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

2005-11-18 Thread Ross Boylan
low. It is basic LaTeX and any LaTeX person > can tell you the answer...(most probably haven't bothered...) > > [EMAIL PROTECTED] wrote: > >Full_Name: Ross Boylan > >Version: 2.2.0 > >OS: Linux > >Submission from: (NULL) (65.175.48.58) > >

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: > > > 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} > > > > s

[Rd] Makefiles and other customization

2005-11-23 Thread Ross Boylan
er option would be to do a clean checkout of the sources for my package, run a special makefile target that would create the necessary files and delete all unwanted files, and then do a regular R CMD build. This might still have trouble with "data.gz". -

Re: [Rd] Makefiles and other customization

2005-11-23 Thread Ross Boylan
On Wed, 2005-11-23 at 15:47 -0800, Kasper Daniel Hansen wrote: > Well you can have a look at etc/Makeconf. I have had some troubles > understanding the make process myself (which probably reveals I am > not a make guru), but it really depends on what you want to > accomplish - and from a cert

[Rd] external pointers

2005-12-09 Thread Ross Boylan
from the C++ run-time, and needs C++ 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 Franc

[Rd] checkpointing

2006-01-02 Thread Ross Boylan
oceed. 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 Epidem

Re: [Rd] checkpointing

2006-01-03 Thread Ross Boylan
On Tue, Jan 03, 2006 at 01:26:39PM +, Prof Brian Ripley wrote: > On Tue, 3 Jan 2006, Kasper Daniel Hansen wrote: > > >On Jan 3, 2006, at 9:36 AM, Brian D Ripley wrote: > > > >>I use save.image() or save(), which seem exactly what you are asking for. > > > >I have the (perhaps unsupported) impr

Re: [Rd] checkpointing

2006-01-06 Thread Ross Boylan
he calling 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 ch

[Rd] an unpleasant interaction of environments and generic functions

2006-01-31 Thread Ross Boylan
.so file. So, is my diagnosis correct? Any suggestions about how to avoid this problem? Maybe sys.source("file", 2)... Seems to work! -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700 [EMAIL PROTECTED] Dept of E

Re: [Rd] an unpleasant interaction of environments and generic functions

2006-01-31 Thread Ross Boylan
On Tue, 2006-01-31 at 15:21 -0800, Ross Boylan wrote: > Any suggestions about how to avoid this problem? > Maybe sys.source("file", 2)... Seems to work! Not quite. The original versions of some stuff from the library hung around, and my efforts to delete them led to m

[Rd] S4 documentation

2006-02-07 Thread Ross Boylan
er to the function generically, how do I do that? I'm using R 2.2.1, and I've found 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

[Rd] Makevars and Makeconf sequencing

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

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=) 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 sta

[Rd] 2 versions of same library loaded

2014-03-12 Thread Ross Boylan
place? How can I stop the madness? Some folks on the openmpi 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 wrote: > > > Can anyone help me understand how I got 2 versions of the same library > > loaded, how to prevent it, and w

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]; se

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"

[Rd] Does R ever move objecsts in memory?

2014-03-16 Thread Ross Boylan
oved that would invalidate the transfer. 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

[Rd] modifying data in a package

2014-03-19 Thread Ross Boylan
ign("mpi.globals", new.env(), environment(mpi.isend)) assign("mpi.isend.obj", vector("list", mpi.request.maxsize(), mpi.globals) 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

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

2014-03-19 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"

[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
ion of your app/system (ie > you're always writing to and reading from the intermediate format). > > > Warm regards, > Brian > > • > Brian Lee Yung Rowe > Founder, Zato Novo > Professor, M.S. Data Analytics, CUNY > > On Aug 1, 2014, at 1:54 PM, Ross Boylan wrote

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

2014-08-01 Thread Ross Boylan
at is unlikely to happen, for many good reasons, but I can still hope :) Ross > > Warm regards, > Brian > > • > Brian Lee Yung Rowe > Founder, Zato Novo > Professor, M.S. Data Analytics, CUNY > > On Aug 1, 2014, at 3:33 PM, Ross Boylan wrote: > &g

