Re: [Rd] head.ts, tail.ts loses time

2024-06-10 Thread Martin Maechler
ad() and tail() are built on `[` very much on purpose. Note that `[` should *not* keep the "ts" property in general, e.g., lynx[c(1:3, 7)] cannot be a regular time series I think I'd consider using windows() for a head.ts() and tail.ts(), but in any case, I am

Re: [Rd] head.ts, tail.ts loses time

2024-06-13 Thread Martin Maechler
7;s proposal, are now simple and "robust", I did not want to make such a "strong" change to such a basic class and its `[` operator. (I'm not *against* it either currently, but I'm not convinced it's worth the effort with possible subsequent changes needed in cod

Re: [Rd] head.ts, tail.ts loses time

2024-06-13 Thread Martin Maechler
>>>>> Spencer Graves >>>>> on Mon, 10 Jun 2024 09:45:46 -0500 writes: > Hi, Martin et al.: > On 6/10/24 9:32 AM, Martin Maechler wrote: >>>>>>> Spencer Graves >>>>>>> on Mon, 10 Jun 2024 07:50

Re: [Rd] R-devel on Windows temporarily broken?

2024-06-13 Thread Martin Maechler
> Dirk Eddelbuettel > on Thu, 13 Jun 2024 07:20:00 -0500 writes: > I had a very routine CI job fail twice this morning on r-devel on Windows; > the package (in fine standard form) doesn't even install under win-builder > r-devel. Whereas on Linux with r86731 everything is

Re: [Rd] 'Fedora' (only!!) -- Certificates are not trusted

2024-08-15 Thread Martin Maechler
ils because of incorrect installation PLEASE !!! Do not spam the R-devel mailing list with things that should've gone to r-sig-fed...@r-project.org { where I *did* CC this (a different msg), a moment ago This E-mail is hopefully the *LAST* one on R-devel with this topic!! } Martin (co-

Re: [Rd] Make factanal accept functions for rotation parameter

2024-08-22 Thread Martin Maechler
stion. unless I'm forgetting something. Can you please provide useful (but *small*) example, which I then also could add to the help page ? Best regards, Martin -- Martin Maechler ETH Zurich and R Core team __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] findInterval

2024-09-17 Thread Martin Maechler
... |.. .|. ..| |.| .|| ## 2 0 0 1 0 0 1 ## 3 0 0 1 0 0 1 ## 4 0 0 1 0 0 1 ## 5 1 1 1 0 1 1 ## 6 1 1 1 1 1 1 ## 7 1 1 1 1 1 1 ## 8 1 1 1 1 1 1 ## 9 1 1 1 1 1 1 ## 10 2 2 2 1

Re: [Rd] Bug in stats::plot.hclust/graphics:::plotHclust/underlying C code (C_dend) in R-3.0?

2013-06-01 Thread Martin Maechler
that happened (between 2.15.x and 3.0.0) when that code was slightly streamlined and moved to the 'graphics' package. > Thanks, > Peter Thank you Peter, for reporting it in such a precise manner! Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] conflicting imports despite using importFrom in NAMESPACE

2013-06-05 Thread Martin Morgan
ended; see section 1.5.1 of Writing R Extensions (though as a lazy programmer I kind of like the pattern "^[^\\.]"). Martin Morgan -pd On Jun 5, 2013, at 18:48 , Jombart, Thibaut wrote: Dear all, It is my understanding that using 'importFrom' in the NAMESPACE o

Re: [Rd] R CMD INSTALL and file permission settings

2013-06-10 Thread Martin Maechler
> Add a new option() [with a to-be-determined name] which, if enabled, turns > on group-write modes for files and directories, ie "664" and "775". [.] > I would be happy to write such a patch (including documentation

Re: [Rd] R CMD INSTALL and file permission settings

2013-06-14 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Mon, 10 Jun 2013 11:44:57 +0200 writes: >>>>> Dirk Eddelbuettel >>>>> on Sat, 8 Jun 2013 11:22:56 -0500 writes: >> Summary: >> The directory /usr/local/lib/R/sit

Re: [Rd] R CMD INSTALL and file permission settings

2013-06-15 Thread Martin Maechler
e (or remove, as you suggest) > -- Bob has no group-write (despite sharing the group) or > world-write rights > -- Hence this fails > -- My patch (reworked by Martin) fixes precisely this > | The implementation of the group-wrtable part of is

