Re: [Rd] Inconsistent rank in qr()

2018-01-22 Thread Martin Maechler
> Serguei Sokol > on Mon, 22 Jan 2018 17:57:47 +0100 writes: > Le 22/01/2018 à 17:40, Keith O'Hara a écrit : >> This behavior is noted in the qr documentation, no? >> >> rank - the rank of x as computed by the decomposition(*): always full rank in the LAPACK case.

Re: [Rd] Why R should never move to git

2018-01-25 Thread Martin Morgan
tandard / best practice for merging branches git checkout master git merge ... a-pull-request git push ... Creating pull requests is a problem for the developer wanting to contribute to R, not for the R-core developer. As we've seen in this thread, R-core would not need to feel responsib

Re: [Rd] sum() returns NA on a long *logical* vector when nb of TRUE values exceeds 2^31

2018-01-27 Thread Martin Maechler
tirely analogously to the behavior of length() which returns integer whenever possible. The advantage of 1) is uniformity. We should (at least provisionally) decide between 1) and 2) and then go for that. It could be that going for 1) may have bad compatibility-consequences in package space, bec

Re: [Rd] withTimeout bug, it does not work properly with nlme anymore

2018-01-30 Thread Martin Maechler
em and shows the problem indeed does not happen in nlminb() -- which I wrongly assumed for a while -- but indeed in nlme's call to own .C() code. I am looking into fixing this (making it interruptable // detect the infinite loop). My guess is that it only happens in degenerate cases like her

Re: [Rd] as.list method for by Objects

2018-02-01 Thread Martin Maechler
uot;") in your code (I see this so often, shockingly to me ...) but rather use if(inherits(obj, "")) instead. Martin > On Tue, Jan 30, 2018 at 3:47 PM, Hervé Pagès wrote: >> On 01/30/2018 02:50 PM, Michael Lawrence wrote: >> >>&

Re: [Rd] as.list method for by Objects

2018-02-01 Thread Martin Maechler
double" to "Date" or "POSIXct" (and many more such cases). For the present case, we should stay with focusing on is.list() being true after as.list() .. the same we would do with as.numeric() and is.numeric(). Martin > However, it would may be too disruptive

Re: [Rd] sum() returns NA on a long *logical* vector when nb of TRUE values exceeds 2^31

2018-02-01 Thread Martin Maechler
>>>>> Hervé Pagès >>>>> on Tue, 30 Jan 2018 13:30:18 -0800 writes: > Hi Martin, Henrik, > Thanks for the follow up. > @Martin: I vote for 2) without *any* hesitation :-) > (and uniformity could be restored at some point in

Re: [Rd] as.list method for by Objects

2018-02-01 Thread Martin Maechler
>>>>> Michael Lawrence >>>>> on Thu, 1 Feb 2018 06:12:20 -0800 writes: > On Thu, Feb 1, 2018 at 1:21 AM, Martin Maechler > wrote: >> >>>>> Michael Lawrence >> >>>>> on Tue, 30 Jan 2018 10

Re: [Rd] as.list method for by Objects

2018-02-02 Thread Martin Maechler
>>>>> Henrik Bengtsson >>>>> on Thu, 1 Feb 2018 10:26:23 -0800 writes: > On Thu, Feb 1, 2018 at 12:14 AM, Martin Maechler > wrote: >>>>>>> Michael Lawrence >>>>>>> on Tue, 30 Jan 2018 15:57:42 -08

Re: [Rd] sum() returns NA on a long *logical* vector when nb of TRUE values exceeds 2^31

2018-02-05 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Thu, 1 Feb 2018 16:34:04 +0100 writes: > >>>>> Hervé Pagès > >>>>> on Tue, 30 Jan 2018 13:30:18 -0800 writes: > > > Hi Martin, Henrik, > > Thanks for the follow u

[Rd] Possible typo in the C source code of R

2018-02-07 Thread Martin Bodin
Good morning, I am Martin Bodin, a postdoc at the CMM in Santiago de Chile, and I am currently in the process of formalising (a part of) the R language into the Coq proof assistant. This work makes me look frequently at the source code of R. I have noticed a strange line in the file src/main

Re: [Rd] Duplicate column names created by base::merge() when by.x has the same name as a column in y

2018-02-22 Thread Martin Maechler
tly), it is little work to introduce an extra argument, I'm calling 'no.dups = TRUE' which when set to false would mirror current R's behavior... and documenting it, then also documents the new behavior (to some extent). My plan is to commit it soonish ;-) Martin > Bes

