Re: [Rd] Problems with ::

2025-04-04 Thread Duncan Murdoch
On 2025-03-19 12:49 p.m., Therneau, Terry M., Ph.D. via R-devel wrote: In response to the tidyverse habit of adding another zillion functions to one's search space, the use of things like survival::coxph is becoming more common. But this practice breaks the use of the specials argument in term

Re: [Rd] Problems with ::

2025-03-21 Thread Mikael Jagan
I've wanted to use specials to detect random effect terms as in ~(f | g), but non-syntactic function names (in this case, '|') are currently not supported. I proposed a patch some time ago: https://bugs.r-project.org/show_bug.cgi?id=18568 I wonder if some of these issues with '::' could be s

Re: [Rd] Problems with ::

2025-03-19 Thread avi.e.gross
rks, could be helpful to some. Assuming dplyr has no compatibility, you can then use dplyr::filter when you want the other one or ... -Original Message- From: R-devel On Behalf Of Therneau, Terry M., Ph.D. via R-devel Sent: Wednesday, March 19, 2025 12:50 PM To: r-devel@r-project.org S

[Rd] Problems with ::

2025-03-19 Thread Therneau, Terry M., Ph.D. via R-devel
In response to the tidyverse habit of adding another zillion functions to one's search space, the use of things like survival::coxph is becoming more common. But this practice breaks the use of the specials argument in terms.formula, something that I make heavy use of in the survival package.

Re: [Rd] Problems with packages fda and splines (PR#13263)

2021-10-24 Thread Bjørn Henrik Auestad via R-devel
Dear Spencer, I'm struggling with the same problem as was mentioned in Re: [Rd] Problems with packages fda and splines (PR#13263). (See also copy below.) I.e. handling NA's with smooth.basis or Data2fd. Would you kindly let me know if it is possible to handle NA's with Data2fd

[Rd] problems with [.terms

2021-08-21 Thread Therneau, Terry M., Ph.D. via R-devel
The survival package uses [.terms a fair bit, in particular it makes use of the index returned in the 'specials' attribute, but the base R code has at least two problems. First, it does not account for offset terms, if present, and also fails for a formula such as  y ~ age + (sex=='male').   Y

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

2017-08-09 Thread Andrzej Oleś
Awesome, thank you Michael! On Mon, Aug 7, 2017 at 7:27 PM, Michael Lawrence wrote: > I ported that over. > > On Tue, Aug 1, 2017 at 5:50 AM, Andrzej Oleś > wrote: > >> Thank you Michael for updating the 3.4 branch, the `callNextMethod()` now >> works for `...` methods as expected. However, I'm

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

2017-08-07 Thread Michael Lawrence
I ported that over. On Tue, Aug 1, 2017 at 5:50 AM, Andrzej Oleś wrote: > Thank you Michael for updating the 3.4 branch, the `callNextMethod()` now > works for `...` methods as expected. However, I'm still missing your other > patch fixing the handling of arguments in `...` methods. It would be

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

2017-08-01 Thread Andrzej Oleś
Thank you Michael for updating the 3.4 branch, the `callNextMethod()` now works for `...` methods as expected. However, I'm still missing your other patch fixing the handling of arguments in `...` methods. It would be really great if this bugfix could be integrated into the 3.4 branch as well, such

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

2017-07-28 Thread Michael Lawrence
I pushed the patch to the 3.4 branch. Feel free to test. Michael On Wed, Jul 26, 2017 at 4:02 AM, Andrzej Oleś wrote: > Hi Michael, > > it seems that your patch to S4 generics dispatching on `...` is still > available only in R-devel, and was not included in the minor R-3.4.1 > release. I was wo

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

2017-07-26 Thread Andrzej Oleś
Hi Michael, it seems that your patch to S4 generics dispatching on `...` is still available only in R-devel, and was not included in the minor R-3.4.1 release. I was wondering what is the policy of incorporating bug fixes from the devel branch into release, and whether there is any chance that the

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

2017-04-25 Thread Andrzej Oleś
You're right, I must have mixed up my R versions when running the example, as the problem seems to be resolved in R-devel. Sorry for the noise and thanks again for fixing this. Andrzej On Tue, Apr 25, 2017 at 3:55 PM, Michael Lawrence wrote: > I attempted to fix it, and that example seems to w

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

2017-04-25 Thread Michael Lawrence
I attempted to fix it, and that example seems to work for me. It's also a (passing) regression test in R. Are you sure you're using a new enough R-devel? On Tue, Apr 25, 2017 at 2:34 AM, Andrzej Oleś wrote: > Hi Michael, > > thanks again for your patch! I've tested it and I'm happy to confirm th

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

2017-04-25 Thread Andrzej Oleś
Hi Michael, thanks again for your patch! I've tested it and I'm happy to confirm that `callNextMethod()` works with methods dispatching on `...`. However, the second issue I reported still seems to be unresolved. Consider the following toy example, where the `f()` calls differ in result depending

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

2017-04-21 Thread Andrzej Oleś
Great, thanks Michael for you quick response! I started off with a question on SO because I was not sure whether this was an actual bug or I was just missing something obvious. I'm looking forward to the patch. Cheers, Andrzej On Thu, Apr 20, 2017 at 10:28 PM, Michael Lawrence < lawrence.mich..

