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Wincent | 1 Jun 2012 11:10
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Re: possible bug in "R Editor"

Dear Professor Ripley, I understand that it is not a real reproducible
example, which may require a Chinese OS. I guess that problem is the
routine does not consider the encoding issue by default. If I open an
existing file and save it rather than save a new file, the editor can
handle it appropriately even the file path contains wide characters.

Best
Ronggui

On 1 June 2012 00:50, Prof Brian Ripley <ripley <at> stats.ox.ac.uk> wrote:
> On 31/05/2012 07:04, Wincent wrote:
>>
>> Dear all,
>>
>> I clicked "File-New Script" to open a R Editor, typed some commands in
>> it and then saved it to a file. If the location where I tried to save
>> the script contained Chinese Character, R Editor complained,
>>
>> Error: invalid input 'E:\Some.Chinese.Characters\new_file.R' in
>> 'utf8towcs'
>>
>>
>>> sessionInfo()
>>
>> R version 2.15.0 (2012-03-30)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
>> [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
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Nick Sabbe | 1 Jun 2012 11:19
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Dependencies on recommended packages

Dear all,

I've recently had some issues getting my package to successfully "check".

This was on R-Forge, so it's not obvious for me to provide SessionInfo or
the likes (if necessary, Stefan can chime in?).

After some research (mainly by Stefan Theussler, driving force behind
R-Forge), this turned out to be the root cause:

On R-Forge, the version of R installed was the latest release (2.15.0),
which includes Matrix 1.0-5 as a recommended package.

My own package depends upon glmnet, which itself depends upon Matrix 1.0-6.

(Note: to avoid issues with that, as a test I've also included an explicit
dependency upon Matrix 1.0-6 in my own package, but this didn't change
anything).

During build and most of R CMD check (with the -as-cran flag), everything
worked out fine (which suggests to me that among others, Matrix 1.0-6 is
present and can be loaded, since one of the checks is that the package and
all its dependencies can be loaded), but while running the examples, somehow
loading of the package failed, with an error message that Matrix 1.0-6 could
not be loaded. Here's the relevant part of the log:

> library('addendum')

Loading required package: glmnet
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Uwe Ligges | 1 Jun 2012 12:10
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Re: Dependencies on recommended packages

Does it still happen with R-2.15.0 patched? Maybe an old version of 
Matrix in a library that is first in the search path? Unfortunately 
glmnet does not import from Matrix and search path issues are likely to 
happen. This needs to be sorted out on R-forge , I think.

Best,
Uwe Ligges

On 01.06.2012 11:19, Nick Sabbe wrote:
> Dear all,
>
>
>
> I've recently had some issues getting my package to successfully "check".
>
> This was on R-Forge, so it's not obvious for me to provide SessionInfo or
> the likes (if necessary, Stefan can chime in?).
>
>
>
> After some research (mainly by Stefan Theussler, driving force behind
> R-Forge), this turned out to be the root cause:
>
> On R-Forge, the version of R installed was the latest release (2.15.0),
> which includes Matrix 1.0-5 as a recommended package.
>
>
>
> My own package depends upon glmnet, which itself depends upon Matrix 1.0-6.
>
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Joan Maspons | 1 Jun 2012 19:38

Re: Patch to add Beta binomial distribution. Mentor needed!

Hi,
I filled a bug [1] and I tried to build a package without success. If there
are no news in a while I'll try some to convince some package developers to
add this distribution

[1] https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14936

Thanks for the feedback,
Joan

2012/5/22 Ben Bolker <bbolker <at> gmail.com>

>
> [various snippage]
>
> also see
>
> library("sos")
> findFn("dbetabin*")
>
> and
>
> http://stackoverflow.com/questions/8065835/
>   proposing-feature-requests-to-the-r-core-team/8066062#8066062
> [url broken]
>
>  for some context on why you should build a package instead
> of trying to get a patch accepted in base R ...
>
>  Ben Bolker
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Tim Triche, Jr. | 1 Jun 2012 19:44
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Re: Patch to add Beta binomial distribution. Mentor needed!

It's in VGAM, remember?  Not a bug.

On Fri, Jun 1, 2012 at 10:38 AM, Joan Maspons <j.maspons <at> creaf.uab.cat>wrote:

> Hi,
> I filled a bug [1] and I tried to build a package without success. If there
> are no news in a while I'll try some to convince some package developers to
> add this distribution
>
> [1] https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14936
>
> Thanks for the feedback,
> Joan
>
> 2012/5/22 Ben Bolker <bbolker <at> gmail.com>
>
> >
> > [various snippage]
> >
> > also see
> >
> > library("sos")
> > findFn("dbetabin*")
> >
> > and
> >
> > http://stackoverflow.com/questions/8065835/
> >   proposing-feature-requests-to-the-r-core-team/8066062#8066062
> > [url broken]
> >
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Joan Maspons | 1 Jun 2012 20:36

Re: Patch to add Beta binomial distribution. Mentor needed!

2012/6/1 Tim Triche, Jr. <tim.triche <at> gmail.com>

> It's in VGAM, remember?  Not a bug.
>
> --
> *A model is a lie that helps you see the truth.*
> *
> *
> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>
>
Yes, it's a wish, not a bug. I would like a faster implementation in c and
including quantile function. pbetabin calls qbetabin and sums from 0 to q
using a loop. It can be avoided using genhypergeo function from hypergeo
package [1] but it adds a dependency and for some parameters it doesn't
converge.

In the other hand I think that these functions should be implemented in a
more neutral place to avoid that packages interested in this distribution
have to depend on VGAM. I'm also interested in the Beta negative binomial
distribution which I think it's not implemented (this will be the second
round). And last but not least I want to learn.

