Re: [Rd] error in install.packages() (PR#14042)

2009-11-04 Thread Prof Brian Ripley
I agree it is a good idea, but a new name seems justified to avoid confusion. On Wed, 4 Nov 2009, Duncan Murdoch wrote: On 11/4/2009 12:15 PM, William Dunlap wrote: -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Duncan Murdo

[Rd] Help with testing (was Re: Request: bring back windows chm help support)

2009-11-03 Thread Prof Brian Ripley
help when you asked for HTML help. Yet no one reported it until after release. On Tue, 3 Nov 2009, Duncan Murdoch wrote: On 11/3/2009 9:49 AM, Michael Dewey wrote: At 10:02 03/11/2009, Prof Brian Ripley wrote: Comment in line below Duncan gave the definitive answer in an earlier reply: the

Re: [Rd] Request: bring back windows chm help support (PR#14034)

2009-11-03 Thread Prof Brian Ripley
Duncan gave the definitive answer in an earlier reply: the active R developers are no longer willing to support CHM help. It is not open for discussion, period. But three comments to ponder (but not discuss). (a) CHM is unusable for many of us. A year or two ago Microsoft disabled it on non

Re: [Rd] unable to compile RODBC (R 2.9.2, AIX)

2009-10-31 Thread Prof Brian Ripley
On Sat, 31 Oct 2009, Chuck White wrote: Hello -- I am trying to compile (linker error, not compiler error) RODBC for R 2.9.2 on AIX 5.3 using gcc. I get the following error: gcc -maix64 -pthread -std=gnu99 -shared -Wl,-brtl -Wl,-G -Wl,-bexpall -Wl,-bnoentry -lc -L/usr/lib -L/usr/X 11R6/lib -L

Re: [Rd] quoted strings in foo.Rd rendered as â

2009-10-31 Thread Prof Brian Ripley
On Sat, 31 Oct 2009, Roger Koenker wrote: On Oct 30, 2009, at 4:11 PM, Prof Brian Ripley wrote: First step to check: update to a released version of R 2.10.0! I see the same behavior with: R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8

Re: [Rd] evince pdf viewing

2009-10-30 Thread Prof Brian Ripley
Yes, it is known: it is described with workarounds (thanks to Marc Schwarz, AFAIR) on the ?pdf help page. On Fri, 30 Oct 2009, Roger Koenker wrote: It was pointed out to me that scatter plots made on our rhel5 system (sessionInfo() below, have the curious feature that when made with pdf() and

Re: [Rd] quoted strings in foo.Rd rendered as â

2009-10-30 Thread Prof Brian Ripley
First step to check: update to a released version of R 2.10.0! If that does not help, using options(useFancyQuotes = TRUE) in the released version should (but possibly not as far back as your alpha pre-release). I suspect that whatever you mean my 'my X11 window' (it is the application runni

Re: [Rd] reg-tests-1.R failure with unstable

2009-10-25 Thread Prof Brian Ripley
consideration. On Sun, 25 Oct 2009, Prof Brian Ripley wrote: On Sun, 25 Oct 2009, Hiroyuki Kawakatsu wrote: On Fri, Oct 23, 2009, Hiroyuki Kawakatsu wrote: Hi, I am getting an error from one of the test files tests/reg-tests-1.R using the unstable version (r50179). (i've learned my le

Re: [Rd] Buglet in optim() SANN

2009-10-25 Thread Prof Brian Ripley
As the posting guide says, please read the help carefully before posting. It does say: ‘maxit’ The maximum number of iterations. Defaults to ‘100’ for the derivative-based methods, and ‘500’ for ‘"Nelder-Mead"’. For ‘"SANN"’ ‘maxit’ gives the total number of function

Re: [Rd] reg-tests-1.R failure with unstable

2009-10-25 Thread Prof Brian Ripley
On Sun, 25 Oct 2009, Hiroyuki Kawakatsu wrote: On Fri, Oct 23, 2009, Hiroyuki Kawakatsu wrote: Hi, I am getting an error from one of the test files tests/reg-tests-1.R using the unstable version (r50179). (i've learned my lessons; this is a clean build.) The tail of reg-tests-1.Rout.fail is L

Re: [Rd] Changing options in R CMD SHLIB

2009-10-19 Thread Prof Brian Ripley
Please see the manual -- 'Writing R Extensions'. If you want to use custom compiler flags, you use a Makevars or personal .Makevars file. Something like PKG_FCFLAGS=-fopenmp (you haven't told us your OS or version of R). On Mon, 19 Oct 2009, Fabio Mathias Corrêa wrote: Dear, When trying to

Re: [Rd] Use of lm on polynomial models (PR#14014)

2009-10-19 Thread Prof Brian Ripley
Others beware: this address does not accept replies, in defiance of the posting guide. On Mon, 19 Oct 2009, Prof Brian Ripley wrote: RTFM time: h^3 is not the cube of h in an R formula (for that you need I(h^3)). See ?formula, for example. Simpler would be lm(w ~ poly(h, 3, raw=TRUE)) On

