler Smith]

This happens even with emacs -q. I've attached the odt file.

Christian Moe m...@christianmoe.com wrote:

Hi,

I cannot reproduce this bug. I copy-pasted the below code, exported
from
Org 8.2.1 and opened the expected two-figure document in LibreOffice
4.0.4.2.

Does this happen with emacs -Q ?

What do you see if you open up the content.xml of the .odt document?

Yours,
Christian Moe


Tyler Smith writes:

 Hi,

 I'm new to org-babel, and having trouble with exporting to .odt. The
 following file works. I can export to .odt no problem, the figure
 shows up as expected:

 +---
 #+PROPERTY: header-args:R  :session rTest

 #+BEGIN_SRC R :results graphics :file test1.jpg :exports both

   plot(1:10)

 #+END_SRC

 #+RESULTS:
 [[file:test1.jpg]]
 +---

 But if I add a second figure, and try to export to .odt, I get a
 Read-Error. Error reading file. error from LibreOffice. I can
export
 to pdf no problem. Here's the problem file:

 +---
 #+PROPERTY: header-args:R  :session rTest

 #+BEGIN_SRC R :results graphics :file test1.jpg :exports both

   plot(1:10)

 #+END_SRC

 #+RESULTS:
 [[file:test1.jpg]]

 #+BEGIN_SRC R :results graphics :file test2.jpg :exports both

 plot(10:1)

 #+END_SRC

 #+RESULTS:
 [[file:test2.jpg]]

 +--

 Thanks,

 Tyler

 Emacs 24.3.50.1
 Org-mode 8.2.1
 Debian Linux
 LibreOffice 4.1.3.2


/sdcard/test.odt
Description: application/vnd.oasis.opendocument.text

[O] Can't export two figures in one document to odt

[Tyler Smith]

Hi,

I'm new to org-babel, and having trouble with exporting to .odt. The
following file works. I can export to .odt no problem, the figure
shows up as expected:

+---
#+PROPERTY: header-args:R  :session rTest

#+BEGIN_SRC R :results graphics :file test1.jpg :exports both

  plot(1:10)

#+END_SRC

#+RESULTS:
[[file:test1.jpg]]
+---

But if I add a second figure, and try to export to .odt, I get a
Read-Error. Error reading file. error from LibreOffice. I can export
to pdf no problem. Here's the problem file:

+---
#+PROPERTY: header-args:R  :session rTest

#+BEGIN_SRC R :results graphics :file test1.jpg :exports both

  plot(1:10)

#+END_SRC

#+RESULTS:
[[file:test1.jpg]]

#+BEGIN_SRC R :results graphics :file test2.jpg :exports both

plot(10:1)

#+END_SRC

#+RESULTS:
[[file:test2.jpg]]

+--

Thanks,

Tyler

Emacs 24.3.50.1
Org-mode 8.2.1
Debian Linux
LibreOffice 4.1.3.2

[O] Bug: = symbol in url converted to %3D [7.9.3f (release_7.9.3f-17-g7524ef @ /usr/local/share/emacs/24.3.50/lisp/org/)]

[Tyler Smith]

MWE:

test.org

* This is a test.
  A link [[http://seqanswers.com/forums/showthread.php?t%3D21][to
seqanswers.com]].

Exporting to latex from org-mode produces the following file:

test.tex

% Created 2013-11-01 Fri 16:37
\documentclass[11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{fixltx2e}
\usepackage{graphicx}
\usepackage{longtable}
\usepackage{float}
\usepackage{wrapfig}
\usepackage{soul}
\usepackage{textcomp}
\usepackage{marvosym}
\usepackage{wasysym}
\usepackage{latexsym}
\usepackage{amssymb}
\usepackage{hyperref}
\tolerance=1000
\providecommand{\alert}[1]{\textbf{#1}}

\title{test}
\author{Tyler Smith}
\date{\today}
\hypersetup{
  pdfkeywords={},
  pdfsubject={},
  pdfcreator={Emacs Org-mode version 7.9.3f}}

\begin{document}

\maketitle

\setcounter{tocdepth}{3}
\tableofcontents
\vspace*{1cm}

\section{This is a test.}
\label{sec-1}

  Here's a line of text with a link
\href{http://seqanswers.com/forums/showthread.php?t%3D21}{to
seqanswers.com}.