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

2017-04-20 Thread Michael Lawrence
Thanks for pointing out these issues. I have a fix that I will commit soon. Btw, I would never have seen the post on Stack Overflow. It's best to report bugs on the bugzilla. Michael On Thu, Apr 20, 2017 at 8:30 AM, Andrzej Oleś wrote: > Hi all, > > I recently encountered some unexpected behavi

[Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

2017-04-20 Thread Andrzej Oleś
Hi all, I recently encountered some unexpected behavior with S4 generics dispatching on `...`, which I described in http://stackoverflow.com/questions/43499203/use-callnextmethod-with-dotsmethods TL;DR: `callNextMethod()` doesn't work in methods dispatching on `...`, and arguments of such methods

[Rd] problems with RdMacros in file DESCRIPTION

2017-03-09 Thread Georgi Boshnakov
Hi, Field RdMacros was introduced in file DESCRIPTION to allow users to import LaTeX-like macros from other packages. Currently 'R CMD Check --as-cran' gives a NOTE: > Unknown, possibly mis-spelled, field in DESCRIPTION: > ‘RdMacros’ A small package demonstrating this is available at http:

[Rd] Problems with sub() due to inability to set encoding of ASCII strings

2016-09-29 Thread Winston Chang
I'm encountering a problem using sub() on strings in R 3.3.1 in Windows, using both RGui and RStudio. The problem happens when the starting string is ASCII, but the replacement string is UTF-8. If we create an ASCII string x1, its encoding is marked as "unknown", and doing a sub() on that string

[Rd] Problems with embedded R, ReplDLL

2015-08-21 Thread Radford Neal
Along with getting pqR to work on Windows, I've also been testing it in the context of embedded R, and in the process have found some problems with the examples given of embedded R use. One problem can be seen in R_ReplDLLinit, in src/main/main.c: void R_ReplDLLinit(void) { SETJMP(R_Toplevel

Re: [Rd] Problems with building a private R-package with Fortran source under Windows

2014-07-22 Thread John Nolan
AM Subject:[Rd] Problems with building a private R-package with Fortran source under Windows Sent by:r-devel-boun...@r-project.org Hi, I recently managed to port the slicot library (http://slicot.org/) to R. I created a new package, put the fortran libs into the src directory

[Rd] Problems with building a private R-package with Fortran source under Windows

2014-07-22 Thread Alexander Braumann
Hi, I recently managed to port the slicot library (http://slicot.org/) to R. I created a new package, put the fortran libs into the src directory together with a Makevars file that include the line: PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) R CMD check did run through on my ubuntu 14.04

Re: [Rd] Problems with MinGW and boost on Windows

2012-11-27 Thread Florian Burkart
Sorry, didn't realize text attachments get stripped as well... here is a link: http://pastebin.com/T3XhsjDY, and for the archives the actual text #define WIN32_LEAN_AND_MEAN #define NOMINMAX 1 #define _WIN32_WINNT 0x0601 #define NTDDI_VERSION 0x0601 #define _MSC_VER_WINNT _MSC_VER_WINNT_WIN7

[Rd] Problems with MinGW and boost on Windows

2012-11-27 Thread Florian Burkart
Hi, I am not sure how widespread this problem is, but definitely occurs for me on 64 bit Win 7 with a 64 bit R. I think I have isolated the issue (to a certain extent) in the attached Test.cpp file. Basically, I think linking with boost serialization is causing the plugin to fail. If I compile T

Re: [Rd] Problems with install.packages when Ncpus > 1

2012-10-06 Thread Uwe Ligges
On 06.10.2012 18:02, Winston Chang wrote: In the code for install.packages, I see that if Ncpus>1, it passes the Ncpus to make, as in 'make -k -j 32'. Is it possible that these packages are failing because of this option to make? It is perfectly correct option: please do your homework before