Re: [Rd] Use of lm on polynomial models (PR#14014)

2009-10-19 Thread Prof Brian Ripley
RTFM time: h^3 is not the cube of h in an R formula (for that you need I(h^3)). See ?formula, for example. Simpler would be lm(w ~ poly(h, 3, raw=TRUE)) On Sun, 18 Oct 2009, michael_ka...@earthlink.net wrote: Full_Name: Michael Aaron Karsh Version: 2.8.0. OS: Windows XP Submission from: (NU

Re: [Rd] Rscript not returning zero

2009-10-17 Thread Prof Brian Ripley
On Sat, 17 Oct 2009, Rodrigo Flores wrote: Hi I'm trying to run a R script in a computer grid using the Rscript interpreter, but the Rscript is not returning zero (even when the scripts processes succesfully) on its exit which causes the scheduler to detect an error and not records the output.

Re: [Rd] (PR#14012)

2009-10-17 Thread Prof Brian Ripley
On Sat, 17 Oct 2009, Seth Falcon wrote: * On 2009-10-16 at 15:00 +0200 sj...@damtp.cam.ac.uk wrote: I think Rscript has a problem running files that have mac encodings for newline (^M rather than ^J on linux). I think those are Mac conventions for end-of-line, not for newline. Even in MacRom

Re: [Rd] linking to package directories is NOT broken in R >= 2.10 beta

2009-10-17 Thread Prof Brian Ripley
When you linked to ../examples/ R was not involved, and what you are seeing is what your browser did with a file:// url. Most browsers will support a wide range of file types, and list directories: but that is not something that was ever (AFAICS) documented to work. The 'issue' is your expect

Re: [Rd] beta build problem

2009-10-13 Thread Prof Brian Ripley
Whatever '/home/paul/Mybin/gtar' is, it is not a tar unpacker so you will need to specify the TAR environment variable when you configure R. 'gtar' is very commonly GNU tar (it is on Fedora Linux for example and on most third-party toolsets for e.g. Solaris and AIX). It is an unwise choice o

Re: [Rd] Possible bug in the Rd parser?

2009-10-11 Thread Prof Brian Ripley
On Sun, 11 Oct 2009, Mathieu Ribatet wrote: Thanks Duncan for all these answers. Indeed I should have checked that the "cases" environment was provided by Rd.sty. Mea culpa. The good point is that before 2.10.0 alpha "R CMD check" finished without any error but the output was wrong - because of

Re: [Rd] (PR#13957) Reading clipboard with read.delim("clipboard") crash

2009-10-08 Thread Prof Brian Ripley
I am having some trouble reproducing this (an example of 3000 rows and 7 columns worked for me, and one of 18000 rows stresses the window manager so it works slowly if at all). But AFAICS you are trying to give your window manager too much data, and the XGetWindowProperty call to determine the

Re: [Rd] Bug (PR#13987)

2009-10-07 Thread Prof Brian Ripley
Please do read the FAQ and R posting guide. (i) You were asked not to report on obselete versions of R (2.9.2 and 2.10.0 alpha are current). (ii) There is no reproducible code here, but the error is almost certainly not in R but in a contributed package or in 'BRB Array tools' (whatever that

Re: [Rd] Help file doesn't display correctly

2009-10-06 Thread Prof Brian Ripley
On Tue, 6 Oct 2009, Ronggui Huang wrote: 2009/10/6 Prof Brian Ripley : On Tue, 6 Oct 2009, Ronggui Huang wrote: Dear R Developer, It seems to be a problem with help file. Not sure if it is related to the new format of Rd parser. Multiple lines are joined together without proper line break

Re: [Rd] Help file doesn't display correctly

2009-10-06 Thread Prof Brian Ripley
On Tue, 6 Oct 2009, Ronggui Huang wrote: Dear R Developer, It seems to be a problem with help file. Not sure if it is related to the new format of Rd parser. Multiple lines are joined together without proper line break. It was a problem with the handling of fancy quotes in a DBCS encoding (a

Re: [Rd] R's --enable-threads does nothing?; gdb needs -lpthread

2009-10-05 Thread Prof Brian Ripley
On Mon, 5 Oct 2009, Andrew Piskorski wrote: In the R-2-9-branch (svn revision 49914, 2009-09-24), R's configure script has an "--enable-threads" option. But, does it do anything useful? When I use "--enable-threads=posix", some of the configure output changes slightly, but it seems to have no

Re: [Rd] R 2.9.2 crashes when sorting latin1-encoded strings

2009-10-05 Thread Prof Brian Ripley
This was a missing PROTECT() in do_order. But I'll echo what Simon Urbanek said: don't do that but rather use the documented ways to re-encode the file as you read it. (Latin-1 used to be needed for collation on Mac OS X as C-level collation in UTF-8 was completely broken -- but we have worke

Re: [Rd] suggest enhancement to segments and arrows to facilitate horizontal and vertical segments

2009-10-05 Thread Prof Brian Ripley
This isn't a one-way street, as it means that some erroneous calls will not be detected, and code written to take advantage of this will only work under R >= 2.10.0. I think we should probably insist that one of x1 and y1 is supplied: if both are omitted arrows() would give a warning, but segm

