Re: [Rd] interfacing R with RFC2445
On Mon, Jan 11, 2010 at 10:10 PM, Jeff Hamann jeff.d.ham...@gmail.comwrote: R Developers, I cannot seem to find an R package that can read/write iCalendar (RFC2445) files. I have found the libical library at sourceforge. I've used it briefly so it may be what I need, but again no R interface. I may have to connect the dots myself. I'm guessing this might be useful for someone other than myself (scrubbing files, performing temporal analysis on events, etc). Since I need to perform these tasks, I will probably do it using R if I can get away with it. Can anyone provide some basic advice for me? A list object of entries? The original data will be coming from an SQL table/view result. Is there any interest in helping with funding such a small project? Small project? The python icalendar package is about 3000 lines of code, plus tests. ical is quite a complex format with all sorts of functionalities. The chances are that if your ical files come from a simple source and don't use all the complications of ical format then you can write an ad-hoc parser that just strips out the event time (or whatever) you need. If you still *do* want to write a full iCalendar reader/parser, the python package might be a good place to start and look for ideas. Barry -- blog: http://geospaced.blogspot.com/ web: http://www.maths.lancs.ac.uk/~rowlings web: http://www.rowlingson.com/ twitter: http://twitter.com/geospacedman pics: http://www.flickr.com/photos/spacedman [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] how to call a function from C
Hi, In Rcpp, we now have a Function class to encapsulate functions (they cover all three kinds, but this may change). To call the function, what we do is generate a call with the function as the first node and then evaluate the call. SEXP stats = PROTECT( R_FindNamespace( mkString( stats) ) ); SEXP rnorm = PROTECT( findVarInFrame( stats, install( rnorm) ) ) ; SEXP call = PROTECT( LCONS( rnorm, CONS( ScalarInteger(10), CONS(ScalarReal(0), R_NilValue ) ) ) ); SEXP res = PROTECT( eval( call , R_GlobalEnv ) ); UNPROTECT(4) ; return res ; It works, but I was wondering if there was another way. I've seen applyClosure, but I'm not sure I should attempt to use it or if using a call like above is good enough. Romain PS: using Rcpp's C++ classes you would express the code above as : Environment stats(package:stats) ; Function rnorm = stats.get( rnorm ) return rnorm( 10, 0.0 ) ; -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/KfKn : Rcpp 0.7.2 |- http://tr.im/JOlc : External pointers with Rcpp `- http://tr.im/JFqa : R Journal, Volume 1/2, December 2009 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] how to call a function from C
Hi,
In Rcpp, we now have a Function class to encapsulate functions
(they cover all three kinds, but this may change).
Just a note on that: there is probably no hurry to do so.
rpy2 is also having CLOSXP, BUILTINSXP, and SPECIALSXP represented as
one function-like class and seems to be behave reasonably while a lot of
other things seem more urgent to sort out.
To call the function, what we do is generate a call with the function
as the first node and then evaluate the call.
SEXP stats = PROTECT( R_FindNamespace( mkString( stats) ) ); SEXP
rnorm = PROTECT( findVarInFrame( stats, install( rnorm) ) ) ; SEXP
call = PROTECT( LCONS( rnorm, CONS( ScalarInteger(10),
CONS(ScalarReal(0), R_NilValue ) ) ) ); SEXP res = PROTECT( eval(
call , R_GlobalEnv ) ); UNPROTECT(4) ; return res ;
It works, but I was wondering if there was another way. I've seen
applyClosure, but I'm not sure I should attempt to use it or if using
a call like above is good enough.
Using R_tryEval() will let you evaluate an expression in a given
environment, as well as capture an eventual error occurring during its
evaluation (and translate it as an exception).
