[Rd] Petition to set warnPartialMatch* options to TRUE during R CMD check by default

Hi all, What it says in the title. This is likely to cause a lot of CRAN packages to fail (I can try and quantify this if seen fit), but I think it's for the best. Packages should not (IMHO) be relying on partial matching in package code / tests. One might be more permissive for vignette/examples

Re: [Rd] [External] Re: Repeated library() of one package with different include.only= entries

. On Mon, Apr 15, 2024 at 6:46 AM Martin Maechler wrote: > I think we should try to advance and hopefully finalize this > thread before we forget about it .. > > >>>>> Michael Chirico n Thu, 11 Apr 2024 09:10:11 -0700 writes: > > >> I would assume that

Re: [Rd] [External] Re: Repeated library() of one package with different include.only= entries

ion to just point to detach()+attachNamespace() is reasonable enough, the rare users that care about this are likely to be able to figure out the rest from there. On Thu, Apr 11, 2024 at 7:37 AM wrote: > On Thu, 11 Apr 2024, Duncan Murdoch wrote: > > > On 11/04/2024 7:0

[Rd] Repeated library() of one package with different include.only= entries

Right now, attaching the same package with different include.only= has no effect: library(Matrix, include.only="fac2sparse") library(Matrix) ls("package:Matrix") # [1] "fac2sparse" ?library does not cover this case -- what is covered is the _loading_ behavior of repeated calls: > [library and

[R-pkg-devel] Removing import(methods) stops exporting S4 "meta name"

other CRAN packages with a similar directive in its NAMESPACE. Michael Chirico __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

[Rd] readChar() could read the whole file by default?

I am curious why readLines() has a default (n=-1L) to read the full file while readChar() has no default for nchars= (i.e., readChar(file) is an error). Is there a technical reason for this? I often[1] see code like paste(readLines(f), collapse="\n") which would be better served by readChar(),

Re: [Rd] c(NA, 0+1i) not the same as c(as.complex(NA), 0+1i)?

c#L418-L425 And indeed! It's not "coercion" in the sense I just described... there's a branch for the 'x == NA_LOGICAL' case to _convert_ to NA_complex_. On Mon, Nov 6, 2023 at 3:08 AM Martin Maechler wrote: > >>>>> Michael Chirico > >>>>> on

[Rd] c(NA, 0+1i) not the same as c(as.complex(NA), 0+1i)?

This is another follow-up to the thread from September "Recent changes to as.complex(NA_real_)". A test in data.table was broken by the changes for NA coercion to complex; the breakage essentially comes from c(NA, 0+1i) # vs c(as.complex(NA), 0+1i) The former is the output we tested against;

Re: [Rd] FR: valid_regex() to test string validity as a regular expression

ular expression '(invalid', reason 'Missing ')'' > In addition: Warning message: > In grepl("(invalid", "subject", perl = FALSE) : > TRE pattern compilation error 'Missing ')'' > > > re2::re2_regexp("(invalid") > Error: missing ): (inval

Re: [Rd] FR: valid_regex() to test string validity as a regular expression

efore any regex is actually executed. At a bare minimum this is a good place to return a classed warning (say invalid_regex_warning) to allow finer control than tryCatch(condition=). On Mon, Oct 9, 2023, 11:30 PM Tomas Kalibera wrote: > > On 10/10/23 01:57, Michael Chirico via R-dev

[Rd] FR: valid_regex() to test string validity as a regular expression

It will be useful to package authors trying to validate input which is supposed to be a valid regular expression. As near as I can tell, the only way we can do so now is to run any regex function and check for the warning and/or condition to bubble up: valid_regex <- function(str) {

[Rd] Unclear provenance of message from S4

MRE to produce the message is the following: setClass("Foo") setOldClass("Bar") setAs("Bar", "Foo", \(x) x) # NOTE: arguments in definition for coerce changed from (x) to (from) In an interactive setting, that may be fine, but I first encountered this message in the install log of a package for

Re: [Rd] Improving user-friendliness of S4 dispatch failure when mis-naming arguments?