Re: [Rd] Windows Laptop specification query

2009-09-28 Thread Prof Brian Ripley
use an open source packages and programming languages for you daily work and make money out of it, and the first time you release something you release it crappy and closed source even if it is legal and allowed of course : ( ) On Monday 28 September 2009 09:16:23 Prof Brian Ripley

Re: [Rd] Windows Laptop specification query

2009-09-28 Thread Prof Brian Ripley
On Mon, 28 Sep 2009, Sean O'Riordain wrote: Good morning Keith, Have a look at http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-a-limit-on-the-memory-it-uses_0021 The short answer is that "it depends"... a) memory is limited under windows Yes, but 64-bit builds can be

Re: [Rd] Compatibility of external C code across platforms

2009-09-26 Thread Prof Brian Ripley
On Sat, 26 Sep 2009, Murray Efford wrote: A package I have written makes considerable use of external C code. There appear to be no problems building a Windows binary with the GNU C compiler, but now I would like to make the package available for other platforms. A stringent check of the code

Re: [Rd] Memory-management crash with UTF-8 on Windows (PR#13955)

2009-09-17 Thread Prof Brian Ripley
Without the file, we can do nothing with this, so please put it somewhere accessible. Also, we need exact reproduction instructions: how did you tell R this was a UTF-8 file? If you copy-pasted it, what did you copy it from? The posting guide and FAQ did ask you not to report on obsolete ve

Re: [Rd] 'make install' fails on Solaris (PR#13946)

2009-09-10 Thread Prof Brian Ripley
p;& make install) || exit 1; \ done make: Fatal error: Command failed for target `install' bash-3.00# and the configure that started it all: ./configure --with-readline=no --with-iconv=no --with-x=no --enable-static=yes --enable-R-static-lib --prefix=/home/dev/scratch/bbownes/R On T

Re: [Rd] 'make install' fails on Solaris (PR#13946)

2009-09-09 Thread Prof Brian Ripley
On Thu, 10 Sep 2009, bow...@gmail.com wrote: Full_Name: Bob Bownes Version: 2.9.2 OS: Solaris 10 Submission from: (NULL) (164.55.254.106) The sed lines in src/unix/Makefile confuse the grep distributed with Solaris that gets configured by ./configure. Well, it calls sed not grep! Which vers

Re: [Rd] question about --with-valgrind-instrumentation=level

2009-09-06 Thread Prof Brian Ripley
On Sun, 6 Sep 2009, Charles Geyer wrote: Does --with-valgrind-instrumentation=2 slow down R when valgrind or gctorture are not in use? I am thinking of compiling the R that the whole department uses for research and teachin with --with-valgrind-instrumentation=2. Is that a good idea or a bad i

Re: [Rd] calling Lapack and BLAS routines from C

2009-09-04 Thread Prof Brian Ripley
On Fri, 4 Sep 2009, Marcin Hitczenko wrote: Hi, I am working on a UNIX machine and I am interfacing R and C with the .C function. I am trying to call LAPACK and BLAS routines, but am running into a problem where, while I am able to run the BLAS routines, I cannot run the LAPACK routines. I com

Re: [Rd] Trouble building R 2.9.2 under solaris 10

2009-09-02 Thread Prof Brian Ripley
Please read the posting guide and the R-admin manual. This is a symptom of a misconfigured compiler/system headers, and you have not told us what you are using. It is not an R issue, so please consult your OS support line (and almost certianly you are not using a Sun compiler here): maybe you

Re: [Rd] [R] R and GNU gcc for OpenMP

2009-09-02 Thread Prof Brian Ripley
On Wed, 2 Sep 2009, Duncan Murdoch wrote: Debabrata Midya wrote: Dear R users, Thanks in advance. I am using R 2.9.1 on Windows XP. May I request you to assist me on the following: I have downloaded Rtools29.exe and installed it today 02 Sep 2009 and I have also provided the appropriate

Re: [Rd] R 2.10.0 devel package check error

2009-08-27 Thread Prof Brian Ripley
AFAICS that is already fixed (r49467). It was a Windows-only problem when building just chm help - I suspect the latter did not work in your package. I should perhaps remind people that R-devel is 'unstable' and as we work on the help system it is likely to be particularly unstable on Window

Re: [Rd] Problems opening R (PR#13908)

2009-08-26 Thread Prof Brian Ripley
Please use R-sig-mac to ask questions about Mac OS X. In particular do not use R-bugs to ask questions. There may be a bug here, but there is nothing to reproduce and it may not be in R (it may be in R.app, the GUI). How about uninstalling R (not re-installing)? See the R-MacOS FAQ, e.g.

