[R-pkg-devel] how to document method arguments that aren't in the signature

2018-05-17 Thread Ross Boylan
"ANY")}: ... } I also considered adding the non-signature arguments in the text. Finally, although datap is formally untyped, there are requirements on what kind of object it can be. In practice it is only likely to be from one of two classes, but I want to allow the users to make their own

[Rd] modifying a persistent (reference) class

2014-08-01 Thread Ross Boylan
I saved objects that were defined using several reference classes. Later I modified the definition of reference classes a bit, creating new functions and deleting old ones. The total number of functions did not change. When I read them back I could only access some of the original data. I asked

Re: [Rd] modifying a persistent (reference) class

2014-08-01 Thread Ross Boylan
• Brian Lee Yung Rowe Founder, Zato Novo Professor, M.S. Data Analytics, CUNY On Aug 1, 2014, at 1:54 PM, Ross Boylan r...@biostat.ucsf.edu wrote: I saved objects that were defined using several reference classes. Later I modified the definition of reference classes a bit, creating

Re: [Rd] modifying a persistent (reference) class

2014-08-01 Thread Ross Boylan
Professor, M.S. Data Analytics, CUNY On Aug 1, 2014, at 3:33 PM, Ross Boylan r...@biostat.ucsf.edu wrote: On Fri, 2014-08-01 at 14:42 -0400, Brian Lee Yung Rowe wrote: Ross, This is generally a hard problem in software systems. The only language I know that explicitly

Re: [Rd] modifying data in a package [a solution]

2014-03-20 Thread Ross Boylan
On Wed, 2014-03-19 at 19:22 -0700, Ross Boylan wrote: I've tweaked Rmpi and want to have some variables that hold data in the package. One of the R files starts mpi.isend.obj - vector(list, 500) #mpi.request.maxsize

[Rd] modifying data in a package

2014-03-19 Thread Ross Boylan
) work? mpi.isend is a function in Rmpi. But I'd guess the first assign will fail because the environment is locked. Thanks. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Does R ever move objecsts in memory?

2014-03-16 Thread Ross Boylan
. I was just using the blocking sends to avoid this problem, but the result is significant delays. Thanks. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] 2 versions of same library loaded

2014-03-13 Thread Ross Boylan
On Thu, 2014-03-13 at 10:46 -0700, Ross Boylan wrote: 1. My premise that R had no references to mpi was incorrect. The logs show 24312: file=libmpi.so.1 [0]; needed by /home/ross/Rlib-3.0.1/Rmpi/libs/Rmpi.so [0] 24312: find library=libmpi.so.1 [0]; searching 24312

Re: [Rd] 2 versions of same library loaded

2014-03-13 Thread Ross Boylan
On Thu, 2014-03-13 at 10:46 -0700, Ross Boylan wrote: It seems very odd that the same Rmpi.so is requiring both the old and new libmpi.so (compare to the first trace in in point 1). There is this code in Rmpi.c: if (!dlopen(libmpi.so.0, RTLD_GLOBAL | RTLD_LAZY) !dlopen

[Rd] 2 versions of same library loaded

2014-03-12 Thread Ross Boylan
list have indicated I need to rebuild R, telling it where my MPI is, but that seems an awfully big hammer for the problem. Thanks. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] 2 versions of same library loaded

2014-03-12 Thread Ross Boylan
Comments/questions interspersed below. On Wed, 2014-03-12 at 22:50 -0400, Simon Urbanek wrote: Ross, On Mar 12, 2014, at 5:34 PM, Ross Boylan r...@biostat.ucsf.edu wrote: Can anyone help me understand how I got 2 versions of the same library loaded, how to prevent it, and what

Re: [Rd] C++ debugging help needed

2013-10-02 Thread Ross Boylan
On Wed, Oct 02, 2013 at 11:05:19AM -0400, Duncan Murdoch wrote: Up to entry #4 this all looks normal. If I go into that stack frame, I see this: (gdb) up #4 Shape::~Shape (this=0x15f8760, __in_chrg=optimized out) at Shape.cpp:13 warning: Source file is more recent than executable.

