[Rd] Latex errors (build on windows)
Where can I found hepl about latex errors:
the R CMD check tells me less, but:
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
pdflatex is not available
Error in running tools::texi2pdf()
The http://win-builder.r-project.org tells me more details but I am
comlpetely lost
especially.:
LaTeX errors found:
! Paragraph ended before \hyper@n@rmalise was complete.
\par
l.575 \end
{ExampleCode}
! You can't use `macro parameter character #' in horizontal mode.
...1,1,1,-1),stringsAsFactors=FALSE) ##
## comment text in the
examples ...
l.575 \end
{ExampleCode}
! Missing $ inserted.
$
l.575 \end
Knut
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Re: [Rd] Latex errors (build on windows)
Can you post the offending package?
On Fri, May 3, 2013 at 8:46 AM, Knut Krueger wrote:
> Where can I found hepl about latex errors:
>
> the R CMD check tells me less, but:
> * checking PDF version of manual ... WARNING
> LaTeX errors when creating PDF version.
> This typically indicates Rd problems.
> * checking PDF version of manual without hyperrefs or index ... ERROR
> Re-running with no redirection of stdout/stderr.
> Hmm ... looks like a package
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
> pdflatex is not available
> Error in running tools::texi2pdf()
>
> The http://win-builder.r-project.org tells me more details but I am
> comlpetely lost
>
> especially.:
>
> LaTeX errors found:
>
>
>
> ! Paragraph ended before \hyper@n@rmalise was complete.
>
>\par
> l.575 \end
>
> {ExampleCode}
> ! You can't use `macro parameter character #' in horizontal mode.
> ...1,1,1,-1),stringsAsFactors=FALSE) ##
> ## comment text in the
> examples ...
> l.575 \end
>
>
> {ExampleCode}
> ! Missing $ inserted.
>
> $
> l.575 \end
>
> Knut
>
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Re: [Rd] Latex errors (build on windows)
Am 03.05.2013 09:58, schrieb R. Michael Weylandt: Can you post the offending package? http://rrepository.konstanze-krueger.de/src/contrib/Dominance_0.9.5.tar.gz Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Latex errors (build on windows)
On 13-05-03 3:46 AM, Knut Krueger wrote:
Where can I found hepl about latex errors:
the R CMD check tells me less, but:
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
pdflatex is not available
You should install MikTeX, from www.miktex.org. I think it will put
itself on your path, but if it does not, you need to make sure the
miktex/bin directory is on your path.
Error in running tools::texi2pdf()
The http://win-builder.r-project.org tells me more details but I am
comlpetely lost
especially.:
LaTeX errors found:
! Paragraph ended before \hyper@n@rmalise was complete.
\par
l.575 \end
{ExampleCode}
! You can't use `macro parameter character #' in horizontal mode.
...1,1,1,-1),stringsAsFactors=FALSE) ##
## comment text in the
examples ...
l.575 \end
{ExampleCode}
! Missing $ inserted.
$
l.575 \end
Once you have pdflatex available, you can run
R CMD Rd2pdf --no-clean
and it will likely give the same error, but will leave behind the files
that caused the errors. Take a look at line 575 (or whatever) of the
.tex file, and you should be able to spot where it came from in your
code. Fix that if the problem is obvious, or show us.
Duncan Murdoch
Knut
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Re: [Rd] Latex errors (build on windows)
Am 03.05.2013 13:03, schrieb Duncan Murdoch: You should install MikTeX, from www.miktex.org. I think it will put itself on your path, but if it does not, you need to make sure the miktex/bin directory is on your path. Thank you, it worked first with a strange error message: File ended while scanning use of \Rhref. there was a % in the DOI path of an URL Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] loading of unwanted namespace
Martin, Your suggestion below did the trick. The issue was obvious once this pointed me to the correct bit of code. Thanks much. Terry T. begin included text --- trace(loadNamespace, quote(if (package == "survival") recover())) will break into ?recover when survival is being loaded. Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Latex errors (build on windows)
Am 03.05.2013 09:58, schrieb R. Michael Weylandt: Can you post the offending package? I solved the problem all is fine now, thanks __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Latex errors (build on windows)
Percent signs are comment markers in .Rd files, so if you want to keep one, you need to escape it by preceding it with a backslash. I know but it was a copy and paste error ... I fixed it just in this way. Duncan Murdoch by the way, what's the next step to get the files on an mirror .. if anybody is interested in that stuff? Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Latex errors (build on windows)
On 03/05/2013 9:35 AM, Knut Krueger wrote: > Percent signs are comment markers in .Rd files, so if you want to keep > one, you need to escape it by preceding it with a backslash. > I know but it was a copy and paste error ... I fixed it just in this way. > Duncan Murdoch > by the way, what's the next step to get the files on an mirror .. if anybody is interested in that stuff? There are several different systems that distribute packages. The main one is CRAN. Their policies and upload instructions are here: http://cran.r-project.org/web/packages/policies.html You might instead want to submit to Bioconductor, R-forge, Rforge, etc. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] submiting a package [was]Latex errors (build on windows)
Am 03.05.2013 16:05, schrieb Duncan Murdoch: On 03/05/2013 9:35 AM, Knut Krueger wrote: > Percent signs are comment markers in .Rd files, so if you want to keep > one, you need to escape it by preceding it with a backslash. > I know but it was a copy and paste error ... I fixed it just in this way. > Duncan Murdoch > by the way, what's the next step to get the files on an mirror .. if anybody is interested in that stuff? There are several different systems that distribute packages. The main one is CRAN. Their policies and upload instructions are here: http://cran.r-project.org/web/packages/policies.html You might instead want to submit to Bioconductor, R-forge, Rforge, etc. I don't know where is the best for that the package is building an ADI (Average Dominance index) building a special sociogramm with igraph, and building a Musicnotation graph http://dx.doi.org/10.1186%2F1742-9994-3-18 all three things are for calculating dominance hierarchies in animals. Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Latex errors (build on windows)
On 03/05/2013 9:12 AM, Knut Krueger wrote: Am 03.05.2013 13:03, schrieb Duncan Murdoch: > > You should install MikTeX, from www.miktex.org. I think it will put > itself on your path, but if it does not, you need to make sure the > miktex/bin directory is on your path. > Thank you, it worked first with a strange error message: File ended while scanning use of \Rhref. there was a % in the DOI path of an URL Percent signs are comment markers in .Rd files, so if you want to keep one, you need to escape it by preceding it with a backslash. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Licence change
Dear list,
For the maintainer of a given package, is it possible to change the
licence of a it from GPL >= 2 to GPL >= 3 ?
