Re: [Rd] On RObjectTables

2012-07-24 Thread Jeroen Ooms
Maybe it is worth considering to document this functionality a bit
more, or expose some wrappers in R? It's a bit obscure right now,
which seems both dangerous in terms of maintenance and a missed
opportunity (especially if people are already building on it).





On Tue, Jul 24, 2012 at 2:06 AM, Michael Lawrence
 wrote:
>
> Luke,
>
> Please keep me advised on this, because the Qt interfaces heavily rely on the 
> ObjectTables (btw, it has worked great for my use cases).
>
> Michael
>
>
> On Fri, Jul 20, 2012 at 7:32 AM,  wrote:
>>
>> I believe everyone who has worked on the relevant files has tried to
>> maintain this functionality, but as it seems to get used and tested
>> very little I can't be sure it is functional at this point. The
>> facility in its current form does complicate the internal code and
>> limit some experiments we might otherwise do, so I would not be
>> surprised if it was at least substantially changed in the next year or
>> two.
>>
>> Best,
>>
>> luke
>>
>>
>> On Thu, 19 Jul 2012, Jeroen Ooms wrote:
>>
>>> I was wondering if anyone knows more about the state of RObjectTables. This
>>> largely undocumented functionality was introduced by Duncan around 2002
>>> somewhere and enables you create an environment where the contents are
>>> dynamically queried by R through a hook function. It is mentioned in R
>>> Internals and ?attach. This functionality is quite powerful and allows you
>>> to e.g. offload a big database of R objects to disk, yet use them as if
>>> they were in your workspace. The recent RProtoBuf package also uses some of
>>> this functionality to dynamically lookup proto definitions.
>>>
>>> I would like to do something similar, but I am not sure if support for this
>>> functionality will be or has been discontinued. The RObjectTables package
>>> is no longer available on OmegaHat and nothing has not been mentioned on
>>> the mailing lists for about 5 years. I found an old version of the package
>>> no github which seems to work, but as far as I understand, the package
>>> still needs the hooks from within R to work. So if this functionality is
>>> actually unsupported and might be removed at some point, I should probably
>>> not invest in it.
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>> --
>> Luke Tierney
>> Chair, Statistics and Actuarial Science
>> Ralph E. Wareham Professor of Mathematical Sciences
>> University of Iowa  Phone: 319-335-3386
>> Department of Statistics andFax:   319-335-3017
>>Actuarial Science
>> 241 Schaeffer Hall  email:   luke-tier...@uiowa.edu
>> Iowa City, IA 52242 WWW:  http://www.stat.uiowa.edu
>>
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

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Re: [Rd] On RObjectTables

2012-07-24 Thread luke-tierney

In my original reply I wrote


The
facility in its current form does complicate the internal code and
limit some experiments we might otherwise do, so I would not be
surprised if it was at least substantially changed in the next year or
two.


This is obviously _not_ the time to invest effort in documenting or
expanding this facility. If you want to use it, go ahead. But you will
have to figure things out from what you have and be prepared for
changes under your feet.

If active bindings can do what you want that may be a safer route to
consider.

luke

On Tue, 24 Jul 2012, Jeroen Ooms wrote:


Maybe it is worth considering to document this functionality a bit
more, or expose some wrappers in R? It's a bit obscure right now,
which seems both dangerous in terms of maintenance and a missed
opportunity (especially if people are already building on it).





On Tue, Jul 24, 2012 at 2:06 AM, Michael Lawrence
 wrote:


Luke,

Please keep me advised on this, because the Qt interfaces heavily rely on the 
ObjectTables (btw, it has worked great for my use cases).

Michael


On Fri, Jul 20, 2012 at 7:32 AM,  wrote:


I believe everyone who has worked on the relevant files has tried to
maintain this functionality, but as it seems to get used and tested
very little I can't be sure it is functional at this point. The
facility in its current form does complicate the internal code and
limit some experiments we might otherwise do, so I would not be
surprised if it was at least substantially changed in the next year or
two.