Re: [Rd] C++ debugging help needed

2013-10-02 Thread Ross Boylan
On Wed, 2013-10-02 at 16:15 -0400, Duncan Murdoch wrote: On 02/10/2013 4:01 PM, Ross Boylan wrote: On Wed, Oct 02, 2013 at 11:05:19AM -0400, Duncan Murdoch wrote: Up to entry #4 this all looks normal. If I go into that stack frame, I see this: (gdb) up #4 Shape

[Rd] Makevars and Makeconf sequencing

2013-08-23 Thread Ross Boylan
in Makevars? Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] problems extracting parts of a summary object

2010-03-22 Thread Ross Boylan
the summary method, the coefficients value is a matrix. I'm trying to pull out the standard errors for some rearranged output. How can I do that? And what's going on? I suspect this may be a namespace issue. Thanks. Ross Boylan P.S. I would appreciate a cc because of some mail problems I'm having

Re: [Rd] problems extracting parts of a summary object

2010-03-22 Thread Ross Boylan
not following the question. Ross On Mon, March 22, 2010 4:03 pm, Ross Boylan wrote: summary(x), where x is the output of lm, produces the expectedd display, including standard errors of the coefficients. summary(x)$coefficients produces a vector (x is r$individual[[2]]): r$individual[[2

Re: [Rd] problems extracting parts of a summary object [solved]

2010-03-22 Thread Ross Boylan
initial email) Doh! Thank you; that was it. This was interacting with another error, which is perhaps how I managed to miss it. Ross -- Tony Plate On Mon, March 22, 2010 4:43 pm, Ross Boylan wrote: On Mon, 2010-03-22 at 16:30 -0600, tpl...@cybermesa.com wrote: Are you sure you're extracting

[Rd] y ~ X -1 , X a matrix

2010-03-17 Thread Ross Boylan
While browsing some code I discovered a call to lm that used a formula y ~ X - 1, where X was a matrix. Looking through the documentation of formula, lm, model.matrix and maybe some others I couldn't find this useage (R 2.10.1). Is it anything I can count on in future versions? Is there

Re: [Rd] y ~ X -1 , X a matrix

2010-03-17 Thread Ross Boylan
On Thu, 2010-03-18 at 00:57 +, ted.hard...@manchester.ac.uk wrote: On 17-Mar-10 23:32:41, Ross Boylan wrote: While browsing some code I discovered a call to lm that used a formula y ~ X - 1, where X was a matrix. Looking through the documentation of formula, lm, model.matrix

Re: [Rd] Rgeneric.py assists in rearranging generic function definitions [inline]

2010-01-25 Thread Ross Boylan
On Thu, 2010-01-21 at 11:38 -0800, Ross Boylan wrote: I've attached a script I wrote that pulls all the setGeneric definitions out of a set of R files and puts them in a separate file, default allGenerics.R. I thought it might help others who find themselves in a similar situation

[Rd] Rgeneric.py assists in rearranging generic function definitions

2010-01-21 Thread Ross Boylan
didn't, and discover you should have, the script automates the conversion. Thanks to everyone who helped me with my packaging problems. The package finally made it to CRAN as http://cran.r-project.org/web/packages/mspath/index.html. I'll send a public notice of that to the general R list. Ross

[Rd] calling setGeneric() twice

2010-01-19 Thread Ross Boylan
seems like the smallest, and therefore safest, change if the duplication is not a problem. Thanks. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] calling setGeneric() twice

2010-01-19 Thread Ross Boylan
an earlier setGeneric to make the whole package work. I am also working on a python script to extract all the generic function defintions (that is, setGeneric()), just in case. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [Rd] calling setGeneric() twice (don't; documentation comments)

2010-01-19 Thread Ross Boylan
On Tue, 2010-01-19 at 12:55 -0800, Seth Falcon wrote: I would expect setGeneric to create a new generic function and nuke/mask methods associated with the generic that it replaces. I tried a test in R 2.7.1, and that is the behavior. I think it would be worthwhile to document it in

Re: [Rd] optional package dependency

2010-01-16 Thread Ross Boylan
On Sat, 2010-01-16 at 07:49 -0800, Seth Falcon wrote: Package authors should be responsible enough to test their codes with and without optional features. It seems unlikely most package authors will have access to a full range of platform types. Ross