Thanks in advance,
Mauricio Zambrano-Bigiarini, Ph.D
--
=
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Institute for Environment and Sustainability (IES)
Joint Research Centre (JRC), European Commission
TP 261, Via Enrico Fermi 2749, 21027 Ispra (VA), IT
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[Rd] Package update for old version of R
Hi, Is is possible to create a release of a package against an older version of R? I would like to release a new version of the package I maintain, but have some errors when I test it against R 3.0.0. Would CRAN accept a new release that works with R 2.15.3 but not R 3.0.0? Thanks, Eilidh Troup -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package update for old version of R
On May 3, 2013, at 14:55 , Eilidh Troup wrote: > Hi, > > Is is possible to create a release of a package against an older version of > R? I would like to release a new version of the package I maintain, but have > some errors when I test it against R 3.0.0. Would CRAN accept a new release > that works with R 2.15.3 but not R 3.0.0? I strongly doubt it. By the CRAN logic, it would move immediately to the Archived folder, which is a fairly obscure place to have your users go look... They're usually helpful in getting you to fix the errors, though. -p -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Licence change
On 03/05/2013 10:34 AM, Mauricio Zambrano-Bigiarini wrote: Dear list, For the maintainer of a given package, is it possible to change the licence of a it from GPL >= 2 to GPL >= 3 ? Are you the author and copyright holder of everything in the package? If so, then I think the answer is yes. If not, then what license did the author give you for the parts you didn't write? You'll need to consult that, to find out if you can still distribute the code with a more restrictive license. For example, if you're using some code that was licensed under GPL 2 (not GPL >= 2), then you need permission from the author of it to distribute it under a different license. If you are distributing the package on CRAN, you'll have to ask them whether they'll still choose to distribute your package after the change. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Licence change
On May 3, 2013, at 10:34 AM, Mauricio Zambrano-Bigiarini wrote:
> Dear list,
>
> For the maintainer of a given package, is it possible to change the licence
> of a it from GPL >= 2 to GPL >= 3 ?
>
In general the maintainer has no such rights. However, if the maintainer is
also the author and holds all copyright, he can release the package under any
license he feels fit. What has been already released cannot be affected,
obviously, but you can release a new version under a different license if you
have the legal right to do so.
(This is not related to the possibility, but one practical problem with
requiring GPL >=3 is that it is not GPL-2 compatible so it's a decision that
better be made very consciously with all the consequences in mind).
Cheers,
Simon
> Thanks in advance,
>
> Mauricio Zambrano-Bigiarini, Ph.D
>
> --
> =
> Water Resources Unit
> Institute for Environment and Sustainability (IES)
> Joint Research Centre (JRC), European Commission
> TP 261, Via Enrico Fermi 2749, 21027 Ispra (VA), IT
> webinfo: http://floods.jrc.ec.europa.eu/
> =
> DISCLAIMER:\ "The views expressed are purely those of th...{{dropped:9}}
>
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Re: [Rd] Minimal build of R ...
Hi All, thanks for the replies. Very helpful to know that it will run with just base. Looks like the best bet, at least to get started, is to not use the usual build-process, but to come up with a simple build-script for just the core. Ultimately, the build script has to be different anyway, as compiling the Fortran code to JS requires a few more steps than the native compile. For a bit of context, the reason I'm toying with this is I've been experimenting recently with analysis-in-the-browser. The kernel of the idea is that if you could do real analysis, without installing anything, and share it on the web then it would be a Good Thing, and could make it easier to engage people with data. I've got a proof-of-concept version running here http://www.monkeycruncher.org that let's you write javascript analysis code in notebook-style documents. It's neat, but it's a bit hamstrung by the lack of javascript libraries to actually do any useful analysis! If you could have R running in there though, that would be a much better proposition ... I'll let you know if I make any progress! Jony -- Centre for Cold Matter, The Blackett Laboratory, Imperial College London, London SW7 2BW T: +44 (0)207 5947741 http://www.imperial.ac.uk/people/jony.hudson http://www.imperial.ac.uk/ccm/research/edm http://www.monkeycruncher.org http://j-star.org/ -- On 3 May 2013, at 01:31, Simon Urbanek wrote: > On May 2, 2013, at 6:18 PM, Gabriel Becker wrote: > >> Jony, >> >> I'm currently writing up the paper for something with a similar result but >> very different implementation. The RBrowserPlugin package/browser plugin >> (joint with my advisor Duncan Temple Lang) embeds R within the web browser >> as an NPAPI plugin. >> >> This approach allows full bi-directional communication between R and the >> javascript engine (including direct function calling and references to >> native objects in both directions) using a user's existing local R >> installation (including packages). >> > > Minor detail: it requires you to have R *and* a special plugin which makes it > pretty much non-deployable. It's completely unrelated to what Jony is > proposing - which doesn't require any dependencies and is actually pretty > cool and would be useful if feasible. FWIW: There are many ways to run R from > a browser that already exist - without the need for plugins or other > client-side hacks - that's the beauty of modern browsers :). > > > To get this back on the actual topic: I have been toying with cross-compiling > R when I was porting it on the iPhone and it's possible, however, you can't > use the build process as-is. It does build core R properly, but the problem > is that you need to bootstrap R to build any packages. I worked around the > problem at the time by building packages on another platform and re-using > those files (things like lazy-loaded DBs, compiled RD files etc.). > > I can imagine that you'll need some equivalent to dynamic linking, but > conceptually it's nothing else but calling functions, so I think you should > be able to compile each package separately and just replace the dynload code > by code that loads another JavaScript. The nice thing is that packages will > simply be just another JS libraries. That's all in theory, I didn't actually > try that