Re: [Rd] R CMD INSTALL and file permission settings

2013-06-15 Thread Martin Maechler
re the > group-writable bit. Which leads us to my point that this > is not what you really want. > | > | Ooops. I'll take another look. > Done. "It works." For fairly generous definitions of > working. I'll detail: > i) My initi

Re: [Rd] str and s3 classes

2013-06-21 Thread Martin Maechler
In such a case (and not only here), using an S4 class instead of an S3 is much more natural IMO. But of course, we can discuss the issue here; that's exactly what I think R-devel is for. With regards (also to the Rstudio team), Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] pretty eerie feeling: Google "down", Twitter "down", R sites up

2013-06-27 Thread Martin Maechler
l fine and up... an eerie feeling indeed. Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] pretty eerie feeling: Google "down", Twitter "down", R sites up

2013-06-27 Thread Martin Maechler
>>>>> Marc Schwartz >>>>> on Thu, 27 Jun 2013 11:26:23 -0500 writes: > On Jun 27, 2013, at 10:32 AM, Martin Maechler wrote: >> Maybe this is just from inside ETH Zurich, >> but I haven't seen this before in many years: &g

Re: [Rd] RFC: a "safe" uniroot() function for future R

2013-07-03 Thread Martin Maechler
>>>>> Berend Hasselman >>>>> on Mon, 3 Jun 2013 09:01:25 +0200 writes: > On 31-05-2013, at 10:34, Martin Maechler > wrote: > ….. >> From the current feedbacks, I'd come to propose / further >> discuss the follow

Re: [Rd] Posting Guide: changed link and other comment

2013-07-22 Thread Martin Maechler
ore generally. Thank you, Scott. I've made both amendments that you've proposed above. The 2nd one is most probably more helpful for non-native English readers/speakers may .. when it may be nice and better style for some flavor of real English .. Martin > Scott > --

Re: [Rd] robustbase compilation problem: probably boneheaded? maybe 32-bit?

2013-07-22 Thread Martin Maechler
> Simon Urbanek > on Thu, 11 Jul 2013 23:10:21 -0400 writes: > On Jul 11, 2013, at 10:57 PM, Ben Bolker wrote: >> >> With a recent SVN build (R Under development (unstable) (2013-07-10 >> r63264) -- "Unsuffered Consequences"), I'm having trouble installing the >>

Re: [Rd] Extending suggestion for stopifnot

2013-08-20 Thread Martin Morgan
On 08/20/2013 11:41 AM, ivo welch wrote: A second enhancement would be a "smart string", which knows that everything inside {{...}} should be evaluated. stopifnot( is.matrix(m), "m is not a matrix, but a {{class(m)}}" ) a variant with more traditional syntax might be if (!is.matrix(m))

Re: [Rd] Packages not found

2013-08-29 Thread Martin Maechler
>>>>> Uwe Ligges >>>>> on Thu, 29 Aug 2013 14:47:21 +0200 writes: > Thanks, we know, this is work in progress. Uwe Ligges and mirrors still work, e.g., http://cran.CH.r-project.org/web/packages/ --- Martin > On 29.08.2013 1

[Rd] Building Windows package .zip files

2013-10-20 Thread Martin Morgan
Section 1.3.3 of Writing R Extensions says "The recommended method of building binary packages is to use R CMD INSTALL --build pkg where pkg is either the name of a source tarball (in the usual .tar.gz format) or the location of the directory of the package source to be built. " (a) vignette

Re: [Rd] R CMD check problem with R 3.0.2

2013-10-28 Thread Martin Maechler
checked for the correct version, etc. Also, by default the vignette rebuilding; manuals etc take time, and it used to need other manual manipulations if you disabled those, and then wanted to check the tarball. I'd be very much inconvenienced if I'd need to build packages every time I want

Re: [Rd] Imports, importFrom slow (for Matrix)

2013-10-30 Thread Martin Maechler
not pre-[load + attach] the 'methods' package. But your bias is only about 0.1 second from my measurements; the time increases from 0.35 to 0.45 not sure if this is still a good enough reason to omit 'methods' from Rscript. Martin > On Tue, Oct 29, 2013 at 10:25 AM, Gáb

Re: [Rd] Imports, importFrom slow (for Matrix)

2013-10-30 Thread Martin Maechler
software, and proposals for changes that speedup the loadNamespace("Matrix") without having to change the R code inside Matrix much are highly appreciated. Martin Maechler, ETH Zurich > On Tue, Oct 29, 2013 at 10:25 AM, Gábor Csárdi > wrote: >> Unfortunately th