Re: [Rd] Problems with install.packages when Ncpus > 1

2012-10-06 Thread Winston Chang
>> In the code for install.packages, I see that if Ncpus>1, it passes the >> Ncpus to make, as in 'make -k -j 32'. Is it possible that these >> packages are failing because of this option to make? > > > It is perfectly correct option: please do your homework before posting as the > posting guide a

Re: [Rd] Problems with install.packages when Ncpus > 1

2012-10-05 Thread Prof Brian Ripley
On 06/10/2012 05:42, Winston Chang wrote: I have a Ubuntu Linux 12.04.1 machine running R 2.15.1. I'm trying to run tests building packages, so install.packages() is trying to install about about 1000 packages from source. I'm running into some strange issues that seem related to using values for

[Rd] Problems with install.packages when Ncpus > 1

2012-10-05 Thread Winston Chang
I have a Ubuntu Linux 12.04.1 machine running R 2.15.1. I'm trying to run tests building packages, so install.packages() is trying to install about about 1000 packages from source. I'm running into some strange issues that seem related to using values for Ncpus other than 1. When I use Ncpus=32, a

Re: [Rd] Problems with 64bit dll compile in R-2.15.0

2012-05-11 Thread Duncan Murdoch
On 12-05-10 2:07 PM, Marian K Talbert wrote: I built my package under the R version 2.14.1 on windows without any problems by first checking for issues using R CMD check (no warnings) and then R CMD build to build the tar.gz. I can install this on version 2.14.1 using install.packages(...). I n

[Rd] Problems with 64bit dll compile in R-2.15.0

2012-05-11 Thread Marian K Talbert
I built my package under the R version 2.14.1 on windows without any problems by first checking for issues using R CMD check (no warnings) and then R CMD build to build the tar.gz. I can install this on version 2.14.1 using install.packages(...). I next tested to see if I could also install o

Re: [Rd] problems with iconv

2011-12-15 Thread RogerP
> I put the header in the /include. Was that right? >Probably not. I would expect something like /usr/local/include, and maybe a -I option to make sure it was >found before the Solaris-supplied one. Does make install (for iconv) not do that for you? Wow! Thanks! That was it! I checked out /us

Re: [Rd] problems with iconv

2011-12-14 Thread peter dalgaard
On Dec 14, 2011, at 19:43 , RogerP wrote: >> I used the --disable-nls and --with-included-gettext options. I also > downloaded the more >up-to-date cairo package. > >> BTW, is there a program I can run to test my iconv binary? I think that > would rule out any >problem with the compilation

Re: [Rd] problems with iconv

2011-12-14 Thread RogerP
>I used the --disable-nls and --with-included-gettext options. I also downloaded the more >up-to-date cairo package. >BTW, is there a program I can run to test my iconv binary? I think that would rule out any >problem with the compilation. >Thanks for you suggestions and for any future hel

Re: [Rd] problems with iconv

2011-12-14 Thread Joshua Ulrich
On Wed, Dec 14, 2011 at 8:15 AM, RogerP wrote: > For some reason when I click on reply and sign-in  - the message I'm replying > to is not carried forward.  As you requested that include your message I > copied and pasted it from my email. > I guess it's some Nabble nonsense then... >> A suitably

Re: [Rd] problems with iconv

2011-12-14 Thread RogerP
For some reason when I click on reply and sign-in - the message I'm replying to is not carried forward. As you requested that include your message I copied and pasted it from my email. > A suitably comprehensive iconv function is essential. The R usage requires > iconv to be able to translate

Re: [Rd] problems with iconv

2011-12-13 Thread Joshua Ulrich
As Uwe asked, please cite the original messages. On Tue, Dec 13, 2011 at 4:10 PM, RogerP wrote: > Sorry, but IMHO saying "read the manual" does not constitute actual help. > > But here it is from the manual: > > A suitably comprehensive iconv function is essential. The R usage requires > iconv to

Re: [Rd] problems with iconv

2011-12-13 Thread RogerP
Sorry, but IMHO saying "read the manual" does not constitute actual help. But here it is from the manual: A suitably comprehensive iconv function is essential. The R usage requires iconv to be able to translate between "latin1" and "UTF-8", to recognize "" (as the current encoding) and "ASCII", a

Re: [Rd] problems with iconv

2011-12-13 Thread Kasper Daniel Hansen
Roger, Since Ripley is usually right, if I was you, I would focus on "You need to ensure that GNU libiconv is actually used: you are obviously not finding it, and I suspect your error is in not setting the path to its header file." Based on your description "I've downloaded and compiled iconv v