Re: [Rd] R CMD on windows 7

2009-08-26 Thread Prof Brian Ripley
On Wed, 26 Aug 2009, Uwe Ligges wrote: As far as I know, nobody of the developers who also work under Windows has access to Windows 7 these days. Patches are welcome, of course! But the described behaviour seems identical to Vista, and the workarounds the same as those in the rw-FAQ. I've n

Re: [Rd] package dependencies specification

2009-08-25 Thread Prof Brian Ripley
On Tue, 25 Aug 2009, Martin Morgan wrote: [...] In addition I am not sure of the consequences of using charset ISO8859-1. It is not portable: the manual says only 'latin1', 'latin2' and 'UTF-8' are known to be. Versions of iconv think the name is ISO8859-1 or ISO-8859-1 or ISO_8859-1 or 8

Re: [Rd] header containing (PR#13834)

2009-08-21 Thread Prof Brian Ripley
Thank you, that's a plausible explanation and probably also explains PR#13899. However, it's not listed by POSIX (not even a 'may fail') at http://www.opengroup.org/onlinepubs/009695399/functions/mkdir.html and nor is it described on man -s2 mkdir on my Solaris 10 system, so it is not surprisin

Re: [Rd] sessionInfo() fails to correctly detect locale settings

2009-08-21 Thread Prof Brian Ripley
On Fri, 21 Aug 2009, Peter Dalgaard wrote: Liviu Andronic wrote: Dear R devels Yesterday I was slightly surprised to notice that R incorrectly detected some of the locale settings. I am not sure whether this is important, but I preferred to drop a message. In the R output below, some entries th

Re: [Rd] R compilation problem on 64 bit SunOS (PR#13898)

2009-08-21 Thread Prof Brian Ripley
On Fri, 21 Aug 2009, Peter Dalgaard wrote: Prof Brian Ripley wrote: [snip] In fact you did not specifically not request nls: use the flag from the gcc specs below to do so (as someone did for gcc). Brian, I see --disable-nls in both places, so you may want to expand on that. (I could well be

Re: [Rd] R compilation problem on 64 bit SunOS (PR#13898)

2009-08-20 Thread Prof Brian Ripley
You are reporting a Solaris error to R-bugs. If the Solaris libintl.h is broken (and it seems yours is), then you need to try one that works (e.g. OpenCSW) or force the use of the one in the R sources by --with-included-gettext use the GNU gettext library included here or dlsable NLS (see b

Re: [Rd] trouble building 2.10?

2009-08-18 Thread Prof Brian Ripley
You currently need builddir != srcdir, which is in any case is strongly recommended for those building from svn checkouts. We will either require that (many projects now do) or test building in the srcdir before the testing period starts. Similar comments hold about needing GNU make -- it is

Re: [Rd] R CMD check --use-valgrind doesn't run valgrind on tests

2009-08-17 Thread Prof Brian Ripley
This was not implemented in R 2.9.x -- the comments in check.in don't agree with the usage, and it seemed unlikely that anyone really wanted this (it can be very slow, so perhaps a test at a time?), so this was intentional (apart from not altering the reported usage). I've added it back for 2.

Re: [Rd] (PR#13789) possible agrep bug; R 2.9.1, Mac OS X 10.5

2009-08-14 Thread Prof Brian Ripley
It transpires this had nothing to do with 'Mac OS X 10.5' (sic, 'ten ten'): it is a 32-bit vs 64-bit issue, and I could not reproduce it even on Mac OS 10.5 with a 64-bit build. The difference is simply the size of 'long' used for internal calculations in the apse.c code, and it seems that has

Re: [Rd] options( "menu" )

2009-08-07 Thread Prof Brian Ripley
There are plans for more wide-ranging GUI hooks, so please be patient. (They are likely to make 2.10.0.) On Fri, 7 Aug 2009, Romain Francois wrote: Hello, The current implementation of the menu function (in utils) makes it difficult for front-ends to hook in and propose an alternative display

Re: [Rd] Section 1.3.1 of R-Ext Documentation lists tests/Examples/pkg-Rex-Rout.save incorrectly (PR#13877)

2009-08-06 Thread Prof Brian Ripley
Same as 13876! On Thu, 6 Aug 2009, ar...@cantab.net wrote: Full_Name: Andrew Thornton Version: Webpage OS: Linux Submission from: (NULL) (81.154.9.63) The Writing R Extensions documentation at: http://cran.r-project.org/doc/manuals/R-exts.html lists two different filenames for making the ex

Re: [Rd] Inconsistent documentation in Writing R Extensions (PR#13876)

2009-08-06 Thread Prof Brian Ripley
On Thu, 6 Aug 2009, brandon.j.whitc...@gsk.com wrote: Greetings, I think there is an inconsistency in the Writing R Extensions document. Please let me know if I am right or wrong on this one. Working from the PDF document (R-exts-2.9.1.pdf) - page 9 states that the file -Ex.Rout.save should

Re: [Rd] update.formula and backticked colons

2009-07-31 Thread Prof Brian Ripley
You can always check the list archives (the ETHZ ones): it did make it. See the thread starting at https://stat.ethz.ch/pipermail/r-devel/2009-July/054184.html I need to look more carefully, but this is not what ... is documented to do and it would need to be an extra argument for this method

Re: [Rd] bug in texi2dvi? (PR#13833)