, y = "double"), \(x, y, ...) x + y) BaseGeneric(X = 1, Y = 2) # Error: unable to find an inherited method for function ‘BaseGeneric’ for signature ‘x="missing", y="missing"’ On Fri, Aug 11, 2023 at 2:26 AM Martin Maechler wrote: > > >>>>> Michael Chir

Re: [Rd] Improving user-friendliness of S4 dispatch failure when mis-naming arguments?

hink it would be very useful and > beneficial to improve S4 to surface that information as well. > > More information about the way that the dispatch failed would be of great > help in situations like the one Michael pointed out. > > ~G > > On Thu, Aug 10, 2023 at 9:

Re: [Rd] Improving user-friendliness of S4 dispatch failure when mis-naming arguments?

n", "statement")) > dbGetQuery(connection = NULL, query = NULL) > #> Error: Can't find method for generic `dbGetQuery(conn, statement)`: > #> - conn : MISSING > #> - statement: MISSING > > Hadley > > On Wed, Aug 9, 2023 at 10:02 PM Michael Chirico v

[Rd] Improving user-friendliness of S4 dispatch failure when mis-naming arguments?

I fielded a debugging request from a non-expert user today. At root was running the following: dbGetQuery(connection = conn, query = query) The problem is that they've named the arguments incorrectly -- it should have been [1]: dbGetQuery(conn = conn, statement = query) The problem is that the

Re: [Rd] tab-complete for non-syntactic names could attempt backtick-wrapping

I personally wouldn't like using a string, and this comment makes me think it's against the r-core preference as well: https://bugs.r-project.org/show_bug.cgi?id=18429#c1 Thanks both for catching the sloppy mistake in vapply() :) Let's continue discussion on the bug/PR. On Thu, Mar 2, 2023 at

Re: [Rd] tab-complete for non-syntactic names could attempt backtick-wrapping

Great suggestion! I've started a patch: https://bugs.r-project.org/show_bug.cgi?id=18479 On Wed, Mar 1, 2023 at 1:56 AM Ivan Krylov wrote: > > В Wed, 1 Mar 2023 01:36:02 -0800 > Michael Chirico via R-devel пишет: > > > +comps[non_syntactic] <- paste0(&qu

[Rd] tab-complete for non-syntactic names could attempt backtick-wrapping

Consider: x <- list(`a b` = 1) x$a (i.e., press the 'tab' key after typing 'x$a') The auto-complete mechanism will fill the buffer like so: x$a b This is not particularly helpful because this is now a syntax error. It seems to me there's a simple fix -- in utils:::specialCompletions(), we can

[Rd] FR: names= argument for load()

issue of static analysis). Michael Chirico __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Line-terminal \ in character consants -- missing from ?Quotes ?

gram.y#L2978-L3008 ('\n' is in the list of valid items after '\') I don't see any special handling for '\r', so there may be a gap in the R parser? Or I just don't understand what I'm reading in the parser :) Mike C On Sun, Feb 12, 2023 at 3:38 AM Duncan Murdoch wrote: > > On 12/02/2023 12:0

[Rd] Line-terminal \ in character consants -- missing from ?Quotes ?

I'm coming across some code that uses the fact the parser ignores a line-terminal '\', e.g. identical("\ ", "\n") # [1] TRUE x = "abc \ def" y = "abc \ndef" identical(x, y) # [1] TRUE However: identical("\\n", "\n") # [1] FALSE This appears to be undocumented behavior; the closest thing I see

[Rd] Shouldn't "Loading" be "Attaching" when referring to library() calls?

require() and library() both emit this message immediately before running library(): "Loading required package: %s" https://github.com/r-devel/r-svn/blob/4198a2941b702d965bb2374c2b908f48c369f40a/src/library/base/R/library.R#L967-L968

Re: [Rd] trace() an S3-classed function in .GlobalEnv

;original" "source" "class" PS one day I hope to master the dark art of choosing r-devel or bugzilla for issues :) On Wed, Jun 8, 2022 at 3:44 AM Martin Maechler wrote: > > >>>>> Michael Chirico > >>>>> on Mon, 6 Jun 2022 23:09:29