Re: [Rd] optional package dependency

2010-01-15 Thread Ross Boylan
On Fri, 2010-01-15 at 09:19 +0100, Kurt Hornik wrote: The idea is that maintainers typically want to fully check their functionality, suggesting to force suggests by default. This might be the nub of the problem. There are different audiences, even for R CMD check. The maintainer probably

Re: [Rd] optional package dependency (enhances)

2010-01-15 Thread Ross Boylan
that logic isn't quite right if the enhanced package is added later. My package only loads/verifies the presence of rmpi if one attempts to use the distributed features, so the relation is at run time, not load time. Ross On Fri, Jan 15, 2010 at 6:00 AM, Ross Boylan r...@biostat.ucsf.edu wrote

Re: [Rd] optional package dependency (suggestions/wishes)

2010-01-15 Thread Ross Boylan
On Fri, 2010-01-15 at 12:34 -0500, Simon Urbanek wrote: On Jan 15, 2010, at 12:18 , Ross Boylan wrote: On Fri, 2010-01-15 at 09:19 +0100, Kurt Hornik wrote: The idea is that maintainers typically want to fully check their functionality, suggesting to force suggests by default

[Rd] optional package dependency

2010-01-14 Thread Ross Boylan
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

Re: [Rd] ?setGeneric garbled (PR#14153)

2009-12-17 Thread Ross Boylan
On Thu, 2009-12-17 at 15:24 +0100, Martin Maechler wrote: Ross Boylan r...@biostat.ucsf.edu on Thu, 17 Dec 2009 02:15:12 +0100 (CET) writes: Full_Name: Ross Boylan Version: 2.10.0 OS: Windows XP Submission from: (NULL) (198.144.201.14) Some of the help

Re: [Rd] group generics

2009-12-03 Thread Ross Boylan
Thanks for your help. I had two concerns about using as: that it would impose some overhead, and that it would require me to code an explicit conversion function. I see now that the latter is not true; I don't know if the overhead makes much difference. On Thu, 2009-12-03 at 13:00 -0800, Martin

Re: [Rd] group generics

2009-12-03 Thread Ross Boylan
the relevant help entries. Ross Ross Boylan wrote: Thanks for your help. I had two concerns about using as: that it would impose some overhead, and that it would require me to code an explicit conversion function. I see now that the latter is not true; I don't know if the overhead makes

Re: [Rd] group generics

2009-11-30 Thread Ross Boylan
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Martin Morgan wrote: Hi Ross -- Ross Boylan r...@biostat.ucsf.edu writes: I have classes A and B, where B contains A. In the implementation of the group generic for B I would like to use the corresponding group generic

[Rd] group generics

2009-11-24 Thread Ross Boylan
] 4 3*t1 Error in getGeneric(f, !optional) : no generic function found for callGeneric Thanks. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] bug in heatmap?

2009-11-05 Thread Ross Boylan
of the row labelled 6 (all 0's and NaN) is white. This is the same color showing for the NaN values. In contrast, all other 0 values appear as dark red. Have I missed some subtlety, or is this a bug? Ross Boylan __ R-devel@r-project.org mailing list

Re: [Rd] mysteriously persistent generic definition

2009-10-28 Thread Ross Boylan
Here's a self-contained example of the problem: foo - function(obj) {return(3);} setGeneric(foo) [1] foo removeGeneric(foo) [1] TRUE foo - function(x) {return(4);} args(foo) function (x) NULL setGeneric(foo) [1] foo args(foo) function (obj) NULL R 2.7.1. I get the same behavior whether

Re: [Rd] mysteriously persistent generic definition

2009-10-28 Thread Ross Boylan
R 2.8.1 on Windows behaves as I expected, i.e., the final args(foo) returns a function of x. The previous example (below) was on Debian GNU/Linux. On Wed, 2009-10-28 at 12:14 -0700, Ross Boylan wrote: Here's a self-contained example of the problem: foo - function(obj) {return(3

[Rd] mysteriously persistent generic definition

2009-10-22 Thread Ross Boylan
the definitions in from a file with ^c^l in ESS; however, I typed the commands above by hand. Thanks. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] user supplied random number generators