Romain
PS: using Rcpp's C++ classes you would express the code above as :
Environment stats(package:stats) ; Function rnorm = stats.get(
rnorm ) return rnorm( 10, 0.0 ) ;
Feel free to snoop in rpy2's rpy/rinterface/rinterface.c and look for
do_try_eval. The behavior looks very similar, the above snippet in
rpy2 would write like:
from rpy2.robjects.packages import importr
stats = importr('stats')
stats.rnorm(10, 0.0)
-- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr |- http://tr.im/KfKn : Rcpp 0.7.2
|- http://tr.im/JOlc : External pointers with Rcpp `-
http://tr.im/JFqa : R Journal, Volume 1/2, December 2009
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Re: [Rd] wiki down?
I see the same problem. The wiki link on the R homepage doesn't seem to respond. A search of r-devel for subjects containing wiki finds this seemingly unanswered recent post. Is it known? -Matthew Ben Bolker bol...@ufl.edu wrote in message news:4b44b12a.60...@ufl.edu... __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] how to call a function from C
On 01/14/2010 12:42 PM, Laurent Gautier wrote:
Hi,
In Rcpp, we now have a Function class to encapsulate functions
(they cover all three kinds, but this may change).
Just a note on that: there is probably no hurry to do so.
rpy2 is also having CLOSXP, BUILTINSXP, and SPECIALSXP represented as
one function-like class and seems to be behave reasonably while a lot of
other things seem more urgent to sort out.
To call the function, what we do is generate a call with the function
as the first node and then evaluate the call.
SEXP stats = PROTECT( R_FindNamespace( mkString( stats) ) ); SEXP
rnorm = PROTECT( findVarInFrame( stats, install( rnorm) ) ) ; SEXP
call = PROTECT( LCONS( rnorm, CONS( ScalarInteger(10),
CONS(ScalarReal(0), R_NilValue ) ) ) ); SEXP res = PROTECT( eval(
call , R_GlobalEnv ) ); UNPROTECT(4) ; return res ;
It works, but I was wondering if there was another way. I've seen
applyClosure, but I'm not sure I should attempt to use it or if using
a call like above is good enough.
Using R_tryEval() will let you evaluate an expression in a given
environment, as well as capture an eventual error occurring during its
evaluation (and translate it as an exception).
Sure. I did not want to over-complicate the question.
I'm currently reviewing tryEval and its underlying R_TopLevelExec which
does not give me enough : when the error occurs, it'd be useful that the
function returns the condition object instead of NULL.
Romain
PS: using Rcpp's C++ classes you would express the code above as :
Environment stats(package:stats) ; Function rnorm = stats.get(
rnorm ) return rnorm( 10, 0.0 ) ;
Feel free to snoop in rpy2's rpy/rinterface/rinterface.c and look for
do_try_eval. The behavior looks very similar, the above snippet in
rpy2 would write like:
from rpy2.robjects.packages import importr
stats = importr('stats')
stats.rnorm(10, 0.0)
nice
--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/KfKn : Rcpp 0.7.2
|- http://tr.im/JOlc : External pointers with Rcpp
`- http://tr.im/JFqa : R Journal, Volume 1/2, December 2009
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Re: [Rd] how to call a function from C
On 1/14/10 1:16 PM, Romain Francois wrote:
On 01/14/2010 12:42 PM, Laurent Gautier wrote:
Hi,
In Rcpp, we now have a Function class to encapsulate functions
(they cover all three kinds, but this may change).
Just a note on that: there is probably no hurry to do so.
rpy2 is also having CLOSXP, BUILTINSXP, and SPECIALSXP represented as
one function-like class and seems to be behave reasonably while a lot of
other things seem more urgent to sort out.
To call the function, what we do is generate a call with the function
as the first node and then evaluate the call.
SEXP stats = PROTECT( R_FindNamespace( mkString( stats) ) ); SEXP
rnorm = PROTECT( findVarInFrame( stats, install( rnorm) ) ) ; SEXP
call = PROTECT( LCONS( rnorm, CONS( ScalarInteger(10),
CONS(ScalarReal(0), R_NilValue ) ) ) ); SEXP res = PROTECT( eval(
call , R_GlobalEnv ) ); UNPROTECT(4) ; return res ;
It works, but I was wondering if there was another way. I've seen
applyClosure, but I'm not sure I should attempt to use it or if using
a call like above is good enough.