Re: [Rd] Duplicate column names created by base::merge() when by.x has the same name as a column in y

2018-02-23 Thread Martin Maechler
>>>>> Scott Ritchie >>>>> on Fri, 23 Feb 2018 12:32:41 +1100 writes: > Thanks Martin! > Can you clarify the functionality of the 'no.dups' argument so I can change > my patch to `data.table:::merge.data.table` accordingly? &g

Re: [Rd] Problem with R_registerRoutines

2018-02-23 Thread Martin Maechler
an-code), so there is still something I don't understand here. > Anyway, does this mean that the package might be accepted on CRAN without further changes? at least not automatically, and not very probably in my gut feeling... but I may be wrong. Did you use R CMD check --as-cra

Re: [Rd] scale.default gives an incorrect error message when is.numeric() fails on a dgeMatrix

2018-03-01 Thread Martin Maechler
methods) > Michael Chirico Yes, 'lars' has _not_ been updated since Spring 2013, notably because its authors have been saying (for rather more than 5 years I think) that one should really use require("glmnet") instead. Your point is still valid that it would be easy to enhance base :: scale.default() so it'd work in more cases. Thank you for that. I do plan to consider such a change in R-devel (planned to become R 3.5.0 in April). Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Unclosed parenthesis in grep.Rd

2018-03-05 Thread Martin Maechler
l be an > integer vector unless the input > There should be a closing parenthesis after \code{invert = > TRUE} Thank you, Hugh! I've added the ')' now. Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Fwd: Re: [EXTERNAL] Re: backquotes and term.labels

2018-03-08 Thread Martin Maechler
I'm open to look at one .. not for the next few days, though. Martin > On Thu, Mar 8, 2018 at 9:39 AM, Therneau, Terry M., Ph.D. via R-devel > wrote: >> Ben, >> >> >> Looking at your notes, it appears that your solution is

Re: [Rd] Bug report - duplicate row names with as.data.frame()

2018-03-08 Thread Martin Maechler
avior which entails that as.data.frame.*(x) (and similar coercions to data frames) should typically _handle_ invalid row names rather than signal errors. Feedback is welcome ! ((though I will be slow in replying, going basicaly off work for my early-starting weekend in the Alps)) Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] importing namespaces from base packages

2018-03-12 Thread Martin Maechler
n it is neither loaded nor attached (e.g., when R runs with only base, say, and suddenly encounters an S4 object), and there still are situations where 'methods' needs to be in the search() path and not just loaded, but these cases should be unrelated to the above DESCRIPTION-Imports vs NAMESPACE-Imports correspondence. Martin Maechler ETH Zurich & R Core Team __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] importing namespaces from base packages

2018-03-13 Thread Martin Maechler
>>>>> Adrian Dușa >>>>> on Tue, 13 Mar 2018 09:17:08 +0200 writes: > On Mon, Mar 12, 2018 at 2:18 PM, Martin Maechler > wrote: >> [...] >> Is that so? Not according to my reading of the 'Writing R >> Ext

Re: [Rd] Inappropriate parens fix for Logic.Rd

2018-03-17 Thread Martin Maechler
typeof(x) is "double", class(x) is "numeric". > When typeof(x) is "integer", class(x) is "integer". It's amazing that we've not done better .. I've tried again now. Thank you Suharto! Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] trivial typo in man/pretty.Rd

2018-03-20 Thread Martin Maechler
ed4c150a/src/library/base/man/pretty.Rd indeed, 20 years and 2 weeks today: then it's good to fix it finally. Thank you Ben! Martin > === > --- pretty.Rd (revision 74426) > +++ pretty.Rd (wo

Re: [Rd] [R-pkg-devel] Warning: rBind is deprecated

2018-03-22 Thread Martin Maechler
Please package authors, do update the source of your packages: a) replace cBind() by cbind() and rBind() by rbind() b) Ensure that your package depends on at least R 3.2.0, i.e. possibly add a 'Depends: R (>= 3.2.0)' to your DESCRIPTION file. Of course feel free to

Re: [Rd] Function 'factor' issues

2018-03-24 Thread Martin Maechler
> , function 'factor' in R devel could be made more consistent and back-compatible. Why not picking it? Thank you for persevering, I'll have a hard look... You have been right before ;-) So I will check this small change for both `factor` and `levels<-.factor` Martin > -

Re: [Rd] Suggesting patch to link DOIs against secure resolver

2018-03-26 Thread Martin Maechler
> Katrin Leinweber > on Sun, 25 Mar 2018 19:04:34 +0200 writes: > Dear Madams and Sirs, > because the DOI foundation recommends a new, secure resolver [1], I > wanted to suggest the attached patch. It > a) updates a static DOI link in the docu, > b) the code chunk