2009-08-18 Thread Ross Boylan
On Sun, 2009-08-16 at 21:24 +0200, Petr Savicky wrote: Dear Ross Boylan: Some time ago, you sent an email to R-devel with the following. I got into this because I'm trying to extend the rsprng code; sprng returns its state as a vector of bytes. Converting these to a vector of integers

[Rd] user supplied random number generators

2009-07-30 Thread Ross Boylan
-project.org/rwiki/doku.php?id=packages:cran:rsprng. Feel free to read, correct, or extend it. Thanks. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] user supplied random number generators

2009-07-30 Thread Ross Boylan
On Thu, 2009-07-30 at 12:32 +0200, Christophe Dutang wrote: This suggests that the type of user_unif_seedloc is Int32*, not int *. It also suggests that user_unif_nseed should return the number of 32 bit integers. The code for PutRNGstate(), for example, uses them in just that way.

Re: [Rd] beginner's guide to C++ programming with R packages?

2009-07-03 Thread Ross Boylan
of the sources; otherwise scraps of my other builds tend to end up in the R package. Thanks, Whit, for the pointers to Rcpp and RAbstraction. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] S4 class redefinition

2009-06-30 Thread Ross Boylan
, define some coerce methods, and then locate and change the relevant instances. Is there a better way? Thanks. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] S4 class redefinition

2009-06-30 Thread Ross Boylan
On Tue, 2009-06-30 at 12:58 -0700, Ross Boylan wrote: I haven't found much on S4 class redefinition; the little I've seen indicates the following is to be expected: 1. setClass(foo, ) 2. create objects of class foo. 3. execute the same setClass(foo, ...) again (source the same file). 4

Re: [Rd] could not find function in R CMD check [solved, but is this an R bug?]

2007-09-12 Thread Ross Boylan
completely and opaquely in this situation? Ross Boylan wrote: During R CMD check I get this: ** building package indices ... Error in eval(expr, envir, enclos) : could not find function readingError Execution halted ERROR: installing package indices failed The check aborts

[Rd] could not find function in R CMD check

2007-09-11 Thread Ross Boylan
} and an example invoking readingError. I'm using R 2.5.1 as packaged for Debian GNU/Linux. Does anyone have an idea what's going wrong here, or how to fix or debug it? The code seems to work OK when I use it from ESS. -- Ross Boylan wk: (415) 514-8146 185 Berry St

[Rd] codetools really optional for R CMD check?

2007-07-25 Thread Ross Boylan
After upgrading to R 2.5.1 on Debian, R CMD check gives * checking Rd cross-references ... WARNING Error in .find.package(package, lib.loc) : there is no package called 'codetools' Execution halted * checking for missing documentation entries ... WARNING etc The NEWS file says (for

[Rd] Reported invalid memory references

2007-06-13 Thread Ross Boylan
? If so, do they indicate problems in R or some other component (e.g., ld.so). Put more practically, should I file one or more bugs, and if so, against what? Thanks. Ross Boylan ==30551== Invalid read of size 4 ==30551==at 0x4016503: (within /lib/ld-2.5.so) ==30551==by 0x4006009: (within

[Rd] undefined symbol: Rf_rownamesgets

2007-04-17 Thread Ross Boylan
I get the error undefined symbol: Rf_rownamesgets when I try to load my package, which include C++ code that calls that function. This is particularly strange since the code also calls Rf_classgets, and it loaded OK with just that. Can anyone tell me what's going on? For the record, I worked

Re: [Rd] undefined symbol: Rf_rownamesgets

2007-04-17 Thread Ross Boylan
On Tue, Apr 17, 2007 at 11:07:12PM -0400, Duncan Murdoch wrote: On 4/17/2007 10:43 PM, Ross Boylan wrote: I get the error undefined symbol: Rf_rownamesgets when I try to load my package, which include C++ code that calls that function. This is particularly strange since the code also calls

[Rd] future plans for missing() in inner functions

2007-04-03 Thread Ross Boylan
Currently, if one wants to test if an argument to an outer function is missing from within an inner function, this works: g5 - function(a) { + inner - function(a) { + if (missing(a)) + outer arg is missing + else + found outer arg! + } + inner(a) + } g5(3) [1] found

Re: [Rd] Replacing slot of S4 class in method of S4 class?