[Rd] S4 class redefinition

2009-06-30 Thread Ross Boylan
at do I do? At the moment it looks as if I'd need to make a new class name, 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

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

2009-07-03 Thread Ross Boylan
get built into a library. It's usually cleaner to build the R library from a fresh version 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] user supplied random number generators

2009-07-29 Thread Ross Boylan
ore of my rsprng adventures are on http://wiki.r-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 >

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. Conve

[Rd] mysteriously persistent generic definition

2009-10-22 Thread Ross Boylan
gt; setGeneric("yearStop") [1] "yearStop" > args(yearStop) function (obj) NULL R 2.7.1. I originally read 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] 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 sam

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 <- fun

[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

[Rd] group generics

2009-11-24 Thread Ross Boylan
nature=c("numeric", "A"))(e1, e2) print(v) new("B", v, xb=e1...@xb) } ) Results: > t1 <- new("B", new("A", xa=4), xb=2) > t1 An object of class “B” Slot "xb": [1] 2 Slot "xa": [1] 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

Re: [Rd] group generics

2009-11-30 Thread Ross Boylan
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Martin Morgan wrote: > Hi Ross -- > > Ross Boylan 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 >> generi

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
w they interacted with callNextMethod, selectMethod, etc. I did study what I thought were 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 requi

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 > >>>>> on Thu, 17 Dec 2009 02:15:12 +0100 (CET) writes: > > > Full_Name: Ross Boylan > > Version: 2.10.0 > > OS: Windows XP > > Sub

[Rd] Rd output garbled in some circumstances

2010-01-13 Thread Ross Boylan
the bug tracker, but couldn't find anything--in fact I had trouble identifying bugs in the documentation system as opposed to bugs in the documentation. Thanks. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] optional package dependency

2010-01-14 Thread Ross Boylan
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] 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 w

Re: [Rd] optional package dependency (enhances)

2010-01-15 Thread Ross Boylan
kipped if the enhanced package was absent. Even 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

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

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 _

[Rd] calling setGeneric() twice

2010-01-19 Thread Ross Boylan
Adding duplicate setGeneric's 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
ing use, and so it would be useful if they could retain setGeneric()'s even if I also need 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 __

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 ?setGene

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

2010-01-21 Thread Ross Boylan
cs.py from the start. If you 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 o

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 >

[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 document

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 o

[Rd] problems extracting parts of a summary object

2010-03-22 Thread Ross Boylan
n I trace through 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 o

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

2010-03-22 Thread Ross Boylan
Plate > class(summary(r$individual[[2]])) [1] "summary.lm" But maybe I'm 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 e

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

2010-03-22 Thread Ross Boylan
what you appeared to be doing from your 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

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

[Rd] One possible use for threads in R

2007-02-08 Thread Ross Boylan
ketched above 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.c

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 10:04:14PM +0100, cstrato wrote: > Ross Boylan wrote: > >On Sun, Feb 04, 2007 at 10:47:37PM +0100, cstrato wrote: > > > >>Seth Falcon wrote: > >> > >>>cstrato <[EMAIL PROTECTED]> writes: > >>> > >&

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 wro

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

2007-02-16 Thread Ross Boylan
uglier: > a <- eval(substitute(function(z) { z; function() z+x}, list(x=k))) > a1 <- a(k1) > k1 <- 5 > a1() [1] 120 -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700 [EMAIL PROTECTED] Dept of Epidemiology

[Rd] R Language Manual: possible error

2007-02-16 Thread Ross Boylan
he front page of the manual says The current version 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:

[Rd] "try"ing to understand condition handling

2007-02-19 Thread Ross Boylan
have in mind the ctl-C handler setting a "time 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

Re: [Rd] "try"ing to understand condition handling

2007-02-20 Thread Ross Boylan
nerates an interrrupt in most (but not all) R > ports. Where 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, >

Re: [Rd] "try"ing 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 hi

Re: [Rd] "try"ing to understand condition handling

2007-02-20 Thread Ross Boylan
murky. 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 Boyl

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

2007-02-25 Thread Ross Boylan
r, you can override the operator new in C++ so that it uses your own allocator, e.g., R_alloc. I'm not sure about all the implications that might make that dangerous (e.g., can the memory be garbage collected? can it be moved?). Overriding new is a bit tricky since there are se

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

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 functi

[Rd] R CMD check ignores .Rbuildignore?