part. I suspect you'll have a lot of work, e.g. you'll need to map > all the I/O operations that load compiled/stored R code, documentation, data > from somewhere etc. Good luck! > If all fails, you can always compile R for JS/Linux ;). > > Cheers, > Simon > > > >> Devel source at https://github.com/gmbecker/RFirefox, release, (hopefully) >> officially cross-platform version to coincide with the paper going off for >> review. >> >> I had toyed with the idea of the emscripten approach, but I think putting R >> in the browser once is enough for me at the moment so I will happily keep >> an eye on your project instead of attacking that myself :). >> >> As for your actual question I can't really say, other than that I suspect >> you will not be able to dispense with base and methods, but that I would >> conjecture that stats is "optional". >> >> ~G >> >> >> On Thu, May 2, 2013 at 9:12 AM, Jony Hudson >> wrote: >> >>> Hi, >>> >>> I'm trying to cross-compile R to javascript so that it can run in a >>> web-browser. Take as long as you need to stop laughing. So, as I was saying >>> - I want to try and get a build of R running in the browser. [If you're not >>> familiar with it already, you might enjoy looking at emscripten.org. It's >>> a remarkably capable tool for translating LLVM bitcode to javascript. Check >>> out some of the demos!] >>> >>> I'm trying to start out with the most minimal build of R possible. I can >>> turn off various options in the configure script, but I'm wondering about >>> the bundled R packages (base, stats etc). I'm guessing that the native code >>> portions of these packages are dynamically loaded at r
Re: [Rd] Licence change
On 03/05/13 16:56, Simon Urbanek wrote: On May 3, 2013, at 10:34 AM, Mauricio Zambrano-Bigiarini wrote: Dear list, For the maintainer of a given package, is it possible to change the licence of a it from GPL >= 2 to GPL >= 3 ? In general the maintainer has no such rights. However, if the maintainer is also the author and holds all copyright, he can release the package under any license he feels fit. What has been already released cannot be affected, obviously, but you can release a new version under a different license if you have the legal right to do so. Thank you very much Duncan and Simon for your replies. The package I'm asking about has 1 author [aut] (me) and 1 contributor [ctb] in the 'Author' field of the DESCRIPTION file. Both of them hold the copyright of the package. In case we want to change the licence. Do the 2 authors write something particular in the next submission to CRAN ? Do we need to provide some written document to CRAN ? What Duncan means with "If you are distributing the package on CRAN, you'll have to ask them whether they'll still choose to distribute your package after the change" May CRAN to decide not to distribute the package because of the change in the licence ? (This is not related to the possibility, but one practical problem with requiring GPL >=3 is that it is not GPL-2 compatible so it's a decision that better be made very consciously with all the consequences in mind). If the package we are talking about is pure R code, with only some dependencies to other R packages, what are the implications of: " one practical problem with requiring GPL >=3 is that it is not GPL-2 compatible" Thanks again, Mauricio -- = Linux user #454569 -- Ubuntu user #17469 = "Study, Practice and Teach" (Jim Rohn) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Minimal build of R ...
Jony, I would caution that while R will run with just base, you won't be able to do much of anything with it. All the statistical analysis and graphing functions reside in additional packages. So practically speaking you'll need the workarounds Simon mentioned involving an alternative to dyn.load so you can attach additional packages. Your project looks pretty cool though! Also, as an aside have you seen the ipython notebook ( http://ipython.org/ipython-doc/dev/interactive/htmlnotebook.html )? It doesn't meet your requirement of not installing anything, and currently has a slightly different focus, but the appearance of the documents is very similar to what you are doing here (other than being server based), and it already understands multiple languages, including python, R, matlab, octave, etc and is being actively developed and supported. ~G On Fri, May 3, 2013 at 8:21 AM, Jony Hudson wrote: > Hi All, > > thanks for the replies. Very helpful to know that it will run with just > base. Looks like the best bet, at least to get started, is to not use the > usual build-process, but to come up with a simple build-script for just the > core. Ultimately, the build script has to be different anyway, as compiling > the Fortran code to JS requires a few more steps than the native compile. > > For a bit of context, the reason I'm toying with this is I've been > experimenting recently with analysis-in-the-browser. The kernel of the idea > is that if you could do real analysis, without installing anything, and > share it on the web then it would be a Good Thing, and could make it easier > to engage people with data. I've got a proof-of-concept version running > here http://www.monkeycruncher.org that let's you write javascript > analysis code in notebook-style documents. It's neat, but it's a bit > hamstrung by the lack of javascript libraries to actually do any useful > analysis! If you could have R running in there though, that would be a much > better proposition ... > > I'll let you know if I make any progress! > > > Jony > > > -- > Centre for Cold Matter, The Blackett Laboratory, > Imperial College London, London SW7 2BW > T: +44 (0)207 5947741 > http://www.imperial.ac.uk/people/jony.hudson > http://www.imperial.ac.uk/ccm/research/edm > http://www.monkeycruncher.org > http://j-star.org/ > -- > > On 3 May 2013, at 01:31, Simon Urbanek > wrote: > > > On May 2, 2013, at 6:18 PM, Gabriel Becker wrote: > > > >> Jony, > >> > >> I'm currently writing up the paper for something with a similar result > but > >> very different implementation. The RBrowserPlugin package/browser plugin > >> (joint with my advisor Duncan Temple Lang) embeds R within the web > browser > >> as an NPAPI plugin. > >> > >> This approach allows full bi-directional communication between R and the > >> javascript engine (including direct function calling and references to > >> native objects in both directions) using a user's existing local R > >> installation (including packages). > >> > > > > Minor detail: it requires you to have R *and* a special plugin which > makes it pretty much non-deployable. It's completely unrelated to what Jony > is proposing - which doesn't require any dependencies and is actually > pretty cool