Re: [Rd] problems with iconv

2011-12-13 Thread Uwe Ligges
Please cite the original messages! On 13.12.2011 21:32, RogerP wrote: As I said in my email: help I appreciate - sarcasm not so much. I re-read the manual - just in case I'd missed something and still do not have any idea. The manual, BTW, needs some serious help for it to be useful to its in

Re: [Rd] problems with iconv

2011-12-13 Thread RogerP
As I said in my email: help I appreciate - sarcasm not so much. I re-read the manual - just in case I'd missed something and still do not have any idea. The manual, BTW, needs some serious help for it to be useful to its intended audiance - people who don't already know how to install R. For exa

Re: [Rd] problems with iconv

2011-12-13 Thread Prof Brian Ripley
On 13/12/2011 17:12, RogerP wrote: I'm at wit's ends here and need some help. Like reading the manual? You need to ensure that GNU libiconv is actually used: you are obviously not finding it, and I suspect your error is in not setting the path to its header file. There are explicit instruc

[Rd] problems with iconv

2011-12-13 Thread RogerP
I'm at wit's ends here and need some help. I've downloaded and compiled iconv versions 1.13 and 1.14 - libiconv.so.2.5.0 and libiconv.so.2.5.1 and copied the iconv all over, replacing the native iconv on my Solaris machine. Still when I try to run the configure I get: checking iconv.h usability

[Rd] Problems with new srcref warnings in R 2.14 (development)

2011-11-19 Thread Vitalie Spinu
Dear R developers, Print method for function now tries to open the source file associated with srcref of the function. It outputs only the warning, if file cannot be open, and forgets to print the function definition. Example: eval(parse(text = "tf <- function(a){ b <- a^4 b }", srcfi

Re: [Rd] Problems with r-help

2011-08-30 Thread Gabor Grothendieck
On Tue, Aug 30, 2011 at 11:42 AM, Gabor Grothendieck wrote: > I am getting messages like this whenever I try to post to r-help.  The > message seems to say that the problem is with on the r-help end (the > recipient domain). > > > Delivery to the following recipient failed permanently: > >    r-h.

[Rd] Problems with r-help

2011-08-30 Thread Gabor Grothendieck
I am getting messages like this whenever I try to post to r-help. The message seems to say that the problem is with on the r-help end (the recipient domain). Delivery to the following recipient failed permanently: r-h...@r-project.org Technical details of permanent failure: Google tried to

Re: [Rd] problems with connections when applied in tryCatch

2011-08-23 Thread Joris Meys
Bug committed with number 14660 Cheers Joris 2011/8/22 Uwe Ligges : > > > On 18.08.2011 17:53, Joris Meys wrote: >> >> Recently on stackoverflow following problem came up : >> >> >> http://stackoverflow.com/questions/7103429/all-the-connections-are-in-use-execution-halted/7108799#7108799 >> >> A r

Re: [Rd] problems with connections when applied in tryCatch

2011-08-22 Thread Uwe Ligges
On 18.08.2011 17:53, Joris Meys wrote: Recently on stackoverflow following problem came up : http://stackoverflow.com/questions/7103429/all-the-connections-are-in-use-execution-halted/7108799#7108799 A reproducible example: When trying replicate(200,tryCatch(read.table("this.is.no.file"),

[Rd] problems with connections when applied in tryCatch

2011-08-18 Thread Joris Meys
Recently on stackoverflow following problem came up : http://stackoverflow.com/questions/7103429/all-the-connections-are-in-use-execution-halted/7108799#7108799 A reproducible example: When trying replicate(200,tryCatch(read.table("this.is.no.file"), warning=function(w){print(showConne

Re: [Rd] Problems with plot and Quartz device (PR#13744)

2009-06-03 Thread Simon Urbanek
Thanks, Thomas. It is indeed a very interesting phenomenon. Apparently the discrete structure in the data interacts with the way the data are plotted on a very small scale. I have committed a work-around - it forces rectangles to retain at least their original width/height when snapping t

Re: [Rd] Problems with plot and Quartz device / What is alpha?

2009-06-03 Thread Thomas Richardson
PS Please forgive my ignorance, but when you say: BTW: you may want to use something like pch=19, cex=0.1 (and maybe add some alpha to get a quick density estimation). I don't know what alpha refers to here. Thanks again. Best wishes, Thomas Cheers, S So I guess it might be related t

Re: [Rd] Problems with plot and Quartz device (PR#13744)

2009-06-03 Thread Thomas Richardson
Dear Simon, Thank you very much for the very rapid response! rna is not defined in R, can you, please, supply a reproducible example? Apologies for including code that could not be run directly. (I had assumed simulating "similar" data would give the same behaviour, but having done more expe

Re: [Rd] Problems with plot and Quartz device / What is alpha?