Best,

luke


On Thu, 19 Jul 2012, Jeroen Ooms wrote:


I was wondering if anyone knows more about the state of RObjectTables. This
largely undocumented functionality was introduced by Duncan around 2002
somewhere and enables you create an environment where the contents are
dynamically queried by R through a hook function. It is mentioned in R
Internals and ?attach. This functionality is quite powerful and allows you
to e.g. offload a big database of R objects to disk, yet use them as if
they were in your workspace. The recent RProtoBuf package also uses some of
this functionality to dynamically lookup proto definitions.

I would like to do something similar, but I am not sure if support for this
functionality will be or has been discontinued. The RObjectTables package
is no longer available on OmegaHat and nothing has not been mentioned on
the mailing lists for about 5 years. I found an old version of the package
no github which seems to work, but as far as I understand, the package
still needs the hooks from within R to work. So if this functionality is
actually unsupported and might be removed at some point, I should probably
not invest in it.

[[alternative HTML version deleted]]

__
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--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa  Phone: 319-335-3386
Department of Statistics andFax:   319-335-3017
   Actuarial Science
241 Schaeffer Hall  email:   luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW:  http://www.stat.uiowa.edu


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--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa  Phone: 319-335-3386
Department of Statistics andFax:   319-335-3017
   Actuarial Science
241 Schaeffer Hall  email:   luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW:  http://www.stat.uiowa.edu

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[Rd] questions on R CMD INSTALL et al

2012-07-24 Thread luxInteg
Greetings,

I am learning R
My machine has these;
CPU: 3cores  amd64 
OS pure-64bit CBLFS liux compiled  from sources  (kernel 3.2.1, gcc-4.6.2 
R-2.15
When I compiled R the compiler spewed  out lines  like these:-

make[3]: Entering directory `/tmp/RtmpiHdDJy/R.INSTALL472339eeb23a/mgcv/src'
gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c 
gcv.c -o gcv.o
gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c 
gdi.c -o gdi.o
gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c 
init.c -o init.o
gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c 
magic.c -o magic.o
gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c 
mat.c -o mat.o
gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c 
matrix.c -o matrix.o
gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c 
mgcv.c -o mgcv.o
gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c 
misc.c -o misc.o
gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c 
qp.c -o qp.o
gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c 
sparse-smooth.c -o sparse-smooth.o
gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c 
tprs.c -o tprs.o
gcc -m64 -std=gnu99 -shared -L/usr/local/atlas/lib -L/usr/local/numerics/lib -
L/usr/lib -o mgcv.so gcv.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o 
qp.o sparse-smooth.o tprs.o -L/home/Rman/R-2.15.0/lib -lRlapack -
L/home/Rman/R-2.15.0/lib -lRblas -lgfortran -lm -L/home/Rman/R-2.15.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpiHdDJy/R.INSTALL472339eeb23a/mgcv/src'
installing to /home/Rman/R-2.15.0/library/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (mgcv)
make[2]: Leaving directory `/home/Rman/R-2.15.0/src/library/Recommended'
make[1]: Leaving directory `/home/Rman/R-2.15.0/src/library/Recommended'

-here is the source_tree   for mgcv ---A
mgcv_SR_tree/mgcv/R
mgcv_SR_tree/mgcv/data
mgcv_SR_tree/mgcv/inst
mgcv_SR_tree/mgcv/man
mgcv_SR_tree/mgcv/po
mgcv_SR_tree/mgcv/src
mgcv_SR_tree/mgcv/DESCRIPTION
mgcv_SR_tree/mgcv/MD5
mgcv_SR_tree/mgcv/NAMESPACE
mgcv_SR_tree/mgcv/changeLog
mgcv_SR_tree/mgcv/gnugpl2.txt
mgcv_SR_tree/mgcv/index

#--and here is the build tree   ---B
mgcv_postBuild_Tree/mgcv/Meta
mgcv_postBuild_Tree/mgcv/R
mgcv_postBuild_Tree/mgcv/data
mgcv_postBuild_Tree/mgcv/help
mgcv_postBuild_Tree/mgcv/html
mgcv_postBuild_Tree/mgcv/libs
mgcv_postBuild_Tree/mgcv/CITATION
mgcv_postBuild_Tree/mgcv/DESCRIPTION
mgcv_postBuild_Tree/mgcv/INDEX
mgcv_postBuild_Tree/mgcv/NAMESPACE