Re: [Rd] .onLoad, packageStartupMessage, and R CMD check

ur linter were using messages from .onLoad for... > > Best, > ~G > > > > On Thu, Nov 4, 2021 at 12:37 PM Duncan Murdoch > wrote: >> >> On 04/11/2021 2:50 p.m., Michael Chirico via R-devel wrote: >> > I wrote a linter to stop users from using package

[Rd] .onLoad, packageStartupMessage, and R CMD check

I wrote a linter to stop users from using packageStartupMessage() in their .onLoad() hook because of the R CMD check warning it triggers: https://github.com/wch/r-source/blob/8b6625e39cd62424dc23399dade37f20fa8afa91/src/library/tools/R/QC.R#L5167 However, this received some pushback which I

[Rd] Should seq.Date() return double storage?

today <- Sys.Date() typeof(today) # [1] "double" typeof(seq(today, by=1, length.out=2)) # [1] "integer" Clearly minor as it doesn't seem to have come up before (e.g. coercion to numeric will happen automatically whenever fractional dates are needed); I only noticed because of a test using

[Rd] translation domain is not inferred correctly from a package's print methods -- intended behavior?

Here is a reprex: # initialize reprex package cd /tmp mkdir myPkg && cd myPkg echo "Package: myPkg" > DESCRIPTION echo "Version: 0.0.1" >> DESCRIPTION mkdir R echo "print.my_class = function(x, ...) { cat(gettext(\"'%s' is deprecated.\"), '\n', gettext(\"'%s' is deprecated.\", domain='R-myPkg'),

[Rd] tools::update_pkg_po() doesn't work on Solaris?

Hi all, I am about 99% sure tools::update_pkg_po() is using an invocation that is not supported by the Solaris version of msgfmt. The invocation[1]: msgfmt -c --statistics -o /path/to/file.mo /path/to/file.po AFAICT neither -c nor --statistics appear to be supported by Solaris [2]: I don't

[R-pkg-devel] gettext on Solaris

My new submission potools failed on Solaris: https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/potools-00check.html Likely reason is that one or more of the SystemRequirements are missing (I put gettext as a catchall in the DESCRIPTION but more specifically it needs msgfmt, msgmerge,

Re: [Rd] Should last default to .Machine$integer.max-1 for substring()

on, Jun 21, 2021 at 1:32 AM Martin Maechler wrote: > > >>>>> Tomas Kalibera > >>>>> on Mon, 21 Jun 2021 10:08:37 +0200 writes: > > > On 6/21/21 9:35 AM, Martin Maechler wrote: > >>>>>>> Michael Chirico > >&g

[Rd] Should last default to .Machine$integer.max-1 for substring()

Currently, substring defaults to last=100L, which strongly suggests the intent is to default to "nchar(x)" without having to compute/allocate that up front. Unfortunately, this default makes no sense for "very large" strings which may exceed 100L in "width". The max width of a string is

[Rd] usage of #import in grDevices/src/qdCocoa.h

be updated to use #include? Other packages appear to have done so, e.g. from GitHub: https://github.com/search?q=%22%23include+cocoa%2Fcocoa.h%22=code Michael Chirico [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list

Re: [Rd] Translations and snprintf on Windows

the issue (AFAICT via trioremap.h). On Thu, Apr 30, 2020 at 4:16 PM Michael Chirico wrote: > [a bit unsure on if this is maybe better for r-package-devel] > > We recently added translations to messages at the R and C level to > data.table. > > At the C level, we did _() wrappi

Re: [Rd] Should 0L * NA_integer_ be 0L?

of logical values even means). FALSE * NA = 0L On Sat, May 23, 2020 at 6:49 PM Martin Maechler wrote: > > >>>>> Michael Chirico > >>>>> on Sat, 23 May 2020 18:08:22 +0800 writes: > > > I don't see this specific case documented anywhere (I also

[Rd] Should 0L * NA_integer_ be 0L?