2009-06-03 Thread Simon Urbanek
On Jun 3, 2009, at 15:00 , Thomas Richardson wrote: PS Please forgive my ignorance, but when you say: BTW: you may want to use something like pch=19, cex=0.1 (and maybe add some alpha to get a quick density estimation). I don't know what alpha refers to here. alpha = alpha component of

Re: [Rd] Problems with plot and Quartz device

2009-06-03 Thread Simon Urbanek
On Jun 3, 2009, at 4:45 , t...@stat.washington.edu wrote: Full_Name: Thomas Richardson Version: R 2.9.0 GUI 1.28 Tiger build 32-bit (5395) OS: 10.4.11 Submission from: (NULL) (216.254.15.72) I have encountered a problem with points in scatterplots disappearing in a quartz window when it i

Re: [Rd] Problems with plot and Quartz device (PR#13744)

2009-06-03 Thread Simon Urbanek
Thomas, rna is not defined in R, can you, please, supply a reproducible example? From your description I think I know roughly what's going on (Quartz attempts to snap rectangles on pixel boundaries to prevent malignant anti-aliasing effects in image plots and this may somehow interact wit

[Rd] Problems with plot and Quartz device (PR#13744)

2009-06-03 Thread tsr
Full_Name: Thomas Richardson Version: R 2.9.0 GUI 1.28 Tiger build 32-bit (5395) OS: 10.4.11 Submission from: (NULL) (216.254.15.72) I have encountered a problem with points in scatterplots disappearing in a quartz window when it is re-sized (to make it larger). I am constructing an 8x12 matrix

Re: [Rd] problems with nls?

2009-03-05 Thread Prof Brian Ripley
I don't see why this is relevant to R-devel rather than R-help. Your script must be very old: the NEWS for R 1.9.0 said Packages ctest, eda, modreg, mva, nls, stepfun and ts have been merged into stats, and lqs has been returned to MASS. That's 5 years ago now. Function nls() s

[Rd] problems with nls?

2009-03-04 Thread per243
I need to make nonlinear regression with the posterior script, but how is the problem? I have error in library (nls), package 'nls' has been merged into 'stats'. I need help? What other forms I have to make nonlinear regression? and how I find to calculate statistics y residuals, scatterplot. tha

Re: [Rd] Problems with packages fda and splines (PR#13263)

2008-11-07 Thread Spencer Graves
Hello, David: Thanks for the comments about NA problems in 'fda'. I'll look into this and get back with you. Spencer [EMAIL PROTECTED] wrote: Full_Name: David D Degras Version: 2.8.0 OS: Mac OS X Submission from: (NULL) (128.135.239.11) I have recently installed the version 2

[Rd] Problems with packages fda and splines (PR#13263)

2008-11-07 Thread degras
Full_Name: David D Degras Version: 2.8.0 OS: Mac OS X Submission from: (NULL) (128.135.239.11) I have recently installed the version 2.8.0 of R along with package fda (v 2.0.2) and its dependencies (including package splines v. 2.8.0). Here are my problems: 1) The package splines should featur

[Rd] Problems with Sweave and pdf.options(encoding="ISOLatin7") (PR#13234)

2008-10-31 Thread zemlys
Hi, Sweave for some reason does not respect encoding setting in pdf.options. Everything is OK with ps.options. Thus when using non-default encoding for graphs, resulting graphics eps file is correct, but pdf file is not. Workaround is very simple, just use latex->dvips->ps2pdf chain to get the in

Re: [Rd] problems with plotting of graphNEL (PR#11993)

2008-08-07 Thread Martin Morgan
Hi Christian -- [EMAIL PROTECTED] writes: > Full_Name: Christian Kuehnert > Version: 2.7.1 > OS: Windows XP > Submission from: (NULL) (91.14.237.109) > > > Hello, > > I've installed the package RBGL (and XML and Rgraphviz) and tried to follow > the > examples in the RBGL-manual > > http://bioc

[Rd] problems with plotting of graphNEL (PR#11993)

2008-08-07 Thread christiankuehnert
Full_Name: Christian Kuehnert Version: 2.7.1 OS: Windows XP Submission from: (NULL) (91.14.237.109) Hello, I've installed the package RBGL (and XML and Rgraphviz) and tried to follow the examples in the RBGL-manual http://bioconductor.org/packages/2.2/bioc/vignettes/RBGL/inst/doc/RBGL.pdf Bu

Re: [Rd] Problems with snowfall

2008-07-17 Thread Arthur Allignol
Hello, Problem is fixed in version 1.52, which is on CRAN for some days now. That missing object was saved in an rda file which somehow got lost on the first release version. Sorry for this. Best, Arthur Allignol [EMAIL PROTECTED] wrote: Guys, Is anyone using snowfall? It seems that the last