2009-07-15 Thread Prof Brian Ripley
On Wed, 15 Jul 2009, Duncan Murdoch wrote: On 15/07/2009 6:00 AM, pa...@idsia.ch wrote: I am trying to call texi2dvi on a very simple tex-file (see below) and it fails with a memory access error. I originally tried to call it on another, meaningful tex file with the same error occuring. I am

Re: [Rd] save() file size (PR#13816)

2009-07-09 Thread Prof Brian Ripley
The evidence contradicts this claim: object.size(x) 4666464 bytes object.size(y) 5812696 bytes so 'y' is indeed larger than 'x' (and compresses less well). Reason: 'x' has automatic row names and 'y' does not. On Thu, 9 Jul 2009, mike.lawre...@dal.ca wrote: Full_Name: Mike Lawrence Versio

[Rd] Removing support for --without-iconv

2009-06-29 Thread Prof Brian Ripley
We made support for a sufficiently general iconv 'essential' in R 2.5.0 and have been giving configure warnings on --without-iconv ever since. We originally announced that --without-iconv would be available in 2.5.x only. The delay in making iconv compulsory was down to problems with install

Re: [Rd] should Sys.glob() cope with a UNC windows path beginning with backslashes?

2009-06-26 Thread Prof Brian Ripley
On Fri, 26 Jun 2009, Tony Plate wrote: I find that Sys.glob() doesn't like UNC paths where the initial slashes are backslashes. The help page for Sys.glob() doesn't specificly mention UNC paths, but does say: "File paths in Windows are interpreted with separator \ or /." Is the failure to tr

Re: [Rd] can't use ATLAS or ACML | 2.9.0

2009-06-26 Thread Prof Brian Ripley
On Fri, 26 Jun 2009, Evan Cooch wrote: So, tried again from scratch. Again, CentOS 5.3, which is essentially RHEL 5.3. ./configure --with-blas="-L/opt/acml4.3.0/gfortran64/lib -lacml" In config.log, get things like configure:37199: checking for dgemm_ in -L/opt/acml4.3.0/gfortran64/lib -lac

Re: [Rd] binding message from R CMD check

2009-06-18 Thread Prof Brian Ripley
On Thu, 18 Jun 2009, Terry Therneau wrote: When I run R CMD check on the survival package I get one error message that I have not been able to figure out: survfitCI: no visible binding for global variable 'n.nevent' I've examined the code and can't see the problem -- the variable in questio

Re: [Rd] Argument as.integer(NA) to a function C

2009-06-18 Thread Prof Brian Ripley
On Thu, 18 Jun 2009, Christophe Genolini wrote: Hi the list, I am writing a R function that call a C function. The C function needs integers but I do not manage to give a NA integer as argument : --- C code --- void essai(int *t){ Rprintf("\nT0=%i T1=%i T2=%i T3=%i",t[0],t[1],t[2],t[3]); }

Re: [Rd] Portuguese translation problem (PR#13756)

2009-06-14 Thread Prof Brian Ripley
You were asked to report problems with translation to the appropriate translation team: see the section 'How to report a bug' of the FAQ. For Brazilian Portuguese the translator listed is Fernando Henrique Ferraz P. da Rosa , not it seems far from you. The Brazilian Portuguese translations ar

Re: [Rd] .Rhistory created with wrong permissions (PR#13752)

2009-06-11 Thread Prof Brian Ripley
Yes, it is by design, and not R's design at that. How (or if) the history is saved is determined by the GUI interface in use. In this case it appears to be command-line R built with readline support, in which case the saving is done by readline's write_history. And although the history.info m

Re: [Rd] Reduce: extra args wishlist?

2009-06-10 Thread Prof Brian Ripley
On Sat, 6 Jun 2009, Ben Bolker wrote: Is there a reason that Reduce() doesn't take a "..." argument that would allow arbitrary extra arguments to be passed through to the function? Here is a little example of how this would be convenient: z <- list( data.frame(state=c("California")

Re: [Rd] CRAN build/checks: Dependencies on non-CRAN packages?

2009-06-08 Thread Prof Brian Ripley
On Mon, 8 Jun 2009, Kurt Hornik wrote: Henrik Bengtsson writes: Hi, how is the CRAN build/check system dealing with dependencies on non-CRAN packages? Are there external repositories that are dealt with in special ways, e.g. Bioconductor and Omegahat? Is this documented somewhere? The mo

Re: [Rd] need help with libtool/aclocal error

2009-06-06 Thread Prof Brian Ripley
Looks like libtool is objecting to a patch-level mismatch in hte R sources (and I'm surprised that such minor mismatches are not allowed). You should be able to solve this by using a current R-patched (>=r48719), or just updating tools/ltmain.sh from https://svn.r-project.org/R/branches/R-2-9-

Re: [Rd] Bug in print.Arima and patch

2009-06-05 Thread Prof Brian Ripley
On Fri, 5 Jun 2009, Gavin Simpson wrote: On Fri, 2009-06-05 at 15:42 +0100, Prof Brian Ripley wrote: Why not use NROW? No reason - had forgotten this existed. I was testing NROW after having seen the R-help message, so will go ahead with that solution. But as I was doing so, something

Re: [Rd] Bug in print.Arima and patch

2009-06-05 Thread Prof Brian Ripley
Why not use NROW? On Fri, 5 Jun 2009, Gavin Simpson wrote: Dear List, A posting to R-Help exposed this problem with the print method for objects of class Arima: set.seed(1) x <- arima.sim(n = 100, list(ar = 0.8897, ma = -0.2279)) mod <- arima(x, order = c(1,0,1)) coefs <- coef(mod) mod2 <- a

Re: [Rd] Show location of workspace image on quit?

