r-devel@r-project.org discussions for September 2012

42	[Rd] if(--as-cran)?

Hello, All: The fda package has tests that run too long for CRAN's current rules. I'd like to wrap some examples in a construct like the following: if(!CRAN()){ ... } I tried the following: CRAN <- ...

Spencer Graves
Sep 3, 2012 at 5:43 am
Sep 6, 2012 at 1:33 pm

11	[Rd] Suggest adding a 'pivot' argument to qr.R

I suggest adding a 'pivot' argument to qr.R, to obtain columns in the same order as the original x, so that a <- qr(x) qr.Q(a) %*% qr.R(a, pivot=TRUE) returns x ...

Tim Hesterberg
Sep 7, 2012 at 3:16 pm
Oct 3, 2012 at 4:20 pm

8	[Rd] problem with vignettes when S4 classes in packages overlap

( A similar problem is also reported by Sebastian P. Luque with library(maptools) library(trip) in the vignette as below ). I am writing a vignette which loads RMySQL and RPostgreSQL. This produces ...

Paul Gilbert
Sep 18, 2012 at 9:40 pm
Sep 19, 2012 at 12:44 pm

6	[Rd] Question about copying arguments in C.

Hi List, I'd imagine this is a question that has been answered before, but I can't seem to track it down, sorry for the duplication if it has. I am writing an interface for a C library and want to ...

Simon Knapp
Sep 15, 2012 at 3:10 am
Sep 16, 2012 at 2:00 pm

6	[Rd] Need to tell R CMD check that a function qr.R is not a method

When creating a package, I would like a way to tell R that a function with a period in its name is not a method. I'm writing a package now with a modified version of qr.R. R CMD check gives ...

Tim Hesterberg
Sep 7, 2012 at 3:05 pm
Sep 7, 2012 at 6:30 pm

5	[Rd] R-devel Digest, Vol 115, Issue 18

My problem is that CRAN demands that I suppress a large fraction of my checks, in order to fit within time constraints. This leaves me with 3 choices. 1. Add lines to my code that tries to guess if ...

Terry Therneau
Sep 19, 2012 at 2:08 pm
Sep 19, 2012 at 6:57 pm

5	[Rd] R crashes when printing a named numeric vector of a specific class - Bug?

Dear useR's, today I stumbled over an interesting phenomenon: First, I created a named numeric vector with a certain class and several attributes via the structure() function. After that, I ...

Basil Abou El-Komboz
Sep 11, 2012 at 2:53 pm
Sep 11, 2012 at 11:57 pm

4	[Rd] error on uneven recycling?

Is there some reason why [1] 2 4 4 Warning message: In (1:2) + (1:3) : longer object length is not a multiple of shorter object length can't be made into an error? I realise it was there in S-PLUS, ...

Thomas Lumley
Sep 25, 2012 at 2:45 am
Sep 25, 2012 at 7:39 am

4	[Rd] Risk of readRDS() not detecting race conditions with parallel saveRDS()?

I hardly know anything about the format used in (non-compressed) serialization/RDS, but hoping someone with more knowledge could give me some feedback; Consider two R processes running in parallel on ...

Henrik Bengtsson
Sep 15, 2012 at 5:21 pm
Sep 15, 2012 at 9:42 pm

4	[Rd] as.data.frame.character lacks nm= argument

Error in as.data.frame.vector(x, ..., nm = nm) : formal argument "nm" matched by multiple actual arguments nm= works for integer arguments: OneToTen 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 Bill ...

William Dunlap
Sep 13, 2012 at 8:32 pm
Sep 14, 2012 at 3:10 pm

4	[Rd] Possible page inefficiency in do_matrix in array.c

In do_matrix in src/array.c there is a type switch containing : case LGLSXP : for (i = 0; i < nr; i++) for (j = 0; j < nc; j++) LOGICAL(ans)[i + j * NR] = NA_LOGICAL; That seems page inefficient, ...

Matthew Dowle
Sep 3, 2012 at 2:04 am
Sep 4, 2012 at 9:05 pm

3	[Rd] non-differentiable evaluation points in nlminb(), follow-up of PR#15052

This is a follow-up question for PR#15052 <http://bugs.r-project.org/bugzilla3/show_bug.cgi?id052 There is another thing I would like to discuss wrt how nlminb() should proceed with NAs. The ...

Sebastian Meyer
Sep 26, 2012 at 9:13 am
Sep 29, 2012 at 7:40 pm

3	[Rd] French Toulouse CRAN mirror always down

Hi! One of the three French CRAN mirrors, cran.cict.fr (Toulouse) seems to be down most of the time, and at least really not reliable. It has currently been down for 28 days (!) [1], and I know that ...