Re: [Rd] tar warnings in R-3.0.2 RC when R is installed by a different (non-root) user

2013-10-31 Thread Martin Morgan
On 09/23/2013 02:53 PM, Prof Brian Ripley wrote: The issue is not the ownership (uname) but the uid. A tarball can only store uids up to 'nobody' (usually 32767), and certainly larger ones cannot be unpacked portably. The many identical warnings can obscure useful messages, e.g., about invalid

[Rd] Determining files opened by an R session

2013-11-04 Thread Martin Gregory
done via the C functions *_open in main/connections.c but don't see anything there that looks like logging. Could someone let me know if it is possible to log which files are opened? Regards, Martin Gregory __ R-devel@r-project.org mailing list

Re: [Rd] cat with backspace and newline characters

2013-11-05 Thread Martin Maechler
you allude to below --- shows that RStudio has changed R in so far that it adds a '\n' even when R, i.e. cat() does not. I can understand that the RStudio programmers want to protect their users (*) from getting funny looking output, but I still don't like the fact that R in

Re: [Rd] cat with backspace and newline characters

2013-11-05 Thread Martin Maechler
>>>>> Brian G Peterson >>>>> on Tue, 5 Nov 2013 07:30:14 -0600 writes: > On 11/05/2013 07:22 AM, Martin Maechler wrote: >> which --- as you allude to below --- shows that RStudio >> has changed R in so far that it adds a

Re: [Rd] [PATCH] minor suggestions for R-ints manual

2013-11-05 Thread Martin Maechler
ommit that introduced the "6 years" string and on the > date of grid 0.1. > Scott I've used "about 2001" and otherwise basically applied your patch (after checking it). Thank you very much for your contribution! Martin Maechler > -- > Scot

Re: [Rd] cat with backspace and newline characters

2013-11-05 Thread Martin Maechler
>>>>> "PhGr" == Philippe Grosjean >>>>> on Tue, 5 Nov 2013 17:02:19 +0100 writes: PhGr> On 05 Nov 2013, at 14:22, Martin Maechler PhGr> wrote: >>>>>>> Kenn Konstabel on Tue, 5 Nov >>>>>&

Re: [Rd] Undocumented S4 method Warning For Bracket

2013-12-11 Thread Martin Morgan
setMethod("[", c("BayMethList", "ANY", "missing"), function(x, i, j, ..., drop=TRUE) {}) so a user providing a 'j' argument would be told that there was no matching method. Martin -- Dario Strbenac Ph

Re: [Rd] External pointers and changing SEXPTYPE

2013-12-16 Thread Martin Morgan
ect, maybe having bundled your ans, ans_nms, R_z, R_a, R_b, R_c into a list. This is suggested by the argument name 'prot' and description in Writing R Extensions section 5.13. Martin I sincerely apologize for posting only several chunks of code. Fortunately for me, the de

Re: [Rd] Sweave trims console output in "tex" mode

2014-01-03 Thread Martin Maechler
k". Anyway, I'm not a > very active user of Sweave. I think in this case, it would be quite useful if strip.white got a new default, say "adaptive", which would becomde FALSE for 'results=tex'. Otherwise, for "safety", we'd have

Re: [Rd] Tab formatting in dummy.coef.R

2014-01-03 Thread Martin Maechler
our not quite correct interpretation. The R internal manual you mention below talks about TABs in specific places in *.Rd files only. *.R (and *.c even more) use TABs in many places, and all of R core have their Emacs / vi / ... settings accordingly. Happy New Year, indeed, to all contributors

Re: [Rd] Sweave trims console output in "tex" mode

2014-01-03 Thread Martin Maechler
>>>>> Duncan Murdoch >>>>> on Fri, 3 Jan 2014 05:52:27 -0500 writes: > On 14-01-03 4:57 AM, Martin Maechler wrote: >>>>>>> Kirill Müller on >>>>>>> Fri, 3 Jan 2014 02:04:06 +0100 writes: >>

Re: [Rd] reference class internals

2014-01-09 Thread Martin Morgan
imicking .self in reference classes] has an infinite (? I didn't wait that long) recursion). I think actually reference classes have a surprising performance _hit_ compared to other R approaches to minimizing copying; this has come up on this or the R mailing list before, but I've lost