2009-06-05 Thread Prof Brian Ripley
Any change here is not so simple to implement as to propose: this is not something in the R engine, but part of the clean-up action in the front end. That means that there are at least 3 versions to handle in the standard front ends (and that for R.app is not in the main source tarball). And

Re: [Rd] (PR#13735) LM/GLM can't find weights vector from within a function

2009-06-01 Thread Prof Brian Ripley
This seems to be as documented. From ?lm All of 'weights', 'subset' and 'offset' are evaluated in the same way as variables in 'formula', that is first in 'data' and then in the environment of 'formula'. We don't have a reproducible example and so do not know where rFormula was

Re: [Rd] edge case concerning NA in dim() (PR#13729)

2009-05-29 Thread Prof Brian Ripley
On Fri, 29 May 2009, asto...@esica.com wrote: Full_Name: Allan Stokes Version: 28.1 OS: XP Submission from: (NULL) (24.108.0.245) I'm trying to use package HDF5 and have discovered some round-trip errors: save, load, save is not idempotent. I started digging into the type system to figure out

Re: [Rd] Bug in "$<-.data.frame" yields corrupt data frame (PR#13724)

2009-05-28 Thread Prof Brian Ripley
Would the above modification work to fix this problem? Yes thank you, and I've incorporated it in R-patched and R-devel. It does catch 3 packages, DescribeDisplay, rgcvpack and BioC:rHVDM. On Wed, 27 May 2009, smckin...@bccrc.ca wrote: Full_Name: Steven McKinney Version: 2.9.0 OS: Mac OS X 1

Re: [Rd] R package installation (PR#13726)

2009-05-27 Thread Prof Brian Ripley
This is a problem in your specification to R of the peculiarities of your system, not in R itself. You have only specified some of the settings you need, and in particular as you are using Fortran 90 code and a shared R library you need more than a typical user would. On Wed, 27 May 2009, l.b

Re: [Rd] [R] sprintf() question

2009-05-26 Thread Prof Brian Ripley
Thank you, incorporated now. As the help page says, %a is a C99 feature that is not available on all platforms. The *printf in msvcrt.dll is a long way from C99-compatible (it dates from ca 10 years ago, but later VC runtimes are also incompatible). Recently MinGW has attempted to supplement

Re: [Rd] plot ignores type= "n" when x is factor (PR#13703)

2009-05-26 Thread Prof Brian Ripley
On Thu, 14 May 2009, paulj...@ku.edu wrote: Full_Name: Paul E. Johnson Version: 2.9.1 Where did you get that? Time travel? OS: Linux (Ubuntu 9.04) Submission from: (NULL) (129.237.61.25) x <- gl(2,50) y <- rnorm(100) plot(x,y) plot(x,y, type="n") I *wish* the last one would draw a blank

Re: [Rd] Fwd: [R] size of point symbols

2009-05-25 Thread Prof Brian Ripley
I don't know where you get your claims from. R graphics is handled internally in inches, with a device-specific mapping to pixels/points etc (which is documented for each device on its help page). This has to be done carefully, as pixels may not be square. What the meaning of pch=1:23 is in

Re: [Rd] (PR#13705) [wishlist, patch] make row() and col() preserve dimnames

2009-05-25 Thread Prof Brian Ripley
On Sun, 17 May 2009, goodr...@fas.harvard.edu wrote: Full_Name: Ben Goodrich Version: 2.9.0 OS: Linux (Debian unstable) Submission from: (NULL) (128.103.220.16) row(x), col(x), and functions that call them like lower.tri(x) and upper.tri(x) do not retain the rownames or colnames of x in the

Re: [Rd] using a "third party" DLL in my package

2009-05-23 Thread Prof Brian Ripley
09, Kasper Daniel Hansen wrote: On May 20, 2009, at 4:32 , Seija Sirkiä wrote: Hello again, thank you for the comments, especially this one: Prof Brian Ripley wrote: My concern would be that there are different cases that fail under Fortran compiler X and you are just sweeping the problem

Re: [Rd] install.packages now intentionally references .Rprofile?

2009-05-20 Thread Prof Brian Ripley
On Wed, 20 May 2009, Martin Morgan wrote: A post on the Bioconductor mailing list https://stat.ethz.ch/pipermail/bioconductor/2009-May/027700.html suggests that install.packages now references .Rprofile (?), whereas in R-2-8 it did not. Is this intentional? Yes. And in fact it did in earli

Re: [Rd] Auto-upgrading a package under Windows ?