\end{document}

Note that the url has been converted from:

http://seqanswers.com/forums/showthread.php?t=21

to:

http://seqanswers.com/forums/showthread.php?t%3D21

This effectively breaks the link. This is not specific to the latex
exporter, it happens also in at least the markdown exporter.

Note also that I have reproduced the problem in a newer version of org:

[8.2.1 (8.2.1-21-g2b3e01-elpa @ /home/tws/.emacs.d/elpa/org-20131028/)]

Thanks,

Tyler

Emacs  : GNU Emacs 24.3.50.1 (i686-pc-linux-gnu, GTK+ Version 3.8.2)
 of 2013-08-20 on ONOTTAR654746
Package: Org-mode version 7.9.3f (release_7.9.3f-17-g7524ef @
/usr/local/share/emacs/24.3.50/lisp/org/)

current state:
==
(setq
 org-export-blocks '((src org-babel-exp-src-block nil)
 (export-comment org-export-blocks-format-comment t)
 (ditaa org-export-blocks-format-ditaa nil)
 (dot org-export-blocks-format-dot nil))
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point
org-babel-execute-safely-maybe)
 org-export-preprocess-before-selecting-backend-code-hook
'(org-beamer-select-beamer-code)
 org-tab-first-hook '(org-hide-block-toggle-maybe
org-src-native-tab-command-maybe
  org-babel-hide-result-toggle-maybe org-babel-header-arg-expand)
 org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-hide-drawers org-cycle-show-empty-lines
  org-optimize-window-after-visibility-change)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-speed-command-hook '(org-speed-command-default-hook
org-babel-speed-command-hook)
 org-babel-pre-tangle-hook '(save-buffer)
 org-occur-hook '(org-first-headline-recenter)
 org-export-interblocks '((src org-babel-exp-non-block-elements))
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-export-latex-format-toc-function 'org-export-latex-format-toc-default
 org-export-preprocess-before-normalizing-links-hook
'(org-remove-file-link-modifiers)
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-export-first-hook '(org-beamer-initialize-open-trackers)
 org-mode-hook '(#[nil \300\301\302\303\304$\207
   [org-add-hook change-major-mode-hook org-show-block-all
append local] 5]
 #[nil \300\301\302\303\304$\207
   [org-add-hook change-major-mode-hook
org-babel-show-result-all append local] 5]
 org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc
   org-beamer-auto-fragile-frames
   org-beamer-place-default-actions-for-lists)
 org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-confirm-shell-link-function 'yes-or-no-p
 )

Re: [O] Bug: = symbol in url converted to %3D [7.9.3f (release_7.9.3f-17-g7524ef @ /usr/local/share/emacs/24.3.50/lisp/org/)]

[Tyler Smith]

Sorry, i screwed up my cut and paste there. In test.org, the link has an = 
sign, not %3D.


Tyler

Sent with AquaMail for Android
http://www.aqua-mail.com


On November 1, 2013 5:10:38 PM Tyler Smith ty...@plantarum.ca wrote:

MWE:

test.org

* This is a test.
  A link [[http://seqanswers.com/forums/showthread.php?t%3D21][to
seqanswers.com]].