[Rd] Problems with snowfall

2008-07-16 Thread giuseppe1 . milicia
Guys, Is anyone using snowfall? It seems that the last version is broken. sfinit contains test code: data("config", package = "snowfall") configM <- as.matrix(t(config)) config <- as.list(configM) names(config) <- dimnames(configM)[[2]] .sfOption$SERVER <<- as.character(confi

Re: [Rd] Problems with R 2.5.0 (PR#9708)

2007-05-24 Thread John Fox
cmaster.ca/jfox > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] > Sent: Thursday, May 24, 2007 1:41 PM > To: [EMAIL PROTECTED] > Cc: [EMAIL PROTECTED] > Subject: [Rd] Problems with R 2.5.0 (PR#9708) > > Full_N

[Rd] Problems with R 2.5.0 (PR#9708)

2007-05-24 Thread fjcaba
Full_Name: FJ Caballero-Granado Version: 2.5.0 OS: Windows Submission from: (NULL) (84.125.163.119) Hi, I usually used R version 2.0.0 and ScViews. I have recently installed version 2.5.0, and I updated ScViews. But the latter does not works well. This is the screen: R version 2.5.0 Patched (20

Re: [Rd] Problems with package containing S4 classes

2007-03-16 Thread cstrato
I must have missed this, thank you. Good night Christian Benilton Carvalho wrote: > Biobase itself does. > b > > On Mar 16, 2007, at 7:43 PM, cstrato wrote: > >> Thank you, I have already read the R-exts manual, but the collate >> field is optional. >> Do you know a package which uses the Collat

Re: [Rd] Problems with package containing S4 classes

2007-03-16 Thread Benilton Carvalho
Biobase itself does. b On Mar 16, 2007, at 7:43 PM, cstrato wrote: > Thank you, I have already read the R-exts manual, but the collate > field is optional. > Do you know a package which uses the Collate field so that I can > study it? > > Best regards > Christian > > Benilton Carvalho wrote:

Re: [Rd] Problems with package containing S4 classes

2007-03-16 Thread cstrato
Thank you, I have already read the R-exts manual, but the collate field is optional. Do you know a package which uses the Collate field so that I can study it? Best regards Christian Benilton Carvalho wrote: > The Collate field gives the order that the files are going to be > concatenated. If t

Re: [Rd] Problems with package containing S4 classes

2007-03-16 Thread Benilton Carvalho
The Collate field gives the order that the files are going to be concatenated. If they're concatenated using the "wrong" order, your installation might fail (for example, the generic is defined after the method). A recommended source is the "Writing R Extensions" http://cran.r-project.org/

Re: [Rd] Problems with package containing S4 classes

2007-03-16 Thread cstrato
I agree, but I hope that "AllGeneric.R" is not the only possibility. BTW, what is a collate field? Best regards Christian Benilton Carvalho wrote: > Well, my understanding is that if you "need" to define it (the > generic) twice you're doing something wrong. > > Do you have a collate field in yo

Re: [Rd] Problems with package containing S4 classes

2007-03-16 Thread Benilton Carvalho
Well, my understanding is that if you "need" to define it (the generic) twice you're doing something wrong. Do you have a collate field in your description file? IMHO, the "AllGeneric.R"/"AllClasses.R" approach is the way to go... keeping your code organized is always a good thing, right? b

Re: [Rd] Problems with package containing S4 classes

2007-03-16 Thread cstrato
Dear Benilton Yes, but the error disappears only when I define it twice. For my package I create three files: 1. MyClasses.R: Here I define the classes only using setClass("baseClass") setClass("derivedClass") 2. methods.baseClass.R Here I define the methods for baseClass setGeneric("export", f

Re: [Rd] Problems with package containing S4 classes

2007-03-16 Thread Benilton Carvalho
do you have a generic for 'export'? On Mar 16, 2007, at 5:38 PM, cstrato wrote: > Dear Benilton > > Thank you, now my package works. > > Do you have an explanation for my second problem: > > * Installing *source* package 'mytest' ... > ** R > ** save image > Error in setMethod("export", "derivedC

Re: [Rd] Problems with package containing S4 classes

2007-03-16 Thread cstrato
Dear Benilton Thank you, now my package works. Do you have an explanation for my second problem: * Installing *source* package 'mytest' ... ** R ** save image Error in setMethod("export", "derivedClass", export.derivedClass) : no existing definition for function "export" Error: unable to