I havent a clue what is happening in the lines prepended by **

Also I used make VERBOSE=1  but the compiler   gave no indication of how one  
arives at  B from A  and  
how the library created mgcv.so) is installed in mgcv_postBuild_Tree/mgcv/libs

advise on hese would be much appreciated


Reading the manual I noticed the way of installing these recommendd packages 
appears to be 
R CMD -l path/to/libraries  recommended_tarball.tar.gz

I  would like to know if the following is possible and if so how so:-
a) obtaining more verbose output from make  (is this makefile related ? )
a) exercising control over the compiler settings for  the creation of the 
library module (mgcv.so in the above case)
b)  manual setting of the source and destination  directroies  and  keeping of  
  
the source tree  where the package is built.

thannks in advance

sincerely
luxInteg

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Re: [Rd] On RObjectTables

2012-07-24 Thread Roger D. Peng
I was thinking that the RObjectTables appeared before the active
binding stuff was introduced. On quick examination, it seems the
active binding mechanism might be a more stable way to go. That's how
it was done in filehash.

-roger

On Tue, Jul 24, 2012 at 9:15 AM,   wrote:
> In my original reply I wrote
>
>
>>> The
>>> facility in its current form does complicate the internal code and
>>> limit some experiments we might otherwise do, so I would not be
>>> surprised if it was at least substantially changed in the next year or
>>> two.
>
>
> This is obviously _not_ the time to invest effort in documenting or
> expanding this facility. If you want to use it, go ahead. But you will
> have to figure things out from what you have and be prepared for
> changes under your feet.
>
> If active bindings can do what you want that may be a safer route to
> consider.
>
> luke
>
>
> On Tue, 24 Jul 2012, Jeroen Ooms wrote:
>
>> Maybe it is worth considering to document this functionality a bit
>> more, or expose some wrappers in R? It's a bit obscure right now,
>> which seems both dangerous in terms of maintenance and a missed
>> opportunity (especially if people are already building on it).
>>
>>
>>
>>
>>
>> On Tue, Jul 24, 2012 at 2:06 AM, Michael Lawrence
>>  wrote:
>>>
>>>
>>> Luke,
>>>
>>> Please keep me advised on this, because the Qt interfaces heavily rely on
>>> the ObjectTables (btw, it has worked great for my use cases).
>>>
>>> Michael
>>>
>>>
>>> On Fri, Jul 20, 2012 at 7:32 AM,  wrote:


 I believe everyone who has worked on the relevant files has tried to
 maintain this functionality, but as it seems to get used and tested
 very little I can't be sure it is functional at this point. The
 facility in its current form does complicate the internal code and
 limit some experiments we might otherwise do, so I would not be
 surprised if it was at least substantially changed in the next year or
 two.

 Best,

 luke


 On Thu, 19 Jul 2012, Jeroen Ooms wrote:

> I was wondering if anyone knows more about the state of RObjectTables.
> This
> largely undocumented functionality was introduced by Duncan around 2002
> somewhere and enables you create an environment where the contents are
> dynamically queried by R through a hook function. It is mentioned in R
> Internals and ?attach. This functionality is quite powerful and allows
> you
> to e.g. offload a big database of R objects to disk, yet use them as if
> they were in your workspace. The recent RProtoBuf package also uses
> some of
> this functionality to dynamically lookup proto definitions.
>
> I would like to do something similar, but I am not sure if support for
> this
> functionality will be or has been discontinued. The RObjectTables
> package
> is no longer available on OmegaHat and nothing has not been mentioned
> on
> the mailing lists for about 5 years. I found an old version of the
> package
> no github which seems to work, but as far as I understand, the package
> still needs the hooks from within R to work. So if this functionality
> is
> actually unsupported and might be removed at some point, I should
> probably
> not invest in it.
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

 --
 Luke Tierney
 Chair, Statistics and Actuarial Science
 Ralph E. Wareham Professor of Mathematical Sciences
 University of Iowa  Phone: 319-335-3386
 Department of Statistics andFax:   319-335-3017
Actuarial Science
 241 Schaeffer Hall  email:   luke-tier...@uiowa.edu
 Iowa City, IA 52242 WWW:  http://www.stat.uiowa.edu


