Re: [Rd] R CMD check pkg and 32/64 bit.

Take a closer look: the differences in output are not just in trailing digits. We solve the latter in R itself mainly by use of e.g. options(digits=5) in the relevant \examples{} sections. However, we also try to remove the numerical instability in the algorithms that leads to this. Perhaps

Re: [Rd] A: ImportFrom(B, ...) -- B: ImportFrom(A, ...)

It is necessary (in most cases, and as implemented). When R goes to load the namespace of A, it has to find the objects you wish to import from B. Remember that objects in R are not standalone: they may have shared components and functions have environments, so the only way to so this is to l

Re: [Rd] nobs() and logLik()

I do wonder why people use zero weights rather than 'subset', and I don't particularly like the discontinuity as a weight goes to zero. But this came up for glm() and it would be better to be consistent, so thanks for pointing out the nls() cases. We'll alter them. On 20/01/2012 05:30, Berwi

Re: [Rd] serialize/unserialize vector improvement

This has languished for a long time, and we should make a decision before FF for 2.15.0. It seems to me that in so far as there is a problem, it is that we serialize via XDR, and that since that was invented little-endian CPUs have taken over the world. So for the only cases I can imagine thi

Re: [Rd] Failure to get compactPDF to compact a pdf file

On 24/01/2012 08:30, John Maindonald wrote: I am failing to get compactPDF to make any change to a pdf file that, a/c to the message from the CRAN upload site, can be very substantially compacted. Any ideas what may be wrong? AFAICS you are quoting a message from R-devel, which tries to find '

Re: [Rd] factor S4 class is NA when as.character method exists

On 24/01/2012 17:17, William Dunlap wrote: Here is code that does make factor() work on a new class like yours. It uses Sv3 methods. Which is necessary as unique() is an S3 generic in the base namespace, and creating some other function named 'unique' elsewhere (which is what setGeneric does

Re: [Rd] serialize/unserialize vector improvement

On 22/01/2012 13:56, Prof Brian Ripley wrote: This has languished for a long time, and we should make a decision before FF for 2.15.0. It seems to me that in so far as there is a problem, it is that we serialize via XDR, and that since that was invented little-endian CPUs have taken over the

Re: [Rd] Unable to reload Rdoc

This is simply not supported. Lazy-load databases are cached, and you cannot expect to change them during the R session once they have been used. Spend the few milliseconds needed to start a new session. And R CMD Rdconv is a much simpler way to check a changed .Rd file. On 27/01/2012 09:47,

Re: [Rd] Numerical instability in new R Windows development version

On 27/01/2012 13:26, Duncan Murdoch wrote: On 12-01-27 7:23 AM, Hans W Borchers wrote: I have a question concerning the new Windows toolchain for R>= 2.14.2. When trying out my package 'pracma' on the win-builder development version it will stop with the following error message: > f3<- function

Re: [Rd] tcltk GUIs (was need gui matrix editor: does R Core team have advice on how?)

On 28/01/2012 22:04, John Fox wrote: Dear Paul and Gabor, The Rcmdr GUI uses the tcltk package, so I have some experience with providing an R tcltk-based GUI for various platforms. As Gabor says, everything works very smoothly on Windows because the R Windows binary includes Tcl/Tk. Maybe, bu

Re: [Rd] zip() containing windows specific code?

On 30/01/2012 17:24, Matthieu Stigler wrote: Dear R devel list I was wondering whether zip() contains a windows specific call to system(), Actually, it does not contain a call to system() as the argument "invisible" seems to be windows specific, yet is used anytime by zip: And what is

Re: [Rd] location of check.Renviron on Windows

On 01/02/2012 19:57, Robert M. Flight wrote: Thanks Simon, that did the ticket. Will remember that next time. It is also an FAQ: http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What-are-HOME-and-working-directories_003f -Robert Robert M. Flight, Ph.D. University of Louisville Bioinfo

Re: [Rd] [ping] panel.first for bxp

This is the wrong place: please file enhancement requests on R-bugs. But I see no case at all for adding this, and all enhancements to base R need convincing cases since you are effectively volunteering someone else to maintain this in perpetuity. The lack of response so far suggests that no

Re: [Rd] Can I use "..." in parallel:::clusterApplyLB?