Re: [Rd] Base R examples that write to current working directory

2018-04-03 Thread Martin Maechler
h' argument to example() is a nice idea, but also changing its default to tempdir() is definitely out of the question for R 3.5.0. Martin > 2. wrap example code in a withTempDir({ ... }) call. > 3. Add an 'eval.path' (*) argument to example() and make > it de

Re: [Rd] [FORGED] recordPlot/replayPlot not working with saveRDS/readRDS

2018-04-03 Thread Martin Maechler
of checkValidSymbolId() or its caller, so that *from R code* one could check if the recordedplot 'x' passed to replayPlot() with its external pointers needs to be fixed up by x <- restoreRecordedPlot(x) or not. But that would be another topic I'd not get envolved deeply jus

Re: [Rd] names lost in functions from packages installed by R-devel r74500

2018-04-03 Thread Martin Maechler
nv, and call it, the JIT kicks in pretty quickly and you can see that 'foo' is byte compiled as well, but it still does not break. This is pretty important, so thank you very much for the nice reproducible report! Martin Maechler ETH Zurich --- *) R-devel CMD INSTALL --no-byte-compile -

Re: [Rd] names lost in functions from packages installed by R-devel r74500

2018-04-03 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Tue, 3 Apr 2018 17:03:02 +0200 writes: >>>>> Francois Rousset >>>>> on Tue, 3 Apr 2018 16:38:42 +0200 writes: >> Dear list members, >> If I install with R-devel r74500 on Win

Re: [Rd] Base R examples that write to current working directory

2018-04-04 Thread Martin Maechler
>>>>> Gabe Becker >>>>> on Tue, 3 Apr 2018 21:16:12 -0700 writes: > Martin et al, > I have submitted a patch on bugzilla which fixes all of the examples I > could easily find which were not already writing only to temporary files or

Re: [Rd] Fwd: suggested patch for messages

2018-04-14 Thread Martin Maechler
#x27;s English. I've committed a change (74593) to R-devel where I've slightly simplified the wording from "this would be:" to "that is:" and really I cannot give a rational reason why I also changed "this" to "that" so I'm open for an

Re: [Rd] packageDate() segfaults, if used without argument

2018-04-16 Thread Martin Maechler
) > My system is FreeBSD 12.0-CURRENT amd64 with R-devel > (r74601). It was a lapsus -- of mine -- not at all related to packageDate(), corrected yesterday (svn r 74604). Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] odd assignInNamespace / setGeneric interaction

2018-04-19 Thread Martin Maechler
ine the active .libPaths() in R, and the fact the R calls R again during 'R CMD check' etc, sometimes drives me crazy when .libPaths() become incompatible for too many reasons yes, I'm diverting: that's another story] If we'd want to allow using (yet another!) envi

[Rd] Spam to R-* list posters

2018-04-19 Thread Martin Maechler
w use your mail providers spam filters to quickly get rid of this. .. or more interestingly and clearly less legally: use R to write "mail bombs". Write an R function sending ca 10 e-mails per hour randomly to that address ... ;-) I did something like that (with a shell script, not

Re: [Rd] Minor glitch in optim()

2018-04-20 Thread Martin Maechler
quot;L-BFGS-B","Brent"))) { > warning("bounds can only be used with method L-BFGS-B (or Brent)") > method <- "L-BFGS-B" > } > Best, JN I aim to go for the first line if((any(lower > -Inf)) || any(upper < Inf)) which is 100

Re: [Rd] R 3.5.0 fails its regression test suite on Linux/x86_64

2018-04-24 Thread Martin Maechler
ocedures to easily workaround the issue, and as Dirk has mentioned, Debian etc have adopted a more robust procedure for packaging both R without rec.pkg. and the rec.pkg.s (and then bundle the two in yet another). Best, Martin Maechler ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] extendrange(): suggested improvement

2018-04-26 Thread Martin Maechler
each side if(!missing(r) && length(r) != 2) stop("'r' must be a \"range\", hence of length 2") f <- if(length(f) == 1L) c(-f,f) else c(-f[1L], f[2L]) r + f * diff(r) } PS: /* I hope the tidy faction will at some time be co