Using R_tryEval() will let you evaluate an expression in a given
environment, as well as capture an eventual error occurring during its
evaluation (and translate it as an exception).
Sure. I did not want to over-complicate the question.
I'm currently reviewing tryEval and its underlying R_TopLevelExec which
does not give me enough : when the error occurs, it'd be useful that the
function returns the condition object instead of NULL.
I possibly went the same path, and ended with R_tryEval. When looking at
it, I could not figure out any way to get what I wanted outside using
geterrmessage in base.
The error string is in the variable errbuf (in src/main/error.c), with
no obvious route to access it (and if truly no route, this might be
something missing from the R C-API).
Romain
PS: using Rcpp's C++ classes you would express the code above as :
Environment stats(package:stats) ; Function rnorm = stats.get(
rnorm ) return rnorm( 10, 0.0 ) ;
Feel free to snoop in rpy2's rpy/rinterface/rinterface.c and look for
do_try_eval. The behavior looks very similar, the above snippet in
rpy2 would write like:p/
I meant do_eval_expr.
from rpy2.robjects.packages import importr
stats = importr('stats')
stats.rnorm(10, 0.0)
nice
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Re: [Rd] how to call a function from C
The Rcpp library in RcppTemplate (the package that Rcpp forked from)
simplifies the process
of calling functions from C++. The design goal was to enable users to focus
on
scientific problem solving rather than interface problems and low-level R
internals (by
hiding these details and documenting everything).
The current Rcpp package is a mashup of the packages RcppTemplate (old
version),
inline, and RInside that involves a fair amount of low-level R hacking, and
this is
probably consistent with the preferences of most readers of this list.
If I am mistaken and there are any users of RcppTemplate please let me know,
as I
am thinking about reoganizing that package to minimize confusion with the
fork.
Thanks,
Dominick
On Thu, Jan 14, 2010 at 7:16 AM, Romain Francois romain.franc...@dbmail.com
wrote:
On 01/14/2010 12:42 PM, Laurent Gautier wrote:
Hi,
In Rcpp, we now have a Function class to encapsulate functions
(they cover all three kinds, but this may change).
Just a note on that: there is probably no hurry to do so.
rpy2 is also having CLOSXP, BUILTINSXP, and SPECIALSXP represented as
one function-like class and seems to be behave reasonably while a lot of
other things seem more urgent to sort out.
To call the function, what we do is generate a call with the function
as the first node and then evaluate the call.
SEXP stats = PROTECT( R_FindNamespace( mkString( stats) ) ); SEXP
rnorm = PROTECT( findVarInFrame( stats, install( rnorm) ) ) ; SEXP
call = PROTECT( LCONS( rnorm, CONS( ScalarInteger(10),
CONS(ScalarReal(0), R_NilValue ) ) ) ); SEXP res = PROTECT( eval(
call , R_GlobalEnv ) ); UNPROTECT(4) ; return res ;
It works, but I was wondering if there was another way. I've seen
applyClosure, but I'm not sure I should attempt to use it or if using
a call like above is good enough.
Using R_tryEval() will let you evaluate an expression in a given
environment, as well as capture an eventual error occurring during its
evaluation (and translate it as an exception).
Sure. I did not want to over-complicate the question.
I'm currently reviewing tryEval and its underlying R_TopLevelExec which
does not give me enough : when the error occurs, it'd be useful that the
function returns the condition object instead of NULL.
