org mode in press

org mode in press

[Andreas Leha]

Hi all,

this just came into my inbox:
http://www.jstatsoft.org/v46/i03

Great work!  Big thanks to the authors.

- Andreas

Re: org mode in press

[Nick Dokos]

Andreas Leha <andreas.leha@med.uni-goettingen.de> wrote:

> Hi all,
> 
> this just came into my inbox:
> http://www.jstatsoft.org/v46/i03
> 
> Great work!  Big thanks to the authors.
> 

I remember reading it with great pleasure back when Eric posted it to
the list: beautiful stuff. I look forward to rereading it.

Congratulations!

Nick

Re: org mode in press

[Eric Schulte]

Hopefully this will serve as the canonical introduction to working with
code blocks in Org-mode.

As we acknowledge in the paper this work would not have been possible
without the ideas and feedback of the Org-mode community, so thanks all!

Nick Dokos <nicholas.dokos@hp.com> writes:

> Andreas Leha <andreas.leha@med.uni-goettingen.de> wrote:
>
>> Hi all,
>> 
>> this just came into my inbox:
>> http://www.jstatsoft.org/v46/i03
>> 
>> Great work!  Big thanks to the authors.
>> 
>
> I remember reading it with great pleasure back when Eric posted it to
> the list: beautiful stuff. I look forward to rereading it.
>
> Congratulations!
>
> Nick
>
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: org mode in press

[Christian Wittern]

I think this is an excellent article, introducing an aspect of org-mode, 
which I think fills a gap that no other software I know of comes even close 
to approach.  I already started mentioning it in conversations and am sure 
it will be very useful to many members of the academic community.

Just to make sure I could answer any follow up questions, I downloaded the 
replication bundle and started installing the dependencies.  I encountered a 
few problems and hope this is the right place to discuss them.  BTW, I am 
working with this on a Mac OS X 10.6 machine.

Most of the dependencies I already had or  installed them from macports.  
One problem I encountered was with installing the RSQLite package.  
Executing the installation command from the README file did not work because 
of permission issues, the command needs to run with superuser rights.  Is it 
possible to give these rights to commands run from babel?  Since I did not 
find a way to do that, I installed from the R commandline, where I found 
that the name of the package is RSQLite, not 'RSQlite' as given in the 
readme file.

The one dependency I could not solve was the 'dot' executable.  I assume 
this is an interpreter for the dot language, for which it seems the program 
on the Mac is named graphviz.  However, I am not sure how to make that work 
with org/babel.  Should I simply symlink to graphviz?  Or is there a babel 
variable to be set?  This is a point that probably needs some explanation, 
at least for Mac users (I realize that the articel might not have been 
intended as such a general introduction with details for all common OSses, 
but it would be nice if this can be gradually supplemented).

One last remark; since this is an online publication, I think using proper 
fontification for the examples and org source code would be even more 
appealing, especially for people who encounter org for the first time.

Keep up the excellent work!!

Christian



On 2012-01-27 23:43, Eric Schulte wrote:
> Hopefully this will serve as the canonical introduction to working with
> code blocks in Org-mode.
>
> As we acknowledge in the paper this work would not have been possible
> without the ideas and feedback of the Org-mode community, so thanks all!
>
> Nick Dokos<nicholas.dokos@hp.com>  writes:
>
>> Andreas Leha<andreas.leha@med.uni-goettingen.de>  wrote:
>>
>>> Hi all,
>>>
>>> this just came into my inbox:
>>> http://www.jstatsoft.org/v46/i03
>>>
>>> Great work!  Big thanks to the authors.
>>>
>> I remember reading it with great pleasure back when Eric posted it to
>> the list: beautiful stuff. I look forward to rereading it.
>>
>> Congratulations!
>>
>> Nick
>>
>>


-- 
Christian Wittern, Kyoto

Re: org mode in press

[rick frankel]

On Jan 28, 2012, at 6:14, Christian Wittern <cwittern@gmail.com> wrote:

> 
> 
> The one dependency I could not solve was the 'dot' executable.  I assume this is an interpreter for the dot language, for which it seems the program on the Mac is named graphviz.  However, I am not sure how to make that work with org/babel.  Should I simply symlink to graphviz?  Or is there a babel variable to be set?  This is a point that probably needs some explanation, at least for Mac users (I realize that the articel might not have been intended as such a general introduction with details for all common OSses, but it would be nice if this can be gradually supplemented).

The dot executable is part of the graphviz package. Installing graphviz should install the dot command line executable alongw w/ neato, circo and and other layout engines. 