2007-03-30 Thread Ross Boylan
programming. Ross Boylan P.S. Regarding the follow up saying that this is the wrong list, the guide to mailing lists says of R-devel This list is intended for questions and discussion about code development in R. Questions likely to prompt discussion unintelligible to non-programmers or topics that are too

Re: [Rd] Rmpi and OpenMPI ?

2007-03-30 Thread Ross Boylan
On Fri, Mar 30, 2007 at 03:01:19PM -0500, Dirk Eddelbuettel wrote: On 30 March 2007 at 12:48, Ei-ji Nakama wrote: | Prof. Nakano(ism Japan) and I wrestled in Rmpi on HP-MPI. | Do not know a method to distinguish MPI well? | It is an ad-hoc patch at that time as follows. There are some

Re: [Rd] R CMD check ignores .Rbuildignore?

2007-03-19 Thread Ross Boylan
On Mon, Mar 19, 2007 at 11:33:37AM +0100, Martin Maechler wrote: RossB == Ross Boylan [EMAIL PROTECTED] on Sun, 18 Mar 2007 12:39:14 -0700 writes: RossB The contents of .Rbuildignore seems to affect RossB R CMD build RossB but not RossB R CMD check. RossB I'm

Re: [Rd] R CMD check ignores .Rbuildignore? [correction]

2007-03-19 Thread Ross Boylan
On Mon, Mar 19, 2007 at 10:38:02AM -0700, Ross Boylan wrote: Kurt Hornick, offlist, also advised this, as well as noting that using Sorry. That should be Kurt Hornik. Ross __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [Rd] R/C++/memory leaks

2007-02-26 Thread Ross Boylan
On Mon, 2007-02-26 at 16:08 +, Ernest Turro wrote: Thanks for your comments Ross. A couple more comments/queries below: On 26 Feb 2007, at 06:43, Ross Boylan wrote: [details snipped] The use of the R api can be confined to a wrapper function. But I can think of no reason

Re: [Rd] R/C++/memory leaks

2007-02-25 Thread Ross Boylan
the memory be garbage collected? can it be moved?). Overriding new is a bit tricky since there are several variants. In particular, there is one with and one without an exception. Also, invdividual classes can define their own new operators; if you have any, you'd need to change those too. Ross

Re: [Rd] R/C++/memory leaks

2007-02-25 Thread Ross Boylan
Here are a few small follow-up comments: On Sun, Feb 25, 2007 at 11:18:56PM +, Ernest Turro wrote: On 25 Feb 2007, at 22:21, Ross Boylan wrote: On Sun, Feb 25, 2007 at 05:37:24PM +, Ernest Turro wrote: Dear all, I have wrapped a C++ function in an R package. I allocate/deallocate

Re: [Rd] trying to understand condition handling

2007-02-20 Thread Ross Boylan
it does, you can set up interrupt handlers (as the help page said) My P.S. concerned whether the code that was interrupted could continue from the point of interruption. As far as I can tell from ?tryCatch there is not, On Mon, 19 Feb 2007, Ross Boylan wrote: I'm confused by the page

Re: [Rd] trying to understand condition handling (interrupts)

2007-02-20 Thread Ross Boylan
[resequencing and deleting for clarity] On Tue, Feb 20, 2007 at 01:15:25PM -0600, Luke Tierney wrote: On Tue, 20 Feb 2007, Ross Boylan wrote: P.S. Is there any mechanism that would allow one to trap an interrupt, like a ctl-C, so that if the user hit ctl-C some state would be changed

Re: [Rd] trying to understand condition handling

2007-02-20 Thread Ross Boylan
. Below, [1] means http://www.stat.uiowa.edu/~luke/R/exceptions/simpcond.html, one of the documents Prof Ripley referred to. That page also has a nice illustration of using the restart facility. On Tue, Feb 20, 2007 at 01:40:11PM -0600, Luke Tierney wrote: On Mon, 19 Feb 2007, Ross Boylan wrote

[Rd] trying to understand condition handling

2007-02-19 Thread Ross Boylan
to finish up flag which the maini code checks from time to time. Thanks. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] pinning down symbol values (Scoping/Promises) question