Exporting to latex from org-mode produces the following file:

test.tex

% Created 2013-11-01 Fri 16:37
\documentclass[11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{fixltx2e}
\usepackage{graphicx}
\usepackage{longtable}
\usepackage{float}
\usepackage{wrapfig}
\usepackage{soul}
\usepackage{textcomp}
\usepackage{marvosym}
\usepackage{wasysym}
\usepackage{latexsym}
\usepackage{amssymb}
\usepackage{hyperref}
\tolerance=1000
\providecommand{\alert}[1]{\textbf{#1}}

\title{test}
\author{Tyler Smith}
\date{\today}
\hypersetup{
  pdfkeywords={},
  pdfsubject={},
  pdfcreator={Emacs Org-mode version 7.9.3f}}

\begin{document}

\maketitle

\setcounter{tocdepth}{3}
\tableofcontents
\vspace*{1cm}

\section{This is a test.}
\label{sec-1}

  Here's a line of text with a link
\href{http://seqanswers.com/forums/showthread.php?t%3D21}{to
seqanswers.com}.

\end{document}

Note that the url has been converted from:

http://seqanswers.com/forums/showthread.php?t=21

to:

http://seqanswers.com/forums/showthread.php?t%3D21

This effectively breaks the link. This is not specific to the latex
exporter, it happens also in at least the markdown exporter.

Note also that I have reproduced the problem in a newer version of org:

[8.2.1 (8.2.1-21-g2b3e01-elpa @ /home/tws/.emacs.d/elpa/org-20131028/)]

Thanks,

Tyler

Emacs  : GNU Emacs 24.3.50.1 (i686-pc-linux-gnu, GTK+ Version 3.8.2)
 of 2013-08-20 on ONOTTAR654746
Package: Org-mode version 7.9.3f (release_7.9.3f-17-g7524ef @
/usr/local/share/emacs/24.3.50/lisp/org/)

current state:
==
(setq
 org-export-blocks '((src org-babel-exp-src-block nil)
 (export-comment org-export-blocks-format-comment t)
 (ditaa org-export-blocks-format-ditaa nil)
 (dot org-export-blocks-format-dot nil))
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point
org-babel-execute-safely-maybe)
 org-export-preprocess-before-selecting-backend-code-hook
'(org-beamer-select-beamer-code)
 org-tab-first-hook '(org-hide-block-toggle-maybe
org-src-native-tab-command-maybe
  org-babel-hide-result-toggle-maybe org-babel-header-arg-expand)
 org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-hide-drawers org-cycle-show-empty-lines
  org-optimize-window-after-visibility-change)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-speed-command-hook '(org-speed-command-default-hook
org-babel-speed-command-hook)
 org-babel-pre-tangle-hook '(save-buffer)
 org-occur-hook '(org-first-headline-recenter)
 org-export-interblocks '((src org-babel-exp-non-block-elements))
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-export-latex-format-toc-function 'org-export-latex-format-toc-default
 org-export-preprocess-before-normalizing-links-hook
'(org-remove-file-link-modifiers)
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-export-first-hook '(org-beamer-initialize-open-trackers)
 org-mode-hook '(#[nil \300\301\302\303\304$\207
   [org-add-hook change-major-mode-hook org-show-block-all
append local] 5]
 #[nil \300\301\302\303\304$\207
   [org-add-hook change-major-mode-hook
org-babel-show-result-all append local] 5]
 org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc
   org-beamer-auto-fragile-frames
   org-beamer-place-default-actions-for-lists)
 org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-confirm-shell-link-function 'yes-or-no-p
 )

[O] accented letters in pdf export

[Tyler Smith]

Hi,

I'm using org 7.9.2, with the new exporter dispatcher from org-export. When
I try to include accented letters, such as \'e, they don't work. When I
export to pdf using C-c C-e p, the resulting tex file shows $\backslash$'e
where I had \'e in the org file. Other macros, like \alpha, work fine.

How do I include accented letters in my pdflatex exports?

Thanks,

Tyler

[O] org-goto bug

[Tyler Smith]

Hi,

According to the manual, and the help window that pops up when you call it,
org-goto should accept a few one-letter commands to move up one level (u),
quit (q), move to the next (n) or previous(p) heading.
However, whenever I try any of these keys, they are interpreted as the
search string for isearch. My set-up is provided below. I have confirmed
that this is also the case when I start emacs with 'emacs -Q', so I don't
think I've done this in my config.