2009-05-20 Thread Prof Brian Ripley
On Wed, 20 May 2009, Dirk Eddelbuettel wrote: On 20 May 2009 at 13:54, Prof Brian Ripley wrote: | On Mon, 18 May 2009, Dirk Eddelbuettel wrote: | | > | > I was trying to be cute with a company-internal package and used | > | >if (Sys.info()["sy

Re: [Rd] Auto-upgrading a package under Windows ?

2009-05-20 Thread Prof Brian Ripley
On Mon, 18 May 2009, Dirk Eddelbuettel wrote: I was trying to be cute with a company-internal package and used if (Sys.info()["sysname"]=="Windows") { update.packages(repos="http://some.where.internal/R";, ask=FALSE) } The commonly used test is .Platform$OS.type == "windows": th

Re: [Rd] Problem building (binary) packages for Windows

2009-05-16 Thread Prof Brian Ripley
On Sat, 16 May 2009, Martin Maechler wrote: "UweL" == Uwe Ligges on Fri, 15 May 2009 20:48:03 +0200 writes: [.] >> Thank you for clarifying this and once again apologies for stirring you >> up with something that had been fixed in the mean-time already. UweL> For R-

Re: [Rd] Spearman's rank correlation test (PR#13574)

2009-05-15 Thread Prof Brian Ripley
On Fri, 15 May 2009, Petr Savicky wrote: Bug report "Spearman's rank correlation test (PR#13574)" was moved to trashcan with empty Notes field. I would like to learn, what was wrong with this bug report. Can i ask the developers to add a note to it? The move was not intended: JitterBug does so

Re: [Rd] View() crashy on Ubuntu 9.04

2009-05-15 Thread Prof Brian Ripley
Thank you, included in R-patched and R-devel now. BTW, it looks like the original problem is in MBCS locales only, which postdate the X11 View() code (but we had patches from Mr Nakama: input contexts are needed for entering CJK languages). I do wonder sometimes if people who only work with d

Re: [Rd] Problem building (binary) packages for Windows

2009-05-15 Thread Prof Brian Ripley
That version of R-devel is not current, so please update it. I think it might have been in an interval where we tried out verious fixes for building bundles and some of them broke other things. In general if you use R-devel or R-patched you need to update before reporting any difficulties. '

Re: [Rd] using a "third party" DLL in my package

2009-05-15 Thread Prof Brian Ripley
On Thu, 14 May 2009, Seija Sirkiä wrote: Hello all, it seems my efforts in reading the manuals and help files aren't enough so here I am. The question is, how would I go about linking a pre-compiled DLL in to my package? I have previously successfully built packages with Fortran and C source

Re: [Rd] Managing DLLs with the same names in an R session

2009-04-24 Thread Prof Brian Ripley
On Fri, 24 Apr 2009, Patrick Aboyoun wrote: I am having a problem using two DLLs with the same name, but obviously located in different directories, in an R session. The troublesome package is the (Bioconductor) Rgraphviz package. It relies on (3rd party software) graphviz and imports function

Re: [Rd] Clarification for options(OutDec)

2009-04-22 Thread Prof Brian Ripley
On Wed, 22 Apr 2009, Stephen Eglen wrote: The documentation for the OutDec option says that it should be a 'one-character string'; yet, if I try a unicode character, it doesn't seem to work. Are unicode chars not counted as one-character? Correct, it has to be a single byte (and the comment

Re: [Rd] history function does not work correctly (PR#13645)

2009-04-08 Thread Prof Brian Ripley
On Wed, 8 Apr 2009, jad...@alum.mit.edu wrote: Full_Name: Joseph Adler Version: 2.8.1 OS: Mac OS X 10.5.6 Submission from: (NULL) (71.142.93.52) According to the help file, the history() function is supposed to show recent command history. However, it does not do this in the current Mac OS X v

Re: [Rd] external equiv to R_serialize()?

2009-03-30 Thread Prof Brian Ripley
On Mon, 30 Mar 2009, Joe Conway wrote: I'm trying to efficiently allow conversion of R objects to PostgreSQL bytea (raw binary) datatype within PL/R for persistent storage in Postgres tables. I have found R_serialize() which looks like what I need, -- e.g. R_serialize(object, NULL, FALSE, NULL

Re: [Rd] Listing of LAPACK error codes

2009-03-25 Thread Prof Brian Ripley
On Wed, 25 Mar 2009, Orlando Döhring wrote: Professor Ripley commented on LAPACK error codes: https://stat.ethz.ch/pipermail/r-help/2007-March/127702.html and says "Internal LAPACK errors are usually problems with arithmetic accuracy, and as such are compiler- and CPU-specific." Is there a list

Re: [Rd] unlink fails to remove symbolic links

2009-03-21 Thread Prof Brian Ripley
On Sat, 21 Mar 2009, Martin Morgan wrote: A little more precisely, unlink fails when the file being unlinked is a broken symbolic link (as in the example below). This is because R_FileExists checks stat() == 0, and stat fails (returns -1) when trying to resolve the broken link. Perhaps lstat() i