and would be useful if feasible. FWIW: There are many ways to > run R from a browser that already exist - without the need for plugins or > other client-side hacks - that's the beauty of modern browsers :). > > > > > > To get this back on the actual topic: I have been toying with > cross-compiling R when I was porting it on the iPhone and it's possible, > however, you can't use the build process as-is. It does build core R > properly, but the problem is that you need to bootstrap R to build any > packages. I worked around the problem at the time by building packages on > another platform and re-using those files (things like lazy-loaded DBs, > compiled RD files etc.). > > > > I can imagine that you'll need some equivalent to dynamic linking, but > conceptually it's nothing else but calling functions, so I think you should > be able to compile each package separately and just replace the dynload > code by code that loads another JavaScript. The nice thing is that packages > will simply be just another JS libraries. That's all in theory, I didn't > actually try that part. I suspect you'll have a lot of work, e.g. you'll > need to map all the I/O operations that load compiled/stored R code, > documentation, data from somewhere etc. Good luck! > > If all fails, you can always compile R for JS/Linux ;). > > > > Cheers, > > Simon > > > > > > > >> Devel source at https://github.com/gmbecker/RFirefox, release, > (hopefully) > >> officially cross-platform version to coincide with the paper going off > for > >> review. > >> > >> I had toyed with the idea of the emscripten approach, but I think > putting R > >> in the browser once is enough for me at the moment so I will happily > keep > >> an eye on your project instead of attacking
Re: [Rd] Minimal build of R ...
Hi Gabriel, yes, packages obviously contain all the good stuff, but need to start somewhere! The ipython notebook project is very impressive, and I've been keeping a close eye on it, although I started out on monkeycruncher long before I was aware of it (I make slow progress). I guess I think of my thing as an experiment in just how much can be done purely in the web client. There are some advantages to pure client-side (rich interactivity, no need for a server, ubiquity) which make it interesting, but it might be a bit "too soon" to be useful! Jony -- Centre for Cold Matter, The Blackett Laboratory, Imperial College London, London SW7 2BW T: +44 (0)207 5947741 http://www.imperial.ac.uk/people/jony.hudson http://www.imperial.ac.uk/ccm/research/edm http://www.monkeycruncher.org http://j-star.org/ -- On 3 May 2013, at 16:46, Gabriel Becker wrote: > Jony, > > I would caution that while R will run with just base, you won't be able to do > much of anything with it. All the statistical analysis and graphing functions > reside in additional packages. So practically speaking you'll need the > workarounds Simon mentioned involving an alternative to dyn.load so you can > attach additional packages. Your project looks pretty cool though! > > Also, as an aside have you seen the ipython notebook ( > http://ipython.org/ipython-doc/dev/interactive/htmlnotebook.html )? It > doesn't meet your requirement of not installing anything, and currently has a > slightly different focus, but the appearance of the documents is very similar > to what you are doing here (other than being server based), and it already > understands multiple languages, including python, R, matlab, octave, etc and > is being actively developed and supported. > > ~G > > > On Fri, May 3, 2013 at 8:21 AM, Jony Hudson > wrote: > Hi All, > > thanks for the replies. Very helpful to know that it will run with just > base. Looks like the best bet, at least to get started, is to not use the > usual build-process, but to come up with a simple build-script for just the > core. Ultimately, the build script has to be different anyway, as compiling > the Fortran code to JS requires a few more steps than the native compile. > > For a bit of context, the reason I'm toying with this is I've been > experimenting recently with analysis-in-the-browser. The kernel of the idea > is that if you could do real analysis, without installing anything, and share > it on the web then it would be a Good Thing, and could make it easier to > engage people with data. I've got a proof-of-concept version running here > http://www.monkeycruncher.org that let's you write javascript analysis code > in notebook-style documents. It's neat, but it's a bit hamstrung by the lack > of javascript libraries to actually do any useful analysis! If you could have > R running in there though, that would be a much better proposition ... > > I'll let you know if I make any progress! > > > Jony > > > -- > Centre for Cold Matter, The Blackett Laboratory, > Imperial College London, London SW7 2BW > T: +44 (0)207 5947741 > http://www.imperial.ac.uk/people/jony.hudson > http://www.imperial.ac.uk/ccm/research/edm > http://www.monkeycruncher.org > http://j-star.org/ > -- > > On 3 May 2013, at 01:31, Simon Urbanek wrote: > > > On May 2, 2013, at 6:18 PM, Gabriel Becker wrote: > > > >> Jony, > >> > >> I'm currently writing up the paper for something with a similar result but > >> very different implementation. The RBrowserPlugin package/browser plugin > >> (joint with my advisor Duncan Temple Lang) embeds R within the web browser > >> as an NPAPI plugin. > >> > >> This approach allows full bi-directional communication between R and the > >> javascript engine (including direct function calling and references to > >> native objects in both directions) using a user's existing local R > >> installation (including packages). > >> > > > > Minor detail: it requires you to have R *and* a special plugin which makes > > it pretty much non-deployable. It's completely unrelated to what Jony is > > proposing - which doesn't require any dependencies and is actually pretty > > cool and would be useful if feasible. FWIW: There are many ways to run R > > from a browser that already exist - without the need for plugins or other > > client-side hacks - that's the beauty of modern browsers :). > > > > > > To get this back on the actual topic: I have been toying with > > cross-compiling R when I was porting it on the iPhone and it's possible, > > however, you can't use the build process as-is. It does build core R > > properly, but the problem is that you need to bootstrap R to build any > > packages. I worked around the problem at the time by building packages on > > another platform and re-using those files (things like lazy-loaded DBs, > > compiled RD files etc.). > > > > I can imagine that you'll need some equivalent to dynamic linking, but > > conceptually it's no
Re: [Rd] Minimal build of R ...