Thanks,

Tyler


Emacs  : GNU Emacs 24.3.50.1 (i686-pc-linux-gnu, GTK+ Version 2.24.10)
 of 2012-12-27 on ONOTTAR654746
Package: Org-mode version 7.9.1 (7.9.1-dist @
/usr/local/share/emacs/site-lisp/org/)

current state:
==
(setq
 org-export-blocks '((src org-babel-exp-src-block nil)
 (export-comment org-export-blocks-format-comment t)
 (ditaa org-export-blocks-format-ditaa nil) (dot
org-export-blocks-format-dot nil))
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point
org-babel-execute-safely-maybe)
 org-export-latex-packages-alist '(( natbib nil) \\bibpunct{(} {)} {;}
{a} {} {,})
 org-reverse-note-order t
 org-agenda-skip-scheduled-if-done t
 org-export-with-drawers t
 org-export-with-tags t
 org-export-preprocess-before-selecting-backend-code-hook
'(org-beamer-select-beamer-code)
 org-tab-first-hook '(org-hide-block-toggle-maybe
org-src-native-tab-command-maybe
  org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
 org-refile-targets '((my-org-refile-targets :maxlevel . 5))
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
 org-cycle-show-empty-lines
  org-optimize-window-after-visibility-change)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-speed-command-hook '(org-speed-command-default-hook
org-babel-speed-command-hook)
 org-blocker-hook '(org-block-todo-from-children-or-siblings-or-parent)
 org-babel-pre-tangle-hook '(save-buffer)
 org-occur-hook '(org-first-headline-recenter)
 org-export-interblocks '((src org-babel-exp-non-block-elements))
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-export-latex-format-toc-function 'org-export-latex-format-toc-default
 org-fast-tag-selection-single-key 'expert
 org-default-notes-file ~/.emacs.d/org/notes.org
 org-export-preprocess-before-normalizing-links-hook
'(org-remove-file-link-modifiers)
 org-cycle-global-at-bob t
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-agenda-ndays 7
 org-agenda-include-diary t
 org-agenda-skip-deadline-if-done t
 org-enforce-todo-dependencies t
 org-export-first-hook '(org-beamer-initialize-open-trackers)
 org-mode-hook '(my-org-mode-hook er/add-org-mode-expansions
 #[nil \300\301\302\303\304$\207
   [org-add-hook change-major-mode-hook org-show-block-all
append local]
 5]
 #[nil \300\301\302\303\304$\207
   [org-add-hook change-major-mode-hook
org-babel-show-result-all append
 local] 5]
 org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-agenda-start-on-weekday nil
 org-directory ~/.emacs.d/org
 org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc
   org-beamer-auto-fragile-frames
   org-beamer-place-default-actions-for-lists)
 org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-confirm-shell-link-function 'yes-or-no-p
 )

[O] syncing with google calendar, file changed on disk

[Tyler Smith]

Hi,

Following the instructions from Worg (
http://orgmode.org/worg/org-tutorials/org-google-sync.html ), I've set
a cron job to download my google calendar, and use Eric Fraga's awk
script to convert it into google.org for inclusion in my agenda. This
works fine, and is currently my only syncing option as my access to
other web services (git, dropbox etc) is blocked at my workplace.

One small issue: the google calendar file changes regularly, even when
I haven't added or modified any appointments. As a consequence, I am
interrupted by Emacs reminding me that google.org has changed on disk,
and I need to respond before I can continue to browse my agenda. This
isn't a big deal, but maybe one of you know how to eliminate this
problem?

For the record, the sort of changes that I see are this:

~/.emacs.d/org$ diff google.org google.org-old
488c488
 ACTION:EMAIL
---
 ACTION:DISPLAY
490,491d489
 SUMMARY:Alarm notification
 ATTENDEE:mailto:x...@gmail.com
495c493
 ACTION:DISPLAY
---
 ACTION:EMAIL
496a495,496
 SUMMARY:Alarm notification
 ATTENDEE:mailto:x...@gmail.com


It seems the ACTION line switches back and forth between DISPLAY and
EMAIL. I don't understand the ics format to know what this means.

