Re: [O] org mode in press
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
Re: [O] org mode in press
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 Dokosnicholas.do...@hp.com writes: Andreas Lehaandreas.l...@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: [O] org mode in press
On Jan 28, 2012, at 6:14, Christian Wittern cwitt...@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: [O] org mode in press
Aloha Christian, Thanks for your comments. It is great to have feedback. Christian Wittern cwitt...@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 Dokosnicholas.do...@hp.com writes: Andreas Lehaandreas.l...@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: [O] org mode in press
Christian Wittern cwitt...@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 |dotfilter 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 | |fdpfilter 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 | |noppretty-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: [O] org mode in press
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 t...@tsdye.com wrote: Aloha Christian, Thanks for your comments. It is great to have feedback. Christian Wittern cwitt...@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 Dokosnicholas.do...@hp.com writes: Andreas Lehaandreas.l...@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: [O] org mode in press
Dov Grobgeld dov.grobg...@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 t...@tsdye.com wrote: Aloha Christian, Thanks for your comments. It is great to have feedback. Christian Wittern cwitt...@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 Dokosnicholas.do...@hp.com writes: Andreas Lehaandreas.l...@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: [O] org mode in press
Christian Wittern cwitt...@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 Dokosnicholas.do...@hp.com writes: Andreas Lehaandreas.l...@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: [O] org mode in press
Nick Dokos nicholas.do...@hp.com wrote: Christian Wittern cwitt...@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: [O] org mode in press
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.do...@hp.com writes: Andreas Leha andreas.l...@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/
[O] org mode in press
Hi all, this just came into my inbox: http://www.jstatsoft.org/v46/i03 Great work! Big thanks to the authors. - Andreas
Re: [O] org mode in press
Andreas Leha andreas.l...@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