 __
 R-devel@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>>>
>>
>
> --
> Luke Tierney
> Chair, Statistics and Actuarial Science
> Ralph E. Wareham Professor of Mathematical Sciences
> University of Iowa  Phone: 319-335-3386
> Department of Statistics andFax:   319-335-3017
>Actuarial Science
> 241 Schaeffer Hall  email:   luke-tier...@uiowa.edu
> Iowa City, IA 52242 WWW:  http://www.stat.uiowa.edu
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



-- 
Roger D. Peng  |  http://www.biostat.jhsph.edu/~rpeng/

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[Rd] Encoding errors in Rd files

2012-07-24 Thread steven mosher
Well, I'm working on project trying to bring back an old package last
published on R 1.9 back to life.
I'm almost there but I am getting killed by an encoding error in the Rd
files

After reading the manual, I decided to try UTF-8.  Mostly because I could
spell it. ha.

That got me a bit closer but I still have these warnings

* checking data for non-ASCII characters ... WARNING
  Warning: found non-ASCII string(s)
  'Tourbihre de la Rivihre-aux-Feu' in object 'modpoll'
  'Lac ` la Fourche' in object 'modpoll'
  'Lac ` la Loutre' in object 'modpoll'
  'Lac Kinogami' in object 'modpoll'
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
 ! Package inputenc Error: Keyboard character used is undefined
(inputenc)in inputencoding `utf8'.

I'll keep searching the help list archives for a clue, but If somebody
could point me at educational material it's really time
that I learn this aspect.

I've readhttp://developer.r-project.org/Encodings_and_R.html

How do I figure out which encoding to use with the error seen above

Steve

[[alternative HTML version deleted]]

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Re: [Rd] questions on R CMD INSTALL et al

2012-07-24 Thread R. Michael Weylandt
On Tue, Jul 24, 2012 at 2:30 PM, luxInteg  wrote:
> Greetings,
>
> I am learning R
> My machine has these;
> CPU: 3cores  amd64
> OS pure-64bit CBLFS liux compiled  from sources  (kernel 3.2.1, gcc-4.6.2
> R-2.15
> When I compiled R the compiler spewed  out lines  like these:-
>
> make[3]: Entering directory `/tmp/RtmpiHdDJy/R.INSTALL472339eeb23a/mgcv/src'
> gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
> I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c
> gcv.c -o gcv.o
> gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
> I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c
> gdi.c -o gdi.o
> gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
> I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c
> init.c -o init.o
> gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
> I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c
> magic.c -o magic.o
> gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
> I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c
> mat.c -o mat.o
> gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
> I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c
> matrix.c -o matrix.o
> gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
> I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c
> mgcv.c -o mgcv.o
> gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
> I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c
> misc.c -o misc.o
> gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
> I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c
> qp.c -o qp.o
> gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
> I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c
> sparse-smooth.c -o sparse-smooth.o
> gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG  -
> I/usr/local/atlas/include  -I/usr/local/numerics/include-fpic  -g -O2  -c
> tprs.c -o tprs.o
> gcc -m64 -std=gnu99 -shared -L/usr/local/atlas/lib -L/usr/local/numerics/lib -
> L/usr/lib -o mgcv.so gcv.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o
> qp.o sparse-smooth.o tprs.o -L/home/Rman/R-2.15.0/lib -lRlapack -
> L/home/Rman/R-2.15.0/lib -lRblas -lgfortran -lm -L/home/Rman/R-2.15.0/lib -lR
> make[3]: Leaving directory `/tmp/RtmpiHdDJy/R.INSTALL472339eeb23a/mgcv/src'
> installing to /home/Rman/R-2.15.0/library/mgcv/libs
> ** R
> ** data
> ** inst
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
>
> * DONE (mgcv)
> make[2]: Leaving directory `/home/Rman/R-2.15.0/src/library/Recommended'
> make[1]: Leaving directory `/home/Rman/R-2.15.0/src/library/Recommended'
>
> -here is the source_tree   for mgcv ---A
> mgcv_SR_tree/mgcv/R
> mgcv_SR_tree/mgcv/data
> mgcv_SR_tree/mgcv/inst
> mgcv_SR_tree/mgcv/man
> mgcv_SR_tree/mgcv/po
> mgcv_SR_tree/mgcv/src
> mgcv_SR_tree/mgcv/DESCRIPTION
> mgcv_SR_tree/mgcv/MD5
> mgcv_SR_tree/mgcv/NAMESPACE
> mgcv_SR_tree/mgcv/changeLog
> mgcv_SR_tree/mgcv/gnugpl2.txt
> mgcv_SR_tree/mgcv/index
>
> #--and here is the build tree   ---B
> mgcv_postBuild_Tree/mgcv/Meta
> mgcv_postBuild_Tree/mgcv/R
> mgcv_postBuild_Tree/mgcv/data
> mgcv_postBuild_Tree/mgcv/help
> mgcv_postBuild_Tree/mgcv/html
> mgcv_postBuild_Tree/mgcv/libs
> mgcv_postBuild_Tree/mgcv/CITATION
> mgcv_postBuild_Tree/mgcv/DESCRIPTION
> mgcv_postBuild_Tree/mgcv/INDEX
> mgcv_postBuild_Tree/mgcv/NAMESPACE
>
> I havent a clue what is happening in the lines prepended by **