On 13/02/2012 06:51, Slava Razbash wrote: Hello, Can I do the following? Is parallel:::clusterApplyLB() designed to work like this? The code below is for illustrative purposes only. It is designed to work with standard R semantics. For ... those are quite complex, and you may have to force e

Re: [Rd] requesting a new SIG mailing list

Have you asked the maintainers of those lists? Or the person who would have to do the work to set the list up (Martin Maechler, who is currently on vacation, or colleagues at ETHZ)? My suspicion is that there would be too little traffic to make a separate list worthwhile to administer. (You

Re: [Rd] Parallel R CMD check?

On 17/02/2012 06:50, Martin Morgan wrote: Running R CMD check on a package can take quite a lot of time. Checks seem like they could be run in parallel (separate processes for, e.g., codoc, examples, tests, ...). Is there a way to do this? My current usage is typically R CMD build R CMD check p

Re: [Rd] executable files R package

On 20/02/2012 17:17, sahir bhatnagar wrote: thanks, I run into the following error message when running R CMD check "Source packages should not contain undeclared executable files" in reference to the following instruction from the help manual: "R CMD check will warn about them unless they are

Re: [Rd] executable files R package

;t you ask your local IT support for help with creating text files? It is not an R topic. On Mon, Feb 20, 2012 at 12:39 PM, Prof Brian Ripley mailto:rip...@stats.ox.ac.uk>> wrote: On 20/02/2012 17:17, sahir bhatnagar wrote: thanks, I run into the following error mes

Re: [Rd] text(1:10, col=NA) is printed in color 1 instead of color 0 (was "is not transparent")

The documentation is out of date (and contradictory for cex). Nowadays NULL and NA for col and font correspond to the par() values, and for cex correspond to 1.0. So it is in fact _plotted_ in par("col"), which by default is 1. On 20/02/2012 18:16, Peter Ruckdeschel wrote: Am 20.02.2012 15:22

Re: [Rd] Controlling simplification in apply()?

On 20/02/2012 16:03, Gavin Simpson wrote: Dear list, Fully according to the documented behaviour, I was bitten by apply() simplifying results to vectors or arrays when the lengths of the individual objects returns by FUN are the same (over simplification). sapply() has argument simplify with de

Re: [Rd] OpenMP and random number generation

On 22/02/2012 08:23, Mathieu Ribatet wrote: Dear all, Now that R has OpenMP facilities, Hmm, not exactly new. I'm trying to use it for my own package but I'm still wondering if it is safe to use random number generation within a OpenMP block. I looked at the R writing extension document bo

Re: [Rd] function remains loaded in the search space after detaching the package

On 24/02/2012 11:20, Martin Maechler wrote: Joris Meys on Fri, 24 Feb 2012 11:24:35 +0100 writes: > I ran into some very irritating behaviour I don't > understand. Let me illustrate with the package gdata() > and the function print.object_size() : >> print(object.

Re: [Rd] function remains loaded in the search space after detaching the package

ntly not in the search space. Any other ideas? R relies very heavily on 'calling a function that's apparently not in the search space': that's much of the point of namespaces. Professor Ripley Cheers Joris On Fri, Feb 24, 2012 at 1:08 PM, Prof Brian Ripley wrote: On 2

Re: [Rd] function remains loaded in the search space after detaching the package

ponents of the package, and is inadvisable. And that is explicitly mentioned on ?unloadNamespace On Fri, 24 Feb 2012, Joris Meys wrote: 2012/2/24 Prof Brian Ripley : As getS3method('print', 'object_size') would have confirmed the expectations of a 'one'

Re: [Rd] improved error message when existing implicit S4 generic is not imported?

I think the message is accurate [*]: you do however need to have a clear understanding of the scoping issues involved, and no message is going to give you that. In short, implicit generics are converted (or not) into explicit functions to be dumped during the dump-for-lazy-loading phase of R C

Re: [Rd] .C clarification

On 03/03/2012 13:42, Terry Therneau wrote: Does .C duplicate unnecessary arguments? For instance fit<- .C("xxx", as.integer(n), x, y, z=double(15)) The first and fourth arguments would have NAMED = 0. Is my guess that .C won't make yet one more (unnecessary) copy correct? .C's internals (d

Re: [Rd] Calling FORTRAN function from R issue?