On Fri, May 3, 2013 at 9:13 AM, Jony Hudson wrote: > ... I guess I think of my thing as an experiment in just how much can be > done purely in the web client. There are some advantages to pure > client-side (rich interactivity, no need for a server, ubiquity) which make > it interesting, > I completely agree. Added to that list, depending on implementation of course, are direct control of the DOM via R code (allowing statisticians to script entire pages using a language they are more comfortable with), the use of R functions directly as event handlers, including for super high-frequency events such as mousemove (which is infeasible in server based approaches due to the required round-trip), and interactive versions of actual R plots (drawn with standard R plotting code), drawn directly to the page via graphics devices which draw primitives via Javascript, among other things As you can probably tell, I have thought a bit about this :) I feel that client-side approaches have a lot of value and can stand alongside server-based approaches. Each approach type has different advantages and disadvantages, neither dominating the other across all scenarios. I will be watching your project with interest. ~G > > Jony > > > -- > Centre for Cold Matter, The Blackett Laboratory, > Imperial College London, London SW7 2BW > T: +44 (0)207 5947741 > http://www.imperial.ac.uk/people/jony.hudson > http://www.imperial.ac.uk/ccm/research/edm > http://www.monkeycruncher.org > http://j-star.org/ > -- > > On 3 May 2013, at 16:46, Gabriel Becker wrote: > > > Jony, > > > > I would caution that while R will run with just base, you won't be able > to do much of anything with it. All the statistical analysis and graphing > functions reside in additional packages. So practically speaking you'll > need the workarounds Simon mentioned involving an alternative to dyn.load > so you can attach additional packages. Your project looks pretty cool > though! > > > > Also, as an aside have you seen the ipython notebook ( > http://ipython.org/ipython-doc/dev/interactive/htmlnotebook.html )? It > doesn't meet your requirement of not installing anything, and currently has > a slightly different focus, but the appearance of the documents is very > similar to what you are doing here (other than being server based), and it > already understands multiple languages, including python, R, matlab, > octave, etc and is being actively developed and supported. > > > > ~G > > > > > > On Fri, May 3, 2013 at 8:21 AM, Jony Hudson > wrote: > > Hi All, > > > > thanks for the replies. Very helpful to know that it will run with just > base. Looks like the best bet, at least to get started, is to not use the > usual build-process, but to come up with a simple build-script for just the > core. Ultimately, the build script has to be different anyway, as compiling > the Fortran code to JS requires a few more steps than the native compile. > > > > For a bit of context, the reason I'm toying with this is I've been > experimenting recently with analysis-in-the-browser. The kernel of the idea > is that if you could do real analysis, without installing anything, and > share it on the web then it would be a Good Thing, and could make it easier > to engage people with data. I've got a proof-of-concept version running > here http://www.monkeycruncher.org that let's you write javascript > analysis code in notebook-style documents. It's neat, but it's a bit > hamstrung by the lack of javascript libraries to actually do any useful > analysis! If you could have R running in there though, that would be a much > better proposition ... > > > > I'll let you know if I make any progress! > > > > > > Jony > > > > > > -- > > Centre for Cold Matter, The Blackett Laboratory, > > Imperial College London, London SW7 2BW > > T: +44 (0)207 5947741 > > http://www.imperial.ac.uk/people/jony.hudson > > http://www.imperial.ac.uk/ccm/research/edm > > http://www.monkeycruncher.org > > http://j-star.org/ > > -- > > > > On 3 May 2013, at 01:31, Simon Urbanek > wrote: > > > > > On May 2, 2013, at 6:18 PM, Gabriel Becker wrote: > > > > > >> Jony, > > >> > > >> I'm currently writing up the paper for something with a similar > result but > > >> very different implementation. The RBrowserPlugin package/browser > plugin > > >> (joint with my advisor Duncan Temple Lang) embeds R within the web > browser > > >> as an NPAPI plugin. > > >> > > >> This approach allows full bi-directional communication between R and > the > > >> javascript engine (including direct function calling and references to > > >> native objects in both directions) using a user's existing local R > > >> installation (including packages). > > >> > > > > > > Minor detail: it requires you to have R *and* a special plugin which > makes it pretty much non-deployable. It's completely unrelated to what Jony > is proposing - which doesn't require any dependencies and is actually > pretty cool and would be useful if feasible. FWIW: There ar
Re: [Rd] Minimal build of R ...