2007-02-16 Thread Ross Boylan
) a1() [1] 101 (by the way, I thought a - eval(substitute(function(z) function() z+k)) would work, but it didn't). This seems to pin the passed in argument as well, though it's even uglier: a - eval(substitute(function(z) { z; function() z+x}, list(x=k))) a1 - a(k1) k1 - 5 a1() [1] 120 -- Ross

[Rd] R Language Manual: possible error

2007-02-16 Thread Ross Boylan
of this document is 2.4.0 (2006-11-25) DRAFT. -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700 [EMAIL PROTECTED] Dept of Epidemiology and Biostatistics fax: (415) 514-8150 University of California, San Francisco San

Re: [Rd] Problem using ofstream in C++ class in package for MacOS X

2007-02-08 Thread Ross Boylan
On Sun, Feb 04, 2007 at 10:47:37PM +0100, cstrato wrote: Seth Falcon wrote: cstrato [EMAIL PROTECTED] writes: Thank you for your fast answer. Sorrowly, I don´t know how to use a debugger on MacOS X, I am using old-style print commands. You should be able to use gdb on OS

[Rd] One possible use for threads in R

2007-02-08 Thread Ross Boylan
is the best approach to this problem (or even that it would be if R were multi-threaded), but it does seem to me this might be one area where threads would be handy in R. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [Rd] Problem using ofstream in C++ class in package for MacOS X

2007-02-08 Thread Ross Boylan
On Thu, Feb 08, 2007 at 11:53:21PM +0100, cstrato wrote: ... Maybe there's some subtle linker problem, or a problem with the representation of strings What do you mean with linker problem? Nothing very specific, but generically wrong options, wrong objects/libraries, or wrong order of

Re: [Rd] encoding issues even w/o accents (background on single quotes)

2007-01-19 Thread Ross Boylan
On Wed, Jan 17, 2007 at 11:56:15PM -0800, Ross Boylan wrote: An earlier thread (in 10/2006) discussed encoding issues in the context of R data and the desire to represent accented characters. It matters in another setting: the output generated by R and the seemingly order character ' (single

Re: [Rd] C vs. C++ as learning and development tool for R

2007-01-19 Thread Ross Boylan
there, is don't use C++ unless you have a compelling reason and a lot of time! Ross Boylan (Among the languages listed, the ones I've used extensively are C, C++, Objective-C, Python, R, and smalltalk.) __ R-devel@r-project.org mailing list https

[Rd] Problems with checking documentation vs data, and a proposal

2007-01-16 Thread Ross Boylan
-arounds? -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700 [EMAIL PROTECTED] Dept of Epidemiology and Biostatistics fax: (415) 514-8150 University of California, San Francisco San Francisco, CA 94107-1739

Re: [Rd] Problems with checking documentation vs data, and a proposal

2007-01-16 Thread Ross Boylan
On Tue, 2007-01-16 at 14:03 -0800, Ross Boylan wrote: I have a single data file inputs.RData that contains 3 objects. I generated an Rd page for each object using prompt(). When I run R CMD check I get * checking for code/documentation mismatches ... WARNING Warning in utils::data(list = al

Re: [Rd] Am I missing something about debugging?

2007-01-04 Thread Ross Boylan
On Thu, 2007-01-04 at 17:06 +1100, [EMAIL PROTECTED] wrote: It is possible to do some of these things with the 'debug' package-- the article in R-news 2003 #3 shows a few of the tricks. Suppose 'b1' calls 'c1'. If 'c1' exists as permanent function defined outside 'b1' (which I generally

Re: [Rd] Which programming paradigm is the most used for make R packages?

2007-01-03 Thread Ross Boylan
. There is a package that permits a more traditional (class-based) OO style; I think it's called R.oo. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Am I missing something about debugging?

2007-01-02 Thread Ross Boylan
. 265); these are conspicuously absent in R. -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700 [EMAIL PROTECTED] Dept of Epidemiology and Biostatistics fax: (415) 514-8150 University of California, San Francisco San

Re: [Rd] Am I missing something about debugging?