On 06/03/2012 13:37, Berwin A Turlach wrote: G'day Berend, On Tue, 6 Mar 2012 13:06:34 +0100 Berend Hasselman wrote: [... big snip ...] But I would really like to hear from an Rexpert why you shouldn't/can't use external here in the Fortran. Probably less a question for an Rexpert but for

Re: [Rd] Calling FORTRAN function from R issue?

On 06/03/2012 06:28, Berwin A Turlach wrote: G'day Dominick, On Mon, 5 Mar 2012 19:21:01 -0500 Dominick Samperi wrote: ... This is consistent with the interface prototype for the BLAS routine zdotc contained in/include/R_ext/BLAS.h, namely, BLAS_extern Rcomplex F77_NAME(zdotc)(Rcomple

Re: [Rd] Rserve compilation error

On 06/03/2012 18:08, jbanerjee wrote: Hi, I am trying to install Rserve 1.7-0 on CentOS 6. But I get this compilation error - /usr/lib64/Revo-5.0/R-2.13.2/lib64/R/lib/libiomp5.so: undefined reference to `pthread_atfork' I tried other versions of Rserve (0.6-5 and 0.6-8) without any success. How

Re: [Rd] --as-cran and need to ignore.svn directories

On 12/03/2012 16:00, Paul Johnson wrote: Good morning: I submitted a package update to CRAN and got a bounce because I had not run R CMD check with "--as-cran". I'd not heard of that before, but I'm glad to know about it now. Well, it has only existed for about a month, but the customizations

Re: [Rd] How to install sqldf to R with version 2.10?

On 17/03/2012 16:25, Uwe Ligges wrote: On 17.03.2012 17:20, Joshua Ulrich wrote: On Sat, Mar 17, 2012 at 9:56 AM, zhu free wrote: Hi, How to install sqldf to R with version 2.10? I used the R in the cluster of university and there seems no way to update the R version to 2.14. However, I do ne

Re: [Rd] parApply vs parCapply

On 17/03/2012 17:03, Ken Knoblauch wrote: I've started to use the parallel package and it works very well speeding things up. Thank you for making this easy to do. Should I have expected that parCapply would return a vector when parApply returns a matrix? Maybe: I would have expected so, and A

Re: [Rd] bzip2'ed data under data/

On 19/03/2012 20:25, Sebastian P. Luque wrote: Hi, R CMD check PACKAGE_VERSION_tar.gz gives warning: Files not of a type allowed in a ‘data’ directory: ‘tser1.csv.bz2’ ‘tser2.csv.bz2’ Please use e.g. ‘inst/extdata’ for non-R data files which I didn't expect, based on section 1.1.5 (Data in

Re: [Rd] R 2.14.1 memory management under Windows

On 22/03/2012 06:11, Peter Meilstrup wrote: My guess would be that it's a matter of having swap space be a dedicated partition or fixed-size file (Linux, usually) versus swapping to a regular file that grows as needed (Windows and OS X, usually.) So if you defragmented your drive and set Windows

Re: [Rd] merge bug fix in R 2.15.0

On Mon, 19 Mar 2012, Stephanie M. Gogarten wrote: I would like to add a vote for keeping blank suffixes in merge(), as I routinely use this functionality. An example use case: But you don't have a vote An exception has been made for "" in R 2.15.0. However, further cases of unintended

Re: [Rd] bzip2'ed data under data/

On 26/03/2012 16:34, Sebastian P. Luque wrote: On Wed, 21 Mar 2012 18:35:15 +, Prof Brian Ripley wrote: On 19/03/2012 20:25, Sebastian P. Luque wrote: Hi, R CMD check PACKAGE_VERSION_tar.gz gives warning: Files not of a type allowed in a ‘data’ directory: ‘tser1.csv.bz2’ ‘tser2

Re: [Rd] Problem with table

On 19/03/2012 17:01, Terry Therneau wrote: R version 2.14.0, started with --vanilla > table(c(1,2,3,4,NA), exclude=2, useNA='ifany') 1 3 4 1 1 1 2 This came from a local user who wanted to remove one particular response from some tables, but also wants to have NA always reported for data chec

[Rd] CRAN policies

life as easy as possible. Kurt Hornik Uwe Ligges Brian Ripley __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] PROTECT help

On 27/03/2012 14:22, Terry Therneau wrote: I received the following note this AM. The problem is, I'm not quite sure how to fix it. Can one use PROTECT(coxlist(eval(PROTECT , do I create an intermediate variable, or otherwise? You can, but I find it easiest to follow if you create an interm

Re: [Rd] CRAN policies

ails a day about why their results were different was taking up far too much time. Paul On 12-03-27 07:52 AM, Prof Brian Ripley wrote: CRAN has for some time had a policies page at http://cran.r-project.org/web/packages/policies.html and we would like to draw this to the attention of pac

Re: [Rd] Missing Windows binary for R-2.15RC?