Re: [Rd] file.exists does not like path names ending in /

2014-01-17 Thread Martin Maechler
different. I agree that this is quite unfortunate, and we all would be happy if OSes were consistent here. I wonder if R couldn't help you (and many others) better to gloss over these OS differences in a helpful way. This list may be a good place to discuss such proposals ... Martin -- Martin Maechler ETH Zurich -- and R Core Team __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] eapply duplicates elements unnecessarily

2014-02-09 Thread Martin Morgan
I think this is because of 'duplicate' in FrameValues (envir.c:2402). It's hard to tell what contract FrameValues is living up to, but is INCREMENT_NAMED() sufficient? (the PROTECT on value in line 2398 also seems unnecessary -- it must already be protected?) Martin -- Comput

Re: [Rd] $new cannot be accessed when running from Rscript and methods package is not loaded

2014-02-11 Thread Martin Morgan
manual. ... * checking R code for possible problems ... NOTE File ‘PkgA/R/binding.R’: .onLoad calls: require(methods) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. with Depends: methods So is there

[Rd] R CMD Sweave tmp.tex doesn't create figures with fig=TRUE, include=FALSE

2014-02-18 Thread Martin Morgan
t file: tmp.pdf and so did $ Rrel --version|head -n 1 R version 3.0.2 Patched (2014-01-02 r64626) -- "Frisbee Sailing" Martin -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location:

[Rd] instantiating a reference class with an initialize() method from .onLoad fails

2014-02-20 Thread Martin Morgan
tle: Documenting reference classes Version: 0.0.1 Date: 2012-08-05 Author: Martin Morgan Maintainer: Martin Morgan Description: This package implements a simple 'reference' class Depends: methods Imports: methods License: Apache License 2.0 Collate: b

Re: [Rd] R and LANGUAGE

2014-02-27 Thread Martin Maechler
UAGE=.." to the locale part of sessionInfo()'s result. b) A new entry LANGUAGE as part of the result. And 'b)' typically should be combined with a tweak to the print.sessionInfo() method. It could say "Language for messages:" instead of "LANGUAGE" Martin - Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R and LANGUAGE

2014-02-27 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Thu, 27 Feb 2014 11:50:04 +0100 writes: > Diverted from ESS-help. > It is really about R's LANGUAGE, locales and > then a wish for sessionInfo() : >>>>> Sparapani, Rodney >>

Re: [Rd] [PATCH] suggestions for R-lang manual

2014-03-03 Thread Martin Maechler
ched with the >> -arguments for the method using the standard argument matching mechanism. >> -The first argument, i.e.@: the object, will have been evaluated. >> - >> >> this information is duplicated. See a few paragraphs up &

[Rd] Sweave provides a misleading error when vignette engine not fully specified

2014-03-05 Thread Martin Morgan
duce graphics output https://stat.ethz.ch/pipermail/r-devel/2014-February/068414.html $ R --version|head -n 3 R Under development (unstable) (2014-03-05 r65124) -- "Unsuffered Consequences" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64

Re: [Rd] [RFC] A case for freezing CRAN

2014-03-24 Thread Martin Maechler
saying it that > it doesn't make sense to serve by default a version that > is known to be incompatible with the version of R being > used. It's very likely to not even install properly. [..] > Also note that back in October 2011, people using R-2.13.2 > would get e.g. ape 2.7-3 on Linux, Windows and > Mac. Wouldn't it make sense that people using R-2.13.2 > today get the same? Why would anybody use R-2.13.2 today > if it's not to run again some code that was written and > used two years ago to obtain some important results? I also tend to agree that it would be great if someone (Karl Millar -> Google ?) would setup a good time-stamping system for CRAN {and Bioconductor and Omegahat and ..?} packages. Ideally that system would work by *using* the CRAN (and ..) infrastructure. > Cheers, H. I'm still unsure if I should agree with you (Hervé) that some freezing / "data base of package timestamps" should happen on-CRAN in addition. Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] "ERROR: installing package indices failed" message when building my package?

2014-03-24 Thread Martin Maechler
e it. It may well be that we (R authors) do require some man pages, and I would not disagree with such a requirement. Do provide at least a man/pRRophetic-package.Rd file if nothing else. You can use promptPackage() to create a prototype for such a file easily. Martin > *** instal

Re: [Rd] "ERROR: installing package indices failed" message when building my package?

2014-03-24 Thread Martin Maechler
>>>>> Paul Geeleher >>>>> on Mon, 24 Mar 2014 09:37:57 -0500 writes: > Hey Martin, > Thanks for your reply. I actually have documentation, but I pasted a > version of the output that was created when I removed the .Rd files > (as I

Re: [Rd] "ERROR: installing package indices failed" message when building my package?