Re: [Rd] predict.glm returns different results for the same model

2018-04-27 Thread Martin Maechler
del.frame.default(), so I thought this should not really be related to glm at all, and I was right. 2) Reading the help page ?makepredictcall --- yes, a good idea, even for experts, believe me, ((notably when it is froma base package, not produced from roxy.. ;-\)) --- reveals what I vaguely remembered: The function was introduced to fix a bug first encountered in lm(. ~ poly(.)) and indeed: -> That help page actually contains an indirect closer to minimal reprex. -> I will also patch the makepredictcall.poly() method. [ as I said: after dinner .. ;-)] -- Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] possible internal (un)tar bug

2018-05-01 Thread Martin Maechler
on a connection, but works fine on a plain file name. This is a bug --> Thank you for the report, Gábor ! I'm investigating. Martin --- my version of your reprex : setwd(tempdir()) dir.create("pkg") cat("this: that\n", file = file.path("pkg", "

Re: [Rd] possible internal (un)tar bug

2018-05-01 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Tue, 1 May 2018 16:14:43 +0200 writes: >>>>> Gábor Csárdi >>>>> on Tue, 1 May 2018 12:05:32 + writes: >> This is a not too old R-devel on Linux, it already fails >> in

Re: [Rd] possible internal (un)tar bug

2018-05-01 Thread Martin Maechler
TLDR: Use gzfile(), not file() .. and you have no problems. >>>>> Martin Maechler >>>>> on Tue, 1 May 2018 16:39:57 +0200 writes: >>>>> Martin Maechler >>>>> on Tue, 1 May 2018 16:14:43 +0200 writes: >>&g

Re: [Rd] issue with model.frame()

2018-05-01 Thread Martin Maechler
per bound allowed currently. (and yes, one could consider increasing that as it has been unchanged in R since the very beginning (I have checked R version 0.49 from 1997). On the other hand, deparse2 (and your older code above) do paste all the parts together via collapse = " " so I don'

Re: [Rd] download.file does not process gz files correctly (truncates them?)

2018-05-03 Thread Martin Morgan
quot;) On windows, the 'mode' argument to download.file() needs to be "wb" (write binary) for binary files. Martin The file is downloaded, but oligo::read.celfiles() returns the following error: Error in checkChipTypes(filenames, verbose, "affymetrix", TRUE) : End o

Re: [Rd] download.file does not process gz files correctly (truncates them?)

2018-05-03 Thread Martin Morgan
d many other utilities outside R) recognize the "foo\n" as "foo\r\n". Obviously this messes up binary files. I guess in the CEL.gz file there are about 8k "\n" characters. Henrik's suggestion (default = "wb") would introduce the complementary proble

Re: [Rd] length of `...`

2018-05-03 Thread Martin Morgan
nargs() provides the number of arguments without evaluating them > f = function(x, ..., y) nargs() > f() [1] 0 > f(a=1, b=2) [1] 2 > f(1, a=1, b=2) [1] 3 > f(x=1, a=1, b=2) [1] 3 > f(stop()) [1] 1 On 05/03/2018 11:01 AM, William Dunlap via R-devel wrote: In R-3.5.0 you can use ...length():

Re: [Rd] download.file does not process gz files correctly (truncates them?)

2018-05-04 Thread Martin Maechler
convincingly. There's one thing I strongly agree with Henrik: The only-on-Windows documented Windows behavior should be documented on all platforms. I'll update the help page, and will also add the .rds extension to the above list [ --- yes, we all should use saveRDS() a

Re: [Rd] download.file does not process gz files correctly (truncates them?)

2018-05-04 Thread Martin Maechler
lso adding '.rds' { OTOH, after reading the thread about this: Shouldn't you make your code more robust and use mode = "wb" (or "ab") in any case? ;-) } Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] length of `...`

2018-05-04 Thread Martin Maechler
no example where current (3.5.0 and newer) ...length() differs from Hadley's dotlength() I'd vert happy to replace ...length 's C based definition by Hadley's beautiful minimal solution. Martin > On 05/03/2018 08:34 AM, Hadley Wickham wrote: >> On Thu, May 3,

Re: [Rd] length of `...`

2018-05-04 Thread Martin Maechler
n spite of the fact that the pure-R solution is slower than a primitive; both are fast enough for all purposes] But such a deprecation cycle typically entails time more writing etc, not something I've time for just these days. Martin > On Fri, May 4, 2018 at 3:02 PM, Martin Maechler

Re: [Rd] unlist errors on a nested list of empty lists

2018-05-10 Thread Martin Maechler
(), and so this old design-bug triggers relatively rarely. Last but not least: I have created an account for you, Steven, on the bugzilla site. Given we have holidays till the weekend and private duties of mine, I won't get to more for now. Best Martin Maechler > On Tue, May 8