I don't see this specific case documented anywhere (I also tried to search the r-devel archives, as well as I could); the only close reference mentions NA & FALSE = FALSE, NA | TRUE = TRUE. And there's also this snippet from R-lang: In cases where the result of the operation would be the same for

[Rd] Translations and snprintf on Windows

but the use of snprintf specifically appears to have caused a crash on Windows: https://github.com/Rdatatable/data.table/issues/4402 Is there any guidance against using gettext with snprintf, or perhaps guidance on which "outputters" *are* OK for translation? Michael Chirico [[a

Re: [Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?

Awesome. Gabe, since you already have a workshopped version, would you like to proceed? Feel free to ping me to review the patch once it's posted. On Mon, Sep 16, 2019 at 3:26 PM Martin Maechler wrote: > >>>>> Michael Chirico > >>>>> on Su

Re: [Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?

Finally read in detail your response Gabe. Looks great, and I agree it's quite intuitive, as well as agree against non-recycling. Once the length(n) == length(dim(x)) behavior is enabled, I don't think there's any need/desire to have head() do x[1:6,1:6] anymore. head(x, c(6, 6)) is quite clear

[Rd] --disable-long-double or --enable-long-double=no?

ambiguity is immediate -- the commit mentions disable-long-double but builds enable-long-double. https://github.com/wch/r-source/commit/fb8e36f8be0aaf47a9c54c9effb219dae34f0e41 Could someone please help to clear the confusion? Thanks Michael Chirico [[alternativ

[Rd] Why no tz argument for format.POSIXlt?

e any reason not to accept a tz argument for format.POSIXlt? It's quite convenient to be able to specify an output timezone format on the fly with format.POSIXct; in the case at hand, I'm trying to force UTC time on input. format(as.POSIXct(x), tz = 'UTC') seems to wo

[Rd] bug: write.dcf converts hyphen in field name to period

.', names(x))) (Or maybe errors for having invalid names) Michael Chirico [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?

I think of head() as a standard helper for "glancing" at objects, so I'm sometimes surprised that head() produces massive output: M = matrix(nrow = 10L, ncol = 10L) print(head(M)) # <- beware, could be a huge print I assume there are lots of backwards-compatibility issues as well as valid

Re: [Rd] rbind has confusing result for custom sub-class (possible bug?)

gt; > Follow-up (inline) on my comment about a potential issue in `[<-.Date`. > > > > On Mon, May 27, 2019 at 9:31 AM Michael Chirico > > wrote: > > > > > > Yes, thanks for following up on thread here. And thanks again for > clearing things up, your email

[Rd] Why is R in Japanese (only in Mac terminal)?

Since a while ago, R on my Mac terminal is being started in Japanese: R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit) R は、自由なソフトウェアであり、「完全に無保証」です。 一定の条件に従えば、自由にこれを再配布することができます。

Re: [Rd] rbind has confusing result for custom sub-class (possible bug?)

on this issue will be in my follow-up thread. Mike C On Mon, May 27, 2019, 10:25 PM Joshua Ulrich wrote: > On Sun, May 26, 2019 at 6:47 AM Joshua Ulrich > wrote: > > > > On Sun, May 26, 2019 at 4:06 AM Michael Chirico > > wrote: > > > > > > Have finally manag

Re: [Rd] rbind has confusing result for custom sub-class (possible bug?)

.Generic), oldClass(x)) # <- restores 'IDate' class So we can fix our bug by defining a [<- class; the question that I still don't see answered in documentation or source code is, why/where is [<- called, exactly? Mike C On Sun, May 26, 2019 at 1:16 PM Michael Chirico wrote: > Debugging t

[Rd] rbind has confusing result for custom sub-class (possible bug?)