2014-03-25 Thread Martin Maechler
>>>>> Paul Geeleher >>>>> on Mon, 24 Mar 2014 09:58:52 -0500 writes: > Hey Martin, > The output looks similar: Well, of course but I assumed you would know how to continue after the error which should have "jumped into the debugger" wi

[Rd] CXX_STD and configure.ac in packages

2014-03-30 Thread Martin Morgan
In C++ code for use in a R-3.1.0 package, my specific problem is that I would like to use if it is available, or if not, or if all else fails. I (think I) can accomplish this with configure.ac as AC_INIT("DESCRIPTION") CXX=`"${R_HOME}/bin/R" CMD config CXX` CXXFLAGS=`"${R_HOME}/bin/R" CMD

Re: [Rd] CXX_STD and configure.ac in packages

2014-03-31 Thread Martin Morgan
On 03/31/2014 04:30 AM, Romain François wrote: Le 31 mars 2014 à 12:20, Martyn Plummer a écrit : On Mon, 2014-03-31 at 07:09 +, Martyn Plummer wrote: Hi Martin, Thanks for the patch. I have applied it. I also added CXX1X and friends to the list of approved variables for R CMD config

Re: [Rd] Typeof for character vector in dataframe returns integer

2014-04-02 Thread Martin Maechler
PLEASE! All this does *not* belong to the R-devel mailing list. It is entirely apt for R-help (or "similar", including stackoverflow). Please do *not* misuse R-devel for basic R questions. Martin Maechler, ETH Zurich __ R-devel@r-project.o

[Rd] Package vignettes share the same environment?

2014-04-05 Thread Martin Morgan
quot; Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) Martin -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

Re: [Rd] attach() outputs messages to stdout - should it be stderr?

2014-04-07 Thread Martin Maechler
tderr, but also be something you can e.g. use suppressMessages( . ) with. I tend to agree to change this from cat() to message(), and will do so after a bit of waiting.. Martin > Here's a patch for the local function checkConflicts() of &

Re: [Rd] attach() outputs messages to stdout - should it be stderr?

2014-04-09 Thread Martin Maechler
>>>>> Henrik Bengtsson >>>>> on Mon, 7 Apr 2014 08:20:27 -0700 writes: > On Mon, Apr 7, 2014 at 1:40 AM, Martin Maechler > wrote: >>>>>>> Henrik Bengtsson on Sun, 6 Apr >>>>>>> 2014 21:33:1

Re: [Rd] R 3.1.0: 'R CMD Sweave' deletes non tex files created upon batch mode exit

2014-04-14 Thread Martin Maechler
the problem, as I seem to always Sweave from ESS (Emacs speaks statistics) which calls Sweave() in R, and that works fine, also in R 3.1.0, as you've already noted Martin Maechler, ETH Zurich % \documentclass[12pt]{article} \usep

Re: [Rd] R 3.1.0: 'R CMD Sweave' deletes non tex files created upon batch mode exit

2014-04-17 Thread Martin Maechler
>>>>> Duncan Murdoch >>>>> on Tue, 15 Apr 2014 08:54:34 -0400 writes: > On 15/04/2014 8:12 AM, peter dalgaard wrote: >> On 15 Apr 2014, at 13:14 , Duncan Murdoch wrote: >> >> > On 14/04/2014, 10:23 AM, Marc Schwartz

Re: [Rd] Can the output of Sys.getenv() be improved?

2014-04-19 Thread Martin Maechler
> William Dunlap > on Fri, 18 Apr 2014 16:50:22 + writes: >> Within an R session, type Sys.getenv() will list all the >> environment variables, but each one of them occupies >> about a page, so scrolling to find one is difficult. Is >> this because I don't know how

Re: [Rd] type.convert and doubles

2014-04-19 Thread Martin Maechler
t is valid, too. But in my view, with the reasoning we have seen here, *and* with the well known software design principle of "least surprise" in mind, I also do think that the default for type.convert() should be what it has been for > 10 years now. Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R 3.1.0: 'R CMD Sweave' deletes non tex files created upon batch mode exit

2014-04-19 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Thu, 17 Apr 2014 11:22:04 +0200 writes: [] > PS: I'm currently testing a patch where 'R CMD Sweave' will > revert to not deleting anything after running the R code by default.