2007-01-02 Thread Ross Boylan
On Tue, 2007-01-02 at 17:24 -0500, Duncan Murdoch wrote: I don't think you're missing anything with the debug() function. It needs updating. Bummer! I don't think there's any structural reason why you shouldn't be able to do the things you're talking about in R, but they haven't been

[Rd] Capturing argument values

2006-12-30 Thread Ross Boylan
would not have the values I needed as well. (Also the frame could later change, though I guess I could convert it to a list to avoid that problem.) Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] setGeneric and file order in a package

2006-12-28 Thread Ross Boylan
test for existence of a generic in the one spot I create it? Since that seems like a half-measure (if a generic exists it may well have different arguments) I suppose I should use namespaces... Thanks. Ross Boylan __ R-devel@r-project.org mailing list

Re: [Rd] promptClass misses methods

2006-12-02 Thread Ross Boylan
On Sat, Dec 02, 2006 at 05:11:22PM +0100, Martin Maechler wrote: RossB == Ross Boylan [EMAIL PROTECTED] on Fri, 1 Dec 2006 11:33:21 -0800 writes: RossB On Fri, Dec 01, 2006 at 11:37:46AM +0100, Martin RossB Maechler wrote: RossB == Ross Boylan [EMAIL PROTECTED

Re: [Rd] promptClass misses methods

2006-12-01 Thread Ross Boylan
On Fri, Dec 01, 2006 at 11:37:46AM +0100, Martin Maechler wrote: RossB == Ross Boylan [EMAIL PROTECTED] on Thu, 30 Nov 2006 22:29:06 -0800 writes: RossB I've had repeated problems with promptClass missing RossB methods, usually telling me a class has no methods RossB when

Re: [Rd] printing coefficients with text

2006-12-01 Thread Ross Boylan
On Fri, Dec 01, 2006 at 10:34:45AM +0100, Martin Maechler wrote: RossB == Ross Boylan [EMAIL PROTECTED] on Thu, 30 Nov 2006 12:17:55 -0800 writes: RossB I want to print the coefficient estimates of a model RossB in a way as consistent with other output in R as RossB

Re: [Rd] Web site link problems (PR#9401)

2006-11-30 Thread Ross Boylan
On Thu, Nov 30, 2006 at 10:59:13AM +0100, Peter Dalgaard wrote: [EMAIL PROTECTED] wrote: 2. http://www.r-project.org/posting-guide.html includes in the section Surprising behavior and bugs, make sure you read R Bugs in the R-faq. The latter is the link

[Rd] printing coefficients with text

2006-11-30 Thread Ross Boylan
of the matrix given as the first argument to the function. Are there any better solutions? Obviously I could just copy the method and modify it, but that creates duplicate code and loses the ability to track future changes to printCoefmat. Thanks. Ross Boylan

[Rd] promptClass misses methods

2006-11-30 Thread Ross Boylan
that I'm running under ESS in emacs. However, I get the same results running R from the command line. Can anyone tell me what's going on here? This is with R 2.4, and I'm not currently using any namespace for my definitions. Thanks. Ross Boylan __ R-devel

Re: [Rd] promptClass misses methods (addendum)

2006-11-30 Thread Ross Boylan
On Thu, Nov 30, 2006 at 10:29:06PM -0800, Ross Boylan wrote: I've had repeated problems with promptClass missing methods, usually telling me a class has no methods when it does. In my current case, I've defined an S4 class mspathCoefficients with a print method setMethod(print, signature(x

Re: [Rd] Missing values for S4 slots [One Solution]

2006-11-24 Thread Ross Boylan
On Fri, Nov 24, 2006 at 11:23:14AM -0800, Ross Boylan wrote: Using R 2.4, the following fails: setClass(testc, representation(a=ANY)) makeC - function(myarg) new(testc, a=myarg) makeC() - Error in initialize(value, ...) : argument myarg is missing, with no default I suspect

[Rd] tail recursion in R

2006-11-14 Thread Ross Boylan
. Thanks. -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700 [EMAIL PROTECTED] Dept of Epidemiology and Biostatistics fax: (415) 514-8150 University of California, San Francisco San Francisco, CA 94107-1739

[Rd] \link to another package

2006-10-19 Thread Ross Boylan
the documentation to work gracefully in that situation. Gracefully means that if Rmpi is not loaded the help still shows; it does not mean that clicking on the link magically produces the Rmpi documentation. -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700

[Rd] documenation duplication and proposed automatic tools

2006-10-02 Thread Ross Boylan
this is not trivial, and I'm not necessarily advocating it as a priority. But I wonder how it strikes people. -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700 [EMAIL PROTECTED] Dept of Epidemiology and Biostatistics fax