You should be capable of building R on Windows from the SVN sources or daily source tarballs. After all, when (as often happens) BioC has an inconsistent set of source or binaries (like released packages depending on unreleased packages, on unreleased versions), the BioC core team tell me to g

Re: [Rd] serialization regression in 2.15.0 beta

On 27/03/2012 22:01, Ben Goodrich wrote: In case anyone is concerned that this regression will affect them, the code was reverted to the 2.14.x behavior by r58842 | ripley | 2012-03-26 08:12:43 -0400 (Mon, 26 Mar 2012) | 1

Re: [Rd] r-forge build failure bafflement

We've seen similar things several times with CRAN submissions. Basic scenario was - INSTALL (via build or check) is trying to install a package that is not already installed, into a private library not on the usual .libPaths(). - Start-up code in that package is looking for the package, and

Re: [Rd] R CMD check returns NOTE about package data set as global variable

On 06/04/2012 19:46, Brad McNeney wrote: I'm developing a package that comes with a data set called RutgersMapB36. One of the package's functions requires this data frame. A toy example is: test<-function() { data(RutgersMapB36) return(RutgersMapB36[,1]) } R CMD check returns a NOTE: t

Re: [Rd] R CMD check returns NOTE about package data set as global variable

ge datasets (at least 100MBs) when you may want to control when they are loaded into memory. In case it matters, I'm check'ing with R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) Brad - Original Message - From: "Prof Brian Ripley" To: "

Re: [Rd] Display instruction text on package load

On 07/04/2012 22:27, Thomas J. Leeper wrote: I'm currently working on a new package for R that interfaces with an API. Most of the package's functionality requires users to supply an access key that allows the package to work with the API. I want to display text immediately upon loading the packa

Re: [Rd] Add DUP = FALSE when tabulate() calls .C("R_tabulate"

On 08/04/2012 19:37, Tim Hesterberg wrote: In base/R/tabulate.R, tabulate() calls .C("R_tabulate"; I suggest adding DUP = FALSE to that call. We can do that. Note that R-patched already does less copying[*], but adding DUP=FALSE may avoid one copy of 'dup' if it is an integer vector. We can

Re: [Rd] Byte compilation of packages on CRAN

On 11/04/2012 20:36, Matthew Dowle wrote: In DESCRIPTION if I set LazyLoad to 'yes' will data.table (for example) then be byte compiled for users who install the binary package from CRAN on Windows? No. LazyLoad is distinct from byte compilation. All installed packages use lazy loading these

Re: [Rd] [patch] giving library() a 'version' argument

A very important point is that library() *had* a 'version' argument for several years, and this is not what it did. So Mr Williams needs to do his homework From such a version of R: version: A character string denoting a version number of the package to be loaded, for use wit

Re: [Rd] R-2.15 compile error: fatal error: internal consistency failure

On 18/04/2012 00:51, Duncan Murdoch wrote: On 12-04-17 5:24 PM, andre zege wrote: I am unable to compile R-2.15.0 source. I configured it without problems with options that i used many times before ./configure --prefix=/home/andre/R-2.15.0 --enable-byte-compiled-packages=no --with-tcltk --enabl

Re: [Rd] R CMD check -- non S3 method warning

On 21/04/2012 14:18, Whit Armstrong wrote: I'm trying to R CMD check a package, and I'm getting the 'checking S3 generic/method consistency' warning. I have written a function 'gamma.dist' which is _not_ an S3 method, but happens to collide with the 'gamma' function from the R::base namespace.