Re: [Rd] Patch for bug 17256 'possible bug in writeForeignSAS in the foreign library when string is NA'

2018-05-17 Thread Martin Maechler
o-email with info. Thank you in advance for helping with this. In this special case, we'd also be happy for other users testing the problem and the fix, as access to SAS may have become difficult for most R core members. Martin Maechler ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Date method of as.POSIXct does not respect tz

2018-05-17 Thread Martin Maechler
using the > character method if one doesn't want the default timezone > (which is often an annoying DST timezone). > This came up on Stack Overflow: > https://stackoverflow.com/q/50373340/1412059 > -- > Roland Thank you Roland for your notice (and

Re: [Rd] Bug on qr.coef when qr is created by a zero matrix with colnames and all y equals zero

2018-05-24 Thread Martin Maechler
n qr.coef shows that when `nam` is not NULL, no branch of code leads to creating `pivotted` before using it finally.  Dear Kun, this is indeed a bug, and I will address it. Thank you very much for the reprex (:= [repr]oducible [ex]ample)! Best, Martin Maechler __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] readLines function with R >= 3.5.0

2018-05-28 Thread Martin Maechler
ber. I can confirm. It "works" if you additionally (the [Enter], i.e., EOL) you also "send" an EOF -- in Unix alikes via -D The same happens if you use 'Rscript ' I'm not the expert here, but am close to sure that we (R core) did not intend this change, whe

Re: [Rd] readLines function with R >= 3.5.0

2018-05-28 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Mon, 28 May 2018 10:28:01 +0200 writes: >>>>> Ralf Stubner >>>>> on Fri, 25 May 2018 19:18:58 +0200 writes: >> Dear all, I would like to draw you attention to this >> questi

Re: [Rd] readLines function with R >= 3.5.0

2018-05-28 Thread Martin Maechler
+ user_input <- readLines(stdin(), n=1) > + user_input <- as.numeric(user_input) > + print(user_input) > + } >> create_matrix() > Write the numbers of vertices: numeric(0) >> oh dear... yes, that is true .. >>>>>

Re: [Rd] readLines function with R >= 3.5.0

2018-05-29 Thread Martin Maechler
>>>>> Ralf Stubner >>>>> on Tue, 29 May 2018 11:21:28 +0200 writes: > On 28.05.2018 16:38, Martin Maechler wrote: >> Then, I now do think this needs to be dealt with as a bug >> (but I'm not delving into fixing it!) > O

Re: [Rd] encoding argument of source() in 3.5.0

2018-06-04 Thread Martin Maechler
> peter dalgaard > on Sun, 3 Jun 2018 23:51:24 +0200 writes: > Looks like this actually comes from readLines(), nothing > to do with source() as such: In current R-devel (still): >> f <- file("http://home.versanet.de/~s-berman/source2.R";, encoding="UTF-8") >> readLi

Re: [Rd] aic() component in GLM-family objects

2018-06-04 Thread Martin Maechler
> Ben Bolker > on Sun, 3 Jun 2018 17:33:18 -0400 writes: > Is it generally known/has it been previously discussed here that the > $aic() component in GLM-family objects (e.g. results of binomial(), > poisson(), etc.) does not as implemented actually return the AIC, but

Re: [Rd] Date class shows Inf as NA; this confuses the use of is.na()

2018-06-11 Thread Martin Maechler
at this will have >> implications in other areas, there is a possibility of >> breaking code and it should be investigated a bit further >> imho. Cheers Joris Indeed. I could argue it is wrong to treat '+/- Inf' as NA for dates (as well as for date times),

Re: [Rd] Date class shows Inf as NA; this confuses the use of is.na()

2018-06-12 Thread Martin Maechler
in : int 0 $ hour : int 0 $ mday : int 23 $ mon : int 5 $ year : int -5879541 $ wday : int 2 $ yday : int 173 $ isdst: int 0 - attr(*, "tzone")= chr "UTC" > we see the integer overflow (to negative here) and that all components but 'sec&#

Re: [Rd] readLines function with R >= 3.5.0

2018-06-13 Thread Martin Maechler
also not yet available in R patched (!) this means using a version of "R-devel", e.g. for Windows available from https://cloud.r-project.org/bin/windows/base/rdevel.html Martin > Sounds like you might want to be running a web service or > something instead though. > M

Re: [Rd] aic() component in GLM-family objects

2018-06-18 Thread Martin Maechler
erred. I've spent quite some time checking this - to some extent. Thank you for the patch. I will use an even slightly extended version ((and using the correct '\eqn{\eta}{eta}' )). Thank you indeed. Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Tiny bug in lm()?