Re: [Rd] Problems with package containing S4 classes

2007-03-16 Thread Benilton Carvalho
your namespace probably contains: useDynLib(testS4) but you don't have any compiled code... remove that line and everything will be fine. btw, if you're playing with S4, you must import 'methods' b On Mar 16, 2007, at 4:55 PM, cstrato wrote: > Dear all, > > Currently, I am trying to create a

[Rd] Problems with package containing S4 classes

2007-03-16 Thread cstrato
Dear all, Currently, I am trying to create a test package "testS4" using S4 classes, which I am attaching. Running R CMD check gives the following error: coeurebooks-computer:/Volumes/CoreData/CRAN cs$ R CMD check testS4_0.1.1.tar.gz * checking for working latex ...sh: line 1: latex: command

[Rd] Problems with metapost colors

2007-02-13 Thread Geoff Russell
Hi all, The developing metapost driver will handle the plots in demo(graphics) putting the lines in the right places, and so on. But the colors are ... to put it politely ... suboptimal :) I can mail an Rplots.mp file to anybody who might be interested in suggesting how I can handle colors. Its

Re: [Rd] Problems with definitions of S4-generics

2007-02-01 Thread Seth Falcon
Jörg Beyer <[EMAIL PROTECTED]> writes: > Hello all, > > I'd like to report a problem related to S4 classes. > > Platform: > Mac G4/400 PCI (PPC-architecture) > Mac OS 10.4.8 > R 2.4.1 for Mac OS X (CRAN binary, 2006-12-19) w/ R.app 1.18 I see the same thing using a fairly recent R-devel: > se

Re: [Rd] Problems with definitions of S4-generics

2007-02-01 Thread Jörg Beyer
Simon, thanks for the clarification, and sorry that I mixed the 'bug' thing up a bit. Yes, you are correct, in fact it was Byron Ellis earlier in the same thread who suggested "to file a bug report". (Maybe I misinterpreted the fact that you didn't contradict. Big mistake.) Jörg Am 31.01.2007 1

Re: [Rd] Problems with definitions of S4-generics

2007-01-31 Thread Simon Urbanek
On Jan 31, 2007, at 10:02 AM, Jörg Beyer wrote: > Hello all, > > I'd like to report a problem related to S4 classes. > > Platform: > Mac G4/400 PCI (PPC-architecture) > Mac OS 10.4.8 > R 2.4.1 for Mac OS X (CRAN binary, 2006-12-19) w/ R.app 1.18 > > Last December, Simon Urbanek confirmed that the

[Rd] Problems with definitions of S4-generics

2007-01-31 Thread Jörg Beyer
Hello all, I'd like to report a problem related to S4 classes. Platform: Mac G4/400 PCI (PPC-architecture) Mac OS 10.4.8 R 2.4.1 for Mac OS X (CRAN binary, 2006-12-19) w/ R.app 1.18 Last December, Simon Urbanek confirmed that the issue is not platform related, and that it is most likely a bug.

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 =

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

2007-01-16 Thread Ross Boylan
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, envir = data_env) : data set 'gold' not found (go

[Rd] Problems with arima function (PR#8743)

2006-04-02 Thread stoffer
I have written before, but to no avail. I have found two minor problems with fitting time series models with R. The thing is, they may be solved with MINOR adjustments to the code. I have posted these problems with detailed examples here: http://www.stat.pitt.edu/stoffer/tsa2/Rissues.htm Brie

[Rd] Problems with R CMD Rdconv and R CMD Sd2Rd (PR#8661)

2006-03-05 Thread timh
I'm using R 2.2.0 on Windows. Doing some conversions of help files. Internal comments indicate that the Sd2Rd conversion is "Converted by Sd2Rd version 1.21." I'm converting .d -> .Rd .sgml -> .Rd using Sd2Rd, then checking by using Rdconv to convert .Rd back to .d or .sgm

Re: [Rd] Problems with calloc function.

2006-01-05 Thread Paul Roebuck
On Tue, 3 Jan 2006, Marcelo Damasceno wrote: > Sorry about my incautiousness, I use the tips, but is > happen same problems. Not really. You definitely skipped over the most important one - don't terminate the host process. > if(temp4 == NULL){ > printf("\n\n No Memory4!"); >

Re: [Rd] Problems with calloc function.

2006-01-05 Thread Hin-Tak Leung
Hi Marcelo, You need to read the R extension manual more carefully... Basically you haven't deference thed pointers. You think you were allocating say, col=2, but instead you were allocating &col in int's, the address of col, which is a large number since user-land memory address starts at a large

Re: [Rd] Problems with calloc function.