Re: [Rd] url, readLines, source behind a proxy

On 18/04/2012 16:04, Joshua Ulrich wrote: Hi Renaud, On Wed, Apr 18, 2012 at 12:22 AM, Renaud Gaujoux wrote: Hi Henrik, Could anybody behind a proxy check if the issue can be reproduced? My proxy is in fact provided by cntml, which acts as a local proxy that takes care of tricky authenti

Re: [Rd] nobs.glm

On 24/04/2012 14:36, Wincent wrote: Hi all, The nobs method of (MASS:::polr class) takes into account of weight, but nobs method of glm does not. I wonder what is the rationale of such design behind nobs.glm. Thanks in advance. Best Regards. library(MASS) house.plr<- polr(Sat ~ Infl + Type +

Re: [Rd] Unable to install rggobi in R 2.15

Do not cross-post. This was answered on R-help. On 28/04/2012 02:47, Indrajit Sengupta wrote: I am currently using R 2.15.0 with R Tools 2.15 (in Windows XP). I downloaded the source for RGgobi and extracted it to a folder. Then I tried compiling and installing with the following command and

Re: [Rd] fast version of split.data.frame or conversion from data.frame to list of its rows

On 01/05/2012 00:28, Antonio Piccolboni wrote: Hi, I was wondering if there is anything more efficient than split to do the kind of conversion in the subject. If I create a data frame as in system.time({fd = data.frame(x=1:2000, y = rnorm(2000), id = paste("x", 1:2000, sep =""))}) user syst

Re: [Rd] Decompressing raw vectors in memory

On 02/05/2012 14:24, Hadley Wickham wrote: Hi all, I'm struggling to decompress a gzip'd raw vector in memory: content<- readBin("http://httpbin.org/gzip";, "raw", 1000) memDecompress(content, type = "gzip") # Error in memDecompress(content, type = "gzip") : # internal error -3 in memDecompre

Re: [Rd] Decompressing raw vectors in memory

On 02/05/2012 16:43, Hadley Wickham wrote: I'm struggling to decompress a gzip'd raw vector in memory: content<- readBin("http://httpbin.org/gzip";, "raw", 1000) memDecompress(content, type = "gzip") # Error in memDecompress(content, type = "gzip") : # internal error -3 in memDecompress(2) I'

Re: [Rd] R Installation Manual - ATLAS BLAS guidance that is not in the current version

On 09/05/2012 19:54, Adler, Avraham wrote: Good afternoon. I am trying to compile a version of Rblas.dll based on ATLAS for the Corei7. I had remembered that there was mention of which file to adjust and that "xerbla" needed to be removed from one of the outputs from the last time I tried a few

Re: [Rd] [patch] Behavior of .C() and .Fortran() when given double(0) or integer(0).

On 04/05/2012 18:42, Pavel N. Krivitsky wrote: Dear R-devel, While tracking down some hard-to-reproduce bugs in a package I maintain, I stumbled on a behavior change between R 2.15.0 and the current R-devel (or SVN trunk). In 2.15.0 and earlier, if you passed an 0-length vector of the right mod

Re: [Rd] StructTS Examples

On 15/05/2012 03:31, R. Michael Weylandt wrote: In the examples for StructTS -- ($RHOME)/library/stats/man/StructTS.Rd -- could par(mfrow = c(4, 1)) plot(log10(UKgas)) plot(cbind(fitted(fit), resids=resid(fit)), main = "UK gas consumption") become plot(log10(UKgas)) par(mfrow = c(4, 1)) plot(c

Re: [Rd] The constant part of the log-likelihood in StructTS

On 30/04/2012 12:37, Jouni Helske wrote: Dear all, I'd like to discuss about a possible bug in function StructTS of stats package. It seems that the function returns wrong value of the log-likelihood, as the added constant to the relevant part of the log-likelihood is misspecified. Here is an si

Re: [Rd] Passing externalptr to .C()

On 16/05/2012 23:30, Rick Sayre wrote: Thanks very much for the quick reply. I'd like to avoid static state in the .so, which is why I'm using the opaque pointer. It is indeed possible to convert everything to .Call(), but the work seems unnecessary given that it used to work just fine and I am

Re: [Rd] r-devel fails tests for parallel

Seems your ancient OS (that compiler has a 6-year-old copyright date) has a broken implementation of affinity with CPU_ZERO but not CPU_COUNT. I've added some checks which should catch this. On 17/05/2012 13:52, Kasper Daniel Hansen wrote: I have been building R-devel daily for years. In the