Rick

Re: org mode in press

[Thomas S. Dye]

Aloha Christian,

Thanks for your comments.  It is great to have feedback.

Christian Wittern <cwittern@gmail.com> writes:

> I think this is an excellent article, introducing an aspect of
> org-mode, which I think fills a gap that no other software I know of
> comes even close to approach.  I already started mentioning it in
> conversations and am sure it will be very useful to many members of
> the academic community.
>
> Just to make sure I could answer any follow up questions, I downloaded
> the replication bundle and started installing the dependencies.  I
> encountered a few problems and hope this is the right place to discuss
> them.  BTW, I am working with this on a Mac OS X 10.6 machine.
>
> Most of the dependencies I already had or  installed them from
> macports.  One problem I encountered was with installing the RSQLite
> package.  Executing the installation command from the README file did
> not work because of permission issues, the command needs to run with
> superuser rights.  Is it possible to give these rights to commands run
> from babel?  Since I did not find a way to do that, I installed from
> the R commandline, where I found that the name of the package is
> RSQLite, not 'RSQlite' as given in the readme file.
>
> The one dependency I could not solve was the 'dot' executable.  I
> assume this is an interpreter for the dot language, for which it seems
> the program on the Mac is named graphviz.  However, I am not sure how
> to make that work with org/babel.  Should I simply symlink to
> graphviz?  Or is there a babel variable to be set?  This is a point
> that probably needs some explanation, at least for Mac users (I
> realize that the articel might not have been intended as such a
> general introduction with details for all common OSses, but it would
> be nice if this can be gradually supplemented).
>
> One last remark; since this is an online publication, I think using
> proper fontification for the examples and org source code would be
> even more appealing, especially for people who encounter org for the
> first time.

Could you be more specific here?  It might be obvious to others, but I
don't understand what you mean by "proper fontification."

All the best,
Tom

>
> Keep up the excellent work!!
>
> Christian
>
>
>
> On 2012-01-27 23:43, Eric Schulte wrote:
>> Hopefully this will serve as the canonical introduction to working with
>> code blocks in Org-mode.
>>
>> As we acknowledge in the paper this work would not have been possible
>> without the ideas and feedback of the Org-mode community, so thanks all!
>>
>> Nick Dokos<nicholas.dokos@hp.com>  writes:
>>
>>> Andreas Leha<andreas.leha@med.uni-goettingen.de>  wrote:
>>>
>>>> Hi all,
>>>>
>>>> this just came into my inbox:
>>>> http://www.jstatsoft.org/v46/i03
>>>>
>>>> Great work!  Big thanks to the authors.
>>>>
>>> I remember reading it with great pleasure back when Eric posted it to
>>> the list: beautiful stuff. I look forward to rereading it.
>>>
>>> Congratulations!
>>>
>>> Nick
>>>
>>>

-- 
Thomas S. Dye
http://www.tsdye.com

Re: org mode in press

[Nick Dokos]

Christian Wittern <cwittern@gmail.com> wrote:

> The one dependency I could not solve was the 'dot' executable.  I
> assume this is an interpreter for the dot language, for which it seems
> the program on the Mac is named graphviz.  However, I am not sure how
> to make that work with org/babel.  Should I simply symlink to
> graphviz?  Or is there a babel variable to be set?  This is a point
> that probably needs some explanation, at least for Mac users (I
> realize that the articel might not have been intended as such a
> general introduction with details for all common OSses, but it would
> be nice if this can be gradually supplemented).
> 

On linux, the graphviz package install a bunch of libraries and a bunch of
commands. The commands are:

,----
|    Graph layout programs
|        dot    filter for hierarchical layouts of graphs
| 
|        neato  filter for symmetric layouts of graphs
| 
|        twopi  filter for radial layouts of graphs
| 
|        circo  filter for circular layout of graphs
| 
|        fdp    filter for symmetric layouts of graphs
| 
|        All of the filters work with either directed or undirected graphs, though dot  is  typically
|        used for directed graphs and neato for undirected graphs.  Note also that neato -n[2] can be
|        used to render layouts produced by the other filters.
| 
|    Graph drawing programs
|        lefty  A Programmable Graphics Editor
| 
|        lneato lefty + neato
| 
|        dotty  lefty + dot
| 
|    Graph layout enhancement
|        gvcolor
|               flow colors through a ranked digraph
| 
|        unflatten
|               adjust directed graphs to improve layout aspect ratio
| 
|        gvpack merge and pack disjoint graphs
| 
|    Graph information and transformation
|        gc     count graph components
| 
|        acyclic
|               make directed graph acyclic
| 
|        nop    pretty-print graph file
| 
|        ccomps connected components filter for graphs
| 
|        sccmap extract strongly connected components of directed graphs
| 
|        tred   transitive reduction filter for directed graphs
| 
|        dijkstra
|               single-source distance filter
| 
|        bcomps biconnected components filter for graphs
| 
|        gvpr   graph pattern scanning and processing language
| 
|        prune  prune directed graphs
| 
|    Other
|        gxl2dot, dot2gxl
|               GXL-DOT converters
`----