Romain
PS: using Rcpp's C++ classes you would express the code above as :
Environment stats(package:stats) ; Function rnorm = stats.get(
rnorm ) return rnorm( 10, 0.0 ) ;
Feel free to snoop in rpy2's rpy/rinterface/rinterface.c and look for
do_try_eval. The behavior looks very similar, the above snippet in
rpy2 would write like:
from rpy2.robjects.packages import importr
stats = importr('stats')
stats.rnorm(10, 0.0)
nice
--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/KfKn : Rcpp 0.7.2
|- http://tr.im/JOlc : External pointers with Rcpp
`- http://tr.im/JFqa : R Journal, Volume 1/2, December 2009
__
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[[alternative HTML version deleted]]
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Re: [Rd] how to call a function from C
On 01/14/2010 03:50 PM, Dominick Samperi wrote: The Rcpp library in RcppTemplate (the package that Rcpp forked from) simplifies the process of calling functions from C++. The design goal was to enable users to focus on scientific problem solving rather than interface problems and low-level R internals (by hiding these details and documenting everything). Hello Dominick, In the Rcpp package, you'd call the rnorm function like this : /* grab the environment called package:stats */ Environment stats(package:stats) ; /* or like this if you want the namespace */ /* Environment stats = Environment::namespace_env(stats) ;*/ /* grab function called 'rnorm' from this environment */ Function rnorm = stats.get(rnorm ) ; /* call the function, about the same way you'd do in R * * rnorm( 10L, sd = 100 ) */ return rnorm( 10, Named( sd, 100.0 ) ) ; All involved SEXP are encapsulated in suitable C++ objects, such as Environment, Function, etc ... the user does not need to know about SEXP, does not need to care about the PROTECT/UNPROTECT dance, etc ... Please let me know which of these three lines of C++ code you consider to be low level R internals. It might be interesting that you post how you would invoke the same using RcppTemplate. The current Rcpp package is a mashup of the packages RcppTemplate (old version), inline, and RInside It is not anything even kind of close to that. There was code from the inline package at some point, but it is now back into inline, which has been improved to support easy inlining of code making use of Rcpp. There is nothing of RInside in Rcpp, it goes the other way, RInside depends on Rcpp and uses its features to ease embedding R into an existing C++ application The Rcpp package is under a lot of changes. See : - http://dirk.eddelbuettel.com/blog/2010/01/12/#rcpp_0.7.2 - http://dirk.eddelbuettel.com/blog/2010/01/02/#rcpp_0.7.1 - http://romainfrancois.blog.free.fr/index.php?post/2010/01/13/Rcpp-0.7.2-is-out - http://romainfrancois.blog.free.fr/index.php?post/2010/01/08/External-pointers-with-Rcpp - http://romainfrancois.blog.free.fr/index.php?post/2009/12/29/new-things-in-Rcpp that involves a fair amount of low-level R hacking, and this is probably consistent with the preferences of most readers of this list. Can you be more specific ? The whole purpose of the package is to hide the R API. The user does not need to know the R API to use the classes of Rcpp. We however indeed use and abuse the R API a lot internally. Romain If I am mistaken and there are any users of RcppTemplate please let me know, as I am thinking about reoganizing that package to minimize confusion with the fork. Thanks, Dominick On Thu, Jan 14, 2010 at 7:16 AM, Romain Francois romain.franc...@dbmail.com mailto:romain.franc...@dbmail.com wrote: On 01/14/2010 12:42 PM, Laurent Gautier wrote: Hi, In Rcpp, we now have a Function class to encapsulate functions (they cover all three kinds, but this may change). Just a note on that: there is probably no hurry to do so. rpy2 is also having CLOSXP, BUILTINSXP, and SPECIALSXP represented as one function-like class and seems to be behave reasonably while a lot of other things seem more urgent to sort out. To call the function, what we do is generate a call with the function as the first node and then evaluate the call. SEXP stats = PROTECT( R_FindNamespace( mkString( stats) ) ); SEXP rnorm = PROTECT( findVarInFrame( stats, install( rnorm) ) ) ; SEXP call = PROTECT( LCONS( rnorm, CONS( ScalarInteger(10), CONS(ScalarReal(0), R_NilValue ) ) ) ); SEXP