Re: [Rd] r-devel fails tests for parallel

On 17/05/2012 15:48, Kasper Daniel Hansen wrote: On Thu, May 17, 2012 at 9:04 AM, Prof Brian Ripley wrote: Seems your ancient OS (that compiler has a 6-year-old copyright date) has a broken implementation of affinity with CPU_ZERO but not CPU_COUNT. I've added some checks which should

Re: [Rd] R-devel on FreeBSD: new C99 functions don't build

On 15/05/2012 20:45, Rainer Hurling wrote: On 15.05.2012 20:49 (UTC+1), Murray Stokely wrote: On Tue, May 15, 2012 at 10:05 AM, Rainer Hurling wrote: About April 25th, there had been some changes within R-devel's src/nmath/pnbeta.c (and probably some other relevant places) and now building R-de

Re: [Rd] Distributing Executables.

On 18/05/2012 16:11, Daniel Fuka wrote: Sorry for this intrusion, but I am confused by two statements that appear to conflict at some level in Writing R Extensions, You may be confused, but the documentation does not conflict. > and wanted to make sure I understand the answer to: Can we distr

Re: [Rd] New S3 methods for optional package

On 24/05/2012 10:38, Jon Olav Skoien wrote: Hi, I have asked this question before, but the solution I ended up with (see below) creates a note when running R CMD check. So I am trying again... I am developing a package B that, among other things, also offers some extra S3-methods for functions

Re: [Rd] Slow do.call when having an error

On 29/05/2012 09:57, Alon Wasserman wrote: Hi, We've encountered a difference in running time between a straight function call and the same call using do.call when the called function generated an error. We've isolated the problem to the following small reproducible example: Consider the followi

Re: [Rd] Out of date instructions to build R using MKL

Hmm, you replied to a message from February and there has been an R release since with a revised manual. That does say (even more clearly) that it refers to version 10.0 of MKL and there have been changes. And since than there had been a change (notified by an Intel engineer) about which vers

Re: [Rd] possible bug in "R Editor"

On 31/05/2012 07:04, Wincent wrote: Dear all, I clicked "File-New Script" to open a R Editor, typed some commands in it and then saved it to a file. If the location where I tried to save the script contained Chinese Character, R Editor complained, Error: invalid input 'E:\Some.Chinese.Character

Re: [Rd] Patch to add Beta binomial distribution. Mentor needed!

On 05/06/2012 09:25, Ben Bolker wrote: Joan Maspons creaf.uab.cat> writes: 2012/6/1 Tim Triche, Jr. gmail.com> It's in VGAM, remember? Not a bug. -- *A model is a lie that helps you see the truth.* * * Howard Skipper Yes,

Re: [Rd] R CMD check: Sys.getenv("R_GSCMD") cannot contain full pathname (contrary to docs)

This is simply not true. Sys.which() should accept absolute paths, and does on my systems (even my Windows system). However, it looks like you gave an unescaped path containing spaces. Most likely you need to include that path in double quotes (just as you would on a Windows shell). On Wed

Re: [Rd] Problems building R on Solaris (gcc 4.6, 64 bit)

On 04/06/2012 19:27, Chander Ganesan wrote: Hello, I'm attempting to build R on Solaris 64-bit using gcc4, and am running into the following error: ld.so.1: R: fatal: relocation error: R_AMD64_PC32: file /home/chander.ganesan/src/r/R-2.15.0/lib/libR.so: symbol main: value 0x28001597b8c does not

Re: [Rd] model.frame and predvars

On 05/06/2012 16:17, Terry Therneau wrote: I was looking at how the model.frame method for lm works and comparing it to my own for coxph. The big difference is that I try to retain xlevels and predvars information for a new model frame, and lm does not. I use a call to model.frame in predict.coxp

Re: [Rd] problem in compililng c code using R CMD SHLIB

On 06/06/2012 18:12, Joshua Ulrich wrote: On Wed, Jun 6, 2012 at 8:20 AM, Simon Urbanek wrote: On Jun 6, 2012, at 6:16 AM, Arathy Ram wrote: Hello all, I was trying to compile a simple C program hello.c using R CMD SHLIB hello.c. MY R software residing in C:\Program Files\R\R-2.15.0, and al