There is no "graphviz" executable as such. I would expect a similar setup
on MacOS. The man page refers to http://www.graphviz.org/Documentation.php
for more info.

HTH,
Nick

Re: org mode in press

[Dov Grobgeld]

[-- Attachment #1: Type: text/plain, Size: 3941 bytes --]

I would also like to thank you for this great article and org-mode in
general. I learned a few things about variables and chaining that I did not
know about. Since I discovered org-mode, I have come to rely upon it as my
extended memory for professional as well as domestic ideas and problems
that I encounter. I keep one big notes.org file in which my first level
headlines is the current date, and my second order headline usually
contains a "Done/Todo" which is a checklist of things that I have to do. I
also love the embedded code (though I wish it was possible to syntax
highlight it!), external links, and tables.

Thanks again!
Dov

On Sat, Jan 28, 2012 at 18:18, Thomas S. Dye <tsd@tsdye.com> wrote:

> Aloha Christian,
>
> Thanks for your comments.  It is great to have feedback.
>
> Christian Wittern <cwittern@gmail.com> writes:
>
> > I think this is an excellent article, introducing an aspect of
> > org-mode, which I think fills a gap that no other software I know of
> > comes even close to approach.  I already started mentioning it in
> > conversations and am sure it will be very useful to many members of
> > the academic community.
> >
> > Just to make sure I could answer any follow up questions, I downloaded
> > the replication bundle and started installing the dependencies.  I
> > encountered a few problems and hope this is the right place to discuss
> > them.  BTW, I am working with this on a Mac OS X 10.6 machine.
> >
> > Most of the dependencies I already had or  installed them from
> > macports.  One problem I encountered was with installing the RSQLite
> > package.  Executing the installation command from the README file did
> > not work because of permission issues, the command needs to run with
> > superuser rights.  Is it possible to give these rights to commands run
> > from babel?  Since I did not find a way to do that, I installed from
> > the R commandline, where I found that the name of the package is
> > RSQLite, not 'RSQlite' as given in the readme file.
> >
> > The one dependency I could not solve was the 'dot' executable.  I
> > assume this is an interpreter for the dot language, for which it seems
> > the program on the Mac is named graphviz.  However, I am not sure how
> > to make that work with org/babel.  Should I simply symlink to
> > graphviz?  Or is there a babel variable to be set?  This is a point
> > that probably needs some explanation, at least for Mac users (I
> > realize that the articel might not have been intended as such a
> > general introduction with details for all common OSses, but it would
> > be nice if this can be gradually supplemented).
> >
> > One last remark; since this is an online publication, I think using
> > proper fontification for the examples and org source code would be
> > even more appealing, especially for people who encounter org for the
> > first time.
>
> Could you be more specific here?  It might be obvious to others, but I
> don't understand what you mean by "proper fontification."
>
> All the best,
> Tom
>
> >
> > Keep up the excellent work!!
> >
> > Christian
> >
> >
> >
> > On 2012-01-27 23:43, Eric Schulte wrote:
> >> Hopefully this will serve as the canonical introduction to working with
> >> code blocks in Org-mode.
> >>
> >> As we acknowledge in the paper this work would not have been possible
> >> without the ideas and feedback of the Org-mode community, so thanks all!
> >>
> >> Nick Dokos<nicholas.dokos@hp.com>  writes:
> >>
> >>> Andreas Leha<andreas.leha@med.uni-goettingen.de>  wrote:
> >>>
> >>>> Hi all,
> >>>>
> >>>> this just came into my inbox:
> >>>> http://www.jstatsoft.org/v46/i03
> >>>>
> >>>> Great work!  Big thanks to the authors.
> >>>>
> >>> I remember reading it with great pleasure back when Eric posted it to
> >>> the list: beautiful stuff. I look forward to rereading it.
> >>>
> >>> Congratulations!
> >>>
> >>> Nick
> >>>
> >>>
>
> --
> Thomas S. Dye
> http://www.tsdye.com
>
>