res = PROTECT( eval( call , R_GlobalEnv ) ); UNPROTECT(4) ; return res ; It works, but I was wondering if there was another way. I've seen applyClosure, but I'm not sure I should attempt to use it or if using a call like above is good enough. Using R_tryEval() will let you evaluate an expression in a given environment, as well as capture an eventual error occurring during its evaluation (and translate it as an exception). Sure. I did not want to over-complicate the question. I'm currently reviewing tryEval and its underlying R_TopLevelExec which does not give me enough : when the error occurs, it'd be useful that the function returns the condition object instead of NULL. Romain PS: using Rcpp's C++ classes you would express the code above as : Environment stats(package:stats) ; Function rnorm = stats.get( rnorm ) return rnorm( 10, 0.0 ) ; Feel free to snoop in rpy2's rpy/rinterface/rinterface.c and look for do_try_eval. The behavior looks very similar, the above
Re: [Rd] how to call a function from C
On Thu, Jan 14, 2010 at 10:20 AM, Romain Francois romain.franc...@dbmail.com wrote: It might be interesting that you post how you would invoke the same using RcppTemplate. Sorry, I will not complete with my own work. The point of my last post was to see if anybody still uses RcppTemplate so I can decide what to do with that package. [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] how to call a function from C
On 01/14/2010 02:27 PM, Laurent Gautier wrote:
On 1/14/10 1:16 PM, Romain Francois wrote:
On 01/14/2010 12:42 PM, Laurent Gautier wrote:
Hi,
In Rcpp, we now have a Function class to encapsulate functions
(they cover all three kinds, but this may change).
Just a note on that: there is probably no hurry to do so.
rpy2 is also having CLOSXP, BUILTINSXP, and SPECIALSXP represented as
one function-like class and seems to be behave reasonably while a lot of
other things seem more urgent to sort out.
To call the function, what we do is generate a call with the function
as the first node and then evaluate the call.
SEXP stats = PROTECT( R_FindNamespace( mkString( stats) ) ); SEXP
rnorm = PROTECT( findVarInFrame( stats, install( rnorm) ) ) ; SEXP
call = PROTECT( LCONS( rnorm, CONS( ScalarInteger(10),
CONS(ScalarReal(0), R_NilValue ) ) ) ); SEXP res = PROTECT( eval(
call , R_GlobalEnv ) ); UNPROTECT(4) ; return res ;
It works, but I was wondering if there was another way. I've seen
applyClosure, but I'm not sure I should attempt to use it or if using
a call like above is good enough.
Using R_tryEval() will let you evaluate an expression in a given
environment, as well as capture an eventual error occurring during its
evaluation (and translate it as an exception).
Sure. I did not want to over-complicate the question.
I'm currently reviewing tryEval and its underlying R_TopLevelExec which
does not give me enough : when the error occurs, it'd be useful that the
function returns the condition object instead of NULL.
I possibly went the same path, and ended with R_tryEval. When looking at
it, I could not figure out any way to get what I wanted outside using
geterrmessage in base.
The error string is in the variable errbuf (in src/main/error.c), with
no obvious route to access it (and if truly no route, this might be
something missing from the R C-API).
It seems to be the regular way around this gap. Martin Morgan gave the
same advice (using geterrmessage) here last week. it only gives you the
error message though
I've been staring at R_ToplevelExec, begincontext and addCondHands. Some
day, I'll understand how to connect the dots. Not today though.
Romain
Romain
PS: using Rcpp's C++ classes you would express the code above as :
Environment stats(package:stats) ; Function rnorm = stats.get(
rnorm ) return rnorm( 10, 0.0 ) ;
Feel free to snoop in rpy2's rpy/rinterface/rinterface.c and look for
do_try_eval. The behavior looks very similar, the above snippet in
rpy2 would write like:p/
I meant do_eval_expr.
thanks.
from rpy2.robjects.packages import importr
stats = importr('stats')
stats.rnorm(10, 0.0)
nice
--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/KfKn : Rcpp 0.7.2
|- http://tr.im/JOlc : External pointers with Rcpp
`- http://tr.im/JFqa : R Journal, Volume 1/2, December 2009
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Re: [Rd] wiki down?