Re: [Rd] sprintf("%d", integer(0)) aborts

2009-03-19 Thread Prof Brian Ripley
On Wed, 18 Mar 2009, William Dunlap wrote: In R's sprintf() if any of the arguments has length 0 the function aborts. E.g., > sprintf("%d", integer(0)) Error in sprintf("%d", integer(0)) : zero-length argument > sprintf(character(), integer(0)) Error in sprintf(character(), integer(0))

Re: [Rd] Bug in Rdconv(.pm) (PR#13575)

2009-03-18 Thread Prof Brian Ripley
This is fixed now in R-devel. Meanwhile a similar issue was found with \kbd in a \value{} preamble, but only in Perl 5.10.x (and the same fix resolves that). On Thu, 5 Mar 2009, Prof Brian Ripley wrote: The problem is that \pkg gets included (unescaped) in a Perl substitution, and in modern

Re: [Rd] Rd \usage clause for an S4 replace method

2009-03-13 Thread Prof Brian Ripley
That's not how you use it, surely? The obvious to me \usage{ \S4method{[}{TimeSeries,TimeDate,missing}(x, i, j, ..., drop) \S4method{[}{TimeSeries,TimeDate,missing,ANY}(x, i, j, ...) <- value } works. There is an example of a replacement method using \method in 'Writing R Extensions', so expe

Re: [Rd] r-devel tarball build failure on windows

2009-03-12 Thread Prof Brian Ripley
I realized that there was a different point tacked on here that has not been answered: On Tue, 10 Mar 2009, Hiroyuki Kawakatsu wrote: [...] By the way, I noticed that -make all recommended- still builds the CHM help files for certain packages (e.g. Matrix) even though I set USE_CHM=FALSE in M

Re: [Rd] iconv.dll in Windows

2009-03-12 Thread Prof Brian Ripley
On Thu, 12 Mar 2009, Uwe Ligges wrote: See .../R/src/gnuwin32/CHANGES: oiconv() is now done by a version of Yukihiro Nakadaira's win_iconv rather than by libiconv. This version is based on Windows' codepages and is not quite as comprehensive as libiconv: it is ho

Re: [Rd] Building R for Vistax64

2009-03-11 Thread Prof Brian Ripley
Look in MkRules and the rw-FAQ. You can easily build R under Mingw64, but no one has reported making it run -- and several have reported failures. Commercail vendors have built 64-bit R under other Windwos compilers. On Wed, 11 Mar 2009, Sim, Fraser wrote: Hi all, I have successfully buil

Re: [Rd] Compiling R-2.8.1 on Sparc Solaris 10: libRlapack.so: symbol __vlog_: referenced symbol not found

2009-03-11 Thread Prof Brian Ripley
Please try the options recommended in the R-admin manual: these do not include using sunperf. But if you want to choose your own options, ask your local Solaris help as this is not an R issue. On Wed, 11 Mar 2009, Mohammad Nikseresht wrote: Hi, I am compiling R2.8.1 on a Sun M4000 machine

Re: [Rd] website feature request - a roadmap (PR#13589)

2009-03-11 Thread Prof Brian Ripley
Have you seen developer.r-project.org? All the relevant information is there. For the medium-term (up to 6 months) the NEWS file in the R-devel version of R indicates currently intended changes. CRAN is a distribution network, and distinct from www.r-project.org and developer.r-project.org.

Re: [Rd] libf95.a: could not read symbols?

2009-03-10 Thread Prof Brian Ripley
Where did FFLAGS come from here (looks like you meant FPICFLAGS)? But that will only postpone the problem: to build R as a shared library you need PIC libraries, and your Fortran library is apparently not PIC (gcc does not generate PIC code by default on x86_64, and g95 as a gcc derivative is

Re: [Rd] bug (PR#13570)

2009-03-10 Thread Prof Brian Ripley
opped for particular predictors? is incorrect -- cross terms are not dropped in this implementation of loess. Thanks, I will incorporate that. Thanks again, Ben Prof Brian Ripley wrote: I've found the discrepancy, so the patched code from current dloess is now available in R-patched and R-de

Re: [Rd] r-devel tarball build failure on windows

2009-03-10 Thread Prof Brian Ripley
This is another of those things which is not yet finished (you will see mention of the removed cross-building scripts in the relevant Makefile.win). Expect it to work from the tarball before GFF in 10 day's time. There's another intermittent problem with dependencies in the current sources th

Re: [Rd] ?as.POSIXct (PR#13587)

2009-03-10 Thread Prof Brian Ripley
On Tue, 10 Mar 2009, lbrag...@gmail.com wrote: Full_Name: Luca Braglia Version: 2.8 OS: Windows Submission from: (NULL) (85.18.136.110) From ?as.POSIXct ## SPSS dates (R-help 2006-02-17) z <- c(10485849600, 10477641600, 10561104000, 10562745600) as.Date(as.POSIXct(z, origin="158

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