Re: [Rd] R 3.1.0: 'R CMD Sweave' deletes non tex files created upon batch mode exit

2014-04-20 Thread Martin Maechler
>>>>> Marc Schwartz >>>>> on Sat, 19 Apr 2014 09:37:30 -0500 writes: > On Apr 19, 2014, at 8:05 AM, Martin Maechler > wrote: >> >>>>>>> Martin Maechler on Thu, >>>>>>> 17 Apr 2

Re: [Rd] type.convert and doubles

2014-04-22 Thread Martin Maechler
aracter/factor, but may > evolve over time to accept arithmetic methods and act more > like a number (e.g. knowing that ³0.1², ³.10² and "1e-1" > are the same number, or that ³-9²<³-0.2"). A class > ³bignum² perhaps? That's another interesting idea.

Re: [Rd] type.convert and doubles

2014-04-22 Thread Martin Maechler
on to have all modeling functions fail upon > seeing a missing value? The na.action argument was only available within lm() etc calls, > with no global override, because "missing values are serious artifacts and should not be > removed without thought". Marti

Re: [Rd] Can the output of Sys.getenv() be improved?

2014-04-26 Thread Martin Maechler
nt for a better S3 class name, we can still change that (longer names are not compelling to me, much shorter ones neither ...) Martin > Bill Dunlap > TIBCO Software > wdunlap tibco.com > > -Original Message- > > From: Martin Maechler [mailto:maech...@stat.math.ethz.ch] >

Re: [Rd] type.convert and doubles

2014-04-26 Thread Martin Maechler
>>>>> Simon Urbanek >>>>> on Sat, 19 Apr 2014 13:06:15 -0400 writes: > On Apr 19, 2014, at 9:00 AM, Martin Maechler wrote: >>>>>>> McGehee, Robert >>>>>>> on Thu, 17 Apr 2014 19:15:47 -0400 writes:

Re: [Rd] type.convert and doubles

2014-04-28 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Sat, 26 Apr 2014 22:59:17 +0200 writes: >>>>> Simon Urbanek >>>>> on Sat, 19 Apr 2014 13:06:15 -0400 writes: >> On Apr 19, 2014, at 9:00 AM, Martin Maechler >> wrote: &

Re: [Rd] type.convert and doubles

2014-04-29 Thread Martin Maechler
>>>>> >>>>> on Tue, 29 Apr 2014 08:25:41 + writes: > [...snip...] > Martin Maecher wrote: >> > I have now committed svn rev 65507 --- to R-devel only for now --- >> > the above: exact = NA

Re: [Rd] type.convert and doubles

2014-04-29 Thread Martin Maechler
>>>>> peter dalgaard >>>>> on Tue, 29 Apr 2014 09:32:21 +0200 writes: > On 28 Apr 2014, at 19:17 , Martin Maechler wrote: >> > [...snip...] >>>> I think there should be two separate discussions: >> &

Re: [Rd] type.convert and doubles

2014-04-29 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Tue, 29 Apr 2014 10:41:19 +0200 writes: >>>>> >>>>> on Tue, 29 Apr 2014 08:25:41 + writes: >> [...snip...] >> Martin Maecher wrote: >>> > I have now c

Re: [Rd] Quantile issue

2014-05-01 Thread Martin Maechler
... this may be the same as PR#15746 : https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15746 on which I commented that it was an example of FAQ 7.31 : > Martin Maechler 2014-04-10 07:10:41 UTC > What really happens is simply > > x0 <- 0.000384478262997113 >

Re: [Rd] Quantile issue

2014-05-01 Thread Martin Maechler
3% of the vector is a single > repeated value. Hmm... this may be the same as PR#15746 : https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15746 on which I commented that it was an example of FAQ 7.31 : > Martin Maechler 2014-04-10 07:10:41 UTC > What really happens i

Re: [Rd] Problem running checks after building R-patched

2014-05-07 Thread Martin Maechler
not TRUE > Execution halted > How do I fix this, if possible? > Berend Well, as it works correctly for others, why don't you execute the above code in your (self installed ?) version of R, and find out why -- I think -- the vignettes of grid were not built / installed correctly ? Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] citEntry handling of encoded URLs

2014-05-22 Thread Martin Morgan
to bibentry points to *Entry Fields*, but the 'url' tag is not mentioned there, even though url appears in the examples; if the list of supported tags is not easy to enumerate, perhaps some insight can be provided at this point as to how the supported tags are determined? Thanks Marti