Milan Bouchet-Valat
Sep 28, 2012 at 7:37 am
Sep 29, 2012 at 6:44 pm

3	[Rd] valgrind crashing

I am trying to do a classic R -d valgrind --vanilla < mypkg-Ex.R as described in http://cs.swan.ac.uk/~csoliver/ok-sat-library/internet_html/doc/doc/R/2.9.1/doc/manual/R-exts.html#Using-valgrind The ...

David
Sep 12, 2012 at 5:38 am
Sep 25, 2012 at 10:03 pm

3	[Rd] Segmentation fault when options(max.print = .Machine$integer.max)

Seemed like a good idea at the time, but [1] Program received signal SIGSEGV, Segmentation fault. because of an integer overflow at src/main/printvector.c:176 R Under development (unstable) ...

Martin Morgan
Sep 24, 2012 at 11:42 pm
Sep 25, 2012 at 3:29 pm

3	[Rd] methods cbind2 bind_activation disrupts cbind everywhere

The methods package ?cbind2 includes the instruction to use via methods:::bind_activation(TRUE). This changes the default definition of cbind globally, disrupting proper evaluation in packages not ...

Martin Morgan
Sep 12, 2012 at 10:23 pm
Sep 15, 2012 at 5:35 pm

2	[Rd] Rbuildignore question

I'm touching up changes to rpart and have a question with .Rbuildignore. Here is my file tmt1014% more .Rbuildignore test.local \.hg src/print_tree.c The source code included a module "print_tree.c", ...

Terry Therneau
Sep 20, 2012 at 5:43 pm
Sep 20, 2012 at 8:37 pm

2	[Rd] Rcmd check problem

Hi, all. I was trying to build my R package with R 2.15.1 32bit and win7. I basically follow the routine in Steven Mosher's blog http://stevemosher.wordpress.com/step-10-build/ After I fixed the ...

Qi Zhang
Sep 19, 2012 at 12:55 am
Sep 19, 2012 at 12:14 pm

2	[Rd] R Segfault reported in Fedora 17

Full details, including all sorts of logs here: https://bugzilla.redhat.com/show_bug.cgi?id�7655 A very quick look doesn't show anything obvious, in fact, it might be a readline bug, but readline is ...

Tom Callaway
Sep 17, 2012 at 5:30 pm
Sep 17, 2012 at 6:59 pm

2	[Rd] Is invokeRestart("abort") unstoppable?

Hi, I'm trying to implement an abort() method that works just like stop() but does not signal the condition such that try() and tryCatch(..., condition=...) are, contrary to stop(), effectively ...

Henrik Bengtsson
Sep 11, 2012 at 11:19 pm
Sep 12, 2012 at 5:08 pm

2	[Rd] Advice on Namespaces

Hi Folks: I'm writing a little package that may not ever hit CRAN or even be distributed beyond a relatively narrow audience at my company. Nevertheless, I have tried to adhere to practices that ...

Bert Gunter
Sep 10, 2012 at 4:11 pm
Sep 11, 2012 at 12:22 pm

2	[Rd] problem building vignette

Hi, I'm trying to get a package to pass through "R CMD check --as-cran" and have run into a problem that gives me no idea where to look to fix it. I'm running R version 15.1 on a Windows 7 64-bit ...

Kevin R. Coombes
Sep 10, 2012 at 6:15 pm
Sep 10, 2012 at 6:29 pm

2	[Rd] Typo (?) in 'aggregate.formula'

In the code for 'aggregate.formula', there is if (as.character(formula[[2L]] == ".")) I believe that it is meant to be if (as.character(formula[[2L]]) == ".") However, if (as.character(formula[[2L]] ...

Suharto Anggono Suharto Anggono
Sep 3, 2012 at 9:06 am
Sep 3, 2012 at 10:05 am

1	[Rd] Defunct of --max-vsize and mem.limits

R-devel, I am migrating from R.2.13.2 to R.2.15.1 and just realize that R command line options --max-nsize and --max-vsize are no longer supported along with the defunct of mem.limits(). To me, the ...

Qwumd
Sep 21, 2012 at 9:52 pm
Mar 6, 2013 at 5:42 pm

1	[Rd] license

R-devel now gives a warning for a non-standard license (this may have happened for a while). In Rgraphviz we include the Graphviz source code, which is under Eclipse. But the rest of the R package is ...

Kasper Daniel Hansen
Sep 24, 2012 at 5:30 pm
Sep 24, 2012 at 9:17 pm

1	[Rd] Question lattice SplomT

This seems to be due to the get.gpar() call in the SplomT() function -- it produces a new page if it is called before any graphics output is drawn. That's not quite correct: The point is that ...

Deepayan Sarkar
Sep 24, 2012 at 5:00 pm
Sep 24, 2012 at 5:00 pm

1	[Rd] example(smooth.spline) fails when function is NOT byte-compiled

Hi, example(smooth.spline) fails with the non byte-compiled version of the smooth.spline function: smth.s require(graphics) smth.s attach(cars) smth.s plot(speed, dist, main = "data(cars) & smoothing ...