2018-07-18 Thread Martin Maechler
rare, so no wonder this has never been reported the last 13.374 years this has been in the sources. Of course, I will still fix it. Thank you, Brett, for reporting! Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] problem with display of complex number

2018-07-19 Thread Martin Maechler
arately, and identically to how double() are print()ed / format()ted in such case, notably, using 'digits' to both parts "separately". 2) We can and probably should keep signif()'s behavior as current, as that has been documented to behave as it does for almost 13 years. Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Should there be a confint.mlm ?

2018-07-20 Thread Martin Maechler
; y1:(Intercept) -1.2261 0.7037 > y1:x1 -0.5100 0.2868 > y1:x2 -2.7554 0.8736 > y2:(Intercept) -0.6980 2.2182 > y2:x1 -0.6162 0.5879 > y2:x2 -3.9724 1.5114 > ``` I'm looking into a relatively small patch to confi

Re: [Rd] Library lib.loc Option Ignored for Dependencies

2018-07-21 Thread Martin Maechler
han one) to be fixed. Notably with the 3.4.x --> 3.5.0 transition and my/our tendency of having quite a few paths in R_LIBS / lib.loc / ... I've been bitten by problems when the wrong version of package was taken from the wrong library path Martin >>

Re: [Rd] Library lib.loc Option Ignored for Dependencies

2018-07-24 Thread Martin Maechler
quietly = quietly) instead of the current code which uses lib.loc = NULL equivalently to lib.loc = .libPaths() Others / ideas? Reproducible examples with small fake packages? Martin > On 07/21/2018 12:34 PM, Martin Maechler wrote: >>>>>>> Benjamin Tyn

Re: [Rd] Suggestion for updating `p.adjust` with new method (BKY 2006)

2018-07-26 Thread Martin Maechler
y we will get a "BKY" method for p.adjust() within a few months. Thank you, indeed, for the proposal! Best, Martin -- Martinhttp://stat.ethz.ch/~maechler Seminar für Statistik, ETH Zürich HG G 16 Rämistrasse 101 CH-8092 Zurich, SWITZERLAND phone: +41-44-632-3408 fax:

Re: [Rd] odd behavior of names

2018-07-30 Thread Martin Maechler
Component: Windows GUI / Window specific Reporter: kevinushey .. gmail .. His minimal REPREX was even much simpler: > list(a = 1, b = 2) $`a` [1] 1 $b [1] 2 Thank you, Bill, for the nice extra example. Martin Maechler ETH Zurich and R Core T

Re: [Rd] apply with zero-row matrix

2018-07-30 Thread Martin Maechler
tions. While that makes sense for high-level R functions that do a lot of things, this would really be a bad idea in general : This would make all of these basic functions larger {more to maintain} and slightly slower for all non-zero cases just to make th

Re: [Rd] apply with zero-row matrix

2018-07-30 Thread Martin Maechler
>>>>> David Hugh-Jones >>>>> on Mon, 30 Jul 2018 10:12:24 +0100 writes: > Hi Martin, Fair enough for R functions in general. But the > behaviour of apply violates the expectation that apply(m, > 1, fun) calls fun n times when m has n rows

Re: [Rd] Code Optimization: print.data.frame + as.data.frame(head(x, n = options("max.print")))

2018-07-31 Thread Martin Maechler
> Juan Telleria Ruiz de Aguirre > on Tue, 31 Jul 2018 08:19:33 +0200 writes: > I polished a little bit more the function: > * Used: getOption("max.print") > * Added comment at the end: cat('[ reached getOption("max.print") -- > omitted ', omitted,' rows ]') > I

Re: [Rd] possible bug in plot.intervals.lmList

2018-08-03 Thread Martin Maechler
it definitely is a buglet in package 'nlme' (maintained by R Core, currently). I've committed a bug fix (and related "cleanup cosmetics") to the nlme package sources which are maintained in subversion / svn at https://svn.r-project.org/R-packages/trunk/nlme/ Thank you for

Re: [Rd] withTimeout bug, it does not work properly with nlme anymore

2018-08-08 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Tue, 30 Jan 2018 15:17:50 +0100 writes: (a bit more than 6 months ago) >>>>> Ramiro Barrantes >>>>> on Mon, 27 Nov 2017 21:02:52 + writes: >> Hello, I was relying on withTimeout (f

Re: [Rd] vctrs: a type system for the tidyverse

2018-08-08 Thread Martin Maechler
ms my own gut feeling which had lead me to agreeing with you, Hadley, that taking the union of all factor levels should be done here. As Gabe mentioned (and you've explained about) the term "type" is really confusing here. As you know, the R internals are all about SEXPs, TYPEOF

Re: [Rd] image() method for Matrix fails on empty matrices (?)