Re: [Rd] citEntry handling of encoded URLs

2014-05-23 Thread Martin Morgan
On 05/23/2014 05:35 AM, Achim Zeileis wrote: On Thu, 22 May 2014, Martin Morgan wrote: The following citEntry includes a url with %3A and other encodings citEntry(entry="article", title = "Software for Computing and Annotating Genomic Ranges", author = p

Re: [Rd] R CMD check for the R code from vignettes

2014-05-31 Thread Martin Morgan
gines that ignore tangle. It is very valuable to all parties to write a vignette with code that is fully evaluated; otherwise, it is too easy for bit rot to seep in, or to 'fake' it in a way that seems innocent but is misleading. Martin Morgan is comfortable with vignettes that do

Re: [Rd] Encourage exit with nonzero error status in ?last.dump

2014-06-13 Thread Martin Maechler
'Details' section of the > help file. I think it would be better to encourage exiting > with a nonzero error status: > options(error = quote({dump.frames(to.file = TRUE); q(status = 1)})) You are right. Thank you for the suggestion: it will be in next release

[Rd] Should a package that indirectly Suggests: a vignette engine pass R CMD check?

2014-06-14 Thread Martin Morgan
using the BiocStyle package for their vignette, and the BiocStyle package suggests the appropriate builder. Martin Morgan -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206

Re: [Rd] index.search

2014-06-16 Thread Martin Maechler
tml#Package-subdirectories ) says |If directory 'tests' has a subdirectory 'Examples' containing a file |'PKG-Ex.Rout.save', this is compared to the output file for running the |examples when the latter are checked. So: A

Re: [Rd] Unfixed bugs in latest R-patched

2014-06-24 Thread Martin Maechler
ou see, there are quite a few cases one could discuss, and have reasons pro and contra some of the changes. I will be too busy till the end of 'useR! 2014' and would want quite a bit of further thoughts before making a quick de

[Rd] RFC: diag(x, n) not preserving integer and logical x

2014-08-07 Thread Martin Maechler
which includes all checks, including those of all recommended packages (including Matrix!) successfully runs through; so at least base + Recommended R never relies on the current behavior, nor should any "well programmed" R code ... Hence my proposal, somewhat tentative for now,

Re: [Rd] RFC: diag(x, n) not preserving integer and logical x

2014-08-11 Thread Martin Maechler
>>>>> Duncan Murdoch >>>>> on Fri, 8 Aug 2014 10:51:10 -0400 writes: Thank you, Duncan (read inline) > On 07/08/2014, 4:51 AM, Martin Maechler wrote: >> This is not at all something new(*). As maintainer of the >> Matrix pac

Re: [Rd] Inconsistent handling of data frames in min(), max(), and mean()

2014-08-22 Thread Martin Maechler
> Gavin Simpson > on Thu, 21 Aug 2014 12:32:31 -0600 writes: > This inconsistency recently came to my attention: >> df <- data.frame(A = 1:10, B = rnorm(10)) >> min(df) > [1] -1.768958 >> max(df) > [1] 10 >> mean(df) > [1] NA Warning message: In mean.d

Re: [Rd] The behaviour of setting names differs between lists and atomic vectors

2014-08-25 Thread Martin Maechler
>> I think there's a bug, but not in names<- (or setNames, >> which calls it). The bug is in the printing, as you'll >> see if you look at names(setNames(list(1), "a\\b")). >> > Yep, slig

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread Martin Maechler
uot;2)" work, apart from using data() on each of the datasets inside the function. As I haven't tried it, that may *still* give a (false) NOTE.. This is a somewhat interesting problem, and I wonder if everyone else has solved it with '1)' rather than a version of '2)'. Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-28 Thread Martin Maechler
have help pages, etc; notably because creating sysdata.rda is not at all part of the package sources, and hence harder for maintenance and "open source transparency". The one additional important in the thread was the special semantic of '::' which here returns something for :: which is *not* part of the 's namespace, whereas the use of '::' does suggest to Joe Average to be working with namespace (as opposed to package) contents. I agree with your suggestion, Peter, that this looks more confusing than it should, and ideally, we'd find a better setup. OTOH, if we additionally allowed something like exportData(), we would additionally get data that is both in the package and namespace environments and other (not exported) data that is only in the package, so add room for even more confusion. Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Martin Morgan
nt infrastructure, so that it makes sense to separate these in distinct packages. It is not uncommon to find 3-5 or more packages in the Depends: field of derived packages for this reason. Martin I am in full agreement that its use should be limited to exceptional situations, and have modifi