On Thu, 14 Jan 2010 11:45:31 -, Matthew Dowle (MD) wrote: I see the same problem. The wiki link on the R homepage doesn't seem to respond. A search of r-devel for subjects containing wiki finds this seemingly unanswered recent post. Is it known? Philippe Grosjean maintains the Wiki, in CC. Best, Fritz -- --- Prof. Dr. Friedrich Leisch Institut für Statistik Tel: (+49 89) 2180 3165 Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308 Ludwigstraße 33 D-80539 München http://www.statistik.lmu.de/~leisch --- Journal Computational Statistics --- http://www.springer.com/180 Münchner R Kurse --- http://www.statistik.lmu.de/R __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] how to call a function from C
On Thu, 14 Jan 2010, Romain Francois wrote:
On 01/14/2010 12:42 PM, Laurent Gautier wrote:
Hi,
In Rcpp, we now have a Function class to encapsulate functions
(they cover all three kinds, but this may change).
Just a note on that: there is probably no hurry to do so.
rpy2 is also having CLOSXP, BUILTINSXP, and SPECIALSXP represented as
one function-like class and seems to be behave reasonably while a lot of
other things seem more urgent to sort out.
To call the function, what we do is generate a call with the function
as the first node and then evaluate the call.
SEXP stats = PROTECT( R_FindNamespace( mkString( stats) ) ); SEXP
rnorm = PROTECT( findVarInFrame( stats, install( rnorm) ) ) ; SEXP
call = PROTECT( LCONS( rnorm, CONS( ScalarInteger(10),
CONS(ScalarReal(0), R_NilValue ) ) ) ); SEXP res = PROTECT( eval(
call , R_GlobalEnv ) ); UNPROTECT(4) ; return res ;
It works, but I was wondering if there was another way. I've seen
applyClosure, but I'm not sure I should attempt to use it or if using
a call like above is good enough.
Using R_tryEval() will let you evaluate an expression in a given
environment, as well as capture an eventual error occurring during its
evaluation (and translate it as an exception).
Sure. I did not want to over-complicate the question.
I'm currently reviewing tryEval and its underlying R_TopLevelExec which does
not give me enough : when the error occurs, it'd be useful that the function
returns the condition object instead of NULL.
R_TopLevelExec, and hence R_tryEval, don't quite do what some users
expect and maybe would like. There are two issues.
The TopLevel part means that conceptually this call runs in its own
stack, which means things like calling error handlers set up outside
this call are not visible, and Sys.whatever functions don't see the
rest of the stack (or at least should not). A call to one of these is
conceptually a bit like asking a separate thread to evaluate the
expression and waiting for the result. (I believe his mechanism was
added to handle finalizer code in the GC, where this makes sense, but
I may have my history wrong.)
The other issue is that what R_tryEval catches is not errors, it is
longjmp attempts. The vast majority of these will come from attempts
to pass errors to exiting handlers, but there are other possibilities,
such as invoking an abort restart (which jumps to top level).
It might be useful to provide a C level interface for catching errors
as well as other jumps and for allowing C code to do cleanup
operations and then continue those jumps if appropriate, but getting
that right is fairly tricky and certainly hasn't risen high enough on
my priority list to warrant the investment of time. The interface
would have to abstract over implementation details though: we
definitely do not want to expose and commit to current details of the
context stack implementation.