On May 3, 2013, at 11:21 AM, Jony Hudson wrote: > Hi All, > > thanks for the replies. Very helpful to know that it will run with just base. > Looks like the best bet, at least to get started, is to not use the usual > build-process, but to come up with a simple build-script for just the core. > Ultimately, the build script has to be different anyway, as compiling the > Fortran code to JS requires a few more steps than the native compile. > > For a bit of context, the reason I'm toying with this is I've been > experimenting recently with analysis-in-the-browser. The kernel of the idea > is that if you could do real analysis, without installing anything, and share > it on the web then it would be a Good Thing, and could make it easier to > engage people with data. I've got a proof-of-concept version running here > http://www.monkeycruncher.org that let's you write javascript analysis code > in notebook-style documents. It's neat, but it's a bit hamstrung by the lack > of javascript libraries to actually do any useful analysis! If you could have > R running in there though, that would be a much better proposition ... > It seems that you want something not unlike RCloud http://stats.research.att.com/RCloud/ It uses WebSockets to talk to R either locally or on a server. The nice thing about using WS is that you can leverage large clusters - are not tied to the local machine. Also it allows you to get the benefits of both worlds: R for computation + static graphics while allowing you do to cool interactive graphics in JavaScript. RCloud is something like iPython notebook but based on R with extra interactive graphics. But this is getting OT ;). Cheers, Simon > I'll let you know if I make any progress! > > > Jony > > > -- > Centre for Cold Matter, The Blackett Laboratory, > Imperial College London, London SW7 2BW > T: +44 (0)207 5947741 > http://www.imperial.ac.uk/people/jony.hudson > http://www.imperial.ac.uk/ccm/research/edm > http://www.monkeycruncher.org > http://j-star.org/ > -- > > On 3 May 2013, at 01:31, Simon Urbanek wrote: > >> On May 2, 2013, at 6:18 PM, Gabriel Becker wrote: >> >>> Jony, >>> >>> I'm currently writing up the paper for something with a similar result but >>> very different implementation. The RBrowserPlugin package/browser plugin >>> (joint with my advisor Duncan Temple Lang) embeds R within the web browser >>> as an NPAPI plugin. >>> >>> This approach allows full bi-directional communication between R and the >>> javascript engine (including direct function calling and references to >>> native objects in both directions) using a user's existing local R >>> installation (including packages). >>> >> >> Minor detail: it requires you to have R *and* a special plugin which makes >> it pretty much non-deployable. It's completely unrelated to what Jony is >> proposing - which doesn't require any dependencies and is actually pretty >> cool and would be useful if feasible. FWIW: There are many ways to run R >> from a browser that already exist - without the need for plugins or other >> client-side hacks - that's the beauty of modern browsers :). >> >> >> To get this back on the actual topic: I have been toying with >> cross-compiling R when I was porting it on the iPhone and it's possible, >> however, you can't use the build process as-is. It does build core R >> properly, but the problem is that you need to bootstrap R to build any >> packages. I worked around the problem at the time by building packages on >> another platform and re-using those files (things like lazy-loaded DBs, >> compiled RD files etc.). >> >> I can imagine that you'll need some equivalent to dynamic linking, but >> conceptually it's nothing else but calling functions, so I think you should >> be able to compile each package separately and just replace the dynload code >> by code that loads another JavaScript. The nice thing is that packages will >> simply be just another JS libraries. That's all in theory, I didn't actually >> try that part. I suspect you'll have a lot of work, e.g. you'll need to map >> all the I/O operations that load compiled/stored R code, documentation, data >> from somewhere etc. Good luck! >> If all fails, you can always compile R for JS/Linux ;). >> >> Cheers, >> Simon >> >> >> >>> Devel source at https://github.com/gmbecker/RFirefox, release, (hopefully) >>> officially cross-platform version to coincide with the paper going off for >>> review. >>> >>> I had toyed with the idea of the emscripten approach, but I think putting R >>> in the browser once is enough for me at the moment so I will happily keep >>> an eye on your project instead of attacking that myself :). >>> >>> As for your actual question I can't really say, other than that I suspect >>> you will not be able to dispense with base and methods, but that I would >>> conjecture that stats is "optional". >>> >>> ~G >>> >>> >>> On Thu, May 2, 2013 at 9:12 AM, Jony Hudson
Re: [Rd] Package update for old version of R
On 03.05.2013 16:47, peter dalgaard wrote: On May 3, 2013, at 14:55 , Eilidh Troup wrote: Hi, Is is possible to create a release of a package against an older version of R? I would like to release a new version of the package I maintain, but have some errors when I test it against R 3.0.0. Would CRAN accept a new release that works with R 2.15.3 but not R 3.0.0? I strongly doubt it. By the CRAN logic, it would move immediately to the Archived folder, which is a fairly obscure place to have your users go look... Right. You could try a version that works both under R-oldrelease and R-release/R-devel which would be accepted, of course. Best, Uwe Ligges They're usually helpful in getting you to fix the errors, though. -p __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Please check link for R-patched.tar.gz
On 02.05.2013 21:01, John Minter wrote: I have been trying to build R-patched from source using the link ftp://ftp.stat.math.ethz.ch/Software/R/R-patched.tar.gz Which the file list says is linked to R-patched_2013-05-01.tar.gz but what I download by both wget and curl (with -R -O --ssl ) is dated 2013-04-23 and builds to an old patch level It could be some hidden cache on my side (I've tried finding and removing) but I think the symbolic link may be wrong on the server. Please let me know if you think I am missing something. You can also try the versions on CRAN: http://cran.r-project.org/src/base-prerelease/ Uwe Ligges Best regards, John Minter [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Licence change