2018-08-20 Thread Martin Maechler
, by install.packages("Matrix", repos="http://R-Forge.R-project.org";) Thank you for the report, Ben! Martin > > library(Matrix) > > m <- Matrix(0,nrow=3,ncol=3) > > m > 3 x 3 sparse Matrix of class "dsCMatrix" > [1,] . . . > [2,] . . .

Re: [Rd] ROBUSTNESS: x || y and x && y to give warning/error if length(x) != 1 or length(y) != 1

2018-08-30 Thread Martin Maechler
be done after checking isNumber(): so then we know we have an atomic and can use XLENGTH() } The 0-length case I don't think we should change as I do find NA (is logical!) to be an appropriate logical answer. Martin Maechler ETH Zurich and R Core team. > Cheers Joris > --

Re: [Rd] Segfault when performing match on POSIXlt object

2018-08-31 Thread Martin Maechler
ecent versions of R. > I think this could be a bug, since even if that match > operation makes no sense, the R session is not supposed to > crash with segmentation fault, but rather throw an > exception. Definitely. It is a bug. > Thanks in advance Thank

Re: [Rd] Segfault when performing match on POSIXlt object

2018-08-31 Thread Martin Maechler
>>>>> Martin Maechler on Fri, 31 Aug 2018 16:00:07 +0200 writes: >>>>> Marco Giuliano on Fri, 31 Aug 2018 08:53:02 +0200 writes: >> Hi All, I found a possible unexpected behavior when >> performing match/%in% on POSIXlt objects,

Re: [Rd] Segfault when performing match on POSIXlt object

2018-08-31 Thread Martin Maechler
>>>>> Marco Giuliano >>>>> on Fri, 31 Aug 2018 16:50:56 +0200 writes: > Hi Martin, should I file a formal bug report somewhere or > you've already done it ? No, I haven't, and as I may not address this bug further myself (in the nea

Re: [Rd] compairing doubles

2018-09-03 Thread Martin Maechler
everything behind a new operator which does not allow to take into account that there are quite a few versions of near-equality --- only partly) mirrored by the existence of extra arguments of all.equal() --- only encourages simplified thinking about the underlying su

Re: [Rd] config.status: error: cannot find input file: `po/Makefile.in'

2018-09-06 Thread Martin Maechler
can easily reproduce also with last night's tar ball. The tar ball is missing 90% of the source files. If you use replace R-devel.tar.gz by R-devel_2018-09-03.tar.gz it works... but of course you want the daily latest version, and I'll have a look on what causes the problem,

Re: [Rd] var() with 0-length vector -- docs inconsistent with result

2018-09-12 Thread Martin Maechler
es an error. I propose also just amend the docu there, and do not change the code (as you Richard also seem favor). After all, `NA` is also pretty close to "not defined", and in that sense valid. Martin > However, I get: > > var(numeric(0)) > [1] NA

Re: [Rd] Poor documentation for "adj" and text()

2018-09-14 Thread Martin Maechler
when that thing has been in R (and S before that) for decades. OTOH^2, improving documentation is often a good and helpful thing and I will look at it now. Thank you, Frederick, for trying to help making R better! Martin > I'd like to get it out of my queue. > Thanks,

Re: [Rd] Bug when calling system/system2 (and request for Bugzilla account)

2018-09-18 Thread Martin Maechler
minimum) of a function before claiming a bug. I've been a bit appalled about the amount of recent e-mails on R-devel of people not having looked at the reference documentation and claiming things... [..omitted..] [..omitted..] and you did note and report a rea

Re: [Rd] A different error in sample()

2018-09-20 Thread Martin Maechler
R version 2.15.3 (2013-03-01) -- "Security Blanket" Here, I clearly think we see a regression bug, and hopefully not one that should trigger often in practice... and -- without any statistics about the consequences out in package space -- I do think we should fix this in code an

Re: [Rd] segfault issue with parallel::mclapply and download.file() on Mac OS X

2018-09-20 Thread Martin Maechler
> Seth Russell > on Wed, 19 Sep 2018 15:19:48 -0600 writes: > I have an lapply function call that I want to parallelize. Below is a very > simplified version of the code: > url_base <- "https://cloud.r-project.org/src/contrib/"; > files <- c("A3_1.0.0.tar.gz", "ABC.RA