I have searched the mailing list and stackoverflow, but if this has
come up before I missed it. Thanks for your help,

Tyler

[O] documentation bug

[Tyler Smith]

Hi,

I'm using org-mode 7.8.03, which shipped with Emacs 24.0.94.1. The
documentation for exporting html includes the following:

12.5.1 HTML export commands
---

`C-c C-e h (`org-export-as-html')'
 Export as HTML file.  [...] If there is an active region(1), only
the region will be
 exported.

However, I think this is incorrect. If there is an active region,
org-export will turn on subtree-p. This results in unexpected
behaviour. For example, if an active region is marked that contains
two subtrees, but point is at the beginning of a third subtree, then
instead of exporting the two subtrees in the active region, you get
only the third subtree which is outside the region. The same problem
appears to hold for C-c C-e R. You actually need to call C-c C-e 1 h
to get the expected behaviour.

I'm not sure if this is a problem with the docs or the code itself,
but they don't seem to match up on this point.

Thanks,

Tyler

[O] syncing with google calendar, file changed on disk

[Tyler Smith]

Hi,

Following the instructions from Worg (
http://orgmode.org/worg/org-tutorials/org-google-sync.html ), I've set
a cron job to download my google calendar, and use Eric Fraga's awk
script to convert it into google.org for inclusion in my agenda. This
works fine, and is currently my only syncing option as my access to
other web services (git, dropbox etc) is blocked at my workplace.

One small issue: the google calendar file changes regularly, even when
I haven't added or modified any appointments. As a consequence, I am
interrupted by Emacs reminding me that google.org has changed on disk,
and I need to respond before I can continue to browse my agenda. This
isn't a big deal, but maybe one of you know how to eliminate this
problem?

For the record, the sort of changes that I see are this:

~/.emacs.d/org$ diff google.org google.org-old
488c488
 ACTION:EMAIL
---
 ACTION:DISPLAY
490,491d489
 SUMMARY:Alarm notification
 ATTENDEE:mailto:x...@gmail.com
495c493
 ACTION:DISPLAY
---
 ACTION:EMAIL
496a495,496
 SUMMARY:Alarm notification
 ATTENDEE:mailto:x...@gmail.com


It seems the ACTION line switches back and forth between DISPLAY and
EMAIL. I don't understand the ics format to know what this means.

I have searched the mailing list and stackoverflow, but if this has
come up before I missed it. Thanks for your help,

Tyler

[Orgmode] problem with remember template

[Tyler Smith]

Hi,

I'm having trouble with a remember template. My template definitions
are:

(setq org-remember-templates
  '((Todo ?t * TODO %^{Brief Description} %^G\n%?Added: %U
~/org/todo.org Tasks)
(Notes   ?n ** %^{Head Line} %U %^G\n%i%?
   ~/org/notes.org Notes)
(Appointment ?a
* %^{What}\n   %^{When}T\n   %^{Where}\n   %? Added: %U
~/org/appts.org Appointments)))

This used to work as expected for all three templates. However, when I
use the appointment template now, it halts processing after I enter the
What string. When it gets to %^{When}T: it deletes the string
%^{When}T, leaving point at that location, and leaves the following
prompt unaltered in the remember buffer.

I have tried various modifications, including emacs -Q and loading only
my org-mode setup. When I do that I get the same result, with the
message text Don't know how to make a let-bound variable an alias
appearing in the minibuffer. This doesn't appear when I use my full
.emacs.d/init.el file.

What have I messed up here?