Thank you very much for all the feedback. I will think about carefully. All the best, Mauricio -- = Linux user #454569 -- Ubuntu user #17469 = "If you torture any data set long enough, it will confess anything!" (Murray Lark) On 05/03/13, Duncan Murdoch wrote: > On 03/05/2013 11:31 AM, Mauricio Zambrano-Bigiarini wrote: > >On 03/05/13 16:56, Simon Urbanek wrote: > >> > >> On May 3, 2013, at 10:34 AM, Mauricio Zambrano-Bigiarini wrote: > >> > >>> Dear list, > >>> > >>> For the maintainer of a given package, is it possible to change the > >>> licence of a it from GPL >= 2 to GPL >= 3 ? > >>> > >> > >> In general the maintainer has no such rights. However, if the maintainer > >> is also the author and holds all copyright, he can release the package > >> under any license he feels fit. What has been already released cannot be > >> affected, obviously, but you can release a new version under a different > >> license if you have the legal right to do so. > > > >Thank you very much Duncan and Simon for your replies. > > > >The package I'm asking about has 1 author [aut] (me) and 1 contributor > >[ctb] in the 'Author' field of the DESCRIPTION file. Both of them hold > >the copyright of the package. > > > >In case we want to change the licence. Do the 2 authors write something > >particular in the next submission to CRAN ? > >Do we need to provide some written document to CRAN ? > > > > > >What Duncan means with > >"If you are distributing the package on CRAN, you'll have to ask them > >whether they'll still choose to distribute your package after the change" > > > >May CRAN to decide not to distribute the package because of the change > >in the licence ? > > You'll have to ask them that. > > > > > >> > >> (This is not related to the possibility, but one practical problem with > >> requiring GPL >=3 is that it is not GPL-2 compatible so it's a decision > >> that better be made very consciously with all the consequences in mind). > > > >If the package we are talking about is pure R code, with only some > >dependencies to other R packages, what are the implications of: > > > >" one practical problem with requiring GPL >=3 is that it is not GPL-2 > >compatible" > > It may mean that one of your users won't be able to use the package, for > example if something else that they need requires GPL-2 licensing. > > Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Licence change
On 03/05/2013 11:31 AM, Mauricio Zambrano-Bigiarini wrote: On 03/05/13 16:56, Simon Urbanek wrote: > > On May 3, 2013, at 10:34 AM, Mauricio Zambrano-Bigiarini wrote: > >> Dear list, >> >> For the maintainer of a given package, is it possible to change the licence of a it from GPL >= 2 to GPL >= 3 ? >> > > In general the maintainer has no such rights. However, if the maintainer is also the author and holds all copyright, he can release the package under any license he feels fit. What has been already released cannot be affected, obviously, but you can release a new version under a different license if you have the legal right to do so. Thank you very much Duncan and Simon for your replies. The package I'm asking about has 1 author [aut] (me) and 1 contributor [ctb] in the 'Author' field of the DESCRIPTION file. Both of them hold the copyright of the package. In case we want to change the licence. Do the 2 authors write something particular in the next submission to CRAN ? Do we need to provide some written document to CRAN ? What Duncan means with "If you are distributing the package on CRAN, you'll have to ask them whether they'll still choose to distribute your package after the change" May CRAN to decide not to distribute the package because of the change in the licence ? You'll have to ask them that. > > (This is not related to the possibility, but one practical problem with requiring GPL >=3 is that it is not GPL-2 compatible so it's a decision that better be made very consciously with all the consequences in mind). If the package we are talking about is pure R code, with only some dependencies to other R packages, what are the implications of: " one practical problem with requiring GPL >=3 is that it is not GPL-2 compatible" It may mean that one of your users won't be able to use the package, for example if something else that they need requires GPL-2 licensing. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Minimal build of R ...
On May 3, 2013, at 12:52 PM, Gabriel Becker wrote: > On Fri, May 3, 2013 at 9:13 AM, Jony Hudson > wrote: > ... I guess I think of my thing as an experiment in just how much can be done > purely in the web client. There are some advantages to pure client-side (rich > interactivity, no need for a server, ubiquity) which make it interesting, > > I completely agree. Added to that list, depending on implementation of > course, are direct control of the DOM via R code (allowing statisticians to > script entire pages using a language they are more comfortable with), the use > of R functions directly as event handlers, including for super high-frequency > events such as mousemove (which is infeasible in server based approaches due > to the required round-trip), and interactive versions of actual R plots > (drawn with standard R plotting code), drawn directly to the page via > graphics devices which draw primitives via Javascript, among other things > This has been attempted quite a few times - literally by the canvas package (in generates JavaScript) and in more general terms by using SVG (this was way back when it was en vogue). The problem is that by design R plots lack the link between data and the objects drawn so you can only add a small amount of interactivity to very specific plots by hand-crafing the links or by trying to apply some heuristics, but it doesn't work in general. That's why all the web-baed interactive graphics typically do it the other way around - define JS-based primitives with interactions and build plots from this. You actually get nice interactive graphics, but you can't re-use R-based graphics (other than re-drawing it interactively, but that's another story). Cheers, Simon > As you can probably tell, I have thought a bit about this :) > > I feel that client-side approaches have a lot of value and can stand > alongside server-based approaches. Each approach type has different > advantages and disadvantages, neither dominating the other across all > scenarios. > > I will be watching your project with interest. > > ~G > > > > Jony > > > -- > Centre for Cold Matter, The Blackett Laboratory, > Imperial College London, London SW7 2BW > T: +44 (0)207 5947741 > http://www.imperial.ac.uk/people/jony.hudson > http://www.imperial.ac.uk/ccm/research/edm > http://www.monkeycruncher.org > http://j-star.org/ > -- > > On 3 May 2013, at 16:46, Gabriel Becker wrote: > > > Jony, > > > > I would caution that while R will run with just base, you won't be able to > > do much of anything with it. All the statistical analysis and graphing > > functions reside in additional packages. So practically speaking you'll > > need the workarounds Simon mentioned involving an alternative to dyn.load > > so you can attach additional packages. Your project looks pretty cool > > though! > > > > Also, as an aside have you seen the ipython notebook ( > > http://ipython.org/ipython-doc/dev/interactive/htmlnotebook.html )? It > > doesn't meet your requirement of not installing anything, and currently has > > a slightly different focus, but the appearance of the documents is very > > similar to what you are doing here (other than being server based), and it > > already understands multiple languages, including python, R, matlab, > > octave, etc and is being actively developed and supported. > > > > ~G > > > > > > On Fri, May 3, 2013 at 8:21 AM, Jony Hudson > > wrote: > > Hi All, > > > > thanks for the replies. Very helpful to know that it will run with just > > base. Looks like the best bet, at least to get started, is to not use the > > usual build-process, but to come up with a simple build-script for just the > > core. Ultimately, the build script has to be different anyway, as compiling > > the Fortran code to JS requires a few more steps than the native compile. > > > > For a bit of context, the reason I'm toying with this is I've been > > experimenting recently with analysis-in-the-browser. The kernel of the idea > > is that if you could do real analysis, without installing anything, and > > share it on the web then it would be a Good Thing, and could make it easier > > to engage people with data. I've got a proof-of-concept version running > > here http://www.monkeycruncher.org that let's you write javascript analysis > > code in notebook-style documents. It's neat, but it's a bit hamstrung by > > the lack of javascript libraries to actually do any useful analysis! If you > > could have R running in there though, that would be a much better > > proposition ... > > > > I'll let you know if I make any progress! > > > > > > Jony > > > > > > -- > > Centre for Cold Matter, The Blackett Laboratory, > > Imperial College London, London SW7 2BW > > T: +44 (0)207 5947741 > > http://www.imperial.ac.uk/people/jony.hudson > > http://www.imperial.ac.uk/ccm/research/edm > > http://www.monkeycruncher.org > > http://j-star.org/ > > -- > > > > On 3 May 2013, at 01:31,