Messages (to you) being given by the build script -- it looks like you
got a good build. (The big "DONE" is a good sign)

>
> Also I used make VERBOSE=1  but the compiler   gave no indication of how one
> arives at  B from A  and
> how the library created mgcv.so) is installed in mgcv_postBuild_Tree/mgcv/libs
>
> advise on hese would be much appreciated
>
>
> Reading the manual I noticed the way of installing these recommendd packages
> appears to be
> R CMD -l path/to/libraries  recommended_tarball.tar.gz

I think you have a command missing after CMD. Usually the format is R
CMD __what_to_do__ -flag options tarball.tar.gz. I.e., if I want to
build xts, I get the source and run

R CMD INSTALL xts_0.8-7.tar.gz

and it all "just works."

Linking uses -l as you noted, but only if you need libraries above and
beyond the R headers (which are included automatically with R CMD
install) that aren't in the package's */src directory. You'll see
above the the appropriate flags were passed to gcc for you in
specifing ATLAS and the gnu c99 extensions. Linking within R should be
done properly for you. I'm not an expert on the package build process,
so I'll wait for someone else to say more / correct me if neede

Re: [Rd] Encoding errors in Rd files

2012-07-24 Thread Prof Brian Ripley

On 24/07/2012 21:08, steven mosher wrote:

Well, I'm working on project trying to bring back an old package last
published on R 1.9 back to life.
I'm almost there but I am getting killed by an encoding error in the Rd
files

After reading the manual, I decided to try UTF-8.  Mostly because I could
spell it. ha.

That got me a bit closer but I still have these warnings

* checking data for non-ASCII characters ... WARNING
   Warning: found non-ASCII string(s)
   'Tourbihre de la Rivihre-aux-Feu' in object 'modpoll'
   'Lac ` la Fourche' in object 'modpoll'
   'Lac ` la Loutre' in object 'modpoll'
   'Lac Kinogami' in object 'modpoll'


How to handle those is in 'Writing R Extensions': basically convert to 
UTF-8 and mark them as UTF-8.



* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
  ! Package inputenc Error: Keyboard character used is undefined
(inputenc)in inputencoding `utf8'.

I'll keep searching the help list archives for a clue, but If somebody
could point me at educational material it's really time
that I learn this aspect.


Without the actual file we can do little.  The message means that 
something in the manual inputs (and it could be the DESCRIPTION file or 
an Rd file) contains a character not known to LaTeX.  Most likely it is 
simply not a UTF-8 character, but it could also be outside LaTeX's gamut.


Normally the LaTeX log (which is in the check output) is more revealing: 
you can also try this part alone with R CMD Rd2pdf (and R CMD Rd2pdf 
--no-description often points the finger at the DESCRIPTION file).




I've readhttp://developer.r-project.org/Encodings_and_R.html

How do I figure out which encoding to use with the error seen above


Assuming this is not something esoteric, UTF-8 is the most comprehensive 
choice, but LaTeX's UTF-8 coverage (and that of the fonts used) is 
heavily biased to Western European scripts.  So for example for 
Lithuanian you may want to choose something else (Latin-7?).





--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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