Thanks,

Tyler
GNU Emacs 24.0.50.2 (i686-pc-linux-gnu, GTK+ Version 2.20.0) of
2010-04-30 on eku238261
org-version 6.35i

my org config file:

;; org-mode
(add-to-list 'auto-mode-alist '(\\.org$ . org-mode))
(define-key global-map \C-cl 'org-store-link)
(define-key global-map \C-ca 'org-agenda)
(global-set-key \C-cb 'org-iswitchb)
(setq org-cycle-global-at-bob t)
(defun my-org-mode-hook ()
  (setq fill-column 80))
(add-hook 'org-mode-hook 'my-org-mode-hook)
(setq my-org-refile-targets (quote (~/org/todo.org
  ~/org/notes.org ~/org/bio131.org ~/org/research.org
  ~/org/multivariate.org)))
(setq org-refile-targets '((my-org-refile-targets . (:maxlevel . 5
(setq org-log-done nil) ;; prompt for closing note? No.
(setq org-todo-keywords
  '((sequence TODO(t) WAIT(w) STARTED(s) |
  DONE(d) CANCELED(c

(define-key mode-specific-map [?a] 'org-agenda)

(require 'remember)

(add-hook 'remember-mode-hook 'org-remember-apply-template)

(define-key global-map [f5] 'remember)

(custom-set-variables
 '(org-agenda-files (quote (~/org/todo.org ~/org/notes.org
~/org/appts.org ~/org/bio131.org
~/org/research.org ~/org/multivariate.org)))
 '(org-default-notes-file ~/org/notes.org)
 '(org-agenda-ndays 7)
 '(org-deadline-warning-days 14)
 '(org-agenda-show-all-dates t)
 '(org-agenda-skip-deadline-if-done t)
 '(org-agenda-skip-scheduled-if-done t)
 '(org-agenda-start-on-weekday nil)
 '(org-reverse-note-order t)
 '(org-fast-tag-selection-single-key (quote expert))
 '(org-remember-store-without-prompt t)
 '(remember-annotation-functions (quote (org-remember-annotation)))
 '(remember-handler-functions (quote (org-remember-handler)))
 '(remember-in-new-frame t))

(setq org-tag-alist '((@office . ?o) (@home . ?h) (@lab . ?l)
  (@errand . ?e) (@computer . ?c)
  (@maywoods . ?m) (@LCW . ?w) (bio131 . ?b)
  (teaching . ?t) (research . ?r)
  (service . ?s) (social . ?S)))

(setq org-remember-templates
  '((Todo ?t * TODO %^{Brief Description} %^G\n%?Added: %U
~/org/todo.org Tasks)
(Notes   ?n ** %^{Head Line} %U %^G\n%i%?
   ~/org/notes.org Notes)
(Appointment ?a
* %^{What}\n   %^{When}t\n   %^{Where}\n   %? Added: %U
~/org/appts.org Appointments)))



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[Orgmode] Scheduling bug? [was: problem with remember template]

[Tyler Smith]

Sorry, I've just realized that the problem described in my previous
email (below) is not a remember template issue at all. I get the same
(or similar) issue when using the schedule function in org.

To reproduce:
run 'emacs -Q'
open a file in org mode (test.org)
Enter a headline (*test)
Try to schedule it (C-c C-s)

At this point I get the message Don't know how to make a let-bound
variable an alias

I get this problem in the latest Emacs on my system:

GNU Emacs 24.0.50.2 (i686-pc-linux-gnu, GTK+ Version 2.20.0) of
2010-04-30 on eku238261
org-version 6.35i

But not in the previous version on my system:

GNU Emacs 23.1.90.2 (i686-pc-linux-gnu, GTK+ Version 2.18.6) of
2010-02-16 on eku238261 
org-version 6.33x

So I think this is a bug that crept into org-mode or emacs, and not a
problem in my config files.