2007-03-18 Thread Ross Boylan
The contents of .Rbuildignore seems to affect R CMD build but not R CMD check. I'm using R 2.4.0 on Debian. Is my understanding correct? And is there anything I can do about it? In my case, some of the excluded files contain references to other libraries, so linking fails under R CMD check. I

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 >

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/mai

Re: [Rd] Rmpi and OpenMPI ?

2007-03-29 Thread Ross Boylan
tegration with Sun Grid Engine. -- 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 Francisc

[Rd] S4 generic surprise

2007-03-29 Thread Ross Boylan
ght the function remain generic, and so did not rebuild it at the next setMethod. If I had practiced the recommended style, I would have done foo<-function(object) 2 setGeneric("foo") and all would have been well. So that's what I'll do. I thought I'd report this in

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

2007-03-30 Thread Ross Boylan
on(object, myname=character(0), ...) { [EMAIL PROTECTED] <- myname; object } Further, if you invoke it with mymethod(myclass, "new name") you will discover myclass is unchanged. You need myclass <- mymethod(myclass, "new name") You might consider us

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 a

[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] "f

[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 particul

[Rd] Reported invalid memory references

2007-06-13 Thread Ross Boylan
y problems? 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 0x400600

Re: [Rd] Using R_MakeExternalPtr

2007-07-25 Thread Ross Boylan
See at bottom for an example. On Wed, 2007-07-25 at 11:26 -0700, Jonathan Zhou wrote: > Hi Hin-Tak, > > Here is the R code function in where I called the two C++ and further below > are the 2 C++ functions I used to create the externalptr and use it : > > soam.Rapply <- function (x, func, ..., >

[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 2.5.0;

[Rd] "could not find function" in R CMD check

2007-09-11 Thread Ross Boylan
, \alias{readingError-class}, \name{readingError-class} 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

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

2007-09-12 Thread Ross Boylan
ond, should R CMD check fail so 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&quo

[Rd] profiling C code

2006-02-20 Thread Ross Boylan
is Mac OS X. Thanks. Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] S4 classes and C

2006-05-18 Thread Ross Boylan
on one line). "Writing R Extensions" (2.3.0 version) makes no reference to this topic that I can see. -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700 [EMAIL PROTECTED] Dept of Epidemiology and Biostatistics

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
recommended R'ish way to approach 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 PROTEC

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: > >

[Rd] S4 accessors

2006-09-25 Thread Ross Boylan
ly the same. Things 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 sp

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

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 contr

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 i

[Rd] documenation duplication and proposed automatic tools

2006-10-02 Thread Ross Boylan
elevant classes. I realize that implementing 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

[Rd] \link to another package

2006-10-19 Thread Ross Boylan
i loaded, so I'd like 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

[Rd] tail recursion in R

2006-11-14 Thread Ross Boylan
in R. 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

[Rd] Missing values for S4 slots

2006-11-24 Thread Ross Boylan
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 On the other hand, this is OK: f <- function(a) g(b=a) g <- function(b) if(missin

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, ...)

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 http://cran.r-project.o

[Rd] printing coefficients with text

2006-11-30 Thread Ross Boylan
f 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 B

[Rd] promptClass misses methods

2006-11-30 Thread Ross Boylan
quot;) Methods may be defined for arguments: x I've looked through the code for promptClass, but nothing popped out at me. It may be relevant 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 o

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