Hervé Pagès
Sep 19, 2012 at 8:41 pm
Sep 20, 2012 at 6:58 am

1	[Rd] different behavior accessing type-specific as.data.frame inside a function vs inside R shell

hello we are developing an R package called ANTsR for which we have some special types. one of these types is an " antsMatrix " type. we implemented a "as.data.frame" function that casts an ...

Brian avants
Sep 19, 2012 at 8:06 pm
Sep 19, 2012 at 10:11 pm

1	[Rd] Cran package checks

Some questions motivated by this discussion. From the CRAN policy page: "Checking the package should take as little CPU time as possible, as the CRAN check farm is a very limited resource and there ...

Terry Therneau
Sep 5, 2012 at 4:08 pm
Sep 6, 2012 at 1:17 am

1	[Rd] Environment when NextMethod is used

I'm running into some hard-to-understand behavior with the evaluation environment when NextMethod is used. I'm using square-bracket indexing into objects, and the evaluation environment of the ...

Winston Chang
Sep 2, 2012 at 4:25 am
Sep 4, 2012 at 2:50 am

0	[Rd] should delete.response(response~predictor) return ~predictor?

Thomas, I noticed the delete.response() just returns its input if the input is not of class "terms". Hence we get surprising (to me) results like y ~ x1 + x2 <environment: 0x3244788 y ~ x1 + x2 ...

William Dunlap
Sep 21, 2012 at 5:57 pm
Sep 21, 2012 at 5:57 pm

0	[Rd] [Repost 3/3] Minor glitch in 'Writing R Extensions'

[ Email repost 3 of 3 ] From: Dirk Eddelbuettel <edd at debian.org To: R-devel org <r-devel at r-project.org Subject: [Patch] Minor glitch in 'Writing R Extensions' Date: Mon, 3 Sep 2012 10:58:32 ...

Dirk Eddelbuettel
Sep 15, 2012 at 6:37 pm
Sep 15, 2012 at 6:37 pm

0	[Rd] [Repost 2/3] Why fix all.equal for POSIXct at 1 msec?

[ Email repost 2 of 3 ] From: Dirk Eddelbuettel <edd at debian.org To: R-core <R-core at r-project.org , Prof Brian D Ripley <ripley at stats.ox.ac.uk Subject: Why fix all.equal for POSIXct at 1 ...

Dirk Eddelbuettel
Sep 15, 2012 at 6:37 pm
Sep 15, 2012 at 6:37 pm

0	[Rd] [Repost 1/3] The X11 device patch

[ Email resend 1 of 3 ] From: Dirk Eddelbuettel <edd at debian.org To: R-core <R-core at r-project.org CC: Philip Johnson <plfjohnson at emory.edu , edd at debian.org Subject: The X11 device patch ...

Dirk Eddelbuettel
Sep 15, 2012 at 6:37 pm
Sep 15, 2012 at 6:37 pm

0	[Rd] Reposting mails to R-Core / R-Devel

Over the last few months, I had sent emails with follow-up suggestions, questions and (minimal) patches to R Core (two) and R-Devel (one). Not one of these emails was met with any follow-up I am ...

Dirk Eddelbuettel
Sep 15, 2012 at 6:37 pm
Sep 15, 2012 at 6:37 pm

0	[Rd] Different behavior of the "showArgs" example (R extension manual) between gcc and Visual C++ compiled code

Hi, I am trying to implement on a Win7 box the showArgs example of section 5.10.2 "Calling .External" of the R extension manual. I am using interchangeably gcc (RTools) and Visual C++ (via ...

Jean-Michel Perraud
Sep 9, 2012 at 11:51 pm
Sep 9, 2012 at 11:51 pm

0	[Rd] all.equal on external pointers and environments

For an external pointer <pointer: (nil) one might expect all.equal to behave as for environments [1] TRUE but it does not Error in unclass(target) : cannot unclass an external pointer A solution is ...

Martin Morgan
Sep 5, 2012 at 8:50 pm
Sep 5, 2012 at 8:50 pm

0	[Rd] Reference classes use a lot more memory after serialization/unserialization

Hello All, I posted this earlier on R-help but received no answers. This touches the implementation of reference classes so maybe R-devel is a better place. The memory consumption of reference ...

Jan Mueller
Sep 4, 2012 at 7:56 am
Sep 4, 2012 at 7:56 am

0	[Rd] [Patch] Minor glitch in 'Writing R Extensions'

The (marked up in info mode) manual Writing R Extensions says in 6.1.3 -- Function: double fprec (double X, double DIGITS) Returns the value of X rounded to DIGITS decimal digits (after the decimal ...

Dirk Eddelbuettel
Sep 3, 2012 at 3:58 pm
Sep 3, 2012 at 3:58 pm

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