I also confirmed that the problem reported below doesn't occur in Emacs
23.1.90.2

Thanks,

Tyler


Tyler Smith tyler.sm...@eku.edu writes:

 Hi,

 I'm having trouble with a remember template. My template definitions
 are:

 (setq org-remember-templates
   '((Todo ?t * TODO %^{Brief Description} %^G\n%?Added: %U
 ~/org/todo.org Tasks)
   (Notes   ?n ** %^{Head Line} %U %^G\n%i%?
~/org/notes.org Notes)
   (Appointment ?a
 * %^{What}\n   %^{When}T\n   %^{Where}\n   %? Added: %U
 ~/org/appts.org Appointments)))

 This used to work as expected for all three templates. However, when I
 use the appointment template now, it halts processing after I enter the
 What string. When it gets to %^{When}T: it deletes the string
 %^{When}T, leaving point at that location, and leaves the following
 prompt unaltered in the remember buffer.

 I have tried various modifications, including emacs -Q and loading only
 my org-mode setup. When I do that I get the same result, with the
 message text Don't know how to make a let-bound variable an alias
 appearing in the minibuffer. This doesn't appear when I use my full
 .emacs.d/init.el file.

 What have I messed up here?

 Thanks,

 Tyler
 GNU Emacs 24.0.50.2 (i686-pc-linux-gnu, GTK+ Version 2.20.0) of
 2010-04-30 on eku238261
 org-version 6.35i

 my org config file:

 ;; org-mode
 (add-to-list 'auto-mode-alist '(\\.org$ . org-mode))
 (define-key global-map \C-cl 'org-store-link)
 (define-key global-map \C-ca 'org-agenda)
 (global-set-key \C-cb 'org-iswitchb)
 (setq org-cycle-global-at-bob t)
 (defun my-org-mode-hook ()
   (setq fill-column 80))
 (add-hook 'org-mode-hook 'my-org-mode-hook)
 (setq my-org-refile-targets (quote (~/org/todo.org
   ~/org/notes.org ~/org/bio131.org ~/org/research.org
   ~/org/multivariate.org)))
 (setq org-refile-targets '((my-org-refile-targets . (:maxlevel . 5
 (setq org-log-done nil) ;; prompt for closing note? No.
 (setq org-todo-keywords
   '((sequence TODO(t) WAIT(w) STARTED(s) |
   DONE(d) CANCELED(c

 (define-key mode-specific-map [?a] 'org-agenda)

 (require 'remember)

 (add-hook 'remember-mode-hook 'org-remember-apply-template)

 (define-key global-map [f5] 'remember)

 (custom-set-variables
  '(org-agenda-files (quote (~/org/todo.org ~/org/notes.org
 ~/org/appts.org ~/org/bio131.org
 ~/org/research.org ~/org/multivariate.org)))
  '(org-default-notes-file ~/org/notes.org)
  '(org-agenda-ndays 7)
  '(org-deadline-warning-days 14)
  '(org-agenda-show-all-dates t)
  '(org-agenda-skip-deadline-if-done t)
  '(org-agenda-skip-scheduled-if-done t)
  '(org-agenda-start-on-weekday nil)
  '(org-reverse-note-order t)
  '(org-fast-tag-selection-single-key (quote expert))
  '(org-remember-store-without-prompt t)
  '(remember-annotation-functions (quote (org-remember-annotation)))
  '(remember-handler-functions (quote (org-remember-handler)))
  '(remember-in-new-frame t))

 (setq org-tag-alist '((@office . ?o) (@home . ?h) (@lab . ?l)
   (@errand . ?e) (@computer . ?c)
   (@maywoods . ?m) (@LCW . ?w) (bio131 . ?b)
 (teaching . ?t) (research . ?r)
   (service . ?s) (social . ?S)))

 (setq org-remember-templates
   '((Todo ?t * TODO %^{Brief Description} %^G\n%?Added: %U
 ~/org/todo.org Tasks)
   (Notes   ?n ** %^{Head Line} %U %^G\n%i%?
~/org/notes.org Notes)
   (Appointment ?a
 * %^{What}\n   %^{When}t\n   %^{Where}\n   %? Added: %U
 ~/org/appts.org Appointments)))



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[Orgmode] Re: Scheduling bug?