luke
Romain
PS: using Rcpp's C++ classes you would express the code above as :
Environment stats(package:stats) ; Function rnorm = stats.get(
rnorm ) return rnorm( 10, 0.0 ) ;
Feel free to snoop in rpy2's rpy/rinterface/rinterface.c and look for
do_try_eval. The behavior looks very similar, the above snippet in
rpy2 would write like:
from rpy2.robjects.packages import importr
stats = importr('stats')
stats.rnorm(10, 0.0)
nice
--
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: l...@stat.uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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[Rd] RcppTemplate user alert
If there are any users of RcppTemplate package Version 6+ please let me know ASAP as I will probably reorganize this package to limit confusion and overlap with the package Rcpp. Since the package Rcpp which forked from an earlier version of RcppTemplate seems to have the support of many people in the R community it is counterproductive for me to continue work on RcppTemplate in its current form. Thanks, Dominick [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Wishlist: system.file(... package) throw an error if package not installed/path not found
Currently, system.file() on a non-existing package returns an empty string: path - system.file(package=foo); print(path); [1] The same goes for non-existing paths in existing package directories: path - system.file(foo, package=base); print(path); [1] Is there a rationale for this, or is it just for historical reasons? Is the empty string used in R to represent a missing file? (e.g. file.exists() == FALSE). I would like to suggest that an error is thrown instead, so that it is caught as soon as possible and not down stream. /Henrik __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Wishlist: system.file(... package) throw an error if package not installed/path not found
On Jan 14, 2010, at 15:01 , Henrik Bengtsson wrote: Currently, system.file() on a non-existing package returns an empty string: path - system.file(package=foo); print(path); [1] The same goes for non-existing paths in existing package directories: path - system.file(foo, package=base); print(path); [1] Is there a rationale for this, or is it just for historical reasons? Is the empty string used in R to represent a missing file? (e.g. file.exists() == FALSE). I would like to suggest that an error is thrown instead, so that it is caught as soon as possible and not down stream. I cannot answer for the original author, but throwing an error is generally a very bad idea since it defeats the vectorization. It is much easier to simply use if(nzchar(system.file(...))) if you want to throw an error in a scalar context than to lose all results because of one vector entry. And, yes, file.exists() will indeed return FALSE (although it is entirely unrelated). Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] adapt package missing because of licensing issue: fix?
I think this is probably known by someone, but I wanted to ask/comment: The 'adapt' package has been removed from CRAN because of an 'unclear' license. That makes sense, but it actually took a bit of digging for me to discover that, and if I had been a student I might not have figured it out. The package is simply missing from the CRAN compiled packages page; I did find information in the check summaries; but I didn't get a clear indication until I found http://cran.r-project.org/web/packages/adapt/index.html by googling (which also gave me a handy link to the archives). https://stat.ethz.ch/pipermail/r-sig-fedora/2009-June/78.html http://packages.debian.org/changelogs/pool/main/a/adapt/adapt_1.0-4-3/r-cran-adapt.copyright give a little more information. library(findFn); sos(multidimensional+integration) found the cubature package for me, which looks like a pretty good replacement but which I haven't tried out yet. My real question: has anyone actually tried to contact the authors and find out if they are willing to put the code under a suitably redistributable license? I can't find anything that suggests that they *don't* want it redistributed ... ? Would it be helpful if I did this, or is this the sort of thing the package maintainer should do? Mike Meyer: mi...@andrew.cmu.edu Alan Genz: g...@gauss.math.wsu.edu cheers Ben Bolker -- Ben Bolker Associate professor, Biology Dep't, Univ. of Florida bol...@ufl.edu / people.biology.ufl.edu/bolker GPG key: people.biology.ufl.edu/bolker/benbolker-publickey.asc signature.asc Description: OpenPGP digital signature __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] optional package dependency