[-- Attachment #2: Type: text/html, Size: 5446 bytes --]

Re: org mode in press

[Eric Schulte]

Dov Grobgeld <dov.grobgeld@gmail.com> writes:

> I would also like to thank you for this great article and org-mode in
> general. I learned a few things about variables and chaining that I did not
> know about. Since I discovered org-mode, I have come to rely upon it as my
> extended memory for professional as well as domestic ideas and problems
> that I encounter. I keep one big notes.org file in which my first level
> headlines is the current date, and my second order headline usually
> contains a "Done/Todo" which is a checklist of things that I have to
> do.

Great to hear, happy it is useful even to those who already have
Org-mode experience.

> I also love the embedded code (though I wish it was possible to syntax
> highlight it!),

It is possible, just add the following to your Emacs configuration.

(setq org-src-fontify-natively t)

Cheers,

> external links, and tables.
>
> Thanks again!
> Dov
>
> On Sat, Jan 28, 2012 at 18:18, Thomas S. Dye <tsd@tsdye.com> wrote:
>
>> Aloha Christian,
>>
>> Thanks for your comments.  It is great to have feedback.
>>
>> Christian Wittern <cwittern@gmail.com> writes:
>>
>> > I think this is an excellent article, introducing an aspect of
>> > org-mode, which I think fills a gap that no other software I know of
>> > comes even close to approach.  I already started mentioning it in
>> > conversations and am sure it will be very useful to many members of
>> > the academic community.
>> >
>> > Just to make sure I could answer any follow up questions, I downloaded
>> > the replication bundle and started installing the dependencies.  I
>> > encountered a few problems and hope this is the right place to discuss
>> > them.  BTW, I am working with this on a Mac OS X 10.6 machine.
>> >
>> > Most of the dependencies I already had or  installed them from
>> > macports.  One problem I encountered was with installing the RSQLite
>> > package.  Executing the installation command from the README file did
>> > not work because of permission issues, the command needs to run with
>> > superuser rights.  Is it possible to give these rights to commands run
>> > from babel?  Since I did not find a way to do that, I installed from
>> > the R commandline, where I found that the name of the package is
>> > RSQLite, not 'RSQlite' as given in the readme file.
>> >
>> > The one dependency I could not solve was the 'dot' executable.  I
>> > assume this is an interpreter for the dot language, for which it seems
>> > the program on the Mac is named graphviz.  However, I am not sure how
>> > to make that work with org/babel.  Should I simply symlink to
>> > graphviz?  Or is there a babel variable to be set?  This is a point
>> > that probably needs some explanation, at least for Mac users (I
>> > realize that the articel might not have been intended as such a
>> > general introduction with details for all common OSses, but it would
>> > be nice if this can be gradually supplemented).
>> >
>> > One last remark; since this is an online publication, I think using
>> > proper fontification for the examples and org source code would be
>> > even more appealing, especially for people who encounter org for the
>> > first time.
>>
>> Could you be more specific here?  It might be obvious to others, but I
>> don't understand what you mean by "proper fontification."
>>
>> All the best,
>> Tom
>>
>> >
>> > Keep up the excellent work!!
>> >
>> > Christian
>> >
>> >
>> >
>> > On 2012-01-27 23:43, Eric Schulte wrote:
>> >> Hopefully this will serve as the canonical introduction to working with
>> >> code blocks in Org-mode.
>> >>
>> >> As we acknowledge in the paper this work would not have been possible
>> >> without the ideas and feedback of the Org-mode community, so thanks all!
>> >>
>> >> Nick Dokos<nicholas.dokos@hp.com>  writes:
>> >>
>> >>> Andreas Leha<andreas.leha@med.uni-goettingen.de>  wrote:
>> >>>
>> >>>> Hi all,
>> >>>>
>> >>>> this just came into my inbox:
>> >>>> http://www.jstatsoft.org/v46/i03
>> >>>>
>> >>>> Great work!  Big thanks to the authors.
>> >>>>
>> >>> I remember reading it with great pleasure back when Eric posted it to
>> >>> the list: beautiful stuff. I look forward to rereading it.
>> >>>
>> >>> Congratulations!
>> >>>
>> >>> Nick
>> >>>
>> >>>
>>
>> --
>> Thomas S. Dye
>> http://www.tsdye.com
>>
>>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: org mode in press

[Eric Schulte]

Christian Wittern <cwittern@gmail.com> writes:

> I think this is an excellent article, introducing an aspect of
> org-mode, which I think fills a gap that no other software I know of
> comes even close to approach.  I already started mentioning it in
> conversations and am sure it will be very useful to many members of
> the academic community.
>

Wonderful.