[Tyler Smith]

Mikael Fornius m...@abc.se writes:

 As you found out the problem is fixed in later versions of emacs, thanks
 for telling!

Sorry, you misunderstood. It's fixed in an earlier version (23), but
broken in the later version (24).

Tyler


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[Orgmode] Re: Scheduling bug?

[Tyler Smith]

Mikael Fornius m...@abc.se writes:

 I was wrong it does work for me with this fresh from today setup:

 GNU Emacs 24.0.50.2 (i686-pc-linux-gnu, GTK+ Version 2.20.1) of 2010-06-01 on 
 eee
 Org-mode version 6.36trans (release_6.36.141.gbc53b)

 (earlier I forgot to load the latest org-mode from $HOME).

 Does it for you?

It does, thanks! Updating to org-mode 6.36trans from the git repository
fixed the problem. 

GNU Emacs 24.0.50.2 (i686-pc-linux-gnu, GTK+ Version 2.20.0) of
2010-04-30 on eku238261
org-version 6.36trans 

Cheers,

Tyler



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[Orgmode] Re: Gmane readers - please subscribe

[Tyler Smith]

Ben Finney ben+em...@benfinney.id.au writes:

 Carsten Dominik carsten.domi...@gmail.com writes:

 If you are reading emacs-orgmode.org through gmane, please read this
 new FAQ to help take load off the maintainers.

 http://orgmode.org/worg/org-faq.php#ml-subscription-and-gmane

 A large part of my reason for reading via Gmane is to avoid yet another
 set of authentication credentials. Especially one that I never use;
 that's a security nightmare waiting to happen. So I'm not interested in
 increasing my security exposure by making a Mailman account on yet
 another site.

Yikes! What nightmare awaits those of us who've foolishly gone ahead and
subscribed? What's my exposure, beyond some nefarious cracker
impersonating me on emacs-orgmode?

Tyler



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[Orgmode] Re: s in agenda saves all org-mode buffers, does not mark entry for bulk action

[Tyler Smith]

Markus Heller helle...@gmail.com writes:

 I'm using org-mode version 6.34a on Windoze XP end emacs 23.1.1.

 In any agenda view, pressing s saves all org mode buffers and does not
 mark the item for bulk action. I went through my .emacs and couldn't
 find anything that looked like re-defining a key binding to configure
 this behaviour.

 How can I find out where this faulty behavior comes from? I don't get
 any error messages ...

I think that's a bug in the documentation. `m' is the default key for
marking items for bulk action, hard-coded into org-agenda.el. The info
page lists s as the key for both `save all org buffers' and `mark for bulk
action'.

Tyler



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[Orgmode] Re: s in agenda saves all org-mode buffers, does not mark entry for bulk action

[Tyler Smith]

Markus Heller helle...@gmail.com writes:

 On 2/4/2010 3:41 PM, Tyler Smith wrote:
 Markus Hellerhelle...@gmail.com  writes:

 I'm using org-mode version 6.34a on Windoze XP end emacs 23.1.1.

 In any agenda view, pressing s saves all org mode buffers and does not
 mark the item for bulk action. I went through my .emacs and couldn't
 find anything that looked like re-defining a key binding to configure
 this behaviour.

 How can I find out where this faulty behavior comes from? I don't get
 any error messages ...

 I think that's a bug in the documentation. `m' is the default key for
 marking items for bulk action, hard-coded into org-agenda.el. The info
 page lists s as the key for both `save all org buffers' and `mark for bulk
 action'.

 Ah, `m' does the trick!  Thanks for pointing this out, Tyler!

 One more question: How can I access the info list you're talking about?


`C-h i' will open the info system, which will give you a window listing
all the help files for your Emacs installation. Move the cursor to `Org
Mode' and press enter. Alternatively, press m orgtabreturn. That
brings you to the menu for the org-info manual. The info regarding the
agenda view is in section 10, titled, funnily enough, `Agenda Views'.

Cheers,

Tyler



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