2006-01-03 Thread Marcelo Damasceno
Hello all and Prof. Brian Ripley , Sorry about my incautiousness, I use the tips, but is happen same problems. Below the R code. rspcplot <- function(file1="dg_01.lab.txt"){ if(is.null(n)) stop("You need first run the function

Re: [Rd] Problems with calloc function.

2005-12-29 Thread Prof Brian Ripley
Rather than trying to reinvent the wheel, why not make use of the functions documented in Writing R Extensions, especially Calloc/Free? And definitely do not call exit() from code linked into R: it is antisocial behaviour to terminate your host's process. Your example is incomplete, and for s

[Rd] Problems with calloc function.

2005-12-29 Thread Marcelo Damasceno
Hi all, I have a C code in Linux, it has 7 pointers and compile e run OK, but when I run in R happens problems with calloc function, it returns NULL. ### > int *temp1,*temp2,*temp3,*temp4; temp1 = (int *)calloc(col,sizeof(int)); if(temp1 == NULL){

Re: [Rd] Problems with Windows Cross compile

2005-12-20 Thread Warnes, Gregory R
Thanks, the default version of R here is 2.1.0, so that must have been the problem. Everything is working now. -Greg > -Original Message- > From: Jun Yan [mailto:[EMAIL PROTECTED] > Sent: Tuesday, December 20, 2005 1:07 PM > To: Warnes, Gregory R > Cc: R-devel (E-mail); Anthony Rossini

Re: [Rd] Problems with Windows Cross compile

2005-12-20 Thread Jun Yan
I've seen that error before. It has to do with the setup of R_EXE. A current linux R is required. The following order worked for me: make linuxR make LinuxFresh=YES mkrules make R Jun On Tue, 20 Dec 2005, Warnes, Gregory R wrote: > > Well, I'm finally getting around to setting up a cross-comp

[Rd] Problems with Windows Cross compile

2005-12-20 Thread Warnes, Gregory R
Well, I'm finally getting around to setting up a cross-compiler for Windows on my local Linux box. I'm using the Yan & Rossini's docuimentation and the latest 'http://cran.r-project.org/doc/contrib/Makefile-rcb' , which is working of the R-2.2.0 sources. After discovering that "cp -p" doesn'

[Rd] Problems with sending data to FORTRAN subrutine

2005-12-12 Thread Ales Ziberna
Dear ExpeRts! I have problem with sending data to FORTRAN subroutine on Windows XP and R 2.1.1. When I call it using .Fortran, I get the following error: R for Windows GUI front-end has encountered a problem and needs to close. We are sorry for the inconvenience. Error signature AppName: rgui.

[Rd] problems with initialize-method, difference between Win XP & Linux

2005-12-06 Thread Matthias Kohl
Dear R devels, I have some questions concerning the use of "initialize". Situation: There are two packages "S4pkg1" and "S4pkg2" which include S4 classes and methods where the first one contains a new S4 class "S4pkg1Class". Then, in "S4pkg2" there is a new S4 class "S4pkg2Class" which has a slo

Re: [Rd] Problems with example(Grid) in grid package

2005-10-24 Thread Gabor Grothendieck
On 10/24/05, Paul Murrell <[EMAIL PROTECTED]> wrote: > Hi > > > Gabor Grothendieck wrote: > > The following: > > > > library(grid) > > grid.newpage() > > example(Grid) > > > > has the yaxis label partly cut off and the x axis label does not appear at > > all. > > Also ?grid.multipanel in that exam

Re: [Rd] Problems with example(Grid) in grid package

2005-10-24 Thread Prof Brian Ripley
On Tue, 25 Oct 2005, Paul Murrell wrote: > hadley wickham wrote: > > I've also noticed the behaviour of grid.rect() has changed in 2.2.0. > > Before the fill defaulted to transparent, but now it defaults to > > white. > > > The initial value of the 'gp' settings for the ROOT grid viewport has > ch

Re: [Rd] Problems with example(Grid) in grid package

2005-10-24 Thread Paul Murrell
Hi Gabor Grothendieck wrote: > The following: > > library(grid) > grid.newpage() > example(Grid) > > has the yaxis label partly cut off and the x axis label does not appear at > all. > Also ?grid.multipanel in that example brings up documentation for > grid-internal but this would not seem to

Re: [Rd] Problems with example(Grid) in grid package

2005-10-24 Thread Paul Murrell
Hi hadley wickham wrote: > I've also noticed the behaviour of grid.rect() has changed in 2.2.0. > Before the fill defaulted to transparent, but now it defaults to > white. The initial value of the 'gp' settings for the ROOT grid viewport has changed in 2.2.0 (see grid/doc/changes.txt). Bef

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