I have a package that can use rmpi, but works fine without it. None of the automatic test code invokes rmpi functionality. (One test file illustrates how to use it, but has quit() as its first command.) What's the best way to handle this? In particular, what is the appropriate form for upload to CRAN? When I omitted rmpi from the DESCRITPION file R CMD check gave quote * checking R code for possible problems ... NOTE alldone: no visible global function definition for ‘mpi.bcast.Robj’ alldone: no visible global function definition for ‘mpi.exit’ quote followed by many more warnings. When I add Suggests: Rmpi in DESCRIPTION the check stops if the package is not installed: quote * checking package dependencies ... ERROR Packages required but not available: Rmpi /quote Rmpi is not required, but I gather from previous discussion on this list that suggests basically means required for R CMD check. NAMESPACE seems to raise similar issues; I don't see any mechanism for optional imports. Also, I have not used namespaces, and am not eager to destabilize things so close to release. At least, I hope I'm close to release :) Thanks for any advice. Ross Boylan P.S. Thanks, Duncan, for your recent advice on my help format problem with R 2.7. I removed the nested \description, and now things look OK. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] optional package dependency
Hi Ross, The quantmod package makes available routines from a variety of contributed packages, but gets around your issues with a bit of, um, trickery. Take a look here (unless your name is Kurt ;-) ): http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/R/buildModel.methods.R?rev=367root=quantmodview=markup It would be nice to have Suggests really mean suggests to check, but I am sure there is a good reason it doesn't. HTH Jeff On Fri, Jan 15, 2010 at 12:00 AM, Ross Boylan r...@biostat.ucsf.edu wrote: I have a package that can use rmpi, but works fine without it. None of the automatic test code invokes rmpi functionality. (One test file illustrates how to use it, but has quit() as its first command.) What's the best way to handle this? In particular, what is the appropriate form for upload to CRAN? When I omitted rmpi from the DESCRITPION file R CMD check gave quote * checking R code for possible problems ... NOTE alldone: no visible global function definition for ‘mpi.bcast.Robj’ alldone: no visible global function definition for ‘mpi.exit’ quote followed by many more warnings. When I add Suggests: Rmpi in DESCRIPTION the check stops if the package is not installed: quote * checking package dependencies ... ERROR Packages required but not available: Rmpi /quote Rmpi is not required, but I gather from previous discussion on this list that suggests basically means required for R CMD check. NAMESPACE seems to raise similar issues; I don't see any mechanism for optional imports. Also, I have not used namespaces, and am not eager to destabilize things so close to release. At least, I hope I'm close to release :) Thanks for any advice. Ross Boylan P.S. Thanks, Duncan, for your recent advice on my help format problem with R 2.7. I removed the nested \description, and now things look OK. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan jeffrey.r...@insightalgo.com ia: insight algorithmics www.insightalgo.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] optional package dependency
On Fri, 2010-01-15 at 00:12 -0600, Jeff Ryan wrote: Hi Ross, The quantmod package makes available routines from a variety of contributed packages, but gets around your issues with a bit of, um, trickery. Take a look here (unless your name is Kurt ;-) ): http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/R/buildModel.methods.R?rev=367root=quantmodview=markup It would be nice to have Suggests really mean suggests to check, but I am sure there is a good reason it doesn't. I agree: it would be nice to have Suggests really mean suggests, and I 'suggested' so in an R-devel message of 20/9/05 with subject Shy Suggestion (but this seems not exist in the R-devel archive?). I got some support, but not from the right people, and so the R suggestion remains the one you can't refuse or you'll wake up with a horse head in your bed. I can live with this forced suggestion, although it is sometimes painful, in particular in Mac or after re-installing everything from scratch in Linux. The main argument was that building may fail later if you don't check suggests early so that you must (de facto) depend on packages you suggest. I'm sure many packages would fail now if the interpretation of suggests was changed because the behaviour of suggests and depends has been near identical for a long time and people have adapted. The window of opportunity for another interpretation was when the checks for undefined request() was added to the R CMD check routines in 2005, but then it was decided that suggests should be near equivalent to depends, and this will stick. Cheers, Jari Oksanen -- Jari Oksanen, Department of Biology, Univ Oulu, FI-90014 Oulu, Finland http://www.oulu.fi/~jarioksa http://vegan.r-forge.r-project.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