Re: [Rd] A different error in sample()

2018-09-20 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Thu, 20 Sep 2018 09:20:46 +0200 writes: >>>>> Wolfgang Huber >>>>> on Thu, 20 Sep 2018 08:47:47 +0200 writes: >> FWIW, I suspect this is related to the function >> R_unif_inde

Re: [Rd] Possible bug, max argument in print.default(), on R-3.5.1-patched

2018-09-25 Thread Martin Maechler
, Gábor, for the report, and Peter for the digging! Martin >> On 22 Sep 2018, at 23:46 , Gábor Csárdi >> wrote: >> >> The max argument of print.default() does not override >> options(max.print), see below. R 3.5.1 and R-devel both >> s

Re: [Rd] as.vector() broken on a matrix or array of type "list"

2018-09-26 Thread Martin Maechler
that the foremost property of 'm' is to be - a list() {with a dim attribute and matrix-like indexing possibility} rather than - a 'matrix' {where every matrix entry is a list()}. At the moment my gut feeling would propose to only update the documentation, adding that one case a

Re: [Rd] Improvement to documentation in dput.Rd

2018-09-29 Thread Martin Maechler
se()'ing [equivalent: dput()] of S4 generics and methods would give an expression which is not only parse()able -- which it is finely here -- but would also be correct when eval()'ed subsequently. So in this sense, one could also for a "bug" fix which

Re: [Rd] Suggested Patch: Adding commas to list of packages after R CMD check

2018-10-02 Thread Martin Maechler
mmitted to R-devel (accidentally already together with the \Sexpr{} related bug fix) in svn rev 75378, last Friday. > This seems like a reasonable suggestion, considering how easy it is to do. > > Another suggestion would be to (optionally) automatically install > m

Re: [Rd] Seg fault stats::runmed

2018-10-05 Thread Martin Maechler
oducibly in R 3.4.3, R3.4.4 (Ubuntu 14.04/Ubuntu 16.04) and also in the latest development version (we call "R-devel"). THank you very much, Hilmar! I will have a look, to ensure missing values (incl NaN) are handled propertly. Martin -- Martin Maechler ETH Zurich and R Core T

Re: [Rd] Redundant code in 'split.default' in R devel

2018-10-08 Thread Martin Maechler
t", length(lf)) > names(y) <- lf Indeed --> removed now. Thank you very much, Suharto! Martin --- "Exercise" (tongue in cheek) to the reader: Write a "code walker" (an R function itself) that takes an argument 'expr', which is an

[Rd] methods(class = class()) - improve for |cl.| > 1 ?

2018-10-17 Thread Martin Maechler
omForest.formula". --- Of course, all this works fine with S4 classes: There the full inheritance is used and all methods are found. Still, would it make sense to improve the underlying .S3methods() ? I assume it will break *some* overzealous package checks out there when .S3methods() and

Re: [Rd] Rmpfr: build vector sequentially -- c(.) not working

2018-10-26 Thread Martin Maechler
f 'NULL' Then, e.g., vec <- mNUL for(i in 1:10) { vec <- c(vec, mpfr(i^2, 88)) } works fine. In the next version of Rmpfr, both as(NULL, "mpfr") mpfr(NULL) will also give the 'mNUL' above. I hope you enjoy using Rmpfr! Best regards, Martin Martin Maechler ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] small bug in formatC?

2018-10-26 Thread Martin Maechler
lem, if it is one, is in .format.zeros: > .format.zeros("0.000", "xx") > Error in strrep(" ", nc - i1) : invalid 'times' value > > R version 3.5.1. > > David Thank you, David. Yes, this looks like a bug / wrong assumption in .format.

Re: [Rd] disappearing paragraphs in html rendering of text from Rd macros

2018-10-30 Thread Martin Maechler
rexes/blob/master/disappearingParagraphs/a.html > and R-3.5.1patched: > https://github.com/GeoBosh/reprexes/blob/master/disappearingParagraphs/a351.html > [..] > Georgi Boshnakov Thank you. I can reproduce what you report, thanks to your 'reprex', an

Re: [Rd] problematic dev.off() after running examples without plots

2018-11-21 Thread Martin Maechler
e in some of *your* examples such as closing all existing devices -- something you should not do: As a good citizen you close graphic devices that you open but not others. > A workaround is to have at least one example which > has some plot. Is there a better solution? Yes, find th

<    1   2   3   4   5   6   7   8   9   10   >