Re: [Rd] S4 accessors

2006-09-27 Thread Ross Boylan
I'm trying to understand what the underlying issues are here--with the immediate goal of how that affects my design and documentation decisions. On Wed, Sep 27, 2006 at 02:08:34PM -0400, John Chambers wrote: Seth Falcon wrote: John Chambers [EMAIL PROTECTED] writes: There is a point

Re: [Rd] S4 accessors

2006-09-26 Thread Ross Boylan
On Tue, 2006-09-26 at 10:43 -0700, Seth Falcon wrote: Ross Boylan [EMAIL PROTECTED] writes: If anyone else is going to extend your classes, then you are doing them a disservice by not making these proper methods. It means that you can control what happens when they are called

[Rd] S4 accessors

2006-09-25 Thread Ross Boylan
are worse for replacement functions; as I understand it, they must use value for their final argument, but the value has different meanings and types in different contexts. Any suggestions or comments? I've attached the .Rd file in case more specifics would help. -- Ross Boylan

Re: [Rd] S4 accessors (corrected)

2006-09-25 Thread Ross Boylan
On Tue, 2006-09-26 at 00:20 +, Ross Boylan wrote: I have a small S4 class for which I've written a page grouping many of the accessors and replacement functions together. I would be interested in people comments on the approach I've taken. The code has a couple of decisions for which I

Re: [Rd] S4 classes and C

2006-05-19 Thread Ross Boylan
On Fri, 2006-05-19 at 11:46 +0200, Martin Maechler wrote: Seth == Seth Falcon [EMAIL PROTECTED] on Thu, 18 May 2006 12:22:36 -0700 writes: Seth Ross Boylan [EMAIL PROTECTED] writes: Is there any good source of information on how S4 classes (and methods) work from C

Re: [Rd] S4 classes and C

2006-05-18 Thread Ross Boylan
On Thu, 2006-05-18 at 13:53 -0400, McGehee, Robert wrote: I believe the paper on which those lecture notes were based can be found here: http://www.ci.tuwien.ac.at/Conferences/DSC-2003/Drafts/BatesDebRoy.pdf Thank you. It looks as if it has some useful stuff in it. Ross

[Rd] Recommended style with calculator and persistent data

2006-05-18 Thread Ross Boylan
the problem? My current approach works, but I'm concerned it is non-standard, and so would be unnatural for users. -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700 [EMAIL PROTECTED] Dept of Epidemiology and Biostatistics

[Rd] S4 documentation

2006-02-07 Thread Ross Boylan
the documentation on documenting S4 a bit too brief (even after looking at the recommended links, which in some cases don't have much on documentation). Since the docs say it's a work in progress, I'm hoping to get the latest word here. Thanks. -- Ross Boylan wk

Re: [Rd] checkpointing

2006-01-06 Thread Ross Boylan
environment (by default). # wrapper to do checkpointing # Ross Boylan [EMAIL PROTECTED] # 06-Jan-2006 # (C) 2006 Regents of University of California # Distributed under the Gnu Public License v2 or later at your option # If you want to checkpoint the optimization of a function f # Use checkpoint(f

[Rd] checkpointing

2006-01-02 Thread Ross Boylan
. In particular, is save a reasonable way to save a few variables to disk? I could also make the code available when/if I get it working. -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700 [EMAIL PROTECTED] Dept of Epidemiology

[Rd] external pointers

2005-12-09 Thread Ross Boylan
++ destructors. -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700 [EMAIL PROTECTED] Dept of Epidemiology and Biostatistics fax: (415) 514-8150 University of California, San Francisco San Francisco, CA 94107-1739

Re: [Rd] problem with \eqn (PR#8322)

2005-11-23 Thread Ross Boylan
On Mon, 2005-11-21 at 10:27 +, Hin-Tak Leung wrote: Kurt Hornik wrote: snipped Definitely a problem in Rdconv. E.g., $ cat foo.Rd \description{ \eqn{{A}}{B} } [EMAIL PROTECTED]:~/tmp$ R-d CMD Rdconv -t latex foo.Rd | grep eqn \eqn{{A}}{A}{{B} shows what is going

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