Re: [Rd] 7 arguments passed to .Internal(identical) which requires 6

On 06/06/2012 21:04, peter dalgaard wrote: FYI, Brian has backed out the changes to identical() in r59533 of R-patched. Please retry your test codes with the new version. (Due to some ISP mess-up, Brian is temporarily unable to reply in detail himself.) -pd Some comments (now my ISP has repa

Re: [Rd] 7 arguments passed to .Internal(identical) which requires 6

On 07/06/2012 11:12, Matthew Dowle wrote: Prof Ripley wrote : (AFAIK the CRAN binary package providers expect users to be using the current version of R.) I guess it's quite common practice for very many users to fail that expectation. I for one do. I'm used to seeing "Warning: package was b

Re: [Rd] 7 arguments passed to .Internal(identical) which requires 6

On 07/06/2012 11:40, Matthew Dowle wrote: Prof Ripley wrote : That Depends line is about source installs. I can't see that documented in either Writing R Extensions or ?install.packages. Is it somewhere else? I thought Depends applied to binaries from CRAN too, which is the default method on

Re: [Rd] 7 arguments passed to .Internal(identical) which requires 6

On 07/06/2012 12:49, Matthew Dowle wrote: On 07/06/2012 11:40, Matthew Dowle wrote: Prof Ripley wrote : That Depends line is about source installs. I can't see that documented in either Writing R Extensions or ?install.packages. Is it somewhere else? I thought Depends applied to binaries fro

Re: [Rd] Vignettes are not being (re)built.

On 22/06/2012 23:01, Jeff Hamann wrote: I'm adding a couple of vignettes to an existing package. Incorrectly, it seems, but you told us no details. You can use R CMD build to get the PDFs (re-)built. R CMD check checks (preferably the tarball), but re-makes nothing. When I make a change

Re: [Rd] Win 64 package build - ERROR: loading failed for 'x64'

On 24/06/2012 02:54, John Nolan wrote: I have developed an R package that works under Win32, but when I attempt to build it on Win64, I get ERROR: loading failed for 'x64' More precisely, I developed and tested the package under Win32 and it works. But when I move to a 64 bit Windows 7 (Ho

Re: [Rd] Fast Kendall's Tau

On 26/06/2012 22:44, Duncan Murdoch wrote: On 12-06-25 2:48 PM, Adler, Avraham wrote: Hello. Has any further action been taken regarding implementing David Simcha's fast Kendall tau code (now found in the package pcaPP as cor.fk) into R-base? It is literally hundreds of times faster, although I

Re: [Rd] Using a function from splines.c in our package

On Mon, 9 Jul 2012, Gordon K Smyth wrote: Dear all, I'm writing to ask for advice as to best practice. A PhD student working with me is writing C++ code that we hope to make public as src code in our Bioconductor package edgeR. He wants to call the function fmm_spline, which is part of the

Re: [Rd] Suggestion / patch to support more Unicode characters in R CMD Rd2pdf

On 04/07/2012 22:01, Mikko Korpela wrote: Hi list, When using R CMD Rd2pdf, it is possible to set environment variable RD2PDF_INPUTENC to value "inputenx" and enjoy better support for UTF-8 characters (see ?Rd2pdf). This enables LaTeX package "inputenx" instead of "inputenc". Even better suppor

Re: [Rd] Understanding tracemem

Read the help carefully as to what 'copy' means: When an object is traced any copying of the object by the C function ‘duplicate’ produces a message to standard output, as does type coercion and copying when passing arguments to ‘.C’ or ‘.Fortran’. If you want to understand w

Re: [Rd] Understanding tracemem

On 12/07/2012 18:20, Hadley Wickham wrote: Read the help carefully as to what 'copy' means: When an object is traced any copying of the object by the C function ‘duplicate’ produces a message to standard output, as does type coercion and copying when passing arguments to ‘.C’ o

Re: [Rd] Warning when sourcing file after require

On 19/07/2012 12:46, Duncan Murdoch wrote: I don't see this in R-patched; I don't have 2.15.1 installed on this machine. But the problem appears to be that XML exports a function called source() (a generic), and you're using it -- but not the current version, which doesn't give the warning. Wh

Re: [Rd] Are R packages supposed to be "relocatable"? (avoiding BioConductor scripts...)