Debugging this issue: https://github.com/Rdatatable/data.table/issues/2008 We have custom class 'IDate' which inherits from 'Date' (it just forces integer storage for efficiency, hence, I). The concatenation done by rbind, however, breaks this and returns a double: library(data.table) DF =

[Rd] \dots used improperly in ?Rprof examples

As it is the first line looks like it's commented out Michael Chirico [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[R-pkg-devel] Getting started with memory debugging

utput from R CMD build . Any help on getting started here would be appreciated :) Michael Chirico PS the source can be found at https://github.com/MichaelChirico/geohashTools [[alternative HTML version deleted]] __ R-package-devel@r-project.org ma

Re: [Rd] strtoi output of empty string inconsistent across platforms

>> Martin Maechler > >>>>> on Fri, 11 Jan 2019 09:44:14 +0100 writes: > > >>>>> Michael Chirico > >>>>> on Fri, 11 Jan 2019 14:36:17 +0800 writes: > > >> Identified as root cause of a bug in data.table: > &

[Rd] strtoi output of empty string inconsistent across platforms

what is the correct output of strtoi("", base = 2L)? Is the cross-platform inconsistency to be expected/documentable? Michael Chirico [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Dead link in documentation of ?timezones

Indeed! Sorry, I need more sleep, should have known better. Thanks! On Fri, Dec 7, 2018 at 6:22 PM Martin Maechler wrote: > >>>>> Michael Chirico > >>>>> on Fri, 7 Dec 2018 10:36:37 +0800 writes: > > > This link is referenced in ?timezones a

[Rd] Dead link in documentation of ?timezones

This link is referenced in ?timezones and appears to have been moved/removed. Is there a replacement? http://www.twinsun.com/tz/tz-link.htm [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list

[Rd] Error message truncation

the entirety of the query and then give some diagnostic information. Queries can get quite long, so it stands to reason that this 8190-length limit might be binding. Thanks, Michael Chirico [[alternative HTML version deleted]] __ R-devel@

[Rd] model.frame strips class as promised, but fails to strip OBJECT in C

meric" is.object(na.omit(DF)$y) # [1] FALSE That is, similarly presented with a classed object, na.omit strips the class *and* the OBJECT attribute. Thanks, Michael Chirico [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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

... On Mar 2, 2018 1:52 AM, "Martin Maechler" <maech...@stat.math.ethz.ch> wrote: > >>>>> Michael Chirico <michaelchiri...@gmail.com> > >>>>> on Tue, 27 Feb 2018 20:18:34 +0800 writes: > > Slightly amended 'Subject': (unimportant mistake

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

needs to be repaired; do we also want to attempt as.numeric(normx) (which I believe would have allowed scale to work in this case)? (I'm aware that there's some import issues in lars, as the offending line to create normx *should* work, as is.numeric(sqrt(drop(rep(1, nrow(x)) %*% (x^2 is TRU

Re: [Rd] Inconsistency in handling of numeric input with %d by sprintf

https://github.com/Rdatatable/data.table/issues/2171 The fix was easy, it's just surprising to see the behavior change almost on a whim. Just wanted to point it out in case this is unknown behavior, but Evan seems to have found this as well. On Tue, May 23, 2017 at 12:00 PM, Michael Chirico

Re: [Rd] Inconsistency in handling of numeric input with %d by sprintf

My particular email had >> to do with the vectors longer than 1 and their positioning vis-a-vis the >> format string.) The safest thing is just to pass the right type. In this >> case, sprintf('%d', as.integer(NA_real_)) works. >> >> Best, >> >> Evan >>

[Rd] Inconsistency in handling of numeric input with %d by sprintf

r other numeric input, why doesn't R just coerce NA_real_ to NA_integer_? Michael Chirico [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] New strptime conversion specification for ordinal suffixes

de superscripts, respectively. With this implemented, converting ord_dates to a Date or POSIXct would be as simple as: as.Date(ord_dates, format = "%B %d%o, %Y") Is there something on the C level preventing this from happening? Michael Chirico [[alternative HTML version dele

[Rd] Suggestions for improvement as regards `as` methods, and a call for consistency in `as.Date` methods

lt;- as.Date("-01-01", ...) - 1 setNames(as.Date(origin, ...) + x, NULL) } as.Date.POSIXct <- function (x, tz = "UTC", ...) { if (tz == "UTC") { z <- floor(unclass(x)/86400) attr(z, "tzone&q