Yours,
--

-- 
Joan Maspons
CREAF (Centre de Recerca Ecològica i Aplicacions Forestals)
Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Catalonia
Tel +34 93 581 2915            j.maspons <at> creaf.uab.cat
http://www.creaf.uab.cat
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Paul Johnson | 1 Jun 2012 20:53
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Requests for vignette clarification (re: Writing R Extensions)

I apologize that these questions are stupid and literal.

I write to ask for clarification of comments in the R extensions
manual about vignettes.  I'm not great at LaTeX, but I'm not a
complete novice either, and some of the comments are puzzling to me.

1. I'm stumbling over this line:

"Make sure all files needed to run the R code in the vignette (data
sets, ...) are accessible by either placing them in the inst/doc
hierarchy of the source package or by using calls to system.file()."

Where it says "inst/doc", can I interpret it to mean "vignettes"?  The
vignette files are under vignettes. Why wouldn't those other files be
in there? Or does that mean I'm supposed to copy the style and bib
files from the vignettes folder to the inst/doc folder?  Or none of
the above :)

2. I'm also curious about the implications of the parenthesized
section of this comment:

"By default R CMD build will run Sweave on all files in Sweave format
in vignettes, or if that does not exist, inst/doc (but not in
sub-directories)."

At first I though that meant it will search vignettes and
subdirectories under vignettes, or it will look under inst/doc, but no
subdirectories under inst/doc.  So I created vignettes in
subdirectories under vignettes and they are ignored by the build
process, so that was obviously wrong.  For clarification, it would
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Paul Gilbert | 3 Jun 2012 21:02
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Re: Requests for vignette clarification (re: Writing R Extensions)

I'll make a guess at some parts of this.

On 12-06-01 02:53 PM, Paul Johnson wrote:
> I apologize that these questions are stupid and literal.
>
> I write to ask for clarification of comments in the R extensions
> manual about vignettes.  I'm not great at LaTeX, but I'm not a
> complete novice either, and some of the comments are puzzling to me.
>
> 1. I'm stumbling over this line:
>
> "Make sure all files needed to run the R code in the vignette (data
> sets, ...) are accessible by either placing them in the inst/doc
> hierarchy of the source package or by using calls to system.file()."
>
> Where it says "inst/doc", can I interpret it to mean "vignettes"?  The
> vignette files are under vignettes. Why wouldn't those other files be
> in there? Or does that mean I'm supposed to copy the style and bib
> files from the vignettes folder to the inst/doc folder?  Or none of
> the above :)

I think the idea is that a user looking at an installed version of the 
package will be able to see things that are in the doc/ directory of the 
installed package. This automatically includes the source files (eg 
*.Stex) from vignettes/ and also the generated *.pdf and the *.R files 
stripped from the *.Stex files. If you want them to have access to other 
files then you should put those somewhere so they get installed, such as 
in the source package /inst/doc directory so they get put in the doc/ 
directory of the installed package. That should probably include 
anything else that is important to reproduce the results in the
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Paul Johnson | 4 Jun 2012 15:29
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Re: Requests for vignette clarification (re: Writing R Extensions)

On Sun, Jun 3, 2012 at 2:02 PM, Paul Gilbert <pgilbert902 <at> gmail.com> wrote:
> I'll make a guess at some parts of this.
>
>
> On 12-06-01 02:53 PM, Paul Johnson wrote:
>>
>> I apologize that these questions are stupid and literal.
>>
>> I write to ask for clarification of comments in the R extensions
>> manual about vignettes.  I'm not great at LaTeX, but I'm not a
>> complete novice either, and some of the comments are puzzling to me.
>>
>> 1. I'm stumbling over this line:
>>
>> "Make sure all files needed to run the R code in the vignette (data
>> sets, ...) are accessible by either placing them in the inst/doc
>> hierarchy of the source package or by using calls to system.file()."
>>
>> Where it says "inst/doc", can I interpret it to mean "vignettes"?  The
>> vignette files are under vignettes. Why wouldn't those other files be
>> in there? Or does that mean I'm supposed to copy the style and bib
>> files from the vignettes folder to the inst/doc folder?  Or none of
>> the above :)
>
>
> I think the idea is that a user looking at an installed version of the
> package will be able to see things that are in the doc/ directory of the
> installed package. This automatically includes the source files (eg *.Stex)
> from vignettes/ and also the generated *.pdf and the *.R files stripped from
> the *.Stex files. If you want them to have access to other files then you
(Continue reading)

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Yihui Xie | 4 Jun 2012 15:55
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Re: Requests for vignette clarification (re: Writing R Extensions)

You should export to Rnw directly from LyX instead of copying the Rnw
document in the LyX temp dir. The former one is a clean TeX document,
and the latter one will mangle all filenames.

Regards,
Yihui
--
Yihui Xie <xieyihui <at> gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA

On Mon, Jun 4, 2012 at 9:29 AM, Paul Johnson <pauljohn32 <at> gmail.com> wrote:
>
>
> I got to the bottom of the problem that made me ask. I had a package
> that failed build check. I wrote the vignette in LyX and when I add a
> bibliography file in LyX, it adds a full path, not just {rockchalk},
> in the Rnw file.
>
> \bibliography{0_home_pauljohn_SVN_rgroup_trunk_rockchalk_rockchalk_vignettes_rockchalk}
>
> LyX does that because it runs its builds in a temporary folder.
>
> When it is like that, the vignette builds for me, but it does not
> survive the package check because the check  won't go looking on the
> long path.
>
> pj
>
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