>
> Just to make sure I could answer any follow up questions, I downloaded
> the replication bundle and started installing the dependencies.  I
> encountered a few problems and hope this is the right place to discuss
> them.  BTW, I am working with this on a Mac OS X 10.6 machine.
>
> Most of the dependencies I already had or  installed them from
> macports.  One problem I encountered was with installing the RSQLite
> package.  Executing the installation command from the README file did
> not work because of permission issues, the command needs to run with
> superuser rights.

This is surprising, on the two GNU/Linux distributions I've tested this
on I am prompted to pick an R install directory which defaults to ~/R in
my home directory so no super-user privileges are required.  My original
motivation for switching from OSX to GNU/Linux was precisely this sort
of weird Mac-specific library install issues across a number of tools
(most notably LaTeX).  Although, a couple of years after switching my
reasons for not switching back are legion. :)

> Is it possible to give these rights to commands run from babel?  Since
> I did not find a way to do that, I installed from the R commandline,
> where I found that the name of the package is RSQLite, not 'RSQlite'
> as given in the readme file.
>
> The one dependency I could not solve was the 'dot' executable.  I
> assume this is an interpreter for the dot language, for which it seems
> the program on the Mac is named graphviz.  However, I am not sure how
> to make that work with org/babel.  Should I simply symlink to
> graphviz?  Or is there a babel variable to be set?  This is a point
> that probably needs some explanation, at least for Mac users (I
> realize that the articel might not have been intended as such a
> general introduction with details for all common OSses, but it would
> be nice if this can be gradually supplemented).
>
> One last remark; since this is an online publication, I think using
> proper fontification for the examples and org source code would be
> even more appealing, especially for people who encounter org for the
> first time.
>
> Keep up the excellent work!!
>

Thanks!,

>
> Christian
>
>
>
> On 2012-01-27 23:43, Eric Schulte wrote:
>> Hopefully this will serve as the canonical introduction to working with
>> code blocks in Org-mode.
>>
>> As we acknowledge in the paper this work would not have been possible
>> without the ideas and feedback of the Org-mode community, so thanks all!
>>
>> Nick Dokos<nicholas.dokos@hp.com>  writes:
>>
>>> Andreas Leha<andreas.leha@med.uni-goettingen.de>  wrote:
>>>
>>>> Hi all,
>>>>
>>>> this just came into my inbox:
>>>> http://www.jstatsoft.org/v46/i03
>>>>
>>>> Great work!  Big thanks to the authors.
>>>>
>>> I remember reading it with great pleasure back when Eric posted it to
>>> the list: beautiful stuff. I look forward to rereading it.
>>>
>>> Congratulations!
>>>
>>> Nick
>>>
>>>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: org mode in press

[Nick Dokos]

Nick Dokos <nicholas.dokos@hp.com> wrote:

> Christian Wittern <cwittern@gmail.com> wrote:
> 
> > The one dependency I could not solve was the 'dot' executable.  I
> > assume this is an interpreter for the dot language, for which it seems
> > the program on the Mac is named graphviz.  However, I am not sure how
> > to make that work with org/babel.  Should I simply symlink to
> > graphviz?  Or is there a babel variable to be set?  This is a point
> > that probably needs some explanation, at least for Mac users (I
> > realize that the articel might not have been intended as such a
> > general introduction with details for all common OSses, but it would
> > be nice if this can be gradually supplemented).
> > 
> 
> On linux, the graphviz package install a bunch of libraries and a bunch of
> commands. The commands are:
> 
> ...

... and afaict, all the commands are symlinks to the dot executable
(/usr/bin/dot).

Nick

> 
> There is no "graphviz" executable as such. I would expect a similar setup
> on MacOS. The man page refers to http://www.graphviz.org/Documentation.php
> for more info.
> 
> HTH,
> Nick
> 
> 

Re: org mode in press

[Christian Wittern]

On 2012-01-28 22:59, rick frankel wrote:
>
> The dot executable is part of the graphviz package. Installing graphviz should install the dot command line executable alongw w/ neato, circo and and other layout engines.
>
> Rick
Thanks to all who pointed this out.
$sudo port install graphviz
did the trick for me, now all dependencies are met.  Yeah!

Christian

-- 
Christian Wittern, Kyoto