Short answer: setRepositories() # chose what you want from BioC install.packages() works and always has. 'Smoke and mirrors' are not actually needed. As for relocatability: I am guessing you are talking about a Linux cluster ... but the details do matter. The distribution of Windows binarie

Re: [Rd] large dataset - confused

On 23/07/2012 18:32, walcotteric wrote: I'm trying to load a dataset into R, but I'm completely lost. This is probably due mostly to the fact that I'm a complete R newb, but it's got me stuck in a research project. I've tried just opening the text file in WordPad and copying the data directly in

Re: [Rd] S4 objects in formulas (really, model frames)

The help for model.frame says Only variables whose type is raw, logical, integer, real, complex or character can be included in a model frame: this includes classed variables such as factors (whose underlying type is integer), but excludes lists. Some S4 objects are of one of

Re: [Rd] Using .onUnload to unload DLLs

On 24/07/2012 07:11, Winston Chang wrote: I've noticed that many of the "base" R packages have an .onUnload() function which automatically unloads compiled shared libraries with library.dynam.unload(). For example: stats:::.onUnload function (libpath) library.dynam.unload("stats", libpath)

Re: [Rd] Encoding errors in Rd files

On 24/07/2012 21:08, steven mosher wrote: Well, I'm working on project trying to bring back an old package last published on R 1.9 back to life. I'm almost there but I am getting killed by an encoding error in the Rd files After reading the manual, I decided to try UTF-8. Mostly because I could

Re: [Rd] pie() bug in r59963

On 26/07/2012 00:37, Hiroyuki Kawakatsu wrote: hi, there appears to be a bug in r-devel (r59963) src/library/graphics/R/pie.R, line 62 P <- t2xy(seq.int(x[i], x[i + 1], n)) meant to be P <- t2xy(seq.int(x[i], x[i + 1], length.out=n)) ? discovered when running demo(graphics). si

Re: [Rd] C code validation

On 27/07/2012 23:52, Adrian Duşa wrote: Dear R-devel, I'm trying to validate the results from a C function, against a (trial and tested) older R function. For reasons unknown to me, the C function seems to give different result sometimes at each trial, even with the very same data. See the adv

Re: [Rd] Shared routines in a dynamic library.

On 30/07/2012 14:48, David L Lorenz wrote: All, I have a question about referring to a subroutine that is in a dynamic library other than the one in my current package. Let's say that I have a package foo and it has some FORTRAN code that contains the subroutines foo1 and foocommon. The packag

Re: [Rd] Problem in vignette packaging of Sweave in utils package

I believe the issue is actually quite simple: you need to run make vignettes when building from a tarball if you want the tangled vignettes and the indices. I'll make that automatic after more testing. On 27/07/2012 21:55, Paul Johnson wrote: On Fri, Jul 27, 2012 at 9:54 AM, Duncan Murdoch

Re: [Rd] Daily snapshots of sources do not work?

On 05/08/2012 08:53, Rainer Hurling wrote: For some days now there had been no more daily snapshots on ftp://ftp.stat.math.ethz.ch/Software/R/ . The latest sources are from 07/26/2012. I think this is not indented? Whatever '07/26/2012' means! __

Re: [Rd] Straight-quotes for usage and examples sections in PDF docs?

On 06/08/12 23:01, Mike Lawrence wrote: Is there any way to ensure that quotation marks are left as straight quotes and not converted to curly quotes in the \usage and \examples sections when the pdf versions of the docs are created? They are not converted ... so there cannot be a way. In stan

Re: [Rd] Performance issues with R2.15.1 built from source on Solaris

On 10/08/2012 17:50, Eberle, Anthony wrote: Yes, the T4 physical host that the zone is configured on is SPARC. Are you saying that this is a function of the hardware or would possibly updating to a newer version of gcc help? I'm actually going to see if I can build a newer version of gcc anyway

Re: [Rd] trouble compiling R-patched from source on Windows 64 bit

On 12/08/2012 19:45, Hodgess, Erin wrote: Hello! I'm trying to install R-patched from source on a Windows 64 bit laptop. See the comments: skipping incompatible ./libRblas.dll.a when searching for -lRblas You are using the wrong compilers: 4.5.2 is not for recent R. I have installed R-tools

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