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Martin Morgan
the class PkgC use PkgB's special functionality without ever manipulating the object of PkgA. Martin Morgan Hadley -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnol

Re: [Rd] Unfixed bugs in latest R-patched

2014-08-29 Thread Martin Maechler
Getting back to 2 months old considerations [more inline]: >>>>> Martin Maechler >>>>> on Tue, 24 Jun 2014 15:08:09 +0200 writes: >>>>> Radford Neal >>>>> on Mon, 23 Jun 2014 11:24:35 -0400 writes: >> A n

Re: [Rd] log(i, base=i) not giving 1

2014-09-02 Thread Martin Maechler
> peter dalgaard > on Tue, 2 Sep 2014 13:43:21 +0200 writes: > Impressive. Never ceases to amaze me what computers can do these days. ;-) Indeed, > It's even more impressive given that we have > static double logbase(double x, double base) > { > #ifdef HAVE_LOG

Re: [Rd] log(i, base=i) not giving 1

2014-09-03 Thread Martin Maechler
>>>>> Prof Brian Ripley >>>>> on Wed, 3 Sep 2014 06:46:47 +0100 writes: > On 02/09/2014 22:43, Ben Bolker wrote: >> On 14-09-02 08:48 AM, Martin Maechler wrote: >>>>>>>> peter dalgaard >>>>>>

Re: [Rd] r wiki

2014-09-09 Thread Martin Maechler
ammers, and the like. Markdown is definitely much better for R users (given knittr and Rmd ..), and github is currently the place to host -- and once it ceases to be that, markdown will be easier to migrate from. Martin > Best, > Philippe On 08 Sep 2014, at 23:12, Gábor Csárdi

Re: [Rd] Problem with order() and I()

2014-09-09 Thread Martin Maechler
and then the internal .gt() where the bug happens because > I("x") > I("\xb5g") [1] NA but really I think the change should happen in xtfrm.Asis(.) which I think should drop the class also in this case. More on this, once we have fixed it. Thank you, Don, very

Re: [Rd] Problem with order() and I()

2014-09-09 Thread Martin Maechler
such cases. Pretty high chance that this will "break" much user (and probably even package) code out there. Still, the other solution, namely order(foo) behaving as order(ch) now does would correspond to the ">" giving FALSE instead of NA, so this solution is not ok in my v

[Rd] install.packages misleads about package availability?

2014-09-10 Thread Martin Morgan
In the context of installing a Bioconductor package using our biocLite() function, install.packages() warns > install.packages("RUVSeq", repos="http://bioconductor.org/packages/2.14/bioc";) Installing package into '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1-2.14' (as 'lib' is unspeci

Re: [Rd] install.packages misleads about package availability?

2014-09-11 Thread Martin Maechler
>>>>> Martin Morgan >>>>> on Wed, 10 Sep 2014 11:49:31 -0700 writes: > In the context of installing a Bioconductor package using our biocLite() > function, install.packages() warns >> install.packages("RUVSeq"

Re: [Rd] last user argument missing from Rscript --verbose

2014-09-19 Thread Martin Maechler
"/usr/local64.sfs/app/R/R-3.1.1-inst/bin/exec/R" [2] "--slave" [3] "--no-restore" [4] "-e" [5] "

Re: [Rd] Bug in new behaviour for all.equal and environments?

2014-09-23 Thread Martin Maechler
hat creative useRs will be able to construct cases where the new all.equal() methods will fail, possibly even end in an infinite loop (which is caught and leads to an error). Please use R-devel svn rev >= 8 for such experiments. Thanking you for testing ..., Martin Maechler ETH Zurich

[Rd] Package Rcpp: Question conerning source code of cpp files and related question

2014-09-30 Thread Martin Spindler
ghly welcome. Thank you very much for your help in advance! Best, Martin crossp.cpp: #include // [[Rcpp::depends(RcppArmadillo)]] using namespace Rcpp; using namespace arma; //[[Rcpp::export]] NumericMatrix crossp3(NumericMatrix Xr) { int n = Xr.nrow(), k = Xr.ncol(); arma::mat X(Xr.begin(), n,

Re: [Rd] debuggingState() analogous to tracingState() ?

2014-10-02 Thread Martin Maechler
is quite technical and assumes you know more about R's debug()ing and trace()ing than an estimated 99.9% of the R users: >>>>> Duncan Murdoch >>>>> on Thu, 2 Oct 2014 07:19:34 -0400 writes: > On 02/10/2014, 6:36 AM, Martin Maechler wrote: >>>&

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