Re: [Rd] Licence change
On May 3, 2013, at 18:42 , Duncan Murdoch wrote: >> >> " one practical problem with requiring GPL >=3 is that it is not GPL-2 >> compatible" > > It may mean that one of your users won't be able to use the package, for > example if something else that they need requires GPL-2 licensing. Actually, with the GPL licenses, usage is not a problem, but distribution can be. These legalities are a bit inane, and I try to forget about them as far as possible, but I think trouble kicks in if someone wants to distribute a work that derives from both GPL-2 and GPL-3 codes. What "derived" means is yet another inane discussion... -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Licence change
On 03/05/2013 2:29 PM, peter dalgaard wrote: On May 3, 2013, at 18:42 , Duncan Murdoch wrote: >> >> " one practical problem with requiring GPL >=3 is that it is not GPL-2 >> compatible" > > It may mean that one of your users won't be able to use the package, for example if something else that they need requires GPL-2 licensing. Actually, with the GPL licenses, usage is not a problem, but distribution can be. Yes, absolutely. Duncan Murdoch These legalities are a bit inane, and I try to forget about them as far as possible, but I think trouble kicks in if someone wants to distribute a work that derives from both GPL-2 and GPL-3 codes. What "derived" means is yet another inane discussion... __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Minimal build of R ...
On Fri, May 3, 2013 at 10:52 AM, Simon Urbanek wrote: > > On May 3, 2013, at 12:52 PM, Gabriel Becker wrote: > > > On Fri, May 3, 2013 at 9:13 AM, Jony Hudson > wrote: > > ... I guess I think of my thing as an experiment in just how much can be > done purely in the web client. There are some advantages to pure > client-side (rich interactivity, no need for a server, ubiquity) which make > it interesting, > > > > I completely agree. Added to that list, depending on implementation of > course, are direct control of the DOM via R code (allowing statisticians to > script entire pages using a language they are more comfortable with), the > use of R functions directly as event handlers, including for super > high-frequency events such as mousemove (which is infeasible in server > based approaches due to the required round-trip), and interactive versions > of actual R plots (drawn with standard R plotting code), drawn directly to > the page via graphics devices which draw primitives via Javascript, among > other things > > > > This has been attempted quite a few times - literally by the canvas > package (in generates JavaScript) and in more general terms by using SVG > (this was way back when it was en vogue). The problem is that by design R > plots lack the link between data and the objects drawn so you can only add > a small amount of interactivity to very specific plots by hand-crafing the > links or by trying to apply some heuristics, but it doesn't work in > general. That's why all the web-baed interactive graphics typically do it > the other way around - define JS-based primitives with interactions and > build plots from this. You actually get nice interactive graphics, but you > can't re-use R-based graphics (other than re-drawing it interactively, but > that's another story). > Simon, I have a working graphics device that ships with RBrowserPlugin which both draws directly into the page via the Raphael js library (which plots to the page via dynamic SVG) and keeps references to the drawn objects around (which is only possible because R can see JS objects and vice-versa). It is a proof-of-concept, but it allows us to add event handlers directly to elements in the plot (and these event handlers can be R functions), and also allows the plot to be updated, including the removal and alteration of individual elements, all via R code *without* redraws or intermediary files. An abstraction layer could certainly be added which formalizes the relationship between the data and the plot elements, but this seems largely orthogonal to the technology used to do the actually plotting, and we can do quite a bit even without it. And if it were added, we could add it in R, and use R computations within it, something that wouldn't work if we are generating strings of JS code and then evaluating them as an entirely separate action in order to make the graphics, because R cannot see the plotted elements at all in this case. The tightly-coupled client-side approach also allows R and Web tech to actually interoperate (a Google Maps display directly controlled and and plotted to via R code in real time in response to user interactions), instead of simply operating side-by-side. Javascript visualization technologies are great, but I don't see why that should prevent us from seeing how much we can leverage of R's extensive statistical visualization capabilities when creating interactive graphics for the web. Also, with the client-side approach we can create AND interact with/modify JS visualizations via R if we do want to go that route, or we can code in JS but have some computations performed in R with 0 latency (e.g. using an R function within a D3 visualization without taking a performance hit). The client side approach has weaknesses, absolutely, and perhaps they are even fatal for some use-cases, but I would argue that more options is very rarely a bad thing, and that, with all due respect, things are perhaps not quite so clear cut as your previous message suggested. ~G > > Cheers, > Simon > > > > As you can probably tell, I have thought a bit about this :) > > > > I feel that client-side approaches have a lot of value and can stand > alongside server-based approaches. Each approach type has different > advantages and disadvantages, neither dominating the other across all > scenarios. > > > > I will be watching your project with interest. > > > > ~G > > > > > > > > Jony > > > > > > -- > > Centre for Cold Matter, The Blackett Laboratory, > > Imperial College London, London SW7 2BW > > T: +44 (0)207 5947741 > > http://www.imperial.ac.uk/people/jony.hudson > > http://www.imperial.ac.uk/ccm/research/edm > > http://www.monkeycruncher.org > > http://j-star.org/ > > -- > > > > On 3 May 2013, at 16:46, Gabriel Becker wrote: > > > > > Jony, > > > > > > I would caution that while R will run with just base, you won't be > able to do much of anything with it. All the statistical analysis and > graphing functions reside in ad
